Publications

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Lab-Affiliated Author, External Collaborator

2022

• Korwek Z, Czerkies M, Jaruszewicz-Błońska J, Prus W, Kosiuk I, Kochańczyk M, Lipniacki T. Non-self RNA rewires IFNβ signaling: A mathematical model of the innate immune response (submitted) bioRxiv

• Zaremba D, Błoński S, Korczyk PM. Concentration on demand – a microfluidic system for precise adjustment of the content of single droplets, Chem Eng J 430(3):132935 (2022) CrossRef

• Grabowski F, Kochańczyk M, Lipniacki T. The spread of SARS-CoV-2 variant Omicron with the doubling time of 2.0–3.3 days can be explained by immune evasion, Viruses 14(2):294 (2022) CrossRef medRxiv | PDF Correspondence

• Liu Z, Moreira RA, Dujmović A, Liu H, Yang B, Poma AB, Nash MA. Mapping mechanostable pulling geometries of a therapeutic anticalin/CTLA-4 protein complex, Nano Lett 22(1):179–187 (2022) CrossRef

• Liguori A, Pandini S, Rinoldi C, Zaccheroni N, Pierini F, Focarete ML, Gualandi C. Thermo-active smart electrospun nanofibers, Macromol Rapid Commun (accepted) CrossRef

• Mahiout LA, Kaźmierczak B, Volpert V. Viral infection spreading and mutation in cell culture, Mathematics 10(2):256 (2022) CrossRef | PDF

2021

• Błoński S, J Aureille, S Badawi, D Zaremba, L Pernet, A Grichine, S Fraboulet, PM Korczyk, P Recho, Ch Guilluy, ME Dolega. Direction of epithelial folding defines impact of mechanical forces on epithelial state, Dev Cell 56:3222–3234 (2021) CrossRef

• M Koehler, A Ray, RA Moreira, B Juniku, AB Poma, D Alsteens. Molecular insights into receptor binding energetics and neutralization of SARS-CoV-2 variants, Nat Commun 12(1):6977 (2021) CrossRef

• Kochańczyk M & Lipniacki T. Pareto-based evaluation of national responses to COVID-19 pandemic shows that saving lives and protecting economy are non-trade-off objectives, Sci Rep 11:2425 (2021)  PubMed CrossRef medRxiv | PDF GitHub

• Grabowski F, Preibisch G, Giziński S, Kochańczyk M, Lipniacki T. SARS-CoV-2 Variant of Concern 202012/01 has about twofold replicative advantage and acquires concerning mutations, Viruses 13(3):392 (2021) CrossRef medRxiv | PDF

• Zaremba D, Błoński S, Korczyk PM. Integration of capillary–hydrodynamic logic circuitries for built-in control over multiple droplets in microfluidic networks, Lab Chip 21:1771 (2021) PubMed CrossRef

• Kaźmierczak B & Sneyd J. Speed of traveling waves for monotone reaction–diffusion systems as a function of diffusion coefficients, Physica D: Nonlin Phenom 424:132940 (2021) CrossRef

• Nienałtowski K, Rigby RE, Walczak J, Zakrzewska KE, Głów E, Rehwinkel J, Komorowski M. Fractional response analysis reveals logarithmic cytokine responses in cellular populations, Nat Commun 12:4175 (2021) CrossRef

• Topolewski P & Komorowski M. Information-theoretic analyses of cellular strategies for achieving high signaling capacity — dynamics, cross-wiring and heterogeneity of cellular states, Curr Opin Syst Biol 27:100352 (2021) CrossRef

• Fiebelkow J, Guendel A, Guendel B, Mehwald N, Jetka T, Komorowski M, Waldherr S, Schaper F, Dittrich A. The tyrosine phosphatase SHP2 increases robustness and information transfer within IL-6-induced JAK/STAT signalling, Cell Commun Signal 19:94 (2021) CrossRef

• Poma A, Thu TTM, Tu LA, Hu C-K, Li MS. Nanomechanical stability of Aβ tetramers and fibril-like structures: Molecular dynamics simulations, J Phys Chem B 125(28):7628−7637 (2021) CrossRef

• Piechocka IK, Keary S, Sosa-Costa A, Lau L, Mohan N, Stanisavljevic J, Borgman KJE, Lakadamyali M, Manzo C, Garcia-Parajo MF. Shear forces induce ICAM-1 nanoclustering onendothelial cells that impact on T-cell migration, Biophys J 120:2644–2656 (2021) CrossRef

• Nakielski P, Rinoldi C, Pruchniewski M, Pawłowska S, Gazińska M, Strojny B, Rybak D, Jezierska-Woźniak K, Urbanek O, Denis P, Sinderewicz E, Czelejewska W, Staszkiewicz-Chodor J, Grodzik M, Ziai Y, Barczewska M, Maksymowicz W, Pierini F. Laser-assisted fabrication of ijectable nanofibrous cell carriers, Small (2021) 2104971 CrossRef

• Rinoldi C, Lanzi M, Fiorelli R, Nakielski P, Zembrzycki K, Kowalewski T, Urbanek O, Grippo V, Jezierska-Woźniak  K, Maksymowicz W, Camposeo A, Bilewicz R, Pisignano D, Sanai N, Pierini F. Three-dimensional printable conductive semi-interpenetrating polymer network hydrogel for neural tissue applications, Biomacromolecules 22(7):3084–3098 (2021) CrossRef | PDF

• Rinoldi C, Zargarian SS, Nakielski P, Li X, Liguori A, Petronella G, Presutti D, Wang Q, Costantini M, De Sio L, Gualandi C, Ding B, Pierini F. Nanotechnology-assisted RNA delivery: From nucleic acid therapeutics to COVID-19 vaccines, Small Meth 5(9):2100402 (2021) CrossRef

• Haghighat Bayan MA, Taromi FA, Lanzi  M, Pierini F. Enhanced efficiency in hollow core electrospun nanofiber-based organic solar cells, Sci Rep 11:21144 (2021) CrossRef

• Lanzi M & Pierini F. Efficient and thermally stable BHJ solar cells based on a soluble hydroxy-functionalized regioregular polydodecylthiophene, React Funct Polym 158:104803 (2021) CrossRef

• De Sio L, Ding B, Focsan M, Kogermann K, Pascoal-Faria P, Petronella F, Mitchell G, Zussmann E, Pierini F. Personalized reusable face masks with smart nano‐assisted destruction of pathogens for COVID‐19: A visionary road, Chem Eur J 27(20):6112–6130 (2021) CrossRef

• Lanzi M, Quadretti D, Marinelli M, Ziai Y, Salatelli E, Pierini F. Influence of the active layer structure on the photovoltaic performance of water-soluble polythiophene-based solar cells, Polymers 13(10):1640 (2021) CrossRef

• Guglielmelli A, Pierini F, Tabiryan N, Umeton C, Bunning TJ, De Sio L. Thermoplasmonics with gold nanoparticles: A new weapon in modern optics and biomedicine, Adv Photonics Res 2000198 (2021) CrossRef

• Marinelli M, Candini A, Monti F, Boschi A, Zangoli M, Salatelli E, Pierini F, Lanzi M, Zanelli A, Gazzano M, Di Maria F. Push–pull thiophene-based small molecules with donor and acceptor units of varying strength for photovoltaic application: Beyond P3HT and PCBM, J Mater Chem C 9:11216–11228 (2021) CrossRef

• Cidonio G, Costantini M, Pierini F, Scognamiglio C, Agarwal T, Barbetta A. 3D printing of biphasic inks: Beyond single-scale architectural control, J Mater Chem C (accepted) CrossRef

• Urbanek O, Wysocka A, Nakielski P, Pierini F, Jagielska E, Sabała I. Staphylococcus aureus specific electrospun wound dressings: Influence of immobilization technique on antibacterial efficiency of novel enzybiotic, Pharmaceutics 13(5), 711 (2021) CrossRef

• La Monac A, Girard G, Savoie S, Bertoni G, Krachkovskiy S, Vijh A, Pierini F, Rosei F, Paolella A. Synthesis of electrospun NASICON Li_1.5Al_0.5Ge_1.5(PO₄)₃ solid electrolyte nanofibers by control of germanium hydrolysis, J Electrochem Soc 168(11):110512 (2021) CrossRef

• Mahmood MI, Poma AB, Okazaki K. Optimizing Gō-MARTINI coarse-grained model for F-BAR protein on lipid membrane, Front Mol Biosci, 8:619381 CrossRef

• Wencel A, Ciezkowska M, Wisniewska M, Zakrzewska KE, Pijanowska DG, Pluta KD. Effects of genetically modified human skin fibroblasts, stably overexpressing hepatocyte growth factor, on hepatic functions of cocultured C3A cells, Biotechnol Bioeng 118(1):72–81 (2021) CrossRef

• Janczewska M, Szkop M, Pikus G, Kopyra K, Świątkowska A, Brygoła K, Karczmarczyk U, Walczak J, Żuk MT, Duszak J, Ciach T. PSMA targeted conjugates based on dextran, Appl Radiat Isot 167:109439 (2021) CrossRef

• Boopathi S, Poma AB, Garduño-Juárez R. An overview of several inhibitors for Alzheimer’s disease: Characterization and failure, Int J Mol Sci 22:10798 (2021) CrossRef

