Orientador: Reginaldo Palazzo Junior / Tese (doutorado) - Universidade Estadual de Campinas, Faculdade de Engenharia Elétrica e de Computação / Made available in DSpace on 2018-08-19T09:31:01Z (GMT). No. of bitstreams: 1 Alves_AlessandroFerreira_D.pdf: 1080224 bytes, checksum: 0748952c3176e9548151bec7e6d9c71d (MD5) Previous issue date: 2011 / Resumo: Para projetarmos um sistema de comunicação digital em espaços hiperbólicos é necessário estabelecer um procedimento sistemático de construção de reticulados como elemento base para a construção de constelações de sinais. De outra forma, em codificação de canal é de fundamental importância a caracterização das estruturas algébrica e geométrica associadas a canais discretos sem memória. Neste trabalho, apresentamos a caracterização geométrica de superfícies a partir dos possíveis emparelhamentos das arestas do polígono fundamental hiperbólico com 3 ? n ? 8 lados associado 'a superfície. Esse tratamento geométrico apresenta propriedades importantes na determinação dos reticulados hiperbólicos a serem utilizados no processo de construção de constelações de sinais, a partir de grupos fuchsianos aritméticos e da superfície de Riemann associada. Além disso, apresentamos como exemplo o desenvolvimento algébrico para a determinação dos geradores do grupo fuchsiano 'gama'8 associado ao polígono hiperbólico 'P IND. 8' / Abstract: In order to design a digital communication system in hyperbolic spaces is necessary to establish a systematic procedure of constructing lattices as the basic element for the construction of the signal constellations. On the other hand, in channel coding is of fundamental importance to characterize the geometric and algebraic structures associated with discrete memoryless channels. In this work, we present a geometric characterization of surfaces from the edges of the possible pairings of fundamental hyperbolic polygon with 3 ? n ? 8 sides associated with the surface. This treatment has geometric properties important in determining the hyperbolic lattices to be used in the construction of sets of signals derived from arithmetic Fuchsian groups and the associated Riemann surface / Doutorado / Telecomunicações e Telemática / Doutor em Engenharia Elétrica

L'objet de cette thèse est l'étude des codes LDPC quantiques. Dans un premier temps, nous travaillons sur des constructions topologiques de codes LDPC quantiques. Nous proposons de construire une famille de codes couleur basée sur des pavages hyperboliques. Nous étudions ensuite les paramètres d'une famille de codes basée sur des graphes de Cayley.Dans une seconde partie, nous examinons les performances de ces codes. Nous obtenons une borne supérieure sur les performances des codes LDPC quantiques réguliers sur le canal à effacement quantique. Ceci prouve que ces codes n'atteignent pas la capacité du canal à effacement quantique. Dans le cas du canal de dépolarisation, nous proposons un nouvel algorithme de décodage des codes couleur basé sur trois décodages de codes de surface. Nos simulations numériques montrent de bonnes performances dans le cas des codes couleur toriques.Pour finir, nous nous intéressons au phénomène de percolation. La question centrale de la théorie de la percolation est la détermination du seuil critique. Le calcul exacte de ce seuil est généralement difficile. Nous relions la probabilité de percolation dans certains pavages réguliers du plan hyperbolique à la probabilité d'erreur de décodage pour une famille de codes hyperboliques. Nous en déduisons une borne sur le seuil critique de ces pavages hyperboliques basée sur des résultats de théorie de l'information quantique. Il s'agit d'une application de la théorie de l'information quantique à un problème purement combinatoire. / This thesis is devoted to the study of quantum LDPC codes. The first part presents some topological constructions of quantum LDPC codes. We introduce a family of color codes based on tilings of the hyperbolic plane. We study the parameters of a family of codes based on Cayley graphs.In a second part, we analyze the performance of these codes. We obtain an upper bound on the performance of regular quantum LDPC codes over the quantum erasure channel. This implies that these codes don't achieve the capacity of the quantum erasure channel. In the case of the depolarizing channel, we propose a new decoding algorithm of color codes based on three surface codes decoding. Our numerical results show good performance for toric color codes.Finally, we focus on percolation theory. The central question in percolation theory is the determination of the critical probability. Computing the critical probability exactly is usually quite difficult. We relate the probability of percolation in some regular tilings of the hyperbolic plane to the probability of a decoding error for hyperbolic codes on the quantum erasure channel. This leads to an upper bound on the critical probability of these hyperbolic tilings based on quantum information. It is an application of quantum information to a purely combinatorial problem.

