A calculus of mobile processes, II
Information and Computation
Information Processing Letters
Theoretical Computer Science - Special issue: Computational systems biology
Graphical rule-based representation of signal-transduction networks
Proceedings of the 2005 ACM symposium on Applied computing
Electronic Notes in Theoretical Computer Science (ENTCS)
Scalable simulation of cellular signaling networks
APLAS'07 Proceedings of the 5th Asian conference on Programming languages and systems
Abstract interpretation of cellular signalling networks
VMCAI'08 Proceedings of the 9th international conference on Verification, model checking, and abstract interpretation
A graphical representation for biological processes in the stochastic pi-calculus
Transactions on Computational Systems Biology VII
From Biochemistry to Stochastic Processes
Electronic Notes in Theoretical Computer Science (ENTCS)
On the computational power of BlenX
Theoretical Computer Science
Modelling self-assembly in BlenX
Transactions on Computational Systems Biology XII
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The object of this paper is to probe the computational limits of an applied concurrent language called @k. This language describes how agents can bind and modify each other. It is meant as a syntactic medium to build, discuss and execute descriptions of cellular signalling pathways. However, it can be studied independently of its intended interpretation, and this is what we are doing here. Specifically, we define a reduction of @k to a fragment where interactions can involve at most two agents at a time. The translation relies on an implicit causality analysis which permits escaping deadlocks. It incurs only a linear blow up in the number of rules. Its correctness is spelt out in terms of the existence of a specific weak bisimulation and is proved in detail. To compensate for the binary restriction, one allows components to create unique names. When using acyclic rules, this additional facility of name creation is not needed and @k can be reduced to a binary form as is.