In eukaryotes the genome adopts a non-random spatial organisation, which is important for gene regulation. However, very little is known about the driving forces behind nuclear organisation. In the simple model eukaryote fission yeast, Schizosaccharomyces pombe, it has been known for a long time that transcriptionally repressed heterochromatin localise to the nuclear membrane (NM); the centromeres attaches to spindle pole body (SPB), while the telomeres are positioned at the NM on the opposite side of the nucleus compared to the SPB. Studies presented in this thesis aimed at advancing our knowledge of nuclear organisation in Schizosaccharomyces pombe. We show that the heterochromatic mating-type region localises to the NM in the vicinity of the SPB. This positioning was completely dependent on Clr4, a histone methyl transferase crucial for the formation of heterochromatin. Additional factors important for localisation were also identified: the chromo domain protein Swi6, and the two boundary elements IR-L and IR-R surrounding this locus. We further identify two other chromo domain proteins; Chp1 and Chp2, as crucial factors for correct subnuclear localisation of this region. From these results we suggest that the boundary elements together with chromodomain proteins in balanced dosage and composition cooperate in organising the mating-type chromatin. Gene regulation can affect the subnuclear localisation of genes. Using nitrogen starvation in S. pombe as a model for gene induction we determined the subnuclear localisation of two gene clusters repressed by nitrogen: Chr1 and Tel1. When repressed these loci localise to the NM, and this positioning is dependent on the histone deacetylase Clr3. During induction the gene clusters moved towards the nuclear interior in a transcription dependent manner. The knowledge gained from work presented in this thesis, regarding nuclear organisation in the S. pombe model system, can hopefully aid to a better understanding of human nuclear organisation.

O presente trabalho apresenta uma formulação misto do MEC (Método dos Elementos de Contorno) e o MEF (Método dos Elementos Finitos). Nessa formulação, as estacas são modeladas através do MEF como elementos de barra e o solo através do MEC, como um meio contínuo, elástico linear, isótropo e homogêneo, utilizando as soluções fundamentais de MINDLIN (1936). Os sistemas de equações do solo e das estacas para elementos verticais são apresentados como uma combinação de ambos, originando um único sistema final de equações. Apresentam-se também as modificações necessárias para um sistema composto por estacas inclinadas. Após a resolução do sistema final, obtém-se os deslocamentos e as tensões de contato solo-estaca. A seguir, apresentam-se alguns exemplos numéricos obtidos a partir da formulação proposta e compara-se com modelos de outros autores. / This work presents a hybrid formulation of BEM (Boundary Elements Method) and FEM (Finite Elements Method). In that formulation, the piles are modeled through FEM as bar elements and the soil through BEM, as an isotropic, homogeneous, semi-infinite and linear-elastic continuum, using the fundamental solutions of MINDLIN (1936). The systems of equations of the soil and of the piles for vertical elements are presented as a combination of both, originating a single final system of equations. Some modifications are accomplished for the system of inclinated piles. After the resolution of the final system, the displacements and the contact tensions between soil and pile are obtained. Numeric examples are obtained starting from the proposed formulation and to proceed they are compared with other authors\' models.

