BWMC2013. Brainstorming Week on Membrane Computing (11th. 2013. Sevilla)
URI permanente para esta colecciónhttps://hdl.handle.net/11441/33342
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Ponencia Flattening P Systems with Active Membranes(Fénix Editora, 2013) Aman, Bogdan; Ciobanu, GabrielLibro Eleventh Brainstorming Week on Membrane Computing Sevilla, February 4-8, 2013 : RGNC REPORT 1/2013(Fénix Editora, 2013) Valencia Cabrera, Luis; García Quismondo, Manuel; Macías Ramos, Luis Felipe; Martínez del Amor, Miguel Ángel; Paun, Gheorghe; Riscos Núñez, Agustín; Universidad de Sevilla. Departamento de Ciencias de la Computación e Inteligencia Artificial; Research Group on Natural Computing; Universidad de Sevilla. TIC193: Computación NaturalPonencia Analysing Gene Networks with PDP Systems. Arabidopsis thaliana, a Case Study(Fénix Editora, 2013) Valencia Cabrera, Luis; García Quismondo, Manuel; Pérez Jiménez, Mario de Jesús; Su, Yansen; Yu, Hui; Pan, Linqiang; Universidad de Sevilla. Departamento de Ciencias de la Computación e Inteligencia Artificial; Ministerio de Ciencia e Innovación (MICIN). España; Junta de Andalucía; Universidad de Sevilla. TIC193: Computación NaturalGene Regulatory Networks (GRNs) are a useful tool for biologists to understand the interactions among genes in living organisms. A special kind of GRNs known as Logic Networks (LNs) has been recently introduced. These networks consider that the state of one or more genes can in uence another one. In a previous work, we proposed a Membrane Computing model which simulates the dynamics of LNs by drawing on the improved LAPP algorithm. In this paper we provide a case study for our LN model on a network which regulates the circadian rhythms of long{term studied plant Arabidopsis thaliana. We outline the software tools employed and propose a methodology for analysing LNs on our Membrane Computing model. At the end of the paper, some conclusions and future work are included.Ponencia Bridging Membrane and Reaction Systems - Further Results and Research Topics(Fénix Editora, 2013) Paun, Gheorghe; Pérez Jiménez, Mario de Jesús; Rozenberg, Grzegorz; Universidad de Sevilla. Departamento de Ciencias de la Computación e Inteligencia Artificial; Junta de Andalucía; Universidad de Sevilla. TIC193: Computación NaturalThis paper continues an investigation into bridging two research areas con- cerned with natural computing: membrane computing and reaction systems. More specif- ically, the paper considers a transfer of two assumptions/axioms of reaction systems, non- permanency and the threshold assumption, into the framework of membrane computing. It is proved that: SN P systems with non-permanency of spikes assumption charac- terize the semilinear sets of numbers, and symport/antiport P systems with threshold assumption (translated as ! multiplicity of objects) can solve SAT in polynomial time. Also, several open research problems are stated.Ponencia Some Open Problems about Numerical P Systems(Fénix Editora, 2013) Paun, Gheorghe; Universidad de Sevilla. Departamento de Ciencias de la Computación e Inteligencia Artificial; Universidad de Sevilla. TIC193: Computación NaturalSome open problems and research topics related to numerical P systems are formulated { also recalling the problems from the corresponding section of the \mega- paper produced for the previous BWMCPonencia The "Catalytic Borderline" Between Universality and Non-Universality of P Systems(Fénix Editora, 2013) Paun, Gheorghe; Universidad de Sevilla. Departamento de Ciencias de la Computación e Inteligencia Artificial; Junta de Andalucía; Universidad de Sevilla. TIC193: Computación NaturalP systems are computing models inspired by the structure and the function- ing of the living cells; they are the basic computing devices of membrane computing, a branch of natural computing. The present note is an overview of results and open prob- lems related to the borderline between the computationally universal and non-universal catalytic P systems. A short introduction to membrane computing is provided, to the use of the reader not familiar with this research areaPonencia Continuous Versus Discrete: Some Topics with a Regard to Membrane Computing(Fénix Editora, 2013) Obtulowicz, AdamSome questions and open problems are formulated in the context of a dilemma continuous approach versus discrete approach to the investigations of dynamics of complex biological and physical systems with a regard to membrane computingPonencia Simulating a Family of Tissue P Systems Solving SAT on the GPU(Fénix Editora, 2013) Martínez del Amor, Miguel Ángel; Pérez Carrasco, Jesús; Pérez Jiménez, Mario de Jesús; Universidad de Sevilla. Departamento de Ciencias de la Computación e Inteligencia Artificial; Junta de Andalucía; Ministerio de Economía y Competitividad (MINECO). España; Universidad de Sevilla. TIC193: Computación NaturalIn order to provide e cient software tools to deal with large membrane systems, high-throughput