Repetitive tetramers of the DNA sequence 5'-CAAT-3' are present in several loci associated with lipooligosaccharide (LOS) phase variation in Haemophilus influenzae type b (Hib). In an attempt to identify H. somnus phase-variable LOS genes, the presence of CAAT repeats within the H. somnus 738 genome was confirmed using a (CAAT)7 probe. A 3.9 kb EcoRI fragment that reacted with the probe was cloned and sequenced. Sequence analysis confirmed the presence of 31 CAAT repeats downstream of two potential start codons, and indicated that small or large proteins would be encoded depending on the number of CAAT repeats. The larger gene products showed 46% amino acid homology to Lex2b from Hib, which influences LOS phase variation in that species. In H. somnus, this gene was named lob1 (lipooligosaccharide biosynthesis gene). Sequence analysis showed that randomly selected colonies most frequently contained 33 CAAT repeats in lob1, corresponding to a 294 amino acid product. Colonies selected for negative reactivity to mAb 5F5 were significantly more likely to have different numbers of CAAT repeats in lob1 than randomly selected colonies. The presence of lob1 in trans altered the LOS profile of a non-phase variable strain of H. somnus, and caused increased levels of reactivity to polyclonal antisera made to purified LOS from strain 738. Based on the ability of this gene to alter the LOS profile of a non-phase varying strain and the correlation of changes in CAAT repeats with mAb 5F5 reactivity, lob1 appears to be involved in LOS biosynthesis and phase variation. / Master of Science

Yes / Coherent subspaces spanned by a finite number of coherent states are introduced, in a quantum system with Hilbert space that has odd prime dimension d. The set of all coherent subspaces is partitioned into equivalence classes, with d 2 subspaces in each class. The corresponding coherent projectors within an equivalence class, have the 'closure under displacements property' and also resolve the identity. Different equivalence classes provide different granularisation of the Hilbert space, and they form a partial order 'coarser' (and 'finer'). In the case of a two-dimensional coherent subspace spanned by two coherent states, the corresponding projector (of rank 2) is different than the sum of the two projectors to the subspaces related to each of the two coherent states. We quantify this with 'non-addditivity operators' which are a measure of quantum interference in phase space, and also of the non-commutativity of the projectors. Generalized Q and P functions of density matrices, which are based on coherent projectors in a given equivalence class, are introduced. Analogues of the Lorenz values and the Gini index (which are popular quantities in mathematical economics) are used here to quantify the inequality in the distribution of the Q function of a quantum state, within the granular structure of the Hilbert space. A comparison is made between Lorenz values and the Gini index for the cases of coarse and also fine granularisation of the Hilbert space. Lorenz values require an ordering of the d 2 values of the Q function of a density matrix, and this leads to the ranking permutation of a density matrix, and to comonotonic density matrices (which have the same ranking permutation). The Lorenz values are a superadditive function and the Gini index is a subadditive function (they are both additive quantities for comonotonic density matrices). Various examples demonstrate these ideas.

High entropy alloys (HEAs) based on refractory elements have shown a great potential for high temperature structural applications. In particular, the ones containing Al, exhibits a microstructure similar to the γ-γ' in Ni-based superalloys. While these alloys exhibit impressive strengths at room temperature (RT) and at elevated temperatures, the continuous B2 matrix in these alloys is likely to be responsible for their brittle behavior at RT. Phase stability of five such alloys are studied by thermo-mechanical treatments and characterization techniques using scanning electron microscopy (SEM) and transmission electron microscopy (TEM). Two of these alloys showed an inverted microstructure, where the disordered BCC phase becomes continuous, and therefore, they were characterized in detail using SEM, TEM, atom probe tomography (APT) and synchrotron x-ray diffraction experiments. The phenomenon of phase inversion lead to a better combination of strength and ductility as compared to the non-inverted microstructure.To enhance the stability of B2 intermetallic phase which provides the strength when present in a BCC matrix, multicomponent B2 phase compositions stable at 1000°C in some of the above studied alloys, were melted separately. The aim was to establish a single phase B2 at 1000°C and understand the mechanical behavior of these single-phase multicomponent B2 intermetallic alloys. These alloys exhibited a ductile behavior under compression and retained ~1 GPa yield strength at temperature up to 600°C. The ductile nature of these alloys is attributed to the change in bonding nature form directional to metallic bonding, possibly resulting from a significantly high configurational entropy compared to binary or ternary stoichiometric B2 compounds.

