Journal
JOURNAL OF CHEMICAL PHYSICS
Volume 136, Issue 17, Pages -Publisher
AMER INST PHYSICS
DOI: 10.1063/1.4704810
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Funding
- Nederlandse organisatie voor Wetenschappelijk Onderzoek (NWO)
- Royal Society
- EPSRC [EP/I030298/1]
- EPSRC [EP/I030298/1, EP/J007404/1] Funding Source: UKRI
- Engineering and Physical Sciences Research Council [EP/J007404/1, EP/I030298/1] Funding Source: researchfish
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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. (C) 2012 American Institute of Physics. [http://dx.doi.org/10.1063/1.4704810]
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