Dominant reaction pathways in high-dimensional systems.

This paper is devoted to the development of a theoretical and computational framework denominated dominant reaction pathways (DRPs) to efficiently sample the statistically significant thermally activated reaction pathways, in multidimensional systems. The DRP approach is consistently derived from the Langevin equation through a systematic expansion in the thermal energy, k(B)T. Its main advantage with respect to existing simulation techniques is that it provides a natural and rigorous framework to perform the path sampling using constant displacement steps, rather than constant time steps. In our previous work, we have shown how to obtain the set of most probable reaction pathways, i.e., the lowest order in the k(B)T expansion. In this work, we show how to compute the corrections to the leading order due to stochastic fluctuations around the most probable trajectories. We also discuss how to obtain predictions for the evolution of arbitrary observables and how to generate conformations, which are representative of the transition state ensemble. We illustrate how our method works in practice by studying the diffusion of a point particle in a two-dimensional funneled external potential.

[1]  T. Woolf,et al.  DYNAMIC REACTION PATHS AND RATES THROUGH IMPORTANCE-SAMPLED STOCHASTIC DYNAMICS , 1999 .

[2]  Ioan Andricioaei,et al.  On the calculation of time correlation functions by potential scaling. , 2006, The Journal of chemical physics.

[3]  Ron Elber,et al.  Long time dynamics of complex systems. , 2002, Accounts of chemical research.

[4]  V. Pande,et al.  On the transition coordinate for protein folding , 1998 .

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

[6]  A. B. Adib,et al.  Stochastic actions for diffusive dynamics: reweighting, sampling, and minimization. , 2007, The journal of physical chemistry. B.

[7]  H. Orland,et al.  Dominant pathways in protein folding. , 2005, Physical review letters.

[8]  C. Caroli,et al.  Diffusion in a bistable potential: A systematic WKB treatment , 1979 .

[9]  H. Scheraga,et al.  An atomically detailed study of the folding pathways of protein A with the stochastic difference equation , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[10]  Oleg Mazonka,et al.  Computing probabilities of very rare events for Langevin processes: a new method based on importance sampling , 1998 .

[11]  P. Bolhuis Rare events via multiple reaction channels sampled by path replica exchange. , 2008, The Journal of chemical physics.

[12]  Grubmüller,et al.  Predicting slow structural transitions in macromolecular systems: Conformational flooding. , 1995, Physical review. E, Statistical physics, plasmas, fluids, and related interdisciplinary topics.

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

[14]  David Chandler,et al.  Transition path sampling: throwing ropes over rough mountain passes, in the dark. , 2002, Annual review of physical chemistry.

[15]  Michael R. Shirts,et al.  Atomistic protein folding simulations on the submillisecond time scale using worldwide distributed computing. , 2003, Biopolymers.

[16]  C. Caroli,et al.  Diffusion in a bistable potential: The functional integral approach , 1981 .

[17]  Peter G. Bolhuis,et al.  A novel path sampling method for the calculation of rate constants , 2003 .

[18]  A. Laio,et al.  Escaping free-energy minima , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[19]  M Sega,et al.  Quantitative protein dynamics from dominant folding pathways. , 2007, Physical review letters.

[20]  Sebastian Doniach,et al.  Simulation of protein folding by reaction path annealing , 2001 .

[21]  Bernard J. Matkowsky,et al.  The Kramers Problem in the Turnover Regime: The Role of the Stochastic Separatrix , 1991 .

[22]  G. Torrie,et al.  Monte Carlo free energy estimates using non-Boltzmann sampling: Application to the sub-critical Lennard-Jones fluid , 1974 .

[23]  V. Muñoz,et al.  Folding dynamics and mechanism of β-hairpin formation , 1997, Nature.

[24]  E. Vanden-Eijnden,et al.  String method for the study of rare events , 2002, cond-mat/0205527.

[25]  P. Faccioli Characterization of protein folding by dominant reaction pathways. , 2008, The journal of physical chemistry. B.

[26]  W. E,et al.  Finite temperature string method for the study of rare events. , 2002, Journal of Physical Chemistry B.