An excursion in reaction systems : from computer science to biology

Reaction systems are a formal model based on the regulation mechanisms of facilitation and inhibition between biochemical reactions, which underlie the functioning of living cells. The aim of this paper is to explore the expressive power of reaction systems as a modeling framework, showing how their basic assumptions and properties can be exploited to formalize computer science and biology oriented problems. In this view, we first provide a reaction-based description of an iterative algorithm to solve the Tower of Hanoi puzzle. Then, we show how the regulation of gene expression in the lac operon, involved in the metabolism of lactose in Escherichia coli cells, can be formalized in terms of reaction systems. Finally, we present a method to derive, given a reaction system with n reactions, a functionally equivalent system with n′ ≤ n reactions using simplification methods of boolean expressions. Some final remarks and directions for future research conclude the paper.