Related papers: A Simulation Algorithm for Brownian Dynamics on Co…
We investigate the usage of a recently introduced noise-cancellation algorithm for Brownian simulations to enhance the precision of measuring transport properties such as the mean-square displacement or the velocity-autocorrelation…
Colloidal solutions posses a wide range of time and length scales, so that it is unfeasible to keep track of all of them within a single simulation. As a consequence some form of coarse-graining must be applied. In this work we use the…
We develop a computational method for modeling electrostatic interactions of arbitrarily-shaped, polarizable objects on colloidal length scales, including colloids/nanoparticles, polymers, and surfactants, dispersed in explicit ion…
Stiff forces, which bind objects together or otherwise confine motion, are found widely in soft-matter systems - colloids with short range attractions, ligand-receptor contacts, particles in optical traps, fibres that resist stretching,…
We present a hybrid Brownian dynamics / Monte Carlo algorithm for simulating solutions of highly entangled semiflexible polymers or filaments. The algorithm combines a Brownian dynamics time-stepping approach with an efficient scheme for…
In colloidal systems, Brownian motion emerges from the massive separation of time and length scales associated to characteristic dynamics of the solute and solvent constituents. This separation of scales produces several temporal regimes in…
Particle suspensions are ubiquitous in our daily life, but are not well understood due to their complexity. During the last twenty years, various simulation methods have been developed in order to model these systems. Due to varying…
We describe in detail how to implement a coarse-grained hybrid Molecular Dynamics and Stochastic Rotation Dynamics simulation technique that captures the combined effects of Brownian and hydrodynamic forces in colloidal suspensions. The…
Two algorithms that combine Brownian dynamics (BD) simulations with mean-field partial differential equations (PDEs) are presented. This PDE-assisted Brownian dynamics (PBD) methodology provides exact particle tracking data in parts of the…
The recent advent of advanced microfabrication capabilities of microfluidic devices has driven attention towards the behavior of particles in inertial flows within microchannels for applications related to the separation and concentration…
We investigate experimentally and theoretically thin layers of colloid particles held adjacent to a solid substrate by gravity. Epifluorescence, confocal, and holographic microscopy, combined with Monte Carlo and hydrodynamic simulations,…
Intraoperative observation of tissue internal structure is often difficult. Hence, real-time soft tissue deformation is essential for the localization of tumor and other internal structures. We propose a method to simulate the internal…
The phoretic Brownian dynamics method is shown here to be an effective approach to simulate the properties of colloidal chemophoretic based systems. The method is then optimized to allow for the comparison with results from multiparticle…
Diffusion processes are fundamental in modelling stochastic dynamics in natural sciences. Recently, simulating such processes on complicated geometries has found applications for example in biology, where toroidal data arises naturally when…
The dynamics of individual colloidal particles in random potential energy landscapes were investigated experimentally and by Monte Carlo simulations. The value of the potential at each point in the two-dimensional energy landscape follows a…
Confocal microscopy of fluorescent labeled particles has been used to study the dynamical and structural properties of colloidal and granular matter in real space. Localization algorithms allow for a fully automatized determination of the…
In this work, we provide a solution to the problem of computing collision stress in particle-tracking simulations. First, a formulation for the collision stress between particles is derived as an extension of the virial stress formula to…
This paper presents a novel formula for the transition density of the Brownian motion on a sphere of any dimension and discusses an algorithm for the simulation of the increments of the spherical Brownian motion based on this formula. The…
In the first part of a series of two papers, we present in considerable detail a collision-driven molecular dynamics algorithm for a system of nonspherical particles, within a parallelepiped simulation domain, under both periodic or…
We propose a new model for the description of complex granular particles and their interaction in molecular dynamics simulations of granular material in two dimensions. The grains are composed of triangles which are connected by deformable…