abstract: DNA nanotechnology is one of the most flourishing interdisciplinary research fields. Through the features of programmability and predictability, DNA nanostructures can be designed to self-assemble into a variety of periodic or aperiodic patterns of different shapes and length scales, and more importantly, they can be used as scaffolds for organizing other nanoparticles, proteins and chemical groups. By leveraging these molecules, DNA nanostructures can be used to direct the organization of complex bio-inspired materials that may serve as smart drug delivery systems and in vitro or in vivo bio-molecular computing and diagnostic devices. In this dissertation I describe a systematic study of the thermodynamic properties of complex DNA nanostructures, including 2D and 3D DNA origami, in order to understand their assembly, stability and functionality and inform future design endeavors. It is conceivable that a more thorough understanding of DNA self-assembly can be used to guide the structural design process and optimize the conditions for assembly, manipulation, and functionalization, thus benefiting both upstream design and downstream applications. As a biocompatible nanoscale motif, the successful integration, stabilization and separation of DNA nanostructures from cells/cell lysate suggests its potential to serve as a diagnostic platform at the cellular level. Here, DNA origami was used to capture and identify multiple T cell receptor mRNA species from single cells within a mixed cell population. This demonstrates the potential of DNA nanostructure as an ideal nano scale tool for biological applications. / Dissertation/Thesis / Ph.D. Chemistry 2014

With the recent growth of the mobile market, companies want to target mobile devices while at the same time keeping product development costs low. One way to do this is to develop web applications, which are accessed from a mobile de- vice’s web browser, instead of native applications. The same web application can then be used on different platforms such as Android and iOS. However, devices such as smart phones and tablets often include cameras and sensors that a web ap- plication may want to access, but which are only accessible from native applica- tions. A framework was developed that enables web applications to communicate with native Android applications. Native applications are launched by clicking a link in the browser, and the result produced is made available to the web applica- tion through a HTTP POST request or a local web server running on the device. Key characteristics of the framework include ease of extension and the ability to enable secure (SSL) communication if desired. The ZXing Barcode Scanner ap- plication was integrated with the framework so that a scanned barcode can be dis- played in the browser. Performance measurements were conducted measuring the time taken from clicking a link to start a test application to the result being avail- able in the browser. The mean times measured were between 323 and 394 mil- liseconds. This indicates that the method used is sufficiently fast to not detract from the user experience. Future work could expand on the measurements or per- form a feature and performance comparison with PhoneGap.

