Publikacje

@article{Varghese2023,

title = {Size-dependent nanoscale soldering of polystyrene colloidal crystals by supercritical fluids},

author = {Jeena Varghese and Reza Mohammadi and Mikołaj Pochylski and Visnja Babacic and Jacek Gapiński and Nicolas Vogel and Hans-Juergen Butt and George Fytas and Bartłomiej Graczykowski},

url = {https://authors.elsevier.com/c/1gA9Z4-sDXVRI},

doi = {10.1016/j.jcis.2022.11.090},

year  = {2023},

date = {2023-03-01},

urldate = {2023-03-01},

journal = {Journal of Colloid and Interface Science},

volume = {633},

pages = {314--322},

publisher = {Elsevier BV},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Vasileiadis2022,

title = {Optomechanical Hot-Spots in Metallic Nanorod–Polymer Nanocomposites},

author = {Thomas Vasileiadis and Adnane Noual and Yuchen Wang and Bartłomiej Graczykowski and Bahram Djafari-Rouhani and Shu Yang and George Fytas},

url = {https://doi.org/10.1021/acsnano.2c06673},

doi = {10.1021/acsnano.2c06673},

year  = {2022},

date = {2022-12-01},

journal = {ACS Nano},

volume = {16},

number = {12},

pages = {20419--20429},

publisher = {American Chemical Society (ACS)},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Piernik2022,

title = {DBFE: distribution-based feature extraction from structural variants in whole-genome data},

author = {Maciej Piernik and Dariusz Brzezinski and Pawel Sztromwasser and Klaudia Pacewicz and Weronika Majer-Burman and Michal Gniot and Dawid Sielski and Oleksii Bryzghalov and Alicja Wozna and Paweł Zawadzki},

editor = {Pier Luigi Martelli},

url = {https://doi.org/10.1093/bioinformatics/btac513},

doi = {10.1093/bioinformatics/btac513},

year  = {2022},

date = {2022-08-01},

journal = {Bioinformatics},

volume = {38},

number = {19},

pages = {4466--4473},

publisher = {Oxford University Press (OUP)},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Szewczyk2022,

title = {In-situ thickness control of centimetre-scale 2D-Like polydopamine films with large scalability},

author = {J. Szewczyk and M. Pochylski and K. Szutkowski and M. Kempiński and R. Mrówczyński and I. Iatsunskyi and J. Gapiński and E. Coy},

url = {https://doi.org/10.1016/j.mtchem.2022.100935},

doi = {10.1016/j.mtchem.2022.100935},

year  = {2022},

date = {2022-06-01},

journal = {Materials Today Chemistry},

volume = {24},

pages = {100935},

publisher = {Elsevier BV},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Vasileiadis2022b,

title = {Phonon transport in the gigahertz to terahertz range: Confinement, topology, and second sound},

author = {Thomas Vasileiadis and Juan Sebastian Reparaz and Bartłomiej Graczykowski},

url = {https://doi.org/10.1063/5.0073508},

doi = {10.1063/5.0073508},

year  = {2022},

date = {2022-05-01},

journal = {Journal of Applied Physics},

volume = {131},

number = {18},

pages = {180901},

publisher = {AIP Publishing},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{MajerBurman2022,

title = {15P Integration of whole genome data with machine learning technology in breast cancer subtyping},

author = {W. Majer-Burman and K. Pacewicz and M. Meler and M. Gniot and D. Sielski and M. Piernik and P. Sztromwasser and A. Wozna and P. Zawadzki},

url = {https://doi.org/10.1016/j.annonc.2022.03.030},

doi = {10.1016/j.annonc.2022.03.030},

year  = {2022},

date = {2022-05-01},

journal = {Annals of Oncology},

volume = {33},

pages = {S130},

publisher = {Elsevier BV},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Kaja2022,

title = {The Thousand Polish Genomes—A Database of Polish Variant Allele Frequencies},

