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We apply a recently developed framework for analyzing the convergence of stochastic algorithms to the general problem of large-scale nonconvex composite optimization more generally, and nonconvex likelihood maximization in particular. Our…
The context of the present paper is stochastic thermodynamics - an approach to nonequilibrium thermodynamics rooted within the broader framework of stochastic control. In contrast to the classical paradigm of Carnot engines, we herein…
Molecular dynamics (MD) simulations are powerful tools for elucidating the macroscopic physical properties of materials from microscopic atomic behaviors. However, the massive, high-dimensional datasets generated by MD simulations pose a…
A new configurational temperature thermostat suitable for molecules with holonomic constraints is derived. This thermostat has a simple set of motion equations, can generate the canonical ensemble in both position and momentum space, acts…
This article presents a new numerical scheme for the discretization of dissipative particle dynamics with conserved energy. The key idea is to reduce elementary pairwise stochastic dynamics (either fluctuation/dissipation or thermal…
We study numerical methods for dissipative particle dynamics (DPD), which is a system of stochastic differential equations and a popular stochastic momentum-conserving thermostat for simulating complex hydrodynamic behavior at mesoscales.…
We investigate the motion of a colloidal particle driven out of equilibrium by an external torque. We use the molecular dynamics simulation that is alternative to the numerical integration approach based on the Langevin equation and is…
Numerical simulations of fast remagnetization processes using the stochastic dynamics are widely used to study various magnetic systems. In this paper we first address several crucial methodological problems of such simulations: (i) the…
The molecular dynamics method is applied to simulate the recrystallization of an amorphous/crystalline silicon interface. The atomic structure of the amorphous material is constructed with the method of Wooten, Winer, and Weaire. The…
Computational studies of the thermodynamic properties of materials at the mesoscopic and macroscopic scales -- involving lengths and times of at least $\mu$m and $\mu$s, respectively -- rely on a coarse-graining approximation such that only…
We introduce a numerical method to sample the distributions of charge, heat, and entropy production in open quantum systems coupled strongly to macroscopic reservoirs, with both temporal and energy resolution and beyond the linear-response…
A thermodynamically consistent particle-based model for fluid dynamics with continuous velocities and a non-ideal equation of state is presented. Excluded volume interactions are modeled by means of biased stochastic multiparticle…
We consider the single-particle velocity distribution of a one-dimensional fluid of inelastic particles. Both the freely evolving (cooling) system and the non-equilibrium stationary state obtained in the presence of random forcing are…
Metadynamics is a powerful method to accelerate molecular dynamics simulations, but its efficiency critically depends on the identification of collective variables that capture the slow modes of the process. Unfortunately, collective…
Many enhanced sampling techniques rely on the identification of a number of collective variables that describe all the slow modes of the system. By constructing a bias potential in this reduced space one is then able to sample efficiently…
The use of the isoconfigurational ensemble to explore structure-dynamic correlations in supercooled liquids is examined. The statistical error of the dynamic propensity and its spatial distribution are determined. The authors present the…
The stochastic dynamics of small elastic objects in fluid are central to many important and emerging technologies. It is now possible to measure and use the higher modes of motion of elastic structures when driven by Brownian motion alone.…
We propose a novel computational strategy to study the glass transition of molecular fluids. Our approach combines the construction of simple yet realistic models with the development of Monte Carlo algorithms to accelerate equilibration…
A Cahn-Hilliard equation with stochastic multiplicative noise and a random convection term is considered. The model describes isothermal phase-separation occurring in a moving fluid, and accounts for the randomness appearing at the…
We investigate the potential of numerical algorithms to decipher the kinetic parameters involved in multi-step chemical reactions. To this end we study a dimerization kinetics of protein as a model system. We follow the dimerization…