Neste trabalho, é desenvolvido um programa de computador para a análise estática e tridimensional de problemas de interação solo-estrutura. O programa permite considerar várias camadas de solo, cada qual com características físicas diferentes. Sobre este solo, o qual pode conter estacas, podem ser apoiados diversos tipos de estruturas, tais como placas e até um edifício. Todos os materiais considerados são homogêneos, isotrópicos, elásticos e lineares. O solo tridimensional é modelado com o método dos elementos de contorno (MEC), empregando as soluções fundamentais de Kelvin e uma técnica alternativa na consideração do maciço não-homogêneo. Esta técnica, que é uma contribuição original deste trabalho, é baseada no relacionamento das soluções fundamentais de deslocamento dos diferentes domínios, permitindo que sejam analisados como um único sólido sem a necessidade de equações de equilíbrio e compatibilidade. Isso reduz o sistema de equações final e melhora a precisão dos resultados, conforme comprovado nos exemplos apresentados. Para reduzir o custo computacional sem prejudicar a precisão dos resultados, é utilizada uma malha de elementos de contorno infinitos (ECI) nas bordas da malha de ECs para modelar o comportamento das variáveis de campo em longas distâncias. A formulação do ECI mapeado utilizado é outra contribuição original deste trabalho, sendo baseado em um EC triangular. É demonstrado por meio de exemplos que tal formulação é eficiente para a redução de malha, contribuindo de forma significativa na redução do custo computacional. Todas as estruturas que interagem com o solo, incluindo as de fundação, são simuladas empregando o método dos elementos finitos (MEF). Cada estaca é modelada como uma linha de carga empregando um único elemento finito com 14 parâmetros nodais, o qual utiliza funções de forma do quarto grau para aproximar os deslocamentos horizontais, do terceiro grau para as forças horizontais e deslocamentos verticais, do segundo grau para as forças cisalhantes verticais e constantes para as reações da base. Este elemento é empregado em outros trabalhos, no entanto os autores utilizam as soluções fundamentais de Mindlin na consideração da presença da estaca no solo. Desta forma, a formulação desenvolvida neste trabalho com as soluções fundamentais de Kelvin pode ser considerada mais uma contribuição original. No edifício, que pode incluir um radier como estrutura de fundação, são utilizados dois tipos de EFs. Os pilares e vigas são simulados com elementos de barra, os quais possuem dois nós e seis graus de liberdade por nó. As lajes e o radier são modelados empregando elementos planos, triangulares e com três nós. Nestes EFs triangulares são superpostos efeitos de membrana e flexão, totalizando também seis graus de liberdade por nó. O acoplamento MEC/MEF é feito transformando as cargas de superfície do MEC em carregamentos nodais reativos no MEF. Além de exemplos específicos nos Capítulos teóricos, um Capítulo inteiro é dedicado a demonstrar a abrangência e precisão da formulação desenvolvida, comparando-a com resultados de outros autores. / In this work, a computer code is developed for the static analysis of three-dimensional soil-structure interaction problems. The program allows considering a layered soil, which may contain piles. This soil may support several structures, such as shells or even an entire building. All materials are considered homogeneous, isotropic, elastic and linear. The three-dimensional soil is modeled with the boundary element method (BEM), employing Kelvin fundamental solutions and an alternative multi-region technique. This technique, which is an original contribution of this work, is based on relating the displacement fundamental solution of the different domains, allowing evaluating them as an unique solid and not requiring compatibility or equilibrium equations. In such a way, the final system of equations is reduced and more accurate results are obtained, as demonstrated in the presented examples. In order to reduce the computational cost maintaining the accuracy, an infinite boundary element (IBE) mesh is employed at the BE mesh limits to model the far field behavior. The mapped IBE utilized, based on a triangular EC, is another original contribution of this work. In the presented examples it is demonstrated that this IBE formulation is efficient for mesh reduction, implying on a significant computational cost reduction. All structures that interact with the soil, including the foundations, are simulated with de finite element method (FEM). The piles are modeled using a one-dimensional 14 parameter finite element, with forth degree shape functions for horizontal displacement approximation, third degree shape functions for horizontal forces and vertical displacement, second degree shape functions for vertical share force, and constant for the base reaction. This element is employed in other works, however the authors utilize Mindlin fundamental solutions for the pile presence consideration in the soil. In such a way, the formulation developed in this work with Kelvin fundamental solutions may be considered one more original contribution. The building, which may include a radier as a foundation structure, is modeled using two types os FEs. Piles and beams are simulated using bar FEs with two nodes and six degrees of freedom per node. The radier and pavements are modeled employing plane triangular three-node FEs. In these FEs plate and membrane effects are superposed, totalizing six degrees of freedom per node. FEM/BEM coupling is made by transforming the BEM tractions in nodal reactions in the FEM. Even though specific examples are presented in the theoretical Chapters, a role Chapter is dedicated for demonstrating the formulation accuracy and coverage. In most examples, the results are compared with the ones obtained by other authors.

