Membrane systems with limited parallelism

Membrane computing is an emerging research field that belongs to the more general area of molecular computing, which deals with computational models inspired from bio-molecular processes. Membrane computing aims at defining models, called membrane systems or P systems, which abstract the functioning and structure of the cell. A membrane system consists of a hierarchical arrangement of membranes delimiting regions, which represent various compartments of a cell, and with each region containing bio-chemical elements of various types and having associated evolution rules, which represent bio-chemical processes taking place inside the cell. This work is a continuation of the investigations aiming to bridge membrane computing (where in a compartmental cell-like structure the chemicals to evolve are placed in compartments defined by membranes) and brane calculi (where one considers again a compartmental cell-like structure with the chemicals/proteins placed on the membranes themselves). We use objects both in compartments and on membranes (the latter are called proteins), with the objects from membranes evolving under the control of the proteins. Several possibilities are considered (objects only moved across membranes or also changed during this operation, with the proteins only assisting the move/change or also changing themselves). Somewhat expected, computational universality is obtained for several combinations of such possibilities. We also present a method for solving the NP-complete SAT problem using P systems with proteins on membranes. The SAT problem is solved in O(nm) time, where n is the number of boolean variables and m is the number of clauses for an instance written in conjunctive normal form. Thus, we can say that the solution for each given instance is obtained in linear time. We succeeded in solving SAT by a uniform construction of a deterministic P system which uses rules involving objects in regions, proteins on membranes, and membrane division. Then, we investigate the computational power of P systems with proteins on membranes in some particular cases: when only one protein is placed on a membrane, when the systems have a minimal number of rules, when the computation evolves in accepting or computing mode, etc. This dissertation introduces also another new variant of membrane systems that uses context-free rewriting rules for the evolution of objects placed inside compartments of a cell, and symport rules for communication between membranes. The strings circulate across membranes depending on their membership to regular languages given by means of regular expressions. We prove that these rewriting-symport P systems generate all recursively enumerable languages. We investigate the computational power of these newly introduced P systems for three particular forms of the regular expressions that are used by the symport rules. A characterization of ET0L languages is obtained in this context

Communication in membrana Systems with symbol Objects.

