The objective of molecular dynamics computations is to infer macroscopic properties of
matter from atomistic models via averages with respect to probability measures dictated by …

The Tinker software, currently released as version 8, is a modular molecular mechanics and
dynamics package written primarily in a standard, easily portable dialect of Fortran 95 with …

For a number of years, we have been exploring the underpinnings of algorithms for
simulating molecular dynamics from a mathematics perspective, ie as outsiders. We have …

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 …

We have recently proposed a new unified theoretical scheme (the “middle” scheme) for
thermostat algorithms for efficient and accurate configurational sampling of the canonical …

Metropolis Monte Carlo simulation is a powerful tool for studying the equilibrium properties
of matter. In complex condensed-phase systems, however, it is difficult to design Monte …

We describe and analyze some Monte Carlo methods for manifolds in euclidean space
defined by equality and inequality constraints. First, we give an MCMC sampler for …

This paper introduces coordinate-independent methods for analyzing multiscale dynamical
systems using numerical techniques based on the transfer operator and its adjoint. In …

Sticky Brownian motion is the simplest example of a diffusion process that can spend finite
time both in the interior of a domain and on its boundary. It arises in various applications in …

We present an approach to Langevin dynamics in the presence of holonomic constraints
based on decomposition of the system into components representing geodesic flow …