68 research outputs found

    TR-2006011: Locally Connected Recursion Categories

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    生化学反応による計算能力の研究

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    早大学位記番号:新6514早稲田大

    Formal models of the extension activity of DNA polymerase enzymes

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    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

    On some modifications and applications of the post correspondence problem

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    The Post Correspondence Problem was introduced by Emil Post in 1946. The problem considers pairs of lists of sequences of symbols, or words, where each word has its place on the list determined by its index. The Post Correspondence Problem asks does there exist a sequence of indices so that, when we write the words in the order of the sequence as single words from both lists, the two resulting words are equal. Post proved the problem to be undecidable, that is, no algorithm deciding it can exist. A variety of restrictions and modifications have been introduced to the original formulation of the problem, that have then been shown to be either decidable or undecidable. Both the original Post Correspondence Problem and its modifications have been widely used in proving other decision problems undecidable. In this thesis we consider some modifications of the Post Correspondence Problem as well as some applications of it in undecidability proofs. We consider a modification for sequences of indices that are infinite to two directions. We also consider a modification to the original Post Correspondence Problem where instead of the words being equal for a sequence of indices, we take two sequences that are conjugates of each other. Two words are conjugates if we can write one word by taking the other and moving some part of that word from the end to the beginning. Both modifications are shown to be undecidable. We also use the Post Correspondence Problem and its modification for injective morphisms in proving two problems from formal language theory to be undecidable; the first problem is on special shuffling of words and the second problem on fixed points of rational functions

    Bibliographie

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    On the closure properties of linear conjunctive languages

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    AbstractLinear conjunctive grammars are conjunctive grammars in which the body of each conjunct contains no more than a single nonterminal symbol. They can at the same time be thought of as a special case of conjunctive grammars and as a generalization of linear context-free grammars that provides an explicit intersection operation.Although the set of languages generated by these grammars is known to include many important noncontext-free languages, linear conjunctive languages are still all square-time, and several practical algorithms have been devised to handle them, which makes this class of grammars quite suitable for use in applications.In this paper we investigate the closure properties of the language family generated by linear conjunctive grammars; the main result is its closure under complement, which implies that it is closed under all set-theoretic operations. We also consider several cases in which the concatenation of two linear conjunctive languages is certain to be linear conjunctive. In addition, it is demonstrated that linear conjunctive languages are closed under quotient with finite languages, not closed under quotient with regular languages, and not closed under ε-free homomorphism

    Complexity and modeling power of insertion-deletion systems

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    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

    Repetitive subwords

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    The central notionof thisthesisis repetitionsin words. We studyproblemsrelated to contiguous repetitions. More specifically we will consider repeating scattered subwords of non-primitive words, i.e. words which are complete repetitions of other words. We will present inequalities concerning these occurrences as well as giving apartial solutionto an openproblemposedby Salomaaet al. We will characterize languages, whichare closed under the operation ofduplication, thatis repeating any factor of a word. We alsogive newbounds onthe number of occurrencesof certain types of repetitions of words. We give a solution to an open problem posed by Calbrix and Nivat concerning regular languages consisting of non-primitive words. We alsopresentsomeresultsregarding theduplication closureoflanguages,among which a new proof to a problem of Bovet and Varricchio

    Acta Cybernetica : Volume 17. Number 1.

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