• Dębska-Vielhaber G, Miller I, Peeva V, Zuschratter W, Walczak J, Schreiber S, Petri S, Machts J, Vogt S, Szczepanowska J, Gellerich FN, Hermann A, Vielhaber S, Kunz WS Impairment of mitochondrial oxidative phosphorylation in skin fibroblasts of SALS and FALS patients is rescued by in vitro treatment with ROS scavengers, Exp Neurol 339:113620 (2021) CrossRef

2020

• Kochańczyk M, Grabowski F, Lipniacki T. Super-spreading events initiated the exponential growth phase of COVID-19 with R₀ higher than initially estimated, R Soc Open Sci 7:200786 (2020) PubMed CrossRef | PDF SuppInfo-PDF Correspondence

• Hat B, Jaruszewicz-Błońska J, Lipniacki T. Model-based optimization of combination protocols for irradiation-insensitive cancers, Sci Rep 10:12652 (2020) CrossRef | PDF

• Bialecki S, Nalecz-Jawecki P, Kazmierczak B, Lipniacki. Traveling and standing fronts on curved surfaces, Physica D 401:132215 (2020) CrossRef

• Kochańczyk M, Grabowski F, Lipniacki T. Dynamics of COVID-19 pandemic at constant and time-dependent contact rates, Math Model Nat Phenom 15:28 (2020) CrossRef | PDF SuppCode

• Chatterjee P, Glimm T, Kaźmierczak B. Mathematical modeling of chondrogenic pattern formation during limb development: Recent advances in continuous models, Math Biosci 322:108319 (2020) CrossRef

• Nakielski P, Pawłowska S, Rinoldi C, Ziai Y, De Sio L, Urbanek O, Zembrzycki K, Pruchniewski M, Lanzi M, Salatelli E, Calogero A, Kowalewski TA, Yarin AL, Pierini F. Multifunctional platform based on electrospun nanofibers and plasmonic hydrogel: A smart nanostructured pillow for near-infrared light-driven biomedical applications, ACS Appl Mater Interfaces 12(49):54328–54342 (2020) CrossRef

• Pierini F, Guglielmelli A, Urbanek O, Nakielski P, Pezzi L, Buda R, Lanzi M, Kowalewski TA, De Sio L. Thermoplasmonic-activated hydrogel based dynamic light attenuator, Adv Opt Mater 2000324 (2020) CrossRef | SuppInfo-PDF SuppMovie-AVI

• Pawłowska S, Rinoldi C, Nakielski P, Ziai Y, Urbanek O, Li X, Kowalewski TA, Ding B, Pierini F. Ultraviolet light-assisted electrospinning of core–shell fully cross-linked P(NIPAAm-co-NIPMAAm) hydrogel-based nanofibers for thermally-induced drug delivery self-regulation, Adv Mater Interfaces 2000247 (2020) CrossRef | SuppInfo-PDF SuppMovie-MP4 CoverPicture

• Blonski S, Zaremba D, Jachimek M, Jakiela S, Wacławczyk T, Korczyk PM. Impact of inertia and channel angles on flow distribution in microfluidic junctions, Microfluid Nanofluid 24:14 (2020) CrossRef

• Sankaran A, Pawłowska S, Pierini F, Kowalewski, Yarin AL. Dynamics of electrospun hydrogel filaments in oscillatory microchannel flows: A theoretical and experimental approach, Phys Fluids 32(7):072008 (2020) CrossRef | PDF

• Chen WC, Kaźmierczak B. Traveling waves in quadratic autocatalytic systems with complexing agent, Discrete Contin Dyn Syst–Ser B (2020) CrossRef

• Moreira RA, Chwastyk M, Baker JL, Guzman HV, Poma AB. Quantitative determination of mechanical stability in the novel coro-navirus spike protein, Nanoscale 12:16409 (2020) CrossRef

• Moreira RA, Guzman HV, Boopathi S, Baker JL, Poma AB. Characterization of structural and energetic differences between conformations of the SARS-CoV-2 spike protein, Materials 13(23):5362 CrossRef

• Zalewska-Piątek B, Olszewski M, Lipniacki T, Błoński S, Wieczór M, Bruździak P, Skwarska A, Nowicki B, Nowicki S, Piątek R. A shear stress micromodel of urinary tract infection by the Escherichia coli producing Dr adhesin, PLOS Pathog 16(1): e1008247 (2020) PubMed CrossRef

• Białobrzeska W, Firganek D, Czerkies M, Lipniacki T, Skwarecka M, Dziąbowska K, Cebula Z, Malinowska N, Bigus D, Bięga E, Pyrć K, Pala K, Żołędowska S, Nidzworski D. Electrochemical immunosensors based on screen-printed gold and glassy carbon electrodes: Comparison of performance for respiratory syncytial virus detection, Biosensors 10(11):175 (2020) CrossRef

• Volpert V, Banerjee M, d’Onofrio A, Lipniacki T, Petrovskii S, Tran VC. Coronavirus – Scientific insights and societal aspects, Math Model Nat Phenom 15:E2 (2020) CrossRef

• Bartali R, Gaixia Z , Tong X, Speranza G, Micheli V, Gottardi G, Fedrizzi M, Pierini F, Sun S, Laidani N, Tavares AC. Graphene oxide/reduced graphene oxide films as protective barriers on lead against differential aeration corrosion induced by water drops, Nanoscale Adv 2:5421 (2020) CrossRef | PDF SuppInfo-PDF

• Wang L, Lv H, Liu L, Zhang Q, Nakielski P, Si Y, Cao J, Li X, Pierini F, Yu J, Ding B. Electrospun nanofiber reinforced three-dimensional chitosan matrices: Architectural, mechanical and biological properties, J Colloid Interface Sci 565(1):416–425 (2020) CrossRef

• Martinez M, Cooper CD, Poma AB, Guzman HV. Free energies of the disassembly of viral capsids from a multiscale molecular simulation approach, J Chem Inf Model 60(2):974–981 (2020) CrossRef

• Boopathi S, Poma AB, Kolandaivel P. Novel 2019 coronavirus structure, mechanism of action, antiviral drug promises and rule out against its treatment, J Biomol Struct Dyn (2020) CrossRef

• Ozen M, Lipniacki T, Levchenko A, Emamian ES, Abdi A. Modeling and measurement of signaling outcomes affecting decision making in noisy intracellular networks using machine learning methods, Itegr Biol 12(5):122–138 (2020) CrossRef |  PDF

2019

• Korczyk PM, van Steijn V, Blonski S, Zaremba D, Beattie DA, Garstecki P. Accounting for corner flow unifies the understanding of droplet formation in microfluidic channels, Nat Commun 10:2528 (2019) PubMed CrossRef | PDF SuppInfo-PDF

• Jetka T, Winarski T, Nienałtowski K, Błoński S, Komorowski M. Information-theoretic analysis of multivariate single-cell signaling responses, PLOS Comput Biol 15(7):e1007132 (2019) PubMed CrossRef | PDF SuppInfo-PDF

• Grabowski F, Czyż P, Kochańczyk , Lipniacki T. Limits to the rate of information transmission through the MAPK pathway, J R Soc Interface 16(152):20180792 (2019) PubMed CrossRef | PDF SuppCode

• Bobrowski A, Lipniacki T. Robin-type boundary conditions in transition from reaction-diffusion equations in 3D domains to equations in 2D domains. J Differ Equ 268(1):239–271 (2019) CrossRef

• Komorowski M, Tawfik DS. The limited information capacity of cross-reactive sensors drives the evolutionary expansion of signaling, Cell Syst 8(1):76–85.e6 (2019) PubMed CrossRef

• Billing U, Jetka T, Nortmann L, Wundrack N, Komorowski M, Waldherr S, Schaper F, Dittrich A. Robustness and information transfer within IL-6-induced JAK/STAT signalling, Commun Biol 2:27 (2019) PubMed CrossRef

• Zaremba D, Blonski S, Marijnissen MJ, Korczyk PM. Fixing the direction of droplets in a bifurcating microfluidic junction, Microfluid Nanofluid 23:55 (2019) CrossRef

• Blonski S, Pregowska A, Michalek T, Szczepanski J. The use of Lempel-Ziv complexity to analyze turbulence and flow randomness based on velocity fluctuations, Bull Polish Acad Sci–Tech Sci 67(5):957–962 CrossRef

• Senapati S, Poma AB, Cieplak M, Filipek S, Park P S-H. Differentiating between inactive and active states of rhodopsin by atomic force microscopy in native membranes, Anal Chem 91(11):7226–7235 (2019) PubMed CrossRef

• Poma AB, Guzman HV, Li Ms, Theodorakis PE. Mechanical and thermodynamic properties of Aβ₄₂, Aβ₄₀, and α-synuclein fibrils: a coarse-grained method to complement experimental studies, Beilstein J Nanotechnol 10:500–513 (2019) PubMed CrossRef

• Enayatiab MS, Neisianya RE, Sajkiewicz P, Behzad T, Denis P, Pierini F. Effect of nanofiller incorporation on thermomechanical and toughness of poly(vinyl alcohol)-based electrospun nanofibrous bionanocomposites, Theor Appl Fract Mech 99:44–50 (2019) CrossRef

• Lanzi M, Salatelli E, Marinelli M, Pierini F. Effect of photocrosslinking of D-A thiophene copolymers on the performance of single-material solar cells, Macromol Chem Phys 1900433 (2019) CrossRef

• Pierini F, Lanzi M. Effect of electron–acceptor content on the efficiency of regioregular double-cable thiophene copolymers in single-material organic solar cells, ACS Omega 4(22):19863–19874 (2019) PubMed CrossRef | PDF SuppInfo-PDF