V této práci představujeme blokovou metodu pro zlepšení lokality v cache paměti u výpočtů typu stencil a dva nástroje, Pluto a PATUS, které tuto metodu používají ke generování optimalizovaného kódu. Provádíme různá měření a zkoumáme zrychlení výpočtu při použití různých optimalizací. Nakonec implementujeme vyhlazovací krok v multigridu s různými optimalizacemi a zkoumáme jak se tyto optimalizace projeví na výkonu multigridu.

Active contours have been proven to be a powerful semiautomatic image segmentation approach, that seems to cope with many applications and different image modalities. However, they exhibit inherent drawbacks, including the sensibility to contour initialization due to the limited capture range of image edges and problems with concave boundary regions. The Gradient Vector Flow replaces the traditional image force and provides an enlarged capture range as well as enhanced concavity extraction capabilities, but it involves an expensive computational effort and considerably increased memory requirements at the time of computation. In this paper, we present an enhancement of the active contour model to facilitate semiautomatic contour detection in huge images. We propose a tile-based image decomposition accompanying an image force computation scheme on demand in order to minimize both computational and memory requirements. We show an efficient implementation of this approach on the basis of general purpose GPU processing providing for continuous active contour deformation without a considerable delay.

This thesis addresses the multi-body assembly (MBA) problem in the context of protein assemblies. [...] In this thesis, we chose the protein assembly domain because accurate and reliable computational modeling, simulation and prediction of such assemblies would clearly accelerate discoveries in understanding of the complexities of metabolic pathways, identifying the molecular basis for normal health and diseases, and in the designing of new drugs and other therapeutics. [...] [We developed] F²Dock (Fast Fourier Docking) which includes a multi-term function which includes both a statistical thermodynamic approximation of molecular free energy as well as several of knowledge-based terms. Parameters of the scoring model were learned based on a large set of positive/negative examples, and when tested on 176 protein complexes of various types, showed excellent accuracy in ranking correct configurations higher (F² Dock ranks the correcti solution as the top ranked one in 22/176 cases, which is better than other unsupervised prediction software on the same benchmark). Most of the protein-protein interaction scoring terms can be expressed as integrals over the occupied volume, boundary, or a set of discrete points (atom locations), of distance dependent decaying kernels. We developed a dynamic adaptive grid (DAG) data structure which computes smooth surface and volumetric representations of a protein complex in O(m log m) time, where m is the number of atoms assuming that the smallest feature size h is [theta](r[subscript max]) where r[subscript max] is the radius of the largest atom; updates in O(log m) time; and uses O(m)memory. We also developed the dynamic packing grids (DPG) data structure which supports quasi-constant time updates (O(log w)) and spherical neighborhood queries (O(log log w)), where w is the word-size in the RAM. DPG and DAG together results in O(k) time approximation of scoring terms where k << m is the size of the contact region between proteins. [...] [W]e consider the symmetric spherical shell assembly case, where multiple copies of identical proteins tile the surface of a sphere. Though this is a restricted subclass of MBA, it is an important one since it would accelerate development of drugs and antibodies to prevent viruses from forming capsids, which have such spherical symmetry in nature. We proved that it is possible to characterize the space of possible symmetric spherical layouts using a small number of representative local arrangements (called tiles), and their global configurations (tiling). We further show that the tilings, and the mapping of proteins to tilings on arbitrary sized shells is parameterized by 3 discrete parameters and 6 continuous degrees of freedom; and the 3 discrete DOF can be restricted to a constant number of cases if the size of the shell is known (in terms of the number of protein n). We also consider the case where a coarse model of the whole complex of proteins are available. We show that even when such coarse models do not show atomic positions, they can be sufficient to identify a general location for each protein and its neighbors, and thereby restricts the configurational space. We developed an iterative refinement search protocol that leverages such multi-resolution structural data to predict accurate high resolution model of protein complexes, and successfully applied the protocol to model gp120, a protein on the spike of HIV and currently the most feasible target for anti-HIV drug design. / text

