Semiconductor nanostructures have attracted great interest owing to their unique physical properties and potential applications in nanoscale functional devices. The enhancement of the physical properties of semiconductor nanostructures and their performance in devices requires a deeper understanding of their fundamental microstructural properties. Thus this thesis is focused on the experimental and theoretical studies of the microstructural properties of two important semiconductor nanostructures: axial heterostructured silicon nanowires with varying doping and indium nitride colloidal nanoparticles. In this thesis, axial heterostructured silicon nanowires with varying doping were synthesized on an oxide-removed Si{111} substrate using a vapour-liquid-solid approach. Their fundamental microstructural properties, including the crystalline structure, wire growth direction and morphologies, were studied using various characterization techniques. It is found that a very small fraction of the silicon nanowires crystallize in a hexagonal (wurtzite) phase, which is thermodynamically unstable in bulk silicon under ambient conditions, while a large majority of the synthesized silicon nanowires exhibit the expected diamond cubic crystalline structure. About 75% of the diamond cubic silicon nanowires synthesized grow in a single <111> direction, while the rest contain growth-related kinks, where the nanowire switches to another direction during the growth. The ~109° silicon nanowire kinks are the most commonly observed, and the growth direction before and after such ~109° kink are both <111>. The sidewalls of silicon nanowires do not change abruptly at the ~109° kink, but exhibit an elbow-shaped structure. It is also found that the nanowire sidewalls exhibit periodic nanofaceting, which is strongly doping-dependent. The nanofaceting is found to occur during the enhanced sidewall growth that arises when the diborane dopant gas is introduced. A thermodynamic model predicting the dependence of nanofacet period on the wire diameter is developed. Another semiconductor nanostructure studied in this thesis is indium nitride colloidal nanoparticles, which were grown using a solution-phase chemical method. The formation of such indium nitride colloidal nanoparticles is confirmed by studying their compositions, crystalline structures and shape using various electron microscopy techniques. The size of the indium nitride colloidal nanoparticles was controlled by varying the time of solution-phase reactions. The most probable size of the colloidal nanoparticles increases and the size distribution broadens with the increase of reaction time. The crystalline structures of the indium nitride colloidal nanoparticles are found to be particle size dependent. The observed dependence of the band gap blueshift of the indium nitride colloidal nanoparticles on the reaction time (hence the particle size) is explained by the quantum-size effect.

The interwall spacing of multi-walled carbon nanotubes has an effect on their physical and chemical properties. Tubes with larger interwall spacing - compared to the spacing where the carbon atoms are in their natural distance to each other - are for instance expected to be mechanically less stable. Considering the MWCNT interwall spacing’s dependence on the tube size, three interesting previous studies with slightly different conclusions can be found. All of them conclude an increase of the interwall spacing with a decreasing tube size. We describe their analysis procedure, compare them to each other and to our own measured data. In the beginning of our analyses, we determine the expected inaccuracy for measured distances out of TEM images being up to 10 % and we show the impacts of the TEM’s defocus, a powerful setting in TEM imaging. Finally, we suppose that the interwall spacings are not as strongly varying as one previous study concludes, but our analyses are relatively in harmony with the two other studies. The interwall spacings from tubes with an inner diameter larger than 5 nm are relatively constant within the whole tube. Furthermore, it appears that the middle spacings (excluding the outer- and innermost ones) show values that are most consistent with the interlayer spacings of turbostratic graphite. In underfocused images, the outer- and innermost spacings tend to have values being slightly smaller than the middle ones from the same tube.

