When an intense laser beam interacts with matter, the Kerr nonlinearity results in self-focusing. Above the critical intensity, self-focusing dominates pulse spreading through diffraction leading to continuous pulse narrowing and thus an increase of the laser peak intensity. Collapse is prevented through the fact that peak intensities ultimately reach a level where ionization occurs. The profile of ionized electrons represents a negative lens which balances Kerr nonlinear self-focusing and causes the formation of stable filaments. From filaments radiation is emitted in a cone around the filament which has been termed conical emission. Filament formation happens at non-perturbative intensities where the formalism of perturbative nonlinear optics loses its validity. This opens the question of how the Kerr nonlinearity behaves in the non-perturbative limit and how large the Kerr nonlinear coefficient is. The expression for the Kerr nonlinearity is derived by perturbation theory; the validity of this expression in the non-perturbative limit is questionable. Further, experimentally the Kerr nonlinear index is extracted from measurements of the self-focusing distance as a function of beam intensity which is called the Z-scan method. This method fails at non-perturbative intensities due to the presence of the negative lens coming from the ionized electrons. The effects of the positive focusing and negative self-defocusing lens cannot be separated by the Z-scan method. As a result, not much is known about the Kerr nonlinearity in the regime of non-perturbative nonlinear optics. The purpose of this thesis is twofold. First, recently it has been discovered that conical emission can be utilized as a broadband and very efficient amplification mechanism in the far infrared. The process has been dubbed Kerr instability amplification. The difference between conical emission and Kerr instability amplification is that they take place in two different regimes of the nonlinear interaction. Whereas conical emission grows out of noise and therewith only takes place once the pump pulse has been substantially restructured due to filamentation, Kerr instability amplification is seeded with a second pulse and therewith occurs long before filamentation happens. The theory developed for Kerr instability amplification has been developed based on a stability analysis of the scalar wave equation. This analysis has shown that with pump lasers in the 1-2 μm range amplification of infrared radiation up to the 10’s of μm can be achieved. For amplification over such a wide range it is not adhoc clear to which exent vectorial wave effects can be neglected. The first part of the thesis closes this gap by developing the vectorial theory of vector instability amplification. The second part uses the results derived for Kerr instability amplification to answer the question of how to measure the Kerr nonlinear index in the nonperturbative laser intensity limit. The idea rests on the fact that Kerr instability amplification is maximum for a specific angle between pump and seed beam which varies as a function of laser pump intensity. A relation is derived that connects this angle with the Kerr nonlinear refractive index. As a result, from the maximum angle measured as a function of pump intensity, both magnitude and functional form of the Kerr nonlinear index as a function of laser intensity can be determined.

Le tendon est un tissu conjonctif fibreux qui transmet les forces du muscle à l'os. Il a une structure hiérarchique formée de faisceaux et de fibrilles de collagène de type I orientées parallèlement à son axe. Leurs propriétés structurales confèrent aux tendons une flexibilité et une résistance à la traction élevées. Cependant, soumis à des sollicitations répétées, les tendons peuvent se déchirer et même rompre, ce qui peut rendre nécessaire Une intervention chirurgicale. Plusieurs stratégies sont en cours de développement comme les autogreffes, les tendons décellularisés ou les fibres synthétiques tressées. Cependant, aucun de ces matériaux ne répond parfaitement au cahier des charges de l'ingénierie tissulaire (cytocompatibilitité, propriétés