2021 |
Richter, Łukasz; Księżarczyk, Karolina; Paszkowska, Karolina; Janczuk-Richter, Marta; Niedziółka-Jönsson, Joanna; Gapiński, Jacek; Łoś, Marcin; Hołyst, Robert; Paczesny, Jan Adsorption of bacteriophages on polypropylene labware affects the reproducibility of phage research Scientific Reports, 11 (1), pp. 7387, 2021, ISSN: 20452322. @article{Richter2021, title = {Adsorption of bacteriophages on polypropylene labware affects the reproducibility of phage research}, author = {Łukasz Richter and Karolina Księżarczyk and Karolina Paszkowska and Marta Janczuk-Richter and Joanna Niedziółka-Jönsson and Jacek Gapiński and Marcin Łoś and Robert Hołyst and Jan Paczesny}, url = {https://www.nature.com/articles/s41598-021-86571-x}, doi = {10.1038/s41598-021-86571-x}, issn = {20452322}, year = {2021}, date = {2021-12-01}, journal = {Scientific Reports}, volume = {11}, number = {1}, pages = {7387}, publisher = {Nature Research}, abstract = {Hydrophobicity is one of the most critical factors governing the adsorption of molecules and objects, such as virions, on surfaces. Even moderate change of wetting angle of plastic surfaces causes a drastic decrease ranging from 2 to 5 logs of the viruses (e.g., T4 phage) in the suspension due to adsorption on polymer vials' walls. The effect varies immensely in seemingly identical containers but purchased from different vendors. Comparison of glass, polyethylene, polypropylene, and polystyrene containers revealed a threshold in the wetting angle of around 95°: virions adsorb on the surface of more hydrophobic containers, while in more hydrophilic vials, phage suspensions are stable. The polypropylene surface of the Eppendorf-type and Falcon-type can accommodate from around 108 PFU/ml to around 1010 PFU/ml from the suspension. The adsorption onto the container's wall might result in complete scavenging of virions from the bulk. We developed two methods to overcome this issue. The addition of surfactant Tween20 and/or plasma treatment provides a remedy by modulating surface wettability and inhibiting virions' adsorption. Plastic containers are essential consumables in the daily use of many bio-laboratories. Thus, this is important not only for phage-related research (e.g., the use of phage therapies as an alternative for antibiotics) but also for data comparison and reproducibility in the field of biochemistry and virology.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Hydrophobicity is one of the most critical factors governing the adsorption of molecules and objects, such as virions, on surfaces. Even moderate change of wetting angle of plastic surfaces causes a drastic decrease ranging from 2 to 5 logs of the viruses (e.g., T4 phage) in the suspension due to adsorption on polymer vials' walls. The effect varies immensely in seemingly identical containers but purchased from different vendors. Comparison of glass, polyethylene, polypropylene, and polystyrene containers revealed a threshold in the wetting angle of around 95°: virions adsorb on the surface of more hydrophobic containers, while in more hydrophilic vials, phage suspensions are stable. The polypropylene surface of the Eppendorf-type and Falcon-type can accommodate from around 108 PFU/ml to around 1010 PFU/ml from the suspension. The adsorption onto the container's wall might result in complete scavenging of virions from the bulk. We developed two methods to overcome this issue. The addition of surfactant Tween20 and/or plasma treatment provides a remedy by modulating surface wettability and inhibiting virions' adsorption. Plastic containers are essential consumables in the daily use of many bio-laboratories. Thus, this is important not only for phage-related research (e.g., the use of phage therapies as an alternative for antibiotics) but also for data comparison and reproducibility in the field of biochemistry and virology. |
Navarro-Urrios, Daniel; Kang, E; Xiao, P; Colombano, M F; Arregui, G; Graczykowski, Bartłomiej; Capuj, N E; Sledzinska, M; Sotomayor-Torres, C M; Fytas, G Optomechanical crystals for spatial sensing of submicron sized particles Scientific Reports, 11 (1), pp. 7829, 2021, ISSN: 2045-2322. @article{Navarro-Urrios2020, title = {Optomechanical crystals for spatial sensing of submicron sized particles}, author = {Daniel Navarro-Urrios and E Kang and P Xiao and M F Colombano and G Arregui and Bartłomiej Graczykowski and N E Capuj and M Sledzinska and C M Sotomayor-Torres and G Fytas}, url = {https://doi.org/10.1038/s41598-021-87558-4 http://www.nature.com/articles/s41598-021-87558-4}, doi = {10.1038/s41598-021-87558-4}, issn = {2045-2322}, year = {2021}, date = {2021-12-01}, journal = {Scientific Reports}, volume = {11}, number = {1}, pages = {7829}, publisher = {Nature Publishing Group UK}, abstract = {Optomechanical crystal cavities (OMC) have rich perspectives for detecting and indirectly analysing biological particles, such as proteins, bacteria and viruses. In this work we demonstrate the working principle of OMCs operating under ambient conditions as a sensor of submicrometer particles by optically monitoring the frequency shift of thermally activated mechanical modes. The resonator has been specifically designed so that the cavity region supports a particular family of low modal-volume mechanical modes, commonly known as -pinch modes-. These involve the oscillation of only a couple of adjacent cavity cells that are relatively insensitive to perturbations in other parts of the resonator. The eigenfrequency of these modes decreases as the deformation is localized closer to the centre of the resonator. Thus, by identifying specific modes that undergo a frequency shift that amply exceeds the mechanical linewidth, it is possible to infer if there are particles deposited on the resonator, how many are there and their approximate position within the cavity region. OMCs have rich perspectives for detecting and indirectly analysing biological particles, such as proteins, viruses and bacteria.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Optomechanical crystal cavities (OMC) have rich perspectives for detecting and indirectly analysing biological particles, such as proteins, bacteria and viruses. In this work we demonstrate the working principle of OMCs operating under ambient conditions as a sensor of submicrometer particles by optically monitoring the frequency shift of thermally activated mechanical modes. The resonator has been specifically designed so that the cavity region supports a particular family of low modal-volume mechanical modes, commonly known as -pinch modes-. These involve the oscillation of only a couple of adjacent cavity cells that are relatively insensitive to perturbations in other parts of the resonator. The eigenfrequency of these modes decreases as the deformation is localized closer to the centre of the resonator. Thus, by identifying specific modes that undergo a frequency shift that amply exceeds the mechanical linewidth, it is possible to infer if there are particles deposited on the resonator, how many are there and their approximate position within the cavity region. OMCs have rich perspectives for detecting and indirectly analysing biological particles, such as proteins, viruses and bacteria. |
Sławski, Jakub; Białek, Rafał; Burdziński, Gotard; Gibasiewicz, Krzysztof; Worch, Remigiusz; Grzyb, Joanna The Journal of Physical Chemistry B, 125 (13), pp. 3307–3320, 2021, ISSN: 1520-6106. @article{Sawski2021, title = {Competition between Photoinduced Electron Transfer and Resonance Energy Transfer in an Example of Substituted Cytochrome c–Quantum Dot Systems}, author = {Jakub Sławski and Rafał Białek and Gotard Burdziński and Krzysztof Gibasiewicz and Remigiusz Worch and Joanna Grzyb}, url = {https://doi.org/10.1021/acs.jpcb.1c00325}, doi = {10.1021/acs.jpcb.1c00325}, issn = {1520-6106}, year = {2021}, date = {2021-04-01}, journal = {The Journal of Physical Chemistry B}, volume = {125}, number = {13}, pages = {3307--3320}, publisher = {American Chemical Society (ACS)}, abstract = {Colloidal quantum dots (QDs) are nanoparticles that are able to photoreduce redox proteins by electron transfer (ET). QDs are also able to transfer energy by resonance energy transfer (RET). Here, we address the question of the competition between these two routes of QDs' excitation quenching, using cadmium telluride QDs and cytochrome c (CytC) or its metal-substituted derivatives. We used both oxidized and reduced versions of native CytC, as well as fluorescent, nonreducible Zn(II)CytC, Sn(II)CytC, and metal-free porphyrin CytC. We found that all of the CytC versions quench QD fluorescence, although the interaction may be described differently in terms of static and dynamic quenching. QDs may be quenchers of fluorescent CytC derivatives, with significant differences in effectiveness depending on QD size. SnCytC and porphyrin CytC increased the rate of Fe(III)CytC photoreduction, and Fe(II)CytC slightly decreased the rate and ZnCytC presence significantly decreased the rate and final level of reduced FeCytC. These might be partially explained by the tendency to form a stable complex between protein and QDs, which promoted RET and collisional quenching. Our findings show that there is a net preference for photoinduced ET over other ways of energy transfer, at least partially, due to a lack of donors, regenerating a hole at QDs and leading to irreversibility of ET events. There may also be a common part of pathways leading to photoinduced ET and RET. The nature of synergistic action observed in some cases allows the hypothesis that RET may be an additional way to power up the ET.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Colloidal quantum dots (QDs) are nanoparticles that are able to photoreduce redox proteins by electron transfer (ET). QDs are also able to transfer energy by resonance energy transfer (RET). Here, we address the question of the competition between these two routes of QDs' excitation quenching, using cadmium telluride QDs and cytochrome c (CytC) or its metal-substituted derivatives. We used both oxidized and reduced versions of native CytC, as well as fluorescent, nonreducible Zn(II)CytC, Sn(II)CytC, and metal-free porphyrin CytC. We found that all of the CytC versions quench QD fluorescence, although the interaction may be described differently in terms of static and dynamic quenching. QDs may be quenchers of fluorescent CytC derivatives, with significant differences in effectiveness depending on QD size. SnCytC and porphyrin CytC increased the rate of Fe(III)CytC photoreduction, and Fe(II)CytC slightly decreased the rate and ZnCytC presence significantly decreased the rate and final level of reduced FeCytC. These might be partially explained by the tendency to form a stable complex between protein and QDs, which promoted RET and collisional quenching. Our findings show that there is a net preference for photoinduced ET over other ways of energy transfer, at least partially, due to a lack of donors, regenerating a hole at QDs and leading to irreversibility of ET events. There may also be a common part of pathways leading to photoinduced ET and RET. The nature of synergistic action observed in some cases allows the hypothesis that RET may be an additional way to power up the ET. |
Vasileiadis, Thomas; Varghese, Jeena; Babacic, Visnja; Gomis-Bresco, Jordi; Urrios, Daniel Navarro; Graczykowski, Bartłomiej Progress and perspectives on phononic crystals Journal of Applied Physics, 129 (16), pp. 160901, 2021, ISSN: 0021-8979. @article{Vasileiadis2021, title = {Progress and perspectives on phononic crystals}, author = {Thomas Vasileiadis and Jeena Varghese and Visnja Babacic and Jordi Gomis-Bresco and Daniel Navarro Urrios and Bartłomiej Graczykowski}, url = {https://aip.scitation.org/doi/10.1063/5.0042337}, doi = {10.1063/5.0042337}, issn = {0021-8979}, year = {2021}, date = {2021-04-01}, journal = {Journal of Applied Physics}, volume = {129}, number = {16}, pages = {160901}, publisher = {AIP Publishing LLC}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Litowczenko, Jagoda; Gapiński, Jacek; Markiewicz, Roksana; Woźniak, Anna; Wychowaniec, Jacek K; Peplińska, Barbara; Jurga, Stefan; Patkowski, Adam Materials Science and Engineering: C, 118 , pp. 111507, 2021, ISSN: 0928-4931. @article{LITOWCZENKO2021111507, title = {Synthesis, characterization and in vitro cytotoxicity studies of poly-N-isopropyl acrylamide gel nanoparticles and films}, author = {Jagoda Litowczenko and Jacek Gapiński and Roksana Markiewicz and Anna Woźniak and Jacek K Wychowaniec and Barbara Peplińska and Stefan Jurga and Adam Patkowski}, url = {http://www.sciencedirect.com/science/article/pii/S0928493120334251}, doi = {https://doi.org/10.1016/j.msec.2020.111507}, issn = {0928-4931}, year = {2021}, date = {2021-01-01}, journal = {Materials Science and Engineering: C}, volume = {118}, pages = {111507}, abstract = {In this work, we show synthesis that leads to thermoreponsive poly-N-isopropyl acrylamide (pNIPAM) nanogels with sizes below 100 nm, irrespectively of the surfactant to crosslinker ratio. We also show that in many environments the temperature induced pNIPAM collapse at Lower Critical Solution Temperature (LCST) of 32.5 °C is accompanied by gel nanoparticles' aggregation. Thus, the proper information on the nanoparticle (NP) structure and deswelling can be obtained only if the routinely measured hydrodynamic radius is supplemented by information on the molecular weight, which can be obtained from the intensity of scattered light. We measured the dynamics and reversibility of the deswelling and subsequent aggregation processes. Furthermore, we show that the highly concentrated pNIPAM gel NPs reversibly form bulk hydrogel networks of varied interconnected porous structure. We show, that in case of drying pNIPAM gel NPs above the LCST, it is possible to obtain films with 20-fold increase in storage modulus (G′) compared to hydrogel networks measured at room temperature. They exhibit temperature hysteresis behavior around LCST of 32.5 °C similar to pNIPAM films. Finally, we show that these hydrogel films, lead to extended proliferation of cells across three different types: fibroblast, endothelial and cancer cells. Additionally, none of the films exhibited any cytotoxic effects. Our study brings new insights into physicochemical characterization of pNIPAM gel NPs and networks behavior in realistic conditions of in vitro measurements, especially by means of dynamic light scattering as well as final unique properties of both gel NPs and formed porous films for possible tissue engineering applications.}, keywords = {}, pubstate = {published}, tppubtype = {article} } In this work, we show synthesis that leads to thermoreponsive poly-N-isopropyl acrylamide (pNIPAM) nanogels with sizes below 100 nm, irrespectively of the surfactant to crosslinker ratio. We also show that in many environments the temperature induced pNIPAM collapse at Lower Critical Solution Temperature (LCST) of 32.5 °C is accompanied by gel nanoparticles' aggregation. Thus, the proper information on the nanoparticle (NP) structure and deswelling can be obtained only if the routinely measured hydrodynamic radius is supplemented by information on the molecular weight, which can be obtained from the intensity of scattered light. We measured the dynamics and reversibility of the deswelling and subsequent aggregation processes. Furthermore, we show that the highly concentrated pNIPAM gel NPs reversibly form bulk hydrogel networks of varied interconnected porous structure. We show, that in case of drying pNIPAM gel NPs above the LCST, it is possible to obtain films with 20-fold increase in storage modulus (G′) compared to hydrogel networks measured at room temperature. They exhibit temperature hysteresis behavior around LCST of 32.5 °C similar to pNIPAM films. Finally, we show that these hydrogel films, lead to extended proliferation of cells across three different types: fibroblast, endothelial and cancer cells. Additionally, none of the films exhibited any cytotoxic effects. Our study brings new insights into physicochemical characterization of pNIPAM gel NPs and networks behavior in realistic conditions of in vitro measurements, especially by means of dynamic light scattering as well as final unique properties of both gel NPs and formed porous films for possible tissue engineering applications. |
Calandra, Pietro; Liveri, Vincenzo Turco; Proietti, Noemi; Capitani, Donatella; Lombardo, Domenico; Gainaru, Catalin; Böhmer, Roland; Kozak, Maciej; Dobies, Maria; Fojud, Zbigniew; Pochylski, Mikołaj Journal of Molecular Liquids, 323 , pp. 114963, 2021, ISSN: 0167-7322. @article{CALANDRA2021114963, title = {Non-ideal mixing behavior in dibutyl phosphate-propylamine binary liquids: Dielectric and nuclear magnetic resonance investigations}, author = {Pietro Calandra and Vincenzo Turco Liveri and Noemi Proietti and Donatella Capitani and Domenico Lombardo and Catalin Gainaru and Roland Böhmer and Maciej Kozak and Maria Dobies and Zbigniew Fojud and Mikołaj Pochylski}, url = {https://www.sciencedirect.com/science/article/pii/S0167732220372056}, doi = {https://doi.org/10.1016/j.molliq.2020.114963}, issn = {0167-7322}, year = {2021}, date = {2021-01-01}, journal = {Journal of Molecular Liquids}, volume = {323}, pages = {114963}, abstract = {Owing to the amphiphilic nature of their constituent molecules, binary mixtures of pure liquid surfactants are usually characterized by enhanced nano-segregation and thus can exhibit interesting transport properties and complex macroscopic behavior. In this ambit it was recently shown by Turco Liveri et al. (J. Mol. Liq. 263 (2018) 274–281) at room temperature that mixtures of short aliphatic chains compounds, such as dibutyl phosphate (DBP) and n-propylamine (PA) liquids, due to their ability to allow for phosphate-to-amine proton transfer, display ionic liquid–like behavior with composition-dependent enhanced conductivity, viscosity, and magnetically-induced birefringence. To understand the molecular mechanisms at the basis of this behavior, in the present study a combination of nuclear magnetic resonance (NMR) and dielectric spectroscopy investigations has been carried out for the same materials for different amine molar ratios. It was found that at certain compositions all studied dynamical processes (conformational changes, local hopping of “free” protons among neighboring polar headgroups, long-range charge migration) exhibit significant deviations from ideal mixing behavior. The microscopic origin of these deviations is discussed.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Owing to the amphiphilic nature of their constituent molecules, binary mixtures of pure liquid surfactants are usually characterized by enhanced nano-segregation and thus can exhibit interesting transport properties and complex macroscopic behavior. In this ambit it was recently shown by Turco Liveri et al. (J. Mol. Liq. 263 (2018) 274–281) at room temperature that mixtures of short aliphatic chains compounds, such as dibutyl phosphate (DBP) and n-propylamine (PA) liquids, due to their ability to allow for phosphate-to-amine proton transfer, display ionic liquid–like behavior with composition-dependent enhanced conductivity, viscosity, and magnetically-induced birefringence. To understand the molecular mechanisms at the basis of this behavior, in the present study a combination of nuclear magnetic resonance (NMR) and dielectric spectroscopy investigations has been carried out for the same materials for different amine molar ratios. It was found that at certain compositions all studied dynamical processes (conformational changes, local hopping of “free” protons among neighboring polar headgroups, long-range charge migration) exhibit significant deviations from ideal mixing behavior. The microscopic origin of these deviations is discussed. |
Coy, Emerson; Babacic, Visnja; Yate, Luis; Załęski, Karol; Kim, Yeonho; Reparaz, Juan Sebastián; Dörling, Bernhard; Graczykowski, Bartłomiej; Iatsunskyi, Igor; Siuzdak, Katarzyna Chemical Engineering Journal, 415 , pp. 128987, 2021, ISSN: 1385-8947. @article{COY2021128987, title = {Study of nanostructured ultra-refractory Tantalum-Hafnium-Carbide electrodes with wide electrochemical stability window}, author = {Emerson Coy and Visnja Babacic and Luis Yate and Karol Załęski and Yeonho Kim and Juan Sebastián Reparaz and Bernhard Dörling and Bartłomiej Graczykowski and Igor Iatsunskyi and Katarzyna Siuzdak}, url = {https://www.sciencedirect.com/science/article/pii/S1385894721005805}, doi = {https://doi.org/10.1016/j.cej.2021.128987}, issn = {1385-8947}, year = {2021}, date = {2021-01-01}, journal = {Chemical Engineering Journal}, volume = {415}, pages = {128987}, abstract = {Transition metal carbides have gathered increasing attention in energy and electrochemistry applications, mainly due to their high structural and physicochemical properties. Their high refractory properties have made them an ideal candidate coating technology and more recently their electronic similarity to the platinum group has expanded their use to energy and catalysis. Here, we demonstrate that the nanostructuring and stoichiometry control of the highest melting point material to this date (Ta-Hf-C) results in outstanding electrochemical stability. Our results show one of the largest windows of stability of a single component electrode in a broad range pH. These experiments provide a new perspective on the electrochemical, thermoelectric and mechanical behavior of Ta-Hf-C nanocomposites, towards a broad range of applications in energy production, catalysis and analytical chemistry.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Transition metal carbides have gathered increasing attention in energy and electrochemistry applications, mainly due to their high structural and physicochemical properties. Their high refractory properties have made them an ideal candidate coating technology and more recently their electronic similarity to the platinum group has expanded their use to energy and catalysis. Here, we demonstrate that the nanostructuring and stoichiometry control of the highest melting point material to this date (Ta-Hf-C) results in outstanding electrochemical stability. Our results show one of the largest windows of stability of a single component electrode in a broad range pH. These experiments provide a new perspective on the electrochemical, thermoelectric and mechanical behavior of Ta-Hf-C nanocomposites, towards a broad range of applications in energy production, catalysis and analytical chemistry. |
2020 |
Wojnarowska, Żaneta; Musiał, Małgorzata; Cheng, Shinian; Gapiński, Jacek; Patkowski, Adam; Pionteck, Jürgen; Paluch, Marian Revealing Fast Proton Transport in Condensed Matter by Means of Density Scaling Concept The Journal of Physical Chemistry C, 124 (29), pp. 15749–15756, 2020. @article{Wojnarowska_2020, title = {Revealing Fast Proton Transport in Condensed Matter by Means of Density Scaling Concept}, author = {Żaneta Wojnarowska and Małgorzata Musiał and Shinian Cheng and Jacek Gapiński and Adam Patkowski and Jürgen Pionteck and Marian Paluch}, url = {https://doi.org/10.1021%2Facs.jpcc.0c03548}, doi = {10.1021/acs.jpcc.0c03548}, year = {2020}, date = {2020-06-01}, journal = {The Journal of Physical Chemistry C}, volume = {124}, number = {29}, pages = {15749--15756}, publisher = {American Chemical Society (ACS)}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Dalvise, Tommaso Marchesi; Harvey, Sean; Hueske, Lisa; Szelwicka, Jolanta; Veith, Lothar; Knowles, Tuomas P J; Kubiczek, Dennis; Flaig, Carolin; Port, Fabian; Gottschalk, Kay-E.; Rosenau, Frank; Graczykowski, Bartłomiej; Fytas, George; Ruggeri, Francesco S; Wunderlich, Katrin; Weil, Tanja Ultrathin Polydopamine Films with Phospholipid Nanodiscs Containing a Glycophorin A Domain Advanced Functional Materials, 30 (8), pp. 2000378, 2020, ISSN: 1616301X. @article{Sledzinska2020b, title = {Ultrathin Polydopamine Films with Phospholipid Nanodiscs Containing a Glycophorin A Domain}, author = {Tommaso Marchesi Dalvise and Sean Harvey and Lisa Hueske and Jolanta Szelwicka and Lothar Veith and Tuomas P J Knowles and Dennis Kubiczek and Carolin Flaig and Fabian Port and Kay-E. Gottschalk and Frank Rosenau and Bartłomiej Graczykowski and George Fytas and Francesco S Ruggeri and Katrin Wunderlich and Tanja Weil}, url = {https://onlinelibrary.wiley.com/doi/abs/10.1002/adfm.201904434 http://doi.wiley.com/10.1002/adfm.202000378}, doi = {10.1002/adfm.202000378}, issn = {1616301X}, year = {2020}, date = {2020-03-01}, journal = {Advanced Functional Materials}, volume = {30}, number = {8}, pages = {2000378}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Graczykowski, Bartłomiej; Vogel, Nicolas; Bley, Karina; Butt, Hans-Jürgen; Fytas, George Nano Letters, 20 (3), pp. 1883–1889, 2020, ISSN: 1530-6984. @article{Sledzinska2020c, title = {Multiband Hypersound Filtering in Two-Dimensional Colloidal Crystals: Adhesion, Resonances, and Periodicity}, author = {Bartłomiej Graczykowski and Nicolas Vogel and Karina Bley and Hans-Jürgen Butt and George Fytas}, url = {https://onlinelibrary.wiley.com/doi/abs/10.1002/adfm.201904434 http://doi.wiley.com/10.1002/adfm.202000378 https://pubs.acs.org/doi/10.1021/acs.nanolett.9b05101}, doi = {10.1021/acs.nanolett.9b05101}, issn = {1530-6984}, year = {2020}, date = {2020-03-01}, journal = {Nano Letters}, volume = {20}, number = {3}, pages = {1883--1889}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Szewczyk, Sebastian; Abram, Mateusz; Białek, Rafał; Haniewicz, Patrycja; Karolczak, Jerzy; Gapiński, Jacek; Kargul, Joanna; Gibasiewicz, Krzysztof Biochimica et Biophysica Acta (BBA) - Bioenergetics, 1861 (2), pp. 148136, 2020, ISSN: 00052728. @article{Szewczyk2020, title = {On the nature of uncoupled chlorophylls in the extremophilic photosystem I-light harvesting I supercomplex}, author = {Sebastian Szewczyk and Mateusz Abram and Rafał Białek and Patrycja Haniewicz and Jerzy Karolczak and Jacek Gapiński and Joanna Kargul and Krzysztof Gibasiewicz}, url = {https://linkinghub.elsevier.com/retrieve/pii/S0005272819301902}, doi = {10.1016/j.bbabio.2019.148136}, issn = {00052728}, year = {2020}, date = {2020-02-01}, journal = {Biochimica et Biophysica Acta (BBA) - Bioenergetics}, volume = {1861}, number = {2}, pages = {148136}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Szewczyk, Sebastian; Białek, Rafał; Giera, Wojciech; Burdziński, G; van Grondelle, Rienk; Gibasiewicz, Krzysztof Excitation dynamics in Photosystem I trapped in TiO2 mesopores Photosynthesis Research, (0123456789), 2020, ISSN: 0166-8595. @article{Szewczyk2020b, title = {Excitation dynamics in Photosystem I trapped in TiO2 mesopores}, author = {Sebastian Szewczyk and Rafał Białek and Wojciech Giera and G Burdziński and Rienk van Grondelle and Krzysztof Gibasiewicz}, url = {https://doi.org/10.1007/s11120-020-00730-1 http://link.springer.com/10.1007/s11120-020-00730-1}, doi = {10.1007/s11120-020-00730-1}, issn = {0166-8595}, year = {2020}, date = {2020-02-01}, journal = {Photosynthesis Research}, number = {0123456789}, publisher = {Springer Netherlands}, abstract = {Excitation decay in closed Photosystem I (PSI) isolated from cyanobacterium Synechocystis sp. PCC 6803 and dissolved in a buffer solution occurs predominantly with a ~ 24-ps lifetime, as measured both by time-resolved fluorescence and transient absorption. The same PSI particles deposited in mesoporous matrix made of TiO2 nanoparticles exhibit significantly accelerated excitation decay dominated by a ~ 6-ps component. Target analysis indicates that this acceleration is caused by ~ 50% increase of the rate constant of bulk Chls excitation quenching. As an effect of this increase, as much as ~ 70% of bulk Chls excitation is quenched before the establishment of equilibrium with the red Chls. Accelerated quenching may be caused by increased excitation trapping by the reaction center and/or quenching properties of the TiO2 surface directly interacting with PSI Chls. Also properties of the PSI red Chls are affected by the deposition in the TiO2 matrix: they become deeper traps due to an increase of their number and their oscillator strength is significantly reduced. These effects should be taken into account when constructing solar cells' photoelectrodes composed of PSI and artificial matrices.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Excitation decay in closed Photosystem I (PSI) isolated from cyanobacterium Synechocystis sp. PCC 6803 and dissolved in a buffer solution occurs predominantly with a ~ 24-ps lifetime, as measured both by time-resolved fluorescence and transient absorption. The same PSI particles deposited in mesoporous matrix made of TiO2 nanoparticles exhibit significantly accelerated excitation decay dominated by a ~ 6-ps component. Target analysis indicates that this acceleration is caused by ~ 50% increase of the rate constant of bulk Chls excitation quenching. As an effect of this increase, as much as ~ 70% of bulk Chls excitation is quenched before the establishment of equilibrium with the red Chls. Accelerated quenching may be caused by increased excitation trapping by the reaction center and/or quenching properties of the TiO2 surface directly interacting with PSI Chls. Also properties of the PSI red Chls are affected by the deposition in the TiO2 matrix: they become deeper traps due to an increase of their number and their oscillator strength is significantly reduced. These effects should be taken into account when constructing solar cells' photoelectrodes composed of PSI and artificial matrices. |
Szewczyk, Sebastian; Białek, Rafał; Burdziński, Gotard; Gibasiewicz, Krzysztof Photosynthesis Research, (0123456789), 2020, ISSN: 0166-8595. @article{Szewczyk2020c, title = {Photovoltaic activity of electrodes based on intact photosystem I electrodeposited on bare conducting glass}, author = {Sebastian Szewczyk and Rafał Białek and Gotard Burdziński and Krzysztof Gibasiewicz}, url = {https://doi.org/10.1007/s11120-020-00722-1 http://link.springer.com/10.1007/s11120-020-00722-1}, doi = {10.1007/s11120-020-00722-1}, issn = {0166-8595}, year = {2020}, date = {2020-02-01}, journal = {Photosynthesis Research}, number = {0123456789}, publisher = {Springer Netherlands}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Śledzińska, Marianna; Graczykowski, Bartłomiej; Maire, Jeremie; Chavez‐Angel, Emigdio; Sotomayor‐Torres, Clivia M; Alzina, Francesc 2D Phononic Crystals: Progress and Prospects in Hypersound and Thermal Transport Engineering Advanced Functional Materials, 30 (8), pp. 1904434, 2020, ISSN: 1616-301X. @article{Sledzinska2020, title = {2D Phononic Crystals: Progress and Prospects in Hypersound and Thermal Transport Engineering}, author = {Marianna Śledzińska and Bartłomiej Graczykowski and Jeremie Maire and Emigdio Chavez‐Angel and Clivia M Sotomayor‐Torres and Francesc Alzina}, url = {https://onlinelibrary.wiley.com/doi/abs/10.1002/adfm.201904434}, doi = {10.1002/adfm.201904434}, issn = {1616-301X}, year = {2020}, date = {2020-02-01}, journal = {Advanced Functional Materials}, volume = {30}, number = {8}, pages = {1904434}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Abram, Mateusz; Białek, Rafał; Szewczyk, Sebastian; Karolczak, Jerzy; Gibasiewicz, Krzysztof; Kargul, Joanna Biochimica et Biophysica Acta (BBA) - Bioenergetics, 1861 (1), pp. 148093, 2020, ISSN: 00052728. @article{Abram2020, title = {Remodeling of excitation energy transfer in extremophilic red algal PSI-LHCI complex during light adaptation}, author = {Mateusz Abram and Rafał Białek and Sebastian Szewczyk and Jerzy Karolczak and Krzysztof Gibasiewicz and Joanna Kargul}, url = {https://linkinghub.elsevier.com/retrieve/pii/S0005272819301409}, doi = {10.1016/j.bbabio.2019.148093}, issn = {00052728}, year = {2020}, date = {2020-01-01}, journal = {Biochimica et Biophysica Acta (BBA) - Bioenergetics}, volume = {1861}, number = {1}, pages = {148093}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Białek, Rafał; Friebe, Vincent; Ruff, Adrian; Jones, Michael R; Frese, Raoul; Gibasiewicz, Krzysztof Electrochimica Acta, 330 , pp. 135190, 2020, ISSN: 00134686. @article{Biaek2020, title = {In situ spectroelectrochemical investigation of a biophotoelectrode based on photoreaction centers embedded in a redox hydrogel}, author = {Rafał Białek and Vincent Friebe and Adrian Ruff and Michael R Jones and Raoul Frese and Krzysztof Gibasiewicz}, url = {https://linkinghub.elsevier.com/retrieve/pii/S0013468619320614}, doi = {10.1016/j.electacta.2019.135190}, issn = {00134686}, year = {2020}, date = {2020-01-01}, journal = {Electrochimica Acta}, volume = {330}, pages = {135190}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Jarzębski, Maciej; Siejak, Przemysław; Przeor, Monika; Gapiński, Jacek; Woźniak, Anna; Baranowska, Hanna Maria; Pawlicz, Jarosław; Baryła-Pankiewicz, Elżbieta; Szwajca, Anna Molecules, 25 (9), 2020, ISSN: 1420-3049. @article{molecules25092013, title = {Fluorescent Submicron-Sized Poly(heptafluoro-n-butyl methacrylate) Particles with Long-Term Stability}, author = {Maciej Jarzębski and Przemysław Siejak and Monika Przeor and Jacek Gapiński and Anna Woźniak and Hanna Maria Baranowska and Jarosław Pawlicz and Elżbieta Baryła-Pankiewicz and Anna Szwajca}, url = {https://www.mdpi.com/1420-3049/25/9/2013}, doi = {10.3390/molecules25092013}, issn = {1420-3049}, year = {2020}, date = {2020-01-01}, journal = {Molecules}, volume = {25}, number = {9}, abstract = {Fluorescent submicron particles of fluorinated methacrylate (HFMBA) with long-term stability have been synthesized and characterized with regard to their potential applications. Rhodamine B (RBITC) isothiocyanate was used as the fluorescent component. The core–shell structure of the particles effectively protected the dye against bleaching. HFBMA nanoparticle (NP) stability was confirmed after seven years of storage. Only slight differences were found in the polydispersity index (pdi) from 0.002 to 0.010. Particle size measurements were carried out using dynamic light scattering (DLS), nanoparticle tracking (NTA), and fluorescence correlation spectroscopy (FCS). The hydrodynamic diameter evaluated by different methods were in good agreement, respectively: 184–550 nm, 218–579 nm, and 236–508 nm. Particle and core morphology was estimated by using scanning and transmission electron microscopy (SEM and TEM). The ability to recognize particles in 3D as a reference sample in biological media has been confirmed by epifluorescence optical microscopy, confocal laser scanning microscopy, and super-resolution confocal microscopy (STED).}, keywords = {}, pubstate = {published}, tppubtype = {article} } Fluorescent submicron particles of fluorinated methacrylate (HFMBA) with long-term stability have been synthesized and characterized with regard to their potential applications. Rhodamine B (RBITC) isothiocyanate was used as the fluorescent component. The core–shell structure of the particles effectively protected the dye against bleaching. HFBMA nanoparticle (NP) stability was confirmed after seven years of storage. Only slight differences were found in the polydispersity index (pdi) from 0.002 to 0.010. Particle size measurements were carried out using dynamic light scattering (DLS), nanoparticle tracking (NTA), and fluorescence correlation spectroscopy (FCS). The hydrodynamic diameter evaluated by different methods were in good agreement, respectively: 184–550 nm, 218–579 nm, and 236–508 nm. Particle and core morphology was estimated by using scanning and transmission electron microscopy (SEM and TEM). The ability to recognize particles in 3D as a reference sample in biological media has been confirmed by epifluorescence optical microscopy, confocal laser scanning microscopy, and super-resolution confocal microscopy (STED). |
Babačić, Višnja; Varghese, Jeena; Coy, Emerson; Kang, Eunsoo; Pochylski, Mikołaj; Gapiński, Jacek; Fytas, George; Graczykowski, Bartłomiej Mechanical reinforcement of polymer colloidal crystals by supercritical fluids Journal of Colloid and Interface Science, 579 , pp. 786 - 793, 2020, ISSN: 0021-9797. @article{BABACIC2020786, title = {Mechanical reinforcement of polymer colloidal crystals by supercritical fluids}, author = {Višnja Babačić and Jeena Varghese and Emerson Coy and Eunsoo Kang and Mikołaj Pochylski and Jacek Gapiński and George Fytas and Bartłomiej Graczykowski}, url = {http://www.sciencedirect.com/science/article/pii/S0021979720308493}, doi = {https://doi.org/10.1016/j.jcis.2020.06.104}, issn = {0021-9797}, year = {2020}, date = {2020-01-01}, journal = {Journal of Colloid and Interface Science}, volume = {579}, pages = {786 - 793}, abstract = {Colloidal crystals realized by self-assembled polymer nanoparticles have prominent attraction as a platform for various applications from assembling photonic and phononic crystals, acoustic metamaterials to coating applications. However, the fragility of these systems limits their application horizon. In this work the uniform mechanical reinforcement and tunability of 3D polystyrene colloidal crystals by means of cold soldering are reported. This structural strengthening is achieved by high pressure gas (N2 or Ar) plasticization at temperatures well below the glass transition. Brillouin light scattering is employed to monitor in-situ the mechanical vibrations of the crystal and thereby determine preferential pressure, temperature and time ranges for soldering, i.e. formation of physical bonding among the nanoparticles while maintaining the shape and translational order. This low-cost method is potentially useful for fabrication and tuning of durable devices including applications in photonics, phononics, acoustic metamaterials, optomechanics, surface coatings and nanolithography.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Colloidal crystals realized by self-assembled polymer nanoparticles have prominent attraction as a platform for various applications from assembling photonic and phononic crystals, acoustic metamaterials to coating applications. However, the fragility of these systems limits their application horizon. In this work the uniform mechanical reinforcement and tunability of 3D polystyrene colloidal crystals by means of cold soldering are reported. This structural strengthening is achieved by high pressure gas (N2 or Ar) plasticization at temperatures well below the glass transition. Brillouin light scattering is employed to monitor in-situ the mechanical vibrations of the crystal and thereby determine preferential pressure, temperature and time ranges for soldering, i.e. formation of physical bonding among the nanoparticles while maintaining the shape and translational order. This low-cost method is potentially useful for fabrication and tuning of durable devices including applications in photonics, phononics, acoustic metamaterials, optomechanics, surface coatings and nanolithography. |
Białek, Rafał; Thakur, Kalyani; Ruff, Adrian; Jones, Michael R; Schuhmann, Wolfgang; Ramanan, Charusheela; Gibasiewicz, Krzysztof Insight into Electron Transfer from a Redox Polymer to a Photoactive Protein The Journal of Physical Chemistry B, 124 (49), pp. 11123-11132, 2020, (PMID: 33236901). @article{doi:10.1021/acs.jpcb.0c08714, title = {Insight into Electron Transfer from a Redox Polymer to a Photoactive Protein}, author = {Rafał Białek and Kalyani Thakur and Adrian Ruff and Michael R Jones and Wolfgang Schuhmann and Charusheela Ramanan and Krzysztof Gibasiewicz}, url = {https://doi.org/10.1021/acs.jpcb.0c08714}, doi = {10.1021/acs.jpcb.0c08714}, year = {2020}, date = {2020-01-01}, journal = {The Journal of Physical Chemistry B}, volume = {124}, number = {49}, pages = {11123-11132}, abstract = {Biohybrid photoelectrochemical systems in photovoltaic or biosensor applications have gained considerable attention in recent years. While the photoactive proteins engaged in such systems usually maintain an internal charge separation quantum yield of nearly 100%, the subsequent steps of electron and hole transfer beyond the protein often limit the overall system efficiency and their kinetics remain largely uncharacterized. To reveal the dynamics of one of such charge-transfer reactions, we report on the reduction of Rhodobacter sphaeroides reaction centers (RCs) by Os-complex-modified redox polymers (P-Os) characterized using transient absorption spectroscopy. RCs and P-Os were mixed in buffered solution in different molar ratios in the presence of a water-soluble quinone as an electron acceptor. Electron transfer from P-Os to the photoexcited RCs could be described by a three-exponential function, the fastest lifetime of which was on the order of a few microseconds, which is a few orders of magnitude faster than the internal charge recombination of RCs with fully separated charge. This was similar to the lifetime for the reduction of RCs by their natural electron donor, cytochrome c2. The rate of electron donation increased with increasing ratio of polymer to protein concentrations. It is proposed that P-Os and RCs engage in electrostatic interactions to form complexes, the sizes of which depend on the polymer-to-protein ratio. Our findings throw light on the processes within hydrogel-based biophotovoltaic devices and will inform the future design of materials optimally suited for this application.}, note = {PMID: 33236901}, keywords = {}, pubstate = {published}, tppubtype = {article} } Biohybrid photoelectrochemical systems in photovoltaic or biosensor applications have gained considerable attention in recent years. While the photoactive proteins engaged in such systems usually maintain an internal charge separation quantum yield of nearly 100%, the subsequent steps of electron and hole transfer beyond the protein often limit the overall system efficiency and their kinetics remain largely uncharacterized. To reveal the dynamics of one of such charge-transfer reactions, we report on the reduction of Rhodobacter sphaeroides reaction centers (RCs) by Os-complex-modified redox polymers (P-Os) characterized using transient absorption spectroscopy. RCs and P-Os were mixed in buffered solution in different molar ratios in the presence of a water-soluble quinone as an electron acceptor. Electron transfer from P-Os to the photoexcited RCs could be described by a three-exponential function, the fastest lifetime of which was on the order of a few microseconds, which is a few orders of magnitude faster than the internal charge recombination of RCs with fully separated charge. This was similar to the lifetime for the reduction of RCs by their natural electron donor, cytochrome c2. The rate of electron donation increased with increasing ratio of polymer to protein concentrations. It is proposed that P-Os and RCs engage in electrostatic interactions to form complexes, the sizes of which depend on the polymer-to-protein ratio. Our findings throw light on the processes within hydrogel-based biophotovoltaic devices and will inform the future design of materials optimally suited for this application. |
Vasileiadis, Thomas; Zhang, Heng; Wang, Hai; Bonn, Mischa; Fytas, George; Graczykowski, Bartłomiej Frequency-domain study of nonthermal gigahertz phonons reveals Fano coupling to charge carriers Science Advances, 6 (51), 2020, ISSN: 23752548. @article{Vasileiadis2020, title = {Frequency-domain study of nonthermal gigahertz phonons reveals Fano coupling to charge carriers}, author = {Thomas Vasileiadis and Heng Zhang and Hai Wang and Mischa Bonn and George Fytas and Bartłomiej Graczykowski}, doi = {10.1126/SCIADV.ABD4540}, issn = {23752548}, year = {2020}, date = {2020-01-01}, journal = {Science Advances}, volume = {6}, number = {51}, abstract = {Telecommunication devices exploit hypersonic gigahertz acoustic phonons to mediate signal processing with microwave radiation, and charge carriers to operate various microelectronic components. Potential interactions of hypersound with charge carriers can be revealed through frequency- and momentum-resolved studies of acoustic phonons in photoexcited semiconductors. Here, we present an all-optical method for excitation and frequency-, momentum-, and space-resolved detection of gigahertz acoustic waves in a spatially confined model semiconductor. Lamb waves are excited in a bare silicon membrane using femtosecond optical pulses and detected with frequency-domain micro-Brillouin light spectroscopy. The population of photoexcited gigahertz phonons displays a hundredfold enhancement as compared with thermal equilibrium. The phonon spectra reveal Stokes–anti-Stokes asymmetry due to propagation, and strongly asymmetric Fano resonances due to coupling between the electron-hole plasma and the photoexcited phonons. This work lays the foundation for studying hypersonic signals in nonequilibrium conditions and, more generally, phonon-dependent phenomena in photoexcited nanostructures.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Telecommunication devices exploit hypersonic gigahertz acoustic phonons to mediate signal processing with microwave radiation, and charge carriers to operate various microelectronic components. Potential interactions of hypersound with charge carriers can be revealed through frequency- and momentum-resolved studies of acoustic phonons in photoexcited semiconductors. Here, we present an all-optical method for excitation and frequency-, momentum-, and space-resolved detection of gigahertz acoustic waves in a spatially confined model semiconductor. Lamb waves are excited in a bare silicon membrane using femtosecond optical pulses and detected with frequency-domain micro-Brillouin light spectroscopy. The population of photoexcited gigahertz phonons displays a hundredfold enhancement as compared with thermal equilibrium. The phonon spectra reveal Stokes–anti-Stokes asymmetry due to propagation, and strongly asymmetric Fano resonances due to coupling between the electron-hole plasma and the photoexcited phonons. This work lays the foundation for studying hypersonic signals in nonequilibrium conditions and, more generally, phonon-dependent phenomena in photoexcited nanostructures. |
Kasprzak, Maciej; Sledzinska, Marianna; Zaleski, Karol; Iatsunskyi, Igor; Alzina, Francesc; Volz, Sebastian; Torres, Clivia Sotomayor M; Graczykowski, Bartłomiej High-temperature silicon thermal diode and switch Nano Energy, 78 (July), 2020, ISSN: 22112855. @article{Kasprzak2020, title = {High-temperature silicon thermal diode and switch}, author = {Maciej Kasprzak and Marianna Sledzinska and Karol Zaleski and Igor Iatsunskyi and Francesc Alzina and Sebastian Volz and Clivia M Sotomayor Torres and Bartłomiej Graczykowski}, doi = {10.1016/j.nanoen.2020.105261}, issn = {22112855}, year = {2020}, date = {2020-01-01}, journal = {Nano Energy}, volume = {78}, number = {July}, publisher = {Elsevier Ltd}, abstract = {A thermal rectifier/diode is a nonreciprocal element or system that enables preferential heat transport in one direction. In this work we demonstrate a single-material thermal diode operating at high temperatures. The diode is made of nanostructured silicon membranes exhibiting spatially and temperature-dependent thermal conductivity and, therefore, falling into the category of spatially asymmetric, nonlinear nonreciprocal systems. We used an all-optical state-of-the-art experimental technique to prove rectification along rigorous criteria of the phenomenon. Using sub-milliwatt power we achieve rectification of about 14%. In addition, we demonstrate air-triggered thermal switching and passive cooling. Our findings provide a CMOS-compatible platform for heat rectification and applications in energy harvesting, thermal insulation and cooling, as well as sensing and potentially thermal logic.}, keywords = {}, pubstate = {published}, tppubtype = {article} } A thermal rectifier/diode is a nonreciprocal element or system that enables preferential heat transport in one direction. In this work we demonstrate a single-material thermal diode operating at high temperatures. The diode is made of nanostructured silicon membranes exhibiting spatially and temperature-dependent thermal conductivity and, therefore, falling into the category of spatially asymmetric, nonlinear nonreciprocal systems. We used an all-optical state-of-the-art experimental technique to prove rectification along rigorous criteria of the phenomenon. Using sub-milliwatt power we achieve rectification of about 14%. In addition, we demonstrate air-triggered thermal switching and passive cooling. Our findings provide a CMOS-compatible platform for heat rectification and applications in energy harvesting, thermal insulation and cooling, as well as sensing and potentially thermal logic. |
2019 |
Pochylski, Mikołaj; Lombardo, Domenico; Calandra, Pietro Applied Sciences, 10 (1), pp. 164, 2019, ISSN: 2076-3417. @article{Pochylski2019b, title = {Optical Birefringence Growth Driven by Magnetic Field in Liquids: The Case of Dibutyl Phosphate/Propylamine System}, author = {Mikołaj Pochylski and Domenico Lombardo and Pietro Calandra}, url = {https://www.mdpi.com/2076-3417/10/1/164}, doi = {10.3390/app10010164}, issn = {2076-3417}, year = {2019}, date = {2019-12-01}, journal = {Applied Sciences}, volume = {10}, number = {1}, pages = {164}, abstract = {Magnetically-induced birefringence is usually low in molecular liquids owing to the low magnetic energy of molecules with respect to the thermal one. Despite this, it has been found that a mixture of dibutyl phosphate and propylamine at propylamine molar ratio (X) around 0.33 surprisingly gives an intense effect (∆n/$łambda$ ≈ −0.1 at 1 Tesla). In this paper the time- and intensity- response to the magnetic field of such mixture have been studied. It was found that the reaction to the magnetic field is unusually slow (from several minutes to hours) depending of the magnetic field intensity. On the basis of the data, the model of orientable dipoles dispersed in a matrix enables to interpret the magnetic field-induced self-assembly in terms of soft molecules-based nanostructures. The analogy with systems made of magnetically polarizable (solid or soft) particles dispersed in liquid carrier allows understanding, at the microscopic scale, the molecular origin and the supra-molecular dynamics involved in the observed behavior. The data present a novel phenomenon in liquid phase where the progressive building up/change of ordered and strongly interacting amphiphiles is driven by the magnetic field.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Magnetically-induced birefringence is usually low in molecular liquids owing to the low magnetic energy of molecules with respect to the thermal one. Despite this, it has been found that a mixture of dibutyl phosphate and propylamine at propylamine molar ratio (X) around 0.33 surprisingly gives an intense effect (∆n/$łambda$ ≈ −0.1 at 1 Tesla). In this paper the time- and intensity- response to the magnetic field of such mixture have been studied. It was found that the reaction to the magnetic field is unusually slow (from several minutes to hours) depending of the magnetic field intensity. On the basis of the data, the model of orientable dipoles dispersed in a matrix enables to interpret the magnetic field-induced self-assembly in terms of soft molecules-based nanostructures. The analogy with systems made of magnetically polarizable (solid or soft) particles dispersed in liquid carrier allows understanding, at the microscopic scale, the molecular origin and the supra-molecular dynamics involved in the observed behavior. The data present a novel phenomenon in liquid phase where the progressive building up/change of ordered and strongly interacting amphiphiles is driven by the magnetic field. |
Comez, L; Fioretto, D; Gapiński, Jacek; Monaco, G; Patkowski, Adam; Steffen, W Condensed Matter Physics, 22 (4), pp. 43603, 2019. @article{Comez2019, title = {Inelastic x-ray scattering reveals the ergodic to nonergodic transition of salol, a liquid with local order}, author = {L. Comez and D. Fioretto and Jacek Gapiński and G. Monaco and Adam Patkowski and W. Steffen}, doi = {10.5488/CMP.22.43603}, year = {2019}, date = {2019-11-01}, journal = {Condensed Matter Physics}, volume = {22}, number = {4}, pages = {43603}, abstract = {We have studied the high-frequency dynamics of salol by inelastic x-ray scattering over a wide temperature range between 50 and 450 K, across the glass transition. We find that salol efficiently realizes the mechanism of dynamical arrest described by the mode-coupling theory, as manifested by a cusp singularity in the behaviour of the non-ergodicity parameter and a Q dependence of the critical non-ergodicity parameter that is in phase with the static structure factor. These results confront positively the mode-coupling theory with liquids with local order.}, keywords = {}, pubstate = {published}, tppubtype = {article} } We have studied the high-frequency dynamics of salol by inelastic x-ray scattering over a wide temperature range between 50 and 450 K, across the glass transition. We find that salol efficiently realizes the mechanism of dynamical arrest described by the mode-coupling theory, as manifested by a cusp singularity in the behaviour of the non-ergodicity parameter and a Q dependence of the critical non-ergodicity parameter that is in phase with the static structure factor. These results confront positively the mode-coupling theory with liquids with local order. |
Śledzińska, Marianna; Graczykowski, Bartłomiej; Marie, Jeremie; Chavez-Angel, Emigdio; Sotomayor-Torres, Clivia M; Alzina, Francesc 2D Phononic Crystals: Progress and Prospects in Hypersound and Thermal Transport Engineering Advanced Functional Materials, pp. 1904434, 2019. @article{Śledzińska2019, title = {2D Phononic Crystals: Progress and Prospects in Hypersound and Thermal Transport Engineering}, author = {Marianna Śledzińska and Bartłomiej Graczykowski and Jeremie Marie and Emigdio Chavez-Angel and Clivia M. Sotomayor-Torres and Francesc Alzina}, doi = {10.1002/adfm.201904434}, year = {2019}, date = {2019-09-11}, journal = {Advanced Functional Materials}, pages = {1904434}, abstract = {The central concept in phononics is the tuning of the phonon dispersion relation, or phonon engineering, which provides a means of controlling related properties such as group velocity or phonon interactions and, therefore, phonon propagation, in a wide range of frequencies depending on the geometries and sizes of the materials. Phononics exploits the present state of the art in nanofabrication to tailor dispersion relations in the range of GHz for the control of elastic waves/phonons propagation with applications toward new information technology concepts with phonons as state variable. Moreover, phonons provide an adaptable approach for supporting a coherent coupling between different state variables, and the development of nanoscale optomechanical systems during the last decade attests this prospect. The most extended approach to manipulate the phonon dispersion relation is introducing an artificial periodic modulation of the elastic properties, which is referred to as phononic crystal (PnC). Herein, the focus is on the recent experimental achievements in the fabrication and application of 2D PnCs enabling the modification of the dispersion relation of surface and membrane modes, and presenting phononic bandgaps, waveguiding, and confinement in the hypersonic regime. Furthermore, these artificial materials offer the potential of modifying and controlling the heat flow to enable new schemes in thermal management.}, keywords = {}, pubstate = {published}, tppubtype = {article} } The central concept in phononics is the tuning of the phonon dispersion relation, or phonon engineering, which provides a means of controlling related properties such as group velocity or phonon interactions and, therefore, phonon propagation, in a wide range of frequencies depending on the geometries and sizes of the materials. Phononics exploits the present state of the art in nanofabrication to tailor dispersion relations in the range of GHz for the control of elastic waves/phonons propagation with applications toward new information technology concepts with phonons as state variable. Moreover, phonons provide an adaptable approach for supporting a coherent coupling between different state variables, and the development of nanoscale optomechanical systems during the last decade attests this prospect. The most extended approach to manipulate the phonon dispersion relation is introducing an artificial periodic modulation of the elastic properties, which is referred to as phononic crystal (PnC). Herein, the focus is on the recent experimental achievements in the fabrication and application of 2D PnCs enabling the modification of the dispersion relation of surface and membrane modes, and presenting phononic bandgaps, waveguiding, and confinement in the hypersonic regime. Furthermore, these artificial materials offer the potential of modifying and controlling the heat flow to enable new schemes in thermal management. |
Pochylski, Mikołaj Structural relaxation in the wave-vector dependence of the longitudinal rigidity modulus Biomed. Opt. Express, 10 (4), pp. 1957–1964, 2019. @article{Pochylski:19, title = {Structural relaxation in the wave-vector dependence of the longitudinal rigidity modulus}, author = {Mikołaj Pochylski}, url = {http://www.osapublishing.org/boe/abstract.cfm?URI=boe-10-4-1957}, doi = {10.1364/BOE.10.001957}, year = {2019}, date = {2019-04-01}, journal = {Biomed. Opt. Express}, volume = {10}, number = {4}, pages = {1957--1964}, publisher = {OSA}, abstract = {Brillouin microscopy recently attracted much attention for being a promising tool for all-optical label-free determination of mechanical properties of biological samples. Before its widespread utilization for biomedical applications, numbers of nuances related with this technique need to be recognized. In this article, we discuss the process of structural relaxation, the phenomena not commonly addressed by the emerging bio-Brillouin community, and its effect on longitudinal rigidity modulus. Using a model aqueous polymer mixture, we show how scattering measurements performed on the same specimen using different experimental geometries can lead to different results.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Brillouin microscopy recently attracted much attention for being a promising tool for all-optical label-free determination of mechanical properties of biological samples. Before its widespread utilization for biomedical applications, numbers of nuances related with this technique need to be recognized. In this article, we discuss the process of structural relaxation, the phenomena not commonly addressed by the emerging bio-Brillouin community, and its effect on longitudinal rigidity modulus. Using a model aqueous polymer mixture, we show how scattering measurements performed on the same specimen using different experimental geometries can lead to different results. |
Stracy, Mathew; Wollman, Adam JM; Kaja, Elżbieta; Gapiński, Jacek; Lee, Ji-Eun; Leek, Victoria A; McKie, Shannon J; Mitchenall, Lesley A; Maxwell, Anthony; Sherratt, David J; Leake, Mark C; Zawadzki, Paweł Single-molecule imaging of DNA gyrase activity in living Escherichia coli Nucleic Acids Research, 47 (1), pp. 210-220, 2019. @article{doi:10.1093/nar/gky1143, title = {Single-molecule imaging of DNA gyrase activity in living Escherichia coli}, author = {Mathew Stracy and Adam JM Wollman and Elżbieta Kaja and Jacek Gapiński and Ji-Eun Lee and Victoria A Leek and Shannon J McKie and Lesley A Mitchenall and Anthony Maxwell and David J Sherratt and Mark C Leake and Paweł Zawadzki}, url = {http://dx.doi.org/10.1093/nar/gky1143}, doi = {10.1093/nar/gky1143}, year = {2019}, date = {2019-01-10}, journal = {Nucleic Acids Research}, volume = {47}, number = {1}, pages = {210-220}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Pochylski, Mikołaj; Gapiński, Jacek; Wojnarowska, Z; Paluch, M; Patkowski, Adam Journal of Molecular Liquids, 282 , pp. 51 - 56, 2019, ISSN: 0167-7322. @article{POCHYLSKI201951, title = {Nature of intramolecular dynamics in protic ionic glass-former: insight from ambient and high pressure Brillouin spectroscopy}, author = {Mikołaj Pochylski and Jacek Gapiński and Z Wojnarowska and M Paluch and Adam Patkowski}, url = {http://www.sciencedirect.com/science/article/pii/S0167732219302417}, doi = {https://doi.org/10.1016/j.molliq.2019.02.131}, issn = {0167-7322}, year = {2019}, date = {2019-01-01}, journal = {Journal of Molecular Liquids}, volume = {282}, pages = {51 - 56}, abstract = {Proton conducting materials play an important role in a variety of electrochemical devices. Especially, the class of protic ionic glass-formers with fast water-independent proton transport within the Grotthuss mechanism has been envisioned as promising fuel cell electrolytes. Nevertheless, despite a number of reports on protic ionic glasses the description of proton transport phenomenon in these systems is still incomplete. Herein, we employed the Brillouin scattering technique to investigate the intramolecular dynamics of acebutolol hydrochloride, protic ionic glass-former with isomerization ability. The studies performed at ambient and elevated pressure revealed the fast relaxation dynamics that may control the proton conductivity, especially at temperatures T < Tg where the vehicle mechanism contribution is negligible.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Proton conducting materials play an important role in a variety of electrochemical devices. Especially, the class of protic ionic glass-formers with fast water-independent proton transport within the Grotthuss mechanism has been envisioned as promising fuel cell electrolytes. Nevertheless, despite a number of reports on protic ionic glasses the description of proton transport phenomenon in these systems is still incomplete. Herein, we employed the Brillouin scattering technique to investigate the intramolecular dynamics of acebutolol hydrochloride, protic ionic glass-former with isomerization ability. The studies performed at ambient and elevated pressure revealed the fast relaxation dynamics that may control the proton conductivity, especially at temperatures T < Tg where the vehicle mechanism contribution is negligible. |
Kasprowicz, D; Chiasera, A; Chappini, A; Zur, L; Gapiński, Jacek; Chrunik, M; Majchrowski, A; Jastrzab, R; Ferrari, M Up-conversion luminescence of RE3+ -doped polymer composites KGd(WO4)2&PMMA 88 , pp. 366 - 371, 2019, ISSN: 0925-3467. @article{KASPROWICZ2019366, title = {Up-conversion luminescence of RE3+ -doped polymer composites KGd(WO4)2&PMMA}, author = {D Kasprowicz and A Chiasera and A Chappini and L Zur and Jacek Gapiński and M Chrunik and A Majchrowski and R Jastrzab and M Ferrari}, url = {http://www.sciencedirect.com/science/article/pii/S0925346718307924}, doi = {https://doi.org/10.1016/j.optmat.2018.12.001}, issn = {0925-3467}, year = {2019}, date = {2019-01-01}, volume = {88}, pages = {366 - 371}, abstract = {Poly(methyl methacrylate) (PMMA)-based luminescent materials are of prime interest for many new optoelectronic devices. This work presents the spectroscopic properties of PMMA-based composites containing KGd(WO4)2:Yb3+/Er3+/Tm3+, KGd(WO4)2:Yb3+/Tm3+ and KGd(WO4)2:Yb3+/Er3+ powders. These systems exhibit effective multicolor up-conversion luminescence in VIS and NIR spectral range under 980 nm excitation. The vibrational properties of the composites were investigated for the first time using the μ-Raman spectroscopy. The obtained results suggest that the KGd(WO4)2:Yb3+/Er3+/Tm3+&PMMA integrated system can be successfully used as a new phosphor for the up-conversion based optoelectronic devices.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Poly(methyl methacrylate) (PMMA)-based luminescent materials are of prime interest for many new optoelectronic devices. This work presents the spectroscopic properties of PMMA-based composites containing KGd(WO4)2:Yb3+/Er3+/Tm3+, KGd(WO4)2:Yb3+/Tm3+ and KGd(WO4)2:Yb3+/Er3+ powders. These systems exhibit effective multicolor up-conversion luminescence in VIS and NIR spectral range under 980 nm excitation. The vibrational properties of the composites were investigated for the first time using the μ-Raman spectroscopy. The obtained results suggest that the KGd(WO4)2:Yb3+/Er3+/Tm3+&PMMA integrated system can be successfully used as a new phosphor for the up-conversion based optoelectronic devices. |
Kang, E; Graczykowski, Bartłomiej; Jonas, U; Christie, D; Gray, L A G; Cangialosi, D; Priestley, R D; Fytas, Georg Macromolecules, 52 (14), pp. 5399-5406, 2019. @article{Kang20195399, title = {Shell Architecture Strongly Influences the Glass Transition, Surface Mobility, and Elasticity of Polymer Core-Shell Nanoparticles}, author = {E Kang and Bartłomiej Graczykowski and U Jonas and D Christie and L A G Gray and D Cangialosi and R D Priestley and Georg Fytas}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85070272667&doi=10.1021%2facs.macromol.9b00766&partnerID=40&md5=2dcd70191d0df0d80f2a608e2ce143cc}, doi = {10.1021/acs.macromol.9b00766}, year = {2019}, date = {2019-01-01}, journal = {Macromolecules}, volume = {52}, number = {14}, pages = {5399-5406}, abstract = {Despite the growing application of nanostructured polymeric materials, there still remains a large gap in our understanding of polymer mechanics and thermal stability under confinement and near polymer-polymer interfaces. In particular, the knowledge of polymer nanoparticle thermal stability and mechanics is of great importance for their application in drug delivery, phononics, and photonics. Here, we quantified the effects of a polymer shell layer on the modulus and glass-transition temperature (Tg) of polymer core-shell nanoparticles via Brillouin light spectroscopy and modulated differential scanning calorimetry, respectively. Nanoparticles consisting of a polystyrene (PS) core and shell layers of poly(n-butyl methacrylate) (PBMA) were characterized as model systems. We found that the high Tg of the PS core was largely unaffected by the presence of an outer polymer shell, whereas the lower Tg of the PBMA shell layer decreased with increasing PBMA thickness. The surface mobility was revealed at a temperature about 15 K lower than the Tg of the PBMA shell layer. Overall, the modulus of the core-shell nanoparticles decreased with increasing PBMA shell layer thickness. These results suggest that the nanoparticle modulus and Tg can be tuned independently through the control of nanoparticle composition and architecture. © 2019 American Chemical Society.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Despite the growing application of nanostructured polymeric materials, there still remains a large gap in our understanding of polymer mechanics and thermal stability under confinement and near polymer-polymer interfaces. In particular, the knowledge of polymer nanoparticle thermal stability and mechanics is of great importance for their application in drug delivery, phononics, and photonics. Here, we quantified the effects of a polymer shell layer on the modulus and glass-transition temperature (Tg) of polymer core-shell nanoparticles via Brillouin light spectroscopy and modulated differential scanning calorimetry, respectively. Nanoparticles consisting of a polystyrene (PS) core and shell layers of poly(n-butyl methacrylate) (PBMA) were characterized as model systems. We found that the high Tg of the PS core was largely unaffected by the presence of an outer polymer shell, whereas the lower Tg of the PBMA shell layer decreased with increasing PBMA thickness. The surface mobility was revealed at a temperature about 15 K lower than the Tg of the PBMA shell layer. Overall, the modulus of the core-shell nanoparticles decreased with increasing PBMA shell layer thickness. These results suggest that the nanoparticle modulus and Tg can be tuned independently through the control of nanoparticle composition and architecture. © 2019 American Chemical Society. |
Graczykowski, Bartłomiej; Gueddida, A; Djafari-Rouhani, B; Butt, H -J; Fytas, Georg Physical Review B, 99 (16), 2019. @article{Graczykowski2019, title = {Brillouin light scattering under one-dimensional confinement: Symmetry and interference self-canceling}, author = {Bartłomiej Graczykowski and A Gueddida and B Djafari-Rouhani and H -J Butt and Georg Fytas}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85065496617&doi=10.1103%2fPhysRevB.99.165431&partnerID=40&md5=fc7596c288a1a9ecba8176296c150eac}, doi = {10.1103/PhysRevB.99.165431}, year = {2019}, date = {2019-01-01}, journal = {Physical Review B}, volume = {99}, number = {16}, abstract = {We present the spontaneous Brillouin light scattering (BLS) under simultaneous one-dimensional confinement of sound and light and show that the photon-phonon coupling results from nontrivial interplay of the photoelastic and moving-interface effects. We reveal two types of BLS self-canceling: governed by mode symmetry and driven by destructive interference of the two effects. We show that the latter can be adjusted by the light polarization and phonon wave number. Furthermore, we present a measurement of the shear-horizontal waves in thin membranes. © 2019 American Physical Society.}, keywords = {}, pubstate = {published}, tppubtype = {article} } We present the spontaneous Brillouin light scattering (BLS) under simultaneous one-dimensional confinement of sound and light and show that the photon-phonon coupling results from nontrivial interplay of the photoelastic and moving-interface effects. We reveal two types of BLS self-canceling: governed by mode symmetry and driven by destructive interference of the two effects. We show that the latter can be adjusted by the light polarization and phonon wave number. Furthermore, we present a measurement of the shear-horizontal waves in thin membranes. © 2019 American Physical Society. |
Jarzębski, Maciej; Peplińska, Barbara; Florczak, Patryk; Gapiński, Jacek; Flak, Dorota; Mała, Patrycja; Ramanavicius, Arunas; Baryła-Pankiewicz, Elżbieta; Cisowska, Joanna Kobus-; Szwajca, Anna Fluorescein ether-ester dyes for labeling of fluorinated methacrylate nanoparticles Journal of Photochemistry and Photobiology A: Chemistry, 382 , pp. 111956, 2019, ISSN: 1010-6030. @article{JARZEBSKI2019111956, title = {Fluorescein ether-ester dyes for labeling of fluorinated methacrylate nanoparticles}, author = {Maciej Jarzębski and Barbara Peplińska and Patryk Florczak and Jacek Gapiński and Dorota Flak and Patrycja Mała and Arunas Ramanavicius and Elżbieta Baryła-Pankiewicz and Joanna Kobus- Cisowska and Anna Szwajca}, url = {http://www.sciencedirect.com/science/article/pii/S1010603019304058}, doi = {https://doi.org/10.1016/j.jphotochem.2019.111956}, issn = {1010-6030}, year = {2019}, date = {2019-01-01}, journal = {Journal of Photochemistry and Photobiology A: Chemistry}, volume = {382}, pages = {111956}, abstract = {Fluorescent core-shell particles are used as versatile fluorophores in confocal microscopy based image analysis and as a colloidal model system to study short and long-range interactions. Bright and stable microspherical probes are proposed as promising materials, especially in bioimaging applications. The release of dyes from fluorescent polymer microspheres is undesirable. Covalent linking of dyes within polymeric spheres during the polymerization process can solve the problem of dye leaching. This requires, e.g. the introduction of reactive groups into the dyes. Its more lipophilic ester-ether derivatives considerably reduced fluorescence. The fluorescent quantum yield of prepared nanoparticles was determined to be below 10%. As-prepared nanoparticles exhibited a low refractive index (1.293–1.349), hence their use is recommended. Scanning electron microscope (SEM) images and the fluorescence correlation spectroscopy (FCS) measurements confirmed high polydispersity of synthesized particles (40–230 nm), and are in agreement with the dynamic light scattering (DLS) and nanoparticle tracking analysis (NTA) results (hydrodynamic diameters 203 ± 9, 548 ± 50, 146 ± 2 nm). The zeta potential of fluorescent 1H,1H-heptafluoro-n-butyl methacrylate (HFBMA) shell nanoparticles (NPs) with propargyl ether-esters, 2-methyl allyl ether-esters and allyl ether-esters of fluorescein was -44.5,-14, -44.7 mV, respectively. The values are different despite the slight difference in the structure of ester-ether derivatives.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Fluorescent core-shell particles are used as versatile fluorophores in confocal microscopy based image analysis and as a colloidal model system to study short and long-range interactions. Bright and stable microspherical probes are proposed as promising materials, especially in bioimaging applications. The release of dyes from fluorescent polymer microspheres is undesirable. Covalent linking of dyes within polymeric spheres during the polymerization process can solve the problem of dye leaching. This requires, e.g. the introduction of reactive groups into the dyes. Its more lipophilic ester-ether derivatives considerably reduced fluorescence. The fluorescent quantum yield of prepared nanoparticles was determined to be below 10%. As-prepared nanoparticles exhibited a low refractive index (1.293–1.349), hence their use is recommended. Scanning electron microscope (SEM) images and the fluorescence correlation spectroscopy (FCS) measurements confirmed high polydispersity of synthesized particles (40–230 nm), and are in agreement with the dynamic light scattering (DLS) and nanoparticle tracking analysis (NTA) results (hydrodynamic diameters 203 ± 9, 548 ± 50, 146 ± 2 nm). The zeta potential of fluorescent 1H,1H-heptafluoro-n-butyl methacrylate (HFBMA) shell nanoparticles (NPs) with propargyl ether-esters, 2-methyl allyl ether-esters and allyl ether-esters of fluorescein was -44.5,-14, -44.7 mV, respectively. The values are different despite the slight difference in the structure of ester-ether derivatives. |
2018 |
Boś-Liedke, Agnieszka; Walawender, Magdalena; Woźniak, Anna; Flak, Dorota; Gapiński, Jacek; Jurga, Stefan; Kucińska, Małgorzata; Plewiński, Adam; Murias, Marek; Elewa, Marwa; Lampp, Lisa; Imming, Peter; Tadyszak, Krzysztof EPR Oximetry Sensor-Developing a TAM Derivative for In Vivo Studies Cell Biochemistry and Biophysics, 76 (1), pp. 19–28, 2018, ISSN: 1559-0283. @article{Boś-Liedke2018, title = {EPR Oximetry Sensor-Developing a TAM Derivative for In Vivo Studies}, author = {Agnieszka Boś-Liedke and Magdalena Walawender and Anna Woźniak and Dorota Flak and Jacek Gapiński and Stefan Jurga and Małgorzata Kucińska and Adam Plewiński and Marek Murias and Marwa Elewa and Lisa Lampp and Peter Imming and Krzysztof Tadyszak}, url = {https://doi.org/10.1007/s12013-017-0824-3}, doi = {10.1007/s12013-017-0824-3}, issn = {1559-0283}, year = {2018}, date = {2018-06-01}, journal = {Cell Biochemistry and Biophysics}, volume = {76}, number = {1}, pages = {19--28}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Szewczyk, Sebastian; Giera, Wojciech; Białek, Rafał; Burdziński, Gotard; Gibasiewicz, Krzysztof Acceleration of the excitation decay in Photosystem I immobilized on glass surface Photosynthesis Research, 136 (2), pp. 171-181, 2018, ISSN: 0166-8595. @article{Szewczyk2018b, title = {Acceleration of the excitation decay in Photosystem I immobilized on glass surface}, author = {Sebastian Szewczyk and Wojciech Giera and Rafał Białek and Gotard Burdziński and Krzysztof Gibasiewicz}, url = {http://link.springer.com/10.1007/s11120-017-0454-z}, doi = {10.1007/s11120-017-0454-z}, issn = {0166-8595}, year = {2018}, date = {2018-05-01}, journal = {Photosynthesis Research}, volume = {136}, number = {2}, pages = {171-181}, abstract = {textcopyright 2017 The Author(s) Femtosecond transient absorption was used to study excitation decay in monomeric and trimeric cyanobacterial Photosystem I (PSI) being prepared in three states: (1) in aqueous solution, (2) deposited and dried on glass surface (either conducting or non-conducting), and (3) deposited on glass (conducting) surface but being in contact with aqueous solvent. The main goal of this contribution was to determine the reason of the acceleration of the excitation decay in dried PSI deposited on the conducting surface relative to PSI in solution observed previously using time-resolved fluorescence (Szewczyk et al., Photysnth Res 132(2):111–126, 2017). We formulated two alternative working hypotheses: (1) the acceleration results from electron injection from PSI to the conducting surface; (2) the acceleration is caused by dehydration and/or crowding of PSI proteins deposited on the glass substrate. Excitation dynamics of PSI in all three types of samples can be described by three main components of subpicosecond, 3–5, and 20–26 ps lifetimes of different relative contributions in solution than in PSI-substrate systems. The presence of similar kinetic components for all the samples indicates intactness of PSI proteins after their deposition onto the substrates. The kinetic traces for all systems with PSI deposited on substrates are almost identical and they decay significantly faster than the kinetic traces of PSI in solution. We conclude that the accelerated excitation decay in PSI-substrate systems is caused mostly by dense packing of proteins.}, keywords = {}, pubstate = {published}, tppubtype = {article} } textcopyright 2017 The Author(s) Femtosecond transient absorption was used to study excitation decay in monomeric and trimeric cyanobacterial Photosystem I (PSI) being prepared in three states: (1) in aqueous solution, (2) deposited and dried on glass surface (either conducting or non-conducting), and (3) deposited on glass (conducting) surface but being in contact with aqueous solvent. The main goal of this contribution was to determine the reason of the acceleration of the excitation decay in dried PSI deposited on the conducting surface relative to PSI in solution observed previously using time-resolved fluorescence (Szewczyk et al., Photysnth Res 132(2):111–126, 2017). We formulated two alternative working hypotheses: (1) the acceleration results from electron injection from PSI to the conducting surface; (2) the acceleration is caused by dehydration and/or crowding of PSI proteins deposited on the glass substrate. Excitation dynamics of PSI in all three types of samples can be described by three main components of subpicosecond, 3–5, and 20–26 ps lifetimes of different relative contributions in solution than in PSI-substrate systems. The presence of similar kinetic components for all the samples indicates intactness of PSI proteins after their deposition onto the substrates. The kinetic traces for all systems with PSI deposited on substrates are almost identical and they decay significantly faster than the kinetic traces of PSI in solution. We conclude that the accelerated excitation decay in PSI-substrate systems is caused mostly by dense packing of proteins. |
Łukarska, M; Jankowska, A; Gapiński, Jacek; Valable, S; Anfray, C; Menard, B; Mintova, S; Kowalak, S Encapsulation of fluorescein into nanozeolites L and Y Microporous and Mesoporous Materials, 260 , pp. 70–75, 2018, ISSN: 13871811. @article{ukarska2018, title = {Encapsulation of fluorescein into nanozeolites L and Y}, author = {M Łukarska and A Jankowska and Jacek Gapiński and S Valable and C Anfray and B Menard and S Mintova and S Kowalak}, url = {https://www.sciencedirect.com/science/article/pii/S1387181117306959 http://linkinghub.elsevier.com/retrieve/pii/S1387181117306959}, doi = {10.1016/j.micromeso.2017.10.040}, issn = {13871811}, year = {2018}, date = {2018-04-01}, journal = {Microporous and Mesoporous Materials}, volume = {260}, pages = {70--75}, publisher = {Elsevier}, abstract = {Fluorescein (F) species were encapsulated inside nanosized zeolites L and Y by their synthesis from adsorbed precursors (phthalic anhydride (Ph) and resorcinol (R)). The applied nanozeolites were modified either with H+ or Zn2+ cations and they played roles of the catalysts for synthesis of F and of the matrices for resulting dye molecules. The F loading, its tautomeric forms and optical properties of obtained composites depended on zeolite structure, morphology and on introduced cations. The composites usually showed higher fluorescence intensity than the pristine dye. The highest fluorescence intensity was noticed for the sample with nano-ZnL matrix. This intensity was much higher than that observed for composite with conventional micro-sized Zn L zeolite. Regarding an efficient fluorescence and nanosize of the obtained composites they seem promising fluorescent tracer for medical (theranostic) applications.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Fluorescein (F) species were encapsulated inside nanosized zeolites L and Y by their synthesis from adsorbed precursors (phthalic anhydride (Ph) and resorcinol (R)). The applied nanozeolites were modified either with H+ or Zn2+ cations and they played roles of the catalysts for synthesis of F and of the matrices for resulting dye molecules. The F loading, its tautomeric forms and optical properties of obtained composites depended on zeolite structure, morphology and on introduced cations. The composites usually showed higher fluorescence intensity than the pristine dye. The highest fluorescence intensity was noticed for the sample with nano-ZnL matrix. This intensity was much higher than that observed for composite with conventional micro-sized Zn L zeolite. Regarding an efficient fluorescence and nanosize of the obtained composites they seem promising fluorescent tracer for medical (theranostic) applications. |
Skupin-Mrugalska, Paulina; Sobotta, Lukasz; Warowicka, Alicja; Wereszczynska, Beata; Zalewski, Tomasz; Gierlich, Piotr; Jarek, Marcin; Nowaczyk, Grzegorz; Kempka, Marek; Gapiński, Jacek; Jurga, Stefan; Mielcarek, Jadwiga Journal of Inorganic Biochemistry, 180 , pp. 1–14, 2018, ISSN: 01620134. @article{Skupin-Mrugalska2018, title = {Theranostic liposomes as a bimodal carrier for magnetic resonance imaging contrast agent and photosensitizer}, author = {Paulina Skupin-Mrugalska and Lukasz Sobotta and Alicja Warowicka and Beata Wereszczynska and Tomasz Zalewski and Piotr Gierlich and Marcin Jarek and Grzegorz Nowaczyk and Marek Kempka and Jacek Gapiński and Stefan Jurga and Jadwiga Mielcarek}, url = {http://linkinghub.elsevier.com/retrieve/pii/S0162013417305366}, doi = {10.1016/j.jinorgbio.2017.11.025}, issn = {01620134}, year = {2018}, date = {2018-03-01}, journal = {Journal of Inorganic Biochemistry}, volume = {180}, pages = {1--14}, abstract = {The present study is focused on the development of liposomes bearing gadolinium chelate (GdLip) providing two functionalities for magnetic resonance imaging (MRI) and photodynamic therapy of cancer. A lipid derivative of gadolinium(III) diethylenetriamine pentaacetic acid salt (GdDTPA1) was inserted in the liposomal membrane and served as MRI contrast agent whereas a zinc phthalocyanine (ZnPc) was used as a model photosensitizer. In addition to conventional liposomes, pegylated lipids were used for the preparation of “stealth” liposomes. The characterization of different GdLip formulations involved evaluation of the liposomes size by nanoparticle tracking analysis, thermal phase behavior by differential scanning calorimetry and ZnPc-mediated singlet oxygen production. Furthermore, relaxivity measurements were performed as well as cytotoxicity and photodynamic activity against cancerous and normal cell lines was studied. Size and thermal behavior were only slightly influenced by GdLip composition, however it distinctly affected singlet oxygen production of ZnPc-loaded GdLip. The quantum yields of singlet oxygen generation by zinc phthalocyanine incorporated in GdLip containing cationic or/and pegylated lipids were smaller than those obtained for non-pegylated carriers with l-$alpha$-phosphatidylglycerol. In general, all formulations of GdLip, irrespectively of composition, were characterized by relaxivities higher than those of commercially used contrast agents (e.g. Magnevisttextregistered). NMR study has shown that the incorporation of ZnPc into the formulations of GdLip increases the relaxation parameters r1 and r2, compared to the values for the non-loaded vesicles. GdDTPA1 did not influence the photodynamic activity of ZnPc against HeLa cells.}, keywords = {}, pubstate = {published}, tppubtype = {article} } The present study is focused on the development of liposomes bearing gadolinium chelate (GdLip) providing two functionalities for magnetic resonance imaging (MRI) and photodynamic therapy of cancer. A lipid derivative of gadolinium(III) diethylenetriamine pentaacetic acid salt (GdDTPA1) was inserted in the liposomal membrane and served as MRI contrast agent whereas a zinc phthalocyanine (ZnPc) was used as a model photosensitizer. In addition to conventional liposomes, pegylated lipids were used for the preparation of “stealth” liposomes. The characterization of different GdLip formulations involved evaluation of the liposomes size by nanoparticle tracking analysis, thermal phase behavior by differential scanning calorimetry and ZnPc-mediated singlet oxygen production. Furthermore, relaxivity measurements were performed as well as cytotoxicity and photodynamic activity against cancerous and normal cell lines was studied. Size and thermal behavior were only slightly influenced by GdLip composition, however it distinctly affected singlet oxygen production of ZnPc-loaded GdLip. The quantum yields of singlet oxygen generation by zinc phthalocyanine incorporated in GdLip containing cationic or/and pegylated lipids were smaller than those obtained for non-pegylated carriers with l-$alpha$-phosphatidylglycerol. In general, all formulations of GdLip, irrespectively of composition, were characterized by relaxivities higher than those of commercially used contrast agents (e.g. Magnevisttextregistered). NMR study has shown that the incorporation of ZnPc into the formulations of GdLip increases the relaxation parameters r1 and r2, compared to the values for the non-loaded vesicles. GdDTPA1 did not influence the photodynamic activity of ZnPc against HeLa cells. |
Meier, G; Gapiński, Jacek; Ratajczyk, M; Lettinga, M P; Hirtz, K; Banachowicz, Ewa; Patkowski, Adam The Journal of Chemical Physics, 148 (9), pp. 094201, 2018. @article{Meier2018, title = {Nano-viscosity of supercooled liquid measured by fluorescence correlation spectroscopy: Pressure and temperature dependence and the density scaling}, author = {G Meier and Jacek Gapiński and M Ratajczyk and M P Lettinga and K Hirtz and Ewa Banachowicz and Adam Patkowski}, url = {https://doi.org/10.1063/1.5011196}, doi = {10.1063/1.5011196}, year = {2018}, date = {2018-01-01}, journal = {The Journal of Chemical Physics}, volume = {148}, number = {9}, pages = {094201}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Ivashchenko, Olena; Peplinska, Barbara; Gapiński, Jacek; Flak, Dorota; Jarek, Marcin; Zaleski, Karol; Nowaczyk, Grzegorz; Pietralik, Zuzanna; Jurga, Stefan Scientific Reports, 8 (1), pp. 4041, 2018, ISSN: 2045-2322. @article{Ivashchenko2018, title = {Silver and ultrasmall iron oxides nanoparticles in hydrocolloids: effect of magnetic field and temperature on self-organization}, author = {Olena Ivashchenko and Barbara Peplinska and Jacek Gapiński and Dorota Flak and Marcin Jarek and Karol Zaleski and Grzegorz Nowaczyk and Zuzanna Pietralik and Stefan Jurga}, url = {https://doi.org/10.1038/s41598-018-22426-2}, doi = {10.1038/s41598-018-22426-2}, issn = {2045-2322}, year = {2018}, date = {2018-01-01}, journal = {Scientific Reports}, volume = {8}, number = {1}, pages = {4041}, abstract = {Micro/nanostructures, which are assembled from various nanosized building blocks are of great scientific interests due to their combined features in the micro- and nanometer scale. This study for the first time demonstrates that ultrasmall superparamagnetic iron oxide nanoparticles can change the microstructure of their hydrocolloids under the action of external magnetic field. We aimed also at the establishment of the physiological temperature (39 textdegreeC) influence on the self-organization of silver and ultrasmall iron oxides nanoparticles (NPs) in hydrocolloids. Consequences of such induced changes were further investigated in terms of their potential effect on the biological activity in vitro. Physicochemical characterization included X-ray diffraction (XRD), optical microscopies (SEM, cryo-SEM, TEM, fluorescence), dynamic light scattering (DLS) techniques, energy dispersive (EDS), Fourier transform infrared (FTIR) and ultraviolet-visible (UV-Vis) spectroscopies, zeta-potential and magnetic measurements. The results showed that magnetic field affected the hydrocolloids microstructure uniformity, fluorescence properties and photodynamic activity. Likewise, increased temperature caused changes in NPs hydrodynamic size distribution and in hydrocolloids microstructure. Magnetic field significantly improved photodynamic activity that was attributed to enhanced generation of reactive oxygen species due to reorganization of the microstructure.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Micro/nanostructures, which are assembled from various nanosized building blocks are of great scientific interests due to their combined features in the micro- and nanometer scale. This study for the first time demonstrates that ultrasmall superparamagnetic iron oxide nanoparticles can change the microstructure of their hydrocolloids under the action of external magnetic field. We aimed also at the establishment of the physiological temperature (39 textdegreeC) influence on the self-organization of silver and ultrasmall iron oxides nanoparticles (NPs) in hydrocolloids. Consequences of such induced changes were further investigated in terms of their potential effect on the biological activity in vitro. Physicochemical characterization included X-ray diffraction (XRD), optical microscopies (SEM, cryo-SEM, TEM, fluorescence), dynamic light scattering (DLS) techniques, energy dispersive (EDS), Fourier transform infrared (FTIR) and ultraviolet-visible (UV-Vis) spectroscopies, zeta-potential and magnetic measurements. The results showed that magnetic field affected the hydrocolloids microstructure uniformity, fluorescence properties and photodynamic activity. Likewise, increased temperature caused changes in NPs hydrodynamic size distribution and in hydrocolloids microstructure. Magnetic field significantly improved photodynamic activity that was attributed to enhanced generation of reactive oxygen species due to reorganization of the microstructure. |
Zawadzka, Katarzyna; Zawadzki, Paweł; Baker, Rachel; Rajasekar, Karthik V; Wagner, Florence; Sherratt, David J; Arciszewska, Lidia K MukB ATPases are regulated independently by the N- and C-terminal domains of MukF kleisin eLife, 7 , 2018. @article{Zawadzka2018, title = {MukB ATPases are regulated independently by the N- and C-terminal domains of MukF kleisin}, author = {Katarzyna Zawadzka and Paweł Zawadzki and Rachel Baker and Karthik V Rajasekar and Florence Wagner and David J Sherratt and Lidia K Arciszewska}, url = {https://doi.org/10.7554/elife.31522}, doi = {10.7554/elife.31522}, year = {2018}, date = {2018-01-01}, journal = {eLife}, volume = {7}, publisher = {eLife Sciences Organisation, Ltd.}, abstract = {The Escherichia coli SMC complex, MukBEF, acts in chromosome segregation. MukBEF shares the distinctive architecture of other SMC complexes, with one prominent difference; unlike other kleisins, MukF forms dimers through its N-terminal domain. We show that a 4-helix bundle adjacent to the MukF dimerisation domain interacts functionally with the MukB coiled-coiled ‘neck’ adjacent to the ATPase head. We propose that this interaction leads to an asymmetric tripartite complex, as in other SMC complexes. Since MukF dimerisation is preserved during this interaction, MukF directs the formation of dimer of dimer MukBEF complexes, observed previously in vivo. The MukF N- and C-terminal domains stimulate MukB ATPase independently and additively. We demonstrate that impairment of the MukF interaction with MukB in vivo leads to ATP hydrolysis-dependent release of MukBEF complexes from chromosomes.}, keywords = {}, pubstate = {published}, tppubtype = {article} } The Escherichia coli SMC complex, MukBEF, acts in chromosome segregation. MukBEF shares the distinctive architecture of other SMC complexes, with one prominent difference; unlike other kleisins, MukF forms dimers through its N-terminal domain. We show that a 4-helix bundle adjacent to the MukF dimerisation domain interacts functionally with the MukB coiled-coiled ‘neck’ adjacent to the ATPase head. We propose that this interaction leads to an asymmetric tripartite complex, as in other SMC complexes. Since MukF dimerisation is preserved during this interaction, MukF directs the formation of dimer of dimer MukBEF complexes, observed previously in vivo. The MukF N- and C-terminal domains stimulate MukB ATPase independently and additively. We demonstrate that impairment of the MukF interaction with MukB in vivo leads to ATP hydrolysis-dependent release of MukBEF complexes from chromosomes. |
Koralewski, Marceli; Balejčíková, Lucia; Mitróová, Zuzana; Pochylski, Mikołaj; Baranowski, Mikołaj; Kopčanský, Peter ACS Applied Materials & Interfaces, 10 (9), pp. 7777-7787, 2018, (PMID: 29417811). @article{Koralewski2018, title = {Morphology and Magnetic Structure of the Ferritin Core during Iron Loading and Release by Magnetooptical and NMR Methods}, author = {Marceli Koralewski and Lucia Balejčíková and Zuzana Mitróová and Mikołaj Pochylski and Mikołaj Baranowski and Peter Kopčanský}, url = {https://doi.org/10.1021/acsami.7b18304}, doi = {10.1021/acsami.7b18304}, year = {2018}, date = {2018-01-01}, journal = {ACS Applied Materials & Interfaces}, volume = {10}, number = {9}, pages = {7777-7787}, abstract = {Ferritins are proteins, which serve as a storage and transportation capsule for iron inside living organisms. Continuously charging the proteins with iron and releasing it from the ferritin is necessary to assure proper management of these important ions within the organism. On the other hand, synthetic ferritins have great potential for biomedical and technological applications. In this work, the behavior of ferritin during the processes of iron loading and release was examined using multiplicity of the experimental technique. The quality of the protein’s shell was monitored using circular dichroism, whereas the average size and its distribution were estimated from dynamic light scattering and transmission electron microscopy images, respectively. Because of the magnetic behavior of the iron mineral, a number of magnetooptical methods were used to gain information on the iron core of the ferritin. Faraday rotation and magnetic linear birefringence studies provide evidence that the iron loading and the iron-release processes are not symmetrical. The spatial organization of the mineral within the protein’s core changes depending on whether the iron was incorporated into or removed from the ferritin’s shell. Magnetic optical rotatory dispersion spectra exclude the contribution of the Fe(II)-composed mineral, whereas joined magnetooptical and nuclear magnetic resonance results indicate that no mineral with high magnetization appear at any stage of the loading/release process. These findings suggest that the iron core of loaded/released ferritin consists of single-phase, that is, ferrihydrite. The presented results demonstrate the usefulness of emerging magnetooptical methods in biomedical research and applications.}, note = {PMID: 29417811}, keywords = {}, pubstate = {published}, tppubtype = {article} } Ferritins are proteins, which serve as a storage and transportation capsule for iron inside living organisms. Continuously charging the proteins with iron and releasing it from the ferritin is necessary to assure proper management of these important ions within the organism. On the other hand, synthetic ferritins have great potential for biomedical and technological applications. In this work, the behavior of ferritin during the processes of iron loading and release was examined using multiplicity of the experimental technique. The quality of the protein’s shell was monitored using circular dichroism, whereas the average size and its distribution were estimated from dynamic light scattering and transmission electron microscopy images, respectively. Because of the magnetic behavior of the iron mineral, a number of magnetooptical methods were used to gain information on the iron core of the ferritin. Faraday rotation and magnetic linear birefringence studies provide evidence that the iron loading and the iron-release processes are not symmetrical. The spatial organization of the mineral within the protein’s core changes depending on whether the iron was incorporated into or removed from the ferritin’s shell. Magnetic optical rotatory dispersion spectra exclude the contribution of the Fe(II)-composed mineral, whereas joined magnetooptical and nuclear magnetic resonance results indicate that no mineral with high magnetization appear at any stage of the loading/release process. These findings suggest that the iron core of loaded/released ferritin consists of single-phase, that is, ferrihydrite. The presented results demonstrate the usefulness of emerging magnetooptical methods in biomedical research and applications. |
Białek, Rafał; Swainsbury, David J K; Wiesner, Maciej; Jones, Michael R; Gibasiewicz, Krzysztof Photosynthesis Research, 0 (0), pp. 0, 2018, ISSN: 0166-8595. @article{Biaek2018, title = {Modelling of the cathodic and anodic photocurrents from Rhodobacter sphaeroides reaction centres immobilized on titanium dioxide}, author = {Rafał Białek and David J K Swainsbury and Maciej Wiesner and Michael R Jones and Krzysztof Gibasiewicz}, url = {http://link.springer.com/10.1007/s11120-018-0550-8}, doi = {10.1007/s11120-018-0550-8}, issn = {0166-8595}, year = {2018}, date = {2018-01-01}, journal = {Photosynthesis Research}, volume = {0}, number = {0}, pages = {0}, publisher = {Springer Netherlands}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Giera, Wojciech; Szewczyk, Sebastian; McConnell, Michael D; Redding, Kevin E; van Grondelle, Rienk; Gibasiewicz, Krzysztof Photosynthesis Research, 137 (2), pp. 321-335, 2018, ISSN: 1573-5079. @article{Giera2018, title = {Uphill energy transfer in photosystem I from Chlamydomonas reinhardtii. Time-resolved fluorescence measurements at 77 K}, author = {Wojciech Giera and Sebastian Szewczyk and Michael D McConnell and Kevin E Redding and Rienk van Grondelle and Krzysztof Gibasiewicz}, url = {https://doi.org/10.1007/s11120-018-0506-z}, doi = {10.1007/s11120-018-0506-z}, issn = {1573-5079}, year = {2018}, date = {2018-01-01}, journal = {Photosynthesis Research}, volume = {137}, number = {2}, pages = {321-335}, abstract = {Energetic properties of chlorophylls in photosynthetic complexes are strongly modulated by their interaction with the protein matrix and by inter-pigment coupling. This spectral tuning is especially striking in photosystem I (PSI) complexes that contain low-energy chlorophylls emitting above 700 nm. Such low-energy chlorophylls have been observed in cyanobacterial PSI, algal and plant PSI--LHCI complexes, and individual light-harvesting complex I (LHCI) proteins. However, there has been no direct evidence of their presence in algal PSI core complexes lacking LHCI. In order to determine the lowest-energy states of chlorophylls and their dynamics in algal PSI antenna systems, we performed time-resolved fluorescence measurements at 77 K for PSI core and PSI--LHCI complexes isolated from the green alga Chlamydomonas reinhardtii. The pool of low-energy chlorophylls observed in PSI cores is generally smaller and less red-shifted than that observed in PSI--LHCI complexes. Excitation energy equilibration between bulk and low-energy chlorophylls in the PSI--LHCI complexes at 77 K leads to population of excited states that are less red-shifted (by textasciitildethinspace12 nm) than at room temperature. On the other hand, analysis of the detection wavelength dependence of the effective trapping time of bulk excitations in the PSI core at 77 K provided evidence for an energy threshold at textasciitildethinspace675 nm, above which trapping slows down. Based on these observations, we postulate that excitation energy transfer from bulk to low-energy chlorophylls and from bulk to reaction center chlorophylls are thermally activated uphill processes that likely occur via higher excitonic states of energy accepting chlorophylls.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Energetic properties of chlorophylls in photosynthetic complexes are strongly modulated by their interaction with the protein matrix and by inter-pigment coupling. This spectral tuning is especially striking in photosystem I (PSI) complexes that contain low-energy chlorophylls emitting above 700 nm. Such low-energy chlorophylls have been observed in cyanobacterial PSI, algal and plant PSI--LHCI complexes, and individual light-harvesting complex I (LHCI) proteins. However, there has been no direct evidence of their presence in algal PSI core complexes lacking LHCI. In order to determine the lowest-energy states of chlorophylls and their dynamics in algal PSI antenna systems, we performed time-resolved fluorescence measurements at 77 K for PSI core and PSI--LHCI complexes isolated from the green alga Chlamydomonas reinhardtii. The pool of low-energy chlorophylls observed in PSI cores is generally smaller and less red-shifted than that observed in PSI--LHCI complexes. Excitation energy equilibration between bulk and low-energy chlorophylls in the PSI--LHCI complexes at 77 K leads to population of excited states that are less red-shifted (by textasciitildethinspace12 nm) than at room temperature. On the other hand, analysis of the detection wavelength dependence of the effective trapping time of bulk excitations in the PSI core at 77 K provided evidence for an energy threshold at textasciitildethinspace675 nm, above which trapping slows down. Based on these observations, we postulate that excitation energy transfer from bulk to low-energy chlorophylls and from bulk to reaction center chlorophylls are thermally activated uphill processes that likely occur via higher excitonic states of energy accepting chlorophylls. |
2017 |
Wojnarowska, Z; Rams-Baron, M; Knapik-Kowalczuk, J; Połatyńska, Agnieszka; Pochylski, Mikołaj; Gapiński, Jacek; Patkowski, Adam; Wlodarczyk, P; Paluch, M Scientific Reports, 7 (1), pp. 7084, 2017, ISSN: 2045-2322. @article{Wojnarowska2017, title = {Experimental evidence of high pressure decoupling between charge transport and structural dynamics in a protic ionic glass-former}, author = {Z Wojnarowska and M Rams-Baron and J Knapik-Kowalczuk and Agnieszka Połatyńska and Mikołaj Pochylski and Jacek Gapiński and Adam Patkowski and P Wlodarczyk and M Paluch}, url = {http://www.nature.com/articles/s41598-017-07136-5}, doi = {10.1038/s41598-017-07136-5}, issn = {2045-2322}, year = {2017}, date = {2017-12-01}, journal = {Scientific Reports}, volume = {7}, number = {1}, pages = {7084}, publisher = {Nature Publishing Group}, abstract = {textcopyright 2017 The Author(s). In this paper the relaxation dynamics of ionic glass-former acebutolol hydrochloride (ACB-HCl) is studied as a function of temperature and pressure by using dynamic light scattering and broadband dielectric spectroscopy. These unique experimental data provide the first direct evidence that the decoupling between the charge transport and structural relaxation exists in proton conductors over a wide T-P thermodynamic space, with the time scale of structural relaxation being constant at the liquid-glass transition ($tau$ $alpha$ = 1000 s). We demonstrate that the enhanced proton transport, being a combination of intermolecular H + hopping between cation and anion as well as tautomerization process within amide moiety of ACB molecule, results in a breakdown of the Stokes-Einstein relation at ambient and elevated pressure with the fractional exponent k being pressure dependent. The dT g /dP coefficient, stretching exponent $beta$ KWW and dynamic modulus E a /$Delta$V # were found to be the same regardless of the relaxation processes studied. This is in contrast to the apparent activation volume parameter that is different when charge transport and structural dynamics are considered. These experimental results together with theoretical considerations create new ideas to design efficient proton conductors for potential electrochemical applications.}, keywords = {}, pubstate = {published}, tppubtype = {article} } textcopyright 2017 The Author(s). In this paper the relaxation dynamics of ionic glass-former acebutolol hydrochloride (ACB-HCl) is studied as a function of temperature and pressure by using dynamic light scattering and broadband dielectric spectroscopy. These unique experimental data provide the first direct evidence that the decoupling between the charge transport and structural relaxation exists in proton conductors over a wide T-P thermodynamic space, with the time scale of structural relaxation being constant at the liquid-glass transition ($tau$ $alpha$ = 1000 s). We demonstrate that the enhanced proton transport, being a combination of intermolecular H + hopping between cation and anion as well as tautomerization process within amide moiety of ACB molecule, results in a breakdown of the Stokes-Einstein relation at ambient and elevated pressure with the fractional exponent k being pressure dependent. The dT g /dP coefficient, stretching exponent $beta$ KWW and dynamic modulus E a /$Delta$V # were found to be the same regardless of the relaxation processes studied. This is in contrast to the apparent activation volume parameter that is different when charge transport and structural dynamics are considered. These experimental results together with theoretical considerations create new ideas to design efficient proton conductors for potential electrochemical applications. |
Coy, Emerson; Graczyk, Piotr; Yate, Luis; Załęski, Karol; Gapiński, Jacek; Kuświk, Piotr; Mielcarek, Sławomir; Stobiecki, Feliks; Mróz, Bogusław; Ferrater, Cesar; Jurga, Stefan Scientific Reports, 7 (1), pp. 11800, 2017, ISSN: 2045-2322. @article{Coy2017, title = {Second Harmonic Generation Response in Thermally reconstructed Multiferroic $beta$′- Gd2(MoO4)3 Thin Films}, author = {Emerson Coy and Piotr Graczyk and Luis Yate and Karol Załęski and Jacek Gapiński and Piotr Kuświk and Sławomir Mielcarek and Feliks Stobiecki and Bogusław Mróz and Cesar Ferrater and Stefan Jurga}, url = {http://www.nature.com/articles/s41598-017-12370-y}, doi = {10.1038/s41598-017-12370-y}, issn = {2045-2322}, year = {2017}, date = {2017-12-01}, journal = {Scientific Reports}, volume = {7}, number = {1}, pages = {11800}, publisher = {Nature Publishing Group}, abstract = {Gd2(MoO4)3 (GMO) is a well-studied multiferroic material that exhibits full ferroelectric and ferroelastic behavior at room temperature. However, its difficult stabilization in thin films has prevented the study and exploitation of its multiferroic properties in different architectures. Here, we report on the study of GMO thin films deposited on Si(001) substrates by Pulsed Laser Deposition (PLD). The physicochemical properties of the films are discussed and studied. Results obtained by X-ray diffraction, X-ray photoelectron spectroscopy, high resolution transmission microscopy and second harmonic generation show that the orthorhombic ($beta$′-GMO) multiferroic phase can be stabilized and homogenized by post deposition thermal reconstruction. Finally, the reconstruction process takes place via a complex surface mechanism with a clear leaf-like behavior.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Gd2(MoO4)3 (GMO) is a well-studied multiferroic material that exhibits full ferroelectric and ferroelastic behavior at room temperature. However, its difficult stabilization in thin films has prevented the study and exploitation of its multiferroic properties in different architectures. Here, we report on the study of GMO thin films deposited on Si(001) substrates by Pulsed Laser Deposition (PLD). The physicochemical properties of the films are discussed and studied. Results obtained by X-ray diffraction, X-ray photoelectron spectroscopy, high resolution transmission microscopy and second harmonic generation show that the orthorhombic ($beta$′-GMO) multiferroic phase can be stabilized and homogenized by post deposition thermal reconstruction. Finally, the reconstruction process takes place via a complex surface mechanism with a clear leaf-like behavior. |
Jarzębski, Maciej; Śliwa, Tomasz; Peplińska, Barbara; Jakubowicz, Jarosław; Kuzioła, Rafał; Kościński, Jeremi; Białopiotrowicz, Tomasz; Gapiński, Jacek Submicron sized fluorescent silica particles characterization Nuclear Instruments and Methods in Physics Research, Section B: Beam Interactions with Materials and Atoms, 411 , pp. 78–84, 2017, ISSN: 0168583X. @article{Jarzebski2017, title = {Submicron sized fluorescent silica particles characterization}, author = {Maciej Jarzębski and Tomasz Śliwa and Barbara Peplińska and Jarosław Jakubowicz and Rafał Kuzioła and Jeremi Kościński and Tomasz Białopiotrowicz and Jacek Gapiński}, url = {https://www.sciencedirect.com/science/article/pii/S0168583X17301118}, doi = {10.1016/j.nimb.2017.01.088}, issn = {0168583X}, year = {2017}, date = {2017-11-01}, journal = {Nuclear Instruments and Methods in Physics Research, Section B: Beam Interactions with Materials and Atoms}, volume = {411}, pages = {78--84}, publisher = {North-Holland}, abstract = {Silica nano- and submicron particles are examples of commonly used nanomaterials with frequently modified surface properties. Various enhanced methods of the fluorescent particles preparations give the opportunities for applications of fluorescent SiO2as a model system for biomedical interactions between the particles and biostructures such as cells, including beam interactions with materials. Fluorescent core-shell structures were prepared by modified Stoeber method, where the fluorescent agent was included in the core and then surrounded by a protective shell. As a fluorescent agent Rhodamine-B isothiocyanate was used. The core-shell tunneling size structure was formed by addition of TEOS (tetraethyl orthosilicate) to the base mixture. The size of the particles were investigated by dynamic light scattering (DLS), nanoparticle tracking analysis (NTA), fluorescence correlation spectroscopy (FCS). Shape and morphology were studied by the transmission and scanning electron microscopy. The fluorescence behavior of the particles was confirmed using NTA in the fluorescent mode and LSM (laser scanning microscope). We confirmed the hydrodynamic diameter in the range between 300 and 1000 nm using the FCS technique. XRD spectra of fluorescent SiO2were also obtained. This study shows practical aspects of use of selected characterization methods for submicron particle characterization, especially with regard to their fluorescent behavior.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Silica nano- and submicron particles are examples of commonly used nanomaterials with frequently modified surface properties. Various enhanced methods of the fluorescent particles preparations give the opportunities for applications of fluorescent SiO2as a model system for biomedical interactions between the particles and biostructures such as cells, including beam interactions with materials. Fluorescent core-shell structures were prepared by modified Stoeber method, where the fluorescent agent was included in the core and then surrounded by a protective shell. As a fluorescent agent Rhodamine-B isothiocyanate was used. The core-shell tunneling size structure was formed by addition of TEOS (tetraethyl orthosilicate) to the base mixture. The size of the particles were investigated by dynamic light scattering (DLS), nanoparticle tracking analysis (NTA), fluorescence correlation spectroscopy (FCS). Shape and morphology were studied by the transmission and scanning electron microscopy. The fluorescence behavior of the particles was confirmed using NTA in the fluorescent mode and LSM (laser scanning microscope). We confirmed the hydrodynamic diameter in the range between 300 and 1000 nm using the FCS technique. XRD spectra of fluorescent SiO2were also obtained. This study shows practical aspects of use of selected characterization methods for submicron particle characterization, especially with regard to their fluorescent behavior. |
Ivashchenko, Olena; Gapiński, Jacek; Peplińska, Barbara; Przysiecka, Łucja; Zalewski, Tomasz; Nowaczyk, Grzegorz; Jarek, Marcin; Marcinkowska-Gapińska, Anna; Jurga, Stefan Materials & Design, 133 , pp. 307–324, 2017, ISSN: 02641275. @article{Ivashchenko2017a, title = {Self-organizing silver and ultrasmall iron oxide nanoparticles prepared with ginger rhizome extract: Characterization, biomedical potential and microstructure analysis of hydrocolloids}, author = {Olena Ivashchenko and Jacek Gapiński and Barbara Peplińska and Łucja Przysiecka and Tomasz Zalewski and Grzegorz Nowaczyk and Marcin Jarek and Anna Marcinkowska-Gapińska and Stefan Jurga}, url = {https://www.sciencedirect.com/science/article/pii/S0264127517307475 http://linkinghub.elsevier.com/retrieve/pii/S0264127517307475}, doi = {10.1016/j.matdes.2017.08.001}, issn = {02641275}, year = {2017}, date = {2017-11-01}, journal = {Materials & Design}, volume = {133}, pages = {307--324}, publisher = {Elsevier}, abstract = {Multimodal nanoparticles (NPs) that may be used for therapies and diagnostics is the most promising trend for efficient therapy. We demonstrate that nanocomposite based on self-organizing silver and ultrasmall magnetic iron oxide NPs (MAg) produced in one-step synthesis revealed unique combination of fluorescence, bactericidal, fungicidal properties and have a potential as magnetic resonance imaging (MRI) contrast agent. Using the green chemistry approach, ginger (Zingiber officinale) rhizome extract was applied as capping agent for MAg synthesis, providing also additional fluorescent properties of NPs and inducing hydrocolloids structuring. The MAg were investigated by X-ray diffraction (XRD), scanning electron microscopy (SEM), transmission electron microscopy (TEM), energy dispersive microanalysis (EDS), fluorescence microscopy, cryo-SEM, dynamic light scattering (DLS) techniques, Fourier transform infrared (FTIR) and ultraviolet–visible (UV–Vis) spectroscopies. MAg dispersions in water and some biological media are very stable which is important for biomedical application. The existence of microstructure in MAg hydrocolloids was proved. The hierarchical character and high ordering of this microstructure were discovered and its level-by-level building blocks were investigated. The microstructure was found to be responsible for fluorescence emittance of MAg hydrocolloids. The properties as well as potential application of the MAg hydrocolloids is yet to be discovered.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Multimodal nanoparticles (NPs) that may be used for therapies and diagnostics is the most promising trend for efficient therapy. We demonstrate that nanocomposite based on self-organizing silver and ultrasmall magnetic iron oxide NPs (MAg) produced in one-step synthesis revealed unique combination of fluorescence, bactericidal, fungicidal properties and have a potential as magnetic resonance imaging (MRI) contrast agent. Using the green chemistry approach, ginger (Zingiber officinale) rhizome extract was applied as capping agent for MAg synthesis, providing also additional fluorescent properties of NPs and inducing hydrocolloids structuring. The MAg were investigated by X-ray diffraction (XRD), scanning electron microscopy (SEM), transmission electron microscopy (TEM), energy dispersive microanalysis (EDS), fluorescence microscopy, cryo-SEM, dynamic light scattering (DLS) techniques, Fourier transform infrared (FTIR) and ultraviolet–visible (UV–Vis) spectroscopies. MAg dispersions in water and some biological media are very stable which is important for biomedical application. The existence of microstructure in MAg hydrocolloids was proved. The hierarchical character and high ordering of this microstructure were discovered and its level-by-level building blocks were investigated. The microstructure was found to be responsible for fluorescence emittance of MAg hydrocolloids. The properties as well as potential application of the MAg hydrocolloids is yet to be discovered. |
Poznar, Monika; Hołubowicz, Rafał; Wojtas, Magdalena; Gapiński, Jacek; Banachowicz, Ewa; Patkowski, Adam; Ożyhar, Andrzej; Dobryszycki, Piotr Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics, 1865 (11), pp. 1358–1371, 2017, ISSN: 15709639. @article{Poznar2017, title = {Structural properties of the intrinsically disordered, multiple calcium ion-binding otolith matrix macromolecule-64 (OMM-64)}, author = {Monika Poznar and Rafał Hołubowicz and Magdalena Wojtas and Jacek Gapiński and Ewa Banachowicz and Adam Patkowski and Andrzej Ożyhar and Piotr Dobryszycki}, url = {https://www.sciencedirect.com/science/article/pii/S1570963917302054?via%3Dihub http://linkinghub.elsevier.com/retrieve/pii/S1570963917302054}, doi = {10.1016/j.bbapap.2017.08.019}, issn = {15709639}, year = {2017}, date = {2017-11-01}, journal = {Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics}, volume = {1865}, number = {11}, pages = {1358--1371}, publisher = {Elsevier}, abstract = {Fish otoliths are calcium carbonate biominerals that are involved in hearing and balance sensing. An organic matrix plays a crucial role in their formation. Otolith matrix macromolecule-64 (OMM-64) is a highly acidic, calcium-binding protein (CBP) found in rainbow trout otoliths. It is a component of high-molecular-weight aggregates, which influence the size, shape and polymorph of calcium carbonate in vitro. In this study, a protocol for the efficient expression and purification of OMM-64 was developed. For the first time, the complete structural characteristics of OMM-64 were described. Various biophysical methods were combined to show that OMM-64 occurs as an intrinsically disordered monomer. Under denaturing conditions (pH, temperature) OMM-64 exhibits folding propensity. It was determined that OMM-64 binds approximately 61 calcium ions with millimolar affinity. The folding-unfolding experiments showed that calcium ions induced the collapse of OMM-64. The effect of other counter ions present in trout endolymph on OMM-64 conformational changes was studied. The significance of disordered properties of OMM-64 and the possible function of this protein is discussed.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Fish otoliths are calcium carbonate biominerals that are involved in hearing and balance sensing. An organic matrix plays a crucial role in their formation. Otolith matrix macromolecule-64 (OMM-64) is a highly acidic, calcium-binding protein (CBP) found in rainbow trout otoliths. It is a component of high-molecular-weight aggregates, which influence the size, shape and polymorph of calcium carbonate in vitro. In this study, a protocol for the efficient expression and purification of OMM-64 was developed. For the first time, the complete structural characteristics of OMM-64 were described. Various biophysical methods were combined to show that OMM-64 occurs as an intrinsically disordered monomer. Under denaturing conditions (pH, temperature) OMM-64 exhibits folding propensity. It was determined that OMM-64 binds approximately 61 calcium ions with millimolar affinity. The folding-unfolding experiments showed that calcium ions induced the collapse of OMM-64. The effect of other counter ions present in trout endolymph on OMM-64 conformational changes was studied. The significance of disordered properties of OMM-64 and the possible function of this protein is discussed. |
Sarbak, Szymon; Sharma, Gargi; Joseph, Cecil S; Kucia, Weronika; Dobek, Krzysztof; Giles, Robert H; Dobek, Andrzej Direct observation of the THz Kerr effect (TKE) in deionized, distilled and buffered (PBS) water Physical Chemistry Chemical Physics, 19 (39), pp. 26749-26757, 2017. @article{Sarbak2017, title = {Direct observation of the THz Kerr effect (TKE) in deionized, distilled and buffered (PBS) water}, author = {Szymon Sarbak and Gargi Sharma and Cecil S Joseph and Weronika Kucia and Krzysztof Dobek and Robert H Giles and Andrzej Dobek}, doi = {10.1039/C7CP04061J}, year = {2017}, date = {2017-09-08}, journal = {Physical Chemistry Chemical Physics}, volume = {19}, number = {39}, pages = {26749-26757}, abstract = {Nonlinear THz pump–optical probe (THz–OKE) measurements in deionized, distilled and buffered (PBS) water are reported. A laser system that produces pulses at 800 nm, 30 fs FWHM, at a repetition rate of 1 kHz and an energy of 6 μJ per pulse, was a source of the probe optical beam and of the pump beam of THz 2 ps pulses. The electric field strength inducing birefringence in water samples was ETHz = 1.35 × 106 V m−1. These samples were chosen in order to study the effect of ionic concentration on water behavior in the ultrafast time scale. Differentiation between ultrafast effects resulting from internal H2O properties and those resulting from H2O–ion interactions was analyzed. These two effects may be connected to a difference in the fluctuations of the network of intermolecular hydrogen bonds of water molecules in the presence and absence of ions in solution. The results indicate that such fluctuations significantly alter water birefringence amplitude and its dynamics.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Nonlinear THz pump–optical probe (THz–OKE) measurements in deionized, distilled and buffered (PBS) water are reported. A laser system that produces pulses at 800 nm, 30 fs FWHM, at a repetition rate of 1 kHz and an energy of 6 μJ per pulse, was a source of the probe optical beam and of the pump beam of THz 2 ps pulses. The electric field strength inducing birefringence in water samples was ETHz = 1.35 × 106 V m−1. These samples were chosen in order to study the effect of ionic concentration on water behavior in the ultrafast time scale. Differentiation between ultrafast effects resulting from internal H2O properties and those resulting from H2O–ion interactions was analyzed. These two effects may be connected to a difference in the fluctuations of the network of intermolecular hydrogen bonds of water molecules in the presence and absence of ions in solution. The results indicate that such fluctuations significantly alter water birefringence amplitude and its dynamics. |
Łukarska, M; Jankowska, A; Gapiński, Jacek; Valable, S; Anfray, C; Menard, B; Mintova, S; Kowalak, S Synthesis of fluorescein by a ship-in-a-bottle method in different zeolites New Journal of Chemistry, 41 (18), pp. 9969–9976, 2017, ISSN: 1144-0546. @article{ukarska2017, title = {Synthesis of fluorescein by a ship-in-a-bottle method in different zeolites}, author = {M Łukarska and A Jankowska and Jacek Gapiński and S Valable and C Anfray and B Menard and S Mintova and S Kowalak}, url = {http://xlink.rsc.org/?DOI=C7NJ01427A}, doi = {10.1039/C7NJ01427A}, issn = {1144-0546}, year = {2017}, date = {2017-09-01}, journal = {New Journal of Chemistry}, volume = {41}, number = {18}, pages = {9969--9976}, publisher = {The Royal Society of Chemistry}, abstract = {Composites consisting of fluorescein (F) entrapped inside various zeolite structures ( i.e. FAU, LTL, MFI, and LTA) were prepared by catalytic synthesis of the dye from its precursors (phthalic anhydride and resorcinol) adsorbed in the zeolites.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Composites consisting of fluorescein (F) entrapped inside various zeolite structures ( i.e. FAU, LTL, MFI, and LTA) were prepared by catalytic synthesis of the dye from its precursors (phthalic anhydride and resorcinol) adsorbed in the zeolites. |
Śliwa, Tomasz; Jarzębski, Maciej; Andrzejewska, Ewa; Szafran, Mikołaj; Gapiński, Jacek Uptake and controlled release of a dye from thermo-sensitive polymer P(NIPAM- co -Vim) Reactive and Functional Polymers, 115 , pp. 102–108, 2017, ISSN: 13815148. @article{Sliwa2017, title = {Uptake and controlled release of a dye from thermo-sensitive polymer P(NIPAM- co -Vim)}, author = {Tomasz Śliwa and Maciej Jarzębski and Ewa Andrzejewska and Mikołaj Szafran and Jacek Gapiński}, url = {https://www.sciencedirect.com/science/article/pii/S1381514817300718?via%3Dihub http://linkinghub.elsevier.com/retrieve/pii/S1381514817300718}, doi = {10.1016/j.reactfunctpolym.2017.04.003}, issn = {13815148}, year = {2017}, date = {2017-06-01}, journal = {Reactive and Functional Polymers}, volume = {115}, pages = {102--108}, publisher = {Elsevier}, abstract = {Copolymers of N-isopropylacrylamide (PNIPAM) are one of the most promising microgel materials for medical applications, especially as a drug carrier. PNIPAMs present unique properties, such as size variation with changing pH and/or temperature. The results of a study on the uptake and release of a dye (Orange II) by microgels of N-isopropylacrylamide copolymer with 1-vinylimidazole (P(NIPAM-co-Vim) are presented. The dye was used as a model low-molecular substance. Hydrodynamic radius (Rh) of P(NIPAM-co-Vim) particles was measured by dynamic light scattering as a function of temperature in two pH environments: acidic and basic. The dye particles contraction was monitored as a function of temperature at pH 4. The measurements of the zeta potential indicated a positive charge of P(NIPAM-co-Vim) particles at pH 4 and a negative one at pH 9. The key experiments were the internalization and the release of the dye. The effectiveness of this process was measured by UV-Vis spectroscopy on the supernatant derived from centrifuged P(NIPAM-co-Vim) suspension. At room temperature the efficiency of trapping of the dye by the microgel at pH 4 was 87%. Changing pH of a sample initially saturated with the dye from 4 to 9 led to a complete release of the trapped dye.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Copolymers of N-isopropylacrylamide (PNIPAM) are one of the most promising microgel materials for medical applications, especially as a drug carrier. PNIPAMs present unique properties, such as size variation with changing pH and/or temperature. The results of a study on the uptake and release of a dye (Orange II) by microgels of N-isopropylacrylamide copolymer with 1-vinylimidazole (P(NIPAM-co-Vim) are presented. The dye was used as a model low-molecular substance. Hydrodynamic radius (Rh) of P(NIPAM-co-Vim) particles was measured by dynamic light scattering as a function of temperature in two pH environments: acidic and basic. The dye particles contraction was monitored as a function of temperature at pH 4. The measurements of the zeta potential indicated a positive charge of P(NIPAM-co-Vim) particles at pH 4 and a negative one at pH 9. The key experiments were the internalization and the release of the dye. The effectiveness of this process was measured by UV-Vis spectroscopy on the supernatant derived from centrifuged P(NIPAM-co-Vim) suspension. At room temperature the efficiency of trapping of the dye by the microgel at pH 4 was 87%. Changing pH of a sample initially saturated with the dye from 4 to 9 led to a complete release of the trapped dye. |
Szewczyk, Sebastian; Giera, Wojciech; D'Haene, Sandrine; van Grondelle, Rienk; Gibasiewicz, Krzysztof Photosynthesis Research, 132 (2), pp. 111–126, 2017, ISSN: 0166-8595. @article{Szewczyk2017b, title = {Comparison of excitation energy transfer in cyanobacterial photosystem I in solution and immobilized on conducting glass}, author = {Sebastian Szewczyk and Wojciech Giera and Sandrine D'Haene and Rienk van Grondelle and Krzysztof Gibasiewicz}, url = {http://link.springer.com/10.1007/s11120-016-0312-4}, doi = {10.1007/s11120-016-0312-4}, issn = {0166-8595}, year = {2017}, date = {2017-05-01}, journal = {Photosynthesis Research}, volume = {132}, number = {2}, pages = {111--126}, publisher = {Springer Netherlands}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Krysztofiak, Katarzyna; Ciężar, Kamila; Kościński, Mikołaj Raman imaging of layered soft contact lenses Journal of Applied Biomaterials & Functional Materials, 15 (2), pp. 0–0, 2017, ISSN: 2280-8000. @article{Krysztofiak2017, title = {Raman imaging of layered soft contact lenses}, author = {Katarzyna Krysztofiak and Kamila Ciężar and Mikołaj Kościński}, url = {http://www.ncbi.nlm.nih.gov/pubmed/27791229 http://www.jab-fm.com/article/c1122e89-9243-410f-9c37-1e338fa1ce62}, doi = {10.5301/jabfm.5000329}, issn = {2280-8000}, year = {2017}, date = {2017-04-01}, journal = {Journal of Applied Biomaterials & Functional Materials}, volume = {15}, number = {2}, pages = {0--0}, publisher = {Wichtig Publishing s.r.l.}, abstract = {BACKGROUND Daily disposable contact lenses are gaining in popularity among practitioners and wearers for the improved ocular health and subjective outcomes they offer. Recently a novel daily disposable contact lens material with water gradient technology was introduced. Delefilcon A lenses consist of a 33% water content silicone hydrogel core and an outer hydrogel layer which is totally free of silicone and contains 80% water. METHODS The aim of the present study was to confirm the layered structure of delefilcon A contact lenses. Thickness of hydrogel coating on the silicone hydrogel core was assessed using Raman spectroscopy. To investigate the layered structure of the material, depth spectra of the lenses were recorded. RESULTS The results obtained suggest that at about 6 $mu$m a boundary between the hydrogel layer and silicone hydrogel core exists, which is in good agreement with the manufacturer's data. CONCLUSIONS Data collected in this experiment confirm a water gradient at the delefilcon A lens surface.}, keywords = {}, pubstate = {published}, tppubtype = {article} } BACKGROUND Daily disposable contact lenses are gaining in popularity among practitioners and wearers for the improved ocular health and subjective outcomes they offer. Recently a novel daily disposable contact lens material with water gradient technology was introduced. Delefilcon A lenses consist of a 33% water content silicone hydrogel core and an outer hydrogel layer which is totally free of silicone and contains 80% water. METHODS The aim of the present study was to confirm the layered structure of delefilcon A contact lenses. Thickness of hydrogel coating on the silicone hydrogel core was assessed using Raman spectroscopy. To investigate the layered structure of the material, depth spectra of the lenses were recorded. RESULTS The results obtained suggest that at about 6 $mu$m a boundary between the hydrogel layer and silicone hydrogel core exists, which is in good agreement with the manufacturer's data. CONCLUSIONS Data collected in this experiment confirm a water gradient at the delefilcon A lens surface. |
Ivashchenko, Olena; Woźniak, Anna; Coy, Emerson; Peplinska, Barbara; Gapiński, Jacek; Jurga, Stefan Colloids and Surfaces B: Biointerfaces, 152 , pp. 85–94, 2017, ISSN: 18734367. @article{Ivashchenko2017b, title = {Release and cytotoxicity studies of magnetite/Ag/antibiotic nanoparticles: An interdependent relationship}, author = {Olena Ivashchenko and Anna Woźniak and Emerson Coy and Barbara Peplinska and Jacek Gapiński and Stefan Jurga}, url = {https://www.sciencedirect.com/science/article/pii/S0927776517300176}, doi = {10.1016/j.colsurfb.2017.01.009}, issn = {18734367}, year = {2017}, date = {2017-04-01}, journal = {Colloids and Surfaces B: Biointerfaces}, volume = {152}, pages = {85--94}, publisher = {Elsevier}, abstract = {Though the cytotoxic properties of magnetite nanoparticles (NPs) are rather well investigated and known to be dose dependent and rather low, surface functionalization can drastically change their properties. To determine whether the cytotoxicity of magnetite/Ag/antibiotic NPs may be associated, among other things, with iron, silver and antibiotic release, this study investigates the release profiles and cytotoxicity of magnetite/Ag/rifampicin and magnetite/Ag/doxycycline NPs compares it similar profiles from magnetite, magnetite/Ag NPs and antibiotics. It was established that the studied NPs released not only water-soluble substances, such as antibiotics, but also poorly-soluble ones, such as iron and silver. The deposition of silver on the magnetite surface promotes the release of iron by the formation of a galvanic couple. Antibiotic adsorbed on the magnetite/Ag surface plays a dual role in the galvanic corrosion processes: as a corrosion inhibitor for iron oxides and as a corrosion promoter for silver. Magnetite/Ag/rifampicin and magnetite/Ag/doxycycline. NPs were found to have greater cytotoxicity towards the HEK293T cell line than magnetite NPs. These results were attributed to the combined toxic action of the released iron, silver ions and antibiotics. Intensive and simultaneous release of the NP components caused cell stress and suppressed their growth.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Though the cytotoxic properties of magnetite nanoparticles (NPs) are rather well investigated and known to be dose dependent and rather low, surface functionalization can drastically change their properties. To determine whether the cytotoxicity of magnetite/Ag/antibiotic NPs may be associated, among other things, with iron, silver and antibiotic release, this study investigates the release profiles and cytotoxicity of magnetite/Ag/rifampicin and magnetite/Ag/doxycycline NPs compares it similar profiles from magnetite, magnetite/Ag NPs and antibiotics. It was established that the studied NPs released not only water-soluble substances, such as antibiotics, but also poorly-soluble ones, such as iron and silver. The deposition of silver on the magnetite surface promotes the release of iron by the formation of a galvanic couple. Antibiotic adsorbed on the magnetite/Ag surface plays a dual role in the galvanic corrosion processes: as a corrosion inhibitor for iron oxides and as a corrosion promoter for silver. Magnetite/Ag/rifampicin and magnetite/Ag/doxycycline. NPs were found to have greater cytotoxicity towards the HEK293T cell line than magnetite NPs. These results were attributed to the combined toxic action of the released iron, silver ions and antibiotics. Intensive and simultaneous release of the NP components caused cell stress and suppressed their growth. |
Połatyńska, Agnieszka; Tomczyk, Karolina; Pochylski, Mikołaj; Meier, Gerd; Gapiński, Jacek; Banachowicz, Ewa; Śliwa, Tomasz; Patkowski, Adam Journal of Chemical Physics, 146 (8), pp. 084506, 2017, ISSN: 00219606. @article{Poatynska2017, title = {Temperature dependent FCS studies using a long working distance objective: Viscosities of supercooled liquids and particle size}, author = {Agnieszka Połatyńska and Karolina Tomczyk and Mikołaj Pochylski and Gerd Meier and Jacek Gapiński and Ewa Banachowicz and Tomasz Śliwa and Adam Patkowski}, url = {http://aip.scitation.org/doi/10.1063/1.4977047}, doi = {10.1063/1.4977047}, issn = {00219606}, year = {2017}, date = {2017-02-01}, journal = {Journal of Chemical Physics}, volume = {146}, number = {8}, pages = {084506}, publisher = {AIP Publishing LLC}, abstract = {In this work, we describe new experimental setups for Fluorescence Correlation Spectroscopy (FCS) where a long working distance objective is used. Using these setups, FCS measurements in a broad temperature range for a small sample volume of about 50 $mu$l can be performed. The use of specially designed cells and a dry long working distance objective was essential for avoiding temperature gradients in the sample. The performance of the new setups and a traditional FCS setup with immersion objectives is compared. The FCS data in combination with the Stokes-Einstein (SE) relation were used to obtain the values of the nanoviscosity of a fluid. We show for selected molecular van der Waals supercooled liquids that despite the fact that in these systems, a characteristic length scale can be defined, the nanoviscosity obtained from FCS is in a very good agreement with the macroscopic (rheometric) viscosity of the sample in a broad temperature range. This result corroborates the applicability of the SE relation to s...}, keywords = {}, pubstate = {published}, tppubtype = {article} } In this work, we describe new experimental setups for Fluorescence Correlation Spectroscopy (FCS) where a long working distance objective is used. Using these setups, FCS measurements in a broad temperature range for a small sample volume of about 50 $mu$l can be performed. The use of specially designed cells and a dry long working distance objective was essential for avoiding temperature gradients in the sample. The performance of the new setups and a traditional FCS setup with immersion objectives is compared. The FCS data in combination with the Stokes-Einstein (SE) relation were used to obtain the values of the nanoviscosity of a fluid. We show for selected molecular van der Waals supercooled liquids that despite the fact that in these systems, a characteristic length scale can be defined, the nanoviscosity obtained from FCS is in a very good agreement with the macroscopic (rheometric) viscosity of the sample in a broad temperature range. This result corroborates the applicability of the SE relation to s... |
