Computational self-assembly

The object of this paper is to appreciate the computational limits inherent in the combinatorics of an applied concurrent (aka agent-based) language . That language is primarily meant as a visual and concise notation for biological signalling pathways. Descriptions in , when enriched with suitable kinetic information, generate simulations as continuous time Markov chains. However, can be studied independently of the intended application, in a purely computational fashion, and this is what we are doing here. Specifically, we define a compilation of into a language where interactions can involve at most two agents at a time. That compilation is generic, the blow up in the number of rules is linear in the total rule set size, and the methodology used in deriving the compilation relies on an implicit causality analysis. The correctness proof is given in details, and correctness is spelt out in terms of the existence of a specific weak bisimulation. To compensate for the binary restricti...

• Type: Journal
• Year: 2008
• Where: TCS
• Authors: Pierre-Louis Curien, Vincent Danos, Jean Krivine, Min Zhang
• Keywords: Biological Signalling Pathways, Suitable Kinetic Information, TCS 2008, Theoretical Computer Science, Time Markov Chains