Multiscale Estimation of Binding Kinetics using Molecular Dynamics, Brownian Dynamics, and Markov State Models

Mr. Lane Votapka
Department of Chemistry and Biochemistry
UC San Diego


A challenge for the field of computational biophysics is to develop approaches that bridge across the disparate time and length scales sampled within different simulation regimes. Methods for combining the speed of rigid-body Brownian dynamics (BD) simulations with the precision of all-atom molecular dynamics (MD) simulations using a Markov state model (MSM) attempt to improve estimates of binding kinetics. We seek to use MSMs to alleviate the computational burden imposed by long time processes by partitioning conformational space into manageable pieces, simulating them in parallel, and then combining the resulting statistics using the MSMs to yield meaningful information.