On the Descriptional Complexity of Limited Propagating Lindenmayer Systems

We investigate the descriptional complexity of limited propagating Lindenmayer systems and their deterministic and tabled variants with respect to the number of rules and the number of symbols. We determine the decrease of complexity when the generative capacity is increased. For incomparable families, we give languages that can be described more efficiently in either of these families than in the other.Comment: In Proceedings DCFS 2010, arXiv:1008.127

On the Number of Membranes in Unary P Systems

We consider P systems with a linear membrane structure working on objects over a unary alphabet using sets of rules resembling homomorphisms. Such a restricted variant of P systems allows for a unique minimal representation of the generated unary language and in that way for an effective solution of the equivalence problem. Moreover, we examine the descriptional complexity of unary P systems with respect to the number of membranes

New variants of insertion and deletion systems in formal languages

In formal language theory, the operations of insertion and deletion are generalizations of the operations of concatenation and left/right quotients. The insertion operation interpolates one word in an arbitrary place within the other while the deletion operation extracts the word from an arbitrary position of another word. Previously, insertion and deletion have been applied to model the recombinance of DNA and RNA molecules in DNA computing, where contexts were used to mimic the site of enzymatic activity. However, in this research, new systems are introduced by taking motivation from the atomic behaviour of chemical compounds during chemical bonding, in which the concept of a balanced arrangement is required for a successful bonding. Besides that, the relation between insertion and deletion systems and group theory are also shown. Here, insertion and deletion systems are constructed with bonds and also interactions; hence new variants of insertion and deletion systems are introduced. The first is bonded systems, which are introduced by defining systems with restrictions that work on the bonding alphabet. The other variant is systems with interactions, which are introduced by utilizing the binary operations of certain groups as the systems’ interactions. From this research, the generative power and closure properties of the newly introduced bonded systems are determined, and a language hierarchy is constructed. In addition, group generating insertion systems are introduced and illustrated using Cayley graphs. Therefore, this research introduced new variants of insertion and deletion systems that contribute to the advancement of DNA computing and also showcased their application in group theory

26. Theorietag Automaten und Formale Sprachen 23. Jahrestagung Logik in der Informatik: Tagungsband

Der Theorietag ist die Jahrestagung der Fachgruppe Automaten und Formale Sprachen der Gesellschaft für Informatik und fand erstmals 1991 in Magdeburg statt. Seit dem Jahr 1996 wird der Theorietag von einem eintägigen Workshop mit eingeladenen Vorträgen begleitet. Die Jahrestagung der Fachgruppe Logik in der Informatik der Gesellschaft für Informatik fand erstmals 1993 in Leipzig statt. Im Laufe beider Jahrestagungen finden auch die jährliche Fachgruppensitzungen statt. In diesem Jahr wird der Theorietag der Fachgruppe Automaten und Formale Sprachen erstmalig zusammen mit der Jahrestagung der Fachgruppe Logik in der Informatik abgehalten. Organisiert wurde die gemeinsame Veranstaltung von der Arbeitsgruppe Zuverlässige Systeme des Instituts für Informatik an der Christian-Albrechts-Universität Kiel vom 4. bis 7. Oktober im Tagungshotel Tannenfelde bei Neumünster. Während des Tre↵ens wird ein Workshop für alle Interessierten statt finden. In Tannenfelde werden • Christoph Löding (Aachen) • Tomás Masopust (Dresden) • Henning Schnoor (Kiel) • Nicole Schweikardt (Berlin) • Georg Zetzsche (Paris) eingeladene Vorträge zu ihrer aktuellen Arbeit halten. Darüber hinaus werden 26 Vorträge von Teilnehmern und Teilnehmerinnen gehalten, 17 auf dem Theorietag Automaten und formale Sprachen und neun auf der Jahrestagung Logik in der Informatik. Der vorliegende Band enthält Kurzfassungen aller Beiträge. Wir danken der Gesellschaft für Informatik, der Christian-Albrechts-Universität zu Kiel und dem Tagungshotel Tannenfelde für die Unterstützung dieses Theorietags. Ein besonderer Dank geht an das Organisationsteam: Maike Bradler, Philipp Sieweck, Joel Day. Kiel, Oktober 2016 Florin Manea, Dirk Nowotka und Thomas Wilk

