Bioinformatics Preprint 05-015
Explicit Collision Simulation of Chemical Reactions in a Graph Based Artifical Chemistry
Gil Benkö, Christoph Flamm, Peter F. Stadler
A Toy Model of an artificial chemistry that treats molecules as graphs was implemented based on a simple Extended Hückel Theory method. Here we describe an extension of the model that models chemical reactions as the result of ``collisions''. In order to avoid a possible bias arising from prescribed generic reaction mechamisms, the reactions are simulated in a way that treats the formation and breakage of individual chemical bonds as elementary operations.
Keywords: Artificial Chemistry, Energy Conservation, Elementary Reactions
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