Tabela A z publikacjami w czasopismach wyróżnionych w Journal Citation Reports (JCR) 
Tabela B z publikacjami w czasopismach zagranicznych i krajowych, wyróżnionych na liście MNSzW
Publikacje konferencyjne indeksowane w bazie Web of Science Core Collection
Inne publikacje w pozostałych czasopismach i wydawnictwach konferencyjnych
Afiliacja IPPT PAN

1.Pierini F., Nakielski P., Urbanek O., Pawłowska S., Lanzi M., De Sio L., Kowalewski T.A., Polymer-Based Nanomaterials for Photothermal Therapy: From Light-Responsive to Multifunctional Nanoplatforms for Synergistically Combined Technologies, BIOMACROMOLECULES, ISSN: 1525-7797, DOI: 10.1021/acs.biomac.8b01138, Vol.0, pp.1-21, 2018
Pierini F., Nakielski P., Urbanek O., Pawłowska S., Lanzi M., De Sio L., Kowalewski T.A., Polymer-Based Nanomaterials for Photothermal Therapy: From Light-Responsive to Multifunctional Nanoplatforms for Synergistically Combined Technologies, BIOMACROMOLECULES, ISSN: 1525-7797, DOI: 10.1021/acs.biomac.8b01138, Vol.0, pp.1-21, 2018

Abstract:
Materials for the treatment of cancer have been studied comprehensively over the past few decades. Among the various kinds of biomaterials, polymer-based nanomaterials represent one of the most interesting research directions in nanomedicine because their controlled synthesis and tailored designs make it possible to obtain nanostructures with biomimetic features and outstanding biocompatibility. Understanding the chemical and physical mechanisms behind the cascading stimuli-responsiveness of smart polymers is fundamental for the design of multifunctional nanomaterials to be used as photothermal agents for targeted polytherapy. In this review, we offer an in-depth overview of the recent advances in polymer nanomaterials for photothermal therapy, describing the features of three different types of polymer-based nanomaterials. In each case, we systematically show the relevant benefits, highlighting the strategies for developing light-controlled multifunctional nanoplatforms that are responsive in a cascade manner and addressing the open issues by means of an inclusive state-of-the-art review. Moreover, we face further challenges and provide new perspectives for future strategies for developing novel polymeric nanomaterials for photothermally assisted therapies.

(45p.)
2.Czerkies M., Korwek Z., Prus W., Kochańczyk M., Jaruszewicz-Błońska J., Tudelska K., Błoński S., Kimmel M., Brasier A.R., Lipniacki T., Cell fate in antiviral response arises in the crosstalk of IRF, NF-κB and JAK/STAT pathways, Nature Communications, ISSN: 2041-1723, DOI: 10.1038/s41467-017-02640-8, Vol.9, pp.493, 2018
Czerkies M., Korwek Z., Prus W., Kochańczyk M., Jaruszewicz-Błońska J., Tudelska K., Błoński S., Kimmel M., Brasier A.R., Lipniacki T., Cell fate in antiviral response arises in the crosstalk of IRF, NF-κB and JAK/STAT pathways, Nature Communications, ISSN: 2041-1723, DOI: 10.1038/s41467-017-02640-8, Vol.9, pp.493, 2018

Abstract:
The innate immune system processes pathogen-induced signals into cell fate decisions. How information is turned to decision remains unknown. By combining stochastic mathematical modelling and experimentation, we demonstrate that feedback interactions between the IRF3, NF-κB and STAT pathways lead to switch-like responses to a viral analogue, poly(I:C), in contrast to pulse-like responses to bacterial LPS. Poly(I:C) activates both IRF3 and NF-κB, a requirement for induction of IFNβ expression. Autocrine IFNβ initiates a JAK/STAT-mediated positive-feedback stabilising nuclear IRF3 and NF-κB in first responder cells. Paracrine IFNβ, in turn, sensitises second responder cells through a JAK/STAT-mediated positive feedforward pathway that upregulates the positive-feedback components: RIG-I, PKR and OAS1A. In these sensitised cells, the ‘live-or-die’ decision phase following poly(I:C) exposure is shorter—they rapidly produce antiviral responses and commit to apoptosis. The interlinked positive feedback and feedforward signalling is key for coordinating cell fate decisions in cellular populations restricting pathogen spread.

