From Maciej.Lisicki at fuw.edu.pl Mon Mar 4 19:49:02 2024 From: Maciej.Lisicki at fuw.edu.pl (Maciej Lisicki) Date: Mon, 4 Mar 2024 12:49:02 -0600 Subject: [Soft-matter] Soft Matter and Complex Systems Seminar on 8 March 2024 Message-ID: <9C32AD74-1C34-4440-B612-0E97B4E2A7F3@fuw.edu.pl> Dear Soft Matter & Complex Systems Colleagues and Friends, On Friday 8 March 2024 at 9:30 AM at the UW Faculty of Physics (Pasteura 5, Warsaw; room 1.40) we are hosting a seminar during which Piotr Bogus?aw Mucha (Faculty of Mathematics, Informatics, and Mechanics, University of Warsaw) who will give a talk Bridging the Micro to Macro: Exploring Agent Dynamics from Communication to Hydrodynamical Limits Abstract This talk presents a simplified approach to modeling the dynamic behavior of agents or particles across various scales. Beginning at the particle (micro) level, we employ kinetic formulations to transition towards hydrodynamical equations. Central to our investigation are Cucker-Smale models, initially developed to simulate the collective motion of fish and birds. By examining the impact of singular communication, we illustrate how these models yield Navier-Stokes type systems, shedding light on the intricate relationship between agent interactions and fluid dynamics. 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 Tue Mar 12 18:57:32 2024 From: Maciej.Lisicki at fuw.edu.pl (Maciej Lisicki) Date: Tue, 12 Mar 2024 12:57:32 -0500 Subject: [Soft-matter] Soft Matter & Complex Systems Seminar on 15 Mar 2024 Message-ID: Dear Soft Matter & Complex Systems Colleagues and Friends, On Friday 15 March 2024 at 9:30 AM at the UW Faculty of Physics (Pasteura 5, Warsaw; room 1.40) we are hosting a seminar during which Mateusz Sikora (Malopolska Centre of Biotechnology, Krakow, Poland & Max Planck Institute of Biophysics, Frankfurt, Germany) will give a talk Integrative modeling of glycoproteins, lessons from the pandemic Abstract Glycans, complex sugars covalently attached to proteins, affect protein stability and function, participate in ?self? recognition, and modulate protein-protein interactions. The glycosylation machinery is frequently hijacked by pathogens, which hide their proteins behind a ?glycan shield?, making them inaccessible to the immune system and complicating pharmacological interventions. Unlike many biomolecules, glycans do not typically form secondary structures and remain highly mobile, posing a challenge for traditional structural biology techniques. In our research, we combined molecular dynamics simulations with cryo-electron tomography and atomic force microscopy to understand how glycans affect viral fusion proteins, particularly the SARS-CoV-2 spike protein. We discovered a surprising flexibility of the spike protein [1,2] and predicted new antibody binding sites accessible through the dynamic glycan shield [3], which can aid in designing novel vaccines. Additionally, we developed a simplified, open-source method for rapidly predicting glycan shielding with minimal computing power. This method has been applied to refine existing cryo-EM maps of glycoproteins [4]. 1. B Turo?ov?, M Sikora, C Sch?rmann, WJH Hagen, S Welsch et al., In situ structural analysis of SARS-CoV-2 spike reveals flexibility mediated by three hinges. Science, 370(6513) 2020 2. R Zhu, D Canena, M Sikora, M Klausberger, H Seferovic, et al., Force-tuned avidity of spike variant-ACE2 interactions viewed on the single-molecule level; Nat Comm, 13(7926) 2022 3. M Sikora, S von B?low, FEC Blanc, M Gecht, R Covino, G Hummer. Computational epitope map of SARS-CoV-2 spike protein. PLoS computational biology, 17(4) 2021 4. Y-X Tsai, N-E Chang, K Reuter, H-T Chang, T-J Yang et al., Rapid simulation of glycoprotein structures by grafting and steric exclusion of glycan conformer libraries. Biorxiv 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 Tue Mar 19 18:59:06 2024 From: Maciej.Lisicki at fuw.edu.pl (Maciej Lisicki) Date: Tue, 19 Mar 2024 13:59:06 -0400 Subject: [Soft-matter] Soft Matter & Complex Systems Seminar on 22 Mar 2024 Message-ID: Dear Soft Matter & Complex Systems Colleagues and Friends, On Friday 22 March 2024 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 (FUW) will give a talk Microscopic time-reversal symmetry versus macroscopic laws 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: