A concepção arquitetônica dos templos dóricos gregos é estudada na perspectiva da Arqueologia da Arquitetura stricto sensu. Verificamos a relevância e o papel que teve a aplicação da geometria e da aritmética como recursos técnicos e metodológicos para o desenvolvimento do projeto do templo dórico grego no século V a.C., visando esclarecer e estabelecer vínculos entre tais ramos da matemática e a lógica subjacente que norteou os arquitetos, tanto em projeto como nas aplicações precisas em obra. Para isso, abordarmos os fundamentos científicos da arquitetura grega a partir da análise de 10 templos clássicos hexastilos (configuração canônica da ordem dórica) fazendo um balanço crítico sobre o alcance e o limite das teorias modernas que desenvolveram modelos de interpretação para o projeto do templo dórico grego. Adotamos como ponto de partida, e referência fundamental, os artigos publicados por J. J. Coulton em meados da década de setenta, no periódico The Annual of the British School at Athens, e vamos sistemáticamente atualizando o debate apoiado nas discussões mais recentes. / The Architectural conception of the Greek Doricos temples has been studied in the perspective of the Archaeology of the Architecture stricto sensu. We had verified the role and the relevance that the geometry and arithmetic applications such as the technical and methodology resources for the design development of the Greek Doric temple in V century B.C., in order to clarify and to establish links between mathematics branches and the underlying logic that had been guiding the architects, as much in projects as in the accuracy applications for the building constructions. In a way to approach the Greek architecture scientific fundamentals from the analysis of 10 hexastilos classic temples (canonic configuration of the Doric order) making a critical balance on the limit and the reach of the modern theories that had developed interpretation models for the design of the Greek Doric temple. We adopt as basic reference and starting point, the articles published for J.J. Coulton in middle of the seventy decade, in the periodic The Annual of the British School at Athens, and systematically go bringing up to date the debate supported in the most recent discussions.

Ce travail étudie comment la mesure des forces hydrodynamiques exercées par un liquide confiné entre une sphère et une surface d'intérêt permet de sonder à distance et sans contact les propriétés mécaniques de cette surface. Nous présentons tout d'abord le principe de cette technique originale de sonde fluide et la machine à forces de surface dynamique que nous utilisons pour mettre en œuvre ces expériences de nano-rhéologie. Puis nous nous intéressons à deux applications que nous avons plus particulièrement étudiées. D'une part, l'étude des propriétés de friction des bicouches lipidiques. Nous mettons en évidence une très faible friction mesurée sur certaines bicouches fluides et son potentiel rôle pour la bio-lubrification. D'autre part l'étude des propriétés élastiques de couche mince d'élastomère. Nous développons pour cela une théorie de l'élastohydrodynamique à géométrie sphère-plan en mode dynamique et présentons des résultats expérimentaux en très bon accord. Nous sommes capables de mesurer le module d'Young de films mince de PDMS d'épaisseur allant jusqu'à 600 nm. Enfin, nous présentons les développements instrumentaux réalisés pour optimiser les performances de la machine à forces de surfaces comme sonde fluide / This work addresses how the measurement of hydrodynamic forces of a liquid confined between a sphere and a surface of interest can lead to probe at a distance and without contact her mechanical properties. Firstly, we introduce this original technique of fluid probe and the dynamic Surface Force Apparatus used to perform these nanorheology experiments. Then, we present two applications for which the fluid probe can be of great importance. The first application is the study of friction properties of lipid bilayers. More particularly we measure very weak fluid friction coefficients on some fluid bilayers, which can be an important issue for biolubrication. The second application is the study of elastic properties of thin elastomer layers. For that we first develop an elasto-hydrodynamic theory for sphere-plan configuration in dynamic mode. Then, we present experimental results in very good agreement with this theory. We are able to measure the Young modulus of thin PDMS films of thickness as small as 600 nm. Finally, we present instrumental developments performed on the Surface Force Apparatus to optimize its potential as fluid probe

