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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]
|Number of pages||18|
|Journal||The Journal of Chemical Physics|
|Publication status||Published - 7 May 2012|
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- 1 Finished
Design Principles for New Soft Materials
Cates, M., Allen, R., Clegg, P., Evans, M., MacPhee, C., Marenduzzo, D. & Poon, W.
7/12/11 → 6/06/17