Titanium based alloys reinforced uniaxially with silicon carbide fibres (Ti/SiC) are advanced and innovative materials for aerospace vehicles. To avoid potential problems, these new materials should be extensively tested and analyzed before application. This research focuses on experimental fracture toughness study on 0.5 mm thick Ti/SiC composite materials for aerospace applications. The fracture toughness tests are mainly based on BS 7448 with some modifications for transversely isotropic behaviour of the composite materials. By loading on specimens in the direction perpendicular to the fibre axis, three critical values of fracture toughness parameters characterizing fracture resistance of material, plane strain fracture toughness [Plane strain fracture toughness }, critical crack tip opening displacement [Critical crack tip opening displacement ] and critical J-integral [Critical at the onset of brittle crack extension or pop-in when Δa is less than 0.2 mm. ]are measured for two kinds of titanium alloy specimens and three kinds of Ti/SiC composites specimens. The values of [Provisional value of Plane strain fracture toughness ] obtained from the fracture toughness tests are not valid [Plane strain fracture toughness ] for these materials, since the thickness of specimens is insufficient to satisfy the minimum thickness criterion; however, the results could be used as particular critical fracture toughness parameter for 0.5 mm thick structures of the materials. The valid values of [Critical J at the onset of brittle crack extension or pop-in when Δa is less than 0.2 mm. ] and [Critical crack tip opening displacement ] could be used as fracture toughness parameters for all thickness of structures of the materials. The results also show that: fracture toughness of the titanium alloys decreases dramatically after being unidirectional reinforced with SiC fibre, which is mainly triggered by poor fibre/matrix bonding condition. Moreover, Ti-Al3-V2.5 reinforced with 25% volume fraction SiC fibre performs better than the other two composites in fracture resistance.

Nowadays, there is a growing demand for high frequency-bandwidth mm-wave (30-300 GHz) electronic wireless transceiver systems to support applications such as high data-rate wireless communication and high resolution imaging. Such mm-wave systems are becoming more feasible due to the extreme transistor downscaling in silicon-based integrated circuits, which enabled densely-integrated high-speed elec- tronics operating up to more than 100 GHz with low fabrication cost. To further enhance system integrability, it is required to implement all wireless system compo- nents on the chip. Presently, the last major barrier to true System-on-Chip (SoC) realization is the antenna implementation on the silicon chip. Although at mm-wave frequencies the antenna size becomes small enough to fit on chip, the antenna performance is greatly deteriorated due the high conductivity and high relative permittivity of the silicon substrate. The negative e↵ects of the silicon substrate could be avoided by using a metallic reflecting surface on top of silicon, which e↵ectively isolates the antenna from the silicon. However, this approach has the shortcoming of having to implement the antenna on the usually very thin silicon oxide layer of a typical CMOS fabrication process (10’s of μm). This forces the antenna to be in a very close proximity (less than one hundredth of a wavelength) to the reflecting surface. In this regime, the use of conventional metallic reflecting surface for silicon shielding has severe e↵ects on the antenna performance as it tends to reduce the antenna radiation resistance resulting in most of the energy being absorbed rather than radiated. In this work, the use of specially patterned reflecting surfaces for improving on- chip antenna performance is investigated. By using a periodic metallic surface on top of a grounded substrate, the structure can mimic the behavior of a perfect mag- netic conductor, hence called Artificial Magnetic Conductor (AMC) surface. Unlike conventional ground plane reflecting surfaces, AMC surfaces generally enhance the radiation and impedance characteristics of close-by antennas. Based on this property, a ring-based AMC reflecting surface has been designed in the oxide layer for on-chip antennas operating at 94 GHz. Furthermore, a folded dipole antenna with its associ- ated planar feeding structures has been optimized and integrated with the developed ring-based AMC surface. The proposed design is then fabricated at KAUST clean- room facilities. Prototype characterization showed very promising results with good correlation to simulations, with the antenna exhibiting an impedance bandwidth of 10% (90-100 GHz) and peak gain of -1.4 dBi, which is the highest gain reported for on-chip antennas at this frequency band without the use of any external o↵-chip components or post-fabrication steps.

This work discusses a methodology developed for robust RF test structure design for SiGe HBTs operating at mm-wave frequencies.

