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This thesis explores theoretical aspects of scanning transmission electron microscopy (STEM) and the comparison of simulation with experiment. / The long standing contrast mismatch problem between theory and experiment in conventional high resolution transmission electron microscopy (HRTEM) is examined using the principle of reciprocity and bright field scanning transmission electron microscopy (BFSTEM). It is found that quantitative agreement between theoretical and experimental images is possible provided that theory suitably accounts for the spatial incoherence of the source, and that experimental images are placed on an absolute scale with respect to the incident beam current. Agreement between theory and experimental image contrast is found to be independent of specimen thickness and probe defocus. / Core-loss electron energy-loss spectroscopy (EELS) is a powerful experimental tool with the potential to provide atomic-resolution information about the electronic structure at defects and interfaces in materials and nanostructures. Interpretation, however, is nonintuitive due to the nonlocal ionization potential. Novel improvements in microscope design and operating environment have enabled two dimensional chemical maps. This has permitted a more thorough theoretical analysis. This thesis compares experimental STEM EELS images of LaMnO3, BiSrMnO3 and Si samples to the relevant theoretical simulations. Image features which at first appear counter intuitive are discussed and explained with the accompanying theoretical simulations. It is demonstrated, using a sample of SrTiO3, that more direct interpretation of atomic resolution chemical maps is possible when using energy dispersive x-ray spectroscopy (EDS) in STEM. / This thesis considers extending chemical mapping in STEM EELS to three dimensions using depth sectioning. It explores, theoretically, the feasibility to depth section zone-axis aligned crystals that contain embedded impurities. In STEM EELS this is found to be possible for point defects but not for larger extended objects such as nanoparticles. / The theory describing the mechanism by which contrast is obtained in elastic scanning confocal electron microscopy (SCEM) is developed. It is shown that there is no first order phase contrast in SCEM and thus low image contrast. Finally, energy filtered scanning transmission electron microscopy (EFSCEM) is developed theoretically. The fundamental equation describing image formation is derived and an efficient computation method is developed to allow the rapid calculation of EFSCEM images.

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Submitted by Geandra Rodrigues (geandrar@gmail.com) on 2018-01-19T16:53:31Z No. of bitstreams: 1 humbertovargasduque.pdf: 4514345 bytes, checksum: 706c4aafb25bb9c14ffc14039c8c53d0 (MD5) / Approved for entry into archive by Adriana Oliveira (adriana.oliveira@ufjf.edu.br) on 2018-01-24T11:47:55Z (GMT) No. of bitstreams: 1 humbertovargasduque.pdf: 4514345 bytes, checksum: 706c4aafb25bb9c14ffc14039c8c53d0 (MD5) / Made available in DSpace on 2018-01-24T11:47:55Z (GMT). No. of bitstreams: 1 humbertovargasduque.pdf: 4514345 bytes, checksum: 706c4aafb25bb9c14ffc14039c8c53d0 (MD5) Previous issue date: 2016-07-29 / O avanço dos estudos teóricos e experimentais dos processos de interação de radiações ionizantes com o DNA [1]–[7] demonstrou que estas radiações, ao interagirem com sistemas biológicos, podem levar à produção de um número significativo de elétrons secundários. Tais elétrons, por sua vez, ao realizarem colisões inelásticas com biomoléculas, as levam a estados excitados (estados vibracionais e eletrônicos) e à produção de estados ressonantes. Estudos recentes [1], [3], [6] reportam que estes processos têm a real capacidade de causar mutação celular ou necrose, devido à simples e dupla quebra da cadeia de DNA, possuindo, portanto, grande potencialidade danosa a qualquer tecido vivo. Com o intuito de entender melhor estas interações de elétrons de baixa energia com as espécies encontradas em sistemas biológicos, no presente trabalho utilizou-se a Espectroscopia de Perda de Energia de Elétrons para estudar as seções de choque diferenciais (SCD) e integrais (SCI). A região de energias de impacto utilizada foi capaz de promover excitação de níveis vibracionais do tetrahidrofurano (THF) e do álcool α-tetrahidrofurfuril (THFA - α-tetrahydrofurfuryl álcool) e bandas de Rydberg de estados eletrônicos do THFA. Estas espécies moleculares foram escolhidas por serem quimicamente análogas aos anéis de açúcar presentes na estrutura do fosfato-desoxirribose, constituintes do DNA, sendo THFA identificado recentemente, como uma melhor opção análoga à estrutura desoxirribose, quando comparado a sua espécie química semelhante, a molécula de THF. As energias de impacto de elétrons utilizadas para o THFA, foram de 20, 