42,659 research outputs found
Graph-Controlled Insertion-Deletion Systems
In this article, we consider the operations of insertion and deletion working
in a graph-controlled manner. We show that like in the case of context-free
productions, the computational power is strictly increased when using a control
graph: computational completeness can be obtained by systems with insertion or
deletion rules involving at most two symbols in a contextual or in a
context-free manner and with the control graph having only four nodes.Comment: In Proceedings DCFS 2010, arXiv:1008.127
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 lingüÃstica 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 mÃnimos 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
Input-Driven Tissue P Automata
We introduce several variants of input-driven tissue P automata where the
rules to be applied only depend on the input symbol. Both strings and multisets are
considered as input objects; the strings are either read from an input tape or defined
by the sequence of symbols taken in, and the multisets are given in an input cell at the
beginning of a computation, enclosed in a vesicle. Additional symbols generated during a
computation are stored in this vesicle, too. An input is accepted when the vesicle reaches a
final cell and it is empty. The computational power of some variants of input-driven tissue
P automata is illustrated by examples and compared with the power of the input-driven
variants of other automata as register machines and counter automata
(Tissue) P Systems with Vesicles of Multisets
We consider tissue P systems working on vesicles of multisets with the very
simple operations of insertion, deletion, and substitution of single objects.
With the whole multiset being enclosed in a vesicle, sending it to a target
cell can be indicated in those simple rules working on the multiset. As
derivation modes we consider the sequential mode, where exactly one rule is
applied in a derivation step, and the set maximal mode, where in each
derivation step a non-extendable set of rules is applied. With the set maximal
mode, computational completeness can already be obtained with tissue P systems
having a tree structure, whereas tissue P systems even with an arbitrary
communication structure are not computationally complete when working in the
sequential mode. Adding polarizations (-1, 0, 1 are sufficient) allows for
obtaining computational completeness even for tissue P systems working in the
sequential mode.Comment: In Proceedings AFL 2017, arXiv:1708.0622
(Tissue) P Systems with Vesicles of Multisets
We consider tissue P systems working on vesicles of multisets with the very
simple operations of insertion, deletion, and substitution of single objects.
With the whole multiset being enclosed in a vesicle, sending it to a target
cell can be indicated in those simple rules working on the multiset. As
derivation modes we consider the sequential mode, where exactly one rule is
applied in a derivation step, and the set maximal mode, where in each
derivation step a non-extendable set of rules is applied. With the set maximal
mode, computational completeness can already be obtained with tissue P systems
having a tree structure, whereas tissue P systems even with an arbitrary
communication structure are not computationally complete when working in the
sequential mode. Adding polarizations (-1, 0, 1 are sufficient) allows for
obtaining computational completeness even for tissue P systems working in the
sequential mode.Comment: In Proceedings AFL 2017, arXiv:1708.0622
Universal power law behaviors in genomic sequences and evolutionary models
We study the length distribution of a particular class of DNA sequences known
as 5'UTR exons. These exons belong to the messanger RNA of protein coding
genes, but they are not coding (they are located upstream of the coding portion
of the mRNA) and are thus less constrained from an evolutionary point of view.
We show that both in mouse and in human these exons show a very clean power law
decay in their length distribution and suggest a simple evolutionary model
which may explain this finding. We conjecture that this power law behaviour
could indeed be a general feature of higher eukaryotes.Comment: 15 pages, 3 figure
Kinetic and Dynamic Delaunay tetrahedralizations in three dimensions
We describe the implementation of algorithms to construct and maintain
three-dimensional dynamic Delaunay triangulations with kinetic vertices using a
three-simplex data structure. The code is capable of constructing the geometric
dual, the Voronoi or Dirichlet tessellation. Initially, a given list of points
is triangulated. Time evolution of the triangulation is not only governed by
kinetic vertices but also by a changing number of vertices. We use
three-dimensional simplex flip algorithms, a stochastic visibility walk
algorithm for point location and in addition, we propose a new simple method of
deleting vertices from an existing three-dimensional Delaunay triangulation
while maintaining the Delaunay property. The dual Dirichlet tessellation can be
used to solve differential equations on an irregular grid, to define partitions
in cell tissue simulations, for collision detection etc.Comment: 29 pg (preprint), 12 figures, 1 table Title changed (mainly
nomenclature), referee suggestions included, typos corrected, bibliography
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