Dissertations / Theses on the topic 'Modelling and theoretical studies'

Understanding the interactions between dye molecules and their constituent moieties will lead to an improvement in the design of new molecules with the appropriate properties. Here, we use computational methods to investigate the relative stability of the three tautomers of hydroxy-triazine, and how they interact with themselves in the gas phase, in aqueous solution and in the solid state. Ab initio and density functional theory (DFT) methods were used to establish the relative gas phase stability of the tautomers, showing two of the tautomers to be significantly more stable than the third. Thermodynamic cycles were calculated using ab initio free energies of salvation and gas phase energies. The crystal phase investigation involved data mining of the Cambridge Structural Database and generating hypothetical crystal structures which were subjected to lattice energy minimisations. The interactions were investigated in the gas phase by minimising small clusters of the tautomers, treated as rigid molecules, from a number of random starting conformations. Molecule dynamics simulations looked at the behaviour in solution, while the lattice energy minimisations and the CSD were again used to look at solid phase interactions. The above methods were also incorporated into further investigations of the interactions between these tautomers and another important dye-related molecule, morpholine, both as an additive and as a covalently bonded fraction. Whole dye molecules containing these substructures, were then studied using the above methods, as well as UV-Vis spectroscopic analysis to calculate dimerisation equilibrium constants. Finally the computational methods were applied to look at the effects of substituents on the interactions of zinc phthalocyanine.

With respect to nitrides being considered as potential fast reactor fuels, research is conducted on the out-of-pile thermophysical properties, sintering and fabrication processes, gas migration mechanisms, self-diffusion and point defect behaviour of actinide nitrides, their surrogate materials, and the inert matrix material ZrN . The experimental research, carried out in the framework of qualifying fuel for the European Lead Cooled Training Reactor (ELECTRA), shows that sintered ZrN and (Dy,Zr)N pellet densities are influenced by the oxygen concentration in the material. The effect is confirmed in sintered (Pu,Zr)N pellets. Oxygen concentration also plays a role in the thermophysical properties of inert matrix nitride fuels, but does not have an impact on the electrical properties of these materials. With the fuel fabrication methods applied here, clean nitride powders can be synthesized. However, the subsequent fabrication phases, including milling and solid solution formation, increases the impurity levels significantly. Research of equal importance is performed on materials free of fabrication-induced impurities, whose properties are studied by employing first-principles methods. ZrN, UN and (U,Zr)N are studied, whereas the results from ZrN are expected to be applicable for actinide nitrides as a first approximation. The migration of noble gases in ZrN, on the atomic scale, confirms the experimentally observed tendency for noble gases with higher atomic number to be retained in the fuel matrix, while the majority of He is released to the fuel pin. Materials modelling implies that self-diffusion of nitrogen and metal atoms in inert matrix nitride fuels is accelerated under irradiation, since noble gas retention reduces migration barriers which govern self-diffusion. Unlike Kr and Xe, He has the capacity to be released into the fuel matrix, after having been trapped in a vacancy. The results are expected to aid in providing an explanation to the macroscopic diffusion phenomena in nitride fuels, as the diffusion behaviour of noble gases is sparsely studied. In addition, a study on the miscibility of ZrN and UN in a narrow composition range suggests solubility, based on the negative mixing energies. The results obtained from research on inert matrix nitride fuel underline several beneficial properties which are desirable in a fast reactor fuel. The relevance of these results is analyzed and contextualized in the thesis, from the perspective of current research and development in the field.

