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
2026-01-09 (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…
2025-12-12 (Piątek)
Zapraszamy do sali 1.40, ul. Pasteura 5 o godzinie 09:30
Anna Niedźwiecka (Laboratory of Biological Physics, Institute of Physics, Polish Academy of Sciences, Warsaw, Poland)From protein disorder to liquid-liquid phase separation and biomineral order
Intrinsically disordered proteins (IDPs) are a class of biomolecules whose conformational flexibility is essential for key biological processes. Highly charged polyanionic proteins, in particular, are responsible for the regulation of biomineralisation by living organisms. We have proposed a physical framework that links the hydrodynamic and electrostatic properties of intrinsically disordered, acid-rich proteins with their function in biomineralisation, whereby the sequence-encoded charge distribution determines the hydrodynamic dimensions and flexibility of the protein chain, the local binding affinity regulates condensation behaviour, and liquid condensates that form in crowded conditions provide microenvironments that control mineral nucleation, growth, and edge development. This cascade—from protein structural disorder, through hydrodynamic behaviour and electrostatic collapse, to the formation of phase-separated liquid precursors of solid phases—represents a universal mechanism by which soft, dynamic biomolecular systems can control the formation of solid-state materials.
2025-12-05 (Piątek)
Zapraszamy do sali 1.40, ul. Pasteura 5 o godzinie 09:30
Antoine Sellier (LadHyX, Ecole Polytechnique, Palaiseau, France)Stokes flow about a collection of slip solid bodies
A boundary efficient and accurate method is proposed and numerically worked out to calculate, in the creeping flow regime, the resistance matrix of a cluster made of N arbitrarily-shaped slip solid bodies. The slip on each body curved surface is modeled using the widely-employed Navier slip condition and there is no restriction on the number N of bodies. Moreover, the task reduces to the treatment of 6N boundary-integral equations on the cluster surface and it is no use calculating the Stokes flow about the moving particles. Comparisons with the literature for one sphere (singularity method) and for two-interacting spheres (multipole method) will be presented. Finally, some numerical results for slip ellipsoids and the gravity-driven motion of two slip interacting spheres will be given and discussed.
2025-11-28 (Piątek)
Zapraszamy do sali 1.40, ul. Pasteura 5 o godzinie 09:30
Michał Klamka (Warsaw University of Technology)Hydrodynamic Levitation of Liquid Droplets on Rotating Surfaces: Experimental and CFD Analysis of Boundary Layer Interactions / Shaking Things Up: A Dynamic Oscillation Framework For Contact Angle Hysteresis Measurement
1. Title: Hydrodynamic Levitation of Liquid Droplets on Rotating Surfaces: Experimental and CFD Analysis of Boundary Layer Interactions
Abstract: The interaction of liquid droplets with solid surfaces is a phenomenon of fundamental importance across numerous industrial processes, including spray coating, spray cooling, and cleaning applications. While thermal effects, such as the well-documented Leidenfrost effect, can induce droplet levitation via a vapor cushion, analogous non-wettable behavior can be achieved at ambient temperatures through hydrodynamic means. A moving surface submerged in a fluid generates a boundary layer capable of preventing direct contact between an impacting droplet and the surface itself. This hydrodynamic levitation has been observed in both low and high-velocity flow regimes.
This investigation presents a comprehensive experimental and computational fluid dynamics (CFD) analysis of the interaction between a liquid droplet and the boundary layer generated by a vertically rotating flat disk. The primary experimental objective was to determine the feasibility of achieving stable droplet levitation within both laminar and turbulent boundary layers. Furthermore, the study aimed to define the operational limits of this levitation, specifically by identifying the critical impact velocity beyond which a free-falling droplet penetrates the boundary layer and makes contact with the disk surface.
The computational portion of this work focuses on elucidating the complex flow field surrounding a levitating droplet. We analyze the mutual interaction between the primary rotating disk flow and the stationary droplet, quantifying the modifications to the base flow caused by the droplet's presence and the resultant aerodynamic forces. A key aspect of this analysis is explaining the origin of observed droplet shape oscillations during levitation by examining flow instabilities and their subsequent effect on the pressure distribution across the droplet's surface. This dual approach provides a detailed understanding of the underlying physics governing hydrodynamic droplet levitation.
