Rules, hypergraphs, and probabilities: the three-level analysis of chemical reaction systems and other stochastic stoichiometric population processes
Eric Smith,
Harrison B. Smith,
Jakob Lykke Andersen
Abstract:We consider problems in the functional analysis and evolution of combinatorial chemical reaction networks as rule-based, or three-level systems. The first level consists of rules, realized here as graph-grammar representations of reaction mechanisms. The second level consists of stoichiometric networks of molecules and reactions, modeled as hypergraphs. At the third level is the stochastic population process on molecule counts, solved for dynamics of population trajectories or probability distributions. Earlie… Show more
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