QC 20130611

This thesis focused on the review and background theory of previous studies on fatigue failure criteria, experimental work and results’ analysis. Several techniques are used for testing fatigue performance for both hot mix asphalt (HMA) and fine aggregate matrix (FAM), such as two-, three- and four-point bending, indirect tension and uniaxial tests. In recent years, a new technique has been introduced using the Dynamic Shear Rheometer (DSR). This technique is based on applying a sinusoidal deformation or loading onto small cylindrical samples, 12 mm diameter and 50 mm height, and the response is analysed to obtain phase angle and deformation data under any given circumstances, such as temperature, frequency, etc. The DSR is limited to test bitumen and fine aggregates matrix FAM samples only; nevertheless, no research efforts have been found that use a DSR to study the performance of full HMA samples. In this work, a successful trial was proposed using a DSR for fatigue testing of HMA under controlled strain and stress modes. Two types of aggregates, limestone and granite with two binder grades, 40/60 and 160/220, were employed to prepare four different mixes of hot rolled asphalt (HRA) and dense bitumen macadam (DBM). A technical procedure was adopted to prepare the DSR samples (12 mm in diameter and 50 mm in height) and a statistical procedure based on histograms and modes for the bulk density of the DSR samples was used to select the samples to be tested for fatigue. An approach was developed based on sweep strain/stress amplitude to arrive at a suitable strain and stress amplitude at the damage region to be used in the fatigue test. A new fatigue index (FIR) parameter was derived from the dissipated pseudo-strain energy for the stress-pseudo-strain relationship to be used for evaluating fatigue performance. Results showed that there is a plateau value for FIR which can be used to evaluate fatigue performance, and this value increases when the normalised shear modulus decreases to less than 0.35 and 0.20 for strain and stress test modes respectively. In addition, the FIR results were in agreement with the results from other reliable approaches that have been used for evaluating fatigue performance, such as the energy ratio (ER) and the traditional approach (TA). A two-point bending (2PB) test for trapezoidal samples was used to verify the DSR technique using FIR, TA and ER approaches; the analysis of results revealed the same conclusions as the DSR technique. The variance in the results of the tested samples was studied using error bars in terms of standard of error for all approaches in both techniques: DSR and 2PB. This variance analysis revealed that FIR has low variation in comparison with the TA and ER approaches in both test techniques. A computational model based on artificial neural networks (ANNs) was used in this work for developing models to predict the fatigue performance of hot mix asphalt (HMA). The fatigue performance was defined according to the criteria of the TA, ER and FIR approaches. The results revealed an excellent correlation between the predicted and experimental data. Bias analysis for ANN models involving average error, intercept and slope showed that the strain test mode was more accurate than the stress test mode. A fracture mechanistic approach was also used to evaluate the fracture performance of HMA tested in DSR. A simple fracture model was developed based on a modified Paris’ law and fatigue test parameters represented by relaxation test coefficient (m) and the dissipated pseudo-strain energy to calculate an internal damage parameter, namely the fracture damage index (FIc). The analysis of the results for FIc was in agreement with the FIR, ER and TA approaches; also, it showed better performance analysis in terms of variation than the TA and ER approaches. The fracture model, FIc, was used as a base for developing a model for predicting fatigue life of HMA in terms of number of cycles for strain and stress test modes. The bias analysis revealed that the strain model’s prediction accuracy was better than that of the stress model. Hysteretic behaviour represents the nonlinear relationship of the stress–strain response for HMA under cyclic loading during fatigue testing. In this regard, a successful trial introduced for modelling the hysteresis loops using Bouc-Wen model for HMA samples tested for fatigue under controlled strain mode using DSR. The nonlinear least squares algorithm was used to estimate the seven parameters for the Bouc-Wen model using experimental results for hysteresis loops of the HMA samples tested in DSR; these parameters control the shape and slope of the degraded hysteresis loops. The outcome of this work confirmed that there is a good agreement between the modelled and experimental hysteresis loops. Due to the variation in the fatigue performance of HMA samples as a result of their properties, the Bouc-Wen model was not able to fully simulate the degradation for different samples when there were changes in the parameters. To improve the Bouc-Wen model’s simulation performance, an ANN technique was used to develop models to predict its parameters; this technique improved the Bouc-Wen model’s performance in Phase I, while its performance in Phase II-III was still poor, despite the degradation simulation being clear. This work revealed the feasibility of using the DSR technique in evaluating the fatigue performance of full HMA according to the developed approaches for preparing and selecting DSR samples and performing fatigue tests. In addition, the work confirmed that limestone has a better fatigue performance for both HRA and DBM mixes than granite. On the other hand, the theoretical part included developing several models based on an ANN and constitutive equations showed the efficiency of these models in predicting the fatigue life of HMA samples tested in the DSR.