Tableau d’honneur de la Faculté des études supérieures et postdoctorales, 2007-2008. / Le positionnement ponctuel de précision (PPP) par satellites GPS requiert encore une longue période d’observations pour atteindre une précision centimétrique, car la résolution des ambiguïtés de phase en mode absolu est contrainte par la présence d’erreurs non modélisées et de biais de phase au récepteur et aux satellites. Afin de mieux comprendre le contexte lié à la résolution des ambiguïtés de phase dans le PPP, un bilan d’erreurs affectant les observations de phase a d’abord été effectué pour évaluer les possibilités de fixer les ambiguïtés à l’entier adéquat. Puis, une approche utilisant un simulateur de signaux GPS a été proposée pour le calibrage des biais de phase d’un récepteur GPS, mais les biais estimés subissent, entre autres, l’influence des biais de code non modélisés et des effets thermiques du récepteur. Finalement, des modifications ont été apportées à la méthodologie actuelle du calibrage des biais de phase des satellites afin d’améliorer la cohérence des biais estimés avec le mod`ele fonctionnel du PPP. Des erreurs non modélisées se propagent toutefois dans les résultats obtenus et, à cet effet, des pistes d’améliorations sont suggérées. Le calibrage des biais de phase est certainement un élément essentiel à l’obtention instantanée d’une précision centimétrique en mode absolu. / GPS Precise Point Positioning (PPP) still requires long observation sessions in order to achieve cm-level accuracy because ambiguity resolution in point positioning is affected by unmodeled errors and by the presence of receiver and satellite phase biases. In order to gain a better understanding of ambiguity resolution in PPP, an error budget has been made to assess the possibilities of accurate ambiguity fixing. Then, an approach using a GPS simulator has been proposed to calibrate receiver phase biases, and the results show evidence of unmodeled code biases and thermal effects in the receiver. Finally, modifications to the actual calibration methods of satellite phase biases have been suggested to improve compatibility with PPP’s functional model. Residual errors still affect the estimated values and suggestions are made to improve the proposed methodology. The calibration of phase biases is an important issue in achieving instantaneous cm-level point positioning.

