<html><head><meta http-equiv="Content-Type" content="text/html; charset=utf-8"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class=""><div class="" style="font-family: HelveticaNeue;"><span class="">Dear Soft Matter & Complex Systems Colleagues and Friends,</span></div><div class="" style="font-family: HelveticaNeue;"><span class=""><br class=""></span></div><div class=""><div class="" style="font-family: HelveticaNeue;">On Friday 26 May 2023 at 9:30 AM at the UW Faculty of Physics (Pasteura 5, Warsaw; room 1.40) we are hosting a seminar during which</div><div class="" style="font-family: HelveticaNeue; margin: 0px; font-stretch: normal; line-height: normal; min-height: 14px;"><font face="HelveticaNeue" class=""><br class=""></font></div><div class="" style="font-family: HelveticaNeue; margin: 0px; font-stretch: normal; line-height: normal;"><font face="HelveticaNeue" class=""><b class="">Paweł Krupa </b>(IF PAN)</font></div><div class="" style="font-family: HelveticaNeue; margin: 0px; font-stretch: normal; line-height: normal; min-height: 14px;"><font face="HelveticaNeue" class=""><br class=""></font></div><div class="" style="font-family: HelveticaNeue; margin: 0px; font-stretch: normal; line-height: normal;"><font face="HelveticaNeue" class="">will give a talk</font></div><div class="" style="font-family: HelveticaNeue; margin: 0px; font-stretch: normal; line-height: normal; min-height: 14px;"><font face="HelveticaNeue" class=""><br class=""></font></div><div class="" style="font-family: HelveticaNeue; margin: 0px; font-stretch: normal; line-height: normal;"><div class="" style="margin: 0px; font-stretch: normal; line-height: normal;"><div class="" style="margin: 0px; font-stretch: normal; line-height: normal;"><b class="">Molecular dynamics simulations to understand biological systems</b></div><div class=""><br class=""></div></div></div><div class="" style="font-family: HelveticaNeue; margin: 0px; font-stretch: normal; line-height: normal;"><b class="">Abstract</b></div><div class="" style="margin: 0px; font-stretch: normal; line-height: normal;"><div class="" style="margin: 0px; font-stretch: normal; line-height: normal;"><font face="HelveticaNeue" class="">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. </font></div><div class="" style="margin: 0px; font-stretch: normal; line-height: normal;"><font face="HelveticaNeue" class="">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]</font></div><div class="" style="margin: 0px; font-stretch: normal; line-height: normal;"><font face="HelveticaNeue" class=""><br class=""></font></div><div class="" style="margin: 0px; font-stretch: normal; line-height: normal;"><font face="HelveticaNeue" class="">References:</font></div><div class="" style="margin: 0px; font-stretch: normal; line-height: normal;"><font face="HelveticaNeue" class="">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.</font></div><div class="" style="margin: 0px; font-stretch: normal; line-height: normal;"><font face="HelveticaNeue" class="">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).</font></div><div class="" style="margin: 0px; font-stretch: normal; line-height: normal;"><font face="HelveticaNeue" class="">3. Gupta, A. et al. Unusual Robustness of Neurotransmitter Vesicle Membranes against Serotonin-Induced Perturbations. J. Phys. Chem. B 127, 1947–1955 (2023).</font></div><div class="" style="margin: 0px; font-stretch: normal; line-height: normal;"><font face="HelveticaNeue" class="">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).</font></div><div class="" style="margin: 0px; font-stretch: normal; line-height: normal;"><font face="HelveticaNeue" class="">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).</font></div></div><div class="" style="font-family: HelveticaNeue; margin: 0px; font-stretch: normal; line-height: normal;"><div class="" style="margin: 0cm; background-color: white;"><div class="" style="margin: 0px; font-stretch: normal; line-height: normal;"><br class=""></div></div></div><div class="" style="font-family: HelveticaNeue; margin: 0px; font-stretch: normal; line-height: normal;">We warmly welcome everyone to attend the talk and the Soft Matter Coffee Break after the seminar, held in room 2.63 (2nd floor).</div></div><div class="" style="font-family: HelveticaNeue;"><br class=""></div><div class="" style="font-family: HelveticaNeue;"><div dir="auto" class="" style="word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;"><div class=""><div class="" style="margin: 0px; font-stretch: normal; line-height: normal;"><font face="HelveticaNeue" class="">Maria Ekiel-Jeżewska</font></div><div class="" style="margin: 0px; font-stretch: normal; line-height: normal;"><font face="HelveticaNeue" class="">Maciej Lisicki</font></div><div class="" style="margin: 0px; font-stretch: normal; line-height: normal;"><font face="HelveticaNeue" class="">Piotr Szymczak</font></div><div class="" style="margin: 0px; font-stretch: normal; line-height: normal;"><font face="HelveticaNeue" class="">Panagiotis Theodorakis</font></div><div class="" style="margin: 0px; font-stretch: normal; line-height: normal;"><font face="HelveticaNeue" class="">Marek Trippenbach</font></div></div></div></div><div class=""><div dir="auto" style="caret-color: rgb(0, 0, 0); color: rgb(0, 0, 0); letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none; word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class=""><div dir="auto" style="caret-color: rgb(0, 0, 0); color: rgb(0, 0, 0); letter-spacing: normal; text-align: start; 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