Related papers: 3D Molecular dynamics simulations using spheropoly…
We provide a two dimensional deformation model to describe how soft squishy circular particles respond to external forces and collisions. This model involves formulating mathematical equations and algorithms for the shape of a deformed…
Droplets form a cornerstone of the spatiotemporal organization of biomolecules in cells. These droplets are controlled using physical processes like chemical reactions and imposed gradients, which are costly to simulate using traditional…
Stochastic models of reaction-diffusion systems are important for the study of biochemical reaction networks where species are present in low copy numbers or if reactions are highly diffusion limited. In living cells many such systems…
The mechanisms of physical and chemical interactions of low temperature plasmas with surfaces can be fruitfully explored using molecular dynamics (MD) simulations. MD simulations follow the detailed motion of sets of interacting atoms…
A general framework for performing event-driven simulations of systems with semi-flexible or rigid bodies interacting under impulsive torques and forces is outlined. Two different approaches are presented. In the first, the dynamics and…
In this review we discuss the recent progress in the simulation of soft active matter systems and in particular the hydrodynamics of microswimmers using the method of multiparticle collision dynamics, which solves the hydrodynamic flows…
In this paper we review the simulation method of the non-smooth contact dynamics. This technique was designed to solve the unilateral and frictional contact problem for a large number of rigid bodies and has proved to be especially valuable…
We present a parallel-scalable method for simulating non-dilute suspensions of deformable particles immersed in Stokesian fluid in three dimensions. A critical component in these simulations is robust and accurate collision handling. This…
A simulation technique is described for quantifying the contribution of three-body interactions to the thermodynamical properties of coarse-grained representations of complex fluids. The method is based on comparing the third virial…
Molecular dynamics simulations are used to investigate the atomic mobility and diffusivity of a generalized Frenkel-Kontorova model which takes into account anharmonic (exponential) interaction of atoms subjected to a three-dimensional…
In this thesis, we develop multiscale models for particle simulations in population dynamics. These models are characterised by prescribing particle motion on two spatial scales: microscopic and macroscopic. At the microscopic level, each…
Three-dimensional (3D) particle-in-cell (PIC) simulations are used to investigate the interaction of ultrahigh intensity lasers ($> 10^{20}$ W/cm$^{-2}$) with matter at overcritical densities. Intense laser pulses are shown to penetrate up…
In this article, two novel numerical methods have been developed for simulating fluid/porous particle interactions in three-dimensional (3D) Stokes flow. The Brinkman-Debye-Bueche model is adopted for the fluid flow inside the porous…
The simplest (2+1)-dimensional mechanical systems associated with light-like curves, already studied by Nersessian and Ramos, are reconsidered. The action is linear in the curvature of the particle path and the moduli spaces of solutions…
Modeling membrane interactions with arbitrarily shaped colloidal particles, such as environmental micro- and nanoplastics, at the cell scale remains particularly challenging, owing to the complexity of particle geometries and the need to…
We develop a numerical a framework to study phoretic particle dynamics in two dimensions. The particles are modeled as chemically active rigid circles, which can emit or absorb a solute into surrounding fluid. The interaction between…
Two-dimensional Molecular Dynamics simulations are used to model the free surface flow of spheres falling down an inclined chute. The interaction between the particles in our model is assumed to be subjected to the Hertzian contact force…
Real-life control tasks involve matters of various substances---rigid or soft bodies, liquid, gas---each with distinct physical behaviors. This poses challenges to traditional rigid-body physics engines. Particle-based simulators have been…
We present, in a unifying way, the main components of three asynchronous event-driven algorithms for simulating physical systems of interacting particles. The first example, hard-particle molecular dynamics, is well-known. We also present a…
Elastic filaments are vital to biological, physical and engineering systems, from cilia driving fluid in the lungs to artificial swimmers and micro-robotics. Simulating slender structures requires intricate balance of elastic, body, active,…