Cette thèse porte sur la modélisation numérique des problèmes de changement de phase. Le but est de proposer un algorithme robuste, basé essentiellement sur la méthode CutFEM, pour résoudre le problème avec la plus grande précision possible. Dans notre démarche, la méthode level-set est employée pour une représentation implicite de l'interface entre différentes phases, tandis que l'imposition des conditions essentielles sur cette dernière se fait à l'aide de la variante symétrique de la méthode de Nitsche. Le premier résultat de la thèse porte sur le développement d'un post-traitement fiable, facile à implémenter, pour une meilleure estimation du flux à travers une frontière immergée. La solution proposée est inspirée de la méthode de l'intégrale de domaine, à la différence que nous introduisons une stabilisation de type Ghost Penalty pour éliminer la sensibilité de la qualité de l'approximation à l'interface par rapport aux nœuds du maillage. L'idée est validée à travers une série d'exemples 2D et 3D.Le deuxième résultat concerne le développement d'un solveur CutFEM pour la simulation des problèmes de Stefan à deux phases sans convection. Dans notre approche, nous nous servons du premier résultat pour une meilleure évaluation de la vitesse de l'interface. Quant à la stabilisation des formulations d'extension de la vitesse et du transport de la fonction level-set, nous avons opté pour la méthode CIP (Continuous Interior Penalty) qui a déjà fait preuve d'une grande efficacité pour des problèmes fortement dominés par la convection. Des exemples numériques 2D permettent de confirmer l'efficacité de notre algorithme puisque des taux de convergence optimaux sont obtenus. Une simulation 3D est également proposée pour démontrer la validité du solveur dans une configuration plus réaliste. Pour le dernier résultat, nous reconsidérons le problème de Stefan, mais cette fois en prenant en compte la convection naturelle dans la phase liquide. L'équation de conduction de la chaleur est alors modifiée par l'ajout d'un terme de convection. De plus, cette équation est couplée aux équations de Navier-Stokes, introduisant de fait des non-linéarités supplémentaires. Un schéma itératif basé sur la méthode de Newton est alors proposé pour une résolution efficace du système. Les autres étapes de résolution sont assez similaires à celles de l'algorithme développé pour les problèmes de Stefan sans convection. Une étude numérique approfondie du solveur est présentée. Premièrement, l'efficacité de la discrétisation en temps et en espace est étudiée pour des problèmes (relativement simples) avec des solutions manufacturées. Ensuite, pour un problème beaucoup plus complexe modélisant la solidification de l'eau, une comparaison des résultats obtenus numériquement avec les résultats expérimentaux connus dans la littérature est présentée. Enfin, d'autres problèmes de changement de phase encore plus complexes tels que la fusion du gallium dans une cavité rectangulaire, ou encore celle du n-octadécane dans une cavité cubique sont considérés, et une comparaison des résultats de simulation avec les données expérimentales est également présentée. / This thesis focuses on the numerical modeling of phase change problems. The aim is to propose a robust CutFEM-based algorithm to solve the problem with the highest possible accuracy. In our approach, the level-set technique is used for an implicit representation of the interface, whereas the imposition of the essential conditions on the interface is done using the symmetric variant of the Nitsche method. The first result of the thesis is the development of a reliable, easy-to-implement post-processing for an accurate estimate of the flux across an interface. The proposed solution is inspired by the domain integral method, with the difference that we introduce Ghost Penalty stabilization to eliminate the sensitivity to the interface location relative to the mesh nodes. The accuracy of the method is validated through a series of two- and three-dimensional examples. The second result concerns the development of a CutFEM method for the numerical simulation of two-phase Stefan's problems without convection. In our approach, we use the idea of the first result for an accurate evaluation of the normal speed of the interface. Regarding the stabilization of the velocity extension and front transportation problems, we opted for the Continuous Interior Penalty method which has shown great effectiveness for convection-dominated problems. Two-dimensional numerical examples are used to confirm the effectiveness of our algorithm since optimal convergence rates are achieved. A three-dimensional simulation is also provided to demonstrate the validity of the solver in a more realistic configuration. For the last result, we reconsider the Stefan problem, but this time taking into account natural convection in the liquid phase. In this phase, the heat conduction equation is then modified by the addition of a convection term. Furthermore, this equation is coupled to the Navier-Stokes equations, thereby introducing additional nonlinearities. An iterative scheme based on Newton's method is then proposed for an efficient solution of the system. The other steps of the proposed solver are quite similar to those of the solver developed for Stefan problems without convection. An in-depth numerical study of the solver is presented. First, the efficiency of discretization in time and space is studied for (relatively simple) problems with manufactured solutions. Then, for a much more complex problem modeling the solidification of water, a comparison of the results obtained numerically with the experimental results known in the literature is presented. Finally, other even more complex phase change problems such as the fusion of gallium in a rectangular cavity, or that of n-octadecane in a cubical test cell are considered, and a comparison of the simulation results with experimental data is also provided.

