Related papers: A Convergent Reaction-Diffusion Master Equation
Diffusion-coagulation can be simply described by a dynamic where particles perform a random walk on a lattice and coalesce with probability unity when meeting on the same site. Such processes display non-equilibrium properties with strong…
We obtain a fast diffusion equation (FDE) as scaling limit of a sequence of zero-range process with symmetric unit rate. Fast diffusion effect comes from the fact that the diffusion coefficient goes to infinity as the density goes to zero.…
One of the main challenges in diffusion-based molecular communication is dealing with the non-linearity of reaction-diffusion chemical equations. While numerical methods can be used to solve these equations, a change in the input signals or…
Standard Reaction-Diffusion (RD) systems are characterized by infinite velocities and no persistence in the movement of individuals, two conditions that are violated when considering living organisms. Here we consider a discrete particle…
This paper proposes a novel reaction-diffusion system approximation tailored for singular diffusion problems, typified by the fast diffusion equation. While such approximation methods have been successfully applied to degenerate parabolic…
We investigate Turing pattern formation in a stochastic and spatially discretized version of a reaction diffusion advection (RDA) equation, which was previously introduced to model synaptogenesis in \textit{C. elegans}. The model describes…
In this paper we present computational techniques to investigate the solutions of two-component, nonlinear reaction-diffusion (RD) systems on arbitrary surfaces. We build on standard techniques for linear and nonlinear analysis of RD…
A class of Brownian dynamics algorithms for stochastic reaction-diffusion models which include reversible bimolecular reactions is presented and analyzed. The method is a generalization of the $\lambda$--$\newrho$ model for irreversible…
We study a system of diffusing point particles in which any triplet of particles reacts and is removed from the system when the relative proximity of the constituent particles satisfies a predefined condition. Proximity-based reaction…
Most biochemical reactions in living cells rely on diffusive search for target molecules or regions in a heterogeneous overcrowded cytoplasmic medium. Rapid re-arrangements of the medium constantly change the effective diffusivity felt…
The stochastic kinetics of BRN are described by a chemical master equation (CME) and the underlying laws of mass action. The CME must be usually solved numerically by generating enough traces of random reaction events. The resulting…
We propose a solution formula for chemical diffusion master equations of birth and death type. These equations, proposed and formalized in the recent paper [5], aim at incorporating the spatial diffusion of molecules into the description…
Smoothed dissipative particle dynamics (SDPD) is a widely used particle-based method for modelling soft matter systems at mesoscopic and macroscopic scales, offering thermodynamic consistency and direct control over the fluid's transport…
In this paper, a new two-relaxation-time regularized (TRT-R) lattice Boltzmann (LB) model for convection-diffusion equation (CDE) with variable coefficients is proposed. Within this framework, we first derive a TRT-R collision operator by…
We design and analyze an approximation method for advection-diffusion-reaction equations where the (generalized) degrees of freedom are polynomials of order $k\ge0$ at mesh faces. The method hinges on local discrete reconstruction operators…
Multiple time scales problems are investigated by combining geometrical and analytical approaches. More precisely, for fast-slow reaction-diffusion systems, we first prove the existence of slow manifolds for the abstract problem under the…
The spatially distributed reaction networks are indispensable for the understanding of many important phenomena concerning the development of organisms, coordinated cell behavior, and pattern formation. The purpose of this brief discussion…
We show that discrete distributions on the $d$-dimensional non-negative integer lattice can be approximated arbitrarily well via the marginals of stationary distributions for various classes of stochastic chemical reaction networks. We…
A simple reaction-diffusion-advection equation is proposed in a dichotomous tree network to discuss an optimal network. An optimal size ratio r is evaluated by the principle of maximization of total reaction rate. In the case of…
A new class of asynchronous discrete-event simulation schemes for advection-diffusion-reaction equations are introduced, which is based on the principle of allowing quanta of mass to pass through faces of a Cartesian finite volume grid. The…