Kiełbowicz-Matuk, Agnieszka; Czarnecka, Jagoda; Banachowicz, Ewa; Rey, Pascal; Rorat, Tadeusz Plant, Cell & Environment, 40 (3), pp. 424–440, 2017, ISSN: 1365-3040, (PCE-16-0763.R1). @article{PCE:PCE12875, title = {Solanum tuberosum ZPR1 encodes a light-regulated nuclear DNA-binding protein adjusting the circadian expression of StBBX24 to light cycle}, author = {Agnieszka Kiełbowicz-Matuk and Jagoda Czarnecka and Ewa Banachowicz and Pascal Rey and Tadeusz Rorat}, url = {http://dx.doi.org/10.1111/pce.12875}, doi = {10.1111/pce.12875}, issn = {1365-3040}, year = {2017}, date = {2017-01-01}, journal = {Plant, Cell & Environment}, volume = {40}, number = {3}, pages = {424--440}, note = {PCE-16-0763.R1}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Pokrzywa, Małgorzata; Pawełek, Katarzyna; Kucia, Weronika; Sarbak, Szymon; Chorell, Erik; Almqvist, Fredrik; Wittung-Stafshede, Pernilla Effects of small-molecule amyloid modulators on a Drosophila model of Parkinson’s disease PLOS ONE, 12 (9), pp. 1-21, 2017. @article{Pokrzywa2017, title = {Effects of small-molecule amyloid modulators on a Drosophila model of Parkinson’s disease}, author = {Małgorzata Pokrzywa and Katarzyna Pawełek and Weronika Kucia and Szymon Sarbak and Erik Chorell and Fredrik Almqvist and Pernilla Wittung-Stafshede}, url = {https://doi.org/10.1371/journal.pone.0184117}, doi = {10.1371/journal.pone.0184117}, year = {2017}, date = {2017-01-01}, journal = {PLOS ONE}, volume = {12}, number = {9}, pages = {1-21}, publisher = {Public Library of Science}, abstract = {Alpha-synuclein (aS) amyloid formation is involved in Parkinson’s disease (PD); therefore, small molecules that target aS and affect its aggregation are of interest as future drug candidates. We recently reported modified ring-fused 2-pyridones that modulate aS amyloid formation in vitro. Here, we describe the effects of such molecules on behavioral parameters of a Drosophila model of PD (i.e., flies expressing human aS), using a new approach (implemented in a commercially available FlyTracker system) to quantify fly mobility. FlyTracker allows for automated analysis of walking and climbing locomotor behavior, as it collects large sequences of data over time in an unbiased manner. We found that the molecules per se have no toxic or kinetic effects on normal flies. Feeding aS-expressing flies with the amyloid-promoting molecule FN075, remarkably, resulted in increased fly mobility at early time points; however, this effect switched to reduced mobility at later time points, and flies had shorter life spans than controls. In contrast, an amyloid inhibitor increased both fly kinetics and life span. In agreement with increased aS amyloid formation, the FN075-fed flies had less soluble aS, and in vitro aS-FN075 interactions stimulated aS amyloid formation. In addition to a new quantitative approach to probe mobility (available in FlyTracker), our results imply that aS regulates brain activity such that initial removal (here, by FN075-triggered assembly of aS) allows for increased fly mobility.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Alpha-synuclein (aS) amyloid formation is involved in Parkinson’s disease (PD); therefore, small molecules that target aS and affect its aggregation are of interest as future drug candidates. We recently reported modified ring-fused 2-pyridones that modulate aS amyloid formation in vitro. Here, we describe the effects of such molecules on behavioral parameters of a Drosophila model of PD (i.e., flies expressing human aS), using a new approach (implemented in a commercially available FlyTracker system) to quantify fly mobility. FlyTracker allows for automated analysis of walking and climbing locomotor behavior, as it collects large sequences of data over time in an unbiased manner. We found that the molecules per se have no toxic or kinetic effects on normal flies. Feeding aS-expressing flies with the amyloid-promoting molecule FN075, remarkably, resulted in increased fly mobility at early time points; however, this effect switched to reduced mobility at later time points, and flies had shorter life spans than controls. In contrast, an amyloid inhibitor increased both fly kinetics and life span. In agreement with increased aS amyloid formation, the FN075-fed flies had less soluble aS, and in vitro aS-FN075 interactions stimulated aS amyloid formation. In addition to a new quantitative approach to probe mobility (available in FlyTracker), our results imply that aS regulates brain activity such that initial removal (here, by FN075-triggered assembly of aS) allows for increased fly mobility. |
2016 |
Łukarska, Małgorzata; Jankowska, Aldona; Gapiński, Jacek; Valable, Samuel; Anfray, Clement; Menard, Benjamin; Mintova, Svetlana; Kowalak, Stanisław Synthesis and encapsulation of fluorescein in zeolite Y Microporous and Mesoporous Materials, 236 , pp. 79–84, 2016, ISSN: 13871811. @article{ukarska2016, title = {Synthesis and encapsulation of fluorescein in zeolite Y}, author = {Małgorzata Łukarska and Aldona Jankowska and Jacek Gapiński and Samuel Valable and Clement Anfray and Benjamin Menard and Svetlana Mintova and Stanisław Kowalak}, url = {https://www.sciencedirect.com/science/article/pii/S138718111630018X http://linkinghub.elsevier.com/retrieve/pii/S138718111630018X}, doi = {10.1016/j.micromeso.2016.02.043}, issn = {13871811}, year = {2016}, date = {2016-12-01}, journal = {Microporous and Mesoporous Materials}, volume = {236}, pages = {79--84}, publisher = {Elsevier}, abstract = {Fluorescein was entrapped inside FAU type zeolite (Y) by generating it from resorcinol and phthalic anhydride. Prior to the formation of fluorescein, zeolite Y was modified with various cations (H, Zn, Ce, Na, K). The modified zeolite acted as catalysts for the fluorescein Friedel–Crafts reaction synthesis, while at the same time it played a role of matrix for the stabilization and homogeneous dispersion of the guest molecules. The nature of the different cations influenced the content of fluorescein generated in the zeolite, and favoured the formation of some dye isomers (i.e. anion, dianion, cation or transition metal complex). The contribution of different fluorescein derivatives in the products was reflected in their absorption and fluorescence properties. The H-, Ce-, and Zn- containing Y zeolites revealed the highest content of fluorescein due to their distinct acid active sites. The composites with H- and ZnY zeolites indicated much higher fluorescence than that of the pristine fluorescein. Moreover, fluorescein in zeolite Y matrices did not show any photobleaching under continuous illumination ($łambda$ = 730 nm, in a two-photon experiment for 180 s), which suggests that these materials could be used for biomedical applications.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Fluorescein was entrapped inside FAU type zeolite (Y) by generating it from resorcinol and phthalic anhydride. Prior to the formation of fluorescein, zeolite Y was modified with various cations (H, Zn, Ce, Na, K). The modified zeolite acted as catalysts for the fluorescein Friedel–Crafts reaction synthesis, while at the same time it played a role of matrix for the stabilization and homogeneous dispersion of the guest molecules. The nature of the different cations influenced the content of fluorescein generated in the zeolite, and favoured the formation of some dye isomers (i.e. anion, dianion, cation or transition metal complex). The contribution of different fluorescein derivatives in the products was reflected in their absorption and fluorescence properties. The H-, Ce-, and Zn- containing Y zeolites revealed the highest content of fluorescein due to their distinct acid active sites. The composites with H- and ZnY zeolites indicated much higher fluorescence than that of the pristine fluorescein. Moreover, fluorescein in zeolite Y matrices did not show any photobleaching under continuous illumination ($łambda$ = 730 nm, in a two-photon experiment for 180 s), which suggests that these materials could be used for biomedical applications. |
Pochylski, Mikołaj; Iwaszkiewicz-Kostka, I; Kaczmarek, M S; Woźniak, Z; Drozdowski, H Molecular orientation in binary liquid mixtures from excess Cotton-Mouton constant Journal of Molecular Liquids, 224 , pp. 146–150, 2016, ISSN: 01677322. @article{Pochylski2016, title = {Molecular orientation in binary liquid mixtures from excess Cotton-Mouton constant}, author = {Mikołaj Pochylski and I Iwaszkiewicz-Kostka and M S Kaczmarek and Z Woźniak and H Drozdowski}, url = {https://www.sciencedirect.com/science/article/pii/S0167732216323121 http://linkinghub.elsevier.com/retrieve/pii/S0167732216323121}, doi = {10.1016/j.molliq.2016.09.124}, issn = {01677322}, year = {2016}, date = {2016-12-01}, journal = {Journal of Molecular Liquids}, volume = {224}, pages = {146--150}, publisher = {Elsevier}, abstract = {We show the results of magnetically induced birefringence measurements performed in binary mixtures of simple molecular liquids. New excess function was introduced based on experimentally determined values of Cotton-Mouton constant - a quantity directly related to the induced orientation of anisotropic molecules. Concentration dependencies of excess molar Cotton-Mouton constant were compared with analogous characteristics of excess molar volume. Both excess functions are well reproduced using Redlich-Kister polynomial expansion. The results suggest that in the examined mixtures binary pairs of unlike molecules are formed in which molecular planes are oriented parallel to each other with simultaneous rotation along the axis perpendicular to benzene plane. Such preferred angular arrangement is independent on the average intermolecular distance within a pair-aggregate.}, keywords = {}, pubstate = {published}, tppubtype = {article} } We show the results of magnetically induced birefringence measurements performed in binary mixtures of simple molecular liquids. New excess function was introduced based on experimentally determined values of Cotton-Mouton constant - a quantity directly related to the induced orientation of anisotropic molecules. Concentration dependencies of excess molar Cotton-Mouton constant were compared with analogous characteristics of excess molar volume. Both excess functions are well reproduced using Redlich-Kister polynomial expansion. The results suggest that in the examined mixtures binary pairs of unlike molecules are formed in which molecular planes are oriented parallel to each other with simultaneous rotation along the axis perpendicular to benzene plane. Such preferred angular arrangement is independent on the average intermolecular distance within a pair-aggregate. |
Kucia, Weronika; Sharma, Gargi; Joseph, Cecil S; Sarbak, Szymon; Oliver, Cameron; Dobek, Andrzej; Giles, Robert H Optical Kerr effect of tRNA solution induced by femtosecond laser pulses Chemical Physics Letters, 662 , pp. 132–136, 2016, ISSN: 00092614. @article{Kucia2016, title = {Optical Kerr effect of tRNA solution induced by femtosecond laser pulses}, author = {Weronika Kucia and Gargi Sharma and Cecil S Joseph and Szymon Sarbak and Cameron Oliver and Andrzej Dobek and Robert H Giles}, url = {https://www.sciencedirect.com/science/article/pii/S0009261416306996 http://linkinghub.elsevier.com/retrieve/pii/S0009261416306996}, doi = {10.1016/j.cplett.2016.09.027}, issn = {00092614}, year = {2016}, date = {2016-10-01}, journal = {Chemical Physics Letters}, volume = {662}, pages = {132--136}, publisher = {North-Holland}, abstract = {The optical Kerr effect (OKE) in a transfer ribonucleic acid (tRNA) solution induced by femtosecond pulses of linearly polarized pump light ($łambda$i=800nm) and sounded by probe light ($łambda$p=800nm) was studied. The measurements were performed to find nonlinear optical parameters describing a single molecule (molecular Kerr constant K, mean nonlinear third order optical polarizability cpi) and to compare them with our previous OKE results obtained in ns and ps time range. The OKE experiment has proven to be an efficient method to obtain the nonlinear parameters of single molecules in solution, which reflects dynamic structure changes.}, keywords = {}, pubstate = {published}, tppubtype = {article} } The optical Kerr effect (OKE) in a transfer ribonucleic acid (tRNA) solution induced by femtosecond pulses of linearly polarized pump light ($łambda$i=800nm) and sounded by probe light ($łambda$p=800nm) was studied. The measurements were performed to find nonlinear optical parameters describing a single molecule (molecular Kerr constant K, mean nonlinear third order optical polarizability cpi) and to compare them with our previous OKE results obtained in ns and ps time range. The OKE experiment has proven to be an efficient method to obtain the nonlinear parameters of single molecules in solution, which reflects dynamic structure changes. |
Babayevska, N; Peplińska, B; Jarek, M; Yate, L; Tadyszak, K; Gapiński, Jacek; Iatsunskyi, I; Jurga, S RSC Advances, 6 (92), pp. 89305–89312, 2016, ISSN: 2046-2069. @article{Babayevska2016, title = {Synthesis, structure, EPR studies and up-conversion luminescence of ZnO:Er 3+ –Yb 3+ @Gd 2 O 3 nanostructures}, author = {N Babayevska and B Peplińska and M Jarek and L Yate and K Tadyszak and Jacek Gapiński and I Iatsunskyi and S Jurga}, url = {http://xlink.rsc.org/?DOI=C6RA18393J}, doi = {10.1039/C6RA18393J}, issn = {2046-2069}, year = {2016}, date = {2016-09-01}, journal = {RSC Advances}, volume = {6}, number = {92}, pages = {89305--89312}, publisher = {The Royal Society of Chemistry}, abstract = {ZnO:Er 3+ –Yb 3+ @Gd 2 O 3 nanostructures were obtained by “ wet ” chemistry methods – the sol–gel technique for the preparation of ZnO and ZnO:Er 3+ –Yb 3+ nanoparticles (NPs), and the seed deposition method for obtaining Gd 2 O 3 .}, keywords = {}, pubstate = {published}, tppubtype = {article} } ZnO:Er 3+ –Yb 3+ @Gd 2 O 3 nanostructures were obtained by “ wet ” chemistry methods – the sol–gel technique for the preparation of ZnO and ZnO:Er 3+ –Yb 3+ nanoparticles (NPs), and the seed deposition method for obtaining Gd 2 O 3 . |
Mazuryk, Jarosław; Deptuła, Tobiasz; Polchi, Alice; Gapiński, Jacek; Giovagnoli, Stefano; Magini, Alessandro; Emiliani, Carla; Kohlbrecher, Joachim; Patkowski, Adam Colloids and Surfaces A: Physicochemical and Engineering Aspects, 502 , pp. 54–65, 2016, ISSN: 09277757. @article{Mazuryk2016, title = {Rapamycin-loaded solid lipid nanoparticles: Morphology and impact of the drug loading on the phase transition between lipid polymorphs}, author = {Jarosław Mazuryk and Tobiasz Deptuła and Alice Polchi and Jacek Gapiński and Stefano Giovagnoli and Alessandro Magini and Carla Emiliani and Joachim Kohlbrecher and Adam Patkowski}, url = {https://www.sciencedirect.com/science/article/pii/S0927775716303259 http://linkinghub.elsevier.com/retrieve/pii/S0927775716303259}, doi = {10.1016/j.colsurfa.2016.05.017}, issn = {09277757}, year = {2016}, date = {2016-08-01}, journal = {Colloids and Surfaces A: Physicochemical and Engineering Aspects}, volume = {502}, pages = {54--65}, publisher = {Elsevier}, abstract = {In recent decades solid lipid nanoparticles (SLN) have become a well-performing tool for the site-targeted delivery of water-insoluble drugs. In this study, Compritoltextregistered 888 ATO-based SLN, coated with polysorbate 80, were loaded with rapamycin (Rap), a lipophilic immunomodulator, broadly-used in therapies of cancer and neurodegenerative diseases. Rap-SLN were formulated using cold high-pressure homogenization and ultrasound-assisted emulsion. The exploitation of these methods yielded the nanoparticles of various values of zeta-potential (from −1mV to −20mV) and efficacies of the Rap entrapment (from 37.5±2.3% to 77.0±5.4%). The SEM and AFM imaging and shape-modeling by the combined DLS-SANS analysis revealed that the Rap-SLN of the hydrodynamic radius of ∼46nm preserve the platelet-like or flat ellipsoidal structure with a thickness as large as 8–9nm. These dimensions correspond to a single lipid bilayer, organized in a triclinic L$beta$ polymorph, and covered with a 1–2-nm shell of the surfactant. Consistently, FT-IR spectra acquired in the range 52–75°C, showed that the Rap incorporation within the lipid matrix decreases the point of the gel-liquid crystalline (L$beta$-L$alpha$) phase transition. These outcomes imply a thermodynamically-driven mechanism of the Rap release from SLN.}, keywords = {}, pubstate = {published}, tppubtype = {article} } In recent decades solid lipid nanoparticles (SLN) have become a well-performing tool for the site-targeted delivery of water-insoluble drugs. In this study, Compritoltextregistered 888 ATO-based SLN, coated with polysorbate 80, were loaded with rapamycin (Rap), a lipophilic immunomodulator, broadly-used in therapies of cancer and neurodegenerative diseases. Rap-SLN were formulated using cold high-pressure homogenization and ultrasound-assisted emulsion. The exploitation of these methods yielded the nanoparticles of various values of zeta-potential (from −1mV to −20mV) and efficacies of the Rap entrapment (from 37.5±2.3% to 77.0±5.4%). The SEM and AFM imaging and shape-modeling by the combined DLS-SANS analysis revealed that the Rap-SLN of the hydrodynamic radius of ∼46nm preserve the platelet-like or flat ellipsoidal structure with a thickness as large as 8–9nm. These dimensions correspond to a single lipid bilayer, organized in a triclinic L$beta$ polymorph, and covered with a 1–2-nm shell of the surfactant. Consistently, FT-IR spectra acquired in the range 52–75°C, showed that the Rap incorporation within the lipid matrix decreases the point of the gel-liquid crystalline (L$beta$-L$alpha$) phase transition. These outcomes imply a thermodynamically-driven mechanism of the Rap release from SLN. |
Stracy, Mathew; Jaciuk, Marcin; Uphoff, Stephan; Kapanidis, Achillefs N; Nowotny, Marcin; Sherratt, David J; Zawadzki, Paweł Single-molecule imaging of UvrA and UvrB recruitment to DNA lesions in living Escherichia coli Nature Communications, 7 , pp. 12568, 2016, ISSN: 2041-1723. @article{Stracy2016, title = {Single-molecule imaging of UvrA and UvrB recruitment to DNA lesions in living Escherichia coli}, author = {Mathew Stracy and Marcin Jaciuk and Stephan Uphoff and Achillefs N Kapanidis and Marcin Nowotny and David J Sherratt and Paweł Zawadzki}, url = {http://www.nature.com/doifinder/10.1038/ncomms12568}, doi = {10.1038/ncomms12568}, issn = {2041-1723}, year = {2016}, date = {2016-08-01}, journal = {Nature Communications}, volume = {7}, pages = {12568}, publisher = {Nature Publishing Group}, abstract = {Nucleotide excision repair is able to identify and remove a wide range of DNA helix distorting lesions from the genome. Here the authors use single molecule imaging of UvrA and UvrB molecules and suggest a two-step ‘scan and recruit' model for UvrA function.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Nucleotide excision repair is able to identify and remove a wide range of DNA helix distorting lesions from the genome. Here the authors use single molecule imaging of UvrA and UvrB molecules and suggest a two-step ‘scan and recruit' model for UvrA function. |
Białek, Rafał; Burdziński, Gotard; Jones, Michael R; Gibasiewicz, Krzysztof Bacteriopheophytin triplet state in Rhodobacter sphaeroides reaction centers Photosynthesis Research, 129 (2), pp. 205–216, 2016, ISSN: 0166-8595. @article{Biaek2016, title = {Bacteriopheophytin triplet state in Rhodobacter sphaeroides reaction centers}, author = {Rafał Białek and Gotard Burdziński and Michael R Jones and Krzysztof Gibasiewicz}, url = {http://link.springer.com/10.1007/s11120-016-0290-6}, doi = {10.1007/s11120-016-0290-6}, issn = {0166-8595}, year = {2016}, date = {2016-08-01}, journal = {Photosynthesis Research}, volume = {129}, number = {2}, pages = {205--216}, publisher = {Springer Netherlands}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Gibasiewicz, Krzysztof; Białek, Rafał; Pajzderska, Maria; Karolczak, Jerzy; Burdziński, Gotard; Jones, Michael R; Brettel, Klaus Photosynthesis Research, 128 (3), pp. 243–258, 2016, ISSN: 0166-8595. @article{Gibasiewicz2016, title = {Weak temperature dependence of P + H A − recombination in mutant Rhodobacter sphaeroides reaction centers}, author = {Krzysztof Gibasiewicz and Rafał Białek and Maria Pajzderska and Jerzy Karolczak and Gotard Burdziński and Michael R Jones and Klaus Brettel}, url = {http://www.ncbi.nlm.nih.gov/pubmed/26942583 http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=PMC4877430 http://link.springer.com/10.1007/s11120-016-0239-9}, doi = {10.1007/s11120-016-0239-9}, issn = {0166-8595}, year = {2016}, date = {2016-06-01}, journal = {Photosynthesis Research}, volume = {128}, number = {3}, pages = {243--258}, abstract = {In contrast with findings on the wild-type Rhodobacter sphaeroides reaction center, biexponential P (+) H A (-) → PH A charge recombination is shown to be weakly dependent on temperature between 78 and 298 K in three variants with single amino acids exchanged in the vicinity of primary electron acceptors. These mutated reaction centers have diverse overall kinetics of charge recombination, spanning an average lifetime from ~2 to ~20 ns. Despite these differences a protein relaxation model applied previously to wild-type reaction centers was successfully used to relate the observed kinetics to the temporal evolution of the free energy level of the state P (+) H A (-) relative to P (+) B A (-) . We conclude that the observed variety in the kinetics of charge recombination, together with their weak temperature dependence, is caused by a combination of factors that are each affected to a different extent by the point mutations in a particular mutant complex. These are as follows: (1) the initial free energy gap between the states P (+) B A (-) and P (+) H A (-) , (2) the intrinsic rate of P (+) B A (-) → PB A charge recombination, and (3) the rate of protein relaxation in response to the appearance of the charge separated states. In the case of a mutant which displays rapid P (+) H A (-) recombination (ELL), most of this recombination occurs in an unrelaxed protein in which P (+) B A (-) and P (+) H A (-) are almost isoenergetic. In contrast, in a mutant in which P (+) H A (-) recombination is relatively slow (GML), most of the recombination occurs in a relaxed protein in which P (+) H A (-) is much lower in energy than P (+) H A (-) . The weak temperature dependence in the ELL reaction center and a YLH mutant was modeled in two ways: (1) by assuming that the initial P (+) B A (-) and P (+) H A (-) states in an unrelaxed protein are isoenergetic, whereas the final free energy gap between these states following the protein relaxation is large (~250 meV or more), independent of temperature and (2) by assuming that the initial and final free energy gaps between P (+) B A (-) and P (+) H A (-) are moderate and temperature dependent. In the case of the GML mutant, it was concluded that the free energy gap between P (+) B A (-) and P (+) H A (-) is large at all times.}, keywords = {}, pubstate = {published}, tppubtype = {article} } In contrast with findings on the wild-type Rhodobacter sphaeroides reaction center, biexponential P (+) H A (-) → PH A charge recombination is shown to be weakly dependent on temperature between 78 and 298 K in three variants with single amino acids exchanged in the vicinity of primary electron acceptors. These mutated reaction centers have diverse overall kinetics of charge recombination, spanning an average lifetime from ~2 to ~20 ns. Despite these differences a protein relaxation model applied previously to wild-type reaction centers was successfully used to relate the observed kinetics to the temporal evolution of the free energy level of the state P (+) H A (-) relative to P (+) B A (-) . We conclude that the observed variety in the kinetics of charge recombination, together with their weak temperature dependence, is caused by a combination of factors that are each affected to a different extent by the point mutations in a particular mutant complex. These are as follows: (1) the initial free energy gap between the states P (+) B A (-) and P (+) H A (-) , (2) the intrinsic rate of P (+) B A (-) → PB A charge recombination, and (3) the rate of protein relaxation in response to the appearance of the charge separated states. In the case of a mutant which displays rapid P (+) H A (-) recombination (ELL), most of this recombination occurs in an unrelaxed protein in which P (+) B A (-) and P (+) H A (-) are almost isoenergetic. In contrast, in a mutant in which P (+) H A (-) recombination is relatively slow (GML), most of the recombination occurs in a relaxed protein in which P (+) H A (-) is much lower in energy than P (+) H A (-) . The weak temperature dependence in the ELL reaction center and a YLH mutant was modeled in two ways: (1) by assuming that the initial P (+) B A (-) and P (+) H A (-) states in an unrelaxed protein are isoenergetic, whereas the final free energy gap between these states following the protein relaxation is large (~250 meV or more), independent of temperature and (2) by assuming that the initial and final free energy gaps between P (+) B A (-) and P (+) H A (-) are moderate and temperature dependent. In the case of the GML mutant, it was concluded that the free energy gap between P (+) B A (-) and P (+) H A (-) is large at all times. |
Dubas, Katarzyna; Baranowski, M; Podhorodecki, A; Jones, M R; Gibasiewicz, Krzysztof The Journal of Physical Chemistry B, 120 (22), pp. 4890–4896, 2016, ISSN: 1520-6106. @article{Dubas2016, title = {Unified Model of Nanosecond Charge Recombination in Closed Reaction Centers from Rhodobacter sphaeroides : Role of Protein Polarization Dynamics}, author = {Katarzyna Dubas and M Baranowski and A Podhorodecki and M R Jones and Krzysztof Gibasiewicz}, url = {http://pubs.acs.org/doi/10.1021/acs.jpcb.6b01459}, doi = {10.1021/acs.jpcb.6b01459}, issn = {1520-6106}, year = {2016}, date = {2016-06-01}, journal = {The Journal of Physical Chemistry B}, volume = {120}, number = {22}, pages = {4890--4896}, publisher = {American Chemical Society}, abstract = {Ongoing questions surround the influence of protein dynamics on rapid processes such as biological electron transfer. Such questions are particularly addressable in light-activated systems. In Rhodobacter sphaeroides reaction centers, charge recombination or back electron transfer from the reduced bacteriopheophytin, HA–, to the oxidized dimeric bacteriochlorophyll, P+, may be monitored by both transient absorption spectroscopy and transient fluorescence spectroscopy. Signals measured with both these techniques decay in a similar three-exponential fashion with lifetimes of ∼0.6–0.7, ∼2–4, and ∼10–20 ns, revealing the complex character of this electron transfer reaction. In this study a single kinetic model was developed to connect lifetime and amplitude data from both techniques. The model took into account the possibility that electron transfer from HA– to P+ may occur with transient formation of the state P+BA–. As a result it was possible to model the impact of nanosecond protein relaxation on the free...}, keywords = {}, pubstate = {published}, tppubtype = {article} } Ongoing questions surround the influence of protein dynamics on rapid processes such as biological electron transfer. Such questions are particularly addressable in light-activated systems. In Rhodobacter sphaeroides reaction centers, charge recombination or back electron transfer from the reduced bacteriopheophytin, HA–, to the oxidized dimeric bacteriochlorophyll, P+, may be monitored by both transient absorption spectroscopy and transient fluorescence spectroscopy. Signals measured with both these techniques decay in a similar three-exponential fashion with lifetimes of ∼0.6–0.7, ∼2–4, and ∼10–20 ns, revealing the complex character of this electron transfer reaction. In this study a single kinetic model was developed to connect lifetime and amplitude data from both techniques. The model took into account the possibility that electron transfer from HA– to P+ may occur with transient formation of the state P+BA–. As a result it was possible to model the impact of nanosecond protein relaxation on the free... |
Kiełbowicz-Matuk, Agnieszka; Banachowicz, Ewa; Turska-Tarska, Anna; Rey, Pascal; Rorat, Tadeusz Plant Science, 246 , pp. 98–111, 2016, ISSN: 01689452. @article{Kiebowicz-Matuk2016, title = {Expression and characterization of a barley phosphatidylinositol transfer protein structurally homologous to the yeast Sec14p protein}, author = {Agnieszka Kiełbowicz-Matuk and Ewa Banachowicz and Anna Turska-Tarska and Pascal Rey and Tadeusz Rorat}, url = {http://linkinghub.elsevier.com/retrieve/pii/S0168945216300267}, doi = {10.1016/j.plantsci.2016.02.014}, issn = {01689452}, year = {2016}, date = {2016-05-01}, journal = {Plant Science}, volume = {246}, pages = {98--111}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Polchi, Alice; Magini, Alessandro; Mazuryk, Jarosław; Tancini, Brunella; Gapiński, Jacek; Patkowski, Adam; Giovagnoli, Stefano; Emiliani, Carla Nanomaterials, 6 (5), pp. 87, 2016, ISSN: 2079-4991. @article{Polchi2016, title = {Rapamycin Loaded Solid Lipid Nanoparticles as a New Tool to Deliver mTOR Inhibitors: Formulation and in Vitro Characterization}, author = {Alice Polchi and Alessandro Magini and Jarosław Mazuryk and Brunella Tancini and Jacek Gapiński and Adam Patkowski and Stefano Giovagnoli and Carla Emiliani}, url = {http://www.mdpi.com/2079-4991/6/5/87}, doi = {10.3390/nano6050087}, issn = {2079-4991}, year = {2016}, date = {2016-05-01}, journal = {Nanomaterials}, volume = {6}, number = {5}, pages = {87}, publisher = {Multidisciplinary Digital Publishing Institute}, abstract = {Recently, the use of mammalian target of rapamycin (mTOR) inhibitors, in particular rapamycin (Rp), has been suggested to improve the treatment of neurodegenerative diseases. However, as Rp is a strong immunosuppressant, specific delivery to the brain has been postulated to avoid systemic exposure. In this work, we fabricated new Rp loaded solid lipid nanoparticles (Rp-SLN) stabilized with polysorbate 80 (PS80), comparing two different methods and lipids. The formulations were characterized by differential scanning calorimetry (DSC), nuclear magnetic resonance (NMR), wide angle X-ray scattering (WAXS), cryo-transmission electron microscopy (cryo-TEM), dynamic light scattering (DLS) and particle tracking. In vitro release and short-term stability were assessed. Biological behavior of Rp-SLN was tested in SH-SY5Y neuroblastoma cells. The inhibition of mTOR complex 1 (mTORC1) was evaluated over time by a pulse-chase study compared to free Rp and Rp nanocrystals. Compritol Rp-SLN resulted more stable and possessing proper size and surface properties with respect to cetyl palmitate Rp-SLN. Rapamycin was entrapped in an amorphous form in the solid lipid matrix that showed partial crystallinity with stable L$beta$, sub-L$alpha$ and L$beta$′ arrangements. PS80 was stably anchored on particle surface. No drug release was observed over 24 h and Rp-SLN had a higher cell uptake and a more sustained effect over a week. The mTORC1 inhibition was higher with Rp-SLN. Overall, compritol Rp-SLN show suitable characteristics and stability to be considered for further investigation as Rp brain delivery system.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Recently, the use of mammalian target of rapamycin (mTOR) inhibitors, in particular rapamycin (Rp), has been suggested to improve the treatment of neurodegenerative diseases. However, as Rp is a strong immunosuppressant, specific delivery to the brain has been postulated to avoid systemic exposure. In this work, we fabricated new Rp loaded solid lipid nanoparticles (Rp-SLN) stabilized with polysorbate 80 (PS80), comparing two different methods and lipids. The formulations were characterized by differential scanning calorimetry (DSC), nuclear magnetic resonance (NMR), wide angle X-ray scattering (WAXS), cryo-transmission electron microscopy (cryo-TEM), dynamic light scattering (DLS) and particle tracking. In vitro release and short-term stability were assessed. Biological behavior of Rp-SLN was tested in SH-SY5Y neuroblastoma cells. The inhibition of mTOR complex 1 (mTORC1) was evaluated over time by a pulse-chase study compared to free Rp and Rp nanocrystals. Compritol Rp-SLN resulted more stable and possessing proper size and surface properties with respect to cetyl palmitate Rp-SLN. Rapamycin was entrapped in an amorphous form in the solid lipid matrix that showed partial crystallinity with stable L$beta$, sub-L$alpha$ and L$beta$′ arrangements. PS80 was stably anchored on particle surface. No drug release was observed over 24 h and Rp-SLN had a higher cell uptake and a more sustained effect over a week. The mTORC1 inhibition was higher with Rp-SLN. Overall, compritol Rp-SLN show suitable characteristics and stability to be considered for further investigation as Rp brain delivery system. |
Michalska, Martyna; Florczak, Anna; Dams-Kozlowska, Hanna; Gapiński, Jacek; Jurga, Stefan; ë, Rapha Acta Biomaterialia, 35 , pp. 293–304, 2016, ISSN: 17427061. @article{Michalska2016, title = {Peptide-functionalized ZCIS QDs as fluorescent nanoprobe for targeted HER2-positive breast cancer cells imaging}, author = {Martyna Michalska and Anna Florczak and Hanna Dams-Kozlowska and Jacek Gapiński and Stefan Jurga and Rapha ë}, url = {https://www.sciencedirect.com/science/article/pii/S1742706116300459 http://linkinghub.elsevier.com/retrieve/pii/S1742706116300459}, doi = {10.1016/j.actbio.2016.02.002}, issn = {17427061}, year = {2016}, date = {2016-04-01}, journal = {Acta Biomaterialia}, volume = {35}, pages = {293--304}, publisher = {Elsevier}, abstract = {In this paper, the synthesis of alloyed CuInZnxS2+x quantum dots (ZCIS QDs), their transfer into aqueous solution via a polymer coating technique, and the use of these nanocrystals to selectively target HER2-positive cells, are reported. By optimizing first the ZnS shell deposition process onto the CuInS2 core, and next the encapsulation of the dots with the amphiphilic poly(maleic anhydride-alt-1-octadecene) (PMAO) polymer, water-dispersible ZCIS QDs were successfully prepared. The nanocrystals with a photoluminescence quantum yield of 35% were purified via centrifugation and ultracentrifugation and high quality nanoparticles with narrow size distributions and surface charges were obtained. After verifying the biocompatibility of PMO-coated ZCIS QDs, we coupled these nanocrystals with the LTVSPWY peptide and demonstrated via MTT assay that both bare and the peptide-linked QDs exhibit low cytotoxicity. The HER2-mediated delivery of the peptide-linked QDs was confirmed by confocal microscopy. This study indicates that as engineered QDs can efficiently be used as fluorescent nanoprobes for selective labelling of HER2-positive SKBR3 cancer cells.}, keywords = {}, pubstate = {published}, tppubtype = {article} } In this paper, the synthesis of alloyed CuInZnxS2+x quantum dots (ZCIS QDs), their transfer into aqueous solution via a polymer coating technique, and the use of these nanocrystals to selectively target HER2-positive cells, are reported. By optimizing first the ZnS shell deposition process onto the CuInS2 core, and next the encapsulation of the dots with the amphiphilic poly(maleic anhydride-alt-1-octadecene) (PMAO) polymer, water-dispersible ZCIS QDs were successfully prepared. The nanocrystals with a photoluminescence quantum yield of 35% were purified via centrifugation and ultracentrifugation and high quality nanoparticles with narrow size distributions and surface charges were obtained. After verifying the biocompatibility of PMO-coated ZCIS QDs, we coupled these nanocrystals with the LTVSPWY peptide and demonstrated via MTT assay that both bare and the peptide-linked QDs exhibit low cytotoxicity. The HER2-mediated delivery of the peptide-linked QDs was confirmed by confocal microscopy. This study indicates that as engineered QDs can efficiently be used as fluorescent nanoprobes for selective labelling of HER2-positive SKBR3 cancer cells. |
Jarzębski, Maciej; Zhang, Yingze; Śliwa, Tomasz; Mazuryk, Jarosław; Deptuła, Tobiasz; Kucinska, Malgorzata; Murias, Marek; Buitenhuis, Johan; Gapiński, Jacek; Patkowski, Adam Journal of Fluorine Chemistry, 183 , pp. 92–99, 2016, ISSN: 00221139. @article{Jarzebski2016, title = {Core–shell fluorinated methacrylate nanoparticles with Rhodamine-B for confocal microscopy and fluorescence correlation spectroscopy applications}, author = {Maciej Jarzębski and Yingze Zhang and Tomasz Śliwa and Jarosław Mazuryk and Tobiasz Deptuła and Malgorzata Kucinska and Marek Murias and Johan Buitenhuis and Jacek Gapiński and Adam Patkowski}, url = {https://www.sciencedirect.com/science/article/pii/S0022113916300148 http://linkinghub.elsevier.com/retrieve/pii/S0022113916300148}, doi = {10.1016/j.jfluchem.2016.01.014}, issn = {00221139}, year = {2016}, date = {2016-03-01}, journal = {Journal of Fluorine Chemistry}, volume = {183}, pages = {92--99}, publisher = {Elsevier}, abstract = {There is a need to develop nanosized and submicron sized stable and efficient fluorescent particles for confocal microscopy and fluorescence correlation spectroscopy, which are useful methods to study dynamics and interactions in complex colloidal systems and living cells. Fluorescent core–transparent shell fluorinated polymer nanoparticles exhibit low refractive index, close to that of water, high fluorescence efficiency, high stability and no cytotoxicity which makes them excellent probes for water based and living systems. Fluorescent core–transparent shell submicron particles were synthesized using 1H,1H-heptafluoro-n-butyl methacrylate (HFBMA) as a monomer and Rhodamine-B-isothiocyanate as a dye. The fluorescent polymeric core was surrounded by a non-fluorescent shell obtained by the seeded growth synthesis. The spherical shape of the particles was confirmed by scanning electron microscopy and the particle size in suspension was characterized by dynamic light scattering (DLS) and fluorescence correlation spectroscopy (FCS). The effect of different reaction parameters, such as initiator concentration and polymerization time on the particle size and charge density as well as their toxicity were studied. The smallest nanoparticles, of diameter d=240nm for the core measured by DLS, were obtained with higher initiator concentration. Repeated confocal imaging, DLS and FCS measurements after a few months up to two years confirmed high fluorescence efficiency, stability and usefulness of prepared particles as versatile systems for confocal microscopy and fluorescence correlation spectroscopy studies in water-based colloidal suspensions. The cytotoxicity tests confirmed a possible use of these nanoparticles also in living cells.}, keywords = {}, pubstate = {published}, tppubtype = {article} } There is a need to develop nanosized and submicron sized stable and efficient fluorescent particles for confocal microscopy and fluorescence correlation spectroscopy, which are useful methods to study dynamics and interactions in complex colloidal systems and living cells. Fluorescent core–transparent shell fluorinated polymer nanoparticles exhibit low refractive index, close to that of water, high fluorescence efficiency, high stability and no cytotoxicity which makes them excellent probes for water based and living systems. Fluorescent core–transparent shell submicron particles were synthesized using 1H,1H-heptafluoro-n-butyl methacrylate (HFBMA) as a monomer and Rhodamine-B-isothiocyanate as a dye. The fluorescent polymeric core was surrounded by a non-fluorescent shell obtained by the seeded growth synthesis. The spherical shape of the particles was confirmed by scanning electron microscopy and the particle size in suspension was characterized by dynamic light scattering (DLS) and fluorescence correlation spectroscopy (FCS). The effect of different reaction parameters, such as initiator concentration and polymerization time on the particle size and charge density as well as their toxicity were studied. The smallest nanoparticles, of diameter d=240nm for the core measured by DLS, were obtained with higher initiator concentration. Repeated confocal imaging, DLS and FCS measurements after a few months up to two years confirmed high fluorescence efficiency, stability and usefulness of prepared particles as versatile systems for confocal microscopy and fluorescence correlation spectroscopy studies in water-based colloidal suspensions. The cytotoxicity tests confirmed a possible use of these nanoparticles also in living cells. |
Gapiński, Jacek; Jarzębski, Maciej; Buitenhuis, Johan; Deptuła, Tobiasz; Mazuryk, Jarosław; Patkowski, Adam Langmuir, 32 (10), pp. 2482–2491, 2016, ISSN: 0743-7463. @article{Gapinski2016, title = {Structure and Dimensions of Core–Shell Nanoparticles Comparable to the Confocal Volume Studied by Means of Fluorescence Correlation Spectroscopy}, author = {Jacek Gapiński and Maciej Jarzębski and Johan Buitenhuis and Tobiasz Deptuła and Jarosław Mazuryk and Adam Patkowski}, url = {http://pubs.acs.org/doi/10.1021/acs.langmuir.5b04605}, doi = {10.1021/acs.langmuir.5b04605}, issn = {0743-7463}, year = {2016}, date = {2016-03-01}, journal = {Langmuir}, volume = {32}, number = {10}, pages = {2482--2491}, publisher = {American Chemical Society}, abstract = {In some applications the dye distribution within fluorescently labeled nanoparticles and its stability over long periods of time are important issues. In this article we study numerically and experimentally the applicability of fluorescence correlation spectroscopy (FCS) to resolve such questions. When the size of fluorescently labeled particles is comparable to or larger than the confocal volume, the effective confocal volume seen in FCS experiments is increasing. Such an effect has already been studied for uniformly labeled spherical particles. In this work we analyze the form of the FCS correlation functions (CFs) for core-labeled and shell-labeled core–shell particles. For shell-labeled particles an additional fast decay was found both in simulations and in experiments on custom-made surface-labeled particles. Universal scaling of FCS correlation times based on the squared ratio of the labeled part radius of gyration to the Gaussian radius of the beam profile was found. Recipes based on the analysis o...}, keywords = {}, pubstate = {published}, tppubtype = {article} } In some applications the dye distribution within fluorescently labeled nanoparticles and its stability over long periods of time are important issues. In this article we study numerically and experimentally the applicability of fluorescence correlation spectroscopy (FCS) to resolve such questions. When the size of fluorescently labeled particles is comparable to or larger than the confocal volume, the effective confocal volume seen in FCS experiments is increasing. Such an effect has already been studied for uniformly labeled spherical particles. In this work we analyze the form of the FCS correlation functions (CFs) for core-labeled and shell-labeled core–shell particles. For shell-labeled particles an additional fast decay was found both in simulations and in experiments on custom-made surface-labeled particles. Universal scaling of FCS correlation times based on the squared ratio of the labeled part radius of gyration to the Gaussian radius of the beam profile was found. Recipes based on the analysis o... |
Pochylski, Mikołaj; Rossi, Cesare Oliviero; Nicotera, Isabella; Liveri, Vincenzo Turco; Calandra, Pietro RSC Advances, 6 (32), pp. 26696–26708, 2016, ISSN: 2046-2069. @article{Pochylski2016a, title = {Nano-demixing as a novel strategy for magnetic field responsive systems: the case of dibutyl phosphate/bis(2-ethylhexyl)amine systems}, author = {Mikołaj Pochylski and Cesare Oliviero Rossi and Isabella Nicotera and Vincenzo Turco Liveri and Pietro Calandra}, url = {http://xlink.rsc.org/?DOI=C6RA02386J}, doi = {10.1039/C6RA02386J}, issn = {2046-2069}, year = {2016}, date = {2016-03-01}, journal = {RSC Advances}, volume = {6}, number = {32}, pages = {26696--26708}, publisher = {The Royal Society of Chemistry}, abstract = {Pure surfactant liquids and their binary mixtures, owing to the amphiphilic nature of the molecules involved, can exhibit nano-segregation and peculiar transport properties with the formation of magnetic field-responsive supramolecular structures.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Pure surfactant liquids and their binary mixtures, owing to the amphiphilic nature of the molecules involved, can exhibit nano-segregation and peculiar transport properties with the formation of magnetic field-responsive supramolecular structures. |
Woźniak, Anna; Noculak, Agnieszka; Gapiński, Jacek; Kociolek, Daria; Boś-Liedke, Agnieszka; Zalewski, Tomasz; Grześkowiak, Bartosz F; Kołodziejczak, Anna; Jurga, Stefan; Banski, Mateusz; Misiewicz, Jan; Podhorodecki, Artur Cytotoxicity and imaging studies of $beta$-NaGdF 4 :Yb 3+ Er 3+ @PEG-Mo nanorods RSC Advances, 6 (98), pp. 95633–95643, 2016, ISSN: 2046-2069. @article{Wozniak, title = {Cytotoxicity and imaging studies of $beta$-NaGdF 4 :Yb 3+ Er 3+ @PEG-Mo nanorods}, author = {Anna Woźniak and Agnieszka Noculak and Jacek Gapiński and Daria Kociolek and Agnieszka Boś-Liedke and Tomasz Zalewski and Bartosz F Grześkowiak and Anna Kołodziejczak and Stefan Jurga and Mateusz Banski and Jan Misiewicz and Artur Podhorodecki}, url = {http://pubs.rsc.org/-/content/articlepdf/2016/ra/c6ra20415e http://xlink.rsc.org/?DOI=C6RA20415E}, doi = {10.1039/C6RA20415E}, issn = {2046-2069}, year = {2016}, date = {2016-01-01}, journal = {RSC Advances}, volume = {6}, number = {98}, pages = {95633--95643}, abstract = {Multimodal imaging based on nanostructures has become a subject of interest for numerous biomedical laboratories.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Multimodal imaging based on nanostructures has become a subject of interest for numerous biomedical laboratories. |
Volz, Sebastian; Ordonez-Miranda, Jose; Shchepetov, Andrey; Prunnila, Mika; Ahopelto, Jouni; Pezeril, Thomas; Vaudel, Gwenaelle; Gusev, Vitaly; Ruello, Pascal; Weig, Eva M; others, Nanophononics: state of the art and perspectives The European Physical Journal B, 89 (1), pp. 15, 2016. @article{volz2016nanophononics, title = {Nanophononics: state of the art and perspectives}, author = {Sebastian Volz and Jose Ordonez-Miranda and Andrey Shchepetov and Mika Prunnila and Jouni Ahopelto and Thomas Pezeril and Gwenaelle Vaudel and Vitaly Gusev and Pascal Ruello and Eva M Weig and others}, year = {2016}, date = {2016-01-01}, journal = {The European Physical Journal B}, volume = {89}, number = {1}, pages = {15}, publisher = {EDP Sciences}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
2015 |
Adamiec, Małgorzata; Gibasiewicz, Krzysztof; Luciński, Robert; Giera, Wojciech; Chełminiak, Przemysław; Szewczyk, Sebastian; Sipińska, Weronika; van Grondelle, Rienk; Jackowski, Grzegorz Journal of Photochemistry and Photobiology B: Biology, 153 , pp. 423–428, 2015, ISSN: 10111344. @article{Adamiec2015, title = {Excitation energy transfer and charge separation are affected in Arabidopsis thaliana mutants lacking light-harvesting chlorophyll a/b binding protein Lhcb3}, author = {Małgorzata Adamiec and Krzysztof Gibasiewicz and Robert Luciński and Wojciech Giera and Przemysław Chełminiak and Sebastian Szewczyk and Weronika Sipińska and Rienk van Grondelle and Grzegorz Jackowski}, url = {http://www.ncbi.nlm.nih.gov/pubmed/26562806 http://linkinghub.elsevier.com/retrieve/pii/S1011134415003619}, doi = {10.1016/j.jphotobiol.2015.11.002}, issn = {10111344}, year = {2015}, date = {2015-12-01}, journal = {Journal of Photochemistry and Photobiology B: Biology}, volume = {153}, pages = {423--428}, abstract = {The composition of LHCII trimers as well as excitation energy transfer and charge separation in grana cores of Arabidopsis thaliana mutant lacking chlorophyll a/b binding protein Lhcb3 have been investigated and compared to those in wild-type plants. In grana cores of lhcb3 plants we observed increased amounts of Lhcb1 and Lhcb2 apoproteins per PSII core. The additional copies of Lhcb1 and Lhcb2 are expected to substitute for Lhcb3 in LHCII trimers M as well as in the LHCII "extra" pool, which was found to be modestly enlarged as a result of the absence of Lhcb3. Time-resolved fluorescence measurements reveal a deceleration of the fast phase of excitation dynamics in grana cores of the mutant by ~15 ps, whereas the average fluorescence lifetime is not significantly altered. Monte Carlo modeling predicts a slowing down of the mean hopping time and an increased stabilization of the primary charge separation in the mutant. Thus our data imply that absence of apoprotein Lhcb3 results in detectable differences in excitation energy transfer and charge separation.}, keywords = {}, pubstate = {published}, tppubtype = {article} } The composition of LHCII trimers as well as excitation energy transfer and charge separation in grana cores of Arabidopsis thaliana mutant lacking chlorophyll a/b binding protein Lhcb3 have been investigated and compared to those in wild-type plants. In grana cores of lhcb3 plants we observed increased amounts of Lhcb1 and Lhcb2 apoproteins per PSII core. The additional copies of Lhcb1 and Lhcb2 are expected to substitute for Lhcb3 in LHCII trimers M as well as in the LHCII "extra" pool, which was found to be modestly enlarged as a result of the absence of Lhcb3. Time-resolved fluorescence measurements reveal a deceleration of the fast phase of excitation dynamics in grana cores of the mutant by ~15 ps, whereas the average fluorescence lifetime is not significantly altered. Monte Carlo modeling predicts a slowing down of the mean hopping time and an increased stabilization of the primary charge separation in the mutant. Thus our data imply that absence of apoprotein Lhcb3 results in detectable differences in excitation energy transfer and charge separation. |
Wendel, Monika; Szot, Dominika; Starzak, Karolina; Tuwalska, Dorota; Gapiński, Jacek; Naskrecki, Ryszard; Prukala, Dorota; Sikorski, Marek; Wybraniec, Slawomir; Burdzinski, Gotard Photophysical properties of betaxanthins: Vulgaxanthin I in aqueous and alcoholic solutions Journal of Luminescence, 167 , pp. 289–295, 2015, ISSN: 00222313. @article{Wendel2015, title = {Photophysical properties of betaxanthins: Vulgaxanthin I in aqueous and alcoholic solutions}, author = {Monika Wendel and Dominika Szot and Karolina Starzak and Dorota Tuwalska and Jacek Gapiński and Ryszard Naskrecki and Dorota Prukala and Marek Sikorski and Slawomir Wybraniec and Gotard Burdzinski}, url = {https://www.sciencedirect.com/science/article/pii/S0022231315003488 http://linkinghub.elsevier.com/retrieve/pii/S0022231315003488}, doi = {10.1016/j.jlumin.2015.06.030}, issn = {00222313}, year = {2015}, date = {2015-11-01}, journal = {Journal of Luminescence}, volume = {167}, pages = {289--295}, publisher = {North-Holland}, abstract = {Betaxanthins are yellow pigments present in Caryophyllales plants and some higher fungi. We characterize photophysical properties of vulgaxanthin I and extracts of Amanita muscaria L. Vulgaxanthin I photoexcitation at $łambda$exc=476nm leads to the S1 excited state with the S1→Sn absorption bands at ca. 390 and 920nm in both aqueous and alcoholic solutions. The S1 state lifetimes (2.9 and 37ps in water) imply that vulgaxanthin I exists in two stereoisomeric forms. An increase in the solvent viscosity extends the S1 lifetimes and fluorescence quantum yields, probably due to hindered internal rotations in the dye. Internal conversion is the major S1 state deactivation path, with fluorescence being a minor channel, and S1→T1 intersystem crossing not observed. Betaxanthins extracted from A. muscaria L. have similar properties. Efficient dissipation of the absorbed light energy as heat supports the postulate of photoprotective role of betaxanthins in vivo.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Betaxanthins are yellow pigments present in Caryophyllales plants and some higher fungi. We characterize photophysical properties of vulgaxanthin I and extracts of Amanita muscaria L. Vulgaxanthin I photoexcitation at $łambda$exc=476nm leads to the S1 excited state with the S1→Sn absorption bands at ca. 390 and 920nm in both aqueous and alcoholic solutions. The S1 state lifetimes (2.9 and 37ps in water) imply that vulgaxanthin I exists in two stereoisomeric forms. An increase in the solvent viscosity extends the S1 lifetimes and fluorescence quantum yields, probably due to hindered internal rotations in the dye. Internal conversion is the major S1 state deactivation path, with fluorescence being a minor channel, and S1→T1 intersystem crossing not observed. Betaxanthins extracted from A. muscaria L. have similar properties. Efficient dissipation of the absorbed light energy as heat supports the postulate of photoprotective role of betaxanthins in vivo. |
Kryjewski, Michal; Tykarska, Ewa; Rebis, Tomasz; Dlugaszewska, Jolanta; Ratajczak, Magdalena; Teubert, Anna; Gapiński, Jacek; Patkowski, Adam; Piskorz, Jaroslaw; Milczarek, Grzegorz; Gdaniec, Maria; Goslinski, Tomasz; Mielcarek, Jadwiga Polyhedron, 98 , pp. 217–223, 2015, ISSN: 02775387. @article{Kryjewski2015, title = {Porphyrazine with bulky 2-(1-adamantyl)-5-phenylpyrrol-1-yl periphery tuning its spectral and electrochemical properties}, author = {Michal Kryjewski and Ewa Tykarska and Tomasz Rebis and Jolanta Dlugaszewska and Magdalena Ratajczak and Anna Teubert and Jacek Gapiński and Adam Patkowski and Jaroslaw Piskorz and Grzegorz Milczarek and Maria Gdaniec and Tomasz Goslinski and Jadwiga Mielcarek}, url = {https://www.sciencedirect.com/science/article/pii/S0277538715002934 http://linkinghub.elsevier.com/retrieve/pii/S0277538715002934}, doi = {10.1016/j.poly.2015.05.033}, issn = {02775387}, year = {2015}, date = {2015-09-01}, journal = {Polyhedron}, volume = {98}, pages = {217--223}, publisher = {Pergamon}, abstract = {The synthesis and physicochemical properties of a novel porphyrazine possessing an alternate system of two peripheral substituents, 2-(1-adamantyl)-5-phenylpyrrol-1-yl and dimethylamino, are presented. Precursor maleonitriles were characterized using X-ray crystallography. Novel porphyrazine was subjected to spectroscopic studies, including the determination of fluorescence quantum yield and singlet oxygen quantum yield. Moreover, its electrochemical and spectroelectrochemical properties were investigated. The antimicrobial photodynamic activities of the novel porphyrazine encapsulated in various liposomal formulations were tested against Staphylococcus aureus and Pseudomonas aeruginosa.}, keywords = {}, pubstate = {published}, tppubtype = {article} } The synthesis and physicochemical properties of a novel porphyrazine possessing an alternate system of two peripheral substituents, 2-(1-adamantyl)-5-phenylpyrrol-1-yl and dimethylamino, are presented. Precursor maleonitriles were characterized using X-ray crystallography. Novel porphyrazine was subjected to spectroscopic studies, including the determination of fluorescence quantum yield and singlet oxygen quantum yield. Moreover, its electrochemical and spectroelectrochemical properties were investigated. The antimicrobial photodynamic activities of the novel porphyrazine encapsulated in various liposomal formulations were tested against Staphylococcus aureus and Pseudomonas aeruginosa. |
Deptuła, Tobiasz; Buitenhuis, Johan; Jarzębski, Maciej; Patkowski, Adam; Gapiński, Jacek Size of Submicrometer Particles Measured by FCS: Correction of the Confocal Volume Langmuir, 31 (24), pp. 6681–6687, 2015, ISSN: 0743-7463. @article{Deptua2015, title = {Size of Submicrometer Particles Measured by FCS: Correction of the Confocal Volume}, author = {Tobiasz Deptuła and Johan Buitenhuis and Maciej Jarzębski and Adam Patkowski and Jacek Gapiński}, url = {http://pubs.acs.org/doi/10.1021/acs.langmuir.5b01225}, doi = {10.1021/acs.langmuir.5b01225}, issn = {0743-7463}, year = {2015}, date = {2015-06-01}, journal = {Langmuir}, volume = {31}, number = {24}, pages = {6681--6687}, publisher = {American Chemical Society}, abstract = {When fluorescence correlation spectroscopy (FCS) in combination with a confocal microscope is used to determine the hydrodynamic radius a of particles comparable to or larger than the linear size $sigma$ of the confocal volume of the microscope, a correction must be used that depends on the a2/$sigma$2 ratio and the distribution of the dye within the particle. Here we present the experimental validation of the theoretically predicted approximate correction necessary for appropriate measurements of the size of uniformly fluorescently labeled spheres of radius comparable to the size of the confocal volume. We also test the approximate correction formula for different ranges of the a/$sigma$ ratio and propose a simple procedure to obtain the correct nanoparticle size from such a measurement.}, keywords = {}, pubstate = {published}, tppubtype = {article} } When fluorescence correlation spectroscopy (FCS) in combination with a confocal microscope is used to determine the hydrodynamic radius a of particles comparable to or larger than the linear size $sigma$ of the confocal volume of the microscope, a correction must be used that depends on the a2/$sigma$2 ratio and the distribution of the dye within the particle. Here we present the experimental validation of the theoretically predicted approximate correction necessary for appropriate measurements of the size of uniformly fluorescently labeled spheres of radius comparable to the size of the confocal volume. We also test the approximate correction formula for different ranges of the a/$sigma$ ratio and propose a simple procedure to obtain the correct nanoparticle size from such a measurement. |
Deptuła, Tobiasz; Warowicka, Alicja; Woźniak, Anna; Grzeszkowiak, Mikołaj; Jarzębski, Maciej; Bednarowicz, Magdalena; Patkowski, Adam; Słomski, Ryszard Acta Biochimica Polonica, 62 (2), pp. 311–316, 2015, ISSN: 0001-527X. @article{Deptua2015a, title = {Cytotoxicity of thermo-responsive polymeric nanoparticles based on N-isopropylacrylamide for potential application as a bioscaffold}, author = {Tobiasz Deptuła and Alicja Warowicka and Anna Woźniak and Mikołaj Grzeszkowiak and Maciej Jarzębski and Magdalena Bednarowicz and Adam Patkowski and Ryszard Słomski}, url = {http://www.ncbi.nlm.nih.gov/pubmed/25980357 http://www.actabp.pl/#File?./html/2_2015/2015_1007.html}, doi = {10.18388/abp.2015_1007}, issn = {0001-527X}, year = {2015}, date = {2015-06-01}, journal = {Acta Biochimica Polonica}, volume = {62}, number = {2}, pages = {311--316}, abstract = {Polymeric nanoparticles based on poly-N-isopropylacrylamide (pNiPAM NPs) and their bio-medical applications have been widely investigated in recent years. These tunable nanoparticles are considered to be great candidates for drug delivery systems, biosensors and bioanalytical devices. Thus, the biocompatibility and toxicity of these nanoparticles is clearly a crucial issue. In this work, the cytotoxicity of thermo-responsive pNiPAM nanoparticles was studied, followed by a detailed analysis of the NPs morphology in growing cell cultures and their 3D structure. Cytotoxic examination was conducted for two cell cultures - HeLa (cervical cancer cell line) and HeK293 (human embryonic kidney cell line), employing MTT (3-4, 5-dimethylthiazol-2-yl-2, 5-diphenyltetrazolium bromide) assay and viability tests. We used Cryo-SEM (scanning electron microscopy) and fluorescence microscopy (IN Cell Analyzer) in order to investigate the morphological structure of the polymer network. We show that pNiPAM nanoparticles do not exhibit any cytotoxicity effects on the investigated cell lines. Additionally, we report that the pNiPAM nanoparticle based scaffold promotes cell growth.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Polymeric nanoparticles based on poly-N-isopropylacrylamide (pNiPAM NPs) and their bio-medical applications have been widely investigated in recent years. These tunable nanoparticles are considered to be great candidates for drug delivery systems, biosensors and bioanalytical devices. Thus, the biocompatibility and toxicity of these nanoparticles is clearly a crucial issue. In this work, the cytotoxicity of thermo-responsive pNiPAM nanoparticles was studied, followed by a detailed analysis of the NPs morphology in growing cell cultures and their 3D structure. Cytotoxic examination was conducted for two cell cultures - HeLa (cervical cancer cell line) and HeK293 (human embryonic kidney cell line), employing MTT (3-4, 5-dimethylthiazol-2-yl-2, 5-diphenyltetrazolium bromide) assay and viability tests. We used Cryo-SEM (scanning electron microscopy) and fluorescence microscopy (IN Cell Analyzer) in order to investigate the morphological structure of the polymer network. We show that pNiPAM nanoparticles do not exhibit any cytotoxicity effects on the investigated cell lines. Additionally, we report that the pNiPAM nanoparticle based scaffold promotes cell growth. |
Pochylski, Mikołaj; Gapiński, Jacek Simple way to analyze Brillouin spectra from turbid liquids. Optics letters, 40 (7), pp. 1456–9, 2015, ISSN: 1539-4794. @article{Pochylski2015, title = {Simple way to analyze Brillouin spectra from turbid liquids.}, author = {Mikołaj Pochylski and Jacek Gapiński}, url = {http://www.ncbi.nlm.nih.gov/pubmed/25831358}, issn = {1539-4794}, year = {2015}, date = {2015-04-01}, journal = {Optics letters}, volume = {40}, number = {7}, pages = {1456--9}, abstract = {The shape of the Brillouin light-scattering spectrum recorded from turbid liquids is distinctly distorted compared to that from a transparent sample. The reason for this is the multiple scattering of light within the medium. The usual expression for the Brillouin spectrum does not apply to the multiple scattering situation. In this Letter, we consider a Brillouin spectrum from opaque samples composed of a distribution of spectra resulting from elementary scattering events, each occurring in single scattering vector conditions. We introduce a one-parameter test function to define the probability distribution of scattering events occurring at a given value of the scattering vector. The proposed procedure was tested on model liquids that consisted of suspensions of sub-micrometer spherical particles of different size and concentration, dispersed in different carrier liquids and studied as a function of temperature. Our analysis made it possible to account for the effect of multiple scattering and to recover the values of mechanical parameters describing the pure solvents.}, keywords = {}, pubstate = {published}, tppubtype = {article} } The shape of the Brillouin light-scattering spectrum recorded from turbid liquids is distinctly distorted compared to that from a transparent sample. The reason for this is the multiple scattering of light within the medium. The usual expression for the Brillouin spectrum does not apply to the multiple scattering situation. In this Letter, we consider a Brillouin spectrum from opaque samples composed of a distribution of spectra resulting from elementary scattering events, each occurring in single scattering vector conditions. We introduce a one-parameter test function to define the probability distribution of scattering events occurring at a given value of the scattering vector. The proposed procedure was tested on model liquids that consisted of suspensions of sub-micrometer spherical particles of different size and concentration, dispersed in different carrier liquids and studied as a function of temperature. Our analysis made it possible to account for the effect of multiple scattering and to recover the values of mechanical parameters describing the pure solvents. |
Gibasiewicz, Krzysztof; Adamiec, Małgorzata; Luciński, Robert; Giera, Wojciech; Chełminiak, Przemysław; Szewczyk, Sebastian; Sipińska, Weronika; Głów, Edyta; Karolczak, Jerzy; van Grondelle, Rienk; Jackowski, Grzegorz Monte Carlo simulations of excitation and electron transfer in grana membranes Biochimica et Biophysica Acta (BBA) - Bioenergetics, 1847 (3), pp. 314–327, 2015, ISSN: 00052728. @article{Gibasiewicz2015, title = {Monte Carlo simulations of excitation and electron transfer in grana membranes}, author = {Krzysztof Gibasiewicz and Małgorzata Adamiec and Robert Luciński and Wojciech Giera and Przemysław Chełminiak and Sebastian Szewczyk and Weronika Sipińska and Edyta Głów and Jerzy Karolczak and Rienk van Grondelle and Grzegorz Jackowski}, url = {http://www.ncbi.nlm.nih.gov/pubmed/25524819 http://linkinghub.elsevier.com/retrieve/pii/S0005272814006628}, doi = {10.1016/j.bbabio.2014.12.004}, issn = {00052728}, year = {2015}, date = {2015-03-01}, journal = {Biochimica et Biophysica Acta (BBA) - Bioenergetics}, volume = {1847}, number = {3}, pages = {314--327}, abstract = {Time-resolved fluorescence measurements on grana membranes with instrumental response function of 3 ps reveal faster excitation dynamics (120 ps) than those reported previously. A possible reason for the faster decay may be a relatively low amount of "extra" LHCII trimers per reaction center of Photosystem II. Monte Carlo modeling of excitation dynamics in C2S2M2 form of PSII-LHCII supercomplexes has been performed using a coarse grained model of this complex, constituting a large majority of proteins in grana membranes. The main factor responsible for the fast fluorescence decay reported in this work was the deep trap constituted by the primary charge separated state in the reaction center (950-1090 cm(-1)). This value is critical for a good fit, whereas typical hopping times between antenna polypeptides (from ~4.5 to ~10.5 ps) and reversible primary charge separation times (from ~4 to ~1.5 ps, respectively) are less critical. Consequently, respective mean migration times of excitation from anywhere in the PSII-LHCII supercomplexes to reaction center range from ~30 to ~80 ps. Thus 1/4-2/3 of the ~120-ps average excitation lifetime is necessary for the diffusion of excitation to reaction center, whereas the remaining time is due to the bottle-neck effect of the trap. Removal of 27% of the Lhcb6 apoprotein pool by mutagenesis of DEG5 gene caused the acceleration of the excitation decay from ~120 to ~100 ps. This effect may be due to the detachment of LHCII-M trimers from PSII-LHCII supercomplexes, accompanied by deepening of the reaction center trap.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Time-resolved fluorescence measurements on grana membranes with instrumental response function of 3 ps reveal faster excitation dynamics (120 ps) than those reported previously. A possible reason for the faster decay may be a relatively low amount of "extra" LHCII trimers per reaction center of Photosystem II. Monte Carlo modeling of excitation dynamics in C2S2M2 form of PSII-LHCII supercomplexes has been performed using a coarse grained model of this complex, constituting a large majority of proteins in grana membranes. The main factor responsible for the fast fluorescence decay reported in this work was the deep trap constituted by the primary charge separated state in the reaction center (950-1090 cm(-1)). This value is critical for a good fit, whereas typical hopping times between antenna polypeptides (from ~4.5 to ~10.5 ps) and reversible primary charge separation times (from ~4 to ~1.5 ps, respectively) are less critical. Consequently, respective mean migration times of excitation from anywhere in the PSII-LHCII supercomplexes to reaction center range from ~30 to ~80 ps. Thus 1/4-2/3 of the ~120-ps average excitation lifetime is necessary for the diffusion of excitation to reaction center, whereas the remaining time is due to the bottle-neck effect of the trap. Removal of 27% of the Lhcb6 apoprotein pool by mutagenesis of DEG5 gene caused the acceleration of the excitation decay from ~120 to ~100 ps. This effect may be due to the detachment of LHCII-M trimers from PSII-LHCII supercomplexes, accompanied by deepening of the reaction center trap. |