author = {Elżbieta Kaja and Adrian Lejman and Dawid Sielski and Mateusz Sypniewski and Tomasz Gambin and Mateusz Dawidziuk and Tomasz Suchocki and Paweł Golik and Marzena Wojtaszewska and Magdalena Mroczek and Maria Stępień and Joanna Szyda and Karolina Lisiak-Teodorczyk and Filip Wolbach and Daria Kołodziejska and Katarzyna Ferdyn and Maciej Dąbrowski and Alicja Woźna and Marcin Żytkiewicz and Anna Bodora-Troińska and Waldemar Elikowski and Zbigniew J. Król and Artur Zaczyński and Agnieszka Pawlak and Robert Gil and Waldemar Wierzba and Paula Dobosz and Katarzyna Zawadzka and Paweł Zawadzki and Paweł Sztromwasser},

url = {https://doi.org/10.3390/ijms23094532},

doi = {10.3390/ijms23094532},

year  = {2022},

date = {2022-04-01},

journal = {International Journal of Molecular Sciences},

volume = {23},

number = {9},

pages = {4532},

publisher = {MDPI AG},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Vasileiadis2021b,

title = {Fast Light-Driven Motion of Polydopamine Nanomembranes},

author = {Thomas Vasileiadis and Tommaso Marchesi DÁlvise and Clara-Magdalena Saak and Mikołaj Pochylski and Sean Harvey and Christopher V. Synatschke and Jacek Gapiński and George Fytas and Ellen H. G. Backus and Tanja Weil and Bartłomiej Graczykowski},

url = {https://doi.org/10.1021/acs.nanolett.1c03165},

doi = {10.1021/acs.nanolett.1c03165},

year  = {2022},

date = {2022-01-01},

journal = {Nano Letters},

volume = {22},

number = {2},

pages = {578--585},

publisher = {American Chemical Society (ACS)},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{molecules27031010,

title = {Nanomolar Nitric Oxide Concentrations in Living Cells Measured by Means of Fluorescence Correlation Spectroscopy},

author = {Roksana Markiewicz and Jagoda Litowczenko and Jacek Gapiński and Anna Woźniak and Stefan Jurga and Adam Patkowski},

url = {https://www.mdpi.com/1420-3049/27/3/1010},

doi = {10.3390/molecules27031010},

issn = {1420-3049},

year  = {2022},

date = {2022-01-01},

urldate = {2022-01-01},

journal = {Molecules},

volume = {27},

number = {3},

abstract = {Measurement of the nitric oxide (NO) concentration in living cells in the physiological nanomolar range is crucial in understanding NO biochemical functions, as well as in characterizing the efficiency and kinetics of NO delivery by NO-releasing drugs. Here, we show that fluorescence correlation spectroscopy (FCS) is perfectly suited for these purposes, due to its sensitivity, selectivity, and spatial resolution. Using the fluorescent indicators, diaminofluoresceins (DAFs), and FCS, we measured the NO concentrations in NO-producing living human primary endothelial cells, as well as NO delivery kinetics, by an external NO donor to the immortal human epithelial living cells. Due to the high spatial resolution of FCS, the NO concentration in different parts of the cells were also measured. The detection of nitric oxide by means of diaminofluoresceins is much more efficient and faster in living cells than in PBS solutions, even though the conversion to the fluorescent form is a multi-step reaction.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@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}

}

@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}

}

@article{Zajaczkowska2021,

title = {Self-Aligned Bilayers for Flexible Free-Standing Organic Field-Effect Transistors},

author = {Hanna Zajaczkowska and Lothar Veith and Witold Waliszewski and Malgorzata A. Bartkiewicz and Michal Borkowski and Piotr Sleczkowski and Jacek Ulanski and Bartlomiej Graczykowski and Paul W. M. Blom and Wojciech Pisula and Tomasz Marszalek},

url = {https://doi.org/10.1021/acsami.1c15208},

doi = {10.1021/acsami.1c15208},

year  = {2021},

date = {2021-12-01},

journal = {ACS Applied Materials &$mathsemicolon$ Interfaces},

volume = {13},

number = {49},

pages = {59012--59022},

publisher = {American Chemical Society (ACS)},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Zajaczkowska2021b,