30, 40 e 50eV, enquanto o intervalo angular dos elétrons espalhados foi de 10°- 90°. Já para a molécula de THF, tais energias foram de 15, 20, 30 e 50eV, enquanto que os processos de espalhamento foram estudados na faixa angular de 15º - 90º. Nesse sentido, as SCD’s e SCI’s de THFA, apresentaram sutil diferença das obtidas por Khakoo et al. [8] para THF, em razão de suas propriedades físico-químicas diversas. A importância do momento de dipolo e polarizabilidade das moléculas nos espalhamentos de elétrons foi verificada, principalmente seus reflexos nas SCD’s para os baixos ângulos de espalhamento (≤30°). Foram utilizados, ainda, cálculos teóricos, realizados pela parte teórica deste grupo de pesquisa, para a comparação com os dados experimentais aqui apresentados, obtendo-se excelente concordância, o que levou a comprovação dos modelos utilizados. Ademais, realizou-se a revisão do trabalho de Garland et al. [9], o que demonstrou que a faixa de energia e os poucos modos vibracionais considerados em seu trabalho, derivados de Allan [10], deixam a desejar no que tange a completude dos estudos das propriedades de transporte. A apresentação do trabalho inclui primeiramente os embasamentos teóricos importantes para a análise dos dados obtidos e dos cálculos teóricos realizados. Posteriormente, é apresentado uma descrição do Espectrômetro de Perda de Energia de Elétrons utilizado e a estrutura de análise de dados. Por fim, são apresentados os dados experimentais e teóricos obtidos no trabalho e as discussões. Adicionalmente, é feita uma revisão do conjunto de dados de excitações de estados vibracionais do THF utilizados em outros estudos publicados na literatura, para a obtenção de propriedades de transporte de elétrons neste gás. / The progress of theoretical and experimental studies of ionizing radiation interaction processes with DNA [1]–[7] demonstrated that such radiation when interacting with biological systems can lead to the production of a significant number of secondary electrons. These electrons, in turn, carry the inelastic collisions with biomolecules, leading to the excited states (vibrational and electronic states) and the production of resonant states. Recent studies [1], [3], [6] report that those processes have the actual ability to cause cell mutation or necrosis, due to single and double break of the DNA chain, having therefore, great potential harmful to any living tissue. In order to better understand these interactions of low-energy electrons with the species found in biological systems, we used in this thesis the Electron Energy Loss Spectroscopy to study the differential (DCS) and integral cross sections (ICS). The region of impact energies used was able to promote excitation of vibrational levels of the tetrahydrofuran (THF) and α-tetrahydrofurfuryl alcohol (THFA), and bands of electronic Rydberg states of TFA. These molecular species were chosen because they are chemically similar to sugar rings present in phosphate-deoxyribose structure, DNA constituents, and the THFA recently identified as a best analogous option for deoxyribose structure, when compared to their similar chemical species, the THF molecule. The electron impact energies used for THFA, were 20, 30, 40 and 50eV, while the angular interval of the scattered electrons was 10 ° - 90 °. The THF molecule was studied for energies of 15, 20, 30 and 50eV, while scattering processes were studied in the angular range of 15º - 90º. In this sense, the DCS's and ICS's of THFA showed subtle difference from those obtained by Khakoo et al. [8] for THF, because of their different physical and chemical properties. The role of the dipole moment and polarizability of the molecules in the electron scattering process was observed, especially its effects on DCS's for low scattering angles (≤30 °). Theoretical calculations, carried out by the theoretical part of this research group, were used also in order to compare with the experimental data presented here, resulting in an excellent agreement, which led to confirmation of the models used. In addition, there was a review of work of Garland et al. [9], which has shown that the energy range and the few vibrational modes considered in their work, derived from Allan [10], were underestimating the role of vibrational excitation with respect to completion of studies of the transport properties. The presentation of this work firstly includes the important theoretical background for data analysis and theoretical calculations performed. Posteriorly, is presented a description of the Electron Energy Loss Spectrometer used and the data analysis framework applied. Finally, the experimental and theoretical data at work and discussions are presented. Additionally, is made a review of the set of vibrational states excitations data of THF used in other studies published in the literature for obtaining electron transport properties of this gas.