Submitted by GLAUCO ALMEIDA (glaucoag@gmail.com) on 2016-03-18T14:17:37Z No. of bitstreams: 1 Glauco Garrido Almeida-TESE-REV.pdf: 3028760 bytes, checksum: f9d5fc9929fc4cee05187b360a597c04 (MD5) / Approved for entry into archive by Sandra Manzano de Almeida (smanzano@marilia.unesp.br) on 2016-03-18T17:11:17Z (GMT) No. of bitstreams: 1 almeida_gg_dr_ilha.pdf: 3028760 bytes, checksum: f9d5fc9929fc4cee05187b360a597c04 (MD5) / Made available in DSpace on 2016-03-18T17:11:17Z (GMT). No. of bitstreams: 1 almeida_gg_dr_ilha.pdf: 3028760 bytes, checksum: f9d5fc9929fc4cee05187b360a597c04 (MD5) Previous issue date: 2015-12-11 / Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES) / Trabalhos experimentais e teóricos desenvolvidos nos últimos anos evidenciaram a capacidade de alcoóis e polialcoóis em mudar características energéticas em proteínas. No entanto, o mecanismo responsável por esse efeito não está totalmente elucidado. Tomando como exemplo o dipeptídeo de alanina, foram realizadas simulações QM/MM em água, etanol e mistura 60-40 % em volume de água-etanol. A molécula de dipeptídeo foi descrita em nível de cálculo quântico MP2/aug-cc-pVDZ. Em solução, apenas confórmeros αR e PPII foram encontrados na população de equilíbrio. A diferença de energia livre em solução αR  PPII é determinada pelo balanço entre energia interna do soluto e energia de interação. Para o dipeptídeo de alanina, qualquer fator que aumente a energia de interação soluto-solvente favorece o aumento da população de αR. Por outro lado fatores que diminuam esse valor, como a adição de etanol, aumentam a população de PPII. Os resultados indicam solvatação preferencial para o sistema, evidenciado pela formação majoritária da primeira camada de solvatação por moléculas de água (na mistura), embora seja possível encontrar moléculas de etanol em pequenas quantidades ao redor do grupo carboxílico da extremidade N-terminal e, cadeias metílicas laterais. Todavia, o comportamento parece não afetar a diferença na estabilidade de equilíbrio conformacional. / Recent papers, both experimental and theoretical, have highlighted the capacity of alcohols and polyalcohol in modifying the energy landscape in proteins. However, the mechanism underlying this effect is not fully elucidated. Taking as a model-system the alanine dipeptide, QM/MM calculations were performed in water, ethanol and solution 60-40% (volume) water-ethanol. The dipeptide molecule was described by MP2/aug-cc-pVDZ level. In solution, only αR and PPII conformers were found in the conformational equilibrium population. The free energy difference in solution αR  PPII is determined by the interplay between internal energy and the interaction energy. It has been found that, for alanine dipeptide, any factor that increases the solute-solvent interaction energy also promotes an increasing on αR stability, moreover factors that decreases this value, such as the addition of ethanol molecules, increases the PPII stability. The results points to a preferential solvation behavior for the system, as evidenced by the composition of the first solvation shell in the mixture mainly populated by water molecules, although it is possible to find small concentration of ethanol molecules around the carboxyl group of the N-terminal end and around methylic side chains. However, this behavior does not seem to affect the differential conformational stability. / CAPES: 99999.014630/2013-03

Made available in DSpace on 2016-06-02T20:34:11Z (GMT). No. of bitstreams: 1 2275.pdf: 3782224 bytes, checksum: 7d2e45951c92f58bd422ef52a5aaddca (MD5) Previous issue date: 2009-02-17 / Universidade Federal de Sao Carlos / Computer simulation methods were used to characterize the structure and molecular properties of natural and synthetic biopolymers in aqueous solution. The polysaccharides chitin and chitosan, and aliphatic polypeptides were studied. The interest on the chitin and chitosan biopolymers is because of their biodegradability, biocompatibility and potential use as pharmaceutical and technological product. Molecular dynamics simulations have been used to characterize the structure and the solubility of the chitins and chitosans in aqueous solution. The simulated systems were composed by solvated chains, and nanoparticles composed by chains packed in a parallel and anti-parallel fashion, with different percentage and distribution of acetyl groups. The 100% acetylated chitin, whether isolated or in the form of α/β-chitin, adopt the 2-fold helix conformation with φ and ψ values similar to those on crystalline state. The ionic strength affects the kinetics, but not the conformational equilibrium. In solution, the intramolecular hydrogen bond HO3(n)···O5(n+1) responsible for the 2-fold helical motif is stabilized by hydrogen bonding to water molecules in a well-defined orientation. On