Related papers: Surface reaction-diffusion kinetics on lattice at …
We analyze response of a macromolecule near to a substrate; the substrate is tiled in the sequential and specific manner so that repeat units of the macromolecule may have different response on its adsorption in different directions onto…
Derivation of macroscopic models for advection-diffusion processes in the presence of dominant heterogeneous (e.g., surface) reactions using homogenisation theory or volume averaging is often deemed unfeasible due to the strong coupling…
We develop a multiscale simulation model for diffusion of solutes through porous triblock copolymer membranes. The approach combines two techniques: self-consistent field theory (SCFT) to predict the structure of the self-assembled,…
Recently, hybrid models have emerged that combine microscopic and mesoscopic regimes in a single stochastic reaction-diffusion simulation. Microscopic simulations track every individual molecule and are generally more accurate. Mesoscopic…
In this paper, a three-dimensional (3D) multiple-relaxation-time (MRT) lattice Boltzmann (LB) model is presented for convection heat transfer in porous media at the representative elementary volume (REV) scale. The model is developed in the…
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…
This study explores the emergence of life through a simulation model approach. The model "Multi-set chemical lattice model" is a model that allows virtual molecules of multiple types to be placed in each lattice cell on a two-dimensional…
In many biological situations, a species arriving from a remote source diffuses in a domain confined between two parallel surfaces until it finds a binding partner. Since such a geometric shape falls in between two- and three-dimensional…
This review article is intended as a practical guide for newcomers to the field of kinetic Monte Carlo (KMC) simulations, and specifically to lattice KMC simulations as prevalently used for surface and interface applications. We will…
The asymmetric stem-cell division of Drosophila SOP precursor cells is driven by the asymmetric localisation of the key protein Lgl (Lethal giant larvae) during mitosis, when Lgl is phosphorylated by the kinase aPKC on a subpart of the…
We address the dynamics of adsorbed molecules (a fundamental issue in surface physics) within the framework of a Master Equation scheme, and study the diffusion of particles in a finite cubic lattice whose boundaries are at the $z=1$ and…
Motivated by models of signaling pathways in B lymphocytes, which have extremely large nuclei, we study the question of how reaction-diffusion equations in thin $2D$ domains may be approximated by diffusion equations in regions of smaller…
A general and local reactive boundary condition (RBC) for studying first-order equilibrium reactions using the lattice Boltzmann method (LBM) is presented. Its main characteristics are accurate reproduction of wall diffusion, invariance to…
The Kinetic Monte Carlo (KMC) method has become an important tool for examination of phenomena like surface diffusion and thin film growth because of its ability to carry out simulations for time scales that are relevant to experiments. But…
The reaction-diffusion master equation (RDME) is a lattice-based stochastic model for spatially resolved cellular processes. It is often interpreted as an approximation to spatially continuous reaction-diffusion models, which, in the limit…
We report an implementation of the lattice Boltzmann method (LBM) to integrate the Bloch-Torrey equation, which describes the evolution of the transverse magnetization vector and the fate of the signal of diffusion magnetic resonance…
We study the deformation and dynamics of droplets in time-dependent flows using 3D numerical simulations of two immiscible fluids based on the lattice Boltzmann model (LBM). Analytical models are available in the literature, which assume…
We analyze diffusion of particles on a two dimensional square lattice. Each lattice site contains an arbitrary number of particles. Interactions affect particles only in the same site, and are macroscopically represented by the excess…
Stochastic reaction-diffusion models are employed to represent many complex physical, biological, societal, and ecological systems. The macroscopic reaction rates describing the large-scale kinetics in such systems are effective,…
A new lattice Boltzmann model (LBM) for chemically reactive mixtures is presented. The approach capitalizes on the recently introduced thermodynamically consistent LBM for multicomponent mixtures of ideal gases. Similar to the non-reactive…