Soft Matter and Complex Systems Seminar
2006/2007 | 2007/2008 | 2008/2009 | 2009/2010 | 2010/2011 | 2011/2012 | 2012/2013 | 2013/2014 | 2014/2015 | 2015/2016 | 2016/2017 | 2017/2018 | 2018/2019 | 2019/2020 | 2020/2021 | 2021/2022 | 2022/2023 | 2023/2024 | 2024/2025 | 2025/2026
2026-04-17 (Piątek)
Zapraszamy do sali 1.40, ul. Pasteura 5 o godzinie 09:30 
Emilia Trudnowska (Institute of Oceanology, Polish Academy of Sciences)Ocean Particles in Motion: Patchiness, Fluxes, and Ecosystem Links from an In Situ Perspective
Particles in the ocean—ranging from microscopic to larger aggregates - marine snow are fundamental carriers of carbon, energy, and ecological interactions. I will present an in situ perspective on those aspects and what are the methodologies and technologies used by oceanographers for direct observations of particles in their natural environment. These include laser counters, underwater vision profilers, sediment traps, and autonomous platforms that resolve particle.
My work has been oscillating around explorations how particle dynamics vary across spatial and temporal scales and the processes that shape particles distribution, transformation, and ecological significance across diverse marine environments: Arctic (Svalbard, Greenland, Barents Sea), Antarctic, sub-Antarctic (Beagle Channel), north Atlantic (Gulf Stream, Norwegian Sea), and Pacific (Monterey Bay). The presented examples of key processes governing particles dynamics include: 1) patchiness, 2) models of secondary production based on size structure, 3) particle–plankton co-existance, 4) classification of particles into morphocategories that reflect their origin and transformation pathways, 5) particle flux and sinking rates in relation to carbon export and ecosystem connectivity, 6) mapping approaches that link particle distributions to food availability for higher trophic levels such as fish and seabirds, 7) the effects of glacier melting o particle pools and transformations, 8) resuspension of particles in kelp forest systems, and 9) seasonal variability in shaping particle abundance and composition.
By integrating observational techniques with process-based understanding, this lecture underscores the importance of particles as a unifying framework for studying marine ecosystems, and aims to stimulate new perspectives for discussion and collaboration.
My work has been oscillating around explorations how particle dynamics vary across spatial and temporal scales and the processes that shape particles distribution, transformation, and ecological significance across diverse marine environments: Arctic (Svalbard, Greenland, Barents Sea), Antarctic, sub-Antarctic (Beagle Channel), north Atlantic (Gulf Stream, Norwegian Sea), and Pacific (Monterey Bay). The presented examples of key processes governing particles dynamics include: 1) patchiness, 2) models of secondary production based on size structure, 3) particle–plankton co-existance, 4) classification of particles into morphocategories that reflect their origin and transformation pathways, 5) particle flux and sinking rates in relation to carbon export and ecosystem connectivity, 6) mapping approaches that link particle distributions to food availability for higher trophic levels such as fish and seabirds, 7) the effects of glacier melting o particle pools and transformations, 8) resuspension of particles in kelp forest systems, and 9) seasonal variability in shaping particle abundance and composition.
By integrating observational techniques with process-based understanding, this lecture underscores the importance of particles as a unifying framework for studying marine ecosystems, and aims to stimulate new perspectives for discussion and collaboration.
2026-04-10 (Piątek)
Zapraszamy do sali 1.40, ul. Pasteura 5 o godzinie 09:30
Jacek Miękisz (MIM UW)Phase transitions in stochastic evolutionary games on graphs
Short abstract, general discussion
We discuss similarities and differences between systems of interacting spins in the ferromagnetic Ising model and systems of interacting players in evolutionary games. We compare Nash equilibria to ground states and phase transitions in both models.
Long abstract, a case study
We examine the impact of the maintenance cost of social links on cooperative behavior in the Prisoner’s Dilemma game on the Barabási-Albert scale-free network with a pairwise stochastic imitation. We show by means of Monte Carlo simulations and pair approximation that the cooperation frequency changes abruptly from an almost full cooperation to a much smaller value when we increase the cost of maintaining links. In the critical region, the stationary distribution is bimodal and the system oscillates between two states: the state with almost full cooperation and one with coexisting strategies. We show that the critical region shrinks with the increasing size of the population. However, the expected time the system spends in a metastable state before switching to the other one does not change as a function of the system’s size, which precludes the existence of two stationary states in the thermodynamic limit of the infinite population.
