The URDME manual Version 1.3

• We have developed URDME, a general software for simulation of stochastic reaction-diffusion processes on unstructured meshes. This allows for a more flexible handling of complicated geometries and curved boundaries compared to simulations on structured, cartesian meshes. The underlying algorithm is the next subvolume method, extended to unstructured meshes by obtaining jump coefficients from a finite element formulation of the corresponding macroscopic equation. This manual describes version 1.3 of the software. URDME 1.3 includes support for Comsol Multiphysics 5.x and PDE Toolbox version 1.5 and above.

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