Design Patterns for an Object-Oriented Computational Chemistry

• Authors: Hugues Bersini
• Venue: ECAL '99 Proceedings of the 5th European Conference on Advances in Artificial Life
• Year: 1999

Chemistry is basically the formation of complexes by combining together basic elements and/or simpler complexes, or by splitting bigger complexes as a result of chemical reactions. The basic elements are glued as a consequence of the affinity that exists between them. This affinity can be explicit, implicit, symmetric or asymmetric. Object-Orientation offers a natural computational framework to capture the very simple and recurrent mechanism which underlies chemistry. The basic elements and the complexes constitute the low-level classes, which can be naturally organized in a hierarchical structure. Every complex is an objet, constructed on the basis of simpler complexes or basic elements, and structured as a special type of ordered computational tree (when affinity is symmetric) and graph (in the asymmetric case). Among the attributes of these objects, one finds their concentration and their reactivity, which are essential values to simulate the dynamics of the whole system. This paper introduces, in a UML type of representation, some basic computational structures and mechanisms which should find a natural place in all simulation interested in complex formation and the time variation of the complexes concentration and reactivity.