• Nakielski P, Pierini F. Blood interactions with nano- and microfibers: recent advances, challenges and applications in nano- and microfibrous hemostatic agents, Acta Biomater 84:63–76 (2019) PubMed CrossRef

2018

• Czerkies M, Korwek Z, Prus W, Kochańczyk M, Jaruszewicz-Błońska J, Tudelska K, Błoński S, Kimmel M, Brasier AR, Lipniacki T. Cell fate in antiviral response arises in the crosstalk of IRF, NF-κB and JAK/STAT pathways, Nat Commun 9:493 (2018) PubMed CrossRef | PDF SuppInfo-PDF SuppData SuppMovies SuppCode

• Jetka T, Nienałtowski K, Filippi S, Stumpf MPH, Komorowski M. An information-theoretic framework for deciphering pleiotropic and noisy biochemical signaling, Nat Commun 9:4591 (2018) PubMed CrossRef | PDF SuppInfo-PDF

• Zuk PJ, Kochańczyk M, Lipniacki T. Sampling rare events in stochastic reaction–diffusion systems within trajectory looping, Phys Rev E 98:022401 (2018) PubMed CrossRef | PDF-ms Www

• Kazmierczak B, Tsai J-C, Bialecki S. The propagation phenomenon of solutions of a parabolic problem on the sphere, Math Model Meth Appl Sci 28(10):2001–2067 (2018) CrossRef

• Zaremba D, Błoński S, Jachimek M, Marijnissen MJ, Jakieła S, Korczyk PM. Investigations of modular microfluidic geometries for passive manipulations on droplets, Bull Polish Acad Sci–Tech Sci 66(2):139–149 (2018) CrossRef

• Skłodowska K, Dębski PR, Michalski JA, Korczyk PM, Dolata M, Zając M, Jakiela S. Simultaneous measurement of viscosity and optical density of bacterial growth and death in a microdroplet, Micromachines 9(5):251 (2018) PubMed CrossRef

• Debski PR, Sklodowska K, Michalski JA, Korczyk PM, Dolata M, Jakiela S. Continuous recirculation of microdroplets in a closed loop tailored for screening of bacteria cultures, Micromachines 9(9):469 PubMed CrossRef

• Pierini F, Nakielski P, Urbanek O, Pawłowska S, Lanzi M, De Sio L, Kowalewski TA. Polymer-based nanomaterials for photothermal therapy: from light-responsive to multifunctional nanoplatforms for synergistically combined technologies, Biomacromolecules 19(11):4147–4167 (2018) PubMed CrossRef

• Pawłowska S, Kowalewski TA, Pierini F. Fibrous polymer nanomaterials for biomedical applications and their transport by fluids: an overview, Soft Matter 14(42):8421–8444 (2018) PubMed CrossRef

• 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 149:273–285 (2018) CrossRef

• Enayati MS, Behzad T, Sajkiewicz PŁ, Bagheri R, Ghasemi-Mobarakeh L, Pierini F. Theoretical and experimental study of the stiffness of electrospun composites of poly(vinyl alcohol), cellulose nanofibers, and nanohydroxy apatite, Cellulose 25(1):65–75 (2018) CrossRef

• Urbanek O, Pierini F, Choińska E, Sajkiewicz P, Bil M, Święszkowski W. Effect of hydroxyapatite nanoparticles addition on structure properties of poly(L-lactide-co-glycolide) after gamma sterilization, Polym Compos 39(4):1024–1031 (2018; e-pub 2016) CrossRef

• Małolepszy A, Błonski S, Chrzanowska-Giżyńska J, Wojasiński M, Płocinski T, Stobinski L, Szymanski Z. Fluorescent carbon and graphene oxide nanoparticles synthesized by the laser ablation in liquid,  Appl Phys A–Mater Sci Process 124:282 (2018) CrossRef

2017

• Tudelska K, Markiewicz J, Kochańczyk M, Czerkies M, Prus W, Korwek Z, Abdi A, Błoński S, Kaźmierczak B, Lipniacki T. Information processing in the NF-κB pathway, Sci Rep 7:15926 (2017) PubMed CrossRef | PDF SuppInfo-PDF SuppCode-BNGL SuppCode-Py

• Jaruszewicz-Błońska J, Lipniacki T. Genetic toggle switch controlled by bacterial growth rate, BMC Syst Biol 11:117 (2017) PubMed CrossRef

• Varga A, Ehrenreiter K, Aschenbrenner B, Kocieniewski P, Kochanczyk M, Lipniacki T, Baccarini M. RAF1/BRAF dimerization integrates the signal from RAS to ERK and ROKα, Sci Signal 10(469):eaai8482 (2017) PubMed CrossRef | SuppCode-BioNetGen

• Kochańczyk M, Kocieniewski P, Kozłowska E, Jaruszewicz-Błońska J, Sparta B, Pargett M, Albeck JG, Hlavacek WS, Lipniacki T. Relaxation oscillations and hierarchy of feedbacks in MAPK signaling, Sci Rep 7:38244 (2017) PubMed CrossRef | PDF SuppInfo-PDF SuppCode-BNG SuppCode-MatCont SuppCode-BNG-noisy SuppCode-Comsol SuppMovie

• Kochańczyk M, Hlavacek WS, Lipniacki T. Spatkin: a simulator for rule-based modeling of biomolecular site dynamics on surfaces, Bioinformatics (2017) 33(22):3667–3669 PubMed CrossRef Www

• Habibi I, Cheong R, Lipniacki T, Levchenko A, Emamian ES, Abdi A. Computation and measurement of cell decision making errors using single cell data, PLOS Comput Biol 13(4):e1005436 (2017) PubMed CrossRef

• Białecki S, Kaźmierczak B, Lipniacki T. Polarization of concave domains by traveling wave pinning, PLOS One 12:e0190372 (2017) PubMed CrossRef

• Bialecki S, Kaźmierczak B, Nowicka D, Tsai J-C. Regularity of solutions to a reaction–diffusion equation on the sphere: the Legendre series approach, Math Meth Appl Sci 40(14):5349–5369 (2017) CrossRef

• Adimy M, Chekroun A, Kaźmierczak B. Traveling waves in a coupled reaction–diffusion and difference model of hematopoiesis, J Differ Equ 262(7):4085–4128 (2017) CrossRef

• Bobrowski A, Kaźmierczak B, Kunze M. An averaging principle for fast diffusions in domains separated by semi-permeable membranes, Math Model Meth Appl Sci 27(4):663–706 (2017) CrossRef arXiv

• Martincuks A, Andryka K, Küster A, Schmitz-Van de Leur H, Komorowski M, Müller-Newen G. Nuclear translocation of STAT3 and NF-κB are independent of each other but NF-κB supports expression and activation of STAT3, Cell Signal 32:36–47 (2017) PubMed CrossRef

• Pawłowska S, Nakielski P, Pierini F, Piechocka IK, Zembrzycki K, Kowalewski TA. Lateral migration of electrospun hydrogel nanofilaments in an oscillatory flow, PLOS One 12(11):e0187815 PubMed CrossRef

• Pierini F, Lanzi M, Nakielski P, Pawłowska S, Urbanek O, Zembrzycki K, Kowalewski TA. Single-material organic solar cells based on electrospun fullerene-grafted polythiophene nanofibers, Macromolecules 50(13):4972–81 (2017) CrossRef

• Pierini F, Lanzi M, Nakielski P, Kowalewski TA. Electrospun polyaniline-based composite nanofibers: Tuning the electrical conductivity by tailoring the structure of thiol-protected metal nanoparticles, J Nanomater 2017:6142140 (2017) CrossRef

• Urbanek O, Sajkiewicz P, Pierini F. The effect of polarity in the electrospinning process on PCL/chitosan nanofibres' structure, properties and efficiency of surface modification, Polymer 124:168–75 (2017) CrossRef

• Urbanek O, Sajkiewicz P, Pierini F, Czerkies M, Kołbuk D. Structure and properties of polycaprolactone/chitosan nonwovens tailored by solvent systems, Biomed Mater 12:015020 (2017) PubMed CrossRef

• Lanzi M, Salatelli E, Di-Nicola FP, Zuppiroli L, Pierini F. A new photocrosslinkable oligothiophene for organic solar cells with enhanced stability, Mater Chem Phys 186:98–107 (2017) CrossRef

• Lanzi M, Salatelli E, Giorgini L, Mucci A, Pierini F, Di-Nicola F. Water-soluble polythiophenes as efficient charge-transport layers for the improvement of photovoltaic performance in bulk heterojunction polymeric solar cells, Eur Polymer J 97:378–388 (2017) CrossRef

2016

• Hat B, Kochańczyk M, Bogdał MN, Lipniacki T. Feedbacks, bifurcations, and cell fate decision-making in the p53 system, PLOS Comput Biol 12(2):e1004787 (2016) PubMed CrossRef | PDF SuppText SuppFigs SuppCode

• Korwek Z, Tudelska K, Nałęcz-Jawecki P, Czerkies M, Prus W, Markiewicz J, Kochańczyk M, Lipniacki T. Importins promote high-frequency NF-κB oscillations increasing information channel capacity, Biol Direct 11:61 (2016) PubMed CrossRef | PDF Scheme-PDF SuppModelInfo-PDF SuppModelCode-BNGL SuppFigs-PDF SuppImages-ZIP