Filmes de óxidos de molibdênio, com ou sem a inclusão de metais, foram eletroquimicamente depositados sobre eletrodos de carbono vítreo em solução de Mo(VI) com pH ajustado em 2,5 ou 3,0. Estes filmes foram caracterizados por Soft X-ray Spectroscopy (SXS), X-ray Diffraction (XRD) e Rutherford Backscattering Spectroscopy (RBS). A coordenação local dos sítios de Mo foram analizadas. As configurações estruturais locais do Mo foram avaliadas quando diferentes números de ciclos de potencial foram empregados na modificação dá superfície do eletrodo. Alguns metais (Pt, Pd, Rh e Cu) foram codepositados com as espécies de Mo e seu efeito nos materiais obtidos foi investigado. O grau de ocupação do orbital 4d do Mo foi examinado como um indicador da existência de interações entre o Mo e o metal codepositado. A incorporação de Pt no filme de óxidos na superfície de um eletrodo de ouro foi caracterizada por espectroscopia PIXE. O eletrodo modificado por óxidos de molibdênio foi estudado em faixas de potencial positivas frente à oxidação de nitrito (NO2-) e de óxido nítrico (NO). A relação entre a porosidade do filme e a presença de água em seus interstícios foi examinada e a capacidade de retenção de NO e NO2 foi também investigada. O eletrodo modificado foi usado como um sensor amperométrico em um sistema de injeção em fluxo (FIA) e o método foi empregado na determinação de nitrito em amostras de lingüiça. A oxidação de H2O2 foi investigada em superfície recoberta por filme de óxidos de Mo com Pt codepositada. O efeito do pH, do potencial e do tempo de pré-redução do filme de Pt e MoOx foi discutida. O comportamento eletroquímico dos filmes codepositados de Rh, Pd, Pt ou Cu e MoOx foi caracterizados comparativamente pela redução do iodato e pela oxidação do nitrito e do etanol nestes substratos. H4MogO26 foi empregado para preparar filmes contendo molibdênio e sua resposta eletroquímica foi comparada com as obtidas com o filme depositado por procedimento usual. O filme de óxidos de molibdênio foi usado com sucesso na imobilização de um complexos de Ru(III) na superfície de carbono vítreo. / Molybdenum oxide films with and without metal inclusion were electrochemically deposited on glassy carbon electrodes from Mo(VI) solutions at pH 2.5 or pH 3.0. These films were characterized by Soft X-ray Spectroscopy (SXS), X-ray Diffraction (XRD) and Rutherford Backscattering Spectroscopy (RBS). The local coordination of Mo sites was analyzed. The Mo local structure configurations were evaluated when different number of potential cycles were employed in the modification of the electrode surface. Some metaIs (Pt, Pd, Rh and Cu) were codeposited with the Mo species and their effect on the obtained material was investigated. The occupancy leveI of the 4d orbital of Mo was examined as an indicator of interactions between Mo and codeposited metals. The incorporation of Pt in the oxide film at a gold electrode surface was characterized by PlXE spectroscopy. The electrode modified by molybdenum oxides was studied at positive potential ranges for the oxidation of nitrite (NO2-) and nitric oxide (NO). The relationship between the porosity of the film and its water content was exarnined and the entrapment of NO and NO2 was also investigated. The modified electrode was used as an amperometric sensor in a flow injection configuration and the method was employed in the deterrnination of nitrite in sausage samples. The oxidation of H2O2 was investigated at surfaces covered by the Mo filrn with codeposited Pt. The effect of pH and potential and time of pre-reduction on the response of the film with Pt was discussed. The electrochemical behaviour of codeposited films of Rh, Pd, Pt or Cu and Mo MoOx was characterized comparatively for the reduction of iodate and the oxidation of nitrite and ethanol. 4MogO26 was also employed to prepare films containing molybdenum and their electrochemical responses were compared with those obtained by using the film electrodeposited by the usual procedure. The molybdenum oxide film was successfully used for the immobilization of Ru(III) complex at glassy carbon surfaces.