mécaniques etc). L'objectif de cette thèse est donc de produire par extrusion et dans des conditions physiologiques une matrice de collagène qui imite le tendon. Tout d'abord, nous avons étudié les instabilités d’extrusion d’un système modèle (alginate de sodium), choisi pour ses propriétés rhéologiques proches du collagène. A partir de cette étude, nous avons ensuite produit des fils de collagène dense ou de mélanges collagène/alginate de diamètre de l’ordre de 500 µm conduisant à l’obtention de structures alignées selon l'axe du fil. Les conditions physico-chimiques ont été sélectionnées afin d'obtenir des fils homogènes avec les meilleures propriétés mécaniques. Enfin, ces fils ont été mis in vitro en contact avec des cellules souches mésenchymateuses. Celles-ci colonisent nos matrices et expriment les différents gènes caractéristiques du tendon, ce qui suggère qu’elles se différencient en cellules tendineuses. / Tendon is a fibrous connective tissue, which transmits forces from muscle to bone. It is mainly composed of collagen I fibrils and fascicles aligned along its axis. Moreover, collagen fascicles exhibit a helical “crimp” which acts as a natural shock-absorber and may play a role in elastic recoil. Due to this hierarchical structure, tendons present both flexibility and a high tensile strength over a wide load range. When an injured tendon is severely ruptured, a heavy surgical procedure is required. To overcome this issue, several strategies have already been developed as autografts, decellularized tendons, braided synthetic fibers. However, none of these materials fully meets chemical, mechanical and cytocompatibility requirements. The aim of this thesis is to produce a collagen matrix which mimics tendon by extrusion under physiological conditions. First, using alginate solutions as a model system for their similar rheological properties, we performed an extensive study of the helical extrusion instability which hinders the formation of regular threads. Based on this work, we then produced micrometric threads of dense collagen or mixtures of collagen and alginate which exhibit structures aligned along the thread axis. The physico-chemical conditions are chosen in order to obtain homogeneous threads with optimized mechanical properties. Finally, mesenchymal stem cells are seeded in vitro on collagen based threads. They colonize our matrices and express characteristic genes which suggests that they differentiate into tendon-like cells.

Master of Arts / Department of English / Katherine Karlin / By the year 2037, climate change has destabilized the world’s ecology, politics, and culture. Hawaii has seceded from the United States, instituting the Cultural Reaffirmation, which champions a sustainable, traditional way of life. Eenie is an astronomer on the Big Island of Hawaii. In order to keep the observatory on Mauna Kea operational, she must appease the newly independent island nation by reenacting a mythical sled race between Poliahu, the Hawaiian snow goddess of Maunakea, and Pele, the fierce goddess of lava, personified by a rival geoscientist from Maunaloa’s volcanic laboratory. Once an Olympic contender in the women’s luge, Eenie has won this race twice before. This year, though, the greenhouse effect has caught up with her; there is no snow on Maunakea. Without it, she cannot prevail, and if she doesn’t, the priests of Hawaii’s Cultural Reaffirmation will pull the telescopes down from their most sacred mountain. Eenie struggles against nature’s increasing wrath, gods, monsters, pigs, and political rivals, though her biggest struggle is within herself. Fire and water must live together takes place in an ecodystopic future, though its story pulls from Hawaiian myth. The story’s projection into the future is based on current events, including the Hawaiian sovereignty movement, climate change science, and technology. An accompanying essay frames the novella through three critical lenses: ecocriticism, eco-politics, and post-colonial hybridity. The essay includes a focused look at the setting of Hawaii as it stands today in terms of environment, politics, and people.