• Chatterjee P, Kaźmierczak B. Eigenfunction approach to transient patterns in a model of chemotaxis, Math Model Nat Phenom 11(2):44–62 (2016) CrossRef

• Pierini F, Zembrzycki K, Nakielski P, Pawłowska S, Kowalewski TA. Atomic force microscopy combined with optical tweezers (AFM/OT), Meas Sci Technol 27:025904 (2016) CrossRef

• Pierini F, Lanzi M, Nakielski P, Pawłowska S, Zembrzycki K, Kowalewski TA. Electrospun poly(3-hexylthiophene)/poly(ethylene oxide)/graphene oxide composite nanofibers: effects of graphene oxide reduction, Polym Adv Technol 27(11):1465–1475 (2016) CrossRef

• Adamowicz J, Pokrywczyńska M, Tworkiewicz J, Kowalczyk T, van Breda SV, Tyloch D, Kloskowski T, Bodnar M, Skopinska-Wisniewska J, Marszałek A, Frontczak-Baniewicz M, Kowalewski TA, Drewa T. New amniotic membrane based biocomposite for future application in reconstructive urology, PLOS One 11(1):e0146012 (2016) PubMed CrossRef

2015

• Szymańska P, Martin KR, MacKeigan JP, Hlavacek WS, Lipniacki T. Computational analysis of an autophagy/translation switch based on mutual inhibition of mTORC1 and ULK1, PLOS One 10(3):e0116550 (2015) PubMed CrossRef | PDF supp-BNGL supp-PDF

• Nałęcz-Jawecki P, Szymańska P, Kochańczyk M, Miękisz J, Lipniacki T. Effective reaction rates for diffusion-limited reaction cycles, J Chem Phys 143(21):215102 (2015) PubMed CrossRef | PDF-ms

• Szymańska P, Kochańczyk M, Miększ J, Lipniacki T. Effective reaction rates in diffusion-limited phosphorylation–dephosphorylation cycles, Phys Rev E 91:022702 (2015) PubMed CrossRef | PDF-ms

• Nienałtowski K, Włodarczyk M, Lipniacki T, Komorowski M. Clustering reveals limits of parameter identifiability in multi-parameter models of biochemical dynamics, BMC Syst Biol 9:65 (2015) PubMed CrossRef | PDF Supp-PDF Supp-Code

• Kellogg RA, Tian C, Lipniacki T, Quake SR, Tay S. Digital signaling decouples activation probability and population heterogeneity, eLife 4:e08931 (2015) PubMed CrossRef | PDF

• Białecki S, Kaźmierczak B, Tsai J-C. Stationary waves on the sphere, SIAM J Appl Math 75(4):1761–1788 (2015) CrossRef

• Szymańska P, Gritti N, Keegstra J, Soltani M, Munsky B. Using noise to control heterogeneity of isogenic populations in homogenous environments, Phys Biol 12:045003 (2015) PubMed CrossRef

• Wronowska W, Charzyńska A, Nienałtowski K, Gambin A. Computational modeling of sphingolipid metabolism, BMC Syst Biol 9:47 (2015) PubMed CrossRef

• Aliper AM, Csoka AB, Buzdin A, Jetka T, Roumiantsev S, Moskalev A, Zhavoronkov A. Signaling pathway activation drift during aging: Hutchinson-Gilford Progeria Syndrome fibroblasts are comparable to normal middle-age and old-age cells, Aging 7(1):26–37 PubMed

• Korczyk PM, Dolega ME, Jakiela S, Jankowski P, Makulska S, Garstecki P. Scaling up the throughput of synthesis and extraction in droplet microfluidic reactors, J Flow Chem 5(2):110–118 (2015) CrossRef

• Samborski A, Jankowski P, Węgrzyn J, Michalski JA, Pawłowska S, Jakieła S, Garstecki P. Blood diagnostics using sedimentation to extract plasma on a fully integrated point-of-care microfluidic system, Eng Life Sci 15(3):333–339 (2015) CrossRef

• Nakielski P, Kowalczyk T, Zembrzycki K, Kowalewski TA. Experimental and numerical evaluation of drug release from nanofiber mats to brain tissue, J Biomed Mater Res B Appl Biomater 103(2):282–291 (2015; e-pub 2014) PubMed CrossRef

• Nakielski P, Pawłowska S, Pierini F, Liwińska W, Hejduk P, Zembrzycki K, Zabost E, Kowalewski TA. Hydrogel nanofilaments via core-shell electrospinning, PLOS One 10(6):e0129816 (2015) PubMed CrossRef Supp Correction

• Noszczyk BH, Kowalczyk T, Łyżniak M, Zembrzycki K, Mikułowski G, Wysocki J, Kawiak J, Pojda Z. Biocompatibility of electrospun human albumin: A pilot study, Biofabrication 7(1):015011 (2015) PubMed CrossRef

• Sielamowicz I, Czech A, Kowalewski TA. Comparative analysis of empirical descriptions of eccentric flow in silo model by the linear and nonlinear regressions. Powder Technol 270:393–410 (2015) CrossRef

• Pierini F, Lanzi M, Lesci IG, Rover N. Comparison between inorganic geomimetic chrysotile and multiwalled carbon nanotubes in the preparation of one-dimensional conducting polymer nanocomposites, Fiber Polym 16(2):426–433 (2015) CrossRef

• Jarecki L, Błoński S, Zachara Z. Modeling of pneumatic melt drawing of poly-L-lactide fibers in the Laval nozzle, Ind Eng Chem Res (2015) 54(43):10796–10810 CrossRef

• Chrzanowska J, Hoffman J, Małolepszy A, Mazurkiewicz M, Kowalewski TA, Szymanski Z, Stobinski L. Synthesis of carbon nanotubes by the laser ablation method: Effect of laser wavelength, Phys Status Solidi B 252(8):1860–1867 (2015) CrossRef

• Oliferuk W, Maj M, Zembrzycki K. Determination of the energy storage rate distribution in the area of strain localization using infrared and visible imaging, Exp Mech 55:753–760 (2015) CrossRef

2014

• Jaruszewicz J, Kimmel M, Lipniacki T. Stability of bacterial toggle switches is enhanced by cell-cycle lengthening by several orders of magnitude, Phys Rev E 89(2):022710 (2014) PubMed CrossRef | PDF-ms

• Bertolusso R, Tian B, Zhao Y, Vergara L, Sabree A, Iwanaszko M, Lipniacki T, Brasier AR, Kimmel M. Dynamic cross talk model of the epithelial innate immune response to double-stranded RNA stimulation: Coordinated dynamics emerging from cell-level noise, PLOS One 9(4):e93396 (2014) PubMed CrossRef | PDF Supp-PDF

• Jetka T, Charzynska A, Gambin A, Stumpf MPH, Komorowski M. StochDecomp—Matlab package for noise decomposition in stochastic biochemical systems, Bioinformatics 30(1):137–138 (2014; e-pub 2013) PubMed CrossRef | PDF-ms Code-Matlab

• Cheng FHC, Aguda BD, Tsai J-C, Kochańczyk M, Lin JMJ, Chen GCW, Lai H-C, Nephew KP, Hwang T-W, Chan MWY. A mathematical model of bimodal epigenetic control of miR-193a in ovarian cancer stem cells, PLOS One 9(12):e116050 (2014) PubMed CrossRef | PDF

• Pokrywczyńska M, Jundziłł A, Adamowicz J, Kowalczyk T, Warda K, Rasmus M, Buchholz Ł, Krzyżanowska S, Nakielski P, Chmielewski T, Bodnar M, Marszałek A, Dębski R, Frontczak-Baniewicz M, Mikułowski G, Nowacki M, Kowalewski TA, Drewa T. Is the poly(L-lactide-co-caprolactone) nanofibrous membrane suitable for urinary bladder regeneration? PLOS One 9(8):105295 (2014) PubMed CrossRef | PDF

• Kloskowski T, Jundziłł A, Kowalczyk T, Nowacki M, Bodnar M, Marszałek A, Pokrywczyńska M, Frontczak-Baniewicz M, Kowalewski TA, Chłosta P, Drewa T. Ureter regeneration—the proper scaffold has to be defined, PLOS One 9(8):106023 (2014) PubMed CrossRef | PDF

• Gomez-Sanchez C, Kowalczyk T, Ruiz De Eguino G, Lopez-Arraiza A, Infante A, Rodriguez CI, Kowalewski TA, Sarrionandia M, Aurrekoetxea J. Electrospinning of poly(lactic acid)/polyhedral oligomeric silsesquioxane nanocomposites and their potential in chondrogenic tissue regeneration, J Biomater Sci–Polym Ed 25(8):802–825 (2014) PubMed CrossRef

• Rafalowska J, Sulejczak D, Chrapusta SJ, Gadamski R, Taraszewska A, Nakielski P, Kowalczyk T, Dziewulska D. Non-woven nanofiber mats – a new perspective for experimental studies of the central nervous system? Folia Neuropathol 52(4): 407-416 (2014) PubMed CrossRef | PDF

• Sulejczak D, Andrychowski J, Kowalczyk T, Nakielski P, Frontczak-Baniewicz M, Kowalewski TA. Electrospun nanofiber mat as a protector against the consequences of brain injury, Folia Neuropathol 52(1):56–69 (2014) PubMed CrossRef | PDF

