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Athabasca asphaltenes were characterized using small-angle X-ray scattering (SAXS) with synchrotron radiation. Two methods were used to separate asphaltenes from Athabasca bitumen. Conventional chemical separation by precipitation with n-pentane, and physical separation realized by passing bitumen through a zirconia membrane with a 20 nm average pore size. The Athabasca permeates and chemically separated samples were dispersed in 1-methylnaphtalene and n-dodecane, with temperature and asphaltene concentration ranges of 50-310 C and 1-8 wt. %, respectively. Two approaches were also taken in the analysis of the SAXS emissions. A model-independent approach provided radii of gyration and scattering coefficients. A model-dependent fit provided size distributions for asphaltenes aggregates assuming that they are dense and spherical. Physically and chemically separated asphaltenes showed significant differences in nominal size and structure, and their structural properties exhibited different temperature dependencies. The results challenge the merits of using chemically separated asphaltene properties as a basis for asphaltene property prediction in crude oil/bitumen.

X-Linked Retinoschisis (XLRS) is a currently incurable, progressive retinal degeneration that affects approximately 1:20,000 males. Sufferers have a loss of retinal structure and visual acuity, leading to blindness. The condition is caused by mutation of the RS1 gene encoding the retinal-specific protein retinoschisin. Retinoschisin is critical in maintaining the normal, ordered retinal architecture, with deletion in mice models leading to loss of both structure and visual processing, analogous to XLRS sufferers. However, re-introduction of retinoschisin using adeno-associated viral vectors leads to complete rescue in these models. Despite the importance of retinoschisin in maintaining retinal architecture, the mechanism by which it maintains this structure remains unknown. As a result, this study aimed to structurally characterise retinoschisin and XLRS-associated point mutants R141H and H207Q to gain insight into the mechanism of retinoschisin action. To this end, retinoschisin was expressed and purified from HEK 293-EBNA cells and the structure of both monomeric and octameric retinoschisin was investigated using Small-Angle X-Ray Scattering (SAXS) and Cryo-electron microscopy (Cryo-EM). Monomeric retinoschisin was found to adopt an elongated structure that allowed for the tight association of the subunits into a planer propeller structure. However, in solution conditions the octamer also stably self-assembled into a dimer of octamers, for which the structure was solved using cryo-EM. This allowed for construction of a quasi-atomic model, enabling mapping of XLRS-associated point mutations on the complex. Two major classes of mutation were identified, in the intra-octamer and inter-octamer interfaces, suggesting a mechanism of pathology for these mutants. Observation of clustered conservative mutations at the inter-octamer interface suggested the dimer of octamers may be physiologically relevant. Furthermore, comparison of the R141H mutant to the wild-type revealed an additional mutated site in the propeller tips. Here, R141H was suggested to induce a small conformational change and alter an interaction site. Another mutant, H207Q, however, induced a destabilization of the assembled retinoschisin molecule. In conclusion, we purified and structurally characterised human retinoschisin, identifying a new hexadecameric oligomer. The structure of this allowed for identification of distinct classes of mutations on the assembled molecule and a hypothesis of the mechanism of retinoschisin action in the retina.

Magnetic films have gained great attention for decades because of their broad industrial application. Their modern functionality more and more relies on their domain structure. Magnetic films usually form complex domain patterns with unique structures at different length scales due to the competition between short range attractive and long range repulsive interactions. The ensemble of domains is topologically disordered, although each of them possesses orientational spin order. Since simplifying complexity is the key step to understand and transform nature, finding new orders from the ostensible disordered structures would be a fascinating topic. Scattering techniques are well-known powerful tools to detect orders. Coherent soft xray magnetic resonant scattering becomes accessible with the development of synchrotron radiation facilities. We applied the technique to study the domain structure of CoPd/MnIr multilayer films with perpendicular magnetic anisotropy. By tuning incident photon energy to Co 2p&rarr3d transition edge we collected small angle magnetic scattering patterns by a charged coupled device