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Arne T. Bittig

ML-Space : hybrid spatial Gillespie and Brownian motion simulation at multiple levels, and a rule-based description language

Universität Rostock, 2017

Abstract: Computer simulations of biological cells as well-stirred systems are well established but neglect the spatial distribution of key actors. In this thesis, a simulation algorithm "ML-Space" for spatial models with dynamic hierarchies is presented. It combines stochastic spatial algorithms in discretized space with individual particles moving in continuous space that have spatial extensions and can contain other particles. For formal descriptions of the systems to be simulated spatially, ML-Space provides a rule-based specification language.

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