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...

The main goal of this paper is to design an efficient sampling technique for dynamic data integration using the Langevin algorithms. Based on a coarse-scale model of the problem, we compute the proposals of the Langevin algorithms using the coarse-scale gradient of the target distribution. To guarantee a correct and efficient sampling, each proposal is first tested by a Metropolis acceptancerej...

A systematic computational approach to describe the conformational dynamics of biomolecules in reduced dimensionality is presented. The method is based on (i) the decomposition of a high-dimensional molecular dynamics trajectory into a few "system" and (many) "bath" degrees of freedom and (ii) a Langevin simulation of the resulting model. Employing principal component analysis, the dimension of...

In this paper, we consider Langevin processes with mechanical constraints. The latter are a fundamental tool in molecular dynamics simulation for sampling purposes and for the computation of free energy differences. The results of this paper can be divided into three parts. (i) We propose a simple discretization of the constrained Langevin process based on a standard splitting strategy. We show...

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...

Intrinsic fluctuations around the solution of the lattice Boltzmann equation are described or modeled by addition of a white Gaussian noise source. For stationary states a fluctuation-dissipation theorem relates the variance of the fluctuations to the linearized Boltzmann collision operator and the pair correlation function.

the determination of gyration radius is a strong research for configuration of a macromolecule. italso reflects molecular compactness shape. in this work, to characterize the behavior of theprotein, we observe quantities such as the radius of gyration and the average energy. we studiedthe changes of these factors as a function of temperature for acetylcholine receptor protein in gasphase with n...

Theoretical tools for adequately treating stochastic effects are important for understanding their role in biological processes. Although master equations provide rigorous means for investigating effects associated with fluctuations of discrete molecular copy numbers, they can be very challenging to treat analytically and numerically. Approaches based on the Langevin approximation are often mor...