Os sistemas de lima única constituem a mais recente tecnologia no que se refere ao preparo dos canais radiculares, e vem sendo objeto de estudo sob diversos aspectos. Uma das preocupações referentes aos sistemas automatizados é a manutenção da qualidade e segurança nos preparos quando da reutilização do instrumento. Este estudo teve como objetivo avaliar as alterações de superfície de dois sistemas de lima única - Wave One e One Shape - e seu desempenho através do tempo de preparo no decorrer dos usos. Duzentos condutos de molares inferiores humanos extraídos foram instrumentados com 10 limas Wave One e 10 limas One Shape, acompanhados de irrigação com 10 ml de Hipoclorito de Sódio 2.5%. Cada instrumento foi utilizado por 10 vezes. Os tempos para o preparo completo do canal foram registrados por um cronômetro digital e anotados em tabelas. Para avaliação em microscopia eletrônica de varredura as limas novas foram observadas assim que removidas da embalagem. Após as utilizações, os instrumentos foram limpos, esterilizados em autoclave e observados após 2, 6, 8 e 10 usos. Três avaliadores calibrados observaram as fotomicrografias e registraram de acordo com os scores propostos a presença ou ausência de alterações superficiais. O teste Kappa de concordância entre os avaliadores apresentou maioria de resultados ótimo a moderado (?=5%). Os dados referentes à avaliação das imagens foram submetidos ao teste Wilcoxon-Mann-Whitney com nível de significância de 5% (?=5%). As alterações mais observadas foram aplainamento e microcavidade. O crack foi observado nos dois instrumentos sendo significante a partir do sexto uso para Wave One e do décimo para One Shape. Os dados relativos aos tempos de preparo foram submetidos à análise estatística pelos testes Wilcoxon-Mann-Whitney, ANOVA e Mc-Nemar com nível de significância de 5% (?=5%). Os tempos de preparo registrados para One Shape foram inferiores aos tempos para Wave One. O uso influenciou os tempos de preparo sendo observado um aumento significativo para os dois instrumentos. Um instrumento One Shape fraturou mas a ocorrência não foi estatisticamente significante. / Single-file systems are the most recent technology in regard to the preparation of root canals and have been studied in several ways. One of the concerns related to automated systems is maintaining quality and safety in preparation when the instrument is reused. This study\'s aim was to evaluate the changes on the surface of two single-file systems - Wave One and One Shape - and their performance through preparation time over the uses. Two hundred root canals of extracted human molars were instrumented with 10 Wave One files and 10 One Shape files, followed by irrigation with 10 ml of sodium hypochlorite 2.5%. Each instrument was used 10 times. The time required to complete each root canal was measured by a digital stopwatch and recorded in tables. New unused files were analysed using a scanning electron microscope. After used, the instruments were cleaned and sterilized, then observed after 2, 6, 8 and 10 uses. Three calibrated evaluators observed these SEM images and listed according to the suggested scores the presence or absence of changes on the surface. The Kappa test showed mostly results from moderate to great (? = 5%). The data relating to evaluation of images was submitted to the Wilcoxon-Mann-Whitney test with a significance level of 5% (? = 5%). The most frequent changes were blunt edges and microcavities. Cracking was observed in both instruments being significant in Wave One after the sixth use and in One Shape after the tenth use. Data on preparation times were statistically analysed by the Wilcoxon-Mann-Whitney, ANOVA and Mc-Nemar tests with a significance level of 5% (? = 5%). Regarding the working time taken to shape the canals, One Shape was significantly faster than Wave One. The preparation time was affected by the number of file use increasing significantly on both instruments. A One Shape instrument fractured but the finding was not statistically significant.