Śliwa, Tomasz; Jarzębski, Maciej Dynamic Light Scattering Investigation of Pnipam-Co-Maa Microgel Solution Current Topics in Biophysics, 37 (1), pp. 29–33, 2015, ISSN: 1232-9630. @article{Sliwa2015, title = {Dynamic Light Scattering Investigation of Pnipam-Co-Maa Microgel Solution}, author = {Tomasz Śliwa and Maciej Jarzębski}, url = {https://www.degruyter.com/downloadpdf/j/ctb.2014.37.issue-1/ctb-2014-0071/ctb-2014-0071.pdf http://www.degruyter.com/view/j/ctb.2014.37.issue-1/ctb-2014-0071/ctb-2014-0071.xml}, doi = {10.2478/ctb-2014-0071}, issn = {1232-9630}, year = {2015}, date = {2015-01-01}, journal = {Current Topics in Biophysics}, volume = {37}, number = {1}, pages = {29--33}, abstract = {The paper presents results of a study of the effect of the environment temperature and pH on the size of particles based on poly N (isopropylacrylamide) chain. The tested substance was the copolymer PNIPAM-co-MAA. The particle size measurements were performed by dynamic light scattering. It was found that the copolymer tested reacts specifically to temperature increase by shrinking more than two times. Important for stabilization of the structure are the chemical groups -COOH present in methacrylic acid that undergoes dissociation. Gradual increase in temperature results in a decrease in the dissociation constant, in binding of protons and thus causes shrinkage of the entire particle. It was also shown that PNIPAM-co-MAA in high concentrations undergoes crystallization.}, keywords = {}, pubstate = {published}, tppubtype = {article} } The paper presents results of a study of the effect of the environment temperature and pH on the size of particles based on poly N (isopropylacrylamide) chain. The tested substance was the copolymer PNIPAM-co-MAA. The particle size measurements were performed by dynamic light scattering. It was found that the copolymer tested reacts specifically to temperature increase by shrinking more than two times. Important for stabilization of the structure are the chemical groups -COOH present in methacrylic acid that undergoes dissociation. Gradual increase in temperature results in a decrease in the dissociation constant, in binding of protons and thus causes shrinkage of the entire particle. It was also shown that PNIPAM-co-MAA in high concentrations undergoes crystallization. |
Śliwa, Tomasz; Jarzębski, Maciej; Szutkowski, Kosma Nanoparticle Tracking Analysis of Latex Standardized Beads Current Topics in Biophysics, 37 (1), pp. 49–53, 2015, ISSN: 1232-9630. @article{Sliwa2015a, title = {Nanoparticle Tracking Analysis of Latex Standardized Beads}, author = {Tomasz Śliwa and Maciej Jarzębski and Kosma Szutkowski}, url = {https://www.degruyter.com/downloadpdf/j/ctb.2014.37.issue-1/ctb-2014-0074/ctb-2014-0074.pdf http://www.degruyter.com/view/j/ctb.2014.37.issue-1/ctb-2014-0074/ctb-2014-0074.xml}, doi = {10.2478/ctb-2014-0074}, issn = {1232-9630}, year = {2015}, date = {2015-01-01}, journal = {Current Topics in Biophysics}, volume = {37}, number = {1}, pages = {49--53}, abstract = {The most popular technique for particle size characterization is the dynamic light scattering (DLS). In recent years new advanced method based on counting each single particle movement was introduced giving perspective for measurement of each component of mixture. This study presents some advantages of nanoparticle tracking analysis (NTA) method in comparison to DLS. For tests standard polystyrene beds were chosen vary diameter of 22, 61 and 150 nm and its mixtures. Experiments showed that the particles size resolution allows to distinguish each population in two population suspension opposed to DLS. The NTA method permits to eliminate the negative effects i.e. dust or aggregates in sample during post processing, that permits to use it in a variety of studies.}, keywords = {}, pubstate = {published}, tppubtype = {article} } The most popular technique for particle size characterization is the dynamic light scattering (DLS). In recent years new advanced method based on counting each single particle movement was introduced giving perspective for measurement of each component of mixture. This study presents some advantages of nanoparticle tracking analysis (NTA) method in comparison to DLS. For tests standard polystyrene beds were chosen vary diameter of 22, 61 and 150 nm and its mixtures. Experiments showed that the particles size resolution allows to distinguish each population in two population suspension opposed to DLS. The NTA method permits to eliminate the negative effects i.e. dust or aggregates in sample during post processing, that permits to use it in a variety of studies. |
Jarzębski, Maciej; Śliwa, Tomasz; Jarzębska, Małgorzata; Szutkowski, Kosma Fabrication of Size-Tunable Silica Particles During Seed-Growth Process Current Topics in Biophysics, 37 (1), pp. 35–41, 2015, ISSN: 1232-9630. @article{Jarzebski2014, title = {Fabrication of Size-Tunable Silica Particles During Seed-Growth Process}, author = {Maciej Jarzębski and Tomasz Śliwa and Małgorzata Jarzębska and Kosma Szutkowski}, url = {https://www.degruyter.com/downloadpdf/j/ctb.2014.37.issue-1/ctb-2014-0072/ctb-2014-0072.pdf http://www.degruyter.com/view/j/ctb.2014.37.issue-1/ctb-2014-0072/ctb-2014-0072.xml}, doi = {10.2478/ctb-2014-0072}, issn = {1232-9630}, year = {2015}, date = {2015-01-01}, journal = {Current Topics in Biophysics}, volume = {37}, number = {1}, pages = {35--41}, abstract = {The size control is one of the most important factors during seed-growth process. Although precise determination of ingredients concentrations is easily controllable during the growth process, there is still a possibility to synthesize oversized particles. Nanosized fluorescent silica particles were synthetized using Stoeber process and verified using three complementary methods of particle size determination, namely Dynamic Light Scattering (DLS), Particle Tracking (PT) as well as by Transmission Electron Microscopy (TEM) and Confocal Microscopy. The final diameter was verified by DLS and estimated to 494 nm. Parameters necessary to control the size were derived.}, keywords = {}, pubstate = {published}, tppubtype = {article} } The size control is one of the most important factors during seed-growth process. Although precise determination of ingredients concentrations is easily controllable during the growth process, there is still a possibility to synthesize oversized particles. Nanosized fluorescent silica particles were synthetized using Stoeber process and verified using three complementary methods of particle size determination, namely Dynamic Light Scattering (DLS), Particle Tracking (PT) as well as by Transmission Electron Microscopy (TEM) and Confocal Microscopy. The final diameter was verified by DLS and estimated to 494 nm. Parameters necessary to control the size were derived. |
Sarbak, Szymon; Kujawa, Melania; Jurga-Nowak, Hanna; Dobek, Andrzej Sodium chloride-induced conformational change in tRNA as measured by circular dichroism Current Topics in Biophysics, 38 (1), pp. 1–5, 2015, ISSN: 1232-9630. @article{Sarbak2015, title = {Sodium chloride-induced conformational change in tRNA as measured by circular dichroism}, author = {Szymon Sarbak and Melania Kujawa and Hanna Jurga-Nowak and Andrzej Dobek}, url = {https://www.degruyter.com/downloadpdf/j/ctb.2015.38.issue-1/ctb-2015-0001/ctb-2015-0001.pdf https://www.degruyter.com/view/j/ctb.2015.38.issue-1/ctb-2015-0001/ctb-2015-0001.xml}, doi = {10.1515/ctb-2015-0001}, issn = {1232-9630}, year = {2015}, date = {2015-01-01}, journal = {Current Topics in Biophysics}, volume = {38}, number = {1}, pages = {1--5}, abstract = {The effect of 0.01-1 M sodium ions on the conformation of the folded brewer's yeast tRNA}, keywords = {}, pubstate = {published}, tppubtype = {article} } The effect of 0.01-1 M sodium ions on the conformation of the folded brewer's yeast tRNA |
2014 |
ł, Miko; Calandra, Pietro; Aliotta, Francesco; Ponterio, Rosina C Electrically induced birefringence in nanoparticle dispersions for electrorheological applications Journal of Physics D: Applied Physics, 47 (46), pp. 465301, 2014, ISSN: 0022-3727. @article{Pochylski2014, title = {Electrically induced birefringence in nanoparticle dispersions for electrorheological applications}, author = {Miko{ł}aj Pochylski and Pietro Calandra and Francesco Aliotta and Rosina C Ponterio}, url = {http://stacks.iop.org/0022-3727/47/i=46/a=465301?key=crossref.9cf2eece206b63d16da1f5c0a4ad2dfb}, doi = {10.1088/0022-3727/47/46/465301}, issn = {0022-3727}, year = {2014}, date = {2014-11-01}, journal = {Journal of Physics D: Applied Physics}, volume = {47}, number = {46}, pages = {465301}, publisher = {IOP Publishing}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Giera, Wojciech; Szewczyk, Sebastian; McConnell, Michael D; Snellenburg, Joris; Redding, Kevin E; van Grondelle, Rienk; Gibasiewicz, Krzysztof Biochimica et Biophysica Acta (BBA) - Bioenergetics, 1837 (10), pp. 1756–1768, 2014, ISSN: 00052728. @article{Giera2014, title = {Excitation dynamics in Photosystem I from Chlamydomonas reinhardtii. Comparative studies of isolated complexes and whole cells}, author = {Wojciech Giera and Sebastian Szewczyk and Michael D McConnell and Joris Snellenburg and Kevin E Redding and Rienk van Grondelle and Krzysztof Gibasiewicz}, url = {http://www.ncbi.nlm.nih.gov/pubmed/24973599 http://linkinghub.elsevier.com/retrieve/pii/S0005272814005192}, doi = {10.1016/j.bbabio.2014.06.004}, issn = {00052728}, year = {2014}, date = {2014-10-01}, journal = {Biochimica et Biophysica Acta (BBA) - Bioenergetics}, volume = {1837}, number = {10}, pages = {1756--1768}, abstract = {Identical time-resolved fluorescence measurements with ~3.5-ps resolution were performed for three types of PSI preparations from the green alga, Chlamydomonas reinhardtii: isolated PSI cores, isolated PSI-LHCI complexes and PSI-LHCI complexes in whole living cells. Fluorescence decay in these types of PSI preparations has been previously investigated but never under the same experimental conditions. As a result we present consistent picture of excitation dynamics in algal PSI. Temporal evolution of fluorescence spectra can be generally described by three decay components with similar lifetimes in all samples (6-8ps, 25-30ps, 166-314ps). In the PSI cores, the fluorescence decay is dominated by the two fastest components (~90%), which can be assigned to excitation energy trapping in the reaction center by reversible primary charge separation. Excitation dynamics in the PSI-LHCI preparations is more complex because of the energy transfer between the LHCI antenna system and the core. The average trapping time of excitations created in the well coupled LHCI antenna system is about 12-15ps longer than excitations formed in the PSI core antenna. Excitation dynamics in PSI-LHCI complexes in whole living cells is very similar to that observed in isolated complexes. Our data support the view that chlorophylls responsible for the long-wavelength emission are located mostly in LHCI. We also compared in detail our results with the literature data obtained for plant PSI.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Identical time-resolved fluorescence measurements with ~3.5-ps resolution were performed for three types of PSI preparations from the green alga, Chlamydomonas reinhardtii: isolated PSI cores, isolated PSI-LHCI complexes and PSI-LHCI complexes in whole living cells. Fluorescence decay in these types of PSI preparations has been previously investigated but never under the same experimental conditions. As a result we present consistent picture of excitation dynamics in algal PSI. Temporal evolution of fluorescence spectra can be generally described by three decay components with similar lifetimes in all samples (6-8ps, 25-30ps, 166-314ps). In the PSI cores, the fluorescence decay is dominated by the two fastest components (~90%), which can be assigned to excitation energy trapping in the reaction center by reversible primary charge separation. Excitation dynamics in the PSI-LHCI preparations is more complex because of the energy transfer between the LHCI antenna system and the core. The average trapping time of excitations created in the well coupled LHCI antenna system is about 12-15ps longer than excitations formed in the PSI core antenna. Excitation dynamics in PSI-LHCI complexes in whole living cells is very similar to that observed in isolated complexes. Our data support the view that chlorophylls responsible for the long-wavelength emission are located mostly in LHCI. We also compared in detail our results with the literature data obtained for plant PSI. |
Aliotta, Francesco; Calandra, Pietro; Pochylski, Mikołaj; Ponterio, Rosina C; Salvato, Gabriele; Vasi, Cirino Is electrospray emission really due to columbic forces? AIP Advances, 4 (9), pp. 097105, 2014, ISSN: 2158-3226. @article{Aliotta2014, title = {Is electrospray emission really due to columbic forces?}, author = {Francesco Aliotta and Pietro Calandra and Mikołaj Pochylski and Rosina C Ponterio and Gabriele Salvato and Cirino Vasi}, url = {http://aip.scitation.org/doi/10.1063/1.4894800}, doi = {10.1063/1.4894800}, issn = {2158-3226}, year = {2014}, date = {2014-09-01}, journal = {AIP Advances}, volume = {4}, number = {9}, pages = {097105}, publisher = {American Institute of Physics}, abstract = {Electrospray ionization (ESI) is a widely adopted soft ionization method for mass spectroscopy (MS). In spite of the undeniable success of the technique, its mechanisms are difficult to be analytically modelled because the process is characterized by non-equilibrium conditions. The common belief is that the formation of gas-phase ions takes place at the apex of the Taylor cone via electrophoretic charging. The charge balance implies that a conversion of electrons to ions should occur at the metal-liquid interface of the injector needle. We have detected that the above description is based on unproved assumptions which are not consistent with the correct evaluation of the problem. The comparison between experiments performed under the usual geometry and observations obtained under symmetric field configurations suggests that the emitted droplets cannot be significantly charged or, at least, that any possible ionization mechanism is so poorly efficient to ensure that columbic forces cannot play a major role...}, keywords = {}, pubstate = {published}, tppubtype = {article} } Electrospray ionization (ESI) is a widely adopted soft ionization method for mass spectroscopy (MS). In spite of the undeniable success of the technique, its mechanisms are difficult to be analytically modelled because the process is characterized by non-equilibrium conditions. The common belief is that the formation of gas-phase ions takes place at the apex of the Taylor cone via electrophoretic charging. The charge balance implies that a conversion of electrons to ions should occur at the metal-liquid interface of the injector needle. We have detected that the above description is based on unproved assumptions which are not consistent with the correct evaluation of the problem. The comparison between experiments performed under the usual geometry and observations obtained under symmetric field configurations suggests that the emitted droplets cannot be significantly charged or, at least, that any possible ionization mechanism is so poorly efficient to ensure that columbic forces cannot play a major role... |
Gapiński, Jacek; Naegele, Gerhard; Patkowski, Adam Freezing lines of colloidal Yukawa spheres. II. Local structure and characteristic lengths The Journal of Chemical Physics, 141 (12), pp. 124505, 2014, ISSN: 0021-9606. @article{Gapinski2014, title = {Freezing lines of colloidal Yukawa spheres. II. Local structure and characteristic lengths}, author = {Jacek Gapiński and Gerhard Naegele and Adam Patkowski}, url = {http://aip.scitation.org/doi/10.1063/1.4895965}, doi = {10.1063/1.4895965}, issn = {0021-9606}, year = {2014}, date = {2014-09-01}, journal = {The Journal of Chemical Physics}, volume = {141}, number = {12}, pages = {124505}, publisher = {American Institute of Physics}, abstract = {Using the Rogers-Young (RY) integral equation scheme for the static pair correlation functions combined with the liquid-phase Hansen-Verlet freezing rule, we study the generic behavior of the radial distribution function and static structure factor of monodisperse charge-stabilized suspensions with Yukawa-type repulsive particle interactions at freezing. In a related article, labeled Paper I [J. Gapinski, G. Naegele, and A. Patkowski, J. Chem. Phys. 136, 024507 (2012)], this hybrid method was used to determine two-parameter freezing lines for experimentally controllable parameters, characteristic of suspensions of charged silica spheres in dimethylformamide. A universal scaling of the RY radial distribution function maximum is shown to apply to the liquid-bcc and liquid-fcc segments of the universal freezing line. A thorough analysis is made of the behavior of characteristic distances and wavenumbers, next-neighbor particle coordination numbers, osmotic compressibility factor, and the Ravache-Mountain-Stre...}, keywords = {}, pubstate = {published}, tppubtype = {article} } Using the Rogers-Young (RY) integral equation scheme for the static pair correlation functions combined with the liquid-phase Hansen-Verlet freezing rule, we study the generic behavior of the radial distribution function and static structure factor of monodisperse charge-stabilized suspensions with Yukawa-type repulsive particle interactions at freezing. In a related article, labeled Paper I [J. Gapinski, G. Naegele, and A. Patkowski, J. Chem. Phys. 136, 024507 (2012)], this hybrid method was used to determine two-parameter freezing lines for experimentally controllable parameters, characteristic of suspensions of charged silica spheres in dimethylformamide. A universal scaling of the RY radial distribution function maximum is shown to apply to the liquid-bcc and liquid-fcc segments of the universal freezing line. A thorough analysis is made of the behavior of characteristic distances and wavenumbers, next-neighbor particle coordination numbers, osmotic compressibility factor, and the Ravache-Mountain-Stre... |
Banachowicz, Ewa; Patkowski, Adam; Meier, Gerd; Klamecka, Kamila; Gapiński, Jacek Successful FCS Experiment in Nonstandard Conditions Langmuir, 30 (29), pp. 8945–8955, 2014, ISSN: 0743-7463. @article{Banachowicz2014, title = {Successful FCS Experiment in Nonstandard Conditions}, author = {Ewa Banachowicz and Adam Patkowski and Gerd Meier and Kamila Klamecka and Jacek Gapiński}, url = {http://pubs.acs.org/doi/10.1021/la5015708}, doi = {10.1021/la5015708}, issn = {0743-7463}, year = {2014}, date = {2014-07-01}, journal = {Langmuir}, volume = {30}, number = {29}, pages = {8945--8955}, publisher = {American Chemical Society}, abstract = {Fluorescence correlation spectroscopy (FCS) is frequently used to measure the self-diffusion coefficient of fluorescently labeled probes in solutions, complex media, and living cells. In a standard experiment water immersion objectives and window thickness in the range of 0.13–0.19 mm are used. We show that successful FCS measurements can be performed using samples of different refractive index placed in cells having windows of different thickness, even much thicker than nominally allowed. Different water, oil, and silicon oil immersion as well as long working distance dry objectives, equipped with the correction collar, were tested and compared. We demonstrate that the requirements for FCS experiments are less stringent than those for high resolution confocal imaging and reliable relative FCS measurements can be performed even beyond the compensation range of the objectives. All these features open new possibilities for construction of custom-made high temperature and high pressure cells for FCS.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Fluorescence correlation spectroscopy (FCS) is frequently used to measure the self-diffusion coefficient of fluorescently labeled probes in solutions, complex media, and living cells. In a standard experiment water immersion objectives and window thickness in the range of 0.13–0.19 mm are used. We show that successful FCS measurements can be performed using samples of different refractive index placed in cells having windows of different thickness, even much thicker than nominally allowed. Different water, oil, and silicon oil immersion as well as long working distance dry objectives, equipped with the correction collar, were tested and compared. We demonstrate that the requirements for FCS experiments are less stringent than those for high resolution confocal imaging and reliable relative FCS measurements can be performed even beyond the compensation range of the objectives. All these features open new possibilities for construction of custom-made high temperature and high pressure cells for FCS. |
Śliwa, Tomasz; Jarzębski, Maciej; Gapiński, Jacek; Grzeszkowiak, M; Kleshchanok, D Stimuli-Responsive PNIPAM Based Copolymers: Modeling and Light Scattering Investigations Acta Physica Polonica A, 125 (5), pp. 1236–1239, 2014, ISSN: 0587-4246. @article{Sliwa2014, title = {Stimuli-Responsive PNIPAM Based Copolymers: Modeling and Light Scattering Investigations}, author = {Tomasz Śliwa and Maciej Jarzębski and Jacek Gapiński and M Grzeszkowiak and D Kleshchanok}, url = {http://przyrbwn.icm.edu.pl/APP/PDF/125/a125z5p31.pdf}, doi = {10.12693/APhysPolA.125.1236}, issn = {0587-4246}, year = {2014}, date = {2014-05-01}, journal = {Acta Physica Polonica A}, volume = {125}, number = {5}, pages = {1236--1239}, abstract = {Temperature dependent behavior of poly(N-isopropylacrylamide) (PNIPAM) copolymers was investigated in three buer-stabilized environments. The tests were performed in thermostabilized goniometer by dynamic and static light scattering. From the dynamic light scattering hydrodynamic radius was obtained. Based on the static light scattering data, calculations of the particle radius from the form factor model were done. Depending of the kind of copolymer, the dierent material response to temperature was observed. Also the characterization of dry particles was done by scanning electron microscope. These scanning electron microscopy micrograms showed the possibility of particles to aggregation.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Temperature dependent behavior of poly(N-isopropylacrylamide) (PNIPAM) copolymers was investigated in three buer-stabilized environments. The tests were performed in thermostabilized goniometer by dynamic and static light scattering. From the dynamic light scattering hydrodynamic radius was obtained. Based on the static light scattering data, calculations of the particle radius from the form factor model were done. Depending of the kind of copolymer, the dierent material response to temperature was observed. Also the characterization of dry particles was done by scanning electron microscope. These scanning electron microscopy micrograms showed the possibility of particles to aggregation. |
2013 |
Danielewicz-Ferchmin, I; Banachowicz, Ewa; Ferchmin, A R Journal of Molecular Liquids, 187 , pp. 157–164, 2013, ISSN: 01677322. @article{Danielewicz-Ferchmin2013, title = {Dielectric saturation in water as quantitative measure of formation of well-defined hydration shells of ions at various temperatures and pressures. Vapor–liquid equilibrium case}, author = {I Danielewicz-Ferchmin and Ewa Banachowicz and A R Ferchmin}, url = {https://www.sciencedirect.com/science/article/pii/S0167732213002079 http://linkinghub.elsevier.com/retrieve/pii/S0167732213002079}, doi = {10.1016/j.molliq.2013.06.005}, issn = {01677322}, year = {2013}, date = {2013-11-01}, journal = {Journal of Molecular Liquids}, volume = {187}, pages = {157--164}, publisher = {Elsevier}, abstract = {Static electric permittivity ϵ of water at equilibrium saturated vapor pressures in electric field in the range 108textlessEtextless1011Vm−1 was calculated. A quantitative measure of the dielectric saturation phenomenon was introduced. It is found that, according to the definition of this measure, well-defined first hydration shells of numerous ions investigated by X-ray and neutron scattering methods described in literature are electrically saturated, and that at various conditions. Calculations show that around some ions, including Ag+, whose hydration shells are not saturated at ambient conditions, dielectric saturation of water can be achieved by increasing temperature and pressure up to the values not far from the critical ones. This is compared with extended X-ray absorption fine structure (EXAFS) and XAFS data for Ag+ and Rb+ found in literature.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Static electric permittivity ϵ of water at equilibrium saturated vapor pressures in electric field in the range 108textlessEtextless1011Vm−1 was calculated. A quantitative measure of the dielectric saturation phenomenon was introduced. It is found that, according to the definition of this measure, well-defined first hydration shells of numerous ions investigated by X-ray and neutron scattering methods described in literature are electrically saturated, and that at various conditions. Calculations show that around some ions, including Ag+, whose hydration shells are not saturated at ambient conditions, dielectric saturation of water can be achieved by increasing temperature and pressure up to the values not far from the critical ones. This is compared with extended X-ray absorption fine structure (EXAFS) and XAFS data for Ag+ and Rb+ found in literature. |
Gibasiewicz, Krzysztof; Pajzderska, Maria; Dobek, Andrzej; Karolczak, Jerzy; Burdziński, Gotard; Brettel, Klaus; Jones, Michael R Physical Chemistry Chemical Physics, 15 (38), pp. 16321-16333, 2013, ISSN: 1463-9076. @article{Gibasiewicz2013a, title = {Analysis of the temperature-dependence of P+HA− charge recombination in the Rhodobacter sphaeroides reaction center suggests nanosecond temperature-independent protein relaxation}, author = {Krzysztof Gibasiewicz and Maria Pajzderska and Andrzej Dobek and Jerzy Karolczak and Gotard Burdziński and Klaus Brettel and Michael R Jones}, url = {http://www.ncbi.nlm.nih.gov/pubmed/23999896 http://xlink.rsc.org/?DOI=c3cp44187c}, doi = {10.1039/c3cp44187c}, issn = {1463-9076}, year = {2013}, date = {2013-10-01}, journal = {Physical Chemistry Chemical Physics}, volume = {15}, number = {38}, pages = {16321-16333}, abstract = {The temperature dependence of charge recombination of the pair P(+)HA(-) in isolated reaction centers from the purple bacterium Rhodobacter sphaeroides with prereduced quinone QA was studied by sub-nanosecond to microsecond time-scale transient absorption. Overall, the kinetics slowed down substantially upon cooling from room temperature to ∼200 K, and then remained virtually unchanged down to 77 K, indicating the coexistence of two competitive pathways of charge recombination, a thermally-activated pathway appearing only above ~200 K and a temperature-independent pathway. In our modelling, the thermally activated pathway includes an uphill electron transfer from HA(-) to BA(-) leading to transient formation of the state P(+)BA(-), whereas the temperature-independent pathway is due to direct downhill electron transfer from HA(-) to P(+). At all temperatures studied, the kinetics could be approximated by a four-component decay. Detailed analysis of the lifetimes and amplitudes of particular phases over the range of temperatures suggests that the kinetically resolved phases reveal the consecutive appearance of three conformational states characterized by an increasing free energy gap between the states P(+)BA(-) and P(+)HA(-). The initial gap between these states was estimated to be only ~8 meV, the intermediate gap being ~92 meV, and the final gap ~135 meV, with no dependence on temperature. It was also calculated through a very straightforward approach that the relaxation process from the initial to the intermediate state occurs within 0.6 ± 0.1 ns, whereas the second step of relaxation from the intermediate to the final state takes 11 ± 2 ns. Both phases of the protein relaxation process are essentially temperature-independent. Possible alternative models to describe the experimental data that cannot be definitely excluded are also discussed.}, keywords = {}, pubstate = {published}, tppubtype = {article} } The temperature dependence of charge recombination of the pair P(+)HA(-) in isolated reaction centers from the purple bacterium Rhodobacter sphaeroides with prereduced quinone QA was studied by sub-nanosecond to microsecond time-scale transient absorption. Overall, the kinetics slowed down substantially upon cooling from room temperature to ∼200 K, and then remained virtually unchanged down to 77 K, indicating the coexistence of two competitive pathways of charge recombination, a thermally-activated pathway appearing only above ~200 K and a temperature-independent pathway. In our modelling, the thermally activated pathway includes an uphill electron transfer from HA(-) to BA(-) leading to transient formation of the state P(+)BA(-), whereas the temperature-independent pathway is due to direct downhill electron transfer from HA(-) to P(+). At all temperatures studied, the kinetics could be approximated by a four-component decay. Detailed analysis of the lifetimes and amplitudes of particular phases over the range of temperatures suggests that the kinetically resolved phases reveal the consecutive appearance of three conformational states characterized by an increasing free energy gap between the states P(+)BA(-) and P(+)HA(-). The initial gap between these states was estimated to be only ~8 meV, the intermediate gap being ~92 meV, and the final gap ~135 meV, with no dependence on temperature. It was also calculated through a very straightforward approach that the relaxation process from the initial to the intermediate state occurs within 0.6 ± 0.1 ns, whereas the second step of relaxation from the intermediate to the final state takes 11 ± 2 ns. Both phases of the protein relaxation process are essentially temperature-independent. Possible alternative models to describe the experimental data that cannot be definitely excluded are also discussed. |
Koralewski, Marceli; Pochylski, Mikołaj; Gierszewski, Jacek Magnetic properties of ferritin and akaganeite nanoparticles in aqueous suspension Journal of Nanoparticle Research, 15 (9), pp. 1902, 2013, ISSN: 1388-0764. @article{Koralewski2013, title = {Magnetic properties of ferritin and akaganeite nanoparticles in aqueous suspension}, author = {Marceli Koralewski and Mikołaj Pochylski and Jacek Gierszewski}, url = {http://link.springer.com/10.1007/s11051-013-1902-0}, doi = {10.1007/s11051-013-1902-0}, issn = {1388-0764}, year = {2013}, date = {2013-09-01}, journal = {Journal of Nanoparticle Research}, volume = {15}, number = {9}, pages = {1902}, publisher = {Springer Netherlands}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Gibasiewicz, Krzysztof; Pajzderska, Maria; Dobek, Andrzej; Brettel, Klaus; Jones, Michael R The Journal of Physical Chemistry B, 117 (38), pp. 11112–11123, 2013, ISSN: 1520-6106. @article{Gibasiewicz2013b, title = {Analysis of the Kinetics of P + H A – Recombination in Membrane-Embedded Wild-Type and Mutant Rhodobacter sphaeroides Reaction Centers between 298 and 77 K Indicates That the Adjacent Negatively Charged Q A Ubiquinone Modulates the Free Energy of P + H A}, author = {Krzysztof Gibasiewicz and Maria Pajzderska and Andrzej Dobek and Klaus Brettel and Michael R Jones}, url = {http://pubs.acs.org/doi/10.1021/jp4011235}, doi = {10.1021/jp4011235}, issn = {1520-6106}, year = {2013}, date = {2013-09-01}, journal = {The Journal of Physical Chemistry B}, volume = {117}, number = {38}, pages = {11112--11123}, publisher = {American Chemical Society}, abstract = {Time-resolved spectroscopic studies of recombination of the P+HA– radical pair in photosynthetic reaction centers (RCs) from Rhodobacter sphaeroides give an opportunity to study protein dynamics triggered by light and occurring over the lifetime of P+HA–. The state P+HA– is formed after the ultrafast light-induced electron transfer from the primary donor pair of bacteriochlorophylls (P) to the acceptor bacteriopheophytin (HA). In order to increase the lifetime of this state, and thus increase the temporal window for the examination of protein dynamics, it is possible to block forward electron transfer from HA– to the secondary electron acceptor QA. In this contribution, the dynamics of P+HA– recombination were compared at a range of temperatures from 77 K to room temperature, electron transfer from HA– to QA being blocked either by prereduction of QA or by genetic removal of QA. The observed P+HA– charge recombination was significantly slower in the QA-deficient RCs, and in both types of complexes, loweri...}, keywords = {}, pubstate = {published}, tppubtype = {article} } Time-resolved spectroscopic studies of recombination of the P+HA– radical pair in photosynthetic reaction centers (RCs) from Rhodobacter sphaeroides give an opportunity to study protein dynamics triggered by light and occurring over the lifetime of P+HA–. The state P+HA– is formed after the ultrafast light-induced electron transfer from the primary donor pair of bacteriochlorophylls (P) to the acceptor bacteriopheophytin (HA). In order to increase the lifetime of this state, and thus increase the temporal window for the examination of protein dynamics, it is possible to block forward electron transfer from HA– to the secondary electron acceptor QA. In this contribution, the dynamics of P+HA– recombination were compared at a range of temperatures from 77 K to room temperature, electron transfer from HA– to QA being blocked either by prereduction of QA or by genetic removal of QA. The observed P+HA– charge recombination was significantly slower in the QA-deficient RCs, and in both types of complexes, loweri... |
Aliotta, F; Calandra, P; Pochylski, Mikołaj; Ponterio, R C; Salvato, G; Vasi, C Enhancement of electrorheological effect by particle-fluid interaction Physical Review E, 87 (6), pp. 062304, 2013, ISSN: 1539-3755. @article{Aliotta2013b, title = {Enhancement of electrorheological effect by particle-fluid interaction}, author = {F Aliotta and P Calandra and Mikołaj Pochylski and R C Ponterio and G Salvato and C Vasi}, url = {https://link.aps.org/doi/10.1103/PhysRevE.87.062304}, doi = {10.1103/PhysRevE.87.062304}, issn = {1539-3755}, year = {2013}, date = {2013-06-01}, journal = {Physical Review E}, volume = {87}, number = {6}, pages = {062304}, publisher = {American Physical Society}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Aliotta, Francesco; Giaquinta, Paolo V; Pochylski, Mikołaj; Ponterio, Rosina C; Prestipino, Santi; Saija, Franz; Vasi, Cirino Volume crossover in deeply supercooled water adiabatically freezing under isobaric conditions The Journal of Chemical Physics, 138 (18), pp. 184504, 2013, ISSN: 0021-9606. @article{Aliotta2013a, title = {Volume crossover in deeply supercooled water adiabatically freezing under isobaric conditions}, author = {Francesco Aliotta and Paolo V Giaquinta and Mikołaj Pochylski and Rosina C Ponterio and Santi Prestipino and Franz Saija and Cirino Vasi}, url = {http://aip.scitation.org/doi/10.1063/1.4803659}, doi = {10.1063/1.4803659}, issn = {0021-9606}, year = {2013}, date = {2013-05-01}, journal = {The Journal of Chemical Physics}, volume = {138}, number = {18}, pages = {184504}, publisher = {American Institute of Physics}, abstract = {The irreversible return of a supercooled liquid to stable thermodynamic equilibrium often begins as a fast process which adiabatically drives the system to solid-liquid coexistence. Only at a later stage will solidification proceed with the expected exchange of thermal energy with the external bath. In this paper we discuss some aspects of the adiabatic freezing of metastable water at constant pressure. In particular, we investigated the thermal behavior of the isobaric gap between the molar volume of supercooled water and that of the warmer ice-water mixture which eventually forms at equilibrium. The available experimental data at ambient pressure, extrapolated into the metastable region within the scheme provided by the reference IAPWS-95 formulation, show that water ordinarily expands upon (partially) freezing under isenthalpic conditions. However, the same scheme also suggests that, for increasing undercoolings, the volume gap is gradually reduced and eventually vanishes at a temperature close to the ...}, keywords = {}, pubstate = {published}, tppubtype = {article} } The irreversible return of a supercooled liquid to stable thermodynamic equilibrium often begins as a fast process which adiabatically drives the system to solid-liquid coexistence. Only at a later stage will solidification proceed with the expected exchange of thermal energy with the external bath. In this paper we discuss some aspects of the adiabatic freezing of metastable water at constant pressure. In particular, we investigated the thermal behavior of the isobaric gap between the molar volume of supercooled water and that of the warmer ice-water mixture which eventually forms at equilibrium. The available experimental data at ambient pressure, extrapolated into the metastable region within the scheme provided by the reference IAPWS-95 formulation, show that water ordinarily expands upon (partially) freezing under isenthalpic conditions. However, the same scheme also suggests that, for increasing undercoolings, the volume gap is gradually reduced and eventually vanishes at a temperature close to the ... |
Aliotta, F; Gapiński, Jacek; Pochylski, Mikołaj; Ponterio, R C; Saija, F; Salvato, G; Vasi, C Physical Review E, 87 (2), pp. 022303, 2013, ISSN: 1539-3755. @article{Aliotta2013, title = {High-frequency propagating density fluctuations in deeply supercooled water: Evidence of a single viscous relaxation}, author = {F Aliotta and Jacek Gapiński and Mikołaj Pochylski and R C Ponterio and F Saija and G Salvato and C Vasi}, url = {http://www.ncbi.nlm.nih.gov/pubmed/23496512 https://link.aps.org/doi/10.1103/PhysRevE.87.022303}, doi = {10.1103/PhysRevE.87.022303}, issn = {1539-3755}, year = {2013}, date = {2013-02-01}, journal = {Physical Review E}, volume = {87}, number = {2}, pages = {022303}, abstract = {We performed a Brillouin scattering experiment on deeply supercooled water and compared the results with similar literature data obtained both at the same and at higher values of the exchanged wave vector. The whole set of available experimental data can be well reproduced with the use of the generalized hydrodynamic model where all the involved thermodynamic parameters are fixed to their literature values. On the contrary, the model based on the memory function approach generates the wrong estimates for measurables when the same values of the thermodynamic parameters are used. This result confirms our recent criticisms against the utilization of models originating from linear response theory [Phys. Rev. E 84, 051202 (2011)]. The inconsistency between models explains apparent discrepancies between the different conclusions on water acoustic behavior which may be found in the literature. We demonstrate that the observed behavior can be explained by assuming only a single relaxation process that is typical of any viscoelastic system. With all thermodynamics quantities fixed, the hydrodynamic description needs only two parameters to model the experimental data, namely, the relaxation time and the high-frequency limit of the sound velocity. The whole body of the experimental data can be well reproduced when the relaxation time behaves in an Arrhenian manner and the difference between the relaxed and not relaxed sound velocities is a constant. The high-frequency sound velocity is never higher than 2200 m/s. We conclude that, at least from experiments performed within the hydrodynamic regime, there is no indication for a fast sound close to the hypersonic velocity observed in ice.}, keywords = {}, pubstate = {published}, tppubtype = {article} } We performed a Brillouin scattering experiment on deeply supercooled water and compared the results with similar literature data obtained both at the same and at higher values of the exchanged wave vector. The whole set of available experimental data can be well reproduced with the use of the generalized hydrodynamic model where all the involved thermodynamic parameters are fixed to their literature values. On the contrary, the model based on the memory function approach generates the wrong estimates for measurables when the same values of the thermodynamic parameters are used. This result confirms our recent criticisms against the utilization of models originating from linear response theory [Phys. Rev. E 84, 051202 (2011)]. The inconsistency between models explains apparent discrepancies between the different conclusions on water acoustic behavior which may be found in the literature. We demonstrate that the observed behavior can be explained by assuming only a single relaxation process that is typical of any viscoelastic system. With all thermodynamics quantities fixed, the hydrodynamic description needs only two parameters to model the experimental data, namely, the relaxation time and the high-frequency limit of the sound velocity. The whole body of the experimental data can be well reproduced when the relaxation time behaves in an Arrhenian manner and the difference between the relaxed and not relaxed sound velocities is a constant. The high-frequency sound velocity is never higher than 2200 m/s. We conclude that, at least from experiments performed within the hydrodynamic regime, there is no indication for a fast sound close to the hypersonic velocity observed in ice. |
Melnikowa, L; Mitroova, Z; Timko, M; Kovac, J; Koralewski, M; Pochylski, Mikołaj; Avdeev, M V; Petrenko, V I; Garamus, V M; Almasy, L; Kopcansky, P Physical characterization of iron oxide nanoparticles in magnetoferritin Magnetohydrodynamics, 49 (3/4), pp. 293–296, 2013. @article{Melnikowa2013, title = {Physical characterization of iron oxide nanoparticles in magnetoferritin}, author = {L Melnikowa and Z Mitroova and M Timko and J Kovac and M Koralewski and Mikołaj Pochylski and M V Avdeev and V I Petrenko and V M Garamus and L Almasy and P Kopcansky}, url = {http://mhd.sal.lv/contents/2013/3/MG.49.3.8.R.html}, year = {2013}, date = {2013-01-01}, journal = {Magnetohydrodynamics}, volume = {49}, number = {3/4}, pages = {293--296}, abstract = {Natural ferritin is the iron-storage protein of animals, plants, and bacteria. It is a spherical biomacromolecule of external diameter about 12 nm composed of 24 protein subunits arranged as a hollow sphere of approximately 8 nm in diameter. Inside the sphere, iron is stored in the ferric oxidation state as a complex molecule with a crystallographic structure similar to mineral ferrihydrite. By a proper chemical process, it is possible to use the empty protein shell of ferritin, i.e. apoferritin, as a confined environment, in which magnetic iron oxide nanoparticles can be synthesized forming a biocompatible ferrofluid called magnetoferritin [1]. The latest studies show that brain ferritin [2] in patients with the Alzheimer's disease [3] has a polyphase structure, incorporating also magnetite. The structure, quality and quantity of the iron core composition in the brain ferritin have not been fully determined yet, and it has not been established whether they are related to the origin of neurodegenerative diseases or to their consequences [4, 5]. For these reasons, by combining different techniques it is necessary to fully characterize the structure and the physico-chemical properties of ferritin and distinguish between magnetic structures, especially for understanding the role of magnetite presence in the development of neurodegenerative diseases. Of particular interest is the search for methods allowing detection of magnetite inside ferritin proteins in vivo and inside magnetoferritin as a model system in vitro, respectively. Magnetoferritin is a relatively new biocompatible nanomaterial with continuously increasing popularity in many fields of science from medicine through nanotechnology up to physics. If compared with physiological ferritin, magnetoferritin contains magnetic nanoparticles (Fe 3O 4, $gamma$-Fe 2O 3) surrounded by the empty protein shell (apoferritin). The problem of toxicity and side effects of magnetic nanoparticles in organs and tissues is minimized due to the protein nature of this unique material, which is important for many possible applications in clinical practice as a drug carrier, contrast medium in radiodiagnostics, or in magnetic hyperthermia therapy. In addition to biocompatibility, another advantage of magnetoferritin for biotechnological applications is a relatively short time of controlled synthesis adapted to the formation of magnetite specifically inside the protein cavity and creation the magnetoferritin molecule. Figs 3, Refs 6.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Natural ferritin is the iron-storage protein of animals, plants, and bacteria. It is a spherical biomacromolecule of external diameter about 12 nm composed of 24 protein subunits arranged as a hollow sphere of approximately 8 nm in diameter. Inside the sphere, iron is stored in the ferric oxidation state as a complex molecule with a crystallographic structure similar to mineral ferrihydrite. By a proper chemical process, it is possible to use the empty protein shell of ferritin, i.e. apoferritin, as a confined environment, in which magnetic iron oxide nanoparticles can be synthesized forming a biocompatible ferrofluid called magnetoferritin [1]. The latest studies show that brain ferritin [2] in patients with the Alzheimer's disease [3] has a polyphase structure, incorporating also magnetite. The structure, quality and quantity of the iron core composition in the brain ferritin have not been fully determined yet, and it has not been established whether they are related to the origin of neurodegenerative diseases or to their consequences [4, 5]. For these reasons, by combining different techniques it is necessary to fully characterize the structure and the physico-chemical properties of ferritin and distinguish between magnetic structures, especially for understanding the role of magnetite presence in the development of neurodegenerative diseases. Of particular interest is the search for methods allowing detection of magnetite inside ferritin proteins in vivo and inside magnetoferritin as a model system in vitro, respectively. Magnetoferritin is a relatively new biocompatible nanomaterial with continuously increasing popularity in many fields of science from medicine through nanotechnology up to physics. If compared with physiological ferritin, magnetoferritin contains magnetic nanoparticles (Fe 3O 4, $gamma$-Fe 2O 3) surrounded by the empty protein shell (apoferritin). The problem of toxicity and side effects of magnetic nanoparticles in organs and tissues is minimized due to the protein nature of this unique material, which is important for many possible applications in clinical practice as a drug carrier, contrast medium in radiodiagnostics, or in magnetic hyperthermia therapy. In addition to biocompatibility, another advantage of magnetoferritin for biotechnological applications is a relatively short time of controlled synthesis adapted to the formation of magnetite specifically inside the protein cavity and creation the magnetoferritin molecule. Figs 3, Refs 6. |
Sikora, Bożena; Fronc, Krzysztof; Kamińska, Izabela; Koper, Kamil; Szewczyk, Sebastian; Paterczyk, Bohdan; Wojciechowski, Tomasz; Sobczak, Kamil; Minikayev, Roman; Paszkowicz, Wojciech; Stępień, Piotr; Elbaum, Danek Transport of NaYF4:Er3+, Yb3+ up-converting nanoparticles into HeLa cells Nanotechnology, 24 (23), pp. 235702, 2013. @article{Sikora2013, title = {Transport of NaYF_{4}:Er^{3+}, Yb^{3+} up-converting nanoparticles into HeLa cells}, author = {Bożena Sikora and Krzysztof Fronc and Izabela Kamińska and Kamil Koper and Sebastian Szewczyk and Bohdan Paterczyk and Tomasz Wojciechowski and Kamil Sobczak and Roman Minikayev and Wojciech Paszkowicz and Piotr Stępień and Danek Elbaum}, url = {http://stacks.iop.org/0957-4484/24/i=23/a=235702}, doi = {10.1088/0957-4484/24/23/235702}, year = {2013}, date = {2013-01-01}, journal = {Nanotechnology}, volume = {24}, number = {23}, pages = {235702}, abstract = {An effective, simple and practically useful method to incorporate fluorescent nanoparticles inside live biological cells was developed. The internalization time and concentration dependence of a frequently used liposomal transfection factor (Lipofectamine 2000) was studied. A user friendly, one-step technique to obtain water and organic solvent soluble Er 3+ and Yb 3+ doped NaYF 4 nanoparticles coated with polyvinylpyrrolidone was obtained. Structural analysis of the nanoparticles confirmed the formation of nanocrystals of the desired sizes and spectral properties. The internalization of NaYF 4 nanoparticles in HeLa cervical cancer cells was determined at different nanoparticle concentrations and for incubation periods from 3 to 24 h. The images revealed a redistribution of nanoparticles inside the cell, which increases with incubation time and concentration levels, and depends on the presence of the transfection factor. The study identifies, for the first time, factors responsible for an effective endocytosis of the up-converting nanoparticles to HeLa cells. Thus, the method could be applied to investigate a wide range of future ‘smart’ theranostic agents. Nanoparticles incorporated into the liposomes appear to be very promising fluorescent probes for imaging real-time cellular dynamics.}, keywords = {}, pubstate = {published}, tppubtype = {article} } An effective, simple and practically useful method to incorporate fluorescent nanoparticles inside live biological cells was developed. The internalization time and concentration dependence of a frequently used liposomal transfection factor (Lipofectamine 2000) was studied. A user friendly, one-step technique to obtain water and organic solvent soluble Er 3+ and Yb 3+ doped NaYF 4 nanoparticles coated with polyvinylpyrrolidone was obtained. Structural analysis of the nanoparticles confirmed the formation of nanocrystals of the desired sizes and spectral properties. The internalization of NaYF 4 nanoparticles in HeLa cervical cancer cells was determined at different nanoparticle concentrations and for incubation periods from 3 to 24 h. The images revealed a redistribution of nanoparticles inside the cell, which increases with incubation time and concentration levels, and depends on the presence of the transfection factor. The study identifies, for the first time, factors responsible for an effective endocytosis of the up-converting nanoparticles to HeLa cells. Thus, the method could be applied to investigate a wide range of future ‘smart’ theranostic agents. Nanoparticles incorporated into the liposomes appear to be very promising fluorescent probes for imaging real-time cellular dynamics. |
Banachowicz, Ewa Wydawnictwo Naukowe Uniwersytetu im. Adama Mickiewicza, 2013, ISBN: 9788323226246. @book{Banachowicz2013, title = {Struktura i parametry fizyczne biopolimerów: badania z zastosowaniem metod rozproszeniowych i modelowania komputerowego}, author = {Ewa Banachowicz}, url = {https://www.nieprzeczytane.pl/Struktura-i-parametry-fizyczne-biopolimerow,product320280.html}, isbn = {9788323226246}, year = {2013}, date = {2013-01-01}, publisher = {Wydawnictwo Naukowe Uniwersytetu im. Adama Mickiewicza}, keywords = {}, pubstate = {published}, tppubtype = {book} } |
2012 |
Pinkney, J N M; Zawadzki, Paweł; Mazuryk, Jarosław; Arciszewska, L K; Sherratt, D J; Kapanidis, A N Proceedings of the National Academy of Sciences, 109 (51), pp. 20871–20876, 2012, ISSN: 0027-8424. @article{Pinkney2012, title = {Capturing reaction paths and intermediates in Cre-loxP recombination using single-molecule fluorescence}, author = {J N M Pinkney and Paweł Zawadzki and Jarosław Mazuryk and L K Arciszewska and D J Sherratt and A N Kapanidis}, url = {http://www.ncbi.nlm.nih.gov/pubmed/23184986 http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=PMC3529024 http://www.pnas.org/cgi/doi/10.1073/pnas.1211922109}, doi = {10.1073/pnas.1211922109}, issn = {0027-8424}, year = {2012}, date = {2012-12-01}, journal = {Proceedings of the National Academy of Sciences}, volume = {109}, number = {51}, pages = {20871--20876}, abstract = {Site-specific recombination plays key roles in microbe biology and is exploited extensively to manipulate the genomes of higher organisms. Cre is a well studied site-specific recombinase, responsible for establishment and maintenance of the P1 bacteriophage genome in bacteria. During recombination, Cre forms a synaptic complex between two 34-bp DNA sequences called loxP after which a pair of strand exchanges forms a Holliday junction (HJ) intermediate; HJ isomerization then allows a second pair of strand exchanges and thus formation of the final recombinant product. Despite extensive work on the Cre-loxP system, many of its mechanisms have remained unclear, mainly due to the transient nature of complexes formed and the ensemble averaging inherent to most biochemical work. Here, we address these limitations by introducing tethered fluorophore motion (TFM), a method that monitors large-scale DNA motions through reports of the diffusional freedom of a single fluorophore. We combine TFM with Foerster resonance energy transfer (FRET) and simultaneously observe both large- and small-scale conformational changes within single DNA molecules. Using TFM-FRET, we observed individual recombination reactions in real time and analyzed their kinetics. Recombination was initiated predominantly by exchange of the "bottom-strands" of the DNA substrate. In productive complexes we used FRET distributions to infer rapid isomerization of the HJ intermediates and that a rate-limiting step occurs after this isomerization. We also observed two nonproductive synaptic complexes, one of which was structurally distinct from conformations in crystals. After recombination, the product synaptic complex was extremely stable and refractory to subsequent rounds of recombination.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Site-specific recombination plays key roles in microbe biology and is exploited extensively to manipulate the genomes of higher organisms. Cre is a well studied site-specific recombinase, responsible for establishment and maintenance of the P1 bacteriophage genome in bacteria. During recombination, Cre forms a synaptic complex between two 34-bp DNA sequences called loxP after which a pair of strand exchanges forms a Holliday junction (HJ) intermediate; HJ isomerization then allows a second pair of strand exchanges and thus formation of the final recombinant product. Despite extensive work on the Cre-loxP system, many of its mechanisms have remained unclear, mainly due to the transient nature of complexes formed and the ensemble averaging inherent to most biochemical work. Here, we address these limitations by introducing tethered fluorophore motion (TFM), a method that monitors large-scale DNA motions through reports of the diffusional freedom of a single fluorophore. We combine TFM with Foerster resonance energy transfer (FRET) and simultaneously observe both large- and small-scale conformational changes within single DNA molecules. Using TFM-FRET, we observed individual recombination reactions in real time and analyzed their kinetics. Recombination was initiated predominantly by exchange of the "bottom-strands" of the DNA substrate. In productive complexes we used FRET distributions to infer rapid isomerization of the HJ intermediates and that a rate-limiting step occurs after this isomerization. We also observed two nonproductive synaptic complexes, one of which was structurally distinct from conformations in crystals. After recombination, the product synaptic complex was extremely stable and refractory to subsequent rounds of recombination. |
Aliotta, F; Pochylski, Mikołaj; Ponterio, R C; Saija, F; Salvato, G; Vasi, C S Structure of bulk water from Raman measurements of supercooled pure liquid and LiCl solutions Physical Review B, 86 (13), pp. 134301, 2012, ISSN: 1098-0121. @article{Aliotta2012, title = {Structure of bulk water from Raman measurements of supercooled pure liquid and LiCl solutions}, author = {F Aliotta and Mikołaj Pochylski and R C Ponterio and F Saija and G Salvato and C S Vasi}, url = {https://link.aps.org/doi/10.1103/PhysRevB.86.134301}, doi = {10.1103/PhysRevB.86.134301}, issn = {1098-0121}, year = {2012}, date = {2012-10-01}, journal = {Physical Review B}, volume = {86}, number = {13}, pages = {134301}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Koralewski, M; Pochylski, Mikołaj; Mitróová, Z; Melníková, L; Kováč, J; Timko, M; Kopčanský, P Magnetic Birefringence Study of the Magnetic Core Structure of Ferritin Acta Physica Polonica A, 121 (5-6), pp. 1237–1239, 2012, ISSN: 0587-4246. @article{Koralewski2012, title = {Magnetic Birefringence Study of the Magnetic Core Structure of Ferritin}, author = {M Koralewski and Mikołaj Pochylski and Z Mitróová and L Melníková and J Kováč and M Timko and P Kopčanský}, url = {http://przyrbwn.icm.edu.pl/APP/PDF/121/a121z5p76.pdf}, doi = {10.12693/APhysPolA.121.1237}, issn = {0587-4246}, year = {2012}, date = {2012-05-01}, journal = {Acta Physica Polonica A}, volume = {121}, number = {5-6}, pages = {1237--1239}, abstract = {Magnetically induced optical birefringence (∆n) was measured for magnetoferritin and horse spleen ferritin aqueous suspensions. The ∆n for magnetoferritin was described in the frame of the Langevin formalism taking into account distribution of core diameter. The established average magnetic dipole moment and core diameter is equal to about 460 µB and 3 nm, respectively. It was shown that magnetic birefringence and the CottonMouton constant can be powerful parameters in identication of the magnetic core structure of ferritin, especially useful in biomedicine.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Magnetically induced optical birefringence (∆n) was measured for magnetoferritin and horse spleen ferritin aqueous suspensions. The ∆n for magnetoferritin was described in the frame of the Langevin formalism taking into account distribution of core diameter. The established average magnetic dipole moment and core diameter is equal to about 460 µB and 3 nm, respectively. It was shown that magnetic birefringence and the CottonMouton constant can be powerful parameters in identication of the magnetic core structure of ferritin, especially useful in biomedicine. |
Szymańska, A; Ślósarek, Genowefa Light Scattering Studies of Hydration and Structural Transformations of Lysozyme Acta Physica Polonica A, 121 (3), pp. 694–698, 2012, ISSN: 0587-4246. @article{Szymanska2012, title = {Light Scattering Studies of Hydration and Structural Transformations of Lysozyme}, author = {A Szymańska and Genowefa Ślósarek}, url = {http://przyrbwn.icm.edu.pl/APP/PDF/121/a121z3p24.pdf}, doi = {10.12693/APhysPolA.121.694}, issn = {0587-4246}, year = {2012}, date = {2012-03-01}, journal = {Acta Physica Polonica A}, volume = {121}, number = {3}, pages = {694--698}, abstract = {We have applied the method of dynamic light scattering to analyse the lysozymeethanol interaction. For low ethanol concentration (below 4.3% (v/v)) no chemical denaturation process is observed. When the ethanol concentration grows above the triggering concentration the hydrodynamic radius of lysozyme increases, indicating the structural changes within the protein molecule. The observed structural modications are attributed to dehydration and preliminary tertiary structure modication of the protein molecule.}, keywords = {}, pubstate = {published}, tppubtype = {article} } We have applied the method of dynamic light scattering to analyse the lysozymeethanol interaction. For low ethanol concentration (below 4.3% (v/v)) no chemical denaturation process is observed. When the ethanol concentration grows above the triggering concentration the hydrodynamic radius of lysozyme increases, indicating the structural changes within the protein molecule. The observed structural modications are attributed to dehydration and preliminary tertiary structure modication of the protein molecule. |
Calandra, Pietro; Mandanici, Andrea; Liveri, Vincenzo Turco; Pochylski, Mikołaj; Aliotta, Francesco Emerging dynamics in surfactant-based liquid mixtures: Octanoic acid/bis(2-ethylhexyl) amine systems The Journal of Chemical Physics, 136 (6), pp. 064515, 2012, ISSN: 0021-9606. @article{Calandra2012, title = {Emerging dynamics in surfactant-based liquid mixtures: Octanoic acid/bis(2-ethylhexyl) amine systems}, author = {Pietro Calandra and Andrea Mandanici and Vincenzo Turco Liveri and Mikołaj Pochylski and Francesco Aliotta}, url = {http://aip.scitation.org/doi/10.1063/1.3684713}, doi = {10.1063/1.3684713}, issn = {0021-9606}, year = {2012}, date = {2012-02-01}, journal = {The Journal of Chemical Physics}, volume = {136}, number = {6}, pages = {064515}, publisher = {American Institute of Physics}, abstract = {This work focuses on the dynamic phenomena emerging in self-assembled transient intermolecular networks formed when two different surfactants are mixed. In particular, the relaxation processes in liquid mixtures composed by bis(2-ethylhexyl)amine (BEEA) and octanoic acid (OA) in the whole composition range has been investigated by dielectric spectroscopy and Brillouin spectroscopy. A thorough analysis of all the experimental data consistently suggests that, mainly driven by acid-base interactions arising when the two surfactants are mixed, supra-molecular aggregates formation causes the slowing down of molecular dynamics. This, in turn, reflects to longer-range relaxations. These changes have been found to be composition-dependent, involving strong departures of the mixture physico-chemical properties from an ideal behaviour, and reflecting the structural and dynamical features of local structures. In particular, the peculiar dynamic processes occurring in these local inter-molecular structures, have been...}, keywords = {}, pubstate = {published}, tppubtype = {article} } This work focuses on the dynamic phenomena emerging in self-assembled transient intermolecular networks formed when two different surfactants are mixed. In particular, the relaxation processes in liquid mixtures composed by bis(2-ethylhexyl)amine (BEEA) and octanoic acid (OA) in the whole composition range has been investigated by dielectric spectroscopy and Brillouin spectroscopy. A thorough analysis of all the experimental data consistently suggests that, mainly driven by acid-base interactions arising when the two surfactants are mixed, supra-molecular aggregates formation causes the slowing down of molecular dynamics. This, in turn, reflects to longer-range relaxations. These changes have been found to be composition-dependent, involving strong departures of the mixture physico-chemical properties from an ideal behaviour, and reflecting the structural and dynamical features of local structures. In particular, the peculiar dynamic processes occurring in these local inter-molecular structures, have been... |
Ślósarek, Genowefa Fizyka - biofizyka - biologia Nauka - Religia - Dzieje, pp. 77–89, Polska Akademia Umiejętności, 2012, 2012. @incollection{Slosarek2012a, title = {Fizyka - biofizyka - biologia}, author = {Genowefa Ślósarek}, year = {2012}, date = {2012-01-01}, booktitle = {Nauka - Religia - Dzieje}, pages = {77--89}, publisher = {Polska Akademia Umiejętności}, address = {2012}, keywords = {}, pubstate = {published}, tppubtype = {incollection} } |
Gapiński, Jacek; Naegele, Gerhard; Patkowski, Adam Freezing lines of colloidal Yukawa spheres. I. A Rogers-Young integral equation study The Journal of Chemical Physics, 136 (2), pp. 024507, 2012, ISSN: 0021-9606. @article{Gapinski2012, title = {Freezing lines of colloidal Yukawa spheres. I. A Rogers-Young integral equation study}, author = {Jacek Gapiński and Gerhard Naegele and Adam Patkowski}, url = {http://www.ncbi.nlm.nih.gov/pubmed/22260603 http://aip.scitation.org/doi/10.1063/1.3675607}, doi = {10.1063/1.3675607}, issn = {0021-9606}, year = {2012}, date = {2012-01-01}, journal = {The Journal of Chemical Physics}, volume = {136}, number = {2}, pages = {024507}, abstract = {Using the Rogers-Young (RY) integral equation scheme for the static structure factor combined with the one-phase Hansen-Verlet (HV) freezing rule, we study the equilibrium structure and two-parameter freezing lines of colloidal particles with Yukawa-type pair interactions representing charge-stabilized silica spheres suspended in dimethylformamide (DMF). Results are presented for a vast range of concentrations, salinities and effective charges covering particles with masked excluded-volume interactions. The freezing lines were obtained for the low-charge and high-charge solutions of the static structure factor, for various two-parameter sets of experimentally accessible system parameters. All RY-HV based freezing lines can be mapped on a universal fluid-solid coexistence line in good agreement with computer simulation predictions. The RY-HV calculations extend the freezing lines obtained in earlier simulations to a broader parameter range. The experimentally observed fluid-bcc-fluid reentrant transition of charged silica spheres in DMF can be explained using the freezing lines obtained in this work.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Using the Rogers-Young (RY) integral equation scheme for the static structure factor combined with the one-phase Hansen-Verlet (HV) freezing rule, we study the equilibrium structure and two-parameter freezing lines of colloidal particles with Yukawa-type pair interactions representing charge-stabilized silica spheres suspended in dimethylformamide (DMF). Results are presented for a vast range of concentrations, salinities and effective charges covering particles with masked excluded-volume interactions. The freezing lines were obtained for the low-charge and high-charge solutions of the static structure factor, for various two-parameter sets of experimentally accessible system parameters. All RY-HV based freezing lines can be mapped on a universal fluid-solid coexistence line in good agreement with computer simulation predictions. The RY-HV calculations extend the freezing lines obtained in earlier simulations to a broader parameter range. The experimentally observed fluid-bcc-fluid reentrant transition of charged silica spheres in DMF can be explained using the freezing lines obtained in this work. |
Szymańska, Agnieszka; Hornowski, Tomasz; Ślósarek, Genowefa Denaturation and aggregation of lysozyme in water-ethanol solution. Acta Biochimica Polonica, 59 (2), pp. 317–21, 2012, ISSN: 1734-154X. @article{Szymanska2012a, title = {Denaturation and aggregation of lysozyme in water-ethanol solution.}, author = {Agnieszka Szymańska and Tomasz Hornowski and Genowefa Ślósarek}, url = {http://www.ncbi.nlm.nih.gov/pubmed/22712059}, issn = {1734-154X}, year = {2012}, date = {2012-01-01}, journal = {Acta Biochimica Polonica}, volume = {59}, number = {2}, pages = {317--21}, abstract = {We have applied rheological methods for the analysis of ethanol-lysozyme interaction during the process of denaturation and aggregation of the protein. At low concentration of ethanol a destruction of the hydration shell of lysozyme is observed. With the increase in the ethanol concentration a structural transformation takes place. It leads to the formation of a protein aggregate with an elongated structure. The rheological characteristics of lysozyme-water-ethanol solution changes from Newtonian to pseudoplastic.}, keywords = {}, pubstate = {published}, tppubtype = {article} } We have applied rheological methods for the analysis of ethanol-lysozyme interaction during the process of denaturation and aggregation of the protein. At low concentration of ethanol a destruction of the hydration shell of lysozyme is observed. With the increase in the ethanol concentration a structural transformation takes place. It leads to the formation of a protein aggregate with an elongated structure. The rheological characteristics of lysozyme-water-ethanol solution changes from Newtonian to pseudoplastic. |