• Stasiek J, Jewartowski M, Kowalewski TA. The use of liquid crystal thermography in selected technical and medical applications—Recent development, J Crystalliz Process Technol 4(1):42466 (2014) CrossRef | PDF

• Blim A, Jarecki L, Błoński S. Modeling of pneumatic melt drawing of polypropylene super-thin fibers in the Laval nozzle, Bull Pol Acad Sci–Tech Sci 62(1):43–54 (2014) CrossRef | PDF

• Korwek Z, Alster O. Rola szlaku indukowanego uszkodzeniami DNA w apoptozie i starzeniu komórkowym [The role of the DNA damage response in apoptosis and cell senescence], Postepy Biochem 60(2):248-62 (2014) PubMed | PDF

• Alster O, Korwek Z. Znaczniki starzenia komórkowego [Markers of cellular senescence], Postepy Biochem 60(2):138-46 (2014) PubMed | PDF

2013

• Pękalski J, Zuk PJ, Kochańczyk M, Junkin M, Kellog R, Tay S, Lipniacki T. Spontaneous NF-κB activation by autocrine TNFα signaling: A computational analysis, PLOS One 8(11):e78887 (2013) PubMed CrossRef | PDF Supp-PDF Code-Matlab Code-BioNetGen Code-MatCont

• Bogdał MN, Hat B, Kochańczyk M, Lipniacki T. Levels of pro-apoptotic regulator Bad and anti-apoptotic regulator Bcl-xL determine the type of the apoptotic logic gate, BMC Syst Biol 7:67 (2013) PubMed CrossRef | PDF Code-Matlab

• Kochańczyk M, Jaruszewicz J, Lipniacki T. Stochastic transitions in a bistable reaction system on the membrane, J R Soc Interface 10(84):20130151 (2013) PubMed CrossRef | PDF Supp-PDF Supp-movies

• Kocieniewski P, Lipniacki T. MEK1 and MEK2 differentially control the duration and amplitude of the ERK cascade response, Phys Biol 10(3):035006 (2013) PubMed CrossRef | PDF-ms Code-BioNetGen

• Jaruszewicz J, Lipniacki T. Toggle switch: Noise determines the winning gene, Phys Biol 10(3):035007 (2013) PubMed CrossRef | PDF-ms

• Jaruszewicz J, Zuk PJ, Lipniacki T. Type of noise defines global attractors in bistable molecular regulatory systems, J Theor Biol 317:140–151 (2013; e-pub 2012) PubMed CrossRef | PDF-ms

• Crooks E, Kazmierczak B, Lipniacki T. A spatially extended model of kinase-receptor interaction, SIAM J Appl Math 73(1):374–400 (2013) CrossRef

• Szopa P, Dyzma M, Kaźmierczak B. Membrane associated complexes in calcium dynamics modelling, Phys Biol 10(3):035004 (2013) PubMed CrossRef

• Kaźmierczak B, Peradzyński Z. Calcium waves with mechano-chemical couplings, Math Biosci Eng 10(3):743-759 (2013) CrossRef

• Piechór K. Calcium waves in thin domains of visco-elastic cells, Math Model Nat Phenom 8(3):206-226 (2013) CrossRef

• Finkenstädt BF, Woodcock DJ, Komorowski M, Harper CV, Davis JRE, White MRH, Rand DA. Quantifying intrinsic and extrinsic noise in gene transcription using the linear noise approximation: an application to single cell data, Ann Appl Stat 7(4):1837-2457 (2013) CrossRef | PDF-ms

• Liepe J, Filippi S, Komorowski M, Stumpf MPH. Maximizing the information content of experiments in systems biology, PLOS Comput Biol 9(1):e1002888 (2013) PubMed CrossRef | PDF

• Komorowski M, Miękisz J, Stumpf MPH. Decomposing noise in biochemical signalling systems highlights the role of protein degradation, Biophys J 104(8):1783-1798 (2013) PubMed CrossRef | PDF

• Woodcock DJ, Vance KW, Komorowski M, Koentges G, Finkenstädt B, Rand DA. A hierarchical model of transcriptional dynamics allows robust estimation of transcription rates in populations of single cells with variable gene copy number, Bioinformatics 29(12):1519-1525 (2013) PubMed CrossRef | PDF

• Schumacher J, Behrends V, Pan Z, Brown DR, Heydenreich F, Lewis MR, Bennett MH, Razzaghi B, Komorowski M, Barahona M, Stumpf MPH, Wigneshweraraj S, Bundy JG, Buck M. Nitrogen and carbon status are integrated at the transcriptional level by the nitrogen regulator NtrC in vivo, mBio 4(6):e00881-13 (2013) PubMed CrossRef | PDF

• Paprocki B, Szczepanski J. Transmission efficiency in ring, brain inspired neuronal networks. Information and energetic aspects, Brain Res 1536:135–143 (2013) PubMed CrossRef

• Paprocki B, Szczepanski J, Kolbuk D. Information transmission efficiency in neuronal communication systems, BMC Neuroscience (2013) 14(Suppl 1):P217 CrossRef | PDF

• Paprocki B, Szczepanski J. How do the amplitude fluctuations affect the neuronal transmission efficiency, Neurocomputing 104:50-56 (2013; e-pub 2012) CrossRef

• Arnold MM, Szczepanski J, Montejo N, Amigo JM, Wajnryb E, Sanchez-Vives MV. Information content in cortical spike trains during brain state transitions, J Sleep Res 22(1):13-21 (2013, e-pub 2012) PubMed CrossRef

• Chmielowiec A. Parallel Algorithm for Multiplying Integer Polynomials and Integers, Lecture Notes in Electrical Engineering 229:605-616 (2013) CrossRef

• Guzowski J, Jakiela S, Korczyk PM, Garstecki P. Custom tailoring multiple droplets one-by-one, Lab Chip 13:4308–4311 (2013) PubMed CrossRef

• Korczyk PM, Derzsi L, Jakiela S, Garstecki P. Microfluidic traps for hard-wired operations on droplets, Lab Chip 13:4096-4102 (2013) PubMed CrossRef

• Churski K, Nowacki M, Korczyk PM, Garstecki P. Simple modular systems for generation of droplets on demand, Lab Chip 13:3689-3697 (2013) PubMed CrossRef

• van Steijn V, Korczyk PM, Derzsi L, Abate AR, Weitz DA , Garstecki P. Block-and-break generation of microdroplets with fixed volume, Biomicrofluidics 7(2):024108 (2013) PubMed CrossRef

• Węgrzyn J, Samborski A, Reissig L, Korczyk PM, Błoński S, Garstecki P. Microfluidic architectures for efficient generation of chemistry gradations in droplets, Microfluid Nanofluid 14(1-2):235–245 (2013, e-pub 2012) CrossRef | PDF

• Andrychowski J, Frontczak-Baniewicz M, Sulejczak D, Kowalczyk T, Chmielewski T, Czernicki Z, Kowalewski TA. Nanofiber nets in prevention of cicatrisation in spinal procedures. Experimental study, Folia Neuropathol 51(2):147-57 (2013) PubMed CrossRef

• Kloskowski T, Kowalczyk T, Nowacki M, Drewa T. Tissue engineering and ureter regeneration, is it possible? Int J Artif Organs 36(6):392-405 (2013) PubMed CrossRef

2012

• Zuk PJ, Kochańczyk M, Jaruszewicz J, Bednorz W, Lipniacki T. Dynamics of a stochastic spatially extended system predicted by comparing deterministic and stochastic attractors of the corresponding birth-death process, Phys Biol 9(5):055002 (2012) PubMed CrossRef | PDF-ms

• Kocieniewski P, Faeder JR, Lipniacki T. The interplay of double phosphorylation and scaffolding in MAPK pathways, J Theor Biol 295:116-124 (2012; e-pub 2011) PubMed CrossRef | PDF-ms

• Barua D, Hlavacek WS, Lipniacki T. A computational model for early events in B cell antigen receptor signaling: analysis of the roles of Lyn and Fyn, J Immunol 189(2):646-658 (2012) PubMed CrossRef | PDF-ms

• El Khatib N, Genieys S, Kazmierczak B, Volpert V. Reaction-diffusion model of artherosclerosis development, J Math Biol 65(2):349-374 (2012) PubMed CrossRef

• Gejji R, Kaźmierczak B, Alber M. Classification and stability of global inhomogeneous solutions of a macroscopic model of cell motion, Math Biosci 238(1):21-31 (2012) PubMed CrossRef

• Dyzma M, Szopa P, Kaźmierczak B. Membrane associated complexes: new approach to calcium dynamics modeling, Math Model Nat Phenom 7(2):32-50 (2012) CrossRef

• Piechór K. Reaction-diffusion equation modelling calcium waves with fast buffering in visco-elastic environment, Arch Mech 64(5):477-509 (2012) PDF

• Korczyk PM, Kowalewski TA, Malinowski SP. Turbulent mixing of clouds with the environment: Small scale two phase evaporating flow investigated in a laboratory by particle image velocimetry, Physica D 241:288-296 (2012) CrossRef

• Guzowski J, Korczyk PM, Jakiela S, Garstecki P. The structure and stability of multiple micro-droplets, Soft Matter 8:7269-7278 (2011) CrossRef

• Jakiela S, Korczyk PM, Makulska S, Cybulski O, Garstecki P. Discontinuous transition in a laminar fluid flow: A change of flow topolgy inside a droplet moving in a micron-size channel, Phys Rev Lett 108(13):134501 (2012) PubMed CrossRef

