Related papers: Systematic errors in diffusion coefficients from l…
We derive diffusive macroscopic equations for the particle and energy density of a system whose time evolution is described by a kinetic equation for the one particle position and velocity function f(r,v,t) that consists of a part that…
Time-dependent density functional theory is widely used to describe excitations of many-fermion systems. In its many applications, 3D coordinate-space representation is used, and infinite-domain calculations are limited to a finite volume…
Single-molecule localization microscopy allows practitioners to locate and track labeled molecules in biological systems. When extracting diffusion coefficients from the resulting trajectories, it is common practice to perform a linear fit…
In this work, we have performed a detailed holographic analysis of the stochastic dynamics of a heavy particle propagating through a strongly coupled plasma moving with a constant velocity along a fixed spatial direction. To model this…
The histogram reweighting technique, widely used to analyze Monte Carlo data, is shown to be applicable to dynamic properties obtained from Molecular Dynamics simulations. The theory presented here is based on the fact that the correlation…
We present a multiscale hybrid particle-field scheme for the simulation of relaxation and diffusion behavior of soft condensed matter systems. It combines particle-based Brownian dynamics and field-based local dynamics in an adaptive sense…
We perform molecular dynamics simulation of a small number of particles in a box with periodic boundary conditions from a view point of chaotic dynamical systems. There is a transition at a critical energy E_c that each particle is confined…
The discretization approximation method commonly used to simulate the dynamics of quantum system coupled to the environment in continuum often suffers from the periodically partial recovery of initial state because of the effect of finite…
The dynamics of open quantum systems can be simulated by unraveling it into an ensemble of pure state trajectories undergoing non-unitary monitored evolution, which has recently been shown to undergo measurement-induced entanglement phase…
We investigate finite-size effects on diffusion in confined fluids using molecular dynamics simulations and hydrodynamic calculations. Specifically, we consider a Lennard-Jones fluid in slit pores without slip at the interface and show that…
This work presents a generalization of the Kraynik-Reinelt (KR) boundary conditions for nonequilibrium molecular dynamics simulations. In the simulation of steady, homogeneous flows with periodic boundary conditions, the simulation box…
We propose a computational method to simulate anomalous self-diffusion in a simple liquid. The method is based on a molecular dynamics simulation on which we impose the following two conditions: firstly, the inter-particle interaction is…
A new method is proposed to numerically extract the diffusivity of a (typically nonlinear) diffusion equation from underlying stochastic particle systems. The proposed strategy requires the system to be in local equilibrium and have…
We consider the increase of the spatial variance of some inhomogeneous, non-equilibrium density (particles, energy, etc.) in a periodic quantum system of condensed matter-type. This is done for a certain class of initial quantum states…
When studying high-dimensional dynamical systems such as macromolecules, quantum systems and polymers, a prime concern is the identification of the most probable states and their stationary probabilities or free energies. Often, these…
We analyze the diffusion of a Brownian particle in a fluid under stationary flow. By using the scheme of non-equilibrium thermodynamics in phase space, we obtain the Fokker-Planck equation which is compared with others derived from kinetic…
In molecular simulations, efficient methods for investigating equilibration and slow relaxation in dense systems are crucial yet challenging. This study focuses on the diffusional characteristics of monodisperse hard disk systems at…
Recent developments in multiscale computation allow the solution of ``coarse equations'' for the expected macroscopic behavior of microscopically/stochastically evolving particle distributions without ever obtaining these coarse equations…
We study by molecular dynamics computer simulation a binary soft-sphere mixture that shows a pronounced decoupling of the species' long-time dynamics. Anomalous, power-law-like diffusion of small particles arises, that can be understood as…
Although an intimate relation between entropy and diffusion has been advocated for many years and even seems to have been verified in theory and experiments, a quantitatively reliable study, and any derivation of an algebraic relation…