Human immunodeficiency virus (HIV-1) is the pathogenic agent of HIV infection thatprecedes the total breakdown of cellular immunity, a condition known as acquiredimmunodeficiency syndrome (AIDS). The pandemic nature of the disease has promptedintense research into its biology. Already, much is known about HIV-1 infection, lifecycle,and progression to aids. Systems biology enables the combination of complex data fromthese studies into a framework where their effect on the various levels of cellularorganization (i.e. Pathways, cells, tissues, organs and the whole body) could be studied insilico. In this thesis, first, we reviewed our knowledge of the HIV-1 Human InteractionDatabase. We examined its contents and identified processes that HIV-1 was not previouslyknown to interact with. Then, we attempted an in silico dynamic model of HIV-1 interaction. We built a model of HIV-1 interaction with the CD4 T cell activation pathway comprised of137 nodes (16 HIV-1, 121 human) and 336 interactions. The model reproduced expectedpatterns of T cell activation. Using interaction graph properties, we identified 26 host cellfactors, including MAPK1&3, Ikkb-Ikky-Ikka and PKA, which contribute to the net activationor inhibition of viral proteins. By following a logical Boolean formalism, we identified 9 hostcell factors essential to the functions of viral proteins in the activation pathway. This wasthe first attempt to model dynamic viral-host interaction relationships. Then, we organize HIV-1 interacting host genes into modules to represent cellular processesneeded by the virus. We combined HIV-1 interactions with host gene GO annotations toclassify host genes according to these needed cellular processes. We obtained 201 modulesand found the same set of viral proteins do not interact with host genes having similarmodules suggesting intelligence in its co-ordination of host processes. This work is one of agrowing list that explores coordination of HIV-1 interactions. But more importantly, it would bebeneficial to functionally downsize the large dynamic HIV-1 interaction network. Finally, in our discussion, we discuss our results and suggest possible ways in which our workon dynamic models could be improved. This work is opening up a new field of systems virologythat studies the effect of viruses on the host in terms of its temporal and spatial aspects.

Cette thèse consiste à étudier l'organisation du système de contrôle des voies métaboliques des bactéries afin de dégager des propriétés systémiques révélant son fonctionnement. Dans un premier temps, nous montrons que le contrôle des voies métaboliques est hautement structuré et peut se décomposer en modules fortement découplés en régime stationnaire. Ces modules possèdent des propriétés mathématiques remarquables ayant des conséquences importantes en biologie. Cette décomposition, basée intrinsèquement sur la vision système de l'Automatique, offre un cadre théorique formel général d'analyse du contrôle des voies métaboliques qui s'est révélé effectif pour analyser des données expérimentales. dans un deuxième temps, nous nous intéressons aux raisons possibles de l'émergence de cette structure de contrôle similaire. Nous identifions un ensemble de contraintes structurelles agissant au niveau de la répartition d'une ressource commune, les protéines, entre les processus cellulaires. Respecter ces contraintes pour un taux de croissance donné conduit à formaliser et résoudre un problème d'optimisation convexe non différentiable, que nous appelons Resource balance Analysis. Ce problème d'optimisation se résout numériquement à l'échelle de la bactérie grâce à un problème de Programmation Linéaire équivalent. plusieurs propriétés sont déduites de l'analyse théorique du critère obtenu. Tout d'abord, le taux de croissance est structurellement limité par la répartition d'une quantité finie de protéines entre les voies métaboliques et les ribosomes. Ensuite, l'émergence des modules dans les voies métaboliques provient d'une politique générale d'économie en protéines chez la bactérie pour gagner du taux de croissance. Certaines stratégies de transport bien connues comme la répression catabolique ou la substitution de transporteurs haute/basse affinités sont prédites par notre méthode et peuvent alors être interprétées comme le moyen de maximiser la croissance tout en minimisant l'investissement en protéines. / This thesis consist in studying the organization of the control system of metabolic pathways of bacteria to identify systemic properties revealing its operation. At first, we show that control of metabolic pathways is highly structured and can be decomposed into modules strongly decoupled in steady-state. These modules are defined by their singular mathematical properties having important implications in biology. This decomposition, based inherently on the system outlook of automatic control, offers a formal theoretical analysis of general control of metabolic pathways, which has been effective in analysing experimental data. In a second step, we consider the possible reasons for the emergence of this modular control structure. We identify a set of structural constraints acting at the distribution of a common resourc, the proteins between cellular processes. Satisfying these constraints for a given growth rate leads to formalize and to solve a non-differentiable convex optimization problem, that we call Resource Balance Analysis. This optimization problem is solved numerically at the scale of the bacteria through an equivalent linear programming problem. Several properties are derived from theoretical analysis of the obtained criterion. Firts, the growth rate is structurally limited by the distribution of a finite amount of proteines between the metabolic pathways and the ribosomes. Second, the emergence of modules in metabolic pathways arises from a policy of economy in proteins in the bacterium to increase the growth rate. Some well known transport strategies such as catabolite repression of the substitution between low/highaffinity transporters are predicted by our methods and could consequently be interpretd as ways to maximize growth while minimizing investment in proteins.