O electrospinning (deposição eletrostática) representa um método simples e conveniente para preparar bras poliméricas e bras cerâmicas com interiores sólidos ou ocos, excepcionalmente longos em comprimento, uniformes no diâmetro, variando no intervalo de dezenas de nanômetros a vários micrômetros, com diversicadas composições. Apesar da potencialidade e versatilidade da Microscopia Eletrônica de Varredura existe um grande problema de caracterizar nanobras, já que este processo não é feito automaticamente. Este trabalho apresenta uma nova metodologia para extração automática de medidas em imagens SEM, como uma alternativa eciente em relação aos softwares semi-automáticos propostos na literatura. A metodologia proposta envolve o processamento das imagens SEM usando Morfologia Matemática e os resultados obtidos são discutidos e comparados àqueles processados por Redes Neurais Celulares e pelo método de Otsu. Imagens coletadas do microscópio foram analisadas por técnicas de processamento de imagens para determinação do diâmetro das nanobras. Os resultados mostraram boa concordância entre as metodologias estudadas e o método padrão-ouro indicando que os mesmos podem substituí-lo para constituir uma alternativa automática na caracterização de nanobras. / The electrospinning technique represents a simple and convenient process to provide polymers and ceramics bers with both solid and hollow interiors that are exceptionally long in length, uniform in diameter, varying within the interval of few nanometers to several microns, and diversied in composition. Despite the versatility and potencially the scanning electron microscopy (SEM) there is a serious problem to characterize nanobers, as it is not made automatically. This work presents novel methodology software for automatic measurement in SEM images, as an eficient alternative in comparison with semi-automatic softwares proposed in literature. The proposed methodology involves the image processing SEM using Mathematical Morphology and the obtained results are argued and compared with those processing for Celullar Neural Network and Otsu method. The microscope images were assessed and analysed by imagery processing techniques to determinate diameters of nanobers. The results has shown good agreement between the investigated and gold standard methods suggesting that the same ones can substitute it to constitute an automatic alternative in the nanobers characterization.

Philosophiae Doctor - PhD / The main objective of this study was to advance kinetic performances of formation and decomposition of magnesium hydride by design strategies which include high energy ball milling in hydrogen (HRBM), in combination with the introduction of catalytic/dopant additives. In this regard, the transformation of Mg → MgH2 by high energy reactive ball milling in hydrogen atmosphere (HRBM) of Mg with various additives to yield nanostructured composite hydrogen storage materials was studied using in situ pressure-temperature monitoring that allowed to get time-resolved results about hydrogenation behaviour during HRBM. The as-prepared and re-hydrogenated nanocomposites were characterized using XRD, high-resolution SEM and TEM, as well as measurements of the mean particle size. Dehydrogenation performances of the nanocomposites were studied by DSC / TGA and TDS; and the re-hydrogenation behaviour was investigated using Sieverts volumetric technique.

Titanium nitride (TiN) films are widely applied as diffusion barrier layers in microelectronic devices. The continued miniaturization of such devices not only poses new challenges to material systems design, but also puts high demands on characterization techniques. To gain understanding of diffusion processes that can eventually lead to failure of the barrier layer and thus of the whole device, it is essential to develop routines to chemically and structurally investigate these layers down to the atomic scale. In the present study, model TiN diffusion barriers with a Cu overlayer acting as the diffusion source were grown by reactive magnetron sputtering on MgO(001) and thermally oxidized Si(001) substrates. Cross-sectional transmission electron microscopy (XTEM) of the pristine samples revealed epitaxial, single-crystalline growth of TiN on MgO(001), while the polycrystalline TiN grown on Si(001) exhibited a [001]-oriented columnar microstructure. Various annealing treatments were carried out to induce diffusion of Cu into the TiN layer. Subsequently, XTEM images were recorded with a high-angle annular dark field detector, which provides strong elemental contrast, to illuminate the correlation between the structure and the barrier efficiency of the single- and polycrystalline TiN layers. Particular regions of interest were investigated more closely by energy dispersive X-ray (EDX) mapping. These investigations are completed by atom probe tomography (APT) studies, which provide a three-dimensional insight into the elemental distribution at the near-interface region with atomic chemical resolution and high sensitivity. In case of the single-crystalline barrier, a uniform Cu-enriched diffusion layer of 12 nm could be detected at the interface after an annealing treatment at 1000 °C for 12 h. This excellent barrier performance can be attributed to the lack of fast diffusion paths such as grain boundaries. Moreover, density-functional theory calculations predict a stoichiometry-dependent atomic diffusion mechanism of Cu in bulk TiN, with Cu diffusing on the N-sublattice for the experimental N/Ti ratio. In comparison, the polycrystalline TiN layers exhibited grain boundaries reaching from the Cu-TiN interface to the substrate, thus providing direct diffusion paths for Cu. However, the microstructure of these columnar layers was still dense without open porosity or voids, so that the onset of grain boundary diffusion could only be found after annealing at 900 °C for 1 h. The present study shows how to combine two high resolution state-of-the-art methods, TEM and APT, to characterize model TiN diffusion barriers. It is shown how to correlate the microstructure with the performance of the barrier layer by two-dimensional EDX mapping and three-dimensional APT. Highly effective Cu-diffusion barrier function is thus demonstrated for single-crystal TiN(001) (up to 1000 °C) and dense polycrystalline TiN (900 °C).

