Related papers: Efficient Reactive Brownian Dynamics
Based on analytical and numerical calculations we study the dynamics of an overdamped colloidal particle moving in two dimensions under time-delayed, non-linear feedback control. Specifically, the particle is subject to a force derived from…
We describe a two-dimensional model for active particles whose self-propulsion speed is not fixed, but varies in time, and whose motion is subject to both translational and rotational diffusion. In the conventional treatment of active…
Stochastic chemical systems with diffusion are modeled with a reaction-diffusion master equation. On a macroscopic level, the governing equation is a reaction-diffusion equation for the averages of the chemical species. On a mesoscopic…
Semimartingale reflecting Brownian motions (SRBMs) are diffusion processes with state space the d-dimensional nonnegative orthant, in the interior of which the processes evolve according to a Brownian motion, and that reflect against the…
We study various combinations of active diffusion with branching, as an extension of standard reaction-diffusion processes. We concentrate on the selection of the asymptotic wavefront speed for thermal run-and-tumble and for thermal active…
The non-thermal nature of self-propelling colloids offers new insights into non-equilibrium physics. The central mathematical model to describe their trajectories is active Brownian motion, where a particle moves with a constant speed,…
We present a diagrammatic formulation of a theory for the time dependence of density fluctuations in equilibrium systems of interacting Brownian particles. To facilitate derivation of the diagrammatic expansion we introduce a basis that…
We proposed a new technique to accelerate sampling methods for solving difficult optimization problems. Our method investigates the intrinsic connection between posterior distribution sampling and optimization with Langevin dynamics, and…
Three coarse-grained molecular dynamics (MD) models are investigated with the aim of developing and analyzing multiscale methods which use MD simulations in parts of the computational domain and (less detailed) Brownian dynamics (BD)…
Stokesian Dynamics (SD) is a numerical framework used for simulating hydrodynamic interactions in particle suspensions at low Reynolds number. It combines far-field approximations with near-field lubrication corrections, offering a balance…
A second-order accurate in time, positivity-preserving, and unconditionally energy stable operator splitting numerical scheme is proposed and analyzed for the system of reaction-diffusion equations with detailed balance. The scheme is…
Up to now, it is not possible to obtain analytical solutions for complex molecular association processes (e.g. Molecule recognition in Signaling or catalysis). Instead Brownian Dynamics (BD) simulations are commonly used to estimate the…
The interplay between stochastic chemical reactions and diffusion can generate rich spatiotemporal patterns. While the timescale for individual reaction or diffusion events may be very fast, the timescales for organization can be much…
Together with the universally recognized SIR model, several approaches have been employed to understand the contagious dynamics of interacting particles. Here, Active Brownian particles (ABP) are introduced to model the contagion dynamics…
We develop and analyze a stochastic genetic interacting particle method (SGIP) for reaction-diffusion-advection (RDA) equations. The SGIP method employs operator splitting to approximate the advection-diffusion and reaction processes,…
In this work animations of the random walk movement using a freeware Algodoo were done in order to support teaching the concepts of Brownian Motion. The random walk movement were simulate considering elastic collision between the particles…
Single-file diffusion (SFD) is a key mechanism underlying transport phenomena in confined physical and biological systems. In a typical SFD process, microscopic particles are restricted to moving in a narrow channel where they cannot pass…
We introduce rd-spiral, an open-source Python library for simulating 2D reaction-diffusion systems using pseudo-spectral methods. The framework combines FFT-based spatial discretization with adaptive Dormand-Prince time integration,…
The ring polymer molecular dynamics (RPMD) rate theory is an efficient and accurate method for estimating rate coefficients of chemical reactions affected by nuclear quantum effects. The commonly used RPMD treatment of gas-phase bimolecular…
Diffusion Schr\"odinger bridges (DSB) have recently emerged as a powerful framework for recovering stochastic dynamics via their marginal observations at different time points. Despite numerous successful applications, existing algorithms…