Ślósarek, Genowefa Współczesna rewolucja naukowa na pograniczu fizyki i biologii Zagadnienia Filozoficzne w Nauce (Philosophical Problems in Science), (51), pp. 96–115, 2012, ISSN: 0867-8296. @article{Slosarek2012b, title = {Współczesna rewolucja naukowa na pograniczu fizyki i biologii}, author = {Genowefa Ślósarek}, url = {http://cejsh.icm.edu.pl/cejsh/element/bwmeta1.element.cejsh-5e0cf13c-1391-4434-8b9a-88e146652db4}, issn = {0867-8296}, year = {2012}, date = {2012-01-01}, journal = {Zagadnienia Filozoficzne w Nauce (Philosophical Problems in Science)}, number = {51}, pages = {96--115}, publisher = {Uniwersytet Papieski Jana Pawła II w Krakowie - Wydawnictwo Naukowe}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Gibasiewicz, Krzysztof; Pajzderska, Maria; Karolczak, Jerzy; Burdziński, Gotard; Dobek, Andrzej; Jones, Michael R Acta Physica Polonica A, 131 (2), pp. 263-268, 2012. @article{Gibasiewicz2012, title = {Primary electron transfer reactions in membrane-bound open and closed reaction centers from purple bacterium Rhodobacter sphaeroides}, author = {Krzysztof Gibasiewicz and Maria Pajzderska and Jerzy Karolczak and Gotard Burdziński and Andrzej Dobek and Michael R Jones}, doi = {10.12693/APhysPolA.122.263}, year = {2012}, date = {2012-01-01}, journal = {Acta Physica Polonica A}, volume = {131}, number = {2}, pages = {263-268}, abstract = {Most ultrafast transient absorption studies of primary electron transfer in reaction centers from purple bacteria have been performed in complexes isolated from their natural lipid membrane environment using detergent. In this contribution we present near-UV-vis transient absorption studies of reaction centers embedded in their natural membrane environment. The evolution of absorption spectra recorded with subpicosecond resolution and reflecting primarily electron transfer reactions has been compared to data obtained previously for isolated reaction centers. We conclude that the overall spectral evolution in both types of samples is similar, and the environment of the reaction center protein has only a minor effect on the primary electron transfer reactions. The differences between the two samples are explained in terms of different energetic levels (and their different temporal evolution) of the two initial charge separated states P+BA- and P+HA-, with P being the primary electron donor and BA and HA the two consecutive electron acceptors. Additionally, in the electric field generated by P+HA-, BA in membrane-bound reaction centers undergoes a stronger electrochromic shift than in isolated reaction centers.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Most ultrafast transient absorption studies of primary electron transfer in reaction centers from purple bacteria have been performed in complexes isolated from their natural lipid membrane environment using detergent. In this contribution we present near-UV-vis transient absorption studies of reaction centers embedded in their natural membrane environment. The evolution of absorption spectra recorded with subpicosecond resolution and reflecting primarily electron transfer reactions has been compared to data obtained previously for isolated reaction centers. We conclude that the overall spectral evolution in both types of samples is similar, and the environment of the reaction center protein has only a minor effect on the primary electron transfer reactions. The differences between the two samples are explained in terms of different energetic levels (and their different temporal evolution) of the two initial charge separated states P+BA- and P+HA-, with P being the primary electron donor and BA and HA the two consecutive electron acceptors. Additionally, in the electric field generated by P+HA-, BA in membrane-bound reaction centers undergoes a stronger electrochromic shift than in isolated reaction centers. |
2011 |
Aliotta, F; Gapiński, Jacek; Pochylski, Mikołaj; Ponterio, R C; Saija, F; Vasi, C Physical Review E, 84 (5), pp. 051202, 2011, ISSN: 1539-3755. @article{Aliotta2011, title = {Collective acoustic modes in liquids: A comparison between the generalized-hydrodynamics and memory-function approaches}, author = {F Aliotta and Jacek Gapiński and Mikołaj Pochylski and R C Ponterio and F Saija and C Vasi}, url = {http://www.ncbi.nlm.nih.gov/pubmed/22181402 https://link.aps.org/doi/10.1103/PhysRevE.84.051202}, doi = {10.1103/PhysRevE.84.051202}, issn = {1539-3755}, year = {2011}, date = {2011-11-01}, journal = {Physical Review E}, volume = {84}, number = {5}, pages = {051202}, abstract = {The most familiar approaches used to describe the dynamical structure factor from adiabatic density fluctuations in liquids are based on generalized hydrodynamics and on the memory function, respectively. We show that, contrary to the common belief, the two approaches are not fully equivalent. In particular, models based on the memory function of a normalized damped oscillator fail in reproducing the correct experimental spectral profiles of systems close to the relaxation process. The discrepancy is due to misleading interpretation of the theoretical memory-function expressions, producing an unavoidable mixing of spectral contribution at different wave vectors when the theory is forced beyond its limits of validity.}, keywords = {}, pubstate = {published}, tppubtype = {article} } The most familiar approaches used to describe the dynamical structure factor from adiabatic density fluctuations in liquids are based on generalized hydrodynamics and on the memory function, respectively. We show that, contrary to the common belief, the two approaches are not fully equivalent. In particular, models based on the memory function of a normalized damped oscillator fail in reproducing the correct experimental spectral profiles of systems close to the relaxation process. The discrepancy is due to misleading interpretation of the theoretical memory-function expressions, producing an unavoidable mixing of spectral contribution at different wave vectors when the theory is forced beyond its limits of validity. |
Gibasiewicz, Krzysztof; Pajzderska, Maria; Potter, Jane A; Fyfe, Paul. K; Dobek, Andrzej; Brettel, Klaus; Jones, Michael R The Journal of Physical Chemistry B, 115 (44), pp. 13037–13050, 2011, ISSN: 1520-6106. @article{Gibasiewicz2011, title = {Mechanism of Recombination of the P + H A – Radical Pair in Mutant Rhodobacter sphaeroides Reaction Centers with Modified Free Energy Gaps Between P + B A – and P + H A –}, author = {Krzysztof Gibasiewicz and Maria Pajzderska and Jane A Potter and Paul. K Fyfe and Andrzej Dobek and Klaus Brettel and Michael R Jones}, url = {http://pubs.acs.org/doi/abs/10.1021/jp206462g}, doi = {10.1021/jp206462g}, issn = {1520-6106}, year = {2011}, date = {2011-11-01}, journal = {The Journal of Physical Chemistry B}, volume = {115}, number = {44}, pages = {13037--13050}, publisher = {American Chemical Society}, abstract = {The kinetics of recombination of the P+HA– radical pair were compared in wild-type reaction centers from Rhodobacter sphaeroides and in seven mutants in which the free energy gap, $Delta$G, between the charge separated states P+BA– and P+HA– was either increased or decreased. Five of the mutant RCs had been described previously, and X-ray crystal structures of two newly constructed complexes were determined by X-ray crystallography. The charge recombination reaction was accelerated in all mutants with a smaller $Delta$G than in the wild-type, and was slowed in a mutant having a larger $Delta$G. The free energy difference between the state P+HA– and the PHA ground state was unaffected by most of these mutations. These observations were consistent with a model in which the P+HA– → PHA charge recombination is thermally activated and occurs via the intermediate state P+BA–, with a mean rate related to the size of the $Delta$G between the states P+BA– and P+HA– and not the $Delta$G between P+HA– and the ground state. A more detailed analys...}, keywords = {}, pubstate = {published}, tppubtype = {article} } The kinetics of recombination of the P+HA– radical pair were compared in wild-type reaction centers from Rhodobacter sphaeroides and in seven mutants in which the free energy gap, $Delta$G, between the charge separated states P+BA– and P+HA– was either increased or decreased. Five of the mutant RCs had been described previously, and X-ray crystal structures of two newly constructed complexes were determined by X-ray crystallography. The charge recombination reaction was accelerated in all mutants with a smaller $Delta$G than in the wild-type, and was slowed in a mutant having a larger $Delta$G. The free energy difference between the state P+HA– and the PHA ground state was unaffected by most of these mutations. These observations were consistent with a model in which the P+HA– → PHA charge recombination is thermally activated and occurs via the intermediate state P+BA–, with a mean rate related to the size of the $Delta$G between the states P+BA– and P+HA– and not the $Delta$G between P+HA– and the ground state. A more detailed analys... |
Graczykowski, Bartłomiej; Dobek, Andrzej Iron–dextran complex: Geometrical structure and magneto-optical features Journal of Colloid and Interface Science, 363 (2), pp. 551–556, 2011, ISSN: 00219797. @article{Graczykowski2011, title = {Iron–dextran complex: Geometrical structure and magneto-optical features}, author = {Bartłomiej Graczykowski and Andrzej Dobek}, url = {http://www.ncbi.nlm.nih.gov/pubmed/21872262 http://linkinghub.elsevier.com/retrieve/pii/S0021979711009465}, doi = {10.1016/j.jcis.2011.07.080}, issn = {00219797}, year = {2011}, date = {2011-11-01}, journal = {Journal of Colloid and Interface Science}, volume = {363}, number = {2}, pages = {551--556}, abstract = {Molecular mass of the iron-dextran complex (M(w)=1133 kDa), diameter of its particles (∼8.3 nm) and the content of iron ions in the complex core (N(Fe)=6360) were determined by static light scattering, measurements of refractive index increment and the Cotton-Mouton effect in solution. The known number of iron ions permitted the calculation of the permanent magnetic dipole moment value to be $mu$(Fe)=3.17×10(-18) erg Oe(-1) and the determination of anisotropy of linear magneto-optical polarizabilities components as $Delta$$chi$=9.2×10(-21) cm(3). Knowing both values and the value of the mean linear optical polarizability $alpha$=7.3×10(-20) cm(3), it was possible to show that the total measured CM effect was due to the reorientation of the permanent and the induced magnetic dipole moments of the complex. Analysis of the measured magneto-optical birefringence indicated very small optical anisotropy of linear optical polarizability components, $kappa$($alpha$), which suggested a homogeneous structure of particles of spherical symmetry.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Molecular mass of the iron-dextran complex (M(w)=1133 kDa), diameter of its particles (∼8.3 nm) and the content of iron ions in the complex core (N(Fe)=6360) were determined by static light scattering, measurements of refractive index increment and the Cotton-Mouton effect in solution. The known number of iron ions permitted the calculation of the permanent magnetic dipole moment value to be $mu$(Fe)=3.17×10(-18) erg Oe(-1) and the determination of anisotropy of linear magneto-optical polarizabilities components as $Delta$$chi$=9.2×10(-21) cm(3). Knowing both values and the value of the mean linear optical polarizability $alpha$=7.3×10(-20) cm(3), it was possible to show that the total measured CM effect was due to the reorientation of the permanent and the induced magnetic dipole moments of the complex. Analysis of the measured magneto-optical birefringence indicated very small optical anisotropy of linear optical polarizability components, $kappa$($alpha$), which suggested a homogeneous structure of particles of spherical symmetry. |
Koralewski, M; Pochylski, Mikołaj; Mitróová, Z; Timko, M; Kopčanský, P; Melníková, L Magnetic birefringence of natural and synthetic ferritin Journal of Magnetism and Magnetic Materials, 323 (18-19), pp. 2413–2417, 2011, ISSN: 03048853. @article{Koralewski2011, title = {Magnetic birefringence of natural and synthetic ferritin}, author = {M Koralewski and Mikołaj Pochylski and Z Mitróová and M Timko and P Kopčanský and L Melníková}, url = {https://www.sciencedirect.com/science/article/pii/S0304885311002861 http://linkinghub.elsevier.com/retrieve/pii/S0304885311002861}, doi = {10.1016/j.jmmm.2011.05.017}, issn = {03048853}, year = {2011}, date = {2011-10-01}, journal = {Journal of Magnetism and Magnetic Materials}, volume = {323}, number = {18-19}, pages = {2413--2417}, publisher = {North-Holland}, abstract = {Magnetically induced optical birefringence ($Delta$n) was measured for magnetoferritin (MFer), horse spleen ferritin (HSF) and nanoscale magnetite aqueous suspensions. The anisotropy of optical polarizability was calculated. The average magnetic dipole moment calculated assuming the Langevin model was about 20,000 and 8500$mu$B per particle, for magnetite nanoparticle and magnetoferritin, respectively. Poor fitting results and the unphysical value of average magnetic moment per Fe ion for MFer excluded the use of the simple Langevin model for description of $Delta$n for this compound. It was deduced that for MFer the estimated average magnetic moment should be about 1125$mu$B per molecule. A magnetic contribution from the protein shell was found to be negligible. Results from the low-field region permit the calculation of the Cotton–Mouton (C–M) constants and their comparison for the substances studied. It was shown that magnetic birefringence and C–M constant can be powerful parameters in identification of the magnetic core structure of ferritins, especially useful in biomedicine.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Magnetically induced optical birefringence ($Delta$n) was measured for magnetoferritin (MFer), horse spleen ferritin (HSF) and nanoscale magnetite aqueous suspensions. The anisotropy of optical polarizability was calculated. The average magnetic dipole moment calculated assuming the Langevin model was about 20,000 and 8500$mu$B per particle, for magnetite nanoparticle and magnetoferritin, respectively. Poor fitting results and the unphysical value of average magnetic moment per Fe ion for MFer excluded the use of the simple Langevin model for description of $Delta$n for this compound. It was deduced that for MFer the estimated average magnetic moment should be about 1125$mu$B per molecule. A magnetic contribution from the protein shell was found to be negligible. Results from the low-field region permit the calculation of the Cotton–Mouton (C–M) constants and their comparison for the substances studied. It was shown that magnetic birefringence and C–M constant can be powerful parameters in identification of the magnetic core structure of ferritins, especially useful in biomedicine. |
Danielewicz-Ferchmin, Irena; Banachowicz, Ewa; Ferchmin, Ryszard A Physical Chemistry Chemical Physics, 13 (39), pp. 17722, 2011, ISSN: 1463-9076. @article{Danielewicz-Ferchmin2011, title = {Role of electromechanical and mechanoelectric effects in protein hydration under hydrostatic pressure}, author = {Irena Danielewicz-Ferchmin and Ewa Banachowicz and Ryszard A Ferchmin}, url = {http://www.ncbi.nlm.nih.gov/pubmed/21897960 http://xlink.rsc.org/?DOI=c1cp21819k}, doi = {10.1039/c1cp21819k}, issn = {1463-9076}, year = {2011}, date = {2011-10-01}, journal = {Physical Chemistry Chemical Physics}, volume = {13}, number = {39}, pages = {17722}, abstract = {Recent measurements of lysozyme hydration water density under non-denaturing pressure show that it is higher than that of bulk water in the same conditions. High protein hydration layer density has earlier been observed at ambient conditions and ascribed to electrostriction. We calculate the pressure-induced protein mean surface charge density increment $Delta$$sigma$. Within the hydration layer, the higher fields due to $Delta$$sigma$ lead to an additional water compression via electrostriction. The increment $Delta$$sigma$ is considered as due to a mechanoelectric effect in protein molecules. The mean value of the effective mechanoelectric coefficient d is calculated and compared with piezoelectric coefficients of amino acids and their compounds.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Recent measurements of lysozyme hydration water density under non-denaturing pressure show that it is higher than that of bulk water in the same conditions. High protein hydration layer density has earlier been observed at ambient conditions and ascribed to electrostriction. We calculate the pressure-induced protein mean surface charge density increment $Delta$$sigma$. Within the hydration layer, the higher fields due to $Delta$$sigma$ lead to an additional water compression via electrostriction. The increment $Delta$$sigma$ is considered as due to a mechanoelectric effect in protein molecules. The mean value of the effective mechanoelectric coefficient d is calculated and compared with piezoelectric coefficients of amino acids and their compounds. |
Koralewski, M; Pochylski, Mikołaj; Gierszewski, J Magnetic birefringence of iron oxyhydroxide nanoparticles stabilised by sucrose Journal of Magnetism and Magnetic Materials, 323 (9), pp. 1140–1144, 2011, ISSN: 03048853. @article{Koralewski2011a, title = {Magnetic birefringence of iron oxyhydroxide nanoparticles stabilised by sucrose}, author = {M Koralewski and Mikołaj Pochylski and J Gierszewski}, url = {https://www.sciencedirect.com/science/article/pii/S0304885310009194 http://linkinghub.elsevier.com/retrieve/pii/S0304885310009194}, doi = {10.1016/j.jmmm.2010.12.024}, issn = {03048853}, year = {2011}, date = {2011-05-01}, journal = {Journal of Magnetism and Magnetic Materials}, volume = {323}, number = {9}, pages = {1140--1144}, publisher = {North-Holland}, abstract = {Magnetically induced optical birefringence is used to investigate pharmaceutically important iron–sucrose aqueous suspensions. XRD and TEM measurements of the system of oxyhydroxide particles stabilised by sucrose have shown that this system contains iron oxyhydroxide in the form of 2–5nm particles. The mineral form of the iron-core is suggested to be akaganeite. Anisotropy of the optical polarizability and magnetic susceptibility of akaganeite nanoparticles are calculated. The permanent dipole moment obtained for the nanoparticles studied was found to be negligible, in agreement with the characteristic superparamagnetic behaviour of the magnetic nanoparticles observed at room temperature. The Neel temperature of these nanoparticles is estimated as below 276K. The results obtained are discussed against a background of the earlier studies of similar nanoscale systems.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Magnetically induced optical birefringence is used to investigate pharmaceutically important iron–sucrose aqueous suspensions. XRD and TEM measurements of the system of oxyhydroxide particles stabilised by sucrose have shown that this system contains iron oxyhydroxide in the form of 2–5nm particles. The mineral form of the iron-core is suggested to be akaganeite. Anisotropy of the optical polarizability and magnetic susceptibility of akaganeite nanoparticles are calculated. The permanent dipole moment obtained for the nanoparticles studied was found to be negligible, in agreement with the characteristic superparamagnetic behaviour of the magnetic nanoparticles observed at room temperature. The Neel temperature of these nanoparticles is estimated as below 276K. The results obtained are discussed against a background of the earlier studies of similar nanoscale systems. |
Kalwarczyk, Tomasz; Ziȩbacz, Natalia; Bielejewska, Anna; Zaboklicka, Ewa; Koynov, Kaloian; Szymański, Jȩdrzej; Wilk, Agnieszka; Patkowski, Adam; Gapiński, Jacek; Butt, Hans-Jürgen; Hołyst, Robert Nano Letters, 11 (5), pp. 2157–2163, 2011, ISSN: 1530-6984. @article{Kalwarczyk2011, title = {Comparative Analysis of Viscosity of Complex Liquids and Cytoplasm of Mammalian Cells at the Nanoscale}, author = {Tomasz Kalwarczyk and Natalia Ziȩbacz and Anna Bielejewska and Ewa Zaboklicka and Kaloian Koynov and Jȩdrzej Szymański and Agnieszka Wilk and Adam Patkowski and Jacek Gapiński and Hans-Jürgen Butt and Robert Hołyst}, url = {http://www.ncbi.nlm.nih.gov/pubmed/21513331 http://pubs.acs.org/doi/abs/10.1021/nl2008218}, doi = {10.1021/nl2008218}, issn = {1530-6984}, year = {2011}, date = {2011-05-01}, journal = {Nano Letters}, volume = {11}, number = {5}, pages = {2157--2163}, abstract = {We present a scaling formula for size-dependent viscosity coefficients for proteins, polymers, and fluorescent dyes diffusing in complex liquids. The formula was used to analyze the mobilities of probes of different sizes in HeLa and Swiss 3T3 mammalian cells. This analysis unveils in the cytoplasm two length scales: (i) the correlation length $xi$ (approximately 5 nm in HeLa and 7 nm in Swiss 3T3 cells) and (ii) the limiting length scale that marks the crossover between nano- and macroscale viscosity (approximately 86 nm in HeLa and 30 nm in Swiss 3T3 cells). During motion, probes smaller than $xi$ experienced matrix viscosity: $eta$(matrix) ≈ 2.0 mPatextperiodcentereds for HeLa and 0.88 mPatextperiodcentereds for Swiss 3T3 cells. Probes much larger than the limiting length scale experienced macroscopic viscosity, $eta$(macro) ≈ 4.4 × 10(-2) and 2.4 × 10(-2) Patextperiodcentereds for HeLa and Swiss 3T3 cells, respectively. Our results are persistent for the lengths scales from 0.14 nm to a few hundred nanometers.}, keywords = {}, pubstate = {published}, tppubtype = {article} } We present a scaling formula for size-dependent viscosity coefficients for proteins, polymers, and fluorescent dyes diffusing in complex liquids. The formula was used to analyze the mobilities of probes of different sizes in HeLa and Swiss 3T3 mammalian cells. This analysis unveils in the cytoplasm two length scales: (i) the correlation length $xi$ (approximately 5 nm in HeLa and 7 nm in Swiss 3T3 cells) and (ii) the limiting length scale that marks the crossover between nano- and macroscale viscosity (approximately 86 nm in HeLa and 30 nm in Swiss 3T3 cells). During motion, probes smaller than $xi$ experienced matrix viscosity: $eta$(matrix) ≈ 2.0 mPatextperiodcentereds for HeLa and 0.88 mPatextperiodcentereds for Swiss 3T3 cells. Probes much larger than the limiting length scale experienced macroscopic viscosity, $eta$(macro) ≈ 4.4 × 10(-2) and 2.4 × 10(-2) Patextperiodcentereds for HeLa and Swiss 3T3 cells, respectively. Our results are persistent for the lengths scales from 0.14 nm to a few hundred nanometers. |
Aliotta, F; Ponterio, R C; Saija, F; Gapiński, J; Pochylski, Mikołaj Relaxation dynamics and evidence of scaling behaviours in aqueous polymer solutions Journal of Molecular Liquids, 159 (1), pp. 105–111, 2011, ISSN: 01677322. @article{Aliotta2011b, title = {Relaxation dynamics and evidence of scaling behaviours in aqueous polymer solutions}, author = {F Aliotta and R C Ponterio and F Saija and J Gapiński and Mikołaj Pochylski}, url = {http://www.events.sbg.ac.at/emlg2009/EMLG2009 Abstracts/PL_Aliotta_abstract2.pdf http://linkinghub.elsevier.com/retrieve/pii/S0167732210003545}, doi = {10.1016/j.molliq.2010.12.006}, issn = {01677322}, year = {2011}, date = {2011-02-01}, journal = {Journal of Molecular Liquids}, volume = {159}, number = {1}, pages = {105--111}, abstract = {The results from some recent Brillouin scattering experiments on aqueous solution of Polyethylene glycol and Polyethylene glycol dimethyl ether are presented. In all the systems a non-Debye relaxation processes have been detected, proceeding on the ps time scale. The average values of the detected relaxation time distributions fail to follow simple Arrhenius behaviors. The temperature evolution of the relaxation time is adequately fitted after the adoption of a phenomenological Vogel-Fulcher-Tammon model. In spite of the different temperature and concentration dependences observed for each system, a unique scaling behavior has been evidenced, at relatively low water contents, when the real and imaginary parts of the loss modulus are plotted as a function of a reduced reverse temperature, T 0 /T, being T 0 the values of the arrest temperature as obtained by the Vogel-Fulcher-Tammon fits. The observation of a unique scaling law for aqueous solutions of polymers characterized by the same average molecular weight but with different end groups suggests for the establishment of similar hydrogen bonded local structures where water plays a main role, acting as a stabilizer bridging neighbouring polymer chains. The possible physical meanings of the obtained phenomenological fitting parameters are discussed and the results are compared with other literature findings. Some excess thermodynamic quantities are analyzed and discussed in the frame of recent approaches. REFERENCES}, keywords = {}, pubstate = {published}, tppubtype = {article} } The results from some recent Brillouin scattering experiments on aqueous solution of Polyethylene glycol and Polyethylene glycol dimethyl ether are presented. In all the systems a non-Debye relaxation processes have been detected, proceeding on the ps time scale. The average values of the detected relaxation time distributions fail to follow simple Arrhenius behaviors. The temperature evolution of the relaxation time is adequately fitted after the adoption of a phenomenological Vogel-Fulcher-Tammon model. In spite of the different temperature and concentration dependences observed for each system, a unique scaling behavior has been evidenced, at relatively low water contents, when the real and imaginary parts of the loss modulus are plotted as a function of a reduced reverse temperature, T 0 /T, being T 0 the values of the arrest temperature as obtained by the Vogel-Fulcher-Tammon fits. The observation of a unique scaling law for aqueous solutions of polymers characterized by the same average molecular weight but with different end groups suggests for the establishment of similar hydrogen bonded local structures where water plays a main role, acting as a stabilizer bridging neighbouring polymer chains. The possible physical meanings of the obtained phenomenological fitting parameters are discussed and the results are compared with other literature findings. Some excess thermodynamic quantities are analyzed and discussed in the frame of recent approaches. REFERENCES |
Graczykowski, Bartłomiej; Dobek, Andrzej Iron--dextran complex: Geometrical structure and magneto-optical features Journal of colloid and interface science, 363 (2), pp. 551–556, 2011. @article{graczykowski2011iron, title = {Iron--dextran complex: Geometrical structure and magneto-optical features}, author = {Bartłomiej Graczykowski and Andrzej Dobek}, year = {2011}, date = {2011-01-01}, journal = {Journal of colloid and interface science}, volume = {363}, number = {2}, pages = {551--556}, publisher = {Elsevier}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
2010 |
Wilk, Agnieszka; Huißmann, S; Stiakakis, E; Kohlbrecher, J; Vlassopoulos, D; Likos, C N; Meier, G; Dhont, J K G; Petekidis, G; Vavrin, R Osmotic shrinkage in star/linear polymer mixtures The European Physical Journal E, 32 (2), pp. 127–134, 2010, ISSN: 1292-8941. @article{Wilk2010, title = {Osmotic shrinkage in star/linear polymer mixtures}, author = {Agnieszka Wilk and S Huißmann and E Stiakakis and J Kohlbrecher and D Vlassopoulos and C N Likos and G Meier and J K G Dhont and G Petekidis and R Vavrin}, url = {http://www.ncbi.nlm.nih.gov/pubmed/20596881 http://www.springerlink.com/index/10.1140/epje/i2010-10607-2}, doi = {10.1140/epje/i2010-10607-2}, issn = {1292-8941}, year = {2010}, date = {2010-06-01}, journal = {The European Physical Journal E}, volume = {32}, number = {2}, pages = {127--134}, abstract = {Multiarm star polymers were used as model grafted colloidal particles with long hairs, to study their size variation due to osmotic forces arising from added linear homopolymers of smaller size. This is the origin of the depletion phenomenon that has been exploited in the past as a means to melt soft colloidal glasses by adding linear chains and analyzed using dynamic light scattering experiments and an effective interactions analysis yielding the depletion potential. Shrinkage is a generic phenomenon for hairy particles, which affects macroscopic properties and state transitions at high concentrations. In this work we present a small-angle neutron scattering study of star/linear polymer mixtures with different size ratios (varying the linear polymer molar mass) and confirm the depletion picture, i.e., osmotic star shrinkage. Moreover, we find that as the linear/star polymer size ratio increases for the same effective linear volume fraction (c/c* with c* the overlapping concentration), the star shrinkage is reduced whereas the onset of shrinkage appears to take place at higher linear polymer volume fractions. A theoretical description of the force balance on a star polymer in solution, accounting for the classic Flory contributions, i.e. elastic and excluded volume, as well as the osmotic force due to the linear chains, accurately predicts the experimental findings of reduced star size as a function of linear polymer concentration. This is done in a parameter-free fashion, in which the size of the cavity created by the star, and from which the chains are excluded, is related to the radius of the former from first principles.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Multiarm star polymers were used as model grafted colloidal particles with long hairs, to study their size variation due to osmotic forces arising from added linear homopolymers of smaller size. This is the origin of the depletion phenomenon that has been exploited in the past as a means to melt soft colloidal glasses by adding linear chains and analyzed using dynamic light scattering experiments and an effective interactions analysis yielding the depletion potential. Shrinkage is a generic phenomenon for hairy particles, which affects macroscopic properties and state transitions at high concentrations. In this work we present a small-angle neutron scattering study of star/linear polymer mixtures with different size ratios (varying the linear polymer molar mass) and confirm the depletion picture, i.e., osmotic star shrinkage. Moreover, we find that as the linear/star polymer size ratio increases for the same effective linear volume fraction (c/c* with c* the overlapping concentration), the star shrinkage is reduced whereas the onset of shrinkage appears to take place at higher linear polymer volume fractions. A theoretical description of the force balance on a star polymer in solution, accounting for the classic Flory contributions, i.e. elastic and excluded volume, as well as the osmotic force due to the linear chains, accurately predicts the experimental findings of reduced star size as a function of linear polymer concentration. This is done in a parameter-free fashion, in which the size of the cavity created by the star, and from which the chains are excluded, is related to the radius of the former from first principles. |
Gapiński, Jacek; Szymański, Jȩdrzej; Wilk, Agnieszka; Kohlbrecher, Joachim; Patkowski, Adam; Hołyst, Robert Size and Shape of Micelles Studied by Means of SANS, PCS, and FCS Langmuir, 26 (12), pp. 9304–9314, 2010, ISSN: 0743-7463. @article{Gapinski2010, title = {Size and Shape of Micelles Studied by Means of SANS, PCS, and FCS}, author = {Jacek Gapiński and Jȩdrzej Szymański and Agnieszka Wilk and Joachim Kohlbrecher and Adam Patkowski and Robert Hołyst}, url = {http://pubs.acs.org/doi/abs/10.1021/la100181d}, doi = {10.1021/la100181d}, issn = {0743-7463}, year = {2010}, date = {2010-06-01}, journal = {Langmuir}, volume = {26}, number = {12}, pages = {9304--9314}, publisher = {American Chemical Society}, abstract = {The hexaethylene glycol monododecyl ether (C12E6) micelles at concentrations up to 10% have been studied in their isotropic phase (10−48 °C) by means of small angle neutron scattering (SANS) and photon correlation spectroscopy (PCS). The SANS data obtained at low temperatures could be unequivocally interpreted as a result of scattering from a suspension of compact globular micelles with the shape of a triaxial ellipsoid or a short end-capped elliptical rod. Different models have been applied to analyze the SANS data obtained at higher temperatures: (i) elongated rod-like micelles with purely sterical interactions, (ii) compact globular micelles with a weak attractive potential, and (iii) globular micelles influenced by the critical phenomena in the whole temperature range studied. The good quality of the experimental data indicated model (i) as the best fit for our data. The diffusion coefficients obtained from the PCS measurements have been compared to the diffusion coefficients calculated for the rod-li...}, keywords = {}, pubstate = {published}, tppubtype = {article} } The hexaethylene glycol monododecyl ether (C12E6) micelles at concentrations up to 10% have been studied in their isotropic phase (10−48 °C) by means of small angle neutron scattering (SANS) and photon correlation spectroscopy (PCS). The SANS data obtained at low temperatures could be unequivocally interpreted as a result of scattering from a suspension of compact globular micelles with the shape of a triaxial ellipsoid or a short end-capped elliptical rod. Different models have been applied to analyze the SANS data obtained at higher temperatures: (i) elongated rod-like micelles with purely sterical interactions, (ii) compact globular micelles with a weak attractive potential, and (iii) globular micelles influenced by the critical phenomena in the whole temperature range studied. The good quality of the experimental data indicated model (i) as the best fit for our data. The diffusion coefficients obtained from the PCS measurements have been compared to the diffusion coefficients calculated for the rod-li... |
Pochylski, Mikołaj; Gapiński, Jacek Brillouin Scattering Study of Polyethylene Glycol/Water System below Crystallization Temperature The Journal of Physical Chemistry B, 114 (8), pp. 2644–2649, 2010, ISSN: 1520-6106. @article{Pochylski2010a, title = {Brillouin Scattering Study of Polyethylene Glycol/Water System below Crystallization Temperature}, author = {Mikołaj Pochylski and Jacek Gapiński}, url = {http://www.ncbi.nlm.nih.gov/pubmed/20146525 http://pubs.acs.org/doi/abs/10.1021/jp910783j}, doi = {10.1021/jp910783j}, issn = {1520-6106}, year = {2010}, date = {2010-03-01}, journal = {The Journal of Physical Chemistry B}, volume = {114}, number = {8}, pages = {2644--2649}, abstract = {We present the results of a Brillouin scattering experiment on aqueous mixtures of polyethylene glycol polymer cooled below their crystallization temperature. The shape of the registered spectrum changed considerably when the phase transition occurs. The Brillouin profile consisted of two peaks which has been interpreted as a result of the scattering of light on the local regions exhibiting different compressibility. Examination of the temperature dependence of the two Brillouin peak positions allows the identification of the specific microstructures present in the studied system. The existence of a complexlike hydration structure, stable against dilution and temperature agitation, was suggested. The nature and the behavior of the hydration complex is discussed in view of the earlier investigations in similar systems.}, keywords = {}, pubstate = {published}, tppubtype = {article} } We present the results of a Brillouin scattering experiment on aqueous mixtures of polyethylene glycol polymer cooled below their crystallization temperature. The shape of the registered spectrum changed considerably when the phase transition occurs. The Brillouin profile consisted of two peaks which has been interpreted as a result of the scattering of light on the local regions exhibiting different compressibility. Examination of the temperature dependence of the two Brillouin peak positions allows the identification of the specific microstructures present in the studied system. The existence of a complexlike hydration structure, stable against dilution and temperature agitation, was suggested. The nature and the behavior of the hydration complex is discussed in view of the earlier investigations in similar systems. |
Stiakakis, E; Wilk, Agnieszka; Kohlbrecher, J; Vlassopoulos, D; Petekidis, G Slow dynamics, aging, and crystallization of multiarm star glasses Physical Review E, 81 (2), pp. 020402, 2010, ISSN: 1539-3755. @article{Stiakakis2010, title = {Slow dynamics, aging, and crystallization of multiarm star glasses}, author = {E Stiakakis and Agnieszka Wilk and J Kohlbrecher and D Vlassopoulos and G Petekidis}, url = {https://link.aps.org/doi/10.1103/PhysRevE.81.020402}, doi = {10.1103/PhysRevE.81.020402}, issn = {1539-3755}, year = {2010}, date = {2010-02-01}, journal = {Physical Review E}, volume = {81}, number = {2}, pages = {020402}, publisher = {American Physical Society}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Pochylski, Mikołaj; Aliotta, F; Ponterio, R C; Saija, F; Gapiński, Jacek Some Evidence of Scaling Behavior in the Relaxation Dynamics of Aqueous Polymer Solutions The Journal of Physical Chemistry B, 114 (4), pp. 1614–1620, 2010, ISSN: 1520-6106. @article{Pochylski2010b, title = {Some Evidence of Scaling Behavior in the Relaxation Dynamics of Aqueous Polymer Solutions}, author = {Mikołaj Pochylski and F Aliotta and R C Ponterio and F Saija and Jacek Gapiński}, url = {http://www.ncbi.nlm.nih.gov/pubmed/20055360 http://pubs.acs.org/doi/abs/10.1021/jp9052456}, doi = {10.1021/jp9052456}, issn = {1520-6106}, year = {2010}, date = {2010-02-01}, journal = {The Journal of Physical Chemistry B}, volume = {114}, number = {4}, pages = {1614--1620}, abstract = {The structural relaxation behavior of aqueous solution of poly(ethylene glycol) and methoxy-capped poly(ethylene glycol), both of mean molecular mass 400 g/mol, is investigated by Brillouin scattering experiments. In both cases non-Debye relaxation processes have been detected, proceeding on the picosecond time scale. The average values of the detected relaxation time distributions fail to follow the simple Arrhenius behavior. The temperature evolution of the relaxation time is adequately fitted using the phenomenological Vogel-Fulcher-Tamman (VFT) model. In spite of the different temperature and concentration dependences observed for the two kinds of systems, with the exception of the highest samples concentrations, a unique scaling behavior has been found for the real and imaginary parts of the loss modulus plotted as a function of the reduced inverse temperature, T(0)/T, T(0) being the VFT arrest temperature. The presence of a unique scaling law in aqueous solutions of polymers characterized by different end groups suggests the establishment of similar hydrogen-bonded local structures. Within this scenario, water acts as a stabilizer and plays the main role bridging neighboring polymer chains. The possible physical interpretation of the obtained fit parameters is discussed, and the results are compared with other literature findings.}, keywords = {}, pubstate = {published}, tppubtype = {article} } The structural relaxation behavior of aqueous solution of poly(ethylene glycol) and methoxy-capped poly(ethylene glycol), both of mean molecular mass 400 g/mol, is investigated by Brillouin scattering experiments. In both cases non-Debye relaxation processes have been detected, proceeding on the picosecond time scale. The average values of the detected relaxation time distributions fail to follow the simple Arrhenius behavior. The temperature evolution of the relaxation time is adequately fitted using the phenomenological Vogel-Fulcher-Tamman (VFT) model. In spite of the different temperature and concentration dependences observed for the two kinds of systems, with the exception of the highest samples concentrations, a unique scaling behavior has been found for the real and imaginary parts of the loss modulus plotted as a function of the reduced inverse temperature, T(0)/T, T(0) being the VFT arrest temperature. The presence of a unique scaling law in aqueous solutions of polymers characterized by different end groups suggests the establishment of similar hydrogen-bonded local structures. Within this scenario, water acts as a stabilizer and plays the main role bridging neighboring polymer chains. The possible physical interpretation of the obtained fit parameters is discussed, and the results are compared with other literature findings. |
Gapiński, Jacek; Patkowski, Adam; Naegele, Gerhard Generic behavior of the hydrodynamic function of charged colloidal suspensions The Journal of Chemical Physics, 132 (5), pp. 054510, 2010, ISSN: 0021-9606. @article{Gapinski2010a, title = {Generic behavior of the hydrodynamic function of charged colloidal suspensions}, author = {Jacek Gapiński and Adam Patkowski and Gerhard Naegele}, url = {http://www.ncbi.nlm.nih.gov/pubmed/20136325 http://aip.scitation.org/doi/10.1063/1.3306397}, doi = {10.1063/1.3306397}, issn = {0021-9606}, year = {2010}, date = {2010-02-01}, journal = {The Journal of Chemical Physics}, volume = {132}, number = {5}, pages = {054510}, abstract = {We discuss the generic behavior of the hydrodynamic function H(q) and diffusion function D(q) characterizing the short-time diffusion in suspensions of charge-stabilized colloidal spheres, by covering the whole fluid regime. Special focus is given to the behavior of these functions at the freezing transition specified by the Hansen-Verlet freezing rule. Results are presented in dependence on scattering wavenumber q, effective particle charge, volume fraction, salt concentration, and particle size, by considering both the low-charge and high-charge branch solutions of static structure factors. The existence of two charge branches leads to the prediction of a re-entrant melting-freezing-melting transition for increasing particle concentration at very low salinity. A universal limiting contour line is derived for the principal peak height value of H(q), independent of particle charge and diameter, and concentration and salinity, which separates the fluid from the fluid-solid coexistence region. This line is only weakly dependent on the value of the structure factor peak height entering the Hansen-Verlet rule. A dynamic freezing criterion is derived in terms of the short-time cage diffusion coefficient, a quantity easily measurable in a scattering experiment. The higher-dimensional parameter scans underlying this study make use of the fast and highly efficient deltagamma-scheme in conjunction with the analytic rescaled mean spherical approximation input for the static structure factor. Our results constitute a comprehensive database useful to researchers performing dynamic scattering experiments on charge-stabilized dispersions.}, keywords = {}, pubstate = {published}, tppubtype = {article} } We discuss the generic behavior of the hydrodynamic function H(q) and diffusion function D(q) characterizing the short-time diffusion in suspensions of charge-stabilized colloidal spheres, by covering the whole fluid regime. Special focus is given to the behavior of these functions at the freezing transition specified by the Hansen-Verlet freezing rule. Results are presented in dependence on scattering wavenumber q, effective particle charge, volume fraction, salt concentration, and particle size, by considering both the low-charge and high-charge branch solutions of static structure factors. The existence of two charge branches leads to the prediction of a re-entrant melting-freezing-melting transition for increasing particle concentration at very low salinity. A universal limiting contour line is derived for the principal peak height value of H(q), independent of particle charge and diameter, and concentration and salinity, which separates the fluid from the fluid-solid coexistence region. This line is only weakly dependent on the value of the structure factor peak height entering the Hansen-Verlet rule. A dynamic freezing criterion is derived in terms of the short-time cage diffusion coefficient, a quantity easily measurable in a scattering experiment. The higher-dimensional parameter scans underlying this study make use of the fast and highly efficient deltagamma-scheme in conjunction with the analytic rescaled mean spherical approximation input for the static structure factor. Our results constitute a comprehensive database useful to researchers performing dynamic scattering experiments on charge-stabilized dispersions. |
Ponterio, R C; Pochylski, Mikołaj; Aliotta, F; Vasi, C; Fontanella, M E; Saija, F Raman scattering measurements on a floating water bridge Journal of Physics D: Applied Physics, 43 (17), pp. 175405, 2010. @article{Ponterio2010, title = {Raman scattering measurements on a floating water bridge}, author = {R C Ponterio and Mikołaj Pochylski and F Aliotta and C Vasi and M E Fontanella and F Saija}, url = {http://stacks.iop.org/0022-3727/43/i=17/a=175405}, doi = {10.1088/0022-3727/43/17/175405}, year = {2010}, date = {2010-01-01}, journal = {Journal of Physics D: Applied Physics}, volume = {43}, number = {17}, pages = {175405}, abstract = {It was observed that when polarized by an intense electric field, water is able to self-arrange into macroscopic cylindrical wires that can hang up and remain floating against gravity. This phenomenon is now known as a 'water bridge'. Several attempts have been made to give an explanation of this apparently unusual behaviour of water. A number of experiments have been performed with the aim of probing any possible structural change of bulk water, after application of the electric field. None of the available findings appear conclusive at the moment. Here we report the results of the first Raman scattering experiment on floating water bridges. The inter-molecular OH-stretching band has been investigated and the results have been compared with those from bulk water. Some changes in the scattering profiles after application of the electric field are shown to have a structural origin. The bridges have been obtained, for the first time, in a vertical geometry and under application of an alternating field. The adopted geometry has allowed us to reveal a clear asymmetry between opposite direct current biasing, which can be related to the nature of the charge carriers.}, keywords = {}, pubstate = {published}, tppubtype = {article} } It was observed that when polarized by an intense electric field, water is able to self-arrange into macroscopic cylindrical wires that can hang up and remain floating against gravity. This phenomenon is now known as a 'water bridge'. Several attempts have been made to give an explanation of this apparently unusual behaviour of water. A number of experiments have been performed with the aim of probing any possible structural change of bulk water, after application of the electric field. None of the available findings appear conclusive at the moment. Here we report the results of the first Raman scattering experiment on floating water bridges. The inter-molecular OH-stretching band has been investigated and the results have been compared with those from bulk water. Some changes in the scattering profiles after application of the electric field are shown to have a structural origin. The bridges have been obtained, for the first time, in a vertical geometry and under application of an alternating field. The adopted geometry has allowed us to reveal a clear asymmetry between opposite direct current biasing, which can be related to the nature of the charge carriers. |
Saija, F; Aliotta, F; Fontanella, M E; Pochylski, Mikołaj; Salvato, G; Vasi, C; Ponterio, R C Communication: An extended model of liquid bridging The Journal of Chemical Physics, 133 (8), pp. 081104, 2010. @article{Saija2010, title = {Communication: An extended model of liquid bridging}, author = {F Saija and F Aliotta and M E Fontanella and Mikołaj Pochylski and G Salvato and C Vasi and R C Ponterio}, url = {https://doi.org/10.1063/1.3483690}, doi = {10.1063/1.3483690}, year = {2010}, date = {2010-01-01}, journal = {The Journal of Chemical Physics}, volume = {133}, number = {8}, pages = {081104}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Zawadzki, Paweł; Ślósarek, Genowefa; Boryski, Jerzy; Wojtaszek, Przemysław Biological Chemistry, 391 (1), pp. 43–53, 2010, ISSN: 1437-4315. @article{Zawadzki2010, title = {A fluorescence correlation spectroscopy study of ligand interaction with cytokinin-specific binding protein from mung bean}, author = {Paweł Zawadzki and Genowefa Ślósarek and Jerzy Boryski and Przemysław Wojtaszek}, url = {http://www.ncbi.nlm.nih.gov/pubmed/19919180 https://www.degruyter.com/view/j/bchm.2010.391.issue-1/bc.2010.005/bc.2010.005.xml}, doi = {10.1515/bc.2010.005}, issn = {1437-4315}, year = {2010}, date = {2010-01-01}, journal = {Biological Chemistry}, volume = {391}, number = {1}, pages = {43--53}, abstract = {Cytokinins are essential plant hormones that regulate numerous physiological processes. Recently, a protein was identified in mung bean (Vigna radiata) and characterized as a cytokinin-specific binding protein (VrCSBP). Fluorescence correlation spectroscopy was used to investigate the interaction between VrCSBP and its ligands. The synthetic cytokinin, N-phenyl-N'-(4-pyridyl) urea, was labeled with two fluorophores, 7-nitro-2,1,3-benzoxadiazole and rhodamine B. Protein-ligand binding was analyzed in an equilibrium saturation binding experiment and confirmed by the competition assay. Surprisingly, it was found that VrCSBP binds not only to cytokinins, but also to gibberellins. In addition, in the presence of natural cytokinins and gibberellins, two populations of VrCSBP that differ in their diffusion coefficients were detected. The diffusion coefficients of these two populations could be related to mono- and dimeric states, which suggests a new mode of operation in ligand binding by VrCSBP, in which dimerization induced by natural ligands enhances the ligand binding capacity of the protein.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Cytokinins are essential plant hormones that regulate numerous physiological processes. Recently, a protein was identified in mung bean (Vigna radiata) and characterized as a cytokinin-specific binding protein (VrCSBP). Fluorescence correlation spectroscopy was used to investigate the interaction between VrCSBP and its ligands. The synthetic cytokinin, N-phenyl-N'-(4-pyridyl) urea, was labeled with two fluorophores, 7-nitro-2,1,3-benzoxadiazole and rhodamine B. Protein-ligand binding was analyzed in an equilibrium saturation binding experiment and confirmed by the competition assay. Surprisingly, it was found that VrCSBP binds not only to cytokinins, but also to gibberellins. In addition, in the presence of natural cytokinins and gibberellins, two populations of VrCSBP that differ in their diffusion coefficients were detected. The diffusion coefficients of these two populations could be related to mono- and dimeric states, which suggests a new mode of operation in ligand binding by VrCSBP, in which dimerization induced by natural ligands enhances the ligand binding capacity of the protein. |
Giera, Wojciech; Ramesh, V M; Webber, Andrew N; van Stokkum, Ivo; van Grondelle, Rienk; Gibasiewicz, Krzysztof Biochimica et Biophysica Acta (BBA) - Bioenergetics, 1797 (1), pp. 106–112, 2010, ISSN: 00052728. @article{Giera2010, title = {Effect of the P700 pre-oxidation and point mutations near A0 on the reversibility of the primary charge separation in Photosystem I from Chlamydomonas reinhardtii}, author = {Wojciech Giera and V M Ramesh and Andrew N Webber and Ivo van Stokkum and Rienk van Grondelle and Krzysztof Gibasiewicz}, url = {https://www.sciencedirect.com/science/article/pii/S000527280900262X http://linkinghub.elsevier.com/retrieve/pii/S000527280900262X}, doi = {10.1016/j.bbabio.2009.09.006}, issn = {00052728}, year = {2010}, date = {2010-01-01}, journal = {Biochimica et Biophysica Acta (BBA) - Bioenergetics}, volume = {1797}, number = {1}, pages = {106--112}, publisher = {Elsevier}, abstract = {Time-resolved fluorescence studies with a 3-ps temporal resolution were performed in order to: (1) test the recent model of the reversible primary charge separation in Photosystem I (Muller et al., 2003; Holwzwarth et al., 2005, 2006), and (2) to reconcile this model with a mechanism of excitation energy quenching by closed Photosystem I (with P700 pre-oxidized to P700+). For these purposes, we performed experiments using Photosystem I core samples isolated from Chlamydomonas reinhardtii wild type, and two mutants in which the methionine axial ligand to primary electron acceptor, A0, has been change to either histidine or serine. The temporal evolution of fluorescence spectra was recorded for each preparation under conditions where the “primary electron donor,” P700, was either neutral or chemically pre-oxidized to P700+. For all the preparations under study, and under neutral and oxidizing conditions, we observed multiexponential fluorescence decay with the major phases of ∼7 ps and ∼25 ps. The relative amplitudes and, to a minor extent the lifetimes, of these two phases were modulated by the redox state of P700 and by the mutations near A0: both pre-oxidation of P700 and mutations caused slight deceleration of the excited state decay. These results are consistent with a model in which P700 is not the primary electron donor, but rather a secondary electron donor, with the primary charge separation event occurring between the accessory chlorophyll, A, and A0. We assign the faster phase to the equilibration process between the excited state of the antenna/reaction center ensemble and the primary radical pair, and the slower phase to the secondary electron transfer reaction. The pre-oxidation of P700 shifts the equilibrium between the excited state and the primary radical pair towards the excited state. This shift is proposed to be induced by the presence of the positive charge on P700+. The same charge is proposed to be responsible for the fast A+A0−→AA0 charge recombination to the ground state and, in consequence, excitation quenching in closed reaction centers. Mutations of the A0 axial ligand shift the equilibrium in the same direction as pre-oxidation of P700 due to the up-shift of the free energy level of the state A+A0−.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Time-resolved fluorescence studies with a 3-ps temporal resolution were performed in order to: (1) test the recent model of the reversible primary charge separation in Photosystem I (Muller et al., 2003; Holwzwarth et al., 2005, 2006), and (2) to reconcile this model with a mechanism of excitation energy quenching by closed Photosystem I (with P700 pre-oxidized to P700+). For these purposes, we performed experiments using Photosystem I core samples isolated from Chlamydomonas reinhardtii wild type, and two mutants in which the methionine axial ligand to primary electron acceptor, A0, has been change to either histidine or serine. The temporal evolution of fluorescence spectra was recorded for each preparation under conditions where the “primary electron donor,” P700, was either neutral or chemically pre-oxidized to P700+. For all the preparations under study, and under neutral and oxidizing conditions, we observed multiexponential fluorescence decay with the major phases of ∼7 ps and ∼25 ps. The relative amplitudes and, to a minor extent the lifetimes, of these two phases were modulated by the redox state of P700 and by the mutations near A0: both pre-oxidation of P700 and mutations caused slight deceleration of the excited state decay. These results are consistent with a model in which P700 is not the primary electron donor, but rather a secondary electron donor, with the primary charge separation event occurring between the accessory chlorophyll, A, and A0. We assign the faster phase to the equilibration process between the excited state of the antenna/reaction center ensemble and the primary radical pair, and the slower phase to the secondary electron transfer reaction. The pre-oxidation of P700 shifts the equilibrium between the excited state and the primary radical pair towards the excited state. This shift is proposed to be induced by the presence of the positive charge on P700+. The same charge is proposed to be responsible for the fast A+A0−→AA0 charge recombination to the ground state and, in consequence, excitation quenching in closed reaction centers. Mutations of the A0 axial ligand shift the equilibrium in the same direction as pre-oxidation of P700 due to the up-shift of the free energy level of the state A+A0−. |
2009 |
Gibasiewicz, Krzysztof; Pajzderska, Maria; Karolczak, J; Dobek, Andrzej Physical Chemistry Chemical Physics, 11 (44), pp. 10484, 2009, ISSN: 1463-9076. @article{Gibasiewicz2009, title = {Excitation and electron transfer in reaction centers from Rhodobacter sphaeroides probed and analyzed globally in the 1-nanosecond temporal window from 330 to 700 nm}, author = {Krzysztof Gibasiewicz and Maria Pajzderska and J Karolczak and Andrzej Dobek}, url = {http://xlink.rsc.org/?DOI=b912431d}, doi = {10.1039/b912431d}, issn = {1463-9076}, year = {2009}, date = {2009-11-01}, journal = {Physical Chemistry Chemical Physics}, volume = {11}, number = {44}, pages = {10484}, publisher = {The Royal Society of Chemistry}, abstract = {Global analysis of a set of room temperature transient absorption spectra of Rhodobacter sphaeroidesreaction centers, recorded in wide temporal and spectral ranges and triggered by femtosecond excitation of accessory bacteriochlorophylls at 800 nm, is presented. The data give a comprehensive review of all spectral dynamics features in the visible and near UV, from 330 to 700 nm, related to the primary events in the Rb. sphaeroidesreaction center: excitation energy transfer from the accessory bacteriochlorophylls (B) to the primary donor (P), primary charge separation between the primary donor and primary acceptor (bacteriopheophytin, H), and electron transfer from the primary to the secondary electron acceptor (ubiquinone). In particular, engagement of the accessory bacteriochlorophyll in primary charge separation is shown as an intermediate electron acceptor, and the initial free energy gap of ∼40 meV, between the states P+BA− and P+HA− is estimated. The size of this gap is shown to be constant for the whole 230 ps lifetime of the P+HA− state. The ultrafast spectral dynamics features recorded in the visible range are presented against a background of results from similar studies performed for the last two decades.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Global analysis of a set of room temperature transient absorption spectra of Rhodobacter sphaeroidesreaction centers, recorded in wide temporal and spectral ranges and triggered by femtosecond excitation of accessory bacteriochlorophylls at 800 nm, is presented. The data give a comprehensive review of all spectral dynamics features in the visible and near UV, from 330 to 700 nm, related to the primary events in the Rb. sphaeroidesreaction center: excitation energy transfer from the accessory bacteriochlorophylls (B) to the primary donor (P), primary charge separation between the primary donor and primary acceptor (bacteriopheophytin, H), and electron transfer from the primary to the secondary electron acceptor (ubiquinone). In particular, engagement of the accessory bacteriochlorophyll in primary charge separation is shown as an intermediate electron acceptor, and the initial free energy gap of ∼40 meV, between the states P+BA− and P+HA− is estimated. The size of this gap is shown to be constant for the whole 230 ps lifetime of the P+HA− state. The ultrafast spectral dynamics features recorded in the visible range are presented against a background of results from similar studies performed for the last two decades. |
Kozak, Maciej; Wlodarczyk, Agnieszka; Dobek, Andrzej Synchrotron radiation small angle scattering studies of d(TTAGGG)4 oligomer in solution Radiation Physics and Chemistry, 78 (10), pp. S134–S136, 2009, ISSN: 0969806X. @article{Kozak2009, title = {Synchrotron radiation small angle scattering studies of d(TTAGGG)4 oligomer in solution}, author = {Maciej Kozak and Agnieszka Wlodarczyk and Andrzej Dobek}, url = {https://www.sciencedirect.com/science/article/pii/S0969806X09002333 http://linkinghub.elsevier.com/retrieve/pii/S0969806X09002333}, doi = {10.1016/j.radphyschem.2009.04.028}, issn = {0969806X}, year = {2009}, date = {2009-10-01}, journal = {Radiation Physics and Chemistry}, volume = {78}, number = {10}, pages = {S134--S136}, publisher = {Pergamon}, abstract = {Telomeric DNA sequences play a crucial role in maintaining chromosome stability and integrity. In human chromosomes telomeres are composed of tandem (TTAGGG)n repeats. The structural parameters and low-resolution structure of a synthetic d(TTAGGG)4 oligomer in solution has been studied in the absence and in the presence of potassium cations, with the use of the small angle scattering of synchrotron radiation. The radii of gyration RG, calculated for d(TTAGGG)4 oligomer (in 10mM Tris/HCl pH 7.3) was 1.42nm, while RG, (in 10mM Tris/HCl pH 7.3; 0.1mM KCl) was 1.32nm. The pair distance distribution function, P(r), yielded a maximum dimension of 4.55and 4.35nm for solutions in the absence and the presence of potassium cations. On the basis of SAXS data, the low-resolution structure in solution has been reconstructed using ab inito methods.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Telomeric DNA sequences play a crucial role in maintaining chromosome stability and integrity. In human chromosomes telomeres are composed of tandem (TTAGGG)n repeats. The structural parameters and low-resolution structure of a synthetic d(TTAGGG)4 oligomer in solution has been studied in the absence and in the presence of potassium cations, with the use of the small angle scattering of synchrotron radiation. The radii of gyration RG, calculated for d(TTAGGG)4 oligomer (in 10mM Tris/HCl pH 7.3) was 1.42nm, while RG, (in 10mM Tris/HCl pH 7.3; 0.1mM KCl) was 1.32nm. The pair distance distribution function, P(r), yielded a maximum dimension of 4.55and 4.35nm for solutions in the absence and the presence of potassium cations. On the basis of SAXS data, the low-resolution structure in solution has been reconstructed using ab inito methods. |
Holyst, Robert; Bielejewska, Anna; Szymański, Jędrzej; Wilk, Agnieszka; Patkowski, Adam; Gapiński, Jacek; żywociński, Andrzej; Kalwarczyk, Tomasz; Kalwarczyk, Ewelina; Tabaka, Marcin; Ziębacz, Natalia; Wieczorek, Stefan A Physical Chemistry Chemical Physics, 11 (40), pp. 9025, 2009, ISSN: 1463-9076. @article{Holyst2009, title = {Scaling form of viscosity at all length-scales in poly(ethylene glycol) solutions studied by fluorescence correlation spectroscopy and capillary electrophoresis}, author = {Robert Holyst and Anna Bielejewska and Jędrzej Szymański and Agnieszka Wilk and Adam Patkowski and Jacek Gapiński and Andrzej żywociński and Tomasz Kalwarczyk and Ewelina Kalwarczyk and Marcin Tabaka and Natalia Ziębacz and Stefan A Wieczorek}, url = {http://xlink.rsc.org/?DOI=b908386c}, doi = {10.1039/b908386c}, issn = {1463-9076}, year = {2009}, date = {2009-10-01}, journal = {Physical Chemistry Chemical Physics}, volume = {11}, number = {40}, pages = {9025}, publisher = {The Royal Society of Chemistry}, abstract = {We measured the viscosity of poly(ethylene glycol) (PEG 6000, 12 000, 20 000) in water using capillary electrophoresis and fluorescence correlation spectroscopy with nanoscopic probes of different diameters (from 1.7 to 114 nm). For a probe of diameter smaller than the radius of gyration of PEG (e.g.rhodamine B or lyzozyme) the measured nanoviscosity was orders of magnitude smaller than the macroviscosity. For sizes equal to (or larger than) the polymer radius of gyration, macroscopic value of viscosity was measured. A mathematical relation for macro and nanoviscosity was found as a function of PEG radius of gyration, Rg, correlation length in semi-dilute solution, $xi$, and probe size, R. For R textless Rg, the nanoviscosity (normalized by water viscosity) is given by exp(b(R/$xi$)a), and for R textgreater Rg, both nano and macroviscosity follow the same curve, exp(b(R/$xi$)a), where a and b are two constants close to unity. This mathematical relation was shown to equally well describe rhodamine (of size 1.7 nm) in PEG 20 000 and the macroviscosity of PEG 8 000 000, whose radius of gyration exceeds 200 nm. Additionally, for the smallest probes (rhodamine B and lysozyme) we have verified, using capillary electrophoresis and fluorescence correlation spectroscopy, that the Stokes–Einstein (SE) relation holds, providing that we use a size-dependent viscosity in the formula. The SE relation is correct even in PEG solutions of very high viscosity (three orders of magnitude larger than that of water).}, keywords = {}, pubstate = {published}, tppubtype = {article} } We measured the viscosity of poly(ethylene glycol) (PEG 6000, 12 000, 20 000) in water using capillary electrophoresis and fluorescence correlation spectroscopy with nanoscopic probes of different diameters (from 1.7 to 114 nm). For a probe of diameter smaller than the radius of gyration of PEG (e.g.rhodamine B or lyzozyme) the measured nanoviscosity was orders of magnitude smaller than the macroviscosity. For sizes equal to (or larger than) the polymer radius of gyration, macroscopic value of viscosity was measured. A mathematical relation for macro and nanoviscosity was found as a function of PEG radius of gyration, Rg, correlation length in semi-dilute solution, $xi$, and probe size, R. For R textless Rg, the nanoviscosity (normalized by water viscosity) is given by exp(b(R/$xi$)a), and for R textgreater Rg, both nano and macroviscosity follow the same curve, exp(b(R/$xi$)a), where a and b are two constants close to unity. This mathematical relation was shown to equally well describe rhodamine (of size 1.7 nm) in PEG 20 000 and the macroviscosity of PEG 8 000 000, whose radius of gyration exceeds 200 nm. Additionally, for the smallest probes (rhodamine B and lysozyme) we have verified, using capillary electrophoresis and fluorescence correlation spectroscopy, that the Stokes–Einstein (SE) relation holds, providing that we use a size-dependent viscosity in the formula. The SE relation is correct even in PEG solutions of very high viscosity (three orders of magnitude larger than that of water). |
Holmqvist, P; Ratajczyk, M; Meier, G; Wensink, H H; Lettinga, M P Supersaturated dispersions of rodlike viruses with added attraction Physical Review E, 80 (3), pp. 031402, 2009, ISSN: 1539-3755. @article{Holmqvist2009, title = {Supersaturated dispersions of rodlike viruses with added attraction}, author = {P Holmqvist and M Ratajczyk and G Meier and H H Wensink and M P Lettinga}, url = {http://www.ncbi.nlm.nih.gov/pubmed/19905111 https://link.aps.org/doi/10.1103/PhysRevE.80.031402}, doi = {10.1103/PhysRevE.80.031402}, issn = {1539-3755}, year = {2009}, date = {2009-09-01}, journal = {Physical Review E}, volume = {80}, number = {3}, pages = {031402}, abstract = {The kinetics of isotropic-nematic (I-N) and nematic-isotropic (N-I) phase transitions in dispersions of rodlike fd viruses are studied. Concentration quenches were applied using pressure jumps in combination with polarization microscopy, birefringence, and turbidity measurements. The full biphasic region could be accessed, resulting in the construction of an experimental analog of the bifurcation diagram. The N-I spinodal points for dispersions of rods with varying concentrations of depletion agent (dextran) were obtained from orientation quenches using cessation of shear flow in combination with small-angle light scattering. We found that the location of the N-I spinodal point is independent of the attraction, which was confirmed by theory. Surprisingly, the experiments showed that also the absolute induction time, the critical nucleus, and the growth rate are insensitive of the attraction if the concentration is scaled to the distance to the phase boundaries.}, keywords = {}, pubstate = {published}, tppubtype = {article} } The kinetics of isotropic-nematic (I-N) and nematic-isotropic (N-I) phase transitions in dispersions of rodlike fd viruses are studied. Concentration quenches were applied using pressure jumps in combination with polarization microscopy, birefringence, and turbidity measurements. The full biphasic region could be accessed, resulting in the construction of an experimental analog of the bifurcation diagram. The N-I spinodal points for dispersions of rods with varying concentrations of depletion agent (dextran) were obtained from orientation quenches using cessation of shear flow in combination with small-angle light scattering. We found that the location of the N-I spinodal point is independent of the attraction, which was confirmed by theory. Surprisingly, the experiments showed that also the absolute induction time, the critical nucleus, and the growth rate are insensitive of the attraction if the concentration is scaled to the distance to the phase boundaries. |
