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.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.19, No.11, pp.4147-4167, 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.19, No.11, pp.4147-4167, 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.

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 -1-14, 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 -1-14, 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

3.Jetka T., Nienałtowski K., Filippi S., Stumpf M.P.H., Komorowski M., An information-theoretic framework for deciphering pleiotropic and noisy biochemical signaling, Nature Communications, ISSN: 2041-1723, DOI: 10.1038/s41467-018-07085-1, Vol.9, pp.4591-1-9, 2018
Jetka T., Nienałtowski K., Filippi S., Stumpf M.P.H., Komorowski M., An information-theoretic framework for deciphering pleiotropic and noisy biochemical signaling, Nature Communications, ISSN: 2041-1723, DOI: 10.1038/s41467-018-07085-1, Vol.9, pp.4591-1-9, 2018

Abstract:
Many components of signaling pathways are functionally pleiotropic, and signaling responses are marked with substantial cell-to-cell heterogeneity. Therefore, biochemical descriptions of signaling require quantitative support to explain how complex stimuli (inputs) are encoded in distinct activities of pathways effectors (outputs). A unique perspective of information theory cannot be fully utilized due to lack of modeling tools that account for the complexity of biochemical signaling, specifically for multiple inputs and outputs. Here, we develop a modeling framework of information theory that allows for efficient analysis of models with multiple inputs and outputs; accounts for temporal dynamics of signaling; enables analysis of how signals flow through shared network components; and is not restricted by limited variability of responses. The framework allows us to explain how identity and quantity of type I and type III interferon variants could be recognized by cells despite activating the same signaling effectors.

4.Nakielski P., Pierini F., Blood interactions with nano- and microfibers: recent advances, challenges and applications in nano- and microfibrous hemostatic agents, Acta Biomaterialia, ISSN: 1742-7061, DOI: 10.1016/j.actbio.2018.11.029, pp.1-48, 2018
Nakielski P., Pierini F., Blood interactions with nano- and microfibers: recent advances, challenges and applications in nano- and microfibrous hemostatic agents, Acta Biomaterialia, ISSN: 1742-7061, DOI: 10.1016/j.actbio.2018.11.029, pp.1-48, 2018

Abstract:
Nanofibrous materials find a wide range of applications, such as vascular grafts, tissue-engineered scaffolds, or drug delivery systems. This phenomenon can be attributed to almost arbitrary biomaterial modification opportunities created by a multitude of polymers used to form nanofibers, as well as by surface functionalization methods. Among these applications, the hemostatic activity of nanofibrous materials is gaining more and more interest in biomedical research. It is therefore crucial to find both materials and nanofiber structural properties that affect organism responses. The present review critically analyzes the response of blood elements to natural and synthetic polymers, and their blends and composites. Also assessed in this review is the incorporation of pro-coagulative substances or drugs that can decrease bleeding time. The review also discusses the main animal models that were used to assess hemostatic agent safety and effectiveness.

Keywords:
Blood-biomaterial interactions, Coagulation, Electrospinning, Nanofibers, Platelets, Hemorrhage

5.Costantini M., Guzowski J., Żuk P.J., Mozetic P., De Panfilis S., Jaroszewicz J., Heljak M., Massimi M., Pierron M., Trombetta M., Dentini M., Święszkowski W., Rainer A., Garstecki P., Barbetta A., Electric Field Assisted Microfluidic Platform for Generation of Tailorable Porous Microbeads as Cell Carriers for Tissue Engineering, Advanced Functional Materials, ISSN: 1616-301X, DOI: 10.1002/adfm.201800874, Vol.28, pp.1800874-1-13, 2018
Costantini M., Guzowski J., Żuk P.J., Mozetic P., De Panfilis S., Jaroszewicz J., Heljak M., Massimi M., Pierron M., Trombetta M., Dentini M., Święszkowski W., Rainer A., Garstecki P., Barbetta A., Electric Field Assisted Microfluidic Platform for Generation of Tailorable Porous Microbeads as Cell Carriers for Tissue Engineering, Advanced Functional Materials, ISSN: 1616-301X, DOI: 10.1002/adfm.201800874, Vol.28, pp.1800874-1-13, 2018