in transmission geometry. Each pattern is an unique fingerprint of the corresponding illuminated domain structure. The patterns were analyzed by an angular correlation method. A variety of striking rotational orders were discovered. Their evolution with applied fields was investigated. The sustainabilities of the orders under the room temperature, exchange biased (EB) state, and non-EB state were compared, which suggests that certain orders can be well manipulated under the EB condition. By simulating magnetic resonant scattering from domain patterns obtained by a direct imaging method, we probed the range of emerging orders and finite size effect. Our study provides a novel approach to characterizing magnetic films and potentially can be extended to any system with a complex microstructure. / 2015-07-11

abstract: In disordered soft matter system, amorphous and crystalline components might be coexisted. The interaction between the two distinct structures and the correlation within the crystalline components are crucial to the macroscopic property of the such material. The spider dragline silk biopolymer, is one of such soft matter material that exhibits exceptional mechanical strength though its mass density is considerably small compare to structural metal. Through wide-angle X-ray scattering (WAXS), the research community learned that the silk fiber is mainly composed of amorphous backbone and $\beta$-sheet nano-crystals. However, the morphology of the crystalline system within the fiber is still not clear. Therefore, a combination of small-angle X-ray scattering experiments and stochastic simulation is designed here to reveal the nano-crystalline ordering in spider silk biopolymer. In addition, several density functional theory (DFT) calculations were performed to help understanding the interaction between amorphous backbone and the crystalline $\beta$-sheets. By taking advantage of the prior information obtained from WAXS, a rather crude nano-crystalline model was initialized for further numerical reconstruction. Using Markov-Chain stochastic method, a hundreds of nanometer size $\beta$-sheet distribution model was reconstructed from experimental SAXS data, including silk fiber sampled from \textit{Latrodectus hesperus}, \textit{Nephila clavipes}, \textit{Argiope aurantia} and \textit{Araneus gemmoides}. The reconstruction method was implemented using MATLAB and C++ programming language and can be extended to study a broad range of disordered material systems. / Dissertation/Thesis / Doctoral Dissertation Physics 2015

A radiação espalhada em radiodiagnóstico, como em mamografia, é usualmente considerada um problema, uma vez que degrada o contraste da imagem. No entanto, pesquisas recentes mostram que a distribuição angular de fótons espalhados (perfil de espalhamento) pode fornecer informações sobre as estruturas que compõem um tecido biológico, permitindo, a partir da análise desta, identificar a presença de anormalidades no tecido. A proposta deste trabalho foi desenvolver medidas do perfil de espalhamento a médio (WAXS) e baixo ângulo (SAXS) de tecidos mamários previamente classificados, como tecidos normais, alterações benignas ou malignas, usando um tubo de raios X e radiação Síncrotron e, posteriormente, identificar as estruturas moleculares e supramoleculares presentes nos tecidos estudados e verificar estatisticamente se as informações contidas conjuntamente nos perfis de espalhamento a médio e baixo ângulo permitem diferenciar tecidos normais de alterados. Este tipo de estudo é potencialmente importante na área da Saúde por estar associado ao desenvolvimento de novas técnicas radiológicas que permitiriam ampliar a capacidade de diagnóstico do câncer mamário. / Scattering radiation in diagnostic radiology, such as mammography, is usually considered a problem, since it degrades the image contrast. However, recent research shows that the angular distribution of scattered photons (scattering profile) can provide information on the structures that compose a biological tissue, allowing, from the analysis of this, identify the presence of abnormalities in the tissue. The purpose of this study was to develop measurements of scattering profile at wide angle x-ray scattering (WAXS) and small angle x-ray scattering (SAXS) from breast tissue previously classified as normal tissue, benign or malignant disease, using a x-ray tube and synchrotron radiation and, subsequently, identify molecular and supra-molecular structures present in these tissues studied and verify statistically, if the information contained in both scattering profiles at wide and small angle allow differentiate normal tissues of changed. This type of study is potentially important in the health area, since to be associated with the development of new radiological techniques that would allow to expand the ability of breast cancer diagnosis.