Enzymes are becoming an effective tool in industrial processes, from crude applications such as bioremediation to fine processes such as chirally selective biocatalysis. The ligninolytic enzymes have recently received considerable attention for industrial application due to both their broad substrate range and their ability to degrade the most recalcitrant natural polymer, lignin. This group of enzymes was therefore identified as the target group for this study. Improved enzyme properties are constantly being sought to enhance the range of applications for enzymes. Biodiversity provides a wide variety of enzymes. Several researchers have concentrated on extremophiles as their primary source of superior enzymes, consequently neglecting temperate environments in their search for these enzymes. The relatively neglected fungal biodiversity of South Africa provided an opportunity to test the hypothesis that potentially important industrial enzymes with unusual properties could be isolated from mesophilic basidiomycetous fungi. Subsequent screening of Eastern Cape biodiversity for thermostable ligninolytic enzymes from basidiomycetes resulted in the isolation of a novel laccase enzyme from a basidiomycetous species. This fungus was identified as Peniophora sp. UD4 by phylogenetic analysis of rDNA ITS sequences. Initial studies indicated a superior optimum temperature of 70°C and thermostability, indicated by no loss in activity at 60°C over nine hours. Further characterization of the laccase revealed a broader than usual substrate range through its unusual ability to oxidatively couple DMAB and MBTH. The laccase also exhibited a broad pH oxidation range for ABTS (pH 2 – 6.8), and a relatively high affinity (K_m_ = 0.0123 mM) and catalytic efficiency (63 252 mM^(-1)^s^(-1)^) for ABTS as a substrate. The laccase activity from Peniophora sp. UD4 was shown to be comprised of three isozymes with a molecular weight of 62 kDa and pI’s of 6.33, 6.45 and 6.50. Investigation of the nutrient and physical factors affecting ligninolytic enzyme production and growth of Peniophora sp. UD4 indicated that the wild-type organism was unsuitable for large scale production of the thermostable laccase due to the low levels of laccase production. The thermostable laccase was applied to defouling of ultrafiltration membranes, bioremediation of industrial waste streams, biocatalysis, and biosensor technology as potential applications. Application of the Peniophora sp. UD4 laccase to defouling of membranes used for ultrafiltration of brown water showed large flux recoveries of 31, 21 and 21% after the first three defouling recycles respectively, compared to 3% for the control without immobilized enzyme. The novel laccase showed potential for the bioremediation of industrial waste streams, the most successful being that of bleach plant effluent, where a reduction of 66% of the phenolic load was achieved. Application of the novel laccase to biocatalytic oxidation of ferulic acid and (±)-α-pinene showed higher product yield as compared to oxidation of these compounds by Trametes versicolor laccase in mediated and non-mediated systems. The major products of (±)-α-pinene oxidation were identified as verbenol and trans-sorberol. The Peniophora sp. UD4 laccase was successfully applied to biosensor technology, which benchmarked significantly better than Trametes versicolor laccase for the detection of 4-chlorophenol. The biosensor developed with laccase from UD4 by covalent binding to a glassy carbon electrode exhibited the best combination of sensitivity and stability. This thesis shows that a laccase with superior properties was obtained from a mesophilic South African basidiomycete. The catalytic properties displayed by the novel laccase from Peniophora sp. UD4 all contribute to the increased industrial applicability of laccases, and may be the most industrially feasible enzyme of its class isolated to date.

A thesis submitted in fulfillment of the requirement for the Degree Master of Technology: Biotechnology, M.L. Sultan technikon, 2000. / The ever-increasing demand for a wide variety of paper products has led to the pulp and paper industry becoming one of the largest industries in the world. In 1988 the United States alone produced almost 71 million metric tonnes of paper and pulp board (Jeffries, 1992). South Africa has also become one of the major international producers of pulp and paper products. Since 1970, the production of paper and board by the South African industry achieved an average growth rate of 5.2% per annum, and in 1997 South Africa was the twelfth largest producer of pulp and 24th biggest supplier of paper and board in the world (Molony, 1999 / M