the other hand, chitosan with small percentage and random distribution of acetil groups can adopt five distinct helical motifs and its conformational equilibrium is highly dependent on pH. The hydrogen bond pattern and solvation around the O3 atom of insoluble chitosan (basic pH) are nearly identical to those quantities in chitin. Chitin and chitosan nanoparticles with block distribution of acetyl groups favor the formation of intermolecular hydrogen bonds and hydrophobic interactions, resulting in more stable aggregates. The water mobility and orientation around polysaccharide chain (highly affected by electrostatic forces) is responsible for the aggregation and solubility of the chitin and chitosan biopolymers. Moreover, a sequential QM/MM methodology is used to study the α-helix stability of aliphatic polypeptides in water solution. The understanding of the folding process is one of the greatest challenges of biophysics, and the first step is the understanding of the formation and stabilization of the secondary structure of a polypeptide. The calculated heat of formation and free energy of solvation showed that the size of side chain is directly related to the α-helix stability. The results suggest that the helix-coil transition of a polypeptide is governed by the equilibrium between the energy used in the folding process and the energy released in the solvation process, showing the solvent effect on α-helix stabilization. The validation of the sequential QM/MM methodology showed that this method is suitable to study the helix-coil transition of polypeptides in solution. The methodology is therefore useful to study solvation effects on the properties of compounds with many conformational degrees of freedom. / Neste trabalho, métodos de simulação computacional foram usados para caracterizar a estrutura e propriedades moleculares de biopolímeros naturais e sintéticos em solução aquosa. Os polissacarídeos quitina e quitosana, e polipeptídeos alifáticos foram os biopolímeros estudados. O interesse nos biopolímeros quitina e quitosana é devido à suas biodegradabilidade, biocompatibilidade e potencial uso como produto farmacêutico ou tecnológico. No presente trabalho, simulações por Dinâmica Molecular foram utilizadas para caracterizar a estrutura e a solubilidade de quitinas e quitosanas em solução aquosa. Os sistemas modelados eram compostos por cadeias solvatadas e nanopartículas formadas por cadeias empacotadas paralelamente e de forma antiparalela, com diferentes percentagens e distribuição de grupos acetil. A quitina 100% acetilada, tanto na forma isolada ou na forma de α/β-quitina adota a conformação de hélice 2, com valores de φ e ψ similares aos da sua estrutura cristalina. A força iônica afeta a cinética, mas não o equilíbrio conformacional. Em solução, as ligações de hidrogênio intramolecular HO3(n)···O5(n+1), responsável por estabilizar o motivo helicoidal hélice 2, são estabilizadas por ligações de hidrogênio com moléculas de água em orientações bem definidas. Por outro lado, a quitosana com pequena percentagem e distribuição randômica de grupos acetil pode adotar cinco motivos estruturais e seu equilíbrio conformacional é altamente dependente do pH. O padrão de ligação de hidrogênio e a solvatação ao redor do átomo O3 da quitina insolúvel (pH básico) é quase idêntico ao observado para a quitina. As nanopartículas de quitina e quitosana com distribuição em blocos de grupos acetil favorece a formação de ligações de hidrogênio intermolecular e interações hidrofóbicas, resultando em agregados mais estáveis. A mobilidade e a orientação das moléculas de água ao redor da cadeia de polissacarídeo (altamente afetada por forças eletrostáticas) é responsável pela agregação e solubilidade dos biopolímeros quitina e quitosana. Além disso, a metodologia QM/MM sequencial foi utilizada para estudar a estabilidade da α-hélice de polipeptídeos alifáticos em solução. Sabe-se que o entendimento do processo de enovelamento é um dos grandes desafios da biofísica, e o primeiro passo consiste em entender a formação e a estabilização da estrutura de polipeptídeos. Os valores de calor de formação e energia livre de solvatação mostraram que o tamanho da cadeia lateral é diretamente proporcional à estabilidade da α-hélice. Os resultados sugerem que o processo de enovelamento-desenovelamento de polipeptídeos é governado pelo equilíbrio entre a energia utilizada para enovelar o peptídeo e a energia liberada pelo processo de solvatação, mostrando o efeito do solvente na estabilização da α-hélice. A validação da metodologia QM/MM sequencial utilizada mostrou ser adequada para o estudo do processo de enovelamento desenovelamento de polipeptídeos em solução, e útil no estudo da estrutura eletrônica e do efeito do solvente em compostos que possuam elevado grau de liberdade conformacional.