The current work is part of the EPSRC MUZIC project, which established the collaboration among several universities to carry out a multidiscipline study on the breakaway oxidation of zirconium alloys. The overall goal of the project is to further understand the mechanisms of the oxidation and breakaway process of zirconium alloys. This thesis describes the nano/micro-structural study and nano-analysis of the corroded zirconium alloys using up-to-date TEM and 3D focused ion beam (FIB) slicing and reconstruction techniques. The work mainly focused on the characterization of ZIRLO. The oxide morphology in general comprises an inner columnar layer and an outer equiaxed layer, except for a post-second transition oxide grown on a Zr-Nb-Ti test alloy with a very poor corrosion resistance, which exhibits generally only equiaxed grains throughout the whole oxide scale. Detailed investigation reveals oxides in a slower oxidation stage exhibit better developed columnar grain structure. All the oxides, independent of different corrosion stages and alloy types, contain predominantly monoclinic oxide and a small amount of tetragonal oxide. Defects at different length scales were examined. In stead of a sudden burst of crack nucleation at the kinetic transition, a gradual introduction of cracks parallel to the metal/oxide interface throughout the pre-transition stage is found, suggesting no direction correlation between the formation of cracks and the transition. Besides cracks, the oxide also contains different forms of nano-porosity: isolated pores of 1-3 nm or interconnected pores at grain boundaries. The density of interconnected porosity, especially those along the oxide growth direction, increases towards the oxide surface, evolving over time. It is suggested that the kinetic transition is related to the development of an interconnected porosity down to the metal/oxide interface, providing easy pathways for the transportation of oxidation species. The metal-oxide interface has a wavy morphology both in the micrometer and nanometer scale. The roughness develops to a maximum just before the first kinetic transition. An intermediate suboxide layer with complex 3D morphology between the bulk oxide and the metal substrate is found. Quantitative EELS analysis shows the composition of this layer to be 40-50 at. % oxygen. The suboxide appears to develop in thickness with increasing oxidation time for the pre-transition oxides, while is very thin or absent in the post-, and post-second transition oxides. In the suboxide region, multiple phases including &alpha;-Zr, &omega;-Zr, tetragonal oxide and a phase with an unidentified structure were found, suggesting different structures can coexist in the suboxide layer. Second-phase particles (SSPs) of &beta;-Nb and hexagonal Zr(Fe,Nb)₂ types were found in ZIRLO samples and FCC Zr(Fe,Cr)₂ was the predominant type in Zircaloy-4. The SPPs showed delayed oxidation compared to surrounding Zr. In ZIRLO, those containing high Fe contents were found to be oxidized and transform into an amorphous state much earlier than &beta;-Nb. Hydrides of different types (&gamma;, &sigma; and &epsilon;) were observed in the metal and metal/oxide region for both Zircaloy-4 and ZIRLO samples. A higher density of hydrides was seen in post-transition oxides of ZIRLO than in pre-transition oxides.

This thesis considers the theory and calculations of image formation mechanisms for various modes of three-dimensional imaging in aberration-corrected scanning transmission electron microscopy. Discrete tomography is used to determine and refine the three-dimensional structure of molecular nanowire bundles. The structure determination is expedited by the use of annular dark-field imaging, an incoherent imaging mode which provides directly interpretable images. The development of spherical aberration correctors and the subsequent reduction in probe sizes, including the depth of field, has made optical depth sectioning a feasible technique. The localisation in three dimensions of substitutional impurity atoms in zone-axis imaging is discussed. Both the channelling of the probe and the pre-focussing effect of the atomic column play an important role in determining the depth response of the impurity atom. Interband scattering within a sample is shown to be influential in imaging crystals containing dislocations and optical depth sectioning is explored as a possible option for overcoming surface relaxation effects in the imaging of screw dislocations end-on. The possibility of extending the optical depth sectioning approach using aberration-corrected scanning confocal electron microscopy is discussed. The coherent and incoherent imaging modes, involving elastically and inelastically scattered electrons respectively, are investigated.

This thesis concerns the experimental application of the technique of optical sectioning in the aberration-corrected scanning transmission electron microscope (STEM). Another aim was to perform optical sectioning experiments on the still relatively new scanning confocal electron microscope (SCEM). To test the feasibility of this technique, experiments were performed on a variety of samples to measure the achievable depth response. Deconvolution methods were explored in an attempt to further improve the depth response. Finally, some of the first optical sectioning experiments were performed in the SCEM using both elastic and inelastically scattered electrons. The results showed a clear need to investigate confocal electron microscopy due to the missing cone problem for incoherent imaging in the STEM. This is particularly evident when imaging objects of greater width than the STEM probe. Confocal electron microscopy using inelastic electrons appeared to be a promising imaging mode for the future with this thesis consisting of early work in the field.

