Institute of Information Science, Academia Sinica

Stemming from the recent  paradigm "computation-as-processes" for logic, novel applications have been emerging of process calculi (such as Milner's

pi) being widely used in biology since the beginning of this twenty-first century. In these applications, logical methods are realised both by syntactic approaches (e.g., rule-based kappa and chemical reaction networks) and by semantics (e.g., stochastic mass action Petri nets, or more generally chemical master equations).

This talk presents my recent work on rule-based modelling of stochastic interaction for RNA (such as interference and transcription elongation). Our modelling represents nucleotide-based interaction for RNA syntactically, using Minsky register machines and semantically, using Markov branching processes. The former representation elucidates the computational power of RNAi, and the latter characterises sustainability of RNAi. We also give a kinetic and thermodynamical meaning of our modelling in chemical terms using Michaelis-Menten kinetics and Boltzmann energy distributions. The aim of this talk is to see how our modelling from the perspective of logic could provide a compact description of complex biological networks and could adequately reflect discreteness and small-numbers of molecular-agents, peculiar to bio-molecular interaction.