Bibliography
J. Miękisz and J. Mohamadichamgavi, Phase transitions in the prisoner’sdilemma game on the Barabási-Albert graph with participation cost, Phys.Rev. E 112: L032302 (2025).
https://www.mimuw.edu.pl/~miekisz/phtrpre.pdf
J. Miękisz, J. Mohamadichamgavi and J. Łacki, Phase transitions in thePrisoner’s Dilemma game on scale-free networks, BioPhysMath 1: 9 pages(2024).
https://www.mimuw.edu.pl/~miekisz/phasetrpdbpm.pdf
We discuss similarities and differences between systems of interacting spins in the ferromagnetic Ising model and systems of interacting players in evolutionary games. We compare Nash equilibria to ground states and phase transitions in both models.
Long abstract, a case study
We examine the impact of the maintenance cost of social links on cooperative behavior in the Prisoner’s Dilemma game on the Barabási-Albert scale-free network with a pairwise stochastic imitation. We show by means of Monte Carlo simulations and pair approximation that the cooperation frequency changes abruptly from an almost full cooperation to a much smaller value when we increase the cost of maintaining links. In the critical region, the stationary distribution is bimodal and the system oscillates between two states: the state with almost full cooperation and one with coexisting strategies. We show that the critical region shrinks with the increasing size of the population. However, the expected time the system spends in a metastable state before switching to the other one does not change as a function of the system’s size, which precludes the existence of two stationary states in the thermodynamic limit of the infinite population.
Bibliography
J. Miękisz and J. Mohamadichamgavi, Phase transitions in the prisoner’sdilemma game on the Barabási-Albert graph with participation cost, Phys.Rev. E 112: L032302 (2025).
https://www.mimuw.edu.pl/~miekisz/phtrpre.pdf
J. Miękisz, J. Mohamadichamgavi and J. Łacki, Phase transitions in thePrisoner’s Dilemma game on scale-free networks, BioPhysMath 1: 9 pages(2024).
https://www.mimuw.edu.pl/~miekisz/phasetrpdbpm.pdf
2026-03-27 (Piątek)
Zapraszamy do sali 1.40, ul. Pasteura 5 o godzinie 09:30
Marcin Napiórkowski (KMMF FUW)Bose-Einstein condensation: an ongoing mathematical challenge
Proving Bose-Einstein condensation in the thermodynamic limit remains a major open problem in mathematical physics. In my talk, I will explain the content of the conjecture and review recent progress in the study of bosonic many-body systems.
2026-03-20 (Piątek)
Zapraszamy do sali 1.40, ul. Pasteura 5 o godzinie 09:30
Rafał Błaszkiewicz (IFT UW)Unsteady Effects in Cilia-Mediated Transport and Microscale Mixing
Authors:
Rafał Błaszkiewicz¹, Margot Young², Albane Théry², Talia Becker Calazans², Arnold J.T.M. Mathijssen², Maciej Lisicki¹
¹University of Warsaw, Warsaw, Poland
²University of Pennsylvania, Philadelphia, USA
Cilia are key drivers of fluid transport in biological systems, from single-celled organisms to human tissues. Traditional models often treat ciliary flows as steady, yet the beating of cilia is inherently unsteady, generating flows that evolve on timescales comparable to viscous diffusion.
In this work, we use a time-dependent linear Stokes framework with Green’s functions and memory kernels to model flows generated by individual and coordinated cilia motion, represented by point-like “Pufflets.” Combining theory, simulations, and experiments, we examine how unsteady actuation affects particle trajectories and flow structures.
Our results show that unsteady effects can modify transport pathways and influence mixing at the microscale, particularly when multiple cilia interact. These findings highlight differences between steady and unsteady Stokes flows and provide insight into the mechanisms underlying cilia-mediated fluid transport.
The full study is available at: https://doi.org/10.48550/arXiv.2603.11020.
