title: Non-stationary forward flux sampling.
abstract: We present a 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. It 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.
authors.affiliation: FOM Institute for Atomic and Molecular Physics (AMOLF), Science Park 104, 1098 XG Amsterdam, The Netherlands.
authors.forename: Nils B
authors.initials: NB
authors.lastname: Becker
authors.forename: Rosalind J
authors.initials: RJ
authors.lastname: Allen
authors.forename: Pieter Rein
authors.initials: PR
authors.lastname: ten Wolde
mesh_terms: D003198:Computer Simulation; D053263:Gene Regulatory Networks; D008957:Models, Genetic; D015233:Models, Statistical; D009010:Monte Carlo Method; D015203:Reproducibility of Results; D013269:Stochastic Processes; D013816:Thermodynamics