Non-stationary forward flux sampling

The Journal of Chemical Physics
Nils B BeckerPieter Rein ten Wolde

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.

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Citations

Feb 21, 2014·Chemical Communications : Chem Comm·Richard S Graham
May 16, 2012·The Journal of Chemical Physics·Nils B Becker, Pieter Rein ten Wolde
May 3, 2013·The Journal of Chemical Physics·Kai KratzerRosalind J Allen
Sep 11, 2012·The Journal of Chemical Physics·Nathan Eidelson, Baron Peters
Sep 28, 2013·The Journal of Chemical Physics·Rory M DonovanDaniel M Zuckerman
Jul 12, 2012·The Journal of Chemical Physics·Nicholas GuttenbergJonathan Weare
Jun 9, 2014·The Journal of Chemical Physics·Matthew R Perkett, Michael F Hagan
Feb 16, 2016·The Journal of Chemical Physics·Ron Elber
Oct 13, 2014·Journal of Molecular Graphics & Modelling·Alexandra T P CarvalhoShina Caroline Lynn Kamerlin
Aug 9, 2016·The European Physical Journal. E, Soft Matter·S Jungblut, C Dellago
Mar 17, 2017·Annual Review of Biophysics·Daniel M Zuckerman, Lillian T Chong
Nov 16, 2013·Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics·Stephen R Williams
Sep 5, 2019·NPJ Systems Biology and Applications·Helena A HerrmannJean-Marc Schwartz
Feb 18, 2020·The Journal of Chemical Physics·Sarwar Hussain, Amir Haji-Akbari
Jul 17, 2020·The Journal of Chemical Physics·Daniel J Sharpe, David J Wales
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Aug 3, 2017·The Journal of Chemical Physics·Jian ZhuZuowei Wang
Aug 24, 2018·The Journal of Chemical Physics·Amir Haji-Akbari
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Jan 24, 2020·The Journal of Chemical Physics·Max C Klein, Elijah Roberts
Sep 2, 2020·NPJ Systems Biology and Applications·Helena A HerrmannJean-Marc Schwartz
Mar 19, 2013·Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics·Tiago RamalhoTorsten A Ensslin
Aug 4, 2021·The Journal of Chemical Physics·Katarina E BlowGabriele C Sosso

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Methods Mentioned

BETA
protein folding

Software Mentioned

PRES
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WE
NS
PERM
FFS

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