Characterization of Rare Events in Molecular Dynamics

A good deal of molecular dynamics simulations aims at predicting and quantifying rare events, such as the folding of a protein or a phase transition. Simulating rare events is often prohibitive, especially if the equations of motion are high-dimensional, as is the case in molecular dynamics. Various...

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Main Authors:	Carsten Hartmann, Ralf Banisch, Marco Sarich, Tomasz Badowski, Christof Schütte
Format:	Article
Language:	English
Published:	MDPI AG 2013-12-01
Series:	Entropy
Subjects:	rare events molecular dynamics optimal pathways stochastic control dynamic programming change of measure cumulant generating function
Online Access:	http://www.mdpi.com/1099-4300/16/1/350

id	doaj-faccba55a07247de8fdb4d2a15bf5195
record_format	Article
spelling	doaj-faccba55a07247de8fdb4d2a15bf51952020-11-24T22:55:59ZengMDPI AGEntropy1099-43002013-12-0116135037610.3390/e16010350e16010350Characterization of Rare Events in Molecular DynamicsCarsten Hartmann0Ralf Banisch1Marco Sarich2Tomasz Badowski3Christof Schütte4Institut für Mathematik, Freie Universität Berlin, Arnimallee 6, 14195 Berlin, GermanyInstitut für Mathematik, Freie Universität Berlin, Arnimallee 6, 14195 Berlin, GermanyInstitut für Mathematik, Freie Universität Berlin, Arnimallee 6, 14195 Berlin, GermanyInstitut für Mathematik, Freie Universität Berlin, Arnimallee 6, 14195 Berlin, GermanyInstitut für Mathematik, Freie Universität Berlin, Arnimallee 6, 14195 Berlin, GermanyA good deal of molecular dynamics simulations aims at predicting and quantifying rare events, such as the folding of a protein or a phase transition. Simulating rare events is often prohibitive, especially if the equations of motion are high-dimensional, as is the case in molecular dynamics. Various algorithms have been proposed for efficiently computing mean first passage times, transition rates or reaction pathways. This article surveys and discusses recent developments in the field of rare event simulation and outlines a new approach that combines ideas from optimal control and statistical mechanics. The optimal control approach described in detail resembles the use of Jarzynski’s equality for free energy calculations, but with an optimized protocol that speeds up the sampling, while (theoretically) giving variance-free estimators of the rare events statistics. We illustrate the new approach with two numerical examples and discuss its relation to existing methods.http://www.mdpi.com/1099-4300/16/1/350rare eventsmolecular dynamicsoptimal pathwaysstochastic controldynamic programmingchange of measurecumulant generating function
collection	DOAJ
language	English
format	Article
sources	DOAJ
author	Carsten Hartmann Ralf Banisch Marco Sarich Tomasz Badowski Christof Schütte
spellingShingle	Carsten Hartmann Ralf Banisch Marco Sarich Tomasz Badowski Christof Schütte Characterization of Rare Events in Molecular Dynamics Entropy rare events molecular dynamics optimal pathways stochastic control dynamic programming change of measure cumulant generating function
author_facet	Carsten Hartmann Ralf Banisch Marco Sarich Tomasz Badowski Christof Schütte
author_sort	Carsten Hartmann
title	Characterization of Rare Events in Molecular Dynamics
title_short	Characterization of Rare Events in Molecular Dynamics
title_full	Characterization of Rare Events in Molecular Dynamics
title_fullStr	Characterization of Rare Events in Molecular Dynamics
title_full_unstemmed	Characterization of Rare Events in Molecular Dynamics
title_sort	characterization of rare events in molecular dynamics
publisher	MDPI AG
series	Entropy
issn	1099-4300
publishDate	2013-12-01
description	A good deal of molecular dynamics simulations aims at predicting and quantifying rare events, such as the folding of a protein or a phase transition. Simulating rare events is often prohibitive, especially if the equations of motion are high-dimensional, as is the case in molecular dynamics. Various algorithms have been proposed for efficiently computing mean first passage times, transition rates or reaction pathways. This article surveys and discusses recent developments in the field of rare event simulation and outlines a new approach that combines ideas from optimal control and statistical mechanics. The optimal control approach described in detail resembles the use of Jarzynski’s equality for free energy calculations, but with an optimized protocol that speeds up the sampling, while (theoretically) giving variance-free estimators of the rare events statistics. We illustrate the new approach with two numerical examples and discuss its relation to existing methods.
topic	rare events molecular dynamics optimal pathways stochastic control dynamic programming change of measure cumulant generating function
url	http://www.mdpi.com/1099-4300/16/1/350
work_keys_str_mv	AT carstenhartmann characterizationofrareeventsinmoleculardynamics AT ralfbanisch characterizationofrareeventsinmoleculardynamics AT marcosarich characterizationofrareeventsinmoleculardynamics AT tomaszbadowski characterizationofrareeventsinmoleculardynamics AT christofschutte characterizationofrareeventsinmoleculardynamics
_version_	1725655379529957376

Characterization of Rare Events in Molecular Dynamics

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