L'objectif de ce travail est de développer et d'évaluer des approches méthodologiques pour la<p>prédiction de séquences cis-régulatrices. Ces approches ont été intégrées dans la suite logicielle<p>RSAT (Regulatory Sequences Analysis Tools). Ces séquences jouent un rôle important dans la<p>régulation de l'expression des gènes. Cette régulation, au niveau transcriptionnel, s'effectue à<p>travers la reconnaissance spécifique entre les facteurs de transcription et leurs sites de fixation<p>(TFBS) au niveau de l'ADN.<p>Nous avons développé et évalué une série d'outils bioinformatiques qui utilisent les matrices<p>position-poids pour prédire les TFBS ainsi que les modules cis-régulateurs (CRM). Nos outils<p>présentent l'avantage d'intégrer les différentes approches déjà proposées par d'autres auteurs tout<p>en proposant des fonctionnalités innovantes.<p>Nous proposons notamment une nouvelle approche pour la prédiction de CRM basé sur la<p>détection de régions significativement enrichies en TFBS. Nous les avons appelés les CRER (pour<p>Cis-Regulatory Elements Enriched Regions). Un autre aspect essentiel de toute notre approche<p>réside dans le fait que nous proposons des mesures statistiques rigoureuses pour estimer<p>théoriquement et empiriquement le risque associé aux différentes prédictions. Les méthodes de<p>prédictions de séquences cis-regulatrices prédisent en effet un taux de fausses prédictions<p>généralement élevé. Nous intégrons un calcul des P-valeurs associées à toutes les prédictions.<p>Nous proposons ainsi une mesure fiable de la probabilité de faux positifs.<p>Nous avons appliqué nos outils pour une évaluation systématique de l'effet du modèle de<p>background sur la précision des prédictions à partir de la base de données de TRANSFAC. Nos<p>résultats suggèrent une grande variabilité pour les modèles qui optimisent la précision des<p>prédictions. Il faut choisir le modèle de background au cas par cas selon la matrice considérée.<p>Nous avons ensuite évalué la qualité des matrices de tous les facteurs de transcription de<p>drosophile de la base de données ORegAnno, c'est à dire leur pouvoir de discrimination entre les<p>TFBS et les séquences génomiques. Nous avons ainsi collecté des matrices des facteurs de<p>transcription de drosophile de bonne qualité.<p>A partir des matrices de drosophile que nous avons collectées, nous avons entamé une analyse<p>préliminaire multi-genome de prédictions de TFBS et de CRM dans la région de lʼenhancer dorsocentral<p>(DCE) du complexe achaete-scute de drosophile. Les gènes de ce complexe jouent un<p>rôle important dans la détermination des cellules système nerveux périphérique de drosophile. Il a<p>été prouvé expérimentalement qu'il existe un lien direct entre le phénotype du système nerveux<p>périphérique et les séquences cis-régulateurs des gènes de ce complexe.<p>Les outils que nous avons développés durant ce projet peuvent s'appliquer à la prédiction des<p>séquences de régulation dans les génomes de tous les organismes. / Doctorat en Sciences / info:eu-repo/semantics/nonPublished

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior / The purpose of this work is to study the relationships between admissible pairs, systems admissible and bialgebras in the category of Yetter-Drinfeld modules, as well as some properties of the Hopf algebra associated (via bosonization) to an admissible pair. We end this dissertation with a family of examples of admissible pairs. / O objetivo deste trabalho é estudar as relações entre pares admissíveis, sistemas admissíveis e biálgebras na categoria dos módulos de Yetter-Drinfeld, bem como algumas propriedades da álgebra de Hopf associada (via bosonização) a um par admissível. Finalizamos esta dissertação com uma família de exemplos de pares admissíveis.

