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
2024-05-17 (Friday)
room 1.40, Pasteura 5 at 09:30 
Yevgen Melikhov (IPPT PAN)Sedimentation Dynamics and Phase Diagram of Attracting Modes for Highly Deformable Fibers in Viscous Media
Sedimentation of elastic objects of different shapes in viscous fluids remains an active research topic due to the importance of such phenomena in numerous biological systems and technological processes. However, even the sedimentation of basic objects, such as fibers or loops, can display rich dynamics if structural flexibility is allowed. This study presents a numerical investigation of the sedimentation of a highly elastic fiber under gravity in a very viscous fluid. We employ the bead model and multipole expansion of the Stokes equations, corrected for lubrication that is implemented in the precise Hydromultipole numerical codes. A dimensionless elasto-gravitation number B, which relates the gravitation and bending forces acting on the fiber, and the fiber aspect ratio N are used to describe the fiber’s flexibility. The fiber evolution is monitored over an extended period to identify the attracting modes by systematically varying B and N in a wide range. An analysis of the characteristic features, such as characteristic time scales and fiber deformation patterns, of all the identified attracting modes is presented. The created phase diagram of these modes clearly illustrates that the existence of each mode depends not only on the elasto-gravitation number B but also on the fiber's aspect ratio N.
2024-04-26 (Friday)
room 1.40, Pasteura 5 at 09:30
Antoni Wrzos (IFT UW)Microscale granular experiments on vascular network formation with computer modeling
The fundamental challenge of tissue engineering is to create a functional vascular network that provides oxygen and nutrients to cells. Effectively constructing such networks requires understanding the processes involved in vascular network formation and identifying the factors influencing its growth. From an experimental perspective, we focus on well-controlled systems consisting of individual plastic microbeads coated with endothelial cells or bead matrices, ie. groups of individual microbeads with adjustable spacing between them. The microbeads are placed in hydrogel, mimicking an extracellular matrix, supplemented with nutrients, fibroblasts, and vascular endothelial growth factors (VEGF) at controlled concentrations.
Numerical tools have been developed for image segmentation of microscopic images with the ability to characterize networks through numerous parameters. One notable observation is that the onset time, marked by the initial growth of capillaries from a microbead, gets shorter with higher concentrations of VEGF. Additionally, higher concentrations of VEGF result in more branched networks, although they do not significantly affect the speed of growth of individual sprouts. The mean bifurcation angle shows weak dependence on VEGF concentration, typically varying between 60 and 75 degrees. This suggests that the sprout tips tend to follow local VEGF gradients. At high VEGF concentrations, we observe exponential distributions of segment lengths, indicating stochastic branching. To simulate growth of capillary networks in vasculogenesis we began to work on a cellular Potts model, consisting off two key factors governing network formation: elastic interactions due to hydrogel deformation by endothelial cells and chemotaxis associated with the diffusion and reaction of VEGF proteins with endothelial cells.
Numerical tools have been developed for image segmentation of microscopic images with the ability to characterize networks through numerous parameters. One notable observation is that the onset time, marked by the initial growth of capillaries from a microbead, gets shorter with higher concentrations of VEGF. Additionally, higher concentrations of VEGF result in more branched networks, although they do not significantly affect the speed of growth of individual sprouts. The mean bifurcation angle shows weak dependence on VEGF concentration, typically varying between 60 and 75 degrees. This suggests that the sprout tips tend to follow local VEGF gradients. At high VEGF concentrations, we observe exponential distributions of segment lengths, indicating stochastic branching. To simulate growth of capillary networks in vasculogenesis we began to work on a cellular Potts model, consisting off two key factors governing network formation: elastic interactions due to hydrogel deformation by endothelial cells and chemotaxis associated with the diffusion and reaction of VEGF proteins with endothelial cells.
