Search

In the area of Natural Computing, Reaction Systems (RSs) are a qualitative abstraction inspired by the functioning of living cells, suitable to model the main mechanisms of biochemical reactions. RSs interact with a context, and pose challenges for modularity, compositionality, extendibility and behavioural equivalence. In this paper we define a modular encoding of RSs as processes in the chained Core Network Algebra (cCNA), which is a new variant of the link-calculus. The encoding represents the behaviour of each entity separately and preserves faithfully their features, and we prove its correctness and completeness. Our encoding provides a Labelled Transition System (LTS) semantics for RSs. Based on the LTS semantics, we adapt the classical notion of bisimulation to define a novel equivalence, called bio-similarity, for studying properties of RSs. In particular, we define a new assertion language based on regular expressions, which allows us to specify the properties of interest, and use it to extend Hennessy-Milner logic to our setting. We prove that our bio-similarity relation and the logical equivalence, that are defined parametrically on some assertion of interest, coincide. Finally, we claim that our encoding contributes to increase the expressiveness of RSs, by exploiting the interaction among different RSs. [ABSTRACT FROM AUTHOR]

A logical theory for interface specification and verification of distributed, concurrent, interactive, real-time systems is worked out based on a semantic foundation including operational and denotational semantics. It supports a calculus for the specification and verification of concurrent interactive systems by interface assertions. Systems are composed acting concurrently and interacting via streams exchanged over their channels forming feedback loops. A denotational semantics is defined handling feedback communication by recursion and fixpoints based on strong causality and realizability instead of monotonicity. The resulting verification calculus for the specification logic is proved to be sound and relatively complete with respect to an operational semantics in terms of generalized Moore machines. Actually, two models of concurrent systems are defined, a more abstract one with communication and interaction modeled by untimed streams and a more concrete one working with timed streams. The untimed model is an abstraction of the timed model. The timed model allows expressing the laws of causality and realizability. Moreover, the timed model can be used to specify real-time properties. [ABSTRACT FROM AUTHOR]