[pt] Este trabalho descreve teoria, simulação e caracterização óptica de microcavidades semicondutoras utilizadas para a mudança de cor de pulsos de luz e geração de pulsos ultra-curtos. Amostras foram fabricadas por MBE com GaAs e AlAs em estruturas compostas de dois espelhos de Bragg e um espaçador de GaAs, formando cavidades de Fabry-Pérot. Espectros de refletância e transmitância foram simulados com o Método da Matriz de Transferência, considerando modelos realísticos para as propriedades ópticas dos materiais. A caracterização óptica foi realizada por FTIR e experimentos de Ring-Down utilizando uma streak camera. Fatores de qualidade maiores que 10(5) foram observados, correspondendo a tempos de armazenamento da luz maiores que 100 ps. Experimentos de troca de cor da luz em uma configuração de pump and probe foram realizados. A geração de pulsos ultra-curtos com cavidades em micropilar foi estudada. Para caracterizá-las, foram empregados o chaveamento óptico de cavidades e a microfotoluminescência resolvida no tempo. O processo completo, ultrarápido, de chaveamento dos modos ressonantes de uma cavidade semicondutora foi claramente observado de maneira inédita. / [en] This work describes the theory, simulation and optical characterization of semiconductor microcavities used to change the color of light and generate ultrashort pulses. Samples were fabricated by MBE with GaAs and AlAs in structures composed of two Bragg mirrors and a GaAs spacer, creating Fabry-Pérot cavities. Reflectance and transmittance spectra were simulated with the transfer-matrix method considering realistic models of the materials optical properties. Optical characterization was performed using FTIR spectroscopy and Ring-Down experiments with a streak camera. Quality factors in excess of 10(5) were observed, corresponding to storage times larger than 100 ps. Color-change experiments using a pump and probe optical setup were performed. The generation of ultra-short pulses with micropillar cavities was investigated. Time-resolved microphotoluminescence and optical cavity switching were employed to characterize the cavities. The complete ultrafast process of switching resonant modes of a semiconductor cavity using all-optical free carrier injection has been clearly observed for the first time.

Le travail présenté dans cette thèse, s’inscrit dans le domaine d'étude de l'interaction des rayonnements ionisants avec les liquides polaires. Bénéficiant de l’accélérateur d'électrons picoseconde ELYSE, les études ont été menées en utilisant les techniques de la radiolyse impulsionnelle associées à la spectrophotométrie d’absorption résolue en temps dans le domaine de la picoseconde. Ce travail est réparti sur deux chapitres distincts. Le premier aborde l’étude la variation temporelle du rendement radiolytique de l’électron solvaté dans l'eau et les alcools simples. Grâce au système de détection original monté sur l’accélérateur ELYSE, composé d’une lampe flash spécialement conçue pour cette détection et d’une streak-camera utilisée pour la première fois en spectroscopie d’absorption, il a été possible d'enregistrer la totalité du déclin du rendement radiolytique de l’électron solvaté d’une façon continue dans un intervalle de temps allant de la dizaine de picoseconde à quelques centaines de nanoseconde. La capture de l’électron solvaté par le méthylviologène, a été mise à profit pour réévaluer le coefficient d’extinction molaire du spectre d'absorption de l’électron solvaté dans l’eau et l’éthanol à partir des points isobestiques qui apparaissent à l'intersection des spectres d'absorption de l’électron solvaté qui disparaît et du méthylviologène qui se forme au cours de la réaction.Le deuxième chapitre est consacré à l’étude des carbonates organiques liquides, tels que le diméthyle carbonate (DMC), le diéthyle carbonate (DEC) et le propylène carbonate (PC). Cette famille de carbonate qui n’a jamais été étudiée auparavant par radiolyse pulsée, entre dans la composition des électrolytes des batteries notamment au lithium. Les études ont été focalisées sur le PC au vu de ces caractéristiques physico-chimiques, notamment sa constante diélectrique très élevée (64) et son très fort moment dipolaire de 4,9 D. Les premiers résultats ont été obtenus d’abord sur des solutions aqueuses contenant du propylène carbonate afin d'observer les réactions de réduction et d'oxydation du PC par les espèces radiolytiques de l'eau (électron solvaté et radicaux OH). Puis après l’identification (spectrale et cinétique) de l’espèce formée par interaction avec le radical OH comme étant le radical PC• résultant de l'abstraction d'un H de la molécule de PC et l’espèce formée par interaction avec l’électron aqueux comme étant l'anion PC-, d’autres mesures ont été effectuées dans le liquide pur ainsi qu’en présence de certains intercepteurs d’électrons (biphényle, anthracène, naphtalène). Elles ont permis d'accéder au rendement radiolytique de PC- ainsi qu'à l'évaluation de son potentiel redox. Les premiers résultats sur le DEC et le DMC sont aussi exposés dans cette partie, portant dans un premier lieu sur le solvant pur et puis en présence de biphényle. / This work is part of the study area of the interaction of radiation with polar liquids. Using the picosecond electron accelerator ELYSE, studies were conducted using the techniques of pulse radiolysis combined with absorption spectrophotometry Time-resolved in the field of a picosecond.This work is divided into two separate chapters. The first study addresses the temporal variation of the radiolytic yield of solvated electron in water and simple alcohols. Due to original detection system mounted on the accelerator ELYSE, composed of a flash lamp specifically designed for the detection and a