Soft Matter and Complex Systems Seminar
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2024-11-22 (Piątek)
Zapraszamy do sali 1.40, ul. Pasteura 5 o godzinie 09:30 
Stanisław Gepner (Warsaw University of Technology)Is the Laminar-Turbulent Edge Crowded? Exploring Multiple Local Attractors in the Edge of Square-Duct Flow
In this work, we present the first streamwise-localized invariant solution for turbulent square duct flow in the moderate Reynolds number range. Through heuristic analysis, we demonstrate that during specific periods within the turbulent time evolution, the flow state approaches the identified localized solution. This finding indicates that the localized solution is embedded within the turbulent attractor, making it the first localized solution identified for square duct flow and a the potential building block of turbulence in this configuration.
We obtain this solution through a bisection process applied within the symmetric subspace of the full state space, which enables the tracking of edge state solutions. Edge states are characterized by a single unstable direction, or a co-dimension one stable manifold, within the symmetric subspace. In the context of the full state space, these solutions are embedded within the turbulent attractor. As relative attractors on the edge of the laminar and turbulent basins, edge states play a significant role in governing the laminar-turbulent transition process. This characteristic makes them particularly interesting for turbulence control applications. In addition to the bisection method, we use Newton-Krylov GMRES-based iterations to converge to invariant solutions. To analyze stability, we apply an Arnoldi-based eigenvalue solver, and an arc-length continuation to track bifurcations. Stability analysis reveals that both branches of our localized solution are unstable in at least one direction. This instability suggests the presence of additional structures that may connect to the branches of the identified solution, indicating that the edge subspace (a co-dimension one subspace of the full space) contains multiple local attractors. Each of these local edge states would have stable manifolds that locally separate initial conditions, leading either toward the laminar attractor, a transient non-laminar excursion or, if it exists, a turbulent attractor. In our ongoing work, we identify and analyze a series of solutions on the edge. We study the positions and potential connections between the lower and upper branches of the identified solutions. By disturbing either the lower or upper branch in the unstable direction, we observe that the system tends either to laminarize smoothly or to experience a transient turbulent excursion. This behavior confirms that both solution branches reside on the edge and that the bifurcation responsible for their creation also lies on the edge. Additionally, we identify a potential heteroclinic connection between these states, which further enriches our understanding of the dynamics governing laminar-turbulent transition in square duct flow.
We obtain this solution through a bisection process applied within the symmetric subspace of the full state space, which enables the tracking of edge state solutions. Edge states are characterized by a single unstable direction, or a co-dimension one stable manifold, within the symmetric subspace. In the context of the full state space, these solutions are embedded within the turbulent attractor. As relative attractors on the edge of the laminar and turbulent basins, edge states play a significant role in governing the laminar-turbulent transition process. This characteristic makes them particularly interesting for turbulence control applications. In addition to the bisection method, we use Newton-Krylov GMRES-based iterations to converge to invariant solutions. To analyze stability, we apply an Arnoldi-based eigenvalue solver, and an arc-length continuation to track bifurcations. Stability analysis reveals that both branches of our localized solution are unstable in at least one direction. This instability suggests the presence of additional structures that may connect to the branches of the identified solution, indicating that the edge subspace (a co-dimension one subspace of the full space) contains multiple local attractors. Each of these local edge states would have stable manifolds that locally separate initial conditions, leading either toward the laminar attractor, a transient non-laminar excursion or, if it exists, a turbulent attractor. In our ongoing work, we identify and analyze a series of solutions on the edge. We study the positions and potential connections between the lower and upper branches of the identified solutions. By disturbing either the lower or upper branch in the unstable direction, we observe that the system tends either to laminarize smoothly or to experience a transient turbulent excursion. This behavior confirms that both solution branches reside on the edge and that the bifurcation responsible for their creation also lies on the edge. Additionally, we identify a potential heteroclinic connection between these states, which further enriches our understanding of the dynamics governing laminar-turbulent transition in square duct flow.