A radiação espalhada em radiodiagnóstico, como em mamografia, é usualmente considerada um problema, uma vez que degrada o contraste da imagem. No entanto, pesquisas recentes mostram que a distribuição angular de fótons espalhados (perfil de espalhamento) pode fornecer informações sobre as estruturas que compõem um tecido biológico, permitindo, a partir da análise desta, identificar a presença de anormalidades no tecido. Neste estudo, foram utilizadas as técnicas de espalhamento de raios X em médio (WAXS) e baixo (SAXS) ângulo para determinar o perfil de espalhamento de tecidos mamários previamente classificados como: tecidos normais (adiposo e fibroglandular), neoplasias benignas e malignas, usando um tubo de raios X e radiação síncrotron. Através das informações de cada perfil foi possível identificar algumas estruturas moleculares e supramoleculares presentes nos tecidos estudados. Além disso, foi construído um modelo de classificação baseado na análise de discriminante dos perfis de espalhamento, o qual permitiu classificar corretamente todas as amostras analisadas neste estudo, quando combinadas as informações das regiões de médio e baixo ângulo. Portanto, os resultados obtidos neste trabalho sugerem a possibilidade do desenvolvimento de novas técnicas radiológicas que permitiriam ampliar a capacidade de diagnóstico do câncer mamário. / Scattering radiation in diagnostic radiology, such as mammography, is usually considered a problem, since it degrades the image contrast. However, recent investigations show that the angular distribution of scattered photons (scattering profile) can provide information about the structures that compose a biological tissue, allowing, from the analysis of the scattering profile, identify the presence of abnormalities in the tissue. In this study, we have used the wide angle x-ray scattering (WAXS) and small angle x-ray scattering (SAXS) techniques to determine the scattering profiles of human breast tissues previously classified as: normal tissue (adipose and fibroglandular), benign or malignant neoplasia, using a x-ray tube and synchrotron radiation. Through the information provide by each profile was possible to identify some molecular and supramolecular structures present in these tissues. In addition, we built a classification model based on discriminant analysis of scattering profiles, which enabled the correct classification of all samples analyzed in this study, when combined information from WAXS and SAXS regions. Therefore, the results obtained in this work suggest the possibility of developing new radiological techniques would expand the capability of breast cancer diagnosis.

Orientador: Maria Izabel Maretti Silveira Bueno / Tese (doutorado) - Universidade Estadual de Campinas, Instituto de Quimica / Made available in DSpace on 2018-08-10T04:20:54Z (GMT). No. of bitstreams: 1 Alexandre_ThaisLevatti_D.pdf: 1122412 bytes, checksum: 5e4072c9674353ddc976abd8cb112ab2 (MD5) Previous issue date: 2006 / Resumo: O uso da região de espalhamento na espectrometria de raios-X (XRS, do inglês, X-Ray Spectrometry) aliada à quimiometria é uma aplicação recente que tem mostrado bons resultados na discriminação de amostras orgânicas. Nesse trabalho, a proposta de se utilizar XRS para solucionar um problema de classificação taxonômica de Lantana sp, utilizando-se folhas desse vegetal não foi alcançada devido à reconhecida evolução contínua desta espécie. No entanto, o estudo de espécies do gênero Musa e das famílias Polemoniaceae, Asteraceae e Portulacaceae, utilizando-se pseudofrutos e sementes, respectivamente foi bem sucedido. A análise de componentes principais (PCA) realizada com os espectros obtidos da irradiação dos pseudofrutos e das sementes mostrou boa correlação entre a disposição das amostras e a classificação nos níveis gênero, espécies e variedades. Variáveis que poderiam justificar a discriminação obtida desses vegetais foram estudadas como exemplo o estudo envolvendo a utilização de carboidratos. Foram realizadas: a regressão de sacarose, frutose e glicose em solução aquosa e frutose e glicose em suco, com bons coeficientes de linearidade (0,998; 0,995; 0,998; 0,994 e 0,991, respectivamente); a discriminação de carboidratos; a regressão do índice de doçura e a rotação específica da luz polarizada de carboidratos; e a regressão da inversão da sacarose. Além da discriminação dos vegetais e do estudo de carboidratos, esse trabalho também apresenta a fundamentação teórica para explicar o surgimento desta técnica e um provável potencial que ela poderá apresenta para o futuro / Abstract: The use of scattering on X-ray Spectrometry (XRS) allied to chemometrics is a new application that is showing good results in discrimination of organics. In the present work the proposal of applying XRS to solve the taxonomic classification of Lantana sp species, using leafs of these plants was not reached due to the evolution process this plant is still undergoing. Nevertheless, this motivated a discrimination study of species of Musa genus (banana) and species of Polemoniaceae, Portulacaceae and Asteraceae families, using fruits and seeds, respectively. Principal component analysis of spectra of fruits and seeds show good correlation between sample arrangement and taxonomic classification in genus, species and