A synthon approach to artificial chemistry

In this work, a co-evolutionary model is discussed that incorporates the logical structure of constitutional chemistry and its kinetics on the one hand and the topological evolution of the chemical reaction network on the other hand. The motivation for designing this model is twofold. First, experiments that should provide insight into chemical problems should be expressed in a syntax that remains as close as possible to real chemistry. Second, the study of physical properties of the complex chemical reaction networks requires growing models that incorporate features realistic from a biochemical perspective. In this article the theory and algorithms underlying the co-evolutionary model are explained and two illustrative examples are provided. These examples show that one needs to be careful in making generalised claims concerning the structure of chemical reaction networks.