Incorporation of probiotic cultures in products in order to replenish or supplement the normal gastrointestinal microflora is a well known and accepted practice. However survival of these cultures is a problem due to a number of reasons including effects of storage conditions. Various researchers from different countries around the world have reported probiotic product instability. Microencapsulation has been used in an attempt to solve this problem. However, most methods involve the use of organic solvents which is not ideal because their toxicity may cause destruction of the microbial cells. A novel encapsulation method for probiotics, which excludes the use of organic solvents, was developed by the Council for Scientific and Industrial Research (CSIR) (US Patent Application no. 20050112205). This thesis investigated the efficiency/potential of this new method for increasing stability of sensitive probiotic cultures, specifically bifidobacteria. Early studies using both culture dependent and culture independent techniques showed reduced numbers of viable cultures in probiotic products, mainly yoghurts, from all around the world. These results were confirmed in this study for similar products sold in South Africa. Most of the product labels did not specify viable numbers of probiotics nor the identity (genus and species names) of the microorganisms incorporated. Successful encapsulation of bifidobacteria was achieved using the CSIR patented method. Complete encapsulation was indicated by absence of cells on surfaces of the encapsulated particles and production of a product with an acceptable particle size distribution was obtained. It was also demonstrated that the encapsulation process produced no visible morphological changes to the bacterial cells nor did it have a negative effect on cell viability over time. The potential of interpolymer complex formation in scCO2 for the encapsulation of sensitive probiotic cultures was demonstrated for the first time. Once ingested, probiotic cultures are exposed to unfavourable acidic conditions in the upper gastrointestinal tract. It is desired that these cultures be protected from this in order to increase the viability of the probiotics for efficient colonization. Interpolymer complex encapsulated B. longum Bb-46 cells were therefore exposed to simulated gastric fluid (SGF) and subsequently to simulated intestinal fluid (SIF). It was found that the interpolymer complex protected bifidobacteria from gastric acidity, displaying pH-responsive release properties, with little to no release in SGF and substantial release in SIF. Thus the interpolymer complex demonstrated desirable characteristics retaining the encapsulated bacteria inside when conditions were unfavourable and only releasing them under favourable conditions. Survival was improved by the incorporation of glyceryl monostearate (GMS) in the matrix and by use of gelatine capsules. Protection efficiency of the interpolymer matrix was better when higher loading of GMS was used. Use of polycaprolactone (PCL) as an alternative to poly (vinylpyrrolidone) (PVP) and incorporation of ethylene oxide-propylene oxide triblock copolymer (PEO-PPO-PEO) affected the interpolymer complex negatively, rendering it swellable in the low pH environment exposing the bifidobacteria to gastric acidity. The use of beeswax seemed to have a more protective effect though results were inconclusive. Probiotic cultures must also remain viable in products during storage. Encapsulated bacteria were either harvested from the reactor after 2 h of equilibration followed by depressurization, and then ground to a fine powder or after 2 h of equilibration the liquefied product was sprayed through a capillary tube with a heated nozzle at the end, into the product chamber. Encapsulated bacteria were stored in either sterile plastic bags or glass bottles under different conditions and then viable counts were determined over time. Survival of bacteria was generally better when the products were stored in glass bottles than in plastic bags. Bacteria encapsulated in an interpolymer complex formed between PVP and vinyl acetate-crotonic acid copolymer (VA-CA), (PVP:VA-CA) survived better than non-encapsulated bacteria under all storage conditions when the product was recovered from the reaction chamber. When the product was recovered from the product chamber, numbers of viable non-encapsulated bacteria were higher than the encapsulated bacteria for all interpolymer complex formulations. This was probably due to some exposure to high shear during spraying into the product chamber. The interpolymer complex between PCL and VA-CA i.e. PCL:VA-CA seemed weaker than the PVP:VA-CA nterpolymer complex as viable counts of bacteria released from it were lower than those from the latter complex. Addition of PEO-PPO-PEO to both the PVP:VA-CA and PCL:VA-CA complexes decreased the protection efficiency. However, results indicated that sufficient release of encapsulated bacteria from the interpolymer complexes was obtained when the encapsulated material was incubated in SIF rather than in Ringer’s solution. When SIF was used for release of encapsulated bacteria, the shelf life of B. longum Bb-46 was doubled. Encapsulation in an interpolymer complex therefore provided protection for encapsulated cells and thus has potential for improving shelf life of probiotic cultures in products. Further studies will investigate the effects of encapsulating probiotics together with prebiotics in the interpolymer complex as well as effects of encapsulating combinations of different probiotic strains together, both on survival in simulated gastrointestinal tract and during storage. The unique particles produced using the patented encapsulation technique increased the stability of probiotic cultures. This technique may find significant application in industries manufacturing probiotic products, especially food and pharmaceuticals, thereby improving the well being of consumers. / Thesis (PhD(Microbiology))--University of Pretoria, 2008. / Microbiology and Plant Pathology / PhD / unrestricted