Esta tesis está dedicada a los sistemas de membranas con objetos-símbolo como marco teórico de los sistemas paralelos y distribuidos de procesamiento de multiconjuntos.Una computación de parada puede aceptar, generar o procesar un número, un vector o una palabra; por tanto el sistema define globalmente (a través de los resultados de todas sus computaciones) un conjunto de números, de vectores, de palabras (es decir, un lenguaje), o bien una función. En esta tesis estudiamos la capacidad de estos sistemas para resolver problemas particulares, así como su potencia computacional. Por ejemplo, las familias de lenguajes definidas por diversas clases de estos sistemas se comparan con las familias clásicas, esto es, lenguajes regulares, independientes del contexto, generados por sistemas 0L tabulados extendidos, generados por gramáticas matriciales sin chequeo de apariciones, recursivamente enumerables, etc. Se prestará especial atención a la comunicación de objetos entre regiones y a las distintas formas de cooperación entre ellos.Se pretende (Sección 3.4) realizar una formalización los sistemas de membranas y construir una herramienta tipo software para la variante que usa cooperación no distribuida, el navegador de configuraciones, es decir, un simulador, en el cual el usuario selecciona la siguiente configuración entre todas las posibles, estando permitido volver hacia atrás. Se considerarán diversos modelos distribuidos. En el modelo de evolución y comunicación (Capítulo 4) separamos las reglas tipo-reescritura y las reglas de transporte (llamadas symport y antiport). Los sistemas de bombeo de protones (proton pumping, Secciones 4.8, 4.9) constituyen una variante de los sistemas de evolución y comunicación con un modo restrictivo de cooperación. Un modelo especial de computación con membranas es el modelo puramente comunicativo, en el cual los objetos traspasan juntos una membrana. Estudiamos la potencia computacional de las sistemas de membranas con symport/antiport de 2 o 3 objetos (Capítulo 5) y la potencia computacional de las sistemas de membranas con alfabeto limitado (Capítulo 6).El determinismo (Secciones 4.7, 5.5, etc.) es una característica especial (restrictiva) de los sistemas computacionales. Se pondrá especial énfasis en analizar si esta restricción reduce o no la potencia computacional de los mismos. Los resultados obtenidos para sistemas de bombeo del protones están transferidos (Sección 7.3) a sistemas con catalizadores bistabiles. Unos ejemplos de aplicación concreta de los sistemas de membranas (Secciones 7.1, 7.2) son la resolución de problemas NP-completos en tiempo polinomial y la resolución de problemas de ordenación.This thesis deals with membrane systems with symbol objects as a theoretical framework of distributed parallel multiset processing systems.A halting computation can accept, generate or process a number, a vector or a word, so the system globally defines (by the results of all its computations) a set of numbers or a set of vectors or a set of words, (i.e., a language), or a function. The ability of these systems to solve particular problems is investigated, as well as their computational power, e.g., the language families defined by different classes of these systems are compared to the classical ones, i.e., regular, context-free, languages generated by extended tabled 0L systems, languages generated by matrix grammars without appearance checking, recursively enumerable languages, etc. Special attention is paid to communication of objects between the regions and to the ways of cooperation between the objects.An attempt to formalize the membrane systems is made (Section 3.4), and a software tool is constructed for the non-distributed cooperative variant, the configuration browser, i.e., a simulator, where the user chooses the next configuration among the possible ones and can go back. Different distributed models are considered. In the evolution-communication model (Chapter 4) rewriting-like rules are separated from transport rules. Proton pumping systems (Sections 4.8, 4.9) are a variant of the evolution-communication systems with a restricted way of cooperation. A special membrane computing model is a purely communicative one: the objects are moved together through a membrane. We study the computational power of membrane systems with symport/antiport of 2 or 3 objects (Chapter 5) and the computational power of membrane systems with a limited alphabet (Chapter 6).Determinism (Sections 4.7, 5.5, etc.) is a special property of computational systems; the question of whether this restriction reduces the computational power is addressed. The results on proton pumping systems can be carried over (Section 7.3) to the systems with bi-stable catalysts. Some particular examples of membrane systems applications are solving NP-complete problems in polynomial time, and solving the sorting problem

In Memoriam, Solomon Marcus

This book commemorates Solomon Marcus’s fifth death anniversary with a selection of articles in mathematics, theoretical computer science, and physics written by authors who work in Marcus’s research fields, some of whom have been influenced by his results and/or have collaborated with him

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

Recent advances in petri nets and concurrency

CEUR Workshop Proceeding

Future of Sustainable Agriculture in Saline Environments

Food production on present and future saline soils deserves the world’s attention particularly because food security is a pressing issue, millions of hectares of degraded soils are available worldwide, freshwater is becoming increasingly scarce, and the global sea-level rise threatens food production in fertile coastal lowlands. Future of Sustainable Agriculture in Saline Environments aims to showcase the global potential of saline agriculture. The book covers the essential topics, such as policy and awareness, soil management, future crops, and genetic developments, all supplemented by case studies that show how this knowledge has been applied. It offers an overview of current research themes and practical cases focused on enhancing food production on saline lands. FEATURES Describes the critical role of the revitalization of salt-degraded lands in achieving sustainability in agriculture on a global scale Discusses practical solutions toward using drylands and delta areas threatened by salinity for sustainable food production Presents strategies for adaptation to climate change and sea-level rise through food production under saline conditions Addresses the diverse aspects of crop salt tolerance and microbiological associations Highlights the complex problem of salinity and waterlogging and safer management of poor-quality water, supplemented by case studies A PDF version of this book is available for free in Open Access at www.taylorfrancis.com. It has been made available under a Creative Commons Attribution-Non Commercial-No Derivatives 4.0 license