Related papers: Understanding Molecular Dynamics with Stochastic P…
Given a particle system obeying overdamped Langevin dynamics, we demonstrate that it is always possible to construct a thermodynamically consistent macroscopic model which obeys a gradient flow with respect to its non-equilibrium free…
Multiple time scale molecular dynamics enhances computational efficiency by updating slow motions less frequently than fast motions. However, in practice the largest outer time step possible is limited not by the physical forces but by…
Stochastic thermodynamics is a framework for describing non-equilibrium processes at the level of fluctuating trajectories, where the state of a system evolves as a stochastic time series, allowing thermodynamic quantities such as work,…
Along with recent progress in structural biology and genome biology, structural dynamics of molecular systems including nucleic acids has attracted attention in the context of gene regulation. Structure-function relationship is an important…
A general formulation of stochastic thermodynamics is presented for open systems exchanging energy and particles with multiple reservoirs. By introducing a partition in terms of "macrostates" (e.g. sets of "microstates"), the consequence on…
Electronic friction and Langevin dynamics is a popular mixed quantum-classical method for simulating the nonadiabatic dynamics of molecules interacting with metal surfaces, as it can be computationally more efficient than fully quantum…
Macroscopic theories of nucleation such as classical nucleation theory envision that clusters of the bulk stable phase form inside the bulk metastable phase. Molecular dynamics simulations are often used to elucidate nucleation mechanisms,…
We develop a formulation for molecular dynamics, Langevin, and hybrid Monte Carlo algorithms in the recently proposed generalized ensemble that is based on a physically motivated realisation of Tsallis weights. The effectiveness of the…
We examine the formulation and numerical treatment of dissipative particle dynamics (DPD) and momentum-conserving molecular dynamics. We show that it is possible to improve both the accuracy and the stability of DPD by employing a pairwise…
Binding and unbinding of ligands to specific sites of a macromolecule are one of the most elementary molecular interactions inside the cell that embody the computational processes of biological regulations. The interaction between…
Classical molecular dynamics simulations of hydrogen plasmas have been performed with emphasis on the analysis of equilibration process. Theoretical basis of simulation model as well as numerically relevant aspects -- such as the proper…
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…
A molecule traveling in a realistic propagation environment can experience stochastic interactions with other molecules and the environment boundary. The statistical behavior of some isolated phenomena, such as dilute unbounded molecular…
Recently, hybrid models have emerged that combine microscopic and mesoscopic regimes in a single stochastic reaction-diffusion simulation. Microscopic simulations track every individual molecule and are generally more accurate. Mesoscopic…
This paper presents a molecular dynamics simulation of an inelastic gas, where collisions between molecules are characterized by a coefficient of restitution less than unity. The simulation employs an event-driven algorithm to efficiently…
This paper is the second in a series devoted to the study of Langevin systems subjected to a continuous time-delayed feedback control. The goal of our previous paper [Phys. Rev. E 91, 042114 (2015)] was to derive second-law-like…
Many physical systems characterized by nonlinear multiscale interactions can be effectively modeled by treating unresolved degrees of freedom as random fluctuations. However, even when the microscopic governing equations and qualitative…
We present a new time-dependent Density Functional approach to study the relaxational dynamics of an assembly of interacting particles subject to thermal noise. Starting from the Langevin stochastic equations of motion for the velocities of…
The stochastic thermodynamics of a dilute, well-stirred mixture of chemically-reacting species is built on the stochastic trajectories of reaction events obtained from the Chemical Master Equation. However, when the molecular populations…
We study thermodynamic processes in contact with a heat bath that may have an arbitrary time-varying periodic temperature profile. Within the framework of stochastic thermodynamics, and for models of thermo-dynamic engines in the idealized…