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In this article we propose a unified framework in order to study reaction-diffusion systems containing self- and cross-diffusion using a free energy approach. This framework naturally leads to the formulation of an energy law, and to a…
Markov chains are fundamental models for stochastic dynamics, with applications in a wide range of areas such as population dynamics, queueing systems, reinforcement learning, and Monte Carlo methods. Estimating the transition matrix and…
Stochastic reaction-diffusion models are now a popular tool for studying physical systems in which both the explicit diffusion of molecules and noise in the chemical reaction process play important roles. The Smoluchowski diffusion-limited…
Morphogenesis is central to biology but remains largely unexplored in chemistry. Reaction-diffusion (RD) mechanisms are, however, essential to understand how shape emerges in the living world. While numerical methods confirm the incredible…
Stochasticity plays important roles in reaction systems. Vector fields of probability flux and velocity characterize time-varying and steady-state properties of these systems, including high probability paths, barriers, checkpoints among…
To analyze possible generalizations of reaction-diffusion schemes for the case of subdiffusion we discuss a simple monomolecular conversion A --> B. We derive the corresponding kinetic equations for local A and B concentrations. Their form…
Subsurface flows are commonly modeled by advection-diffusion equations. Insufficient measurements or uncertain material procurement may be accounted for by random coefficients. To represent, for example, transitions in heterogeneous media,…
A new method is introduced allowing to solve exactly the reactions A+A->inert and A+A->A on the 1D lattice with synchronous diffusional dynamics (simultaneous hopping of all particles). Exact connections are found relating densities and…
We derive diffusive macroscopic equations for the particle and energy density of a system whose time evolution is described by a kinetic equation for the one particle position and velocity function f(r,v,t) that consists of a part that…
In the first part of this paper math-ph/0612078, a complete description of Q-conditional symmetries for two classes of reaction-diffusion-convection equations with power diffusivities is derived. It was shown that all the known results for…
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,…
This study deals with continuous limits of interacting one-dimensional diffusive systems, arising from stochastic distortions of discrete curves with various kinds of coding representations. These systems are essentially of a…
The nonlinear coupled reaction-diffusion (NCRD) systems are important in the formation of spatiotemporal patterns in many scientific and engineering fields, including physical and chemical processes, biology, electrochemical processes,…
We consider the Cauchy problem on nonlinear scalar conservation laws with a diffusion-type source term related to an index $s\in \R$ over the whole space $\R^n$ for any spatial dimension $n\geq 1$. Here, the diffusion-type source term…
We address the numerical treatment of source terms in algebraic flux correction schemes for steady convection-diffusion-reaction (CDR) equations. The proposed algorithm constrains a continuous piecewise-linear finite element approximation…
Physics-guided sampling with diffusion priors has recently shown strong performance in solving complex systems of partial differential equations (PDEs) from sparse observations. However, these methods are typically evaluated on benchmark…
We are interested in the numerical solution of nonsymmetric linear systems arising from the discretization of convection-diffusion partial differential equations with separable coefficients and dominant convection. Preconditioners based on…
We study the coupled two-species non-equilibrium reaction-controlled diffusion model introduced by Trimper et al. [Phys. Rev. E 62, 6071 (2000)] by means of detailed Monte Carlo simulations in one and two dimensions. Particles of type A may…
Traditional chemical kinetics may be inappropriate to describe chemical reactions in micro-domains involving only a small number of substrate and reactant molecules. Starting with the stochastic dynamics of the molecules, we derive a…
The Metropolis Monte Carlo (MC) method is used to extract reaction kinetics from a given equilibrium distribution of states of a complex system. The approach is illustrated by the folding/unfolding reaction for two proteins - a model…