Abstract:
Injection of cell‐laden scaffolds in the form of mesoscopic particles directly to the site of treatment is one of the most promising approaches to tissue regeneration. Here, a novel and highly efficient method is presented for preparation of porous microbeads of tailorable dimensions (in the range ≈300–1500 mm) and with a uniform and fully interconnected internal porous texture. The method starts with generation of a monodisperse oil‐in‐water emulsion inside a flow‐focusing microfluidic device. This emulsion is later broken‐up, with the use of electric field, into mesoscopic double droplets, that in turn serve as a template for the porous microbeads. By tuning the amplitude and frequency of the electric pulses, the template droplets and the resulting porous bead scaffolds are precisely produced. Furthermore, a model of pulsed electrodripping is proposed that predicts the size of the template droplets as a function of the applied voltage. To prove the potential of the porous microbeads as cell carries, they are tested with human mesenchymal stem cells and hepatic cells, with their viability and degree of microbead colonization being monitored. Finally, the presented porous microbeads are benchmarked against conventional microparticles with nonhomogenous internal texture, revealing their superior performance.

6.Kaźmierczak B., Tsai J.C., Białecki S., The propagation phenomenon of solutions of a parabolic problem on the sphere, MATHEMATICAL MODELS AND METHODS IN APPLIED SCIENCES, ISSN: 0218-2025, DOI: 10.1142/S0218202518500483, Vol.28, No.10, pp.2001-2067, 2018
Kaźmierczak B., Tsai J.C., Białecki S., The propagation phenomenon of solutions of a parabolic problem on the sphere, MATHEMATICAL MODELS AND METHODS IN APPLIED SCIENCES, ISSN: 0218-2025, DOI: 10.1142/S0218202518500483, Vol.28, No.10, pp.2001-2067, 2018

Abstract:
In this paper, we study propagation phenomena on the sphere using the bistable reaction–diffusion formulation. This study is motivated by the propagation of waves of calcium concentrations observed on the surface of oocytes, and the propagation of waves of kinase concentrations on the B-cell membrane in the immune system. To this end, we first study the existence and uniqueness of mild solutions for a parabolic initial-boundary value problem on the sphere with discontinuous bistable nonlinearities. Due to the discontinuous nature of reaction kinetics, the standard theories cannot be applied to the underlying equation to obtain the existence of solutions. To overcome this difficulty, we give uniform estimates on the Legendre coefficients of the composition function of the reaction kinetics function and the solution, and a priori estimates on the solution, and then, through the iteration scheme, we can deduce the existence and related properties of solutions. In particular, we prove that the constructed solutions are of C2,1 class everywhere away from the discontinuity point of the reaction term. Next, we apply this existence result to study the propagation phenomenon on the sphere. Specifically, we use stationary solutions and their variants to construct a pair of time-dependent super/sub-solutions with different moving speeds. When applied to the case of sufficiently small diffusivity, this allows us to infer that if the initial concentration of the species is above the inhomogeneous steady state, then the species will exhibit the propagating behavior.

Keywords:
Propagation, sphere, bistable kinetics

7.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.

8.Poma Bernaola A., 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 Bernaola A., 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

9.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

10.Hussain M., Misbah-ul-Islam , Meydan T., Cuenca J.A., Melikhov Y., Mustafa G., Murtaza G., Jamil Y., Microwave absorption properties of CoGd substituted ZnFe2O4 ferrites synthesized by co-precipitation technique, CERAMICS INTERNATIONAL, ISSN: 0272-8842, DOI: 10.1016/j.ceramint.2017.12.145, Vol.44, No.6, pp.5909-5914, 2018
Hussain M., Misbah-ul-Islam , Meydan T., Cuenca J.A., Melikhov Y., Mustafa G., Murtaza G., Jamil Y., Microwave absorption properties of CoGd substituted ZnFe2O4 ferrites synthesized by co-precipitation technique, CERAMICS INTERNATIONAL, ISSN: 0272-8842, DOI: 10.1016/j.ceramint.2017.12.145, Vol.44, No.6, pp.5909-5914, 2018

Abstract:
A series of co-precipitated Zn1-xCoxGdyFe2-yO4 spinel ferrites (x = 0.0-0.5, y = 0.00-0.10) sintered at 1000 degrees C were characterized by X-ray diffraction (XRD), Fourier transform infrared spectroscopy (FTIR), scanning electron microscopy (SEM), vibrating sample magnetometery (VSM) and microwave cavity perturbation (MCP). XRD patterns and FTIR spectra reveal formation of the spinel phase along with few traces of GdFeO3 second phase. The lattice constant decreases with an increasing amount of CoGd ions due to the segregation of Gd3+ on the grain boundaries and due to replacement of lager Zn2+ ions with smaller Co2+ ions. SEM shows grain size to decrease with the increase of CoGd contents due to grain growth inhibition by the second phase. VSM results show remanence and saturation magnetization to exhibit an increasing trend due to Co substitution on octahedral sites and presence of a second phase. The coercivity increases with the increase of CoGd contents due to anisotropic nature of Co. MCP shows the complex magnetic permeability to increase with CoGd concentration while the complex permittivity decreases.

