This thesis discusses various large multi-dimensional dataset analysis methods and their applications. Particular attention is paid to non-linear optimization analyses and general processing algorithms and frameworks when the datasets are significantly larger than the available computer memory. All new presented algorithms and frameworks were implemented in the HyperSpy analysis toolbox. A novel Smart Adaptive Multi-dimensional Fitting (SAMFire) algorithm is presented and applied across a range of scanning transmission electron microscope (STEM) experiments. As a result, the Stark effect in quantum disks was mapped in a cathodoluminescence STEM experiment, and fully quantifiable 3D atomic distributions of a complex boron nitride core-shell nanoparticle were reconstructed from an electron energy loss spectrum (EELS) tilt-series. The EELS analysis also led to the development of two new algorithms to extract EELS near-edge structure fingerprints from the original dataset. Both approaches do not rely on standards, are not limited to thin or constant thickness particles and do not require atomic resolution. A combination of the aforementioned fingerprinting techniques and SAMFire allows robust quantifiable EELS analysis of very large regions of interest. A very large dataset loading and processing framework, “LazySignal”, was developed and tested on scanning precession electron diffraction (SPED) data. A combination of SAMFire and LazySignal allowed efficient analysis of large diffraction datasets, successfully mapping strain across an extended (ca. 1 μm × 1 μm) region and classifying the strain fields around precipitate needles in an aluminium alloy.

abstract: ABSTRACT Along with the fast development of science and technology, the studied materials are becoming more complicated and smaller. All these achievements have advanced with the fast development of powerful tools currently, such as Scanning electron microscopy (SEM), Focused Ion Beam (FIB), Transmission electron microscopy (TEM), Energy dispersive X-ray spectroscopy (EDX), Electron energy loss spectroscopy (EELS) and so on. SiTiO3 thin film, which is grown on Si (100) single crystals, attracts a lot of interest in its structural and electronic properties close to its interface. Valence EELS is used to investigate the Plasmon excitations of the ultrathin SrTiO3 thin film which is sandwiched between amorphous Si and crystalline Si layers. On the other hand, theoretical simulations based on dielectric functions have been done to interpret the experimental results. Our findings demonstrate the value of valence electron energy-loss spectroscopy in detecting a local change in the effective electron mass. Recently it is reported that ZnO-LiYbO2 hybrid phosphor is an efficient UV-infrared convertor for silicon solar cell but the mechanism is still not very clear. The microstructure of Li and Yb co-doped ZnO has been studied by SEM and EDX, and our results suggest that a reaction (or diffusion) zone is very likely to exist between LiYbO2 and ZnO. Such diffusion regions may be responsible for the enhanced infrared emission in the Yb and Li co-doped ZnO. Furthermore, to help us study the diffusion zone under TEM in future, the radiation damage on synthesized LiYbO2 has been studied at first, and then the electronic structure of the synthesized LiYbO2 is compared with Yb2O3 experimentally and theoretically, by EELS and FEFF8 respectively. / Dissertation/Thesis / Ph.D. Materials Science and Engineering 2013

No description available.

M.Sc. / Please refer to full text to view abstract

The research work presented in this thesis comprises an electron microscopy and spectroscopy study of crystal defects that relate to the occurrence of different colours in natural and synthetic diamonds. Two principal lines of investigation have been covered, each with its own objective. The first aims to identify the source of brown colour in natural and synthetic diamond and the second to ascertain the distribution of colour inducing point defects in synthetic diamond. An outline of both areas of research is given below.1) Brown colour in natural and synthetic diamondsColour is a physical property that can be very difficult to characterise in diamond and consequently it receives regular attention from scientists working in the gem industry. In this work, the crystal structures of brown and colourless natural type IIa diamonds are compared along with brown coloured synthetic diamonds manufactured using the chemical vapour deposition (CVD) process. Numerous attempts have been made to trace the origin of brown tints in natural diamond, with the most likely sources, dislocations and nitrogen impurities, ruled out through the application of various analytical techniques. Recently more emphasis has been placed on the study of vacancy related defects in natural diamond and their influence on colour. Differences between the annealing characteristics of brown coloured natural and CVD diamonds suggest that the defect or defects responsible for the brown colour might be different for each type of diamond. The focus of this research work is the analysis of vacancy defects of the order of 1nm in size using aberration corrected scanning transmission electron microscopy (AC-STEM). The sub-nanometre size probe afforded by this technique allows such defect structures to be resolved much more readily than with conventional high resolution transmission electron microscopy (HR-TEM). Small-scale contrast variations are apparent in the lattice images of brown diamonds but not of the colourless variety. These features have been compared to simulated phase contrast images of vacancy clusters in diamond.2) Yellow / Green coloured synthetic diamonds grown using metal solvent catalystSynthetic diamonds for jewellery and industrial applications are routinely manufactured under high pressure-temperature (HPHT) conditions that closely resemble those found during the creation of natural diamonds. Although the manufacturing equipment can vary in design, the HPHT process that occurs inside the reaction vessel remains essentially the same. During processing, the carbon source material is dissolved into a molten metal and then precipitated onto tiny seed diamonds that are added to the reaction chamber. Much time and effort has been expended in refining this process to reduce impurities and defects in the finished diamonds. The presence of remnant transition metal atoms (e.g. nickel) in the crystal structure influences the electronic properties and in particular the colour of the diamonds. The position and configuration of these metallic defects has previously been studied by a variety of analytical techniques, including optical absorption-luminescence spectroscopy and electron paramagnetic resonance spectroscopy (EPR). These studies have proposed a number of optically active nickel centres at both substitutional and interstitial sites. Their association with vacancies and nitrogen atoms has also been highlighted. This work uses electron microscopy and spectroscopy to characterise the nickel defects in synthetic type 1b diamonds.