streak-camera used for the first time in absorption spectroscopy, it was possible to record the time-dependent radiolytic yields of the solvated electron from ten picoseconds to a few hundred nanoseconds. The scavenging of the electron solvated by methyl viologen, was utilized to reevaluate the molar extinction coefficient of the absorption spectrum of solvated electron in water and ethanol from isobestic points which corresponds to the intersection of the absorption spectra of solvated electron which disappears and methyl viologen which is formed during the reaction.The second chapter is devoted to the study of liquid organic carbonates such as dimethyl carbonate (DMC), diethyl carbonate (DEC) and propylene carbonate (PC). This family of carbonate wich compose the electrolytes lithium batteries, has never been investigated by pulse radiolysis. The studies were focused on the PC in the light of these physicochemical characteristics, including its very high dielectric constant (64) and its strong dipole moment of 4.9 D. The first results were obtained on aqueous solutions containing propylene carbonate to observe the reactions of reduction and oxidation of PC by radiolytic species of water (solvated electron and OH radicals). Then, after the identification (spectral and kinetic) of the species formed by interaction with the OH radical as the PC• radical resulting from the abstraction of a H from the molecule of PC and the species formed by the interaction with electron as the anion aqueous PC-, other measurements were made in the pure liquid and in the presence of some electron interceptors (biphenyl, anthracene, naphthalene). They give access to the radiolytic yield of PC- and the evaluation of its redox potential. The first results of the DEC and the DMC are also outlined in this section, the pure solvent and then in the presence of biphenyl.

Maize is the staple food for a majority of people in Southern Africa, but plant diseases are responsible for at least 10% of crop production losses. Bacterial leaf streak (BLS) of maize was first reported in South Africa in 1949 and has not been reported elsewhere. Very little is known about the pathogen involved and therefore it is deemed necessary to compile a characteristic profile for the pathogen to prevent the possibility of major crop losses as a result of this disease. This study aimed to use biochemical and phenotypic methods to determine the specific characteristics of the causal agent of BLS. Diseased plant material showing symptoms of BLS were collected during the maize production seasons of 2012 and 2013 within South Africa’s maize production regions namely the North West, Free State, Gauteng and Northern Cape provinces. To prevent contamination, maize leaves were surface sterilised thoroughly before bacterial isolation commenced. Sections of the infected maize leaves were placed on GYC agar plates on which yellow, mucoid bacterial colonies after incubation for 24 to 48 hrs. The isolated bacteria were purified and the molecular identification of the bacteria was conducted in a related study. Although literature indicates that Xanthomonas campestris pv. zeae is the causal agent of BLS, pure cultures obtained from maize leaves showing characteristic symptoms of BLS were identified as species of Xanthomonas, Pantoea, and Enterobacter. To elucidate the pathogenicity of the isolated strains, pathogenicity tests based on Koch’s postulates were performed. Results from the pathogenicity tests confirmed that only the isolate Xanthomonas species was capable of inducing the characteristic BLS symptoms when healthy maize plants were inoculated with the suspected pathogens. It is important to inoculate the maize seedlings at the correct age (four-leaf stage) and the spray method is recommended. Re-isolation was repeated from the same plant material used during the initial isolation process but the isolation method was amended. The optimised isolation method involved the use of a dilution range and spread plate method. Colonies from this isolation technique grew as bright yellow colonies that were identified as Xanthomonas spp. This outcome indicates the importance of surface sterilisation, pulverisation and subsequent dilution of plant materials for isolation of bacterial pathogens from diseases plants. These isolates were used to create protein profiles with SDS-PAGE electrophoresis and carbon utilisation patterns with the Biolog® GN2 system. Protein profiling banding patterns was assessed based on presence/absence criteria. Highly similar protein profiles were observed among the X. campestris pv. zeae isolates but groupings of different protein profiles were determined when minor differences in the protein profiles was taken into account. Xanthomonas campestris pv. zeae was successfully distinguished from the X. axonopodis pv. vasculorum reference strain through unique SDS banding patterns. Banding patterns obtained from cultures grown in a liquid medium (tryptic soy broth) were of a higher quality than the banding patterns obtained from bacteria harvested from solid media (CYG agar plates). Carbon source utilisation data was used to evaluate the average well colour development obtained from each isolate. Statistically significant differences were found among some of the isolates, with some isolates being metabolically more active than other isolates. Substrate utilisation patterns produced by the isolates corresponded to previously published studies on various Xanthomonas species. The cell count of the samples used during carbon utilisation patterns must be standardised in order to obtain reliable results. During this study, the application of Koch’s postulates and two inoculation techniques confirmed that Xanthomonas campestris pv. zeae is