Thin film arrays of molecules or supramolecules are active subjects of investigation because of their potential value in electronics, chemical sensing, catalysis, and other areas. Scanning probe microscopes (SPMs), including scanning tunneling microscopes (STMs) and atomic force microscopes (AFMs) are commonly used for the characterization and metrology of thin film arrays. As opposed to transmission electron microscopy (TEM), SPMs have the advantage that they can often make observations of thin films in air or liquid, while TEM requires highly specialized techniques if the sample is to be in anything but vacuum. SPM is a surface imaging technique, while TEM typically images a 2D projection of a thin 3D sample. Additionally, variants of SPM can make observations of more than just topography; for instance, magnetic force microscopy measures nanoscale magnetic properties. Thin film arrays are typically two-dimensionally periodic. A perfect, infinite two-dimensionally periodic array is mathematically constrained to belong to one of only 17 possible 2D plane symmetry groups. Any real image is both finite and imperfect. Crystallographic Image Processing (CIP) is an algorithm that Fourier transforms a real image into a 2D array of complex numbers, the Fourier coefficients of the image intensity, and then uses the relationship between those coefficients to first ascertain the 2D plane symmetry group that the imperfect, finite image is most likely to possess, and then adjust those coefficients that are symmetry-related so as to perfect the symmetry. A Fourier synthesis of the symmetrized coefficients leads to a perfectly symmetric image in direct space (when accumulated rounding and calculation errors are ignored). The technique is, thus, an averaging technique over the direct space experimental data that were selected from the thin film array. The image must have periodicity in two dimensions in order for this technique to be applicable. CIP has been developed over the past 40 years by the electron crystallography community, which works with 2D projections from 3D samples. Any periodic sample, whether it is 2D or 3D has an "ideal structure" which is the structure absent any crystal defects. The ideal structure can be considered one average unit cell, propagated by translation into the whole sample. The "real structure" is an actual sample containing vacancies, dislocations, and other defects. Typically the goal of electron and other types of microscopy is examination of the real structure, as the ideal structure of a crystal is already known from X-ray crystallography. High resolution transmission electron microscope image based electron crystallography, on the other hand, reveals the ideal crystal structure by crystallographic averaging. The ideal structure of a 2D thin film cannot be easily in a spatially selective fashion examined by grazing incidence X-ray or low energy electron diffraction based crystallography. SPMs straightforwardly observe thin films in direct space, but SPM accuracy is hampered by blunt or multiple tips and other unavoidable instrument errors. Especially since the film is often of a supramolecular system whose molecules are weakly bonded (via pi bonds, hydrogen bonds, etc.) both to the substrate and to each other, it is relatively easy for a molecule from the film to adhere to the scanning tip during the scan and become part of the tip during subsequent observation. If the thin film array has two-dimensional periodicity, CIP is a unique and effective tool both for image enhancement (determination of ideal structure) and for the quantification of overall instrument error. In addition, if a sample of known 2D periodicity is scanned, CIP can return information about the contribution of the instrument itself to the image. In this thesis we show how the technique is applied to images of two dimensionally periodic samples taken by SPMs. To the best of our knowledge, this has never been done before. Since 2D periodic thin film arrays have an ideal structure that is mathematically constrained to belong to one of the 17 plane symmetry groups, we can use CIP to determine that group and use it for a particularly effective averaging algorithm. We demonstrate that the use of this averaging algorithm removes noise and random error from images more effectively than translational averaging, also known as "lattice averaging" or "Fourier filtering". We also demonstrate the ability to correct systematic errors caused by hysteresis in the scanning process. These results have the effect of obtaining the ideal structure of the sample, averaging out the defects crystallographically, by providing an average unit cell which, when translated, represents the ideal structure. In addition, if one has recorded a scanning probe image of a 2D periodic sample of known symmetry, we demonstrate that it is possible to use the Fourier coefficients of the image transform to solve the inverse problem and calculate the point spread function (PSF) of the instrument. Any real scanning probe instrument departs from the ideal PSF of a Dirac delta function, and CIP allows us to quantify this departure as far as point symmetries are concerned. The result is a deconvolution of the "effective tip", which includes any blunt or multiple tip effects, as well as the effects caused by adhesion of a sample molecule to the scanning tip, or scanning irregularities unrelated to the physical tip. We also demonstrate that the PSF, once known, can be used on a second image taken by the same instrument under approximately the same experimental conditions to remove errors introduced during that second imaging process. The preponderance of two-dimensionally periodic samples as subjects of SPM observation makes the application of CIP to SPM images a valuable technique to extract a maximum amount of information from these images. The improved resolution of current SPMs creates images with more higher-order Fourier coefficients than earlier, "softer" images; these higher-order coefficients are especially amenable to CIP, which can then effectively magnify the resolution improvement created by better hardware. The improved resolution combined with the current interest in supramolecular structures (which although 3D usually start building on a 2D periodic surface) appears to provide an opportunity for CIP to significantly contribute to SPM image processing.