Orientador: Jose Roberto de França Arruda / Tese (doutorado) - Universidade Estadual de Campinas, Faculdade de Engenharia Mecanica / Made available in DSpace on 2018-08-13T08:53:33Z (GMT). No. of bitstreams: 1 Nascimento_RangelFerreirado_D.pdf: 7547341 bytes, checksum: 0793f0ff7763f81b44868f59db73aab6 (MD5) Previous issue date: 2009 / Resumo: Esta tese estuda e investiga o problema de propagação de ondas em estruturas periódicas usando o método de elemento espectral, a relação entre a matriz dinâmica e a matriz de transferência é mostrada para alguns casos, tais como, viga, barra, placa de Levy e modelo de Minddlin Hermman. A partir destas teorias, o método de propagação de ondas usando um modelo de elementos finitos de uma fatia do guia de ondas, WFEM é apresentado e o problema de prever os modos de propagação e os números de onda correspondentes. O objetivo deste trabalho é mostrar que usando o método WFEM e uma fatia do guia de onda modelado com elementos finitos sólido é possível construir elementos finitos espectrais para ser usado em guias de ondas homogêneos sem precisar de malha de refinamento. Tais elementos podem ser usados para modelar guias de ondas com seção transversal constante. A matriz de rigidez dinâmica para o elemento de barra elementar e para o elemento de viga de Euler Bernoulli são obtidos usando a formulação espectral padrão e obtidas usando uma fatia do guia de onda modelado pelo método FEM, são mostrados resultados do método proposto. / Abstract: This thesis, studies and investigates wave propagation problem in periodic structures using the spectral element method, the relation between the dynamic matrix and the transfer matrix is shown for some cases, such as, beam, bar, Levy plate and Mindlin-Herrmann's model. From these theories, the Wave Finite Element Method, WFEM is presented and the problem of predicting the wave propagation modes and the respective wavenumbers. The purpose of this work is to show that using the WFEM method and a slice of the waveguide modeled with solid finite elements, it is possible to develop spectral finite elements to be used in long homogeneous waveguides without the need of mesh refinement. Such elements can be used to model waveguides with constant cross section and long spans. The dynamic stiffness matrix of a simple rod and Bernoulli Euler beam element obtained using the standard spectral formulation and obtained via the FEM model of a slice are shown to be similar, thus validating the proposed method. / Doutorado / Mecanica dos Sólidos e Projeto Mecanico / Doutor em Engenharia Mecânica

[pt] O Método Híbrido dos Elementos de Contorno foi introduzido em 1987. Desde então, o método foi aplicado com sucesso a diferentes tipos de problemas de elasticidade e potencial, inclusive problemas dependentes do tempo. Esta Tese apresenta uma tentativa para consolidar a formulação simplificada do Método Híbrido dos Elementos de Contorno para a análise geral da resposta dinâmica de sistemas elásticos. Baseado em um método de superposição modal, um conjunto acoplado de equações diferenciais de movimento de alta ordem é transformado em um conjunto desacoplado de equações diferenciais de segunda ordem que podem ser integradas normalmente por meio de procedimentos conhecidos. Este método também é uma extensão de uma formulação introduzida por J. S. Przemieniecki, para a análise de vibração livre de barras e elementos de viga baseada em uma série de freqüências. O método trata estruturas restringidas, com condições iniciais não homogêneas dadas como valores nodais e também através de campos prescritos no domínio, assim como forças genéricas de massa (além de forças inerciais). Esta tese também tem por objetivo estabelecer a consolidação conceitual da aplicação da versão simplificada do Método Híbrido dos Elementos de Contorno a materiais com gradação funcional. São obtidas várias classes de soluções fundamentais para problemas de potencial dependentes e independentes do tempo, para a análise no domínio da freqüência combinada com uma técnica avançada (mencionada acima) de superposição modal baseada em séries de freqüências. Com isso, consegue- se a utilização de integrais somente no contorno mesmo para materiais heterogêneos. Apresenta-se um grande número de resultados numéricos de problemas bidimensionais, para validação dos desenvolvimentos teóricos realizados. / [en] The hybrid boundary element method was introduced in 1987. Since then, the method has been successfully applied to different problems of elasticity and potential, including time-dependent problems. This thesis presents an attempt to