Le présent travail concerne l’élaboration et la caractérisation de matériaux phosphatés pour l’électronique et l’optique compatibles avec l’environnement et avec les procédés d’un développement durable. Nos recherches ont surtout porté sur les composés phosphatés non linéaires et plus particulièrement sur les phases eulytines de type BII3MIII(XO4)3 (avec BII = cation bivalent, MIII = cation trivalent, X = P, As, V). Bien évidement seuls les phosphatés exempts d’éléments toxiques seront considérés pour des applications. Les autres complèteront nos études fondamentales. Tous ces composés cristallisent dans le groupe d’espace I-43d non centrosymétrique compatible avec des propriétés non linéaires optiques et piézoélectriques. Une analyse de nos données structurales et celles disponibles dans la littérature nous a conduit aux conclusions suivantes pour les phases stoichiométriques de type BII3MIII(XO4)3 sus-indiquées : i) seules les phases Pb3Bi(AsO4)3 et Pb3Bi(PO4)3 ont été rapportées dans la littérature, ii) les phosphates de type eulytines semblent se stabiliser facilement à la température ordinaire pour toutes les combinaisons possibles de cations BII et MIII, pourvu que le rayon ionique moyen du site (16c) soit de l’ordre ou supérieur à environ 1Å. Les mesures diélectriques réalisées ont permis de mettre en évidence des comportements thermiques totalement inédits. Nous avons mis en évidence des transitions de phases originales au voisinage de la température ambiante 300K. Les transitions de phases ainsi mises en évidence ne peuvent être de nature ferroélectriques car aucun changement de symétrie n’a été observé aux températures de ces transitions. Ainsi à partir des transitions 5D0→7F0 de Eu3+ nous avons observé deux émissions proches mais distinctes. Ce qui montre bien l’existence de deux sites à 20K, tendant à se confondre en seul vers 300K, température correspondant aux pics diélectriques. Ce phénomène signifie que l'environnement de Eu3+ varie avec la température présageant l’existence de transitions de phases de nature très particulière. Cependant la nature de ces transitions n’est pas encore clarifiée même si elle a été par ailleurs confirmée par DSC et même par la variation du déclin de fluorescence de Eu3+ avec la température. Des changements de pentes des graphes aux mêmes températures (150K et 300K) ont été mis en évidence à partir des résolutions structurales en fonction de la température 100 - 400K. / The objective of the present thesis is to place our research work into the perspectives of a sustainable development with a sound design of materials for optics and electronics containing zero toxic element substance. Indeed free toxic elements phosphates are the most appropriate as raw materials for the fabrications of electronic & optical devices. With the aim to conceive such devices in the present research work, we try to correlate the chemical composition, the crystal structure and the physical properties of various phosphate eulytites BII3MIII(PO4)3 (BII = Ca, Sr, Ba, Pb; MIII = Y, Bi). We have also considered the analysis of the structural parameters that “condition” and influence the phase stability of the eulytite families. From the present study it appeared that eulytite under normal conditions of pressure and temperature could be stabilized mainly with big size cations in the (16c) Wickoff positions. The minimum mean size required for such cations is about 1Å. The dielectric investigations have shown very original behaviors totally unexpected with unknown peaks of the thermal plots of dielectric parameters. These peaks are all located close to room temperature (300K). Our preliminary structural investigations versus temperature have evidenced the stability of the space group I-43d all along the temperature domain 100 – 400K. The dielectric transitions are real as corroborated by the thermal variation of the lattice parameters and some chemical bonds, length and angles showing evidence of a slope change at the same temperature of dielectric peaks. As local probe, Eu3+ photoluminescence has also evidenced the existence two Eu3+ positions in (16c) sites at very low temperature. At a temperature of the dielectric transitions (300K) only one Eu3+ site is evidenced. This may explain the origin of the dielectric transitions. Our optical laser spectroscopy also showed a very original behavior along the thermal plots of the decay time of Eu3+ emission.

Magister Educationis - MEd / The study was located within the project : Relevance of school mathematics Education (ROSME) of the Department of Dicactics at the University of the Western Cape. The research was undertaken in the belief that mathematics enables creative and logical reasoning about contextualised problems in the realm of the physical and social world as well as in the discipline mathematics itself. This research attempted to investigate the contextual issues that teachers have to deal with in mathematics education. / South Africa

Master of Science / Department of Computer Science / Antonio R. Asebedo / Mitchell L. Neilsen / Small unmanned aircraft systems (sUAS) have been in commercial use since the1980’s and over 8-12% of its current uses are in the agricultural sector, but only involving limited uses like surveying, mapping and imaging, which is expected to increase to 47% according to AUVSI with the association of Artificial Intelligence over the next decade. Our research is one such effort to help farmers utilize advanced sUAS technology coupled with Artificial Intelligence and give them meaningful results in a widely used and user friendly interface, like a mobile application. The vision for this application is to provide a completely automated experience to the farmer for a repetitive and periodic analysis of his/her crops where all the instruction needed from the farmer is a push of a button on a one time configured application and ultimately providing results in seconds. This would help the farmer scout their crops, assess yield potential, and determine if additional inputs are needed for increasing grain yield and profit per acre. For making this application we focused on user-friendliness by abstracting crop algorithms, minimized necessary user inputs, and automate the construction of flight paths. Due to internet connection not always being available at farm fields, processing was kept to on-board compute systems and the mobile device to give live results to farmers without reliance on cloud-based analytics. The application is configured to work with DJI Aircraft using OpenCv for video processing and mobile vision, GIS and GPS data for accurate mapping, locating device, sUAS on the mobile application, and FFMPEG for encoding and decoding compressed video data. An algorithm developed by Precision-Ag Lab at the K-State Agronomy Department was implemented into the sUAS application for providing real time yield estimations and nitrogen recommendation algorithm for winter wheat.

