A thesis submitted to the Faculty of Science, University of the Witwatersrand, Johannesburg, in fulfilment of the requirements for the degree of Doctor of Philosophy / In this dissertation the physical and chemical alterations induced by mastication and manipulation of wax by the worker bee in honeycomb construction, and the subsequent contribution afforded the structural integrity of the nest, are elucidated. In comb building, the freshly secreted wax scales are mandibulated together with a frothy salivary emulsion, and added piece-meal to form honeycomb. Textural modifications were revealed using X-ray crystallography. While virgin scale wax is highly structured, with the crystallites aligned approximately perpendicular to the planar surface, comb wax has a random crystallographic arrangement. This reflects a disruption of the crystallite structure following the mechanical insult of mastication. Chemical analyses included investigation of both lipid and proteinaceous elements. Lipid composition was evaluated by enzyme-catalyzed as well as thin-layer and gas-liquid chromatographic methods. The results indicate a reduction in scale diacylglycerols with a corresponding increase in comb saturated monoaeylglycerols. Such modifications are highly suggestive of lipase activity within the salivary addition. The proteins of comb and scale wax were analyzed electrophoretically, under reduced conditions. Each wax possesses unique polypeptide fractions, in addition to sharing common protein species, It is speculated that those in common represent integral proteins, such as transport molecules, while the disparities noted may be due to salivary enzymatic degradation, or even glycosylation. The effects of these textural and chemical alterations on the mechanical behaviour of the waxes was assessed. Tensile tests were performed on a variety of scale and comb wax preparations over the range of temperatures likely to impinge on the honeybee nest. These investigations reveal the specific structural contributions made by each of the physico-chemical alterations described. Further, they demonstrate that while scales are ideal moulding materials due to their high distensibility and low stiffness, the greater resistance to deformation and lower potential for extension makes comb wax a superior structural material. The mechanical advantage for including propolis and cocoon silk within the comb structure was also investigated. Tensile testing indicates that the resultant composite material is structurally superior, largely due to the presence of silk reinforcement. / Andrew Chakane 2018

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The sex comb an array of specialized bristles on the foreleg, is a highly variable male trait of Drosophila that provides an ideal system for integrative studies of morphological evolution. Here, studies of the genetic and developmental architecture of sex comb bristle number variation in Drosophila melanogaster are described. Analysis of the response to twenty-four generations of divergent artificial selection indicated high genetic variance underlying this trait, and demonstrated a weak relationship with other, developmentally related non-sex bristle systems. I also present evidence showing bristle number is associated with mating success. Manipulation of diet in full-sib families confirmed that this trait is condition dependent, and that there is a genetic basis for condition dependence. Further partitioning of variance components using a half-sib mating design revealed a strong maternal, dominance and/or X chromosome effect on sex comb bristle number variation. Finally, sex comb bristle number was not correlated with comb orientation in wild type, High and Low artificial selection lines, or the mutant strain bric a brac PR72. Analysis of patterns of variation in comb orientation over ontogeny in these lines showed that this aspect of the sex comb phenotype is highly canalized. This body of work provides important insight into D. melanogaster sex comb evolvability, and represents a timely approach to bridging the gap between population genetics and development in studies of phenotypic evolution. / Thesis / Doctor of Philosophy (PhD)

La spectroscopie par transformation de Fourier par peignes de fréquences femtosecondes tire parti d’un interféromètre sans partie mobile. Il mesure les interférences entre deux peignes de fréquences, sources lasers à large bande spectrale constituée de raies fines et équidistantes. Il améliore significativement le temps de mesure et la limite de résolution spectrale des spectromètres de Fourier. Néanmoins, les conditions sur la stabilité à court terme des peignes ne peuvent pas être remplies par les techniques d’asservissement classique. Jusqu’à présent, aucun spectre de qualité n’a pu être mesuré avec un très faible temps d’acquisition. Cette thèse présente le développement d’une méthode de correction en temps réel capable de compenser les fluctuations résiduelles des peignes et de restituer des spectres sans artefacts. La méthode, analogique, ne nécessite aucun asservissement ou traitement informatique a posteriori. Ses performances sont démontrées dans le proche infrarouge (1,5 µm) et le visible (520 nm), à l’aide d’oscillateurs femtosecondes fibrés. Des spectres moléculaires couvrant 12 THz sont mesurés en 500 µs à limite de résolution Doppler. Ils sont en excellent accord avec les données de la littérature. Pour la première fois, le plein potentiel de la spectroscopie de Fourier par peignes de fréquences est démontré. Le domaine de l’infrarouge moyen est la région de prédilection de la spectroscopie moléculaire car la plupart des molécules y présentent des absorptions fortes et caractéristiques. Étendre la spectroscopie par peignes de fréquences à cette région est donc l’objectif suivant à atteindre. Dans cette optique, un peigne émettant autour de 3 µm est caractérisé. Il est basé sur la conversion non-linéaire par différence de fréquences d’un oscillateur à erbium élargi spectralement par une fibre fortement non-linéaire. / Dual-comb Fourier-transform spectroscopy takes advantage of an interferometer without moving parts. Interferences pattern between two femtosecond frequency combs, broadband laser sources whose spectra consist of evenly-spaced narrow lines, is measured. The measurement time and the spectral resolution are significantly improved compared to traditional Fourier spectrometers. However, the required short-term stability of the combs cannot be achieved by classic locking methods. Until now, no high-quality spectra could be recorded within a very short acquisition time. This thesis reports on the development of a real-time correction method able to compensate for the combs’ residual fluctuations and to restore non-distorted spectra. This analog technique does not require any locking system or a posteriori calculation. Its performance is demonstrated in the near-infrared (1.5 µm) and in the visible (520 nm) with fiber-based femtosecond lasers. Doppler-limited molecular spectra spanning 12 THz are measured within 500 µs. They are in excellent agreement with databases. For the first time, the full potential of dual-comb spectroscopy is demonstrated. The mid-infrared region is an attractive spectral range for molecular spectroscopy due to the molecules’ strong and characteristic absorptions. Therefore, extending dual-comb spectroscopy to this region is the next goal to achieve. Toward this goal, a comb emitting around 3 µm is characterized. It is based on the non-linear difference frequency generation from an erbium oscillator spectrally broadened with a highly non-linear fiber.

