Chronic kidney disease (CKD) and end stage renal disease (ESRD) are significant causes of adult morbidity and mortality worldwide. Though these conditions are common, the mechanisms of pathogenesis in kidney disease are poorly understood. Genetic predisposition has been established in the African American population; however this does not explain the ubiquity of CKD in the United States and abroad. Diabetes and hypertension are the two most frequently occurring co-morbidities in kidney disease and both have been identified as putative sources of injury to the delicate filtering structures of the kidney. Furthermore, the intrinsic functional relationship between the cardiovascular and renal organ systems adds to the plausibility of a hemodynamic cause. In light of this knowledge, we aim to explore the roles of genetic predisposition and hypertension in the pathogenesis and progression of CKD. The filtering apparatus of the kidney, the glomerulus, is a looping tuft of capillaries specialized to allow the passage of water and certain substances from the blood while restricting others. Glomeruli at the corticomedullary boundary of the kidney experience blood pressures closer to those in systemic arterioles and are subject to similar hemodynamic stresses. To evaluate the role of hypertension in CKD, we employed a well-known model of hypertensive kidney disease in mice involving uninephrectomy (UNX), subcutaneous implantation of a timed-release pellet containing the active aldosterone precursor deoxycorticosterone acetate (DOCA), and a high-salt diet. Given the role of heritability in human CKD pathogenesis, we applied the DOCA-UNX model in two strains of mice with differing susceptibility to kidney damage, the 129S6 and C57BL/6 strains, to evaluate the effects of genetic predisposition. Mice were subjected to varying lengths of hypertension exposure and their kidneys were subsequently examined by transmission electron microscopy (TEM). Ultrastructural lesions of glomeruli were evaluated by a renal pathologist and assigned subjective pathology scores based on the extent and severity of involvement. We hypothesized that certain glomerular lesions, particularly those involving the podocytes of the visceral epithelium, would increase in severity in mice with heritable susceptibility (129S6) as well as those with longer exposure to glomerular hypertension. Our observations demonstrate these hypotheses are partially correct. By TEM histopathology, mouse strain was found to have a significant effect on the severity of certain epithelial lesions while duration of hypertension had a significant effect on the overall morphological pathology of the podocytes, glomerular basement membrane, and glomerulus as a whole. These results provide a promising foundation for further investigation of the pathogenesis of CKD in mice.

Developments in scanning transmission electron microscopy (STEM) have opened up new possibilities for time-resolved imaging at the atomic scale. However, rapid imaging of single atom dynamics brings with it a new set of challenges, particularly regarding noise and the interaction between the electron beam and the specimen. This thesis develops a set of analytical tools for capturing atomic motion and analyzing the dynamic behaviour of materials at the atomic scale. Machine learning is increasingly playing an important role in the analysis of electron microscopy data. In this light, new unsupervised learning tools are developed here for noise removal under low-dose imaging conditions and for identifying the motion of surface atoms. The scope for real-time processing and analysis is also explored, which is of rising importance as electron microscopy datasets grow in size and complexity. These advances in image processing and analysis are combined with computational modelling to uncover new chemical and physical insights into the motion of atoms adsorbed onto surfaces. Of particular interest are systems for heterogeneous catalysis, where the catalytic activity can depend intimately on the atomic environment. The study of Cu atoms on a graphene oxide support reveals that the atoms undergo anomalous diffusion as a result of spatial and energetic disorder present in the substrate. The investigation is extended to examine the structure and stability of small Cu clusters on graphene oxide, with atomistic modelling used to understand the significant role played by the substrate. Finally, the analytical methods are used to study the surface reconstruction of silicon alongside the electron beam-induced motion of adatoms on the surface. Taken together, these studies demonstrate the materials insights that can be obtained with time-resolved STEM imaging, and highlight the importance of combining state-ofthe- art imaging with computational analysis and atomistic modelling to quantitatively characterize the behaviour of materials with atomic resolution.