Keywords:
cellular signalling networks, innate immunity, regulatory networks, stochastic modelling

(45p.)
3.Gruziel M., Thyagarajan K., Dietler G., Stasiak A., Ekiel-Jeżewska M.L., Szymczak P., Periodic Motion of Sedimenting Flexible Knots, PHYSICAL REVIEW LETTERS, ISSN: 0031-9007, DOI: 10.1103/PhysRevLett.121.127801, Vol.121, No.12, pp.127801-1-6, 2018
Gruziel M., Thyagarajan K., Dietler G., Stasiak A., Ekiel-Jeżewska M.L., Szymczak P., Periodic Motion of Sedimenting Flexible Knots, PHYSICAL REVIEW LETTERS, ISSN: 0031-9007, DOI: 10.1103/PhysRevLett.121.127801, Vol.121, No.12, pp.127801-1-6, 2018

Abstract:
We study the dynamics of knotted deformable closed chains sedimenting in a viscous fluid. We show experimentally that trefoil and other torus knots often attain a remarkably regular horizontal toroidal structure while sedimenting, with a number of intertwined loops, oscillating periodically around each other. We then recover this motion numerically and find out that it is accompanied by a very slow rotation around the vertical symmetry axis. We analyze the dependence of the characteristic timescales on the chain flexibility and aspect ratio. It is observed in the experiments that this oscillating mode of the dynamics can spontaneously form even when starting from a qualitatively different initial configuration. In numerical simulations, the oscillating modes are usually present as transients or final stages of the evolution, depending on chain aspect ratio and flexibility, and the number of loops.

(45p.)
4.Poma A.B., Li M.S., Theodorakis P.E., Generalization of the elastic network model for the study of large conformational changes in biomolecules, Physical Chemistry Chemical Physics, ISSN: 1463-9076, DOI: 10.1039/C8CP03086C, Vol.20, pp.17020-17028, 2018
Poma A.B., Li M.S., Theodorakis P.E., Generalization of the elastic network model for the study of large conformational changes in biomolecules, Physical Chemistry Chemical Physics, ISSN: 1463-9076, DOI: 10.1039/C8CP03086C, Vol.20, pp.17020-17028, 2018

Abstract:
The elastic network (EN) is a prime model that describes the long-time dynamics of biomolecules. However, the use of harmonic potentials renders this model insufficient for studying large conformational changes of proteins (e.g. stretching of proteins, folding and thermal unfolding). Here, we extend the capabilities of the EN model by using a harmonic approximation described by Lennard-Jones (LJ) interactions for far contacts and native contacts obtained from the standard overlap criterion as in the case of Gō-like models. While our model is validated against the EN model by reproducing the equilibrium properties for a number of proteins, we also show that the model is suitable for the study of large conformation changes by providing various examples. In particular, this is illustrated on the basis of pulling simulations that predict with high accuracy the experimental data on the rupture force of the studied proteins. Furthermore, in the case of DDFLN4 protein, our pulling simulations highlight the advantages of our model with respect to Gō-like approaches, where the latter fail to reproduce previous results obtained by all-atom simulations that predict an additional characteristic peak for this protein. In addition, folding simulations of small peptides yield different folding times for α-helix and β-hairpin, in agreement with experiment, in this way providing further opportunities for the application of our model in studying large conformational changes of proteins. In contrast to the EN model, our model is suitable for both normal mode analysis and molecular dynamics simulation. We anticipate that the proposed model will find applications in a broad range of problems in biology, including, among others, protein folding and thermal unfolding.

Keywords:
Free Energy, protein, elastic network, molecular dynamics, normal mode analysis

(40p.)
5.Malińska D., Szymański J., Patalas-Krawczyk P., Michalska B., Wojtala A., Prill M., Partyka M., Drabik K., Walczak J., Sewer A., Johne S., Luettich K., Peitsch M.C., Hoeng J., Duszyński J., Szczepanowska J., van der Toorn M., Więckowski M.R., Assessment of mitochondrial function following short- and long-term exposure of human bronchial epithelial cells to total particulate matter from a candidate modified-risk tobacco product and reference cigarettes, Food and Chemical Toxicology, ISSN: 0278-6915, DOI: 10.1016/j.fct.2018.02.013, Vol.115, pp.1-12, 2018
Malińska D., Szymański J., Patalas-Krawczyk P., Michalska B., Wojtala A., Prill M., Partyka M., Drabik K., Walczak J., Sewer A., Johne S., Luettich K., Peitsch M.C., Hoeng J., Duszyński J., Szczepanowska J., van der Toorn M., Więckowski M.R., Assessment of mitochondrial function following short- and long-term exposure of human bronchial epithelial cells to total particulate matter from a candidate modified-risk tobacco product and reference cigarettes, Food and Chemical Toxicology, ISSN: 0278-6915, DOI: 10.1016/j.fct.2018.02.013, Vol.115, pp.1-12, 2018

