Literature DB >> 30736684

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

Alexander M Berezhkovskii1, Attila Szabo2.   

Abstract

Milestoning on a one-dimensional potential starts by choosing a set of points, called milestones, and initiating short trajectories from each milestone, which are terminated when they reach an adjacent milestone for the first time. From the average duration of these trajectories and the probabilities of where they terminate, a rate matrix can be constructed and then used to calculate the mean first-passage time (MFPT) between any two milestones. All these MFPT's turn out to be exact. Here we adopt a point of view from which this remarkable result is not unexpected. In addition, we clarify the nature of the "states" whose interconversion is described by the rate matrix constructed using information obtained from short trajectories and provide a microscopic expression for the "equilibrium population" of these states in terms of equilibrium averages of the committors.

Year:  2019        PMID: 30736684      PMCID: PMC6910584          DOI: 10.1063/1.5079742

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


  14 in total

1.  Transition path sampling: throwing ropes over rough mountain passes, in the dark.

Authors:  Peter G Bolhuis; David Chandler; Christoph Dellago; Phillip L Geissler
Journal:  Annu Rev Phys Chem       Date:  2001-10-04       Impact factor: 12.703

2.  Computing time scales from reaction coordinates by milestoning.

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

3.  From transition paths to transition states and rate coefficients.

Authors:  Gerhard Hummer
Journal:  J Chem Phys       Date:  2004-01-08       Impact factor: 3.488

4.  How the diffusivity profile reduces the arbitrariness of protein folding free energies.

Authors:  M Hinczewski; Y von Hansen; J Dzubiella; R R Netz
Journal:  J Chem Phys       Date:  2010-06-28       Impact factor: 3.488

5.  Coarse master equations for peptide folding dynamics.

Authors:  Nicolae-Viorel Buchete; Gerhard Hummer
Journal:  J Phys Chem B       Date:  2008-01-31       Impact factor: 2.991

6.  Diffusion along the splitting/commitment probability reaction coordinate.

Authors:  Alexander M Berezhkovskii; Attila Szabo
Journal:  J Phys Chem B       Date:  2013-07-03       Impact factor: 2.991

7.  Exact rate calculations by trajectory parallelization and tilting.

Authors:  Eric Vanden-Eijnden; Maddalena Venturoli
Journal:  J Chem Phys       Date:  2009-07-28       Impact factor: 3.488

8.  Exact milestoning.

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

9.  Foundations and latest advances in replica exchange transition interface sampling.

Authors:  Raffaela Cabriolu; Kristin M Skjelbred Refsnes; Peter G Bolhuis; Titus S van Erp
Journal:  J Chem Phys       Date:  2017-10-21       Impact factor: 3.488

10.  On the assumptions underlying milestoning.

Authors:  Eric Vanden-Eijnden; Maddalena Venturoli; Giovanni Ciccotti; Ron Elber
Journal:  J Chem Phys       Date:  2008-11-07       Impact factor: 3.488

View more
  4 in total

1.  Hierarchical Markov State Model Building to Describe Molecular Processes.

Authors:  David K Wolfe; Joseph R Persichetti; Ajeet K Sharma; Phillip S Hudson; H Lee Woodcock; Edward P O'Brien
Journal:  J Chem Theory Comput       Date:  2020-02-17       Impact factor: 6.006

2.  A Companion Guide to the String Method with Swarms of Trajectories: Characterization, Performance, and Pitfalls.

Authors:  Haochuan Chen; Dylan Ogden; Shashank Pant; Wensheng Cai; Emad Tajkhorshid; Mahmoud Moradi; Benoît Roux; Christophe Chipot
Journal:  J Chem Theory Comput       Date:  2022-02-09       Impact factor: 6.006

3.  Diffusive barrier crossing rates from variationally determined eigenvalues.

Authors:  Alexander M Berezhkovskii; Irina V Gopich; Attila Szabo
Journal:  J Chem Phys       Date:  2021-07-21       Impact factor: 4.304

4.  Stochastic Model of Solvent Exchange in the First Coordination Shell of Aqua Ions.

Authors:  Luca Sagresti; Lorenzo Peri; Giacomo Ceccarelli; Giuseppe Brancato
Journal:  J Chem Theory Comput       Date:  2022-04-26       Impact factor: 6.006

  4 in total

北京卡尤迪生物科技股份有限公司 © 2022-2023.