Literature DB >> 19655850

Exact rate calculations by trajectory parallelization and tilting.

Eric Vanden-Eijnden1, Maddalena Venturoli.   

Abstract

A sampling procedure to compute exactly the rate of activated processes arising in systems at equilibrium or nonequilibrium steady state is presented. The procedure is a generalization of the method proposed in [A. Warmflash et al., J. Chem. Phys. 127, 154112 (2007); A. Dickson et al., J. Chem. Phys. 130, 074104 (2009)] in which one performs simulations restricted into cells by using a reinjection rule at the boundaries of the cells which is consistent with the exact probability fluxes through these boundaries. Our generalization uses results from transition path theory which indicate how to tilt the dynamics to calculate reaction rates.

Year:  2009        PMID: 19655850     DOI: 10.1063/1.3180821

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


  28 in total

1.  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

2.  Perspective: Computer simulations of long time dynamics.

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

3.  Kinetics of O2 Entry and Exit in Monomeric Sarcosine Oxidase via Markovian Milestoning Molecular Dynamics.

Authors:  Anthony Bucci; Tang-Qing Yu; Eric Vanden-Eijnden; Cameron F Abrams
Journal:  J Chem Theory Comput       Date:  2016-05-19       Impact factor: 6.006

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.  Exact milestoning.

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

6.  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

7.  Committors, first-passage times, fluxes, Markov states, milestones, and all that.

Authors:  Alexander M Berezhkovskii; Attila Szabo
Journal:  J Chem Phys       Date:  2019-02-07       Impact factor: 3.488

8.  Multiple Ligand Unbinding Pathways and Ligand-Induced Destabilization Revealed by WExplore.

Authors:  Alex Dickson; Samuel D Lotz
Journal:  Biophys J       Date:  2017-02-28       Impact factor: 4.033

9.  Predicting ligand binding affinity using on- and off-rates for the SAMPL6 SAMPLing challenge.

Authors:  Tom Dixon; Samuel D Lotz; Alex Dickson
Journal:  J Comput Aided Mol Des       Date:  2018-08-23       Impact factor: 3.686

10.  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

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