Abstract:
Mitochondrial dysfunction caused by cigarette smoke is involved in the oxidative stress-induced pathology of airway diseases. Reducing the levels of harmful and potentially harmful constituents by heating rather than combusting tobacco may reduce mitochondrial changes that contribute to oxidative stress and cell damage. We evaluated mitochondrial function and oxidative stress in human bronchial epithelial cells (BEAS 2B) following 1- and 12-week exposures to total particulate matter (TPM) from the aerosol of a candidate modified-risk tobacco product, the Tobacco Heating System 2.2 (THS2.2), in comparison with TPM from the 3R4F reference cigarette. After 1-week exposure, 3R4F TPM had a strong inhibitory effect on mitochondrial basal and maximal oxygen consumption rates compared to TPM from THS2.2. Alterations in oxidative phosphorylation were accompanied by increased mitochondrial superoxide levels and increased levels of oxidatively damaged proteins in cells exposed to 7.5 μg/mL of 3R4F TPM or 150 μg/mL of THS2.2 TPM, while cytosolic levels of reactive oxygen species were not affected. In contrast, the 12-week exposure indicated adaptation of BEAS-2B cells to long-term stress. Together, the findings indicate that 3R4F TPM had a stronger effect on oxidative phosphorylation, gene expression and proteins involved in oxidative stress than TPM from the candidate modified-risk tobacco product THS2.2.

Keywords:
Mitochondria, Mitochondrial respiratory chain, Oxidative stress, BEAS-2B cells, Cigarette, Tobacco heating system

(40p.)
6.Lanzi M., Salatelli E., Giorgini L., Marinelli M., Pierini F., Effect of the incorporation of an Ag nanoparticle interlayer on the photovoltaic performance of green bulk heterojunction water-soluble polythiophene solar cells, POLYMER, ISSN: 0032-3861, DOI: 10.1016/j.polymer.2018.07.012, Vol.149, pp.273-285, 2018
Lanzi M., Salatelli E., Giorgini L., Marinelli M., Pierini F., Effect of the incorporation of an Ag nanoparticle interlayer on the photovoltaic performance of green bulk heterojunction water-soluble polythiophene solar cells, POLYMER, ISSN: 0032-3861, DOI: 10.1016/j.polymer.2018.07.012, Vol.149, pp.273-285, 2018

Abstract:
Two water-soluble regioregular poly(3-alkylthiophene)s, incorporating aminic groups at the end of the side chains, have been synthesized using a post-polymerization functionalization procedure on a ω-bromine substituted polyalkylthiophene. The high solubility of the obtained polymers in water allowed for the preparation of “green” bulk heterojunction solar cells which reached a power conversion efficiency of 4.85% when PC61BM was used as electron-acceptor material. Improved optical absorption and photocurrent have been obtained by interposing a layer of Ag nanoparticles between the buffer and the photoactive layer, leading to a final power conversion efficiency of 5.51%.

Keywords:
Water-soluble polythiophene, Bulk heterojunction solar cell, Organic photovoltaic

(40p.)
7.Bukowicki M., Ekiel-Jeżewska M.L., Different bending models predict different dynamics of sedimenting elastic trumbbells, SOFT MATTER, ISSN: 1744-683X, DOI: 10.1039/C8SM00604K, Vol.14, pp.5786-5799, 2018
Bukowicki M., Ekiel-Jeżewska M.L., Different bending models predict different dynamics of sedimenting elastic trumbbells, SOFT MATTER, ISSN: 1744-683X, DOI: 10.1039/C8SM00604K, Vol.14, pp.5786-5799, 2018

Abstract:
The main goal of this paper is to examine theoretically and numerically the impact of a chosen bending model on the dynamics of elastic filaments settling in a viscous fluid under gravity at low-Reynolds-number. We use the bead-spring approximation of a filament and the Rotne–Prager mobility matrix to describe hydrodynamic interactions between the beads. We analyze the dynamics of trumbbells, for which bending angles are typically larger than for thin and long filaments. Each trumbbell is made of three beads connected by springs and it exhibits a bending resistance, described by the harmonic or – alternatively – by the ‘cosine’ (also called the Kratky–Porod) bending models, both often used in the literature. Using the harmonic bending potential, and coupling it to the spring potential by the Young's modulus, we find simple benchmark solutions: stable stationary configurations of a single elastic trumbbell and attraction of two elastic trumbbells towards a periodic long-lasting orbit. As the most significant result of this paper, we show that for very elastic trumbbells at the same initial conditions, the Kratky–Porod bending potential can lead to qualitatively and quantitatively different spurious dynamics, with artificially large bending angles and unrealistic shapes. We point out that for the bead models of an elastic filament, the range of applicability of the Kratky–Porod model might not go beyond bending angles smaller than π/2 for touching beads and beyond an even much lower value for beads well-separated from each other. The existence of stable stationary configurations of elastic trumbbells and a family of periodic oscillations of two elastic trumbbells are very important findings on their own.

