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
2023-06-16 (Friday)
room 1.40, Pasteura 5 at 09:30 
Jonasz Słomka (ETH Zürich)How BioEncounters at the microscale prime microbial interactions in the ocean
Microbial interactions critically depend on the rate of physical cell-cell or cell-resource encounters: these microscale processes control the rate of many fundamental ecological functions. In the ocean, a prominent example is the encounters among phytoplankton that lead to the formation of marine snow following a phytoplankton bloom. Another example is bacterial encounters with sinking marine snow particles that bacteria degrade, exerting an important control on carbon export from the upper ocean (the ‘biological pump’). Microscale encounters are nearly always modeled as encounters between inanimate spheres, borrowing from physical models of gases, coagulating colloids, and rain formation. However, these physics-based approaches fail to account for important traits of microorganisms, for example, cell elongation. Yet, certain traits of microorganisms combined with environmental conditions significantly impact many types of encounters in the ocean. For example, cell shape, in conjunction with buoyancy and turbulence, can increase encounter rates and thus speed up the formation of marine snow by elongated phytoplankton nearly ten-fold: this result provides a mechanistic explanation for the rapid clearance of blooms of elongated phytoplankton species. Similarly, encounters between bacteria and sinking marine snow depend on cell shape, motility, and fluid shear, and these factors can alter the encounter rate by orders of magnitude. Finally, microbes can harness encounters - Trichodesmium, a key marine nitrogen fixer, uses smart reversals to convert random encounters between cells into organized active aggregates. I will outline how more realistic models of encounters and aggregation at the microscale can contribute to our understanding of fundamental ecological processes controlled by microbes.
2023-06-02 (Friday)
room 1.40, Pasteura 5 at 09:30
Małgorzata Przerwa, Russell Kajouri, Soheil Arbabi (IFT UW)Student Talks
Małgorzata Przerwa (FUW)
Sedimentation of mass-asymmetric dumbbells in Stokes flow.
We investigate the dynamics of a mass-asymmetric dumbbells sedimentation in a low Reynolds number regime, in a pseudo-2D environment. We numerically and analytically predict the motion, and compare the trajectories to experimental data.
Russell Kajouri (IF PAN)
Anti-durotaxis motion onto Gradient Brushes Without External Energy Supply
Durotaxis motion usually takes place from softer to stiffer parts of a substrate with stiffness gradient, as has been demonstrated in the case of cell motion on cancer tissues in the context of biology, or more recently for droplets on gradient brush substrates (https://doi.org/10.1021/acs.langmuir.2c03381). In this presentation, we will demonstrate a new brush substrate design with stiffness gradient, which is able to sustain anti-dutoraxis motion, that is cause the motion of a fluid from its stiffer to its softer parts of the brush substrate. For this case, we will present the influence of the various, key system parameters and the underlying mechanism of the fluid motion.
Soheil Arbabi (IF PAN)
Coalescence of surfactant-laden droplets
Droplet coalescence is commonly encountered in nature and is also relevant for various technologies, such as inkjet printing. In this presentation, we present our results on the coalescence ofsurfactant-laden water droplets, which have been obtained by means of molecular dynamics simulation of a coarse-grained (CG) force-field. In particular, we will discuss the details of thecoalescence mechanism and the bridge growth dynamics.
Sedimentation of mass-asymmetric dumbbells in Stokes flow.
We investigate the dynamics of a mass-asymmetric dumbbells sedimentation in a low Reynolds number regime, in a pseudo-2D environment. We numerically and analytically predict the motion, and compare the trajectories to experimental data.
Russell Kajouri (IF PAN)
Anti-durotaxis motion onto Gradient Brushes Without External Energy Supply
Durotaxis motion usually takes place from softer to stiffer parts of a substrate with stiffness gradient, as has been demonstrated in the case of cell motion on cancer tissues in the context of biology, or more recently for droplets on gradient brush substrates (https://doi.org/10.1021/acs.langmuir.2c03381). In this presentation, we will demonstrate a new brush substrate design with stiffness gradient, which is able to sustain anti-dutoraxis motion, that is cause the motion of a fluid from its stiffer to its softer parts of the brush substrate. For this case, we will present the influence of the various, key system parameters and the underlying mechanism of the fluid motion.
Soheil Arbabi (IF PAN)
Coalescence of surfactant-laden droplets
Droplet coalescence is commonly encountered in nature and is also relevant for various technologies, such as inkjet printing. In this presentation, we present our results on the coalescence ofsurfactant-laden water droplets, which have been obtained by means of molecular dynamics simulation of a coarse-grained (CG) force-field. In particular, we will discuss the details of thecoalescence mechanism and the bridge growth dynamics.