京都大学 / 新制・課程博士 / 博士(理学) / 甲第23459号 / 理博第4753号 / 新制||理||1681(附属図書館) / 京都大学大学院理学研究科化学専攻 / (主査)教授 倉田 博基, 教授 島川 祐一, 教授 寺西 利治 / 学位規則第4条第1項該当 / Doctor of Science / Kyoto University / DGAM

In the last two decades, advances in the dark field detectors and microscopes of scanning transmission electron microscopy (STEM) have inspired a resurgence of interest in quantitative STEM analysis. One promising avenue is the use of STEM as a nanothermometric probe. In this application, thermal diffuse scattering, captured by a CCD camera or an annular dark field detector, acts as an indirect measurement of the specimen temperature. One challenge with taking such a measurement is achieving adequate sensitivity to quantify a change in scattered electron signal on the order of 1% or less of the full electron beam. Another difficulty is decoupling the thermal effect on electron scattering from scattering changes due to differing specimen thicknesses and materials. To address these issues, we have developed a method using STEM, combined with electron energy loss spectroscopy (EELS), to produce a material-specific calibration curve. On silicon, across the range 89 K to 294 K, we measured a monotonically increasing HAADF signal ranging from 4.0% to 4.4% of the direct beam intensity at a thickness-to-mean-free-path ratio of 0.5. This yielded a calibration curve of temperature versus full-beam-normalized, thickness-normalized HAADF signal. The method enables thermal measurements on a specimen of varying local thickness at a spatial resolution of a few nanometers. We demonstrated the potential of the technique for testing electron scattering models by applying single-electron scattering theory to the data collected to extract a measurement of the mean atomic vibration amplitude in silicon at 294 K. The measured value, 0.00738 ± 0.00002 nm, agrees well with reported measurement using X-rays.

Japanese eels (Anguilla japonicas) are snakelike fishes living in waters in the Asian region. In contrast to most fishes which are stenohalines that can only live in waters with a narrow range of salinity, Japanese eels are classified as euryhalines that can habitat in a broad range of salinity. As the lifecycle of Japanese eels consists of stages across fresh and seawater districts, a well-developed osmoregulation mechanism is needed to balance the intra- and extra- cellular osmolarity of the fishes throughout the seawater acclimation process. While fish gills are one of the organs that separating the ambient water and the inner body fluid of the fish, the fish gills of the Japanese eels have been studied as one of the most crucial organs for osmoregulation purposes. Yet, the osmoregulation and survival strategies of Japanese eels under hyperosmotic stress has not been fully elucidated. In chapter 2, this study has performed a transcriptome study on the ex vivo gill filament model of the Japanese eel to profile the molecular responses after a hypertonic treatment of 4 hours or 8 hours. The experiment is aimed to mimic the gill cells exposed to seawater in the seawater acclimation process of Japanese eels. A profile of differential expressed genes (DEGs) has been revealed that 577 DEGs were commonly upregulated and 711 DEGs were commonly downregulated in both 4- and 8-hours hypertonic treatment. Functional analysis and annotation have been processed with these DEGs, including Ingenuity Canonical Pathways analysis and gene ontology. These analyses have revealed that the cellular homeostasis of the gill cells has been disrupted and cell death responses has been induced by osmotic stress. The results have raises a concern that the maintenance of cellular viability and a cell death regulation mechanism are needed for the fishes to survive in the early stage of seawater acclimation. In chapter 3, this chapter demonstrated that gill cells in Japanese eels are susceptible to apoptosis when they are exposed to hyperosmotic treatments in both in vitro gill cell and the ex vivo gill filament model. To maintain the viability of the gills cells, two inhibitors of apoptosis, XIAP, and survivin, were seen to be expressed in gills cells. The expression of XIAP and survivin were upregulated by dexamethasone, which is an agonist mimicking the effect of cortisol on fishes in seawater acclimation. Meanwhile, the expression levels of the apoptosis executor, caspase 3, were downregulated. These data suggested that with the regulation of cortisol express in the fishes, XIAP and survivin are effective apoptosis regulators in the gill cells of Japanese eels. The study has demonstrated the molecular responses of the gills of Japanese eels exposed to hyperosmotic stress at the transcriptional level and post-translational level by using transcriptome studies and protein study respectively. The study has paved cell death regulation to be another the key field to study in understanding the ability of salinity tolerance in euryhalines.

