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250
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 34 (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.
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 26 (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 23 (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
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 22 (10 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
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 22 (7 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.
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 21 (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.
Membrane Systems with Symport/Antiport: Universality Results
 in Membrane Computing. Intern. Workshop WMCCdeA2002, Revised Papers
, 2002
"... We consider tissue P systems using symport / antiport rules of only one symbol where in each link (channel) between two cells at most one rule is applied, but in each channel a symport / antiport rule has to be used if possible. We prove that any recursively enumerable set of kdimensional vectors o ..."
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Cited by 18 (7 self)
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We consider tissue P systems using symport / antiport rules of only one symbol where in each link (channel) between two cells at most one rule is applied, but in each channel a symport / antiport rule has to be used if possible. We prove that any recursively enumerable set of kdimensional vectors of natural numbers can be generated (accepted) by such a tissue P system with symport / antiport rules of one symbol using at most 2k + 5 (at most 3k + 7) cells.
On P Systems as a Modelling Tool for Biological Systems
 in: PreProceedings of WMC6  Vienna 2005
, 2005
"... Abstract. We introduce a variant of P systems where rules have associated a real number providing a measure for the “intrinsic reactivity”of the rule and roughly corresponding to the kinetic coefficient which, in biochemistry, is usually associated to each molecular reaction. The behaviour of these ..."
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Cited by 18 (9 self)
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Abstract. We introduce a variant of P systems where rules have associated a real number providing a measure for the “intrinsic reactivity”of the rule and roughly corresponding to the kinetic coefficient which, in biochemistry, is usually associated to each molecular reaction. The behaviour of these P systems is then defined according to a strategy which, in each step, randomly selects the next rule to be applied depending upon a certain distribution of probabilities. As an application, we present a P system model of the quorum sensing regulatory networks of the bacterium Vibrio Fischeri. In this respect, a formalisation of the network in terms of P systems is provided and some simulation results concerning the behaviour of a colony of such bacteria are reported. We also briefly describe the implementation techniques adopted by pointing out the generality of our approach which appears to be fairly independent from the particular choice of P system variant and the language used to implement it. 1
Catalytic P systems, semilinear sets, and vector addition systems
 THEORETICAL COMPUTER SCIENCE
, 2004
"... We look at 1region membrane computing systems which only use rules of the form Ca Cv, where C is a catalyst anoncatalW:k and v is a(possiblW:kky string ofnoncatal sts. There are norulk of the form a v. Thus, we can think of these systems as"purelx catalxyMWe consider two types: (1) when thein ..."
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Cited by 16 (3 self)
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We look at 1region membrane computing systems which only use rules of the form Ca Cv, where C is a catalyst anoncatalW:k and v is a(possiblW:kky string ofnoncatal sts. There are norulk of the form a v. Thus, we can think of these systems as"purelx catalxyMWe consider two types: (1) when theinitial configuration containsonl onecatalxkA and (2) when theinitial configuration contains mulains catalsy" We show that systems of the first type are equivalyM to communicationfree Petri nets, which are aly equivalyM to commutative contextfree grammars. They defin epreciselkq semilel sets. ThispartialkyM:W"k an open question (in: WMCCdeA'02, Lecture Notes in Computer Science,vol 2597, Springer,Berlge 2003, pp. 400  409; Computational" universal P systems without priorities: two catal"k# are su#cient, availt,y at http://psystems.disco.unimib.it, 2003). Systems of the second type define exactl""# recursivelMkq""yl sets oftupl# (i.e., Turing machinecomputablWk Weal" studyan extended model where therul are of the form q :(p; Ca Cv) (where q and p are states), i.e., the appl":xyMk of therul is guided bya #nitestatecontrol For thisgeneral"yM model type (1) aswel as type (2) with some restriction correspond to vector addition systems. Finally, we briefly investigate the closure properties of catalytic systems.