Aula Magna di Anatomia Comparata - BES - Via Selmi, 3 (second floor) 7th september 2009 at 16.00 pm

Luca Cardelli (Microsoft Research)

Title:
"Molecules as Automata"


Abstract

We describe chemical and biochemical systems as collectives of interacting stochastic automata: each automaton represents a molecule that undergoes state transitions. This framework constitutes an artificial biochemistry, where automata interact by the equivalent of the law of mass action. We analyze systems and networks, both by stochastic and continuous methods, and relate the two approaches, building a formal connection between automata theory and the standard chemistry of diluted well-mixed solutions. From a systems biology perspective, interacting automata are a computational framework inspired by biochemistry, used to model and analyze biochemical systems. But conversely, from a synthetic biology perspective, it is also possible to take an arbitrary set of automata and implement them as molecules. In particular, recent advances in DNA strand displacement techniques provide a systematic and compositional implementation of heterogeneous concurrent collections of interacting automata.