4,816 research outputs found
Model checking probabilistic and stochastic extensions of the pi-calculus
We present an implementation of model checking for probabilistic and stochastic extensions of the pi-calculus, a process algebra which supports modelling of concurrency and mobility. Formal verification techniques for such extensions have clear applications in several domains, including mobile ad-hoc network protocols, probabilistic security protocols and biological pathways. Despite this, no implementation of automated verification exists. Building upon the pi-calculus model checker MMC, we first show an automated procedure for constructing the underlying semantic model of a probabilistic or stochastic pi-calculus process. This can then be verified using existing probabilistic model checkers such as PRISM. Secondly, we demonstrate how for processes of a specific structure a more efficient, compositional approach is applicable, which uses our extension of MMC on each parallel component of the system and then translates the results into a high-level modular description for the PRISM tool. The feasibility of our techniques is demonstrated through a number of case studies from the pi-calculus literature
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
Reactive Systems over Cospans
The theory of reactive systems, introduced by Leifer and Milner and previously extended by the authors, allows the derivation of well-behaved labelled transition systems (LTS) for semantic models with an underlying reduction semantics. The derivation procedure requires the presence of certain colimits (or, more usually and generally, bicolimits) which need to be constructed separately within each model. In this paper, we offer a general construction of such bicolimits in a class of bicategories of cospans. The construction sheds light on as well as extends Ehrig and Konig’s rewriting via borrowed contexts and opens the way to a unified treatment of several applications
A framework for protein and membrane interactions
We introduce the BioBeta Framework, a meta-model for both protein-level and
membrane-level interactions of living cells. This formalism aims to provide a
formal setting where to encode, compare and merge models at different
abstraction levels; in particular, higher-level (e.g. membrane) activities can
be given a formal biological justification in terms of low-level (i.e.,
protein) interactions. A BioBeta specification provides a protein signature
together a set of protein reactions, in the spirit of the kappa-calculus.
Moreover, the specification describes when a protein configuration triggers one
of the only two membrane interaction allowed, that is "pinch" and "fuse". In
this paper we define the syntax and semantics of BioBeta, analyse its
properties, give it an interpretation as biobigraphical reactive systems, and
discuss its expressivity by comparing with kappa-calculus and modelling
significant examples. Notably, BioBeta has been designed after a bigraphical
metamodel for the same purposes. Hence, each instance of the calculus
corresponds to a bigraphical reactive system, and vice versa (almost).
Therefore, we can inherith the rich theory of bigraphs, such as the automatic
construction of labelled transition systems and behavioural congruences
Types for BioAmbients
The BioAmbients calculus is a process algebra suitable for representing
compartmentalization, molecular localization and movements between
compartments. In this paper we enrich this calculus with a static type system
classifying each ambient with group types specifying the kind of compartments
in which the ambient can stay. The type system ensures that, in a well-typed
process, ambients cannot be nested in a way that violates the type hierarchy.
Exploiting the information given by the group types, we also extend the
operational semantics of BioAmbients with rules signalling errors that may
derive from undesired ambients' moves (i.e. merging incompatible tissues).
Thus, the signal of errors can help the modeller to detect and locate unwanted
situations that may arise in a biological system, and give practical hints on
how to avoid the undesired behaviour
- …