2012/01/18 by Nils B. Becker, Rosalind J. Allen, Pieter Rein ten Wolde · 1 citation
Biochemistry, Genetics and Molecular Biology · Physics and Astronomy · #cond-mat.stat-mech #physics.comp-ph #q-bio.MN
paper · pdf · doi:10.1063/1.4704810
18 pages, 10 figures
arxiv created 2012/01/18 · arxiv updated 2015/06/03
We present a new method, Non-Stationary Forward Flux Sampling, that allows efficient simulation of rare events in both stationary and non-stationary stochastic systems. The method uses stochastic branching and pruning to achieve uniform sampling of trajectories in phase space and time, leading to accurate estimates for time-dependent switching propensities and time-dependent phase space probability densities. The method is suitable for equilibrium or non-equilibrium systems, in or out of stationary state, including non-Markovian or externally driven systems. We demonstrate the validity of the technique by applying it to a one-dimensional barrier crossing problem that can be solved exactly, and show its usefulness by applying it to the time-dependent switching of a genetic toggle switch.