La bio-informatique est un champ pluridisciplinaire qui utilise la biologie, l’informatique, la physique et les mathématiques pour résoudre des problèmes posés par la biologie. L’une des thématiques de la bio-informatique est l’analyse des séquences génomiques et la prédiction de gènes d’ARN non codants. Les ARN non codants sont des molécules d’ARN qui sont transcrites mais pas traduites en protéine et qui ont une fonction dans la cellule. Trouver des gènes d’ARN non codants par des techniques de biochimie et de biologie moléculaire est assez difficile et relativement coûteux. Ainsi, la prédiction des gènes d’ARNnc par des méthodes bio-informatiques est un enjeu important. Cette recherche décrit un travail d’analyse informatique pour chercher des nouveaux ARNnc chez le pathogène Candida albicans et d’une validation expérimentale. Nous avons utilisé comme stratégie une analyse informatique combinant plusieurs logiciels d’identification d’ARNnc. Nous avons validé un sous-ensemble des prédictions informatiques avec une expérience de puces à ADN couvrant 1979 régions du génome. Grace à cette expérience nous avons identifié 62 nouveaux transcrits chez Candida albicans. Ce travail aussi permit le développement d’une méthode d’analyse pour des puces à ADN de type tiling array. Ce travail présente également une tentation d’améliorer de la prédiction d’ARNnc avec une méthode se basant sur la recherche de motifs d’ARN dans les séquences. / Bioinformatics is a multidisciplinary field that uses biology, computer science, physics and mathematics to solve problems in biology. One of the topics of bioinformatics is the analysis of genomic sequences and prediction of genes from non-coding RNA (ncRNA). The non-coding RNAs are RNA molecules that are transcribed but not translated into protein and have a function in the cell. The use of biochemistry and molecular biology techniques in order to find non-coding RNA genes is rather difficult and relatively expensive. Thus, the prediction of genes by bioinformatics methods is an important issue. This research describes a computer analysis to search for new ncRNA in the pathogen Candida albicans and an experimental validation. The strategy used was to combine several algorithms and to validate a subset of computer predictions with a microarray experience covering 1979 regions of the genome. We have identified 62 new transcripts in Candida albicans. We have also developed an analytical method for tiling array and attempted to improve the prediction of ncRNAs this with a method based on the search of RNA motifs in the sequences.

Demonstration videos can be found on fr.linkedin.com/in/doriangomez/ / Cette thèse porte sur la modélisation procédurale de mondes virtuels étendus dans le domaine de l’informatique graphique. Nous proposons d’exploiter les propriétés de visibilité entre régions élémentaires de la scène, que nous appelons tuiles, pour contrôler sa construction par pavage rectangulaire. Deux objectifs distincts sont visés par nos travaux : (1) fournir aux infographistes un moyen efficace pour générer du contenu 3D pour ces scènes virtuelles de très grande taille, et (2) garantir, dès la création du monde, des performances de rendu et de visualisation efficace. Pour cela, nous proposons plusieurs méthodes de détermination de la visibilité en 2D et en 3D. Ces méthodes permettent l’évaluation d’ensembles potentiellement visibles (PVS) en temps interactif ou en temps réel. Elles sont basées sur les calculs de lignes séparatrices et de lignes de support des objets, mais aussi sur l’organisation hiérarchique des objets associés aux tuiles. La première technique (2D) garantit l’occultation complète du champ visuel à partir d’une distance fixe, spécifiée par le concepteur de la scène, depuis n’importe quel endroit sur le pavage. La seconde permet d’estimer et de localiser les tuiles où se propage la visibilité, et de construire le monde en conséquence. Afin de pouvoir générer des mondes variés, nous présentons ensuite l’extension de cette dernière méthode à la 3D. Enfin, nous proposons deux méthodes d’optimisation du placement des objets sur les tuiles permettant d’améliorer leurs propriétés d’occultation et leurs impacts sur les performances de rendu tout en conservant l’atmosphère créée par l’infographiste par ses choix de placement initiaux. / This thesis deals with procedural modeling applied to extended worlds for computer graphics.We study visibility applied to tiling patterns, aiming at two distinct objectives : (1) providing artists with efficient tools to generate 3D content for very extended virtual scenes, and (2) guaranteeing that this content improves performance of subsequent renderings, during its construction. We propose several methods for 2D and 3D visibility determination, in order to achieve interactive or real-time evaluation of potentially visible sets (PVS). They are based on the concepts of separating and supporting lines/planes, as well as objects hierarchies over tiles. Our first 2D method guarantees full occlusion of the visual field (view frustum) beyond a fixed distance, regardless of the observer’s location on a tiling. The second method enables fast estimation and localization of visible tiles, and builds up a virtual world accordingly. We also extend this method to 3D. Finally, we present two methods to optimize objects locations on tiles, and show how to improve rendering performance for scenes generated on the fly.

Pražské metro jako prostor pro realizaci geologických exkurzí Abstract: The aim of this diploma thesis is to evaluate and explore the potential of the tiling materials used in the Prague metro and to create guidelines suitable for organizing geological excursions. Ysdfvwavweefawfbaljehbrrkvjasdhbflavjsdhbf alskdjfbalksjdfnaůksjdnaůkjsdfnaůksjsa Sdfasdfasdfasfavsdfvaskedjfnalksjdfnca weuifhmacskdjfmcapisdjfcaksdjnfcamůskdjfnmacsdkjfnmacůskjdfmnacůs kdjfmnaclskdjfnmacůskdjfnacf askdjfaůksjdf nasdkfjn askdjfn aůksjdnf aůskjdfn aůkjsdf akjsdn fakůjsd fnaůksjdfnaůksrjng adg