J'ai réalisé pour cette thèse des travaux expérimentaux à l'aide de la microscopie et de la spectroscopie électronique portant sur l'étude de nanostructures plasmoniques et de nanocristaux semi-conducteurs. Le but étant d'etudier leurs propriétés optiques sur des dimensions spatiales de l'ordre du nm. A cette échelle il est possible d'observer le champs proche électrique associé aux modes de résonances plasmons de surface supportées par des nanostructures métalliques. Ainsi j'ai pu étudier l'effet de la présence de rugosités sur des nano-bâtonnets d'or et constater que leur présence modifiait localement la structure du champs proche électrique. Des mesures combinées par spectroscopie de perte d'énergie des électrons (EELS) et de cathodoluminescence ont permis de comparer les réponses mesurées en champs proches à celle effectuées en champs lointain. Une étude faite par EELS portant sur le couplage entre deux nano-bâtonnets métalliques positionnés bout à bout et séparés par une distance de quelques dizaines de nanomètres a permis de cartographier la localisation de modes hybridés séparément sur chaque branche. Enfin des études comparatives de cathodoluminescence et de photoluminescence sur des points quantiques isolés ont permis de constater l'équivalence de l'information collectées par ces deux techniques sur ce type d'émetteurs de lumière / For this thesis, I have realised some experimental works using electron microscopy and electron spectroscopies for the study of plasmonic nanostructures and semiconductor nanocrystals . The aim being to study their optical properties with spatial resolutions of the order of a few nm. At this level it is possible to observe the electric near-field associated to the localised surface plasmon resonances supported by metallic nanostructures . So I was able to study the effect due to the presence of roughness on single gold nanorods and I have found that their presence locally alterate the structure of the electric near-field . Combined measurement of electron energy loss spectroscopy (EELS ) and cathodoluminescence spectroscopy were used to compare the near-field and far-field responses respectively. A study by EELS on the coupling between two metal nanorods positioned end to end and separated by a disance of tens of nanometers was used to map the localisation of hybridised modes separately on each branch of the dimers. Finally, comparative studies of cathodoluminescence and photoluminescence on single quantum dots have shown the equivalence of the information collected by these two techniques for such light emitters

Dynamical effects are known to reduce the signal to noise ratio in EMCD measurements making them highly dependent on sample thickness. Precession of the electron beam has been shown to reduce these effects in ordinary crystallography. This work investigates precession of the electron beam as a method of reducing the dynamical effects in EMCD using simulations. Simulations are run on BCC Fe in two and three beam conditions. The results show significant effects on the EMCD signal. However, whether these improve the signal quality seems dependent on sample orientation and thickness range. The initial findings reported here are promising and motivate further research.

abstract: Recent improvements in energy resolution for electron energy-loss spectroscopy in the scanning transmission electron microscope (STEM-EELS) allow novel effects in the low-loss region of the electron energy-loss spectrum to be observed. This dissertation explores what new information can be obtained with the combination of meV EELS energy resolution and atomic spatial resolution in the STEM. To set up this up, I review nanoparticle shape effects in the electrostatic approximation and compare the “classical” and “quantum” approaches to EELS simulation. Past the electrostatic approximation, the imaging of waveguide-type modes is modeled in ribbons and cylinders (in “classical" and “quantum" approaches, respectively), showing how the spatial variations of such modes can now be imaged using EELS. Then, returning to the electrostatic approximation, I present microscopic applications of low-loss STEM-EELS. I develop a “classical” model coupling the surface plasmons of a sharp metallic nanoparticle to the dipolar vibrations of an adsorbate molecule, which allows expected molecular signal enhancements to be quantified and the resultant Fano-type asymmetric spectral line shapes to be explained, and I present “quantum” modelling for the charged nitrogen-vacancy (NV-) and neutral silicon-vacancy (SiV0) color centers in diamond, including cross-sections and spectral maps from density functional theory. These results are summarized before concluding. Many of these results have been previously published in Physical Review B. The main results of Ch. 2 and Ch. 4 were packaged as “Enhanced vibrational electron energy-loss spectroscopy of adsorbate molecules” (99, 104110), and much of Ch. 5 appeared as “Prospects for detecting individual defect centers using spatially resolved electron energy loss spectroscopy” (100, 134103). The results from Ch. 3 are being prepared for a forthcoming article in the Journal of Chemical Physics. / Dissertation/Thesis / Doctoral Dissertation Physics 2020

