Related papers: Discrete state model of a self-aggregating colloid…
Systems driven by Brownian motion are ubiquitous. A prevailing challenge is inferring, from data, the diffusion and kinetic parameters that describe these stochastic processes. In this work, we investigate a multi-state diffusion process…
We demonstrate a simple method by which time-dependent interactions can be exploited to improve self-assembly in colloidal systems. We apply this method to two systems: a model colloid with short-ranged attractive potentials that undergoes…
We present a stochastic approach to modeling the dynamics of coexistence of prey and predator populations. It is assumed that the space of coexistence is explicitly subdivided in a grid of cells. Each cell can be occupied by only one…
Understanding the organization of collective motion in biological systems is an ongoing challenge. In this Paper we consider a minimal model of self-propelled particles with variable speed. Inspired by experimental data from schooling fish,…
Markov state models (MSMs) have become a popular approach for investigating the conformational dynamics of proteins and other biomolecules. MSMs are typically built from numerous molecular dynamics simulations by dividing the sampled…
We review recent experimental, numerical, and analytical results on active suspensions of self-propelled colloidal beads moving in (quasi) two dimensions. Active colloids form part of the larger theme of active matter, which is noted for…
A method to couple interparticle contact models with Stokesian dynamics (SD) is introduced to simulate colloidal aggregates under flow conditions. The contact model mimics both the elastic and plastic behavior of the cohesive connections…
Colloidal gels are a prototypical example of a heterogeneous network solid whose complex properties are governed by thermally-activated dynamics. In this Letter we experimentally establish the connection between the intermittent dynamics of…
Markov state models (MSMs) have been successful in computing metastable states, slow relaxation timescales and associated structural changes, and stationary or kinetic experimental observables of complex molecules from large amounts of…
We demonstrate how direct simulation of stochastic, individual-based models can be combined with continuum numerical analysis techniques to study the dynamics of evolving diseases. % Sidestepping the necessity of obtaining explicit…
Understanding the out-of-equilibrium properties of noisy microscale systems and the extent to which they can be modulated externally, is a crucial scientific and technological challenge. It holds the promise to unlock disruptive new…
We reconsider the structure-based route to coarse graining in which the coarse-grained model is defined in such a way to reproduce some distributions functions of the original system as accurately as possible. We consider standard…
In this study, a coarse-graining framework for discrete models is formulated on the basis of multiscale homogenization. The discrete model considered in this paper is the Lattice Discrete Particle Model (LDPM), which simulates concrete at…
We study a set of models of self-propelled particles that achieve collective motion through similar alignment-based dynamics, considering versions with and without repulsive interactions that do not affect the heading directions. We explore…
We study clustering in a stochastic system of particles sliding down a fluctuating surface in one and two dimensions. In steady state, the density-density correlation function is a scaling function of separation and system size.This scaling…
We propose a kinetic model for the self-aggregation by amyloid proteins. By extending several well-known models for protein aggregation, the time evolution of aggregate concentrations containing $r$ proteins, denoted $c_r(t)$, can be…
We systematically derive an exact coarse-grained description for interacting particles with thermodynamically consistent stochastic dynamics, applicable across different observation scales, the mesoscopic and the macroscopic. We implement…
We introduce a stochastic agent-based model for the flocking dynamics of self-propelled particles that exhibit velocity-alignment interactions with neighbours within their field of view. The stochasticity in the dynamics of the model arises…
Depending on the pH value and salt concentration of Al2O3 suspensions different microstructures can form. Especially the clustered one is of major interest for industrial purposes as found in the production of ceramics. In this paper we…
Non-equilibrium collective behavior of self-propelled colloidal rods in a confining channel is studied using Brownian dynamics simulations and dynamical density functional theory. We observe an aggregation process in which rods…