Finite temperature string method for the study of rare events.

A method is presented for the study of rare events such as conformational changes arising in activated processes whose reaction coordinate is not known beforehand and for which the assumptions of transition state theory are invalid. The method samples the energy landscape adaptively and determines the isoprobability surfaces for the transition: by definition the trajectories initiated anywhere on one of these surfaces has equal probability to reach first one metastable set rather than the other. Upon weighting these surfaces by the equilibrium probability distribution, one obtains an effective transition pathway, i.e., a tube in configuration space inside which conformational changes occur with high probability, and the associated rate. The method is first validated on a simple two-dimensional example; then it is applied to a model of solid-solid transformation of a condensed system.

[1]  刘金明,et al.  IL-13受体α2降低血吸虫病肉芽肿的炎症反应并延长宿主存活时间[英]/Mentink-Kane MM,Cheever AW，Thompson RW，et al//Proc Natl Acad Sci U S A , 2005 .

[2]  Sabine Attinger,et al.  Multiscale Modelling and Simulation , 2004 .

[3]  Berend Smit,et al.  Understanding Molecular Simulation , 2001 .

[4]  Tom Ziegler,et al.  First-Principle Molecular Dynamic Simulations along the Intrinsic Reaction Paths , 2001 .

[5]  M. Parrinello,et al.  Action-derived molecular dynamics in the study of rare events. , 2001, Physical review letters.

[6]  Alexander D. MacKerell,et al.  Computational Biochemistry and Biophysics , 2001 .

[7]  G. Henkelman,et al.  Improved tangent estimate in the nudged elastic band method for finding minimum energy paths and saddle points , 2000 .

[8]  Russell P. Cowburn,et al.  The attractions of magnetism for nanoscale data storage , 2000, Philosophical Transactions of the Royal Society of London. Series A: Mathematical, Physical and Engineering Sciences.

[9]  D. Berkov.  Numerical calculation of the energy barrier distribution in disordered many-particle systems: the path integral method , 1998 .

[10]  C. Dellago,et al.  Transition path sampling and the calculation of rate constants , 1998 .

[11]  Giovanni Ciccotti,et al.  Book Review: Classical and Quantum Dynamics in Condensed Phase Simulations , 1998 .

[12]  Christoph Dellago,et al.  Efficient transition path sampling: Application to Lennard-Jones cluster rearrangements , 1998 .

[13]  M. Tuckerman,et al.  IN CLASSICAL AND QUANTUM DYNAMICS IN CONDENSED PHASE SIMULATIONS , 1998 .

[14]  Ron Elber,et al.  Yet another look at the steepest descent path , 1997 .

[15]  Ron Elber,et al.  Calculation of classical trajectories with a very large time step: Formalism and numerical examples , 1996 .

[16]  Berend Smit,et al.  Understanding molecular simulation: from algorithms to applications , 1996 .

[17]  Oppenheim,et al.  Dynamics of hard-sphere suspensions. , 1994, Physical review. E, Statistical physics, plasmas, fluids, and related interdisciplinary topics.

[18]  Braun,et al.  Thermally activated magnetization reversal in elongated ferromagnetic particles. , 1993 .

[19]  E. Carter,et al.  Ridge method for finding saddle points on potential energy surfaces , 1993 .

[20]  P. Hänggi,et al.  Reaction-rate theory: fifty years after Kramers , 1990 .

[21]  C. Kelley.  Iterative Methods for Linear and Nonlinear Equations , 1987 .

[22]  Graeme E. Murch,et al.  Diffusion in solids : recent developments , 1985 .

[23]  M. Freidlin,et al.  Random Perturbations of Dynamical Systems , 1984 .

[24]  C. Gardiner.  Handbook of Stochastic Methods , 1983 .

[25]  A. Nowick,et al.  Diffusion in solids: recent developments , 1975 .