BWMC2005. Brainstorming Week On Membrane Computing (3rd. 2005. Sevilla)
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Ponencia On a Class of P Automata as a Machine Model for Languages over Infinite Alphabets(Fénix Editora, 2005) Vaszil, GyörgyWe show how P automata having a finite description and working with a finite object-alphabet can be used to describe languages over countably infinite alphabets. We propose to relate the language classes characterized by different types of P automata to some of the existing characterizations of language classes over infinite alphabets, and give an upper bound for the class of languages accepted by the class of one of the most straightforward and least complicated variants of these types of P automata.Ponencia Recognizing Membrane Structures with Tree Automata(Fénix Editora, 2005) Sempere, José M.; López, DamiánIn this work we propose a new model of tree automata based on multisets of states and symbols linked to the finite control. This new model accepts a set of trees with symmetries between their internal nodes. We name this property as mirroring. We propose an application of these automata to solve a problem related to P systems such as recognizing identic membrane structures.Ponencia Further Results on P Systems with Promoters/Inhibitors(Fénix Editora, 2005) Sburlan, DragosThe paper gives several results regarding P systems with non-cooperative rules and promoters/inhibitors at the level of rules. For the class of P systems using inhibitors, generating families of sets of vectors of numbers, the equivalence with the family of Parikh sets of ET0L languages is presented. In case of P systems with non- cooperative promoted rules even if an upper bound was not given, the inclusion of the family PsET0L was proved. Moreover, a characterization of such systems by means of a particular form of random context grammars, therefore a sequential formal device, is proposed.Ponencia Dynamical Probabilistic P Systems: Definitions and Applications(Fénix Editora, 2005) Pescini, Dario; Besozzi, Daniela; Zandron, Claudio; Mauri, GiancarloWe introduce dynamical probabilistic P systems, a variant where probabilities associated to the rules change during the evolution of the system, as a new approach to the analysis and simulation of the behavior of complex systems. We define the notions for the analysis of the dynamics and we show some applications for the investigation of the properties of the Brusselator (a simple scheme for the Belousov-Zabothinskii reaction), the Lotka-Volterra system and the decay process.Ponencia One More Universality Result for P Systems with Objects on Membranes(Fénix Editora, 2005) Paun, Gheorghe; Universidad de Sevilla. Departamento de Ciencias de la Computación e Inteligencia Artificial; Universidad de Sevilla. TIC193: Computación NaturalWe continue here the attempt to bridge brane calculi with membrane com- puting, following the investigation started in. Specifically, we consider P systems with objects placed on the membranes, and processed by membrane operations. The operations used in this paper are membrane creation (cre), and membrane dissolution (dis), defined in a way which reminds the operations pino, exo from a brane calculus from. For P systems based on these operations we prove the universality, for one of the two possible variants of the operations; for the other variant the problem remains open.Ponencia Further Twenty Six Open Problems in Membrane Computing(Fénix Editora, 2005) Paun, Gheorghe; Universidad de Sevilla. Departamento de Ciencias de la Computación e Inteligencia Artificial; Universidad de Sevilla. TIC193: Computación NaturalThis is a sort of personal list of problems and research topics, compiled with the occasion of the Third Brainstorming Week on Membrane Computing, Sevilla, 2005.Ponencia Christiansen Grammar for Some P Systems(Fénix Editora, 2005) Ortega de la Puente, Alfonso; Núñez Hervás, Rafael; Cruz Echeandía, Marina de la; Alfonseca, ManuelThe main goal of this work is to formally describe P systems. This is a necessary step to subsequently apply Christiansen grammar evolution (an evolutionary tool developed by the authors) for automatic designing of P systems. Their complex structure suggests us two decisions: to restrict our study to a subset of P systems that ease the representation while keeping a suitable complexity and to select a powerful enough formal tool. Our work is restricted to a kind of P system that can simulate any logical function by means of delay symbols and two mobile catalysts. Like in general P systems, some components of these "logical" P systems depend on other components (for example, the number of axioms and regions and the set of possible indexes for the symbols in their rules depend on the membrane structure). So, a formal representation able to handle context dependent constructions is needed. Our work uses Christiansen grammars to describe P systems.Ponencia A Tool for Using the SBML Format to Represent P Systems which Model Biological Reaction Networks(Fénix Editora, 2005) Nepomuceno Chamorro, Isabel de los Ángeles; Nepomuceno Chamorro, Juan Antonio; Romero Campero, Francisco José; Universidad de Sevilla. Departamento de Ciencias de la Computación e Inteligencia Artificial; Universidad de Sevilla. TIC193: Computación NaturalIn this paper we present a software tool to represent P systems modelling signalling networks of biochemical reactions using SBML (Systems Biology Markup Language), a machine-readable format for describing qualitative and quantitative models of biochemical networks. CLIPS (C Language Integrated Production System), a tool which provides a complete environment for the construction of rule and/or object based expert systems, has been used to simulated membrane system. Our