Related papers: Systematic errors in diffusion coefficients from l…
The simulation of stochastic reaction-diffusion systems using fine-grained representations can become computationally prohibitive when particle numbers become large. If particle numbers are sufficiently high then it may be possible to…
There is a great need for improved statistical sampling in a range of physical, chemical and biological systems. Even simulations based on correct algorithms suffer from statistical error, which can be substantial or even dominant when slow…
This paper introduces a novel dynamical pressure boundary condition for weakly-compressible smoothed particle hydrodynamics (WCSPH). Unlike previous methods that rely on indirect approaches or ghost particles, our method integrates the…
Recently, an analytical expression for the system size dependence and direction-dependence of self-diffusion coefficients for neat liquids due to hydrodynamic interactions has been derived for molecular dynamics (MD) simulations using…
Diffusive transport is a universal phenomenon, throughout both biological and physical sciences, and models of diffusion are routinely used to interrogate diffusion-driven processes. However, most models neglect to take into account the…
Diffusive transport of a particle in spatially correlated random energy landscape having exponential density of states has been considered. We exactly calculate the diffusivity in the nondispersive quasi-equilibrium transport regime and…
Brownian motion in a granular gas in a homogeneous cooling state is studied theoretically and by means of molecular dynamics. We use the simplest first-principle model for the impact-velocity dependent restitution coefficient, as it follows…
We study the Brownian motion of a classical particle in one-dimensional inhomogeneous environments where the transition probabilities follow quasiperiodic or aperiodic distributions. Exploiting an exact correspondence with the…
This paper uses dynamical invariants to describe the evolution of collisionless systems subject to time-dependent gravitational forces without resorting to maximum-entropy probabilities. We show that collisionless relaxation can be viewed…
The diffusion equation is the primary tool to study the movement dynamics of a free Brownian particle, but when spatial heterogeneities in the form of permeable interfaces are present, no fundamental equation has been derived. Here we…
Recent molecular dynamics simulations show that a dilute relativistic gas equilibrates to a Juettner velocity distribution if ensemble velocities are measured simultaneously in the observer frame. The analysis of relativistic Brownian…
Dynamics simulations of constrained particles can greatly aid in understanding the temporal and spatial evolution of biological processes such as lateral transport along membranes and self-assembly of viruses. Most theoretical efforts in…
We present a multiscale simulation algorithm for amorphous materials, which we illustrate and validate in a canonical case of dense granular flow. Our algorithm is based on the recently proposed Spot Model, where particles in a dense random…
Particle-in-Cell (PIC) methods have achieved widespread recognition as simple and flexible approaches to model collisionless plasma physics in fully kinetic simulations of astrophysical environments. However, in many situations the standard…
The piston system (particles in a box) is the simplest and paradigmatic model in traditional thermodynamics. However, the recently established framework of stochastic thermodynamics (ST) fails to apply to this model system due to the…
In this paper we develop a stochastic boundary conditions (SBC) for event-driven molecular dynamics simulations of a finite volume embedded within an infinite environment. In this method, we first collect the statistics of…
Dynamic facilitation theory assumes short-ranged dynamic constraints to be the essential feature of supercooled liquids and draws much of its conclusions from the study of kinetically constrained models. While deceptively simple, these…
In the coarse grained Brownian Dynamics simulation method the many solvent molecules are replaced by random thermal kicks and an effective friction acting on the particles of interest. For Brownian Dynamics the friction has to be so strong…
Computational modelling of diffusion in heterogeneous media is prohibitively expensive for problems with fine-scale heterogeneities. A common strategy for resolving this issue is to decompose the domain into a number of non-overlapping…
Kinetic equations model the position-velocity distribution of particles subject to transport and collision effects. Under a diffusive scaling, these combined effects converge to a diffusion equation for the position density in the limit of…