Literature DB >> 20614962

Steady-state simulations using weighted ensemble path sampling.

Divesh Bhatt1, Bin W Zhang, Daniel M Zuckerman.   

Abstract

We extend the weighted ensemble (WE) path sampling method to perform rigorous statistical sampling for systems at steady state. A straightforward steady-state implementation of WE is directly practical for simple landscapes, but not when significant metastable intermediates states are present. We therefore develop an enhanced WE scheme, building on existing ideas, which accelerates attainment of steady state in complex systems. We apply both WE approaches to several model systems, confirming their correctness and efficiency by comparison with brute-force results. The enhanced version is significantly faster than the brute force and straightforward WE for systems with WE bins that accurately reflect the reaction coordinate(s). The new WE methods can also be applied to equilibrium sampling, since equilibrium is a steady state.

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Year:  2010        PMID: 20614962      PMCID: PMC2912933          DOI: 10.1063/1.3456985

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


  21 in total

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Authors:  Anton K Faradjian; Ron Elber
Journal:  J Chem Phys       Date:  2004-06-15       Impact factor: 3.488

2.  Simulating rare events in equilibrium or nonequilibrium stochastic systems.

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Journal:  J Chem Phys       Date:  2006-01-14       Impact factor: 3.488

3.  Forward flux sampling-type schemes for simulating rare events: efficiency analysis.

Authors:  Rosalind J Allen; Daan Frenkel; Pieter Rein ten Wolde
Journal:  J Chem Phys       Date:  2006-05-21       Impact factor: 3.488

4.  Reaction coordinates and transition pathways of rare events via forward flux sampling.

Authors:  Ernesto E Borrero; Fernando A Escobedo
Journal:  J Chem Phys       Date:  2007-10-28       Impact factor: 3.488

5.  Umbrella sampling for nonequilibrium processes.

Authors:  Aryeh Warmflash; Prabhakar Bhimalapuram; Aaron R Dinner
Journal:  J Chem Phys       Date:  2007-10-21       Impact factor: 3.488

6.  Computing stationary distributions in equilibrium and nonequilibrium systems with forward flux sampling.

Authors:  Chantal Valeriani; Rosalind J Allen; Marco J Morelli; Daan Frenkel; Pieter Rein ten Wolde
Journal:  J Chem Phys       Date:  2007-09-21       Impact factor: 3.488

7.  Minimum free energy pathways and free energy profiles for conformational transitions based on atomistic molecular dynamics simulations.

Authors:  Arjan van der Vaart; Martin Karplus
Journal:  J Chem Phys       Date:  2007-04-28       Impact factor: 3.488

8.  Rapid equilibrium sampling initiated from nonequilibrium data.

Authors:  Xuhui Huang; Gregory R Bowman; Sergio Bacallado; Vijay S Pande
Journal:  Proc Natl Acad Sci U S A       Date:  2009-09-29       Impact factor: 11.205

9.  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

10.  Weighted-ensemble Brownian dynamics simulations for protein association reactions.

Authors:  G A Huber; S Kim
Journal:  Biophys J       Date:  1996-01       Impact factor: 4.033

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  30 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.  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

3.  A comparison of weighted ensemble and Markov state model methodologies.

Authors:  Haoyun Feng; Ronan Costaouec; Eric Darve; Jesús A Izaguirre
Journal:  J Chem Phys       Date:  2015-06-07       Impact factor: 3.488

4.  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

5.  Statistical Uncertainty Analysis for Small-Sample, High Log-Variance Data: Cautions for Bootstrapping and Bayesian Bootstrapping.

Authors:  Barmak Mostofian; Daniel M Zuckerman
Journal:  J Chem Theory Comput       Date:  2019-05-07       Impact factor: 6.006

6.  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

7.  Simulating rare events using a weighted ensemble-based string method.

Authors:  Joshua L Adelman; Michael Grabe
Journal:  J Chem Phys       Date:  2013-01-28       Impact factor: 3.488

Review 8.  Path-sampling strategies for simulating rare events in biomolecular systems.

Authors:  Lillian T Chong; Ali S Saglam; Daniel M Zuckerman
Journal:  Curr Opin Struct Biol       Date:  2016-12-13       Impact factor: 6.809

9.  WESTPA: an interoperable, highly scalable software package for weighted ensemble simulation and analysis.

Authors:  Matthew C Zwier; Joshua L Adelman; Joseph W Kaus; Adam J Pratt; Kim F Wong; Nicholas B Rego; Ernesto Suárez; Steven Lettieri; David W Wang; Michael Grabe; Daniel M Zuckerman; Lillian T Chong
Journal:  J Chem Theory Comput       Date:  2015-02-10       Impact factor: 6.006

10.  Simulating Current-Voltage Relationships for a Narrow Ion Channel Using the Weighted Ensemble Method.

Authors:  Joshua L Adelman; Michael Grabe
Journal:  J Chem Theory Comput       Date:  2015-04-14       Impact factor: 6.006

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