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
ABSTRACT
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.
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