Acknowledgments: This research was carried out with the support of the Interdisciplinary Centre for Mathematical and Computational Modelling University of Warsaw (ICM UW) under computational allocation no G100-2222. Research was funded by the Warsaw University of Technology within the Excellence Initiative: Research University (IDUB) programme.
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2. Title: Shaking Things Up: A Dynamic Oscillation Framework For Contact Angle Hysteresis Measurement
Abstract: This work presents a dynamic method for determining contact angle hysteresis (CAH) by placing droplets on a harmonically oscillating substrate, providing new kinetic insights into surface wettability. We designed a custom experimental setup featuring a lightweight, 3D-printed motion carriage actuated by a high-performance linear motor capable of sinusoidal oscillations with accelerations up to 9g, and equipped with a high-speed optical system for millisecond-scale imaging and analysis. Silicon wafers were used as substrates with Glaco superhydrophobic surface treatment, and deionised water was chosen as the working fluid due to its well-characterized and reproducible physicochemical properties, ensuring comparability and minimizing variability. The integrated imaging and analysis approach, including precise droplet deposition and a robust MATLAB processing pipeline, enabled accurate measurement of contact angle dynamics and improved uncertainty quantification. Results show this oscillation-based method effectively probes the thresholds required for depinning, advances the study of dynamic droplet mobility, and facilitates detection of local surface heterogeneities, outperforming conventional static and quasi-static CAH measurement techniques.
Abstract: The interaction of liquid droplets with solid surfaces is a phenomenon of fundamental importance across numerous industrial processes, including spray coating, spray cooling, and cleaning applications. While thermal effects, such as the well-documented Leidenfrost effect, can induce droplet levitation via a vapor cushion, analogous non-wettable behavior can be achieved at ambient temperatures through hydrodynamic means. A moving surface submerged in a fluid generates a boundary layer capable of preventing direct contact between an impacting droplet and the surface itself. This hydrodynamic levitation has been observed in both low and high-velocity flow regimes.
This investigation presents a comprehensive experimental and computational fluid dynamics (CFD) analysis of the interaction between a liquid droplet and the boundary layer generated by a vertically rotating flat disk. The primary experimental objective was to determine the feasibility of achieving stable droplet levitation within both laminar and turbulent boundary layers. Furthermore, the study aimed to define the operational limits of this levitation, specifically by identifying the critical impact velocity beyond which a free-falling droplet penetrates the boundary layer and makes contact with the disk surface.
The computational portion of this work focuses on elucidating the complex flow field surrounding a levitating droplet. We analyze the mutual interaction between the primary rotating disk flow and the stationary droplet, quantifying the modifications to the base flow caused by the droplet's presence and the resultant aerodynamic forces. A key aspect of this analysis is explaining the origin of observed droplet shape oscillations during levitation by examining flow instabilities and their subsequent effect on the pressure distribution across the droplet's surface. This dual approach provides a detailed understanding of the underlying physics governing hydrodynamic droplet levitation.
Acknowledgments: This research was carried out with the support of the Interdisciplinary Centre for Mathematical and Computational Modelling University of Warsaw (ICM UW) under computational allocation no G100-2222. Research was funded by the Warsaw University of Technology within the Excellence Initiative: Research University (IDUB) programme.
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2. Title: Shaking Things Up: A Dynamic Oscillation Framework For Contact Angle Hysteresis Measurement
Abstract: This work presents a dynamic method for determining contact angle hysteresis (CAH) by placing droplets on a harmonically oscillating substrate, providing new kinetic insights into surface wettability. We designed a custom experimental setup featuring a lightweight, 3D-printed motion carriage actuated by a high-performance linear motor capable of sinusoidal oscillations with accelerations up to 9g, and equipped with a high-speed optical system for millisecond-scale imaging and analysis. Silicon wafers were used as substrates with Glaco superhydrophobic surface treatment, and deionised water was chosen as the working fluid due to its well-characterized and reproducible physicochemical properties, ensuring comparability and minimizing variability. The integrated imaging and analysis approach, including precise droplet deposition and a robust MATLAB processing pipeline, enabled accurate measurement of contact angle dynamics and improved uncertainty quantification. Results show this oscillation-based method effectively probes the thresholds required for depinning, advances the study of dynamic droplet mobility, and facilitates detection of local surface heterogeneities, outperforming conventional static and quasi-static CAH measurement techniques.
