The Algorithms and Implementation of MesoRD

The next subvolume method, NSM, is a novel procedure for the simulation of the Markov process corresponding to the reaction–diffusion master equation. Unlike many other stochastic simulation algorithms, the NSM does not require spatial homogeneity, and is therefore applicable to a wider range of models. MesoRD, a portable, open source software implementing the NSM, attempts to make the method available to a larger audience. The aims are (i) to permit as general input model descriptions as possible, (ii) interacting with the user through sensible interfaces, while (iii) preventing the two aforementioned goals from negatively impacting performance. This text describes the design of MesoRD and its underlying algorithms, and discusses possible directions for future development.