In dieser Arbeit werden die grundlegenden Wachstumsprozesse von Ga2O3 , mittels Transmissionselektronenmikroskopie analysiert. Dazu gehört die Untersuchung des heteroepitaktischen Wachstums von Galliumoxidschichten welche mittels Molekularstrahlepitaxie (molekular beam epitaxy MBE), der gepulsten Laser Abscheidung (pulsed laser deposition (PLD)) und der metallorganischen Gasphasenepitaxie (metalorganic vapor phase epitaxy (MOVPE)) auf (0001) orientierte Saphir Substraten abgeschieden wurden. Heteroepitaktisches Wachstum von Ga2O3 auf Saphir (0001) erfolgt bis zu einer Dicke von 3 Monolagen pseudomorph als α-Ga2O3 welches durch die Gitterfehlpassung zwischen Galliumoxid und dem Saphire Substrat induzierte Gitterverspannung stabilisiert wir. Weiterhin, im Fokus der Arbeit stehend, wird das homoepitaktische Wachstum von Galliumoxid auf (100) orientierten Galliumoxidsubstraten untersucht. Neben den Besonderheiten des Schichtwachstums, die sich aus den eingesetzten metallorganischen Präkursoren und Sauerstoffquellen ergeben, wird die Schichtstruktur in Abhängigkeit der typischen Wachstumsparameter (Wachstumstemperatur, Wachstumsrate, Kammerdruck und Fehlorientierung des Substrates) analysiert. Dabei wird gezeigt das homoepitaktischen Wachstum auf (100) orientiertem, β-Ga2O3, mittels MOVPE, die kristalline Perfektion der gewachsenen Schichten stark von den verwendeten Präkursoren (Trimethylgallium (TMGa) und Triethylgallium (TEGa) als metallorganische Ausgangsstoffe und H2 O oder purer Sauerstoff als Oxidant) und den chemischen Prozessen an der Oberfläche bestimmt wird. Des Weiteren wird die Entstehung von Zwillingslammelen in abhähngigkeit der Fehlorientierung untersucht. Durch die Einführung von vorbestimmten Fehlorientierungswinkeln der Substrate ist es möglich das Entstehen der Zwillingslamellen zu verhindern, und ein Stufenflusswachstum zu generieren. Durch die Anwendung eines Ratengleichungsansatzes ist es möglich die experimentell beobachteten Dichten an Zwillingslamellen zu erklären und einen Diffusionskoeffizienten zu bestimmen. (i) Heteroepitaktisches Wachstum von Ga2O3 auf Saphir (0001) erfolgt bis zu einer Dicke von 3 Monolagen pseudomorph als alpha-Ga2O3. Oberhalb dieser Schicht wächst relaxiertes ß-Ga2O3 in Form von 3 Rotationsdomänen auf. Die Stabilisation der dünnen alpha-Ga2O3 Schicht wird, durch die Gitterfehlpassung zwischen Galliumoxid und dem Saphire Substrat induzierte Gitterverspannung bewirkt. (ii) Beim homoepitaktischen Wachstum auf (100) orientiertem ß-Ga2O3 mittels MOVPE wird die kristalline Perfektion der gewachsenen Schichten stark von den verwendeten Präkursoren (Trimethylgallium (TMGa) und Triethylgallium (TEGa) als metallorganische Ausgangsstoffe und H2O oder purer Sauerstoff als Oxidant) und den chemischen Prozessen an der Oberfläche bestimmt. Während beim Wachstum mittels TMGa und O2 vorwiegend polykristalline Schichten entstehen, ergeben sich beim Wachstum mittels TMGa und H2O sowie TEGa und O2 geschlossenen epitaktische Schichten. Dieser signifikante Unterschiede lässt sich durch die unterschiedlichen Reaktionswege der Ausgangsstoffe sowie durch die katalytische Wirkung der (100) Flächen des ß-Ga2O3 erklären. (iii) Die Perfektion, mittels MOVPE gewachsener, homoepitaktischer Schichten, auf (100) orientierten Substraten, ist stark von der Fehlorientierung des Substrates bestimmt. Schichten die auf Substraten mit geringen Fehlorientierungen abgeschieden werden (< 2° bei Wachstumstemperaturen < 850°C) sind durch eine hohe Dichte an Zwillingslamellen gekennzeichnet. Die Entstehung der Zwillingslamellen ist ein Resultat eines Doppelpositionierungsprozesses der Atome auf der Oberfläche der Wachstumsebene. Durch die Einführung von vorbestimmten Fehlorientierungswinkeln der Substrate ist es möglich das Entstehen der Zwillingslamellen zu verhindern, und ein Stufenflusswachstum zu generieren. Durch die Anwendung eines Ratengleichungsansatzes, welcher die konkurrierenden Prozesse des Einbaus von Atomen in Oberflächenstufen sowie der Nukleation und des Wachstum von zweidimensionalen Inseln beschreibt, ist es möglich die experimentell beobachteten Dichten an Zwillingslamellen zu erklären und einen Diffusionskoeffizienten zu bestimmen, Dieser ist um zwei Größenordnungen geringer als bei klassischen Halbleitern, wie z. B. GaAs. In dieser Arbeit werden die grundlegenden Wachstumsprozesse