Thesis (MSc)--University of Stellenbosch, 2006. / Bibliography. Also available via the Internet.

Thesis (Ph.D.)--University of Melbourne, School of Earth Sciences, 2009. / Typescript. Includes bibliographical references.

abstract: Genomic structural variation (SV) is defined as gross alterations in the genome broadly classified as insertions/duplications, deletions inversions and translocations. DNA sequencing ushered structural variant discovery beyond laboratory detection techniques to high resolution informatics approaches. Bioinformatics tools for computational discovery of SVs however are still missing variants in the complex cancer genome. This study aimed to define genomic context leading to tool failure and design novel algorithm addressing this context. Methods: The study tested the widely held but unproven hypothesis that tools fail to detect variants which lie in repeat regions. Publicly available 1000-Genomes dataset with experimentally validated variants was tested with SVDetect-tool for presence of true positives (TP) SVs versus false negative (FN) SVs, expecting that FNs would be overrepresented in repeat regions. Further, the novel algorithm designed to informatically capture the biological etiology of translocations (non-allelic homologous recombination and 3&ndashD; placement of chromosomes in cells –context) was tested using simulated dataset. Translocations were created in known translocation hotspots and the novel&ndashalgorithm; tool compared with SVDetect and BreakDancer. Results: 53% of false negative (FN) deletions were within repeat structure compared to 81% true positive (TP) deletions. Similarly, 33% FN insertions versus 42% TP, 26% FN duplication versus 57% TP and 54% FN novel sequences versus 62% TP were within repeats. Repeat structure was not driving the tool's inability to detect variants and could not be used as context. The novel algorithm with a redefined context, when tested against SVDetect and BreakDancer was able to detect 10/10 simulated translocations with 30X coverage dataset and 100% allele frequency, while SVDetect captured 4/10 and BreakDancer detected 6/10. For 15X coverage dataset with 100% allele frequency, novel algorithm was able to detect all ten translocations albeit with fewer reads supporting the same. BreakDancer detected 4/10 and SVDetect detected 2/10 Conclusion: This study showed that presence of repetitive elements in general within a structural variant did not influence the tool's ability to capture it. This context-based algorithm proved better than current tools even with half the genome coverage than accepted protocol and provides an important first step for novel translocation discovery in cancer genome. / Dissertation/Thesis / Ph.D. Biomedical Informatics 2014

The contribution of the clamping force in the technique used in this study to stretch-bend low carbon steel samples was investigated to support the subsequent changes in the microstructure and properties of the formed material with regard to parent material. Although plastic deformation by cold working is known to induce texture or preferred orientation to the grains of a formed material while decreasing its ductility and increasing the strength, as well as inducing residual stress, it is not known how the different directions (rolling, transverse and oblique/45°) of the sheet steel will respond to this stretch bending technique. The first part of the research work involved a thorough literature review on sheet metal forming processes and their effect on the formed material with interest on the above mentioned directions of the sheet. It became clear from the literature overview that cold working of a material will induce strain-hardening which varies with the magnitude of cold work, resulting in changes in the strength and ductility of the material. Besides, when plastic deformation is not uniform (e.g., tensile and compressive) throughout the entire cross section of the formed part, residual stresses remain in the material with the grains been elongated along the direction of the maximum strain. The main parameters that were considered and controlled in this study are as follows: strain experienced / stress induced into the form sample, the sample direction, the stroke length and the clamping torque, the generated radius of curvature. The chapters that follow the literature review, deal with the set-up of the different equipment used in this study, the specimen preparation as well as the recording, the calculation and interpretation of the results. It was found that the stress magnitude that generated the different radii of curvature (120 mm, 150 mm and 185 mm) was between 1 percent & 13 percent higher than the parent material’s yield strength with the lower stress been associated to the smaller radius of curvature and the higher stress to the higher radius. The stress induced into the sample during forming was not only proportional to the stroke length but also to the distance between the punch’s tip and the sample and the sample to the die’s nadir. The clamping torque adopted was restricted to the manual capacity of the operator who used a preset torque wrench to fasten the plate sample into the jig. Plate samples of low carbon steel were cut to angles of 0°, 45°, and 90° to the rolling direction of the sheet material and stretch-bent on a single-action mechanical press to 120 mm, 150 mm, and 185 mm radii of curvature. The preliminary results indicate that stretch-bent samples had increased hardness to the parent plate, in particular below the surface layers up to around 1.1 mm depth. Since there is a well established relationship between hardness, yield and tensile strengths for steel, the yield and tensile strengths of the formed material were estimated using the Nobre et al [34] incremental relation, which relates the linearity between relative increments of hardness and yield strength. Changes were not noticeable at the microstructural level of the formed samples. Meanwhile, samples from which higher plastic deformation stress values were calculated were not those absorbing higher impact energy when Charpy specimen cut from plate and stretch-bent samples were tested. The maximum relieved residual stress in the parent material was predominantly compressive and represents in magnitude approximately 12 percent (average for the three directions) of its original yield strength. In the stretch-bent samples, the relieved residual stress was compressive in the outer curved section with a magnitude about 50 percent of the parent material yield strength and tensile in the inner curved section with a magnitude approximately 25 percent of the parent material yield strength.