2024-04-19 (Friday)
room 1.40, Pasteura 5 at 09:30
Piotr Korczyk (IPPT PAN)Droplets in Micro-Channels
Microfluidics has demonstrated significant potential across various research and technological domains. In this presentation, I will provide an overview of the microfluidics research conducted by me and my collaborators at the Institute of Fundamental Technological Research. Specifically, I will focus on droplet microfluidics and share our latest discoveries concerning the mechanisms underlying droplet formation at micro-channel junctions.
2024-04-12 (Friday)
room 1.40, Pasteura 5 at 09:30
Alina Ciach (IChF PAN)Self-assembly in mixtures with competing interactions
I will present theoretical and simulation results for a mixture of oppositely charged hydrophilic and hyrophobic particles immersed in a near-critical binary solvent. In such a mixture, the potential between like particles can have the form of short-range attraction long-range repulsion, and the cross-interaction is repulsive at short- and attractive at large distances. A theory combining the density functional and field-theoretical methods and the MD simulations show coexistence of a low-density disordered phase with a high-density phase with alternating layers rich in the first and second components. In these layers, crystalline structure is present in the solid, and absent in the liquid crystals. The density and the degree of order of the ordered phase decrease with increasing temperature, up to a temperature where the theory predicts a narrow two-phase region with increasing density of both disordered and ordered phases for increasing temperature. MD simulations show that monocrystals of the solid and liquid crystals have a prolate shape with the axis parallel to the direction of concentration oscillations, and the deviation from the spherical shape increases with increasing periodic order.
2024-04-05 (Friday)
room 1.40, Pasteura 5 at 09:30
Michał Matuszewski (Center for Theoretical Physics, Polish Academy of Sciences)Quantum and classical computing with exciton-polaritons
Exciton-polaritons are quantum quasiparticles that appear in the regime of strong light-matter coupling. They can be realized in a wide range of semiconductor materials, including inorganic semiconductors such as GaAs and CdTe, organic semiconductors, two-dimensional materials and perovskites. Their uniqueness lies in that they combine the properties of both light and matter, resulting in excellent transport and strong interparticle interactions. In this talk I will discuss the applications of exciton-polaritons in classical and quantum computing, including reservoir computing, all-optical systems, and quantum neural networks.
2024-03-22 (Friday)
room 1.40, Pasteura 5 at 09:30
Bogdan Cichocki (IFT UW)Microscopic time-reversal symmetry versus macroscopic laws
2024-03-15 (Friday)
room 1.40, Pasteura 5 at 09:30
Mateusz Sikora (Malopolska Centre of Biotechnology, Krakow, Poland & Max Planck Institute of Biophysics, Frankfurt, Germany)Integrative modeling of glycoproteins, lessons from the pandemic
Glycans, complex sugars covalently attached to proteins, affect protein stability and function, participate in ‘self’ recognition, and modulate protein-protein interactions. The glycosylation machinery is frequently hijacked by pathogens, which hide their proteins behind a “glycan shield”, making them inaccessible to the immune system and complicating pharmacological interventions. Unlike many biomolecules, glycans do not typically form secondary structures and remain highly mobile, posing a challenge for traditional structural biology techniques. In our research, we combined molecular dynamics simulations with cryo-electron tomography and atomic force microscopy to understand how glycans affect viral fusion proteins, particularly the SARS-CoV-2 spike protein. We discovered a surprising flexibility of the spike protein [1,2] and predicted new antibody binding sites accessible through the dynamic glycan shield [3], which can aid in designing novel vaccines. Additionally, we developed a simplified, open-source method for rapidly predicting glycan shielding with minimal computing power. This method has been applied to refine existing cryo-EM maps of glycoproteins [4].
1. B Turoňová, M Sikora, C Schürmann, WJH Hagen, S Welsch et al., In situ structural analysis of SARS-CoV-2 spike reveals flexibility mediated by three hinges.
