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A rewriting logic framework for operational semantics of membrane systems,
 Theoretical Computer Science,
, 2007
"... Abstract Existing results in membrane computing refer mainly to P systems' characterization of Turing computability, also to some polynomial solutions to NPcomplete problems by using an exponential workspace created in a "biological way". In this paper we define an operational seman ..."
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Abstract Existing results in membrane computing refer mainly to P systems' characterization of Turing computability, also to some polynomial solutions to NPcomplete problems by using an exponential workspace created in a "biological way". In this paper we define an operational semantics of a basic class of P systems, and give two implementations of the operational semantics using rewriting logic. We present some results regarding these implementations, including two operational correspondence results, and discuss why these implementations are relevant in order to take advantage of good features of both structural operational semantics and rewriting logic. c 2007 Elsevier B.V. All rights reserved. Keywords: Membrane systems; Operational semantics; Rewriting logic; Maude Membrane systems Membrane systems represent a new abstract model of parallel and distributed computing inspired by cell compartments and molecular membranes A detailed description of P systems can be found in
Quorum sensing P systems
, 2006
"... This paper continues the investigation of population P systems model [F. Bernardini, M. Gheorghe, Population P systems, Journal of Universal Computer Science 10 (5) (2004) 509–539] by considering bacterium quorum sensing (QS) phenomena as the basis of the new approach. A new computational model call ..."
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Cited by 10 (5 self)
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This paper continues the investigation of population P systems model [F. Bernardini, M. Gheorghe, Population P systems, Journal of Universal Computer Science 10 (5) (2004) 509–539] by considering bacterium quorum sensing (QS) phenomena as the basis of the new approach. A new computational model called QS P system is introduced. It is proved that QS P systems are able to simulate counter machines, and hence they are equivalent in power to Turing machines. An example of a QS P system modelling the behaviour of Vibrio fischeri bacteria colonies is also presented and the emergence of the QS mechanism is illustrated.
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 8 (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
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.
On P systems with bounded parallelism
 Proceedings of the 1st International Workshop on Theory and Application of P Systems (TAPS ’05
, 2005
"... A framework that describes the evolution of P systems with bounded parallelism is defined by introducing basic formal features that can be then integrated into a structural operational semantics. This approach investigates a generic strategy of selecting membranes and rules and applying the rules. P ..."
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Cited by 5 (4 self)
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A framework that describes the evolution of P systems with bounded parallelism is defined by introducing basic formal features that can be then integrated into a structural operational semantics. This approach investigates a generic strategy of selecting membranes and rules and applying the rules. P systems with boundary rules are used to illustrate the case and an example dealing with an evolution strategy involving bounded parallelism is discussed. 1
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
Expressing Control Mechanisms in P systems by Rewriting Strategies
 of LNCS
, 2006
"... Abstract. In this paper we provide a semantics for membrane systems given by rewriting strategies. We describe some control mechanisms in membrane computing defined over sets of rules rather than individual rules. Then we present the rewriting strategy formalism together with its operational semanti ..."
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Abstract. In this paper we provide a semantics for membrane systems given by rewriting strategies. We describe some control mechanisms in membrane computing defined over sets of rules rather than individual rules. Then we present the rewriting strategy formalism together with its operational semantics. We use strategies to define the semantics of the maximal parallel rewriting and priorities. Rewriting strategies are not enough to express the membrane computation involving promoters or inhibitors. 1 Control Mechanisms in Membrane Systems In membrane systems (called also P systems) [8], the objects to evolve and the rules governing this evolution are chosen in a nondeterministic way. Moreover, this choice is exhaustive in the sense that no rule can be further applied in the same evolution step: this is the maximal parallel rewriting. A global clock is assumed, that is the same clock for all the regions of a membrane system. At each tick of this clock, a current configuration of the system is transformed
Supervisor:
, 2005
"... Membrane computing is an emerging research field that belongs to the more general area of molecular computing, which deals with models of computation inspired by biomolecular processes, which are seen as informationprocessing mechanisms. Membrane computing aims at defining computational models, cal ..."
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Membrane computing is an emerging research field that belongs to the more general area of molecular computing, which deals with models of computation inspired by biomolecular processes, which are seen as informationprocessing mechanisms. Membrane computing aims at defining computational models, called membrane systems or P systems, which abstract from the functioning and structure of the cell. A membrane system consists of a hierarchical arrangement of membranes delimiting regions, which represent various compartments of a cell, and with each region containing biochemical elements of various types and having associated rules, which represent biochemical processes taking place inside the cell. This thesis investigates variants of membrane systems as models for molecular computing and as modelling paradigms for biological systems. On one hand, we follow the standard approach of research in membrane computing: defining a notion of computation for membrane systems, and investigating the computational power of such computing devices. Specifically, we address issues concerning the power of “simple ” bioinspired
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.