Literature DB >> 15268572

Rate constants for diffusive processes by partial path sampling.

Daniele Moroni1, Peter G Bolhuis, Titus S van Erp.   

Abstract

We introduce a path sampling method for the computation of rate constants for complex systems with a highly diffusive character. Based on the recently developed transition interface sampling (TIS) algorithm this procedure increases the efficiency by sampling only parts of complete transition trajectories. The algorithm assumes the loss of memory for diffusive progression along the reaction coordinate. We compare the new partial path technique to the TIS method for a simple diatomic system and show that the computational effort of the new method scales linearly, instead of quadratically, with the width of the diffusive barrier. The validity of the memory loss assumption is also discussed. Copyright 2004 American Institute of Physics

Entities:  

Year:  2004        PMID: 15268572     DOI: 10.1063/1.1644537

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


  28 in total

1.  Markov state modeling and dynamical coarse-graining via discrete relaxation path sampling.

Authors:  B Fačkovec; E Vanden-Eijnden; D J Wales
Journal:  J Chem Phys       Date:  2015-07-28       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.  Kinetic pathways of beta-hairpin (un)folding in explicit solvent.

Authors:  Peter G Bolhuis
Journal:  Biophys J       Date:  2004-10-29       Impact factor: 4.033

4.  Reaction coordinates for the flipping of genetic switches.

Authors:  Marco J Morelli; Sorin Tanase-Nicola; Rosalind J Allen; Pieter Rein ten Wolde
Journal:  Biophys J       Date:  2008-01-25       Impact factor: 4.033

5.  An experimentally guided umbrella sampling protocol for biomolecules.

Authors:  Maria Mills; Ioan Andricioaei
Journal:  J Chem Phys       Date:  2008-09-21       Impact factor: 3.488

6.  Building Markov state models along pathways to determine free energies and rates of transitions.

Authors:  Albert C Pan; Benoît Roux
Journal:  J Chem Phys       Date:  2008-08-14       Impact factor: 3.488

7.  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

8.  Exact milestoning.

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

9.  On approximating a weak Markovian process as Markovian: Are we justified when discarding longtime correlations.

Authors:  Kai-Yang Leong; Feng Wang
Journal:  J Chem Phys       Date:  2019-02-28       Impact factor: 3.488

10.  ScMile: A Script to Investigate Kinetics with Short Time Molecular Dynamics Trajectories and the Milestoning Theory.

Authors:  Wei Wei; Ron Elber
Journal:  J Chem Theory Comput       Date:  2020-01-30       Impact factor: 6.006

View more

北京卡尤迪生物科技股份有限公司 © 2022-2023.