No description available.

The evaluation of fluid forces on vibrating framed structures in a fluid environment is of current significance in view of the activity in ocean engineering. Accurate knowledge of the fluid forces under conditions of variable separated flow is lacking. In this study an attempt has been made to find a general method of evaluation of fluid forces on cylinders for variable flow, using published data from tests of constant velocity flow, uniformly accelerated flow and wave motion. The parameters that appear to govern the variable flow forces are discussed and models for relating force magnitudes to these parameters are suggested. The dynamic response of framed structures in an ocean environment has not been investigated except for linear sinusoidal wave motion in deep water conditions. The response of shallow water structures to various types of wave forces, as well as to earthquake excitation, has been analysed numerically here, taking into account the interaction between the structure and fluid motions. The effect of the mass and drag parameters on the structure response has been studied. Governing load cases for the design of framed structures have been related to structural period and water depth. / Applied Science, Faculty of / Civil Engineering, Department of / Graduate

This thesis investigated the application of seismic analysis methods and the response of idealized shear frames subjected to seismic loading. To complete this research, a Design Basis Earthquake (DBE) for a project site in San Luis Obispo, CA, and five past earthquake records were considered. The DBE was produced per the American Society of Civil Engineers’ Minimum Design Loads for Buildings and Other Structures (ASCE 7-10) and used for application of the Equivalent Lateral Force Procedure (ELFP) and Response Spectrum Analysis (RSA). When applying RSA, the modal peak responses were combined using the Absolute Sum (ABS), Square-Root-of-the-Sum-of-Squares (SRSS), and Complete Quadratic Combination (CQC) method. MATLAB scripts were developed to produce several displacement, velocity, and acceleration spectrums for each earthquake. Moreover, MATLAB scripts were written to yield both analytical and numerical solutions for each system through application of Linear Time History Analysis (THA). To obtain analytical solutions, two implicit forms of the Newmark-beta Method were employed: the Average Acceleration Method and the Linear Acceleration Method. To generate a comparison, the ELFP, RSA, and THA methods were applied to shear frames up to ten stories in height. The system parameters that impacted the accuracy of each method and the response of the systems were analyzed, including the effects of classical damping and nonclassical damping models. In addition to varying levels of Rayleigh damping, non-linear hysteric friction spring dampers (FSDs) were implemented into the systems. The design of the FSDs was based on target stiffness values, which were defined as portions of the system’s lateral stiffness. To perform the required Nonlinear Time History Analysis (NTHA), a SAP2000 model was developed. The efficiencies of the FSDs at each target stiffness, with and without the addition of low levels of viscous modal damping are analyzed. It was concluded that the ELFP should be supplemented by RSA when performing seismic response analysis. Regardless of system parameters, the ELFP yielded system responses 30% to 50% higher than RSA when combing responses with the SRSS or CQC method. When applying RSA, the ABS method produced inconsistent and inaccurate results, whereas the SRSS and CQC results were similar for regular, symmetric systems. Generally, the SRSS and CQC results were within 5% of the analytical solution yielded through THA. On the contrary, for irregular structures, the SRSS method significantly underestimated the response, and the CQC method was four to five times more accurate. Additionally, both the Average Acceleration Method and Linear Acceleration Method yielded numerical solutions with errors typically below 1% when compared with the analytical solution. When implemented into the systems, the FSDs proved to be most efficient when designed to have stiffnesses that were 50% of the lateral stiffness of each story. The addition of 1% modal damping to the FSDs resulted in quicker energy dissipation without significantly reducing the peak response of the system. At a stiffness of 50%, the FSDs reduced the displacement response by 40% to 60% when compared with 5% modal damping. Additionally, the FSDs at low stiffnesses exhibited the effects of negative lateral stiffness due to P-delta effects when the earthquake ground motions were too weak to induce sliding in the ring assemblies.