Canola (Brassica napus) contributes $19.3 billion dollars to the Canadian economy each year as a result of its oil- and protein-rich seeds. These economically important seed products are produced in highest concentration in the embryo. Embryo development is supported nutritionally and structurally by the maternal subregions, which include the inner (ISC) and outer distal seed coat (OSC), the chalazal seed coat (CZSC), and the chalazal proliferating tissue (CPT). Research on the maternal seed subregions is limited to the SC as a result of its accessibility; the embedded CZSC and CPT subregions have yet to be characterized in canola. Using light and transmission electron microscopy, I found the CZSC and CPT to be anatomically distinct and experience profound changes throughout seed development. To understand these changes at the RNA level, laser microdissection and RNA sequencing were used to profile these subregions spatially and temporally from the ovule to mature green stage of seed development. Employing vigorous bioinformatics analyses, I found that the maternal subregions are transcriptomically distinct and possess unique RNA populations. From here I began to elucidate the biological processes operating within the maternal subregions. As a whole, the maternal subregions appear to have a critical role in transporting nutrients to the filial subregions as well as in coping with oxidative stress produced during these energy-rich processes. Additionally, using CanEnrich, I was able to generate predictive transcriptional circuits regulating the biological processes occurring within the maternal seed. This research has produced the most comprehensive dataset on the canola seed to date and will provide a valuable resource for research on seed development as well as seed improvement. / October 2016

The processing and properties of novel polymer-based nano-composite (PNC) dielectrics for capacitor applications has been studied. PNCs were fabricated via a vacuum based deposition technique and their micro/nano-structure, chemical and dielectric properties investigated. After process development and optimisation, co-deposited Al and nylon-6 PNCs had a dielectric constant k&sim;7 at an approximate Al volume fraction of 0.3 that agreed with analytical predictions if it was assumed that the Al transformed to an oxide in-situ and/or after deposition. The significant effect of absorbed water vapour and temperature on PNC dielectric properties was revealed using different types of post-deposition heat treatment. Alternately-deposited PNCs consisting of Al or Ag 2-20 nm layers sandwiched between nylon-6 layers were fabricated in which the overall PNC Al or Ag volume fraction was controlled by varying the nominal Al or Ag layer thickness. Ag layers comprised of discrete nano-islands that produced a nano-capacitor network effect that increased k to &sim;11. In the case of Al layers, when the layer thickness was &ge; 5 nm, corresponding to a nominal volume fraction of 0.1, Al (core)-oxide (shell) nanoparticles were formed and the PNC dielectric constant increased to &sim;19. The detailed nano-structure of the core-shell particles was studied using various types of transmission electron microscopy (TEM), and the elevations in dielectric constant ascribed to multiple-interface polarisation effects dependent on the formation of the core-shell structure. PNCs based on alternate deposition of Ti sandwiched in nylon-6, and then both Ti and Ag in nylon-6 were also fabricated, with k reaching &sim;73 for Ag+Ti/nylon-6 PNCs. As well as Ti-based core (metal)-shell (oxide) particles, the Ag volume fraction was sufficiently high in the 10 nm nylon-6 layers to again form a nano-capacitor network that contributed to the overall device capacitance and effective dielectric constant. Again, various types of high magnification TEM were critical in resolving the Ti-based core-shell structure and its role in high-k behaviour. The vacuum-based alternate deposition technique has been developed to offer ease of operation, reliability, flexibility and applicability to chemically different filler and matrix systems in the fabrication of high-k PNC based capacitors, in which high-k performance relies critically on the formation of core (metal)-shell (oxide) particles in both Al and Ti based systems.

No description available.