Metallophthalocyanine-single walled carbon nanotube conjugates were successfully synthesized and applied in the electrochemical characterizations of pesticides (amitrole and diuron) and 2-mercaptoethanol (2-ME). The formation of conjugates was confirmed through the use of the following analytical techniques: UV-vis, FTIR, Raman and XRD spectroscopies, atomic force and transmission electron microscopies and voltammetry. Chemically linking SWCNT to MPcs created platforms that offered efficient transfer of electrons and this was confirmed through electrochemical impedance studies (EIS) and voltammetry as shown by lower ΔEp values observed in conjugates. Carboxy carrying MPcs have very poor electron transfer kinetics (both tetrasubstituted and low symmetry), but the presence of SWCNTs activates their catalysis. All electrochemical studies were done at pH 4. Cyclic voltammetry, rotating disk linear sweep voltammetry, chronoamperometry and EIS were used in the electrochemical characterization of 2-ME and the pesticides on poly-Ni(OH)TAPc and MPc-SWCNT modified glassy carbon electrodes (GCEs). High Tafel slopes were observed for the pesticides relative to 2-ME, an indication of the passivating nature of their oxidation products. However, conjugates showed very high resistances to passivation and were easily regenerated by shaking in methanol. Improved catalysis of the conjugates is also indicated by the high catalytic rate constants for the analytes, observed on these electrodes. Conjugates of low symmetry MPcs with SWCNTs gave the highest catalytic rate constants, confirming better catalysis on these electrode surfaces. The nature of SWCNT functionalization also affected catalysis, with amine functionalized SWCNTs inducing better catalytic properties into the MPcs than carboxylic acid terminated CNTs. The presence of amine functionalized SWCNTs activates the catalysis of non-catalytic carboxy-carrying MPcs and this is more pronounced in conjugates of tetrasubstituted MPcs relative to those of low symmetry Pcs. Ethylene amine (EA) functionalized SWCNTs reduced redox overpotentials of the MPcs more than the phenyl-amine (PA) functionalized counterparts. Poly-NiTAPc was successfully converted to poly-Ni(OH)TAPc through cyclisation in pH 4 buffer and showed very good catalytic properties towards diuron, relative to the former.

abstract: Because of their favorable ionic and/or electronic conductivity, non-stoichiometric oxides are utilized for energy storage, energy conversion, sensing, catalysis, gas separation, and information technologies, both potential and commercialized. Charge transport in these materials is influenced strongly by grain boundaries, which exhibit fluctuations in composition, chemistry and atomic structure within Ångstroms or nanometers. Here, studies are presented that elucidate the interplay between macroscopic electrical conductivity, microscopic character, and local composition and electronic structure of grain boundaries in polycrystalline ceria-based (CeO2) solid solutions. AC impedance spectroscopy is employed to measure macroscopic electrical conductivity of grain boundaries, and electron energy-loss spectroscopy (EELS) in the aberration-correction scanning transmission electron microscope (AC-STEM) is used to quantify local composition and electronic structure. Electron diffraction orientation imaging microscopy is employed to assess microscopic grain boundary character, and links these macro- and nanoscopic techniques across length scales. A model system, CaxCe1-xO2-x-δ, is used to systematically investigate relationships between nominal Ca2+ concentration, grain boundary ionic conductivity, microscale character, and local solute concentration. Grain boundary conductivity varied by several orders of magnitude over the composition range, and assessment of grain boundary character highlighted the critical influence of local composition on conductivity. Ceria containing Gd3+ and Pr3+/4+ was also investigated following previous theoretical work predicting superior ionic conductivity relative to state-of-the-art GdxCe1-xO2-x/2-δ. The grain boundary conductivity was nearly 100 times greater than expected and a factor four enrichment of Pr concentration was observed at the grain boundary, which suggested electronic conduction that was cited as the origin of the enhanced conductivity. This finding inspired the development of two EELS-based experimental approaches to elucidate the effect of Pr enrichment on grain boundary conductivity. One employed ultra-high energy resolution (~10 meV) monochromated EELS to characterize Pr inter-bandgap electronic states. Alternatively, STEM nanodiffraction orientation imaging coupled with AC-STEM EELS was employed to estimate the composition of the entire grain boundary population in a polycrystalline material. These compositional data were the input to a thermodynamic model used to predict electrical properties of the grain boundary population. These results suggest improved DC ionic conduction and enhanced electronic conduction under AC conditions. / Dissertation/Thesis / Doctoral Dissertation Materials Science and Engineering 2016

abstract: Nanocrystalline (nc) thin films exhibit a wide range of enhanced mechanical properties compared to their coarse-grained counterparts. Furthermore, the mechanical behavior and microstructure of nc films is intimately related. Thus, precise control of the size, aspect ratio and spatial distribution of grains can enable the synthesis of thin films with exceptional mechanical properties. However, conventional bottom-up techniques for synthesizing thin films are incapable of achieving the microstructural control required to explicitly tune their properties. This dissertation focuses on developing a novel technique to synthesize metallic alloy thin films with precisely controlled microstructures and subsequently characterizing their mechanical properties using in situ transmission electron microscopy (TEM). Control over the grain size and distribution was achieved by controlling the recrystallization process of amorphous films by the use of thin crystalline seed layers. The novel technique was used to manipulate the microstructure of structural (TiAl) and functional (NiTi) thin films thereby exhibiting its capability and versatility. Following the synthesis of thin films with tailored microstructures, in situ TEM techniques were employed to probe their mechanical properties. Firstly, a novel technique was developed to measure local atomic level elastic strains in metallic glass thin films during in situ TEM straining. This technique was used to detect structural changes and anelastic deformation in metallic glass thin films. Finally, as the electron beam (e-beam) in TEMs is known to cause radiation damage to specimen, systematic experiments were carried out to quantify the effect of the e-beam on the stress-strain response of nc metals. Experiments conducted on Al and Au films revealed that the e-beam enhances dislocation activity leading to stress relaxation. / Dissertation/Thesis / Supplementary Video S1 / Supplementary Video S2 / Supplementary Video S3 / Doctoral Dissertation Materials Science and Engineering 2017