Keywords:
Spinel ferrites, Magnetization, Permittivity, Permeability

11.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

12.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.

13.Pawłowska S., Kowalewski T.A., Pierini F., Fibrous polymer nanomaterials for biomedical applications and their transport by fluids: an overview, SOFT MATTER, ISSN: 1744-683X, DOI: 10.1039/C8SM01269E, Vol.14, pp.8421-8444, 2018
Pawłowska S., Kowalewski T.A., Pierini F., Fibrous polymer nanomaterials for biomedical applications and their transport by fluids: an overview, SOFT MATTER, ISSN: 1744-683X, DOI: 10.1039/C8SM01269E, Vol.14, pp.8421-8444, 2018

Abstract:
Over the past few decades, there has been strong interest in the development of new micro- and nanomaterials for biomedical applications. Their use in the form of capsules, particles or filaments suspended in body fluids is associated with conformational changes and hydrodynamic interactions responsible for their transport. The dynamics of fibres or other long objects in Poiseuille flow is one of the fundamental problems in a variety of biomedical contexts, such as mobility of proteins, dynamics of DNA or other biological polymers, cell movement, tissue engineering, and drug delivery. In this review, we discuss several important applications of micro and nanoobjects in this field and try to understand the problems of their transport in flow resulting from material-environment interactions in typical, crowded, and complex biological fluids. Our aim is to elucidate the relationship between the nano- and microscopic structures of elongated polymer particles and their flow properties, thus opening the possibility to design nanoobjects that can be efficiently transported by body fluids for targeted drug release or local tissue regeneration.

14.Sosa-Costa A., Piechocka I.K., Gardini L., Pavone F.S., Capitanio M., Garcia-Parajo M.F., Manzo C., PLANT: A Method for Detecting Changes of Slope in Noisy Trajectories, BIOPHYSICAL JOURNAL, ISSN: 0006-3495, DOI: 10.1016/j.bpj.2018.04.006, Vol.114, No.9, pp.2044-2051, 2018
Sosa-Costa A., Piechocka I.K., Gardini L., Pavone F.S., Capitanio M., Garcia-Parajo M.F., Manzo C., PLANT: A Method for Detecting Changes of Slope in Noisy Trajectories, BIOPHYSICAL JOURNAL, ISSN: 0006-3495, DOI: 10.1016/j.bpj.2018.04.006, Vol.114, No.9, pp.2044-2051, 2018

Abstract:
Time traces obtained from a variety of biophysical experiments contain valuable information on underlying processes occurring at the molecular level. Accurate quantification of these data can help explain the details of the complex dynamics of biological systems. Here, we describe PLANT (Piecewise Linear Approximation of Noisy Trajectories), a segmentation algorithm that allows the reconstruction of time-trace data with constant noise as consecutive straight lines, from which changes of slopes and their respective durations can be extracted. We present a general description of the algorithm and perform extensive simulations to characterize its strengths and limitations, providing a rationale for the performance of the algorithm in the different conditions tested. We further apply the algorithm to experimental data obtained from tracking the centroid position of lymphocytes migrating under the effect of a laminar flow and from single myosin molecules interacting with actin in a dual-trap force-clamp configuration.

Keywords:
TETHERED PARTICLE MOTION, CHANGE-POINT DETECTION, OPTICAL TWEEZERS, CELL-ADHESION, UNKNOWN POINT, SINGLE, MYOSIN, MODEL, MIGRATION, TRACKING

15.Żuk P.J., Cichocki B., Szymczak P., GRPY: An Accurate Bead Method for Calculation of Hydrodynamic Properties of Rigid Biomacromolecules, BIOPHYSICAL JOURNAL, ISSN: 0006-3495, DOI: 10.1016/j.bpj.2018.07.015, Vol.115, No.5, pp.782-800, 2018
Żuk P.J., Cichocki B., Szymczak P., GRPY: An Accurate Bead Method for Calculation of Hydrodynamic Properties of Rigid Biomacromolecules, BIOPHYSICAL JOURNAL, ISSN: 0006-3495, DOI: 10.1016/j.bpj.2018.07.015, Vol.115, No.5, pp.782-800, 2018

Abstract:
Two main problems that arise in the context of hydrodynamic bead modeling are an inaccurate treatment of bead overlaps and the necessity of using volume corrections when calculating intrinsic viscosity. We present a formalism based on the generalized Rotne-Prager-Yamakawa approximation that successfully addresses both of these issues. The generalized Rotne-Prager-Yamakawa method is shown to be highly effective for the calculation of transport properties of rigid biomolecules represented as assemblies of spherical beads of different sizes, both overlapping and nonoverlapping. We test the method on simple molecular shapes as well as real protein structures and compare its performance with other computational approaches.