Astronomy with gravitational-wave observations is now a reality. Much of the theoretical research in this field falls under three broad themes: the mathematical description and physical understanding of gravitational radiation and its effects; the construction of accurate and computationally efficient waveform models for astrophysical sources; and the improved statistical analysis of noisy data from interferometric detectors, so as to extract and characterise source signals. The doctoral thesis presented in this dissertation is an investigation of various topics across these themes. Under the first theme, we examine the direct interaction between gravitational waves and electromagnetic fields in a self-contained theoretical study; this is done with a view to understanding the observational implications for highly energetic astrophysical events that radiate in both the gravitational and electromagnetic sectors. We then delve into the second theme of source modelling by developing and implementing an improved waveform model for the extreme-mass-ratio inspirals of stellar-mass compact objects into supermassive black holes, which are an important class of source for future space-based detectors such as the Laser Interferometer Space Antenna. Two separate topics are explored under the third theme of data analysis. We begin with the procedure of searching for gravitational-wave signals in detector data, and propose several combinatorial compression schemes for the large banks of waveform templates that are matched against putative signals, before studying the usefulness of these schemes for accelerating searches. After a gravitational-wave source is detected, the follow-up process is to measure its parameters in detail from the data; this is addressed as we apply the machine-learning technique of Gaussian process regression to gravitational-wave data analysis, and in particular to the formidable problem of parameter estimation for extreme-mass-ratio inspirals.

Dans cette thèse, nous nous proposons d'étudier et de traiter conjointement plusieurs problèmes phares en traitement d'images incluant le recalage d'images qui vise à apparier deux images via une transformation, la segmentation d'images dont le but est de délimiter les contours des objets présents au sein d'une image, et la décomposition d'images intimement liée au débruitage, partitionnant une image en une version plus régulière de celle-ci et sa partie complémentaire oscillante appelée texture, par des approches variationnelles locales et non locales. Les relations étroites existant entre ces différents problèmes motivent l'introduction de modèles conjoints dans lesquels chaque tâche aide les autres, surmontant ainsi certaines difficultés inhérentes au problème isolé. Le premier modèle proposé aborde la problématique de recalage d'images guidé par des résultats intermédiaires de segmentation préservant la topologie, dans un cadre variationnel. Un second modèle de segmentation et de recalage conjoint est introduit, étudié théoriquement et numériquement puis mis à l'épreuve à travers plusieurs simulations numériques. Le dernier modèle présenté tente de répondre à un besoin précis du CEREMA (Centre d'Études et d'Expertise sur les Risques, l'Environnement, la Mobilité et l'Aménagement) à savoir la détection automatique de fissures sur des images d'enrobés bitumineux. De part la complexité des images à traiter, une méthode conjointe de décomposition et de segmentation de structures fines est mise en place, puis justifiée théoriquement et numériquement, et enfin validée sur les images fournies
In this thesis, we study and jointly address several important image processing problems including registration that aims at aligning images through a deformation, image segmentation whose goal consists in finding the edges delineating the objects inside an image, and image decomposition closely related to image denoising, and attempting to partition an image into a smoother version of it named cartoon and its complementary oscillatory part called texture, with both local and nonlocal variational approaches. The first proposed model addresses the topology-preserving segmentation-guided registration problem in a variational framework. A second joint segmentation and registration model is introduced, theoretically and numerically studied, then tested on various numerical simulations. The last model presented in this work tries to answer a more specific need expressed by the CEREMA (Centre of analysis and expertise on risks, environment, mobility and planning), namely automatic crack recovery detection on bituminous surface images. Due to the image complexity, a joint fine structure decomposition and segmentation model is proposed to deal with this problem. It is then theoretically and numerically justified and validated on the provided images

1. The Force Field Accuracy Problem. The utility and applicability of MD simulations to model biomolecular systems goes only as far as its ability to sufficiently sample the conformational space and the correct description of the potential in terms of the force field functional form and parameter set. Clearly, the force field defines the shape of the conformational space for a given set of atomic positions and also the accessibility of energy minima. When simulating systems at equilibrium, especially quite stable systems such as DNA, the force fields strive to generate ensembles that reproduce well real systems and this does not have to come as a big trade-off with sampling power. In recent years it has become the business of computer engineers and software developers to address the issue of achieving long and biologically relevant time scales. Convergence and reproducibility of atomistic DNA simulations with state-of-the-art force fields such as our parmbsc1 has been convincingly demonstrated. It also seems that until a significant revolution, where milliseconds of simulation become routine, current sampling ranges completely cover the internal structures and dynamics of B-DNAs at this time scale. The growing confidence has allowed many researchers to use MD for very detailed studies on the sequence-dependent nature of DNA oligomers and on