von Ga2O3 , mittels Transmissionselektronenmikroskopie analysiert. Dazu gehört die Untersuchung des heteroepitaktischen Wachstums von Galliumoxidschichten welche mittels Molekularstrahlepitaxie (molekular beam epitaxy MBE), der gepulsten Laser Abscheidung (pulsed laser deposition (PLD)) und der metallorganischen Gasphasenepitaxie (metalorganic vapor phase epitaxy (MOVPE)) auf (0001) orientierte Saphir Substraten abgeschieden wurden. Heteroepitaktisches Wachstum von Ga2O3 auf Saphir (0001) erfolgt bis zu einer Dicke von 3 Monolagen pseudomorph als α-Ga2O3 welches durch die Gitterfehlpassung zwischen Galliumoxid und dem Saphire Substrat induzierte Gitterverspannung stabilisiert wir. Weiterhin, im Fokus der Arbeit stehend, wird das homoepitaktische Wachstum von Galliumoxid auf (100) orientierten Galliumoxidsubstraten untersucht. Neben den Besonderheiten des Schichtwachstums, die sich aus den eingesetzten metallorganischen Präkursoren und Sauerstoffquellen ergeben, wird die Schichtstruktur in Abhängigkeit der typischen Wachstumsparameter (Wachstumstemperatur, Wachstumsrate, Kammerdruck und Fehlorientierung des Substrates) analysiert. Dabei wird gezeigt das homoepitaktischen Wachstum auf (100) orientiertem, β-Ga2O3, mittels MOVPE, die kristalline Perfektion der gewachsenen Schichten stark von den verwendeten Präkursoren (Trimethylgallium (TMGa) und Triethylgallium (TEGa) als metallorganische Ausgangsstoffe und H2 O oder purer Sauerstoff als Oxidant) und den chemischen Prozessen an der Oberfläche bestimmt wird. Des Weiteren wird die Entstehung von Zwillingslammelen in abhähngigkeit der Fehlorientierung untersucht. Durch die Einführung von vorbestimmten Fehlorientierungswinkeln der Substrate ist es möglich das Entstehen der Zwillingslamellen zu verhindern, und ein Stufenflusswachstum zu generieren. Durch die Anwendung eines Ratengleichungsansatzes ist es möglich die experimentell beobachteten Dichten an Zwillingslamellen zu erklären und einen Diffusionskoeffizienten zu bestimmen. Des Weiteren wird das Wachstum im Mischsystem (InxGa1-x)2O3 untersucht und gezeigt das Indium als grenzflächenaktive Substanz wirken kann. / In this work we study the basic growth processes of epitaxial Ga2O3 films, by means of transmission electron microscopy. We investigate the heteroepitaxial growth of thin layers Ga2O3 on the (0001) plane of sapphire grown by molecular beam epitaxy (MBE), pulsed laser deposition (PLD) and metal organic vapor phase epitaxy (MOVPE). Furthermore, we will focus on the homoepitaxial growth on the (100) plane by MOVPE. Beside the peculiarities of the layer growth dependence on different metal organic precursors and oxygen sources, we investigate the influence of typical growth parameters (i.e. growth temperature, growth-rate, chamber pressure and miscut angle of the substrate) on the layer morphology. Incase of heteroepitaxial growth of β-Ga2O3 on (0001) plane of sapphire, independent of the growth method, the formation of a 3 monolayer thick α-Ga2O3 layer is observed, which is stabilized through strain, as a result of the lattice mismatch between sapphire and α-Ga2O3. In case of homoepitaxial growth by MOVPE on (100) oriented β-Ga2O3, the crystalline quality of the grown layer strongly depends on the used precursor (tri-methyl-gallium (TMGa) or tri-ethyl-gallium (TEGa) as metal precursor and H2O or pure oxygen as oxidant) and the chemical processes on the surface, respectively. Further on is the crystalline perfection of homoepitaxial layers grown by MOVPE on (100) oriented β-Ga2O3 substrates strongly dependent on the miscut-angle of the substrates. Layer grown on substrate with a small miscut-angle (< 2°) show high amount of twin lamella. These twin lamella are a result of a possible double positioning mechanism of ad-atoms on the growth surface. By introducing appropriate miscut-angles of the substrate it is possible to suppress the formation of these twin lamellae, and enable step flow growth. By applying a rate equation approach, describing the competing processes of incorporation of ad-atoms at kink sites or nucleation and growth of two dimensional island, it is possible to quantitatively reproduce the experimentally observed twin lamella densities and to determine a surface diffusion coefficient of the ad-atoms. Furthermore, in case of the alloy system (InxGa1-x)2O3, it is shown that indium can act as an surfactant, by increasing the surface diffusion.