2023-05-26 (Friday)
room 1.40, Pasteura 5 at 09:30
Paweł Krupa (IF PAN)Molecular dynamics simulations to understand biological systems
Molecular modeling and simulations have become powerful tools for examining the structure, dynamics, and function of biological systems at atomic and molecular levels. As these methods continue to evolve, driven by advancements in software and hardware development, we can investigate larger and more complicated systems, extend simulation timescales, run more trajectories, and obtain more realistic results. Such capabilities allow us to reevaluate certain topics and uncover the limitations of oversimplified models used in both experimental and computational studies, which can produce physically correct outcomes that do not accurately represent much more complex physiological conditions.
In this talk, I will present examples demonstrating how we can construct reliable models of lipid bilayers and investigate their behavior, as well as the impact of other molecules, including ions, neurotransmitters, and proteins as by proper employment of molecular dynamics simulations, we can gain valuable insights into the intricate interactions and dynamics of complex biological systems, which often are not possible to be investigated experimentally [1–5]
References:
1. Rodziewicz-Motowidło, S., Krupa, P., Karska, N., Zhukov, I. & Lipińska, A. Why does the UL49.5 of herpes simplex 1 virus fail to inhibit the TAP-dependent antigen presentation? (2023) doi:10.26434/chemrxiv-2023-91b0s.
2. Graul, M. et al. The N-terminal Proline Hinge Motif Controls the Structure of Bovine Herpesvirus 1-encoded Inhibitor of the Transporter Associated with Antigen Processing Required for its Immunomodulatory Function. J. Mol. Biol. 435, 167964 (2023).
3. Gupta, A. et al. Unusual Robustness of Neurotransmitter Vesicle Membranes against Serotonin-Induced Perturbations. J. Phys. Chem. B 127, 1947–1955 (2023).
4. Huy Pham, D. Q., Krupa, P., Nguyen, H. L., La Penna, G. & Li, M. S. Computational Model to Unravel the Function of Amyloid-β Peptides in Contact with a Phospholipid Membrane. J. Phys. Chem. B 124, 3300–3314 (2020).
5. Krupa, P., Quoc Huy, P. D. & Li, M. S. Properties of monomeric Aβ42 probed by different sampling methods and force fields: Role of energy components. J. Chem. Phys. 151, 055101 (2019).
In this talk, I will present examples demonstrating how we can construct reliable models of lipid bilayers and investigate their behavior, as well as the impact of other molecules, including ions, neurotransmitters, and proteins as by proper employment of molecular dynamics simulations, we can gain valuable insights into the intricate interactions and dynamics of complex biological systems, which often are not possible to be investigated experimentally [1–5]
References:
1. Rodziewicz-Motowidło, S., Krupa, P., Karska, N., Zhukov, I. & Lipińska, A. Why does the UL49.5 of herpes simplex 1 virus fail to inhibit the TAP-dependent antigen presentation? (2023) doi:10.26434/chemrxiv-2023-91b0s.
2. Graul, M. et al. The N-terminal Proline Hinge Motif Controls the Structure of Bovine Herpesvirus 1-encoded Inhibitor of the Transporter Associated with Antigen Processing Required for its Immunomodulatory Function. J. Mol. Biol. 435, 167964 (2023).
3. Gupta, A. et al. Unusual Robustness of Neurotransmitter Vesicle Membranes against Serotonin-Induced Perturbations. J. Phys. Chem. B 127, 1947–1955 (2023).
4. Huy Pham, D. Q., Krupa, P., Nguyen, H. L., La Penna, G. & Li, M. S. Computational Model to Unravel the Function of Amyloid-β Peptides in Contact with a Phospholipid Membrane. J. Phys. Chem. B 124, 3300–3314 (2020).
5. Krupa, P., Quoc Huy, P. D. & Li, M. S. Properties of monomeric Aβ42 probed by different sampling methods and force fields: Role of energy components. J. Chem. Phys. 151, 055101 (2019).
2023-05-19 (Friday)
room 1.40, Pasteura 5 at 09:30
Alexander Chamolly (Institut Pasteur, Paris)The mechanics of a bird embryo
For decades, biologists have sought to understand the development of an embryo in terms of genes, proteins and biochemistry. Recently however there has been a revolution in the field with the introduction of physical ideas. In this seminar I will talk about the early bird embryo, how we can use a mechanical model to understand how it performs reliably the developmental stage of gastrulation, how we measure its rheological properties as a soft matter system, and how we can manipulate it to further understand the impact of mechanics on genetic expression and cell fate.