Made available in DSpace on 2014-06-12T15:50:50Z (GMT). No. of bitstreams: 1 license.txt: 1748 bytes, checksum: 8a4605be74aa9ea9d79846c1fba20a33 (MD5) Previous issue date: 2008 / O grande diferencial dos LMS (Learning Management System) mais sofisticados está no fato deles disponibilizarem uma maior aproximação e facilidade de entendimento do conteúdo gerenciado e disponibilizado ao aluno ou aprendiz. Para isso, o uso de recursos multimídia como áudio, imagens, vídeos e objetos de realidade virtual, inseridos no conteúdo oferecido, permite um aprendizado mais agradável e mais atrativo para o aluno que usa o LMS com estes recursos. Devido à grande dificuldade de se manipular, inserir e recuperar tais objetos multimídia e de realidade virtual nos conteúdos gerenciados por LMS, sentiu-se a necessidade de especificar e implementar um servidor de dados que facilitasse tal manipulação integrada a um LMS O objetivo principal deste trabalho é desenvolver um Servidor de Dados para manipulação e gerenciamento de objetos multimídia e objetos de realidade virtual em um LMS, tendo sido escolhido como estudo de caso o LMS AMADEUS-MM. O referido servidor tem como finalidade principal o gerenciamento de conteúdo multimídia em ambientes virtuais de ensino, com particular eficiência no armazenamento e transferência de dados multimídia (imagens, áudios, vídeos) e mundos de realidade virtual. O Servidor de Dados Multimídia provê uma estrutura de dados para o gerenciamento do conteúdo multimídia em um ambiente virtual de ensino, além de fornecer componentes (armazenamento, negócio e interface) para dar suporte à gestão de componentes multimídia (imagens, áudio e vídeo) e mundos de realidade virtual (VRML e X3D). Sua arquitetura permite a integração com plataformas de ensino a distância via troca de mensagens XML de forma que a plataforma de ensino possa usufruir de maneira transparente os serviços que o Servidor de Dados Multimídia provê. Para isso, foi feito um estudo sobre cada tipo de objeto multimídia e de realidade virtual e de como são armazenados tais objetos em banco de dados; foi elaborado e implementado um conjunto de protótipos, um para cada forma de armazenamento estudada, e foi feito um conjunto de avaliações baseadas em engenharia de desempenho de forma a definir a melhor abordagem para armazenar e recuperar estes objetos multimídia para ambientes de ensino a distância. Além disso, foi proposto um modelo de integração entre o servidor e plataformas de ensino a distância de forma que tais 4 plataformas possam usufruir dos serviços oferecidos de forma transparente. O servidor proposto nessa pesquisa faz parte de um projeto de pesquisa intitulado Projeto Amadeus_MM1, cujo objetivo é desenvolver um ambiente virtual para ensino baseado em uma proposta pedagógica centrada em processos de medição e avaliação, coordenado pelos professores Fernando Fonseca e Alex Sandro Gomes (Cin/UFPE).

