Related papers: A Minimally-Resolved Immersed Boundary Model for R…
The numerical simulation of multiphase flows involving dispersed components with large scale disparities, such as the collisions between millimeter-sized bubbles and micron-sized mineral particles in flotation, poses a significant…
We consider a model system consisting of two reaction-diffusion equations, where one species diffuses in a volume while the other species diffuses on the surface which surrounds the volume. The two equations are coupled via a nonlinear…
We present a versatile open-source pipeline for simulating inhomogeneous reaction-diffusion processes in highly resolved, image-based geometries of porous media with reactive boundaries. Resolving realistic pore-scale geometries in…
The simulation of stochastic reaction-diffusion systems using fine-grained representations can become computationally prohibitive when particle numbers become large. If particle numbers are sufficiently high then it may be possible to…
In a continuum model of the solvation of charged molecules in an aqueous solvent, the classical Poisson-Boltzmann (PB) theory is generalized to include the solute point charges and the dielectric boundary that separates the high-dielectric…
Reaction-diffusion models with nonlocal constraints naturally arise as limiting cases of coupled bulk-surface models of intracellular signalling. In this paper, a minimal, mass-conserving model of cell-polarization on a curved membrane is…
The aim of this paper is to discuss the appropriate modelling of in- and outflow boundary conditions for nonlinear drift-diffusion models for the transport of particles including size exclusion and their effect on the behaviour of…
A simulation framework based on the level-set and the immersed boundary methods (LS-IBM) has been developed for reactive transport problems in porous media involving a moving solid-fluid interface. The interface movement due to surface…
We present a high order parameter-robust numerical method for a system of (M>=2) coupled singularly perturbed parabolic reaction-diffusion problems. A small perturbation parameter {\epsilon} is multiplied with the second order spatial…
We develop a Split Reactive Brownian Dynamics (SRBD) algorithm for particle simulations of reaction-diffusion systems based on the Doi or volume reactivity model, in which pairs of particles react with a specified Poisson rate if they are…
Diffusion-induced Ramsey narrowing that appears when atoms can leave the interaction region and repeatedly return without lost of coherence is investigated using strong collisions approximation. The effective diffusion equation is obtained…
We develop a Fluctuating Immersed Boundary (FIB) method for performing Brownian dynamics simulations of confined particle suspensions. Unlike traditional methods which employ analytical Green's functions for Stokes flow in the confined…
The Immersed Boundary Method (IBM) is one of the popular one-fluid mixed Eulerian-Lagrangian methods to simulate motion of droplets. While the treatment of a moving complex boundary is an extremely time consuming and formidable task in a…
We propose enforcing constraints on Model-Based Diffusion by introducing emerging barrier functions inspired by interior point methods. We demonstrate that the standard Model-Based Diffusion algorithm can lead to catastrophic performance…
We study mean-field inclusion processes with an additional slow phase, in which particle interactions occur at a vanishing rate proportional to the inverse system size. In the thermodynamic limit, such systems exhibit condensation at high…
This paper presents eigensolution and non-modal analyses for immersed boundary methods (IBMs) based on volume penalization for the linear advection equation. This approach is used to analyze the behavior of flux reconstruction (FR)…
The problem of mass diffusion in layered systems has relevance to applications in different scientific disciplines, e.g., chemistry, material science, soil science, and biomedical engineering. The mathematical challenge in these type of…
This work presents an intermediate resolution model of the hydrodynamics of colloidal particles based on a mixed Eulerian-Lagrangian formulation. The particle is constructed with a small set of overlapping Peskin's Immersed Boundary kernels…
We study the mass-conserved reaction-diffusion system known as the wave-pinning model, which serves as a minimal framework for describing cell polarity. In this model, the interplay between reaction kinetics and slow diffusion forms a sharp…
Several classic problems for particles diffusing outside an arbitrary configuration of non-overlapping partially reactive spherical traps in three dimensions are revisited. For this purpose, we describe the generalized method of separation…