Gibasiewicz, Krzysztof; Pajzderska, Maria; Ziółek, M; Karolczak, J; Dobek, Andrzej The Journal of Physical Chemistry B, 113 (31), pp. 11023–11031, 2009, ISSN: 1520-6106. @article{Gibasiewicz2009b, title = {Internal Electrostatic Control of the Primary Charge Separation and Recombination in Reaction Centers from Rhodobacter sphaeroides Revealed by Femtosecond Transient Absorption}, author = {Krzysztof Gibasiewicz and Maria Pajzderska and M Ziółek and J Karolczak and Andrzej Dobek}, url = {http://pubs.acs.org/doi/abs/10.1021/jp811234q}, doi = {10.1021/jp811234q}, issn = {1520-6106}, year = {2009}, date = {2009-08-01}, journal = {The Journal of Physical Chemistry B}, volume = {113}, number = {31}, pages = {11023--11031}, publisher = {American Chemical Society}, abstract = {We report the observation of two conformational states of closed RCs from Rhodobacter sphaeroides characterized by different P+HA− → PHA charge recombination lifetimes, one of which is of subnanosecond value (700 ± 200 ps). These states are also characterized by different primary charge separation lifetimes. It is proposed that the distinct conformations are related to two protonation states either of reduced secondary electron acceptor, QA−, or of a titratable amino acid residue localized near QA. The reaction centers in the protonated state are characterized by faster charge separation and slower charge recombination when compared to those in the unprotonated state. Both effects are explained in terms of the model assuming modulation of the free energy level of the state P+HA− by the charges on or near QA and decay of the P+HA− state via the thermally activated P+BA− state.}, keywords = {}, pubstate = {published}, tppubtype = {article} } We report the observation of two conformational states of closed RCs from Rhodobacter sphaeroides characterized by different P+HA− → PHA charge recombination lifetimes, one of which is of subnanosecond value (700 ± 200 ps). These states are also characterized by different primary charge separation lifetimes. It is proposed that the distinct conformations are related to two protonation states either of reduced secondary electron acceptor, QA−, or of a titratable amino acid residue localized near QA. The reaction centers in the protonated state are characterized by faster charge separation and slower charge recombination when compared to those in the unprotonated state. Both effects are explained in terms of the model assuming modulation of the free energy level of the state P+HA− by the charges on or near QA and decay of the P+HA− state via the thermally activated P+BA− state. |
Gibasiewicz, Krzysztof; Rutkowski, M; van Grondelle, R Fluorescence hole-burning and site-selective studies of LHCII Photosynthetica, 47 (2), pp. 232–240, 2009, ISSN: 0300-3604. @article{Gibasiewicz2009a, title = {Fluorescence hole-burning and site-selective studies of LHCII}, author = {Krzysztof Gibasiewicz and M Rutkowski and R van Grondelle}, url = {http://link.springer.com/10.1007/s11099-009-0037-0}, doi = {10.1007/s11099-009-0037-0}, issn = {0300-3604}, year = {2009}, date = {2009-06-01}, journal = {Photosynthetica}, volume = {47}, number = {2}, pages = {232--240}, publisher = {Springer Netherlands}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Giera, Wojciech; Gibasiewicz, Krzysztof; Ramesh, V M; Lin, Su; Webber, Andrew Physical Chemistry Chemical Physics, 11 (25), pp. 5186, 2009, ISSN: 1463-9076. @article{Giera2009, title = {Electron transfer from A−0 to A1 in Photosystem I from Chlamydomonas reinhardtii occurs in both the A and B branch with 25–30-ps lifetime}, author = {Wojciech Giera and Krzysztof Gibasiewicz and V M Ramesh and Su Lin and Andrew Webber}, url = {http://xlink.rsc.org/?DOI=b822938d}, doi = {10.1039/b822938d}, issn = {1463-9076}, year = {2009}, date = {2009-06-01}, journal = {Physical Chemistry Chemical Physics}, volume = {11}, number = {25}, pages = {5186}, publisher = {The Royal Society of Chemistry}, abstract = {We have recorded transient absorption kinetics at 390 nm with picosecond resolution in order to observe electron transfer from the reduced primary acceptor, A−0, to the secondary acceptor, A1, in wild type and mutated Photosystem I from Chlamydomonas reinhardtii. In the mutants, the methionine axial ligand to the primary electron acceptor in either the A- or B-branch of electron transfer cofactors, was replaced with histidine. Both of the mutations reduced the formation of a positive signal at 390 nm, characteristic of A−1 to a level approximately half of that observed in wild type Photosystem I. It is concluded that in the mutated branch of Photosystem I, electron transfer from A−0 to A1 does not occur. The absorption kinetics resulting from subtraction of either of the mutants' traces from that of wild type is interpreted to reflect the kinetics of A- or B-side electron transfer from A−0 to A1 in the the wild type Photosystem I. Each of these traces could be fitted with a monoexpoenential decay characterized by the same amplitude and 25–30-ps lifetime. The almost identical effect of both mutations on A−1 formation confirm a similar engagement of both the A- ad B-branches in electron transfer to A1 in Photosystem I from C. reinhardtii. This observation is in contrast to the unidirectional electron transfer concluded from the studies on similar mutants of cyanobacterial Photosystem I.1 Thus, this contribution provides further evidence for functional differences between these two model Photosystems.}, keywords = {}, pubstate = {published}, tppubtype = {article} } We have recorded transient absorption kinetics at 390 nm with picosecond resolution in order to observe electron transfer from the reduced primary acceptor, A−0, to the secondary acceptor, A1, in wild type and mutated Photosystem I from Chlamydomonas reinhardtii. In the mutants, the methionine axial ligand to the primary electron acceptor in either the A- or B-branch of electron transfer cofactors, was replaced with histidine. Both of the mutations reduced the formation of a positive signal at 390 nm, characteristic of A−1 to a level approximately half of that observed in wild type Photosystem I. It is concluded that in the mutated branch of Photosystem I, electron transfer from A−0 to A1 does not occur. The absorption kinetics resulting from subtraction of either of the mutants' traces from that of wild type is interpreted to reflect the kinetics of A- or B-side electron transfer from A−0 to A1 in the the wild type Photosystem I. Each of these traces could be fitted with a monoexpoenential decay characterized by the same amplitude and 25–30-ps lifetime. The almost identical effect of both mutations on A−1 formation confirm a similar engagement of both the A- ad B-branches in electron transfer to A1 in Photosystem I from C. reinhardtii. This observation is in contrast to the unidirectional electron transfer concluded from the studies on similar mutants of cyanobacterial Photosystem I.1 Thus, this contribution provides further evidence for functional differences between these two model Photosystems. |
Banachowicz, Ewa; Kozak, Maciej; Patkowski, Adam; Meier, Gerhard; Kohlbrecher, Joachim High-pressure small-angle neutron scattering studies of glucose isomerase conformation in solution Journal of Applied Crystallography, 42 (3), pp. 461–468, 2009, ISSN: 0021-8898. @article{Banachowicz2009, title = {High-pressure small-angle neutron scattering studies of glucose isomerase conformation in solution}, author = {Ewa Banachowicz and Maciej Kozak and Adam Patkowski and Gerhard Meier and Joachim Kohlbrecher}, url = {http://scripts.iucr.org/cgi-bin/paper?S0021889809007456}, doi = {10.1107/S0021889809007456}, issn = {0021-8898}, year = {2009}, date = {2009-06-01}, journal = {Journal of Applied Crystallography}, volume = {42}, number = {3}, pages = {461--468}, publisher = {International Union of Crystallography}, abstract = {Small-angle neutron scattering (SANS) of solutions of glucose/xylose isomerase from Streptomyces rubiginosus was measured as a function of pressure. It is shown that the structure of the enzyme in solution as seen by SANS is practically the same as that in the crystal and does not change with pressure up to 150 MPa. This reflects the unusually high structural stability of this material, which makes it extremely interesting to use as a secondary standard for pressure-dependent SANS experiments. This lack of pressure dependence of the SANS data also indicates that any possible change in hydration of the protein induced by pressure is not visible in the SANS curves. An appropriate correction procedure must be used for the SANS data in order to account for the distortion of the intensity curve due to hard-sphere and electrostatic interactions. After this correction, the isomerase can be readily used as a secondary standard for SANS measurements.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Small-angle neutron scattering (SANS) of solutions of glucose/xylose isomerase from Streptomyces rubiginosus was measured as a function of pressure. It is shown that the structure of the enzyme in solution as seen by SANS is practically the same as that in the crystal and does not change with pressure up to 150 MPa. This reflects the unusually high structural stability of this material, which makes it extremely interesting to use as a secondary standard for pressure-dependent SANS experiments. This lack of pressure dependence of the SANS data also indicates that any possible change in hydration of the protein induced by pressure is not visible in the SANS curves. An appropriate correction procedure must be used for the SANS data in order to account for the distortion of the intensity curve due to hard-sphere and electrostatic interactions. After this correction, the isomerase can be readily used as a secondary standard for SANS measurements. |
Vavrin, R; Kohlbrecher, J; Wilk, Agnieszka; Ratajczyk, M; Lettinga, M P; Buitenhuis, J; Meier, G The Journal of Chemical Physics, 130 (15), pp. 154903, 2009, ISSN: 0021-9606. @article{Vavrin2009, title = {Structure and phase diagram of an adhesive colloidal dispersion under high pressure: A small angle neutron scattering, diffusing wave spectroscopy, and light scattering study}, author = {R Vavrin and J Kohlbrecher and Agnieszka Wilk and M Ratajczyk and M P Lettinga and J Buitenhuis and G Meier}, url = {http://www.ncbi.nlm.nih.gov/pubmed/19388768 http://aip.scitation.org/doi/10.1063/1.3103245}, doi = {10.1063/1.3103245}, issn = {0021-9606}, year = {2009}, date = {2009-04-01}, journal = {The Journal of Chemical Physics}, volume = {130}, number = {15}, pages = {154903}, abstract = {We have applied small angle neutron scattering (SANS), diffusing wave spectroscopy (DWS), and dynamic light scattering (DLS) to investigate the phase diagram of a sterically stabilized colloidal system consisting of octadecyl grafted silica particles dispersed in toluene. This system is known to exhibit gas-liquid phase separation and percolation, depending on temperature T, pressure P, and concentration phi. We have determined by DLS the pressure dependence of the coexistence temperature and the spinodal temperature to be dP/dT=77 bar/K. The gel line or percolation limit was measured by DWS under high pressure using the condition that the system became nonergodic when crossing it and we determined the coexistence line at higher volume fractions from the DWS limit of turbid samples. From SANS measurements we determined the stickiness parameter tau(B)(P,T,phi) of the Baxter model, characterizing a polydisperse adhesive hard sphere, using a global fit routine on all curves in the homogenous regime at various temperatures, pressures, and concentrations. The phase coexistence and percolation line as predicted from tau(B)(P,T,phi) correspond with the determinations by DWS and were used to construct an experimental phase diagram for a polydisperse sticky hard sphere model system. A comparison with theory shows good agreement especially concerning the predictions for the percolation threshold. From the analysis of the forward scattering we find a critical scaling law for the susceptibility corresponding to mean field behavior. This finding is also supported by the critical scaling properties of the collective diffusion.}, keywords = {}, pubstate = {published}, tppubtype = {article} } We have applied small angle neutron scattering (SANS), diffusing wave spectroscopy (DWS), and dynamic light scattering (DLS) to investigate the phase diagram of a sterically stabilized colloidal system consisting of octadecyl grafted silica particles dispersed in toluene. This system is known to exhibit gas-liquid phase separation and percolation, depending on temperature T, pressure P, and concentration phi. We have determined by DLS the pressure dependence of the coexistence temperature and the spinodal temperature to be dP/dT=77 bar/K. The gel line or percolation limit was measured by DWS under high pressure using the condition that the system became nonergodic when crossing it and we determined the coexistence line at higher volume fractions from the DWS limit of turbid samples. From SANS measurements we determined the stickiness parameter tau(B)(P,T,phi) of the Baxter model, characterizing a polydisperse adhesive hard sphere, using a global fit routine on all curves in the homogenous regime at various temperatures, pressures, and concentrations. The phase coexistence and percolation line as predicted from tau(B)(P,T,phi) correspond with the determinations by DWS and were used to construct an experimental phase diagram for a polydisperse sticky hard sphere model system. A comparison with theory shows good agreement especially concerning the predictions for the percolation threshold. From the analysis of the forward scattering we find a critical scaling law for the susceptibility corresponding to mean field behavior. This finding is also supported by the critical scaling properties of the collective diffusion. |
Gapiński, Jacek; Patkowski, Adam; Banchio, A J; Buitenhuis, J; Holmqvist, P; Lettinga, M P; Meier, G; Naegele, G The Journal of Chemical Physics, 130 (8), pp. 084503, 2009, ISSN: 0021-9606. @article{Gapinski2009, title = {Structure and short-time dynamics in suspensions of charged silica spheres in the entire fluid regime}, author = {Jacek Gapiński and Adam Patkowski and A J Banchio and J Buitenhuis and P Holmqvist and M P Lettinga and G Meier and G Naegele}, url = {http://aip.scitation.org/doi/10.1063/1.3078408}, doi = {10.1063/1.3078408}, issn = {0021-9606}, year = {2009}, date = {2009-02-01}, journal = {The Journal of Chemical Physics}, volume = {130}, number = {8}, pages = {084503}, publisher = {American Institute of Physics}, abstract = {We present an experimental study of short-time diffusion properties in fluidlike suspensions of monodisperse charge-stabilized silica spheres suspended in dimethylformamide. The static structure factor S(q), the short-time diffusion function D(q), and the hydrodynamic function H(q) have been probed by combining x-ray photon correlation spectroscopy experiments with static small-angle x-ray scattering. Our experiments cover the full liquid-state part of the phase diagram, including de-ionized systems right at the liquid-solid phase boundary. We show that the dynamic data can be consistently described by the renormalized density fluctuation expansion theory of Beenakker and Mazur over a wide range of concentrations and ionic strengths. In accordance with this theory and Stokesian dynamics computer simulations, the measured short-time properties cross over monotonically, with increasing salt content, from the bounding values of salt-free suspensions to those of neutral hard spheres. Moreover, we discuss an u...}, keywords = {}, pubstate = {published}, tppubtype = {article} } We present an experimental study of short-time diffusion properties in fluidlike suspensions of monodisperse charge-stabilized silica spheres suspended in dimethylformamide. The static structure factor S(q), the short-time diffusion function D(q), and the hydrodynamic function H(q) have been probed by combining x-ray photon correlation spectroscopy experiments with static small-angle x-ray scattering. Our experiments cover the full liquid-state part of the phase diagram, including de-ionized systems right at the liquid-solid phase boundary. We show that the dynamic data can be consistently described by the renormalized density fluctuation expansion theory of Beenakker and Mazur over a wide range of concentrations and ionic strengths. In accordance with this theory and Stokesian dynamics computer simulations, the measured short-time properties cross over monotonically, with increasing salt content, from the bounding values of salt-free suspensions to those of neutral hard spheres. Moreover, we discuss an u... |
Dobek, Andrzej Magneto-optics of ferritin Dubnickowa, A; Dubnicka, S; Granja, C; Leroy, C; Stekl, I (Ed.): Nuclear Physics Methods and Accelerators in Biology and Medicine, pp. 143–146, AIP Conference Proceedings, New York, 2009. @inproceedings{Dobek2009, title = {Magneto-optics of ferritin}, author = {Andrzej Dobek}, editor = {A Dubnickowa and S Dubnicka and C Granja and C Leroy and I Stekl}, year = {2009}, date = {2009-01-01}, booktitle = {Nuclear Physics Methods and Accelerators in Biology and Medicine}, pages = {143--146}, publisher = {AIP Conference Proceedings}, address = {New York}, keywords = {}, pubstate = {published}, tppubtype = {inproceedings} } |
Pankowska, M; Dobek, Andrzej Linear and nonlinear magneto-optics of ferritin The Journal of Chemical Physics, 131 , pp. 01505-1-10, 2009. @article{Pankowska2009, title = {Linear and nonlinear magneto-optics of ferritin}, author = {M Pankowska and Andrzej Dobek}, doi = {10.1063/1.3159844}, year = {2009}, date = {2009-01-01}, journal = {The Journal of Chemical Physics}, volume = {131}, pages = {01505-1-10}, abstract = {Measurements of Rayleigh light scattering and Cotton–Mouton (CM) effect are carried out at room temperature for 100 mM NaCl solutions of apoferritin/ferritin loaded with 0, 90, 100, 500, 700, and 1500 Fe atoms/molecule. Because of the spherical shape, ferritin macromolecule should not manifest magnetic anisotropy; however, in solution it shows the induced magnetic birefringence (CM effect) and changes in intensity of the scattered light components. The newly obtained data support the previously reported conclusions indicating that the deformation of linear optical polarizability induced in the ferritin by a magnetic field and the orientation of the induced magnetic dipole moment by this field are the main sources of the magneto-optical phenomena observed. Nevertheless, it is also found that the orientation of the permanent magnetic dipole moment contributes to both effects. The magnetic field induced changes in the light scattering and the CM effect theoretically depend on the linear magneto-optical polarizability, χχ, on the nonlinear magneto-optical polarizability, ηη, and square of the permanent magnetic dipole moment value of the macromolecule, μ2μ2. On the basis of the theory describing both effects as well as the experimental data, the values of the anisotropy of linear magneto-optical polarizabilities components, the values of the linear optical polarizability and its anisotropy, nonlinear magneto-optical polarizability and its anisotropy, are estimated. Also the magnetic dipole moment of the ferritin macromolecule is found. Interestingly, not all iron atoms in the ferritin are indicated to be in the superparamagnetic state, some of them occur in the diamagnetic form.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Measurements of Rayleigh light scattering and Cotton–Mouton (CM) effect are carried out at room temperature for 100 mM NaCl solutions of apoferritin/ferritin loaded with 0, 90, 100, 500, 700, and 1500 Fe atoms/molecule. Because of the spherical shape, ferritin macromolecule should not manifest magnetic anisotropy; however, in solution it shows the induced magnetic birefringence (CM effect) and changes in intensity of the scattered light components. The newly obtained data support the previously reported conclusions indicating that the deformation of linear optical polarizability induced in the ferritin by a magnetic field and the orientation of the induced magnetic dipole moment by this field are the main sources of the magneto-optical phenomena observed. Nevertheless, it is also found that the orientation of the permanent magnetic dipole moment contributes to both effects. The magnetic field induced changes in the light scattering and the CM effect theoretically depend on the linear magneto-optical polarizability, χχ, on the nonlinear magneto-optical polarizability, ηη, and square of the permanent magnetic dipole moment value of the macromolecule, μ2μ2. On the basis of the theory describing both effects as well as the experimental data, the values of the anisotropy of linear magneto-optical polarizabilities components, the values of the linear optical polarizability and its anisotropy, nonlinear magneto-optical polarizability and its anisotropy, are estimated. Also the magnetic dipole moment of the ferritin macromolecule is found. Interestingly, not all iron atoms in the ferritin are indicated to be in the superparamagnetic state, some of them occur in the diamagnetic form. |
2008 |
Szymańska, A; Ślósarek, Genowefa; Hornowski, T; Kozak, M The SAXS and Rheological Studies of HEWL Amyloid Formation Acta Physica Polonica A, 114 (2), pp. 447–454, 2008, ISSN: 0587-4246. @article{Szymanska2008, title = {The SAXS and Rheological Studies of HEWL Amyloid Formation}, author = {A Szymańska and Genowefa Ślósarek and T Hornowski and M Kozak}, url = {http://przyrbwn.icm.edu.pl/APP/PDF/114/a114z216.pdf}, doi = {10.12693/APhysPolA.114.447}, issn = {0587-4246}, year = {2008}, date = {2008-08-01}, journal = {Acta Physica Polonica A}, volume = {114}, number = {2}, pages = {447--454}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Patkowski, Adam; Gapiński, Jacek; Fluerasu, A; Holmqvist, P; Meier, G; Lettinga, M P; Naegele, G Structure and Dynamics of Colloidal Suspensions Studied by Means of XPCS Acta Physica Polonica A, 114 (2), pp. 339–350, 2008, ISSN: 0587-4246. @article{Patkowski2008, title = {Structure and Dynamics of Colloidal Suspensions Studied by Means of XPCS}, author = {Adam Patkowski and Jacek Gapiński and A Fluerasu and P Holmqvist and G Meier and M P Lettinga and G Naegele}, url = {http://przyrbwn.icm.edu.pl/APP/PDF/114/a114z204.pdf}, doi = {10.12693/APhysPolA.114.339}, issn = {0587-4246}, year = {2008}, date = {2008-08-01}, journal = {Acta Physica Polonica A}, volume = {114}, number = {2}, pages = {339--350}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Meier, G; Vavrin, R; Kohlbrecher, J; Buitenhuis, J; Lettinga, M P; Ratajczyk, M Measurement Science and Technology, 19 (3), pp. 034017, 2008, ISSN: 0957-0233. @article{Meier2008, title = {SANS and dynamic light scattering to investigate the viscosity of toluene under high pressure up to 1800 bar}, author = {G Meier and R Vavrin and J Kohlbrecher and J Buitenhuis and M P Lettinga and M Ratajczyk}, url = {http://stacks.iop.org/0957-0233/19/i=3/a=034017?key=crossref.bfbdaf02abacd76a9551bd29e8590a14}, doi = {10.1088/0957-0233/19/3/034017}, issn = {0957-0233}, year = {2008}, date = {2008-03-01}, journal = {Measurement Science and Technology}, volume = {19}, number = {3}, pages = {034017}, publisher = {IOP Publishing}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Gibasiewicz, Krzysztof; Pajzderska, Maria The Journal of Physical Chemistry B, 112 (6), pp. 1858–1865, 2008, ISSN: 1520-6106. @article{Gibasiewicz2008, title = {Primary Radical Pair P + H - Lifetime in Rhodobacter sphaeroides with Blocked Electron Transfer to Q A . Effect of o -Phenanthroline}, author = {Krzysztof Gibasiewicz and Maria Pajzderska}, url = {http://www.ncbi.nlm.nih.gov/pubmed/18215032 http://pubs.acs.org/doi/abs/10.1021/jp075184j}, doi = {10.1021/jp075184j}, issn = {1520-6106}, year = {2008}, date = {2008-02-01}, journal = {The Journal of Physical Chemistry B}, volume = {112}, number = {6}, pages = {1858--1865}, abstract = {Transient absorption spectroscopy with a time resolution of approximately 1 ns was applied to study the decay of the primary radical pair P+H- in Rhodobacter sphaeroides R-26 reaction centers with blocked electron transfer from H- to QA. The block in the electron transfer was realized in two ways: by either reducing or removing QA. We found very different kinetics of the P+H- decay in these two cases. Convolution of the multiexponential decay with the instrument response function allowed resolution of as many as three kinetic components of textless1-, 3-4-, and 9-12-ns lifetimes in chromatophores with QA reduced and in isolated reaction centers both with QA either reduced or removed (with or without o-phenanthroline) but with variable relative amplitudes. Removing QA or adding o-phenanthroline to isolated reaction centers increased the amplitude of the slowest decay phase relative to that of the fastest phase. On the basis of these observations, we propose that reaction centers adopt three conformational states characterized by different decay kinetics of P+H-. These conformational states appear to be controlled by the charges in the vicinity of the QA site as revealed by the effects of QA reduction and o-phenanthroline-mediated protonation of the sites close to QA.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Transient absorption spectroscopy with a time resolution of approximately 1 ns was applied to study the decay of the primary radical pair P+H- in Rhodobacter sphaeroides R-26 reaction centers with blocked electron transfer from H- to QA. The block in the electron transfer was realized in two ways: by either reducing or removing QA. We found very different kinetics of the P+H- decay in these two cases. Convolution of the multiexponential decay with the instrument response function allowed resolution of as many as three kinetic components of textless1-, 3-4-, and 9-12-ns lifetimes in chromatophores with QA reduced and in isolated reaction centers both with QA either reduced or removed (with or without o-phenanthroline) but with variable relative amplitudes. Removing QA or adding o-phenanthroline to isolated reaction centers increased the amplitude of the slowest decay phase relative to that of the fastest phase. On the basis of these observations, we propose that reaction centers adopt three conformational states characterized by different decay kinetics of P+H-. These conformational states appear to be controlled by the charges in the vicinity of the QA site as revealed by the effects of QA reduction and o-phenanthroline-mediated protonation of the sites close to QA. |
Kaczmarek, Michał S; Ładziński, Piotr; Woźniak, Zenon; Błaszczak, Zdzisław; Surma, Marian; Pochylski, Mikołaj Journal of Molecular Liquids, 138 (1), pp. 168 - 172, 2008, ISSN: 0167-7322. @article{Kaczmarek2008b, title = {Dynamics of transportation of glucose and urea water solutions through a porous polyethyleneterephthalate membrane studied by optical interference}, author = {Michał S Kaczmarek and Piotr Ładziński and Zenon Woźniak and Zdzisław Błaszczak and Marian Surma and Mikołaj Pochylski}, url = {http://www.sciencedirect.com/science/article/pii/S0167732207001948}, doi = {10.1016/j.molliq.2007.10.002}, issn = {0167-7322}, year = {2008}, date = {2008-01-01}, journal = {Journal of Molecular Liquids}, volume = {138}, number = {1}, pages = {168 - 172}, abstract = {The paper reports an interferometric method for characterisation of the dynamics of transportation of glucose and urea water solutions through a porous polyethyleneterephthalate membrane. The method is based on measurements of the changes in the light refraction indices of solutions partitioned by the membrane, using a Jamina interferometer. Synthetic membranes have been used among others in haemodialysis. In this process selective transportation of substances through a membrane permits elimination of toxic substances form the patient's blood employing the phenomena of osmosis, filtration, ultrafiltration and diffusion. The process efficiency depends on the parameters of the membrane pores (diameter, channel length, number of channels per diffusion active area). The process of haemodialysis can be optimised by changing the parameters influencing its course, whose effect is determined by measurements of diffusion rate of substances of the known molar weight, molecule size and permeability (glucose, urea) in laboratory conditions. In this paper, assuming the porous model of the membrane structure, the permeability P and mean number of pores m per a unit of the diffusion active area have been determined in order to establish the parameters at which the course of haemodialysis will be the most effective.}, keywords = {}, pubstate = {published}, tppubtype = {article} } The paper reports an interferometric method for characterisation of the dynamics of transportation of glucose and urea water solutions through a porous polyethyleneterephthalate membrane. The method is based on measurements of the changes in the light refraction indices of solutions partitioned by the membrane, using a Jamina interferometer. Synthetic membranes have been used among others in haemodialysis. In this process selective transportation of substances through a membrane permits elimination of toxic substances form the patient's blood employing the phenomena of osmosis, filtration, ultrafiltration and diffusion. The process efficiency depends on the parameters of the membrane pores (diameter, channel length, number of channels per diffusion active area). The process of haemodialysis can be optimised by changing the parameters influencing its course, whose effect is determined by measurements of diffusion rate of substances of the known molar weight, molecule size and permeability (glucose, urea) in laboratory conditions. In this paper, assuming the porous model of the membrane structure, the permeability P and mean number of pores m per a unit of the diffusion active area have been determined in order to establish the parameters at which the course of haemodialysis will be the most effective. |
Kasprzak, W; Nadolny, Z; Kaczmarek, M S; Woźniak, Z; Pochylski, Mikołaj Kerr effect in liquids with various electro-optic properties Przegląd Elektrotechniczny, 84 (10), pp. 166-169, 2008. @article{Kasprzak2008, title = {Kerr effect in liquids with various electro-optic properties}, author = {W Kasprzak and Z Nadolny and M.S Kaczmarek and Z. Woźniak and Mikołaj Pochylski}, year = {2008}, date = {2008-01-01}, journal = {Przegląd Elektrotechniczny}, volume = {84}, number = {10}, pages = {166-169}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Ślósarek, Genowefa Odkrycie struktury komórkowej tkanki nerwowej Kosmos. Problemy Nauk Biologicznych, 57 (1-2), pp. 103–107, 2008. @article{Slosarek2008, title = {Odkrycie struktury komórkowej tkanki nerwowej}, author = {Genowefa Ślósarek}, year = {2008}, date = {2008-01-01}, journal = {Kosmos. Problemy Nauk Biologicznych}, volume = {57}, number = {1-2}, pages = {103--107}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Kriegs, H; Meier, G; Gapiński, Jacek; Patkowski, Adam The Journal of Chemical Physics, 128 (1), pp. 014507, 2008, ISSN: 0021-9606. @article{Kriegs2008, title = {The effect of intramolecular relaxations on the damping of longitudinal and transverse phonons in polysiloxanes studied by Brillouin spectroscopy}, author = {H Kriegs and G Meier and Jacek Gapiński and Adam Patkowski}, url = {http://www.ncbi.nlm.nih.gov/pubmed/18190204 http://aip.scitation.org/doi/10.1063/1.2816136}, doi = {10.1063/1.2816136}, issn = {0021-9606}, year = {2008}, date = {2008-01-01}, journal = {The Journal of Chemical Physics}, volume = {128}, number = {1}, pages = {014507}, abstract = {The effect of intramolecular relaxations on the damping of longitudinal and transverse phonons was studied in poly(methylphenylsiloxane) (PMPS) and poly(ethylmethylsiloxane) (PEMS) polymers by means of Brillouin spectroscopy. It is shown that studies of the polarized and depolarized Brillouin spectra as functions of temperature and pressure allow for the separation of the contributions of the internal and structural relaxations to the damping of longitudinal and transverse phonons, respectively. In polymers with intramolecular relaxations these processes contribute not only to the damping of longitudinal phonons, according to theoretical predictions, but also transverse phonons, in contradiction to the theory.}, keywords = {}, pubstate = {published}, tppubtype = {article} } The effect of intramolecular relaxations on the damping of longitudinal and transverse phonons was studied in poly(methylphenylsiloxane) (PMPS) and poly(ethylmethylsiloxane) (PEMS) polymers by means of Brillouin spectroscopy. It is shown that studies of the polarized and depolarized Brillouin spectra as functions of temperature and pressure allow for the separation of the contributions of the internal and structural relaxations to the damping of longitudinal and transverse phonons, respectively. In polymers with intramolecular relaxations these processes contribute not only to the damping of longitudinal phonons, according to theoretical predictions, but also transverse phonons, in contradiction to the theory. |
Szymański, Jędrzej; Wilk, Agnieszka; Hołyst, Robert; Roberts, Geraint; Sinclair, Kirsty; Kowalski, Adam Micro- and macro-shear viscosity in dispersed lamellar phases Journal of Non-Newtonian Fluid Mechanics, 148 (1-3), pp. 134–140, 2008, ISSN: 03770257. @article{Szymanski2008, title = {Micro- and macro-shear viscosity in dispersed lamellar phases}, author = {Jędrzej Szymański and Agnieszka Wilk and Robert Hołyst and Geraint Roberts and Kirsty Sinclair and Adam Kowalski}, url = {https://www.sciencedirect.com/science/article/pii/S0377025707001024 http://linkinghub.elsevier.com/retrieve/pii/S0377025707001024}, doi = {10.1016/j.jnnfm.2007.04.008}, issn = {03770257}, year = {2008}, date = {2008-01-01}, journal = {Journal of Non-Newtonian Fluid Mechanics}, volume = {148}, number = {1-3}, pages = {134--140}, publisher = {Elsevier}, abstract = {Surfactant phases, such as dispersed lamellar gels, are extremely useful in commercial products because they are very weight-effective at building viscosity. An enduring challenge is to determine the microstructural features responsible for the bulk rheology so that we can design products with improved performance. The samples described here have very different rheological profiles as exemplified by an order-of-magnitude difference in their zero-shear-rate viscosity, and infinite-shear-rate viscosities which differ by half an order of magnitude. As a first approximation we consider the dispersed lamellar system to be analogous to a high-internal-phase-volume emulsion which is described by the well-known Kreiger–Dougherty equation. This requires us to establish the value of a number of parameters of which the continuous phase viscosity is the one that defines the baseline viscosity. We measured this in situ by a micro-viscosity technique involving Fluorescence Correlation Spectroscopy using microscopic probes: viz. a fluorescent dye molecule (rhodamine) of size 0.85nm; a lyzozyme protein of 2nm size and a quantum dot of 12.5nm size. We show that the continuous phase has a viscosity about twice that of water. Moreover, this viscosity is the same for the all three probes indicating that the system is quite uniform at the microscopic level investigated. Interestingly, this micro-viscosity was practically the same for all the samples and thus could not be correlated with zero-shear-rate viscosity or other rheological characteristics. We conclude that the macro-viscosity arises from structures much larger than 25nm (twice the hydrodynamic diameter of the quantum dot). Our future intention is to use larger probes to establish the length-scale at which the microstructure begins to be apparent in the bulk rheology characteristics.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Surfactant phases, such as dispersed lamellar gels, are extremely useful in commercial products because they are very weight-effective at building viscosity. An enduring challenge is to determine the microstructural features responsible for the bulk rheology so that we can design products with improved performance. The samples described here have very different rheological profiles as exemplified by an order-of-magnitude difference in their zero-shear-rate viscosity, and infinite-shear-rate viscosities which differ by half an order of magnitude. As a first approximation we consider the dispersed lamellar system to be analogous to a high-internal-phase-volume emulsion which is described by the well-known Kreiger–Dougherty equation. This requires us to establish the value of a number of parameters of which the continuous phase viscosity is the one that defines the baseline viscosity. We measured this in situ by a micro-viscosity technique involving Fluorescence Correlation Spectroscopy using microscopic probes: viz. a fluorescent dye molecule (rhodamine) of size 0.85nm; a lyzozyme protein of 2nm size and a quantum dot of 12.5nm size. We show that the continuous phase has a viscosity about twice that of water. Moreover, this viscosity is the same for the all three probes indicating that the system is quite uniform at the microscopic level investigated. Interestingly, this micro-viscosity was practically the same for all the samples and thus could not be correlated with zero-shear-rate viscosity or other rheological characteristics. We conclude that the macro-viscosity arises from structures much larger than 25nm (twice the hydrodynamic diameter of the quantum dot). Our future intention is to use larger probes to establish the length-scale at which the microstructure begins to be apparent in the bulk rheology characteristics. |
Giera, Wojciech; Gibasiewicz, Krzysztof; Ramesh, V M; Ziółek, Marcin; Karolczak, Jerzy; Dobek, Andrzej; Webber, A N A0 → A1 Electron Transfer in Chlamydomonas reinhardtii PS I with Replaced A0 Axial Ligand Allen, J F; Gantt, E; Golbeck, J H; Osmond, B (Ed.): Photosynthesis. Energy from the Sun. 14th International Congress on Photosynthesis, pp. 65-68, Springer, 2008, ISBN: 978-1-4020-6709-9. @inproceedings{Giera2008, title = {A0 → A1 Electron Transfer in Chlamydomonas reinhardtii PS I with Replaced A0 Axial Ligand}, author = {Wojciech Giera and Krzysztof Gibasiewicz and V M Ramesh and Marcin Ziółek and Jerzy Karolczak and Andrzej Dobek and A N Webber}, editor = {J F Allen and E Gantt and J H Golbeck and B Osmond}, doi = {10.1007/978-1-4020-6709-9_15}, isbn = {978-1-4020-6709-9}, year = {2008}, date = {2008-01-01}, booktitle = {Photosynthesis. Energy from the Sun. 14th International Congress on Photosynthesis}, pages = {65-68}, publisher = {Springer}, abstract = {Replacement of methionine, the natural axial ligand to the primary electron acceptor (A0) in Photosystem I, with a series of different amino acids results in dramatic increase of the A0− lifetime from ̃20 ps in wild type to a few nanoseconds in the mutants in the case of Chlamydomonas reinhardtii (Ramesh et al. 2004, 2007). This effect is similar independently if the mutation affects A-side or B-side A0. This observation confirms an existence of two equivalent primary electron acceptors in both symmetric branches of Photosystem I in Chlamydomonas reinhardtii, which makes this photosystem unusual among other photosystems (from purple bacteria, PS II), which are essentially unidirectional. However, it is still not clear if the bidirectionality of electron transfer in Photosystem I is complete, i.e. if the electron from A0− reaches A1 in both branches or takes another route in the “non-active” branch. In order to solve this issue, in this contribution we attempted to compare kinetics of A0− reoxidation to the kinetics of A1− formation in the case of B-side A0 mutant with methionine replaced by serine.}, keywords = {}, pubstate = {published}, tppubtype = {inproceedings} } Replacement of methionine, the natural axial ligand to the primary electron acceptor (A0) in Photosystem I, with a series of different amino acids results in dramatic increase of the A0− lifetime from ̃20 ps in wild type to a few nanoseconds in the mutants in the case of Chlamydomonas reinhardtii (Ramesh et al. 2004, 2007). This effect is similar independently if the mutation affects A-side or B-side A0. This observation confirms an existence of two equivalent primary electron acceptors in both symmetric branches of Photosystem I in Chlamydomonas reinhardtii, which makes this photosystem unusual among other photosystems (from purple bacteria, PS II), which are essentially unidirectional. However, it is still not clear if the bidirectionality of electron transfer in Photosystem I is complete, i.e. if the electron from A0− reaches A1 in both branches or takes another route in the “non-active” branch. In order to solve this issue, in this contribution we attempted to compare kinetics of A0− reoxidation to the kinetics of A1− formation in the case of B-side A0 mutant with methionine replaced by serine. |
2007 |
żywociński, Andrzej; Korda, Anna; Gosk, Joanna; Wieczorek, Stefan A; Wilk, Agnieszka; Hołyst, Robert Kinetic Trapping of Large Amount of Long Polymers in Nanopores Journal of the American Chemical Society, 129 (44), pp. 13398–13399, 2007, ISSN: 0002-7863. @article{Zywocinski2007, title = {Kinetic Trapping of Large Amount of Long Polymers in Nanopores}, author = {Andrzej żywociński and Anna Korda and Joanna Gosk and Stefan A Wieczorek and Agnieszka Wilk and Robert Hołyst}, url = {http://pubs.acs.org/doi/abs/10.1021/ja0762590}, doi = {10.1021/ja0762590}, issn = {0002-7863}, year = {2007}, date = {2007-11-01}, journal = {Journal of the American Chemical Society}, volume = {129}, number = {44}, pages = {13398--13399}, publisher = {American Chemical Society}, abstract = {It is well-established that when polymer size exceeds the size of a confining space, the equilibrium partition of polymer between the confined space and the bulk solution is zero. Surprisingly, we found that the long water-soluble polymers with a small hydrophobic group can be efficiently trapped inside the water channels (nanopores) of the hexagonal phase of non-ionic surfactant.}, keywords = {}, pubstate = {published}, tppubtype = {article} } It is well-established that when polymer size exceeds the size of a confining space, the equilibrium partition of polymer between the confined space and the bulk solution is zero. Surprisingly, we found that the long water-soluble polymers with a small hydrophobic group can be efficiently trapped inside the water channels (nanopores) of the hexagonal phase of non-ionic surfactant. |
Marcinkowska-Gapińska, Anna; Gapiński, Jacek; Elikowski, Waldemar; Jaroszyk, Feliks; Kubisz, Leszek Medical & Biological Engineering & Computing, 45 (9), pp. 837–844, 2007, ISSN: 0140-0118. @article{Marcinkowska-Gapinska2007, title = {Comparison of three rheological models of shear flow behavior studied on blood samples from post-infarction patients}, author = {Anna Marcinkowska-Gapińska and Jacek Gapiński and Waldemar Elikowski and Feliks Jaroszyk and Leszek Kubisz}, url = {http://www.ncbi.nlm.nih.gov/pubmed/17674068 http://link.springer.com/10.1007/s11517-007-0236-4}, doi = {10.1007/s11517-007-0236-4}, issn = {0140-0118}, year = {2007}, date = {2007-09-01}, journal = {Medical & Biological Engineering & Computing}, volume = {45}, number = {9}, pages = {837--844}, abstract = {Quantitative analysis of blood viscosity was performed on the basis of mathematical models of non-Newtonian fluid shear flow behavior (Casson, Ree-Eyring and Quemada). A total of 100 blood samples were drawn from clinically stable survivors of myocardial infarction, treated with aspirin or acenocoumarol and controls to these drugs. Whole blood and plasma viscosity were measured at a broad range of shear rates using a rotary-oscillating viscometer Contraves LS40. Numerical analysis of the experimental data was carried out by means of linear (for Casson) and non-linear regression for the remaining models. In the evaluation of the results, both the fit quality and physical interpretation of the models' parameters were considered. The Quemada model fitted most precisely with the experimental findings and, despite the controversies concerning the relationship between in vivo tissue perfusion and in vitro rheological measurements, seemed to be a valuable method enhancing investigation possibilities of cardiovascular patients. Our results suggest that aspirin does not affect blood rheological properties, while acenocoumarol may slightly alter red cell deformability and rouleaux formation.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Quantitative analysis of blood viscosity was performed on the basis of mathematical models of non-Newtonian fluid shear flow behavior (Casson, Ree-Eyring and Quemada). A total of 100 blood samples were drawn from clinically stable survivors of myocardial infarction, treated with aspirin or acenocoumarol and controls to these drugs. Whole blood and plasma viscosity were measured at a broad range of shear rates using a rotary-oscillating viscometer Contraves LS40. Numerical analysis of the experimental data was carried out by means of linear (for Casson) and non-linear regression for the remaining models. In the evaluation of the results, both the fit quality and physical interpretation of the models' parameters were considered. The Quemada model fitted most precisely with the experimental findings and, despite the controversies concerning the relationship between in vivo tissue perfusion and in vitro rheological measurements, seemed to be a valuable method enhancing investigation possibilities of cardiovascular patients. Our results suggest that aspirin does not affect blood rheological properties, while acenocoumarol may slightly alter red cell deformability and rouleaux formation. |
Danielewicz-Ferchmin, I; Banachowicz, Ewa; Ferchmin, A R Water phases under high electric field and pressure applied simultaneously Journal of Molecular Liquids, 135 (1-3), pp. 75–85, 2007, ISSN: 01677322. @article{Danielewicz-Ferchmin2007, title = {Water phases under high electric field and pressure applied simultaneously}, author = {I Danielewicz-Ferchmin and Ewa Banachowicz and A R Ferchmin}, url = {https://www.sciencedirect.com/science/article/pii/S0167732207000074 http://linkinghub.elsevier.com/retrieve/pii/S0167732207000074}, doi = {10.1016/j.molliq.2006.10.006}, issn = {01677322}, year = {2007}, date = {2007-07-01}, journal = {Journal of Molecular Liquids}, volume = {135}, number = {1-3}, pages = {75--85}, publisher = {Elsevier}, abstract = {The rigorous equation of state of an open system containing water in an electric field above 108 V m−1 under pressure applied in the range 10−4≤Po≤0.8 GPa leads to phase diagrams with two possible kinds of phase transitions at 293 K. The first one is the discontinuous phase transition under pressure applied in the range 10−4≤Po≤0.05 GPa in the $Pi$, $sigma$ coordinates ($Pi$ is the electrostriction pressure and $sigma$ denotes the surface charge density at an adjacent charged surface). The second one represents the continuous phase transition under pressure applied in the range 10−4≤Po≤0.8 GPa; it occurs at higher values of $sigma$ than the former one.}, keywords = {}, pubstate = {published}, tppubtype = {article} } The rigorous equation of state of an open system containing water in an electric field above 108 V m−1 under pressure applied in the range 10−4≤Po≤0.8 GPa leads to phase diagrams with two possible kinds of phase transitions at 293 K. The first one is the discontinuous phase transition under pressure applied in the range 10−4≤Po≤0.05 GPa in the $Pi$, $sigma$ coordinates ($Pi$ is the electrostriction pressure and $sigma$ denotes the surface charge density at an adjacent charged surface). The second one represents the continuous phase transition under pressure applied in the range 10−4≤Po≤0.8 GPa; it occurs at higher values of $sigma$ than the former one. |
Gibasiewicz, Krzysztof; Ramesh, V M; Lin, Su; Redding, Kevin; Woodbury, Neal W; Webber, Andrew N Photosynthesis Research, 92 (1), pp. 55–63, 2007, ISSN: 0166-8595. @article{Gibasiewicz2007, title = {Two equilibration pools of chlorophylls in the Photosystem I core antenna of Chlamydomonas reinhardtii}, author = {Krzysztof Gibasiewicz and V M Ramesh and Su Lin and Kevin Redding and Neal W Woodbury and Andrew N Webber}, url = {http://www.ncbi.nlm.nih.gov/pubmed/17611814 http://link.springer.com/10.1007/s11120-006-9125-1}, doi = {10.1007/s11120-006-9125-1}, issn = {0166-8595}, year = {2007}, date = {2007-07-01}, journal = {Photosynthesis Research}, volume = {92}, number = {1}, pages = {55--63}, abstract = {Femtosecond transient absorption spectroscopy was applied for a comparative study of excitation decay in several different Photosystem I (PSI) core preparations from the green alga Chlamydomonas reinhardtii. For PSI cores with a fully interconnected network of chlorophylls, the excitation energy was equilibrated over a pool of chlorophylls absorbing at approximately 683 nm, independent of excitation wavelength [Gibasiewicz et al. J Phys Chem B 105:11498-11506, 2001; J Phys Chem B 106:6322-6330, 2002]. In preparations with impaired connectivity between chlorophylls, we have found that the spectrum of chlorophylls connected to the reaction center (i.e., with approximately 20 ps decay time) over which the excitation is equilibrated becomes excitation-wavelength-dependent. Excitation at 670 nm is finally equilibrated over chlorophylls absorbing at approximately 675 nm, whereas excitation at 695 nm or 700 nm is equilibrated over chlorophylls absorbing at approximately 683 nm. This indicates that in the vicinity of the reaction center there are two spectrally different and spatially separated pools of chlorophylls that are equally capable of effective excitation energy transfer to the reaction center. We propose that they are related to the two groups of central PSI core chlorophylls lying on the opposite sides of reaction center.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Femtosecond transient absorption spectroscopy was applied for a comparative study of excitation decay in several different Photosystem I (PSI) core preparations from the green alga Chlamydomonas reinhardtii. For PSI cores with a fully interconnected network of chlorophylls, the excitation energy was equilibrated over a pool of chlorophylls absorbing at approximately 683 nm, independent of excitation wavelength [Gibasiewicz et al. J Phys Chem B 105:11498-11506, 2001; J Phys Chem B 106:6322-6330, 2002]. In preparations with impaired connectivity between chlorophylls, we have found that the spectrum of chlorophylls connected to the reaction center (i.e., with approximately 20 ps decay time) over which the excitation is equilibrated becomes excitation-wavelength-dependent. Excitation at 670 nm is finally equilibrated over chlorophylls absorbing at approximately 675 nm, whereas excitation at 695 nm or 700 nm is equilibrated over chlorophylls absorbing at approximately 683 nm. This indicates that in the vicinity of the reaction center there are two spectrally different and spatially separated pools of chlorophylls that are equally capable of effective excitation energy transfer to the reaction center. We propose that they are related to the two groups of central PSI core chlorophylls lying on the opposite sides of reaction center. |
Aliotta, F; Gapiński, Jacek; Pochylski, Mikołaj; Ponterio, R C; Saija, F; Salvato, G Excess compressibility in binary liquid mixtures The Journal of Chemical Physics, 126 (22), pp. 224508, 2007, ISSN: 0021-9606. @article{Aliotta2007, title = {Excess compressibility in binary liquid mixtures}, author = {F Aliotta and Jacek Gapiński and Mikołaj Pochylski and R C Ponterio and F Saija and G Salvato}, url = {http://www.ncbi.nlm.nih.gov/pubmed/17581064 http://aip.scitation.org/doi/10.1063/1.2745292}, doi = {10.1063/1.2745292}, issn = {0021-9606}, year = {2007}, date = {2007-06-01}, journal = {The Journal of Chemical Physics}, volume = {126}, number = {22}, pages = {224508}, abstract = {Brillouin scattering experiments have been carried out on some mixtures of molecular liquids. From the measurement of the hypersonic velocities we have evaluated the adiabatic compressibility as a function of the volume fraction. We show how the quadratic form of the excess compressibility dependence on the solute volume fraction can be derived by simple statistical effects and does not imply any interaction among the components of the system other than excluded volume effects. This idea is supported by the comparison of the experimental results with a well-established prototype model, consisting of a binary mixture of hard spheres with a nonadditive interaction potential. This naive model turns out to be able to produce a very wide spectrum of structural and thermodynamic features depending on values of its parameters. An attempt has made to understand what kind of structural information can be gained through the analysis of the volume fraction dependence of the compressibility.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Brillouin scattering experiments have been carried out on some mixtures of molecular liquids. From the measurement of the hypersonic velocities we have evaluated the adiabatic compressibility as a function of the volume fraction. We show how the quadratic form of the excess compressibility dependence on the solute volume fraction can be derived by simple statistical effects and does not imply any interaction among the components of the system other than excluded volume effects. This idea is supported by the comparison of the experimental results with a well-established prototype model, consisting of a binary mixture of hard spheres with a nonadditive interaction potential. This naive model turns out to be able to produce a very wide spectrum of structural and thermodynamic features depending on values of its parameters. An attempt has made to understand what kind of structural information can be gained through the analysis of the volume fraction dependence of the compressibility. |
Kang, Kyongok; Wilk, Agnieszka; Patkowski, Adam; Dhont, Jan K G The Journal of Chemical Physics, 126 (21), pp. 214501, 2007, ISSN: 0021-9606. @article{Kang2007, title = {Diffusion of spheres in isotropic and nematic networks of rods: Electrostatic interactions and hydrodynamic screening}, author = {Kyongok Kang and Agnieszka Wilk and Adam Patkowski and Jan K G Dhont}, url = {http://www.ncbi.nlm.nih.gov/pubmed/17567202 http://aip.scitation.org/doi/10.1063/1.2737446}, doi = {10.1063/1.2737446}, issn = {0021-9606}, year = {2007}, date = {2007-06-01}, journal = {The Journal of Chemical Physics}, volume = {126}, number = {21}, pages = {214501}, abstract = {Translational diffusion of a small charged tracer sphere in isotropic and nematic suspensions of long and thin charged rods is investigated as a function of ionic strength and rod concentration. A theory for the diffusive properties of a small sphere is developed, where both (screened) hydrodynamic interactions and charge interactions between the tracer sphere and the rod network are analyzed. Hydrodynamic interactions are formulated in terms of the hydrodynamic screening length. As yet, there are no independent theoretical predictions for the hydrodynamic screening length for rod networks. Experimental tracer-diffusion data are presented for various ionic strengths as a function of the rod concentration, both in the isotropic and nematic states. Orientational order parameters are measured for the same ionic strengths as a function of the rod concentration. The hydrodynamic screening length is determined from these experimental data and scaling relations obtained from the above mentioned theory. For the isotropic networks, a master curve is found for the hydrodynamic screening length as a function of the rod concentration. For the nematic networks the screening length turns out to be a very sensitive function of the orientational order parameter.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Translational diffusion of a small charged tracer sphere in isotropic and nematic suspensions of long and thin charged rods is investigated as a function of ionic strength and rod concentration. A theory for the diffusive properties of a small sphere is developed, where both (screened) hydrodynamic interactions and charge interactions between the tracer sphere and the rod network are analyzed. Hydrodynamic interactions are formulated in terms of the hydrodynamic screening length. As yet, there are no independent theoretical predictions for the hydrodynamic screening length for rod networks. Experimental tracer-diffusion data are presented for various ionic strengths as a function of the rod concentration, both in the isotropic and nematic states. Orientational order parameters are measured for the same ionic strengths as a function of the rod concentration. The hydrodynamic screening length is determined from these experimental data and scaling relations obtained from the above mentioned theory. For the isotropic networks, a master curve is found for the hydrodynamic screening length as a function of the rod concentration. For the nematic networks the screening length turns out to be a very sensitive function of the orientational order parameter. |
Szymański, Jȩdrzej; Poboży, Ewa; Trojanowicz, Marek; Wilk, Agnieszka; Garstecki, Piotr; Hołyst, Robert The Journal of Physical Chemistry B, 111 (19), pp. 5503–5510, 2007, ISSN: 1520-6106. @article{Szymanski2007, title = {Net Charge and Electrophoretic Mobility of Lysozyme Charge Ladders in Solutions of Nonionic Surfactant}, author = {Jȩdrzej Szymański and Ewa Poboży and Marek Trojanowicz and Agnieszka Wilk and Piotr Garstecki and Robert Hołyst}, url = {http://www.ncbi.nlm.nih.gov/pubmed/17441752 http://pubs.acs.org/doi/abs/10.1021/jp067511d}, doi = {10.1021/jp067511d}, issn = {1520-6106}, year = {2007}, date = {2007-05-01}, journal = {The Journal of Physical Chemistry B}, volume = {111}, number = {19}, pages = {5503--5510}, abstract = {We report on the electrophoretic mobility and on the thermal diffusion of lysozyme proteins dissolved in aqueous solutions of a nonionic surfactant (C12E6) at a wide range of concentrations of the surfactant (0-20% by weight). We want to estimate the influence of a dense network of elongated micelles of C12E6 on the effective charge of the proteins as observed in the capillary electrophoresis experiments. The possible mechanism leading to the change in the effective charge of protein could involve the deformation of the cloud of counterions around the protein when it squeezes through the narrow (of the order of a protein diameter) aqueous channels formed in the solution of elongated micelles. The combination of independent measurements of the electrophoretic mobility of a family of modified proteins (lysozyme charge ladder [Colton et al. J. Am. Chem. Soc. 1997, 119, 12701]), of the microviscosity of the solutions of surfactant (obtained via fluorescence correlation spectroscopy), and of the hydrodynamic radius of the proteins (photon correlation spectroscopy) allow us to conclude that the effective charge of the proteins is not affected by the presence of surfactant, even at high concentrations.}, keywords = {}, pubstate = {published}, tppubtype = {article} } We report on the electrophoretic mobility and on the thermal diffusion of lysozyme proteins dissolved in aqueous solutions of a nonionic surfactant (C12E6) at a wide range of concentrations of the surfactant (0-20% by weight). We want to estimate the influence of a dense network of elongated micelles of C12E6 on the effective charge of the proteins as observed in the capillary electrophoresis experiments. The possible mechanism leading to the change in the effective charge of protein could involve the deformation of the cloud of counterions around the protein when it squeezes through the narrow (of the order of a protein diameter) aqueous channels formed in the solution of elongated micelles. The combination of independent measurements of the electrophoretic mobility of a family of modified proteins (lysozyme charge ladder [Colton et al. J. Am. Chem. Soc. 1997, 119, 12701]), of the microviscosity of the solutions of surfactant (obtained via fluorescence correlation spectroscopy), and of the hydrodynamic radius of the proteins (photon correlation spectroscopy) allow us to conclude that the effective charge of the proteins is not affected by the presence of surfactant, even at high concentrations. |
Gapiński, Jacek; Patkowski, Adam; Banchio, A J; Holmqvist, P; Meier, G; Lettinga, M P; Naegele, G Collective diffusion in charge-stabilized suspensions: Concentration and salt effects The Journal of Chemical Physics, 126 (10), pp. 104905, 2007, ISSN: 0021-9606. @article{Gapinski2007, title = {Collective diffusion in charge-stabilized suspensions: Concentration and salt effects}, author = {Jacek Gapiński and Adam Patkowski and A J Banchio and P Holmqvist and G Meier and M P Lettinga and G Naegele}, url = {http://www.ncbi.nlm.nih.gov/pubmed/17362085 http://aip.scitation.org/doi/10.1063/1.2538891}, doi = {10.1063/1.2538891}, issn = {0021-9606}, year = {2007}, date = {2007-03-01}, journal = {The Journal of Chemical Physics}, volume = {126}, number = {10}, pages = {104905}, abstract = {The authors present a joint experimental-theoretical study of collective diffusion properties in aqueous suspensions of charge-stabilized fluorinated latex spheres. Small-angle x-ray scattering and x-ray photon correlation spectroscopy have been used to explore the concentration and ionic-strength dependence of the static and short-time dynamic properties including the hydrodynamic function H(q), the wave-number-dependent collective diffusion coefficient D(q), and the intermediate scattering function over the entire accessible range. They show that all experimental data can be quantitatively described and explained by means of a recently developed accelerated Stokesian dynamics simulation method, in combination with a modified hydrodynamic many-body theory. In particular, the behavior of H(q) for de-ionized and dense suspensions can be attributed to the influence of many-body hydrodynamics, without any need for postulating hydrodynamic screening to be present, as it was done in earlier work. Upper and lower boundaries are provided for the peak height of the hydrodynamic function and for the short-time self-diffusion coefficient over the entire range of added salt concentrations.}, keywords = {}, pubstate = {published}, tppubtype = {article} } The authors present a joint experimental-theoretical study of collective diffusion properties in aqueous suspensions of charge-stabilized fluorinated latex spheres. Small-angle x-ray scattering and x-ray photon correlation spectroscopy have been used to explore the concentration and ionic-strength dependence of the static and short-time dynamic properties including the hydrodynamic function H(q), the wave-number-dependent collective diffusion coefficient D(q), and the intermediate scattering function over the entire accessible range. They show that all experimental data can be quantitatively described and explained by means of a recently developed accelerated Stokesian dynamics simulation method, in combination with a modified hydrodynamic many-body theory. In particular, the behavior of H(q) for de-ionized and dense suspensions can be attributed to the influence of many-body hydrodynamics, without any need for postulating hydrodynamic screening to be present, as it was done in earlier work. Upper and lower boundaries are provided for the peak height of the hydrodynamic function and for the short-time self-diffusion coefficient over the entire range of added salt concentrations. |
Ramesh, V M; Gibasiewicz, Krzysztof; Lin, Su; Bingham, Scott E; Webber, Andrew N Biochimica et Biophysica Acta (BBA) - Bioenergetics, 1767 (2), pp. 151–160, 2007, ISSN: 00052728. @article{Ramesh2007, title = {Replacement of the methionine axial ligand to the primary electron acceptor A0 slows the A0− reoxidation dynamics in Photosystem I}, author = {V M Ramesh and Krzysztof Gibasiewicz and Su Lin and Scott E Bingham and Andrew N Webber}, url = {http://www.ncbi.nlm.nih.gov/pubmed/17316554 http://linkinghub.elsevier.com/retrieve/pii/S0005272806003896}, doi = {10.1016/j.bbabio.2006.12.013}, issn = {00052728}, year = {2007}, date = {2007-02-01}, journal = {Biochimica et Biophysica Acta (BBA) - Bioenergetics}, volume = {1767}, number = {2}, pages = {151--160}, abstract = {The recent crystal structure of photosystem I (PSI) from Thermosynechococcus elongatus shows two nearly symmetric branches of electron transfer cofactors including the primary electron donor, P(700), and a sequence of electron acceptors, A, A(0) and A(1), bound to the PsaA and PsaB heterodimer. The central magnesium atoms of each of the putative primary electron acceptor chlorophylls, A(0), are unusually coordinated by the sulfur atom of methionine 688 of PsaA and 668 of PsaB, respectively. We [Ramesh et al. (2004a) Biochemistry 43:1369-1375] have shown that the replacement of either methionine with histidine in the PSI of the unicellular green alga Chlamydomonas reinhardtii resulted in accumulation of A(0)(-) (in 300-ps time scale), suggesting that both the PsaA and PsaB branches are active. This is in contrast to cyanobacterial PSI where studies with methionine-to-leucine mutants show that electron transfer occurs predominantly along the PsaA branch. In this contribution we report that the change of methionine to either leucine or serine leads to a similar accumulation of A(0)(-) on both the PsaA and the PsaB branch of PSI from C. reinhardtii, as we reported earlier for histidine mutants. More importantly, we further demonstrate that for all the mutants under study, accumulation of A(0)(-) is transient, and that reoxidation of A(0)(-) occurs within 1-2 ns, two orders of magnitude slower than in wild type PSI, most likely via slow electron transfer to A(1). This illustrates an indispensable role of methionine as an axial ligand to the primary acceptor A(0) in optimizing the rate of charge stabilization in PSI. A simple energetic model for this reaction is proposed. Our findings support the model of equivalent electron transfer along both cofactor branches in Photosystem I.}, keywords = {}, pubstate = {published}, tppubtype = {article} } The recent crystal structure of photosystem I (PSI) from Thermosynechococcus elongatus shows two nearly symmetric branches of electron transfer cofactors including the primary electron donor, P(700), and a sequence of electron acceptors, A, A(0) and A(1), bound to the PsaA and PsaB heterodimer. The central magnesium atoms of each of the putative primary electron acceptor chlorophylls, A(0), are unusually coordinated by the sulfur atom of methionine 688 of PsaA and 668 of PsaB, respectively. We [Ramesh et al. (2004a) Biochemistry 43:1369-1375] have shown that the replacement of either methionine with histidine in the PSI of the unicellular green alga Chlamydomonas reinhardtii resulted in accumulation of A(0)(-) (in 300-ps time scale), suggesting that both the PsaA and PsaB branches are active. This is in contrast to cyanobacterial PSI where studies with methionine-to-leucine mutants show that electron transfer occurs predominantly along the PsaA branch. In this contribution we report that the change of methionine to either leucine or serine leads to a similar accumulation of A(0)(-) on both the PsaA and the PsaB branch of PSI from C. reinhardtii, as we reported earlier for histidine mutants. More importantly, we further demonstrate that for all the mutants under study, accumulation of A(0)(-) is transient, and that reoxidation of A(0)(-) occurs within 1-2 ns, two orders of magnitude slower than in wild type PSI, most likely via slow electron transfer to A(1). This illustrates an indispensable role of methionine as an axial ligand to the primary acceptor A(0) in optimizing the rate of charge stabilization in PSI. A simple energetic model for this reaction is proposed. Our findings support the model of equivalent electron transfer along both cofactor branches in Photosystem I. |