Nanostructures were formed on diced specimens of several silicon carbide polytypes and silicon using electron beam lithography. A general introduction to nanostructure synthesis and electron beam lithography,are presented. A scanning electron microscope was retrofitted with a commercially available electron beam lithography package and an electrostatic beam blanker to permit nanoscale lithography to be performed. A process was first developed and optimized on silicon substrates to expose, poly-methyl-methacrylate (PMMA) resist with an electron beam to make nanoscale nickel masks for reactive ion etching. The masks consist of an array of nickel dots that range in size from 20 to 100 nm in diameter. Several nanoscale structures were then fabricated in silicon carbide using electron beam lithography. The structures produced are characterized by field emission Scanning Electron Microscopy.

L'utilisation récente des nanoparticules (NPs) comme vecteurs pour l'imagerie et l'adressage d'agents thérapeutiques en nano-médecine nécessite la compréhension de leurs mécanismes d'internalisation et de transport au niveau des barrières biologiques. Dans ce contexte, l'objectif de cette étude est de caractériser l'interaction et la transcytose de NPs de silice fluorescentes en fonction de leur taille (15, 50 et 100 nm) dans un modèle in-vitro de barrière endothéliale pulmonaire humaine. L'internalisation et le transport trans-endothélial des NPs a été analysé quantitativement à l'échelle nanométrique par microscopie électronique à transmission (MET) combinée à de la stéréologie. Un transport trans-endothélial a été observé pour toutes les tailles de NPs. Néanmoins, l'analyse de la distribution intracellulaire révèle une tendance à l'accumulation dans les voies de dégradation cellulaires pour les NPs de 50 et 100 nm. Cette accumulation est moindre pour les NPs de 15 nm. L'internalisation des NPs a également été analysée par cytométrie en flux et MET en présence de différents inhibiteurs de l'endocytose dans le but d'identifier leurs voies d'internalisation. En fonction de la taille des NPs, les mécanismes d'endocytose varient, suggérant une dépendance du transport trans-cellulaire à certains mécanismes d'endocytose. L'internalisation des NPs de 15 nm par la voie d'endocytose cavéole dépendante pourrait ainsi expliquer l'efficacité de leur transport du côté basal. Les méthodologies développées pour l'étude du transport trans-cellulaire des NPs de silice peuvent être appliquées à l'étude de NPs synthétiques plus complexes ou de NPs biologiques, telles que les lipoprotéines de basse-densité, et ce dans un contexte pathologique. / The recent use of nanoparticles (NPs) as carriers for imaging and delivery of therapeutics agents in nanomedecine involves understanding their endocytosis and transcytosis mechanisms at biological barriers. In this context, the aim of this study was to characterize the interaction and transcytosis of fluorescent silica NPs in function of their size (15, 50, and 100 nm) in an in-vitro model of human pulmonary endothelial barrier. NPs internalization and trans-endothelial transport has been quantitatively analyzed at nanometer resolution using transmission electron microscopy (TEM) combined with stereology. Trans-endothelial transport has been observed for each size of NPs. However cellular distribution analysis shows an accumulation in the cellular degradation pathways for 50 nm and 100 nm NPs. Whereas 15 nm NPs are less accumulated. NPs uptake was also analyzed by flow cytometry and TEM in the presence of different inhibitors to decipher NPs internalization pathways. Depending on NPs size, the involved endocytosis pathways were different, suggesting a dependency of trans-cellular transport toward endocytic mechanisms. The specific internalization of 15 nm NPs by the caveolin dependant pathway could explain the efficacy of their release at the basal side. Techniques developed for the study of the trans-cellular transport of silica NPs can also be applied to more complex synthetic NPs or biological NPs, such as low-density lipoproteins, in a pathological context.

