One conventional method for studying dislocations uses the Transmission Electron Microscope (TEM), a complex and expensive piece of equipment which requires extensive specimen preparation in order to thin the specimens to electron transparent thickness. Newer High Resolution Electron Backscatter Diffraction (HREBSD) methods of determining geometrically necessary dislocation content via cross-correlation promise to be able to produce estimates of the dislocation density of the sample over a larger area with considerably less preparation time and using a much more accessible instrument. However, the accuracy of the new EBSD technique needs more experimental verification, including consideration of possible changes in the specimen dislocation density due to the different preparation methods. By comparing EBSD and TEM dislocation measurements of Electron Transparent platinum specimens prepared using the Focused Ion Beam (FIB), along with EBSD dislocations measurements of specimens prepared by both FIB and mechanical polishing techniques, this paper seeks to verify the accuracy of the new method and identify any changes in the specimens’ apparent dislocation density caused by the different preparation processes.

The breast cancer susceptibility protein, BRCA1, is a tumor suppressor that helps maintain genomic integrity. Changes in BRCA1 that effect DNA repair processes can fuel cancer induction. The Kelly lab, at the Virginia Tech Carilion Research Institute, has recently developed a new methodology that employs silicon nitride (SiN) microchips to isolate BRCA1 assemblies from the nuclear material of breast cancer cells. These microchips are coated with adaptor proteins that include antibodies against target proteins of interest. The adaptor proteins are added in sequential steps to the coated microchips, followed by an aliquot of sample containing the protein of interest, such as BRCA1. The Kelly lab, partnered with Protochips Inc., developed these devices as a robust, tunable platform to monitor molecular processes, and refer to them as 'Cryo-SiN' in cryo-Electron Microscopy (EM) imaging. We are currently using Cryo-SiN to recruit BRCA1 protein assemblies to the microchip surface under mild conditions, while simultaneously preparing them for cryogenic preservation and EM imaging. This strategy presents a viable alternative to antibody affinity columns that require stringent elution steps to obtain protein complexes from the column. Another advantage of the microchip strategy is that it requires only a 30-minute nuclear extraction, a 60-minute enrichment procedure, and a 5-minute microchip capture step--a total of 95 minutes from initially lysing the cells to plunge-freezing the EM specimens. Therefore, these novel approaches represent a major departure from classical separation procedures that often require days to complete, during which time active protein assemblies can readily dissociate or become inactive. Overall, our use of BRCA1-specific microchips may reveal changes in the BRCA1 architecture during various stages of cancer progression--a major gap in knowledge that persists in cancer research. / M. S. / Modern advances in the imaging technology used for cryogenic electron microscopy (cryo-EM) have offered researchers an extraordinary view into the world of biology at the nanoscale. Supplemental to these technical innovations is the development of tunable substrates based on functional new materials that revolutionize the sequestering of biological components from human cells, such as protein complexes formed in breast cancer cells. New developments of novel viewing substrates, given traditional electron microscopy viewing grids have remained unchanged for decades, is the logical next step into the future of enhanced cryo-EM imaging. Tunable microchip substrates, made using recently enhanced micro-engineering techniques, are currently under development for use in cryo-EM imaging. In this work I have examined these microchip substrates for their capacity to streamline the isolation of biomolecules such as the protein most prominently cited in breast cancer, known as the breast cancer susceptibility protein (BRCA1). Utilizing these novel microchip substrates in the Kelly Lab, I have collected and analyzed data containing BRCA1 proteins, formed in human breast cancer cells, toward the development of 3-dimensional protein structures that allow us to peer into the structure-function relationships of these proteins. New and exciting Cryo-EM data, collected using these newly developed microchips, has the potential to reveal obscure disease mechanisms being propagated at the molecular level in modern clinical practice, such as breast cancer.