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Orbicular and comb layer textures in igneous environments are evidence of an unusual heating and cooling regime in small pockets at the edges of crystallizing magmas. Changes in the composition of a magma spark rapid changes in temperature, which cause the temporary suppression of normal crystal nucleation. As the superheated or supercooled magma returns to equilibrium temperature, crystallization occurs exclusively on pre-existing nucleation surfaces (floating xenoliths or wall rocks), creating orbicular and comb layering textures. Orbs and comb layers collected from two localities in the central Sierra Nevada Batholith were analyzed to determine 1) how they formed and 2) what their formation history reveals about the emplacement histories of their respective host plutons. Geochemical analysis including XRF, U-Pb dating and Sr-Nd and O isotope analysis was used to constrain the characteristics of the orbicular magma. Cathodoluminescence as well as macro and microscale petrography was used to determine the specific growth history of the orbs and comb layers. This study shows that orbs and comb layers from both localities formed due to superheating caused by the influx of water into the orbicular melt. Subsequent cooling was caused by mixing–induced depolymerization and fluid enrichment (Big Meadows Creek) or emplacement into a cooler host rock (Deer Creek). Both locations studied are 2–3 Ma younger than their host plutons, indicating that the processes which form orb and comb layers may cause late melting and magma remobilization in larger plutons.

Synthetic aperture sonar (SAS) is a wide-beam sonar technique commonly used for mapping the seafloor at high resolution. The Acoustics Research Group at the University of Canterbury operates a towed SAS system known as KiwiSAS-IV. This is currently being redesigned with the aim of reducing the weight, size and power requirements of the system. The long term goal is to make it capable of being mounted on an autonomous underwater vehicle (AUV) so that mapping of remote and/or dangerous waters can be accomplished without human interaction. This thesis presents the design of the front-end electronics used to drive the 36 transducers to produce the acoustic beam and receive the returning signals after they have reflected off a target. To achieve sufficient range, the transducers are driven with a 200 Vₚ₋ₚ signal with a maximum frequency of 110 kHz. This design uses class D switching amplifiers to generate these waveforms. The AD9271 integrated circuit, which can handle eight transducers simultaneously, is used to amplify the incoming signals and sample them at up to 50 MHz. This high sampling rate multiplied by all 36 transducers results in an amount of data which is too great for a conventional microprocessor-based system to handle. Instead, an FPGA is used to receive this data, decimate it using multiplier-free cascaded integrator-comb (CIC) filters, and then pass it to the back-end system for further processing and storage. A prototype circuit was created to test the theory developed in this thesis. This showed that the system is capable of generating the necessary waveforms and amplifying, capturing, and decimating the returning signals. However, further refinement is required before it is able to be used in the sonar system.

Doctor of Philosophy / Department of Physics / Brian R. Washburn / Optical frequency combs produced by mode-locked fiber lasers are useful tools for high precision frequency metrology and molecular spectroscopy in a robust and portable format. We have specifically investigated erbium doped fiber mode-locked lasers that use single-walled carbon nanotubes as a saturable absorber. We have, for the first time, developed and phase- stabilized a carbon nanotube fiber laser (CNFL) frequency comb. The carbon nanotube saturable absorber, which was fabricated using an optically driven deposition method, permits a high repetition frequency (>150 MHz) since an optical nonlinearity of fibers is not used for mode-locking. The CNFL comb combined with a parabolic pulse erbium doped fiber amplifier (EDFA) has shown a compact, robust, and cost-effective supercontinuum source. The amplified pulse from the parabolic pulse EDFA was compressed with a hollow-core photonic bandgap fiber, which produced a wave-breaking-free pulse with an all-fiber set-up. The stabilized comb has demonstrated a fractional instability of 1.2 ×10[superscript]-11 at 1 sec averaging time, the reference-limited instability. We have performed optical frequency metrology with the CNFL comb and have measured an optical frequency, P(13) which is a molecular overtone transition of C2H2. The measured frequency has shown a good agreement with the known value within an uncertainty of 10 kHz. In order to extend the application of the CNFL comb such as multi-heterodyne dual comb spectroscopy, we have investigated the noise of the CNFL comb and particularly, the broad carrier envelope offset frequency (f[subscript]0) linewidth of the CNFL comb. The primary noise source is shown to be white amplitude noise on the oscillator pump laser combined with the sensitivity of the mode-locked laser to pump power fluctuations. The control bandwidth of f[subscipt]0 was limited by the response dynamics of the CNFL comb. The significant reduction of comb noise has been observed by implementing a phase-lead compensation to extend control bandwidth of the comb and by reducing the pump relative intensity noise simultaneously. Therefore the f[subscipt]0 linewidth has been narrower from 850 kHz to 220 kHz. The integrated phase noise for the f[subscipt]0 lock is 1.6 radians from 100 Hz to 102 kHz.