Internal instability of a widely graded cohesionless soil refers to a phenomenon in which its finer particles migrate within the void network of its coarser particles, as a result of seepage flow. Onset of internal instability of a soil is governed by a combination of geometric and hydromechanical constraints. Much concern exists for embankment dams and levees built using soils with a potential for internal instability. Migration of finer particles to a boundary where they can exit, by washing out, may cause erosion or piping failure and, occasionally, induce collapse of these soil structures. There is a need, in professional practice, to better understand the phenomenon and to develop improved methods to evaluate the susceptibility of a soil. A series of permeameter tests was performed on six widely-graded cohesionless materials. The objectives are to assess the geometric indices proposed for evaluation of susceptibility, and examine hydromechanical factors influence the onset of internal instability. A modified slurry mixing technique, with discrete deposition, was found satisfactory for reconstitution of the homogeneous saturated test specimens. The onset of internal instability was founded to be triggered by a combination of effective stress and hydraulic gradient. The finding yields a hydromechanical envelope, unique for a particular gradation shape, at which internal instability initiated. Three commonly used geometric criteria were comprehensively evaluated with reference to these experimental data and also a database compiled from the literature. The relative conservatism of each criterion was examined and a modified semi-empirical geometric rule then proposed based on the capillary tube model. A theoretical framework for plotting the hydromechanical envelope was established based on an extension of the α concept of Skempton and Brogan, and subsequently verified by test data. Finally, a novel unified approach was proposed to assess the onset of internal instability, based on combining geometric and hydromechanical indices of a soil. / Applied Science, Faculty of / Civil Engineering, Department of / Graduate

The integrity of the genome is critical to organisms and it is affected by many factors. Radiation, for example, poses a serious threat to genome stability of human beings. While physical monitors for radiation hazard are present, the biological consequences of long term exposure to radiation are not well understood. With the opportunity as part of the International Caenorhabditis elegans Experiment-1 flight project, several approaches using C. elegans were taken to measure mutational changes that occurred during the spaceflight. Among these methods, the eT1 balancer system was demonstrated to be well-suited as an integrating biological dosimeter for spaceflight. The dog-1 gene in C. elegans is required to prevent mutations at poly-G/poly-C tracts, and previous work has described that in the absence of DOG-1, small deletions initiate within these tracts, most likely as a consequence of improperly repaired replication blocks. The eT1 balancer system was adapted to investigate the broad mutational spectrum of dog-1 mutants. Using this system, I was able to determine a forward mutation rate of approximately 1 x 10-3, 10 fold higher than spontaneous. Both small deletions as reported previously and unreported large chromosome rearrangements were observed, and most of mutations analyzed are associated with G/C tracts. Thus, I propose that following dog-1-induced replication blocks, repair leads to a wide range of mutational events and chromosomal instabilities, similar to those seen in human cancers. The existence of the G/C tracts in C. elegans creates a fortuitous but perplexing problem. They are hotspots for genome instability and need enzymatic protection. In the genome of C. elegans, approximately 400 G/C tracts exist and are distributed along every chromosome in a non-random pattern. G/C tracts are also over-represented in another Caenorhabditis species, C. briggsae. However, the positions and distribution differ from those in C. elegans. Furthermore, in C. elegans, analysis of SAGE data showed that the position of the G/C tracts correlated with the level of gene expression. Although being a threat to genome stability, the genomic distribution of G/C tracts in C. elegans and their effect on regional transcription levels suggest a role for G/C tracts in chromatin structure. / Medicine, Faculty of / Medical Genetics, Department of / Graduate

The present work investigates the dynamics and stability of shock waves in granular gases. The problem was modelled for a piston propagating into a system of disks that can undergo inelastic collisions if an impact threshold is exceeded. The model was addressed numerically at the microscopic and macroscopic levels. The molecular dynamics methodology employed the Event-Driven Molecular Dynamics method, and the continuum model was formulated using the Navier-Stokes equations for granular gases with the transport terms of Jenkins and Richman and a modified cooling rate term. The inviscid steady state shock structure was derived and analyzed. The results indicated that a relaxing shock structure is expected for sufficiently strong shock waves. Beyond this limit the structure was shown to be independent of the initial energy, a finding similar to the strong shock approximation in molecular gases. One-dimensional simulations demonstrated that the molecular dynamics and continuum models yield similar evolutions and structures of the shock wave, validating the continuum description of this study. Two-dimensional results showed that sufficiently strong shock waves can exhibit multi-dimensional instability with high density non-uniformities and convective rolls within the structure, with the size of instabilities shown to scale with the relaxation length of the shock structure. Instabilities were observed with the continuum description only with the inclusion of statistical fluctuations to density mimicking the molecular model. The cases that were unstable were shown to be in a regime whereby statistical fluctuations can become important, following the description for this regime by Bird. Based on these findings, it is proposed that unstable shock behaviour can be observed for highly dissipative shock waves that yield short relaxation length scales, where fluctuations become important. The current work may shed light on unstable shock behaviour observed in dissipative gases, having implications for both granular media and molecular gases.

