منابع مشابه
Robust and efficient configurational molecular sampling via Langevin dynamics.
A wide variety of numerical methods are evaluated and compared for solving the stochastic differential equations encountered in molecular dynamics. The methods are based on the application of deterministic impulses, drifts, and Brownian motions in some combination. The Baker-Campbell-Hausdorff expansion is used to study sampling accuracy following recent work by the authors, which allows determ...
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This chapter reviews numerical simulations of quantum field theories based on stochastic quantization and the Langevin equation. The topics discussed include renormalization of finite stepsize algorithms, Fourier acceleration, and the relation of the Langevin equation to hybrid stochastic algorithms and hybrid Monte Carlo. Invited chapter to appear in the special supplement “Stochastic Quantiza...
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We generalize the Langevin Dynamics through the mirror descent framework for first-order sampling. The näıve approach of incorporating Brownian motion into the mirror descent dynamics, which we refer to as Symmetric Mirrored Langevin Dynamics (S-MLD), is shown to connected to the theory of Weighted Hessian Manifolds. The S-MLD, unfortunately, contains the hard instance of Cox–Ingersoll–Ross pro...
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Proteins and other macromolecules have coupled dynamics over multiple time scales (from femtosecond to millisecond and beyond) that make resolving molecular dynamics challenging. We present an approach based on periodically decomposing the dynamics of a macromolecule into slow and fast modes based on a scalable coarse-grained normal mode analysis. A Langevin equation is used to propagate the sl...
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In this paper we generalize a result by Rubin and Ungar on Hamiltonian systems containing a strong constraining potential to Langevin dynamics. Such highly oscillatory systems arise, for example, in the context of molecular dynamics. We derive constrained equations of motion for the slowly varying solution components. This includes in particular the derivation of a correcting force-term that st...
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ژورنال
عنوان ژورنال: Physical Review E
سال: 2007
ISSN: 1539-3755,1550-2376
DOI: 10.1103/physreve.75.056707