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

Impact of Membrane Computing and P Systems in ISI WoS. Celebrating the 65th Birthday of Gheorghe Păun

Membrane Computing is a branch of Computer Science initiated by Gheorghe Păun in 1998, in a technical report of Turku Centre for Computer Science published as a journal paper ("Computing with Membranes" in Journal of Computer and System Sciences) in 2000. Membrane systems, as Gheorghe Păun called the models he has introduced, are known nowadays as "P Systems" (with the letter P coming from the initial of the name of this research area "father"). This note is an overview of the impact in ISI WoS of Gheorghe Păun’s works, focused on Membrane Computing and P Systems field, on the occasion of his 65th birthday anniversary

Two Refinements of the Template-Guided DNA Recombination Model of Ciliate Computing

To solve the mystery of the intricate gene unscrambling mechanism in ciliates, various theoretical models for this process have been proposed from the point of view of computation. Two main models are the reversible guided recombination system by Kari and Landweber and the template-guided recombination (TGR) system by Prescott, Ehrenfeucht and Rozenberg, based on two categories of DNA recombination: the pointer guided and the template directed recombination respectively. The latter model has been generalized by Daley and McQuillan. In this thesis, we propose a new approach to generate regular languages using the iterated TGR system with a finite initial language and a finite set of templates, that reduces the size of the template language and the alphabet compared to that of the Daley-McQuillan model. To achieve computational completeness using only finite components we also propose an extension of the contextual template-guided recombination system (CTGR system) by Daley and McQuillan, by adding an extra control called permitting contexts on the usage of templates. Then we prove that our proposed system, the CTGR system using permitting contexts, has the capability to characterize the family of recursively enumerable languages using a finite initial language and a finite set of templates. Lastly, we present a comparison and analysis of the computational power of the reversible guided recombination system and the TGR system. Keywords: ciliates, gene unscrambling, in vivo computing, DNA computing, cellular computing, reversible guided recombination, template-guided recombination

Grammars with Restricted Derivation Trees

V této disertační práci jsou studovány teoretické vlastnosti gramatik s omezenými derivačními stromy. Po uvedení současného stavu poznání v této oblasti je výzkum zaměřen na tři základní typy omezení derivačních stromů. Nejprve je představeno zcela nové téma, které je založeno na omezení řezů a je zkoumána vyjadřovací síla takto omezené gramatiky. Poté je zkoumáno několik nových vlastností omezení kladeného na cestu derivačních stromů. Zejména je studován vliv vymazávacích pravidel na vyjadřovací sílu gramatik s omezenou cestou a pro tyto gramatiky jsou zavedeny dvě normální formy. Následně je popsána nová souvislost mezi gramatikami s omezenou cestou a některými pseudouzly. Dále je prezentován protiargument k vyjadřovací síle tohoto modelu, která byla dosud považována za dobře známou vlastnost. Nakonec je zavedeno zobecnění modelu s omezenou cestou na ne jednu, ale několik cest. Tento model je následně studován zejména z hlediska vlastností vkládání, uzávěrových vlastností a vlastností syntaktické analýzy.This doctoral thesis studies theoretical properties of grammars with restricted derivation trees. After presenting the state of the art concerning this investigation area, the research is focused on the three main kinds of the restrictions placed upon the derivation trees. First, it introduces completely new investigation area represented by cut-based restriction and examines the generative power of the grammars restricted in this way. Second, it investigates several new properties of path-based restriction placed upon the derivation trees. Specifically, it studies the impact of erasing productions on the generative power of grammars with restricted path and introduces two corresponding normal forms. Then, it describes a new relation between grammars with restricted path and some pseudoknots. Next, it presents a counterargument to the generative power of grammars with controlled path that has been considered as well-known so far. Finally, it introduces a generalization of path-based restriction to not just one but several paths. The model generalized in this way is studied, namely its pumping, closure, and parsing properties.