Building Markov state models using optimal transport theory
Year: 2019
Type: article
Abstract: Markov State Models (MSMs) describe the rates and routes in conformational dynamics of biomolecules. Computational estimation of MSMs can be expensive because molecular simulations are slow to find and sample the rare transient events. We describe here an efficient approximate way to determine MSM rate matrices by combining maximum caliber (maximizing path entropies) with optimal transport theory (minimizing some path cost function, as when routing trucks on transportation networks) to patch together transient dynamical information from multiple non-equilibrium simulations. We give toy examples.
Source: The Journal of Chemical Physics
DOI: 10.1063/1.5086681
Authors: Purushottam D. Dixit, Ken A. Dill
Institutions: Columbia University, Stony Brook University
Language: English
Subfield: Molecular Biology
Domain: Life Sciences
Open Access status: green
Funder: National Science Foundation
OpenAlex ID: W2913155865