Personalized recommender systems aim to assist users in retrieving and accessing interesting items by automatically acquiring user preferences from the historical data and matching items with the preferences. In the last decade, recommendation services have gained great attention due to the problem of information overload. However, despite recent advances of personalization techniques, several critical issues in modern recommender systems have not been well studied. These issues include: (1) understanding the accessing patterns of users (i.e., how to effectively model users' accessing behaviors); (2) understanding the relations between users and other objects (i.e., how to comprehensively assess the complex correlations between users and entities in recommender systems); and (3) understanding the interest change of users (i.e., how to adaptively capture users' preference drift over time). To meet the needs of users in modern recommender systems, it is imperative to provide solutions to address the aforementioned issues and apply the solutions to real-world applications. The major goal of this dissertation is to provide integrated recommendation approaches to tackle the challenges of the current generation of recommender systems. In particular, three user-oriented aspects of recommendation techniques were studied, including understanding accessing patterns, understanding complex relations and understanding temporal dynamics. To this end, we made three research contributions. First, we presented various personalized user profiling algorithms to capture click behaviors of users from both coarse- and fine-grained granularities; second, we proposed graph-based recommendation models to describe the complex correlations in a recommender system; third, we studied temporal recommendation approaches in order to capture the preference changes of users, by considering both long-term and short-term user profiles. In addition, a versatile recommendation framework was proposed, in which the proposed recommendation techniques were seamlessly integrated. Different evaluation criteria were implemented in this framework for evaluating recommendation techniques in real-world recommendation applications. In summary, the frequent changes of user interests and item repository lead to a series of user-centric challenges that are not well addressed in the current generation of recommender systems. My work proposed reasonable solutions to these challenges and provided insights on how to address these challenges using a simple yet effective recommendation framework.

The adsorption and separation of Pd(II) from Pt(IV), Ir(IV) and Rh(III) by silica microparticles functionalized with triethylenetetramine (TETA), 2-(2-aminoethylthio)ethanamine (NSN) and 2-(2-(2-aminoethyl)ethylthio)ethanamine (NSSN) in 1 M hydrochloric acid medium was investigated by continuous column studies. The functionalized sorbent materials were characterized by microanalysis, SEM-EDS and FT-IR. Palladium selectivity of the sorbent materials was achieved by stripping of rhodium, iridium and platinum chlorido species with 0.5 M of NaClO4 in 1 M HCl while [PdCl4]2 was eluted with 3% w/v thiourea. The desorption efficiency of thiourea was confirmed by the SEM-EDS analysis of the materials after Pd(II) elution. Palladium loading capacity of the sorbents were in the order S-NSSN (23.85 mg/g) > S-NSN (12.70 mg/g) > S-TETA (4.97 mg/g). The extraction patterns on the sorbent materials were explained by considering the coordination chemistry of the ligand with [PdCl4]2ˉ and ionic interactions of [PtCl6]2ˉ and [IrCl5(H2O]ˉ. The square planar complexes, [Pd(HNSSNH)Cl2]Cl2 and [Pd(NSNH)Cl2][PdCl4]2, were isolated, analyzed by spectroscopy and single crystal X-ray, whereas evidence of the fraction of Pd(II)-TETA complex was obtained by HPLC studies. This provided proof of the inner sphere coordination mechanism as the mode of interaction of these ligands with [PdCl4]2ˉ. Trace amounts of Brˉ anions in ligands resulted in the inadvertent isolation of bromide coordinated Pd(II) NSN and NSSN complexes. The ion-pair salts of [TETAH4]4+ with [PtCl6]2ˉ, [IrCl6]3ˉ and [RhCl6]3ˉ were also isolated and characterized by microanalysis and IR to further explain the extraction patterns.