simulators are required. Parallel computing platforms are good candidates, since they are capable of partially implementing the inherently parallel nature of the model. In this concern, today GPUs (Graphics Processing Unit) are considered as highly parallel processors, and they are being consolidated as accelerators for scienti c applications. In fact, previous attempts to design P systems simulators on GPUs have shown that a parallel architecture is better suited in performance than traditional single CPUs. In 2010, a GPU-based simulator was introduced for a family of P systems with active membranes solving SAT in linear time. This is the starting point of this paper, which presents a new GPU simulator for another polynomial-time solution to SAT by means of tissue P systems with cell division, trading space for time. The aim of this simulator is to further study which ingredients of di erent P systems models are well suited to be managed by the GPU.Ponencia Improving Universality Results on Parallel Enzymatic Numerical P Systems(Fénix Editora, 2013) Leporati, Alberto; Porreca, Antonio E.; Zandron, Claudio; Mauri, GiancarloWe improve previously known universality results on enzymatic numerical P systems (EN P systems, for short) working in all-parallel and one-parallel modes. By using a attening technique, we rst show that any EN P system working in one of these modes can be simulated by an equivalent one-membrane EN P system working in the same mode. Then we show that linear production functions, each depending upon at most one variable, su ce to reach universality for both computing modes. As a byproduct, we propose some small deterministic universal enzymatic numerical P systems.Ponencia Turing Incompleteness of Asynchronous P Systems with Active Membranes(Fénix Editora, 2013) Leporati, Alberto; Manzoni, Luca; Porreca, Antonio E.We prove that asynchronous P systems with active membranes without divi- sion rules can be simulated by place/transition Petri nets, and hence are computationally weaker than Turing machines. This result holds even if the synchronisation mechanisms provided by electrical charges and membrane dissolution are exploited.Ponencia An Application of the PCol Automata in Robot Control(Fénix Editora, 2013) Langer, Miroslav; Cienciala, Ludek; Ciencialová, Lucie; Perdek, Michal; Kelemenová, AliceThe P colonies were introduced in as a variant of the bio-inspired com- putational models called membrane systems or P systems. In we divided agents into the groups according the function they provide; we introduced the modularity on the P colonies. PCol automata are an extension of the P colonies by the tape (see). This is an accepting computational device based on the very simple computational units. In this paper we combine the approach of the modules in the P colonies and of the PCol automata and we introduce the PCol automaton driven robot.Ponencia On Controlled P Systems(Fénix Editora, 2013) Krithivasan, Kamala; Paun, Gheorghe; Ramanujan, AjeeshWe introduce and brie y investigate P systems with controlled computations. First, P systems with label restricted transitions are considered (in each step, all rules used have either the same label, or, possibly, the empty label, ), then P systems with the computations controlled by languages (as in context-free controlled grammars). The relationships between the families of sets of numbers computed by the various classes of controlled P systems are investigated, also comparing them with length sets of languages in Chomsky and Lindenmayer hierarchies (characterizations of the length sets of ET0L and of recursively enumerable languages are obtained in this framework). A series of open problems and research topics are formulated.Ponencia Rete Algorithm for P System Simulators(Fénix Editora, 2013) Graciani Díaz, Carmen; Gutiérrez Naranjo, Miguel Ángel; Riscos Núñez, Agustín; Universidad de Sevilla. Departamento de Ciencias de la Computación e Inteligencia Artificial; Junta de Andalucía; Ministerio de Economía y Competitividad (MINECO). España; Universidad de Sevilla. TIC193: Computación NaturalThe Rete algorithm is a well-known algorithm in rule-based production systems which builds directed acyclic graphs that represent higher-level rule sets. This allows the rule-based systems to avoid complete re-evaluation of all conditions of the rules each step in order to check the applicability of the rules and, therefore, the computational e ciency of the production systems is improved. In this paper we study how these ideas can be applied in the improvement of the design of computational simulators in the framework of Membrane Computing.Ponencia Kernel P Systems - Version 1(Fénix Editora, 2013) Gheorgue, Marian; Ipate, Florentin; Dragomir, Ciprian; Mierla, Laurentiu; Valencia Cabrera, Luis; García Quismondo, Manuel; Pérez Jiménez, Mario de Jesús; Universidad de Sevilla. Departamento de Ciencias de la Computación e Inteligencia Artificial; Ministerio de