Class of 2012 Abstract / Specific Aims: Autologous stem cell transplant (ASCT) is the current gold standard following induction therapy to improve survival of multiple myeloma (MM). Lenalidomide (LEN) is used for treatment of MM before ASCT, but exposure may impair autologous peripheral blood stem cell (PBSC) mobilization. Chemomobilization with cyclophosphamide (CTX) has not been evaluated in this setting. CTX + filgrastim was investigated to determine if LEN-associated mobilization impairment can be abrogated. Methods: 36 pts (group A=12 pts who received ≥2 cycles of LEN and group B=24 pts without LEN) were analyzed retrospectively. Baseline characteristics were matched (p>0.05 for all variables). All pts received CTX (median group B, 1.5g/m2; median group A, 3gm/m2(p=0.18)) and filgrastim 10µg/kg/day. Primary outcomes include number of CD34+ cells collected and number of leukapheresis sessions. Secondary outcomes include failure to collect CD34+ cells and total CD34+ cells collected after second leukapheresis. Main Results: Total median number of CD34+ cells collected in group B=9.15x106/kg CD34+ cells and group A=7.43x106/kg CD34+ cells (p=0.159). Median number of apheresis sessions in group B=2 and group A=3 (p=0.42). Two of 12 pts with antecedent LEN usage failed to collect while no patient without previous LEN exposure failed to collect (p=0.105). Total number of CD34+ cells collected after 2 apheresis sessions for group B=8.13x106/kg CD34+ cells and group A=3.34x106/kg CD34+ cells (p=0.06). Conclusions: Chemomobilization with CTX + filgrastim yields robust PBSC collections irrespective of antecedent lenalidomide. There was a trend towards lesser PBSC collection in LEN-treated pts.

Ce travail porte sur le développement de nouvelles méthodes de caractérisation in-situ basées sur les spectroscopies électroniques XPS et MM-EPES associées à des calculs théoriques obtenus grâce à des simulations Monte-Carlo afin de réaliser des études quantitatives fines et précises. La première partie de ce travail, a été consacrée à l’analyse quantitative de signaux XPS et MM-EPES. Pour cela, dans un premier temps, la fonction de correction de l’analyseur hémisphérique (HSA) qui est une combinaison de l’aire d’analyse (A) et de la transmission (T) a été déterminée en utilisant une nouvelle méthode basée sur des images élastiques. Pour la première fois, la dépendance de A en énergie cinétique des électrons a été mise en évidence. Avec l’utilisation de cette nouvelle fonction, une méthode de caractérisation in situ basée sur la modélisation théorique des signaux XPS et MM-EPES a été développée. Cette méthode a permis d’étudier le dépôt d’un film d’or sur un substrat de silicium oxydé et a montré une grande précision dans le cas de très faibles quantités de matière déposée (< 2 nm) alors que les techniques microscopiques classiques se sont révélées inefficaces. La deuxième partie a porté sur le développement d’une nouvelle technique d’imagerie in-situ appelé MM-EPEM qui consiste à scanner la surface par un faisceau d’électrons et de collecter les électrons rétrodiffusés élastiquement afin de construire une image en intensité de la surface. Les étapes d’obtention des images MM-EPEM et les procédures d’exploitation de ces dernières ont été décrites et optimisées. Ensuite, cette technique a été utilisée pour l’étude de l’état de surface de dépôts d’or sur différents substrats. Cette technique s’avère être non destructive et très sensible aux éléments présents à la surface. Et elle permet de déterminer la cartographie chimique et la nano-organisation de la surface. / This thesis focuses on the development of new in-situ methods of characterization based on the electron spectroscopies (XPS and EPES) coupled with theoretical calculations obtained through Monte-Carlo simulations in order to perform very precise quantitative studies. The first part of this thesis was devoted to quantitative studies of XPS and MM-EPES measurements. Firstly, the correction function of a hemispherical analyzer (HSA) which is a combination of the analysis area (A) and the transmission (T) was determined using a new method based on the elastic images. For the first time, the dependence of A on the kinetic energy of electrons was highlighted. Using this function, an in-situ method based on the combination of XPS and MM-EPES modeling was setting up. This method was used to determine the organization of gold film deposed on oxidized silicon substrate. Measurements show that this method is able to determine surface parameters when the microscopy techniques do not give any information in the case of a small quantity of gold deposit (less than 2 nm). The second part of this work was directed towards developing a new generation of microscopy called MM-EPEM which is based on the detection of elastic electrons. The stages required to obtain these images are well described and optimized here. The MM-EPEM images processing was used to study gold growth on different substrates. This technique is a non-destructive method and allows the operator to construct chemical tomography and to determine the nano-organization of the surface.