Single-particle cryogenic electron microscopy (cryo-EM) has become a powerful mainstay tool in high resolution structural biology thanks to advances in hardware, software and sample preparation technology. In my thesis, I utilized this technique to unravel the function of various challenging biological macromolecules. My first focus was bacterial ribosomal biogenesis: understanding how bacteria assemble their ribosomes. Ribosomes are the factories of the cell, responsible for manufacturing all proteins. Ribosomes themselves are huge, with the bacterial version made of 52 proteins and 4566 RNA nucleotides. How these components assemble has long been a mystery. Early groundbreaking work sketched out a biogenesis pathway using purified components in vitro – but under non-physiological conditions. We sought to understand how the bacterial ribosome – specifically the large subunit 50S – is built inside the cell. To achieve this, we engineered a conditional knock-out bacterial strain that lacked one specific ribosomal protein (L17). This caused the cells to accumulate incomplete intermediates along the 50S biogenesis pathway. These intermediates were purified and examined with mass spectrometry and single-particle cryo-EM. Two major hurdles arose in this project: firstly, the biogenesis intermediates exhibited a preferred orientation when vitrified for cryo-EM analysis. This means that instead of showing many different views required for reconstruction of the 3D structure, the intermediates only adopted one view on the cryo-EM grid. To overcome this problem, we engineered a method to induce additional views on the microscope by tilting the stage. Using another test protein that also exhibited preferred orientation (hemagglutinin), we optimized and characterized this new tilt methodology and showed it was generally applicable to overcoming preferred orientation, regardless of type of specimen. We also created a software tool, called 3DFSC (3dfsc.salk.edu), for other microscopists to calculate the degree of directional anisotropy in their structures due to preferred orientation. Using this tilt strategy finally enabled the structural elucidation of our 50S intermediates. The second challenge in the project was the large amount of heterogeneity present in the sample. Through hierarchical 3D classification schemes using the latest software tools, we obtained 14 different 50S intermediate structures, all from imaging a single cryo-EM grid. By analyzing the missing components of each intermediate, and corroborating these observations with mass spectrometry data, we outlined the first in vivo 50S assembly pathway, and showed that ribosome assembly occurs step-wise and in parallel pathways. My second focus was on pushing the resolution limits of single-particle cryo-EM using adeno-associated virus (AAV) serotype 2 homogeneous virus-like particles (VLPs) that lack DNA. Exploiting several technical advances to improve resolution, including use of gold grids, per-particle CTF refinement, and correction for Ewald sphere curvature, we managed to obtain a 1.86 Å resolution reconstruction of the AAV2L336C variant VLP, the highest resolution icosahedral virus reconstruction solved by single-particle cryo-EM to date. Using our structure, we were able to show improvements using Ewald sphere curvature correction and shed light on the mechanistic basis as to why the L336C mutation resulted in defects in genome packaging and infectivity compared to the WT viral particles. My third focus was the understanding of small membrane proteins involved in infectious diseases. Membrane proteins are a challenge to work with due to the need for them to be extracted from the lipid bilayer for studies as compared to soluble proteins. Infectious diseases have a huge burden on society, with the top three infectious agents accounting for 2.7 million deaths in 2016. The third most deadly infectious disease is malaria, a mosquito-borne parasite which kills 450,000 people annually. One drug used early on for treating malaria was chloroquine but its usefulness waned due to development of resistance. Chloroquine resistance is mediated by the chloroquine resistance transporter (PfCRT). Although small (49 kDa) for single-particle cryo-EM, we solved its structure by using fragment antibody technology to add mass and help with image alignment and 3D reconstruction. The 3.2 Å structure resembles other drug metabolite transporters, and the chloroquine resistance mutations map to a ring around the central