Year: 2024
Type: article
Abstract: Many chemical reactions and molecular processes occur on time scales that are significantly longer than those accessible by direct simulations. One successful approach to estimating dynamical statistics for such processes is to use many short time series of observations of the system to construct a Markov state model, which approximates the dynamics of the system as memoryless transitions between a set of discrete states. The dynamical Galerkin approximation (DGA) is a closely related framework for estimating dynamical statistics, such as committors and mean first passage times, by approximating solutions to their equations with a projection onto a basis. Because the projected dynamics are generally not memoryless, the Markov approximation can result in significant systematic errors. Inspired by quasi-Markov state models, which employ the generalized master equation to encode memory resulting from the projection, we reformulate DGA to account for memory and analyze its performance on two systems: a two-dimensional triple well and the AIB9 peptide. We demonstrate that our method is robust to the choice of basis and can decrease the time series length required to obtain accurate kinetics by an order of magnitude.
Source: The Journal of Chemical Physics
DOI: 10.1063/5.0187145
Language: English
Subfield: Statistical and Nonlinear Physics
Field: Physics and Astronomy
Domain: Physical Sciences
Open Access status: green
Awards: G2589448798, DMS/NIGMS 1: Design and Analysis of Machine Learning Approaches for Long Timescale Prediction from Short Trajectory Data, Rare-event simulation and analysis for elucidating mechanisms of development and disease, Graduate Research Fellowship Program (GRFP), Beagle-3: A Shared GPU Cluster for Biomolecular Sciences
OpenAlex ID: W4392103594