Pochylski, Mikołaj; Aliotta, F; Błaszczak, Z; Gapiński, J High-Frequency Dynamical Behavior of Poly(ethylene glycol)+H2O Mixtures by Brillouin Spectroscopy Macromolecular Symposia, 251 (1), pp. 47-53, 2007, ISSN: 1521-3900. @article{MASY:MASY200750507, title = {High-Frequency Dynamical Behavior of Poly(ethylene glycol)+H2O Mixtures by Brillouin Spectroscopy}, author = {Mikołaj Pochylski and F Aliotta and Z Błaszczak and J Gapiński}, url = {http://dx.doi.org/10.1002/masy.200750507}, doi = {10.1002/masy.200750507}, issn = {1521-3900}, year = {2007}, date = {2007-01-01}, journal = {Macromolecular Symposia}, volume = {251}, number = {1}, pages = {47-53}, publisher = {WILEY-VCH Verlag}, abstract = {Brillouin spectroscopy has been used to examine high-frequency dynamical behavior of aqueous solutions of poly(ethylene glycol) (Mw ≈ 400g/mol) at 298K in the entire concentration region. It was found that a relaxation process takes place in the experimental frequency window that significantly affects the shape of experimentally recorded spectrum of the density fluctuations (dynamical structure factor). The process detected was attributed to segmental motion of the flexible polymeric chain. The full spectrum analysis of Brillouin spectra has been performed taking advantage of the relaxation function previously used in describing a single relaxation process in dielectric examination of water solutions of PEG 400. The proposed data processing procedure permits a qualitative reproduction of concentration dependencies of the hypersonic wave velocity and absorption measured. The shapes of the concentration dependencies of the relaxation times obtained from the Brillouin and the dielectric spectroscopies are in good agreement over a very broad concentration range, although their absolute values are scaled by the factor of 3. This result indicate that the two processes revealed independently by dielectric and Brillouin spectroscopies, apparently separated in time-scale, are just the same relaxation process.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Brillouin spectroscopy has been used to examine high-frequency dynamical behavior of aqueous solutions of poly(ethylene glycol) (Mw ≈ 400g/mol) at 298K in the entire concentration region. It was found that a relaxation process takes place in the experimental frequency window that significantly affects the shape of experimentally recorded spectrum of the density fluctuations (dynamical structure factor). The process detected was attributed to segmental motion of the flexible polymeric chain. The full spectrum analysis of Brillouin spectra has been performed taking advantage of the relaxation function previously used in describing a single relaxation process in dielectric examination of water solutions of PEG 400. The proposed data processing procedure permits a qualitative reproduction of concentration dependencies of the hypersonic wave velocity and absorption measured. The shapes of the concentration dependencies of the relaxation times obtained from the Brillouin and the dielectric spectroscopies are in good agreement over a very broad concentration range, although their absolute values are scaled by the factor of 3. This result indicate that the two processes revealed independently by dielectric and Brillouin spectroscopies, apparently separated in time-scale, are just the same relaxation process. |
Pochylski, Mikołaj; Blaszczak, Zdzislaw Brillouin spectroscopy investigations of poly(ethylene glycol) water and organic solvent mixtures Proc. SPIE, 6598 , pp. 65980X, 2007. @article{Pochylski2007, title = {Brillouin spectroscopy investigations of poly(ethylene glycol) water and organic solvent mixtures}, author = {Mikołaj Pochylski and Zdzislaw Blaszczak}, doi = {10.1117/12.726588}, year = {2007}, date = {2007-01-01}, journal = {Proc. SPIE}, volume = {6598}, pages = {65980X}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Dobek, Andrzej Optical and Electric Gradients in Photosynthesis Granja, Carlos; Leroy, Claude; Stekl, Ivan (Ed.): Nuclear Physics Methods and Accelerators in Biology and Medicine: Fourth International Summer School on Nuclear Physics Methods and Accelerators in Biology and Medicine, pp. 169–174, AIP Conference Proceedings, 2007, ISSN: 0094243X. @inproceedings{Dobek2007, title = {Optical and Electric Gradients in Photosynthesis}, author = {Andrzej Dobek}, editor = {Carlos Granja and Claude Leroy and Ivan Stekl}, url = {http://aip.scitation.org/doi/abs/10.1063/1.2825772}, doi = {10.1063/1.2825772}, issn = {0094243X}, year = {2007}, date = {2007-01-01}, booktitle = {Nuclear Physics Methods and Accelerators in Biology and Medicine: Fourth International Summer School on Nuclear Physics Methods and Accelerators in Biology and Medicine}, volume = {958}, pages = {169--174}, publisher = {AIP Conference Proceedings}, keywords = {}, pubstate = {published}, tppubtype = {inproceedings} } |
Pacławski, K; Gapiński, Jacek Static and dynamic light scattering method for analysis of gold colloidal growth in aqueous solution Archives of Metallurgy and Materials, 52 (1), pp. 121–128, 2007. @article{Pacawski2007, title = {Static and dynamic light scattering method for analysis of gold colloidal growth in aqueous solution}, author = {K Pacławski and Jacek Gapiński}, url = {http://yadda.icm.edu.pl/baztech/element/bwmeta1.element.baztech-article-BSW3-0029-0017}, year = {2007}, date = {2007-01-01}, journal = {Archives of Metallurgy and Materials}, volume = {52}, number = {1}, pages = {121--128}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Patkowski, Adam; Gapiński, Jacek; Meier, G; Kriegs, H Isotropic Brillouin spectra of liquids having an internal degree of freedom The Journal of Chemical Physics, 126 (1), pp. 014508, 2007, ISSN: 0021-9606. @article{Patkowski2007, title = {Isotropic Brillouin spectra of liquids having an internal degree of freedom}, author = {Adam Patkowski and Jacek Gapiński and G Meier and H Kriegs}, url = {http://aip.scitation.org/doi/10.1063/1.2426347}, doi = {10.1063/1.2426347}, issn = {0021-9606}, year = {2007}, date = {2007-01-01}, journal = {The Journal of Chemical Physics}, volume = {126}, number = {1}, pages = {014508}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Dwiecki, Krzysztof; Górnas, Paweł; Wilk, Agnieszka; Nogala-Kałucka, Małgorzata; Polewski, Krzysztof Cellular and Molecular Biology Letters, 12 (1), pp. 51–69, 2007, ISSN: 1689-1392. @article{Dwiecki2007, title = {Spectroscopic studies of D-$alpha$-tocopherol concentration-induced transformation in egg phosphatidylcholne vesicles}, author = {Krzysztof Dwiecki and Paweł Górnas and Agnieszka Wilk and Małgorzata Nogala-Kałucka and Krzysztof Polewski}, url = {http://www.ncbi.nlm.nih.gov/pubmed/17124545 http://www.degruyter.com/view/j/cmble.2007.12.issue-1/s11658-006-0059-6/s11658-006-0059-6.xml}, doi = {10.2478/s11658-006-0059-6}, issn = {1689-1392}, year = {2007}, date = {2007-01-01}, journal = {Cellular and Molecular Biology Letters}, volume = {12}, number = {1}, pages = {51--69}, abstract = {The effects of embedding up to 60 mol% of $alpha$-tocopherol ($alpha$-Toc) on the morphology and structure of the egg phosphatidylcholine (PC) membrane were studied using spectroscopic techniques. The resulting vesicles were subjected to turbidometric and dynamic light scattering measurements to evaluate their size distribution. The $alpha$-Toc intrinsic fluorescence and its quenching was used to estimate the tocopherol position in the membrane. Optical microscopy was used to visualize morphological changes in the vesicles during the inclusion of tocopherol into the 2 mg/ml PC membrane. The incorporation of up to 15 mol% of tocopherol molecules into PC vesicles is accompanied by a linear increase in the fluorescence intensity and the simultaneous formation of larger, multilamellar vesicles. Increasing the tocopherol concentration above 20 mol% induced structural and morphological changes leading to the disappearance of micrometer-sized vesicles and the formation of small unilamellar vesicles of size ranging from 30 to 120 nm, mixed micelles and non-lamellar structures.}, keywords = {}, pubstate = {published}, tppubtype = {article} } The effects of embedding up to 60 mol% of $alpha$-tocopherol ($alpha$-Toc) on the morphology and structure of the egg phosphatidylcholine (PC) membrane were studied using spectroscopic techniques. The resulting vesicles were subjected to turbidometric and dynamic light scattering measurements to evaluate their size distribution. The $alpha$-Toc intrinsic fluorescence and its quenching was used to estimate the tocopherol position in the membrane. Optical microscopy was used to visualize morphological changes in the vesicles during the inclusion of tocopherol into the 2 mg/ml PC membrane. The incorporation of up to 15 mol% of tocopherol molecules into PC vesicles is accompanied by a linear increase in the fluorescence intensity and the simultaneous formation of larger, multilamellar vesicles. Increasing the tocopherol concentration above 20 mol% induced structural and morphological changes leading to the disappearance of micrometer-sized vesicles and the formation of small unilamellar vesicles of size ranging from 30 to 120 nm, mixed micelles and non-lamellar structures. |
2006 |
Szymański, Jedrzej; Patkowski, Adam; Wilk, Agnieszka; Garstecki, Piotr; Holyst, Robert Diffusion and Viscosity in a Crowded Environment: from Nano- to Macroscale The Journal of Physical Chemistry B, 110 (51), pp. 25593–25597, 2006, ISSN: 1520-6106. @article{Szymanski2006a, title = {Diffusion and Viscosity in a Crowded Environment: from Nano- to Macroscale}, author = {Jedrzej Szymański and Adam Patkowski and Agnieszka Wilk and Piotr Garstecki and Robert Holyst}, url = {http://pubs.acs.org/doi/abs/10.1021/jp0666784}, doi = {10.1021/jp0666784}, issn = {1520-6106}, year = {2006}, date = {2006-12-01}, journal = {The Journal of Physical Chemistry B}, volume = {110}, number = {51}, pages = {25593--25597}, publisher = {American Chemical Society}, abstract = {Although water is the chief component of living cells, food, and personal care products, the supramolecular components make their viscosity larger than that of water by several orders of magnitude. Using fluorescence correlation spectroscopy (FCS), photon correlation spectroscopy (PCS), NMR, and rheology data, we show how the viscosity changes from the value for water at the molecular scale to the large macroviscosity. We determined the viscosity experienced by nanoprobes (of sizes from 0.28 to 190 nm) in aqueous micellar solution of hexaethylene-glycol-monododecyl-ether (in a range of concentration from 0.1% w/w to 35% w/w) and identified a clear crossover at the length scale of 17 ± 2 nm (slightly larger than persistence length of micelles) at which viscosity acquires its macroscopic value. The sharp dependence of the viscosity coefficients on the size of the probe in the nanoregime has important consequences for diffusion-limited reactions in crowded environments (e.g., living cells).}, keywords = {}, pubstate = {published}, tppubtype = {article} } Although water is the chief component of living cells, food, and personal care products, the supramolecular components make their viscosity larger than that of water by several orders of magnitude. Using fluorescence correlation spectroscopy (FCS), photon correlation spectroscopy (PCS), NMR, and rheology data, we show how the viscosity changes from the value for water at the molecular scale to the large macroviscosity. We determined the viscosity experienced by nanoprobes (of sizes from 0.28 to 190 nm) in aqueous micellar solution of hexaethylene-glycol-monododecyl-ether (in a range of concentration from 0.1% w/w to 35% w/w) and identified a clear crossover at the length scale of 17 ± 2 nm (slightly larger than persistence length of micelles) at which viscosity acquires its macroscopic value. The sharp dependence of the viscosity coefficients on the size of the probe in the nanoregime has important consequences for diffusion-limited reactions in crowded environments (e.g., living cells). |
Pochylski, Mikołaj; Aliotta, F; Blaszczak, Z; Gapiński, Jacek The Journal of Physical Chemistry B, 110 (41), pp. 20533–20539, 2006, ISSN: 1520-6106. @article{Pochylski2006a, title = {Structuring Effects and Hydration Phenomena in Poly(Ethylene Glycol)/Water Mixtures Investigated by Brillouin Scattering}, author = {Mikołaj Pochylski and F Aliotta and Z Blaszczak and Jacek Gapiński}, url = {http://www.ncbi.nlm.nih.gov/pubmed/17034240 http://pubs.acs.org/doi/abs/10.1021/jp0620973}, doi = {10.1021/jp0620973}, issn = {1520-6106}, year = {2006}, date = {2006-10-01}, journal = {The Journal of Physical Chemistry B}, volume = {110}, number = {41}, pages = {20533--20539}, abstract = {Aqueous solutions of poly(ethylene glycol) (PEG) of mean molecular mass of 600 g/mol (PEG600) are investigated by Brillouin scattering technique. At high PEG content, a relaxation phenomenon is observed, which is related to a local rearrangement of the polymer structure where the interaction, via hydrogen bonding, with the solvent molecules plays a role. The obtained values of the relaxation times match the literature data very well for a fast relaxation time revealed by dielectric relaxation measurements in very similar mixtures. The calculated concentration behaviors of the excess adiabatic compressibility turns out in good agreement with the previous findings from ultrasonic measurements at 3 MHz. The observed minimum in the adiabatic compressibility is interpreted as the result of the interaction between water and the EO units of the PEG chain, which results in a structure tighter then that typical of bulk water and of pure PEG600. Such a hypothesis is supported by the observation that volume fraction value of about 0.3 coincides with the concentration value at which full hydration of EO units takes place. The observation that at the same concentration, the polymer coils start to overlap each other further supports the idea that the adiabatic compressibility behavior is monitoring the structural evolution of the mixture. However, similar results are obtained for largely different binary mixture which suggests caution in taking this conclusion too literally. In particular, the hypothesis that the occurrence of an extreme in the excess adiabatic compressibility could be simply originated by statistical effects and that further work is required for disentangling entropic contribution from effects of hetero-association and self-aggregation of one or both the components.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Aqueous solutions of poly(ethylene glycol) (PEG) of mean molecular mass of 600 g/mol (PEG600) are investigated by Brillouin scattering technique. At high PEG content, a relaxation phenomenon is observed, which is related to a local rearrangement of the polymer structure where the interaction, via hydrogen bonding, with the solvent molecules plays a role. The obtained values of the relaxation times match the literature data very well for a fast relaxation time revealed by dielectric relaxation measurements in very similar mixtures. The calculated concentration behaviors of the excess adiabatic compressibility turns out in good agreement with the previous findings from ultrasonic measurements at 3 MHz. The observed minimum in the adiabatic compressibility is interpreted as the result of the interaction between water and the EO units of the PEG chain, which results in a structure tighter then that typical of bulk water and of pure PEG600. Such a hypothesis is supported by the observation that volume fraction value of about 0.3 coincides with the concentration value at which full hydration of EO units takes place. The observation that at the same concentration, the polymer coils start to overlap each other further supports the idea that the adiabatic compressibility behavior is monitoring the structural evolution of the mixture. However, similar results are obtained for largely different binary mixture which suggests caution in taking this conclusion too literally. In particular, the hypothesis that the occurrence of an extreme in the excess adiabatic compressibility could be simply originated by statistical effects and that further work is required for disentangling entropic contribution from effects of hetero-association and self-aggregation of one or both the components. |
Danielewicz-Ferchmin, Irena; Banachowicz, Ewa; Ferchmin, Ryszard A ChemPhysChem, 7 (10), pp. 2126–2133, 2006, ISSN: 1439-4235. @article{Danielewicz-Ferchmin2006, title = {Properties of Hydration Shells of Protein Molecules at their Pressure- and Temperature-Induced Native-Denatured Transition}, author = {Irena Danielewicz-Ferchmin and Ewa Banachowicz and Ryszard A Ferchmin}, url = {http://www.ncbi.nlm.nih.gov/pubmed/16955512 http://doi.wiley.com/10.1002/cphc.200600289}, doi = {10.1002/cphc.200600289}, issn = {1439-4235}, year = {2006}, date = {2006-10-01}, journal = {ChemPhysChem}, volume = {7}, number = {10}, pages = {2126--2133}, abstract = {Properties of water at the surface of biomolecules are important for their conformational stability. The behaviour of hydrating water at protein transition (t) pressures P(t) and temperatures T(t) , with the points (P(t),T(t) ) lying in the Native-Denatured (N-D) transition line, is studied. Hydration shells at the hydrophilic regions of protein molecules with surface charge density sigma are investigated with the help of the equation of state of water in an open system. The local values of sigma rather close to each other (sigma(D) approximately 0.3 C m(-2)) are found for six different experimental lines of the N-D transition found in the literature. The values sigma(D) correspond to the crossings of the total pressure (P(t)+Pi) vs sigma isotherms at different T(t) (Pi-electrostriction pressure). The pressures P(t) and temperatures T(t) appear to be related with some selected sites at the surfaces of the protein molecules.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Properties of water at the surface of biomolecules are important for their conformational stability. The behaviour of hydrating water at protein transition (t) pressures P(t) and temperatures T(t) , with the points (P(t),T(t) ) lying in the Native-Denatured (N-D) transition line, is studied. Hydration shells at the hydrophilic regions of protein molecules with surface charge density sigma are investigated with the help of the equation of state of water in an open system. The local values of sigma rather close to each other (sigma(D) approximately 0.3 C m(-2)) are found for six different experimental lines of the N-D transition found in the literature. The values sigma(D) correspond to the crossings of the total pressure (P(t)+Pi) vs sigma isotherms at different T(t) (Pi-electrostriction pressure). The pressures P(t) and temperatures T(t) appear to be related with some selected sites at the surfaces of the protein molecules. |
Patkowski, Adam; Gapiński, Jacek; Pakula, T; Meier, G Polymer, 47 (20), pp. 7231–7240, 2006, ISSN: 00323861. @article{Patkowski2006a, title = {Physical nature of complex structural relaxation in polysiloxane – PMpTS: $alpha$ and $alpha$′ relaxations}, author = {Adam Patkowski and Jacek Gapiński and T Pakula and G Meier}, url = {https://www.sciencedirect.com/science/article/pii/S0032386106006860 http://linkinghub.elsevier.com/retrieve/pii/S0032386106006860}, doi = {10.1016/j.polymer.2006.05.065}, issn = {00323861}, year = {2006}, date = {2006-09-01}, journal = {Polymer}, volume = {47}, number = {20}, pages = {7231--7240}, publisher = {Elsevier}, abstract = {Structural relaxation processes in poly(methyl-para-tolyl-siloxane) (PMpTS) polymers of three molecular weights were studied using dynamic light scattering. Two relaxation processes: the usual $alpha$ and an additional slow one $alpha$′ were observed and studied as function of temperature and molecular weight. Contrary to the structural relaxation, we find that in a plot T–Tg the relaxation times for the $alpha$′ process for all molecular weights do not collapse to a single curve. For one of the samples the light scattering correlation functions were compared with the corresponding functions obtained by means of mechanical relaxation, dielectric spectroscopy and computer simulations. The simulations show that the bimodal distribution, i.e. the $alpha$ relaxation and the slow ($alpha$′) process are contained in the correlation functions of most of the probes (optical anisotropy, dipole moment, chain bond, density) in agreement with experimental observations.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Structural relaxation processes in poly(methyl-para-tolyl-siloxane) (PMpTS) polymers of three molecular weights were studied using dynamic light scattering. Two relaxation processes: the usual $alpha$ and an additional slow one $alpha$′ were observed and studied as function of temperature and molecular weight. Contrary to the structural relaxation, we find that in a plot T–Tg the relaxation times for the $alpha$′ process for all molecular weights do not collapse to a single curve. For one of the samples the light scattering correlation functions were compared with the corresponding functions obtained by means of mechanical relaxation, dielectric spectroscopy and computer simulations. The simulations show that the bimodal distribution, i.e. the $alpha$ relaxation and the slow ($alpha$′) process are contained in the correlation functions of most of the probes (optical anisotropy, dipole moment, chain bond, density) in agreement with experimental observations. |
Rathgeber, Silke; Pakula, Tadeusz; Wilk, Agnieszka; Matyjaszewski, Krzysztof; Lee, Hyung-il; Beers, Kathryn L Polymer, 47 (20), pp. 7318–7327, 2006, ISSN: 00323861. @article{Rathgeber2006, title = {Bottle-brush macromolecules in solution: Comparison between results obtained from scattering experiments and computer simulations}, author = {Silke Rathgeber and Tadeusz Pakula and Agnieszka Wilk and Krzysztof Matyjaszewski and Hyung-il Lee and Kathryn L Beers}, url = {https://www.sciencedirect.com/science/article/pii/S0032386106006872 http://linkinghub.elsevier.com/retrieve/pii/S0032386106006872}, doi = {10.1016/j.polymer.2006.06.010}, issn = {00323861}, year = {2006}, date = {2006-09-01}, journal = {Polymer}, volume = {47}, number = {20}, pages = {7318--7327}, publisher = {Elsevier}, abstract = {We addressed the structure of bottle-brush macromolecules under good solvent conditions by means of scattering techniques and computer simulations. Architectural parameters, such as backbone length, side chain length and side chain stiffness were varied systematically. A consistent description of the form factors was achieved by describing the bottle-brush polymers as flexible cylinders with internal density fluctuations. The model leads to direct conclusions about parameters, such as the brush persistence length, describing the overall shape of the bottle-brush polymers. Indirect conclusions about the side chain and backbone conformation can be drawn. Experimental results were compared to those obtained from computer simulations carried out for single bottle-brush polymers using the cooperative motion algorithm. The simulation gives direct access to the pair correlation function, allowing an independent determination of the form factor. In addition direct information about the side chain and backbone conformation can be obtained. The critical parameter for lyotropic behavior of bottle-brush polymer solutions is the ratio of brush persistence length to diameter which should be of order 10 or larger. Thus the discussion of the results is focused on the impact of the architectural parameters on the persistence of the bottle-brush polymers. Experimental results on the lyotropic behavior of a bottle-brush polymer are presented.}, keywords = {}, pubstate = {published}, tppubtype = {article} } We addressed the structure of bottle-brush macromolecules under good solvent conditions by means of scattering techniques and computer simulations. Architectural parameters, such as backbone length, side chain length and side chain stiffness were varied systematically. A consistent description of the form factors was achieved by describing the bottle-brush polymers as flexible cylinders with internal density fluctuations. The model leads to direct conclusions about parameters, such as the brush persistence length, describing the overall shape of the bottle-brush polymers. Indirect conclusions about the side chain and backbone conformation can be drawn. Experimental results were compared to those obtained from computer simulations carried out for single bottle-brush polymers using the cooperative motion algorithm. The simulation gives direct access to the pair correlation function, allowing an independent determination of the form factor. In addition direct information about the side chain and backbone conformation can be obtained. The critical parameter for lyotropic behavior of bottle-brush polymer solutions is the ratio of brush persistence length to diameter which should be of order 10 or larger. Thus the discussion of the results is focused on the impact of the architectural parameters on the persistence of the bottle-brush polymers. Experimental results on the lyotropic behavior of a bottle-brush polymer are presented. |
Hoffmann, Marcin; Eitner, Krystian; von Grotthuss, Marcin; Rychlewski, Leszek; Banachowicz, Ewa; Grabarkiewicz, Tomasz; Szkoda, Tomasz; Kolinski, Andrzej Journal of Computer-Aided Molecular Design, 20 (5), pp. 305–319, 2006, ISSN: 0920-654X. @article{Hoffmann2006, title = {Three dimensional model of severe acute respiratory syndrome coronavirus helicase ATPase catalytic domain and molecular design of severe acute respiratory syndrome coronavirus helicase inhibitors}, author = {Marcin Hoffmann and Krystian Eitner and Marcin von Grotthuss and Leszek Rychlewski and Ewa Banachowicz and Tomasz Grabarkiewicz and Tomasz Szkoda and Andrzej Kolinski}, url = {http://www.ncbi.nlm.nih.gov/pubmed/16972168 http://link.springer.com/10.1007/s10822-006-9057-z}, doi = {10.1007/s10822-006-9057-z}, issn = {0920-654X}, year = {2006}, date = {2006-05-01}, journal = {Journal of Computer-Aided Molecular Design}, volume = {20}, number = {5}, pages = {305--319}, abstract = {The modeling of the severe acute respiratory syndrome coronavirus helicase ATPase catalytic domain was performed using the protein structure prediction Meta Server and the 3D Jury method for model selection, which resulted in the identification of 1JPR, 1UAA and 1W36 PDB structures as suitable templates for creating a full atom 3D model. This model was further utilized to design small molecules that are expected to block an ATPase catalytic pocket thus inhibit the enzymatic activity. Binding sites for various functional groups were identified in a series of molecular dynamics calculation. Their positions in the catalytic pocket were used as constraints in the Cambridge structural database search for molecules having the pharmacophores that interacted most strongly with the enzyme in a desired position. The subsequent MD simulations followed by calculations of binding energies of the designed molecules were compared to ATP identifying the most successful candidates, for likely inhibitors - molecules possessing two phosphonic acid moieties at distal ends of the molecule.}, keywords = {}, pubstate = {published}, tppubtype = {article} } The modeling of the severe acute respiratory syndrome coronavirus helicase ATPase catalytic domain was performed using the protein structure prediction Meta Server and the 3D Jury method for model selection, which resulted in the identification of 1JPR, 1UAA and 1W36 PDB structures as suitable templates for creating a full atom 3D model. This model was further utilized to design small molecules that are expected to block an ATPase catalytic pocket thus inhibit the enzymatic activity. Binding sites for various functional groups were identified in a series of molecular dynamics calculation. Their positions in the catalytic pocket were used as constraints in the Cambridge structural database search for molecules having the pharmacophores that interacted most strongly with the enzyme in a desired position. The subsequent MD simulations followed by calculations of binding energies of the designed molecules were compared to ATP identifying the most successful candidates, for likely inhibitors - molecules possessing two phosphonic acid moieties at distal ends of the molecule. |
Szymański, Jȩdrzej; Patkowski, Adam; Gapiński, Jacek; Wilk, Agnieszka; Hołyst, Robert The Journal of Physical Chemistry B, 110 (14), pp. 7367–7373, 2006, ISSN: 1520-6106. @article{Szymanski2006b, title = {Movement of Proteins in an Environment Crowded by Surfactant Micelles: Anomalous versus Normal Diffusion}, author = {Jȩdrzej Szymański and Adam Patkowski and Jacek Gapiński and Agnieszka Wilk and Robert Hołyst}, url = {http://www.ncbi.nlm.nih.gov/pubmed/16599511 http://pubs.acs.org/doi/abs/10.1021/jp055626w}, doi = {10.1021/jp055626w}, issn = {1520-6106}, year = {2006}, date = {2006-04-01}, journal = {The Journal of Physical Chemistry B}, volume = {110}, number = {14}, pages = {7367--7373}, abstract = {Small proteins move in crowded cell compartments by anomalous diffusion. In many of them, e.g., the endoplasmic reticulum, the proteins move between lipid membranes in the aqueous lumen. Molecular crowding in vitro offers a systematic way to study anomalous and normal diffusion in a well controlled environment not accessible in vivo. We prepared a crowded environment in vitro consisting of hexaethylene glycol monododecyl ether (C(12)E(6)) nonionic surfactant and water and observed lysozyme diffusion between elongated micelles. We have fitted the data obtained in fluorescence correlation spectroscopy using an anomalous diffusion model and a two-component normal diffusion model. For a small concentration of surfactant (below 4 wt %) the data can be fitted by single-component normal diffusion. For larger concentrations the normal diffusion fit gave two components: one very slow and one fast. The amplitude of the slow component grows with C(12)E(6) concentration. The ratio of diffusion coefficients (slow to fast) is on the order of 0.1 for all concentrations of surfactant in the solution. The fast diffusion is due to free proteins while the slow one is due to the protein-micelle complexes. The protein-micelle interaction is weak since even in a highly concentrated solution (35% of C(12)E(6)) the amplitude of the slow mode is only 10%, despite the fact that the average distance between the micelles is the same as the size of the protein. The anomalous diffusion model gave the anomaly index (r(2)(t) approximately t(alpha)), alpha monotonically decreasing from alpha = 1 (at 4% surfactant) to alpha = 0.88 (at 37% surfactant). The fits for two-component normal diffusion and anomalous diffusion were of equally good quality, but the physical interpretation was only straightforward for the former.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Small proteins move in crowded cell compartments by anomalous diffusion. In many of them, e.g., the endoplasmic reticulum, the proteins move between lipid membranes in the aqueous lumen. Molecular crowding in vitro offers a systematic way to study anomalous and normal diffusion in a well controlled environment not accessible in vivo. We prepared a crowded environment in vitro consisting of hexaethylene glycol monododecyl ether (C(12)E(6)) nonionic surfactant and water and observed lysozyme diffusion between elongated micelles. We have fitted the data obtained in fluorescence correlation spectroscopy using an anomalous diffusion model and a two-component normal diffusion model. For a small concentration of surfactant (below 4 wt %) the data can be fitted by single-component normal diffusion. For larger concentrations the normal diffusion fit gave two components: one very slow and one fast. The amplitude of the slow component grows with C(12)E(6) concentration. The ratio of diffusion coefficients (slow to fast) is on the order of 0.1 for all concentrations of surfactant in the solution. The fast diffusion is due to free proteins while the slow one is due to the protein-micelle complexes. The protein-micelle interaction is weak since even in a highly concentrated solution (35% of C(12)E(6)) the amplitude of the slow mode is only 10%, despite the fact that the average distance between the micelles is the same as the size of the protein. The anomalous diffusion model gave the anomaly index (r(2)(t) approximately t(alpha)), alpha monotonically decreasing from alpha = 1 (at 4% surfactant) to alpha = 0.88 (at 37% surfactant). The fits for two-component normal diffusion and anomalous diffusion were of equally good quality, but the physical interpretation was only straightforward for the former. |
Banchio, Adolfo J; Gapiński, Jacek; Patkowski, Adam; Haeußler, Wolfgang; Fluerasu, Andrei; Sacanna, Stefano; Holmqvist, Peter; Meier, Gerhard; Lettinga, Paul M; Naegele, Gerhard Many-Body Hydrodynamic Interactions in Charge-Stabilized Suspensions Physical Review Letters, 96 (13), pp. 138303, 2006, ISSN: 0031-9007. @article{Banchio2006, title = {Many-Body Hydrodynamic Interactions in Charge-Stabilized Suspensions}, author = {Adolfo J Banchio and Jacek Gapiński and Adam Patkowski and Wolfgang Haeußler and Andrei Fluerasu and Stefano Sacanna and Peter Holmqvist and Gerhard Meier and Paul M Lettinga and Gerhard Naegele}, url = {http://www.ncbi.nlm.nih.gov/pubmed/16712043 https://link.aps.org/doi/10.1103/PhysRevLett.96.138303}, doi = {10.1103/PhysRevLett.96.138303}, issn = {0031-9007}, year = {2006}, date = {2006-04-01}, journal = {Physical Review Letters}, volume = {96}, number = {13}, pages = {138303}, abstract = {In this joint experimental-theoretical work we study hydrodynamic interaction effects in dense suspensions of charged colloidal spheres. Using x-ray photon correlation spectroscopy we have determined the hydrodynamic function H(q), for a varying range of electrosteric repulsion. We show that H(q) can be quantitatively described by means of a novel Stokesian dynamics simulation method for charged Brownian spheres, and by a modification of a many-body theory developed originally by Beenakker and Mazur. Very importantly, we can explain the behavior of H(q) for strongly correlated particles without resorting to the controversial concept of hydrodynamic screening, as was attempted in earlier work by Riese [Phys. Rev. Lett. 85, 5460 (2000)].}, keywords = {}, pubstate = {published}, tppubtype = {article} } In this joint experimental-theoretical work we study hydrodynamic interaction effects in dense suspensions of charged colloidal spheres. Using x-ray photon correlation spectroscopy we have determined the hydrodynamic function H(q), for a varying range of electrosteric repulsion. We show that H(q) can be quantitatively described by means of a novel Stokesian dynamics simulation method for charged Brownian spheres, and by a modification of a many-body theory developed originally by Beenakker and Mazur. Very importantly, we can explain the behavior of H(q) for strongly correlated particles without resorting to the controversial concept of hydrodynamic screening, as was attempted in earlier work by Riese [Phys. Rev. Lett. 85, 5460 (2000)]. |
Banachowicz, Ewa Light scattering studies of proteins under compression Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics, 1764 (3), pp. 405–413, 2006, ISSN: 15709639. @article{Banachowicz2006a, title = {Light scattering studies of proteins under compression}, author = {Ewa Banachowicz}, url = {http://www.ncbi.nlm.nih.gov/pubmed/16510323 http://linkinghub.elsevier.com/retrieve/pii/S157096390600032X}, doi = {10.1016/j.bbapap.2006.01.014}, issn = {15709639}, year = {2006}, date = {2006-03-01}, journal = {Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics}, volume = {1764}, number = {3}, pages = {405--413}, abstract = {The scattering techniques are very convenient and effective in investigation of the shape, size and interactions of biological molecules close to their natural states in solution. However, it seems that from among a wide spectrum of scattering techniques, the light scattering ones have been relatively rarely used for the study of proteins under elevated hydrostatic pressure. This paper gives a brief description of the well developed possibilities of this technique for potential applications in the study of dissociation, aggregation and structural changes in proteins under compression. A short review of the already known applications is also given. Finally, the high-pressure dynamic light scattering results obtained by author on the lysozyme solution are shown and discussed.}, keywords = {}, pubstate = {published}, tppubtype = {article} } The scattering techniques are very convenient and effective in investigation of the shape, size and interactions of biological molecules close to their natural states in solution. However, it seems that from among a wide spectrum of scattering techniques, the light scattering ones have been relatively rarely used for the study of proteins under elevated hydrostatic pressure. This paper gives a brief description of the well developed possibilities of this technique for potential applications in the study of dissociation, aggregation and structural changes in proteins under compression. A short review of the already known applications is also given. Finally, the high-pressure dynamic light scattering results obtained by author on the lysozyme solution are shown and discussed. |
Kriegs, H; Gapiński, Jacek; Meier, G; Paluch, M; Pawlus, S; Patkowski, Adam Pressure effects on the $alpha$ and $alpha$′ relaxations in polymethylphenylsiloxane The Journal of Chemical Physics, 124 (10), pp. 104901, 2006, ISSN: 0021-9606. @article{Kriegs2006, title = {Pressure effects on the $alpha$ and $alpha$′ relaxations in polymethylphenylsiloxane}, author = {H Kriegs and Jacek Gapiński and G Meier and M Paluch and S Pawlus and Adam Patkowski}, url = {http://aip.scitation.org/doi/10.1063/1.2177242}, doi = {10.1063/1.2177242}, issn = {0021-9606}, year = {2006}, date = {2006-03-01}, journal = {The Journal of Chemical Physics}, volume = {124}, number = {10}, pages = {104901}, publisher = {American Institute of Physics}, abstract = {In some polymers, in addition to the usual structural $alpha$ relaxation, a slower $alpha$′ relaxation is observed with a non-Arrhenius temperature dependence. In order to understand better the molecular origin of this $alpha$′ relaxation in poly(methylphenylsiloxane) (PMPS) we have studied, for the first time, the pressure dependence of its relaxation time, together with the usual temperature dependence, by means of dynamic light scattering (DLS). For the same material the $alpha$ relaxation was also studied by means of DLS and dielectric spectroscopy (DS) in broad temperature and pressure ranges. We find that the temperature dependence of both $alpha$ and $alpha$′ relaxation times, at all pressures studied, can be described by a double Vogel-Fulcher-Tammann (VFT) law. The pressure dependence of the characteristic temperatures Tg (glass transition temperature) and T0 (Vogel temperature) as well as the activation volumes for both $alpha$ and $alpha$′ processes are very similar, indicating, that both relaxation processes originate from similar local mol...}, keywords = {}, pubstate = {published}, tppubtype = {article} } In some polymers, in addition to the usual structural $alpha$ relaxation, a slower $alpha$′ relaxation is observed with a non-Arrhenius temperature dependence. In order to understand better the molecular origin of this $alpha$′ relaxation in poly(methylphenylsiloxane) (PMPS) we have studied, for the first time, the pressure dependence of its relaxation time, together with the usual temperature dependence, by means of dynamic light scattering (DLS). For the same material the $alpha$ relaxation was also studied by means of DLS and dielectric spectroscopy (DS) in broad temperature and pressure ranges. We find that the temperature dependence of both $alpha$ and $alpha$′ relaxation times, at all pressures studied, can be described by a double Vogel-Fulcher-Tammann (VFT) law. The pressure dependence of the characteristic temperatures Tg (glass transition temperature) and T0 (Vogel temperature) as well as the activation volumes for both $alpha$ and $alpha$′ processes are very similar, indicating, that both relaxation processes originate from similar local mol... |
Banachowicz, Ewa; Danielewicz-Ferchmin, I Physics and Chemistry of Liquids, 44 (1), pp. 95–105, 2006, ISSN: 0031-9104. @article{Banachowicz2006b, title = {Static permittivity of water in electric field higher than 10 8 V m −1 and pressure varying from 0.1 to 600 MPa at room temperature}, author = {Ewa Banachowicz and I Danielewicz-Ferchmin}, url = {http://www.tandfonline.com/doi/abs/10.1080/00319100500338912}, doi = {10.1080/00319100500338912}, issn = {0031-9104}, year = {2006}, date = {2006-02-01}, journal = {Physics and Chemistry of Liquids}, volume = {44}, number = {1}, pages = {95--105}, publisher = {Taylor & Francis Group}, abstract = {A recently proposed statistical approach to the permittivity $epsilon$ of water in the high electric field E (I. Danielewicz-Ferchmin, A.R. Ferchmin. Phys. Chem. Chem. Phys., 6, 1332 (2004)) has been applied to water at T = 293 K subjected to external pressure. Results are shown in the form of the set of isobars $epsilon$(E), which reveal abrupt falls at E∼109 V m−1.}, keywords = {}, pubstate = {published}, tppubtype = {article} } A recently proposed statistical approach to the permittivity $epsilon$ of water in the high electric field E (I. Danielewicz-Ferchmin, A.R. Ferchmin. Phys. Chem. Chem. Phys., 6, 1332 (2004)) has been applied to water at T = 293 K subjected to external pressure. Results are shown in the form of the set of isobars $epsilon$(E), which reveal abrupt falls at E∼109 V m−1. |
Patkowski, Adam; Gapiński, Jacek; Meier, G; Kriegs, H; Grand, Le A; Dreyfus, C Unexpected effect of internal degrees of freedom on transverse phonons in supercooled liquids Europhysics Letters (EPL), 73 (4), pp. 607–613, 2006, ISSN: 0295-5075. @article{Patkowski2006b, title = {Unexpected effect of internal degrees of freedom on transverse phonons in supercooled liquids}, author = {Adam Patkowski and Jacek Gapiński and G Meier and H Kriegs and Le A Grand and C Dreyfus}, url = {http://stacks.iop.org/0295-5075/73/i=4/a=607?key=crossref.8b86e9eb8242607bf9be17b90e358bd2}, doi = {10.1209/epl/i2005-10429-y}, issn = {0295-5075}, year = {2006}, date = {2006-02-01}, journal = {Europhysics Letters (EPL)}, volume = {73}, number = {4}, pages = {607--613}, publisher = {IOP Publishing}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
von Grotthuss, Marcin; Plewczynski, Dariusz; Ginalski, Krzysztof; Rychlewski, Leszek; Shakhnovich, EugeneI BMC Bioinformatics, 7 (1), pp. 53, 2006, ISSN: 14712105. @article{VonGrotthuss2006, title = {PDB-UF: database of predicted enzymatic functions for unannotated protein structures from structural genomics}, author = {Marcin von Grotthuss and Dariusz Plewczynski and Krzysztof Ginalski and Leszek Rychlewski and EugeneI Shakhnovich}, url = {http://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-7-53}, doi = {10.1186/1471-2105-7-53}, issn = {14712105}, year = {2006}, date = {2006-02-01}, journal = {BMC Bioinformatics}, volume = {7}, number = {1}, pages = {53}, publisher = {BioMed Central}, abstract = {The number of protein structures from structural genomics centers dramatically increases in the Protein Data Bank (PDB). Many of these structures are functionally unannotated because they have no sequence similarity to proteins of known function. However, it is possible to successfully infer function using only structural similarity. Here we present the PDB-UF database, a web-accessible collection of predictions of enzymatic properties using structure-function relationship. The assignments were conducted for three-dimensional protein structures of unknown function that come from structural genomics initiatives. We show that 4 hypothetical proteins (with PDB accession codes: 1VH0, 1NS5, 1O6D, and 1TO0), for which standard BLAST tools such as PSI-BLAST or RPS-BLAST failed to assign any function, are probably methyltransferase enzymes. We suggest that the structure-based prediction of an EC number should be conducted having the different similarity score cutoff for different protein folds. Moreover, performing the annotation using two different algorithms can reduce the rate of false positive assignments. We believe, that the presented web-based repository will help to decrease the number of protein structures that have functions marked as "unknown" in the PDB file. http://paradox.harvard.edu/PDB-UF and http://bioinfo.pl/PDB-UF}, keywords = {}, pubstate = {published}, tppubtype = {article} } The number of protein structures from structural genomics centers dramatically increases in the Protein Data Bank (PDB). Many of these structures are functionally unannotated because they have no sequence similarity to proteins of known function. However, it is possible to successfully infer function using only structural similarity. Here we present the PDB-UF database, a web-accessible collection of predictions of enzymatic properties using structure-function relationship. The assignments were conducted for three-dimensional protein structures of unknown function that come from structural genomics initiatives. We show that 4 hypothetical proteins (with PDB accession codes: 1VH0, 1NS5, 1O6D, and 1TO0), for which standard BLAST tools such as PSI-BLAST or RPS-BLAST failed to assign any function, are probably methyltransferase enzymes. We suggest that the structure-based prediction of an EC number should be conducted having the different similarity score cutoff for different protein folds. Moreover, performing the annotation using two different algorithms can reduce the rate of false positive assignments. We believe, that the presented web-based repository will help to decrease the number of protein structures that have functions marked as "unknown" in the PDB file. http://paradox.harvard.edu/PDB-UF and http://bioinfo.pl/PDB-UF |
Ślósarek, Genowefa; Kozak, M; Gierszewski, J; Pietraszko, A Structure of N 6 -furfurylaminopurine (kinetin) dihydrogenphosphate Acta Crystallographica Section B Structural Science, 62 (1), pp. 102–108, 2006, ISSN: 0108-7681. @article{Slosarek2006, title = {Structure of N 6 -furfurylaminopurine (kinetin) dihydrogenphosphate}, author = {Genowefa Ślósarek and M Kozak and J Gierszewski and A Pietraszko}, url = {http://scripts.iucr.org/cgi-bin/paper?S010876810502673X}, doi = {10.1107/S010876810502673X}, issn = {0108-7681}, year = {2006}, date = {2006-02-01}, journal = {Acta Crystallographica Section B Structural Science}, volume = {62}, number = {1}, pages = {102--108}, publisher = {International Union of Crystallography}, abstract = {The crystal structure of kinetin dihydrogenphosphate has been determined at 115 and 293 K. Kinetin dihydrogenphosphate undergoes a polymorphic phase transition at 291.1 K. In both phases the crystal belongs to the triclinic system with the symmetry described by the space group P$backslash$bar 1. In the low-temperature phase, the unit cell is doubled along the a axis. There is a dynamic equilibrium between different tautomeric forms of the adenine residue, determined by the distribution of H atoms within the network of hydrogen bonds.}, keywords = {}, pubstate = {published}, tppubtype = {article} } The crystal structure of kinetin dihydrogenphosphate has been determined at 115 and 293 K. Kinetin dihydrogenphosphate undergoes a polymorphic phase transition at 291.1 K. In both phases the crystal belongs to the triclinic system with the symmetry described by the space group P$backslash$bar 1. In the low-temperature phase, the unit cell is doubled along the a axis. There is a dynamic equilibrium between different tautomeric forms of the adenine residue, determined by the distribution of H atoms within the network of hydrogen bonds. |
Pochylski, Mikołaj; Aliotta, F; Błaszczak, Z; Gapiński, Jacek The Journal of Physical Chemistry B, 110 (1), pp. 485–493, 2006, ISSN: 1520-6106. @article{Pochylski2006b, title = {Evidences of Nonideal Mixing in Poly(ethylene Glycol)/Organic Solvent Mixtures by Brillouin Scattering}, author = {Mikołaj Pochylski and F Aliotta and Z Błaszczak and Jacek Gapiński}, url = {http://www.ncbi.nlm.nih.gov/pubmed/16471559 http://pubs.acs.org/doi/abs/10.1021/jp053813o}, doi = {10.1021/jp053813o}, issn = {1520-6106}, year = {2006}, date = {2006-01-01}, journal = {The Journal of Physical Chemistry B}, volume = {110}, number = {1}, pages = {485--493}, abstract = {The concentration dependence of the hypersonic properties of solutions of poly(ethylene glycol) of mean molecular mass 600 g/mol (PEG600) in benzene and toluene has been investigated by Brillouin scattering. The two solvents are very similar in structure and chemical properties, but while benzene is nonpolar, toluene possess a modest dipole. In both solvents a high-frequency relaxation process has been observed at high concentrations which has been assigned to conformational rearrangements of the polymeric chains, triggered by reorientation of the side groups. In both cases, the concentration dependence of the adiabatic compressibility deviates significantly from linearity, indicating the existence of nonideal mixing phenomena driven by aggregation processes taking place in the systems. However, there is no temperature dependence for solutions of PEG600 in benzene; on the contrary, the results obtained for solutions of PEG600 in toluene are noticeably dependent on the temperature. The comparison of the experimental data with the results of previous experiments on similar systems allows a general picture for weakly interacting mixtures of hydrogen-bonded systems and organic solvents to be developed. In particular, in the presence of a nonpolar solvent molecule the local structure of the mixture is dominated by solute self-association processes and any resulting solute-solvent correlation is barely induced by excluded volume effects. At high enough dilution the self-aggregation of solute molecules produces a variety of new local topologies that cannot be observed in bulk solute, and as a consequence, the concentration evolution of the system is too rich to be described in terms of a linear combination of a few components over the whole concentration range. The situation seems to be simpler for the polar toluene solvent molecules, where a three-component model seems able to fit the experimental concentration dependence of the hypersonic velocity. This result is interpreted to imply that the interaction between the solvent dipoles and the active sites of the solute produces a relatively stable heterocoordination, while the relevance of self-association is partially reduced.}, keywords = {}, pubstate = {published}, tppubtype = {article} } The concentration dependence of the hypersonic properties of solutions of poly(ethylene glycol) of mean molecular mass 600 g/mol (PEG600) in benzene and toluene has been investigated by Brillouin scattering. The two solvents are very similar in structure and chemical properties, but while benzene is nonpolar, toluene possess a modest dipole. In both solvents a high-frequency relaxation process has been observed at high concentrations which has been assigned to conformational rearrangements of the polymeric chains, triggered by reorientation of the side groups. In both cases, the concentration dependence of the adiabatic compressibility deviates significantly from linearity, indicating the existence of nonideal mixing phenomena driven by aggregation processes taking place in the systems. However, there is no temperature dependence for solutions of PEG600 in benzene; on the contrary, the results obtained for solutions of PEG600 in toluene are noticeably dependent on the temperature. The comparison of the experimental data with the results of previous experiments on similar systems allows a general picture for weakly interacting mixtures of hydrogen-bonded systems and organic solvents to be developed. In particular, in the presence of a nonpolar solvent molecule the local structure of the mixture is dominated by solute self-association processes and any resulting solute-solvent correlation is barely induced by excluded volume effects. At high enough dilution the self-aggregation of solute molecules produces a variety of new local topologies that cannot be observed in bulk solute, and as a consequence, the concentration evolution of the system is too rich to be described in terms of a linear combination of a few components over the whole concentration range. The situation seems to be simpler for the polar toluene solvent molecules, where a three-component model seems able to fit the experimental concentration dependence of the hypersonic velocity. This result is interpreted to imply that the interaction between the solvent dipoles and the active sites of the solute produces a relatively stable heterocoordination, while the relevance of self-association is partially reduced. |
Kang, Kyongok; Wilk, Agnieszka; Buitenhuis, J; Patkowski, Adam; Dhont, Jan K G Diffusion of spheres in isotropic and nematic suspensions of rods The Journal of Chemical Physics, 124 (4), pp. 044907, 2006, ISSN: 0021-9606. @article{Kang2006, title = {Diffusion of spheres in isotropic and nematic suspensions of rods}, author = {Kyongok Kang and Agnieszka Wilk and J Buitenhuis and Adam Patkowski and Jan K G Dhont}, url = {http://aip.scitation.org/doi/10.1063/1.2161204}, doi = {10.1063/1.2161204}, issn = {0021-9606}, year = {2006}, date = {2006-01-01}, journal = {The Journal of Chemical Physics}, volume = {124}, number = {4}, pages = {044907}, publisher = {American Institute of Physics}, abstract = {Diffusion of a small tracer sphere (apoferritin) in isotropic and nematic networks [of fd virus] is discussed. For a tracer sphere that is smaller than the mesh size of the network, screened hydrodynamic interactions between the sphere and the network determine its diffusion coefficient. A theory is developed for such interactions as well as their relation to the long-time self-diffusion coefficient. Fluorescence correlation spectroscopy measurements on mixtures of apoferritin and fd virus are presented. The long-time self-diffusion coefficient of apoferritin is measured as a function of the fd-virus concentration, both in the isotropic and nematic state, in directions parallel and perpendicular to the nematic director. The hydrodynamic screening length of the fd-virus network as a function of fd concentration is obtained by combining these experimental data with the theory. Surprisingly, the screening length increases with increasing concentration in nematic networks. This is due to the increase in the d...}, keywords = {}, pubstate = {published}, tppubtype = {article} } Diffusion of a small tracer sphere (apoferritin) in isotropic and nematic networks [of fd virus] is discussed. For a tracer sphere that is smaller than the mesh size of the network, screened hydrodynamic interactions between the sphere and the network determine its diffusion coefficient. A theory is developed for such interactions as well as their relation to the long-time self-diffusion coefficient. Fluorescence correlation spectroscopy measurements on mixtures of apoferritin and fd virus are presented. The long-time self-diffusion coefficient of apoferritin is measured as a function of the fd-virus concentration, both in the isotropic and nematic state, in directions parallel and perpendicular to the nematic director. The hydrodynamic screening length of the fd-virus network as a function of fd concentration is obtained by combining these experimental data with the theory. Surprisingly, the screening length increases with increasing concentration in nematic networks. This is due to the increase in the d... |
2005 |
Gibasiewicz, Krzysztof; Szrajner, Anna; Ihalainen, Janne A; Germano, Marta; Dekker, Jan P; van Grondelle, Rienk The Journal of Physical Chemistry B, 109 (44), pp. 21180–21186, 2005, ISSN: 1520-6106. @article{Gibasiewicz2005a, title = {Characterization of Low-Energy Chlorophylls in the PSI-LHCI Supercomplex from Chlamydomonas r einhardtii . A Site-Selective Fluorescence Study}, author = {Krzysztof Gibasiewicz and Anna Szrajner and Janne A Ihalainen and Marta Germano and Jan P Dekker and Rienk van Grondelle}, url = {http://www.ncbi.nlm.nih.gov/pubmed/16853744 http://pubs.acs.org/doi/abs/10.1021/jp0530909}, doi = {10.1021/jp0530909}, issn = {1520-6106}, year = {2005}, date = {2005-11-01}, journal = {The Journal of Physical Chemistry B}, volume = {109}, number = {44}, pages = {21180--21186}, abstract = {Almost all photosystem I (PSI) complexes from oxygenic photosynthetic organisms contain chlorophylls that absorb at longer wavelength than that of the primary electron donor P700. We demonstrate here that the low-energy pool of chlorophylls in the PSI-LHCI complex from the green alga Chlamydomonas reinhardtii, containing five to six pigments, is significantly blue-shifted (A(max) at 700 nm at 4 K) compared to that in the PSI core preparations from several species of cyanobacteria and in PSI-LHCI particles from higher plants. This makes them almost isoenergetic with the primary donor. However, they keep the other characteristic features of "red" chlorophylls: clear spectral separation from the bulk chlorophylls, big Stokes shift revealing pronounced electron-phonon coupling, and large homogeneous and inhomogeneous broadening of approximately 170 and approximately 310 cm(-1), respectively.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Almost all photosystem I (PSI) complexes from oxygenic photosynthetic organisms contain chlorophylls that absorb at longer wavelength than that of the primary electron donor P700. We demonstrate here that the low-energy pool of chlorophylls in the PSI-LHCI complex from the green alga Chlamydomonas reinhardtii, containing five to six pigments, is significantly blue-shifted (A(max) at 700 nm at 4 K) compared to that in the PSI core preparations from several species of cyanobacteria and in PSI-LHCI particles from higher plants. This makes them almost isoenergetic with the primary donor. However, they keep the other characteristic features of "red" chlorophylls: clear spectral separation from the bulk chlorophylls, big Stokes shift revealing pronounced electron-phonon coupling, and large homogeneous and inhomogeneous broadening of approximately 170 and approximately 310 cm(-1), respectively. |
Ziolek, Marcin; Pawlowicz, Natalia; Naskrecki, Ryszard; Dobek, Andrzej The Journal of Physical Chemistry B, 109 (38), pp. 18171–18176, 2005, ISSN: 1520-6106. @article{Ziolek2005, title = {Electron Transfer in the Reaction Center of the Rb. s phaeroides R-26 Studied by Transient Absorption}, author = {Marcin Ziolek and Natalia Pawlowicz and Ryszard Naskrecki and Andrzej Dobek}, url = {http://www.ncbi.nlm.nih.gov/pubmed/16853333 http://pubs.acs.org/doi/abs/10.1021/jp050682i}, doi = {10.1021/jp050682i}, issn = {1520-6106}, year = {2005}, date = {2005-09-01}, journal = {The Journal of Physical Chemistry B}, volume = {109}, number = {38}, pages = {18171--18176}, abstract = {Electron transfer at the reaction center of the purple photosynthetic bacterium Rb. sphaeroides R-26 was measured at room temperature by the time-resolved transient absorption spectroscopy technique with 200 fs temporal resolution. The absorbance changes characteristic of the excited state of the primary donor and extending over the whole spectral range investigated from 350 nm up to 720 nm appeared after excitation with a laser pulse of about 100 fs duration at 800 nm. The time evolution of the spectra reflected the excitation of bacteriochlorophylls (BChl) M and L and the subsequent transfer of this excitation to the primary electron donor (P), with the time constant shorter than 1 ps. The decay time constant of the excited primary donor P was determined as about 3 ps, and it was faster than the rise of the reduced intermediary acceptor bacteriopheophytin (BPhe(L)). Photoreduction of BPhe(L) and its further reoxidation was clearly observed as an increase in its bleaching band intensity at around 540 nm in about 4 ps and its decrease in about 200 ps. Our findings support the theoretical model assuming the involvement of the intermediate state P(+)BChl- in the so-called "two-step" model. In this model an electron is transferred in a sequence from the excited special pair P* to bacteriochlorophyll, BChl(L), then to bacteriopheophytin, BPhe(L), and further on to quinone, Q(A). The branched charge separation, partially via P and partially via BChl(L), was also observed.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Electron transfer at the reaction center of the purple photosynthetic bacterium Rb. sphaeroides R-26 was measured at room temperature by the time-resolved transient absorption spectroscopy technique with 200 fs temporal resolution. The absorbance changes characteristic of the excited state of the primary donor and extending over the whole spectral range investigated from 350 nm up to 720 nm appeared after excitation with a laser pulse of about 100 fs duration at 800 nm. The time evolution of the spectra reflected the excitation of bacteriochlorophylls (BChl) M and L and the subsequent transfer of this excitation to the primary electron donor (P), with the time constant shorter than 1 ps. The decay time constant of the excited primary donor P was determined as about 3 ps, and it was faster than the rise of the reduced intermediary acceptor bacteriopheophytin (BPhe(L)). Photoreduction of BPhe(L) and its further reoxidation was clearly observed as an increase in its bleaching band intensity at around 540 nm in about 4 ps and its decrease in about 200 ps. Our findings support the theoretical model assuming the involvement of the intermediate state P(+)BChl- in the so-called "two-step" model. In this model an electron is transferred in a sequence from the excited special pair P* to bacteriochlorophyll, BChl(L), then to bacteriopheophytin, BPhe(L), and further on to quinone, Q(A). The branched charge separation, partially via P and partially via BChl(L), was also observed. |
Gapiński, Jacek; Wilk, Agnieszka; Patkowski, Adam; Haeußler, W; Banchio, A J; Pecora, R; Naegele, G The Journal of Chemical Physics, 123 (5), pp. 054708, 2005, ISSN: 0021-9606. @article{Gapinski2005, title = {Diffusion and microstructural properties of solutions of charged nanosized proteins: Experiment versus theory}, author = {Jacek Gapiński and Agnieszka Wilk and Adam Patkowski and W Haeußler and A J Banchio and R Pecora and G Naegele}, url = {http://www.ncbi.nlm.nih.gov/pubmed/16108686 http://aip.scitation.org/doi/10.1063/1.1996569}, doi = {10.1063/1.1996569}, issn = {0021-9606}, year = {2005}, date = {2005-08-01}, journal = {The Journal of Chemical Physics}, volume = {123}, number = {5}, pages = {054708}, abstract = {We have reanalyzed our former static small-angle x-ray scattering and photon correlation spectroscopy results on dense solutions of charged spherical apoferritin proteins using theories recently developed for studies of colloids. The static structure factors S(q), and the small-wave-number collective diffusion coefficient D(c) determined from those experiments are interpreted now in terms of a theoretical scheme based on a Derjaguin-Landau-Verwey-Overbeek-type continuum model of charged colloidal spheres. This scheme accounts, in an approximate way, for many-body hydrodynamic interactions. Stokesian dynamics computer simulations of the hydrodynamic function have been performed for the first time for dense charge-stabilized dispersions to assess the accuracy of the theoretical scheme. We show that the continuum model allows for a consistent description of all experimental results, and that the effective particle charge is dependent upon the protein concentration relative to the added salt concentration. In addition, we discuss the consequences of small ions dynamics for the collective protein diffusion within the framework of the coupled-mode theory.}, keywords = {}, pubstate = {published}, tppubtype = {article} } We have reanalyzed our former static small-angle x-ray scattering and photon correlation spectroscopy results on dense solutions of charged spherical apoferritin proteins using theories recently developed for studies of colloids. The static structure factors S(q), and the small-wave-number collective diffusion coefficient D(c) determined from those experiments are interpreted now in terms of a theoretical scheme based on a Derjaguin-Landau-Verwey-Overbeek-type continuum model of charged colloidal spheres. This scheme accounts, in an approximate way, for many-body hydrodynamic interactions. Stokesian dynamics computer simulations of the hydrodynamic function have been performed for the first time for dense charge-stabilized dispersions to assess the accuracy of the theoretical scheme. We show that the continuum model allows for a consistent description of all experimental results, and that the effective particle charge is dependent upon the protein concentration relative to the added salt concentration. In addition, we discuss the consequences of small ions dynamics for the collective protein diffusion within the framework of the coupled-mode theory. |
Hołyst, R; Staniszewski, K; Patkowski, Adam; Gapiński, Jacek The Journal of Physical Chemistry B, 109 (18), pp. 8533–8537, 2005, ISSN: 1520-6106. @article{Hoyst2005, title = {Hidden Minima of the Gibbs Free Energy Revealed in a Phase Separation in Polymer/Surfactant/Water Mixture}, author = {R Hołyst and K Staniszewski and Adam Patkowski and Jacek Gapiński}, url = {http://www.ncbi.nlm.nih.gov/pubmed/16852004 http://pubs.acs.org/doi/abs/10.1021/jp050634y}, doi = {10.1021/jp050634y}, issn = {1520-6106}, year = {2005}, date = {2005-05-01}, journal = {The Journal of Physical Chemistry B}, volume = {109}, number = {18}, pages = {8533--8537}, abstract = {We observed a very unusual kinetic pathway in a separating C(12)E(6)/PEG/H(2)O ternary mixture. We let the mixture separate above the spinodal temperature (cloud point temperature) for some time and next cool it into a metastable region of a phase diagram, characterized by two minima of the Gibbs potential, one corresponding to the homogeneous mixture and one to the fully separated PEG-rich and C(12)E(6)-rich phases. Despite the fact that in the metastable region the thermodynamic equilibrium corresponds to the separated phases (global minimum of the Gibbs free energy), we observe perfect mixing of the initially separated phase. The homogeneous state, obtained in this way, does not separate, if left undisturbed. However, many cooling-heating cycles or full separation with visible meniscus above the cloud point temperature induce the phase separation in the metastable region. The metastable region can exist tens of degrees below the cloud point temperature. This effect is not observed in the binary mixture of C(12)E(6)/H(2)O.}, keywords = {}, pubstate = {published}, tppubtype = {article} } We observed a very unusual kinetic pathway in a separating C(12)E(6)/PEG/H(2)O ternary mixture. We let the mixture separate above the spinodal temperature (cloud point temperature) for some time and next cool it into a metastable region of a phase diagram, characterized by two minima of the Gibbs potential, one corresponding to the homogeneous mixture and one to the fully separated PEG-rich and C(12)E(6)-rich phases. Despite the fact that in the metastable region the thermodynamic equilibrium corresponds to the separated phases (global minimum of the Gibbs free energy), we observe perfect mixing of the initially separated phase. The homogeneous state, obtained in this way, does not separate, if left undisturbed. However, many cooling-heating cycles or full separation with visible meniscus above the cloud point temperature induce the phase separation in the metastable region. The metastable region can exist tens of degrees below the cloud point temperature. This effect is not observed in the binary mixture of C(12)E(6)/H(2)O. |
Gibasiewicz, Krzysztof; Croce, R; Morosinotto, T; Ihalainen, J A; van Stokkum, I H M; Dekker, J P; Bassi, R; van Grondelle, R Excitation Energy Transfer Pathways in Lhca4 Biophysical Journal, 88 (3), pp. 1959–1969, 2005, ISSN: 00063495. @article{Gibasiewicz2005b, title = {Excitation Energy Transfer Pathways in Lhca4}, author = {Krzysztof Gibasiewicz and R Croce and T Morosinotto and J A Ihalainen and I H M van Stokkum and J P Dekker and R Bassi and R van Grondelle}, url = {http://www.ncbi.nlm.nih.gov/pubmed/15653744 http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=PMC1305248 http://linkinghub.elsevier.com/retrieve/pii/S0006349505732586}, doi = {10.1529/biophysj.104.049916}, issn = {00063495}, year = {2005}, date = {2005-03-01}, journal = {Biophysical Journal}, volume = {88}, number = {3}, pages = {1959--1969}, publisher = {The Biophysical Society}, abstract = {EET in reconstituted Lhca4, a peripheral light-harvesting complex from Photosystem I of Arabidopsis thaliana, containing 10 chlorophylls and 2 carotenoids, was studied at room temperature by femtosecond transient absorption spectroscopy. Two spectral forms of Lut were observed in the sites L1 and L2, characterized by significantly different interactions with nearby chlorophyll a molecules. A favorable interpretation of these differences is that the efficiency of EET to Chls is about two times lower from the "blue" Lut in the site L1 than from the "red" Lut in the site L2 due to fast IC in the former case. A major part of the energy absorbed by the "red" Lut, approximately 60%-70%, is transferred to Chls on a sub-100-fs timescale from the state S(2) but, in addition, minor EET from the hot S(1) state within 400-500 fs is also observed. EET from the S(1) state to chlorophylls occurs also within 2-3 ps and is ascribed to Vio and/or "blue" Lut. EET from Chl b to Chl a is biphasic and characterized by time constants of approximately 300 fs and 3.0 ps. These rates are ascribed to EET from Chl b spectral forms absorbing at approximately 644 nm and approximately 650 nm, respectively. About 25% of the excited Chls a decays very fast-within approximately 15 ps. This decay is proposed to be related to the presence of the interacting Chls A5 and B5 located next to the carotenoid in the site L2 and may imply some photoprotective role for Lhca4 in the photosystem I super-complex.}, keywords = {}, pubstate = {published}, tppubtype = {article} } EET in reconstituted Lhca4, a peripheral light-harvesting complex from Photosystem I of Arabidopsis thaliana, containing 10 chlorophylls and 2 carotenoids, was studied at room temperature by femtosecond transient absorption spectroscopy. Two spectral forms of Lut were observed in the sites L1 and L2, characterized by significantly different interactions with nearby chlorophyll a molecules. A favorable interpretation of these differences is that the efficiency of EET to Chls is about two times lower from the "blue" Lut in the site L1 than from the "red" Lut in the site L2 due to fast IC in the former case. A major part of the energy absorbed by the "red" Lut, approximately 60%-70%, is transferred to Chls on a sub-100-fs timescale from the state S(2) but, in addition, minor EET from the hot S(1) state within 400-500 fs is also observed. EET from the S(1) state to chlorophylls occurs also within 2-3 ps and is ascribed to Vio and/or "blue" Lut. EET from Chl b to Chl a is biphasic and characterized by time constants of approximately 300 fs and 3.0 ps. These rates are ascribed to EET from Chl b spectral forms absorbing at approximately 644 nm and approximately 650 nm, respectively. About 25% of the excited Chls a decays very fast-within approximately 15 ps. This decay is proposed to be related to the presence of the interacting Chls A5 and B5 located next to the carotenoid in the site L2 and may imply some photoprotective role for Lhca4 in the photosystem I super-complex. |