Three-dimensional porous single crystals (PSCs) are a recent development in the growing world of mesoporous material. The mesoporosity allows for the material to retain their nanoproperties whilst being bulk in size. The current work concentrates on chromium oxide and cobalt oxide PSCs formed in the templates SBA-15 and KIT-6. HRTEM is the main technique used in this investigation, looking at the morphology and single crystallinity of these materials. A growth mechanism for the PSC material is proposed based on HRTEM observations. XRD studies revealed that the confinement effect, caused by the mesopores, reduces the temperature for both cobalt and chromium oxide crystallisation, as well as a different intermediate route from the metal nitrates. The properties of chromium oxide PSC are also investigated magnetically and catalytically. Some metal oxides in different templates are also presented, despite no PSC forming. HRTEM work on other nanomaterials, based on collaboration, is also presented.

M.Tech. (Department of Chemistry, Faculty of Applied Sciences), Vaal University of Technology / Many oxidic iron compounds—iron oxides; oxy-hydroxides and hydroxides—not only play an important role in a variety of disciplines but also serve as a model system of reduction and catalytic reactions. There are more than 16 identifiable oxidic iron compounds. The reduction of these compounds has been investigated for centuries. Despite this, the reduction behavior of the oxides is not fully understood as yet. To date the reduction mechanism is still plagued with uncertainties and conflicting theories, partly due to the complex nature of these oxides and intermediates formed during the reduction. Thermodynamically, the reduction of iron oxide occurs in steps. For example, during the reduction of hematite (a-Fe2O3) magnetite (Fe3O4) is first formed followed by non-stoichiometric wüstite (Fe1-yO) and lastly metallic iron (a-Fe). The rate of transformation depends on the reduction conditions. Further, this reduction is accompanied by changes in the crystal structure. The reduction behavior of iron oxides using graphite under ball-milling conditions was investigated using Planetary mono mill (Fritsch Pulverisette 6), Mössbauer Spectroscopy (MS), X-ray Diffraction (XRD), Scanning electron microscopy (SEM) and Transmission Electron Microscopy (TEM). It was found that hematite transformed into magnetite, Wüstite and or cementite depending on the milling conditions. The study shows that by increasing the milling time, the rotational speed and / or the ball to powder ratio, the extent of the conversion of hematite to its reduction products increased. Further investigations are required for the elucidation of the reduction mechanism. The reaction og magnetite and graphite at different milling conditions lead to the formation of Fe2+ and Fe3+ species, the former increasing at the expense of Fe3O4. Fe3O4 completely disappeared after a BPR of 50:1 and beyond. The Fe2+ species was confirmed to be due to FeO using XRD analysis. HRSEM images Fe2O3 using scanning electron microscopy prior to and after milling at different times showed significant changes while the milling period was increased, HRSEM images showed that the once well defined hematite particles took ill-defined shapes and also became smaller in size, which was a results of the milling action that induced reaction between the two powders to form magnetite. EDX spectra at different milling times also confirmed formation of magnetite. EDX elemental analysis and quantification confirmed the elemental composition of starting material consisting mainly of iron. Similarly, HRSEM images of Fe3O4 using Scanning electron microscopy (SEM) prior to and after milling at different BPR showed significant changes when the milling period was increased. EDX spectra at different milling times also confirmed formation of partial FeO and EDX elemental analysis and quantification confirmed the elemental composition of starting material consisting mainly of iron than Fe2O3. TEM images of both Fe2O3 and Fe3O4 particles at different milling conditions displayed observable particle damages as a function of milling period.The once well - defined particles (Fe2O3 and Fe3O4 ) successively took ill – defined shapes, possibly accompanied by crystallite size reduction. MAS showed that the reactive milling of α- Fe2O3 and C resulted in reduction to Fe3O4 , FeO and or cementite depending on the milling conditions etc Time, milling speed and BPR variation which influenced the reduction. The study shows that by increasing the milling time, the rotational speed and / or the ball to powder ratio, the extent of the conversion of hematite to its reduction products increased. XRD study investigations even though were unable to detect spm species (Fe2+ and Fe3+ ) which has smaller crystallites below detection limits ,the variation in time showed an increment in the magnetite peaks accompanied by recession of hematite and graphite peaks as the milling time was increased which relates to the MAS observation.XRD also corroborated the data obtained from MAS that showed that the main constituent was magnetite and further evidence in support of the reduction of hematite to magnetite under reactive milling was obtained using XRD . Overall, the work demonstrated selective reduction of Fe2O3 to Fe3O4 and Fe3O4 to FeO by fine tuning the milling conditions. It is envisaged that the reduction of FeO to Fe and possible carburization to FexC could also be achieved.

