16,992 research outputs found

    Free energy reconstruction from steered dynamics without post-processing

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    Various methods achieving importance sampling in ensembles of nonequilibrium trajectories enable to estimate free energy differences and, by maximum-likelihood post-processing, to reconstruct free energy landscapes. Here, based on Bayes theorem, we propose a more direct method in which a posterior likelihood function is used both to construct the steered dynamics and to infer the contribution to equilibrium of all the sampled states. The method is implemented with two steering schedules. First, using non-autonomous steering, we calculate the migration barrier of the vacancy in Fe-alpha. Second, using an autonomous scheduling related to metadynamics and equivalent to temperature-accelerated molecular dynamics, we accurately reconstruct the two-dimensional free energy landscape of the 38-atom Lennard-Jones cluster as a function of an orientational bond-order parameter and energy, down to the solid-solid structural transition temperature of the cluster and without maximum-likelihood post-processing.Comment: Accepted manuscript in Journal of Computational Physics, 7 figure

    Fluctuation-dissipation relations far from equilibrium

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    The fluctuation-dissipation (F-D) theorem is a fundamental result for systems near thermodynamic equilibrium, and justifies studies between microscopic and macroscopic properties. It states that the nonequilibrium relaxation dynamics is related to the spontaneous fluctuation at equilibrium. Most processes in Nature are out of equilibrium, for which we have limited theory. Common wisdom believes the F-D theorem is violated in general for systems far from equilibrium. Recently we show that dynamics of a dissipative system described by stochastic differential equations can be mapped to that of a thermostated Hamiltonian system, with a nonequilibrium steady state of the former corresponding to the equilibrium state of the latter. Her we derived the corresponding F-D theorem, and tested with several examples. We suggest further studies exploiting the analogy between a general dissipative system appearing in various science branches and a Hamiltonian system. Especially we discussed the implications of this work on biological network studies.Comment: 12 pages, 4 figures, major revision over the first versio

    Stochastic Methods for Zero Energy Quantum Scattering

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    We investigate the use of stochastic methods for zero energy quantum scattering based on a path integral approach. With the application to the scattering of a projectile from a nuclear many body target in mind, we use the potential scattering of a particle as a test for the accuracy and efficiency of several methods. To be able to deal with complex potentials, we introduce a path sampling action and a modified scattering observable. The approaches considered are the random walk, where the points of a path are sequentially generated, and the Langevin algorithm, which updates an entire path. Several improvements are investigated. A cluster algorithm for dealing with scattering problems is finally proposed, which shows the best accuracy and stability.Comment: 40 pages LaTeX, 1 Postscript file containig 20 figures; execute main.tex file, which automatically will include other file
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