title: Markov state modeling and dynamical coarse-graining via discrete relaxation path sampling.
abstract: A method is derived to coarse-grain the dynamics of complex molecular systems to a Markov jump process (MJP) describing how the system jumps between cells that fully partition its state space. The main inputs are relaxation times for each pair of cells, which are shown to be robust with respect to positioning of the cell boundaries. These relaxation times can be calculated via molecular dynamics simulations performed in each cell separately and are used in an efficient estimator for the rate matrix of the MJP. The method is illustrated through applications to Sinai billiards and a cluster of Lennard-Jones discs.
authors.affiliation: Department of Chemistry, University of Cambridge, Lensfield Road, CB2 1EW Cambridge, United Kingdom.
authors.forename: B
authors.initials: B
authors.lastname: Fačkovec
authors.affiliation: Courant Institute, New York University, 251 Mercer Street, New York, New York 10012, USA.
authors.forename: E
authors.initials: E
authors.lastname: Vanden-Eijnden
authors.affiliation: Department of Chemistry, University of Cambridge, Lensfield Road, CB2 1EW Cambridge, United Kingdom.
authors.forename: D J
authors.initials: DJ
authors.lastname: Wales
mesh_terms: D000465:Algorithms; D017276:Friction; D046911:Macromolecular Substances / Q000737:chemistry*; D008390:Markov Chains; D056004:Molecular Dynamics Simulation; D009010:Monte Carlo Method; D059010:Single-Cell Analysis
chemical_list: D046911:Macromolecular Substances