Literature DB >> 17949137

Umbrella sampling for nonequilibrium processes.

Aryeh Warmflash1, Prabhakar Bhimalapuram, Aaron R Dinner.   

Abstract

The authors introduce an algorithm for determining the steady-state probability distribution of an ergodic system arbitrarily far from equilibrium. By enforcing equal sampling of different regions of phase space, as in umbrella sampling simulations of systems at equilibrium, low probability regions are explored to a much greater extent than in physically weighted simulations. The algorithm can be used to accumulate joint statistics for an arbitrary number of order parameters for a system governed by any stochastic dynamics. They demonstrate the efficiency of the algorithm by applying it to a model of a genetic toggle switch which evolves irreversibly according to a continuous time Monte Carlo procedure.

Year:  2007        PMID: 17949137     DOI: 10.1063/1.2784118

Source DB:  PubMed          Journal:  J Chem Phys        ISSN: 0021-9606            Impact factor:   3.488


  33 in total

1.  Simulations of the alternating access mechanism of the sodium symporter Mhp1.

Authors:  Joshua L Adelman; Amy L Dale; Matthew C Zwier; Divesh Bhatt; Lillian T Chong; Daniel M Zuckerman; Michael Grabe
Journal:  Biophys J       Date:  2011-11-15       Impact factor: 4.033

2.  Steady-state simulations using weighted ensemble path sampling.

Authors:  Divesh Bhatt; Bin W Zhang; Daniel M Zuckerman
Journal:  J Chem Phys       Date:  2010-07-07       Impact factor: 3.488

3.  Perspective: Computer simulations of long time dynamics.

Authors:  Ron Elber
Journal:  J Chem Phys       Date:  2016-02-14       Impact factor: 3.488

4.  Efficient stochastic simulation of chemical kinetics networks using a weighted ensemble of trajectories.

Authors:  Rory M Donovan; Andrew J Sedgewick; James R Faeder; Daniel M Zuckerman
Journal:  J Chem Phys       Date:  2013-09-21       Impact factor: 3.488

5.  The "weighted ensemble" path sampling method is statistically exact for a broad class of stochastic processes and binning procedures.

Authors:  Bin W Zhang; David Jasnow; Daniel M Zuckerman
Journal:  J Chem Phys       Date:  2010-02-07       Impact factor: 3.488

6.  Estimating first-passage time distributions from weighted ensemble simulations and non-Markovian analyses.

Authors:  Ernesto Suárez; Adam J Pratt; Lillian T Chong; Daniel M Zuckerman
Journal:  Protein Sci       Date:  2015-09-09       Impact factor: 6.725

7.  Exact milestoning.

Authors:  Juan M Bello-Rivas; Ron Elber
Journal:  J Chem Phys       Date:  2015-03-07       Impact factor: 3.488

8.  Galerkin approximation of dynamical quantities using trajectory data.

Authors:  Erik H Thiede; Dimitrios Giannakis; Aaron R Dinner; Jonathan Weare
Journal:  J Chem Phys       Date:  2019-06-28       Impact factor: 3.488

9.  An adaptive weighted ensemble procedure for efficient computation of free energies and first passage rates.

Authors:  Divesh Bhatt; Ivet Bahar
Journal:  J Chem Phys       Date:  2012-09-14       Impact factor: 3.488

10.  Coupled folding and binding with 2D Window-Exchange Umbrella Sampling.

Authors:  Alex Dickson; Logan S Ahlstrom; Charles L Brooks
Journal:  J Comput Chem       Date:  2015-08-06       Impact factor: 3.376

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