consolidate a formulation for the general analysis of the dynamic response of elastic systems. Based on a mode- superposition technique, a set of coupled, higher-order differential equations of motion is transformed into a set of uncoupled second order differential equations, which may be integrated by means of standard procedures. The first motivation for these theoretical developments is the hybrid boundary element method, a generalization of T. H. H. Pian`s previous achievements for finite elements, which, requiring only boundary integrals, yields a stiffness matrix for arbitrary domain shapes and any number of degrees of freedom. The method is also an extension of a formulation introduced by J. S. Przemieniecki, for the free vibration analysis of bar and beam elements based on a power series of frequencies. It handles constrained and unconstrained structures, non-homogeneous initial conditions given as nodal values as well as prescribed domain fields and general domain forces (other than inertial forces). This thesis also focuses on establishing the conceptual framework for applying the simplified version of the hybrid boundary element method to functionally graded materials. Several classes of fundamental solutions for steady-state and time-dependent problems of potential are derived for a frequency-domain analysis combined with an advanced mode superposition technique based on a power series of frequencies. Thus, the boundary-only feature of the method is preserved even with such spatially varying material property.Several numerical examples are given in terms of an efficient patch test for irregular bounded, unbounded and multiply connected regions submitted to high gradients.

The traditional construction practice used in masonry buildings throughout the world is limited to walls with rectangular cross sections that, when reinforced with steel bars, typically accommodate only single-leg horizontal ties and a single layer of vertical reinforcement. This arrangement provides no confinement at the wall toes, and it may lead to instability in critical wall zones and significant structural damage during seismic events. Conversely, the development of a new building system, constructed with reinforced masonry (RM) walls with boundary elements, allows closed ties to be used as confinement reinforcement, thus minimizing such instability and its negative consequences. Relative to traditional walls, walls with boundary elements have enhanced performance because they enable the compression reinforcement to remain effective up to much larger displacement demands, resulting in a damage tolerant system and eventually, more resilient buildings under extreme events. Research on the system-level (complete building) performance of RM walls with boundary elements is, at the time of publication of this dissertation, nonexistent in open literature. What little research has been published on this innovative building system has focused only on investigating the component-level performance of RM walls with boundary elements under lateral loads. To address this knowledge gap, the dissertation presents a comprehensive research program that covered: component-level performance simulation; system-level (complete building) experimental testing; seismic risk assessment tools; and simplified analytical models to facilitate adoption of the developed new building system. In addition, and in order to effectively mobilize the knowledge generated through the research program to stakeholders, the work has been directly related to building codes in Canada and the USA (NBCC and ASCE-7) as well as other standards including FEMA P695 (FEMA 2009) (Chapter 2), TMS 402 and CSA S304 (Chapter 3), FEMA P58 (FEMA 2012) (Chapter 4), and ASCE-41 (Chapter 5). Chapter 1 of the dissertation highlights its objectives, focus, scope and general organization. The simulation in Chapter 2 is focused on evaluating the component-level overstrength, period-based ductility, and seismic collapse margin ratios under the maximum considered earthquakes. Whereas previous studies have shown that traditional RM walls might not meet the collapse risk criteria established by FEMA P695, the analysis presented in this chapter clearly shows that RM shear walls with boundary elements not only meet the collapse risk criteria, but also exceed it with a significant margin. Following the component-level simulation presented in Chapter 2, Chapter 3 focused on presenting the results of a complete two-story asymmetrical RM shear wall building with boundary elements, experimentally tested under simulated seismic loading. This