Molecular recognition is essential to all biological interactions and processes. Knowledge of the structural basis of recognition offers a powerful mechanism for understanding, predicting and controlling the behaviour of biological systems. In this thesis, we present, firstly a computational and crystallographic analysis of molecular recognition in protein-ligand systems; and secondly, progress towards the synthesis of a fluorescent probe for calcium ion recognition. Class I phosphoinositide 3-kinases (PI3Ks), in particular PI3Kγ, have long been considered promising drug targets for the treatment of inflammatory and autoimmune disorders. As a step towards improved understanding of PI3K binding preferences, we examine the basis on which PI3Kγ distinguishes γ-selective inhibitors AS-605240 and AS-604850, with a ~30-fold preference for the former. Interestingly, despite the chemical similarity of the two ligands, the X-ray structures for their PI3Kγ complexes exhibit the molecules in different conformers, s-cis for AS-604850 and s-trans for AS-605240. Here, we re-examine the PI3Kγ/AS-605240 crystallographic data and find that not only is a s-cis conformation possible but in fact it has a much higher occupancy (87%) than the originally modelled s-trans isomer (13%). Subsequently, to account for the isomeric complexities presented by the ligands, we perform 140 ns MD simulations of the four PI3Kγ complexes in explicit solvent: this reveals similar conformational flexibility at the active site for all systems. Yet, the conformations sampled by the s-cis isomers are more consistent with the conformations reported by the X-ray crystal structures. Subsequent energetic analysis was performed incorporating ensemble-averaging and desolvation effects via the Poisson-Boltzmann continuum solvent model. For both inhibitors the s-cis isomers are predicted to be the most favourable conformations. Additionally, the results indicate a preference for AS-605240, as observed experimentally. The molecular basis for this preference is discussed, together with a comparison of molecular mechanical and quantum chemical treatments of the key ligand-Val882 interaction. This study provides structural, dynamical and energetic insights into the subtle basis of molecular recognition by PI3Kγ.Fluorescent probes have evolved into an extremely useful tool for the detection of calcium in biological systems. Benzothiazole derivatives BTC, and its iminocoumarin analogue BTIC, are two low affinity calcium indicators featuring many desirable properties for cellular calcium measurement. In an effort to produce fluorophores that can be chemically conjugated with a screening protein, such as Green Fluorescent Protein (GFP), we aimed to derivatise BTC and BTIC. Two synthetic approaches towards the synthesis of these potential fluorescent probes are outlined.

Chloroperoxidase (CPO) is a potential biocatalyst for use in asymmetric synthesis. The mechanisms of CPO catalysis are therefore of interest. The halogenation reaction, one of several chemical reactions that CPO catalyzes, is not fully understood and is the subject of this dissertation. The mechanism by which CPO catalyzes halogenation is disputed. It has been postulated that halogenation of substrates occurs at the active site. Alternatively, it has been proposed that hypochlorous acid, produced at the active site via oxidation of chloride, is released prior to reaction, so that halogenation occurs in solution. The free-solution mechanism is supported by the observation that halogenation of most substrates often occurs non-stereospecifically. On the other hand, the enzyme-bound mechanism is supported by the observation that some large substrates undergo halogenation stereospecifically. The major purpose of this research is to compare chlorination of the substrate beta-cyclopentanedione in the two environments. One study was of the reaction with limited hydration because such a level of hydration is typical of the active site. For this work, a purely quantum mechanical approach was used. To model the aqueous environment, the limited hydration environment approach is not appropriate. Instead, reaction precursor conformations were obtained from a solvated molecular dynamics simulation, and reaction of potentially reactive molecular encounters was modeled with a hybrid quantum mechanical/molecular mechanical approach. Extensive work developing parameters for small molecules was pre-requisite for the molecular dynamics simulation. It is observed that a limited and optimized (active-site-like) hydration environment leads to a lower energetic barrier than the fully solvated model representative of the aqueous environment at room temperature, suggesting that the stable water network near the active site is likely to facilitate the chlorination mechanism. The influence of the solvent environment on the reaction barrier is critical. It is observed that stabilization of the catalytic water by other solvent molecules lowers the barrier for keto-enol tautomerization. Placement of water molecules is more important than the number of water molecules in such studies. The fully-solvated model demonstrates that reaction proceeds when the instantaneous dynamical water environment is close to optimal for stabilizing the transition state.