2025-11-07 (Piątek)
Zapraszamy do sali 1.40, ul. Pasteura 5 o godzinie 09:30
Tomasz Szawełło (IFT UW)Diffusive transport in network models of dissolution in porous media
Dissolution in porous media emerges from the interplay of fluid flow, reactant transport, chemical reactions, and evolving structure. Reactant transport combines advection and diffusion: advection promotes channeling instabilities, whereas diffusion stabilizes fronts. Pore network models provide an efficient framework to simulate dissolution, but often assume advection-dominated axial transport in pores—an assumption frequently violated in natural and industrial systems such as groundwater flows or catalytic reactors.
In this seminar I first motivate the need to include axial diffusion in pore network models and derive the classical Graetz solution for advection–reaction in a cylindrical pore with reactive walls. I next show how retaining axial diffusion modifies the solution structure, inducing additional dependence on Damköhler and Péclet numbers. Building on this, I present a solution to the 1D advection–diffusion–reaction problem for pores in the network that incorporates axial diffusion. Finally, I map dissolution outcomes on Damköhler–Péclet phase diagrams, highlighting transitions in morphology and comparing them with laboratory benchmarks.
In this seminar I first motivate the need to include axial diffusion in pore network models and derive the classical Graetz solution for advection–reaction in a cylindrical pore with reactive walls. I next show how retaining axial diffusion modifies the solution structure, inducing additional dependence on Damköhler and Péclet numbers. Building on this, I present a solution to the 1D advection–diffusion–reaction problem for pores in the network that incorporates axial diffusion. Finally, I map dissolution outcomes on Damköhler–Péclet phase diagrams, highlighting transitions in morphology and comparing them with laboratory benchmarks.
2025-10-24 (Piątek)
Zapraszamy do sali 1.40, ul. Pasteura 5 o godzinie 09:30
Akash Unnikrishnan (IFT UW)Taylor-Couette flow: from table-top experiments to planetary patterns
The Taylor-Couette system-the flow between two concentric rotating cylinders, has served as a model problem for studying flow instabilities and transitions to turbulence. In the first part of this seminar, I will briefly trace its historical importance and discuss how simple variations in rotation rates and geometry give rise to a hierarchy of flow states, from steady Taylor vortices to complex wavy and turbulent regimes. Extending the problem to non-circular enclosures introduces additional confinement effects and even Moffatt-like vortices, enriching the dynamics further.
In the second part, I will outline how meshless numerical methods can be employed to simulate such flows efficiently without requiring structured grids. Finally, I will present results from simulations, some using these meshless methods, that exhibit vortex patterns, including one reminiscent of the hexagonal jet observed in Saturn’s atmosphere. While not being an exact planetary model, the similarity highlights the universality of pattern-forming mechanisms in rotating shear-driven flows.
In the second part, I will outline how meshless numerical methods can be employed to simulate such flows efficiently without requiring structured grids. Finally, I will present results from simulations, some using these meshless methods, that exhibit vortex patterns, including one reminiscent of the hexagonal jet observed in Saturn’s atmosphere. While not being an exact planetary model, the similarity highlights the universality of pattern-forming mechanisms in rotating shear-driven flows.
2025-10-17 (Piątek)
Zapraszamy do sali 1.40, ul. Pasteura 5 o godzinie 09:30
Jenna Poonoosamy (Forschungszentrum Jülich)Deciphering interface coupled mineral dissolution and precipitation processes: experiments and modelling
Interface-coupled dissolution and precipitation (ICDP) processes control the evolution of reactive mineral/fluid systems in many subsurface environments, from CO₂ sequestration and concrete carbonation to steel corrosion in nuclear waste repositories and natural hydrogen generation. ICDP involves the dissolution of a primary mineral and the precipitation of a secondary phase directly on its surface, forming a rim. This rim may facilitate complete replacement of the parent phase or lead to passivation or mineral armoring. Despite its importance, the mechanisms governing mineral passivation and the fate of co-evolving gas phases remain poorly understood.