Septinas são GTPases consideradas como um novo componente do citoesqueleto. Essas proteínas interagem entre si para formar heterocomplexos filamentosos e estruturas de alta ordem que são importantes para a citocinese e uma variedade de outros processos celulares. Existem muitos aspectos mecânicos dessas proteínas que não são totalmente compreendidos, incluindo a forma como os heterocomplexos se agrupam corretamente. Em humanos, há 13 genes que codificam septinas, classificadas em quatro grupos quanto à similaridade em relação à estrutura primária. O complexo hexamérico SEPT7-SEPT6-SEPT2-SEPT2-SEPT6-SEPT7 foi o melhor caracterizado, com uma estrutura cristalina resolvida à 4 &Aring;. Segundo às Regras de Kinoshita, as septinas desse complexo podem ser substituídas nesse arranjo por outras pertencentes ao mesmo grupo. Neste trabalho utilizamos a técnica de microscopia eletrônica de transmissão com análise de partícula única para estudar dois complexos de septinas. Um dos complexos estudados neste projeto é formado por septinas humanas, para as quais atualmente não há informações estruturais disponíveis. O complexo SEPT5-SEPT6-SEPT7 foi expresso heterólogamente em E. coli e purificado em alta concentração salina para evitar a polimerização. A análise de partículas únicas de imagens por contrastação negativa mostrou a presença de partículas alongadas de aproximadamente 25 nm de comprimento, compostos por seis monômeros, como esperado. Com o objetivo de localizar a posição da SEPT5 no complexo, foi realizada uma fusão com MBP (Maltose Binding Protein) e imunomarcação com anticorpo monoclonal anti-SEPT5, concluindo que a SEPT5 está localizada na extremidade do complexo hexamérico. Porém, a SEPT5 pertence ao mesmo grupo da SEPT2, que foi relatada estar localizada no centro do hexâmero. Este resultado possibilitou uma nova discussão sobre a maneira que as septinas formam os complexos e, como a sensibilidade à concentração salina está relacionada com a fragilidade da interface NC, análogo ao observado em complexos de Saccharomyces cerevisiae. Um complexo de Ciona intestinalis incluindo a SEPT2, SEPT6, SEPT7 e SEPT9, também expresso heterólogamente em E. coli, foi preparado por contrastação negativa. A análise de partícula única das imagens coletadas mostrou um heterocomplexo aparentemente hexamérico, embora fosse esperado um octâmero devido à presença das quatro septinas diferentes, sendo uma pertencente à cada um dos quatro grupos. Os resultados deste trabalho proporcionaram um avanço na compreensão da formação de heterocomplexos de septinas e como essas proteínas interagem umas com as outras nesta montagem. / Septins are GTPases that appear to be a novel component of the cytoskeleton. These proteins interact with each other to form filamentous heterocomplexes and high order structures which are important for cytokinesis and a variety of other cellular processes. There are many mechanistic aspects of these proteins that are not fully understood, including how the heterocomplexes correctly assemble. In humans, there are 13 genes encoding septins, classified in four groups based on primary structure. The SEPT7-SEPT6-SEPT2-SEPT2-SEPT6-SEPT7 hexameric complex was the best characterized, with a crystalline structure solved at 4 &Aring;. According to Kinoshita´s Rules, the septins of this complex can be replaced in this arrangement by others belonging to the same group. In this work, we used transmission electron microscopy with single particle analysis to study two septin complexes. One of the complexes studied in this project is composed of three human septins, for which there is currently no structural information available. The SEPT5-SEPT6-SEPT7 complex was heterologously expressed in E. coli and purified at high salt concentration to avoid polymerization. Single particle analysis of negatively stained samples showed the presence of elongated particles of approximately 25 nm in length. To locate SEPT5 in the complex, a fusion with MBP (Maltose Binding Protein) and immunoblotting with anti-SEPT5 monoclonal antibody was performed, concluding that SEPT5 is located at the end of the hexameric complex. However, SEPT5 belongs to the same group as SEPT2, which was reported to be located in the center of the hexamer. This result allowed for a new discussion on the way that septins form heterocomplexes and also, on how the sensitivity of the NC interface in related to salt concentration, analogous to that observed in the heterocomplex of Saccharomyces cerevisiae. A Ciona intestinalis complex including SEPT2, SEPT6, SEPT7 and SEPT9, also expressed heterologously in E. coli, was prepared by negative staining. The single particle analysis of the collected images showed an apparently hexameric heterocomplex, although an octamer was expected due to the presence of the four different septins, one belonging to each of the four groups. The results of this work represent advances in the understanding of the formation of septin heterocomplexes and how these proteins interact with each other during assembly.