16.Demchenko I.N., Syryanyy Y., Melikhov Y., Nittler L., Gladczuk L., Lasek K., Cozzarini L., Dalmiglio M., Goldoni A., Konstantynov P., Chernyshova M., X-ray photoelectron spectroscopy analysis as a tool to assess factors influencing magnetic anisotropy type in Co/MgO system with gold interlayer, SCRIPTA MATERIALIA, ISSN: 1359-6462, DOI: 10.1016/j.scriptamat.2017.10.006, Vol.145, pp.50-53, 2018
Demchenko I.N., Syryanyy Y., Melikhov Y., Nittler L., Gladczuk L., Lasek K., Cozzarini L., Dalmiglio M., Goldoni A., Konstantynov P., Chernyshova M., X-ray photoelectron spectroscopy analysis as a tool to assess factors influencing magnetic anisotropy type in Co/MgO system with gold interlayer, SCRIPTA MATERIALIA, ISSN: 1359-6462, DOI: 10.1016/j.scriptamat.2017.10.006, Vol.145, pp.50-53, 2018

Abstract:
X-ray photoelectron spectroscopy (XPS) studies of Au/Co/Au(0.3 nm)/MgO and Au/Co/MgO systems were conducted in order to monitor the electronic structure modification at Co/MgO interface with/without gold interlayer. A detailed analysis of Co 2p states revealed that the amount of minor oxygen contribution at Co/MgO interface decreased after the Au interlayer was added. The obtained XPS results together with density functional theory (DFT) allowed explanation of the increase of surface anisotropy energy in the sample with the gold interlayer in terms of (i) noble and transitional metal d-d orbital hybridization; (ii) interfacial Co 3d and O 2p; and (iii) interface imperfection.

17.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.

18.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

19.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

20.Chernyshova M., Malinowski K., Melikhov Y., Kowalska-Strzęciwilk E., Czarski T., Wojeński A., Linczuk P., Krawczyk R.D., Study of the optimal configuration for a Gas Electron Multiplier aimed at plasma impurity radiation monitoring, Fusion Engineering and Design, ISSN: 0920-3796, DOI: 10.1016/j.fusengdes.2018.03.031, Vol.136, pp.592-596, 2018
Chernyshova M., Malinowski K., Melikhov Y., Kowalska-Strzęciwilk E., Czarski T., Wojeński A., Linczuk P., Krawczyk R.D., Study of the optimal configuration for a Gas Electron Multiplier aimed at plasma impurity radiation monitoring, Fusion Engineering and Design, ISSN: 0920-3796, DOI: 10.1016/j.fusengdes.2018.03.031, Vol.136, pp.592-596, 2018

Abstract:
For the purpose of monitoring the level of plasma impurity (especially tungsten) and its distribution reconstruction at tokamaks (ITER in particular), a Soft X-Ray (SXR) tomographic diagnostics based on Gas Electron Multiplier (GEM) detectors with energy discrimination has been extensively considered for a while. Coupled with advanced electronics, GEM detectors offer excellent time and space resolution, as well as a charge spectrum from which the SXR photon spectrum can be deconvolved. In addition, they are less subjected to a neutron damage as compared to standard semiconductor diodes. This contribution highlights the latest studies supporting the development of such diagnostics focusing on laboratory tests to examine: (a) the impact of GEM holes geometry on the properties and distribution of the electron avalanche; (b) the effect of the high rate photon flux on GEM foil performance; and (c) the optimal electric field distribution.

Keywords:
Nuclear instruments for hot plasma diagnostics, X-ray detectors, Electron multipliers (gas), Micropattern gaseous detectors (MSGC; GEM; THGEM; RETHGEM; MHSP; MICROPIC; MICROMEGAS; InGrid; etc.)