[pt] Injeção de dependências, uma forma de inversão de controle, é uma forma de estruturar a configuração e composição de componentes de software que traz vários benefícios como um acoplamento reduzido entre componentes. No entanto, um framework genérico de injeção de dependências requer instrospecção em tempo de execução, o que explica por que injeção de dependências é popular em Java mas praticamente inexistente em C Mais Mais. Neste trabalho apresentamos um sistema de introspecção para C Mais Mais 11 e mostramos como ele pode ser usado para melhorar uma implementação de Service Component Architecture (SCA) para C Mais Mais. Usamos vários novas funcionalidades de C Mais Mais 11 como perfect forwarding, variadic templates e lvalue references para melhorar a usabilidade da API de reflexão e minimizar o overhead de execução. / [en] Dependency injection, a form of inversion of control, is a way of structuring the configuration and composition of software components that brings many benefits such as a loose coupling of components. However, a generic dependency injection framework requires runtime type introspection and this is why dependency injection is popular in Java and almost non-existent in C plus plus. In this work we present a introspection system for C plus plus 11 and show how to use it to improve an implementation of the Service Component Architecture (SCA) for C plus plus. It uses several features of C plus plus 11 such as perfect forwarding, variadic templates and lvalue references to improve usability and minimize overhead.

Renewable energy sources normally require power converters to convert their energy into standardized regulated ac output. The motivation for this thesis is to design and control power converters for renewable energy systems to ensure very good power quality, efficiency and reliability. The renewable energy sources considered are low voltage dc sources such as photovoltaic (PV) modules. Two transformer-isolated power circuit topologies with input voltage of less than 50V are designed and developed for low and medium power applications. Various design and control issues of these converters are identified and new solutions are proposed. For low power rating of a few hundred watts, a line-frequency transformer interfaced inverter is developed. In the grid connected operation, it is observed that this topology injects considerable lower order odd and even harmonics in the grid current. The reasons for this are identified. A new current control method using adaptive harmonic compensation technique and a proportional-resonant-integral (PRI) controller is proposed. The proposed current controller is designed to ensure that the grid current harmonics are within the limits set by the IEEE 1547-2003 standard. Phase-locked loops (PLLs) are used for grid synchronization of power converters in grid-tied operation and for closed-loop control reference generation. Analysis and design of synchronous reference frame PLL (SRF-PLL) and second-order generalized integrator (SOGI) based PLLs considering unit vector distortion under the possible non-ideal grid conditions of harmonics, unbalance, dc offsets and frequency deviations are proposed and validated. Both SRF-PLL and SOGI-PLL are low-complexity PLLs. The proposed designs achieve fastest settling time for these PLLs for a given worst-case input condition. The harmonic distortion and dc offsets in the resulting unit vectors are limited to be well within the limits set by the IEEE 1547-2003 standard. The proposed designs can be used to achieve very good performance using conventional low-complexity PLLs without the requirement of advanced PLLs which can be computationally intensive. A high-frequency (HF) transformer interfaced ac link inverter with a lossless snubber is developed medium power level in the order of few kilowatts. The HF transformer makes the topology compact and economical compared to an equally rated line frequency transformer. A new synchronized modulation method is proposed to suppress the possible over-voltages due to current commutation in the leakage inductance of the HF transformer. The effect of circuit non-ideality of turn-on delay time is analyzed. The proposed modulation mitigates the problem of spurious turn-on that can occur due to the turn-on delay time. The HF inverter, rectifier and snubber devices have soft switching with this modulation. A new reliable start-up method is proposed for this inverter topology without any additional start- up circuitry. This solves the problems of over-voltages and inrush currents during start-up. The overall research work reported in the thesis shows that it is possible to have compact, reliable and high performance power converters for renewable energy conversion systems. It is also shown that high control performance and power quality can be achieved using the proposed control techniques of low implementation complexity.