varieties. Looking for variables that could justify the discriminations obtained, studies were developed involving carbohydrates. It was realized: sucrose, fructose and glucose regression in aqueous solutions and fructose and glucose calibration in juice solutions with good linear coefficients (0.998; 0.995; 0.998; 0.994 e 0.991, respectively); carbohydrates discrimination; X-ray spectra correlation with sweetness degrees and specific rotation of polarized light of carbohydrates; and regression of kinetics of sucrose inversion. Besides the vegetable classifications and the carbohydrate studies, this work presents a theorical basis to explain the XRS characteristics, the history before the arising of this method and its potentialities for the future / Doutorado / Quimica Analitica / Mestre em Química

Orientador: Iris Concepcion Kinares de Torriani / Dissertação (mestrado) - Universidade Estadual de Campinas, Instituto de Fisica Gleb Wataghin / Made available in DSpace on 2018-08-08T07:14:14Z (GMT). No. of bitstreams: 1 Silva_JulioCesarda_M.pdf: 3602925 bytes, checksum: ebc541d863211845fb7a5a80d72ed5b5 (MD5) Previous issue date: 2007 / Resumo: Durante as últimas décadas, o estudo de mudanças conformacionais de macromoléculas biológicas tem se tornado um grande desafio para os cientistas, além de ser um tema de interesse biotecnológico e de engenharia de proteínas. O processo de enovelamento (desenovelamento) de proteínas tem sido intensivamente estudado, pois isso pode contribuir para o conhecimento do processo de síntese de proteínas, além de ajudar a entender o desenvolvimento de algumas doenças associadas ao mau enovelamento ou agregação de certas proteínas. Nesse contexto, o Espalhamento de Raios-X a Baixo Ângulo (SAXS) aparece como uma técnica valiosa para esse estudo, pois ela permite obter informações estruturais da molécula em solução. Além de permitir estudos dinâmicos, as experiências de SAXS possibilitam a observação das moléculas em condições fisiológicas. Neste trabalho, a potencialidade da técnica de SAXS foi evidenciada no estudo de mudanças conformacionais de biomoléculas. O processo de desnaturação da proteína lisozima em solução foi estudado através de experiências em equilíbrio. Mudanças conformacionais foram observadas durante o processo de desnaturação por ação de uréia na solução e por altas temperaturas. Os resultados mostraram que a lisozima é uma proteína com certa resistência para se desenovelar completamente, mesmo em condições extremas de concentração de uréia e de altas temperaturas. A molécula tende a não perder totalmente sua compacidade. Além disso, foram observados somente dois estados conformacionais (enovelado e desenovelado). Um estado intermediário reportado na literatura, mas contestado por vários autores, não foi observado. Isso mostra a alta cooperatividade dessa proteína no processo de desnaturação. Outro processo estudado foi a oligomerização da proteína -Lactoglobulina sob ação de irradiação com radiação gama. A proteína foi estudada na forma sólida, com diferentes atividades de água, e em solução, em diferentes concentrações. As amostras foram irradiadas com radiação gama em diferentes doses e as mudanças foram registradas através de experiências de SAXS. Os dados experimentais foram usados para o cálculo de modelos dos oligômeros formados por ação da radiação. Concluindo, este estudo mostrou que a técnica de SAXS é uma ferramenta versátil e muito útil para o estudo de processos de mudanças nas estruturas terciária e quaternária de proteínas em solução / Abstract: During the last decades, the study of conformational changes in biological macromolecules has been a great challenge for the scientists, and continues to be an important subject of biotechnological interest and protein engineering. The process of folding (unfolding) of protein molecules has been intensively studied, because this investigation can contribute to the knowledge of the process of protein synthesis, thus helping to understand the development of some illnesses associated with misfolding or aggregation processes of certain proteins. In this context, the technique of Small Angle X-ray Scattering (SAXS) appears as a valuable technique, because it provides structural information of the molecules in solution. This technique allows dynamical studies and makes possible the study of the protein in physiological conditions. In this work the potentiality of the SAXS technique was evidenced in the study of conformational changes of biological molecules. The process of denaturation of the protein lysozyme in solution was studied using SAXS measurements in equilibrium conditions. Conformational changes were observed during the process of denaturation by the action of urea in the solution and for high temperatures. The results showed that lysozyme is a protein with certain resistance to unfold completely. Even in extreme conditions of high concentration of urea and high temperatures, this protein does not totally lose its compactness. Moreover, only two conformational states (folded and unfolded) were observed. An intermediate state was not observed. This study showed the high cooperativity of the unfolding process of this protein during its denaturation process. Another process studied was the oligomerization of the protein -Lactoglobulin under the effect of gamma irradiation. The protein was studied in the solid form, in different water activities, and in solution, in different concentrations. The samples were exposed to several doses of -radiation. The SAXS technique was used to obtain dimensional parameters of the proteins and models were calculated from the experimental scattering data. Finally, this study showed that the SAXS technique as a versatile and very useful tool for the study of changes in the tertiary and quaternary structures of proteins in solution / Mestrado / Física / Mestre em Física

