From Maciej.Lisicki at fuw.edu.pl Tue Nov 7 21:28:15 2023 From: Maciej.Lisicki at fuw.edu.pl (Maciej Lisicki) Date: Tue, 7 Nov 2023 21:28:15 +0100 Subject: [Soft-matter] Soft Matter and Complex Systems Seminar on 10 Nov 2023 Message-ID: <36FDFB0E-5AD6-4B6F-959B-C83FE5B0421E@fuw.edu.pl> Dear Soft Matter & Complex Systems Colleagues and Friends, On Friday 10 November 2023 at 9:30 AM at the UW Faculty of Physics (Pasteura 5, Warsaw; room 1.40) we are hosting a seminar during which Dorota Niedzia?ek (Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw & Molecure S.A. Warsaw) will give a talk The rocket science behind enzymatic machinery Abstract The understanding of the catalytic process of a targeted enzyme might be a very important step for successful drug design process. Having an experimentally resolved structure is a must. Yet, it is merely a starting point of the way towards understanding the full picture of the enzyme's mechanism of action. There are several levels of theory we can use for studying an enzymatic machinery. The classical models fail to properly describe catalytic reactions. I would like to show you how we can overcome that limitations by using a combination of polarizable force field models and quantum mechanical calculations. 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 Wed Nov 15 08:05:35 2023 From: Maciej.Lisicki at fuw.edu.pl (Maciej Lisicki) Date: Wed, 15 Nov 2023 07:05:35 +0000 Subject: [Soft-matter] Soft Matter and Complex Systems Seminar on 17 Nov 2023 Message-ID: <4ECE3E5F-1372-4875-A81A-4E8A8CCB1065@fuw.edu.pl> Dear Soft Matter & Complex Systems Colleagues and Friends, On Friday 17 November 2023 at 9:30 AM at the UW Faculty of Physics (Pasteura 5, Warsaw; room 1.40) we are hosting a seminar during which Annemiek Cornellissen and Camille Le Scao (Universit? Paris Cit?) will give a talk Morphogenesis of branching networks in jellyfish and fern leaves Abstract Transport networks in living organisms show a variance of architecture, with either ramified or looped networks. These transport networks develop in parallel with the organisms, arising from local interactions and feedback mechanisms, resulting in self-organizing patterns. In this presentation, we will first introduce general concepts used in morphogenesis, such as noise, instabilities and emergent patterns. We will then focus on the morphogenesis of the gastrovascular network of the jellyfish Aurelia aurita and on the vascular system of leaves. 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 Wed Nov 22 08:40:09 2023 From: Maciej.Lisicki at fuw.edu.pl (Maciej Lisicki) Date: Wed, 22 Nov 2023 02:40:09 -0500 Subject: [Soft-matter] Soft Matter and Complex Systems Seminar on 24 Nov 2023 Message-ID: Dear Soft Matter & Complex Systems Colleagues and Friends, On Friday 24 November 2023 at 9:30 AM at the UW Faculty of Physics (Pasteura 5, Warsaw; room 1.40) we are hosting a seminar during which Daniel W?jcik (Nencki Institute for Experimental Biology, PAS) will give a talk Statistical framework for identification of individual and social aspects of animal learning in intelligent cages Abstract Several recent cage designs support studies of multiple animals housed for weeks with minimal human intervention in a single or multiple compartments where they can interact with cage elements and with each other, and their behavior can be tracked in various ways. Here we focus on Intellicage system where up to 14 female mice housed together can be identified with an RFID transponder interacting with intelligent corners providing reward, and the behavior is described in terms of discrete events. We present a general conceptual, analytical and computational framework for stochastic description, analysis and modeling of data from such cages. This framework combines the theory of point processes (as used in spike train analysis) with reinforcement learning models. We demonstrate how individual and social aspects of learning can be identified within the data, and show different specific approaches which facilitate study of effects of the whole group on an animal or formation of a hierarchy of social effects in group learning. The results of the analysis are validated with equivalent simulated data. To illustrate this conceptual framework and our analytical approach we designed an experimental paradigm where rewards are offered depending on an arbitrary assignment of an animal to one of two groups, ?majority? or ?minority?. The two groups were assigned different locations with reward availability, changing in consecutive phases of the experiment. We show that the data support importance of the social effects in animal learning of the reward and may also be used to identify a social structure within the group. Corresponding generative models can be used for validation of various analytical methods and for prediction of mice behavior. 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 27 11:41:00 2023 From: Maciej.Lisicki at fuw.edu.pl (Maciej Lisicki) Date: Mon, 27 Nov 2023 11:41:00 +0100 Subject: [Soft-matter] Soft Matter & Complex Systems Seminar on 1 Dec 2023 Message-ID: <50B94A1A-F709-431A-B8EB-F86E3723282D@fuw.edu.pl> Dear Soft Matter & Complex Systems Colleagues and Friends, On Friday 1 December 2023 at 9:30 AM at the UW Faculty of Physics (Pasteura 5, Warsaw; room 1.40) we are hosting a seminar during which Bogdan Cichocki & Jeffrey Everts (FUW) will give a talk Chiral active fluids in the creeping flow regime (Part I) Abstract Viscosity is a property that tells us how easy it is to cause flow in a fluid. For incompressible isotropic systems, the most well-known type of viscosity is the shear viscosity, which quantifies how much of the fluid's available energy dissipates when a symmetric velocity gradient is induced into the system. However, the situation differs in so-called chiral active fluids, which are manifestly out-of-equilibrium systems. Here, the fluid particles are set into motion by activity or uniform rotation of the system and are, therefore, characterised by a non-trivial angular momentum density. Consequently, the flow properties of such a fluid are not just described by the shear viscosity. There are additional so-called odd viscosity coefficients that do not contribute to viscous dissipation in a direct manner. Because of the fundamental interest in this problem and recent experiments, we study such chiral active fluids in the creeping flow regime in more detail. In Part 1 of the seminar (1 December), we show that the fundamental solution can be explicitly constructed without any approximation for stationary three-dimensional incompressible flow. Our calculations form the basis for solving more complicated flow problems and for constructing the theory of hydrodynamic interactions in chiral active fluids. In Part 2 of the talk (8 December), we will demonstrate how we can use the Green's function to construct an analytical exact solution for the single-particle problem. Furthermore, we will then explicitly demonstrate that odd viscosity can contribute to viscous dissipation via alteration of the fluid 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: