Computing stationary distributions in equilibrium and non-equilibrium systems with Forward Flux Sampling

Abstract

We present a method for computing stationary distributions for activated processes in equilibrium and non-equilibrium systems using Forward Flux Sampling (FFS). 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 non-equilibrium rare event problem proposed by Maier and Stein, to nucleation in a 2-dimensional Ising system, and to the flipping of a genetic switch.

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Cited by in corpus (34)

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• Automatic, optimized interface placement in forward flux sampling simulations
• Importance sampling large deviations in nonequilibrium steady states. I
• Forward-Flux Sampling with Jumpy Order Parameters
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• Reaction coordinates for the flipping of genetic switches
• Analytic methods for modeling stochastic regulatory networks
• Crystallization of hard spheres revisited. II. Thermodynamic modeling, nucleation work, and the surface of tension
• Eliminating fast reactions in stochastic simulations of biochemical networks: a bistable genetic switch
• Variational control forces for enhanced sampling of nonequilibrium molecular dynamics simulations
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• Transition path sampling algorithm for discrete many-body systems
• The barrier to ice nucleation in monatomic water
• Crystallization of hard spheres revisited. I. Extracting kinetics and free energy landscape from forward flux sampling
• Optimal modularity for nucleation in network-organized Ising model
• Folding Kinetics of a Polymer
• The Barrier Method: A Technique for Calculating Very Long Transition Times
• Computation of nucleation of a non-equilibrium first-order phase transition using a rare-event algorithm
• Variational deep learning of equilibrium transition path ensembles
• Numerical calculation of free-energy barriers for entangled polymer nucleation
• Weighted-ensemble Brownian dynamics simulation: Sampling of rare events in non-equilibrium systems
• Nucleation in scale-free networks
• Estimating time-correlation functions by sampling and unbiasing dynamically activated events
• Trajectory reweighting for non-equilibrium steady states
• Nucleation pathways on complex networks
• Heterogeneous nucleation on complex networks with mobile impurities
• Kinetic reconstruction of free energies as a function of multiple order parameters
• Noise induces rare events in granular media