A series of computational studies were carried out on Group 14 (C, Si and Ge) elements in organometallic and biological compounds. Theoretical studies on classical and H-bridged A3H3+ (A=C, Si and Ge) as p ligands with different organometallic fragments at B3LYP and B3P86 level reveal a reverse charge transfer from ligand to metal in Si and Ge complexes whereas in C complexes there is a small charge transfer from metal to ligand. The H-bridged complexes are more stable than the complexes based on Si3H3+ and Ge3H3+ ligands with terminal hydrogens. The stability of the bridged systems increases from Si to Ge. Corrective scale factors for computed harmonic CºO vibrational frequencies for 31 organometallic complexes have been determined at the HF and B3LYP levels. The scaled B3LYP frequencies exhibit a greater reliability than do HF frequencies. Experimental data have shown that Si/Ge-substituted decapeptides are advantageous over their C analog in vitro and in vivo studies in modern hormone therapy. A computational investigation was carried out on the synthesized decapeptides focusing on position 5 containing Si and Ge. The results have shown that there are some differences in C, Si and Ge-containing analogs. However, further investigations are needed to elucidate the observed advantages of Si/Ge over C analogs.

In this thesis, we investigate the regularity and approximation of a hyperbolic-elliptic coupled problem. In particular, we consider the Poisson and the transport equation where both are assigned nonhomogeneous Dirichlet boundary conditions. The coupling of the two problems is executed as follows. The right hand side function of the Poisson equation is the solution ρ of the transport equation whereas the gradient field E = −∇u, with u being solution of the Poisson problem, is the convective field for the transport equation. The analysis is done throughout on a nonconvex, not simply connected domain that is supposed to be homeomorph to an annular domain. In the first part of this thesis, we will focus on the existence and uniqueness of a classical solution to this highly nonlinear problem using the framework of Hölder continuous functions. Herein, we distinguish between a time dependent and time independent formulation. In both cases, we investigate the streamline functions defined by the convective field E. These are used in the time dependent case to derive an operator equation whose fixed point is the streamline function to the gradient of the classical solution u. In the time independent setting, we formulate explicitly the solution operators L for the Poisson and T for the transport equation and show with a fixed point argument the existence and uniqueness of a classical solution (u,ρ). The second part of this thesis deals with the approximation of the coupled problem in Sobolev spaces. First, we show that the nonlinear transport equation can be formulated equivalently as variational inequality and analyse its Galerkin finite element discretization. Due to the nonlinearity of the coupled problem, it is necessary to use iterative solvers. We will introduce the staggered algorithm which is an iterative method solving alternating the Poisson and transport equation until convergence is obtained. Assuming that LοT is a contraction in the Sobolev space H1(Ω), we will investigate the convergence of the discrete staggered algorithm and obtain an error estimate. Subsequently, we present numerical results in two and three dimensions. Beside the staggered algorithm, we will introduce other iterative solvers that are based on linearizing the coupled problem by Newton’s method. We illustrate that all iterative solvers converge satisfactorily to the solution (u, ρ).

