A new method of in situ extraction of alcohols from fermentation broth was investigated. The extraction method exploited the latent advantages of the non-equilibrium phase interaction of the fluid system in the flash tank to effectively recover the alcohol. Carbon dioxide gas ranging from 4.2L/min to 12.6L/min was used to continuously strip 2 and 12% (v/v) ethanol solution in a fermentor with a recycle. Ethanol and water in the stripped gas was recovered by compressing and then flashing into a flash tank that was maintained at 5 to 70bar and 5 to 55oC where two immiscible phases comprising CO2-rich phase (top layer) and H2O-rich phase (bottom layer) were formed. The H2O-rich bottom layer was collected as the Bottoms. The CO2-rich phase was continuously throttled producing a condensate (Tops) as a result of the Joule-Thompson cooling effect. The total ethanol recovered from the extraction scheme was 46.0 to 80% for the fermentor containing 2% (v/v) ethanol and 57 to 89% for the fermentor containing 12% (v/v) ethanol. The concentration of ethanol in the Bottoms ranged from 8.0 to 14.9 %(v/v) for the extraction from the 2 %(v/v) ethanol solution and 40.0 to 53.8 %(v/v) for the 12% (v/v) fermentor ethanol extraction. The Bottoms concentration showed a fourfold increase compared to the feed. The ethanol concentration of the Tops were much higher with the highest at approx. 90% (v/v) ethanol, however the yields were extremely low. Compression work required ranged from 6.4 to 20.1 MJ/kg ethanol recovered from the gas stream in the case of 12% (v/v) ethanol in fermentor. The energy requirement for the 2% (v/v) extraction was 84MJ/kg recovered ethanol. The measured Joule-Thompson cooling effect for the extraction scheme was in the range of 10 to 20% the work of compressing the gas. The lowest measured throttle valve temperature was -47oC at the flash tank conditions of 70bar and 25oC. Optimization of the extraction scheme showed that increasing the temperature of the flash tank reduced the amount of ethanol recovered. Increasing the pressure of the flash tank increased the total ethanol recovered but beyond 45bar it appeared to reduce the yield. The 12.6L/min carbon dioxide flow rate favored the high pressure(70bar) extraction whiles 4.2L/min appeared to favor the low pressure(40bar) extraction. The studies showed that the extraction method could potentially be used to recover ethanol and other fermentation products. / Master of Science

Doctor of Philosophy / Department of Physics / Kristan L. Corwin / Optical frequency references have been widely used in applications such as navigation, remote sensing, and telecommunication industry. For stable frequency references in the near-infrared (NIR), lasers can be locked to narrow absorption features in gases such as acetylene. Currently, most Near NIR references are realized in free space setups. In this thesis, a low-loss hollow-core optical fiber with a diameter of sub millimeters is integrated into the reference setup to provide long interaction lengths between the filling gas and the laser field, also facilitate the optical interaction with low power levels. To make portable NIR reference, gas can be sealed inside the hollow-core fiber, by creating a photonic microcell. This work has demonstrated all-fiber optical frequency references in the Near IR by fabricating and integrating gas sealed photonic microcells in the reference setup. Also, a thoughtful study regarding the lineshape of the fiber-based reference has been accomplished. According the proper modeling of a shift due to lineshape, a correction was applied to our previous absolute frequency measurement of an NIR optical frequency reference. Furthermore, effects of the hollow-core fibers, including mode-dependence frequency shift related to surface modes are explored. In addition, angle splicing techniques, which will improve the performance of the fiber-based frequency reference have been created. Low transmission and return loss angle splices of photonic bandgap fiber, single mode PCF, and large core kagome to SMF-28 are developed and those fibers are demonstrated to be promising for photonic microcell based optical frequency references. Finally, a potentially portable optical metrology system is demonstrated by stabilizing a fiber-laser based frequency comb to an acetylene-filled optical fiber frequency reference. Further work is necessary to fabricate an all-fiber portable optical metrology system with high optical transmission and low molecular contamination.