L'étude de stabilité des systèmes différentiels issus des équations de Navier-Stokes consiste à analyser la réponse du système linéarisé à une perturbation en onde plane. Elle ne peut pas rendre compte de tous les mécanismes possibles d'instabilité non linéaire. De telles analyses de stabilité non linéaire ont été abordées pour des discrétisations en différences finies de l'équation scalaire non visqueuse de Burgers. Elles sont basées sur l'analyse en ondes résonantes, en considérant un ensemble d'ondes qui forment un groupe fermé pour l'équation discrétisée. Une conclusion importante de ces travaux est que quelques mécanismes non linéaires instables existent qui échappent à l'analyse linéaire, comme le mécanisme de focalisation étudié et expliqué à l'aide des modes de side band, introduits pour amorcer les instabilités. Cette approche d'ondes résonantes est étendue à l'analyse non linéaire de stabilité pour les méthodes LBM (Lattice Boltzmann Method). Nous présentons pour la première fois une équation vectorielle à la place de l' équation scalaire de Burgers, car la méthode LBM considère une fonction de distribution par vitesses discrètes. L'application du principe des ondes résonantes aux équations de Boltzmann sur réseau pour un écoulement monodimensionnel, compressible et isotherme dans un schéma D1Q3 donne des cartes d'instabilité, dans le cas de 1 ou plusieurs modes résonants, très dépendantes des conditions initiales. Le phénomène de focalisation n'a pas été obtenu dans la formulation LBM. Des croissances transitoires dues à la non-normalité des opérateurs peuvent exister. Elles sont calculées par une méthode d'optimisation Lagrangienne utilisant les équations adjointes de LBM. L'application du principe des ondes résonantes est étendue à un modèle 2D. On montre que les instabilités deviennent prépondérantes. / The stability study of differential systems derived from the Navier- Stokes equations consists in analysing the response of the planar linearized system from a disturbance on a flat wave. It cannot account for all possible mechanisms of nonlinear instability. Such non-linear stability analyses were discussed for finite difference of the scalar non-viscous Burger equation. They are based on the analysis in resonant waves, considering a set of waves that form a closed group for the discretized equation. An important conclusion of this work is that some unstable nonlinear mechanisms exist that are beyond the linear analysis, as the focusing mechanism studied and explained using the methods of side band, introduced to initiate instabilities. This approach of resonant waves is extended to non-linear stability analysis for LBM (Lattice Boltzmann Method) methods. We report for the first time a vector equation instead of the scalar Burgers equation, because the LBM method considers a distribution function by discrete speeds. The principle of resonant waves to lattice Boltzmann equations for one-dimensional flow in a compressible and isothermal D1Q3 scheme gives instability maps, in the case of one or more resonant modes , highly dependent upon the initial conditions. The phenomenon of focus has not been obtained in the LBM formulation. Transient growth due to non-normality of operators may exist. They are calculated by a Lagrangian optimization method combined with LBM equations. The principle of resonant waves is extended to a 2D model. We show that the instabilities become dominant.