• Sikora M, Adam D, Korczyk PM, Prodi-Schwab A, Szymczak P, Cieplak M. Geometrical and electrical properties of indium tin oxide clusters in ink dispersions, Langmuir 28(2):1523-1530 (2012) PubMed CrossRef

• Baranowska-Korczyc A, Reszka A, Sobczak K, Sikora B, Dziawa P, Aleszkiewicz M, Kłopotowski Ł, Paszkowicz W, Dłużewski P, Kowalski BJ, Kowalewski TA, Sawicki M, Elbaum D, Fronc K, Magnetic Fe doped ZnO nanofibers obtained by electrospinning, J Sol-Gel Sci Techn 61(3):494-500 (2012) CrossRef

• Jarecki L, Błoński S, Blim A, Zachara A. Modeling of Pneumatic Melt Spinning Processes, J Appl Polym Sci 125(6):4402–4415 (2012) CrossRef

• Kołbuk D, Sajkiewicz P, Kowalewski TA, Optical birefringence and molecular orientation of electrospun polycaprolactone fibers by polarizing-interference microscopy, Eur Polym J 48:275-283 (2012) CrossRef

• Blim A, Kowalczyk T. Dynamic lattice liquid (DLL) model in computer simulation of the structure and dynamics of polymer condensed systems, e-Polymers 079:1-11 (2012) PDF

2011

• Hat B, Kaźmierczak B, Lipniacki T. B cell activation triggered by the formation of the small receptor cluster: A computational study, PLoS Comput Biol 7(10):e1000448 (2011) PubMed CrossRef | PDF

• Szopa P, Lipniacki T, Kaźmierczak B. Exact solutions to a spatially extended model of kinase-receptor interaction, Phys Biol 8(5):055005 (2011) PubMed CrossRef

• Kaźmierczak B, Peradzyński Z. Calcium waves with fast buffers and mechanical effects, J Math Biol 62:1-38 (2011, e-pub 2010) PubMed CrossRef

• Kaźmierczak B, Piechór K. Traveling wave solutions of a model of skin pattern formation in a singular case, Math Method Appl Sci 34(3):325–337 (2011; e-pub 2010) CrossRef

• Kochańczyk M. Prediction of functionally important residues in globular proteins from unusual central distances of amino acids, BMC Struct Biol 11(1):34 (2011) PubMed CrossRef | PDF PDF+supp Code Server

• Guzowski J, Korczyk PM, Jakiela S, Garstecki P. Automated high-throughtput generation of droplets, Lab Chip 11:3593–3595 (2011) PubMed CrossRef

• Jakiela S, Makulska S, Korczyk PM, Garstecki P. Speed of flow of individual droplets in microfluidic channels as a function of the capillary number, volume of droplets and contrast of viscosities, Lab Chip 11(21):3603–3608 (2011) PubMed CrossRef

• Sielamowicz I, Czech M, Kowalewski TA. Empirical analysis of eccentric flow registered by the DPIV technique inside a silo model, Powder Technol 212:38–56 (2011) CrossRef

• Sielamowicz I, Czech M, Kowalewski TA. Empirical description of granular flow inside a model silo with vertical walls, Biosyst Eng 108(4):334–344 (2011) CrossRef

• Szczepański J, Arnold M, Wajnryb E, Amigó JM, Sanchez-Vives MV. Mutual information and redundancy in spontaneous communication between cortical neurons, Biol Cybern 104:161–174 (2011) PubMed CrossRef

• Paprocki B, Szczepański J. Efficiency of neural transmission as a function of synaptic noise, threshold, and source characteristics, Biosystems 105(1):62–72 (2011) PubMed CrossRef

• Kursa M, Bajer K, Lipniacki T. Cascade of vortex loops initiated by a single reconnection of quantum vortices, Phys Rev B 83(1):014515 (2011) CrossRef | PDF-ms

• Chylek LA, Hu B, Blinov ML, Emonet T, Faeder JR, Goldstein B, Gutenkunst RN, Haugh JM, Lipniacki T, Posner RG, Yang J, Hlavacek WS. Guidelines for visualizing and annotating rule-based models, Mol Biosyst 7(10):2779-95 (2011) PubMed CrossRef | PDF-ms

• Błoński S, Domagalski P, Dziubiński M, Kowalewski TA. Hydrodynamically modified seeding for micro-PIV, Arch Mech 63:163–182 (2011) PDF

• Jarecki L, Błoński S, Zachara A, Blim A. Computer modeling of pneumatic formation of superthin fibres, Comp Meth Mat Sci 11(1): 74–80 (2011)

• Szumbarski J, Błoński S. Destabilization of laminar flow in a rectangular channel by transversely-oriented wall corrugation, Arch Mech 63(4):393–428 (2011) PDF

• Szymborski T, Korczyk PM, Hołyst R, Garstecki P. Ionic polarization of liquid-liquid interfaces; dynamic control of the rate of electro-coalescence, Appl Phys Lett 99:094101 (2011) CrossRef

• Korczyk PM, Cybulski O, Makulska S, Garstecki P. Effects of unsteadiness of the rates of flow on the dynamics of formation of droplets in microfluidic systems, Lab Chip 11:173–175 (2011) PubMed CrossRef

2010

• Tay S, Hughey J, Lee T, Lipniacki T, Covert M, Quake S. Single-cell NF-κB dynamics reveal digital activation and analogue information processing, Nature 466:267-271 (2010) PubMed CrossRef | PDF Code

• Kaźmierczak B, Dyzma M. Mechanical effects coupled with calcium waves, Arch Mech 62:121-133 (2010). PDF

• Kaźmierczak B, Lipniacki T. Spatial gradients in kinase cascade regulation, IET Syst Biol 4:348-355 (2010) PubMed CrossRef | PDF-ms

• Peradzyński Z. Diffusion of calcium in biological tissues and accompanying mechano-chemical effects, Arch Mech 62(6):423-440 (2010) PDF

• Sadlej K, Wajnryb E, Ekiel-Jeżewska ML, Lamparska D, Kowalewski TA. Dynamics of nanofibres conveyed by low Reynolds number flow in a microchannel, Int J Heat Fluid Fl 31:996-1004 (2010) CrossRef

• Sielamowicz I, Czech M, Kowalewski TA. Empirical description of flow parameters in eccentric flow inside a silo model, Powder Technol 198:381-394 (2010) CrossRef

• Piechór K. Forms of travelling waves admitted by a mechanochemical model of tumour angiogenesis, Math Method Appl Sci 33:1482-1495 (2010) CrossRef

• Churski K, Korczyk P, Garstecki P. High-throughput automated droplet microfluidic system for screening of reaction conditions, Lab Chip 10:816 (2010) PubMed CrossRef

2009

• Szczepański J. On the distribution function of the complexity of finite sequences, Inform Sciences 179:1217-1220 (2009) CrossRef

• Alber M, Gejji R, Kaźmierczak B. Existence of global solutions of a macroscopic model of cellular motion in a chemotactic field, Appl Math Lett 22:1645-1648 (2009) CrossRef

• Hat B, Puszyński K, Lipniacki T. Exploring mechanisms of oscillations in p53 and NF-κB systems, IET Syst Biol 3(5):342-355 (2009) PubMed CrossRef | PDF-ms

• Puszyński K, Bertolusso R, Lipniacki T. Crosstalk between p53 and NF-κB systems: pro- and anti-apoptotic functions of NF-κB, IET Syst Biol 3(5):356-367 (2009) PubMed CrossRef | PDF-ms Code

• Kaźmierczak B, Lipniacki T. Regulation of kinase activity by diffusion and feedback, J Theor Biol 259:291-296 (2009) PubMed CrossRef

• Alabrudziński S, Ekiel-Jeżewska ML, Chehata-Gomez D, Kowalewski TA. Particle clusters settling under gravity in a viscous fluid, Phys Fluids 21:073302 (2009) CrossRef

• Peradzyński Z, Barral S, Makowski K, Dudeck M. Causality violation in analysis of Hall thruster plasma instabilities, J Tech Phys 49(3-4):315-327 (2009)

• El Khatib N, Génieys S, Kaźmierczak B, Volpert V. Mathematical modelling of atherosclerosis as an inflammatory disease, Phil Trans R Soc A 367(1908):4877-4886 (2009) PubMed CrossRef

• Fryczkowski R, Kowalczyk T. Nanofibres from polianiline/polihydroxybutyrate blends, Synthetic Met 159:2266-2268 (2009) CrossRef

• Bretcanu O, Misra SK, Yunos DM, Boccaccini AR, Roy I, Kowalczyk T, Błoński S, Kowalewski TA. Electrospun nanofibrous biodegradable polyester coatings on Bioglass-based glass-ceramics for tissue engineering, Mater Chem Phys 118:420-426 (2009) CrossRef

2008

• Kaźmierczak B. Existence of global solutions to a model of chondrogenesis, Math Meth Appl Sci 32(3):264-283 (2008) CrossRef

• Kaźmierczak B, Volpert V. Calcium waves in systems with immobile buffers as a limit of waves for systems with non zero diffusion, Nonlinearity 21:71 (2008) CrossRef

• Kaźmierczak B, Volpert V. Travelling calcium waves in systems with non diffusing buffers, Math Mod Meth Appl Sci 18(6):883-912 (2008) CrossRef