Science, 370(6513) 2020
2. R Zhu, D Canena, M Sikora, M Klausberger, H Seferovic, et al., Force-tuned avidity of spike variant-ACE2 interactions viewed on the single-molecule level
Nat Comm, 13(7926) 2022
3. M Sikora, S von Bülow, FEC Blanc, M Gecht, R Covino, G Hummer. Computational epitope map of SARS-CoV-2 spike protein.
PLoS computational biology, 17(4) 2021
4. Y-X Tsai, N-E Chang, K Reuter, H-T Chang, T-J Yang et al., Rapid simulation of glycoprotein structures by grafting and steric exclusion of glycan conformer libraries.
Biorxiv
1. B Turoňová, M Sikora, C Schürmann, WJH Hagen, S Welsch et al., In situ structural analysis of SARS-CoV-2 spike reveals flexibility mediated by three hinges.
Science, 370(6513) 2020
2. R Zhu, D Canena, M Sikora, M Klausberger, H Seferovic, et al., Force-tuned avidity of spike variant-ACE2 interactions viewed on the single-molecule level
Nat Comm, 13(7926) 2022
3. M Sikora, S von Bülow, FEC Blanc, M Gecht, R Covino, G Hummer. Computational epitope map of SARS-CoV-2 spike protein.
PLoS computational biology, 17(4) 2021
4. Y-X Tsai, N-E Chang, K Reuter, H-T Chang, T-J Yang et al., Rapid simulation of glycoprotein structures by grafting and steric exclusion of glycan conformer libraries.
Biorxiv
2024-03-08 (Friday)
room 1.40, Pasteura 5 at 09:30
Piotr Bogusław Mucha (Faculty of Mathematics, Informatics, and Mechanics, University of Warsaw)Bridging the Micro to Macro: Exploring Agent Dynamics from Communication to Hydrodynamical Limits
This talk presents a simplified approach to modeling the dynamic behaviorof agents or particles across various scales. Beginning at the particle(micro) level, we employ kinetic formulations to transition towardshydrodynamical equations. Central to our investigation are Cucker-Smalemodels, initially developed to simulate the collective motion of fish andbirds. By examining the impact of singular communication, we illustratehow these models yield Navier-Stokes type systems, shedding light on theintricate relationship between agent interactions and fluid dynamics.
2024-03-01 (Friday)
room 1.40, Pasteura 5 at 09:30
A. Dziarmaga-Działyńska, A. Lis, D. Woś, P. Śmieja (IFT UW)Student talks
On Friday 1 March 2024 at 9:30 AM at the UW Faculty of Physics (Pasteura 5, Warsaw; room 1.40) we are hosting a series of student talks:
Anna Dziarmaga-Działyńska
Epidemic on a graph
The Justinian Plague epidemic took place in the mid-6th century, and reached most of the Mediterranean Basin, Western Europe and Persia. The disease is caused by the bacteria Yersinia pestis, and the main reservoir are rodents, particularly rats. Plague is transmitted to humans (and between humans) mainly through the bites of fleas and lice. The aim of our simulation is meant to determine the principal tramsmission vector of the pathogen which are either rats, or humans themselves. We make use of the differences between transport networks for the rats (that traveled with grain shipments) and for people, who mainly traveled via extensive road network.
Antoni Lis
Removal kinetics from the cell nucleus
In my presentation, I aim to provide a concise overview of our current understanding of mRNA export from the cell nucleus to the cytoplasm, and to offer insights gained from our experimental investigations into this intricate process.
Dawid Woś
Physics of Concretion Growth
A concretion is a dense, solid mass created through the deposition of mineral cement within the interstices among particles, commonly discovered in sedimentary rock or soil. While concretions typically exhibit ovoid or spherical shapes, irregular forms are also observed. The discussion will center on exploring the various physical processes underlying the formation of these structures.