(40p.)
8.Żuk P.J., Kochańczyk M., Lipniacki T., Sampling rare events in stochastic reaction-diffusion systems within trajectory looping, PHYSICAL REVIEW E, ISSN: 1539-3755, DOI: 10.1103/PhysRevE.98.022401, Vol.98, pp.022401-1-10, 2018
Żuk P.J., Kochańczyk M., Lipniacki T., Sampling rare events in stochastic reaction-diffusion systems within trajectory looping, PHYSICAL REVIEW E, ISSN: 1539-3755, DOI: 10.1103/PhysRevE.98.022401, Vol.98, pp.022401-1-10, 2018

Abstract:
In bistable reaction–diffusion systems, transitions between stable states typically occur on timescales orders of magnitude longer than the chemical equilibration time. Estimation of transition rates within explicit Brownian dynamics simulations is computationally prohibitively costly. We present a method that exploits a single trajectory, generated by a prior simulation of diffusive motions of molecules, to sample chemical kinetic processes on timescales several orders of magnitude longer than the duration of the diffusive trajectory. In this approach, we “loop” the diffusive trajectory by transferring chemical states of the molecules from the last to the first time step of the trajectory. Trajectory looping can be applied to enhance sampling of rare events in biochemical systems in which the number of reacting molecules is constant, as in cellular signal transduction pathways. As an example, we consider a bistable system of autophosphorylating kinases, for which we calculate state-to-state transition rates and traveling wave velocities. We provide an open-source implementation of the method.

(35p.)
9.Skłodowska K., Dębski P.R., Michalski J.A., Korczyk P.M., Dolata M., Zając M., Jakiela S., Simultaneous Measurement of Viscosity and Optical Density of Bacterial Growth and Death in a Microdroplet, Micromachines, ISSN: 2072-666X, DOI: 10.3390/mi9050251, Vol.9, No.5, pp.1-13, 2018
Skłodowska K., Dębski P.R., Michalski J.A., Korczyk P.M., Dolata M., Zając M., Jakiela S., Simultaneous Measurement of Viscosity and Optical Density of Bacterial Growth and Death in a Microdroplet, Micromachines, ISSN: 2072-666X, DOI: 10.3390/mi9050251, Vol.9, No.5, pp.1-13, 2018

Abstract:
Herein, we describe a novel method for the assessment of droplet viscosity moving inside microfluidic channels. The method allows for the monitoring of the rate of the continuous growth of bacterial culture. It is based on the analysis of the hydrodynamic resistance of a droplet that is present in a microfluidic channel, which affects its motion. As a result, we were able to observe and quantify the change in the viscosity of the dispersed phase that is caused by the increasing population of interacting bacteria inside a size-limited system. The technique allows for finding the correlation between the viscosity of the medium with a bacterial culture and its optical density. These features, together with the high precision of the measurement, make our viscometer a promising tool for various experiments in the field of analytical chemistry and microbiology, where the rigorous control of the conditions of the reaction and the monitoring of the size of bacterial culture are vital.

Keywords:
droplet microfluidics, cell growth, viscosity, rheology, Escherichia coli

(30p.)
10.Dębski P.R., Skłodowska K., Michalski J.A., Korczyk P.M., Dolata M., Jakiela S., Continuous Recirculation of Microdroplets in a Closed Loop Tailored for Screening of Bacteria Cultures, Micromachines, ISSN: 2072-666X, DOI: 10.3390/mi9090469, Vol.9, pp.1-11, 2018
Dębski P.R., Skłodowska K., Michalski J.A., Korczyk P.M., Dolata M., Jakiela S., Continuous Recirculation of Microdroplets in a Closed Loop Tailored for Screening of Bacteria Cultures, Micromachines, ISSN: 2072-666X, DOI: 10.3390/mi9090469, Vol.9, pp.1-11, 2018

