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18
The Topological Structures of Membrane Computing
 FUNDAMENTA INFORMATICAE
, 2001
"... In its initial presentation, the P system formalism describes the topology of the membranes as a set of nested regions. This description is too rough and presents several shortcommings: only the nesting of membranes is taken into account, not their adjacency and there is an artificial distinction be ..."
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Cited by 15 (11 self)
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In its initial presentation, the P system formalism describes the topology of the membranes as a set of nested regions. This description is too rough and presents several shortcommings: only the nesting of membranes is taken into account, not their adjacency and there is an artificial distinction between a membrane and its enclosed region. To answer
Data structure as topological spaces
 In Proceedings of the 3nd International Conference on Unconventional Models of Computation UMC02
, 2002
"... Abstract. In this paper, we propose a topological metaphor for computations: computing consists in moving through a path in a data space and making some elementary computations along this path. This idea underlies an experimental declarative programming language called mgs. mgs introduces the notion ..."
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Cited by 15 (5 self)
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Abstract. In this paper, we propose a topological metaphor for computations: computing consists in moving through a path in a data space and making some elementary computations along this path. This idea underlies an experimental declarative programming language called mgs. mgs introduces the notion of topological collection: a set of values organized by a neighborhood relationship. The basic computation step in mgs relies on the notion of path: a path C is substituted for a path B in a topological collection A. This step is called a transformation and several features are proposed to control the transformation applications. By changing the topological structure of the collection, the underlying computational model is changed. Thus, mgs enables a unified view on several computational mechanisms. Some of them are initially inspired by biological or chemical processes (Gamma and the CHAM, Lindenmayer systems, Paun systems and cellular automata).
CAPSULE: Hardwareassisted parallel execution of componentbased programs
 In Proceedings of the 39th Annual International Symposium on Microarchitecture
, 2006
"... Since processor performance scalability will now mostly be achieved through threadlevel parallelism, there is a strong incentive to parallelize a broad range of applications, including those with complex control flow and data structures. And writing parallel programs is a notoriously difficult task ..."
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Cited by 11 (0 self)
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Since processor performance scalability will now mostly be achieved through threadlevel parallelism, there is a strong incentive to parallelize a broad range of applications, including those with complex control flow and data structures. And writing parallel programs is a notoriously difficult task. Beyond processor performance, the architect can help by facilitating the task of the programmer, especially by simplifying the model exposed to the programmer. In this article, among the many issues associated with writing parallel programs, we focus on finding the appropriate parallelism granularity, and efficiently mapping tasks with complex control and data flow to threads. We propose to relieve the user and compiler of both tasks by delegating the parallelization decision to the architecture at runtime, through a combination of hardware and
Chemical Computing
, 2004
"... All information processing systems found in living organisms are based on chemical processes. Harnessing the power of chemistry for computing might lead to a new unifying paradigm coping with the rapidly increasing complexity and autonomy of computational systems. Chemical computing refers to compu ..."
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Cited by 8 (0 self)
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All information processing systems found in living organisms are based on chemical processes. Harnessing the power of chemistry for computing might lead to a new unifying paradigm coping with the rapidly increasing complexity and autonomy of computational systems. Chemical computing refers to computing with real molecules as well as to programming electronic devices using principles taken from chemistry. The paper focuses on the latter, called artificial chemical computing, and discusses several aspects of how the metaphor of chemistry can be employed to build technical information processing systems. In these systems, computation emerges out of an interplay of many decentralized relatively simple components analogized to molecules. Chemical programming encompassed then the definition of molecules, reaction rules, and the topology and dynamics of the reaction space. Due to the selforganizing nature of chemical dynamics, new programming methods are required. Potential approaches for chemical programming are discussed and a road map for developing chemical computing into a unifying and well grounded approach is sketched.
The Calculus of Looping Sequences
"... Abstract. We describe the Calculus of Looping Sequences (CLS) which is suitable for modeling microbiological systems and their evolution. We present two extensions, CLS with links (LCLS) and Stochastic CLS. LCLS simplifies the description of protein interaction at a lower level of abstraction, namel ..."
