Thesis (MEng)--Stellenbosch University, 2015. / ENGLISH ABSTRACT: Tana River, the largest river in Kenya, is an important habit that supports numerous types of life, which creates an attractive environment. Occasionally loss of life and damage to property are experienced during floods. Upstream development of hydropower generation dams without consideration of downstream impacts is well documented in literature and the aftermaths are being well exhibited currently. The aim of the thesis is to investigate and identify factors that affect the flood levels in the Tana River Delta by using a two dimensional model and eventually drawing up a velocity- water depth interaction hazard classification map. Reviews of the literature clearly established that the floods in the delta are not generated by internal rainfall only but also operation of upstream dams accounting for 95% of the flood levels. Consequently, investigations of the impacts of dams have on flow regime were carried out. Probabilistic analysis revealed that post dam seasonal patterns has not been impacted but the magnitude of flood peaks has generally declined due to the attenuation of small peaks. However, large/flash floods (10 year Annual Recurrence Interval (ARI) spill at the dams causing major flooding downstream. Further probabilistic analysis on river discharges and sea water level was carried out to determine various ARI peaks. This incorporated climate change based on the 4th IPCC report. A two-dimensional hydrodynamic model was set up and calibrated with recorded discharges and theoretically derived parameters. Impacts of extreme tidal levels were investigated on the water levels and other factors limiting flood propagation. Finally, the model was used to simulate the 2, 50 and 100 year ARI inclusive of climate change floods and, based on Australian guidelines, flood lines and hazard maps were drawn. The results show that high tides elevate water levels in the delta in combination with the bottleneck effect at the rechanneled canal. The road crossing through the delta has inadequate bridges to convey the floods. The derived flood maps drawn (Figure 6-4) highlight that settlements in the lower delta are located within the 2 year ARI flood lines and that the extent of flooding is similar or less so in 50 and 100 year ARI flood peaks simulated. The model predicted the velocity and water depths with sufficient accuracy and recommendations are made that the study area should be extended upstream, and more field data should be collected to aid in calibration and that land use should be incorporated in flood map classification. In conclusion, the thesis has identified the flood hotspots and factors governing floods. These findings could assist in decision making by various agencies proposing flood mitigation or advocating post dam flooding scenarios. / AFRIKAANSE OPSOMMING: Die Tanarivier is die grootste rivier in Kenia en ’n belangrike habitat vir verskeie tipes diere en plante wat ‘n aantreklike omgewing skep.Verlies aan lewens en skade aan eiendom vind egter somtyds tydens oorstromings plaas. Die bou van damme vir die ontwikkeling van hidrokrag hoër op in die rivier sonder om die impak laer af in ag te neem, asook die gevolge daarvan, word dikwels in die lireratuur beskryf. Die doel met hierdie tesis is om die faktore wat die vloedhoogtes in die Tanarivier beïnvloed met die gebruik van ’n twee-dimensionele hidrodinamiese model te ondersoek en te identifiseer en om dan ’n gevaarsonekaart te teken wat die interaksie tussen waterspoed en -diepte toon. Die oorsig van die literatuur het getoon dat die oorstromings in die delta nie die gevolg is van reën in die binneland nie, maar dat die damme hoër op in die rivier verantwoordelik is vir 95% van die oorstromings. Dus is die impak van die damme op oorstromings ondersoek. Waarskynlikheidsontleding het oor die algemeen getoon dat die na-dam seisoenale vloeipatrone nie beinvloed is nie, maar dat veral die kleiner vloedpieke in die algemeen afgeneem het as gevolg van vloedattenuasie deur die damme. Groter en frats oorstromings (>1:10 ARI) veroorsaak egter steeds dat die damme oorloop en lei tot ernstige oorstromings. Die verdere waarskynlikheidsontleding van riviervloei en die seewatervlak is uitgevoer om die verskillende Jaarlikse Herhaling Periode (JHP) vlakke vas te stel. Dit het klimaatsverandering gegrond op die 4de IPCC verslag ingesluit. ʼn Twee dimensionele hidrodinamiese model is opgestel en gekalibreer teen waargenome vloei en teoreties-afgeleide parameters is gekalibreer. Die impak van uiterste getyvlakke asook faktore wat die oorstromings beperk is ondersoek. Die model is toe gebruik om die 2, 50 en 100 JHP vloedoorstromings te simuleer en vloedlyne en gevaarkaarte is volgens die Australiese riglyne geteken. Die resultate toon dat hooggety die watervlak in die delta laat styg veral in kombinasie met die bottelnek effek van die nuwe kanaal. Daar is te min brûe op die pad wat die delta deurkruis, om die vloede se vloei deur te laat Die kaarte wat geteken is toon dat daar nedersettings in die laer delta binne die 2 JHP jaar vloedarea is en dat die omvang van oorstromings dieselfde of laer is as die 50 en 100 JHP jaar vloedpieke wat gesimuleer is. Die model kan gebruik word om die vloeispoed en waterdieptes redelik akkuraat te voorspel en die volgende aanbevelings word gemaak. Toestande hoër op teen die rivier moet ondersoek word, meer data wat gedurende kalibrasie gebruik kan word moet versamel word en grondgebruik moet in die kaartklassifikasie ingesluit word. Ten slotte is die gevaarpunte vir oorstromings en die faktore wat oorstromings veroorsaak aangetoon. Hierdie bevindinge kan van nut wees as besluite geneem moet word veral wat betref die voorkoming van oorstromings nadat damme gebou is.