[pt] Este trabalho apresenta a previsão do desempenho de três acessórios de união (manilha de união, elo Kenter e elo Multifuncional) utilizados em sistemas de ancoragem de unidades offshore, sob carregamentos monotônicos e cíclicos. Cinqüenta e sete modelos foram analisados pelo método de Elementos Finitos utilizando o software Ansys 10. Inicialmente, com o objetivo de quantificar a influência do contato e mensurar a área onde este ocorre, três modelos com contatos entre manilha de união e elos foram analisados com variações no diâmetro (76, 95 e 120 mm) e mantendo-se constante as propriedades mecânicas do material e a carga aplicada. Em seqüência, cinqüenta e quatro outros modelos foram elaborados sem condições de contato, isto é, com as cargas aplicadas diretamente nos componentes de estudo, que sofreram variações de diâmetros (76, 95 e 120 mm), de propriedades mecânicas (limites de escoamento e resistência mecânica) e de carregamento (proof load e minimum break load). Comparativamente, as manilhas de união apresentaram os menores níveis de tensões e as melhores distribuições de tensões dentre os três componentes para todos os casos analisados. Dos cinqüenta e quatro modelos citados acima, três foram selecionados para análise da vida em fadiga com o software FE-Fatigue. Estes representavam um acessório de união de cada tipo com o diâmetro considerado crítico (120 mm) e sem variações nas propriedades mecânicas do material. Os resultados mostraram que a geometria do componente é determinante para os valores das tensões e da vida-fadiga. A manilha apresentou os melhores resultados de resistência e de vida-fadiga, que para o diâmetro e material escolhidos, foi cerca de três vezes maior do que aquela relativa aos elos Kenter e Multifuncional. / [en] This work represents an approach to predict the performance of three joining accessories (shackle, Kenter link and Multifunctional link) for offshore mooring systems under monotonic and cyclic loading. Fifty seven models were analyzed by the Finite Element method using the software Ansys 10. Initially, in order to quantify the influence of the contact conditions and to measure the area where it occurs, three models presenting contacts between the joining shackle and chain links were analyzed varying the diameter (76, 95, 120 mm) and maintaining constant the material’s mechanical properties as well as the applied loads. In sequence, fifty four other models were created without contact conditions, which means that the loads were applied directly on the components in question, with variations in link diameter (76, 95 and 120 mm), in mechanical properties (yield stress and ultimate strength) and in load conditions (proof and minimum break loads). Comparing the joining shackles with the other accessories, the shackles present the lowest stress levels and the best stress distributions with regard to all the cases studied. Three of the fifty four models cited above were selected for predicting their fatigue life making use of the FE-Fatigue software. These represented one of each joining accessory with a diameter considered critical (120 mm), keeping constant the mechanical properties of the material. The results showed that the influence of the component geometry is determinant for the stress values developed during the loading tests as well as its fatigue life. The shackle presented the best results in terms of strength and fatigue life, which was about three times greater than that for the Kenter and Multifunctional links.

A thesis submitted for the degree of Doctor of Philosophy in the Faculty of Science at the University of the Witwatersrand. / The present thesis is divided into three parts. The study described in Part I arose out of a request by the Chamber of Mines Mining Research Laboratory to the National Institute for Metallurgy to undertake a preliminary study of whether it would be feasible, in Witwatersrand conglomerates, to carry out rapid delimitation of areas rich in gold and/or uranium at the rock face, a procedure which would permit areas of rich ore to be removed selectively by means of the "rock-cutter". The approach adopted in this study was essentially geochemical, while conventional mineralogical techniques (macro-auto radiographs , thin section and polished section analyses) provided a control. The samples were drawn from the Vaal Reef at Hartebeestfontein and Zandpan and from the Ventersdorp Contact Reef at Venterspost, and were analysed quantitatively for gold, silver, uranium, pyrite, muscovite, pyrophyllite, chlorite, quartz, iron, potassium, nickel, titanium, zirconium and chromium. The intensity of the interrelationships between the elements and minerals analysed for was examined statistically by means of correlation covariance and factor analysis programmes written for an IBM 360/50 digital computer. A sympathetic relationship -- defined as significant positive correlation (with a correlation coefficient r> 0. 7) -- was found to exist between gold and uranium in both the Vaal Reef and Ventersdorp Contact Reef samples. These findings suggest that gold and uranium can be removed Simultaneously by means of the rock-cutter, and that radioactivity can be used as an indicator for on-site delimitation of areas rich in gold. In the course of the study described in Part I, it became evident that little detailed mineralogical work had ever been done on the phyllosilicates occurring in the Witwatersrand System. Accordingly, certain phyllosilicates from Witwatersrand conglomerate bands and other sources were examined in detail, this study being described in Part II of the present thesis. This study called for detailed chemical, optical, X-ray crystallographic, infra-red, differential thermal and thermogravimetric analyses, the results of which are presented. The findings were examined in the light of variolls classification schemes that have bep proposed for the phyllosilicates. This investigation revealed the need for a universally acceptable system of classification for the phyllosilicates, which should preferably be drawn up under the auspices of the International Mineralogical Association to avoid the confusion that exists at present. Part III of the present thesis is devoted to a discussion and description of various analytical techniques that had to be modified or developed to meet th8 requirements of the studies described in Parts I and II. The techniques described include: (1) An X-ray diffraction method which was developed for the quantitative analysis of pyrite, muscovite, pyrophyllite, chlorite and quartz in crushed ore from Witwatersrand conglomerates. This method makes use of novacul iie as an external standard and of binary mixtures as analytical standards, and had a mean absolute error of 1. 1 %. This method may be expanded to permit analysis of an n-component mixture. (2) A whole rock pressed powder technique of X-ray fluorescence analysis which was used for the quantitative determination of iron, potassium, nickel, titanium, zirconium and chromium. This method makes use of internstional rock standards as external standards. Six computer programmes used for the computation of the analytical results and in the statistical and crystallographic calculations are also presented in Part III. / AC2017

