SMBP Group Meeting: David Silva Sanchez

Tuesday Jul 9, 2024, 2:00 PM → 3:00 PM America/New_York

3rd Floor Classroom (162 Fifth Avenue )

Speaker: David Silva Sanchez 

Topic: Technical details of the development of computational methods that combine Molecular Dynamics and Experimental Data

Abstract: In this talk, I will share my experience developing methods that use experimental data to bias molecular dynamics simulations. In particular, I will talk about methods related to solving heterogeneity in Cryo-Electron Microscopy. For the first half of the talk, I will start by giving a brief introduction to existing methods, and something I have been developing for the last year. In the second half, I will talk about the difficulties I have found while developing these methods: What are the downsides of using MD engines such as GROMACS or OpenMM? What are the main bottlenecks? Is there any way to alleviate the cost of comparing simulated structures to experimental data? To finish, I would like to have an open discussion on Coarse-Grained Molecular Dynamics, and how it might affect the user retention of the developed application.