In the first part of this work, we describe a theory of the ground states and charge gaps in the fractional quantum Hall states of graphene. The theory relies on knowledge of these properties for filling fractions smaller than one. Then, by the application of two mapping rules, one is able to obtain these properties for fractional quantum Hall states at arbitrary fillings, by conceiving the quantum Hall ferromagnets as vacua on which correlated electrons or correlated holes are added. The predicted charge gaps and phase transitions between different fractional quantum Hall states are in good agreement with recent experiments. In the second part, we investigate the low energy theory for the neutral Landau level of bilayer graphene. We closely analyze the way different terms in the Hamiltonian transform under the action of particle-hole conjugation symmetries, and identify several terms that are relevant in explaining the lack of such symmetry in experiments. Combining an accurate parametrization of the electronic structure of bilayer graphene with a systematic account of the impact of screening we are able to explain the absence of particle-hole symmetry reported in recent experiments. We also study the energetics of fractional quantum Hall states with coherence between n=0 and n=1 cyclotron quantum numbers, and obtain a general formula to map the two-point correlation function from their well-known counterparts made from only n=0 quantum numbers. Bilayer graphene has the potential for realizing these states which have no analogue in other two-dimensional electron systems such as Gallium Arsenide. We apply this formula to describe the properties of the n=0/n=1 coherent Laughlin state which displays nematic correlations. / text

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An investigation is presented into methods of characterising cirrus ice crystals from in-situ light scattering data. A database of scattering patterns from modelled crystals was created using the Ray Tracing with Diffraction on Facets (RTDF) model from the University of Hertfordshire, to which experimental and modelled data was fitted. Experimental data was gathered in the form of scattering patterns from ice analogue crystals with similar optical properties and hexagonal symmetry to ice, yet stable at room temperature. A laboratory rig is described which images scattering patterns from single particles while allowing precise control over the orientation of the particle with respect to the incident beam. Images of scattering patterns were captured and compared to patterns from modelled crystals with similar geometry. Methods for introducing particles en-masse and individually to the Small Ice Detector (SID) instruments are discussed, with particular emphasis on the calibration of the gain of the SID-2 instrument. The variation in gain between detector elements is found to be significant, variable over the life of the detector, and different for different detectors. Fitting was performed by comparison of test scattering patterns (either modelled or experimental) to the reference database. Representation of the two dimensional scattering patterns by asymmetry factor, moment invariants, azimuthal intensity patterns (AIP) and the Fourier transform of the AIP are compared for fitting accuracy. Direct comparison of the AIP is found to be the most accurate method. Increased resolution of the AIP is shown to improve the fitting substantially. Case studies are presented for the fitting of two ice analogue crystals to the modelled database. Fitting accuracy is found to be negatively influenced by small amounts of surface roughness and detail not currently considered by the RTDF model. Fitting of in-situ data gathered by the SID-3 instrument during the HALO 02 campaign at the AIDA cloud chamber in Germany is presented and discussed. Saturation of detector pixels is shown to affect pattern fitting. In-flight operation of the instrument involves the variation of gain of the whole detector (as opposed to individual elements) in order to obtain unsaturated images of both large and small particles.