Thesis (MScEng (Mechanical and Mechatronic Engineering))--Stellenbosch University, 2008. / This thesis is concerned with the development and testing of a non-invasive device that is unassailable, and can be placed on an aggressive psychiatric patient to monitor the vital signs of this patient. Two devices, a glove measuring oxygen saturation and another on the dorsal part (back) of the patient measuring heart rate via electrocardiography (ECG), skin temperature and respiratory rate were designed and implemented. The data is transmitted using wireless technology. Both devices connect to one central monitoring station using two separate Bluetooth connections ensuring a total wireless setup. All the hardware and software to measure these variables have been designed and implemented. A Matlab graphical user interface (GUI) was developed for signal processing and monitoring of the vital signs of the psychiatric patient. Detection algorithms were implemented to detect ECG arrhythmias such as premature ventricular contraction and atrial fibrillation. The prototype was manufactured and tested in a laboratory setting on five volunteers. Satisfactory test results were obtained and the primary objectives of the thesis were fulfilled

Optical Coherence Tomography (OCT) is a non-invasive three-dimensional imaging technique. OCT synthesizes a cross-sectional image from a series of lateral adjacent depth scans, and with a two-dimensional scanning scheme, three-dimensional intensity image of sample can be constructed. Due to its non-invasive capability, OCT has been widely applied in ophthalmology, cardiology and dermatology; and in addition to three-dimensional intensity image construction, various functional OCT imaging techniques have been developed for clinical application. My research is focused on developing functional OCT systems for application in ophthalmology, including polarization-sensitive optical coherence tomography (PS-OCT) for retinal nerve fiber layer (RNFL) birefringence measurement and dual-wavelength photothermal optical coherence tomography (DWP-OCT) for microvasculature blood oxygen saturation (SO2) measurement. In the study, a single-mode-fiber based polarization-sensitive swept-source OCT (PS-SS-OCT) with polarization modulator, polarization-sensitive bulk-optics balanced detection module is constructed and polarization processing methods based on Stokes vectors are applied to determine birefringence. PS-OCT is able to provide human subject's RNFL thickness, phase retardation, and birefringence information. Degradation in the degree of polarization (DOP) along depth is investigated and its difference between four quadrants of RNFL (superior, temporal, inferior and nasal) indicates the structural property difference. DWP-OCT is a novel functional OCT system consisting of a phase-sensitive optical coherence tomography system (PhS-OCT) and two photothermal excitation lasers. PhS-OCT is based on a swept-source laser operating in the 1060 nm wavelength range; the two photothermal excitation lasers with wavelength 770 nm and 800 nm are intensity modulated at different frequencies. PhS-OCT probe beam and two photothermal excitation beams are combined and incident on the sample, optical pathlength (op) change on the sample introduced by two photothermal excitation beams are measured and used for blood SO2 estimation. A polarization microscope is proposed for future study. The polarization microscope is an imaging technique providing molecular structure and orientation based on probe light's polarization state information. The polarization microscope uses a wavelength tunable light source, and can achieve any incident polarization state by a retarder-rotator combination. Specimen's birefringence can be determined based on the changing of detected light amplitude. / text

The hypothesis of horizontal gene transfer of a hybrid gene from bacteria to the filamentous Ascomycota was tested using constrained phylogenetic analyses and tests of topological congruence. Results suggest that the hybrid gene was acquired from bacteria by a single transfer before the radiation of the Leotiomyceta. The phylogenetic relationship among Nimbya and Embellisia was investigated using both morphological and molecular data. Examination of conidia morphology revealed that Nimbya and Embellisia comprise two and four distinct morphological groups, respectively. Molecular analyses support all morphological groups of Nimbya and Embellisia and reveal that both genera are polyphyletic. Results suggest the circumscription of these genera is based upon convergent morphological characters. To further understand the evolutionary relationship among Alternaria and closely related genera, ten protein-coding genes were sequenced across 176 species. Three genes possessed significant substitution saturation and two other genes did not possess sufficient phylogenetic signal to assess relationships among the asexual Alternaria. The remaining five loci revealed strong support for asexual Alternaria and the order of divergence among eight asexual Alternaria species-groups. The current polyphyly of Alternaria was resolved using morphological and molecular data. Morphological examination revealed that most members of the infectoria clade (sexual Alternaria) produce diagnostic colony characters on dichloran rose bengal yeast extract sucrose agar (DRYES) and weak potato dextrose agar (WPDA) that are fundamentally different as compared to other small-spored Alternaria species. These data also revealed that all members of the infectoria clade produce arachnoid vegetative hyphae with multiple primary conidiophores, whereas other small-spored Alternaria species do not. Phylogenetic analyses revealed that the sexual infectoria clade clusters with other sexual genera phylogenetically distant to the asexual Alternaria. Lastly, the validity of taxonomy and the phylogenetic relationship among three small-spored Alternaria species was examined. Total ortholog comparisons and whole-genome comparisons revealed that the DNA sequence of A. alternata ATCC 11680 has a higher percent similarity to A. tenuissima EGS 34-015 than to A. alternata EGS 34-016. This suggests that these two isolates share a more recent common ancestor and A. alternata EGS 34-016 is more distantly related.