Thesis advisor: Gabor T. Marth / This thesis concerns itself with the development of methods for comparing genomes. Chapter 2 is a comparative genomics investigation of coding regions across multiple species. Regions of the genome coding for proteins show higher conservation than non-coding regions. Furthermore, we show that a portion of coding regions are conserved beyond the requirements of protein conservation, supporting functions such as microRNA binding and splicing enhancement, providing the non-coding functional impetus to conservation. In Chapter 3, we focus on the detection and characterization of a particular type of structural variation - mobile element insertions (MEIs). While there are many types of mobile elements in the human genome, three of these are active and cause most of the MEI variation observed in humans: ALU, L1 and SVA elements. We detect variation across 1000 Genomes Pilot populations caused by these elements, assemble ALU elements to single nucleotide resolution, and determine actively copying species of this element. We've developed a variety of algorithmic approaches to MEI detection, and present these. Chapter 4 outlines an approach to remedy reference bias via the incorporation of variation data into the reference. In particular, we construct a pan-genome reference, demonstrated concretely via resolving ALU regions, and develop new alignment software to align against this enriched reference structure. / Thesis (PhD) — Boston College, 2014. / Submitted to: Boston College. Graduate School of Arts and Sciences. / Discipline: Biology.

South Africa remains the 5th largest producer and 4th largest exporter of coal in the world. It is also the largest supplier of coal to the European Union. This fact is significant as the European Union has recently supported the environmental lobby that threatens the combined full scale use of coal in Europe and other first world countries. This promotes the development of clean coal technologies in order to counter the ever increasing number of environmental constraints threatening the export market. One critical development in clean coal technologies is coal beneficiation, which allows the reduction of ash and inert content. Permian coals from South Africa have characteristically high ash and inertinite contents and therefore require further beneficiation. The Witbank coalfield No. 4 seam is no exception. It can be described as being more inert and having a higher mineral content compared to the No. 2 seam in the same coalfield also mined for export purposes. With the increase in environmental legislation and the push towards “clean coal” this raises a concern in terms of the performance and marketability of export coal produced from the No. 4 seam. This seam will in the future be economically significant and is still a great source for export steam coal. Due to the nature and composition of the No. 4 seam, coal beneficiation is essential to reduce the mineral and inert content to be in line with export quality specification levels. Washability characteristics of the No. 4 seam coal indicate that the No. 4 seam is difficult to beneficiate. Until recently the main clean-ability parameters evaluated in South African export coals as per customer specification included mainly heating value, moisture and ash reduction with little to no work being done on trace element concentration reduction. This paper focuses on the partitioning of the trace elements within the seam in relation to the organic and inorganic affinity of the trace elements and possible methods of trace element reduction by removal using coal beneficiation techniques. The techniques investigated include reduction by washing using dense medium beneficiation and flotation. In each evaluation the focus was on trace-element-tomineral and trace-element-to-organic matter relationship and hence setting the basis for liberation analysis to evaluate reducibility. By the evaluation of the coal mineralogy, petrography and trace element relationships, methods of optimum trace element reduction can be established. With the focus on marketing it was shown that carbon loss need not be sacrificed in the reduction of specific trace elements in the No. 4 seam and that the trace element distribution itself allows for beneficiation whilst maintaining acceptable yields. Processes and possible beneficiation techniques for optimum trace element reduction and marketability in the case of the No.4 seam are proposed.

