Literature DB >> 27059558

Kramers turnover: From energy diffusion to spatial diffusion using metadynamics.

Pratyush Tiwary1, B J Berne1.   

Abstract

We consider the rate of transition for a particle between two metastable states coupled to a thermal environment for various magnitudes of the coupling strength using the recently proposed infrequent metadynamics approach [P. Tiwary and M. Parrinello, Phys. Rev. Lett. 111, 230602 (2013)]. We are interested in understanding how this approach for obtaining rate constants performs as the dynamics regime changes from energy diffusion to spatial diffusion. Reassuringly, we find that the approach works remarkably well for various coupling strengths in the strong coupling regime, and to some extent even in the weak coupling regime.

Mesh:

Year:  2016        PMID: 27059558      PMCID: PMC4818276          DOI: 10.1063/1.4944577

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


  12 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.  Role of water and steric constraints in the kinetics of cavity-ligand unbinding.

Authors:  Pratyush Tiwary; Jagannath Mondal; Joseph A Morrone; B J Berne
Journal:  Proc Natl Acad Sci U S A       Date:  2015-09-14       Impact factor: 11.205

3.  Assessing the Reliability of the Dynamics Reconstructed from Metadynamics.

Authors:  Matteo Salvalaglio; Pratyush Tiwary; Michele Parrinello
Journal:  J Chem Theory Comput       Date:  2014-03-10       Impact factor: 6.006

4.  Diffusive model of protein folding dynamics with Kramers turnover in rate.

Authors:  Robert B Best; Gerhard Hummer
Journal:  Phys Rev Lett       Date:  2006-06-07       Impact factor: 9.161

5.  Accurate sampling using Langevin dynamics.

Authors:  Giovanni Bussi; Michele Parrinello
Journal:  Phys Rev E Stat Nonlin Soft Matter Phys       Date:  2007-05-25

6.  Well-tempered metadynamics: a smoothly converging and tunable free-energy method.

Authors:  Alessandro Barducci; Giovanni Bussi; Michele Parrinello
Journal:  Phys Rev Lett       Date:  2008-01-18       Impact factor: 9.161

7.  A time-independent free energy estimator for metadynamics.

Authors:  Pratyush Tiwary; Michele Parrinello
Journal:  J Phys Chem B       Date:  2014-07-21       Impact factor: 2.991

8.  Generic mechanism of optimal energy transfer efficiency: a scaling theory of the mean first-passage time in exciton systems.

Authors:  Jianlan Wu; Robert J Silbey; Jianshu Cao
Journal:  Phys Rev Lett       Date:  2013-05-13       Impact factor: 9.161

9.  From metadynamics to dynamics.

Authors:  Pratyush Tiwary; Michele Parrinello
Journal:  Phys Rev Lett       Date:  2013-12-03       Impact factor: 9.161

10.  Kinetics of protein-ligand unbinding: Predicting pathways, rates, and rate-limiting steps.

Authors:  Pratyush Tiwary; Vittorio Limongelli; Matteo Salvalaglio; Michele Parrinello
Journal:  Proc Natl Acad Sci U S A       Date:  2015-01-20       Impact factor: 11.205

View more
  2 in total

1.  How wet should be the reaction coordinate for ligand unbinding?

Authors:  Pratyush Tiwary; B J Berne
Journal:  J Chem Phys       Date:  2016-08-07       Impact factor: 3.488

2.  Predicting reaction coordinates in energy landscapes with diffusion anisotropy.

Authors:  Pratyush Tiwary; B J Berne
Journal:  J Chem Phys       Date:  2017-10-21       Impact factor: 3.488

  2 in total

北京卡尤迪生物科技股份有限公司 © 2022-2023.