Pochylski, Mikołaj; Aliotta, F; Błaszczak, Z; Gapiński, Jacek Structural Relaxation Processes in Polyethylene Glycol/CCl 4 Solutions by Brillouin Scattering The Journal of Physical Chemistry B, 109 (9), pp. 4181–4188, 2005, ISSN: 1520-6106. @article{Pochylski2005, title = {Structural Relaxation Processes in Polyethylene Glycol/CCl 4 Solutions by Brillouin Scattering}, author = {Mikołaj Pochylski and F Aliotta and Z Błaszczak and Jacek Gapiński}, url = {http://www.ncbi.nlm.nih.gov/pubmed/16851480 http://pubs.acs.org/doi/abs/10.1021/jp045130z}, doi = {10.1021/jp045130z}, issn = {1520-6106}, year = {2005}, date = {2005-03-01}, journal = {The Journal of Physical Chemistry B}, volume = {109}, number = {9}, pages = {4181--4188}, abstract = {We present results of a Brillouin scattering experiment on solutions of poly(ethylene glycol) of mean molecular mass 600 g/mol (PEG600) in CCl4. The relaxation process detected has been assigned to conformational rearrangements of the polymeric chains, triggered by reorientation of the side groups. The concentration dependencies of the hypersound velocity and normalized absorption are compared against the indications from several models proposed in the literature. The concentration evolution of the system is described in terms of two distinct regimes. At high polymer content, the system is dominated by the structure of the dense polymer, where polymer-polymer interactions, together with excluded volume effects, induce the existence of a preferred local arrangement resulting in a narrow distribution of the relaxation times, with the average value of the relaxation time following a simple Arrhenius temperature dependence. As the concentration decreases, the original structure of the hydrogen bonded polymer network is destroyed, and a number of different local configuration coexist, giving rise to a wider distribution of relaxation times or to a multiple relaxation. At low concentrations, the experimental data are well fitted assuming a Vogel-Fulker-Tammon behavior for the average relaxation time. In addition, the observed deviation from the ideal behavior for the refractive index and the density suggests that CCl4 does not behave as an inert solvent, and due to polarization effects, it can develop local hetero-associated structures via electrostatic interaction with the O-H end groups of the polymeric chains. The hypothesis has been successfully tested by fitting the concentration behavior of the hypersonic velocity to a recent three-component model, suitable to describe the concentration dependence of sound velocity in moderately interacting fluids. The indication of the model furnishes a very high value for the association constant of the PEG600, confirming the literature indication that, in polymeric systems capable of developing long liner aggregates via hydrogen bonding interaction, the Brillouin probe is insensitive to the true length of the polymeric chains. The Brillouin scattering experiment just sees an effective hydrogen bonded aggregate that is huge relative to the length of the single polymeric chain and becomes sensitive only to the density fluctuations of the local segmental motions.}, keywords = {}, pubstate = {published}, tppubtype = {article} } We present results of a Brillouin scattering experiment on solutions of poly(ethylene glycol) of mean molecular mass 600 g/mol (PEG600) in CCl4. The relaxation process detected has been assigned to conformational rearrangements of the polymeric chains, triggered by reorientation of the side groups. The concentration dependencies of the hypersound velocity and normalized absorption are compared against the indications from several models proposed in the literature. The concentration evolution of the system is described in terms of two distinct regimes. At high polymer content, the system is dominated by the structure of the dense polymer, where polymer-polymer interactions, together with excluded volume effects, induce the existence of a preferred local arrangement resulting in a narrow distribution of the relaxation times, with the average value of the relaxation time following a simple Arrhenius temperature dependence. As the concentration decreases, the original structure of the hydrogen bonded polymer network is destroyed, and a number of different local configuration coexist, giving rise to a wider distribution of relaxation times or to a multiple relaxation. At low concentrations, the experimental data are well fitted assuming a Vogel-Fulker-Tammon behavior for the average relaxation time. In addition, the observed deviation from the ideal behavior for the refractive index and the density suggests that CCl4 does not behave as an inert solvent, and due to polarization effects, it can develop local hetero-associated structures via electrostatic interaction with the O-H end groups of the polymeric chains. The hypothesis has been successfully tested by fitting the concentration behavior of the hypersonic velocity to a recent three-component model, suitable to describe the concentration dependence of sound velocity in moderately interacting fluids. The indication of the model furnishes a very high value for the association constant of the PEG600, confirming the literature indication that, in polymeric systems capable of developing long liner aggregates via hydrogen bonding interaction, the Brillouin probe is insensitive to the true length of the polymeric chains. The Brillouin scattering experiment just sees an effective hydrogen bonded aggregate that is huge relative to the length of the single polymeric chain and becomes sensitive only to the density fluctuations of the local segmental motions. |
Włodarczyk, Agnieszka; Grzybowski, Przemysław; Patkowski, Adam; Dobek, Andrzej The Journal of Physical Chemistry B, 109 (8), pp. 3594–3605, 2005, ISSN: 1520-6106. @article{Wodarczyk2005, title = {Effect of Ions on the Polymorphism, Effective Charge, and Stability of Human Telomeric DNA. Photon Correlation Spectroscopy and Circular Dichroism Studies}, author = {Agnieszka Włodarczyk and Przemysław Grzybowski and Adam Patkowski and Andrzej Dobek}, url = {http://www.ncbi.nlm.nih.gov/pubmed/16851398 http://pubs.acs.org/doi/abs/10.1021/jp045274d}, doi = {10.1021/jp045274d}, issn = {1520-6106}, year = {2005}, date = {2005-03-01}, journal = {The Journal of Physical Chemistry B}, volume = {109}, number = {8}, pages = {3594--3605}, abstract = {The effect of different ions on the formation and behavior of quadruplex structures of the human telomere sequence d(TTAGGG)(4) has been studied by photon correlation spectroscopy (PCS) and circular dichroism (CD). The saturation and melting curves obtained in the presence of K(+), Na(+), Rb(+), Li(+), Cs(+), and Sr(2+) ions were recorded by CD spectroscopy and indicated the formation of monomeric quadruplexes. Analysis of the saturation curves obtained at 2 degrees C has shown that the presence of a single Sr(2+) ion per oligomer is sufficient for the formation of a monomeric quadruplex of the DNA sequence studied. In the presence of SrCl(2) at a concentration of 50 mM, the formation of tetrameric quadruplexes has been detected. The effect of Sr(2+) ions on the formation of quadruplex structures by the human telomere sequence d(TTAGGG)(4) is stronger and different from that of the other ions tested. The paper also presents results of a study of electrostatic interactions in solution. The translation diffusion coefficients D(T) of the structures present in solution have been determined by photon correlation spectroscopy and the effective charges on the structures have been calculated by combining the experimental data with the results based on the coupled mode theory. Analysis of the melting points monitored by the CD method has permitted a determination of Deltan, the number of ions released in the process of thermal denaturation. All the results are in good agreement with the predictions based on the theory of polyelectrolytes. The effect of ions on the formation and behavior of quadruplex structures of the human telomere sequence d(TTAGGG)(4) has been studied by photon correlation spectroscopy and circular dichroism.}, keywords = {}, pubstate = {published}, tppubtype = {article} } The effect of different ions on the formation and behavior of quadruplex structures of the human telomere sequence d(TTAGGG)(4) has been studied by photon correlation spectroscopy (PCS) and circular dichroism (CD). The saturation and melting curves obtained in the presence of K(+), Na(+), Rb(+), Li(+), Cs(+), and Sr(2+) ions were recorded by CD spectroscopy and indicated the formation of monomeric quadruplexes. Analysis of the saturation curves obtained at 2 degrees C has shown that the presence of a single Sr(2+) ion per oligomer is sufficient for the formation of a monomeric quadruplex of the DNA sequence studied. In the presence of SrCl(2) at a concentration of 50 mM, the formation of tetrameric quadruplexes has been detected. The effect of Sr(2+) ions on the formation of quadruplex structures by the human telomere sequence d(TTAGGG)(4) is stronger and different from that of the other ions tested. The paper also presents results of a study of electrostatic interactions in solution. The translation diffusion coefficients D(T) of the structures present in solution have been determined by photon correlation spectroscopy and the effective charges on the structures have been calculated by combining the experimental data with the results based on the coupled mode theory. Analysis of the melting points monitored by the CD method has permitted a determination of Deltan, the number of ions released in the process of thermal denaturation. All the results are in good agreement with the predictions based on the theory of polyelectrolytes. The effect of ions on the formation and behavior of quadruplex structures of the human telomere sequence d(TTAGGG)(4) has been studied by photon correlation spectroscopy and circular dichroism. |
Rathgeber, Silke; Pakula, Tadeusz; Wilk, Agnieszka; Matyjaszewski, Krzysztof; Beers, Kathryn L On the shape of bottle-brush macromolecules: Systematic variation of architectural parameters The Journal of Chemical Physics, 122 (12), pp. 124904, 2005, ISSN: 0021-9606. @article{Rathgeber2005, title = {On the shape of bottle-brush macromolecules: Systematic variation of architectural parameters}, author = {Silke Rathgeber and Tadeusz Pakula and Agnieszka Wilk and Krzysztof Matyjaszewski and Kathryn L Beers}, url = {http://www.ncbi.nlm.nih.gov/pubmed/15836421 http://aip.scitation.org/doi/10.1063/1.1860531}, doi = {10.1063/1.1860531}, issn = {0021-9606}, year = {2005}, date = {2005-03-01}, journal = {The Journal of Chemical Physics}, volume = {122}, number = {12}, pages = {124904}, abstract = {We measured the form factor of bottle-brush macromolecules under good solvent conditions with small-angle neutron scattering and static light scattering. The systems under investigation are brushes, synthesized via the grafting-from route, built from a poly(alkyl methacrylate) backbone to which poly(n-butyl acrylate) side chains are densely grafted. The aim of our work is to study how the systematic variation of structural parameters such as the side chain length and backbone length change the conformation of the polymer brushes in solution. All spectra can be consistently described by a model, considering the bottle-brush polymers as flexible rods with internal density fluctuations. Parameters discussed are (1) the contour length per main chain monomer l(b), (2) the fractal dimension of the side chains Ds, as well as (3) the fractal dimension D, and (4) the Kuhn length lambdak of the overall brush. l(b)=0.253+/-0.008 nm is found to be independent of the side chain length and equal to the value found for the bare main chain, indicating a strongly stretched conformation for the backbone due to the presence of the side chains. The fractal dimension of the side chains is determined to be Ds=1.75+/-0.07 which is very close to the value of 10.588 approximately 1.70 expected for a three-dimensional self-avoiding random walk (3D-SAW) under good solvent conditions. On larger length scales the overall brush appears to be a 3D-SAW itself (D=1.64+/-0.08) with a Kuhn-step length of lambdak=70+/-4 nm. The value is independent of the side chain length and 46 times larger than the Kuhn length of the bare backbone (lambdak=1.8+/-0.2 nm). The ratio of Kuhn length to brush diameter lambda(k)dtextgreateror=20 determines whether lyotropic behavior can be expected or not. Since longer side chains do not lead to more persistent structures, lambda(k)d decreases from 8 to 4 with increasing side chain length and lyotropic behavior becomes unlikely.}, keywords = {}, pubstate = {published}, tppubtype = {article} } We measured the form factor of bottle-brush macromolecules under good solvent conditions with small-angle neutron scattering and static light scattering. The systems under investigation are brushes, synthesized via the grafting-from route, built from a poly(alkyl methacrylate) backbone to which poly(n-butyl acrylate) side chains are densely grafted. The aim of our work is to study how the systematic variation of structural parameters such as the side chain length and backbone length change the conformation of the polymer brushes in solution. All spectra can be consistently described by a model, considering the bottle-brush polymers as flexible rods with internal density fluctuations. Parameters discussed are (1) the contour length per main chain monomer l(b), (2) the fractal dimension of the side chains Ds, as well as (3) the fractal dimension D, and (4) the Kuhn length lambdak of the overall brush. l(b)=0.253+/-0.008 nm is found to be independent of the side chain length and equal to the value found for the bare main chain, indicating a strongly stretched conformation for the backbone due to the presence of the side chains. The fractal dimension of the side chains is determined to be Ds=1.75+/-0.07 which is very close to the value of 10.588 approximately 1.70 expected for a three-dimensional self-avoiding random walk (3D-SAW) under good solvent conditions. On larger length scales the overall brush appears to be a 3D-SAW itself (D=1.64+/-0.08) with a Kuhn-step length of lambdak=70+/-4 nm. The value is independent of the side chain length and 46 times larger than the Kuhn length of the bare backbone (lambdak=1.8+/-0.2 nm). The ratio of Kuhn length to brush diameter lambda(k)dtextgreateror=20 determines whether lyotropic behavior can be expected or not. Since longer side chains do not lead to more persistent structures, lambda(k)d decreases from 8 to 4 with increasing side chain length and lyotropic behavior becomes unlikely. |
Kahle, S; Gapiński, Jacek; Hinze, G; Patkowski, Adam; Meier, G The Journal of Chemical Physics, 122 (7), pp. 074506, 2005, ISSN: 0021-9606. @article{Kahle2005, title = {A comparison of relaxation processes in structurally related van der Waals glass formers: The role of internal degrees of freedom}, author = {S Kahle and Jacek Gapiński and G Hinze and Adam Patkowski and G Meier}, url = {http://www.ncbi.nlm.nih.gov/pubmed/15743253 http://aip.scitation.org/doi/10.1063/1.1846653}, doi = {10.1063/1.1846653}, issn = {0021-9606}, year = {2005}, date = {2005-02-01}, journal = {The Journal of Chemical Physics}, volume = {122}, number = {7}, pages = {074506}, abstract = {Depolarized dynamic light scattering (DLS), dielectric relaxation (DS), and deuterium NMR studies of fragile van der Waals glass forming liquids phenylphthalein-dimethylether (PDE) and cresolphthalein-dimethylether (KDE) are presented. In PDE a new dielectric loss process was found, which can be attributed to the 180 degrees flip of the phenyl rings. The previous finding that the distribution of the structural relaxation times measured for PDE and KDE by DS is substantially narrower than that measured by DLS is explained by partial decoupling of the dynamics of the dipole moment from the structural relaxation of the sample. The dynamics of PDE and KDE is compared with the previous studies of two other structurally similar liquids: 1,1'-di(4-methoxy-5-methylphenyl)cyclohexane (BMMPC) and 1,1'-bis(p-methoxyphenyl)cyclohexane (BMPC) in order to relate dynamical features with the chemical structure of the material. The evidence for the intramolecular character of the secondary relaxations observed in BMPC and PDE is presented.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Depolarized dynamic light scattering (DLS), dielectric relaxation (DS), and deuterium NMR studies of fragile van der Waals glass forming liquids phenylphthalein-dimethylether (PDE) and cresolphthalein-dimethylether (KDE) are presented. In PDE a new dielectric loss process was found, which can be attributed to the 180 degrees flip of the phenyl rings. The previous finding that the distribution of the structural relaxation times measured for PDE and KDE by DS is substantially narrower than that measured by DLS is explained by partial decoupling of the dynamics of the dipole moment from the structural relaxation of the sample. The dynamics of PDE and KDE is compared with the previous studies of two other structurally similar liquids: 1,1'-di(4-methoxy-5-methylphenyl)cyclohexane (BMMPC) and 1,1'-bis(p-methoxyphenyl)cyclohexane (BMPC) in order to relate dynamical features with the chemical structure of the material. The evidence for the intramolecular character of the secondary relaxations observed in BMPC and PDE is presented. |
Ihalainen, Janne A; van Stokkum, Ivo H M; Gibasiewicz, Krzysztof; Germano, Marta; van Grondelle, Rienk; Dekker, Jan P Biochimica et Biophysica Acta (BBA) - Bioenergetics, 1706 (3), pp. 267–275, 2005, ISSN: 00052728. @article{Ihalainen2005, title = {Kinetics of excitation trapping in intact Photosystem I of Chlamydomonas reinhardtii and Arabidopsis thaliana}, author = {Janne A Ihalainen and Ivo H M van Stokkum and Krzysztof Gibasiewicz and Marta Germano and Rienk van Grondelle and Jan P Dekker}, url = {http://www.ncbi.nlm.nih.gov/pubmed/15694355 http://linkinghub.elsevier.com/retrieve/pii/S0005272804003299}, doi = {10.1016/j.bbabio.2004.11.007}, issn = {00052728}, year = {2005}, date = {2005-02-01}, journal = {Biochimica et Biophysica Acta (BBA) - Bioenergetics}, volume = {1706}, number = {3}, pages = {267--275}, abstract = {We measured picosecond time-resolved fluorescence of intact Photosystem I complexes from Chlamydomonas reinhardtii and Arabidopsis thaliana. The antenna system of C. reinhardtii contains about 30-60 chlorophylls more than that of A. thaliana, but lacks the so-called red chlorophylls, chlorophylls that absorb at longer wavelength than the primary electron donor. In C. reinhardtii, the main lifetimes of excitation trapping are about 27 and 68 ps. The overall lifetime of C. reinhardtii is considerably shorter than in A. thaliana. We conclude that the amount and energies of the red chlorophylls have a larger effect on excitation trapping time in Photosystem I than the antenna size.}, keywords = {}, pubstate = {published}, tppubtype = {article} } We measured picosecond time-resolved fluorescence of intact Photosystem I complexes from Chlamydomonas reinhardtii and Arabidopsis thaliana. The antenna system of C. reinhardtii contains about 30-60 chlorophylls more than that of A. thaliana, but lacks the so-called red chlorophylls, chlorophylls that absorb at longer wavelength than the primary electron donor. In C. reinhardtii, the main lifetimes of excitation trapping are about 27 and 68 ps. The overall lifetime of C. reinhardtii is considerably shorter than in A. thaliana. We conclude that the amount and energies of the red chlorophylls have a larger effect on excitation trapping time in Photosystem I than the antenna size. |
Błaszczak, Zdzisław; Pochylski, Mikołaj; Iwaszkiewicz-Kostka, Iwona; Ziobrowski, Piotr; Drozdowski, Mirosław Temperature study of Brillouin light scattering in selected dimethacrylates Journal of Molecular Structure, 737 (1), pp. 11 - 15, 2005, ISSN: 0022-2860. @article{Błaszczak2005, title = {Temperature study of Brillouin light scattering in selected dimethacrylates}, author = {Zdzisław Błaszczak and Mikołaj Pochylski and Iwona Iwaszkiewicz-Kostka and Piotr Ziobrowski and Mirosław Drozdowski}, url = {http://www.sciencedirect.com/science/article/pii/S0022286004007239}, doi = {j.molstruc.2004.09.030}, issn = {0022-2860}, year = {2005}, date = {2005-01-01}, journal = {Journal of Molecular Structure}, volume = {737}, number = {1}, pages = {11 - 15}, abstract = {Selected dimethacrylates forming multifunctional monomers have been studied using Brillouin spectroscopy. The hypersound wave propagation velocity and adiabatic compressibility of the compounds studied have been determined. It has been revealed that these quantities depend on both temperature and the structure of the molecule chain of the monomer. Some characteristic features obtained from the Brillouin study have been discussed in terms of molecular interactions.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Selected dimethacrylates forming multifunctional monomers have been studied using Brillouin spectroscopy. The hypersound wave propagation velocity and adiabatic compressibility of the compounds studied have been determined. It has been revealed that these quantities depend on both temperature and the structure of the molecule chain of the monomer. Some characteristic features obtained from the Brillouin study have been discussed in terms of molecular interactions. |
Mikusińska-Planner, A; Gągalska, J; Pochylski, Mikołaj; Kaczmarek, M M X-Ray method of detection of neoplasmic changes Physics and Chemistry of Liquids, 43 (2), pp. 167-174, 2005. @article{doi:10.1080/00319100412331333904, title = {X-Ray method of detection of neoplasmic changes}, author = {A Mikusińska-Planner and J Gągalska and Mikołaj Pochylski and M M Kaczmarek}, url = {https://doi.org/10.1080/00319100412331333904}, doi = {10.1080/00319100412331333904}, year = {2005}, date = {2005-01-01}, journal = {Physics and Chemistry of Liquids}, volume = {43}, number = {2}, pages = {167-174}, publisher = {Taylor & Francis}, abstract = {The article presents an X-ray method of detection of neoplasmic changes in people based on measurements from human blood serum. A new X-ray marker Ωrtg is defined and determined directly from the experimental angular distributions of radiation scattered by human blood serum samples. The numerical values of the marker Ωrtg are related directly to the character of the angular distribution of the scattered radiation intensity. The values of Ωrtg markers obtained for cancer patients were compared with the levels of the PSA marker. Statistical computer analysis of the correlation between the markers Ωrtg and PSA was made with the use of Statistica software by the method of classification trees. The threshold value of the Ωrtg marker, allowing distinction between the healthy and neoplasmically changed blood serum, was determined.}, keywords = {}, pubstate = {published}, tppubtype = {article} } The article presents an X-ray method of detection of neoplasmic changes in people based on measurements from human blood serum. A new X-ray marker Ωrtg is defined and determined directly from the experimental angular distributions of radiation scattered by human blood serum samples. The numerical values of the marker Ωrtg are related directly to the character of the angular distribution of the scattered radiation intensity. The values of Ωrtg markers obtained for cancer patients were compared with the levels of the PSA marker. Statistical computer analysis of the correlation between the markers Ωrtg and PSA was made with the use of Statistica software by the method of classification trees. The threshold value of the Ωrtg marker, allowing distinction between the healthy and neoplasmically changed blood serum, was determined. |
Błaszczak, Zdzisław; Pochylski, Mikołaj; Iwaszkiewicz-Kostka, Iwona; Ziobrowski, Piotr; Drozdowski, Mirosław; Farhoud, Maher Brillouin scattering study of polyethylene glycol different solutions Journal of Molecular Liquids, 121 (2), pp. 75 - 79, 2005, ISSN: 0167-7322. @article{Błaszczak2005b, title = {Brillouin scattering study of polyethylene glycol different solutions}, author = {Zdzisław Błaszczak and Mikołaj Pochylski and Iwona Iwaszkiewicz-Kostka and Piotr Ziobrowski and Mirosław Drozdowski and Maher Farhoud}, url = {http://www.sciencedirect.com/science/article/pii/S016773220400340X}, doi = {j.molliq.2004.10.034}, issn = {0167-7322}, year = {2005}, date = {2005-01-01}, journal = {Journal of Molecular Liquids}, volume = {121}, number = {2}, pages = {75 - 79}, abstract = {Abstract Brillouin spectroscopy was used to study the elastic properties of polyethylene glycol solutions in water, benzene and toluene. It has been shown that the spectroscopic features, characterizing the elastic properties of polymer solutions being under study, strongly depend on both polymer concentration and the kind of solvent. The non-monotonic character of the concentration dependencies of the hypersound velocity and adiabatic compressibility indicate the occurrence of the polymer–solvent interactions.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Abstract Brillouin spectroscopy was used to study the elastic properties of polyethylene glycol solutions in water, benzene and toluene. It has been shown that the spectroscopic features, characterizing the elastic properties of polymer solutions being under study, strongly depend on both polymer concentration and the kind of solvent. The non-monotonic character of the concentration dependencies of the hypersound velocity and adiabatic compressibility indicate the occurrence of the polymer–solvent interactions. |
Kang, Kyongok; Gapiński, Jacek; Lettinga, M P; Buitenhuis, J; Meier, G; Ratajczyk, M; Dhont, Jan K G; Patkowski, Adam Diffusion of spheres in crowded suspensions of rods The Journal of Chemical Physics, 122 (4), pp. 044905, 2005, ISSN: 0021-9606. @article{Kang2005, title = {Diffusion of spheres in crowded suspensions of rods}, author = {Kyongok Kang and Jacek Gapiński and M P Lettinga and J Buitenhuis and G Meier and M Ratajczyk and Jan K G Dhont and Adam Patkowski}, url = {http://www.ncbi.nlm.nih.gov/pubmed/15740296 http://aip.scitation.org/doi/10.1063/1.1834895}, doi = {10.1063/1.1834895}, issn = {0021-9606}, year = {2005}, date = {2005-01-01}, journal = {The Journal of Chemical Physics}, volume = {122}, number = {4}, pages = {044905}, abstract = {Translational tracer diffusion of spherical macromolecules in crowded suspensions of rodlike colloids is investigated. Experiments are done using several kinds of spherical tracers in fd-virus suspensions. A wide range of size ratios L/2a of the length L of the rods and the diameter 2a of the tracer sphere is covered by combining several experimental methods: fluorescence correlation spectroscopy for small tracer spheres, dynamic light scattering for intermediate sized spheres, and video microscopy for large spheres. Fluorescence correlation spectroscopy is shown to measure long-time diffusion only for relatively small tracer spheres. Scaling of diffusion coefficients with a/xi, predicted for static networks, is not found for our dynamical network of rods (with xi the mesh size of the network). Self-diffusion of tracer spheres in the dynamical network of freely suspended rods is thus fundamentally different as compared to cross-linked networks. A theory is developed for the rod-concentration dependence of the translational diffusion coefficient at low rod concentrations for freely suspended rods. The proposed theory is based on a variational solution of the appropriate Smoluchowski equation without hydrodynamic interactions. The theory can, in principle, be further developed to describe diffusion through dynamical networks at higher rod concentrations with the inclusion of hydrodynamic interactions. Quantitative agreement with the experiments is found for large tracer spheres, and qualitative agreement for smaller spheres. This is probably due to the increasing importance of hydrodynamic interactions as compared to direct interactions as the size of the tracer sphere decreases.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Translational tracer diffusion of spherical macromolecules in crowded suspensions of rodlike colloids is investigated. Experiments are done using several kinds of spherical tracers in fd-virus suspensions. A wide range of size ratios L/2a of the length L of the rods and the diameter 2a of the tracer sphere is covered by combining several experimental methods: fluorescence correlation spectroscopy for small tracer spheres, dynamic light scattering for intermediate sized spheres, and video microscopy for large spheres. Fluorescence correlation spectroscopy is shown to measure long-time diffusion only for relatively small tracer spheres. Scaling of diffusion coefficients with a/xi, predicted for static networks, is not found for our dynamical network of rods (with xi the mesh size of the network). Self-diffusion of tracer spheres in the dynamical network of freely suspended rods is thus fundamentally different as compared to cross-linked networks. A theory is developed for the rod-concentration dependence of the translational diffusion coefficient at low rod concentrations for freely suspended rods. The proposed theory is based on a variational solution of the appropriate Smoluchowski equation without hydrodynamic interactions. The theory can, in principle, be further developed to describe diffusion through dynamical networks at higher rod concentrations with the inclusion of hydrodynamic interactions. Quantitative agreement with the experiments is found for large tracer spheres, and qualitative agreement for smaller spheres. This is probably due to the increasing importance of hydrodynamic interactions as compared to direct interactions as the size of the tracer sphere decreases. |
2004 |
Dreyfus, C; Grand, Le A; Gapiński, Jacek; Steffen, W; Patkowski, Adam Scaling the $backslashalpha $ -relaxation time of supercooled fragile organic liquids The European Physical Journal B - Condensed Matter and Complex Systems, 42 (3), pp. 309–319, 2004, ISSN: 1434-6028. @article{Dreyfus2004, title = {Scaling the $backslashalpha $ -relaxation time of supercooled fragile organic liquids}, author = {C Dreyfus and A Le Grand and Jacek Gapiński and W Steffen and Adam Patkowski}, url = {http://link.springer.com/10.1140/epjb/e2004-00386-3}, doi = {10.1140/epjb/e2004-00386-3}, issn = {1434-6028}, year = {2004}, date = {2004-12-01}, journal = {The European Physical Journal B - Condensed Matter and Complex Systems}, volume = {42}, number = {3}, pages = {309--319}, publisher = {EDP Sciences}, abstract = {It was shown recently [1] that the structural $alpha$-relaxation time $backslashtau $ of supercooled o-terphenyl depends on a single control parameter $backslashGamma $, which is the product of a function of density $E(backslashrho )$, by the inverse temperature T -1. We extend this finding to other fragile glassforming liquids using light scattering data. Available experimental results do not allow to discriminate between several analytical forms of the function $E(backslashrho )$, the scaling arising from the separation of density and temperature in $backslashGamma $. We also propose a simple form for $backslashtau (backslashGamma )$, which depends only on three material-dependent parameters, reproducing relaxation times over 12 orders of magnitude.}, keywords = {}, pubstate = {published}, tppubtype = {article} } It was shown recently [1] that the structural $alpha$-relaxation time $backslashtau $ of supercooled o-terphenyl depends on a single control parameter $backslashGamma $, which is the product of a function of density $E(backslashrho )$, by the inverse temperature T -1. We extend this finding to other fragile glassforming liquids using light scattering data. Available experimental results do not allow to discriminate between several analytical forms of the function $E(backslashrho )$, the scaling arising from the separation of density and temperature in $backslashGamma $. We also propose a simple form for $backslashtau (backslashGamma )$, which depends only on three material-dependent parameters, reproducing relaxation times over 12 orders of magnitude. |
Wilk, Agnieszka; Gapiński, Jacek; Patkowski, Adam; Pecora, R The Journal of Chemical Physics, 121 (21), pp. 10794–10802, 2004, ISSN: 0021-9606. @article{Wilk2004, title = {Self-diffusion in solutions of a 20 base pair oligonucleotide: Effects of concentration and ionic strength}, author = {Agnieszka Wilk and Jacek Gapiński and Adam Patkowski and R Pecora}, url = {http://www.ncbi.nlm.nih.gov/pubmed/15549965 http://aip.scitation.org/doi/10.1063/1.1811599}, doi = {10.1063/1.1811599}, issn = {0021-9606}, year = {2004}, date = {2004-12-01}, journal = {The Journal of Chemical Physics}, volume = {121}, number = {21}, pages = {10794--10802}, abstract = {The long-time self-diffusion coefficients of a 20 base pair duplex oligonucleotide are measured as functions of 20-mer and added NaCl salt concentrations. The self-diffusion coefficients decrease monotonically with increasing 20-mer concentrations for the high-added salt sample and display non-monotonically decreasing 20-mer concentration dependences at lower added salt concentrations. The non-monotonic behavior is attributed to the opposing effects of the tendency to increase the interactions between 20-mers as the concentration is increased and to a decrease in the extent of the Coulomb forces as counterions from the 20-mer increasingly screen them. Attempts to account for the effect of the Coulomb forces on the self-diffusion coefficients by using effective dimensions in the hard rod theory give good agreement with experiment at the highest salt concentration studied. For the lower salt concentrations there appear to be two scaling regimes--one at low polyion concentration in which the high salt scaling of the rod dimensions by adding the Debye screening to the length and diameter of the rod is appropriate and one at high polyion concentrations where the scaling of the dimensions is the addition of 1/2 the Debye screening length. Estimates of the "overlap" concentration C*=1/L(eff) indicate that the non-monotonic decrease occurs at concentrations lower than C*. Finally, the fluorescence correlation spectroscopy self-diffusion coefficients measured here are compared with the mutual diffusion coefficients measured by dynamic light scattering.}, keywords = {}, pubstate = {published}, tppubtype = {article} } The long-time self-diffusion coefficients of a 20 base pair duplex oligonucleotide are measured as functions of 20-mer and added NaCl salt concentrations. The self-diffusion coefficients decrease monotonically with increasing 20-mer concentrations for the high-added salt sample and display non-monotonically decreasing 20-mer concentration dependences at lower added salt concentrations. The non-monotonic behavior is attributed to the opposing effects of the tendency to increase the interactions between 20-mers as the concentration is increased and to a decrease in the extent of the Coulomb forces as counterions from the 20-mer increasingly screen them. Attempts to account for the effect of the Coulomb forces on the self-diffusion coefficients by using effective dimensions in the hard rod theory give good agreement with experiment at the highest salt concentration studied. For the lower salt concentrations there appear to be two scaling regimes--one at low polyion concentration in which the high salt scaling of the rod dimensions by adding the Debye screening to the length and diameter of the rod is appropriate and one at high polyion concentrations where the scaling of the dimensions is the addition of 1/2 the Debye screening length. Estimates of the "overlap" concentration C*=1/L(eff) indicate that the non-monotonic decrease occurs at concentrations lower than C*. Finally, the fluorescence correlation spectroscopy self-diffusion coefficients measured here are compared with the mutual diffusion coefficients measured by dynamic light scattering. |
Patkowski, Adam; Gapiński, Jacek; Meier, Gerhard Dynamics of supercooled van der Waals liquid under pressure. A dynamic light scattering study Colloid & Polymer Science, 282 (8), pp. 874–881, 2004, ISSN: 0303-402X. @article{Patkowski2004, title = {Dynamics of supercooled van der Waals liquid under pressure. A dynamic light scattering study}, author = {Adam Patkowski and Jacek Gapiński and Gerhard Meier}, url = {http://link.springer.com/10.1007/s00396-004-1102-7}, doi = {10.1007/s00396-004-1102-7}, issn = {0303-402X}, year = {2004}, date = {2004-06-01}, journal = {Colloid & Polymer Science}, volume = {282}, number = {8}, pages = {874--881}, publisher = {Springer-Verlag}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Angelini, R; Fioretto, D; Gapiński, Jacek; Monaco, G; Patkowski, Adam Study of the Rytov dip for liquid o -terphenyl Philosophical Magazine, 84 (13-16), pp. 1463–1469, 2004, ISSN: 1478-6435. @article{Angelini2004, title = {Study of the Rytov dip for liquid o -terphenyl}, author = {R Angelini and D Fioretto and Jacek Gapiński and G Monaco and Adam Patkowski}, url = {http://www.tandfonline.com/doi/abs/10.1080/14786430310001644224}, doi = {10.1080/14786430310001644224}, issn = {1478-6435}, year = {2004}, date = {2004-05-01}, journal = {Philosophical Magazine}, volume = {84}, number = {13-16}, pages = {1463--1469}, publisher = {Taylor & Francis Group}, abstract = {Light scattering spectra in the depolarized configuration are presented for the fragile glass former o-terphenyl in the temperature range between 350 and 421 K. These spectra are characterized by the presence of the Rytov dip and have been analysed in terms of the two-variable model of Andersen and Pecora. This model works well in the whole temperature range explored, that is over a range where the shear viscosity varies by almost one decade. The coupling parameter R is extracted and turns out to be almost temperature independent and very similar to that derived for other studied systems.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Light scattering spectra in the depolarized configuration are presented for the fragile glass former o-terphenyl in the temperature range between 350 and 421 K. These spectra are characterized by the presence of the Rytov dip and have been analysed in terms of the two-variable model of Andersen and Pecora. This model works well in the whole temperature range explored, that is over a range where the shear viscosity varies by almost one decade. The coupling parameter R is extracted and turns out to be almost temperature independent and very similar to that derived for other studied systems. |
Petekidis, G; Gapiński, Jacek; Seymour, P; van Duijneveldt, J S; Vlassopoulos, D; Fytas, G Dynamics of core-shell particles in concentrated suspensions Physical Review E, 69 (4), pp. 042401, 2004, ISSN: 1539-3755. @article{Petekidis2004, title = {Dynamics of core-shell particles in concentrated suspensions}, author = {G Petekidis and Jacek Gapiński and P Seymour and J S van Duijneveldt and D Vlassopoulos and G Fytas}, url = {http://www.ncbi.nlm.nih.gov/pubmed/15169049 https://link.aps.org/doi/10.1103/PhysRevE.69.042401}, doi = {10.1103/PhysRevE.69.042401}, issn = {1539-3755}, year = {2004}, date = {2004-04-01}, journal = {Physical Review E}, volume = {69}, number = {4}, pages = {042401}, abstract = {The dynamics of soft colloidal particles in a concentrated suspension was studied by two color dynamic light scattering. The short-time diffusion coefficient, D(s)(q), revealed a weak slowing down around the peak of S(q) in contrast to the much stronger dependence observed in hard sphere systems, and the absence of any slowing down in ultrasoft diblock micelles. The low-q limit of the diffusion coefficient, D(s)(q=0), reflecting the cooperative nature of the dynamics was found to decrease from its dilute limit value in contrast to the weak increase observed in hard sphere systems. The behavior of D(s)(q) reflects distinct polymer-layer-induced hydrodynamic effects present in concentrated suspensions of core-shell particles.}, keywords = {}, pubstate = {published}, tppubtype = {article} } The dynamics of soft colloidal particles in a concentrated suspension was studied by two color dynamic light scattering. The short-time diffusion coefficient, D(s)(q), revealed a weak slowing down around the peak of S(q) in contrast to the much stronger dependence observed in hard sphere systems, and the absence of any slowing down in ultrasoft diblock micelles. The low-q limit of the diffusion coefficient, D(s)(q=0), reflecting the cooperative nature of the dynamics was found to decrease from its dilute limit value in contrast to the weak increase observed in hard sphere systems. The behavior of D(s)(q) reflects distinct polymer-layer-induced hydrodynamic effects present in concentrated suspensions of core-shell particles. |
Krzaczkowska, J; Gierszewski, J; Ślósarek, Genowefa Solubility of Adenine and Kinetin in Water–Ethanol Solutions Journal of Solution Chemistry, 33 (4), pp. 395–406, 2004, ISSN: 0095-9782. @article{Krzaczkowska2004, title = {Solubility of Adenine and Kinetin in Water–Ethanol Solutions}, author = {J Krzaczkowska and J Gierszewski and Genowefa Ślósarek}, url = {http://link.springer.com/10.1023/B:JOSL.0000036309.37357.70}, doi = {10.1023/B:JOSL.0000036309.37357.70}, issn = {0095-9782}, year = {2004}, date = {2004-04-01}, journal = {Journal of Solution Chemistry}, volume = {33}, number = {4}, pages = {395--406}, publisher = {Kluwer Academic Publishers-Plenum Publishers}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Skibinska, Lidia; Banachowicz, Ewa; Gapiński, Jacek; Patkowski, Adam; Barciszewski, Jan Structural similarity ofE. coli 5S rRNA in solution and within the ribosome Biopolymers, 73 (3), pp. 316–325, 2004, ISSN: 0006-3525. @article{Skibinska2004, title = {Structural similarity ofE. coli 5S rRNA in solution and within the ribosome}, author = {Lidia Skibinska and Ewa Banachowicz and Jacek Gapiński and Adam Patkowski and Jan Barciszewski}, url = {http://doi.wiley.com/10.1002/bip.10598}, doi = {10.1002/bip.10598}, issn = {0006-3525}, year = {2004}, date = {2004-02-01}, journal = {Biopolymers}, volume = {73}, number = {3}, pages = {316--325}, publisher = {Wiley Subscription Services, Inc., A Wiley Company}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Ramesh, V M; Gibasiewicz, Krzysztof; Lin, Su; Bingham, Scott E; Webber, Andrew N Biochemistry, 43 (5), pp. 1369–1375, 2004, ISSN: 0006-2960. @article{Ramesh2004, title = {Bidirectional Electron Transfer in Photosystem I: Accumulation of A 0 - in A-Side or B-Side Mutants of the Axial Ligand to Chlorophyll A 0 †}, author = {V M Ramesh and Krzysztof Gibasiewicz and Su Lin and Scott E Bingham and Andrew N Webber}, url = {http://www.ncbi.nlm.nih.gov/pubmed/14756574 http://pubs.acs.org/doi/abs/10.1021/bi0354177}, doi = {10.1021/bi0354177}, issn = {0006-2960}, year = {2004}, date = {2004-02-01}, journal = {Biochemistry}, volume = {43},< |
Publikacje
2021 |
Adsorption of bacteriophages on polypropylene labware affects the reproducibility of phage research Scientific Reports, 11 (1), pp. 7387, 2021, ISSN: 20452322. |
Optomechanical crystals for spatial sensing of submicron sized particles Scientific Reports, 11 (1), pp. 7829, 2021, ISSN: 2045-2322. |
The Journal of Physical Chemistry B, 125 (13), pp. 3307–3320, 2021, ISSN: 1520-6106. |
Progress and perspectives on phononic crystals Journal of Applied Physics, 129 (16), pp. 160901, 2021, ISSN: 0021-8979. |
Materials Science and Engineering: C, 118 , pp. 111507, 2021, ISSN: 0928-4931. |
Journal of Molecular Liquids, 323 , pp. 114963, 2021, ISSN: 0167-7322. |
Chemical Engineering Journal, 415 , pp. 128987, 2021, ISSN: 1385-8947. |
2020 |
Revealing Fast Proton Transport in Condensed Matter by Means of Density Scaling Concept The Journal of Physical Chemistry C, 124 (29), pp. 15749–15756, 2020. |
Ultrathin Polydopamine Films with Phospholipid Nanodiscs Containing a Glycophorin A Domain Advanced Functional Materials, 30 (8), pp. 2000378, 2020, ISSN: 1616301X. |
Nano Letters, 20 (3), pp. 1883–1889, 2020, ISSN: 1530-6984. |
Biochimica et Biophysica Acta (BBA) - Bioenergetics, 1861 (2), pp. 148136, 2020, ISSN: 00052728. |
Excitation dynamics in Photosystem I trapped in TiO2 mesopores Photosynthesis Research, (0123456789), 2020, ISSN: 0166-8595. |
Photosynthesis Research, (0123456789), 2020, ISSN: 0166-8595. |
2D Phononic Crystals: Progress and Prospects in Hypersound and Thermal Transport Engineering Advanced Functional Materials, 30 (8), pp. 1904434, 2020, ISSN: 1616-301X. |
Biochimica et Biophysica Acta (BBA) - Bioenergetics, 1861 (1), pp. 148093, 2020, ISSN: 00052728. |
Electrochimica Acta, 330 , pp. 135190, 2020, ISSN: 00134686. |
Molecules, 25 (9), 2020, ISSN: 1420-3049. |
Mechanical reinforcement of polymer colloidal crystals by supercritical fluids Journal of Colloid and Interface Science, 579 , pp. 786 - 793, 2020, ISSN: 0021-9797. |
Insight into Electron Transfer from a Redox Polymer to a Photoactive Protein The Journal of Physical Chemistry B, 124 (49), pp. 11123-11132, 2020, (PMID: 33236901). |
Frequency-domain study of nonthermal gigahertz phonons reveals Fano coupling to charge carriers Science Advances, 6 (51), 2020, ISSN: 23752548. |
High-temperature silicon thermal diode and switch Nano Energy, 78 (July), 2020, ISSN: 22112855. |
2019 |
Applied Sciences, 10 (1), pp. 164, 2019, ISSN: 2076-3417. |
Condensed Matter Physics, 22 (4), pp. 43603, 2019. |
2D Phononic Crystals: Progress and Prospects in Hypersound and Thermal Transport Engineering Advanced Functional Materials, pp. 1904434, 2019. |
Structural relaxation in the wave-vector dependence of the longitudinal rigidity modulus Biomed. Opt. Express, 10 (4), pp. 1957–1964, 2019. |
Single-molecule imaging of DNA gyrase activity in living Escherichia coli Nucleic Acids Research, 47 (1), pp. 210-220, 2019. |
Journal of Molecular Liquids, 282 , pp. 51 - 56, 2019, ISSN: 0167-7322. |
Up-conversion luminescence of RE3+ -doped polymer composites KGd(WO4)2&PMMA 88 , pp. 366 - 371, 2019, ISSN: 0925-3467. |
Macromolecules, 52 (14), pp. 5399-5406, 2019. |
Physical Review B, 99 (16), 2019. |
Fluorescein ether-ester dyes for labeling of fluorinated methacrylate nanoparticles Journal of Photochemistry and Photobiology A: Chemistry, 382 , pp. 111956, 2019, ISSN: 1010-6030. |
2018 |
EPR Oximetry Sensor-Developing a TAM Derivative for In Vivo Studies Cell Biochemistry and Biophysics, 76 (1), pp. 19–28, 2018, ISSN: 1559-0283. |
Acceleration of the excitation decay in Photosystem I immobilized on glass surface Photosynthesis Research, 136 (2), pp. 171-181, 2018, ISSN: 0166-8595. |
Encapsulation of fluorescein into nanozeolites L and Y Microporous and Mesoporous Materials, 260 , pp. 70–75, 2018, ISSN: 13871811. |
Journal of Inorganic Biochemistry, 180 , pp. 1–14, 2018, ISSN: 01620134. |
The Journal of Chemical Physics, 148 (9), pp. 094201, 2018. |
Scientific Reports, 8 (1), pp. 4041, 2018, ISSN: 2045-2322. |
MukB ATPases are regulated independently by the N- and C-terminal domains of MukF kleisin eLife, 7 , 2018. |
ACS Applied Materials & Interfaces, 10 (9), pp. 7777-7787, 2018, (PMID: 29417811). |
Photosynthesis Research, 0 (0), pp. 0, 2018, ISSN: 0166-8595. |
Photosynthesis Research, 137 (2), pp. 321-335, 2018, ISSN: 1573-5079. |
2017 |
Scientific Reports, 7 (1), pp. 7084, 2017, ISSN: 2045-2322. |
Scientific Reports, 7 (1), pp. 11800, 2017, ISSN: 2045-2322. |
Submicron sized fluorescent silica particles characterization Nuclear Instruments and Methods in Physics Research, Section B: Beam Interactions with Materials and Atoms, 411 , pp. 78–84, 2017, ISSN: 0168583X. |
Materials & Design, 133 , pp. 307–324, 2017, ISSN: 02641275. |
Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics, 1865 (11), pp. 1358–1371, 2017, ISSN: 15709639. |
Direct observation of the THz Kerr effect (TKE) in deionized, distilled and buffered (PBS) water Physical Chemistry Chemical Physics, 19 (39), pp. 26749-26757, 2017. |
Synthesis of fluorescein by a ship-in-a-bottle method in different zeolites New Journal of Chemistry, 41 (18), pp. 9969–9976, 2017, ISSN: 1144-0546. |
Uptake and controlled release of a dye from thermo-sensitive polymer P(NIPAM- co -Vim) Reactive and Functional Polymers, 115 , pp. 102–108, 2017, ISSN: 13815148. |
Photosynthesis Research, 132 (2), pp. 111–126, 2017, ISSN: 0166-8595. |
Raman imaging of layered soft contact lenses Journal of Applied Biomaterials & Functional Materials, 15 (2), pp. 0–0, 2017, ISSN: 2280-8000. |
Colloids and Surfaces B: Biointerfaces, 152 , pp. 85–94, 2017, ISSN: 18734367. |
Journal of Chemical Physics, 146 (8), pp. 084506, 2017, ISSN: 00219606. |
Plant, Cell & Environment, 40 (3), pp. 424–440, 2017, ISSN: 1365-3040, (PCE-16-0763.R1). |
Effects of small-molecule amyloid modulators on a Drosophila model of Parkinson’s disease PLOS ONE, 12 (9), pp. 1-21, 2017. |
2016 |
Synthesis and encapsulation of fluorescein in zeolite Y Microporous and Mesoporous Materials, 236 , pp. 79–84, 2016, ISSN: 13871811. |
Molecular orientation in binary liquid mixtures from excess Cotton-Mouton constant Journal of Molecular Liquids, 224 , pp. 146–150, 2016, ISSN: 01677322. |
Optical Kerr effect of tRNA solution induced by femtosecond laser pulses Chemical Physics Letters, 662 , pp. 132–136, 2016, ISSN: 00092614. |
RSC Advances, 6 (92), pp. 89305–89312, 2016, ISSN: 2046-2069. |
Colloids and Surfaces A: Physicochemical and Engineering Aspects, 502 , pp. 54–65, 2016, ISSN: 09277757. |
Single-molecule imaging of UvrA and UvrB recruitment to DNA lesions in living Escherichia coli Nature Communications, 7 , pp. 12568, 2016, ISSN: 2041-1723. |
Bacteriopheophytin triplet state in Rhodobacter sphaeroides reaction centers Photosynthesis Research, 129 (2), pp. 205–216, 2016, ISSN: 0166-8595. |
Photosynthesis Research, 128 (3), pp. 243–258, 2016, ISSN: 0166-8595. |
The Journal of Physical Chemistry B, 120 (22), pp. 4890–4896, 2016, ISSN: 1520-6106. |
Plant Science, 246 , pp. 98–111, 2016, ISSN: 01689452. |
Nanomaterials, 6 (5), pp. 87, 2016, ISSN: 2079-4991. |
Acta Biomaterialia, 35 , pp. 293–304, 2016, ISSN: 17427061. |
Journal of Fluorine Chemistry, 183 , pp. 92–99, 2016, ISSN: 00221139. |
Langmuir, 32 (10), pp. 2482–2491, 2016, ISSN: 0743-7463. |
RSC Advances, 6 (32), pp. 26696–26708, 2016, ISSN: 2046-2069. |
Cytotoxicity and imaging studies of $beta$-NaGdF 4 :Yb 3+ Er 3+ @PEG-Mo nanorods RSC Advances, 6 (98), pp. 95633–95643, 2016, ISSN: 2046-2069. |
Nanophononics: state of the art and perspectives The European Physical Journal B, 89 (1), pp. 15, 2016. |
2015 |
Journal of Photochemistry and Photobiology B: Biology, 153 , pp. 423–428, 2015, ISSN: 10111344. |
Photophysical properties of betaxanthins: Vulgaxanthin I in aqueous and alcoholic solutions Journal of Luminescence, 167 , pp. 289–295, 2015, ISSN: 00222313. |
Polyhedron, 98 , pp. 217–223, 2015, ISSN: 02775387. |
Size of Submicrometer Particles Measured by FCS: Correction of the Confocal Volume Langmuir, 31 (24), pp. 6681–6687, 2015, ISSN: 0743-7463. |
Acta Biochimica Polonica, 62 (2), pp. 311–316, 2015, ISSN: 0001-527X. |
Simple way to analyze Brillouin spectra from turbid liquids. Optics letters, 40 (7), pp. 1456–9, 2015, ISSN: 1539-4794. |
Monte Carlo simulations of excitation and electron transfer in grana membranes Biochimica et Biophysica Acta (BBA) - Bioenergetics, 1847 (3), pp. 314–327, 2015, ISSN: 00052728. |
Dynamic Light Scattering Investigation of Pnipam-Co-Maa Microgel Solution Current Topics in Biophysics, 37 (1), pp. 29–33, 2015, ISSN: 1232-9630. |
Nanoparticle Tracking Analysis of Latex Standardized Beads Current Topics in Biophysics, 37 (1), pp. 49–53, 2015, ISSN: 1232-9630. |
Fabrication of Size-Tunable Silica Particles During Seed-Growth Process Current Topics in Biophysics, 37 (1), pp. 35–41, 2015, ISSN: 1232-9630. |
Sodium chloride-induced conformational change in tRNA as measured by circular dichroism Current Topics in Biophysics, 38 (1), pp. 1–5, 2015, ISSN: 1232-9630. |
2014 |
Electrically induced birefringence in nanoparticle dispersions for electrorheological applications Journal of Physics D: Applied Physics, 47 (46), pp. 465301, 2014, ISSN: 0022-3727. |
Biochimica et Biophysica Acta (BBA) - Bioenergetics, 1837 (10), pp. 1756–1768, 2014, ISSN: 00052728. |
Is electrospray emission really due to columbic forces? AIP Advances, 4 (9), pp. 097105, 2014, ISSN: 2158-3226. |
Freezing lines of colloidal Yukawa spheres. II. Local structure and characteristic lengths The Journal of Chemical Physics, 141 (12), pp. 124505, 2014, ISSN: 0021-9606. |
Successful FCS Experiment in Nonstandard Conditions Langmuir, 30 (29), pp. 8945–8955, 2014, ISSN: 0743-7463. |
Stimuli-Responsive PNIPAM Based Copolymers: Modeling and Light Scattering Investigations Acta Physica Polonica A, 125 (5), pp. 1236–1239, 2014, ISSN: 0587-4246. |
2013 |
Journal of Molecular Liquids, 187 , pp. 157–164, 2013, ISSN: 01677322. |
Physical Chemistry Chemical Physics, 15 (38), pp. 16321-16333, 2013, ISSN: 1463-9076. |
Magnetic properties of ferritin and akaganeite nanoparticles in aqueous suspension Journal of Nanoparticle Research, 15 (9), pp. 1902, 2013, ISSN: 1388-0764. |
The Journal of Physical Chemistry B, 117 (38), pp. 11112–11123, 2013, ISSN: 1520-6106. |
Enhancement of electrorheological effect by particle-fluid interaction Physical Review E, 87 (6), pp. 062304, 2013, ISSN: 1539-3755. |
Volume crossover in deeply supercooled water adiabatically freezing under isobaric conditions The Journal of Chemical Physics, 138 (18), pp. 184504, 2013, ISSN: 0021-9606. |
Physical Review E, 87 (2), pp. 022303, 2013, ISSN: 1539-3755. |
Physical characterization of iron oxide nanoparticles in magnetoferritin Magnetohydrodynamics, 49 (3/4), pp. 293–296, 2013. |
Transport of NaYF4:Er3+, Yb3+ up-converting nanoparticles into HeLa cells Nanotechnology, 24 (23), pp. 235702, 2013. |
Wydawnictwo Naukowe Uniwersytetu im. Adama Mickiewicza, 2013, ISBN: 9788323226246. |
2012 |
Proceedings of the National Academy of Sciences, 109 (51), pp. 20871–20876, 2012, ISSN: 0027-8424. |
Structure of bulk water from Raman measurements of supercooled pure liquid and LiCl solutions Physical Review B, 86 (13), pp. 134301, 2012, ISSN: 1098-0121. |
Magnetic Birefringence Study of the Magnetic Core Structure of Ferritin Acta Physica Polonica A, 121 (5-6), pp. 1237–1239, 2012, ISSN: 0587-4246. |
Light Scattering Studies of Hydration and Structural Transformations of Lysozyme Acta Physica Polonica A, 121 (3), pp. 694–698, 2012, ISSN: 0587-4246. |
Emerging dynamics in surfactant-based liquid mixtures: Octanoic acid/bis(2-ethylhexyl) amine systems The Journal of Chemical Physics, 136 (6), pp. 064515, 2012, ISSN: 0021-9606. |
Fizyka - biofizyka - biologia Nauka - Religia - Dzieje, pp. 77–89, Polska Akademia Umiejętności, 2012, 2012. |
Freezing lines of colloidal Yukawa spheres. I. A Rogers-Young integral equation study The Journal of Chemical Physics, 136 (2), pp. 024507, 2012, ISSN: 0021-9606. |
Denaturation and aggregation of lysozyme in water-ethanol solution. Acta Biochimica Polonica, 59 (2), pp. 317–21, 2012, ISSN: 1734-154X. |
Współczesna rewolucja naukowa na pograniczu fizyki i biologii Zagadnienia Filozoficzne w Nauce (Philosophical Problems in Science), (51), pp. 96–115, 2012, ISSN: 0867-8296. |
Acta Physica Polonica A, 131 (2), pp. 263-268, 2012. |
2011 |
Physical Review E, 84 (5), pp. 051202, 2011, ISSN: 1539-3755. |
The Journal of Physical Chemistry B, 115 (44), pp. 13037–13050, 2011, ISSN: 1520-6106. |
Iron–dextran complex: Geometrical structure and magneto-optical features Journal of Colloid and Interface Science, 363 (2), pp. 551–556, 2011, ISSN: 00219797. |
Magnetic birefringence of natural and synthetic ferritin Journal of Magnetism and Magnetic Materials, 323 (18-19), pp. 2413–2417, 2011, ISSN: 03048853. |
Physical Chemistry Chemical Physics, 13 (39), pp. 17722, 2011, ISSN: 1463-9076. |
Magnetic birefringence of iron oxyhydroxide nanoparticles stabilised by sucrose Journal of Magnetism and Magnetic Materials, 323 (9), pp. 1140–1144, 2011, ISSN: 03048853. |
Nano Letters, 11 (5), pp. 2157–2163, 2011, ISSN: 1530-6984. |
Relaxation dynamics and evidence of scaling behaviours in aqueous polymer solutions Journal of Molecular Liquids, 159 (1), pp. 105–111, 2011, ISSN: 01677322. |
Iron--dextran complex: Geometrical structure and magneto-optical features Journal of colloid and interface science, 363 (2), pp. 551–556, 2011. |
2010 |
Osmotic shrinkage in star/linear polymer mixtures The European Physical Journal E, 32 (2), pp. 127–134, 2010, ISSN: 1292-8941. |
Size and Shape of Micelles Studied by Means of SANS, PCS, and FCS Langmuir, 26 (12), pp. 9304–9314, 2010, ISSN: 0743-7463. |
Brillouin Scattering Study of Polyethylene Glycol/Water System below Crystallization Temperature The Journal of Physical Chemistry B, 114 (8), pp. 2644–2649, 2010, ISSN: 1520-6106. |
Slow dynamics, aging, and crystallization of multiarm star glasses Physical Review E, 81 (2), pp. 020402, 2010, ISSN: 1539-3755. |
Some Evidence of Scaling Behavior in the Relaxation Dynamics of Aqueous Polymer Solutions The Journal of Physical Chemistry B, 114 (4), pp. 1614–1620, 2010, ISSN: 1520-6106. |
Generic behavior of the hydrodynamic function of charged colloidal suspensions The Journal of Chemical Physics, 132 (5), pp. 054510, 2010, ISSN: 0021-9606. |
Raman scattering measurements on a floating water bridge Journal of Physics D: Applied Physics, 43 (17), pp. 175405, 2010. |
Communication: An extended model of liquid bridging The Journal of Chemical Physics, 133 (8), pp. 081104, 2010. |
Biological Chemistry, 391 (1), pp. 43–53, 2010, ISSN: 1437-4315. |
Biochimica et Biophysica Acta (BBA) - Bioenergetics, 1797 (1), pp. 106–112, 2010, ISSN: 00052728. |
2009 |
Physical Chemistry Chemical Physics, 11 (44), pp. 10484, 2009, ISSN: 1463-9076. |
Synchrotron radiation small angle scattering studies of d(TTAGGG)4 oligomer in solution Radiation Physics and Chemistry, 78 (10), pp. S134–S136, 2009, ISSN: 0969806X. |
Physical Chemistry Chemical Physics, 11 (40), pp. 9025, 2009, ISSN: 1463-9076. |
Supersaturated dispersions of rodlike viruses with added attraction Physical Review E, 80 (3), pp. 031402, 2009, ISSN: 1539-3755. |
The Journal of Physical Chemistry B, 113 (31), pp. 11023–11031, 2009, ISSN: 1520-6106. |
Fluorescence hole-burning and site-selective studies of LHCII Photosynthetica, 47 (2), pp. 232–240, 2009, ISSN: 0300-3604. |
Physical Chemistry Chemical Physics, 11 (25), pp. 5186, 2009, ISSN: 1463-9076. |
High-pressure small-angle neutron scattering studies of glucose isomerase conformation in solution Journal of Applied Crystallography, 42 (3), pp. 461–468, 2009, ISSN: 0021-8898. |
The Journal of Chemical Physics, 130 (15), pp. 154903, 2009, ISSN: 0021-9606. |
The Journal of Chemical Physics, 130 (8), pp. 084503, 2009, ISSN: 0021-9606. |
Magneto-optics of ferritin Dubnickowa, A; Dubnicka, S; Granja, C; Leroy, C; Stekl, I (Ed.): Nuclear Physics Methods and Accelerators in Biology and Medicine, pp. 143–146, AIP Conference Proceedings, New York, 2009. |
Linear and nonlinear magneto-optics of ferritin The Journal of Chemical Physics, 131 , pp. 01505-1-10, 2009. |
2008 |
The SAXS and Rheological Studies of HEWL Amyloid Formation Acta Physica Polonica A, 114 (2), pp. 447–454, 2008, ISSN: 0587-4246. |
Structure and Dynamics of Colloidal Suspensions Studied by Means of XPCS Acta Physica Polonica A, 114 (2), pp. 339–350, 2008, ISSN: 0587-4246. |
Measurement Science and Technology, 19 (3), pp. 034017, 2008, ISSN: 0957-0233. |
The Journal of Physical Chemistry B, 112 (6), pp. 1858–1865, 2008, ISSN: 1520-6106. |
Journal of Molecular Liquids, 138 (1), pp. 168 - 172, 2008, ISSN: 0167-7322. |
Kerr effect in liquids with various electro-optic properties Przegląd Elektrotechniczny, 84 (10), pp. 166-169, 2008. |
Odkrycie struktury komórkowej tkanki nerwowej Kosmos. Problemy Nauk Biologicznych, 57 (1-2), pp. 103–107, 2008. |
The Journal of Chemical Physics, 128 (1), pp. 014507, 2008, ISSN: 0021-9606. |
Micro- and macro-shear viscosity in dispersed lamellar phases Journal of Non-Newtonian Fluid Mechanics, 148 (1-3), pp. 134–140, 2008, ISSN: 03770257. |
A0 → A1 Electron Transfer in Chlamydomonas reinhardtii PS I with Replaced A0 Axial Ligand Allen, J F; Gantt, E; Golbeck, J H; Osmond, B (Ed.): Photosynthesis. Energy from the Sun. 14th International Congress on Photosynthesis, pp. 65-68, Springer, 2008, ISBN: 978-1-4020-6709-9. |
2007 |
Kinetic Trapping of Large Amount of Long Polymers in Nanopores Journal of the American Chemical Society, 129 (44), pp. 13398–13399, 2007, ISSN: 0002-7863. |
Medical & Biological Engineering & Computing, 45 (9), pp. 837–844, 2007, ISSN: 0140-0118. |
Water phases under high electric field and pressure applied simultaneously Journal of Molecular Liquids, 135 (1-3), pp. 75–85, 2007, ISSN: 01677322. |
Photosynthesis Research, 92 (1), pp. 55–63, 2007, ISSN: 0166-8595. |
Excess compressibility in binary liquid mixtures The Journal of Chemical Physics, 126 (22), pp. 224508, 2007, ISSN: 0021-9606. |
The Journal of Chemical Physics, 126 (21), pp. 214501, 2007, ISSN: 0021-9606. |
The Journal of Physical Chemistry B, 111 (19), pp. 5503–5510, 2007, ISSN: 1520-6106. |
Collective diffusion in charge-stabilized suspensions: Concentration and salt effects The Journal of Chemical Physics, 126 (10), pp. 104905, 2007, ISSN: 0021-9606. |
Biochimica et Biophysica Acta (BBA) - Bioenergetics, 1767 (2), pp. 151–160, 2007, ISSN: 00052728. |
High-Frequency Dynamical Behavior of Poly(ethylene glycol)+H2O Mixtures by Brillouin Spectroscopy Macromolecular Symposia, 251 (1), pp. 47-53, 2007, ISSN: 1521-3900. |
Brillouin spectroscopy investigations of poly(ethylene glycol) water and organic solvent mixtures Proc. SPIE, 6598 , pp. 65980X, 2007. |
Optical and Electric Gradients in Photosynthesis Granja, Carlos; Leroy, Claude; Stekl, Ivan (Ed.): Nuclear Physics Methods and Accelerators in Biology and Medicine: Fourth International Summer School on Nuclear Physics Methods and Accelerators in Biology and Medicine, pp. 169–174, AIP Conference Proceedings, 2007, ISSN: 0094243X. |
Static and dynamic light scattering method for analysis of gold colloidal growth in aqueous solution Archives of Metallurgy and Materials, 52 (1), pp. 121–128, 2007. |
Isotropic Brillouin spectra of liquids having an internal degree of freedom The Journal of Chemical Physics, 126 (1), pp. 014508, 2007, ISSN: 0021-9606. |
Cellular and Molecular Biology Letters, 12 (1), pp. 51–69, 2007, ISSN: 1689-1392. |
2006 |
Diffusion and Viscosity in a Crowded Environment: from Nano- to Macroscale The Journal of Physical Chemistry B, 110 (51), pp. 25593–25597, 2006, ISSN: 1520-6106. |
The Journal of Physical Chemistry B, 110 (41), pp. 20533–20539, 2006, ISSN: 1520-6106. |
ChemPhysChem, 7 (10), pp. 2126–2133, 2006, ISSN: 1439-4235. |
Polymer, 47 (20), pp. 7231–7240, 2006, ISSN: 00323861. |
Polymer, 47 (20), pp. 7318–7327, 2006, ISSN: 00323861. |
Journal of Computer-Aided Molecular Design, 20 (5), pp. 305–319, 2006, ISSN: 0920-654X. |
The Journal of Physical Chemistry B, 110 (14), pp. 7367–7373, 2006, ISSN: 1520-6106. |
Many-Body Hydrodynamic Interactions in Charge-Stabilized Suspensions Physical Review Letters, 96 (13), pp. 138303, 2006, ISSN: 0031-9007. |
Light scattering studies of proteins under compression Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics, 1764 (3), pp. 405–413, 2006, ISSN: 15709639. |
Pressure effects on the $alpha$ and $alpha$′ relaxations in polymethylphenylsiloxane The Journal of Chemical Physics, 124 (10), pp. 104901, 2006, ISSN: 0021-9606. |
Physics and Chemistry of Liquids, 44 (1), pp. 95–105, 2006, ISSN: 0031-9104. |
Unexpected effect of internal degrees of freedom on transverse phonons in supercooled liquids Europhysics Letters (EPL), 73 (4), pp. 607–613, 2006, ISSN: 0295-5075. |
BMC Bioinformatics, 7 (1), pp. 53, 2006, ISSN: 14712105. |
Structure of N 6 -furfurylaminopurine (kinetin) dihydrogenphosphate Acta Crystallographica Section B Structural Science, 62 (1), pp. 102–108, 2006, ISSN: 0108-7681. |
The Journal of Physical Chemistry B, 110 (1), pp. 485–493, 2006, ISSN: 1520-6106. |
Diffusion of spheres in isotropic and nematic suspensions of rods The Journal of Chemical Physics, 124 (4), pp. 044907, 2006, ISSN: 0021-9606. |
2005 |
The Journal of Physical Chemistry B, 109 (44), pp. 21180–21186, 2005, ISSN: 1520-6106. |
The Journal of Physical Chemistry B, 109 (38), pp. 18171–18176, 2005, ISSN: 1520-6106. |
The Journal of Chemical Physics, 123 (5), pp. 054708, 2005, ISSN: 0021-9606. |
The Journal of Physical Chemistry B, 109 (18), pp. 8533–8537, 2005, ISSN: 1520-6106. |
Excitation Energy Transfer Pathways in Lhca4 Biophysical Journal, 88 (3), pp. 1959–1969, 2005, ISSN: 00063495. |
Structural Relaxation Processes in Polyethylene Glycol/CCl 4 Solutions by Brillouin Scattering The Journal of Physical Chemistry B, 109 (9), pp. 4181–4188, 2005, ISSN: 1520-6106. |
The Journal of Physical Chemistry B, 109 (8), pp. 3594–3605, 2005, ISSN: 1520-6106. |
On the shape of bottle-brush macromolecules: Systematic variation of architectural parameters The Journal of Chemical Physics, 122 (12), pp. 124904, 2005, ISSN: 0021-9606. |
The Journal of Chemical Physics, 122 (7), pp. 074506, 2005, ISSN: 0021-9606. |
Biochimica et Biophysica Acta (BBA) - Bioenergetics, 1706 (3), pp. 267–275, 2005, ISSN: 00052728. |
Temperature study of Brillouin light scattering in selected dimethacrylates Journal of Molecular Structure, 737 (1), pp. 11 - 15, 2005, ISSN: 0022-2860. |
X-Ray method of detection of neoplasmic changes Physics and Chemistry of Liquids, 43 (2), pp. 167-174, 2005. |
Brillouin scattering study of polyethylene glycol different solutions Journal of Molecular Liquids, 121 (2), pp. 75 - 79, 2005, ISSN: 0167-7322. |
Diffusion of spheres in crowded suspensions of rods The Journal of Chemical Physics, 122 (4), pp. 044905, 2005, ISSN: 0021-9606. |
2004 |
Scaling the $backslashalpha $ -relaxation time of supercooled fragile organic liquids The European Physical Journal B - Condensed Matter and Complex Systems, 42 (3), pp. 309–319, 2004, ISSN: 1434-6028. |
The Journal of Chemical Physics, 121 (21), pp. 10794–10802, 2004, ISSN: 0021-9606. |
Dynamics of supercooled van der Waals liquid under pressure. A dynamic light scattering study Colloid & Polymer Science, 282 (8), pp. 874–881, 2004, ISSN: 0303-402X. |
Study of the Rytov dip for liquid o -terphenyl Philosophical Magazine, 84 (13-16), pp. 1463–1469, 2004, ISSN: 1478-6435. |
Dynamics of core-shell particles in concentrated suspensions Physical Review E, 69 (4), pp. 042401, 2004, ISSN: 1539-3755. |
Solubility of Adenine and Kinetin in Water–Ethanol Solutions Journal of Solution Chemistry, 33 (4), pp. 395–406, 2004, ISSN: 0095-9782. |
Structural similarity ofE. coli 5S rRNA in solution and within the ribosome Biopolymers, 73 (3), pp. 316–325, 2004, ISSN: 0006-3525. |
Biochemistry, 43 (5), pp. 1369–1375, 2004, ISSN: 0006-2960. |