Chemical exchange saturation transfer (CEST) MRI has the ability to noninvasively measure endogenous biomarkers and exogenous agents relevant to various diseases and medical conditions. My work has focused on the development of MRI pulse sequences and data analysis methods to more accurately estimate endogenous and exogenous CEST contrast measurements at 7 T and 3 T magnetic field strengths. Chapter 1 discusses the various sources of signal that have been measured with CEST MRI in the clinic, the acquisition methods used to acquire these signals, and the data analysis methods used to quantify the CEST effects from these signals. Appendix A describes the development of a respiration gated CEST pulse sequence that was ultimately used with a lung fibrosis mouse model to measure extracellular pH (pHe) of the fibrotic lesions. Appendix B describes the development of a data processing algorithm that used the Bloch equations modified for chemical exchange to generate more accurate and precise pHe estimates both at 7 T and 3 T magnetic field strengths relative to a previous data processing algorithm. Appendix C describes the development of a retrospective gating technique for the lung that generates more accurate and precise endogenous CEST contrast measurements.

The Grenville orogeny was a protracted (~200 m.y.) series of “hot” magmatic- metamorphic events that contributed to the growth of the Laurentian margin in the late Mesoproterozoic. The granites contain remarkably high Zr content, lack xenocrysts, and become zircon saturated at high temperatures, which are all unusual for felsic magmas. The “hot Grenville granite” hypothesis is tested and use of high-Zr granitoids as potential zones of crustal magma generation through: U-Pb geochronology and cathodoluminescence imaging to assess inherited zircon components; quantitative modeling of zircon crystallization history using rhyolite-MELTS; and Ti-in-zircon thermometry. U-Pb zircon ages for two samples from the Virginia Blue Ridge are 1168 ± 25 Ma (2209 ppm Zr; Tzr = 1032°C) and 1050 ± 13 Ma (918 ppm Zr; Tzr = 898°C). A sample from the NJ – Hudson Highlands has been dated at 1018 ± 11 Ma (1238 ppm Zr; Tzr = 960°C). These samples produce crystallization histories that range over higher temperatures (983–1060°C) than colder, low-Zr counterparts and contain Ti concentrations of 2 to 86 ppm. This analytical approach will further the understanding of zircon’s utility and limitations as a proxy in granite petrogenesis, and constrain thermal models that produced uncommon lithospheric conditions that led to widespread hot granite production at a unique period in Earth history.

Differential protection is the unit protection system which is applied to protect a particular unit of power systems. Unit is known as zone in protection terminology which is equivalent to simple electrical node. In recent time, low impedance current differential protection schemes based on percentage restrained characteristics are widely used in power systems to protect busbar systems. The main application issue of these schemes is mis-operation due to current transformer (CT) saturation during close-in external faults. Researchers have suggested various solution of this problem; however, individually they are not sufficient to puzzle out all mis-operational scenarios. This thesis presents a new bus differential algorithm by defining alternative partial operating current characteristics of a differential protection zone and investigating its performance for all practical bus faults. Mathematical model of partial operating current and operating principle of the proposed bus differential relay are described in details. A CT saturation detection algorithm which includes fast and late CT saturation detection techniques is incorporated in relay design to increase the sensitivity of partial operating current based internal-external fault discriminator for high impedance internal faults. Performance of the proposed relay is validated by an extensive test considering all possible fault scenarios.

Current transformer saturation will cause the secondary current distortion. When saturation occurs, the secondary current will not be linearly proportional to the primary current, which may lead to maloperation of protection devices. This thesis researches and tests two detecting methods: Fast Fourier Transform (FFT) and Wavelet Transform based methods. Comparing these two methods, FFT has a better performance in steady state saturation, and Wavelet Transform can determine singularity to provide the moment of distortion. The Jiles-Atherton (J-A) theory of ferromagnetic hysteresis is one approach used in electromagnetics transient modeling. With decades of development, the J-A model has evolved into different versions. The author summarizes the different models and implements J-A model in both MATLAB and Simulink.

Bacteria classified in the family Methylomonadaceae must derive their carbon from one-carbon compounds. They are characterized by the possession of internal membranes of two types. Type I membranes are layered and fill the middle of the cells while type II membranes form concentric layers around the periphery of the cells. Also, there are two metabolic pathways by which the methylobacteria assimilate one-carbon compounds. Further evidence of this dichotomy was sought by DNA-DNA saturation hybridization of DNAs from both types of methylobacteria. Very low DNA-DNA homology was seen between types I and II or within the types. It was not possible, therefore, to correlate the degree of genetic relatedness with either the nature of the internal membranes or the pathway of carbon assimilation.