In this dissertation, we explore the possibilities of systematically constructing large structural mechanisms using existing spatial overconstrained linkages with only revolute joints as basic elements. The first part of the dissertation is devoted to structural mechanisms (networks) based on the Bennett linkage, a well-known spatial 4R linkage. This special linkage has been used as the basic element. A particular layout of the structures has been identified allowing unlimited extension of the network by repeating elements. As a result, a family of structural mechanisms has been found which form single-layer structural mechanisms. In general, these structures deploy into profiles of cylindrical surface. Meanwhile, two special cases of the single-layer structures have been extended to form multi-layer structures. In addition, according to the mathematical derivation, the problem of connecting two similar Bennett linkages into a mobile structure, which other researchers were unable to solve, has also been solved. A study into the existence of alternative forms of the Bennett linkage has also been done. The condition for the alternative forms to achieve the compact folding and maximum expansion has been derived. This work has resulted in the creation of the most effective deployable element based on the Bennett linkage. A simple method to build the Bennett linkage in its alternative form has been introduced and verified. The corresponding networks have been obtained following the similar layout of the original Bennett linkage. The second effort has been made to construct large overconstrained structural mechanisms using hybrid Bricard linkages as basic elements. The hybrid Bricard linkage is a special case of the Bricard linkage, which is overconstrained and with a single degree of mobility. Starting with the derivation of the compatibility condition and the study of its deployment behaviour, it has been found that for some particular twists, the hybrid Bricard linkage can be folded completely into a bundle and deployed to a flat triangular profile. Based on this linkage, a network of hybrid Bricard linkages has been produced. Furthermore, in-depth research into the deployment characteristics, including kinematic bifurcation and the alternative forms of the hybrid Bricard linkage, has also been conducted. The final part of the dissertation is a study into tiling techniques in order to develop a systematic approach for determining the layout of mobile assemblies. A general approach to constructing large structural mechanisms has been proposed, which can be divided into three steps: selection of suitable tilings, construction of overconstrained units and validation of compatibility. This approach has been successfully applied to the construction of the structural mechanisms based on Bennett linkages and hybrid Bricard linkages. Several possible configurations are discussed including those described previously. All of the novel structural mechanisms presented in this dissertation contain only revolute joints, have a single degree of mobility and are geometrically overconstrained. Research work reported in this dissertation could lead to substantial advancement in building large spatial deployable structures.

La bio-informatique est un champ pluridisciplinaire qui utilise la biologie, l’informatique, la physique et les mathématiques pour résoudre des problèmes posés par la biologie. L’une des thématiques de la bio-informatique est l’analyse des séquences génomiques et la prédiction de gènes d’ARN non codants. Les ARN non codants sont des molécules d’ARN qui sont transcrites mais pas traduites en protéine et qui ont une fonction dans la cellule. Trouver des gènes d’ARN non codants par des techniques de biochimie et de biologie moléculaire est assez difficile et relativement coûteux. Ainsi, la prédiction des gènes d’ARNnc par des méthodes bio-informatiques est un enjeu important. Cette recherche décrit un travail d’analyse informatique pour chercher des nouveaux ARNnc chez le pathogène Candida albicans et d’une validation expérimentale. Nous avons utilisé comme stratégie une analyse informatique combinant plusieurs logiciels d’identification d’ARNnc. Nous avons validé un sous-ensemble des prédictions informatiques avec une expérience de puces à ADN couvrant 1979 régions du génome. Grace à cette expérience nous avons identifié 62 nouveaux transcrits chez Candida albicans. Ce travail aussi permit le développement d’une méthode d’analyse pour des puces à ADN de type tiling array. Ce travail présente également une tentation d’améliorer de la prédiction d’ARNnc avec une méthode se basant sur la recherche de motifs d’ARN dans les séquences. / Bioinformatics is a multidisciplinary field that uses biology, computer science, physics and mathematics to solve problems in biology. One of the topics of bioinformatics is the analysis of genomic sequences and prediction of genes from non-coding RNA (ncRNA). The non-coding RNAs are RNA molecules that are transcribed but not translated into protein and have a function in the cell. The use of biochemistry and molecular biology techniques in order to find non-coding RNA genes is rather difficult and relatively expensive. Thus, the prediction of genes by bioinformatics methods is an important issue. This research describes a computer analysis to search for new ncRNA in the pathogen Candida albicans and an experimental validation. The strategy used was to combine several algorithms and to validate a subset of computer predictions with a microarray experience covering 1979 regions of the genome. We have identified 62 new transcripts in Candida albicans. We have also developed an analytical method for tiling array and attempted to improve the prediction of ncRNAs this with a method based on the search of RNA motifs in the sequences.