Enhanced Sampling of Nonequilibrium Steady States

被引:74
作者
Dickson, Alex [1 ]
Dinner, Aaron R.
机构
[1] Univ Chicago, James Franck Inst, Dept Chem, Chicago, IL 60637 USA
来源
ANNUAL REVIEW OF PHYSICAL CHEMISTRY, VOL 61 | 2010年 / 61卷
关键词
nonequilibrium umbrella sampling; forward flux sampling; transition rates; path sampling; string method; STOCHASTIC SIMULATION; DYNAMICS SIMULATIONS; SINGLE-MOLECULE; MODELS; TRANSITIONS; SUSPENSIONS; ROBUSTNESS; ENSEMBLE; KINETICS;
D O I
10.1146/annurev.physchem.012809.103433
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
We review recent progress in methods for accelerating the convergence of simulations of nonequilibrium systems, specifically nonequilibrium umbrella sampling (NEUS) and forward flux sampling (FFS). These methods account for statistics of dynamical paths between interfaces to enforce sampling of low probability regions of phase space for computing steady-state averages, including transition rates, for systems driven arbitrarily far from equilibrium. Recent advances in NEUS allow for efficient sampling of complex systems by focusing sampling in the vicinity of a one-dimensional manifold (string) that connects regions of interest in phase space; this procedure can be extended to the case of two strings that describe the forward and backward transition ensembles separately, which is useful, as they do not, in general, coincide. We recast FFS in the framework of NEUS to facilitate comparison of the two methods. We conclude by discussing selected applications of interest.
引用
收藏
页码:441 / 459
页数:19
相关论文
共 95 条
[1]  
Allen M. P., 2017, COMPUTER SIMULATION
[2]   Sampling rare switching events in biochemical networks [J].
Allen, RJ ;
Warren, PB ;
ten Wolde, PR .
PHYSICAL REVIEW LETTERS, 2005, 94 (01)
[3]   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)
[4]   Homogeneous nucleation under shear in a two-dimensional Ising model: Cluster growth, coalescence, and breakup [J].
Allen, Rosalind J. ;
Valeriani, Chantal ;
Tanase-Nicola, Sorin ;
ten Wolde, Pieter Rein ;
Frenkel, Daan .
JOURNAL OF CHEMICAL PHYSICS, 2008, 129 (13)
[5]   Integrative mathematical oncology [J].
Anderson, Alexander R. A. ;
Quaranta, Vito .
NATURE REVIEWS CANCER, 2008, 8 (03) :227-234
[6]  
[Anonymous], 1987, Nonnegative Matrices and Applicable Topics in Linear Algebra
[7]   Shear ordering in thin films of spherical block copolymer [J].
Arya, G ;
Rottler, J ;
Panagiotopoulos, AZ ;
Srolovitz, DJ ;
Chaikin, PM .
LANGMUIR, 2005, 21 (24) :11518-11527
[8]   Fast Monte Carlo simulations and singularities in the probability distributions of nonequilibrium systems [J].
Bandrivskyy, A ;
Beri, S ;
Luchinsky, DG ;
Mannella, R ;
McClintock, PVE .
PHYSICAL REVIEW LETTERS, 2003, 90 (21) :4
[9]   SHEAR-THICKENING (DILATANCY) IN SUSPENSIONS OF NONAGGREGATING SOLID PARTICLES DISPERSED IN NEWTONIAN LIQUIDS [J].
BARNES, HA .
JOURNAL OF RHEOLOGY, 1989, 33 (02) :329-366
[10]   Crystal nucleation of colloidal suspensions under shear -: art. no. 068303 [J].
Blaak, R ;
Auer, S ;
Frenkel, D ;
Löwen, H .
PHYSICAL REVIEW LETTERS, 2004, 93 (06) :068303-1