2023-05-15 (Monday)
room B0.14, Pasteura 5 at 09:30
Tony Ladd (University of Florida)Bayesian Monte-Carlo for photovoltaic materials characterization
Quantifying rates of charge carrier recombination is an important step in developing solar cells with high power conversion efficiencies (PCE). However, recovering characteristic parameters such as carrier mobility, dopant concentration, and recombination rate constants is hindered by the interplay between carrier dynamics and the various recombination mechanisms. Interpretation of optoelectronic measurements, such as time-resolved photoluminescence (TRPL), usually relies on analytically tractable simplifications of the underlying physics models for carrier mobility and recombination, which can sacrifice much of the information content of the measurement.
Bayesian inference is a means of efficiently solving inverse problems. Rather than trying to locate a single optimum solution, it creates a probability distribution in the parameter space, based on the differences between simulated and measured data. In this case the forward problem is straightforward – given a set of material parameters, what does the TRPL curve look like. The inverse problem is to determine the material parameters from a given set of experimental data. I will present results to show that a small number of TRPL scans are sufficient to determine accurate values for most of the key optoelectronic parameters: carrier mobility, doping level, Auger and radiative recombination rates, and the bulk and surface contributions to the non-radiative decay. Minimizing non-radiative decay is a key to designing solar cells with high PCE.
Bayesian inference is quite computationally expensive, requiring a numerical solution of the classical drift-diffusion equations (in 1D) for each parameter set. To reduce the computational demands to manageable proportions, we have implemented a Metropolis Monte Carlo sampling, which can efficiently locate and sample the high probability region of the distribution.
Please note that, since it is outside of the Soft Matter and Complex Systems seminar schedule, attendance is not compulsory (although warmly encouraged!) for students taking the seminar.
Bayesian inference is a means of efficiently solving inverse problems. Rather than trying to locate a single optimum solution, it creates a probability distribution in the parameter space, based on the differences between simulated and measured data. In this case the forward problem is straightforward – given a set of material parameters, what does the TRPL curve look like. The inverse problem is to determine the material parameters from a given set of experimental data. I will present results to show that a small number of TRPL scans are sufficient to determine accurate values for most of the key optoelectronic parameters: carrier mobility, doping level, Auger and radiative recombination rates, and the bulk and surface contributions to the non-radiative decay. Minimizing non-radiative decay is a key to designing solar cells with high PCE.
Bayesian inference is quite computationally expensive, requiring a numerical solution of the classical drift-diffusion equations (in 1D) for each parameter set. To reduce the computational demands to manageable proportions, we have implemented a Metropolis Monte Carlo sampling, which can efficiently locate and sample the high probability region of the distribution.
Please note that, since it is outside of the Soft Matter and Complex Systems seminar schedule, attendance is not compulsory (although warmly encouraged!) for students taking the seminar.
2023-05-05 (Friday)
room 1.40, Pasteura 5 at 09:30
Tomasz Wacławczyk (MEiL PW)On relation between sharp and diffusive interface models: statistical model of the interphase region
My seminar will concern physical, mathematical and numerical modeling of the physical system localized between two phases. In literature, this system is known as interface/interphase region. Basing on the recent experimental and (MD based) numerical results, I will argue that sharp and diffusive interface models used in fluid mechanics do not explain why topological changes (break up, coalescence) can be predicted so effectively by solution of their governing equations. To address this problem, more general: statistical interphase region model is put forward. It provides clear physical interpretation of its all ingredients and allows to derive the governing equation of the sharp and diffusive interface/interphase models in the conservative form. I will argue, that the statistical model of the interphase region is integrating existing deterministic sharp/diffusive interface models into one coherent framework. In addition, the new statistical model avoids numerical problems that plague numerical solutions of the equations governing deterministic models.
2023-04-28 (Friday)
room 1.40, Pasteura 5 at 09:30
Endre Joachim L. Mossige (University of Oslo, Norway)Culinary fluid mechanics and other currents in food science
Innovations in fluid mechanics are leading to better food since ancient history, while creativity in cooking inspires applied and fundamental science. In this talk, I will discuss how recent advances in hydrodynamics are changing food science, and how the surprising phenomena that arise in the kitchen lead to discoveries and technologies across the disciplines, including rheology and soft matter. Central topics include cocktails and champagne (multiphase flows), whipped cream (complex fluids) and pancake making (viscous flows). For every topic, I will present the state-of-the-art knowledge, the open problems, and likely directions for future research.
The speaker will connect via Zoom.
The speaker will connect via Zoom.
