BWMC2006. Brainstorming Week On Membrane Computing (4th. 2006. Sevilla)

URI permanente para esta colecciónhttps://hdl.handle.net/11441/34355

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Reaction Cycles in Membrane Systems and Molecular Dynamics
(Fénix Editora, 2006) Muskulus, Michael; Houweling, Sanne; Rozenberg, Grzegorz; Besozzi, Daniela; Cazzaniga, Paolo; Pescini, Dario; Brijder, Robert
We are considering molecular dynamics and (sequential) membrane systems from the viewpoint of Markov chain theory. The first step is to understand the structure of the configuration space, with respect to communicating classes. Instead of a reachability analysis by traditional methods, we use the explicit monoidal structure of this space with respect to rule applications. This leads to the notion of precycle, which is an element of the integer kernel of the stoichiometric matrix. The generators of the set of precycles can be effectively computed by an incremental algorithm due to Contejean and Devie. To arrive at a characterization of cycles, we introduce the notion of defect, which is a set of geometric constraints on a configuration to allow a precycle to be enabled, that is, be a cycle. An important open problem is the effcient calculation of the defects. We also discuss aspects of asymptotic behavior and connectivity, as well as give a biological example, showing the usefulness of the method for model checking.
Some Notes on the Interplay Between P Systems and Chemotaxis in Bacteria
(Fénix Editora, 2006) Ardelean, Ioan I.; Besozzi, Daniela
We describe some chemotactic behaviors of bacteria, that is, their movement response to changes in the environment, and the underlying molecular mechanisms. We outline how such processes could be linked to membrane computing, by taking inspiration from them for new type of rules or new features to be introduced in P systems, as well as by considering how the application of recent P system-based models can produce relevant results for the description and the analysis of chemotaxis processes.
Stochastic Approaches in P Systems for Simulating Biological Systems
(Fénix Editora, 2006) Cazzaniga, Paolo; Pescini, Dario; Romero Campero, Francisco José; Besozzi, Daniela; Mauri, Giancarlo; Universidad de Sevilla. Departamento de Ciencias de la Computación e Inteligencia Artificial; Universidad de Sevilla. TIC193: Computación Natural
Different stochastic strategies for modeling biological systems with P systems are reviewed in this paper, such as the multi-compartmental approach and dynamical probabilistic P systems. The respective results obtained from the simulations of a test case study (the quorum sensing phenomena in Vibrio Fischeri colonies) are shown, compared and discussed.
Two Universality Results for (Mem)Brane Systems
(Fénix Editora, 2006) Besozzi, Daniela; Busi, Nadia; Franco, Giuditta; Freund, Rudolf; Paun, Gheorghe; Universidad de Sevilla. Departamento de Ciencias de la Computación e Inteligencia Artificial; Universidad de Sevilla. TIC193: Computación Natural
We prove that P systems with mate and drip operations and using at most five membranes during any step of a computation are universal. This improves a recent similar result from, where eleven membranes are used. The proof of this result has the "drawback" that the output of a computation is obtained on an inner membrane of the system. A universality proof is then given for the case when the result of a computation is found on the skin membrane (on its external side, hence "visible" from the environment), but in this case we use one more membrane, as well as another basic brane operation exo; moreover, the operations are now of the projective type, as introduced in.

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Examinando BWMC2006. Brainstorming Week On Membrane Computing (4th. 2006. Sevilla) por Autor "Besozzi, Daniela"