title = {Self-Aligned Bilayers for Flexible Free-Standing Organic Field-Effect Transistors},

author = {Hanna Zajaczkowska and Lothar Veith and Witold Waliszewski and Malgorzata A. Bartkiewicz and Michal Borkowski and Piotr Sleczkowski and Jacek Ulanski and Bartłomiej Graczykowski and Paul W. M. Blom and Wojciech Pisula and Tomasz Marszalek},

url = {https://doi.org/10.1021/acsami.1c15208},

doi = {10.1021/acsami.1c15208},

year  = {2021},

date = {2021-12-01},

journal = {ACS Applied Materials &$mathsemicolon$ Interfaces},

volume = {13},

number = {49},

pages = {59012--59022},

publisher = {American Chemical Society (ACS)},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Wojtaszewska2021,

title = {Validation of HER2 Status in Whole Genome Sequencing Data of Breast Cancers with the Ploidy-Corrected Copy Number Approach},

author = {Marzena Wojtaszewska and Rafał Stępień and Alicja Woźna and Maciej Piernik and Pawel Sztromwasser and Maciej Dąbrowski and Michał Gniot and Sławomir Szymański and Maciej Socha and Piotr Kasprzak and Rafał Matkowski and Paweł Zawadzki},

url = {https://doi.org/10.1007/s40291-021-00571-1},

doi = {10.1007/s40291-021-00571-1},

year  = {2021},

date = {2021-12-01},

journal = {Molecular Diagnosis &$mathsemicolon$ Therapy},

volume = {26},

number = {1},

pages = {105--116},

publisher = {Springer Science and Business Media LLC},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Zawadzi_2021,

title = {Autoantibodies neutralizing type I IFNs are present in ~4% of uninfected individuals over 70 years old and account for ~20% of COVID-19 deaths},

author = {Paul Bastard and Paweł Zawadzki},

url = {https://doi.org/10.1126/sciimmunol.abl4340},

doi = {10.1126/sciimmunol.abl4340},

year  = {2021},

date = {2021-08-01},

journal = {Science Immunology},

volume = {6},

number = {62},

pages = {1-26},

publisher = {science group},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Babacic2021,

title = {Thickness-Dependent Elastic Softening of Few-Layer Free-Standing MoSe 

 $łess$sub$greater$2$łess$/sub$greater$},

author = {Visnja Babacic and David Saleta Reig and Sebin Varghese and Thomas Vasileiadis and Emerson Coy and Klaas-Jan Tielrooij and Bartłomiej Graczykowski},

url = {https://doi.org/10.1002/adma.202008614},

doi = {10.1002/adma.202008614},

year  = {2021},

date = {2021-05-01},

journal = {Advanced Materials},

volume = {33},

number = {23},

pages = {2008614},

publisher = {Wiley},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@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}

}

@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}

}

@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}

}

@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}

}

@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}

}

@article{Dubas2021,

title = {Antagonistic Effects of Point Mutations on Charge Recombination and a New View of Primary Charge Separation in Photosynthetic Proteins},

author = {Katarzyna Dubas and Sebastian Szewczyk and Rafał Białek and G Burdziński and M R Jones and Krzysztof Gibasiewicz},

url = {https://doi.org/10.1021/acs.jpcb.1c03978},

doi = {10.1021/acs.jpcb.1c03978},

year  = {2021},

date = {2021-01-01},

journal = {The Journal of Physical Chemistry B},

volume = {125},

number = {31},

pages = {8742--8756},

publisher = {American Chemical Society (ACS)},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Gibasiewicz2021,

title = {Temperature dependence of nanosecond charge recombination in mutant Rhodobacter sphaeroides reaction centers: modelling of the protein dynamics},

author = {Krzysztof Gibasiewicz and Maria Pajzderska and Rafał Białek and Michael R Jones},

url = {https://doi.org/10.1007/s43630-021-00069-z},

doi = {10.1007/s43630-021-00069-z},

year  = {2021},

date = {2021-01-01},

journal = {Photochemical & Photobiological Sciences},

volume = {20},

number = {7},

pages = {913--922},

publisher = {Springer Science and Business Media LLC},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Ciar2020,

title = {2D fourier transform for global analysis and classification of meibomian gland images},

author = {Kamila Ciężar and Mikołaj Pochylski},

url = {https://doi.org/10.1016/j.jtos.2020.09.005},

doi = {10.1016/j.jtos.2020.09.005},

year  = {2020},

date = {2020-10-01},

journal = {The Ocular Surface},

volume = {18},

number = {4},

pages = {865--870},

publisher = {Elsevier BV},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@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}