effort was aimed at demonstrating the discrepancies between the way engineers design buildings (as individual components) and the way these buildings actually behave as an integrated system, comprised of these components. In addition, to evaluate the enhanced resilience of the new building system, the tested building was designed to have the same lateral resistance as previously tested building with traditional RM shear walls, thus facilitating direct comparison. The experimental results yielded two valuable findings: 1) it clearly demonstrated the overall performance enhancements of the new building system in addition to its reduced reinforcement cost; and 2) it highlighted the drawbacks of the building acting as a system compared to a simple summation of its individual components. In this respect, although the slab diaphragm-wall coupling enhanced the building lateral capacity, this enhancement also meant that other unpredictable and undesirable failure modes could become the weaker links, and therefore dominate the performance of the building system. Presentation of these findings has attracted much attention of codes and standards committees (CSA S304 and TMS 402/ACI 530/ASCE 5) in Canada and the USA, as it resulted in a paradigm shift on how the next-generation of building codes (NBCC and ASCE-7) should be developed to address system-levels performance aspects. Chapter 4 introduced an innovative system-level risk assessment methodology by integrating the simulation and experimental test results of Chapters 2 and 3. In this respect, the experimentally validated simulations were used to generate new system-level fragility curves that provide a realistic assessment of the overall building risk under different levels of seismic hazard. Although, within the scope of this dissertation, the methodology has been applied only on buildings constructed with RM walls with boundary elements, the developed new methodology is expected to be adopted by stakeholders of other new and existing building systems and to be further implemented in standards based on the current FEMA P58 risk quantification approaches. Finally, and in order to translate the dissertation findings into tools that can be readily used by stakeholders to design more resilient buildings in the face of extreme events, simplified backbone and hysteretic models were developed in Chapter 5 to simulate the nonlinear response of RM shear wall buildings with different configurations. These models can be adapted to perform the nonlinear static and dynamic procedures that are specified in the ASCE-41 standards for both existing and new building systems. The research in this chapter is expected to have a major positive impact, not only in terms of providing more realistic model parameters for exiting building systems, but also through the introduction of analytical models for new more resilient building systems to be directly implemented in future editions of the ASCE-41. This dissertation presents a cohesive body of work that is expected to influence a real change in terms of how we think about, design, and construct buildings as complex systems comprised of individual components. The dissertation’s overarching hypothesis is that previous disasters have not only exposed the vulnerability of traditional building systems, but have also demonstrated the failure of the current component-by-component design approaches to produce resilient building systems and safer communities under extreme events. / Dissertation / Doctor of Philosophy (PhD)

No description available.

No / New representations and efficient calculation methods are derived for the problem of propagation from an infinite regularly spaced array of coherent line sources above a homogeneous impedance plane, and for the Green's function for sound propagation in the canyon formed by two infinitely high, parallel rigid or sound soft walls and an impedance ground surface. The infinite sum of source contributions is replaced by a finite sum and the remainder is expressed as a Laplace-type integral. A pole subtraction technique is used to remove poles in the integrand which lie near the path of integration, obtaining a smooth integrand, more suitable for numerical integration, and a specific numerical integration method is proposed. Numerical experiments show highly accurate results across the frequency spectrum for a range of ground surface types. It is expected that the methods proposed will prove useful in boundary element modeling of noise propagation in canyon streets and in ducts, and for problems of scattering by periodic surfaces.

