Related papers: Surface reaction-diffusion kinetics on lattice at …
Lattice-based stochastic simulators are commonly used to study biological reaction-diffusion processes. Some of these schemes that are based on the reaction-diffusion master equation (RDME), can simulate for extended spatial and temporal…
Pattern formation in reaction-diffusion systems is of great importance in surface micro-patterning [Grzybowski et al. Soft Matter. 1, 114 (2005)], self-organization of cellular micro-organisms [Schulz et al. Annu. Rev. Microbiol. 55, 105…
Several stochastic simulation algorithms (SSAs) have been recently proposed for modelling reaction-diffusion processes in cellular and molecular biology. In this paper, two commonly used SSAs are studied. The first SSA is an on-lattice…
Stochastic modeling of reaction-diffusion kinetics has emerged as a powerful theoretical tool in the study of biochemical reaction networks. Two frequently employed models are the particle-tracking Smoluchowski framework and the on-lattice…
Reaction-diffusion systems where transition rates exhibit quenched disorder are common in physical and chemical systems. We study pair reactions on a periodic two-dimensional lattice, including continuous deposition and spontaneous…
Kinetic Monte-Carlo (KMC) simulations are a well-established numerical tool to investigate the time-dependent surface morphology in molecular beam epitaxy (MBE) experiments. In parallel, simplified approaches such as limited mobility (LM)…
The reaction-diffusion master equation (RDME) is a lattice stochastic reaction-diffusion model that has been used to study spatially distributed cellular processes. The RDME is often interpreted as an approximation to spatially-continuous…
The reaction-diffusion master equation (RDME) is a model that allows for efficient on-lattice simulation of spatially resolved stochastic chemical kinetics. Compared to off-lattice hard-sphere simulations with Brownian Dynamics (BD) or…
We introduce a distribution-free lattice Boltzmann formulation for general compartmental reaction--diffusion systems arising in mathematical epidemiology. The proposed scheme, termed a single-step simplified lattice Boltzmann method…
A new lattice Boltzmann model (LBM) is presented to describe chemically reacting multicomponent fluid flow in homogenised porous media. In this work, towards further generalizing the multicomponent reactive lattice Boltzmann model, we…
In this paper, a boundary scheme is proposed for the two-dimensional five-velocity (D2Q5) lattice Boltzmann method with heterogeneous surface reaction, in which the unknown distribution function is determined locally based on the kinetic…
Rate-equation models are a widely-used and inexpensive tool for the simulation of interstellar chemistry under a range of physical conditions. However, their application to grain-surface chemical systems necessitates a number of simplifying…
We study the effect of confinement on diffusion limited bimolecular reactions within a lattice model where a small number of reactants diffuse amongst a much larger number of inert particles. When the number of inert particles is held…
Computational systems biology has provided plenty of insights into cell biology. Early on, the focus was on reaction networks between molecular species. Spatial distribution only began to be considered mostly within the last decade.…
We study diffusion-reaction processes on periodic square planar lattices and simple cubic (sc) lattices. Considered first is a single diffusing reactant undergoing an irreversible reaction upon first encounter with a stationary co-reactant…
In this work, we first develop a general mesoscopic multiple-relaxation-time lattice Boltzmann (MRT-LB) model for the two-dimensional diffusion equation with the constant diffusion coefficient and source term, where the D2Q5 (five discrete…
Over the last decade, the Lattice Boltzmann method has found major scope for the simulation of a large spectrum of problems in soft matter, from multiphase and multi-component microfluidic flows, to foams, emulsions, colloidal flows, to…
The reaction-diffusion master equation is a stochastic model often utilized in the study of biochemical reaction networks in living cells. It is applied when the spatial distribution of molecules is important to the dynamics of the system.…
The birth of the lattice Boltzmann method (LBM) fulfils a dream that simple arithmetic calculations can simulate complex fluid flows without solving complicated partial differential flow equations. Its power and potential of resolving more…
Microfluidics provides a powerful and versatile technology to accurately control spatial and temporal conditions for cell culturing and can therefore be used to study cellular responses to gradients. Here we use Lattice Boltzmann methods…