Matching Items (18)

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Damage-free vibrational spectroscopy of biological materials in the electron microscope

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Vibrational spectroscopy in the electron microscope would be transformative in the study of biological samples, provided that radiation damage could be prevented. However, electron beams typically create high-energy excitations that

Vibrational spectroscopy in the electron microscope would be transformative in the study of biological samples, provided that radiation damage could be prevented. However, electron beams typically create high-energy excitations that severely accelerate sample degradation. Here this major difficulty is overcome using an ‘aloof’ electron beam, positioned tens of nanometres away from the sample: high-energy excitations are suppressed, while vibrational modes of energies <1 eV can be ‘safely’ investigated. To demonstrate the potential of aloof spectroscopy, we record electron energy loss spectra from biogenic guanine crystals in their native state, resolving their characteristic C–H, N–H and C=O vibrational signatures with no observable radiation damage. The technique opens up the possibility of non-damaging compositional analyses of organic functional groups, including non-crystalline biological materials, at a spatial resolution of ∼10 nm, simultaneously combined with imaging in the electron microscope.

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  • 2016-03-10

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Determination of Renal Stone Composition with Dual-Energy CT

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This research evaluates the capabilities of typical radiological measures and dual-energy systems to differentiate common kidney stones materials: uric acid, oxalates, phosphates, struvite, and cystine. Two different X-ray spectra (80

This research evaluates the capabilities of typical radiological measures and dual-energy systems to differentiate common kidney stones materials: uric acid, oxalates, phosphates, struvite, and cystine. Two different X-ray spectra (80 kV and 120 kV) were applied and the dual-energy ratio of individual kidney stones was used to figure out the discriminability of different materials. A CT cross-section with a prospective kidney stone was analyzed to see the capabilities of such a technique. Typical radiological measures suggested that phosphates and oxalate stones can be distinguished from uric acid stones while dual-energy seemed to prove similar effectiveness.

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  • 2020-05

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Effect of Defects on Calculation of Electron Energy Loss Spectra of Ceria and Titania

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Climate change is one of the biggest challenges facing today's society.Since the late 19th century, the global average temperature has been rising. In order to minimize the temperature increase of

Climate change is one of the biggest challenges facing today's society.Since the late 19th century, the global average temperature has been rising. In order to minimize the temperature increase of the earth, it is necessary to develop alternative energy technologies that do not depend on fossil fuels. Solar fuels are one potential energy source for the future. Solar fuel technologies use catalysts to convert low energy molecules into fuels via artificial photosynthesis. TiO2, or titania, is an important model photocatalyst for studying these reactions. It is also important to use remaining fossil fuel resources efficiently and with the lowest possible greenhouse gas emissions. Fuel cells are electrochemical devices that aim to accomplish this goal and CeO2, or ceria, is an important material used in these devices. One way to observe the atomic structure of a material is with a transmission electron microscope (TEM). A traditional transmission electron microscope employs a beam of fast electrons to form atomic resolution images of a material. While imaging gives information about the positions of the atoms in the material, spectroscopy gives information about the composition and bonding of the material. A type of spectroscopy that can be performed inside the transmission electron microscope is electron energy loss spectroscopy (EELS), which provides a fundamental understanding of the electronic structure of a material. The energy loss spectrum also contains information on the chemical bonding in the material, and theoretical calculations that model the spectra are essential to correctly interpreting this bonding information. FEFF is a software that performs EELS calculations. Calculations of the oxygen K edges of TiO2 and CeO2 were made using FEFF in order to understand the changes that occur in the spectrum when oxygen vacancies are introduced as well as the changes near a grain boundary.

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  • 2013-12

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Zeolites: structural properties and benchmarks of feasibility

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Zeolites are a class of microporous materials that are immensely useful as molecular sieves and catalysts. While there exist millions of hypothetical zeolite topologies, only 206 have been recognized to

Zeolites are a class of microporous materials that are immensely useful as molecular sieves and catalysts. While there exist millions of hypothetical zeolite topologies, only 206 have been recognized to exist in nature, and the question remains: What distinguishes known zeolite topologies from their hypothetical counterparts? It has been found that all 206 of the known zeolites can be represented as networks of rigid perfect tetrahedra that hinge freely at the connected corners. The range of configurations over which the corresponding geometric constraints can be met has been termed the "flexibility window". Only a small percentage of hypothetical types exhibit a flexibility window, and it is thus proposed that this simple geometric property, the existence of a flexibility window, provides a reliable benchmark for distinguishing potentially realizable hypothetical structures from their infeasible counterparts. As a first approximation of the behavior of real zeolite materials, the flexibility window provides additional useful insights into structure and composition. In this thesis, various methods for locating and exploring the flexibility window are discussed. Also examined is the assumption that the tetrahedral corners are force-free. This is a reasonable approximation in silicates for Si-O-Si angles above ~135°. However, the approximation is poor for germanates, where Ge-O-Ge angles are constrained to the range ~120°-145°. Lastly, a class of interesting low-density hypothetical zeolites is evaluated based on the feasibility criteria introduced.