the pathogen responsible for bacterial leaf streak of maize. Members of the Pantoea and Enterobacter genera were found on the leaf surface of maize plants infected with BLS but inoculations of healthy maize plants with these bacteria did not result in bacterial leaf streak symptoms on the maize plants. These bacteria were not pathogenic and were considered endophytes. The identified pathogen was characterised through protein and metabolic profiling. The protein profiles of the pathogen obtained through analysis of the major bands of the SDS-PAGE gels were highly similar and distinguishable from the Xanthomonas reference culture. Groupings within the X. campestris pv. zeae group was found when major and minor bands were considered, this may however be altered when the intensities of the bands are used during analysis. Carbon utilisation patterns were assessed using Biolog® GN2 plates. A metabolic fingerprint was created for the pathogen of BLS, it was possible to distinguish between X. campestris pv. zeae and other Xanthomonas strains based on the fingerprint. This fingerprint could be used to identify the pathogen. / MSc (Environmental Sciences), North-West University, Potchefstroom Campus, 2015

Maize is the staple food for a majority of people in Southern Africa, but plant diseases are responsible for at least 10% of crop production losses. Bacterial leaf streak (BLS) of maize was first reported in South Africa in 1949 and has not been reported elsewhere. Very little is known about the pathogen involved and therefore it is deemed necessary to compile a characteristic profile for the pathogen to prevent the possibility of major crop losses as a result of this disease. This study aimed to use biochemical and phenotypic methods to determine the specific characteristics of the causal agent of BLS. Diseased plant material showing symptoms of BLS were collected during the maize production seasons of 2012 and 2013 within South Africa’s maize production regions namely the North West, Free State, Gauteng and Northern Cape provinces. To prevent contamination, maize leaves were surface sterilised thoroughly before bacterial isolation commenced. Sections of the infected maize leaves were placed on GYC agar plates on which yellow, mucoid bacterial colonies after incubation for 24 to 48 hrs. The isolated bacteria were purified and the molecular identification of the bacteria was conducted in a related study. Although literature indicates that Xanthomonas campestris pv. zeae is the causal agent of BLS, pure cultures obtained from maize leaves showing characteristic symptoms of BLS were identified as species of Xanthomonas, Pantoea, and Enterobacter. To elucidate the pathogenicity of the isolated strains, pathogenicity tests based on Koch’s postulates were performed. Results from the pathogenicity tests confirmed that only the isolate Xanthomonas species was capable of inducing the characteristic BLS symptoms when healthy maize plants were inoculated with the suspected pathogens. It is important to inoculate the maize seedlings at the correct age (four-leaf stage) and the spray method is recommended. Re-isolation was repeated from the same plant material used during the initial isolation process but the isolation method was amended. The optimised isolation method involved the use of a dilution range and spread plate method. Colonies from this isolation technique grew as bright yellow colonies that were identified as Xanthomonas spp. This outcome indicates the importance of surface sterilisation, pulverisation and subsequent dilution of plant materials for isolation of bacterial pathogens from diseases plants. These isolates were used to create protein profiles with SDS-PAGE electrophoresis and carbon utilisation patterns with the Biolog® GN2 system. Protein profiling banding patterns was assessed based on presence/absence criteria. Highly similar protein profiles were observed among the X. campestris pv. zeae isolates but groupings of different protein profiles were determined when minor differences in the protein profiles was taken into account. Xanthomonas campestris pv. zeae was successfully distinguished from the X. axonopodis pv. vasculorum reference strain through unique SDS banding patterns. Banding patterns obtained from cultures grown in a liquid medium (tryptic soy broth) were of a higher quality than the banding patterns obtained from bacteria harvested from solid media (CYG agar plates). Carbon source utilisation data was used to evaluate the average well colour development obtained from each isolate. Statistically significant differences were found among some of the isolates, with some isolates being metabolically more active than other isolates. Substrate utilisation patterns produced by the isolates corresponded to previously published studies on various Xanthomonas species. The cell count of the samples used during carbon utilisation patterns must be standardised in order to obtain reliable results. During this study, the application of Koch’s postulates and two inoculation techniques confirmed that Xanthomonas campestris pv. zeae is the pathogen responsible for bacterial leaf streak of maize. Members of the Pantoea and Enterobacter genera were found on the leaf surface of maize plants infected with BLS but inoculations of healthy maize plants with these bacteria did not result in bacterial leaf streak symptoms on the maize plants. These bacteria were not pathogenic and were considered endophytes. The identified pathogen was characterised through protein and metabolic profiling. The protein profiles of the pathogen obtained through analysis of the major bands of the SDS-PAGE gels were highly similar and distinguishable from the Xanthomonas reference culture. Groupings within the X. campestris pv. zeae group was found when major and minor bands were considered, this may however be altered when the intensities of the bands are used during analysis. Carbon utilisation patterns were assessed using Biolog® GN2 plates. A metabolic fingerprint was created for the pathogen of BLS, it was possible to distinguish between X. campestris pv. zeae and other Xanthomonas strains based on the fingerprint. This fingerprint could be used to identify the pathogen. / MSc (Environmental Sciences), North-West University, Potchefstroom Campus, 2015