Tomography of crystal defects in the electron microscope was first attempted in 2005 by the author and colleagues. This thesis further develops the technique, using a variety of samples and methods. Use of a more optimised, commercial tomographic reconstruction program on the original GaN weak beam dark-field (WBDF) tilt series gave a finer reconstruction with lower background, line width 10-20 nm. Four WBDF tilt series were obtained of a microcrack surrounded by dislocations in a sample of indented silicon, tilt axes parallel to g = 220, 220, 400 and 040. Moiré fringes in the defect impaired alignment and reconstruction. The effect on reconstruction of moiré fringe motion with tilt was simulated, resulting in an array of rods, not a flat plane. Dislocations in a TiAl alloy were reconstructed from WBDF images with no thickness contours, giving an exceptionally clear reconstruction. The effect of misalignment of the tilt axis with systematic row g(ng) was assessed by simulating tilt series with diffraction condition variation across the tilt range of Δn = 0, 1 and 2. Misalignment changed the inclination of the reconstructed dislocation with the foil surfaces, and elongated the reconstruction in the foil normal direction; this may explain elongation additional to the missing wedge effect in experiments. Tomography from annular dark-field (ADF) STEM dislocation images was also attempted. A tilt series was obtained from the GaN sample; the reconstructed dislocations had a core of bright intensity of comparable width to WBDF reconstructions, with a surrounding region of low intensity to 60 nm width. An ADF STEM reconstruction was obtained from the Si sample at the same microcrack as for WBDF; here automatic specimen drift correction in tomography acquisition software succeeded, a significant improvement. The microcrack surfaces in Si reconstructed as faint planes and dislocations were recovered as less fragmented lines than from the WBDF reconstruction. ADF STEM tomography was also carried out on the TiAl sample, using a detector inner angle (βin) that included the first order Bragg spots (in other series βin had been 4-6θ B). Extinctions occurred which were dependent on tilt; this produced only weak lines in the reconstruction. Bragg scattering in the ADF STEM image was estimated by summing simulated dark-field dislocation images from all Bragg beams at a zone axis; a double line was produced. It was hypothised that choosing the inner detector angle to omit these first Bragg peaks may preclude most dynamical image features. Additional thermal diffuse scattering (TDS) intensity due to dilatation around an edge dislocation was estimated and found to be insignificant. The Huang scattering cross section was estimated and found to be 9Å, ten times thinner than experimental ADF STEM dislocation images. The remaining intensity may be from changes to TDS from Bloch wave transitions at the dislocation; assessing this as a function of tilt is for further work. On simple assessment, only three possible axial channeling orientations were found over the tilt range for GaN; if this is typical, dechanneling contrast probably does not apply to defect tomography.

Optoelectronic devices fabricated from nitride semiconductors include blue and green light emitting diodes (LEDs) and laser diodes (LDs). To design efficient devices, the structure and composition of the constituent materials must be well-characterised. Traditional microscopy techniques used to examine nitride semiconductors include transmission electron microscopy (TEM), and atomic force microscopy (AFM). This thesis describes the study of nitride semiconductor materials using these traditional methods, as well as atom probe tomography (APT), a technique more usually applied to metals that provides three-dimensional (3D) compositional information at the atomic scale. By using both APT and correlative microscopy techniques, a more complete understanding of the material can be gained, which can potentially lead to higher-efficiency, longer-lasting devices. Defects, such as threading dislocations (TDs), can harm device performance. An AFM-based technique was used to show that TDs affect the local electrical properties of nitride materials. To investigate any compositional changes around the TD, APT studies of TDs were attempted, and evidence for oxygen enrichment near the TD was observed. The dopant level in nitride devices also affects their optoelectronic properties, and the combination of APT and TEM was used to show that Mg dopants were preferentially incorporated into pyramidal inversion domains, with a Mg content two orders of magnitude above the background level. Much debate has been focused on the microstructural origin of charge carrier localisation in InGaN. Alloy inhomogeneities have often been suggested to provide this localisation, yet APT has revealed InGaN quantum wells to be a statistically random alloy. Electron beam irradiation in the TEM caused damage to the InGaN, however, and a statistically significant deviation from a random alloy distribution was then observed by APT. The alloy homogeneity of InAlN was also studied, and this alloy system provided a unique opportunity to study gallium implantation damage to the APT sample caused during sample preparation by the focused ion beam (FIB). The combination of APT with traditional microscopy techniques made it possible to achieve a thorough understanding of a wide variety of nitride semiconductor materials.