• Puszyński K, Hat B, Lipniacki T. Oscillations and bistability in the stochastic model of p53, J Theor Biol 254(2):452-465 (2008) PubMed CrossRef | Code

• Lipniacki T, Hat B, Faeder JR, Hlavacek WS. Stochastic effects and bistability in T cell receptor signaling, J Theor Biol 254(1):110-122 (2008) PubMed CrossRef | PDF-ms Code-ODE Code-Gillespie Code-BioNetGen

• Amigó JM, Kocarev L, Szczepański J. On some properties of the discrete Lyapunov exponent, Phys Lett A 372:6265-6268 (2008) CrossRef

• Nagarajan R, Szczepański J, Wajnryb E. Interpreting non-random signatures in biomedical signals using Lempel-Ziv complexity, Physica D 237(3):359-364 (2008) CrossRef

• Kowalewski TA, Błoński S, Korczyk P. Eksperymentalna analiza przepływów w skali mikro i nano [Experimental analysis of micro- and nanoscale flows], in Wybrane zagadnienia przepływów i wymiany ciepła, Oficyna Wyd. Polit. Warsz. 6:127-149 (2008)

• Licznar P, Łomotowski J, Błoński S, Ciach GJ. Microprocessor Field Impactometer Calibration: Do We Measure Drops Momentum or Their Kinetic Energy?, J Atmos Ocean Tech 25:742-753 (2008) CrossRef

• Kowalczyk T, Nowicka A, Elbaum D, Kowalewski TA. Electrospinning of bovine serum albumin. Optimization and the use for production of biosensors, Biomacromolecules 9:2087-2090 (2008) PubMed CrossRef

• Piechór K. Non-local Korteweg stresses from kinetic theory point of view, Arch Mech 60(1):23-58 (2008) PDF

• Malinowski SP, Andrejczuk M, Grabowski W, Korczyk P, Kowalewski TA, Smolarkiewicz PK. Laboratory and modeling studies of cloud–clear air interfacial mixing: anisotropy of small-scale turbulence due to evaporative cooling, New J Phys 10:075020 (2008) CrossRef

2007

• Błoński S, Korczyk PM, Kowalewski TA. Analysis of turbulence in a micro-channel emulsifier, Int J Therm Sci 46:1126–1141 (2007) CrossRef

• Lipniacki T, Puszyński K, Paszek P, Brasier AR, Kimmel M. Single TNFα trimers mediating NF-κB activation: Stochastic robustness of NF-κB signaling, BMC Bioinformatics 8:376 (2007) PubMed CrossRef | PDF PDF-supp1 PDF-supp2 PDF-supp3 Code Code-supp

• Alber M, Glimm T, Hentschel HG, Kazmierczak B, Zhang YT, Zhu J, Newman SA. The morphostatic limit for a model of skeletal pattern formation in the vertebrate limb, Bull Math Biol 69:460-483 (2007) PubMed CrossRef

• Newman SA, Christley S, Glimm T, Hentschel HG, Kazmierczak B, Zhang YT, Zhu J, Alber M. Multiscale models for vertebrate limb development, Curr Top Dev Biol 81:311-340 (2007) PubMed CrossRef

• Amigo JM, Kocarev L, Szczepanski J. Theory and practice of chaotic cryptography, Phys Lett A 366:211-216 (2007) CrossRef

• Lipniacki T, Kimmel M. Deterministic and stochastic models of NF-κB pathway, Cardiovasc Toxicol 7(4):215-234 (2007) PubMed CrossRef

• Bobrowski A, Lipniacki T, Pichor K, Rudnicki R. Asymptotic behavior of distributions of mRNA and protein levels in a model of stochastic gene expression, J Math Anal Appl 333:753-769 (2007) CrossRef

• Hat B, Paszek P, Kimmel M, Piechor K, Lipniacki T. How the number of alleles influences gene expression, J Stat Phys 128:511-533 (2007) CrossRef

• Fujarewicz K, Kimmel M, Lipniacki T, Swierniak A. Adjoint systems for models of cell signalling pathways and their application to parameter fitting, IEEE/ACM T Comput Biol Bioinform 4:322-335 (2007) PubMed CrossRef

• Kowalewski TA. Thermochromic Liquid Crystals, in Springer Handbook of Experimental Fluid Mechanics, chap. B 7.1, 487-499 (2007)

• Amigo JM, Kocarev L, Szczepanski J, Discrete Lyapunov exponent and resistance to differential cryptanalysis, IEEE T Circuits II 54:882-886 (2007) CrossRef

• Kazmierczak B, Volpert V. Travelling waves in partially degenerated reaction-diffusion systems, Mathematical Modelling of Natural Phenomena 2:106-125 (2007) CrossRef

• Kazmierczak B, Volpert V. Calcium waves in systems with immobile buffers as a limit of waves for systems with nonzero diffusion, Nonlinearity 21:71-98 (2007) CrossRef

• Błoński S, Kowalewski TA. PIV analysis of turbulent flow in a micro-channel, J Theor Appl Mech 45:489-503 (2007) PDF

2006

• Lipniacki T, Paszek P, Brasier AR, Luxon B, Kimmel M. Stochastic regulation in early immune response, Biophys J 90:725-742 (2006) PubMed CrossRef | PDF Code

• Lipniacki T, Paszek P, Marciniak-Czochra A, Brasier AR, Kimmel M. Transcriptional stochasticity in gene expression, J Theor Biol 238:348-367 (2006) PubMed CrossRef

• Lipniacki T. Dynamics of superfluid ⁴He: Two-scale approach, Eur J Mech B-Fluid 25(4):435-458 (2006) CrossRef

• Kocarev L, Szczepanski J, Amigo JM, Tomovski I. Discrete Chaos-I: Theory, IEEE T Circuits Sys 53:1300-1309 (2006) CrossRef

• Amigo JM, Kocarev L, Szczepanski J. Order patterns and chaos, Phys Lett A 355:27-31 (2006) CrossRef |

• Korczyk P, Malinowski SP, Kowalewski TA. Mixing of cloud and clear air in centimeter scales observed in laboratory by means of Particle Image Velocimetry, Atmospheric Res 82:173-182 (2006) CrossRef

• Sielamowicz I, Błoński S, Kowalewski TA Digital Particle Image Velocimetry (DPIV) technique in measurements of granular material flows, Part 2 of 3 - converging hoppers, Chem Eng Sci 61(16):5307-5317(2006) CrossRef

2005

• Paszek P, Lipniacki T, Brasier AR, Tian B, Nowak DE, Kimmel M. Stochastic effects of multiple regulators on expression profiles in eukaryotes, J Theor Biol 233:423-433 (2005) PubMed CrossRef

• Chaturvedi R, Huang C, Schneider T, Izaguirre J, Glimm T, Hentschel G, Glazier J, Kazmierczak B, Newman S, Alber M. On multiscale approaches to three-dimensional modeling of morphogenesis, J R Soc Interface 2:237-253 (2005) PubMed CrossRef | PDF

• Alber M, Hentschel HGE, Kazmierczak B, Newman S. Existence of solutions to a new model of biological pattern formation, J Math Anal Appl 308:175-194 (2005) CrossRef

• Alber M, Glimm T, Hentschel HGE, Kazmierczak B, Newman S. Stability of n-dimensional patterns in a generalized Turing system: implications for a biological patterns formation, Nonlinearity 18:125 (2005) CrossRef

• Belk M, Kazmierczak B, Volpert V. Existence of reaction-diffusion-convection waves in unbounded strips, Int J Math Math Sci 2005(2):169-193 (2005) CrossRef

• Kazmierczak B. Fale biegnące w ośrodkach z dyfuzją, Pismo PTM - Matematyka Stosowana. Matematyka dla Społeczeństwa 6, 47:29-47 (2005)

• Szczepanski J, Amigo JM, Michalek T, Kocarev L. Cryptographically Secure Substitutions Based on the Approximation of Mixing Maps, IEEE T Circuits Sys 52:443-453 (2005) CrossRef

• Amigó JM, Szczepanski J, Kocarev L. A Chaos-based approach to the design of cryptographically secure substitutions, Phys Lett A 343:55-60 (2005) CrossRef

• Peradzyński Z, Kazmierczak B. On mechanochemical calcium waves, Arch Appl Mech 74:827-833 (2005) CrossRef

• Barral S, Makowski K, Peradzyński Z, Dudek M. Transit time instability in Hall Thruster, Phys Plasmas 12, 073504 (2005) CrossRef

• Kowalewski TA, Blonski S, Barral S. Experiments and modelling of electrospinning process, B Pol Acad Sci-Tech 53:385-394 (2005) PDF

• Sielamowicz I, Błoński S, Kowalewski TA. Optical technique DPIV in measurements of granular material flows, Part 1 of 3 - plane hoppers, Chem Eng Sci 60(2):589-598 (2005) CrossRef

• Michalek T, Kowalewski TA, Saler B. Natural convection for anomalous density variation of water - numerical benchmark, Prog In Comput Fluid Dyn 5:158-170 (2005) CrossRef

2004

• Kaźmierczak B, Piechór K. Some heteroclinic solutions of a model of skin pattern formation, Math Meth Appl Sci 27:1317-1345 (2004) CrossRef

• Szczepański J, Amigó JM, Wajnryb E, Sanchez-Vives MV. Characterizing spike trains with Lempel–Ziv complexity, Neurocomputing 58-60:79-84 (2004) CrossRef

