Viruses and their morphology have been detected and studied with electron microscopy (EM) since the end of the 1930s. The technique has been vital for the discovery of new viruses and in establishing the virus taxonomy. Today, electron microscopy is an important technique in clinical diagnostics. It both serves as a routine diagnostic technique as well as an essential tool for detecting infectious agents in new and unusual disease outbreaks. The technique does not depend on virus specific targets and can therefore detect any virus present in the sample. New or reemerging viruses can be detected in EM images while being unrecognizable by molecular methods. One problem with diagnostic EM is its high dependency on experts performing the analysis. Another problematic circumstance is that the EM facilities capable of handling the most dangerous pathogens are few, and decreasing in number. This thesis addresses these shortcomings with diagnostic EM by proposing image analysis methods mimicking the actions of an expert operating the microscope. The methods cover strategies for automatic image acquisition, segmentation of possible virus particles, as well as methods for extracting characteristic properties from the particles enabling virus identification. One discriminative property of viruses is their surface morphology or texture in the EM images. Describing texture in digital images is an important part of this thesis. Viruses show up in an arbitrary orientation in the TEM images, making rotation invariant texture description important. Rotation invariance and noise robustness are evaluated for several texture descriptors in the thesis. Three new texture datasets are introduced to facilitate these evaluations. Invariant features and generalization performance in texture recognition are also addressed in a more general context. The work presented in this thesis has been part of the project Panvirshield, aiming for an automatic diagnostic system for viral pathogens using EM. The work is also part of the miniTEM project where a new desktop low-voltage electron microscope is developed with the aspiration to become an easy to use system reaching high levels of automation for clinical tissue sections, viruses and other nano-sized particles.

Contamination from various sources has a huge impact on soil health and microbial community composition. Metal contamination of soil in mining scenarios is of concern and is not adequately addressed, particularly with respect to the microbial community. The mining industry is one of the largest contributors to heavy metal contamination of soil in South Africa, especially since the country is one of the major mining countries in the world. Platinum mining is of special importance, since the largest percentage of the world’s reserves of platinum group metals are found and mined in South Africa. Metals from mining activities become irreversibly immobilized in soil systems because they cannot be degraded and has a huge impact on soil systems. In this study, bacteria was isolated from soil samples collected from a platinum mine tailings dam outside Rustenburg. During the warm sampling season (March 2006) most isolates were found, especially in sites 3 and 4. During the colder and drier season (May 2006) there were less isolates. Most of the isolated cultures also displayed a wide temperature growth range, mostly between 24°C - 37°C. Paenibacillus lautus and Bacillus subtilus DN-10 had a growth range between 5°C - 40°C. Culturable metal tolerant bacteria were isolated, purified and identified using 16S rDNA sequences. Nine different species were found namely Paenibacillus lautus strain DS19, Paenibacillus lautus, Paenibacillus sp. C15, uncultured Paenibacillaceae, Bacillus subtilis strain DN-10, Bacillus sp. KDNB5, Bacillus cereus, Stenotrophomonas maltophilia and Alcaligenes sp. DJWH 146-2. The ability of these strains to tolerate metal concentrations were explored by determining their minimum inhibitory concentrations for a selection of metals e.g. aluminum, barium, cobalt, chromium, cadmium, copper, iron, lead, manganese, nickel and mercury. Most isolates were able to tolerate >5mM of the Al\Ni alloy and cobalt. Transmission electron microscopy was used to determine the location of metals inside bacterial cells and electron dispersive X-ray analysis was used to determine the levels of metals inside microbial cells. Bacillus subtilis DN-10 (LDK0306) showed a high MIC (>5mM) for most metals used, except Hg. This strain also had a high percentage (10.26%) of Pb detected in its cells by EDX. This was the highest percentage detected. Plasmids were extracted from the identified strains and can help gain a better understanding of metal tolerance mechanisms used by these isolates. / Thesis(MSc (Environmental Sciences))--North-West University, Potchefstroom Campus, 2013