2024-11-15 (Piątek)
Zapraszamy do sali 1.40, ul. Pasteura 5 o godzinie 09:30
Alina Ciach (IChF PAN)Anomalous underscreening in concentrated ionic systems
Concentrated ionic systems can find practical applications in energystorage devices, and in living cells the density of ions is large.Classical theories developed for dilute electrolytes, however, are notvalid when the average distance between the ions becomes comparable withtheir diameters. Different experimental techniques, approximate theoriesand simulations give contradictory results for the distribution of theions and for screening of charged objects, and a commonly acceptedtheory is still to be developed.
I will very briefly present the experimental and simulation results.Next I'll discuss major differences between dilute and concentratedionic systems, and introduce the mesoscopic approach for ionic systemswith any density. In the theory, the finite size of the ions and thevariance of the local charge are taken into account.The correlationfunctions obtained within the theory will be compared with experiments.The remaining open questions will be discussed.
I will very briefly present the experimental and simulation results.Next I'll discuss major differences between dilute and concentratedionic systems, and introduce the mesoscopic approach for ionic systemswith any density. In the theory, the finite size of the ions and thevariance of the local charge are taken into account.The correlationfunctions obtained within the theory will be compared with experiments.The remaining open questions will be discussed.
2024-11-08 (Piątek)
Zapraszamy do sali 1.40, ul. Pasteura 5 o godzinie 09:30
Tony Ladd (University of Florida at Gainesville)Using molecular flexibility to purify DNA from a cell lysate
DNA is a semi-flexible polyelectrolyte with a persistence length of about 50 nm. At equilibrium, entropic forces cause the individual molecules to form compact spherical coils, which can be easily stretched by a weak shear flow into a cigar-like conformation that is not, on average, aligned with the flow direction. Because the electrophorectic mobility of the sheared polyelectrolyte is no longer isotropic, DNA can be driven to the walls of a confining channel by an electric field that pushes the DNA in the opposite direction to the flow. The migration velocity is sufficient to keep the DNA in a thin layer next to the wall. With a suitable choice of field strengths, the DNA can be driven against the flow (since it is next to the channel walls), while all the other components of a cell lysate are flushed in the opposite direection by the flow. This is a much stronger separation than in typical microfluidic processes, which rely on mobility contrast between the species. A simple microfludic device, assembled from acrylic sheets for less than $1, can provide a chemical-free purification of DNA. In this talk I will outline the physics underpinning the separation and describe experiments that purify DNA in sufficient quantities (up to 40 ng) for PCR amplification and gel electrophoresis.
2024-10-25 (Piątek)
Zapraszamy do sali 1.40, ul. Pasteura 5 o godzinie 09:30
Łukasz Klotz (Warsaw University of Technology)Influence of porous material on the flow behind backward-facing step - experimental study
We investigate effect of porous insert located upstream of the separation edge of backward facing step (BFS) in early transitional regime as a function of Reynolds number. This is an example of hydrodynamic system that is a combination of separated shear flow with large amplification potential and porous materials known for efficient flow destabilisation. Spectral analysis reveals that dynamics of backward-facing step is dominated by spectral modes that remain globally coherent along the streamwise direction. We detect two branches of characteristic frequencies in the flow and with Hilbert transform we characterise their spatial support. For low Reynolds numbers, the dynamics of the flow is dominated by lower frequency, whereas for sufficiently large Reynolds numbers cross-over to higher frequencies is observed. Increasing permeability of the porous insert results in decrease in Reynolds number value, at which frequency cross-over occurs. By comparing normalized frequencies on each branch with local stability analysis, we attribute Kelvin-Helmholtz and Tollmien-Schlichting instabilities to upper and lower frequency branches, respectively. Finally, our results show that porous inserts enhance Kelvin-Helmholtz instability and promote transition to oscillator type dynamics. Specifically, the amplitude of vortical (BFS) structures associated with higher frequency branch follows Landau model prediction for all investigated porous inserts.
