Related papers: Advanced Thermostats for Molecular Dynamics
We introduce a variation of the dissipative particle dynamics (DPD) thermostat that allows for controlling transport properties of molecular fluids. The standard DPD thermostat acts only on a relative velocity along the interatomic axis.…
A new Thermodynamic Uncertainty Relation (TUR) is derived for systems described by linearly coupled Langevin equations in the presence of non-linear frictional forces. In our scheme, the main variable represents the velocity of a particle,…
We analyze a system coupled to a bath of independent harmonic oscillators. We transform the bath in chain structure by solving an inverse eigenvalue problem. We solve the equations of motion for the collective variables defined by this…
In this article we derive the effective pairwise interactions in a Langevin type united atoms model of water. The interactions are determined from the trajectories of a detailed molecular dynamics simulation of simple point charge water. A…
Coarse-graining of fully atomistic molecular dynamics simulations is a long-standing goal in order to allow the description of processes occurring on biologically relevant timescales. For example, the prediction of pathways, rates and…
By using the effective non-Markovian measure [H.P. Breuer, E.M. Laine, J. Piilo, Phys. Rev. Lett. 103, 210401 (2009)], we investigate non-Markovian dynamics of a pair of two-level atoms (TLAs) system, each of which interacting with a local…
Inspired by one--dimensional light--particle systems, the dynamics of a non-Hamiltonian system with long--range forces is investigated. While the molecular dynamics does not reach an equilibrium state, it may be approximated in the…
We study the non-equilibrium diffusion dynamics of supersonic lattice solitons in a classical chain of atoms with nearest-neighbor interactions coupled to a heat bath. As a specific example we choose an interaction with cubic anharmonicity.…
The analysis of the dynamics of tracer particles in a complex bath can provide valuable information about the microscopic behaviour of the bath. In this work, we study the dynamics of a forced tracer in a colloidal bath by means of Langevin…
We study heat exchange in temperature-biased metal-molecule-metal molecular junctions by employing the LAMMPS atomic molecular dynamics simulator. Generating the nonequilibrium steady state with Langevin thermostats at the boundaries of the…
We show through a nonlinear Fokker-Planck formalism, and confirm by molecular dynamics simulations, that the overdamped motion of interacting particles at T=0, where T is the temperature of a thermal bath connected to the system, can be…
We recently showed that the dynamics of coarse-grained observables in systems out of thermal equilibrium are governed by the non-stationary generalized Langevin equation [J. Chem. Phys. 147, 214110 (2017), J. Chem. Phys. 150, 174118…
We study the dynamics of a tracer in a dense mixture of particles connected to different thermostats. Starting from the overdamped Langevin equations that describe the evolution of the system, we derive the expression of the self-diffusion…
Many coarse-grained models have been developed for equilibrium studies of lipid bilayer membranes. To achieve in simulations access to length-scales and time-scales difficult to attain in fully atomistic molecular dynamics, these…
Based on a microscopic system reservoir model,where the associated bath is not in thermal equilibrium, we simulate the nonstationary Langevin dynamics and obtained the generalized nonstationary fluctuation dissipation relation (FDR) which…
A model for the thermodynamics of a quantum heat bath is introduced. Under the assumption that the bath molecules have finitely many degrees of freedom and are weakly interacting, we present a general derivation of the equation of state of…
We consider a chain of anharmonic oscillators immersed in a heat bath with a temperature gradient and a time varying tension applied to one end of the chain while the other side is fixed to a point. We prove that under diffusive space-time…
This article covers thermodynamic, dynamic, and kinetic models that are suitable for the analysis of wetting, adsorption, and related interfacial phenomena in colloidal and multiphase systems. Particular emphasis is made on describing…
The search for departures from standard hydrodynamics in many-body systems has yielded a number of promising leads, especially in low dimension. Here we study one of the simplest classical interacting lattice models, the nearest-neighbour…
Adaptive Langevin dynamics is a method for sampling the Boltzmann-Gibbs distribution at prescribed temperature in cases where the potential gradient is subject to stochastic perturbation of unknown magnitude. The method replaces the…