Orientador: Maria Izabel Maretti Silveira Bueno / Tese (doutorado) - Universidade Estadual de Campinas, Instituto de Quimica / Made available in DSpace on 2018-08-08T20:31:04Z (GMT). No. of bitstreams: 1 Bortoleto_GiseleGoncalves_D.pdf: 1848402 bytes, checksum: 97da7589f57febbd17ac608c4ed98640 (MD5) Previous issue date: 2007 / Resumo: Esta tese de doutorado apresenta uma inovação na química analítica abordando novas aplicações da técnica de fluorescência de raios-X, na qual o espalhamento da radiação X e a quimiometria exercem papel fundamental. Os sinais de espalhamento dos raios X provenientes da interação de diferentes fontes de excitação com amostras essencialmente orgânicas foram avaliados a partir de estudos realizados com um espectrômetro de bancada com tubo de Rh, como também com luz síncrotron, da linha de fluorescência de raios-X do Laboratório Nacional de Luz Síncrotron (LNLS), Campinas, SP, Brasil. Os resultados mostraram diferentes perfis de espalhamento da radiação para as diferentes fontes de excitação empregadas. Uma banda contínua em toda região espectral foi obtida como sinal, no caso do uso da luz síncrotron, e intensos picos em determinadas regiões espectrais caracterizaram os espalhamentos Compton e Rayleigh, quando o tubo de Rh foi utilizado. A alta intensidade da luz síncrotron resolveu os problemas de precisão intermediária observados nas medidas das amostras de álcoois realizadas com tubo de Rh. Em outro estudo, no qual os espectros de XRF de amostras de adoçantes dietéticos e óleos vegetais foram analisados por PCA, os resultados revelaram agrupamentos entre compostos com composições químicas ligeiramente distintas. Nesse caso, o uso do tubo de Rh foi adequado para atingir os objetivos propostos. Nas análises de óleos, a formação dos diversos grupos foi baseada nas variedades de óleos de soja, canola, girassol e milho. Nos testes realizados com adoçantes, os resultados mostraram uma tendência de diferenciação entre as amostras compostas por diferentes edulcorantes, principalmente entre aqueles que contêm ou que não contêm o átomo de enxofre em suas moléculas. O estudo realizado com amostra de urina conclui este trabalho, ressaltando mais uma vantagem do uso da XRF aliada a quimiometria: a possibilidade de realizar quantificações diretas e simultâneas de elementos inorgânicos e compostos orgânicos em amostras líquidas complexas. Nesse caso, um método para determinação de Ca, P, Na, K, Mg, Cl, uréia, glicose e creatinina em amostra de urina é apresentado, no qual os coeficientes de regressão da ordem de 0,99, obtidos para os modelos de calibração dos diferentes analitos, mostram a potencialidade da técnica para ser implementada em laboratórios de rotina. / Abstract: This work presents an innovation in analytical chemistry dealing with new applications of X-ray fluorescence technique in which the X-ray scattering effects and the chemometric tools play essential roles. X-ray scattering spectra resulting from interaction of simple organic samples were obtained with two sources, a common bench top spectrometer equipped with a Rh tube and also with synchrotron radiation (from the XRF beam line of the Laboratório Nacional de Luz Síncrotron (LNLS), Campinas, SP, Brazil). Distinct scattering profiles are observed for both excitation sources: a continuum for synchrotron light and intense peaks related to Compton and Rayleigh effects when a Rh tube is used. After processing the spectra from both sources, it was observed that the high intensity of synchrotron radiation solved the intermediate precision problems found in measuring samples via Rh tube. In another study, the spectra of sweetners and vegetable oils were analysed by XRF with PCA and the results showed distinct groupings for distinct samples. In this case, the Rh source was adequate to reach the objectives. In oil analyses, different groupings are based on the varieties of soybean, corn, canola and sunflower oils. In the case of sweetners, the results show a tendence to diferentiate samples of dissimilar artificial sweetners, especially when the presence of sulfur is of major importance. A study performed with urine samples is the final part of this work, poiting out one more advantage of using X-ray fluorescence with chemometrics, that is, the possibility of simultaneous and direct quantifications of inorganic elements and organic compounds in complex liquid samples. In this case a method for determining Ca, P, Na, K, Mg, Cl, urea, glucose and creatinine is presented with good regression coefficients being obtained for the different analytes. This can be taken as a good indication of the potential of the technique for implementation in routine laboratories. / Doutorado / Quimica Analitica / Doutor em Ciências