Literature DB >> 11531506

Action-derived molecular dynamics in the study of rare events.

D Passerone1, M Parrinello.   

Abstract

We present a practical method to generate classical trajectories with fixed initial and final boundary conditions. Our method is based on the minimization of a suitably defined discretized action. The method finds its most natural application in the study of rare events. Its capabilities are illustrated by nontrivial examples. The algorithm lends itself to straightforward parallelization, and when combined with ab initio molecular dynamics it promises to offer a powerful tool for the study of chemical reactions.

Mesh:

Year:  2001        PMID: 11531506     DOI: 10.1103/PhysRevLett.87.108302

Source DB:  PubMed          Journal:  Phys Rev Lett        ISSN: 0031-9007            Impact factor:   9.161


  10 in total

1.  Escaping free-energy minima.

Authors:  Alessandro Laio; Michele Parrinello
Journal:  Proc Natl Acad Sci U S A       Date:  2002-09-23       Impact factor: 11.205

2.  A self-learning algorithm for biased molecular dynamics.

Authors:  Gareth A Tribello; Michele Ceriotti; Michele Parrinello
Journal:  Proc Natl Acad Sci U S A       Date:  2010-09-27       Impact factor: 11.205

3.  Perspective: Computer simulations of long time dynamics.

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

4.  Gauging the flexibility of the active site in soybean lipoxygenase-1 (SLO-1) through an atom-centered density matrix propagation (ADMP) treatment that facilitates the sampling of rare events.

Authors:  Prasad Phatak; Isaiah Sumner; Srinivasan S Iyengar
Journal:  J Phys Chem B       Date:  2012-08-17       Impact factor: 2.991

5.  Combining optimal control theory and molecular dynamics for protein folding.

Authors:  Yaman Arkun; Mert Gur
Journal:  PLoS One       Date:  2012-01-06       Impact factor: 3.240

6.  Finding multiple reaction pathways via global optimization of action.

Authors:  Juyong Lee; In-Ho Lee; InSuk Joung; Jooyoung Lee; Bernard R Brooks
Journal:  Nat Commun       Date:  2017-05-26       Impact factor: 14.919

Review 7.  Neural Network for Principle of Least Action.

Authors:  Beibei Wang; Shane Jackson; Aiichiro Nakano; Ken-Ichi Nomura; Priya Vashishta; Rajiv Kalia; Mark Stevens
Journal:  J Chem Inf Model       Date:  2022-07-05       Impact factor: 6.162

8.  Transition pathway and its free-energy profile: a protocol for protein folding simulations.

Authors:  In-Ho Lee; Seung-Yeon Kim; Jooyoung Lee
Journal:  Int J Mol Sci       Date:  2013-08-02       Impact factor: 5.923

9.  A Folding Pathway Model of Mini-Protein BBA5.

Authors:  In-Ho Lee; Seung-Yeon Kim; Jooyoung Lee
Journal:  Biomed Res Int       Date:  2015-09-20       Impact factor: 3.411

10.  Dynamic folding pathway models of the Trp-cage protein.

Authors:  In-Ho Lee; Seung-Yeon Kim
Journal:  Biomed Res Int       Date:  2013-06-24       Impact factor: 3.411

  10 in total

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