21.Ekiel-Jeżewska M.L., Boniecki R., Bukowicki M., Gruca M., Stokes velocity generated by a point force in various geometries, EUROPEAN PHYSICAL JOURNAL E, ISSN: 1292-8941, DOI: 10.1140/epje/i2018-11727-3, Vol.41, No.120, pp.1-7, 2018
Ekiel-Jeżewska M.L., Boniecki R., Bukowicki M., Gruca M., Stokes velocity generated by a point force in various geometries, EUROPEAN PHYSICAL JOURNAL E, ISSN: 1292-8941, DOI: 10.1140/epje/i2018-11727-3, Vol.41, No.120, pp.1-7, 2018

Abstract:
In this short review, we visualize the fluid velocity generated by a point force close to a plane free surface or a plane rigid wall. We present separately contributions from all the multipoles which form the corresponding classical systems of images. Such graphical images might be useful in the theoretical and numerical modeling of the dynamics of micro-objects moving close to an interface.

22.Demchenko I.N., Melikhov Y., Syryanyy Y., Zaytseva I., Konstantynov P., Chernyshov M., Effect of argon sputtering on XPS depth-profiling results of Si/Nb/Si, JOURNAL OF ELECTRON SPECTROSCOPY AND RELATED PHENOMENA, ISSN: 0368-2048, DOI: 10.1016/j.elspec.2017.09.009, Vol.224, pp.17-22, 2018
Demchenko I.N., Melikhov Y., Syryanyy Y., Zaytseva I., Konstantynov P., Chernyshov M., Effect of argon sputtering on XPS depth-profiling results of Si/Nb/Si, JOURNAL OF ELECTRON SPECTROSCOPY AND RELATED PHENOMENA, ISSN: 0368-2048, DOI: 10.1016/j.elspec.2017.09.009, Vol.224, pp.17-22, 2018

Abstract:
Ultrathin Si/Nb/Si trilayer is an excellent example of a system for which dimensionality effects, together with other factors like type of a substrate material and growth method, influence strongly its superconducting properties. This study offers some important insights into experimental investigation of density of states of such a system with the aim to identify an electronic structure of the interface as a function of niobium layer thickness. For that, two Si/Nb/Si trilayers with 9.5 and 1.3 nm thick niobium layer buried in amorphous silicon were studied using high-resolution (HR) XPS depth-profile techniques. Strong influence of sputtering was observed, which resulted in severe intermixture of Si and Nb atoms. Nevertheless, a sharp top interface and metallic phase of niobium were detected for the thicker layer sample. On the contrary, a Nb-rich mixed alloy at top interface was observed for the thinner layer sample.

Keywords:
High-resolution X-ray photoelectron spectroscopy, XPS, Si/Nb/Si, NbSi, Depth profiling

23.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

24.Chernyshova M., Czarski T., Malinowski K., Melikhov Y., Kasprowicz G., Kowalska-Strzęciwilk E., Linczuk P., Wojeński A., Krawczyk R.D., 2D GEM based imaging detector readout capabilities from perspective of intense soft x-ray plasma radiation, REVIEW OF SCIENTIFIC INSTRUMENTS, ISSN: 0034-6748, DOI: 10.1063/1.5039278, Vol.89, No.10, pp.10G106-1-5, 2018
Chernyshova M., Czarski T., Malinowski K., Melikhov Y., Kasprowicz G., Kowalska-Strzęciwilk E., Linczuk P., Wojeński A., Krawczyk R.D., 2D GEM based imaging detector readout capabilities from perspective of intense soft x-ray plasma radiation, REVIEW OF SCIENTIFIC INSTRUMENTS, ISSN: 0034-6748, DOI: 10.1063/1.5039278, Vol.89, No.10, pp.10G106-1-5, 2018

Abstract:
A detecting system based on the Gas Electron Multiplier (GEM) technology is considered for tokamak plasma radiation monitoring. In order to estimate its capabilities in processing and recording intense photon flux (up to similar to 0.1 MHz/mm(2)), the imaging effectiveness of GEM detectors was tested with different patterned anode planes (i. e., different signal readouts): a simple hexagonal readout structure and three structures with interconnected electrodes (XY square, XY rectangular, and UXV). It was found that under intense photon flux, all the readouts fail to account for a considerable amount of the incoming signals due to mostly photon position determination ambiguity and overlapped signals. Analysis of the signals that can be used to determine photon position and energy unambiguously showed that the UXV readout structure is more effective among the readouts with interconnected electrodes. Along with similar spatial resolution and accuracy, the UXV based layout could be considered as a quite promising base of the interconnected anode electrodes configuration, keeping in mind that the photon rate capability has to be improved for the final application.

25.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