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  • 2013

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Ultrafast electrons and x-rays as probe of biomolecular dynamics

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The structure-function relation in Biology suggests that every biological molecule has evolved its structure to carry out a specific function. However, for many of these processes (such as those with

The structure-function relation in Biology suggests that every biological molecule has evolved its structure to carry out a specific function. However, for many of these processes (such as those with catalytic activity) the structure of the biomolecule changes during the course of a reaction. Understanding the structure-function relation thus becomes a question of understanding biomolecular dynamics that span a variety of timescales (from electronic rearrangements in the femtoseconds to side-chain alteration in the microseconds and more). This dissertation deals with the study of biomolecular dynamics in the ultrafast timescales (fs-ns) using electron and X-ray probes in both time and frequency domains.

It starts with establishing the limitations of traditional electron diffraction coupled with molecular replacement to study biomolecular structure and proceeds to suggest a pulsed electron source Hollow-Cone Transmission Electron Microscope as an alternative scheme to pursue ultrafast biomolecular imaging. In frequency domain, the use of Electron Energy Loss Spectroscopy as a tool to access ultrafast nuclear dynamics in the steady state, is detailed with the new monochromated NiON UltraSTEM and examples demonstrating this instrument’s capability are provided.

Ultrafast X-ray spectroscopy as a tool to elucidate biomolecular dynamics is presented in studying X-ray as a probe, with the study of the photolysis of Methylcobalamin using time-resolved laser pump – X-ray probe absorption spectroscopy. The analysis in comparison to prior literature as well as DFT based XAS simulations offer good agreement and understanding to the steady state spectra but are so far inadequate in explaining the time-resolved data. However, the trends in the absorption simulations for the transient intermediates show a strong anisotropic dependence on the axial ligation, which would define the direction for future studies on this material to achieve a solution.

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Date Created
  • 2016

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Towards High Spatial Resolution Vibrational Spectroscopy in a Scanning Transmission Electron Microscope

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Vibrational spectroscopy is a ubiquitous characterization tool in elucidating atomic structure at the bulk and nanoscale. The ability to perform high spatial resolution vibrational spectroscopy in a scanning transmission electron

Vibrational spectroscopy is a ubiquitous characterization tool in elucidating atomic structure at the bulk and nanoscale. The ability to perform high spatial resolution vibrational spectroscopy in a scanning transmission electron microscope (STEM) with electron energy-loss spectroscopy (EELS) has the potential to affect a variety of materials science problems. Since 2014, instrumentation development has pushed for incremental improvements in energy resolution, with the current best being 4.2 meV. Although this is poor in comparison to what is common in photon or neutron vibrational spectroscopies, the spatial resolution offered by vibrational EELS is equal to or better than the best of these other techniques.

The major objective of this research program is to investigate the spatial resolution of the monochromated energy-loss signal in the transmission-beam mode and correlate it to the excitation mechanism of the associated vibrational mode. The spatial variation of dipole vibrational signals in SiO2 is investigated as the electron probe is scanned across an atomically abrupt SiO2/Si interface. The Si-O bond stretch signal has a spatial resolution of 2 – 20 nm, depending on whether the interface, bulk, or surface contribution is chosen. For typical TEM specimen thicknesses, coupled surface modes contribute strongly to the spectrum. These coupled surface modes are phonon polaritons, whose intensity and spectral positions are strongly specimen geometry dependent. In a SiO2 thin-film patterned with a 2x2 array, dielectric theory simulations predict the simultaneous excitation of parallel and uncoupled surface polaritons and a very weak excitation of the orthogonal polariton.

It is demonstrated that atomic resolution can be achieved with impact vibrational signals from optical and acoustic phonons in a covalently bonded material like Si. Sub-nanometer resolution mapping of the Si-O symmetric bond stretch impact signal can also be performed in an ionic material like SiO2. The visibility of impact energy-loss signals from excitation of Brillouin zone boundary vibrational modes in hexagonal BN is seen to be a strong function of probe convergence, but not as strong a function of spectrometer collection angles. Some preliminary measurements to detect adsorbates on catalyst nanoparticle surfaces with minimum radiation damage in the aloof-beam mode are also presented.

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  • 2020

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Microstructure of BAlN and InGaN epilayers for optoelectronic applications

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In this dissertation, various characterization techniques have been used to investigate many aspects of the properties of III-nitride materials and devices for optoelectronic applications.

The first part of this work

In this dissertation, various characterization techniques have been used to investigate many aspects of the properties of III-nitride materials and devices for optoelectronic applications.

