Stochastic simulation of reaction-diffusion systems: A fluctuating-hydrodynamics approach

Stochastic simulation of reaction-diffusion systems: A fluctuating-hydrodynamics approach.

We develop numerical methods for stochastic reaction-diffusion systems based on approaches used for fluctuatinghydrodynamics (FHD). For hydrodynamicsystems, the FHD formulation is formally described by stochastic partial differential equations (SPDEs). In the reaction-diffusion systems we consider, our model becomes similar to the reaction-diffusion master equation (RDME) description when our S...

Fluctuating Hydrodynamics of Reaction-Diffusion Systems

We develop numerical methods for reaction-diffusion systems based on the equations of fluctuating hydrodynamics (FHD). While the FHD formulation is formally described by stochastic partial differential equations (SPDEs), it becomes similar to the reaction-diffusion master equation (RDME) description when those SPDEs are spatially discretized and reactions are modeled as a source term having Poi...

Spatial-Stochastic Simulation of Reaction-Diffusion Systems

In biological systems, biochemical networks play a crucial role, implementing a broad range of vital functions from regulation and communication to resource transport and shape alteration. While biochemical networks naturally occur at low copy numbers and in a spatial setting, this fact often is ignored and well-stirred conditions are assumed for simplicity. Yet, it is now increasingly becoming...

Stochastic Simulation of Reaction-Diffusion Systems

Stochastic Simulation of Reaction-Diffusion Systems

Reactiondiffusion systems are mathematical models that describe how the concentration of one or more substances distributed in space changes under the influence of local chemical reactions in which the substances are converted into each other, and diffusion which causes the substances to spread out in space. The classical representation of a reaction-diffusion system is given by semi-linear par...