Os primatas neotropicais, ou primatas do novo mundo, são pertencentes a um grupo diverso e variado de animais, com características anatômicas, comportamentais e taxonômicas próprias, que os diferem dos primatas do velho mundo. Estima-se que representem 31% dos primatas não-humanos do planeta. Têm sofrido com as altas taxas de crescimento populacional e perturbação antrópica resultante do desflorestamento, agricultura e criação de gado. Com o intuito de reverter esta situação e maximizar o potencial reprodutivo das espécies, o desenvolvimento de biotecnologias associadas à reprodução tem sido amplamente justificado nos dias de hoje, por representarem importantes ferramentas reprodutivas, contribuindo para a preservação da biodiversidade e manutenção da diversidade genética. Assim, o objetivo do presente estudo foi padronizar a colheita de sêmen de Alouatta guariba clamitans por eletroejaculação por via retal com posterior análise do sêmen fresco, procedimentos nunca descritos para a espécie, e adaptar o método de preparo de sêmen de Leontopithecus chrysomelas, Alouatta caraya e Alouatta guariba clamitans para microscopia eletrônica de transmissão, permitindo a comparação da ultraestrutura dos espermatozoides das três espécies e apresentando resultados também inéditos na literatura científica. Para este estudo, foram utilizados quatro exemplares de L. chrysomelas, dois exemplares de A. caraya e dois exemplares de A.g. clamitans, machos adultos mantidos em cativeiro. L. chrysomelas tiveram o sêmen colhido por vibroestimulação peniana, e A. caraya e A.g. clamitans foram submetidos à eletroejaculação por via retal. Após a obtenção dos ejaculados, o sêmen foi avaliado quanto ao volume, pH, concentração, motilidade, integridade de membrana plasmática, integridade de membrana acrossomal e morfologia, e posteriormente preparado para microscopia eletrônica de transmissão. A análise dos 12 espermatozoides das três espécies estudadas revelou que todos apresentam os componentes básicos descritos para o espermatozoide humano cabeça, colo e cauda, formada pelas peças intermediária, principal e terminal com variações na forma e tamanho de cada componente. As diferenças mais significativas encontradas entre os espermatozoides comparados foram extensão de acrossomo, comprimento, largura e organização de peça intermediária. O presente estudo atingiu os objetivos propostos, apresentando resultados inéditos na literatura científica / The neotropical primates, also known as primates of the new world, are a diverse and varied group of animals, with unique anatomical and taxonomic characteristics, as well a unique behaviour, that distinguish those from the old world primates. It is estimated that these present 31% of the non-human primate population of the planet. High taxes of populational growth and anthropological disturbance have been undergoing due to deforestation, agriculture and cattle farms. In order to revert this situation and maximize the reproductive potential of the species, the development of biotechnologies associated to the reproduction are widely justified nowadays, for representing important reproductive tools, contributing to the preservation of the biodiversity and maintenance of genetic diversity. Hence, the purpose of this study was to collect Alouatta guariba clamitans semen by rectal electroejaculation then analyze the fresh semen, procedures never before described for the species, and adapt the preparation method of Leontopithecus chrysomelas, Alouatta caraya and Alouatta guariba clamitans semen for electron transmission microscope, allowing the comparison of the spermatozoa ultrastructure from the three species and also presenting new results to the scientific literature. For this study, it was used four specimens of L. chrysomelas, two specimens of A. caraya and two specimens of A.g. clamitans, adult males kept in captivity. L. chrysomelas had the semen taken by penine vibratory stimulation, and A. caraya and A.g. clamitans were submitted to rectal electroejaculation. After the semen was obtained, it was evaluated regarding the volume, pH, concentration, motility, sperm membrane integrity, acrosome integrity and morphology, and then prepared for electron transmission microscopy. The analysis of the spermatozoa of the three studied species revealed that all present the basic components described for the human spermatozoa - head, neck region and tail, formed by middle, principal and terminal pieces - with variations in 14 shape and size of each component. The most significant differences found between the compared spermatozoa were the acrosome extension and middle piece length, thickness and organization. The present study attained the proposed goals, presenting unprecedented results for the scientific literature