Thesis (PhD)--Stellenbosch University, 2013. / ENGLISH ABSTRACT: In this thesis the structural dynamics, upon photo-excitation, of the charge-densitywave (CDW) material 4Hb-TaSe2 is investigated on the time-scale of atomic motion and simultaneously on the spatial-scale of atomic dimensions. CDW materials have been of interest since their discovery in the 1970’s because of their remarkable non-linear and anisotropic electrical properties, gigantic dielectric constants, unusual elastic properties and rich dynamical behaviour. Some of these exotic properties were extensively investigated in thermal equilibrium soon after their discovery but only recently have ultrafast techniques like femtosecond spectroscopy become available to study their out-of-equilibrium behaviour on the time-scale of atomic motion. By studying their behaviour on this time-scale a more in-depth understanding of their macroscopic properties can be gained. However, to do investigations on the atomic time-scale and simultaneously directly observe the evolution of the atomic arrangements is another challenge. One approach is through the previously mentioned technique of femtosecond pump-probe spectroscopy but converting the usual ultrashort optical probing source to an ultrashort electron or x-ray source that can diffract off the sample and reveal structural detail on the atomic level. Here, the femto-to-picosecond out-of-equilibrium behaviour upon photo-excitation in 4Hb-TaSe2 is investigated using an ultrashort electron probe source. Two variations of using an electron probe source are used: conventional scanning Femtosecond Electron Diffraction (FED) and a new approach namely Femtosecond Streaked Electron Diffraction (FSED). The more established FED technique, based on femtosecond pumpprobe spectroscopy, is used as the major investigating tool while the FSED technique, based on ultrafast streak camera technology, is an attempt at broadening the scope of available techniques to study structural dynamics in crystalline material on the subpicosecond time-scale. With these two techniques, the structural dynamics during the phase transition from the commensurate- to incommensurate-CDW phase in 4Hb-TaSe2 is observed through diffraction patterns with a temporal resolution of under 500 fs. The study reveals strong coupling between the electronic and lattice systems of the material and several time-constants of under and above a picosecond are extracted from the data. Using these time-constants, the structural evolution during the phase transition is better understood and with the newly gained knowledge, a model of all the processes involved after photo-excitation is proposed. / AFRIKAANSE OPSOMMING: In hierdie tesis word die strukturele dinamika van die lading-digtheid-golf (LDG) materiaal 4Hb-TaSe2 ondersoek op die tydskaal van atomiese bewegings en gelyktydig op die ruimtelikeskaal van atomiese dimensies. LDG materie is al van belang sedert hul ontdekking in die 1970’s as gevolg van hul merkwaardige nie-lineêre en anisotrope elektriese eienskappe, reuse diëlektriese konstantes, ongewone elastiese eienskappe en ryk dinamiese gedrag. Sommige van hierdie eksotiese eienskappe is omvattend ondersoek in termiese ewewig kort na hul ontdekking, maar eers onlangs is dit moontlik deur middle van ultravinnige tegnieke soos femtosekonde spektroskopie om hulle uit-ewewigs gedrag te bestudeer op die tydskaal van atomiese beweging. Deur die gedrag op hierdie tydskaal te bestudeer kan ’n meer insiggewende begrip van hul makroskopiese eienskappe verkry word. Om ondersoeke in te stel op die atomiese tydskaal en gelyktydig direk die evolusie van die atoom posisie te waarneem is egter ’n moeilike taak. Een benadering is deur middle van femtosekonde “pump-probe” spektroskopie maar dan die gewone optiese “probe” puls om te skakel na ’n electron of x-straal puls wat van die materiaal kan diffrak en dus strukturele inligting op die atomiese vlak kan onthul. Hier word die femto-tot-pico sekonde uit-ewewig gedrag in 4Hb-TaSe2 ondersoek met behulp van elektron pulse. Twee variasies van die gebruik van ’n elektron bron word gebruik: konvensionele “Femtosecond Electron Diffraction” (FED) en ’n nuwe benadering, naamlik, “Femtosecond Streaked Electron Diffraction” (FSED). Die meer gevestigde FED tegniek, wat gebaseer is op femtosekonde “pump-probe” spektroskopie, word gebruik as die hoof ondersoek metode terwyl die FSED tegniek, wat gebaseer is op die ultra vinnige “streak camera” tegnologie, ’n poging is om beskikbare tegnieke uit te brei wat gebruik kan word om strukturele dinamika in materie te bestudeer op die sub-picosekonde tydskaal. Met behulp van hierdie twee tegnieke, word die strukturele dinamika tydens die fase oorgang van die ooreenkomstige tot nie-ooreenkomstige LDG fase in 4Hb-TaSe2 deur diffraksie patrone met ’n tydresolusie van minder as 500 fs waargeneem. Die studie toon ’n sterk korrelasie tussen die elektroniese sisteem en kristalrooster. Verskeie tydkonstantes van onder en bo ’n picosekonde kon ook uit die data onttrek word en gebruik word om die strukturele veranderinge beter te verstaan. Hierdie nuwe kennis het ons in staat gestel om ’n model van al die betrokke prosesse voor te stel.

