Transition-Path Theory and Path-Finding Algorithms for the Study of Rare Events

被引：418

作者：

E, Weinan ^{[1
,2
]}

Vanden-Eijnden, Eric ^{[3
]}

机构：

[1] Princeton Univ, Dept Math, Princeton, NJ 08544 USA

[2] Princeton Univ, Program Appl & Computat Math, Princeton, NJ 08544 USA

[3] NYU, Courant Inst Math Sci, New York, NY 10012 USA

来源：

ANNUAL REVIEW OF PHYSICAL CHEMISTRY, VOL 61 | 2010年 / 61卷

关键词：

string method; activated process; minimum free energy path; transition-state theory; NUDGED ELASTIC BAND; MOLECULAR-DYNAMICS SIMULATIONS; PROTEIN-FOLDING KINETICS; STRING METHOD; FREE-ENERGY; SADDLE-POINTS; STATES; MODELS;

D O I：

10.1146/annurev.physchem.040808.090412

中图分类号：

O64 [物理化学（理论化学）、化学物理学];

学科分类号：

070304 ; 081704 ;

摘要：

Transition-path theory is a theoretical framework for describing rare events in complex systems. It can also be used as a starting point for developing efficient numerical algorithms for analyzing such rare events. Here we review the basic components of transition-path theory and path-finding algorithms. We also discuss connections with the classical transition-state theory.

引用

页码：391 / 420

页数：30

共 88 条

[1] Forward flux sampling-type schemes for simulating rare events: Efficiency analysis [J].

Allen, Rosalind J. ;

Frenkel, Daan ;

ten Wolde, Pieter Rein .

JOURNAL OF CHEMICAL PHYSICS, 2006, 124 (19)

[2]

[Anonymous], 2007, J CHEM PHYS

[3]

[Anonymous], 2002, PHYS REV B

[4]

Bass R. F., 1997, Diffusions and elliptic operators

[5]

Bennett C.H., 1975, Diffusion in Solids: Recent Developments, P73

[6] Reactive flux and folding pathways in network models of coarse-grained protein dynamics [J].

Berezhkovskii, Alexander ;

Hummer, Gerhard ;

Szabo, Attila .

JOURNAL OF CHEMICAL PHYSICS, 2009, 130 (20)

[7] DIFFUSION-CONTROLLED REACTIONS - A VARIATIONAL FORMULA FOR THE OPTIMUM REACTION COORDINATE [J].

BERKOWITZ, M ;

MORGAN, JD ;

MCCAMMON, JA ;

NORTHRUP, SH .

JOURNAL OF CHEMICAL PHYSICS, 1983, 79 (11) :5563-5565

[8] Transition path sampling: Throwing ropes over rough mountain passes, in the dark [J].

Bolhuis, PG ;

Chandler, D ;

Dellago, C ;

Geissler, PL .

ANNUAL REVIEW OF PHYSICAL CHEMISTRY, 2002, 53 :291-318

[9] Transition-path sampling of β-hairpin folding [J].

Bolhuis, PG .

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2003, 100 (21) :12129-12134

[10] From A to B in free energy space [J].

Branduardi, Davide ;

Gervasio, Francesco Luigi ;

Parrinello, Michele .

JOURNAL OF CHEMICAL PHYSICS, 2007, 126 (05)

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