From Biochemistry to Stochastic Processes

The nanoκ calculus is a formalism that models biochemical systems by defining its set of reactions. We study the implementation of nanoκ into the Stochastic Pi Machine where biochemical systems are defined by regarding molecules as processes, and deriving the overall behaviour by means of communication rules. Our implementation complies with the stochastic behaviors of systems, thus allowing one to use nanoκ as an intelligible front-end for a process-oriented simulator. This study also permits to reuse, in nanoκ, the theories and tools already developed for process calculi.