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.

Dental amalgams have been used for centuries as major restorative materials for decaying teeth. Amalgams are prepared by mixing alloy particles which contain Ag, Sn, and Cu as the major constituent elements with liquid Hg. The study of microstructure is essential in understanding the setting reactions and improving the properties of amalgams. Until the work reported in this dissertation, optical microscopy (OM), scanning electron microscopy (SEM), and x-ray diffractometry (XRD) were used commonly to analyze amalgam microstructures. No previous systematic transmission electron microscopy (TEM) study has been performed due to sample preparation difficulties and composite structure of dental amalgams. The goal of this research was to carry out detailed microstructural and compositional studies of dental amalgams. This was accomplished using the enhanced spatial resolution of the TEM and its associated microanalytical techniques, namely, scanning transmission electron microscopy (STEM), x-ray energy dispersive spectroscopy (XEDS) and micro-microdiffraction (μμD). A new method was developed for thinning amalgam samples to electron transparency using the "wedge technique." Velvalloy, a low-Cu amalgam, and Tytin, a high-Cu amalgam, were the two amalgams characterized. Velvalloy is composed of a Ag₂Hg₃ (γ₁)/HgSn₇₋₉ (γ₂) matrix surrounding unreacted Ag₃Sn (γ) particles. In addition, hitherto uncharacterized reaction layers between Ag₃Sn(γ)/Ag₂Hg₃ (γ₂) and Ag₂Hg₃ (γ₁)/HgSn₇₋₉ (γ₂) were observed and analyzed. An Ag-Hg-Sn (β₁) phase was clearly identified for the first time. In Tytin, the matrix consists of Ag₂Hg₃ (γ₁) grains. Fine precipitates of Cu₆Sn₅ (η') are embedded inside the γ₁ and at the grain boundaries. These precipitates are responsible for the improved creep resistance of Tytin compared to Velvalloy. The additional Cu has completely eliminated the γ₂ phase which is the weakest component of amalgams. Ag-Hg-Sn (β₁) and large grains of Cu₆Sn₅ (η') are found adjacent to the unreacted alloy particles. Tytin alloy particles contain Cu₃Sn (ε) precipitates in a matrix of Ag₃Sn (γ) and Ag₄Sn (β). SEM was used to correlate the TEM findings in the context of the general microstructure. The results are in good agreement with those published in the literature. The microstructural details reported here, many of which were not previously available, will help provide insight into the deformation mechanisms of dental amalgams.

We propose to interpret Cryogenic Electron Microscopy (CryoEM) data as a supervision for learning parameters of CryoEM microscopes. Following this formulation, we present a differentiable version of Transmission Electron Microscopy (TEM) Simulator that provides differentiability of all continuous inputs in a simulation. We demonstrate the learning capability of our simulator with two examples, detector parameter estimation and denoising. With our differentiable simulator, detector parameters can be learned from real data without time-consuming handcrafting. Besides, our simulator enables new way to denoising micrographs. We develop this simulator with the combination of Taichi and PyTorch, exploiting kernel-based and operator-based parallel differentiable programming, which results in good speed, low memory footprint and expressive code. We call our work as Differentiable TEM Detector as there are still challenges to implement a fully differentiable transmission electron microscope simulator that can further differentiate with respect to particle positions. This work presents first steps towards a fully differentiable TEM simulator. Finally, as a subsequence of our work, we abstract out the fuser that connects Taichi and PyTorch as an open-source library, Stannum, facilitating neural rendering and differentiable rendering in a broader context. We publish our code on GitHub.

