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425
Artificial Chemistries  A Review
, 2000
"... This article reviews the growing body of scientific work in Artificial Chemistry. First, common motivations and fundamental concepts are introduced. Second, current research activities are discussed along three application dimensions: modelling, information processing and optimization. Finally, comm ..."
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Cited by 58 (4 self)
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This article reviews the growing body of scientific work in Artificial Chemistry. First, common motivations and fundamental concepts are introduced. Second, current research activities are discussed along three application dimensions: modelling, information processing and optimization. Finally, common phenomena among the different systems are summarized. It is argued here that Artificial Chemistries are "the right stuff" for the study of prebiotic and biochemical evolution, and they provide a productive framework for questions regarding the origin and evolution of organizations in general. Furthermore, Artificial Chemistries have a broad application range to practical problems as shown in this review.
The Social System
"... into cally to a process of national selection. This article describes the process used, presents feedback from the assessors and candidates involved, and discusses possible improvements for future rounds. ..."
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Cited by 40 (0 self)
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into cally to a process of national selection. This article describes the process used, presents feedback from the assessors and candidates involved, and discusses possible improvements for future rounds.
MGS: a RuleBased Programming Language for Complex Objects and Collections
, 2001
"... We present the first results in the development of a new declarative programming language called MGS. This language is devoted to the simulation of biological processes, especially those whose state space must be computed jointly with the current state of the system. MGS proposes a unified view on s ..."
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Cited by 39 (13 self)
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We present the first results in the development of a new declarative programming language called MGS. This language is devoted to the simulation of biological processes, especially those whose state space must be computed jointly with the current state of the system. MGS proposes a unified view on several computational mechanisms initially inspired by biological or chemical processes (Gamma and the CHAM, Lindenmayer systems, Paun systems and cellular automata). The basic computation step in MGS replaces in a collection A of elements, some subcollection B, by another collection C. The collection C only depends on B and its adjacent elements in A. The pasting of C into A B depends on the shape of the involved collections. This step is called a transformation. The specification of the collection to be substituted can be done in many ways. We propose here a pattern language based on the neighborhood relationship induced by the topology of the collection. Several features to control the transformation applications are then presented.
P systems, a new computational modelling tool for Systems Biology
 Transactions on Computational Systems Biology VI. Lecture
, 2006
"... Abstract. In this paper we present P systems as a reliable computational modelling tool for Systems Biology that takes into account the discrete character of the quantity of components of biological systems, the inherently randomness in biological phenomena and the key role played by membranes in th ..."
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Cited by 31 (14 self)
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Abstract. In this paper we present P systems as a reliable computational modelling tool for Systems Biology that takes into account the discrete character of the quantity of components of biological systems, the inherently randomness in biological phenomena and the key role played by membranes in the function of living cells. We will introduce two different strategies for the evolution of P systems, namely, Multicompartmental Gillespie’s Algorithm based on the well known Gillespie’s Algorithm but running on more than one compartment; and Deterministic Waiting Times Algorithm, an exact deterministic method. In order to illustrate these two strategies we have modelled two biological systems: the EGFR Signalling Cascade and the Quorum Sensing System in the bacterium Vibrio Fischeri. Our simulations results show that for the former system a deterministic approach is valid whereas for the latter a stochastic approach like Multicompartmental Gillespie’s Algorithm is necessary. 1
Networks of evolutionary processors
 Acta Informatica
, 2003
"... Abstract. In this paper we consider networks of evolutionary processors as language generating and computational devices. When the filters are regular languages one gets the computational power of Turing machines with networks of size at most six, depending on the underlying graph. When the filters ..."
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Cited by 30 (7 self)
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Abstract. In this paper we consider networks of evolutionary processors as language generating and computational devices. When the filters are regular languages one gets the computational power of Turing machines with networks of size at most six, depending on the underlying graph. When the filters are defined by random context conditions, we obtain an incomparability result with the families of regular and contextfree languages. Despite their simplicity, we show how the latter networks might be used for solving an NPcomplete problem, namely the “3colorability problem”, in linear time and linear resources (nodes, symbols, rules). 1
From cells to computers: Computing with membranes (P systems
 Biosystems
, 2001
"... The aim of this paper is to introduce to the reader the main ideas of computing with membranes, a recent branch of (theoretical) molecular computing. In short, in a celllike system, multisets of objects evolve according to given rules in the compartments defined by a membrane structure and compute ..."
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Cited by 28 (0 self)
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The aim of this paper is to introduce to the reader the main ideas of computing with membranes, a recent branch of (theoretical) molecular computing. In short, in a celllike system, multisets of objects evolve according to given rules in the compartments defined by a membrane structure and compute natural numbers as the result of halting sequences of transitions. The model is parallel, nondeterministic. Many variants have already been considered and many problems about them were investigated. We present here some of these variants, focusing on two central classes of results: (1) characterizations of the recursively enumerable sets of numbers and (2) possibilities to solve NPcomplete problems in polynomial — even linear — time (of course, by making use of an exponential space). The results are given without proofs. An almost complete bibliography of the domain, at the middle of October 2000, is
Solving NPcomplete problems with networks of evolutionary processors
 Proceedings of IWANN 2001, LNCS 2084, SpringerVerlag
, 2001
"... We propose a computational device based on evolutionary rules and communication within a network, similar to that introduced in [4], called network of evolutionary processors. An NPcomplete problem is solved by networks of evolutionary processors of linear size in linear time. Some furher direction ..."
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Cited by 24 (6 self)
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We propose a computational device based on evolutionary rules and communication within a network, similar to that introduced in [4], called network of evolutionary processors. An NPcomplete problem is solved by networks of evolutionary processors of linear size in linear time. Some furher directions of research are finally discussed.
Principles of chemical programming
 In RULE’04, ENTCS. Elsevier
, 2004
"... Abstract The chemical reaction metaphor describes computation in terms of a chemical solution in which molecules interact freely according to reaction rules. Chemical models use the multiset as their basic data structure. Computation proceeds by rewritings of the multiset which consume elements acco ..."
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Cited by 23 (11 self)
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Abstract The chemical reaction metaphor describes computation in terms of a chemical solution in which molecules interact freely according to reaction rules. Chemical models use the multiset as their basic data structure. Computation proceeds by rewritings of the multiset which consume elements according to reaction conditions and produce new elements according to specific transformation rules. Since the introduction of Gamma in the mideighties, many other chemical formalisms have been proposed such as the Cham, the Psystems and various higherorder extensions. The main objective of this paper is to identify a basic calculus containing the very essence of the chemical paradigm and from which extensions can be derived and compared to existing chemical models. 1