Thesis (PhD (Physics))--University of Stellenbosch, 2010. / ENGLISH ABSTRACT: Ultrafast Electron Diffraction (UED) is a rapidly maturing field which allows investigation of the evolution of atomic arrangement in solids on timescales comparable to the vibrational period of their constituent atoms (~10-13 s). The technique is an amalgamation of conventional high energy electron diffraction methods and pump-probe spectroscopy with femtosecond (1 fs = 10-15 s) laser pulses. Ultrafast pulsed electron sources generally suffer from limitations on the attainable electron number per pulse (brightness) due to Coulomb repulsion among the electrons. In this dissertation, the design and construction of a compact UED source capable of delivering sub-300 fs electron pulses suitable for diffraction experiments and containing about 5000 electrons per shot is described. The setup has been characterised by measurement of the transverse beam size and angular spread, and through recording and analyzing an electron diffraction pattern from a titanium foil. Measurement of the temporal duration of fs electron pulses is not trivial, and a specialised compact streak camera operating in accumulation mode has been developed as part of this study. A sub-200 fs temporal resolution has been achieved, and the dependence of temporal duration on electron number per pulse was investigated for the current UED source. The observed trends correlate well with detailed electron bunch simulations. In order to investigate ultrafast processes on samples that cannot be probed repeatedly, it becomes necessary to significantly increase the brightness of current state of the art compact sources such as the one constructed in the present study. UED sources employing electron pulse compression techniques offer this possibility. Traditional pulse compression schemes based on RF cavities, while simple in principle, pose significant technical challenges in their realisation. The current thesis describes two novel UED pulse compression methods developed by the author: achromatic reflectron compression and pulsed cavity compression. Both concepts are expected to be easier to realise than conventional RF compression. Detailed simulations predict that such sources can attain a brightness improvement of more than one order of magnitude over compact sources that do not employ compression techniques. In addition, such sources show much promise for the attainment of pulse durations in the sub-100 fs range. / AFRIKAANSE OPSOMMING: Ultra vinnige elektron diffraksie is ‘n meettegniek wat tans in die proses is om vinnige ontwikkeling te ondergaan. Die tegniek het ten doel om strukturele omsettingsprosesse op ‘n lengteskaal van atoombindings en ‘n tydskaal van die vibrasie periode van atome in materie, ongeveer 10-13 s, te ondersoek. Dit word bewerkstellig deur die spasieresolusievermoë van gewone hoë energie elektron diffraksie met die tydresolusievermoë van femtosekonde (1 fs = 10-15 s) laserspektroskopie te kombineer. Die aantal elektrone per puls (intensiteit) van ultravinnige gepulsde elektronbronne word beperk deur die Coulomb afstootingskragte tussen die elektrone. Hierdie dissertasie beskryf die ontwerp en konstruksie van ‘n kompakte ultravinnige elektron bron. Die elektronpulse wat geproduseer word bevat tot 5000 elektrone per puls met ‘n tyd durasie van minder as 300 fs, en is geskik vir diffraksie eksperimente. Die aparaat is gekarakteriseer deur die volgende metings: elektronpulsdiameter, straaldivergensie, en ‘n titaan foelie se statiese diffraksie patroon. Dit is nie triviaal om die durasie van femtosekonde elektronpulse te meet nie, en n spesiale kompakte akkumulerende “streak camera” is vir die doeleindes van hierdie projek onwikkel. Die tydresolusie van hierdie “streak camera” is beter as 200 fs, en die afhanklikheid van die pulsdurasie wat deur die ultravinnige elektron bron geproduseer word as n funksie van die elektrongetal per puls is met behulp van hierdie toestel bepaal. Die resultate klop redelik goed met gedetaileerde simulasies van die elektron puls dinamika. Die karakterisasie van monsters wat nie herhaaldelik gemeet kan word nie vereis verkieslik ‘n nog hoër pulsintensiteit as wat met huidige bronne bereik kan word. ‘N verdere doelstelling is dus om ultravinnige elektron bronne te ontwikkel wat pulse met meer elektrone per puls kan genereer. Dit kan bewerkstellig word deur bronne wat van elektron puls kompressie tegnieke gebruik maak. Die tradisionele manier waarop dít gedoen word is deur middel van n kontinu gedrewe radio frekwensie holte. Hierdie metode gaan egter gepaard met aanmerklik hoë tegniese uitdagings. Om hierdie rede het die outeur twee alternatiewe puls kompressie konsepte ontwikkel: akromatiese reflektron kompressie and gepulsde holte kompressie. Albei konsepte sal waarskeinlik makliker wees om te realiseer as die tradisionele radio frekwensie kompressie, en is deur middel van gedetaileerde simulasies geverifiseer. Hierdie simulasies voorspel dat die intensiteit van genoemde bronne met ten minste n grooteorde meer kan wees as wat tans met kompakte ultravinnige elektron bronne moontlik is. Verder blyk dit dat sulke bronne n pulsdurasie van minder as 100 fs kan bereik.