This project relates to the non-classical growth of inorganic crystals with interesting morphologies that are highly desirable in industry. All crystals were synthesized via hydrothermal or solvothermal methods and their growth was studied by stopping each reaction at a range of different times, extracting the particles and analysing them using a variety of characterisation techniques. The main techniques used were scanning electron microscopy and transmission electron microscopy but other techniques, such as powder X-ray diffraction and thermal gravimetric analysis, were also employed. Decorated ZnO microstadiums were studied where ZnO nanocones coat the inner and outer columnar walls of ZnO microstadiums. It was revealed that the polymer in the synthetic solution enhanced the aggregation of nanocrystallites of precursor ions on the microstadium surfaces, which then underwent recrystallization, forming ZnO nanocones. The presence of organic agents was also found to be crucial in the non-classical growth mechanisms of CaCO₃ and RHO-ZIF crystals as the presence of charged groups on the organic molecules led to the aggregation of precursor molecules/ions, preventing classical growth. The disordered aggregates underwent surface recrystallization, forming ‘core-shell' structures where a thin layer of single crystal encased a disordered core. Over time the crystallisation extended from the surface inwards, towards the core, until true single crystals were formed. Organic molecules were also shown to play a role in the non-classical growth of 8-branched Cu₂O structures. In this case, however, studies of the electronic configuration of the main terminating facets of Cu₂O crystals revealed another key factor in their non-classical growth. Terminating hydroxyl groups on the Cu₂O surfaces could have different charges depending on the number of Cu⁺ ions they were coordinated to. The terminating {111} faces were the only ones to be coated with negatively charged hydroxyl groups, which explained the rapid growth on these surfaces as they were able to attract the positively charged metal/polymer precursor clusters. This new phenomenon was also found to be the main driving force in the rapid growth of branches in snowflake-like Fe₂O₃ crystals despite no organic agent being used. In this case, the {11-20} faces of the seed crystals had positively charged hydroxyl groups that were able to rapidly attract the negatively charged [Fe(CN) ₆]³⁻ ions in the aqueous solution.

During recent years, new types of materials have been discovered with unique properties. One family of such materials are two-dimensional materials, which include graphene and MXene. These materials are stronger, more flexible, and have higher conductivity than other materials. As such they are highly interesting for new applications, e.g. specialized in vivo drug delivery systems, hydrogen storage, or as replacements of common materials in e.g. batteries, bulletproof clothing, and sensors. The list of potential applications is long for these new materials. As these materials are almost entirely made up of surfaces, their properties are strongly influenced by interaction between their surfaces, as well as with molecules or adatoms attached to the surfaces (surface groups). This interaction can change the materials and their properties, and it is therefore imperative to understand the underlying mechanisms. Surface groups on two-dimensional materials can be studied by Transmission Electron Microscopy (TEM), where high energy electrons are transmitted through a sample and the resulting image is recorded. However, the high energy needed to get enough resolution to observe single atoms damages the sample and limits the type of materials which can be analyzed. Lowering the electron energy decreases the damage, but the image resolution at such conditions is severely limited by inherent imperfections (aberrations) in the TEM. During the last years, new TEM models have been developed which employ a low acceleration voltage together with aberration correction, enabling imaging at the atomic scale without damaging the samples. These aberration-corrected TEMs are important tools in understanding the structure and chemistry of two-dimensional materials. In this thesis the two-dimensional materials graphene and Ti3C2Tx MXene have been investigated by low-voltage, aberration-corrected (scanning) TEM. High temperature annealing of graphene covered by residues from the synthesis is studied, as well as the structure and surface groups on single and double Ti3C2Tx MXene. These results are important contributions to the understanding of this class of materials and how their properties can be controlled.

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