Recent experiences from the Darfield and Canterbury, New Zealand earthquakes have shown that the soft soil condition of saturated liquefiable sand has a profound effect on seismic response of buildings, bridges and other lifeline infrastructure. For detailed evaluation of seismic response three dimensional integrated analysis comprising structure, foundation and soil is required; such an integrated analysis is referred to as Soil Foundation Structure Interaction (SFSI) in literatures. SFSI is a three-dimensional problem because of three primary reasons: first, foundation systems are three-dimensional in form and geometry; second, ground motions are three-dimensional, producing complex multiaxial stresses in soils, foundations and structure; and third, soils in particular are sensitive to complex stress because of heterogeneity of soils leading to a highly anisotropic constitutive behaviour. In literatures the majority of seismic response analyses are limited to plane strain configuration because of lack of adequate constitutive models both for soils and structures, and computational limitation. Such two-dimensional analyses do not represent a complete view of the problem for the three reasons noted above. In this context, the present research aims to develop a three-dimensional mathematical formulation of an existing plane-strain elasto-plastic constitutive model of sand developed by Cubrinovski and Ishihara (1998b). This model has been specially formulated to simulate liquefaction behaviour of sand under ground motion induced earthquake loading, and has been well-validated and widely implemented in verifcation of shake table and centrifuge tests, as well as conventional ground response analysis and evaluation of case histories. The approach adopted herein is based entirely on the mathematical theory of plasticity and utilises some unique features of the bounding surface plasticity formalised by Dafalias (1986). The principal constitutive parameters, equations, assumptions and empiricism of the existing plane-strain model are adopted in their exact form in the three-dimensional version. Therefore, the original two-dimensional model can be considered as a true subset of the three-dimensional form; the original model can be retrieved when the tensorial quantities of the three dimensional version are reduced to that of the plane-strain configuration. Anisotropic Drucker-Prager type failure surface has been adopted for the three-dimensional version to accommodate triaxial stress path. Accordingly, a new mixed hardening rule based on Mroz’s approach of homogeneous surfaces (Mroz, 1967) has been introduced for the virgin loading surface. The three-dimensional version is validated against experimental data for cyclic torsional and triaxial stress paths.

A plume of process-affected groundwater was identified in a shallow sand aquifer adjacent to a tailings impoundment at Syncrude Canada Ltd. Quantitative and qualitative Naphthenic Acid (NA) analyses were performed on groundwater samples to investigate NA fate and transport properties in the subsurface. Analysis of dissolved organic and inorganic components was undertaken to identify, quantify and assess the mobility of other dissolved components of environmental significance. NAs at concentrations up to 87 mg/L were found to represent the major contributor to aquatic toxicity. Attenuation of NAs by biodegradation is not observed based on screening techniques developed to date. Retardation of NAs observed at the field scale, is consistent with weak sorption observed in the laboratory by other authors. Concentrations of ammonium approached 4 mg/L in the plume, however mobility is limited by cation exchange. Aromatics and trace metals are present in low quantities (i. e. <10 ??g/L) and are only detected in groundwater immediately adjacent to the toe of the tailings impoundment. Cl and Na are found at concentrations of up 282 and 579 mg/L respectively. Dissolved oxygen is typically < 1 mg/L within the plume, while redox indicators Mn(II), Fe(II) and methane are detected between <0. 1 - 2. 6, 0. 2 - 3. 5 and <0. 1 - 2. 1 mg/L respectively within the plume. Solid phase geochemistry, determined through solid phase extractions, was coupled with aqueous geochemistry and reactive transport modeling to identify the dominant geochemical processes occurring within the plume. Based on scenarios evaluated using reactive transport modeling, the most likely origin for the presently observed, weakly reducing conditions in the plume appears to be the presence of a small amount of disssolved, degradable organic carbon. The dominant terminal electron acceptors appear to be Fe(III) and Mn(III/IV) in the plume core and dissolved oxygen at the plume fringe. Dissolved Fe and Mn are observed to enter the domain at the upgradient boundary at maximal concentrations of 4. 2 and 0. 7 mg/L respectively. Trace metal geochemistry of the aquifer material was also assessed using solid phase extractions. The potential for trace metal release via reductive dissolution of the native geologic material is considered minimal in this case, based on the weakly reducing nature of the plume and a lack of excessive trace metal content in the aquifer material.