An arched structure provides an effective load carrying system for large span structures. When it comes to long span roof structures, timber arches are one of the best solutions from both structural and aesthetical point of view. Glulam arched structures are often designed using slender elements due to economic consideration. Such slender cross-section shape increases the risk of instability. Instability analysis of straight members such as beam and column are explicitly defined in Eurocode. However, for instability of curved members no analytical approach is provided in the code, thus some numerical method is required. Nonetheless, an approximation is frequently used to obtain the effective buckling length for the arched structures in the plane of arches. In this master thesis a linear buckling analysis is carried out in Abaqus to obtain an optimal effective buckling length both in-plane and out-of-plane for circular glulam arched structures. The elastic springs are used to simulate the overall stiffness of the bracing system. The results obtained by the FE simulations are compared with a simple approximation method. Besides, the forces acting on the bracings system is obtained based on 3D geometric nonlinear stress analysis of the timber trusses. Our findings conclude that the approximation method overestimates the effective buckling length for the circular glulam arched structures. In addition, the study indicates that the position of the lateral supports along the length of the arch is an important design aspect for buckling behaviour of the arched structures. Moreover, in order to acquire an effective structure lateral supports are needed both in extrados and intrados. Furthermore, instead of using elastic spring elements to simulate the overall stiffness of the bracing system, a full 3D simulation of two parallel arches was performed. It was shown that the springs are stronger than the real bracing system for the studied arch.

A model examining underground smouldering peat combustion is presented. A one-step chemical reaction is considered where the gas and solid are assumed to be in thermal equilibrium. The full model allows porosity, permeability and gas density to vary and considers a buoyant velocity field determined by Darcy's law. Due to the low bulk thermal conductivity of peat, the diffusion of oxygen through it is characterised by a Lewis number much less than one. This results in thermal-diffusive instabilities. These instabilities can cause flame balls to arise in gaseous combustion and a fingering regime to arise in solid combustion. Analytical solutions to simplified spherically symmetrical equations are derived. These equations assume diffusion to be the dominant transport mechanism as well as taking that the porosity, gas molecular weight and gas density all remain constant. The underlying structure of the combustion region is found to be analogous to that of a flame ball. When studied in cylindrical symmetry a single, stable finger can be modelled propagating against an imposed air flow. The effects of heat losses, velocity magnitude and the Lewis number can be studied and results are compared to existing experimental smouldering combustion data. Although no detailed experiments have studied this phenomenon in peat, predicted results capture key qualitative trends found in both filtration combustion of polyurethane foam and in the fingering combustion of paper. In addition to this, when the imposed air flow is reduced to zero a propagating combustion front is predicted, analogous to a self-travelling flame ball. When the velocity field is determined by Darcy's law the dimensionless permeability of the peat plays a key role in determining the range of values over which fingering combustion can occur. Whilst there is little impact of taking the gas molecular weight to be constant, when porosity is allowed to vary and a relationship between porosity and permeability is included an over-blowing extinction limit is identified. This limit is not found in the constant-porosity model where a low-fuel extinction limit is predicted. Peats of differing ages and locations can possess significantly different characteristics. However, the fingering regime is predicted to occur within the range of parameters in which peat soils lie. Experiments suggest that fingering combustion can take the form of both sparse fingers and a complex fingering regime. The cylindrically symmetrical model can not capture tip-splitting. Hence the model does not explicitly account for the distance between two neighbouring fingers. However, an estimate for this value can be made if peat smouldering were to occur in a regime of multiple fingering. An averaged continuum model describing the spread of an ember storm is also presented. The dominant mechanism determining the spread-rate of the fire is the lofting and landing of embers and individual fires are taken to grow in an elliptical manner under the influence of the wind. When an ember storm is spreading at a steady speed, its spread rate is found to be described by a single similarity solution.