Piotr Śmieja
Docking Dihydrobacillaene to CYP107 from Bacillus subtilis
It has been established that the P450 enzymes from the PksX gene cluster in Bacillus Subtilis participate in the biosynthesis of bacillane, the known antibiotic. In my presentation I discuss the process of docking dihydrobacillaene, a substrate in this process, to the P450 from Bacillus Subtilis, as well as the homolog proteins from Bacillus amyloliquefaciens and Bacillus atrophaeus.
We warmly welcome everyone to attend the talk and the Soft Matter Coffee Break after the seminar, held in room 2.63 (2nd floor).
Anna Dziarmaga-Działyńska
Epidemic on a graph
The Justinian Plague epidemic took place in the mid-6th century, and reached most of the Mediterranean Basin, Western Europe and Persia. The disease is caused by the bacteria Yersinia pestis, and the main reservoir are rodents, particularly rats. Plague is transmitted to humans (and between humans) mainly through the bites of fleas and lice. The aim of our simulation is meant to determine the principal tramsmission vector of the pathogen which are either rats, or humans themselves. We make use of the differences between transport networks for the rats (that traveled with grain shipments) and for people, who mainly traveled via extensive road network.
Antoni Lis
Removal kinetics from the cell nucleus
In my presentation, I aim to provide a concise overview of our current understanding of mRNA export from the cell nucleus to the cytoplasm, and to offer insights gained from our experimental investigations into this intricate process.
Dawid Woś
Physics of Concretion Growth
A concretion is a dense, solid mass created through the deposition of mineral cement within the interstices among particles, commonly discovered in sedimentary rock or soil. While concretions typically exhibit ovoid or spherical shapes, irregular forms are also observed. The discussion will center on exploring the various physical processes underlying the formation of these structures.
Piotr Śmieja
Docking Dihydrobacillaene to CYP107 from Bacillus subtilis
It has been established that the P450 enzymes from the PksX gene cluster in Bacillus Subtilis participate in the biosynthesis of bacillane, the known antibiotic. In my presentation I discuss the process of docking dihydrobacillaene, a substrate in this process, to the P450 from Bacillus Subtilis, as well as the homolog proteins from Bacillus amyloliquefaciens and Bacillus atrophaeus.
We warmly welcome everyone to attend the talk and the Soft Matter Coffee Break after the seminar, held in room 2.63 (2nd floor).
2024-01-26 (Friday)
room 1.40, Pasteura 5 at 09:30
Laura Meissner, Franciszek Myck, Wojciech Niedziółka, Michalina Szpak (IFT UW)Student talks
On Friday 26 January 2024 at 9:30 AM at the UW Faculty of Physics (Pasteura 5, Warsaw; room 1.40) we are hosting a series of student talks:
Laura Meissner (FUW)
Liquid-liquid phase separation in eukaryotic cells
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Franciszek Myck (FUW)
Under pressure - the physics of brewing a perfect espresso
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Wojciech Niedziółka (FUW)
Sod shock tube problem - a playground for shock capturing schemes
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Michalina Szpak (FUW)
Viscous oil on a rotating table
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Jakub Wysocki (FUW)
Oscillons in Granular Media
We will continue with student talks at the first seminar in summer term in March. We warmly welcome everyone to attend the talk and the Soft Matter Coffee Break after the seminar, held in room 2.63 (2nd floor).
Laura Meissner (FUW)
Liquid-liquid phase separation in eukaryotic cells
= = =
Franciszek Myck (FUW)
Under pressure - the physics of brewing a perfect espresso
= = =
Wojciech Niedziółka (FUW)
Sod shock tube problem - a playground for shock capturing schemes
= = =
Michalina Szpak (FUW)
Viscous oil on a rotating table
= = =
Jakub Wysocki (FUW)
Oscillons in Granular Media
We will continue with student talks at the first seminar in summer term in March. We warmly welcome everyone to attend the talk and the Soft Matter Coffee Break after the seminar, held in room 2.63 (2nd floor).