the complex arsenal of mechanisms that govern its behavior. In any such studies careful validation of results is necessary since it is not yet entirely clear how well and to what degree are sequence effects reproduced in MD. The fact that the latest-generation of force fields agree very well between themselves and that they fit with the sparse experimental data is surely very encouraging, but it will be some time until small differences in sequence geometries can be validated. Our own extensive validation of the parmbsc1 force field, as well as a large number of other works that have, since its publication, either specifically set out to assess its performance, or have just applied it with success, speak of a very stable parametrization able to deal with a wide range of DNAs. It is worth to mention that in special conditions small improvements might be necessary, which could be achieved with the inclusion of polarization terms. However, up to date, no force field has been able to model polarization without eventually destabilizing the system and this at a huge cost (a factor of 10) to calculation speed. To sum up, based on the remarkable performance of parmbsc1, we and other groups can employ it with confidence in the detailed study of DNA dynamics and we expect that the number of supporting results will only increase. 2. 2. Sequence-dependence and polymorphisms of B-DNA. So what is it that we actually learn from analyzing the conformation variability of DNA over its sequence space at the tetramer level? It is well established that different bps have different preferences regarding their internal geometries, and to some extent, Calladine’s set of heuristic rules is able to make sense of these differences. At the bps level, some sequences are extremely stable, such as ApT, and some sequences, such as CpG, have a bi-stable equilibrium and they convert between different arrangements of their internal geometries. There are cases where this frustration can be explained by their charge distribution, bulkiness or the strength of their stacking and h-bonding interactions, but in many cases in requires a more holistic view, taking higher-level sequence effects into account. In multi-microsecond MD simulations, intra-base-pair parameters are always unimodal since alternative states that might be accessed through base opening are not sampled in at this time scale. However, their ensemble averages show sizeable differences according to the change in sequence. Inter- base-pair parameters can be bimodal, but only in certain tetranulceotide combinations that make up about 5% of cases. This can be explained considering that the central bps of a particular combination of four nucleotides has a structural preference that is in conflict with those of its neighboring steps. In order to minimize the energy cost and satisfy as best as possible all conformational requirements, a more flexible bps will populate several states, usually a maximum of two. Optimization of geometries between several bps generally involve backbone rearrangements, with the sugar-phosphate acting as a hinge that allows consecutive bps to coordinate in a complex choreography often involving other factors, such as subtle changes in the solvent environment environment. In B-DNA the most important backbone transition is the BI/BII, which can be related to the base chemistry through the sequence-dependent relative strength of unconventional h-bonds that stabilize BII conformations. In a tetramer model of B-DNA, the backbone transitions of different tetramers are translated into motions along different internal degrees of freedom, depending on the sequence. Therefore, we are able now to build a picture of the interconnected conformational space of DNA as an overlap of tetranucleotide sequences with transferable structural descriptors. It is still a matter of speculation how these properties might be exploited by proteins and other binders for biological function. 3. Information transfer through the DNA. There are however a few special cases where the tetramer model does not seem to be sufficient. The CTAG is one such case that demonstrates that for a highly flexible and polymorphic tetramer, long-range sequence composition can have a notable effect on the structural properties of the central bps. Analyzing the mechanism behind this long-range communication through the DNA has meant more than anything else an opportunity to understand rare events of sequence modulation that might be a lot more general in cases of larger, induced distortions on the helix. In CTAG we could observe sequence influence not only from the hexamer level, but even from beyond, and the data points to a complex mechanism of information transfer across DNA through coordinated backbone movements. In performing biological function, DNA is often mistakenly viewed as an inert lattice onto which proteins assemble to replicate or transcribe genes. However, experiments demonstrate that information transfer in the DNA can happen even over long distances and can produce allosteric effects upon ligand binding. Without question, the binding of proteins or small molecules to the DNA can produce coupled conformational changes that may affect a neighboring binding site and increase its affinity for the secondary binding protein. Such changes need not alter ensemble averages and only potentiate modifications in the shape of the energy well at the secondary binding site. As seen from the dynamic information provided by an MD trajectory, maybe in more than one case of protein couples, DNA acts as a wire transmitting pulses of information originated at the primary binding site that travel to distant regions. We show that MD methods can provide reasonable explanations for cooperative binding phenomena on the DNA and open for the first time the possibility of the “allostery without conformational change” in the recruitment of proteins of the DNA scaffold. From a thermodynamic point of view, this type of cooperative binding seems to be entropy-driven. Thus, the first binding event freezes some of the degrees of freedom around it’s own binding region, but also reduces the entropy cost associated to the second binding.