Surface plasmon resonances at the nanoscale hold great potential for applications in many areas, and the characterization of plasmonic nanostructures plays a critical role in the realization of these applications. Electron energy loss spectroscopy (EELS) has emerged as a powerful characterization tool to study the response of plasmonic nanostructures due to its high spatial-resolution and the capability to probe bright as well as dark plasmonic modes. The main limiting factor of EELS is the energy resolution. However, in this thesis, we overcome this limitation using a combination of electron monochromation and the use of the Richardson-Lucy algorithm. We show that the algorithm could be used to obtain effective energy resolutions up to 10 meV. Using EELS we analyze the resonances of planar nanostructures, and we found that the supported resonances can be described as edge and cavity or film modes, behaving as 1D and 2D modes respectively. We also demonstrate that edge modes are unaffected by the presence of bends up to the critical angle of 90◦ where the modes start self-interacting producing large energy shifts. The interaction of plasmon resonances is also studied, and we show that the coupling can be reduced to three behaviors: coupling through the edge, coupling through a corner, and non-coupling. We propose a method to control the coupling through the edge in offset nanowires, by tuning the nodal alignment and spectral overlap of the edge modes. Finally, we analyze the plasmon modes supported by Koch snowflake fractal antennas, and we demonstrate that modes present in the fractals are formed by the edge modes supported by their characteristic edges. This thesis provides a complete picture of the surface plasmon resonances supported by planar nanostructures and demonstrates the ability of EELS to probe and image a wide variety of plasmonic resonances. / Thesis / Doctor of Philosophy (PhD)

La présence de lacunes d’oxygène dans les diélectriques est supposée dégrader les propriétés électriques des transistors « high-k metal gate ». Nous avons donc étudié les possibilités d’une nouvelle méthodologie pour analyser ces défauts dans des couches minces de HfO2. Il s’agit d’utiliser des techniques optimisées pour la caractérisation de nano-dispositifs i.e. la spectroscopie de perte d'énergie des électrons (EELS) en microscopie électronique en transmission et la cathodoluminescence (CL)calibrées par la spectroscopie d’annihilation de positons (PAS). Des films de HfO2 ont été déposés par ALD et PVD sur des substrats de silicium. Pour les besoins du PAS, des couches d’épaisseur (10 à 100nm) supérieure au standard de la nanoélectronique ont été élaborées. D’après leurs analyses par DRX,RBS/NRA, MEB, TEM. Ces couches présentent majoritairement une structure complexe et un excès d’oxygène important. Les résultats PAS dépendent de la technique de dépôt et du traitement thermique.Leur comparaison avec des caractérisations électriques sur les couches les plus minces indique la génération de champs électriques dans la couche, à l’interface avec le substrat et dans le substrat. Ces observations confirment la présence de charges évoquée dans la littérature. Ces études ont permis de mettre au point la méthodologie et les conditions d’acquisition et d’analyse des spectres EELS et CL.Ceux-ci dépendent de la technique de dépôt et du traitement thermique. Cependant la qualité des couches n’a pas permis d’isoler les effets de la stoechiométrie. Ce travail ouvre de nombreuses perspectives pour approfondir la compréhension des phénomènes se déroulant au sein des nano-dispositifs. / The presence of oxygen vacancies in high-k oxides is fore seen to have detrimental effects in high-kmetal gate MOS transistors. To validate this hypothesis, we investigate the possibility of using electron energy loss spectroscopy in an electron transmission microscope (EELS) and the cathodoluminescence(CL) calibrated by the positron annihilation spectroscopy (PAS) to analyze these defects in thin HfO2 layers.To develop this methodology, HfO2 films have been deposited both by ALD and PVD on silicon substrates. To make the samples adapted to the PAS depth resolution, the layers thicknesses (10 to100 nm) are higher than those used in microelectronics. According to XRD, RBS/NRA, MEB, TEM results, these layers present a complex structure and a large excess of oxygen.PAS results depend both on the deposition technique and on the heat treatment. They evidence the presence of electric fields in the oxide layer or at the interface with the substrate. Electrical measurements in the thinnest layers, confirm the presence of charges in the oxide layer as already mentioned in the literature. The sign of these charges changes with heat treatment and is in agreement with the PAS results.EELS improved data acquisition has been developed. The EELS and CL spectra have been analyzed using a systematic methodology allowing to extracting characteristic parameters. They depend on the deposition technique and the heat treatment. However, due to the poor quality of the layers, it has not been possible to isolate the effects of the stoichiometry. This work opens many perspectives to improve knowledge on phenomena occurring in devices.