Proton radiotherapy has recently become a popular form of cancer treatment. For maximum effectiveness, accurate models are needed to calculate proton angular scattering and energy loss. Scattering events are statistically independent and may be calculated from the effective number of events per reciprocal multiple scattering angle or energy loss. It is shown that multiple scattering distributions from Molière’s scattering law can be convolved by depth for accurate numerical calculation of angular distributions in several example materials. This obviates the need for correction factors to the analytic solution and its approximations. It is also shown that numerically solving Molière’s scattering law in terms of the complete (non-small angle) differential cross section and large angle approximations extends the validity of Molière theory to large angles. To calculate probability energy loss distributions, Landau-Vavilov theory is adapted to Fourier transforms and extended to very thick targets through convolution over the probability energy loss distributions in each depth interval. When the depth is expressed in terms of the continuous slowing down approximation (CSDA) the resulting probability energy loss distributions rely on the mean excitation energy as the sole material dependent parameter. Through numerical calculation of the CSDA over the desired energy loss, this allows the energy loss cross section to vary across the distribution and accurately accounts for broadening and skewness for thick targets in a compact manner. An analytic, Fourier transform solution to Vavilov’s integral is shown. A single scattering nuclear model that calculates large angle dose distributions that have a similar functional form to FLUKA (FLUktuierende KAskade) Monte Carlo, is also introduced. For incorporation into Monte Carlo or a treatment planning system, lookup tables of the number of scattering events or cross sections for different clinical energies may be used to determine angular or energy loss distributions.

Interfacial interactions between materials in complex heterostructures can dominate the material's response in manymodern-day energy-related devices and processes. Considerable research has been dedicated towards addressing the profound effects of interfaces. Here, first-principles-based quantum mechanical simulations are discussed to characterize the interfacial materials properties of two systems. First, density-functional theory (DFT) calculations were performed for ceramic oxide grain boundaries in undoped and doped CeO2. Second, the development, theoretical framework, and utilization of high-throughput, workflow-based, DFT calculations are presented to model the synthesis of two-dimensional (2D) heterostructured materials. Utilizing this workflow, predictive machine learning models were created to elucidate key interface-property relationships in 2D heterostructured materials. The DFT simulations reveal that the Σ3(111)/[101] grain boundary was energetically more stable than theΣ3(121)/[101]grain boundary due to the larger atomic coherency in the Σ3(111)/[101] grain boundary plane. The alkaline-earth metal-doped grain boundary energies demonstrate a parabolic dependence on the size of the solutes, interfacial strain, and packing density of the grain boundary. The grain boundary energies were stabilized upon Ca, Sr, and Ba doping whereas Be and Mg render them energetically unstable. The electronic density of states reveals that no defect states were present in/above the band gap. The thermodynamic trapping of oxygen vacancies in the near grain boundary region was not significantly impacted by the presence of Ca-solute ions. However, the migration energy barriers within the grain boundary core were dramatically reduced with high local Ca-solute concentrations, around 0.3 eV-0.5 eV. Chapter 5 and Chapter 6 discusses the development of the open-source, high-throughput computational "synthesis"based workflow package Hetero2d and the application of Hetero2d using 52 Janus 2D materials and 19 metallic, cubic phase, elemental substrates. The 438 Janus 2D-substrate pairs were analyzed by identifying substrate surfaces that stabilize metastable Janus 2D materials, characterizing their effects on the post-adsorbed 2D materials, and identifying the bonding between the 2D material and substrate. Machine learning models were applied to predict the binding energy, z-separation, and charge transfer of the Janus 2D-substrate pairs providing insight into the critical properties which factor into these properties.

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.

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.

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.

A highly uniform and repeatable method for synthesizing the single-layer transition metal dichalcogenides (TMDs) molybdenum disulfide, MoS2, and tungsten disulfide, WS2, was developed. This method employed chemical vapor deposition (CVD) of precursors in a custom built cold-wall reaction chamber designed to allow independent control over the growth parameters. Iterations of this reaction chamber were employed to overcome limitations to the growth method. First, molybdenum trioxide, MoO3, and S were co-evaporated from alumina coated W baskets to grow MoS2 on SiO2/Si substrates. Using this method, films were found to have repeatable coverage, but unrepeatable morphology. Second, the reaction chamber was modified to include a pair of custom bubbler delivery systems to transport diethyl sulfide (DES) and molybdenum hexacarbonyl (MHC) to the substrate as a S and Mo precursors. Third, tungsten hexacarbonyl (WHC) replaced MHC as a transition metal precursor for the synthesis of WS2 on Al2O3, substrates. This method proved repeatable in both coverage and morphology allowing the investigation of the effect of varying the flow of Ar, varying the substrate temperature and varying the flux of DES to the sample. Increasing each of these parameters was found to decrease the nucleation density on the sample and, with the exception of the Ar flow, induce multi-layer feature growth. This combination of precursors was also used to investigate the reported improvement in feature morphology when NaCl is placed upstream of the substrate. This was found to have no effect on experiments in the configurations used. A final effort was made to adequately increase the feature size by switching from DES to hydrogen sulfide, H2S, as a source of S. Using H2S and WHC to grow WS2 films on Al2O3, it was found that increasing the substrate temperature and increasing the H2S flow both decrease nucleation density. Increasing the H2S flow induced bi-layer growth. Ripening of synthesized WS2 crystals was demonstrated to occur when the sample was annealed, post-growth, in an Ar, H2, and H2S flow. Finally, it was verified that the final H2S and WHC growth method yielded repeatability and uniformity matching, or improving upon, the other methods and precursors investigated.

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.

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.

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.