Le Positionnement Ponctuel Précis (PPP) est une technique de positionnement qui utilise un seul récepteur GNSS. Cette approche diffère nettement des méthodes différentielles qui sont largement utilisées et qui nécessitent deux ou plusieurs récepteurs. Le PPP est une technique économique, autonome par station, avec une précision centimétrique qui a ouvert la possibilité à une large gamme d'applications. Cependant, dans les applications qui nécessitent une convergence rapide et une haute précision, la performance du PPP n'est pas encore suffisante. Le PPP peut prendre jusqu’à 30 minutes pour converger vers des solutions avec une précision décimétrique. Cette longue période d’initiation est principalement consacrée à la stabilisation des ambiguïtés de phase vers des valeurs flottantes constantes. Compte tenu de ce problème, il est démontré que la Résolution des Ambigüités (RA) améliore la stabilité du modèle d’estimation, réduit le temps de convergence et améliore la précision des coordonnées. Cette étude vise donc à améliorer la performance du PPP pour obtenir une meilleure précision plus rapidement. À cette fin, les biais de phase des satellites qui perturbent la résolution des ambiguïtés sont estimées du côté producteur et résolues du côté utilisateur. Une modélisation judicieuse de paramètres et une sélection rigoureuse des modèles de correction sont effectuées afin de réduire la propagation des erreurs non-corrigées dans les biais de phase des satellites estimés. Du côté producteur, une nouvelle approche modulaire à deux étapes est proposée et implémentée comprenant l'estimation de biais de phase des satellites à partir de chaque site et l'intégration séquentielle des solutions. Ces deux étapes ont des structures simples et elles permettent d'estimer précisément les biais de phase de chaque satellite. L’algorithme de l’intégration séquentielle garde un bon compromis entre la charge de calcul, la charge et la capacité de mémoire de l’ordinateur, l'efficacité du traitement des paramètres et la précision des estimations. Du coté producteur, chaque observation est modélisée individuellement et intégrée dans le processus d'estimation. Ceci facilite l'intégration des fréquences supplémentaires (par exemple, la troisième fréquence L5 ou des observations multi-GNSS) pour améliorer davantage la performance de PPP en fonction de la modernisation du GNSS. Du côté utilisateur, un modèle d’observation de plein rang au niveau de récepteur mono-fréquence est proposé et implémenté. Cela donne de la flexibilité aux utilisateurs avec les récepteurs mono-fréquence pour utiliser notre solution PPP-RA lorsque les produits d'ionosphère de haute précision sont disponibles. Le modèle proposé est compatible avec les horloges de satellite standards actuelles fournies par IGS, CODE, JPL, par exemple. Le délai ionosphérique est corrigé et estimé en parallèle. Cela permet à l'utilisateur d’utiliser une correction ionosphérique de faible ou de haute précision et obtenir une performance améliorée en ajustant uniquement la précision de l'estimation de ce paramètre. La performance du PPP-RA du côté utilisateur a été comparée au PPP conventionnel en termes du temps de convergence et de la précision des coordonnées. En résumé, on a obtenu une amélioration importante en temps de convergence (jusqu'à 80 %) et en précision planimétrique (jusqu'à 60 %) par rapport au PPP conventionnel. De plus, une étude comparative est effectuée pour distinguer les caractéristiques de notre approche des autres méthodes PPP-RA. L’avantage de notre PPP-RA est aussi démontré par son approche unique à éliminer les défauts de rang et résoudre les ambiguïtés libre-de-biais. / Precise Point Positioning (PPP) is a single receiver GNSS positioning technique developed in contrast to broadly used differential methods that require two or more receivers. Employing a single receiver makes PPP a cost-effective and per-site autonomous technique with centimetre precision that has opened up the possibility of a wide range of applications. In many applications where short time period is required to reach high precisions, the performance of PPP is not yet sufficient. Typically, PPP takes up to 30 minutes in order to converge to coordinate solutions with acceptable precision. This limitation is mostly due to the long period required for stabilizing the float carrier phase ambiguities to constant values. Given this problem, it is showed that Ambiguity Resolution (AR) improves drastically the stability of the estimation model that in turn reduces the convergence time, and increases the precision of estimated coordinates. Thus, this study seeks to enhance the performance of PPP to obtain higher precision at a faster convergence time. For this reason, the hardware dependent satellite phase biases are estimated at the producer-side and by applying them as corrections the integer ambiguities can be resolved at the user-side. A judicious modelling of all parameters and a careful selection of the correction models is accomplished to reduce the impact of error propagation on the precision of parameters estimation. At the producer-side, a novel modular approach is proposed and established including the per-site satellite phase bias estimation and the sequential integration of the solutions. The two-steps of the producer-side have simple structures and allows for estimating the satellite phase biases. The proposed sequential network solution, keeps a good compromise between the computational burden, the computer memory load, the efficiency of handling parameters and the precision of estimations. In addition, all observables are modelled individually and integrated in the estimation process that facilitates the extension of algorithms for integrating additional frequencies or mutli-GNSS observables with respect to the GNSS modernization. At the user side, a novel full rank design matrix in the single frequency level is proposed and implemented. This gives the flexibility to the users with single-frequency receivers to benefit from our PPP-AR while the high precision ionosphere products are available. The proposed model is compatible with the current standard satellite clocks available, for example, from IGS, CODE, and JPL. The ionosphere is corrected and estimated at the same time. This gives the user the possibility to take advantage of low or high precision ionosphere products for obtaining an enhanced performance with our PPP-AR by only adjusting the precision of the ionosphere delay estimation. The performance of our PPP-AR user-side is then compared to the conventional PPP in terms of convergence time and coordinate precision. A substantial improvement has been obtained in terms of planimetric precision (up to 60%) and the convergence time (up to 80%) compared to the conventional PPP method. In addition, the characteristics of our PPP-AR are compared in detail with other PPP-AR methods. The advantage of our method is discussed by its unique approach of removing the rank deficiencies and resolving bias-free ambiguities.

