Measurable Stochastics for Brane Calculus

We give a stochastic extension of the Brane Calculus, along the lines of recent work by Cardelli and Mardare. In this presentation, the semantics of a Brane process is a measure of the stochastic distribution of possible derivations. To this end, we first introduce a labelled transition system for Brane Calculus, proving its adequacy w.r.t. the usual reduction semantics. Then, brane systems are presented as Markov processes over the measurable space generated by terms up-to syntactic congruence, and where the measures are indexed by the actions of this new LTS. Finally, we provide a SOS presentation of this stochastic semantics, which is compositional and syntax-driven.Comment: In Proceedings MeCBIC 2010, arXiv:1011.005

A flat process calculus for nested membrane interactions

The link-calculus has been recently proposed as a process calculus for representing interactions that are open (i.e. that the number of processes may vary), and multiparty (i.e. that may involve more than two processes). Here, we apply the link-calculus for expressing, possibly hierarchical and non dyadic, biological interactions. In particular, we provide a natural encoding of Cardelli's Brane calculus, a compartment-based calculus, introduced to model the behaviour of nested membranes. Notably, the link-calculus is at, but we can model membranes just as special processes taking part in the biological reaction. Moreover, we give evidence that the link-calculus allows one to directly model biological phenomena at the more appropriate level of abstraction

A Flat Process Calculus for Nested Membrane Interactions

The link-calculus has been recently proposed as a process calculus for representing interactions that are open (i.e., that the number of processes may vary), and multiparty (i.e., that may involve more than two processes). Here, we apply the link-calculus for expressing, possibly hierarchical and non dyadic, biological interactions. In particular, we provide a natural encoding of Cardelli's Brane calculus, a compartment-based calculus, introduced to model the behaviour of nested membranes. Notably, the link-calculus is flat, but we can model membranes just as special processes taking part in the biological reaction. Moreover, we give evidence that the link-calculus allows one to directly model biological phenomena at the more appropriate level of abstraction

Measurable stochastics for Brane Calculus

AbstractThe main aim of this work is to give a stochastic extension of the Brane Calculus, along the lines of recent work by Cardelli and Mardare (2010) [12]. In this approach, the semantics of a process is a measure of the stochastic distribution of possible derivations. To this end, we first introduce a compositional, finitely branching labelled transition system for Brane Calculus; interestingly, the associated strong bisimulation is a congruence. Then, we give a stochastic semantics to Brane systems by defining them as Markov processes over the measurable space generated by terms up-to syntactic congruence, and where the measures are indexed by the actions of this new LTS. Finally, we provide an SOS presentation of this stochastic semantics, which is compositional and syntax-driven, and moreover the induced rate bisimilarity is a congruence

RPO Semantics for Mobile Ambients

The paper focuses on the synthesis of labelled transition systems (LTSs) for process calculi, choosing as testbed Mobile Ambients (MAs). The proposal is based on a graphical encoding: a process is mapped into a graph equipped with interfaces, such that the denotation is fully abstract with respect to the standard structural congruence. Graphs with interfaces are amenable to the synthesis mechanism based on borrowed contexts (BCs), an instance of relative pushouts (RPOs). The BC mechanism allows the effective construction of a LTS that has graphs with interfaces as states and labels, and such that the associated bisimilarity is a congruence. Our paper focuses on the analysis of a LTS over processes as graphs with interfaces: we use the LTS on graphs to recover a LTS directly defined over the structure of MAs processes, further defining a set of SOS inference rules capturing the same operational semantics

Characterizing contextual equivalence in calculi with passivation

AbstractWe study the problem of characterizing contextual equivalence in higher-order languages with passivation. To overcome the difficulties arising in the proof of congruence of candidate bisimilarities, we introduce a new form of labeled transition semantics together with its associated notion of bisimulation, which we call complementary semantics. Complementary semantics allows to apply the well-known Howeʼs method for proving the congruence of bisimilarities in a higher-order setting, even in the presence of an early form of bisimulation. We use complementary semantics to provide a coinductive characterization of contextual equivalence in the HOπP calculus, an extension of the higher-order π-calculus with passivation, obtaining the first result of this kind. We then study the problem of defining a more effective variant of bisimilarity that still characterizes contextual equivalence, along the lines of Sangiorgiʼs notion of normal bisimilarity. We provide partial results on this difficult problem: we show that a large class of test processes cannot be used to derive a normal bisimilarity in HOπP, but we show that a form of normal bisimilarity can be defined for HOπP without restriction

Adequacy Issues in Reactive Systems: Barbed Semantics for Mobile Ambients

Reactive systems represent a meta-framework aimed at deriving behavioral congruences for those specification formalisms whose operational semantics is provided by rewriting rules. The aim of this thesis is to address one of the main issues of the framework, concerning the adequacy of the standard observational semantics (the IPO and the saturated one) in modelling the concrete semantics of actual formalisms. The problem is that IPO-bisimilarity (obtained considering only minimal labels) is often too discriminating, while the saturated one (via all labels) may be too coarse, and intermediate proposals should then be put forward. We then introduce a more expressive semantics for reactive systems which, thanks to its flexibility, allows for recasting a wide variety of observational, bisimulation-based equivalences. In particular, we propose suitable notions of barbed and weak barbed semantics for reactive systems, and an efficient characterization of them through the IPO-transition systems. We also propose a novel, more general behavioural equivalence: L-bisimilarity, which is able to recast both its IPO and saturated counterparts, as well as the barbed one. The equivalence is parametric with respect to a set L of reactive systems labels, and it is shown that under mild conditions on L it is a congruence. In order to provide a suitable test-bed, we instantiate our proposal over the asynchronous CCS and, most importantly, over the mobile ambients calculus, whose semantics is still in a flux