Program, Workshop in Hünfeld, April 3‐4, 2020 “COMPUTER SIMULATION AND THEORY OF MACROMOLECULES”

Friday, April 03, 2020

11:00 – 13:00 Arrival, registration and lunch

13:00 – 13:05 Welcome Maiia Shulman ( University / Center for Protein Diagnostics) 13:05 – 13:30 Facilitation of Protein Design for Optogenetic Applications by Computer‐aided Protein Modeling and Theoretical UV/VIS Spectroscopy Natalia Ostrowska (University of Warsaw) 13:30 – 13:55 Reduced Spherical Crowders for Explicit Water Simulations and Where to Find Them Marvin Scherlo ( / Center for Protein Diagnostics) 13:55 – 14:20 The Ras Dimer Interface Identified by Protein Docking, MD Simulations and FRET Experiments Laura Schulz (Max‐Planck‐Institute of Biophysics, Frankfurt) 14:20 – 14:45 Sampling of Ligand‐Induced Conformational Changes in Renin and Factor VIIa Andrea Vaiana (Max Planck Institute for Biophysical , Göttingen) 14:45 – 15:10 Automated Cryo‐EM Structure Refinement using Correlation‐driven Molecular Dynamics

15:10 – 15:25 Coffee break

Daniel Mann (Research Center Jülich) 15:25 – 15:50 Maintenance of Lipid Asymmetry in Gram‐Negative Bacteria Camilo Aponte‐Santamaría (University of Los Andes, Bogotá) 15:50 – 16:15 Localization of Cholesterol Around the Metabotropic Glutamate Receptor 2 Anna Kahler (Friedrich Alexander University of Erlangen‐Nuremberg) 16:15 – 16:40 Intrinsic Flexibility and Structural Stability of Proteins Patrick Quoika (University of Innsbruck) 16:40 – 17:05 Computational Approaches towards Explaining the Thermodynamics of the Coil‐Globule Transition of N‐(Isopropylacrylamide) Yani Zhao (Max Planck Institute for Polymer Research, Mainz) 17:05 – 17:30 Why Do Elastin‐Like Polypeptides Have Different Solvation Behaviors in Water‐Ethanol and ‐Urea Mixtures? Michaela Černeková (University of Chemistry and Technology, Prague) 17:30 – 17:55 Computational Analysis of Proteins Intervening Ribosome Exit Tunnel

18:00 – 19:00 Dinner

19:30 – Poster Session / Beer

Program, Workshop in Hünfeld, April 3‐4, 2020 “COMPUTER SIMULATION AND THEORY OF MACROMOLECULES”

Saturday, April 4, 2020

8:00 – 8:50 Breakfast

Gerhard Hummer (Max Planck Institute for Biophysics, Frankfurt) 8:55 – 9:35 What's Wrong with Diffusion? Benjamin Lickert (Albert‐Ludwigs‐University Freiburg) 9:35 – 10:00 Langevin Modeling of Multisecond Dynamics Based on Atomistic Simulations Alessio Lapolla (Max Planck Institute for Biophysical Chemistry, Göttingen) 10:00 – 10:25 Fingerprints of Non‐Markovian Dynamics in Free Energy Landscapes

10:25 – 10:45 Coffee break

Martin Reinhardt (Max Planck Institute for Biophysical Chemistry, Göttingen) 10:45 – 11:10 Determining Free Energy Differences Through Variational Morphing Sebastian Wingbermuehle (Ruhr University Bochum) 11:10 – 11:35 Capturing the Flexibility of a Protein‐Ligand Complex with Enhanced Sampling Techniques: Binding Free Energies from Umbrella Sampling, REST2, and Bias Exchange Martin Werner (Max Planck Institute for Biophysical Chemistry, Göttingen) 11:35 – 12:00 Triangular Coupling of Correlated Amino Acid Mutations

12:00 – 13:00 Lunch Philipp Althoff (Ruhr University Bochum / Center for Protein Diagnostics) 13:00 – 13:25 Tracing Water Molecule Migration and Gating Mechanisms of Light‐activated Channel Proteins by Extracting Contact Patterns from MD Trajectories Ruo‐Xu Gu (Max Planck Institute for Biophysical Chemistry, Göttingen) 13:25 – 13:50 Lipid‐Protein Interactions Modulate the Conformatioal Equilibrium of a Potassium Channel Andrei Kostritskii (Research Center Jülich) 13:50 – 14:15 Ion Conduction by TMEM16 Lipid Scramblases: Insights from MD Simulations David Bickel (Heinrich Heine University Düsseldorf) 14:15 – 14:40 Potential of Mean Force Calculations on the Permeation of the Inner Mitochondrial Membrane by Phomoxanthone A Species Leonie Chatzimagas ( University, Saarbrücken) 14:40 – 15:05 Simulations of Liquid Jet Explosion and Shock Waves Induced by X‐Ray Free‐Electron Lasers 15:05 – 15:20 Coffee break Robert Becker (University of Saarland, Saarbrücken) 15:20 – 15:45 Collective Motions of RNA Helicases Involved in RNA Translocation Qiang Zhang (Karlsruhe Institute of Technology) 15:45 – 16:10 Investigation on the Growth Mechanism of HKUST‐1 via Simulation Mariana Kozlowska (Karlsruhe Institute of Technology) 16:10 – 16:35 Functionality of Chemically Modified Chitosans from Molecular Dynamics Simulations Sergio Cruz‐Leon (Max Planck Institute of Biophysics, Frankfurt) 16:35 – 17:00 Helical Twist of dsDNA Depends on Cation Type and Concentration

17:00 – 17:30 Poster prize, final remarks

18:00 Dinner / Departure