138 research outputs found
Ciliate Gene Unscrambling with Fewer Templates
One of the theoretical models proposed for the mechanism of gene unscrambling
in some species of ciliates is the template-guided recombination (TGR) system
by Prescott, Ehrenfeucht and Rozenberg which has been generalized by Daley and
McQuillan from a formal language theory perspective. In this paper, we propose
a refinement of this model that generates regular languages using the iterated
TGR system with a finite initial language and a finite set of templates, using
fewer templates and a smaller alphabet compared to that of the Daley-McQuillan
model. To achieve Turing completeness using only finite components, i.e., a
finite initial language and a finite set of templates, 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.Comment: In Proceedings DCFS 2010, arXiv:1008.127
Word Blending and Other Formal Models of Bio-operations
As part of ongoing efforts to view biological processes as computations, several formal models of DNA-based processes have been proposed and studied in the formal language literature. In this thesis, we survey some classical formal language word and language operations, as well as several bio-operations, and we propose a new operation inspired by a DNA recombination lab protocol known as Cross-pairing Polymerase Chain Reaction, or XPCR. More precisely, we define and study a word operation called word blending which models a special case of XPCR, where two words x w p and q w y sharing a non-empty overlap part w generate the word x w y. Properties of word blending that we study include closure properties of the Chomsky families of languages under this operation and its iterated version, existence of solution to equations involving this operation, and its state complexity
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
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
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 Left and Right Insertion and Deletion
Summary. In this article we investigate the operations of insertion and deletion performed at the ends of a string. We show that using these operations in a P systems framework (which corresponds to using specific variants of graph control), computational completeness can even be achieved with the operations of left and right insertion and deletion of only one symbol.
Linearly bounded infinite graphs
Linearly bounded Turing machines have been mainly studied as acceptors for
context-sensitive languages. We define a natural class of infinite automata
representing their observable computational behavior, called linearly bounded
graphs. These automata naturally accept the same languages as the linearly
bounded machines defining them. We present some of their structural properties
as well as alternative characterizations in terms of rewriting systems and
context-sensitive transductions. Finally, we compare these graphs to rational
graphs, which are another class of automata accepting the context-sensitive
languages, and prove that in the bounded-degree case, rational graphs are a
strict sub-class of linearly bounded graphs
P Systems with Minimal Left and Right Insertion and Deletion
In this article we investigate the operations of insertion and deletion performed
at the ends of a string. We show that using these operations in a P systems
framework (which corresponds to using specific variants of graph control), computational
completeness can even be achieved with the operations of left and right insertion and
deletion of only one symbol
Transducers based on networks of evolutionary processors LOS FINANCIADORES NO ESTÁN BIEN
We consider a new type of transducer that does not scan sequentially the input word. Instead, it consists of a directed graph whose nodes are processors which work in parallel and are specialized in just one type of a very simple evolutionary operation: inserting, deleting or substituting a symbol by another one. The computation on an input word starts with this word placed in a designated node, the input node, of the network an alternates evolutionary and communication steps. The computation halts as soon as another designated node, the output node, is nonempty. The translation of the input word is the set of words existing in the output node when the computation halts. We prove that these transducers can simulate the work of generalized sequential machines on every input. Furthermore, all words obtained by a given generalized sequential machine by the shortest computations on a given word can also be computed by the new transducers. Unlike the case of generalized sequential machines, every recursively enumerable language can be the transduction de?ned by the new transducer of a very simple regular language. The same idea may be used for proving that these transducers can simulate the shortest computations of an arbitrary Turing machine, used as a transducer, on every input word. Finally, we consider a restricted variant of NEP transducer, namely pure NEP transducers and prove that there are still regular languages whose pure NEP transductions are not semilinear
- …