Tutorial

The tutorial presents a new model of diffusion coefficient for a non-homogeneous non-well-stirred reaction-diffusion system. In this model the diffusion coefficient explicitly depends on the local concentration of solute, frictional coefficient and temperature. The derivation of the diffusivity consists of five main steps: 1. calculation of the local virtual force per molecules as the spatial derivative of the chemical potential 2. calculation of the particles mean drift velocity in terms of the local force and local frictional coefficient; 3. estimation of the flux of particles as the product of the mean drift velocity and the local concentration; 4. definition of diffusion coefficients as function of local activity and frictional coefficients and concentration, and 5. calculation of diffusion rates as the negative first spatial derivative of the flux of particles. The tutorial presents also the software tool Redi (REaction-DIffusion simulator) that implements our diffusion model into a Gillespie-like stochastic simulation algorithm.