La modélisation des problèmes d'interactions sol-structure et fluide-structure couvre plusieurs domaines de recherche très actifs qui traitent une multitude d'aspects tels que la géométrie non bornée du sol et dans certains cas du fluide stocké, les effets dissipatifs visqueux et radiatifs, l'application du chargement sismique, le choix des variables de base, les propriétés algébriques des systèmes d'équations résultant du couplage,... etc. Dans le présent travail, différents modèles numériques de couplage sol-structure et fluide-structure ont été examinés. Les limites de troncature géométrique du sol et du fluide on été traitées avec des éléments infinis dont les performances ont été comparées à celles des conditions de radiations. Le problème de vibrations libres couplées des systèmes fluide-structure a été résolu en introduisant de nouvelles techniques de symétrisation efficaces. De plus, une nouvelle formulation symétrique en éléments de frontière a été proposée. Cette formulation permet de produire une matrice symétrique définie positive et aboutit ainsi à un système algébrique similaire à celui qui découle de la discrétisation en éléments finis. La matrice bâtie dite "raideur équivalente" peut facilement être assemblée ou couplée avec les matrices de la formulation en éléments finis. Toutes les applications qui ont servi soit à comparer des modèles soit à valider les programmes développés, ont été effectué es dans le cas des barrages poids en béton. Ce cas constitue un problème de couplage fluide-sol-structure typique / Modeling fluid-structure and soil-structure interaction problems covers several research fields dealing with multiple aspects such as : unbounded geometry of soil media and in some cases of retained fluid, viscous and radiation dissipative effects, application of seismic loading, choice of the basic variables, algebraic properties of the resulting coupled system, ... etc. In this work, different numerical models of soil-structure and fluid-structure coupling have been studied. The truncation boundaries of the soil and of the fluid domains have been considered by using infinite elements whose performances were compared to those of radiation conditions. The problem of the free coupled vibrations of the fluid-structure systems has been solved by introducing efficient symmetrization techniques. In addition, a new symmetric boundary element formulation is proposed. It allows to produce a positive definite and symmetric matrix and therefore to conduct to an algebraic system similar to the one obtained from finite element discretization. The produced matrix called "equivalent stiffness matrix" can easily be assembled or coupled to finite element matrices. All of the applications which have been done in order to compare models or to validate the developed programs were built in the case of concrete gravity dams, which constitute typical coupled fluid- soil-structure problems

O objetivo do presente trabalho é o desenvolvimento de formulações e de códigos computacionais que possibilitem a análise bidimensional estática de meios contínuos anisotrópicos viscoplásticos reforçados ou não por fibras. Especificamente, as análises numéricas envolvem aplicações dos métodos dos elementos de contorno (MEC) e dos elementos finitos (MEF), comparando-se os resultados obtidos com respostas analíticas e experimentais, disponíveis na literatura, buscando-se assim, subsídios teóricos que permitam o entendimento de problemas mais gerais envolvendo meios anisotrópicos. Para tanto são empregados elementos finitos triangulares com aproximações cúbica e quadrática para os deslocamentos na modelagem dos domínios. Na consideração do reforço com fibras, elementos finitos de barras simples são empregados. A formulação desenvolvida proporciona também a consideração de distribuição randômica das fibras imersas no meio sem qualquer aumento dos graus de liberdade do problema analisado, diferindo-se assim, das formulações conhecidas até o momento. Com o MEC, a análise de plasticidade e viscoplasticidade em meios com anisotropia geral é feita de maneira original no trabalho, destacando-se a consideração de lei de fluxo plástico não-associativa e o tratamento de viscosidade apenas com integrais de contorno, sem a utilização de aproximações de domínio. Uma quantidade significativa de exemplos é apresentada, possibilitando a verificação da eficiência das formulações e dos códigos desenvolvidos / The objective of the present work is the development of formulations and computational codes that enable the static bidimensional analysis of the viscoplastic anisotropic medias reinforced, or not, by fibers. Specifically, the numerical analysis involve applications of the boundary elements method (BEM) and finite elements (FEM), comparing the results obtained with analytical and experimental solutions available in the literature, allowing the understanding of general problems in anisotropic media. Two-dimensional finite elements with cubic and quadrate approximations for the displacements are used to model domains. Reinforcements are modeled by truss finite elements. The developed formulation provides the consideration of random distribution of the fibers, without any additional degree of freedom of the problem. With the BEM, the plasticity and viscoplasticity analysis in general anisotropic medias is originally developed in the present work, emphasizing the consideration of non-associative plastic flow and the treatment of viscosity just with boundary integrals, without domain approximation. Various examples are shown in order to verify the efficiency of the proposed formulation and developed computational codes