Literature DB >> 17328617

Transition-event durations in one-dimensional activated processes.

Bin W Zhang1, David Jasnow, Daniel M Zuckerman.   

Abstract

Despite their importance in activated processes, transition-event durations--which are much shorter than first passage times--have not received a complete theoretical treatment. The authors therefore study the distribution rhob(t) of durations of transition events over a barrier in a one-dimensional system undergoing overdamped Langevin dynamics. The authors show that rhob(t) is determined by a Fokker-Planck equation with absorbing boundary conditions and obtain a number of results, including (i) the analytic form of the asymptotic short-time transient behavior, which is universal and independent of the potential function; (ii) the first nonuniversal correction to the short-time behavior leading to an estimate of a key physical time scale; (iii) following previous work, a recursive formulation for calculating, exactly, all moments of rhob based solely on the potential function-along with approximations for the distribution based on a small number of moments; and (iv) a high-barrier approximation to the long-time (t-->infinity) behavior of rhob(t). The authors also find that the mean event duration does not depend simply on the barrier-top frequency (curvature) but is sensitive to details of the potential. All of the analytic results are confirmed by transition-path-sampling simulations implemented in a novel way. Finally, the authors discuss which aspects of the duration distribution are expected to be general for more complex systems.

Entities:  

Mesh:

Year:  2007        PMID: 17328617     DOI: 10.1063/1.2434966

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


  30 in total

1.  Tabulation as a high-resolution alternative to coarse-graining protein interactions: Initial application to virus capsid subunits.

Authors:  Justin Spiriti; Daniel M Zuckerman
Journal:  J Chem Phys       Date:  2015-12-28       Impact factor: 3.488

2.  Disordered proteins follow diverse transition paths as they fold and bind to a partner.

Authors:  Jae-Yeol Kim; Hoi Sung Chung
Journal:  Science       Date:  2020-06-12       Impact factor: 47.728

3.  Efficient and verified simulation of a path ensemble for conformational change in a united-residue model of calmodulin.

Authors:  Bin W Zhang; David Jasnow; Daniel M Zuckerman
Journal:  Proc Natl Acad Sci U S A       Date:  2007-11-01       Impact factor: 11.205

4.  A dynamic view of enzyme catalysis.

Authors:  Aurora Jiménez; Pere Clapés; Ramon Crehuet
Journal:  J Mol Model       Date:  2008-03-06       Impact factor: 1.810

5.  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

Review 6.  Protein folding transition path times from single molecule FRET.

Authors:  Hoi Sung Chung; William A Eaton
Journal:  Curr Opin Struct Biol       Date:  2017-11-05       Impact factor: 6.809

7.  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

8.  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

9.  Exact Solutions for Distributions of First-Passage, Direct-Transit, and Looping Times in Symmetric Cusp Potential Barriers and Wells.

Authors:  Alexander M Berezhkovskii; Leonardo Dagdug; Sergey M Bezrukov
Journal:  J Phys Chem B       Date:  2019-04-23       Impact factor: 2.991

10.  Stratified UWHAM and Its Stochastic Approximation for Multicanonical Simulations Which Are Far from Equilibrium.

Authors:  Bin W Zhang; Nanjie Deng; Zhiqiang Tan; Ronald M Levy
Journal:  J Chem Theory Comput       Date:  2017-09-28       Impact factor: 6.006

View more

北京卡尤迪生物科技股份有限公司 © 2022-2023.