37 research outputs found

    ML-Space: hybrid spatial Gillespie and Brownian motion simulation at multiple levels, and a rule-based description language

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    Computer simulations of biological cells as well-stirred systems are well established but neglect the spatial distribution of key actors. In this thesis, a simulation algorithm "ML-Space" for spatial models with dynamic hierarchies is presented. It combines stochastic spatial algorithms in discretized space with individual particles moving in continuous space that have spatial extensions and can contain other particles. For formal descriptions of the systems to be simulated spatially, ML-Space provides a rule-based specification language.Computersimulationen mikrobiologischer Prozesse, bei denen eine homogene Verteilung der Akteure einer Zelle angenommen wird, sind gut etabliert. In dieser Arbeit wird ein räumlicher Simulationsalgorithmus "ML-Space" für Mehrebenenmodelle vorgestellt, der auch dynamische Hierarchien abdeckt. Er vereint stochastische räumliche Algorithmen in diskretisiertem Raum mit individuellen Partikeln mit kontinuierlichen Koordinaten, die andere Partikel enthalten können. Zur formalen Beschreibung der räumlich zu simulierenden Systeme bietet ML-Space eine regelbasierte Modellierungssprache

    The Applied Pi Calculus: Mobile Values, New Names, and Secure Communication

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    We study the interaction of the programming construct " new " , which generates statically scoped names, with communication via messages on channels. This interaction is crucial in security protocols, which are the main motivating examples for our work; it also appears in other programming-language contexts. We define the applied pi calculus, a simple, general extension of the pi calculus in which values can be formed from names via the application of built-in functions, subject to equations, and be sent as messages. (In contrast, the pure pi calculus lacks built-in functions; its only messages are atomic names.) We develop semantics and proof techniques for this extended language and apply them in reasoning about security protocols. This paper essentially subsumes the conference paper that introduced the applied pi calculus in 2001. It fills gaps, incorporates improvements, and further explains and studies the applied pi calculus. Since 2001, the applied pi calculus has been the basis for much further work, described in many research publications and sometimes embodied in useful software, such as the tool ProVerif, which relies on the applied pi calculus to support the specification and automatic analysis of security protocols. Although this paper does not aim to be a complete review of the subject, it benefits from that further work and provides better foundations for some of it. In particular, the applied pi calculus has evolved through its implementation in ProVerif, and the present definition reflects that evolution

    A Semantic Theory of the Internet of Things (extended abstract)

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    We propose a process calculus for modelling and reasoning on systems in the Internet of Things paradigm. Our systems interact both with the physical environment, via sensors and actuators, and with smart devices, via short-range and Internet channels. The calculus is equipped with a standard notion of labelled bisimilarity which represents a fully abstract characterisation of a well-known contextual equivalence. We use our semantic proof-methods to prove run-time properties of a non-trivial case study as well as system equalities

    A Flat Process Calculus for Nested Membrane Interactions

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    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

    A general theory of barbs, contexts and labels

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    Barbed bisimilarity is a widely-used behavioural equivalence for interactive systems: given a set of predicates (denoted “barbs” and representing basic observations on states) and a set of contexts (representing the possible execution environments), two systems are deemed to be equivalent if they verify the same barbs whenever inserted inside any of the chosen contexts. Despite its flexibility and expressiveness, this definition of equivalence is unsatisfactory, since often the quantification is over an infinite set of contexts, thus making barbed bisimilarity very hard to be verified. Should a labelled operational semantics be available, more efficient observational equivalences might be adopted. To this end, a series of techniques have been proposed to derive labelled transition systems (LTSs) from unlabeled ones, the main example being Leifer and Milner’s theory of reactive systems. The underlying intuition is that labels should be the “minimal” contexts that allow for a reduction step to be performed. However, minimality is difficult to asses, while the set of “intuitively” correct labels is often easily devised by the ingenuity of the researcher. This paper introduces a framework that characterises (weak) barbed bisimilarity via LTSs whose labels are (not necessarily minimal) contexts. Differently from previous proposals, our theory is not dependent on the way the labelled transitions are built, and it relies on a simple set-theoretical presentation for identifying those properties such an LTS should verify in order to (1) capture the barbed bisimilarities of the underlying system and (2) ensure that such bisimilarities are congruences. Furthermore, we adopt suitable proof techniques in order to make feasible the verification of such properties. To provide a test-bed for our formalism, we instantiate it by addressing the semantics of the Mobile Ambients calculus, recasting its (weak) barbed bisimilarities via label-based behavioural equivalences

    A flat process calculus for nested membrane interactions

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    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

    Dynamic Input/Output Automata: a Formal and Compositional Model for Dynamic Systems

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    We present dynamic I/O automata (DIOA), a compositional model of dynamic systems, based on I/O automata. In our model, automata can be created and destroyed dynamically, as computation proceeds. In addition, an automaton can dynamically change its signature, that is, the set of actions in which it can participate. This allows us to model mobility, by enforcing the constraint that only automata at the same location may synchronize on common actions. Our model features operators for parallel composition, action hiding, and action renaming. It also features a notion of automaton creation, and a notion of trace inclusion from one dynamic system to another, which can be used to prove that one system implements the other. Our model is hierarchical: a dynamically changing system of interacting automata is itself modeled as a single automaton that is "one level higher." This can be repeated, so that an automaton that represents such a dynamic system can itself be created and destroyed. We can thus model the addition and removal of entire subsystems with a single action. We establish fundamental compositionality results for DIOA: if one component is replaced by another whose traces are a subset of the former, then the set of traces of the system as a whole can only be reduced, and not increased, i.e., no new behaviors are added. That is, parallel composition, action hiding, and action renaming, are all monotonic with respect to trace inclusion. We also show that, under certain technical conditions, automaton creation is monotonic with respect to trace inclusion: if a system creates automaton Ai instead of (previously) creating automaton A'i, and the traces of Ai are a subset of the traces of A'i,then the set of traces of the overall system is possibly reduced, but not increased. Our trace inclusion results imply that trace equivalence is a congruence relation with respect to parallel composition, action hiding, and action renaming. Our trace inclusion results enable a design and refinement methodology based solely on the notion of externally visible behavior, and which is therefore independent of specific methods of establishing trace inclusion. It permits the refinement of components and subsystems in isolation from the entire system, and provides more flexibility in refinement than a methodology which is, for example, based on the monotonicity of forward simulation with respect to parallel composition. In the latter, every automaton must be refined using forward simulation, whereas in our framework different automata can be refined using different methods. The DIOA model was defined to support the analysis of mobile agent systems, in a joint project with researchers at Nippon Telegraph and Telephone. It can also be used for other forms of dynamic systems, such as systems described by means of object-oriented programs, and systems containing services with changing access permissions

    A Network-Aware Process Calculus for Global Computing and its Categorical Framework

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    An essential aspect of distributed systems is resource management, concerning how resources can be accessed and allocated. This aspect should also be taken into account when modeling and verifying such systems. A class of formalisms with the desired features are nominal calculi: they represent resources as atomic objects called names and have linguistic constructs to express creation of new resources. The paradigmatic nominal calculus is the π-calculus, which is well-studied and comes with models and logics. The first objective of this thesis is devising a natural and seamless extension of the π-calculus where resources are network nodes and links. The motivation is provided by a recent, successful networking paradigm called Software Defined Networks, which allows the network structure to be manipulated at runtime via software. We devise a new calculus called Network Conscious π-calculus (NCPi), where resources, namely nodes and links, are represented as names, following the π-calculus guidelines. This allows NCPi to reuse the π-calculus name-handling machinery. The semantics allows observing end-to-end routing behavior, in the form of routing paths through the network. As in the π-calculus, bisimilarity is not closed under input prefix. Interestingly, closure under parallel composition does not hold either. Taking the greatest bisimulation closed under all renamings solves the issue only for the input prefix. We conjecture that such closure yields a full congruence for the subcalculus with only guarded sums. We introduce an extension of NCPi (κNCPi) with some features that makes it closer to real-life routing. Most importantly, we add concurrency, i.e. multiple paths can be observed at the same time. Unlike the sequential version, bisimilarity is a congruence from the very beginning, due to the richer observations, so κNCPi can be considered the “right” version of NCPi when compositionality is needed. This extended calculus is used to model the peer- to-peer architecture Pastry. The second objective is constructing a convenient operational model for NCPi. We consider coalgebras, that are categorical representation of system. Coalgebras have been studied in full generality, regardless of the specific structure of systems, and algorithms and logics have been developed for them. This allows for the application of general results and techniques to a variety of systems. The main difficulty in the coalgebraic treatment of nominal calculi is the presence of name binding: it introduces α-conversion and makes SOS rules and bisimulations non-standard. The consequence is that coalgebras on sets are not able to capture these notions. The idea of the seminal paper by Fiore and Turi is resorting to coalgebras on presheaves, i.e. functors C → Set. Intuitively, presheaves allow associating to collections of names, seen as objects of C, the set of processes using those names. Fresh names generation strategies can be formalized as endofunctors on C, which are lifted to presheaves in a standard way and used to model name binding. Within this framework, a coalgebra for the π-calculus transition system is constructed: the benefit is that ordinary coalgebraic bisimulations for such coalgebra are π-calculus bisimulations. Moreover, Fiore and Turi show a technique to obtain a new coalgebra whose bisimilarity is closed under all renamings. This relation is a congruence for the π-calculus. Presheaves come with a rich theory that can help deriving new results, but coalgebras on presheaves are impractical to implement: the state space can be infinite, for instance when a process recursively creates names. However, if we restrict to a class of presheaves (according to Ciancia et al.), coalgebras admit a concrete implementation in terms of HD-automata, that are finite-state automata suitable for verification. In this thesis we adapt and extend Fiore-Turi’s approach to cope with network resources. First we provide a coalgebraic semantics for NCPi whose bisimulations are bisimulations in the NCPi sense. Then we compute coalgebras and equivalences that are closed under all renamings. The greatest such equivalence is a congruence w.r.t. the input prefix and we conjecture that, for the NCPi with only guarded sums, it is a congruence also w.r.t. parallel composition. We show that this construction applies a form of saturation. Then we prove the existence of a HD-automaton for NCPi. The treatment of network resources is non-trivial and paves the way to modeling other calculi with complex resources
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