7,587 research outputs found
A Unifying Approach to Decide Relations for Timed Automata and their Game Characterization
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
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
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
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
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
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
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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