Fifth Biological Diffusion and Brownian Dynamics Brainstorm Meeting March 24-25th, 2021


All times are given in CET. PDT times are given via the link on the time. The link also allows to convert to your local time (https:// Please be aware that daylight saving starts at different dates in different countries.

Please note, talks in session 3 and 4 are swapped compared to a previous version of the schedule.

The given schedule is the final version of the program.

Wednesday 24.03

5:00 pm
Welcome (Prof. Rebecca Wade, Heidelberg Institute for Theoretical Studies, Germany)

Session 1 - Crowding: Diffusion in cells and membranes

Chaired by Prof. Rommie Amaro
5:10 pm
Keynote Speaker:
Prof. Syma Khalid (University of Southampton, United Kingdom)
Molecular choreography within the periplasm of E. coli
Contributed lectures
5:50 pm
CT1: Dr. Debabrata Dey (Weizmann Institute of Science, Israel)
Line-FRAP, a versatile method to measure diffusion rates in vitro and in vivo
6:05 pm
CT2: Dr. Ariane Nunes Alves (Heidelberg Institute for Theoretical Studies, Germany)
Fluorescence recovery curves from Brownian dynamics simulations
6:20 pm
CT3: Dr. Francesco Reina (Leibniz IPHT, Germany)
Comparison between simulation and experimental data to estimate diffusion parameters on living cell membranes
6:35 pm
CT4: Agnes Koerfer (Friedrich-Schiller Univeristät Jena, Germany)
Simulation of Molecular Membrane Diffusion Models for an Understanding of Different Experimental Dynamic Microscopy Data
6:50 pm
15 min break

Session 2 - Advances in Brownian dynamics and motion

Chaired by Dr. Lane Votapka
Contributed lectures
7:05 pm
CT5: Dr. Goutam Mukherjee (Heidelberg Institute for Theoretical Studies, Germany)
How are Electrons Transferred from Cytochrome P450 Reductase to Cytochrome P450 Enzymes? Towards a Structural and Dynamic Understanding
7:20 pm
CT6: Martin Reinhardt (Heidelberg Institute for Theoretical Studies, Germany)
Brownian Dynamics Simulations of Proteins in the Presence of Surfaces
7:35 pm
CT7: Dr. Angélica Sandoval-Pérez (University of California San Francisco, United States)
Double stranded DNA binds to a specific site of the adhesive blood-protein von Willebrand factor guided by electrostatic interactions
7:50 pm
CT8: Dr. Olivier Walker (University of Lyon, France)
Combining NMR and molecular dynamics to explore protein motions
8:05 pm
Keynote Speaker:
Prof. Aleksei Aksimentiev (University of Illinois, USA)
Multi-resolution simulations of biomolecular systems with ARBD
8:45 pm
9:00 pm
End of day 1

Thursday 25.03

5:00 pm
Welcome (NN)

Session 3 - Binding and aggregation of proteins and lipids

Chaired by Dr. Ariane Nunes Alves
5:05 pm
Keynote Speaker:
Prof Gerhard Hummer (Max Planck Institute for Biophysics, Frankfurt, Germany)
Diffusion in membranes and dense protein solutions
Contributed lectures
5:45 pm
CT13: Vijay Phanindra Srikanth Kompella (Curtin University, Australia)
Characterization of slow and sub-diffusive behaviour in crowded protein solutions and discerning the underlying causal relations
6:00 pm
CT14: Dr. Ioana M. Ilie (University of Zurich, Switzerland)
Simulating Biological Complexity beyond the spherical cow
6:15 pm
CT15: Matheus Ferraz (Federal University of Pernambuco/Aggeu Magalhaes Institute, Brazil)
Insights into the binding mechanism reveal the molecular selectivity of VHH-72 against SARS-CoV-1 but not for SARS-CoV-2 RBD
6:30 pm
CT16: Dr. Xavier Prasanna Anthony Raj (University of Helsinki, Finland)
Role of seipin in early stages of lipid droplet biogenesis
6:45 pm
15 min break

Session 4 - Kinetics of protein-ligand binding

Chaired by Prof. Rebecca Wade
Contributed lectures
7:00 pm
CT9: Dr. Lane Votapka (University of California San Diego, United States)
Expanding the Capabilities and Usability of SEEKR to Estimate the Kinetics of Molecular Processes
7:15 pm
CT10: Dr. Steffen Wolf (University of Freiburg, Germany)
Coarse-graining Hamiltonian dynamics into free energies and friction profiles for the acceleration of the prediction of dynamics MD simulations
7:30 pm
CT11: Abraham Muñiz Chicharro (Heidelberg Institute for Theoretical Studies, Germany)
A multiscale approach to compute conformation-gated ligand-receptor binding kinetics
7:45 pm
CT12: Dr. Mauricio del Razo Sarmina (University of Amsterdam, Netherlands)
Molecular kinetics as hybrid switching diffusions: a general framework for MSM/RD simulation
8:00 pm
Keynote Speaker:
Prof. Roseanna Zia (Stanford University, USA)
Physical transport modulates protein synthesis rates and can explain increasing ribosome productivity as growth quickens
8:40 pm
Final discussion
9:00 pm
End of conference

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