This thesis essentially reports an investigation of the behaviour of buried (0.12 to 0.25m diameter) single-walled PVC-U and vitrified clay pipes during installation in a uniform sand surround and when subjected to applied surface loading. An additional simple study of tail void displacements due to tunnelling in sand is also presented. Controlled laboratory tests were conducted in a glass-faced, steel-sided box. The buried pipes were installed perpendicular to the glass face and were subjected to static and cyclic loading, simulating increasing overburden stress and the passing of traffic over a shallow buried pipe respectively. The simulated shallow tunnel tests were also conducted perpendicular to the glass and involved withdrawal of the outer of two concentrically placed tubes. Photographs were taken of the sand particles and the buried structure in the plane of the cross section together with strain gauge readings on the pipe or tunnel wall throughout installation and loading/shield withdrawal. The resulting sand displacements are presented in the form of horizontal and vertical contour plots. Pipe deflections and volumetric and shear strain contours of the sand were also determined for the buried pipe tests. The shape of the deformed pipe and the imposed stress at the pipe springline were inferred from the pipe wall strains. During the PVC-U pipe tests, the deformation of the pipe caused the applied stress to be transferred to the sidefill via arching in the surrounding soil. This was associated with a reduction of applied stress reaching the pipe. Increasing the initial soil stiffness reduced the magnitude of the pipe and soil displacements and the stress carried by the pipe. Use of a vitrified clay pipe however, caused the soil surround to settle relative to the pipe. Soil shear strain contour plots are used to highlight the mechanisms of the transfer of applied stress onto, or away from, the buried pipes, and are related to the shape of the deformed pipe in the PVC-U pipe tests. The test data also allowed standard buried pipe design methods and installation procedures to be critically appraised. The soil movements recorded during the tunnel tests were shown to be similar to those recorded during the buried PVC-U pipe tests, indicating a similar soil loading transfer mechanism.

This thesis set out to improve our current understanding specifically of the role of permeability and carbon sources for the metabolic functioning of permeable sands.  Sampling of an intertidal sandy sediment in a shallow estuary over a 1-yr period revealed that permeability, being influenced by natural seasonal changes in biology and environmental conditions, varied temporally.  More specifically, the extracellular polymeric substances in the sediment were proven to substantially contribute to this temporal variability.  Sediment oxygen consumption also demonstrated seasonal variation and could be related to changes in temperature and total organic carbon, but, more importantly, also to permeability. Different carbon (C) sources were shown to influence the time series station but were also identified for other parts of the estuary.  A better understanding of the sedimentary C_org pool and the C_orgundergoing mineralization was furthermore obtained with the novel application of methods developed in the soil sciences comparing the δ¹³C of respired CO₂ to that of available source material and sedimentary C_org.  Overall, the results presented here demonstrate the crucial importance of permeability and carbon sources to metabolic processes and their mediation by biological factors. This thesis highlights the importance of continued research into the complexities of these permeable sands.

Machair is a habitat found predominantly in coastal areas of the north–west of Scotland and is characterised by a low-input, rotational arable system interspersed with semi-natural grasslands. Land management is an essential part of the machair system as both intensification and abandonment threaten its future. Little is known about this system in terms of its below ground communities. A survey was conducted over a three season, two year period for molecular determination of bacterial, AM fungal and nematode community structure. Cropped, fallow and undisturbed grassland were sampled; soil and roots associated with two commonly occurring species and composite soil samples were collected. In addition the effect of edaphic factors and vegetation composition on soil communities was assessed, both in the field and in greenhouse experiments. Results show that although all of the examined factors impacted the community structure of the three soil groups to some degree, the strength of this effect varied between groups. Bacterial communities were mainly affected by temporal factors, particularly year, possibly due to variation in soil moisture content. AM fungal community structure also varied considerably with season, but the mechanisms behind this were less obvious, with both abiotic and plant factors playing a role. AM fungal community structure varied with different plant hosts but also with soil moisture content. In contrast to both bacteria and AM fungi, nematode communities showed a strong response to land use although temporal factors and differences between locations were also observed. Grasslands harboured a distinctly different community structure from cropped and fallow, largely as a result of variation in bacterivores and carnivores. Vegetation composition and soil moisture content were also found to affect nematode community structure. This study has revealed that machair soil communities seem to be highly complex, dynamic and adapted to the changeable conditions that persist.

Leishmania development in their vectors is closely connected with bloodmeal digestion. This thesis focuses on factors affecting bloodmeal digestion, egg development and Leishmania infection within the sand fly gut. First, we compared the effect of mammalian (rabbit) and avian (chicken) blood on digestion and eggs development in Phlebotomus duboscqi. Sand flies fed on chickens had twice lower protein concentrations in the midgut and significantly lower trypsin activity compared to those fed on rabbits. The highest differences in the trypsin activity were observed during first 24 hours post bloodmeal. In addition, females fed on chickens had slower eggs development and their eggs were 10 % smaller compared to those fed on rabbits. In the second part of the thesis we tested the effect of mosquito hormone TMOF on the trypsin activity and eggs development of Lutzomyia longipalpis. Rabbit blood with TMOF (28 mg/ml) was presented to the females via a membrane feeding system. Sand flies fed on blood with TMOF had 15 - 35 % less trypsin activity than control females fed on only rabbit blood. In addition, females fed on blood with TMOF had developed 30 % less eggs and their eggs were 12 - 24 % smaller compared to control group. However the effect of TMOF we observed was lower than that described previously...