}

@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}

}

@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}

}

@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}

}

@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}

}

@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}

}

@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}

}

@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}

}

@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}

}

@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}

}

@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  = {2020},

date = {2020-01-01},

urldate = {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}

}

@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}

}

@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}

}

@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}

}

@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}

}

@article{Bastard2020,

title = {Autoantibodies against type I IFNs in patients with life-threatening COVID-19},

author = {Paul Bastard and Lindsey B Rosen and Qian Zhang and Eleftherios Michailidis and Hans-Heinrich Hoffmann and Yu Zhang and Karim Dorgham and Quentin Philippot and Jérémie Rosain and Vivien Béziat and Jérémie Manry and Elana Shaw and Liis Haljasmägi and Pärt Peterson and Lazaro Lorenzo and Lucy Bizien and Sophie Trouillet-Assant and Kerry Dobbs and Adriana Almeida de Jesus and Alexandre Belot and Anne Kallaste and Emilie Catherinot and Yacine Tandjaoui-Lambiotte and Jeremie Le Pen and Gaspard Kerner and Benedetta Bigio and Yoann Seeleuthner and Rui Yang and Alexandre Bolze and Andr á and Ottavia M Delmonte and Michael S Abers and Alessandro Aiuti and Giorgio Casari and Vito Lampasona and Lorenzo Piemonti and Fabio Ciceri and Kaya Bilguvar and Richard P Lifton and Marc Vasse and David M Smadja and M é and J é and Benjamin Terrier and Darragh Duffy and Lluis Quintana-Murci and Diederik van de Beek and Lucie Roussel and Donald C Vinh and Stuart G Tangye and Filomeen Haerynck and David Dalmau and Javier Martinez-Picado and Petter Brodin and Michel C Nussenzweig and St é and Carlos Rodr í and Guillaume Vogt and Trine H Mogensen and Andrew J Oler and Jingwen Gu and Peter D Burbelo and Jeffrey I Cohen and Andrea Biondi and Laura Rachele Bettini and Mariella D textquotesingle and Paolo Bonfanti and Patrick Rossignol and Julien Mayaux and Fréd é and Eystein S Husebye and Francesca Fusco and Matilde Valeria Ursini and Luisa Imberti and Alessandra Sottini and Simone Paghera and Eugenia Quiros-Roldan and Camillo Rossi and Riccardo Castagnoli and Daniela Montagna and Amelia Licari and Gian Luigi Marseglia and Xavier Duval and Jade Ghosn and John S Tsang and Raphaela Goldbach-Mansky and Kai Kisand and Michail S Lionakis and Anne Puel and Shen-Ying Zhang and Steven M Holland and Guy Gorochov and Emmanuelle Jouanguy and Charles M Rice and Aur é and Luigi D Notarangelo and Laurent Abel and Helen C Su and Jean-Laurent Casanova and Paweł Zawadzki and ...},

url = {https://doi.org/10.1126/science.abd4585},

doi = {10.1126/science.abd4585},

year  = {2020},

date = {2020-01-01},

journal = {Science},

volume = {370},

number = {6515},

pages = {eabd4585},

publisher = {American Association for the Advancement of Science (AAAS)},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Zhang2020,

title = {Inborn errors of type I IFN immunity in patients with life-threatening COVID-19},