cavity, suggesting this central pore as the drug binding site. Tuberculosis (TB) is the top killer, above malaria and HIV/AIDS, being responsible for 1.3 million deaths. In TB, a common antibiotic target is the bacterium’s cell wall synthesis machinery. One family of such enzymes is the arabinosyltransferases, which synthesize the critical arabinose sugars. Using single-particle cryo-EM, we solved two high resolution structures of one such essential enzyme, AftD. Due to the low yield of the protein, a picoliter automated sample dispensing robot was crucial to allow for initial cryo-EM analysis. We then performed mutagenesis studies in M. smegmatis, a TB model organism, which uncovered the critical amino acid residues in the active site and determined that a bound acyl-carrier-protein was likely involved in allosteric inhibition of AftD’s active site. Another member of the family, EmbB, is the target of a widely used frontline TB drug called ethambutol. We have solved the high resolution structures of the apo and putative drug-bound states of EmbB, allowing us to map out, for the first time, both the active site and drug-resistance mutations of this crucial enzyme. The atomic structures of the functional pockets of Mycobacterial AftD and malarial PfCRT will hopefully enable structure-based drug design to improve existing drugs or potentially even develop new treatments against these infectious maladies. In conclusion, the continual and breathtaking improvements in single-particle cryo-EM methodology has been instrumental in allowing the elucidation of the aforementioned biological macromolecules from ribosome biogenesis intermediates, to AAV2 vehicle, Plasmodium drug resistance transporter to mycobacterial glycosyltransferases – structures of which help explain biological function.

The deformation mechanisms operating in diamond-like carbon (DLC) coatings on (100) and (111) Si, has been investigated. The effect of coating thickness, indenter geometry, substrate orientation and deposition technique on the deformation of DLC coatings and the underlying substrate was studied by undertaking nanoindentation followed by subsurface microstructural characterization. Uncoated (111) Si was also investigated for comparison. The observed microstructural features were correlated to the indentation response of the coatings and compared with simulation studies, as well as observations on uncoated Si. In uncoated (111) Si, phase transformation was found to be responsible for the discontinuities in the load-displacement curves, similar to (100) Si. However, slip was activated on {311} planes instead of on {111} planes. Moreover, the density of defects was also significantly lower and their distribution asymmetric. The coatings were adherent, uniformly thick and completely amorphous. The load-displacement curves displayed several pop-ins and a pop-out, the indentation loads for the first pop-in and the pop-out depending primarily on the thickness of the coating. The coatings exhibited localized compressive deformation in the direction of loading without any through-thickness cracks. The extent of this localized deformation increased with indentation load. Hardness and thickness of the coatings and the geometry of the indenter influenced the magnitude of compressive strains. Harder and thinner coatings and a blunt indenter exhibited the minimum degree of deformation. Densification by rearrangement of molecules has been suggested as the mechanism responsible for plastic compression. At indentation loads corresponding to the first pop-in, (100) and (111) silicon substrates initially deformed by <111> and <311> slip respectively. Higher indentation loads caused phase transformation. Therefore, unlike in uncoated Si, dislocation nucleation in the Si substrate has been proposed as the mode responsible for the first pop-in. Subsequent pop-ins were attributed to further deformation by slip and twinning, phase transformation and extensive cracking (median and secondary cracks) of the substrate. The pop-out, however, was ascribed to phase transformation. Extensive deformation in the substrate, parallel to the interface, is attributed to the wider distribution of the stress brought about by the DLC coating. Good correlation was obtained between the nanoindentation response, microstructural features and simulation studies.