Rate constants for diffusive processes by partial path sampling

被引:140
作者
Moroni, D
Bolhuis, PG
van Erp, TS
机构
[1] Univ Amsterdam, Dept Chem Engn, NL-1018 WV Amsterdam, Netherlands
[2] Ecole Normale Super Lyon, Ctr Europeen Calcul Atom & Mol, Phys Lab, F-69364 Lyon 07, France
关键词
D O I
10.1063/1.1644537
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 introduce a path sampling method for the computation of rate constants for complex systems with a highly diffusive character. Based on the recently developed transition interface sampling (TIS) algorithm this procedure increases the efficiency by sampling only parts of complete transition trajectories. The algorithm assumes the loss of memory for diffusive progression along the reaction coordinate. We compare the new partial path technique to the TIS method for a simple diatomic system and show that the computational effort of the new method scales linearly, instead of quadratically, with the width of the diffusive barrier. The validity of the memory loss assumption is also discussed. (C) 2004 American Institute of Physics.
引用
收藏
页码:4055 / 4065
页数:11
相关论文
共 19 条
[1]   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
[2]   Sampling ensembles of deterministic transition pathways [J].
Bolhuis, PG ;
Dellago, C ;
Chandler, D .
FARADAY DISCUSSIONS, 1998, 110 :421-436
[3]   Transition path sampling on diffusive barriers [J].
Bolhuis, PG .
JOURNAL OF PHYSICS-CONDENSED MATTER, 2003, 15 (01) :S113-S120
[4]   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
[5]   NEW ALGORITHM FOR MONTE-CARLO SIMULATION OF ISING SPIN SYSTEMS [J].
BORTZ, AB ;
KALOS, MH ;
LEBOWITZ, JL .
JOURNAL OF COMPUTATIONAL PHYSICS, 1975, 17 (01) :10-18
[6]   STATISTICAL-MECHANICS OF ISOMERIZATION DYNAMICS IN LIQUIDS AND TRANSITION-STATE APPROXIMATION [J].
CHANDLER, D .
JOURNAL OF CHEMICAL PHYSICS, 1978, 68 (06) :2959-2970
[7]   On the calculation of reaction rate constants in the transition path ensemble [J].
Dellago, C ;
Bolhuis, PG ;
Chandler, D .
JOURNAL OF CHEMICAL PHYSICS, 1999, 110 (14) :6617-6625
[8]   Transition path sampling and the calculation of rate constants [J].
Dellago, C ;
Bolhuis, PG ;
Csajka, FS ;
Chandler, D .
JOURNAL OF CHEMICAL PHYSICS, 1998, 108 (05) :1964-1977
[9]   Transition path sampling [J].
Dellago, C ;
Bolhuis, PG ;
Geissler, PL .
ADVANCES IN CHEMICAL PHYSICS, VOL 123, 2002, 123 :1-78
[10]   THEORETICAL FOUNDATIONS OF DYNAMIC MONTE-CARLO SIMULATIONS [J].
FICHTHORN, KA ;
WEINBERG, WH .
JOURNAL OF CHEMICAL PHYSICS, 1991, 95 (02) :1090-1096