Preserving correlations between trajectories for efficient path sampling

作者: Todd R. Gingrich , Phillip L. Geissler

DOI: 10.1063/1.4922343

关键词: Sampling (statistics)Importance samplingSequenceMarkov processTrajectoryMathematical optimizationStatistical physicsPath (graph theory)Monte Carlo methodStochastic processComputer science

摘要: Importance sampling of trajectories has proved a uniquely successful strategy for exploring rare dynamical behaviors complex systems in an unbiased way. Carrying out this sampling, however, requires ability to propose changes pathways that are substantial, yet sufficiently modest obtain reasonable acceptance rates. Satisfying requirement becomes very challenging the case long trajectories, due characteristic divergences chaotic dynamics. Here, we examine schemes addressing problem, which engineer correlation between trial trajectory and its reference path, instance using artificial forces. Our analysis is facilitated by modern perspective on Markov chain Monte Carlo inspired non-equilibrium statistical mechanics, clarifies types strategies can scale trajectories. Viewed light, most promising such guides manipulating sequence random numbers advan...

参考文章(43)
Joel L. Lebowitz, Herbert Spohn, A GALLAVOTTI-COHEN-TYPE SYMMETRY IN THE LARGE DEVIATION FUNCTIONAL FOR STOCHASTIC DYNAMICS Journal of Statistical Physics. ,vol. 95, pp. 333- 365 ,(1999) , 10.1023/A:1004589714161
John D. Weeks, David Chandler, Hans C. Andersen, Role of Repulsive Forces in Determining the Equilibrium Structure of Simple Liquids The Journal of Chemical Physics. ,vol. 54, pp. 5237- 5247 ,(1971) , 10.1063/1.1674820
Gabriel Stoltz, Path sampling with stochastic dynamics: Some new algorithms Journal of Computational Physics. ,vol. 225, pp. 491- 508 ,(2007) , 10.1016/J.JCP.2006.12.006
Jakob Mehl, Thomas Speck, Udo Seifert, Large deviation function for entropy production in driven one-dimensional systems. Physical Review E. ,vol. 78, pp. 011123- ,(2008) , 10.1103/PHYSREVE.78.011123
D. Collin, F. Ritort, C. Jarzynski, S. B. Smith, I. Tinoco, C. Bustamante, Verification of the Crooks fluctuation theorem and recovery of RNA folding free energies Nature. ,vol. 437, pp. 231- 234 ,(2005) , 10.1038/NATURE04061
Gavin E. Crooks, David Chandler, Efficient transition path sampling for nonequilibrium stochastic dynamics Physical Review E. ,vol. 64, pp. 026109- ,(2001) , 10.1103/PHYSREVE.64.026109
Haye Hinrichsen, Eytan Domany, Damage spreading in the Ising model Physical Review E. ,vol. 56, pp. 94- 98 ,(1997) , 10.1103/PHYSREVE.56.94
J. P. Nilmeier, G. E. Crooks, D. D. L. Minh, J. D. Chodera, Nonequilibrium candidate Monte Carlo is an efficient tool for equilibrium simulation Proceedings of the National Academy of Sciences of the United States of America. ,vol. 108, pp. 18199- 18200 ,(2011) , 10.1073/PNAS.1106094108
Michael Grünwald, Christoph Dellago, Phillip L. Geissler, Precision shooting: Sampling long transition pathways. Journal of Chemical Physics. ,vol. 129, pp. 194101- 194101 ,(2008) , 10.1063/1.2978000