Contamination from various sources has a huge impact on soil health and microbial community composition. Metal contamination of soil in mining scenarios is of concern and is not adequately addressed, particularly with respect to the microbial community. The mining industry is one of the largest contributors to heavy metal contamination of soil in South Africa, especially since the country is one of the major mining countries in the world. Platinum mining is of special importance, since the largest percentage of the world’s reserves of platinum group metals are found and mined in South Africa. Metals from mining activities become irreversibly immobilized in soil systems because they cannot be degraded and has a huge impact on soil systems. In this study, bacteria was isolated from soil samples collected from a platinum mine tailings dam outside Rustenburg. During the warm sampling season (March 2006) most isolates were found, especially in sites 3 and 4. During the colder and drier season (May 2006) there were less isolates. Most of the isolated cultures also displayed a wide temperature growth range, mostly between 24°C - 37°C. Paenibacillus lautus and Bacillus subtilus DN-10 had a growth range between 5°C - 40°C. Culturable metal tolerant bacteria were isolated, purified and identified using 16S rDNA sequences. Nine different species were found namely Paenibacillus lautus strain DS19, Paenibacillus lautus, Paenibacillus sp. C15, uncultured Paenibacillaceae, Bacillus subtilis strain DN-10, Bacillus sp. KDNB5, Bacillus cereus, Stenotrophomonas maltophilia and Alcaligenes sp. DJWH 146-2. The ability of these strains to tolerate metal concentrations were explored by determining their minimum inhibitory concentrations for a selection of metals e.g. aluminum, barium, cobalt, chromium, cadmium, copper, iron, lead, manganese, nickel and mercury. Most isolates were able to tolerate >5mM of the Al\Ni alloy and cobalt. Transmission electron microscopy was used to determine the location of metals inside bacterial cells and electron dispersive X-ray analysis was used to determine the levels of metals inside microbial cells. Bacillus subtilis DN-10 (LDK0306) showed a high MIC (>5mM) for most metals used, except Hg. This strain also had a high percentage (10.26%) of Pb detected in its cells by EDX. This was the highest percentage detected. Plasmids were extracted from the identified strains and can help gain a better understanding of metal tolerance mechanisms used by these isolates. / Thesis(MSc (Environmental Sciences))--North-West University, Potchefstroom Campus, 2013

In order to improve understanding of diesel soot oxidation, an experimental rig was designed and set up, in which the soot oxidation conditions, such as temperature, oxygen partial pressure, and CO2 partial pressure, could be varied independently of each other. The oxidizing gas flow in the oxidizer was under laminar condition. This test rig comprised a naturally-aspirated single cylinder engine which acted as the soot generator, and a separate premixed oxidation burner system in which soot extracted from the engine was oxidized under controlled conditions. Diesel soot was extracted from the engine exhaust pipe and from the engine pre-combustion chamber, and the soot-laden gas was then conveyed to the burner where it was oxidized. The burner was positioned vertically and it had a flat flame whose thickness was only a few millimetres. The hot gases from the flame flew upwards through a quartz transparent tube which acted as the soot oxidation duct. The soot-laden gas from the engine was premixed with the feedgas (itself a premixed mixture of methane, air, oxygen, and nitrogen) to the burner. The soot particles passed vertically through the flame front and continued burning in the post-flame gas flowing through the quartz tube oxidation duct. The oxygen concentration and temperature of the post-flame soot oxidation gas were controllable by adjusting the flowrate and composition of the burner feedgas. Diesel soot particles were sampled at different heights along the centreline of the quartz tube above the burner. Profiles of oxygen concentration, temperature, and soot particle velocity in the oxidation zone were thus measured. Morphology and size distributions of the sampled diesel soot particles were analyzed by means of Transmission Electron Microscopy (TEM) and a computer software called ImagePro Plus. Subsequently, the specific surface oxidation rates of the soot particles were worked out based on soot particle size distributions. The TEM micrographs obtained in this study showed that the diesel soot agglomerates existed in forms of clusters and chains, each containing between a small number and thousands of individual, mostly spherical tiny particles. Of order 97% of the individual spherical particles (spherules) had a size range from 10 to 80 nm. Occasionally, individual spherules of about 150 nm in diameter could be observed. The diesel soot particles sampled from the pre-chamber of the engine had different size distributions from those sampled from the exhaust of the engine, indicating that the soot underwent an oxidation process in the combustion chamber. Soot oxidation experiments were performed in the burner post-flame gas under oxygen partial pressures ranging from 0.010 to 0.050 atm and temperatures from 1520 to 1820 K. The test results showed that the oxidation rates of the diesel soot extracted from the diesel engine were generally lower than those predicted by the well-known Nagle and Strickland-Constable formula; however, the measured oxidation rates were higher than the predictions made with another well-known formula - the Lee formula. The soot extracted from the engine pre-chamber appeared not to oxidize as fast as the soot extracted from the exhaust of the engine. CO2 gas injection to the post-flame oxidation gas at constant oxygen partial pressure and oxidation temperature seemed to have accelerated the diesel soot oxidation rate. Based on the experimental results of this study and the results of other researchers, modifications to the Nagle and Strickland-Constable formula and to the Lee formula were accomplished. Also, an empirical expression, as an alternative to semi-empirical formulae, was worked out and presented in the thesis.

