Journal Papers Simulating Stochastic Dynamic Interactions with Spatial Information and Flux


We present a conservative extension to rule based modeling languages with constructs for component attributes and functions that modify these attributes; the language has a stochastic semantics, and it is equipped with flux analysis. We show that the constructs of this language, called M, bring an ease especially in modeling biological systems, where spatial information is of essence. We discuss the language on models from molecular biology such as membrane diffusion systems, and actin polymerization networks, as well as models from ecology, where spatial behavior of animals as in bird flocks and fish schools are studied.

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