In this thesis, we present a detailed investigation of the electronic properties of particular transition-metal dichalcogenides. Applying electron-energy loss spectroscopy, the connection between the negative plasmon dispersion of tantalum diselenide and the occurrence of a charge-density wave state (CDW) in this compound as well as related materials is observed. Our studies include doping experiments with alkali metal addition altering the charge density of the compounds. This is known to suppress the CDW. We show that it further changes the plasmon dispersion from negative to positive slope. To estimate the doping rate of the investigated tantalum diselenide samples, a density functional theory approach is introduced, giving reliable results for a quantitative analysis of our findings. We refer to a theoretical model to describe the connection of the charge ordering and the plasmon dynamics. Investigations of the non-CDW compound niobium disulfide give further insights into the proposed interaction. Experimental results are further evaluated by a Kramers-Kronig-analysis. A structural analysis, by means of elastic electron scattering, shows the CDW to be suppressed upon doping, giving space for an emerging superstructure related to the introduced K atoms. / In der vorliegenden Arbeit wird eine detaillierte Untersuchung der elektronischen Eigenschaften von ausgewählten Übergangsmetall-Dichalcogeniden präsentiert. Unter Anwendung von Elektronenenergieverlust-Spektroskopie wird die Verbindung der negativen Plasmomendispersion in Tantaldiselenid zum Auftreten eines Ladungsdichtewelle-Zustands (CDW) in diesem und in verwandten Materialien untersucht. Die Untersuchungen schließen Dotierungsexperimente mit dem Zusatz von Alkalimetallen ein, die die Ladungsdichte der Proben beeinflussen. Einerseits unterdrückt dies die CDW. Es wird außerdem gezeigt, dass sich der Anstieg der Plasmonendispersion von negativ zu positiv ändert. Ein Dichtefunktional-Theorie-Zugang zur Abschätzung der Dotierungsraten der untersuchten Tantaldiselenid-Proben wird genutzt, um verlässliche Ergebnisse für die quantitative Analyse unserer Messungen zu erhalten. Ein theoretisches Modell wird einbezogen, welches die Verbindung der Ladungsordung zur kollektiven Anregung der Ladungsdichte beschreibt, Untersuchungen der nicht-CDW Substanz Niobdisulfid geben weitere Einblicke in die Verbindung der beiden Phänomene. Die experimentellen Resultate werden weiterhin mit einer Kramers-Kronig-Analyse ausgewertet. Strukturelle Untersuchungen mit elastischer Elektronenstreuung zeigen, wie die CDW unterdrückt wird und einer auftauchenden Überstruktur, verursacht von den interkalierten K-Atomen, Raum gibt.

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<p>This thesis presents studies of the X-ray linear dichroism (XLD) in individual single-walled (SW) and multi-walled (MW) carbon nanotubes (CNT) measured by a scanning transmission X-ray microscope (STXM). The C 1s spectra of CNT showed a large XLD at the C 1s→π* transition. The magnitude of the XLD was found to be related to the quality of CNT such that in high quality CNT, it was fairly large and as the quality lowered it decreased. This dichroic effect was used to map defects along individual CNT. In addition, STXM was employed to map chemical components in pristine, purified, and dodecyl functionalized SWCNT bundles to investigate the changes occurring in them due to chemical functionalization.<br />STXM has limited spatial resolution. Thus, electron energy loss spectroscopy (EELS) in a transmission electron microscope (TEM) was used to obtain similar information about CNT, but at much higher spatial resolution. The measurements performed in the scanning transmission electron microscopy (STEM) mode produced signals analogous to the XLD when the orientation of the momentum transfer (q) was resolved. This was achieved by displacing the pattern of electron scattering from CNT relative to the EELS entrance aperture. TEM-EELS was also utilized to map defects in pristine and focused ion beam (FIB) modified CNT.</p> / Doctor of Philosophy (PhD)