author = {Qian Zhang and Paul Bastard and Zhiyong Liu and Jér é and Marcela Moncada-Velez and Jie Chen and Masato Ogishi and Ira K D Sabli and Stephanie Hodeib and Cecilia Korol and Jeremie Rosain and Kaya Bilguvar and Junqiang Ye and Alexandre Bolze and Benedetta Bigio and Rui Yang and Andres Augusto Arias and Qinhua Zhou and Yu Zhang and Fanny Onodi and Sarantis Korniotis and Lea Karpf and Quentin Philippot and Marwa Chbihi and Lucie Bonnet-Madin and Karim Dorgham and Nikaïa Smith and William M Schneider and Brandon S Razooky and Hans-Heinrich Hoffmann and Eleftherios Michailidis and Leen Moens and Ji Eun Han and Lazaro Lorenzo and Lucy Bizien and Philip Meade and Anna-Lena Neehus and Aileen Camille Ugurbil and Aur é and Gaspard Kerner and Peng Zhang and Franck Rapaport and Yoann Seeleuthner and Jeremy Manry and Cecile Masson and Yohann Schmitt and Agatha Schlüter and Tom Le Voyer and Taushif Khan and Juan Li and Jacques Fellay and Lucie Roussel and Mohammad Shahrooei and Mohammed F Alosaimi and Davood Mansouri and Haya Al-Saud and Fahd Al-Mulla and Feras Almourfi and Saleh Zaid Al-Muhsen and Fahad Alsohime and Saeed Al Turki and Rana Hasanato and Diederik van de Beek and Andrea Biondi and Laura Rachele Bettini and Mariella DÁngio' and Paolo Bonfanti and Luisa Imberti and Alessandra Sottini and Simone Paghera and Eugenia Quiros-Roldan and Camillo Rossi and Andrew J Oler and Miranda F Tompkins and Camille Alba and Isabelle Vandernoot and Jean-Christophe Goffard and Guillaume Smits and Isabelle Migeotte and Filomeen Haerynck and Pere Soler-Palacin and Andrea Martin-Nalda and Roger Colobran and Pierre-Emmanuel Morange and Sevgi Keles and Fatma Colkesen and Tayfun Ozcelik and Kadriye Kart Yasar and Sevtap Senoglu and Semsi Nur Karabela and Carlos Rodr í and Giuseppe Novelli and Sami Hraiech and Yacine Tandjaoui-Lambiotte and Xavier Duval and Cedric Laouenan and Andrew L Snow and Clifton L Dalgard and Joshua D Milner and Donald C Vinh and Trine H Mogensen and Nico Marr and Andr á and Bertrand Boisson and Stephanie Boisson-Dupuis and Jacinta Bustamante and Anne Puel and Michael J Ciancanelli and Isabelle Meyts and Tom Maniatis and Vassili Soumelis and Ali Amara and Michel Nussenzweig and Adolfo Garcia-Sastre and Florian Krammer and Aurora Pujol and Darragh Duffy and Richard P Lifton and Shen-Ying Zhang and Guy Gorochov and Vivien Beziat and Emmanuelle Jouanguy and Vanessa Sancho-Shimizu and Charles M Rice and Laurent Abel and Luigi D Notarangelo and Aur é and Helen C Su and Jean-Laurent Casanova and Paweł Zawadzki and ...},

url = {https://doi.org/10.1126/science.abd4570},

doi = {10.1126/science.abd4570},

year  = {2020},

date = {2020-01-01},

journal = {Science},

volume = {370},

number = {6515},

pages = {eabd4570},

publisher = {American Association for the Advancement of Science (AAAS)},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{SowiskaSeidler2020,

title = {The First Report of Biallelic Missense Mutations in the SFRP4 Gene Causing Pyle Disease in Two Siblings},

author = {Anna Sowińska-Seidler and Paweł Sztromwasser and Katarzyna Zawadzka and Dawid Sielski and Ewelina Bukowska-Olech and Paweł Zawadzki and Kazimierz Kozłowski and Aleksander Jamsheer},

url = {https://doi.org/10.3389/fgene.2020.593407},

doi = {10.3389/fgene.2020.593407},

year  = {2020},

date = {2020-01-01},

journal = {Frontiers in Genetics},

volume = {11},

publisher = {Frontiers Media SA},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Casanova2020,