Dans le domaine des structures en Béton Armé (BA) et plus spécifiquement, lors de la conception d'éléments non-flexibles tels que les corbeaux, les poutres bayonets et les poutres profondes, la Méthode Bielle-Tirant (MBT) présente des avantages par rapport aux algorithmes classiques de calcul de ferraillage basé sur l'analyse FE (par exemple Wood-Armor ou Capra-Maury).La Methode Bielle-Tirant reste une alternative adaptée pour la conception de structures en béton présentant un comportement élastique ou plastique dont le cadre d'application est bien défini dans les codes de conception des structures en béton comme les EuroCodes et les spécifications de conception des ponts AASHTO-LRFD.Néanmoins, cette méthode présente l'inconvénient majeur de nécessiter un investissement important en ressources humaines ou en capacité de calcul pour, respectivement, son application manuelle ou une approche automatique par optimisation de topologie.Le document propose une alternative légère, en termes d'itérations requises, à l'automatisation de la MBT, qui part de l'affirmation que les entretoises résultantes et les attaches d'un modèle ST approprié peuvent être distribuées selon la direction des contraintes principales, $sigma_{III}$ et $sigma_{I}$, obtenus à partir d'un planaire modèle aux EF / Within the field of Reinforced Concrete (RC) structures and more specifically, at the design of non-flexural elements such as corbels, nibs, and deep beams, the rational procedure of conception and justification referred as Strut-and-Tie Method (STM) has shown some advantages over classical algorithms of reinforcement computation based on FE analysis (eg. Wood-Armer or Capra-Maury).The STM remains a suitable alternative for the design of concrete structures presenting either elastic or plastic behaviour whose application framework is well defined in concrete structures’ design codes like the EuroCodes and the AASHTO-LRFD Bridge Design Specifications.Nevertheless, this method has the main inconvenient of requiring a high amount of resources investment in terms of highly experienced personal or in terms of computational capacity for, respectively, its manual application or an automatic approach through topology optimisation.The document proposes a light alternative, in terms of required iterations, to the automation of the STM, which starts from the statement that the resultant struts and ties of a suitable ST model can be distributed according to the direction of the principal stresses, $sigma_{III}$ and $sigma_{I}$ , obtained from a planar or a three-dimensional FE model

Este trabalho avaliou, utilizando o Método dos Elementos Finitos, o comportamento mecânico em seis ensaios, quatro de flexo compressão com variação apenas no comprimento da haste de fixação, um de flexão ântero-posterior e um de flexão lateral, em um modelo tridimensional de fixador externo construído com auxílio do computador. Para a validação desses ensaios os mesmos testes também foram realizados na máquina universal de ensaio e depois comparados com o método dos elementos finitos. A rigidez no ensaio de flexão lateral obtida no método dos elementos finitos apresentou um valor 106% maior do que o obtido na máquina universal de ensaio, possivelmente por ocorrência de afrouxamento entre as partes adjacentes elo fixador externo no ensaio mecânico, e no ensaio de flexo compressão (número 1) a rigidez obtida pelo método dos elementos finitos foi 7,39% menor elo que a obtida na máquina universal de ensaio. No ensaio número 4 (flexo-compressão) os deslocamentos obtidos, correspondentes a aplicação de uma carga de 15,4 N, utilizando tanto o método dos elementos finitos como a máquina universal ele ensaio, divergiram em 8,5%. Já no ensaio número 5 (flexão ântero-posterior) a divergência foi de 0,9%, para os deslocamentos correspondentes a aplicação de uma carga de 14,4 N. O Métodos dos Elementos Finitos é um eficiente método para prever comportamento mecânico de estruturas complexas. / This work evaluates the mechanical behavior of an external device on a CAD (Computer Aided Design) 3D model in six tests, four of them of flexion-compression with a single variation of the external device stick length, one of longitudinal flexion and one of lateral flexion. They all were carried out applying the Method of the Finite Elements (MFE). For the comparison with the MFE the same mechanical testes were made. The stiffness achieved in the MFE showed a value 106% greater than that of the mechanical test. The test number one of flexion-compression showed a value 7,39% smaller in the MFE than that of the mechanical test. In the test number four (flexion-compression) the corresponding displacement after the application of a 15,4 N working stress showed a difference of 8,5%. The variation of the number five test was of 0,9% for the displacement after the application of a 14,4N working stress. The MEF showed efficient to evaluate the behavior of complex mechanical structures.