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Cited by 7 (3 self)
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Abstract. We describe the Calculus of Looping Sequences (CLS) which is suitable for modeling microbiological systems and their evolution. We present two extensions, CLS with links (LCLS) and Stochastic CLS. LCLS simplifies the description of protein interaction at a lower level of abstraction, namely at the domain level. Stochastic CLS allows us to describe quantitative aspects of the modeled systems, such as the frequency of chemical reactions. As examples of application to real biological systems, we show the simulation of the activity of the lactose operon in E.coli and the quorum sensing process in P.aeruginosa, both described with Stochastic CLS. 1
A HigherOrder Graph Calculus for Autonomic Computing
 GRAPH THEORY, COMPUTATIONAL INTELLIGENCE AND THOUGHT. A CONFERENCE CELEBRATING MARTIN CHARLES GOLUMBIC'S 60TH BIRTHDAY (2008)
, 2008
"... In this paper, we present a highlevel formalism based on port graph rewriting, strategic rewriting, and rewriting calculus. We argue that this formalism is suitable for modeling autonomic systems and briefly illustrate its expressivity for modeling properties of such systems. ..."
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Cited by 4 (1 self)
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In this paper, we present a highlevel formalism based on port graph rewriting, strategic rewriting, and rewriting calculus. We argue that this formalism is suitable for modeling autonomic systems and briefly illustrate its expressivity for modeling properties of such systems.
Cell communication in tissue P systems and cell division in population P systems
 Second Brainstorming Week on Membrane Computing. Seville 27 February 2004, Technical Report 01/2004, pages 74–91. Dept. of Computer Sciences and Artificial Intelligence, Univ. of Sevilla
, 2004
"... Abstract. Two classes of tissue P systems based on evolution communication rules are introduced, some results are proved, but many more are listed as further research problems. A framework to develop population P systems is defined and a number of variants formulated with a strong biological motivat ..."
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Cited by 3 (1 self)
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Abstract. Two classes of tissue P systems based on evolution communication rules are introduced, some results are proved, but many more are listed as further research problems. A framework to develop population P systems is defined and a number of variants formulated with a strong biological motivation. 1
Patternmatching and rewriting rules for group indexed data structures
 ACM SIGPLAN NOTICES
, 2002
"... In this report, we present a new framework for the definition of various datastructures (including trees and arrays) together with a generic language of filters enabling a rulebased programming style of functions. This framework is implemented in an experimental language called MGS. The underlying ..."
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Cited by 3 (1 self)
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In this report, we present a new framework for the definition of various datastructures (including trees and arrays) together with a generic language of filters enabling a rulebased programming style of functions. This framework is implemented in an experimental language called MGS. The underlying notions funding our framework have a topological nature and make possible to extend the casebased definition of functions found in modern functional languages beyond algebraic datastructures.
Accretive Rules in Cayley P Systems
 in Procs. 3th Worshop on Membrane Computing, WMC2, Curtea de Arges, Romania, 2002, Gh. Paun et
, 2003
"... During a discussion taking place at WMC'01, G. Paun put the question of what could be computed only by moving symbols between membranes. In this paper we provide some elements of the answer, in a setting similar to tissue P systems, where the set of membranes is organized into a finite graph or ..."
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Cited by 2 (0 self)
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During a discussion taking place at WMC'01, G. Paun put the question of what could be computed only by moving symbols between membranes. In this paper we provide some elements of the answer, in a setting similar to tissue P systems, where the set of membranes is organized into a finite graph or into a Cayley graph, and using a very simple propagation process characterizing accretive growth. Our main result is to characterize the final configuration as a least fixed point and to establish two series of approximations that converge to it. All the notions introduced (Cayley graph of membranes, accretive rule and iteration) have been implemented in the MGS programming language and the two approximation series can be e#ectively computed in Pressburger arithmetics using the omega calculator in the case of Abelian Cayley graphs.