Thesis (PhD. (Geography)) --University of Limpopo, 2019 / Of late climate change and consequently, the spread of crop diseases has been identified as one of the major threat to crop production and food security in subSaharan Africa. This research, therefore, aims to evaluate the role of in situ hyperspectral and new generation multispectral data in detecting maize crop viral and fungal diseases, that is maize streak virus and grey leaf spot respectively. To accomplish this objective; a comparison of two variable selection techniques (Random Forest’s Forward Variable, (FVS) and Guided Regularized Random Forest: (GRRF) was done in selecting the optimal variables that can be used in detecting maize streak virus disease using in-situ resampled hyperspectral data. The findings indicated that the GRRF model produced high classification accuracy (91.67%) whereas the FVS had a slightly lower accuracy (87.60%) based on Hymap when compared to the AISA. The results have shown that the GRRF algorithm has the potential to select compact feature sub sets, and the accuracy performance is better than that of RF’s variable selection method. Secondly, the utility of remote sensing techniques in detecting the geminivirus infected maize was evaluated in this study based on experiments in Ofcolaco, Tzaneen in South Africa. Specifically, the potential of hyperspectral data in detecting different levels of maize infected by maize streak virus (MSV) was tested based on Guided Regularized Random Forest (GRRF). The findings illustrate the strength of hyperspectral data in detecting different levels of MSV infections. Specifically, the GRRF model was able to identify the optimal bands for detecting different levels of maize streak disease in maize. These bands were allocated at 552 nm, 603 nm, 683 nm, 881 nm, and 2338 nm. This study underscores the potential of using remotely sensed data in the accurate detection of maize crop diseases such as MSV and its severity which is critical in crop monitoring to foster food security, especially in the resource-limited subSaharan Africa. The study then investigated the possibility to upscale the previous findings to space borne sensor. RapidEye data and derived vegetation indices were tested in detecting and mapping the maize streak virus. The results revealed that the use of RapidEye spectral bands in detection and mapping of maize streak virus disease yielded good classification results with an overall accuracy of 82.75%. The inclusion of RapidEye derived vegetation indices improved the classification accuracies by 3.4%. Due to the cost involved in acquiring commercial images, like xviii RapidEye, a freely available Landsat-8 data can offer a new data source that is useful for maize diseases estimation, in environments which have limited resources. This study investigated the use of Landsat 8 and vegetation indices in estimating and predicting maize infected with maize streak virus. Landsat 8 data produced an overall accuracy of 50.32%. The inclusion of vegetation indices computed from Landsat 8 sensor improved the classification accuracies by 1.29%. Overally, the findings of this study provide the necessary insight and motivation to the remote sensing community, particularly in resource-constrained regions, to shift towards embracing various indices obtained from the readily-available and affordable multispectral Landsat-8 OLI sensor. The results of the study show that the mediumresolution multispectral Landsat 8-OLI data set can be used to detect and map maize streak virus disease. This study demonstrates the invaluable potential and strength of applying the readily-available medium-resolution, Landsat-8 OLI data set, with a large swath width (185 km) in precisely detecting and mapping maize streak virus disease. The study then examined the influence of climatic, environmental and remotely sensed variables on the spread of MSV disease on the Ofcolaco maize farms in Tzaneen, South Africa. Environmental and climatic variables were integrated together with Landsat 8 derived vegetation indices to predict the probability of MSV occurrence within the Ofcolaco maize farms in Limpopo, South Africa. Correlation analysis was used to relate vegetation indices, environmental and climatic variables to incidences of maize streak virus disease. The variables used to predict the distribution of MSV were elevation, rainfall, slope, temperature, and vegetation indices. It was found that MSV disease infestation is more likely to occur on low-lying altitudes and areas with high Normalised Difference Vegetation Index (NDVI) located at an altitude ranging of 350 and 450 m.a.s.l. The suitable areas are characterized by temperatures ranging from 24°C to 25°C. The results indicate the potential of integrating Landsat 8 derived vegetation indices, environmental and climatic variables to improve the prediction of areas that are likely to be affected by MSV disease outbreaks in maize fields in semi-arid environments. After realizing the potential of remote sensing in detecting and predicting the occurrence of maize streak virus disease, the study further examined its potential in mapping the most complex disease; Grey Leaf Spot (GLS) in maize fields using WorldView-2, Quickbird, RapidEye, and Sentinel-2 resampled from hyperspectral data. To accomplish this objective, field spectra were acquired from healthy, moderate and xix severely infected maize leaves during the 2013 and 2014 growing seasons. The spectra were then resampled to four sensor spectral resolutions – namely WorldView-2, Quickbird, RapidEye, and Sentinel-2. In each case, the Random Forest algorithm was used to classify the 2013 resampled spectra to represent the three identified disease severity categories. Classification accuracy was evaluated using an independent test dataset obtained during the 2014 growing season. Results showed that Sentinel-2 achieved the highest overall accuracy (84%) and kappa value (0.76), while the WorldView-2, produced slightly lower accuracies. The 608 nm and 705nm were selected as the most valuable bands in detecting the GLS for Worldview 2, and Sentinel-2. Overall, the results imply that opportunities exist for developing operational remote sensing systems for detection of maize disease. Adoption of such remote sensing techniques is particularly valuable for minimizing crop damage, improving yield and ensuring food security.

