Computing stationary distributions in equilibrium and nonequilibrium systems with forward flux sampling.
We present a method for computing stationary distributions for activated processes in equilibrium and nonequilibrium systems using forward flux sampling. In this method, the stationary distributions are obtained directly from the rate constant calculations for the forward and backward reactions; there is no need to perform separate calculations for the stationary distribution and the rate constant. We apply the method to the nonequilibrium rare event problem proposed by Maier and Stein, to nucleation in a 2-dimensional Ising system, and to the flipping of a genetic switch.
Valeriani
Chantal
C
FOM Institute for Atomic and Molecular Physics, Kruislaan 407, 1098 SJ Amsterdam, The Netherlands. valeriani@amolf.nl
Allen
Rosalind J
RJ
Morelli
Marco J
MJ
Frenkel
Daan
D
Rein ten Wolde
Pieter
P
D002627:Chemistry, Physical / Q000379:methods*; D003198:Computer Simulation; D008957:Models, Genetic; D015233:Models, Statistical; D008962:Models, Theoretical; D009010:Monte Carlo Method; D009068:Movement; D010825:Physics / Q000379:methods; D017510:Protein Folding; D015203:Reproducibility of Results; D013816:Thermodynamics