Complexity and modeling power of insertion-deletion systems

SISTEMAS DE INSERCIÓN Y BORRADO: COMPLEJIDAD Y CAPACIDAD DE MODELADO El objetivo central de la tesis es el estudio de los sistemas de inserción y borrado y su capacidad computacional. Más concretamente, estudiamos algunos modelos de generación de lenguaje que usan operaciones de reescritura de dos cadenas. También consideramos una variante distribuida de los sistemas de inserción y borrado en el sentido de que las reglas se separan entre un número finito de nodos de un grafo. Estos sistemas se denominan sistemas controlados mediante grafo, y aparecen en muchas áreas de la Informática, jugando un papel muy importante en los lenguajes formales, la lingüística y la bio-informática. Estudiamos la decidibilidad/ universalidad de nuestros modelos mediante la variación de los parámetros de tamaño del vector. Concretamente, damos respuesta a la cuestión más importante concerniente a la expresividad de la capacidad computacional: si nuestro modelo es equivalente a una máquina de Turing o no. Abordamos sistemáticamente las cuestiones sobre los tamaños mínimos de los sistemas con y sin control de grafo.COMPLEXITY AND MODELING POWER OF INSERTION-DELETION SYSTEMS The central object of the thesis are insertion-deletion systems and their computational power. More specifically, we study language generating models that use two string rewriting operations: contextual insertion and contextual deletion, and their extensions. We also consider a distributed variant of insertion-deletion systems in the sense that rules are separated among a finite number of nodes of a graph. Such systems are refereed as graph-controlled systems. These systems appear in many areas of Computer Science and they play an important role in formal languages, linguistics, and bio-informatics. We vary the parameters of the vector of size of insertion-deletion systems and we study decidability/universality of obtained models. More precisely, we answer the most important questions regarding the expressiveness of the computational model: whether our model is Turing equivalent or not. We systematically approach the questions about the minimal sizes of the insertiondeletion systems with and without the graph-control

P Systems with Minimal Insertion and Deletion

In this paper we consider insertion-deletion P systems with priority of deletion over the insertion.We show that such systems with one symbol context-free insertion and deletion rules are able to generate PsRE. If one-symbol one-sided context is added to insertion or deletion rules but no priority is considered, then all recursively enumerable languages can be generated. The same result holds if a deletion of two symbols is permitted. We also show that the priority relation is very important and in its absence the corresponding class of P systems is strictly included in MAT

When Stars Control a Grammar's Work

Graph-controlled insertion-deletion (GCID) systems are regulated extensions of insertion-deletion systems. Such a system has several components and each component contains some insertion-deletion rules. The components are the vertices of a directed control graph. A rule is applied to a string in a component and the resultant string is moved to the target component specified in the rule. The language of the system is the set of all terminal strings collected in the final component. We impose the restriction in the structure of the underlying graph to be a star structure where there is a central, control component which acts like a master and transmits a string (after applying one of its rules) to one of the components specified in the (applied) rule. A component which receives the string can process the obtained string with any applicable rule available in it and sends back the resultant string only to the center component. With this restriction, we obtain computational completeness for some descriptional complexity measuresComment: In Proceedings AFL 2023, arXiv:2309.0112

On the Power of Small Size Insertion P Systems

In this article we investigate insertion systems of small size in the framework of P systems. We consider P systems with insertion rules having one symbol context and we show that they have the computational power of context-free matrix grammars. If contexts of length two are permitted, then any recursively enumerable language can be generated. In both cases a squeezing mechanism, an inverse morphism, and a weak coding are applied to the output of the corresponding P systems. We also show that if no membranes are used then corresponding family is equal to the family of context-free languages

Formal models of the extension activity of DNA polymerase enzymes

The study of formal language operations inspired by enzymatic actions on DNA is part of ongoing efforts to provide a formal framework and rigorous treatment of DNA-based information and DNA-based computation. Other studies along these lines include theoretical explorations of splicing systems, insertion-deletion systems, substitution, hairpin extension, hairpin reduction, superposition, overlapping concatenation, conditional concatenation, contextual intra- and intermolecular recombinations, as well as template-guided recombination. First, a formal language operation is proposed and investigated, inspired by the naturally occurring phenomenon of DNA primer extension by a DNA-template-directed DNA polymerase enzyme. Given two DNA strings u and v, where the shorter string v (called the primer) is Watson-Crick complementary and can thus bind to a substring of the longer string u (called the template) the result of the primer extension is a DNA string that is complementary to a suffix of the template which starts at the binding position of the primer. The operation of DNA primer extension can be abstracted as a binary operation on two formal languages: a template language L1 and a primer language L2. This language operation is called L1-directed extension of L2 and the closure properties of various language classes, including the classes in the Chomsky hierarchy, are studied under directed extension. Furthermore, the question of finding necessary and sufficient conditions for a given language of target strings to be generated from a given template language when the primer language is unknown is answered. The canonic inverse of directed extension is used in order to obtain the optimal solution (the minimal primer language) to this question. The second research project investigates properties of the binary string and language operation overlap assembly as defined by Csuhaj-Varju, Petre and Vaszil as a formal model of the linear self-assembly of DNA strands: The overlap assembly of two strings, xy and yz, which share an overlap y, results in the string xyz. In this context, we investigate overlap assembly and its properties: closure properties of various language families under this operation, and related decision problems. A theoretical analysis of the possible use of iterated overlap assembly to generate combinatorial DNA libraries is also given. The third research project continues the exploration of the properties of the overlap assembly operation by investigating closure properties of various language classes under iterated overlap assembly, and the decidability of the completeness of a language. The problem of deciding whether a given string is terminal with respect to a language, and the problem of deciding if a given language can be generated by an overlap assembly operation of two other given languages are also investigated