This thesis describes the design, construction and application of a novel vacuum system for the preparation of thin films of organic charge-transfer compounds. The method of thermal evaporation was used for four materials: tetrathiafulvalene (TTF) and three of its derivatives, dimethyltetrathiafiilvalene (DiMe-TTF), trimethyltetrathiafiilvalene (TriMe-TTF) and bis(ethylenedithio)tetrathiafiilvalene (BEDT-TTF). The resulting thin layers were characterised using optical and electron microscopy, infrared/visible spectroscopy and dc conductivity measurements down to 77K.Thin films of tetrathiafulvalene, after doping with iodine, exhibited a maximum value of dc, in-plane room temperature conductivity σ of 8.0+2.4 S cm(^-1). Semiconducting behaviour was exhibited over the range 77-300 K with AE = 0.09+0.02 eV. The effect of the deposition rate on fihn morphology is reported. TTF iodide layers were also prepared by co- evaporating the two components. These films exhibited a maximum conductivity of 2.9+0.4 S cm(^-1) at room temperature. Again, semiconducting behaviour was noted over the range 77- 300 K with AE = 0.2+0.02 eV. A comparison of the optical, structural and electrical properties of the two types of films is made. DiMe-TTF and TriMe-TTF thin films were also successfully prepared. Doping with iodine resulted in in-plane, dc room temperature conductivities of 10(^-6) and 10(^-7) S cm(^-1), respectively. These values, together with data from optical spectroscopy, suggested that both salts were in the full charge-transfer state. (BEDT-TTF) iodide thin films were deposited by evaporating the organic compound and subsequent doping. Doped films possessed a dc, in-plane room temperature conductivity of 10(^-3) S cm(^-1).Annealing these layers at 60ºC resulted in an increase in conductivity with a final value of 1.6 S cm(^-1). Semiconducting behaviour over the range 77-300 K was exhibited by the annealed films (ΔE = 0.028 eV).Finally, thin film transistors, incorporating TTF and BEDT-TTF doped layers, were fabricated and their electrical characteristics measured.

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Applications of zinc oxide (ZnO) for optoelectronic devices, including light emitting diodes, semiconductor lasers, and solar cells have not yet been realized due to the lack of high-quality p-type ZnO. In the research presented herein, pulsed laser deposition is employed to grow Ag-doped ZnO thin films, which are characterized in an attempt to understand the ability of Ag to act as a p-type dopant. By correlating the effects of the substrate temperature, oxygen pressure, and laser energy on the electrical and microstructural properties of Ag-doped ZnO films grown on c-cut sapphire substrates, p-type conductivity is achieved under elevated substrate temperatures. Characteristic stacking fault features have been continuously observed by transmission electron microscopy in all of the p-type films. Photoluminescence studies on n-type and p-type Ag-doped ZnO thin films demonstrate the role of stacking faults in determining the conductivity of the films. Exciton emission attributed to basal plane stacking faults suggests that the acceptor impurities are localized nearby the stacking faults in the n-type films. The photoluminescence investigation provides a correlation between microstructural characteristics and electrical properties of Ag- doped ZnO thin films; a link that enables further understanding of the doping nature of Ag impurities in ZnO. Under optimized deposition conditions, various substrates are investigated as potential candidates for ZnO thin film growth, including r -cut sapphire, quartz, and amorphous glass. Electrical results indicated that despite narrow conditions for obtaining p-type conductivity at a given substrate temperature, flexibility in substrate choice enables improved electrical properties. In parallel, N+-ion implantation at elevated temperatures is explored as an alternative approach to achieve p-type ZnO. The ion implantation fluence and temperature have been optimized to achieve p-type conductivity. Transmission electron microscopy reveals that characteristic stacking fault features are present throughout the p-type films, however in n-type N-doped films high-density defect clusters are observed. These results suggest that the temperature under which ion implantation is performed plays a critical role in determining the amount of dynamic defect re- combination that can take place, as well as defect cluster formation processes. Ion implantation at elevated temperatures is shown to be an effective method to introduce increased concentrations of p-type N dopants while reducing the amount of stable post-implantation disorder. Finally, the fabrication and properties of p-type Ag-doped ZnO/n-type ZnO and p-type N-doped ZnO/n-type ZnO thin film junctions were reported. For the N-doped sample, a rectifying behavior was observed in the I-V curve, consistent with N-doped ZnO being p-type and forming a p-n junction. The turn-on voltage of the device was ∼2.3 V under forward bias. The Ag-doped samples did not result in rectifying behavior as a result of conversion of the p-type layer to n-type behavior under the n- type layer deposition conditions. The systematic studies in this dissertation provide possible routes to grow p-type Ag-doped ZnO films and in-situ thermal activation of N-implanted dopant ions, to overcome the growth temperature limits, and to push one step closer to the future integration of ZnO-based devices.

The objective of this thesis is to present the fabrication of a multiphoton microscope and the underlying theory responsible for its proper functioning. A basic introduction to nonlinear optics will give the necessary knowledge to the reader to understand the optical effects involved. Femtosecond laser pulses will be presented and characterized. Each part of the microscope, their integration and the design of the microscope will be discussed. The basic concepts of laser scanning microscopy are also required to explain the design of the scanning optics. Fast scanning problems and their solutions are also briefly viewed. As a working proof, the first images taken with the microscope will be presented. Fluorescent beads, rat tail tendon, gold nanoparticles and pollen grain images using various nonlinear effects will be shown and discussed.