tool acts as a translator from SBML to CLIPS; that is, besides providing an environment for writing SBML code it also parses this code and generates automatically the CLIPS code that simulates the membrane system represented in SBML.Ponencia First Steps Towards a Geometry of Computation(Fénix Editora, 2005) Muskulus, Michael; Brijder, RobertWe introduce a geometrical setting which seems promising for the study of computation in multiset rewriting systems, but could also be applied to register machines and other models of computation. This approach will be applied here to membrane systems (also known as P systems) without dynamical membrane creation. We discuss the role of maximum parallelism and further simplify our model by considering only one membrane and sequential application of rules, thereby arriving at asynchronous multiset rewriting systems (AMR systems). Considering only one membrane is no restriction, as each static membrane system has an equivalent AMR system. It is further shown that AMR systems without a priority relation on the rules are equivalent to Petri Nets. For these systems we introduce the notion of asymptotically exact computation, which allows for stochastic appearance checking in a priori bounded (for some complexity measure) computations. The geometrical analogy in the lattice Nd0 ; d 2 N, is developed, in which a computation corresponds to a trajectory of a random walk on the directed graph induced by the possible rule applications. Eventually this leads to symbolic dynamics on the partition generated by shifted positive cones C+ p , p 2 Nd0 , which are associated with the rewriting rules, and their intersections. Complexity measures are introduced and we consider non-halting, loop-free computations and the conditions imposed on the rewriting rules. Eventually, two models of information processing, control by demand and control by availability are discussed and we end with a discussion of possible future developments.Ponencia Simulating Avascular Tumors with Membrane Systems(Fénix Editora, 2005) Gutiérrez Naranjo, Miguel Ángel; Pérez Jiménez, Mario de Jesús; Romero Campero, Francisco José; Universidad de Sevilla. Departamento de Ciencias de la Computación e Inteligencia Artificial; Ministerio de Ciencia y Tecnología (MCYT). España; Universidad de Sevilla. TIC193: Computación NaturalTumor growth has received a considerable attention by the scientific community. In the earliest stages of development, tumor growth seems to be regulated by direct diffusion of nutrients and wastes from and to surrounding tissue. In this paper we present an approach of the use of membrane computing techniques to simulate and predict the growth of a tumor in the avascular stage. We present a preliminary version of our software to simulate this growth and some future research lines.Ponencia A Simulator for Confluent P Systems(Fénix Editora, 2005) Gutiérrez Naranjo, Miguel Ángel; Pérez Jiménez, Mario de Jesús; Riscos Núñez, Agustín; Universidad de Sevilla. Departamento de Ciencias de la Computación e Inteligencia Artificial; Ministerio de Ciencia y Tecnología (MCYT). España; Universidad de Sevilla. TIC193: Computación NaturalSoftware simulators for P system are nowadays the main tool to carry out experiments in the field of Membrane Computing. Although the simulation of a P system is a quite complex task, current simulators have been successfully used for pedagogical purposes and also as assistant tools for researchers. Up to now, simulators have always been designed to deal with a specific model of P systems. In this paper we present a new simulator which is not oriented to only one model of systems, but it allows the researcher to experiment with many existing models or even to create new ones.Ponencia Matrix Languages, Register Machines, Vector Addition Systems(Fénix Editora, 2005) Freund, Rudolf; Ibarra, Óscar H.; Paun, Gheorghe; Yen, Hsu-Chen; Universidad de Sevilla. Departamento de Ciencias de la Computación e Inteligencia Artificial; Universidad de Sevilla. TIC193: Computación NaturalWe give a direct and simple proof of the equality of Parikh images of lan- guages generated by matrix grammars with appearance checking with the sets of vectors generated by register machines. As a particular case, we get the equality of the Parikh images of languages generated by matrix grammars without appearance checking with the sets of vectors generated by partially blind register machines. Then, we consider pure matrix grammars (i.e., grammars which do not distinguish terminal and nonterminal symbols), and prove the inclusion of the family of Parikh images of languages generated by such grammars (without appearance checking) in the family of sets of vectors generated by blind register machines, as well as the inclusion of reachability sets of vector addition systems in the family of Parikh images of pure matrix languages. For pure matrix grammars with a certain restriction on the form of matrices, also the converse of the latter inclusion is obtained. Thus, in view of the result from, we obtain the semilin- earity of languages generated by pure matrix grammars (without appearance checking) with alphabets with at most five letters, with the considered restrictions on the form of matrices. A pure matrix grammar with five symbols, but without restrictions on the form of matrices, is produced which generates a non-semilinear language.Ponencia Editing Configurations of P Systems(Fénix Editora, 2005) Csuhaj Varjú, Erzsébet; Nola, Antonio di; Paun, Gheorghe; Pérez Jiménez, Mario de Jesús; Vaszil, György; Universidad de Sevilla. Departamento de Ciencias de la Computación e Inteligencia Artificial; Universidad de Sevilla. TIC193: Computación NaturalThis paper proposes and preliminarily investigates the possibility of