title = {A Global Effort to Define the Human Genetics of Protective Immunity to SARS-CoV-2 Infection},

author = {Jean-Laurent Casanova and Helen C Su and Laurent Abel and Alessandro Aiuti and Saleh Almuhsen and Andres Augusto Arias and Paul Bastard and Catherine Biggs and Dusan Bogunovic and Bertrand Boisson and Stephanie Boisson-Dupuis and Alexandre Bolze and Anastasia Bondarenko and Aziz Bousfiha and Petter Brodin and Jacinta Bustamante and Manish Butte and Giorgio Casari and Michael Ciancanelli and Aurelie Cobat and Antonio Condino-Neto and Megan Cooper and Clifton Dalgard and Sara Espinosa and Hagit Feldman and Jacques Fellay and Jose Luis Franco and David Hagin and Yuval Itan and Emmanuelle Jouanguy and Carrie Lucas and Davood Mansouri and Isabelle Meyts and Joshua Milner and Trine Mogensen and Tomohiro Morio and Lisa Ng and Luigi D Notarangelo and Satoshi Okada and Tayfun Ozcelik and Pere Soler Palacin and Anna Planas and Carolina Prando and Anne Puel and Aurora Pujol and Claire Redin and Laurent Renia and Jose Carlos Rodriguez Gallego and Lluis Quintana-Murci and Vanessa Sancho-Shimizu and Vijay Sankaran and Mikko R J Seppanen and Mohammad Shahrooei and Andrew Snow and Andras Spaan and Stuart Tangye and Jordi Perez Tur and Stuart Turvey and Donald C Vinh and Horst von Bernuth and Xiaochuan Wang and Paweł Zawadzki and Qian Zhang and Shenying Zhang},

url = {https://doi.org/10.1016/j.cell.2020.05.016},

doi = {10.1016/j.cell.2020.05.016},

year  = {2020},

date = {2020-01-01},

journal = {Cell},

volume = {181},

number = {6},

pages = {1194--1199},

publisher = {Elsevier BV},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@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}

}

@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}

}

@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}

}

@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}

}

@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}

}

@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}

}

@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}

}

@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}

}

@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}

}

@article{TurcoLiveri2018,

title = {Molecular association of small amphiphiles: Origin of ionic liquid properties in dibutyl phosphate/propylamine binary mixtures},

author = {Vincenzo Turco Liveri and Domenico Lombardo and Mikolaj Pochylski and Pietro Calandra},

url = {https://doi.org/10.1016/j.molliq.2018.05.003},

doi = {10.1016/j.molliq.2018.05.003},

year  = {2018},

date = {2018-08-01},

journal = {Journal of Molecular Liquids},

volume = {263},

pages = {274--281},

publisher = {Elsevier BV},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@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}

}

@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}

}

@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}

}

@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}

}

@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}

}

@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}

}

@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}

}

@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}

}

@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}

}

@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}

}

@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}

}

@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}

}

@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}

}

@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}

}

@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}

}

@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}

}

@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}

}

@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}

}

@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}

}

@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}

}

@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}

}

@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}

}

@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}

}

@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}

}

@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}

}

@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}

}

@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}

}

@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}

}

@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}

}

@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}

}

@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}

}

@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}

}

@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}

}

@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}

}

@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}

}

@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}

}

@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}

}

@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}

}

@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}

}

@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}

}

@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}

}

@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}

}

@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}

}

@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}

}

@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}

}

@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}

}

@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}

}

@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}

}

@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}

}

@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}

}

@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}

}

@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}

}

@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}

}

@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}

}

@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}

}

@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}

}

@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}

}

@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}

}

@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}

}

@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}

}

@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}

}

@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}

}

@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}

}

@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}

}

@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}

}

@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}

}

@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}

}

@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}

}

@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}

}

@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}

}

@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}

}

@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}

}

@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}

}

@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}

}

@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}

}

@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}

}

@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}

}

@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}

}

@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}

}

@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}

}

@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}

}

@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}

}

@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}

}

@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}

}

@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}

}

@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}

}

@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}

}

@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}

}

@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}

}

@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}

}