Explicit collision simulation of chemical reactions in a graph based artificial chemistry

Abstract

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