The first part of this work is focused on the evolution of microstructures of BAlN thin films. The films were grown by flow-modulated epitaxy at 1010 oC, with B/(B+Al) gas-flow ratios ranging from 0.06 to 0.18. The boron content obtained from X-ray diffraction (XRD) patterns ranges from x = 0.02 to 0.09, while Rutherford backscattering spectrometry (RBS) measures x = 0.06 to 0.16. Transmission electron microscopy indicates the sole presence of the wurtzite crystal structure in the BAlN films, and a tendency towards twin formation and finer microstructure for B/(B+Al) gas-flow ratios greater than 0.15. The RBS data suggest that the incorporation of B is highly efficient, while the XRD data indicate that the epitaxial growth may be limited by a solubility limit in the crystal phase at about 9%. Electron energy loss spectroscopy has been used to profile spatial variations in the composition of the films. It has also located point defects in the films with nanometer resolution. The defects are identified as B and Al interstitials and N vacancies by comparison of the observed energy thresholds with results of density functional theory calculations.

The second part of this work investigates dislocation clusters observed in thick InxGa1-xN films with 0.07 ≤ x ≤ 0.12. The clusters resemble baskets with a higher indium content at their interior. Threading dislocations at the basket boundaries are of the misfit edge type, and their separation is consistent with misfit strain relaxation due the difference in indium content between the baskets and the surrounding matrix. The base of the baskets exhibits no observable misfit dislocations connected to the threading dislocations, and often no net displacements like those due to stacking faults. It is argued that the origin of these threading dislocation arrays is associated with misfit dislocations at the basal plane that dissociate, forming stacking faults. When the stacking faults form simultaneously satisfying the crystal symmetry, the sum of their translation vectors does add up to zero, consistent with our experimental observations.

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Date Created
  • 2018

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Excursions in Electron Energy-Loss Spectroscopy

Description

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

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.

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  • 2020

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Fluctuation electron microscopy of amorphous and polycrystalline materials

Description

Fluctuation Electron Microscopy (FEM) has become an effective materials' structure characterization technique, capable of probing medium-range order (MRO) that may be present in amorphous materials. Although its sensitivity to MRO

Fluctuation Electron Microscopy (FEM) has become an effective materials' structure characterization technique, capable of probing medium-range order (MRO) that may be present in amorphous materials. Although its sensitivity to MRO has been exercised in numerous studies, FEM is not yet a quantitative technique. The holdup has been the discrepancy between the computed kinematical variance and the experimental variance, which previously was attributed to source incoherence. Although high-brightness, high coherence, electron guns are now routinely available in modern electron microscopes, they have not eliminated this discrepancy between theory and experiment. The main objective of this thesis was to explore, and to reveal, the reasons behind this conundrum.

The study was started with an analysis of the speckle statistics of tilted dark-field TEM images obtained from an amorphous carbon sample, which confirmed that the structural ordering is sensitively detected by FEM. This analysis also revealed the inconsistency between predictions of the source incoherence model and the experimentally observed variance.

FEM of amorphous carbon, amorphous silicon and ultra nanocrystalline diamond samples was carried out in an attempt to explore the conundrum. Electron probe and sample parameters were varied to observe the scattering intensity variance behavior. Results were compared to models of probe incoherence, diffuse scattering, atom displacement damage, energy loss events and multiple scattering. Models of displacement decoherence matched the experimental results best.

Decoherence was also explored by an interferometric diffraction method using bilayer amorphous samples, and results are consistent with strong displacement decoherence in addition to temporal decoherence arising from the electron source energy spread and energy loss events in thick samples.

It is clear that decoherence plays an important role in the long-standing discrepancy between experimental FEM and its theoretical predictions.

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Date Created
  • 2015

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Development and application of operando TEM to a ruthenium catalyst for CO oxidation

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Operando transmission electron microscopy (TEM) is an extension of in-situ TEM in which the performance of the material being observed is measured simultaneously. This is of great value, since structure-performance

Operando transmission electron microscopy (TEM) is an extension of in-situ TEM in which the performance of the material being observed is measured simultaneously. This is of great value, since structure-performance relationships lie at the heart of materials science. For catalyst materials, like the SiO2-supported Ru nanoparticles studied, the important performance metric, catalyst activity, is measured inside the microscope by determining the gas composition during imaging. This is accomplished by acquisition of electron energy loss spectra (EELS) of the gas in the environmental TEM while catalysis is taking place. In this work, automated methods for rapidly quantifying low-loss and core-loss EELS of gases were developed. A new sample preparation method was also established to increase catalytic conversion inside a differentially-pumped environmental TEM, and the maximum CO conversion observed was about 80%. A system for mixing gases and delivering them to the environmental TEM was designed and built, and a method for locating and imaging nanoparticles in zone axis orientations while minimizing electron dose rate was determined.

After atomic resolution images of Ru nanoparticles observed during CO oxidation were obtained, the shape and surface structures of these particles was investigated. A Wulff model structure for Ru particles was compared to experimental images both by manually rotating the model, and by automatically determining a matching orientation using cross-correlation of shape signatures. From this analysis, it was determined that most Ru particles are close to Wulff-shaped during CO oxidation. While thick oxide layers were not observed to form on Ru during CO oxidation, thin RuO2 layers on the surface of Ru nanoparticles were imaged with atomic resolution for the first time. The activity of these layers is discussed in the context of the literature on the subject, which has thus far been inconclusive. We conclude that disordered oxidized ruthenium, rather than crystalline RuO2 is the most active species.

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Date Created
  • 2016