2023-04-21 (Friday)
room 1.40, Pasteura 5 at 09:30
Debasish Das (University of Strathclyde)On the absence of collective motion in a bulk suspension of spontaneously rotating dielectric particles
A suspension of dielectric particles rotating spontaneously when subjected to a DC electric field in two-dimensions next to a no-slip electrode have proven to be an ideal model for active matter [Bricard et al., 2013]. In this system, an electrohydrodynamic (EHD) instability called Quincke rotation was exploited to create self-propelling particles which aligned with each other due to EHD interactions giving rise to collective motion. It is natural to question whether a suspension of such particles in three-dimensions will also display collective motion and spontaneously flow like bacterial suspensions do. Using molecular dynamics type simulations, we show that dielectrophoretic forces responsible for chaining in the direction of the applied electric field in conventional electrorheological fluids prevent collective motion in suspensions with individual particle rotation. Our simulations discover that the fundamental microstructural unit of a suspension under Quincke rotation is a pair of counter-rotating spheres aligned in the direction of the electric field. We perform a linear stability that explains this observation [Das and Saintillan, 2023].
A. Bricard, J.-B. Caussin, N. Desreumaux, O. Dauchot, and D. Bartolo. Emergence of macroscopic directed motion in populations of motile colloids. Nature, 503:95–98, 2013.
D. Das and D. Saintillan. On the absence of collective motion in a bulk suspension of spontaneously rotating dielectric particles. sub judice, 2023.
A. Bricard, J.-B. Caussin, N. Desreumaux, O. Dauchot, and D. Bartolo. Emergence of macroscopic directed motion in populations of motile colloids. Nature, 503:95–98, 2013.
D. Das and D. Saintillan. On the absence of collective motion in a bulk suspension of spontaneously rotating dielectric particles. sub judice, 2023.
2023-04-14 (Friday)
room 1.40, Pasteura 5 at 09:30
Russell Kajouri, Soheil Arbabi, Luis Carnevale (IF PAN)1. Unidirectional Droplet Propulsion onto Gradient Brushes Without External Energy Supply 2. Coalescence of surfactant-laden droplets 3.Liquid thread breakup and the formation of satellite droplets
1) Russell Kajouri
Title: Unidirectional Droplet Propulsion onto Gradient Brushes Without External Energy Supply
Durotaxis motion due to stiffness gradient is a process in which an agent, e.g.. a droplet or a cell, exhibits a unidirectional movement without consuming the energy of an external source. In our recent research, we describe the possibility of durotaxis motion of polymer-brush substrates and its dependence on various parameters. We also explain the mechanism of this phenomenon.
2) Soheil Arbabi
Title: Coalescence of surfactant-laden droplets
Droplet coalescence is commonly encountered in nature and is also relevant for various technologies, such as inkjet printing. In this presentation, we present our results on the coalescence ofsurfactant-laden water droplets, which have been obtained by means of molecular dynamics simulation of a coarse-grained (CG) force-field. In particular, we will discuss the details of thecoalescence mechanism and the bridge growth dynamics.
3) Luis Carnevale
Title: Liquid thread breakup and the formation of satellite droplets
The breakup of liquid threads into smaller droplets is a fundamental problem in fluid dynamics. Here, we estimate the characteristic wavelength of the breakup process by means of many-body dissipative particle dynamics and discuss the power-law dependence of the number of satellite droplets as a function of the Ohnesorge and thermal capillary number. We also elucidate the breakup mechanism and the conditions under satellite droplets form.
Title: Unidirectional Droplet Propulsion onto Gradient Brushes Without External Energy Supply
Durotaxis motion due to stiffness gradient is a process in which an agent, e.g.. a droplet or a cell, exhibits a unidirectional movement without consuming the energy of an external source. In our recent research, we describe the possibility of durotaxis motion of polymer-brush substrates and its dependence on various parameters. We also explain the mechanism of this phenomenon.
2) Soheil Arbabi
Title: Coalescence of surfactant-laden droplets
Droplet coalescence is commonly encountered in nature and is also relevant for various technologies, such as inkjet printing. In this presentation, we present our results on the coalescence ofsurfactant-laden water droplets, which have been obtained by means of molecular dynamics simulation of a coarse-grained (CG) force-field. In particular, we will discuss the details of thecoalescence mechanism and the bridge growth dynamics.
3) Luis Carnevale
Title: Liquid thread breakup and the formation of satellite droplets
The breakup of liquid threads into smaller droplets is a fundamental problem in fluid dynamics. Here, we estimate the characteristic wavelength of the breakup process by means of many-body dissipative particle dynamics and discuss the power-law dependence of the number of satellite droplets as a function of the Ohnesorge and thermal capillary number. We also elucidate the breakup mechanism and the conditions under satellite droplets form.
2023-03-31 (Friday)
room 1.40, Pasteura 5 at 09:30
Karol Makuch (IChF PAN)Steady-state thermodynamics
There is mounting evidence that the exchange of energy of a macroscopic steady-state system with its environment can be described in an equilibrium thermodynamic-like fashion. I will discuss the progress in the above direction during the seminar and present our recent results.