SUMMARY MesoRD is a tool for simulating stochastic reaction-diffusion systems as modeled by the reaction diffusion master equation. The simulated systems are defined in the Systems Biology Markup Language with additions to define compartment geometries. MesoRD 1.0 supports scale-dependent reaction rate constants and reactions between reactants in neighbouring subvolumes. These new features make...

We introduce a DNA-based reaction-diffusion (RD) system in which reaction and diffusion terms can be precisely and independently controlled. The effective diffusion coefficient of an individual reaction component, as we demonstrate on a traveling wave, can be reduced up to 2.7-fold using a self-assembled hydrodynamic drag. The intrinsic programmability of this RD system allows us to engineer, f...

the stochastic reaction diffusion systems may suffer sudden shocks‎, ‎in order to explain this phenomena‎, ‎we use markovian jumps to model stochastic reaction diffusion systems‎. ‎in this paper‎, ‎we are interested in almost sure exponential stability of stochastic reaction diffusion systems with markovian jumps‎. ‎under some reasonable conditions‎, ‎we show that the trivial solution of stocha...

We propose a kind of reaction-diffusion equations for cell differentiation, which exhibits the Turing instability. If the diffusivity of some variables is set to be infinity, we get coupled competitive reaction-diffusion equations with a global feedback term. The size ratio of each cell type is controlled by a system parameter in the model. Finally, we extend the model to a cascade model of cel...

A nanoparticle growth model is developed to predict and guide the syntheses of monodisperse colloidal nanoparticles in the liquid phase. The model, without any a priori assumptions, is based on the Fick's law of diffusion, conservation of mass and the Gibbs-Thomson equation for crystal growth. In the limiting case, this model reduces to the same expression as the currently accepted model that r...

Behavior of catalytic reactions in narrow pores is controlled by a delicate interplay between fluctuations in adsorption-desorption at pore openings, restricted diffusion, and reaction. This behavior is captured by a generalized hydrodynamic formulation of appropriate reaction-diffusion equations (RDE). These RDE incorporate an unconventional description of chemical diffusion in mixed-component...

in this paper, the effect of surface area of reaction layers in gas diffusion electrodes on oxygen reduction reaction was investigated. for this purpose, various amounts (0.1, 0.2, 0.3, 0.4, 0.5, 1, 1.5 and zero %wt of total loading of reaction layer) of single walled carbon nanotube (swcnt) were inserted in the reaction layer. the performance of gas diffusion electrodes for oxygen reduction re...

We present simple explicit estimates for the apparent reaction rate constant for threemolecular reactions. For small concentrations and d > 1, it depends only on the diffusion coefficients and sizes of the particles. For small concentrations and d ≤ 1, it is also time – dependent. For large concentrations, it gains the dependence on concentrations. Typeset using REVTEX 1