Doctor of Philosophy / Department of Entomology / Marcelo Ramalho-Ortigao / Kun Yan Zhu / Microbial communities residing within the midgut of insect vectors play a critical role in the response to various zoonotic and human pathogens, and can directly alter the development and survival of the insects. Sand flies are the primary vector of Leishmania, the causative pathogen of leishmaniasis, a neglected tropical disease. Sand flies acquire many microbes from the soil where immature stages develop until emergence as adults. Gram-negative Pantoea agglomerans and gram-positive Bacillus subtilis are two bacteria commonly associated with sand fly populations. Here, I demonstrated that an EGFP- and a GFP-expressing version of these two bacteria localize to different compartments of the midgut; a phenomenon that is achieved, in part, to pH differences found across the length of the gut. Additionally, P. agglomerans is able to selectively induce midgut epithelial apoptosis while B. subtilis does not. This is accompanied by differential immune and homeostasis responses to both bacteria highlighted by immune pathway suppression via the Poor Immune Response upon Knock-in (Pirk) gene. These effects may actually be representative of a broader type of response to bacterial infection that might be present across several insect species. Finally, I demonstrated that during metamorphosis the sand fly relies, at least in part, upon the activation of multiple genes from the autophagy pathway to aid in generating adult tissues. More specifically, I demonstrate, using microscopy, the presence of ATG6 in the cytoplasm of developing midgut epithelial cells of the sand fly pupae.

Folded map in pocket.

M.Sc. / The Mining of sand in South Africa is rapidly growing to sustain an increasing demand of sand for building purposes. Although mining of sand is regulated by environmental legislation, such as the National Environmental Management Act 107 of 1998, previous poor mining practices have left areas of land degraded and vulnerable to erosion. These areas need to be rehabilitated by restoring the vegetation and habitats to a natural state. This study was conducted in the Seringveld Conservancy, where the mining of sand has left the landscape with a degraded and unsightly appearance, and where little rehabilitation of the original vegetation has taken place. The aim of the study was to develop rehabilitation techniques for the degraded mined soils and to develop an overall strategy of revegetation by regenerating key plant species. Techniques for regenerating indigenous tree species cover, using modified mined sludge if topsoil is not available, were used to develop a practical and cost effective strategy to be used in revegetation. A comparative trial was used to cultivate indigenous tree species in different soil mixtures. Monitoring was done weekly to determine the growth performance and to ascertain which plant species would be most suitable and easy to cultivate. The study is important as it provides new information on the rehabilitation and revegetation of sand mined areas in the Seringveld Conservancy. This study will determine if alternatives could be used to replace topsoil on mined areas where none is available. The study is needed to determine whether revegetation of the mined areas would be possible using indigenous plant species that are often difficult to grow. The overall results indicate that replacing topsoil was successful for various modified soil mixtures that could sustain the growth of indigenous vegetation on the sand mines. Different indigenous tree species require different modified soil mixtures for successful propagation. A revegetation strategy was developed to complement and enable the rehabilitation of the mined in the Seringveld Conservancy. The revegetation initiative will benefit the restructuring of the degraded mined areas in the Seringveld Conservancy and will provide a benchmark for revegetation efforts in future in similar sand mining areas.

The interest in superhydrophobic coatings have increased exponentially in the recentdecades due to their potential and versatility in their applications. The use forsuperhydrophobic surfaces range from water repellent fabric, to self cleaning surfacesand numerous applications in industry. In this project the durability of 6 differentsuperhydrophobic coatings have been examined. The durability was tested bydropping sand on the surfaces from a set hight of 10 cm and a flow of 40 g/min. Thesurfaces were mounted on a 45° angle. The surfaces were abraded for 30 seconds ata time and the static, receding, and advancing contact angles along with the roll-ofangle was measured. Five of the surfaces were built up with nano particles and onewas sand blasted and anodized to create a superhydrophobic structure. The surfacesthat withstood the most abrasion was the surface that had been calcined to improveadhesion and the surface that had been sand blasted and anodized. Measurementsshowed that the roll-off angle and the receding contact angle were the two bestindicators of the deterioration of a surface, while the static contact angle and theadvancing contact angle varied little with abrasion. The project was done at thecompany Technical Research Institute of Sweden (SP) at their chemistry, surfaces andmaterials department in Stockholm. All coatings and equipment was supplied by SP.