While much is known about the attachment of the chlamydiae to the host cell and intracellular events during the developmental cycle, little is known about the mechanism(s) by which elementary bodies exit the cell. In this report, we use the guinea-pig conjunctival model of Chlamydia caviae infection to present in vivo ultrastructural evidence supporting two mechanisms for release of chlamydiae from the mucosal epithelia. Four days after infection, histopathologic observation shows an intense infiltration of polymorphonuclear leukocytes (PMN) in the conjunctival epithelium. Using transmission electron microscopy, a gradient-directed PMN response to chlamydiae-infected epithelial cells was observed. As PMN infiltration intensifies, epithelial hemidesmosome/integrin/focal adhesion adherence with the basal lamina is disconnected and PMNs literally lift off and release infected superficial epithelia from the mucosa. Many of these infected cells appear to be healthy with intact microvilli, nuclei, and mitochondria. While lysis of some infected cells occurs with release of chlamydiae into the extracellular surface milieu, the majority of infected cells are pushed off the epithelium. We propose that PMNs play an active role in detaching infected cells from the epithelium and that these infected cells eventually die releasing organisms but, in the process, move to new tissue sites via fluid dynamics.

No description available.

<p> The fatigue softening behaviour of copper single crystals was investigated as a function of temperature. Copper crystals, prestrained in tension, were softened by "push-pull" cycling at constant plastic strain amplitude, in the low amplitude range, and the cyclic stress-strain curves determined at various temperatures. Transmission electron microscopy was employed to determine the detailed microstructural changes which occured during softening while X-ray and slip line observations were utilized to indicate the overall structural changes on a macroscopic scale. The results were correlated and a rationale, based on dipole production, proposed for the observed softening behaviour. </p> / Thesis / Master of Science (MSc)

Supporting videos attached / The nanoscale structure of fully dense human cortical bone is explored using advanced transmission electron microscopy (TEM) techniques. Studies of fully dense cortical bone are rare because of the sample preparation challenges. In this work, cryogenic ion milling is compared favourably with traditional ultramicrotoming methods because of the clearer imaging results and better preservation of biological structures in the ion milled samples. Ion milled samples were prepared parallel, perpendicular and at a 45 degree angle to the long axis of a human femur. The samples are cooled with liquid nitrogen while being milled to prevent heating damage to the bone structure. Bright-field and dark-field imaging show that mineral mainly occurs as 65 nm wide, 5 nm thick mineral structures, external to the collagen fibrils, and with the long axis of the mineral running parallel to the fibrils. In samples cut parallel to the long axis of the bone, the mineral structures have their c-axes aligned with the collagen fibril long axis. In these sections the mineral structures extend up to 200 nm and are grouped into stripe-like bunches, 53 nm apart. Samples cut perpendicular to the long axis of the bone show open areas roughly 45 nm in diameter. These open areas are assumed to be the location of collagen fibrils within the structure and are tangentially surrounded by 65 nm wide, 5 nm thick mineral structures. On average, there are 22 nm of mineral structures between adjoining collagen fibrils. Samples cut at 45 degrees to the long axis of the bone confirm that the open structure seen in the perpendicular section is not an artefact of sample preparation. By tilting the sample, the 45 degree sample shows the structure of both the parallel and perpendicular sections. The parallel structure strongly resembles images of embryonic bone and other mineralized tissues seen in the literature, so the perpendicular open structure is not caused by sample preparation. An examination of ultramicrotoming’s effect on mineral structure size compared with that of ion milling shows that the mineral structures in ion milled samples are twice as long as in ultramicrotomed samples, indicating that bone mineral may be damaged by the forces applied to the complex composite structure existing in fully dense cortical bone. Using energy dispersive X-ray spectroscopy (EDXS) results and a simplified model of the locations of mineral within the collagen/mineral framework, a calculation of the percentage of external mineral was performed. The result showed that 80+_ 6 % of the mineral in fully dense cortical bone must be external to the collagen fibrils to obtain the EDXS results. Finally, Z-contrast tomography, based on the use of high angle annular darkfield (HAADF) imaging, was used to prepared tomographic reconstructions of the external mineral in fully dense cortical bone. Unlike bright-field tomography, the Z-contrast technique allows examination of crystalline materials as the contrast in HAADF images is mass-thickness dependent instead of diffraction based. These reconstructions again showed the mineral tangentially surrounding 50 nm diameter cylindrical holes, assumed to be the location of collagen fibrils in all directions. This work shows the importance of mineral that is external to the collagen fibrils to the nanoscale structure of fully dense cortical bone. / Thesis / Doctor of Philosophy (PhD)