transforming a configuration (membrane structure and multisets of symbol-objects present in the compartments of this membrane structure) of a P system into another configuration, by means of a given set of rules acting both on the membranes and on the multisets of objects. Although such a transformation can be obtained during a computation of a P system, we consider it as a goal per se, as a pre-computation phase, when the system itself is built. In this framework, several important topics appear, such as the edit-distance be- tween configurations (with respect to a given set of editing rules; actually, this is a weak metric, because it is not necessarily symmetric), normal forms, reachability, existence of single configurations from which a given family of configurations can be constructed, etc. We investigate here only a few of these questions; the paper is mainly devoted to formulating problems in the new framework, calling attention to the possible extensions and usefulness of the present approach.Ponencia EP-colonies: Micro-Organisms in a Cell-like Environment(Fénix Editora, 2005) Csuhaj Varjú, ErzsébetThe aim of this note is to introduce a model for describing populations of extremely simple organisms which live in and interact with a dynamically changing cell-like environment. In addition to the definition of the notion, we present examples illustrating some possible properties of these constructs and propose some bio-inspired problems to study.Ponencia Event-Related Outputs of Computations in P Systems(Fénix Editora, 2005) Cavaliere, Matteo; Freund, Rudolf; Leitsch, Alexander; Paun, Gheorghe; Universidad de Sevilla. Departamento de Ciencias de la Computación e Inteligencia Artificial; Universidad de Sevilla. TIC193: Computación NaturalWe briefly investigate the idea to consider as the result of a computation in a P system the number of steps elapsed between two events produced during the computation. Specifically, we first consider the case when the result of a computation is defined in terms of events related to using rules, introducing objects, or meeting objects. Universality is easily obtained in each case for symport/antiport P systems. Then, we address the case when the number computed by a system is the length of a computation itself. We obtain a few results both for catalytic multiset-rewriting and for symport/antiport systems (in each case, also with using membrane dissolution) showing that non-semilinear sets of vectors can be computed in this way. A general non-universality result is proved for this case - no system, of any type, can have as the length of its halting computations all sets of numbers computable by Turing machines. The general problem, of characterizing the sets of numbers computed in this way, remains open.Ponencia Specifying Dynamic Software Architectures by Using Membrane Systems(Fénix Editora, 2005) Cavaliere, Matteo; Deufemia, VincenzoWe present a formalism for the definition of dynamic software architectures in terms of membrane systems, distributed computational models inspired from the structure and the functioning of living cells. The dynamics (the evolution) of the overall architecture is defined by rules that modify the contents (data) and structure of the membrane system. The evolution of the membrane system can be statically checked to ensure that some properties imposed by the architecture are preserved.Ponencia Abstract Machines of Systems Biology (Extended Abstract)(Fénix Editora, 2005) Cardelli, LucaLiving cells are extremely well-organized autonomous systems, consisting of discrete interacting components. Key to understanding and modelling their behavior is modelling their system organization, which can be described as a collection of distinct but interconnected abstract machines. Biologists have invented a number of notations attempting to describe, abstractly, these abstract machines and the processes that they implement. Systems biology aims to understand how these abstract machines work, separately and together.Ponencia WebPS: A Web-based P System Simulator with Query Facilities(Fénix Editora, 2005) Bonchis, Cosmin; Izbasa, Cornel; Petcu, Dana; Ciobanu, GabrielIn this paper we present an open-source web-enabled simulator for P sys- tems. We use CLIPS embedded in C, and make the simulator available as a web application, complemented by a query language to specify the results.Ponencia Metabolic Algorithm with Time-varying Reaction Maps(Fénix Editora, 2005) Bianco, Luca; Fontana, Federico; Manca, VincenzoA symbolic-based approach to modelling biochemical processes and cellular dynamics is likely to turn useful in computational biology, where attempts to represent the cell as a huge, complex dynamic system must trade with the linguistic nature of the DNA and the individual behavior of the organelles living within. The early version of the metabolic algorithm gave a first answer to the problem of representing oscillatory biological phenomena, so far being treated with traditional (differential) mathematical tools, in terms of rewriting systems. We are now working on a further version of this algorithm, in which the rule application is tuned by reaction maps depending on the specific phenomenon under consideration. Successful simulations of the Brusselator, the Lotka-Volterra population dynamics and the PKC activation foster potential applications of the algorithm in systems biology.Ponencia On Modelling Ion Fluxes Across Biological Membranes with P Systems(Fénix Editora, 2005) Ardelean, Ioan I.; Besozzi, DanielaIn this report we address the challenge of using P systems to integrate at the whole cell level both active and passive transport of different ions, done by different types of membrane transport proteins which work simultaneously and concurrently.