The focus of the projects presented here was to develop possible solutions to three issues commonly encountered during chemometric analysis of comprehensive two-dimensional liquid chromatography diode array detector (LCxLC-DAD) data. The focus of the first project was to determine a means of performing background correction that removed two background ridges. The methods of simply subtracting out a mean blank sample, singular value decomposition based background correction (SVD-BC) and asymmetrically weighted least squares (AWLS) were compared. AWLS was found to be the only background correction technique to fully remove the ridges. However, AWLS was also found to attenuate the peak intensity by approximately 25% due to over fitting of the background at the lower wavelengths. The focus of the second project was the investigation of five common interpolation strategies for the reconstruction of the sampled first dimension peak. The interpolation strategy that best reproduced the original first dimension retention time was Gaussian fitting. This was expected given that the simulated data set was generated using a Gaussian model for the peak shape. An algorithm, semi-automated alignment method (SAAM), was then developed that allowed for each peak to be aligned independently of the other peaks in the data set. SAAM was validated using both simulated and experimental data. The simulated results indicated that SAAM produced percent recoveries close to 100%. SAAM was also compared to iterative key set factor analysis-alternating least squares (IKSFA-ALS) for the analysis of phenytoin in a waste water treatment plant effluent. SAAM produced a concentration of 26±3 ppb compared to 39±9 ppb from IKSFA-ALS. While these results are very different, the result produced by SAAM is still within the experimental error of the reference 2D-LC/MS/MS method, 42±19. Finally, SAAM was compared to two existing literature methods. A mixture of simulated and experimental data sets was used to measure the accuracy and precision of the results. SAAM was found to be impacted less by intra- and inter-sample retention time shifting then PARAFAC2. SAAM and shifted candecomp/PARAFAC were found to produce very similar results. However, SAAM was found to experience some difficulty producing accurate and precise results with some of the experimental data sets.

This research project sought to explore, compare and develop chemometric methods with the goal of resolving chromatographically overlapped peaks though the use of spectral information gained from the four-way data sets associated with comprehensive two-dimensional liquid chromatography with diode array detection (LC ´ LC-DAD). A chemometric method combining iterative key set factor analysis (IKSFA) and multivariate curve resolution-alternating least squares (MCR-ALS) was developed. In the section of urine data analyzed, over 50 peaks were found, with 18 visually observable and 32 additional compounds found only after application of the chemometric method. Upon successful chemometric resolution of chromatographically overlapped peaks, accurate and precise quantification was then necessary. Of the compared methods for quantification, the manual baseline method was determined to offer the best precisions. Of the 50 found peaks from the urine analysis, 34 were successfully quantified using the manual baseline method with percent relative standard deviations ranging from 0.09 to 16. The accuracy of quantification was then investigated by the analysis of wastewater treatment plant effluent (WWTPE) samples. The chemometrically determined concentration of the unknown phenytoin sample was found to not exhibit a significant difference from the result obtained by the LC-MS/MS reference method, and the precision of the IKSFA-ALS method was better than that of the precision of the LC-MS/MS analysis. Chromatographic factors (data complexity, large dynamic range, retention time shifting, chromatographic and spectral peak overlap and background removal, were all found to affect the quantification results. The last part of this work focused on rapid screening methods that were capable of locating peaks between samples that exhibited significant differences in concentration. The aim here was to reduce the amount of data required to be resolved and quantified to only those peaks that were of interest. This would then reduce the time required to analyze large, complex samples by eliminating the need to first quantify all peaks in a given sample for many different samples. Both the similarity index (SI) method and the Fisher ratio (FR) method were found to fulfill this requirement in a rapid means of screening fifteen wine samples.