2024-10-18 (Piątek)
Zapraszamy do sali 1.40, ul. Pasteura 5 o godzinie 09:30
Krzysztof Kuczera (Department of Chemistry and Department of Molecular Biosciences, The University of Kansas, Lawrence, KS, USA)Discovery and Characterization of Blood-Brain Barrier Modulating Peptides based on E-cadherin
AbstractThe delivery of pharmaceutical agents to the central nervous system is hindered by the Blood-Brain Barrier (BBB), a network of inter-cellular interactions of the epithelium. Here, we present a search for novel peptides able to modulate the BBB, focusing on the E-cadherin protein, which is involved in the formation of these intercellular junctions. Previously, two classes of peptides, HAV and ADT, were known to modulate BBB permeability in vitro and in vivo. Here we use computational methods to perform a systematic search for novel peptides which can effectively interfere with E-cadherin interactions. Employing protein-protein and peptide-protein docking methods with varied levels of flexibility, we propose 115 different peptides with a high binding affinity for E-cadherin as candidates for disrupting the BBB. Several strongest binders have been selected for experimental validation and further sequence optimization. Additionally, conformations of selected peptides in aqueous solution were explored with molecular dynamics simulations, showing a general preference for extended structures and fast conformational equilibria, on the 10-100 ns time scales. Thus, this work presents a systematic computational approach for generating novel peptides with high potential for disrupting the BBB and enabling drug delivery to the central nervous system.
2024-10-11 (Piątek)
Zapraszamy do sali 1.40, ul. Pasteura 5 o godzinie 09:30
Andrej Vilfan (J. Stefan Institute, Ljubljana, Slovenia)Minimum dissipation theorems for microswimmers
Microswimmers are natural or artificial self-propelled microscaleobjects moving through a fluid at low Reynolds numbers. The entropyproduction of microswimmers, related to their dissipated power,consists of two contributions. The external dissipation takes place inthe viscous fluid surrounding the microswimmer. Internal dissipationtakes place in the propulsive layer on the swimmer's surface. We haveshown that a lower bound on the external dissipation can be derivedwith the knowledge of drag coefficients of two bodies of the sameshape, one with a no-slip and one with a perfect slip boundarycondition [1]. This approach can be generalized to take into accountthe internal dissipation, which is often the dominant contribution. Bycombining the Helmholtz minimum dissipation theorem and the principleof linear superposition, we solve the combined minimum dissipationproblem for different classes of swimmers including surface-drivenviscous droplets, Marangoni surfers, etc. [2,3]. We show that theminimum entropy production in suspensions of active microswimmersdiffers fundamentally from particles driven by external forces.
[1] B. Nasouri, A. Vilfan and R. Golestanian, Phys. Rev. Lett., 126,034503 (2021)
[2] A. Daddi-Moussa-Ider, R. Golestanian and A. Vilfan, Nat. Commun.14, 6060 (2023)
[3] A. Daddi-Moussa-Ider, R. Golestanian and A. Vilfan, J. Fluid Mech.986, A32 (2024)
[1] B. Nasouri, A. Vilfan and R. Golestanian, Phys. Rev. Lett., 126,034503 (2021)
[2] A. Daddi-Moussa-Ider, R. Golestanian and A. Vilfan, Nat. Commun.14, 6060 (2023)
[3] A. Daddi-Moussa-Ider, R. Golestanian and A. Vilfan, J. Fluid Mech.986, A32 (2024)
2024-10-04 (Piątek)
Zapraszamy do sali 1.40, ul. Pasteura 5 o godzinie 09:30
Panagiotis Theodorakis (Institute of Physics, Polish Academy of Sciences)Soft Matter Matters
In this presentation, I will talk about a range of different soft matter matters (problems) that have recently been tackled in the group of Soft Matter and Fluids Physics by using a wide spectrum of methods from molecular to continuum scales. This soft matter matters for various applications ranging from printing and spayring technologies to cooling and employs different soft-matter matters. A series of key simulation results will be discussed for various interesting phenomena, providing understanding of underlying mechanisms and design principles for functional matter (materials) in specific applications. On the modeling side, I will also talk about the ongoing development of the general-purpose many-body dissipative particle dynamics force-field based on the MARTINI coarse-graining approach (MDPD-MARTINI), which enables us to simulate a wide spectrum of soft matter systems with a significant speed-up with respect to molecular dynamics.
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