Technological progress in commercializing ultrafast lasers and detectors has allowed realization of cooperative processes on an ultrashort time scale, which demand a re-evaluation of the conventional cooperative phenomena with a new insight. Ultrafast cooperative phenomena in coherently prepared media and various applications of superfluorescence and coherent Raman scattering are studied in this dissertation. In particular, a simple theoretical testimony on analogy between a cooperative emission and coherent Raman scattering is presented by offering an opportunity to perform parallel research on these two processes from a unified point of view. On one hand, the superfluorescent pulse with a time duration of a few tens of picoseconds (ps) from alkali metal vapor is observed for the first time, even though cooperative phenomena in atomic vapor have been extensively studied for more than five decades. A dense rubidium vapor pumped by ultrashort (100 femtosecond, fs) pulses allows a realization of the ultrafast superfluorescence while a time-resolved study of superfluorescence is accomplished by using a streak camera with 2 ps time resolution. Experimental research on quantum nature of cooperative emissions has been “frozen” over the years (three decades) possibly because of the technical difficulties. Quantum fluctuations of superfluorescence development are explored experimentally by taking advantage of the ultra fast streak camera. Presumable applications of the superfluorescent pulse in e.g., a remote sensing, and an ultraviolet upconversion of the input infrared laser pulse are presented. The quantum interference due to different excitation pathways is revealed by the temporal coherent control technique while observing interferometric signals from alkali metal vapors. On the other hand, a new spectroscopic technique based on ultrafast coherent Raman scattering is developed. The key advantage of the presented technique is to suppress the non-resonant background noise which usually obscures possible applications of the other conventional coherent Raman techniques in practice. A reduction of the background noise is achieved by shaping and delaying the third pulse which probes the coherence of the medium (i.e., an enhancement of specific vibrations of the target molecules in unison) firstly prepared by two broadband pulses. We demonstrate a robustness and superiority of signal-to-noise ratio of the developed technique by identifying as few as 10000 bacterial spores at a single laser shot level. Finally, several comparative studies between cooperative and uncooperative processes are presented. A picosecond cooperative phenomenon in a three-photon resonant medium induced by a single as well as two-color ultrashort pulses is investigated. A time-resolved study shows that a picosecond cooperative effect is crucial in the well-established fields of resonant-enhanced multiphoton ionizations and harmonic generations. We also present a quantitative analysis for spontaneous versus broadband coherent Raman scattering on pyridine molecules. The spontaneous Raman signal is enhanced by 5 orders as a result of cooperative phenomena.

Sugarcane bacilliform virus (SCBV) is an economically important pathogen of sugarcane in Australia which limits access to foreign sugarcane germplasm. Although SCBV is present in the major cane growing regions worldwide, very little is known about its variability, virulence and the yield losses resulting from infection. The limited information on SCBV has resulted in quarantine measures being introduced to protect the Australian sugarcane industry, with a major consequence being restricted access to imported sugarcane germplasm for breeding programs. Foreign sugarcane germplasm plays an important role in breeding of new commercial varieties for the Australian sugar industry and is essential for the long term productivity, profitability and sustainability of the sugar industry. This study was aimed at characterising Australian isolates of SCBV to enable the development of reliable and robust molecular and/or antibody-based diagnostic tests which could be used to not only assess the impact of SCBV on the Australian sugarcane industry, but could also be used to screen imported sugarcane germplasm for the virus. SCBV virions (SCBV-IM) were purified from the sugarcane accession "Ireng Maleng" and the dsDNA genome was cloned and sequenced. The genome of SCBV-IM comprised 7687 bp with an organisation typical of other badnaviruses. When the entire nucleotide sequence of SCBV-IM was compared to that of the Moroccan SCBV isolate (SCBV-Mo), less than 75% similarity was present. Within the coding regions, ORF I, ORF II and ORF III had 83%, 71% and 73% nucleotide similarity to SCBV-Mo, respectively. At the amino acid level, ORFs I, II and III from SCBV-IM showed 91%, 84% and 85% similarity to the equivalent regions in SCBV-Mo, respectively. To further investigate the level of sequence variability within Australian SCBV isolates, virions were purified from three further sugarcane accessions and a 220 bp fragment of the reverse transcriptase-coding region was amplified. Five clones from each sub-population were selected and sequenced. Analysis of these sequences revealed considerable variability in the virus population with variability within one plant as great as it was between isolates. However, since the use of specific primers could also be selecting for a sub-population of SCBV sequences, it was possible that the variability may actually be greater than that reported. These results indicated that SCBV isolates are complex and variable and may represent a continuum of genetic variability. High molecular weight DNA species larger than the SCBV 7.6 kbp unit-length genome were found in DNA extracted from purified SCBV-IM virions. We confirmed that these high molecular weight nucleic acids were virus-specific and open circular in conformation. Using field inversion gel