No Cycles in Compartments. Starting from Conformon-P Systems

Starting from proofs of results about the computing power of conformon- P systems, we infer several results about the power of certain classes of tissue-like P systems with (cooperative) rewriting rules used in an asynchronous way, without cycles in compartments. This last feature is related to an important restriction appearing when dealing with lab implementations of P systems, that of avoiding local evolution loops of objects

A computacional model to predict land-use and cover changes in mountain landscapes

Since the second half of the 20th century, an expansion of the forest in European mountain areas due to agricultural abandonment has been observed. The reduction of the agricultural intensity implies the disappearance of semi-natural alpine meadows and pastures of great ecological and aesthetic value. This thesis proposes a computational model, using P systems, to simulate the future agricultural landscape evolution in the Catalan Pyrenees and in the Stubai Valley, located in central Alps, for a period of 30 years. In these regions, three simulated scenarios have been established: (1) Continuation of the observed farming trends, or maintenance of the status quo, (2) significant and (3) strong stocking rate reductions. The results show how the traditional agricultural surfaces decrease in all simulated scenarios in both study areas. Therefore, it is important to apply new strategies to preserve these cultural surfaces and the multiple ecosystem services for future generations before they disappear definitively.D'ençà de la segona meitat del segle XX s'ha observat una expansió del bosc a les zones de muntanya europees, originada per l'abandonament de l'agricultura. La reducció de la intensitat agrícola comporta la desaparició de prats i pastures alpins seminaturals de gran valor ecològic i estètic. Aquesta tesi proposa un model computacional utilitzant P sistemes per simular l'evolució futura del paisatge agrícola als Pirineus catalans i a la Vall de Stubai, situada als Alps centrals, durant un període de 30 anys. En aquestes regions s'han establert tres escenaris a simular: (1) continuació de la tendència ramadera observada, o manteniment del statu quo, (2) reducció significativa i (3) molt forta de la càrrega ramadera. Els resultats obtinguts mostren com la superfície agrícola tradicional es redueix en tots els escenaris simulats en ambdues àrees d'estudi. Per tant, és important aplicar noves estratègies per preservar aquestes superfícies culturals i els múltiples serveis de l'ecosistema per a les futures generacions, abans que desapareguin definitivament.Desde la segunda mitad del siglo XX se ha observado un expansión del bosque en las zonas de montaña europeas, originada por el abandono de la agricultura. La reducción de la intensidad agrícola implica la desaparición de prados y pastos alpinos seminaturales de gran valor ecológico y estético. Esta tesis propone un modelo computacional utilizando P sistemas para simular la evolución futura del paisaje agrícola en los Pirineos catalanes y en el Valle de Stubai, situado en los Alpes centrales, durante un periodo de 30 años. En estas regiones se han establecido tres escenarios a simular: (1) continuación de la tendencia ganadera observada, o mantenimiento del statu quo, (2) reducción significativa y (3) muy fuerte de la carga ganadera. Los resultados obtenidos muestran como la superficie agrícola tradicional se reduce en todos los escenarios simulados en las dos áreas de estudio. Por lo tanto, es importante aplicar nuevas estrategias para preservar estas superficies culturales y los múltiples servicios del ecosistema para las futuras generaciones, antes de que desaparezcan definitivamente

Modeling formalisms in systems biology

Systems Biology has taken advantage of computational tools and high-throughput experimental data to model several biological processes. These include signaling, gene regulatory, and metabolic networks. However, most of these models are specific to each kind of network. Their interconnection demands a whole-cell modeling framework for a complete understanding of cellular systems. We describe the features required by an integrated framework for modeling, analyzing and simulating biological processes, and review several modeling formalisms that have been used in Systems Biology including Boolean networks, Bayesian networks, Petri nets, process algebras, constraint-based models, differential equations, rule-based models, interacting state machines, cellular automata, and agent-based models. We compare the features provided by different formalisms, and discuss recent approaches in the integration of these formalisms, as well as possible directions for the future.Research supported by grants SFRH/BD/35215/2007 and SFRH/BD/25506/2005 from the Fundacao para a Ciencia e a Tecnologia (FCT) and the MIT-Portugal Program through the project "Bridging Systems and Synthetic Biology for the development of improved microbial cell factories" (MIT-Pt/BS-BB/0082/2008)

Frontiers of Membrane Computing: Open Problems and Research Topics

This is a list of open problems and research topics collected after the Twelfth Conference on Membrane Computing, CMC 2012 (Fontainebleau, France (23 - 26 August 2011), meant initially to be a working material for Tenth Brainstorming Week on Membrane Computing, Sevilla, Spain (January 30 - February 3, 2012). The result was circulated in several versions before the brainstorming and then modified according to the discussions held in Sevilla and according to the progresses made during the meeting. In the present form, the list gives an image about key research directions currently active in membrane computing

Modelling tools and methodologies for rapid protocell prototyping

The field of unconventional computing considers the possibility of implementing computational devices using novel paradigms and materials to produce computers which may be more efficient, adaptable and robust than their silicon based counterparts. The integration of computation into the realms of chemistry and biology will allow the embedding of engineered logic into living systems and could produce truly ubiquitous computing devices. Recently, advances in synthetic biology have resulted in the modification of microorganism genomes to create computational behaviour in living cells, so called “cellular computing”. The cellular computing paradigm offers the possibility of intelligent bacterial agents which may respond and communicate with one another according to chemical signals received from the environment. However, the high levels of complexity when altering an organism which has been well adapted to certain environments over millions of years of evolution suggests an alternative approach in which chemical computational devices can be constructed completely from the bottom up, allowing the designer exquisite control and knowledge about the system being created. This thesis presents the development of a simulation and modelling framework to aid the study and design of bottom-up chemical computers, involving the encapsulation of computational re-actions within vesicles. The new “vesicle computing” paradigm is investigated using a sophisticated multi-scale simulation framework, developed from mesoscale, macroscale and executable biology techniques

Implementación sobre hardware reconfigurable de una arquitectura no determinista, paralela y distribuida de alto rendimiento, basada en modelos de computación con membranas

Falta palabras clavesEn este documento se presenta el trabajo de tesis doctoral realizado dentro del Programa de Doctorado “Informática Industrial” del Departamento de Tecnología Electrónica de la Universidad de Sevilla. Recoge la investigación centrada en el desarrollo de una implementación en hardware reconfigurable, FPGA, de modelos de computación basados en membranas, también denominados sistemas P. Estos sistemas, de inspiración biológica, son de reciente creación, y tienen aplicaciones directas en procesos de simulación, especialmente de sistemas y procesos biológicos. Se engloban dentro de la computación natural, y se trata de modelos paralelos maximales orientados a máquinas. Este hecho supone un desafío en el desarrollo de implementaciones hardware, ya que es precisa la generación de un diseño diferente para cada problema, incluso para cada instancia. Como consecuencia directa, es necesario el desarrollo de una arquitectura hardware dedicada parametrizada, junto con un desarrollo software, que analice los sistemas de entrada y, en base a sus características, construya un diseño sintetizable dedicado para esa instancia concreta. Además, al ser la disciplina de reciente creación, existen distintos tipos de sistemas P, por lo que es preciso un análisis previo, seguido de una selección, con el propósito de implementar el mayor subconjunto posible de los mismos