Abstract:
Emerging microfluidic technology has introduced new precision controls over reaction conditions. Owing to the small amount of reagents, microfluidics significantly lowers the cost of carrying a single reaction. Moreover, in two-phase systems, each part of a dispersed fluid can be treated as an independent chemical reactor with a volume from femtoliters to microliters, increasing the throughput. In this work, we propose a microfluidic device that provides continuous recirculation of droplets in a closed loop, maintaining low consumption of oil phase, no cross-contamination, stabilized temperature, a constant condition of gas exchange, dynamic feedback control on droplet volume, and a real-time optical characterization of bacterial growth in a droplet. The channels (tubing) and junction cubes are made of Teflon fluorinated ethylene propylene (FEP) to ensure non-wetting conditions and to prevent the formation of biofilm, which is particularly crucial for biological experiments. We show the design and operation of a novel microfluidic loop with the circular motion of microdroplet reactors monitored with optical sensors and precision temperature controls. We have employed the proposed system for long term monitoring of bacterial growth during the antibiotic chloramphenicol treatment. The proposed system can find applications in a broad field of biomedical diagnostics and therapy.

Keywords:
microfluidic loop, bacteria cultures, screening, antibiotic treatment, Escherichia coli

(30p.)
11.Małolepszy A., Błoński S., Chrzanowska-Giżyńska J., Wojasiński M., Płociński T., Stobiński L., Szymański Z., Fluorescent carbon and graphene oxide nanoparticles synthesized by the laser ablation in liquid, APPLIED PHYSICS A-MATERIALS SCIENCE AND PROCESSING, ISSN: 0947-8396, DOI: 10.1007/s00339-018-1711-5, pp.124-282, 2018
Małolepszy A., Błoński S., Chrzanowska-Giżyńska J., Wojasiński M., Płociński T., Stobiński L., Szymański Z., Fluorescent carbon and graphene oxide nanoparticles synthesized by the laser ablation in liquid, APPLIED PHYSICS A-MATERIALS SCIENCE AND PROCESSING, ISSN: 0947-8396, DOI: 10.1007/s00339-018-1711-5, pp.124-282, 2018

Abstract:
The results of synthesis of the fluorescent carbon dots (CDots) from graphite target and reduced graphene oxide (rGO) nanoparticles performed by the nanosecond laser ablation in polyethylene glycol 200 (PEG200) are shown. Two-step laser irradiation (first graphite target, next achieved suspension) revealed a very effective production of CDots. However, the ablation in PEG appeared to be effective with 1064 nm laser pulse in contrast to the ablation with 355 nm laser pulse. In the case of rGO nanoparticles similar laser irradiation procedure was less efficient. In both cases, received nanoparticles exhibited strong, broadband photoluminescence with a maximum dependent on the excitation wavelength. The size distribution for obtained CDots was evaluated using the DLS technique and HRTEM images. The results from both methods show quite good agreement in nanoparticle size estimation although the DLS method slightly overestimates nanoparticle’s diameter

(25p.)
12.Zaremba D., Błoński S., Jachimek M., Marijnissen M.J., Jakieła S., Korczyk P.M., Investigations of modular microfluidic geometries for passive manipulations on droplets, BULLETIN OF THE POLISH ACADEMY OF SCIENCES: TECHNICAL SCIENCES, ISSN: 0239-7528, DOI: 10.24425/119068, Vol.66, No.2, pp.139-149, 2018
Zaremba D., Błoński S., Jachimek M., Marijnissen M.J., Jakieła S., Korczyk P.M., Investigations of modular microfluidic geometries for passive manipulations on droplets, BULLETIN OF THE POLISH ACADEMY OF SCIENCES: TECHNICAL SCIENCES, ISSN: 0239-7528, DOI: 10.24425/119068, Vol.66, No.2, pp.139-149, 2018

Abstract:
Multiple pipetting is a standard laboratory procedure resulting in the compartmentalisation of a liquid sample. Microfluidics offers techniques which can replace this process by the use of tiny droplets. Passive manipulation on droplets is an interesting and promising approach for the design of microfluidic devices which on one hand are easy-to-use and on the other, execute complex laboratory procedures. We present a comprehensive study of the geometry of microfluidic components which encode different operations on droplets into the structure of the device. The understanding of hydrodynamic interactions between the continuous flow and a droplet travelling through confined space of nontrivial microfluidic geometries is crucial for a rational and efficient design of new generation of modular microfluidic processors with embedded instructions.

Keywords:
microfluidics, two-phase flows, droplets

(25p.)