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12
Compositional Semantics and Behavioral Equivalences for P Systems
, 2008
"... The aim of the paper is to give a compositional semantics in the style of the Structural Operational Semantics (SOS) and to study behavioral equivalence notions for P Systems. Firstly, we consider P Systems with maximal parallelism and without priorities. We define a process algebra, called P Algebr ..."
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Cited by 7 (7 self)
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The aim of the paper is to give a compositional semantics in the style of the Structural Operational Semantics (SOS) and to study behavioral equivalence notions for P Systems. Firstly, we consider P Systems with maximal parallelism and without priorities. We define a process algebra, called P Algebra, whose terms model membranes, we equip the algebra with a Labeled Transition System (LTS) obtained through SOS transition rules, and we study how some equivalence notions defined over the LTS model apply in our case. Then, we consider P Systems with priorities and extend the introduced framework to deal with them. We prove that our compositional semantics reflects correctly maximal parallelism and priorities.
Causality in Membrane Systems
"... Summary. P systems are a biologically inspired model introduced by Gheorghe Păun with the aim of representing the structure and the functioning of the cell. P systems are usually equipped with the maximal parallelism semantics; however, since their introduction, some alternative semantics have been ..."
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Cited by 6 (0 self)
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Summary. P systems are a biologically inspired model introduced by Gheorghe Păun with the aim of representing the structure and the functioning of the cell. P systems are usually equipped with the maximal parallelism semantics; however, since their introduction, some alternative semantics have been proposed and investigated. We propose a semantics that describes the causal dependencies occurring between the reactions of a P system. We investigate the basic properties that are satisfied by such a semantics. The notion of causality turns out to be quite relevant for biological systems, as it permits to point out which events occurring in a biological pathway are necessary for another event to happen. 1
A P Systems Flat Form Preserving Step–by–step Behaviour
, 2008
"... Starting from a compositional operational semantics of transition P Systems we have previously defined, we face the problem of developing an axiomatization that is sound and complete with respect to some behavioural equivalence. To achieve this goal, we propose to transform the systems into a normal ..."
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Cited by 6 (6 self)
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Starting from a compositional operational semantics of transition P Systems we have previously defined, we face the problem of developing an axiomatization that is sound and complete with respect to some behavioural equivalence. To achieve this goal, we propose to transform the systems into a normal form with an equivalent semantics. As a first step, we introduce axioms which allow the transformation of membrane structures into flat membranes. We leave as future work the further step that leads to the wanted normal form.
A Formal Framework for P Systems
"... Summary. The formalism of P systems is known for many years, yet just recently new derivation modes and halting conditions have been proposed. For developing comparable results, a formal description of their functioning, in particular, of the derivation step is necessary. We introduce a formal gener ..."
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Cited by 3 (3 self)
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Summary. The formalism of P systems is known for many years, yet just recently new derivation modes and halting conditions have been proposed. For developing comparable results, a formal description of their functioning, in particular, of the derivation step is necessary. We introduce a formal general framework for static membrane systems that aims to capture most of the essential features of (tissue) P systems and to define their functioning in a formal way. 1
MeCBIC 2008 Translating Stochastic CLS into Maude
"... This paper describes preliminary results on the application of statistical modelchecking to systems described with Stochastic CLS. Stochastic CLS is a formalism based on term rewriting that allows biomolecular systems to be described by taking into account their structure and by allowing very gener ..."
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This paper describes preliminary results on the application of statistical modelchecking to systems described with Stochastic CLS. Stochastic CLS is a formalism based on term rewriting that allows biomolecular systems to be described by taking into account their structure and by allowing very general events to be modelled. Statistical modelchecking is an analysis technique that permits properties of a system to be studied on the results of a number of stochastic simulations. We choose RealTime Maude as a tool that supports the modelling and analysis of systems with realtime properties. We adapt Gillespie’s algorithm for simulating chemical systems into our approach. The resulting method is applied to analyse some simple examples and a model of the lactose operon regulation in E.coli.
Towards a P Systems Normal Form Preserving Step–by–step Behaviour
"... Starting from a compositional operational semantics of transition P Systems we have previously defined, we face the problem of developing an axiomatization that is sound and complete with respect to some behavioural equivalence. To achieve this goal, we propose to transform the systems into a unique ..."
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Starting from a compositional operational semantics of transition P Systems we have previously defined, we face the problem of developing an axiomatization that is sound and complete with respect to some behavioural equivalence. To achieve this goal, we propose to transform the systems into a unique normal form which preserves the semantics. As a first step, we introduce axioms which allow the transformation of membrane structures with no dissolving rules into flat membranes. We discuss the problems which arise when dissolving rules are allowed and we suggest possible solutions. We leave as future work the further step that leads to the wanted normal form. 1
Compositional Semantics of Spiking Neural P Systems
, 2010
"... The aim of the paper is to give a formal compositional semantics for Spiking Neural P systems (SNP systems) by following the Structural Operational Semantics (SOS) approach. A process algebra is introduced whose terms represent SNP systems. The algebra is equipped with a semantics, given as a labell ..."
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The aim of the paper is to give a formal compositional semantics for Spiking Neural P systems (SNP systems) by following the Structural Operational Semantics (SOS) approach. A process algebra is introduced whose terms represent SNP systems. The algebra is equipped with a semantics, given as a labelled transition system. This semantics allows notions of behavioural equivalences over SNP systems to be studied. Some known equivalences are considered and their definition based on the given semantics is provided. Such equivalences are proved to be congruences.
AN OVERVIEW ON OPERATIONAL SEMANTICS IN MEMBRANE COMPUTING
, 2010
"... The aim of this paper is to give motivations for the development of operational semantics in membrane computing, and to survey existing proposals. In particular, the definitions are compared of three operational semantics available in the literature, namely a semantics proposed by Andrei, Ciobanu an ..."
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The aim of this paper is to give motivations for the development of operational semantics in membrane computing, and to survey existing proposals. In particular, the definitions are compared of three operational semantics available in the literature, namely a semantics proposed by Andrei, Ciobanu and Lucanu, another proposed by Busi, and another one proposed by the authors of the present paper. These definitions are different since they are given with different aims. However, we show that there is an operational correspondence among the three.
Modeling, Verification and Testing of P Systems Using
"... Summary. In this paper we present an approach to modelling, verification and testing for celllike Psystems based on EventB and the Rodin platform. We present a general framework for modelling P systems using EventB, which we then use to implement two Psystem models in the Rodin platform. For ea ..."
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Summary. In this paper we present an approach to modelling, verification and testing for celllike Psystems based on EventB and the Rodin platform. We present a general framework for modelling P systems using EventB, which we then use to implement two Psystem models in the Rodin platform. For each of the two models, we use the associated ProB model checker to verify properties and we present some of the results obtained. 1