electrophoresis (FIGE), the SCBV-IM DNA was separated into four discrete bands with sizes ranging from between 1 to 4 genome copies. The DNA was shown to comprise overlapped individual genome-length molecules and not covalently-bonded continuous DNA strands. We presume that these DNA molecules are concatamers formed during replication as a result of a terminal overlap on the sense strand. The presence of these concatamers within virions may explain the observation of particles with lengths corresponding to one, two or three times the modal length of 130 nm. Four SCBV-infected Saccharum officinarum plants were examined for the presence of integrated viral DNA. Southern blot analysis of viral DNA and total DNA extracted from the same plant source were compared with, or without, restriction digestion. The resulting restriction patterns from viral and total DNA were almost identical suggesting that there were no integrated SCBV sequences in the sugarcane cultivars tested. Although larger-than-single-genome copy bands were detected in both the viral and the total DNA samples, this was probably due to the presence of genomic concatamers. SCBV integration studies using Southern analyses were further complicated by high sequence variability which precluded the restriction digestion of all viral DNA species. As such, some of the SCBV DNA species remain as concatamers which appear as larger-than-unit-length SCBV products. An antiserum derived from a mixture of purified SCBV isolates has been used routinely in the past to screen for SCBV infection, but the heterogeneity reported for badnaviruses has cast doubt on the ability of this antiserum to detect all SCBV isolates. We attempted to determine whether antiserum generated against proteins other than the viral capsid could be used to detect SCBV infections, thus improving the reliability and robustness of SCBV diagnosis. The complete coding regions of SCBV ORF I and ORF II were bacterially expressed and used as antigens for antiserum production. Both ORF I and II proteins were found to be highly immunogenic and generated high-titre antisera, designated AS-I and AS-II, respectively. The diagnostic utility of both antisera to detect SCBV in six different infected sugarcane plants was tested using both immunosorbent electron microscopy (ISEM) and western blots. The currently used SCBV antiserum (AS-V), generated against a mixture of purified SCBV isolates, was included for comparison. In western analyses, neither AS-I nor AS-V was able to conclusively detect SCBV in any of the six infected plants due to reactivity with numerous non-specific proteins. In contrast, AS-II reacted specifically with a protein of the expected size (~13.5 kDa) in 2/6 infected plants. When compared using ISEM, AS-V, AS-I and AS-II trapped virions from 6/6, 6/6 and 2/6 SCBV-infected plants, respectively. However, the number of virions trapped using AS-V was approximately 30-fold more than that trapped using either AS-I or AS-II. These results highlight the variability between SCBV isolates and suggest that ISEM with antisera raised against mixtures of viral proteins may be a useful tool for the detection of viral isolates.

Une étude de prévalence des espèces BSOLV, BSGFV et BSIMV a montré que les espèces BSOLV et BSGFV sont très présentes dans les variétés hybrides interspécifiques MxH et FHIA-21 et que le niveau de prévalence de l’espèce BSGFV est significativement plus élevé chez FHIA-21 que chez MxH. Des résultats complémentaires suggèrent que la transmission des espèces virales BSOLV et BSGFV chez MxH et FHIA-21 résulte principalement de l’activation d’allèles eBSV infectieux plutôt que d’une transmission vectorielle par cochenille. La cinétique d’activation des allèles infectieux OL1 et GF7 dans les variétés MxH et FHIA-21 a été suivie durant 15 mois en conditions de culture au champ. Cette étude montre que les allèles infectieux OL1 et GF7 ne sont pas exprimés au même niveau ni dans les variétés MxH et FHIA-21ni pour une même variété (FHIA-21) et que le niveau d’activation dépend du mode de multiplication du matériel végétal. Des résultats préliminaires suggèrent que les infections par les espèces BSOLV et BSGFV n’ont que peu d’incidence sur la production fruitière chez les variétés MxH et FHIA. Globalement, cette thèse apporte une contribution significative à l’évaluation et à la gestion du risque BSV associé à la culture à grande échelle de variétés interspécifiques de bananier, notamment par la mise au point d’approches d’évaluation de ce risque transposables à d’autres variétés. / This thesis focuses on the risk of spreading Banana streak viruses in the Dominican Republic through the large scale cultivation of hybrid varieties Macho x Hembra and FHIA-21, which both harbor infectious eBSVs. An unprecedented survey showed that BSOLV and BSGFV are widespread in both varieties, with BSGFV being the most prevalent species, and that BSIMV is not present. BSGFV prevalence level was significantly higher in FHIA-21 than in MxH. Analyses of molecular taxonomical data of the natural mealybug vectors of BSVs and eBSV patterns of MxH and FHIA-21 were carried out and pointed to a marginal role of mealybugs in the transmission of BSGFV and BSOLV in the Dominican Republic in MxH and FHIA-21.The kinetics of activation of infectious eBSOLV and eBSGFV in MxH and FHIA-21 was monitored under field conditions. Results collected over 15 months showed that infectious alleles OL1 (BSOLV) and GF7 (eBSGFV) are differentially expressed in MxH and FHIA-21and that the mode of multiplication of the planting material influences expression levels. Preliminary results also suggest that BSV infection does not have a major effect on fruit production. Overall, this thesis contributes significantly to the development and implementation of appropriate strategies for evaluating and mitigating the risks of spreading BSVs that are associated with the cultivation of banana interspecific hybrids.