2014/02/14 by Purushottam D. Dixit, Dixit, Purushottam D., Ken A. Dill +1
Biochemistry, Genetics and Molecular Biology · Neuroscience · Physics and Astronomy · #Diffusion and Search Dynamics #FOS: Physical sciences #Gene Regulatory Network Analysis #Neural dynamics and brain function #Soft Condensed Matter (cond-mat.soft) #Statistical Mechanics (cond-mat.stat-mech) #cond-mat.soft #cond-mat.stat-mech
paper · pdf · doi:10.48550/arxiv.1402.3340
arxiv created 2014/02/14 · openalex publication_date 2014/02/14 · arxiv updated 2014/02/17 · openalex created_date 2025/10/10 · openalex updated_date 2026/07/28
We present a principled approach for estimating the matrix of microscopic rates among states of a Markov process, given only its stationary state population distribution and a single average global kinetic observable. We adapt Maximum Caliber, a variational principle in which a path entropy is maximized over the distribution of all the possible trajectories, subject to basic kinetic constraints and some average dynamical observables. We show that this approach leads, under appropriate conditions, to the continuous-time master equation and a Smoluchowski-like equation that is valid for both equilibrium and non-equilibrium stationary states. We illustrate the method by computing the solvation dynamics of water molecules from molecular dynamics trajectories.