Preserving correlations between trajectories for efficient path sampling.

Importance sampling of trajectories has proved a uniquely successful strategy for exploring rare dynamical behaviors of complex systems in an unbiased way. Carrying out this sampling, however, requires an ability to propose changes to dynamical pathways that are substantial, yet sufficiently modest to obtain reasonable acceptance rates. Satisfying this requirement becomes very challenging in the case of long trajectories, due to the characteristic divergences of chaotic dynamics. Here, we examine schemes for addressing this problem, which engineer correlation between a trial trajectory and its reference path, for instance using artificial forces. Our analysis is facilitated by a modern perspective on Markov chain Monte Carlo sampling, inspired by non-equilibrium statistical mechanics, which clarifies the types of sampling strategies that can scale to long trajectories. Viewed in this light, the most promising such strategy guides a trial trajectory by manipulating the sequence of random numbers that advance its stochastic time evolution, as done in a handful of existing methods. In cases where this "noise guidance" synchronizes trajectories effectively, as the Glauber dynamics of a two-dimensional Ising model, we show that efficient path sampling can be achieved for even very long trajectories.

[1]  Sanghyun Park,et al.  Comparison of the serial and parallel algorithms of generalized ensemble simulations: an analytical approach. , 2008, Physical review. E, Statistical, nonlinear, and soft matter physics.

[2]  Gavin E. Crooks,et al.  Excursions in Statistical Dynamics , 1999 .

[3]  R. Rosenfeld Nature , 2009, Otolaryngology--head and neck surgery : official journal of American Academy of Otolaryngology-Head and Neck Surgery.

[4]  John D. Chodera,et al.  Using Nonequilibrium Fluctuation Theorems to Understand and Correct Errors in Equilibrium and Nonequ , 2011, 1107.2967.

[5]  C. Dellago,et al.  Reaction coordinates of biomolecular isomerization. , 2000, Proceedings of the National Academy of Sciences of the United States of America.

[6]  C. Jarzynski Nonequilibrium Equality for Free Energy Differences , 1996, cond-mat/9610209.

[7]  H. C. Andersen,et al.  Role of Repulsive Forces in Determining the Equilibrium Structure of Simple Liquids , 1971 .

[8]  U. Seifert Stochastic thermodynamics, fluctuation theorems and molecular machines , 2012, Reports on progress in physics. Physical Society.

[9]  J. Herskowitz,et al.  Proceedings of the National Academy of Sciences, USA , 1996, Current Biology.

[10]  Jonathan Weare,et al.  Steered transition path sampling. , 2012, The Journal of chemical physics.

[11]  G. Crooks,et al.  Efficient transition path sampling for nonequilibrium stochastic dynamics. , 2001, Physical review. E, Statistical, nonlinear, and soft matter physics.

[12]  J. P. Garrahan,et al.  Dynamic Order-Disorder in Atomistic Models of Structural Glass Formers , 2009, Science.

[13]  Alexander K Hartmann High-precision work distributions for extreme nonequilibrium processes in large systems. , 2014, Physical review. E, Statistical, nonlinear, and soft matter physics.

[14]  O. Bagasra,et al.  Proceedings of the National Academy of Sciences , 1914, Science.

[15]  P. R. ten Wolde,et al.  Sampling rare switching events in biochemical networks. , 2004, Physical review letters.

[16]  John D. Chodera,et al.  Time Step Rescaling Recovers Continuous-Time Dynamical Properties for Discrete-Time Langevin Integration of Nonequilibrium Systems , 2013, The journal of physical chemistry. B.

[17]  L. de Arcangelis,et al.  Comparative study of damage spreading in the Ising model using heat-bath, glauber, and metropolis dynamics , 1990 .

[18]  Manuel Athènes,et al.  Measurement of nonequilibrium entropy from space-time thermodynamic integration. , 2008, The Journal of chemical physics.

[19]  J. L. Lebowitz,et al.  Exact Large Deviation Function in the Asymmetric Exclusion Process , 1998 .

[20]  K. Schulten,et al.  Free energy calculation from steered molecular dynamics simulations using Jarzynski's equality , 2003 .

[21]  W. K. Hastings,et al.  Monte Carlo Sampling Methods Using Markov Chains and Their Applications , 1970 .

[22]  C. Jarzynski,et al.  Verification of the Crooks fluctuation theorem and recovery of RNA folding free energies , 2005, Nature.

[23]  October I Physical Review Letters , 2022 .

[24]  D. Frenkel,et al.  Homogeneous nucleation under shear in a two-dimensional Ising model: cluster growth, coalescence, and breakup. , 2008, The Journal of chemical physics.

[25]  I. Tinoco,et al.  Equilibrium Information from Nonequilibrium Measurements in an Experimental Test of Jarzynski's Equality , 2002, Science.

[26]  K. Schulten,et al.  Steered molecular dynamics and mechanical functions of proteins. , 2001, Current opinion in structural biology.

[27]  K. Pearson,et al.  Biometrika , 1902, The American Naturalist.

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

[29]  Gabriel Stoltz Path sampling with stochastic dynamics: Some new algorithms , 2007, J. Comput. Phys..

[30]  Thomas Speck,et al.  Large deviation function for entropy production in driven one-dimensional systems. , 2008, Physical review. E, Statistical, nonlinear, and soft matter physics.

[31]  N. Metropolis,et al.  Equation of State Calculations by Fast Computing Machines , 1953, Resonance.

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

[33]  J. A. Crowther Reports on Progress in Physics , 1941, Nature.

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

[35]  Wayne A Hendrickson,et al.  What is 'current opinion' in structural biology? , 2011, Current opinion in structural biology.

[36]  Udo Seifert Entropy production along a stochastic trajectory and an integral fluctuation theorem. , 2005, Physical review letters.

[37]  C. Dellago,et al.  Precision shooting: Sampling long transition pathways. , 2008, The Journal of chemical physics.

[38]  J. Lebowitz,et al.  A Gallavotti–Cohen-Type Symmetry in the Large Deviation Functional for Stochastic Dynamics , 1998, cond-mat/9811220.

[39]  V. Lecomte,et al.  Thermodynamic Formalism for Systems with Markov Dynamics , 2007 .

[40]  Berend Smit,et al.  Chapter 3 – Monte Carlo Simulations , 2002 .

[41]  宁北芳,et al.  疟原虫var基因转换速率变化导致抗原变异[英]/Paul H, Robert P, Christodoulou Z, et al//Proc Natl Acad Sci U S A , 2005 .

[42]  C. Dellago,et al.  Autoionization in Liquid Water , 2001, Science.

[43]  R. Gillan New Editor-in-Chief for Journal of Physics A: Mathematical and Theoretical , 2014 .

[44]  Aaron R Dinner,et al.  A two-step nucleotide-flipping mechanism enables kinetic discrimination of DNA lesions by AGT , 2008, Proceedings of the National Academy of Sciences.

[45]  Eytan Domany,et al.  Damage spreading in the Ising model , 1997 .

[46]  J. P. Garrahan,et al.  First-order dynamical phase transition in models of glasses: an approach based on ensembles of histories , 2008, 0810.5298.

[47]  C. Dellago,et al.  Biased sampling of nonequilibrium trajectories: can fast switching simulations outperform conventional free energy calculation methods? , 2005, The journal of physical chemistry. B.

[48]  Journal of Chemical Physics , 1932, Nature.