Molecules as Automata

Lecturer: Prof. Luca Cardelli (Microsoft Research, Cambridge, UK).

About the lecturer | Course Summary | Slides and Exercises

About the lecturer: Luca Cardelli graduated from the University of Pisa and reveived a Ph.D. in computer science from the University of Edinburgh. He worked at Bell Labs in Murray Hill, Digital Equipment Corporation, Systems Research Center in Palo Alto, before assuming a position at Microsoft Research, in Cambridge UK, where he is currently Principal Researcher and head of the Programming Principles and Tools and Security groups.

His main interests are in type theory and operational semantics (for applications to language design, semantics, and implementation), and in concurrency theory (for applications to computer networks and to modeling biological systems). He implemented the first compiler for ML (one of the most popular typed functional language, whose recent incarnations are Caml and F#) and one of the earliest direct-manipulation user-interface editors. He was a member of the Modula-3 design committee, and has designed a few experimental languages, including Obliq: a distributed higher-order scripting language (voted most influential POPL'95 paper 10 years later), and Polyphonic C#, a distributed extension of C#. His more protracted research activity has been in establishing the semantic and type-theoretic foundations of object-oriented languages, resulting in the 1996 book "A Theory of Objects" with Martin Abadi. More recently he has focused on modeling global and mobile computation, via the Ambient Calculus and Spatial Logics, which indirectly led to a current interest in Systems Biology and stochastic systems.

He has published over 100 papers, 1 book, and 2 proceedings as chair/editor (POPL'98 and ECOOP'03). He has served in over 80 Program Committees, and as editor of 7 journals. He is a Fellow of the Royal Society, an ACM Fellow, an Elected Member of the Academia Europaea, an Elected Member of AITO, and a long-standing member of EATCS. In terms of unreliable statistics, he has a Hirsch index of ~58, he is the ~45th most cited computer scientist, and the 3rd most acknowledged computer scientist. [Extracted from]

Course summary:
Chemical and biochemical systems are described 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 by discrete and continuous methods, and relate the two approaches.

Slides and Exercises Please send the solutions to Luca (luca AT microsoft DOT com) not later than on June, 1.

Here is the SPiM simulator website.
Solutions [PDF]