The dynamical solution of a well-mixed, nonlinear stochastic chemical kinetic system, described by the Master equation, may be exactly computed using the stochastic simulation algorithm. However, because the computational cost scales with the number of reaction occurrences, systems with one or more "fast" reactions become costly to simulate. This paper describes a hybrid stochastic method that ...

1.2 Melt Phase System Initialization. Isolated chains in the fully extended conformation were first subjected to elevated temperature (800 K) simulations using Langevin dynamics (damping parameter = 3800 fs, time step = 2 fs). Random conformations were outputted on nanosecond intervals. This protocol resulted in 60 uncorrelated chain conformation for each polymer simulated. These chains were ne...

Computer simulations of colloidal suspensions are discussed. The simulations are based on the Langevin equations, pairwise interaction between colloidal particles and take into account Brownian, hydrodynamic and colloidal forces. Comparison of two models, one taking into account inertial term in Langevin equation and another based on diffusional approximation proposed in [D.L. Ermak, J.A. McCam...

Diffusion studies of adsorbates moving on a surface are often analyzed using 2D Langevin simulations. These simulations are computationally cheap and offer valuable insight into the dynamics, however, they simplify the complex interactions between the substrate and adsorbate atoms, neglecting correlations in the motion of the two species. The effect of this simplification on the accuracy of obs...

High-performance computing approaches that combine molecular-scale and macroscale continuum mechanics have long been anticipated in various fields. Such approaches may enrich our understanding of the links between microscale molecular mechanisms and macroscopic properties in the continuum. However, there have been few successful examples to date owing to various difficulties associated with ove...

A broad array of canonical sampling methods are available for molecular simulation based on stochastic-dynamical perturbation of Newtonian dynamics, including Langevin dynamics, Stochastic Velocity Rescaling, and methods that combine Nosé-Hoover dynamics with stochastic perturbation. In this article we discuss several stochasticdynamical thermostats in the setting of simulating systems with hol...

The prediction of ionic currents in protein channels of biological membranes is one of the central problems of computational molecular biophysics. Existing continuum descriptions of ionic permeation fail to capture the rich phenomenology of the permeation process, so it is therefore necessary to resort to particle simulations. Brownian dynamics (BD) simulations require the connection of a small...