vii, 54 p. : ill. A print copy of this thesis is available through the UO Libraries. Search the library catalog for the location and call number. / We investigate the existence of a stable homotopy category (SHC) associated to the category of p -complete abelian groups [Special characters omitted]. First we examine [Special characters omitted] and prove [Special characters omitted] satisfies all but one of the axioms of an abelian category. The connections between an SHC and homology functors are then exploited to draw conclusions about possible SHC structures for [Special characters omitted]. In particular, let [Special characters omitted] denote the category whose objects are chain complexes of [Special characters omitted] and morphisms are chain homotopy classes of maps. We show that any homology functor from any subcategory of [Special characters omitted] containing the p-adic integers and satisfying the axioms of an SHC will not agree with standard homology on free, finitely generated (as modules over the p -adic integers) chain complexes. Explicit examples of common functors are included to highlight troubles that arrise when working with [Special characters omitted]. We make some first attempts at classifying small objects in [Special characters omitted]. / Committee in charge: Hal Sadofsky, Chairperson, Mathematics; Boris Botvinnik, Member, Mathematics; Daniel Dugger, Member, Mathematics; Sergey Yuzvinsky, Member, Mathematics; Elizabeth Reis, Outside Member, Womens and Gender Studies

Submitted by Luciana Ferreira (lucgeral@gmail.com) on 2014-08-12T15:13:32Z No. of bitstreams: 2 license_rdf: 23148 bytes, checksum: 9da0b6dfac957114c6a7714714b86306 (MD5) dissertacao rommel cc.pdf: 1665635 bytes, checksum: 9f894f847272036c011387e2de71507f (MD5) / Made available in DSpace on 2014-08-12T15:13:32Z (GMT). No. of bitstreams: 2 license_rdf: 23148 bytes, checksum: 9da0b6dfac957114c6a7714714b86306 (MD5) dissertacao rommel cc.pdf: 1665635 bytes, checksum: 9f894f847272036c011387e2de71507f (MD5) Previous issue date: 2009-03-12 / Given a graph G = (V;E) and a set of vertices D V, a vertice v 2 V is dominated by D if jN[v] \ Dj 1. When jN(v) \ Dj = 1 for all v 2 V, G is efficiently dominable. A generalization of this concept is called efficient multiple domination, which requires all vertices must be dominated by a set D V exactly k times. The aim of this dissertation is to study these topics, describing the theoretical knowledge needed for advanced researches. For this reason, many of the theorems and its proofs are detailed. Furthermore, some results on the efficient multiple domination are presented, including bounds for the size of efficient k-dominating sets, the complement and iterated line graphs of efficiently (r + 1)-dominable r-regular graphs and a N P-completeness proof for the efficient multiple domination problem in arbitrary graphs. It is expected that this work contribute to the development of future researches on the efficient domination and in the resolution of some open problems. / Dado um grafo G = (V;E) e um subconjunto de vértices D V, define-se D como um conjunto dominante de G se todo vértice v 2 V que não estiver incluído no conjunto D for adjacente a pelo menos um vértice de D. Na situação em que, para todo v 2 V, jN[v]\Dj = 1, diz-se que o grafo G é eficientemente dominado. Uma generalização desse conceito consiste na múltipla dominação eficiente, em que é requerido que todo vértice do grafo seja dominado exatamente k vezes. O objetivo deste trabalho é realizar um estudo exploratório sobre esses temas, de modo a reunir o conhecimento teórico requerido para pesquisas avançadas. Para isso, buscou-se a apresentação e o detalhamento das demonstrações dos teoremas estudados. Além disso, foram fornecidos alguns resultados sobre a múltipla dominação eficiente no que se refere aos limites para o tamanho de um conjunto k-dominante eficiente, à relação da k-dominação eficiente entre grafos regulares, seu complemento e seus grafos linha iterados, bem como à caracterização da N P-completude para o problema da múltipla dominação eficiente em grafos arbitrários. Espera-se que esta dissertação forneça subsídios teóricos para estudos futuros voltados à dominação eficiente, bem como à resolução de algumas questões em aberto.

Cette thèse porte sur deux sujets intrinsèquement liés : le calcul de la constante de normalisation d’un champ de Markov et l’estimation de l’affinité de liaison d’un complexe de protéines. Premièrement, afin d’aborder ce problème de comptage #P complet, nous avons développé Z*, basé sur un élagage des quantités de potentiels négligeables. Il s’est montré plus performant que des méthodes de l’état de l’art sur des instances issues d’interaction protéine-protéine. Par la suite, nous avons développé #HBFS, un algorithme avec une garantie anytime, qui s’est révélé plus performant que son prédécesseur. Enfin, nous avons développé BTDZ, un algorithme exact basé sur une décomposition arborescente qui a fait ses preuves sur des instances issues d’interaction intermoléculaire appelées “superhélices”. Ces algorithmes s’appuient sur des méthodes issuse des modèles graphiques : cohérences locales, élimination de variable et décompositions arborescentes. A l’aide de méthodes d’optimisation existantes, de Z* et des fonctions d’énergie de Rosetta, nous avons développé un logiciel open source estimant la constante d’affinité d’un complexe protéine protéine sur une librairie de mutants. Nous avons analysé nos estimations sur un jeu de données de complexes de protéines et nous les avons confronté à deux approches de l’état de l’art. Il en est ressorti que notre outil était qualitativement meilleur que ces méthodes. / This thesis is focused on two intrinsically related subjects : the computation of the normalizing constant of a Markov random field and the estimation of the binding affinity of protein-protein interactions. First, to tackle this #P-complete counting problem, we developed Z*, based on the pruning of negligible potential quantities. It has been shown to be more efficient than various state-of-the-art methods on instances derived from protein-protein interaction models. Then, we developed #HBFS, an anytime guaranteed counting algorithm which proved to be even better than its predecessor. Finally, we developed BTDZ, an exact algorithm based on tree decomposition. BTDZ has already proven its efficiency on intances from coiled coil protein interactions. These algorithms all rely on methods stemming from graphical models : local consistencies, variable elimination and tree decomposition. With the help of existing optimization algorithms, Z* and Rosetta energy functions, we developed a package that estimates the binding affinity of a set of mutants in a protein-protein interaction. We statistically analyzed our esti- mation on a database of binding affinities and confronted it with state-of-the-art methods. It appears that our software is qualitatively better than these methods.