From Maciej.Lisicki at fuw.edu.pl Sun Nov 3 18:41:00 2024 From: Maciej.Lisicki at fuw.edu.pl (Maciej Lisicki) Date: Sun, 3 Nov 2024 18:41:00 +0100 Subject: [Soft-matter] Soft Matter & Complex Systems Seminar on 8 Nov 2024 Message-ID: Dear Soft Matter & Complex Systems Colleagues and Friends, On Friday 8 November 2024 at 9:30 AM at the UW Faculty of Physics (Pasteura 5, Warsaw; room 1.40) we are hosting a seminar during which Anthony Ladd (University of Florida at Gainesville) will give a talk Using molecular flexibility to purify DNA from a cell lysate Abstract 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. We warmly welcome everyone to attend the talk and the Soft Matter Coffee Break after the seminar, held in room 2.63 (2nd floor). Maria Ekiel-Je?ewska Maciej Lisicki Piotr Szymczak Panagiotis Theodorakis Marek Trippenbach -------------- next part -------------- An HTML attachment was scrubbed... URL: From Maciej.Lisicki at fuw.edu.pl Sun Nov 3 18:41:00 2024 From: Maciej.Lisicki at fuw.edu.pl (Maciej Lisicki) Date: Sun, 3 Nov 2024 18:41:00 +0100 Subject: [Soft-matter] Soft Matter & Complex Systems Seminar on 8 Nov 2024 Message-ID: Dear Soft Matter & Complex Systems Colleagues and Friends, On Friday 8 November 2024 at 9:30 AM at the UW Faculty of Physics (Pasteura 5, Warsaw; room 1.40) we are hosting a seminar during which Anthony Ladd (University of Florida at Gainesville) will give a talk Using molecular flexibility to purify DNA from a cell lysate Abstract 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. We warmly welcome everyone to attend the talk and the Soft Matter Coffee Break after the seminar, held in room 2.63 (2nd floor). Maria Ekiel-Je?ewska Maciej Lisicki Piotr Szymczak Panagiotis Theodorakis Marek Trippenbach -------------- next part -------------- An HTML attachment was scrubbed... URL: From Maciej.Lisicki at fuw.edu.pl Mon Nov 11 22:12:44 2024 From: Maciej.Lisicki at fuw.edu.pl (Maciej Lisicki) Date: Mon, 11 Nov 2024 22:12:44 +0100 Subject: [Soft-matter] Soft Matter & Complex Systems Seminar on 15 Nov 2024 Message-ID: <3810544E-964A-497A-9BF4-70D0EFD9E8B9@fuw.edu.pl> Dear Soft Matter & Complex Systems Colleagues and Friends, On Friday 15 November 2024 at 9:30 AM at the UW Faculty of Physics (Pasteura 5, Warsaw; room 1.40) we are hosting a seminar during which Alina Ciach (IChF PAN) will give a talk Anomalous underscreening in concentrated ionic systems Abstract Concentrated ionic systems can find practical applications in energy storage devices, and in living cells the density of ions is large. Classical theories developed for dilute electrolytes, however, are not valid when the average distance between the ions becomes comparable with their diameters. Different experimental techniques, approximate theories and simulations give contradictory results for the distribution of the ions and for screening of charged objects, and a commonly accepted theory is still to be developed. I will very briefly present the experimental and simulation results. Next I'll discuss major differences between dilute and concentrated ionic systems, and introduce the mesoscopic approach for ionic systems with any density. In the theory, the finite size of the ions and the variance of the local charge are taken into account.The correlation functions obtained within the theory will be compared with experiments. The remaining open questions will be discussed. We warmly welcome everyone to attend the talk and the Soft Matter Coffee Break after the seminar, held in room 2.63 (2nd floor). Maria Ekiel-Je?ewska Maciej Lisicki Piotr Szymczak Panagiotis Theodorakis Marek Trippenbach -------------- next part -------------- An HTML attachment was scrubbed... URL: From Maciej.Lisicki at fuw.edu.pl Mon Nov 18 22:12:42 2024 From: Maciej.Lisicki at fuw.edu.pl (Maciej Lisicki) Date: Mon, 18 Nov 2024 22:12:42 +0100 Subject: [Soft-matter] Soft Matter & Complex Systems Seminar on 22 Nov 2024 Message-ID: <12D2E011-6100-4976-A739-9515D3F85BC0@fuw.edu.pl> Dear Soft Matter & Complex Systems Colleagues and Friends, On Friday 22 November 2024 at 9:30 AM at the UW Faculty of Physics (Pasteura 5, Warsaw; room 1.40) we are hosting a seminar during which Stanis?aw Gepner (Warsaw University of Technology) will give a talk Is the Laminar-Turbulent Edge Crowded? Exploring Multiple Local Attractors in the Edge of Square-Duct Flow Abstract 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 warmly welcome everyone to attend the talk and the Soft Matter Coffee Break after the seminar, held in room 2.63 (2nd floor). Maria Ekiel-Je?ewska Maciej Lisicki Piotr Szymczak Panagiotis Theodorakis Marek Trippenbach -------------- next part -------------- An HTML attachment was scrubbed... URL: From Maciej.Lisicki at fuw.edu.pl Mon Nov 25 13:44:33 2024 From: Maciej.Lisicki at fuw.edu.pl (Maciej Lisicki) Date: Mon, 25 Nov 2024 13:44:33 +0100 Subject: [Soft-matter] Soft Matter & Complex Systems Seminar on 29 Nov 2024 Message-ID: <798DB0F1-C4A2-42DC-85F2-99A13005AEAF@fuw.edu.pl> Dear Soft Matter & Complex Systems Colleagues and Friends, On Friday 29 November 2024 at 9:30 AM at the UW Faculty of Physics (Pasteura 5, Warsaw; room 1.40) we are hosting a seminar during which Wojciech G??d? (Institute of Physical Chemistry, PAS) will give a talk Influence of obstacles on the collective motion of self-propelled particles forming traveling bands Abstract The influence of regularly distributed disk-like obstacles on the motion of self-propelled particles is investigated within the framework of the Vicsek model. We focus on systems with a large number of self-propelled particles that form ordered structures such as traveling bands. The obstacles are arranged in a square lattice. We investigate the influence of their size and their separation on the formation and stability of ordered patterns of moving particles. We have discovered new structures stabilized by different arrangements of obstacles. We warmly welcome everyone to attend the talk and the Soft Matter Coffee Break after the seminar, held in room 2.63 (2nd floor). Maria Ekiel-Je?ewska Maciej Lisicki Piotr Szymczak Panagiotis Theodorakis Marek Trippenbach -------------- next part -------------- An HTML attachment was scrubbed... URL: