7,587 research outputs found

    A Unifying Approach to Decide Relations for Timed Automata and their Game Characterization

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    In this paper we present a unifying approach for deciding various bisimulations, simulation equivalences and preorders between two timed automata states. We propose a zone based method for deciding these relations in which we eliminate an explicit product construction of the region graphs or the zone graphs as in the classical methods. Our method is also generic and can be used to decide several timed relations. We also present a game characterization for these timed relations and show that the game hierarchy reflects the hierarchy of the timed relations. One can obtain an infinite game hierarchy and thus the game characterization further indicates the possibility of defining new timed relations which have not been studied yet. The game characterization also helps us to come up with a formula which encodes the separation between two states that are not timed bisimilar. Such distinguishing formulae can also be generated for many relations other than timed bisimilarity.Comment: In Proceedings EXPRESS/SOS 2013, arXiv:1307.690

    A Survey on Continuous Time Computations

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    We provide an overview of theories of continuous time computation. These theories allow us to understand both the hardness of questions related to continuous time dynamical systems and the computational power of continuous time analog models. We survey the existing models, summarizing results, and point to relevant references in the literature

    Flexible RNA design under structure and sequence constraints using formal languages

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    The problem of RNA secondary structure design (also called inverse folding) is the following: given a target secondary structure, one aims to create a sequence that folds into, or is compatible with, a given structure. In several practical applications in biology, additional constraints must be taken into account, such as the presence/absence of regulatory motifs, either at a specific location or anywhere in the sequence. In this study, we investigate the design of RNA sequences from their targeted secondary structure, given these additional sequence constraints. To this purpose, we develop a general framework based on concepts of language theory, namely context-free grammars and finite automata. We efficiently combine a comprehensive set of constraints into a unifying context-free grammar of moderate size. From there, we use generic generic algorithms to perform a (weighted) random generation, or an exhaustive enumeration, of candidate sequences. The resulting method, whose complexity scales linearly with the length of the RNA, was implemented as a standalone program. The resulting software was embedded into a publicly available dedicated web server. The applicability demonstrated of the method on a concrete case study dedicated to Exon Splicing Enhancers, in which our approach was successfully used in the design of \emph{in vitro} experiments.Comment: ACM BCB 2013 - ACM Conference on Bioinformatics, Computational Biology and Biomedical Informatics (2013

    Coupling of quantum angular momenta: an insight into analogic/discrete and local/global models of computation

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    In the past few years there has been a tumultuous activity aimed at introducing novel conceptual schemes for quantum computing. The approach proposed in (Marzuoli A and Rasetti M 2002, 2005a) relies on the (re)coupling theory of SU(2) angular momenta and can be viewed as a generalization to arbitrary values of the spin variables of the usual quantum-circuit model based on `qubits' and Boolean gates. Computational states belong to finite-dimensional Hilbert spaces labelled by both discrete and continuous parameters, and unitary gates may depend on quantum numbers ranging over finite sets of values as well as continuous (angular) variables. Such a framework is an ideal playground to discuss discrete (digital) and analogic computational processes, together with their relationships occuring when a consistent semiclassical limit takes place on discrete quantum gates. When working with purely discrete unitary gates, the simulator is naturally modelled as families of quantum finite states--machines which in turn represent discrete versions of topological quantum computation models. We argue that our model embodies a sort of unifying paradigm for computing inspired by Nature and, even more ambitiously, a universal setting in which suitably encoded quantum symbolic manipulations of combinatorial, topological and algebraic problems might find their `natural' computational reference model.Comment: 17 pages, 1 figure; Workshop `Natural processes and models of computation' Bologna (Italy) June 16-18 2005; to appear in Natural Computin

    Integrated Structure and Semantics for Reo Connectors and Petri Nets

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    In this paper, we present an integrated structural and behavioral model of Reo connectors and Petri nets, allowing a direct comparison of the two concurrency models. For this purpose, we introduce a notion of connectors which consist of a number of interconnected, user-defined primitives with fixed behavior. While the structure of connectors resembles hypergraphs, their semantics is given in terms of so-called port automata. We define both models in a categorical setting where composition operations can be elegantly defined and integrated. Specifically, we formalize structural gluings of connectors as pushouts, and joins of port automata as pullbacks. We then define a semantical functor from the connector to the port automata category which preserves this composition. We further show how to encode Reo connectors and Petri nets into this model and indicate applications to dynamic reconfigurations modeled using double pushout graph transformation

    Models of Quantum Cellular Automata

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    In this paper we present a systematic view of Quantum Cellular Automata (QCA), a mathematical formalism of quantum computation. First we give a general mathematical framework with which to study QCA models. Then we present four different QCA models, and compare them. One model we discuss is the traditional QCA, similar to those introduced by Shumacher and Werner, Watrous, and Van Dam. We discuss also Margolus QCA, also discussed by Schumacher and Werner. We introduce two new models, Coloured QCA, and Continuous-Time QCA. We also compare our models with the established models. We give proofs of computational equivalence for several of these models. We show the strengths of each model, and provide examples of how our models can be useful to come up with algorithms, and implement them in real-world physical devices

    Adaptable transition systems

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    We present an essential model of adaptable transition systems inspired by white-box approaches to adaptation and based on foundational models of component based systems. The key feature of adaptable transition systems are control propositions, imposing a clear separation between ordinary, functional behaviours and adaptive ones. We instantiate our approach on interface automata yielding adaptable interface automata, but it may be instantiated on other foundational models of component-based systems as well. We discuss how control propositions can be exploited in the specification and analysis of adaptive systems, focusing on various notions proposed in the literature, like adaptability, control loops, and control synthesis
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