The design of steel framed buildings must take into consideration the lateral drift of the structure due to wind loading and any serviceability issues that may arise from this lateral movement. This thesis focuses on one of these issues, damage to nonstructural components. Although there are no specific requirements in the United States governing the effects of wind drift, it is an important issue which may significantly impact the buildings structural performance and economy. Furthermore, because these serviceability issues are not codified, there is a wide variation among design firms in how they are dealt with, leading to a greater economic disparity. This thesis begins with a comprehensive review of the literature that covers all pertinent aspects of wind drift in steel framed buildings. Next an analytical study of the variations in modeling parameters is performed to demonstrate how simple assumptions can affect the overall buildings stiffness and lateral displacements. A study is then carried out to illustrate the different sources of elastic deformation in a variety of laterally loaded steel frames. The different modeling variables demonstrate how deformation sources vary with bay width, the number of bays and the number of stories, providing a useful set of comparisons. To ascertain how serviceability issues are dealt with from firm to firm, a survey of the practice is developed to update the one conducted in 1988 (ASCE). In effect, the thesis is presented with the intention of suggesting and establishing a comprehensive, performance based approach to the wind drift design of steel framed buildings. / Master of Science

<p>A study has been conducted in mildly aggressive saline solutions to indentify subtle yet important difference in the anodic and cathodic process of three Mg-Al alloys, AZ31B, AM30 and AM60B in a partially passive state and a localized corrosion state. The influence of metallurgical factors and environment variables on the corrosion resistance and surface film breakdown process has been investigated using potentiodynamic and potentiostatic tests combined with optical microscopy.</p> <p>All three Mg-Al alloys corroded in a partially protected state under open circuit conditions in the test solution and the surface film formed on each exhibited a similar breakdown potential. This indicates that metallurgical factors such as alloying additions and the presence of the β-phase (Mg₁₇Al₁₂) did not significantly influence the surface film breakdown process. AM60B exhibited improved corrosion resistance at potentials below the breakdown potential due to the formation of a more protective surface film. The β- phase, however, did not strongly influence either the anodic process at potentials above the breakdown potential or the cathodic process. It was determined that increasing the alloy Al content increases the corrosion potential of Mg-Al alloys, but also increases the risk of localized corrosion. The similar anodic and cathodic polarization behaviour exhibited by AZ31B and AM30 indicates that a 1 wt % Zn alloying addition does not strongly influence the corrosion resistance of these alloys. The die-cast skin of AM60B exhibited better corrosion resistance than the interior at potentials below the breakdown potential due to the higher fraction of Al-rich β-phase, which improved the protective ability of the surface film. The semi-continuous β-phase network did not provide a strong micro-galvanic activity to drive anodic dissolution of the α-phase, therefore, did not significantly affect the corrosion resistance above the breakdown potential. The crystallographic texture exhibited by the extruded AM30 did not strongly affect the short-term and long-term corrosion resistance. AM30 showed a relatively steady passive state during long time exposures in a room temperature 0.01 M NaCl solution.</p> / Master of Science (MSc)

Current and future space exploration operations rely heavily on space-borne telescopes, of which mirrors are an integral component. However, traditional solid mirrors are heavy and require a big storage space. Deploying membrane mirrors can alleviate many of these obstacles. Membrane mirrors are light and can be compactly stowed resulting in cheap launching costs. It was also demonstrated that membrane mirror would provide quality optical imaging capabilities. However, membrane mirrors exhibit undesirable vibrations that can be caused by thermal gradients or internally-induced excitations. The undesirable vibration degrades the performance of these mirrors. Hence, it is proposed to augment membrane mirrors with smart actuators around their outer rim. Smart actuators can be used to suppress the undesirable vibration. More importantly, such a system provide the capability to form appropriate surfaces to correct for aberrations in an incoming wavefront. In this spirit, this work aims at modeling and control a membrane mirror augmented with smart actuators. The approach here to consider a membrane strip augmented with smart actuators as a prelude for studying circular membranes. We consider strips of membrane material, and treat two such structures: a membrane strip augmented with a single piezoceramic bimorph acting in bending, and a membrane strip augmented with multiple macro-fiber composite bimorphs. The later structure is studied under two actuation configurations. In the first configuration, both actuators act in bending. In the other configuration, one actuator acts in bending and the second acts in tension. The developed models of both structures were validated experimentally. Then, control laws were derived for both structures. An optimal proportional-integral controller is used for the membrane strip augmented with a single piezoceramic bimorph. For the membrane strip augmented with two macro-fiber composite bimorphs, a sliding mode controller with a switching command is used. Simulation results are presented to demonstrate the efficacy of the proposed control laws. Then, a circular membrane augmented with macro-fiber composite bimorph actuators is considered. We derive the governing equation of the structure for the general configuration, where actuators are producing bending moments and radial loading. Then, we seek a reduced order model of the structure. We work on obtaining a Galerkin expansion of the model where the test functions used are the mode shapes of the structure as obtained from a finite element analysis conducted in a commercial software package. Then the control problem is considered. The objective is to correct for optical aberrations, so the Zernike polynomial basis functions are used. A transformation from the optical modes to the mechanical modes is presented and an augmented adaptive controller is used to correct for image aberrations. The results presented show the efficacy of the controller. / Ph. D.