PMID: 22587212May 17, 2012Paper

Transition path sampling algorithm for discrete many-body systems

Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics
Thierry MoraFrancesco Zamponi

Abstract

We propose a Monte Carlo method for efficiently sampling trajectories with fixed initial and final conditions in a system with discrete degrees of freedom. The method can be applied to any stochastic process with local interactions, including systems that are out of equilibrium. We combine the proposed path sampling algorithm with thermodynamic integration to calculate transition rates. We demonstrate our method on the well-studied two-dimensional Ising model with periodic boundary conditions, and show agreement with other results for both large and small system sizes. The method scales well with the system size, allowing one to simulate systems with many degrees of freedom, and providing complementary information with respect to other algorithms.

References

Feb 9, 2005·Physical Review Letters·Rosalind J AllenPieter Rein Ten Wolde
May 13, 2005·Nature·Murat AcarAlexander van Oudenaarden
Mar 24, 2006·Nature·Gürol M SüelMichael B Elowitz
Jul 21, 2006·The Journal of Physical Chemistry. B·Weinan EEric Vanden-Eijnden
Sep 27, 2006·The Journal of Chemical Physics·Jie HuAaron R Dinner
Sep 25, 2007·The Journal of Chemical Physics·Chantal ValerianiPieter Rein ten Wolde
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Nov 18, 2009·Journal of Physics. Condensed Matter : an Institute of Physics Journal·Rosalind J AllenPieter Rein Ten Wolde
Jul 27, 2011·The Journal of Chemical Physics·Massimiliano PiccianiJulien Tailleur

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Citations

Jul 21, 2015·Soft Matter·Alireza Mashaghi, Abolfazl Ramezanpour
May 20, 2020·Physical Review. E·Loredana M VasiloiuJuan P Garrahan
Dec 20, 2014·Physical Review Letters·Manuel Athènes, Vasily V Bulatov
Jul 17, 2020·The Journal of Chemical Physics·Daniel J Sharpe, David J Wales

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