Os problemas freqüentes de patologias ortopédicas e traumáticas da coluna vertebral envolvem a colocação de fixadores internos (parafusos longos, os quais são inseridos nos pedículos posteriores até os corpos vertebrais e conectados por fios nas hastes longitudinais podendo ser fixados em todas as posições pelas porcas). Estes fixadores foram simulados no computador através da construção de modelos geométricos dos mesmos, utilizando o software ANSYS 5.5, que consiste de várias ferramentas para análise do projeto baseado no método dos elementos finitos. Foi também utilizado um software para a modelagem das peças e do conjunto do fixador já existente chamado SOLID EDGE, e logo em seguida o mesmo foi transferido para o software ANSYS 5.5 e simulado. Esta comparação servirá como complemento para possíveis modificações das montagens, dimensões e aplicações, não necessitando de novos ensaios mecânicos na máquina universal de ensaios e sim realizando simulações computadorizadas / The frequent problems of orthopedic and traumatic pathologies of the spinal column that involves the placement of an internal fixator (long screws, which are inserted in the subsequent pedicle until the vertebral and connected by bodies for wires in the longitudinal stems could be fastened in all the positions by the screw). These fixators were simulate in the computer through the construction of geometric models of the same ones, using the software ANSYS 5.5, that consists of several tools for analysis of the project based on the method of the finite elements. It was also used a software for the modelling of the pieces and of the group of the fixador already called existent SOLID EDGE, and then the same was transferred to the software ANSYS 5.5 and simulated. This comparison will serve a complement for possible modifications of the assemblies, dimensions and applications, not needing new mechanical test in the universal machine test but accomplishing computerized simulations

Os elementos transponíveis (TEs) constituem grande parte do material genético de diversos eucariotos, alcançando entre 50-80% do genoma de gramíneas. Os projetos genoma proporcionaram um aumento das informações disponíveis sobre estes elementos, o que evidenciou sua importância e possibilitou o desenvolvimento de novas abordagens para seu estudo. O sistema Mutator (Mu) de milho é o mais ativo e mutagênico transposon de plantas. Além do elemento autônomo, MuDR, o sistema compreende ainda um conjunto de elementos bastante heterogêneo em sua seqüência e estrutura, chamados MuLEs, que podem conter até mesmo fragmentos de genes do hospedeiro. As seqüências de transposons mais abundantemente expressas no transcriptoma de cana-de-açúcar são relacionadas a MuDR e se agrupam em quatro clados (nomeados Classes I, II, II e IV), existentes antes da divergência entre Mono e Eudicotiledôneas. O trabalho apresentado aqui teve o objetivo de aprofundar o conhecimento sobre o sistema Mutator em cana-de-açúcar a partir da análise comparativa entre seqüências dessa planta e de arroz (cujo genoma está totalmente seqüenciado). Foi possível avaliar a abundância e diversidade do sistema Mu em gramíneas, ficando evidente uma amplificação de elementos clado-específica, tendo a Classe II sofrido uma explosão no número de cópias ao longo da evolução destas plantas. Análises estruturais revelaram que, enquanto as Classes I e II compreendem elementos com características de transposons, as Classes III e IV são, na verdade, transposases domesticadas. Foram completamente seqüenciados dois clones de BAC de cana-de-açúcar, um proveniente de cada parental do híbrido (Saccharum officinarum e Saccharum spontaneum), ambos contendo elementos da Classe III. Estes elementos foram caracterizados e a seqüência genômica de cana foi comparada com sua ortóloga em arroz, revelando um acúmulo de TEs nas regiões intergênicas. / Transposable elements (TEs) constitute great part of eukaryote genetic material, in grasses, they comprise between 50-80% of the genome. Genome projects have significantly increased the amount of information about these elements, revealing their importance and allowing the development of new approaches for their study. The Mutator system (Mu) of maize is the most active and mutagenic plant transposon. Beyond the autonomous element, MuDR, the system comprises a very heterogeneous, in sequence and structure, set of elements, called MuLEs, that can contain even host gene fragments. The most abundant transposon related sequences expressed in sugarcane transcriptoma are the MuDR-like. They group into four clades (called Classes I, II, III and IV) that exist prior to the Mono and Eudicot split. The aim of this work is to gain knowledge about the Mutator system in sugarcane through the comparative analysis against rice (whose genome is completely sequenced). The results described the abundance and diversity of the Mu system in grasses, evidencing a clado-specific amplification with a burst of Class II along the evolution of this plant group. Structural analyses showed that, while Classes I and II comprise elements with transposon characteristics, Classes III and IV are domesticated transposases. One BAC clone from each sugarcane parental genotype (Saccharum officinarum and Saccharum spontaneum) have been completely sequenced, both containing Class III elements. These elements have been characterized and the sugarcane genomic sequences were compared with their orthologues in rice. The comparative analyses showed an accumulation of TEs in the intergenic regions.