Economía y Competitividad (MINECO). España; Junta de Andalucía; Universidad de Sevilla. TIC193: Computación NaturalA basic P system, called kernel P system4 (kP system for short), combining features of di erent P systems introduced and studied so far is de ned and discussed. The structure of such systems is de ned as a dynamic graph, similar to tissue-like P systems, the objects are organised as multisets, and the rules in each compartment, rewriting and communication together with system structure changing rules, are applied in accordance with a speci c execution strategy. The de nition of kP systems is introduced and some examples illustrate this concept. Two classes of P systems, namely neural-like and generalised communicating P systems are simulated by kP systems. Some case studies prove the expressive power of these systems.Ponencia Universal P Systems: One Catalyst Can Be Suficient(Fénix Editora, 2013) Freund, Rudolf; Paun, Gheorghe; Universidad de Sevilla. Departamento de Ciencias de la Computación e Inteligencia Artificial; Junta de Andalucía; Universidad de Sevilla. TIC193: Computación NaturalWhether P systems with only one catalyst can already be universal, is still an open problem. Here we establish universality (computational completeness) by using speci c variants of additional control mechanisms. At each step using only multiset rules from one set of a nite number of sets of rules allows for obtaining computational completeness with one catalyst and only one membrane. If the targets are used for choosing the multiset of rules to be applied, for getting computational completeness with only one catalyst more than one membrane is needed. If the available sets of rules change periodically with time, computational completeness can be obtained with one catalyst in one membrane. Moreover, we also improve existing computational completeness results for P systems with mobile catalysts and for P systems with membrane creation.Ponencia Scenario Based P Systems(Fénix Editora, 2013) Ciobanu, Gabriel; Sburlan, DragosIn this paper we de ne and study Scenario Based P Systems, a model of computation inspired by the metabolic pathways and networks. Starting from the classical de nition of P systems with symbol objects and multiset rewriting rules, we de ne regular expressions able to capture the causal dependencies among di erent executions of the rules. The results show the computational power of this model.Ponencia 2D P Colonies and Modelling of Liquid Flow Over the Earth's Surface(Fénix Editora, 2013) Cienciala, Ludek; Ciencialová, Lucie; Langer, MiroslavWe continue the investigation of 2D P colonies introduced in [1], a class of abstract computing devices composed of independent agents, acting and evolving in a shared 2D environment where the agents are located. Agents have limited information about the contents of the environment where they can move in four directions.Ponencia A GPU Simulation for Evolution-Communication P Systems with Energy Having no Antiport Rules(Fénix Editora, 2013) Bangalan, Zylynn F.; Soriano, Krizia Ann N.; Juayong, Richelle Ann B.; Cabarle, Francis George C.; Adorna, Henry N.; Martínez del Amor, Miguel Ángel; Universidad de Sevilla. Departamento de Ciencias de la Computación e Inteligencia Artificial; Junta de Andalucía; Ministerio de Ciencia e Innovación (MICIN). España; Universidad de Sevilla. TIC193: Computación NaturalEvolution-Communication P system with energy (ECPe systems) is a cell- like variant P system which establishes a dependence between evolution and communi- cation through special objects, called `energy,' produced during evolution and utilized during communication. This paper presents our initial progress and e orts on the im- plementation and simulation of ECPe systems using Graphics Processing Units (GPUs). Our implementation uses matrix representation and operations presented in a previous work. Speci cally, an implementation of computations on ECPe systems without antiport rules is discussed.Ponencia Studying the Chlorophyll Fluorescence in Cyanobacteria with Membrane Computing Techniques(Fénix Editora, 2013) Ardelean, Ioan I.; Díaz Pernil, Daniel; Gutiérrez Naranjo, Miguel Ángel; Peña Cantillana, Francisco; Sarchizian, Iris; Universidad de Sevilla. Departamento de Ciencias de la Computación e Inteligencia Artificial; Universidad de Sevilla. Departamento de Matemática Aplicada I (ETSII); Junta de Andalucía; Ministerio de Economía y Competitividad (MINECO). España; Universidad de Sevilla. TIC193: Computación Natural; Universidad de Sevilla. FQM296: Topología Computacional y Matemática AplicadaIn this paper, we report a pioneer study of the decrease in chlorophyll uorescence produced by the reduction of MTT (a dimethyl thiazolyl diphenyl tetrazolium salt) monitored using an epi uorescence microscope coupled to automate image analysis in the framework of P systems. Such analysis has been performed by a family of tissue P systems working on the images as data inpu