This study aims to explore whether human intentions to move or cease to move right and left hands can be decoded from spatiotemporal features in non-invasive electroencephalography (EEG) in order to control a discrete two-dimensional cursor movement for a potential multi-dimensional Brain-Computer interface (BCI). Five naïve subjects performed either sustaining or stopping a motor task with time locking to a predefined time window by using motor execution with physical movement or motor imagery. Spatial filtering, temporal filtering, feature selection and classification methods were explored. The performance of the proposed BCI was evaluated by both offline classification and online two-dimensional cursor control. Event-related desynchronization (ERD) and post-movement event-related synchronization (ERS) were observed on the contralateral hemisphere to the hand moved for both motor execution and motor imagery. Feature analysis showed that EEG beta band activity in the contralateral hemisphere over the motor cortex provided the best detection of either sustained or ceased movement of the right or left hand. The offline classification of four motor tasks (sustain or cease to move right or left hand) provided 10-fold cross-validation accuracy as high as 88% for motor execution and 73% for motor imagery. The subjects participating in experiments with physical movement were able to complete the online game with motor execution at the average accuracy of 85.5±4.65%; Subjects participating in motor imagery study also completed the game successfully. The proposed BCI provides a new practical multi-dimensional method by noninvasive EEG signal associated with human natural behavior, which does not need long-term training.

Apesar da importância econômica e ambiental que a madeira representa como fonte natural e renovável de energia e fibras, pouco é conhecido sobre os processos celulares, moleculares e bioquímicos envolvidos com a sua formação. Usando metodologias proteômicas como 2D-PAGE e espectrometria de massas foi iniciada a análise do proteoma do caule de Eucalyptus grandis em diferentes estádios de desenvolvimento (5 meses, 3 anos e 6 anos). O presente trabalho baseou-se especificamente na idade de cinco meses. As plantas tiveram suas folhas, raízes e cascas removidas e seus caules foram macerados em almofariz com nitrogênio líquido e as proteínas extraídas pelo método de extração fenólica. As proteínas foram separadas por eletroforese bidimensional em fitas IPG com gradiente de pH imobilizado linear de 4-7 na primeira dimensão e gel de poliacrilamida (12,5%) na segunda dimensão. A coloração dos géis foi realizada com coomassie G250. Foram detectados 438 spots e um total de 168 spots foram retirados do gel, digeridos com tripsina e submetidos ao sequenciamento por espectrometria de massas através do sistema LCMS/ MS. O sequenciamento por MS apresentou uma eficiência de 72,02% possibilitando a identificação de 121 spots, enquanto que 35 (20,83%) não apresentaram homologia com nenhuma base de dados. Entre as proteínas identificadas 22 foram representadas por mais de um spot, podendo indicar a ocorrência e eventos provenientes do splicing alternativo, modificações pós-traducional, variações alélicas de uma mesma proteína ou degradação da amostra. Entre os spots analisados, 22,02% estão relacionados com a produção de energia, (17,86%) metabolismo, (13,69%) processes celulares, (0,60%) transporte, (8,33%) componentes estruturais, (5,36%) metabolismo macromolecular, (4,17%) proteínas putativas, (20,83%) não apresentaram homologia com nenhuma base de dados e (7,14%) não demonstraram resultado. A comparação realizada entre o volume de 59 proteínas e os seus respectivos transcritos demonstrou que não existe correlação entre mRNA e as proteínas do caule. O método possibilitou uma rápida e precisa separação e identificação das proteínas do caule de Eucalyptus grandis que são diferencialmente expressas durante a fase de crescimento de cinco meses. / The process of wood formation is an important economical factor for the forestry industry and it is also of ecological importance, although little is known about the proteins involved in wood formation. The sequencing, identification and analysis of proteins provides such information of wood formation. Using proteomics techniques such as two-dimensional gel electrophoresis and mass spectrometry we have started a proteomic analysis of wood formation in Eucalyptus grandis at different stages of development (5 months, 3 and 6 years old). This work presents data related to the stage of 5 months. Using high resolution 2DE with linear pH gradient ranging from 4 to 7, a total of 438 spots were detected. However, only 168 spots were analyzed by LC ESIMS/ MS and 121 were identified (72.02%) while 35 (20.83%) presented no homology in the database used. Overall, 22 proteins appeared as multiple spots and accounted for most of the proteins found in the group. This observation may reflect post-translation modification, alternative splicing events, isozyme variation, allelic variation of the same protein, but also protein degradation. Over the 168 spots analysed, (22.02%) play a role in energy, (17.86%) metabolism, (13.69%) cellular processes, (0.60%) transport, (8.33%) structural components, (5.36%) macromolecular metabolism, (4.17%) putative protein, (20.83%) no homology and (7.14%) no result. For 59 proteins, the spot volume was compared with their respective transcript with mRNAs extracted from wood forming tissue. The method provided a faster and accurate tool for separation and identify of protein which are differentially expressed under different stages of development in Eucalyptus grandis.