Publications in journals ranked by Journal Citation Reports (JCR) 
Publications in other journals ranked by Ministry of Science and Higher Education
Conference publications indexed in the Web of Science Core Collection
Publications in other journals and conference proceedings
Affiliation to IPPT PAN

1.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

2.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

3.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.

4.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.022401-1-022401-10, 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.022401-1-022401-10, 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.

5.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

6.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

7.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