Rafał Błaszkiewicz¹, Margot Young², Albane Théry², Talia Becker Calazans², Arnold J.T.M. Mathijssen², Maciej Lisicki¹
¹University of Warsaw, Warsaw, Poland
²University of Pennsylvania, Philadelphia, USA
Cilia are key drivers of fluid transport in biological systems, from single-celled organisms to human tissues. Traditional models often treat ciliary flows as steady, yet the beating of cilia is inherently unsteady, generating flows that evolve on timescales comparable to viscous diffusion.
In this work, we use a time-dependent linear Stokes framework with Green’s functions and memory kernels to model flows generated by individual and coordinated cilia motion, represented by point-like “Pufflets.” Combining theory, simulations, and experiments, we examine how unsteady actuation affects particle trajectories and flow structures.
Our results show that unsteady effects can modify transport pathways and influence mixing at the microscale, particularly when multiple cilia interact. These findings highlight differences between steady and unsteady Stokes flows and provide insight into the mechanisms underlying cilia-mediated fluid transport.
The full study is available at: https://doi.org/10.48550/arXiv.2603.11020.
2026-03-06 (Piątek)
Zapraszamy do sali 1.40, ul. Pasteura 5 o godzinie 09:30
Jonasz Słomka (FUW)How encounters at the microscale prime microbial interactions
Microbial interactions often critically depend on the rate of physical cell-cell or cell-resourceencounters. In a liquid environment, many prominent examples include encounters amongphytoplankton in the ocean that lead to the formation of marine snow, the formation of livingaggregates by cyanobacteria, bacterial chemotaxis towards leaky phytoplankton, andhorizontal gene transfer between bacteria. Microscale encounters are nearly alwaysquantified as encounters between inanimate spheres, borrowing from the physics of gases,coagulating colloids, and rain formation. However, these classical approaches often fail toaccount for important traits of microorganisms, such as cell elongation, motility, or gradientsensing. Even more importantly, experimental assays typically do not control cell-cellencounters. In my talk, I will outline how more realistic models of encounters at themicroscale can contribute to our understanding of fundamental ecological processescontrolled by microbes, from active aggregation through chemotaxis to gene exchanges. Iwill close by presenting our recent experimental evidence that encounters driven by fluidshear strongly control the rates of horizontal gene transfer between bacteria.
2026-02-27 (Piątek)
Zapraszamy do sali 1.40, ul. Pasteura 5 o godzinie 09:30
Alicja Domańska, Tomasz Pniewski, Jakub Wróbel, Łukasz Białas, Maria Puciata-Mroczynska, Michalina Szpak (IFT UW)Student Talks
The schedule of talks:
- Alicja Domańska – Flow-Driven Precipitation from Supersaturated Solutions
- Tomasz Pniewski – Modeling angiogenesis with the Cellular Potts model
- Jakub Wróbel – Thermodynamic analysis of thermo-osmotic flow
- Łukasz Białas – Grounds for Investigation: CT Scan Analysis of Coffee Pucks
- Maria Puciata-Mroczynska – Single grain dynamics ona rough inclined plane
- Michalina Szpak – Optical microscopy investigation of the coffee ring effect
2026-01-23 (Piątek)
Zapraszamy do sali 1.40, ul. Pasteura 5 o godzinie 09:30
Jan Kossacki, Aleksander Syrewicz, Gabriela Niechwiadowicz, Mark Passia, Maciej Pawlus (IFT UW)Student Talks
The schedule of talks:
- Jan Kossacki – Origin of the banded structure in agates
- Aleksander Syrewicz – The shape of ideal stratovolcanoes
- Gabriela Niechwiadowicz – Challenges of reconstructions in time-dependent CT reconstructions
- Mark Passia – Challenges of real time classification of radar echoes
- Maciej Pawlus – The growth of a transport network with a coevolving boundary
2026-01-16 (Piątek)
Zapraszamy do sali 1.40, ul. Pasteura 5 o godzinie 09:30
Piotr Zdybel (IPPT PAN)Three-Dimensional Buckling of Slender Filaments in Shear Flow
We study the onset of 3D buckling of a slender elastic filament in a viscous shear flow at low Reynolds number and high Péclet number. Using the Euler–Bernoulli (elastica) description linearized about a straight configuration of arbitrary orientation, we show that the 3D stability problem can be reduced to a universal spectral problem governed by an orientation-dependent combination of the elastoviscous number and the shear geometry. Building on earlier in-plane eigenmodes, we solve the 3D eigenproblem and propose a simple analytic approximation of the unstable eigenfunctions as Gaussian wave packets. This yields the central scaling result: for highly flexible filaments, the characteristic wavenumber of the most unstable mode grows proportionally to the square root of this elastoviscous measure. Finally, we validate the predicted eigenshapes by numerical simulations of finite-thickness filaments using a bead model and the HYDROMULTIPOLE codes. The talk is based on our paper: P. Sznajder, P. Zdybel, L. Liu, and M. L. Ekiel-Jeżewska, Phys. Rev. E 110, 025104 (2024).
