URDME v. 1.1: User's manual

Details URDME v. 1.1: User's manual URDME v. 1.1: User's manual

2009-02-17

arxiv.org/abs/0902.2912v2

Biology

Quantitative Biology

Molecular Networks

The latest version of URDME is available from http://www.urdme.org. URDME 1.0 is available from http://user.it.uu.se/~stefane

Scientific paper

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 (NSM), extended to unstructured meshes by obtaining jump coefficients from the finite element formulation of the corresponding macroscopic equation. This manual describes version 1.1 of the software.

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