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Hybrid particle-field methods are computationally efficient approaches for modelling soft matter systems. So far applications of these methodologies have been limited to constant volume conditions. Here, we reformulate particle-field…
In this paper, we perform molecular dynamics (MD) simulations to study the two-dimensional packing process of both monosized and random size particles with radii ranging from $1.0 \, \mu m$ to $7.0 \, \mu m$. The system was allowed to…
We analytically study quantum dissipative dynamics described by the Caldirola-Kanai model with inter-particle interactions. We have found that the dissipative quantum dynamics of the Caldirola-Kanai model can be exactly mapped to a…
The algorithm for Dissipative Particle Dynamics (DPD), as modified by Espagnol and Warren, is used as a starting point for proving an H-theorem for the free energy and deriving hydrodynamic equations. Equilibrium and transport properties of…
We describe and implement a technique for extracting forces from the relaxation of an overdamped thermal system with normal modes. At sufficiently short time intervals, the evolution of a normal mode is well described by a one-dimensional…
The optimal conversion of a continuous inter-particle potential to a discrete equivalent is considered here. Existing and novel algorithms are evaluated to determine the best technique for creating accurate discrete forms using the minimum…
A density functional theory for colloidal dynamics is presented which includes hydrodynamic interactions between the colloidal particles. The theory is applied to the dynamics of colloidal particles in an optical trap which switches…
This work proposes stochastic partial differential equations (SPDEs) as a practical tool to replicate clustering effects of more detailed particle-based dynamics. Inspired by membrane-mediated receptor dynamics on cell surfaces, we…
An efficient Path Integral Monte Carlo procedure is proposed to simulate the behavior of quantum many-body dissipative systems described within the framework of the influence functional. Thermodynamic observables are obtained by Monte Carlo…
Over the last few decades, classical density-functional theory (DFT) and its dynamic extensions (DDFTs) have become powerful tools in the study of colloidal fluids. Recently, previous DDFTs for spherically-symmetric particles have been…
We explore the dynamics of a tracer in an active particle harmonic chain, investigating the influence of interactions. Our analysis involves calculating mean-squared displacements (MSD) and space-time correlations through Green's function…
The cooperative dynamics of a 1-D collection of Markov jump, interacting stochastic processes is studied via a mean-field approach. In the time-asymptotic regime, the resulting nonlinear master equation is analytically solved. The…
Plastic deformation in microscale differs from the macroscopic plasticity in two respects: (i) the flow stress of small samples depends on their size (ii) the scatter of plasticity increases significantly. In this work we focus on the…
In recent years, a number of dynamical density functional theories (DDFTs) have been developed for describing the dynamics of the one-body density of both colloidal and atomic fluids. In the colloidal case, the particles are assumed to have…
The path probability of stochastic motion of non dissipative or quasi-Hamiltonian systems is investigated by numerical experiment. The simulation model generates ideal one-dimensional motion of particles subject only to conservative forces…
We investigate a system of co-oriented active particles interacting only via hydrodynamic and steric interactions. We offer a new method of calculating the flow created by any active particle in a 2D fluid, focusing on the dynamics of flow…
Subdiffusion has been proposed as an explanation of various kinetic phenomena inside living cells. In order to fascilitate large-scale computational studies of subdiffusive chemical processes, we extend a recently suggested mesoscopic model…
A machine learning technique is proposed for quantifying uncertainty in power system dynamics with spatiotemporally correlated stochastic forcing. We learn one-dimensional linear partial differential equations for the probability density…
We use functional, Fr\'echet, derivatives to quantify how thermodynamic outputs of a molecular dynamics (MD) simulation depend on the potential used to compute atomic interactions. Our approach quantifies the sensitivity of the quantities…
Two dimensional simulations of non-cohesive granular matter in a biaxial shear tester are discussed. The effect of particle elasticity on the mechanical behavior is investigated using two complementary distinct element methods (DEM): Soft…