2026-01-09 (Piątek)
Zapraszamy do sali 1.40, ul. Pasteura 5 o godzinie 09:30
Tomasz Lipniacki (IPPT PAN)Antagonism between viral infection and innate immunity at the single-cell level
Authors: Frederic Grabowski, Marek Kochańczyk, Zbigniew Korwek, Maciej Czerkies, Wiktor Prus, Tomasz Lipniacki
(Institute of Fundamental Technological Research, Polish Academy of Sciences)
When infected with a virus, cells may secrete interferons (IFNs) that prompt nearby cells to prepare for upcoming infection. Reciprocally, viral proteins often interfere with IFN synthesis and IFN-induced signaling. We modeled the crosstalk between the propagating virus and the innate immune response using an agent-based stochastic approach. By analyzing immunofluorescence microscopy images we observed that the mutual antagonism between the respiratory syncytial virus (RSV) and infected A549 cells leads to dichotomous responses at the single-cell level and complex spatial patterns of cell signaling states. Our analysis indicates that RSV blocks innate responses at three levels: by inhibition of IRF3 activation, inhibition of IFN synthesis, and inhibition of STAT1/2 activation. In turn, proteins coded by IFN-stimulated (STAT1/2-activated) genes inhibit the synthesis of viral RNA and viral proteins. The striking consequence of these inhibitions is a lack of coincidence of viral proteins and IFN expression within single cells.
PloS Pathogens, 2023
(Institute of Fundamental Technological Research, Polish Academy of Sciences)
When infected with a virus, cells may secrete interferons (IFNs) that prompt nearby cells to prepare for upcoming infection. Reciprocally, viral proteins often interfere with IFN synthesis and IFN-induced signaling. We modeled the crosstalk between the propagating virus and the innate immune response using an agent-based stochastic approach. By analyzing immunofluorescence microscopy images we observed that the mutual antagonism between the respiratory syncytial virus (RSV) and infected A549 cells leads to dichotomous responses at the single-cell level and complex spatial patterns of cell signaling states. Our analysis indicates that RSV blocks innate responses at three levels: by inhibition of IRF3 activation, inhibition of IFN synthesis, and inhibition of STAT1/2 activation. In turn, proteins coded by IFN-stimulated (STAT1/2-activated) genes inhibit the synthesis of viral RNA and viral proteins. The striking consequence of these inhibitions is a lack of coincidence of viral proteins and IFN expression within single cells.
PloS Pathogens, 2023
2025-12-19 (Piątek)
Zapraszamy do sali 1.40, ul. Pasteura 5 o godzinie 09:30
Rafał Demkowicz-Dobrzański (IFT UW)Quantum Metrology - an almost perfect theory with just a few cracks
Recent theoretical developments have rendered quantum metrology a mature field, where some of the most fundamental question have been answered and efficient computational tools developed. We have now a full understanding of quantum metrological potential in case of noisy single parameter estimation models, provided the noise may be assumed to be Markovian. Nevertheless, non-Markovian models remain challenging and efficient universal theoretical tools are still missing. Apart from that, multi-parameter estimation scenarios may pose a challenge even in the Markovian regime, not to mention non-Markovian one. Do not despair, though, some progress is being made…