Modeling Interactions between Biochemical Reactions

Abstract

From the information processing point of view a living cell consists of a (huge) number of biochemical reactions that interact with each other. Two main mechanisms through which biochemical reactions influence each other are facilitation and inhibition. Therefore it is reasonable to base a formal model of interactions between biochemical reactions on a suitable formalization of these two mechanisms. Recently introduction reaction systems is a formal model following this way of reasoning.

We have made a number of assumptions that hold for a great number of biochemical reactions and therefore underlie the model of reaction systems. The assumptions are:

• Reactions are primary, while structures are secondary.

• There is a “threshold supply” of elements: either an element is present and then there is “enough” of it, or an element is not present. Thus there is no counting in the basic model.

• There is no “permanency” of elements: if “nothing” happens to an element, then it ceases to exist. Sustaining an element requires an effort (“life/existence must be sustained”).

We will argue that assumptions underlying the functioning of biochemical reactions are very different to the underlying axioms of standard models in theoretical computer science (including the model of Petri nets).