MOLECULAR PATHWAYS AS CONCURRENT SYSTEMS
We realized that molecules, which are structures, could be represented by their potential behavior: the process in which they may participate. For example, according to this approach, an enzyme is the enzymatic reaction it may catalyze [example]. In fact, biochemical processes and concurrent communication systems share many features. In both cases, multiple entities exist concurrently, interact and modify each other. Based on this analogy, the Pi-calculus, originally developed for the specification of computational processes, could also be used to model biochemical ones.
We employ 5 major principles in modeling biochemical processes as concurrent systems:
Pathways, molecules and molecular domains as computational processes [example]
Complementary molecular determinants correspond as communication channels [example]
Molecular interaction and modification as communication and change of channel names [example]
The integrity of molecules, complexes and compartment as channels with restricted scope [example]
The formation of complexes and translocation of molecule as extrusion of restricted channels [example]
Based on this strong correspondence between the calculus and biochemical networks, we can incrementally represent detailed information on biochemical systems in a structured, biologically faithful fashion. The resulting representations can be used in simulation, analysis and verification.