Fatores de transcrição (FT) são proteínas que se ligam em sequências específicas e bem conservadas de nucleotídeos no DNA, denominadas sítios de ligação dos fatores de transcrição (SLFT), localizadas em regiões de regulação gênica conhecidas como módulos cis-reguladores (CRM). Ao reconhecer o SLFT, o fator de transcrição se liga naquele sítio e influencia a transcrição gênica positiva ou negativamente. Existem técnicas experimentais para a identificação dos locais dos SLFTs em um genoma, como footprinting, ChIP-chip ou ChIP-seq. Entretanto, a execução de tais técnicas implica em custos e tempo elevados. Alternativamente, pode-se utilizar as sequências de SLFTs já conhecidas para um determinado fator de transcrição e aplicar técnicas de aprendizado computacional supervisionado para criar um modelo computacional para tal sítio e então realizar a predição computacional no genoma. Entretanto, a maioria das ferramentas computacionais existentes para esse fim considera independência entre as posições entre os nucleotídeos de um sítio - como as baseadas em PWMs (position weight matrix) - o que não é necessariamente verdade. Este projeto teve como objetivo avaliar a utilização de gramáticas regulares estocásticas (GRE) como técnica alternativa às PWMs neste problema, uma vez que GREs são capazes de caracterizar dependências entre posições consecutivas dos sítios. Embora as diferenças de desempenho tenham sido sutis, GREs parecem mesmo ser mais adequadas do que PWMs na presença de valores mais altos de dependência de bases, e PWMs nos demais casos. Por fim, uma ferramenta de predição computacional de SLFTs foi criada baseada tanto em GREs quanto em PWMs. / Transcription factors (FT) are proteins that bind to specific and well-conserved sequences of nucleotides in the DNA, called transcription factor binding sites (TFBS), contained in regions of gene regulation known as cis-regulatory modules (CRM). By recognizing TFBA, the transcription factor binds to that site and positively or negatively influence the gene transcription. There are experimental procedures for the identification of TFBS in a genome such as footprinting, ChIP-chip or ChIP-Seq. However, the implementation of these techniques involves high costs and time. Alternatively, one may utilize the TFBS sequences already known for a particular transcription factor and applying computational supervised learning techniques to create a computational model for that site and then perform the computational prediction in the genome. However, most existing software tools for this purpose considers independence between nucleotide positions in the site - such as those based on PWMs (position weight matrix) - which is not necessarily true. This project aimed to evaluate the use of stochastic regular grammars (SRG) as an alternative technique to PWMs in this problem, since SRGs are able to characterize dependencies between consecutive positions in the sites. Although differences in performance have been subtle, SRGs appear to be more suitable than PWMs in the presence of higher base dependency values, and PWMs in other cases. Finally, a computational TFBS prediction tool was created based on both SRGs and PWMs.

Os atuais avanços na área das Tecnologias da Informação e da Comunicação (TIC) estão mudando a Educação, com a disponibilização de sistemas educativos para apoiar as atividades no processo de ensino e de aprendizagem. Embora o tópico de combinatória seja relevante para o ensino médio e para os cursos de Ciências Exatas, este tópico tem sido desconsiderado nos avanços da Informática na Educação, principalmente ao se considerar o uso de ambientes de aprendizagem via Web. Atualmente, o iComb é, no melhor de nosso conhecimento, o único sistema Web integrável a tais ambientes. Ele é um Módulo de Aprendizagem Interativa (iMA) integrável ao Sistema Gerenciador de Cursos (SGC) Moodle, por meio do plugin iTarefa. O iComb oferece atividades de autoria de exercícios, bem como, sua avaliação automática. No entanto, considerando sua usabilidade, foram detectados alguns problemas na interface. O foco deste trabalho está relacionado ao reprojeto do sistema iComb e seu impacto na aprendizagem de combinatória. Para a reconstrução do iComb adotou-se o método de design de interação, buscando-se a participação efetiva de usuários finais do sistema, em todas as atividades desse processo, com (i) sessões de teste de usabilidade utilizando a versão Java do iComb para identificar problemas e guiar o redesenho do sistema, e (ii) prototipagem e avaliação da interface do sistema redesenhado. Esse processo permitiu implementar uma nova versão do iComb utilizando tecnologias associadas ao HTML5, que será brevemente disponibilizado como software livre. / Current advances in Information and Communication Technologies (ICT) are changing Education with delivering software to support learning/teaching activities. Although being relevant for Science, Technology, Engineering, and Mathematics (STEM) courses, Combinatorial Analysis is almost disregarded in these advances, mostly if we consider their integration with earning Management Systems. Currently, iComb is, at the best of our knowledge, the only system with such a possibility. It is an interactive Learning Module (iLM) that can be integrated to Moodle, through the iAssign plugin. iComb provides authoring activities as well as their automatic assessment. Nevertheless, considering the system usability, several interaction problems were detected during sessions with teachers and students. In this work it is described the process of redesigning the iComb system by adopting Interactive Design, to conduct controlled sessions of system use for (i) identifying usability issues for guiding the system redesign; and (ii) prototyping and evaluate the redesigned system interface, with end-users. This process allowed to implement new version of iComb using HTML5 related technologies that will be sooner available as free software, in order to reach a larger audience. Preliminary results on the interface evaluation indicate that both students and teachers felt more comfortable using the new interface of iComb and found it easier to execute common tasks.