Fundamenta Informaticae - Volume 49, issue 1-3

Authors: Martín-Vide, Carlos | Păun, Gheorghe

Article Type: Other

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Citation: Fundamenta Informaticae, vol. 49, no. 1-3, pp. i-ii, 2002

Authors: Martín-Vide, Carlos | Păun, Andrei | Păun, Gheorghe | Rozenberg, Grzegorz

Article Type: Research Article

Abstract: This paper continues research on membrane systems which function by communication only, meaning that there are no evolving rules for molecules. The whole computation process relies on passage of molecules through membranes -- this provides communication between regions of the membrane system. Next to transport of single molecules through membranes (uniport) we also study a coupled transport of molecules, with two molecules passing either in the same direction (symport) or in opposite directions (antiport). We study …the computational power of such membrane systems and prove that using only symport one gets Turing universality. Moreover, we prove that five membranes suffice to get Turing universality, and the number of membranes can be decreased to three if forbidding context conditions for transport are used. Show more

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Citation: Fundamenta Informaticae, vol. 49, no. 1-3, pp. 1-15, 2002

Authors: Aguado, Joaquin | Balanescu, Tudor | Cowling, Tony | Gheorghe, Marian | Holcombe, Mike | Ipate, Florentin

Article Type: Research Article

Abstract: The aim of this paper is to show how the P systems with replicated rewriting can be modeled by X-machines (also called Eilenberg machines). In the first approach, the parallel behaviour of the regions of a P system is simulated by a sequential process involving a single X-machine. This allows the application of the X-machine testing procedures in order to prove the correctness of P systems. In the second approach, a P system is simulated by a …communicating system of X-machines. Each component of such a system is an X-machine associated with a region of the given P system. The components act in parallel, as their counterparts do in a P system, and use some specific mechanism for communication and synchronisation. Show more

Keywords: P Systems, Finite state machines, (Stream) X-machines, Formal specifications

Citation: Fundamenta Informaticae, vol. 49, no. 1-3, pp. 17-33, 2002

Authors: Ardelean, Ioan I.

Article Type: Research Article

Abstract: This paper presents the stucture, organization (hierarchy) and function of cell membrane in bacteria, with special emphasis on: i) the hierarchy of cell membranes in Gram-negative and Gram-positive bacteria, ii) two main criteria for the classification of transport of ions and molecules across cell membrane, iii) two important mechanisms of transport – symport and antiport, and iv) the relevance of these biological realities for working concepts in P systems such as membrane hierarchy and developmental rules. …The biological reality not only illustrates some central concepts in P systems but also could give some suggestions for the theoretical development of P systems and their possible implementation. Show more

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Citation: Fundamenta Informaticae, vol. 49, no. 1-3, pp. 35-43, 2002

Authors: Atanasiu, Adrian | Martín-Vide, Carlos

Article Type: Research Article

Abstract: P systems are computing models where certain objects evolve in parallel in a hierarchical membrane structure. Recent results show that this model is a promising framework for solving NP-complete problems in polynomial time. A variant of P systems with active membranes is proposed in this paper. It uses a new operation called "subordonation", based on the process of "endocytosis" of membranes: a membrane can be entirely absorbed by another membrane, preserving its content. This class of …P systems with active membranes can compute all Turing computable mappings. Arithmetical operations defined in [1] can be obtained as particular cases of primitive recursive functions, but with a higher complexity degree. Show more

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Citation: Fundamenta Informaticae, vol. 49, no. 1-3, pp. 45-59, 2002

Authors: Ciobanu, Gabriel | Paraschiv, Dorin

Article Type: Research Article

Abstract: We present a software application that is intended to be a tool for people working with P~systems. This software tool is called the Membrane Simulator and it provides a graphical simulation for two variants of P systems: the initial version of the catalytic hierarchical cell system and the active membrane system.

Citation: Fundamenta Informaticae, vol. 49, no. 1-3, pp. 61-66, 2002

Authors: Ciobanu, Gabriel | Tanasă, Bogdan

Article Type: Research Article

Abstract: This paper describes the molecular interactions and coordination of cell processes using computer operating system concepts related to synchronization and communication. We argue that in molecular biology, the genes and their chromatin context provide communication and interaction with various cell processes in a similar way to that in which computer processes synchronize and communicate with each other.

Keywords: Cell biology, operating systems, process communication, pipe, signals, modules

Citation: Fundamenta Informaticae, vol. 49, no. 1-3, pp. 67-80, 2002

Authors: Freund, Rudolf | Oswald, Marion

Article Type: Research Article

Abstract: We consider extended variants of GP systems, i.e., membrane systems with sequential applications of evolution rules. The main features we explore are applicability conditions (context conditions) on single objects as well as on the remaining contents of the underlying compartment. For a special very restricted variant only using forbidding context conditions we already obtain universal computational power.

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Citation: Fundamenta Informaticae, vol. 49, no. 1-3, pp. 81-102, 2002

Authors: Frisco, Pierluigi | Hoogeboom, Hendrik Jan | Sant, Paul

Article Type: Research Article

Abstract: We present a direct universal P system based on splicing. Our approach differs from those shown in previous papers as the P system we construct takes as input an encoding of another P system. Previous results were based on the simulation of universal type-0 grammars or Turing machines. We think that the approach we use can be applied to other variants of P systems.

Keywords: DNA computing, P systems, Splicing, Direct universal system

Citation: Fundamenta Informaticae, vol. 49, no. 1-3, pp. 103-122, 2002

Authors: Giavitto, Jean-Louis | Michel, Olivier

Article Type: Research Article

Abstract: In its initial presentation, the P system formalism describes the topology of the membranes as a set of nested regions. In this paper, we present an algebraic structure developped in combinatorial topology that can be used to describe finer adjacency relationships between membranes. Using an appropriate abstract setting, this technical device enables us to reformulate also the computation within a membrane and proposes a unified view on several computational mechanisms initially inspired by biological processes. …These theoretical tools are instantiated in MGS, an experimental programming language handling various types of membrane structures in a homogeneous and uniform syntax. Show more

Keywords: membrane computing, Gamma, CHAM, P system, L system, cellular automata, group based fields, rewriting, topological collection, declarative programming language

Citation: Fundamenta Informaticae, vol. 49, no. 1-3, pp. 123-145, 2002