M.Sc. / Despite several decades of extensive research and development in pharmaceutical chemistry, the poor solubility of lipophilic compounds in aqueous media remains a major barrier to their absorption, bioavailability and clinical efficacy. This poor solubility is also a problem in other areas such as the flavour and fragrance industry. In cosmetics, for example, poor aqueous solubility and instability of oily compounds causes problems in formulation and fragrance stability. One approach to overcome these difficulties is to encapsulate oily compounds in biocompatible materials. As a drug delivery system such an approach is attractive if the size of the capsule is reduced to the micrometer or nanometer scale. Naturally occurring polysaccharides like sodium alginate (NaALG) and chitosan (CS) are generally regarded as safe (GRAS) for use in human use and have therefore gained much attention recently. As a drug delivery system, this polymer matrix can be used to prevent drug degradation in the gastro intestinal tract (GIT) and often provides controlled release of the encapsulant. Cyclodextrins (CDs) on the other hand offer an alternative approach. These cyclic oligosaccharides have the ability to form non-covalent inclusion complexes with a range of organic compounds, and in so doing alter their physiochemical properties such as solubility. This study was aimed at exploring these concepts by using ALG and CS as an entrapment matrix for an essential oil, tagette oil (used as a model oily drug) that is insoluble in aqueous media. Alginate/chitosan (ALG/CS) nanoparticles were prepared in a 3-step procedure; emulsification of tagette oil in aqueous Na-ALG solution, followed by ionotropic pre-gelation of the ALG core with CaCl2 and further crosslinking with CS. Morphology and particle size measurements were performed by scanning and transmission electron microscopy (SEM and TEM), and Malvern Zetasizer.

>Magister Scientiae - MSc / There are limited reports on virus population in haloalkaline environments; therefore the aim of this study was to investigate the genetic diversity and biology of bacteriophage communities in these environments. Bacteria were isolated to be used as phage hosts. One bacterium from Lake Magadi and four bacteria from Lake Shala were successfully isolated from sediment samples. A further two Lake Shala bacterial hosts from the IMBM culture collection were also used to isolate bacteriophages. Bacterial isolates were identified to be most closely related to Bacillius halodurans, Halomonas axialensis, Virgibacillus salarius, Bacillus licheniformis, Halomonas venusta, Bacillus pseudofirmus and Paracoccus aminovorans. Bacteriophages were screened using all bacteria against sediment samples from both Lake Shala and Lake Magadi. One phage was identified from Lake Magadi sediments (MGBH1) and two phages from Lake Shala sediments (SHBH1 and SHPA). TEM analysis showed that these phages belong to three different dsDNA phage families; Siphoviridae (MGBH1), Myoviridae (SHBH1) and Podoviridae (SHPA). All phages showed different genome sizes on agarose gel. Due to the small genome size, phage SHPA was chosen for further investigation. Partial, genome sequence analysis showed homology to both bacterial and phage proteins. A further investigation of phage diversity in this environment is essential using metagenomic approaches to understand these unique communities.

Transmission electron microscopy (TEM) is an important tool for the characterization of materials as it can provide clear understanding of the relationship between structure, property and composition of nanomaterials. For this, the in-situ TEM analysis is performed and requires specially manufactured sample holders. In particular, those designed to carry out electrical biasing can be used to understand not just the I-V characteristics but also the failure mechanism, structure-property relationship, Joule heating dynamics, electromigration, field emission properties, etc. at the nanoscale. The platforms holding the sample in most modern in-situ TEM holders rely on an insulating ceramic membrane which needs to be (almost) transparent to the imaging electron beam. Electrodes are defined through lithography and patterned on this membrane. Unfortunately, the presence of this membranes introduces several limitations such as electrostatic charging, reduction of image contrast and poor mechanical stability. To circumvent this issue it is necessary to fabricate a novel type of sample platform which does not rely on the presence of a membrane. In this work, novel membraneless sample-holding platforms were designed and manufactured using advanced microfabrication methods and tools. Besides fitting into an array of analytical tools, the novel platforms (or “chips”) can be subjected to thermal and/or chemical processing without compromising their function or structure. To test these, the electrical response of one-, two- and zero-dimensional nanoparticles were studied. Firstly, we investigated current-induced modifications in silver nanowires and expandable graphite flakes and studied various phenomenon involved. Along with these, corresponding ex-situ studies were also performed. Next, graphene oxide was explored as an alternative support platform for in-situ TEM. We successfully achieved temperature as high as 2000o C by Joule heating of graphene oxide. Furthermore, this graphene oxide platform was used as a heater and chemical processing substrate for investigating thermal stability and synthesis of inorganic nanoparticles, respectively.