• Kocarev L, Szczepanski J. Finite-Space Lyapunov exponents and pseudochaos, Phys Rev Lett 93 (2004) PubMed CrossRef

• Szczepanski J, Wajnryb E, Amigó JM, Sanchez-Vives MV, Slater M. Biometric random number generators, Comput Secur 23:77-84 (2004) CrossRef

• Amigó JM, Szczepański J, Wajnryb E, Sanchez-Vives MV. Estimating the entropy rate of spike trains via Lempel-Ziv complexity, Neural Comput 16:717-736 (2004) PubMed CrossRef

• Lipniacki T, Paszek P, Brasier AR, Luxon B, Kimmel M. Mathematical model of NF-κB regulatory module, J Theor Biol 228:195-215 (2004) PubMed CrossRef

• Kucaba-Pietal A, Walenta Z, Peradzynski Z. Size and wall effects in flows in nanochannels, Turbulence 10:77-81 (2004)

• Kazmierczak B, Vakulenko S, Genieys S. Pattern formation capacity of spatially extended systems, Phys Rev E 69, 016215 (2004) PubMed CrossRef

• Kowalewski TA. Experimental Methods for Quantitative Analysis of Thermally Driven Flows in Phase Change with Convection, eds. T. Kowalewski, D. Gobin, CISM Course Lecture Notes 449:167-215 (2004)

• Kowalewski TA. Fluids in Motion, Academia 32-34 (2004)

• Kowalewski TA, Pakleza J, Trzcinski R, Zachara A. Experimental analysis of vapour bubble growth on heated surface, Archives of Theromdynamics 25:1-12 (2004)

• Sielamowicz I, Kowalewski TA, Błoński S. Central and Eccentric Granular Material Flows in Bins/Hoppers Registered by Optical Technique DPIV, Acta Agrophysica 4(2):519-531 (2004)

2003

• Kazmierczak B, Piechór K. Some heteroclinic solutions of a model of skin pattern formation, Math Meth Appl Sci 27:1317-1345 (2004) CrossRef

• Kazmierczak B, Volpert V. Existence of heteroclinic orbits for systems satysfying monotonicity conditions, Nonlinear Anal-Theor 55:467-491 (2003) CrossRef

• Amigó JM, Szczepański J. Approximations of dynamical systems and their applications to cryptography, Int J Bifurcat Chaos 13:1937-1948 (2003) CrossRef

• Szczepanski J, Amigo JM, Wajnryb E, Sanchez-Vives MV. Application of Lempel–Ziv complexity to the analysis of neural discharges, Network: Comput Neural Syst 14:335-350 (2003) PubMed CrossRef

• Amigó JM, Szczepański J, Wajnryb E, Sanchez-Vives MV. On the number of states of the neuronal sources, BioSystems 68:57-66 (2003) PubMed CrossRef

• Szczepanski J, Michalek T. Random fields approach to the study of DNA chains, J Biol Phys 29:39-54 (2003) CrossRef

• Lipniacki T. Shape-preserving solutions for quantum vortex motion under localized induction approximation, Phys Fluids 15:1381-1395 (2003) CrossRef

• Michalek T, Kowalewski TA. Simualtion of the water freezing process - numerical benchmarks, TASK Quarterly 7:389-408 (2003)

• Kowalewski TA, Mosyak A, Hetsroni G. Tracking of coherent thermal structures on a heated wall. Part 2: DNS Simulation, Exp in Fluids 34:390-396 (2003) CrossRef

• Peradzynski Z, da Silva ML, Lago V, Bedjamin E, Lebehot A, Mazouffre S, Dudeck M, Szymanski Z, Chikaou A, Boubert M. Modeling of radiative plasma sorrounding a space probe entering Mars atmosphere, High Temp Mat Pr-Isr 7:115-125 (2003)

2002

• Kazmierczak B, Lipniacki T. Homoclinic solutions in mechanical systems with small dissipation. Application to DNA dynamics, J Math Biol 44:309-329 (2002) PubMed CrossRef

• Lipniacki T. Quasi-static solution for quantum vortex motion under the localized induction approximation, J Fluid Mech 477:321-337 (2002) CrossRef

• Kucaba-Pietal A, Walenta Z, Peradzynski Z. What are the limits of applicability of the theory of micropolar fluids for description of real fluid flows through narrow channels, Proc Appl Math Mech 1:308-309 (2002) CrossRef

• Gorska A, Gorski K, Kotulski Z, Paszkiewicz A, Szczepanski J. New experimental results in differential-linear cryptanalysis of reduced variants of DES, Int Ser Eng 664:335-348 (2002)

• Kazmierczak B. Existence of heteroclinic orbits for systems satisfying monotonicity conditions, Lecture Notes in Nonlinear Analysis, 3:93-107 (2002)

• Kazmierczak B, Piechor K. Parametric dependence of phase boundary solution to model kinetic equations on parameters, ZAMP 53:539-568 (2002) CrossRef

• Kazmierczak B, Piechor K. Phase boundary solutions to model kinetic equations via the conley index theory, Part II, Math Comput Model 36:1393-1408 (2002) CrossRef

• Kazmierczak B, Massot M, Volpert V, Peradzynski Z. Solvability conditions for elliptic problems with non-Fredholm operators, Applicationes Mathematicae 29:219-238 (2002)

• Kurzyna J, Gascon N, Bonhomme G, Dudeck M, Makowski K, Peradzynski Z, Lago V, Lebehot A. Oscillations of discharge current in stationary plasma thruster, High Temp Mat Pr-Isr 6:181-190 (2002)

• Pakleza J, Duluc MC, Kowalewski TA. Experimental investigation of vapour bubble growth, Heat Transfer 3:479-485 (2002)

• Stasiek J, Kowalewski TA. Thermochromic liquid crystals applied for heat transfer research, Opto-electron Rev 10:1-10 (2002) CrossRef

• Monti P, Fernando HJ, Princevac M, Kowalewski TA, Chan WC, Padyjak ER. Observations of flow and turbulence in the nocturnal boundary layer over a slope, J Atmospheric Sci 59:2513-2534 (2002) <2513:OOFATI>2.0.CO;2 CrossRef |

• Kowalewski TA, Cybulski A, Michalek T. Experimental benchmark for casting problems, Heat Transfer 4:813-819 (2002)

• Kowalewski TA. Particle Image Velocimetry and Thermometry in two phase problems, in Visualization and Imaging in Transport Phenomena, Annals of New York Academy of Sciences 972:213-222, edts. S Siedeman & A Landesberg, NY (2002)

2001

• Szczepański J. A new result on the Nirenberg problem for expanding maps, Nonlinear Anal 43:91-99 (2001) CrossRef

• Szczepanski J, Kotulski Z. Pseudorandom Number Generators Based on Chaotic Dynamical Systems, Open Syst Inf Dyn 8:137-146 (2001) CrossRef

• Lipniacki T. Evolution of line-length density and anisotropy of quantum tangle in ⁴He, Phys Rev B 64:214516-1-9 (2001) CrossRef

• Lipniacki T. Thermodynamics of local DNA openings, Phys Rev E 64: 051919-1-5 (2001) PubMed CrossRef

• Lipniacki T. On quantum turbulence in superfluid Helium, Arch Mech 53:23-43 (2001)

• Lipniacki T. Torsional travelling waves in DNA, J Nonlinear Math Phys 8:188-194 (2001) CrossRef | PDF-ms

• Lipniacki T. Statics of rigid units chain, Int J Bifurcat Chaos 11:845-854 (2001) CrossRef

2000 and older

• Lipniacki T. Evolution of quantum vortices following reconnection, Eur J Mech B-Fluids, 19:361-378 (2000) CrossRef

• Lipniacki T. Chemically driven traveling waves in DNA, Phys Rev E 60:7253-7561 (1999) CrossRef

• Kotulski Z, Szczepański J. Application of discrete chaotic dynamical systems in cryptography-DCC method, Int J Bifurcat Chaos 9:1121-1135 (1999)

• Lipniacki T. Dynamics of quantum vortices in superfluid He, Arch Mech 50:439-454 (1998)

• Lipniacki T. Non-linear mechanical model of DNA dynamics, Nuovo Cimento D 20:831-843 (1998) CrossRef

• Lipniacki T. Can the system of discrete vortices imitate boundary layer, Arch Mech 49:103-109 (1998)

• Szczepański J, Kotulski Z. On two motions of a particle driven by equivalent ergodic and chaotic reflection laws, Arch Mech 50:865-875 (1998)

• Lipniacki T. Dynamics of superfluid Helium - Limits of the Vinen model, Arch Mech 49:615-633 (1997)

• Kotulski Z, Szczepański J. Discrete chaotic cryptography, Ann Phys 6:381-394 (1997) CrossRef

• Szczepański J, Wajnryb E. Do Ergodic or Chaotic Properties of the Reflection Law Imply Ergodicity or Chaotic Behavior of a Particle’s Motion? Chaos Soliton Fract 5:77-89 (1995) CrossRef

• Szczepański J. On a problem of Nirenberg concerning expanding maps in Hilbert space, Proc AMS 116:1041-1044 (1992) CrossRef

• Szczepański J, E. Wajnryb. Long time behavior of the one-particle distribution function for the Knudsen gas for the convex domain, Phys Rev A 44:3615-3621 (1991) CrossRef

• Szczepański J. On the basis of the statistical mechanics. The Liouville equation for systems with an infinite countable number of degrees of freedom, Physica A 157:955-982 (1989) CrossRef