Master of Science / Department of Electrical and Computer Engineering / Andrew Rys / Clock and data recovery (CDR) circuits form the backbone of high speed receivers. These receivers are used in various applications such as chip to chip interconnects, optical communications and backplane routing. The received data in CDR circuits are potentially noisy and asynchronous, i.e. they are not accompanied by a clock. The CDR circuit has to generate a clock from the data and then retime the data. The CDR circuit that recovers the clock and retimes the data has to remove the jitter that is accumulated during its transport through channels due to inter symbol interference (ISI). There are stringent jitter specifications defined by various communication standards that must be addressed by CDR circuits. These make the design of CDR circuits more difficult for system designers as well the circuit designer. Many parameters have to be taken into consideration while designing a CDR circuit. The problem becomes even more interesting as there are various tradeoffs in the design. As speeds of communications increase, the maximum allowable jitter decreases. Jitter in CDR circuits arises due to a lot of factors and is also dependent on the method used for clock and data recovery. In CDR circuits that use phase locked loops to recover the clock and retime the data, jitter may be caused by the metastability of sequential elements used in phase detectors. Jitter is also caused by the phase noise of the VCO used in the PLL. In CDR circuits that use the delay locked loop to recover the clock and data, jitter may be caused by the metastability of sequential elements in phase detectors as well as the quality of reference clock that is used to re-time the data. Additional effects that can cause jitter in CDR circuits include the use of spread spectrum clocking, delta sigma noise shaping performance, etc. In this thesis a non-sequential linear phase detector has been proposed which does not use any sequential elements to avoid metastability issues in phase detectors. The output jitter in a CDR circuit that uses the proposed phase detector is measured and compared to a Hogge Phase Detector [5].

ITC/USA 2009 Conference Proceedings / The Forty-Fifth Annual International Telemetering Conference and Technical Exhibition / October 26-29, 2009 / Riviera Hotel & Convention Center, Las Vegas, Nevada / We derive bounds on the performance of data-aided joint estimators for timing offset, carrier phase offset, and carrier frequency offset for use in an APSK packet-based communication link. It is shown that the Cramér-Rao Bound (CRB) is a function of the training sequence, the signal-to-noise ratio (SNR), and the pulse shape. We also compute APSK training sequences of different lengths that minimize the CRB for each of the parameters.

No description available.

Phase equilibrium data is vital for designing chemical separation equipment. Traditionally, such data is obtained through laboratory experiments by sampling and analysing each phase of an equilibrated chemical mixture. An alternative means of generating such data is via molecular simulations, which also gives insight into the microscopic structure of the phases. This project was undertaken due to the lack of work on molecular simulations in predicting vapour-liquid-liquid equilibrium (VLLE). Gibbs Ensemble Monte Carlo molecular simulations were performed in the isochoricisothermal (NVT) and isobaric-isothermal (NVT) ensembles to determine the ability and limitations of the Transferable Potentials for Phase Equilibria (United-Atom) and Extended Simple Point Charge (SPC-E) force fields in predicting three-phase fluid equilibrium for two binary and three ternary industrially relevant mixtures: n-hexane/water (1), ethane/ethanol (2), methane/n-heptane/water (3), n-butane/1-butene/water (4) and nhexane/ ethanol/water (5). The NPT ensemble proved inadequate for predicting VLLE for binary mixtures, as for both binary mixtures (1 and 2), the simulations reverted to two phases. This was due in part to the unlike-pair interactions between pseudoatoms in different molecules not being accurately predicted at the specified simulation conditions to reproduce experimental mixture densities and vapour pressures. It was also due to the sensitivity of the NPT ensemble to perturbations which probably removed the system from its three-phase trajectory in Gibbs phase space, since specifying even the correct pressure corresponding to the potential models was unsuccessful in obtaining stable VLLE. Furthermore, ternary VLLE could not be obtained for a mixture exhibiting an extremely narrow three-phase region (4) and simulations for a miscible, non-ideal mixture (5) gave mole fractions that were in poor agreement with experiment. Good results were obtained for mixture 3 which exhibits limited mutual solubilities and a large three phase region. The NVT ensemble overcame the shortcomings of the NPT ensemble by producing three stable phases for the binary mixtures, revealing that the three-phase pressures were shifted by as much as 12%. Also, the narrow three-phase region of mixture 4 was overcome by adjusting the total system volume, producing three stable phases. These were also the first successful binary VLLE simulations involving complex polyatomic molecules. / Thesis (M.Sc.Eng.)-University of KwaZulu-Natal, Durban, 2008.