To address these gaps, we combined controlled column and microfluidic experiments with advanced microstructural characterization and pore-scale modelling. Using a model system which is redox- and pH-insensitive with the primary mineral celestine (SrSO4) covered with secondary barite (BaSO4), we quantified the role of barite nucleation dynamics, barite porosity, and the heterogeneity of celestine surface reactivity in driving mineral armoring. Three-dimensional FIB-SEM and HAADF-STEM analyses revealed nanoporosity in the secondary barite rim, while microfluidic experiments coupled with in-situ Raman and AFM imaging demonstrated how spatial variations in surface reactivity govern localized dissolution–precipitation patterns. Pore-scale modelling further showed that selective ion diffusion and electric double layer effects contribute to mineral passivation.
We extended this framework to ICDP systems involving gas generation. Using witherite (BaCO3) dissolution in sulfate-rich acidic solutions, we observed that the concomitant precipitation of barite and CO₂ exsolution forms distinctive “cauliflower-like”, mineral precipitates encrusting gas bubbles. These textures arise from electrostatic enrichment of ions around gas bubbles, promoting barite nucleation and trapping water droplets within mineral shells. When precipitation outpaces dissolution, these structures inhibit further mineral reaction and clog pore spaces, potentially impeding CO₂ storage, hydrogen recovery, and metal corrosion processes.
Together, our results reveal the coupled roles of surface chemistry, microstructure, and fluid dynamics in controlling ICDP kinetics and the evolution of reactive interfaces, key to predicting the long-term reactivity and permeability of subsurface systems.
To address these gaps, we combined controlled column and microfluidic experiments with advanced microstructural characterization and pore-scale modelling. Using a model system which is redox- and pH-insensitive with the primary mineral celestine (SrSO4) covered with secondary barite (BaSO4), we quantified the role of barite nucleation dynamics, barite porosity, and the heterogeneity of celestine surface reactivity in driving mineral armoring. Three-dimensional FIB-SEM and HAADF-STEM analyses revealed nanoporosity in the secondary barite rim, while microfluidic experiments coupled with in-situ Raman and AFM imaging demonstrated how spatial variations in surface reactivity govern localized dissolution–precipitation patterns. Pore-scale modelling further showed that selective ion diffusion and electric double layer effects contribute to mineral passivation.
We extended this framework to ICDP systems involving gas generation. Using witherite (BaCO3) dissolution in sulfate-rich acidic solutions, we observed that the concomitant precipitation of barite and CO₂ exsolution forms distinctive “cauliflower-like”, mineral precipitates encrusting gas bubbles. These textures arise from electrostatic enrichment of ions around gas bubbles, promoting barite nucleation and trapping water droplets within mineral shells. When precipitation outpaces dissolution, these structures inhibit further mineral reaction and clog pore spaces, potentially impeding CO₂ storage, hydrogen recovery, and metal corrosion processes.
Together, our results reveal the coupled roles of surface chemistry, microstructure, and fluid dynamics in controlling ICDP kinetics and the evolution of reactive interfaces, key to predicting the long-term reactivity and permeability of subsurface systems.
2025-10-03 (Piątek)
Zapraszamy do sali 1.40, ul. Pasteura 5 o godzinie 09:30
Jordan Orchard (IFT UW)Anomalous diffusion in billiard channels
Polygonal billiard channels are examples of pseudo-chaotic dynamics, a combination of integrable evolution and sudden jumps due to singular points that arise from the corners of the polygon. Such pseudo-chaotic behaviour, often characterised by an algebraic separation of nearby trajectories, is believed to be linked to the wild dependence that particle transport has on billiard geometry. Borrowing ideas from the Zemlyakov-Katok construction, we derive an exact expression of a scattering map of the cell connecting the outgoing flow of trajectories to the unconstrained incoming flow.