1. Problema de exactitud del campo de fuerza La utilidad y aplicabilidad de las simulaciones de DM para modelar sistemas biomoleculares depende de su capacidad para muestrear suficientemente el espacio conformacional y la descripción correcta del potencial en términos de la forma funcional del campo de fuerza y el conjunto de parámetros. Claramente, el campo de fuerza define la forma del espacio conformacional para un conjunto dado de posiciones atómicas y también el acceso a los mínimos energéticos. Al simular sistemas en equilibrio, especialmente en sistemas bastante estables como el ADN, los campos de fuerza se esfuerzan por generar conjuntos que reproducen sistemas reales y no tiene por qué ser una gran desventaja con el poder de muestreo. En los últimos años, se ha convertido en tarea de los ingenieros informáticos y los desarrolladores de software abordar el problema de lograr escalas de tiempo largas y biológicamente relevantes. La convergencia y reproducibilidad de simulaciones de ADN atomístico con campos de fuerza de última generación, como nuestro parmbsc1, se ha demostrado de forma convincente. También parece que hasta llegar a una revolución significativa, donde los milisegundos de simulación se vuelven rutinarios, los rangos de muestreo actuales cubren por completo las estructuras internas y la dinámica de los ADN-B en esta escala de tiempo. La creciente confianza ha permitido a muchos investigadores utilizar DM para estudios muy detallados sobre la naturaleza dependiente de la secuencia de oligómeros de ADN y sobre el complejo arsenal de mecanismos que rigen su comportamiento. En cualquiera de estos estudios es necesaria una validación cuidadosa de los resultados ya que aún no está del todo claro qué tan bien y en qué grado se reproducen los efectos de secuencia en DM. El hecho de que la última generación de campos de fuerza coincida muy bien entre sí y que se ajusten a los escasos datos experimentales es seguramente muy alentador, pero pasará algún tiempo hasta que se puedan validar pequeñas diferencias en las geometrías de las secuencias. Nuestra propia validación extensiva del campo de fuerza parmbsc1, así como una gran cantidad de otros trabajos que, desde su publicación, se han establecido específicamente para evaluar su rendimiento, o simplemente lo han aplicado con éxito, hablan de una parametrización muy estable capaz de tratar con una amplia gama de ADN. Vale la pena mencionar que en condiciones especiales podrían ser necesarias pequeñas mejoras, lo que podría lograrse con la inclusión de términos de polarización. Sin embargo, hasta la fecha, ningún campo de fuerza ha sido capaz de modelar la polarización sin desestabilizar finalmente el sistema y esto a un costo enorme (un factor de 10) a la velocidad de cálculo. En resumen, con base en el notable desempeño de parmbsc1, nosotros y otros grupos podemos emplearlo con confianza en el estudio detallado de la dinámica del ADN y esperamos que el número de resultados de soporte solo aumente. 2. Dependencia de la secuencia y polimorfismos del ADN-B. Entonces, ¿qué es lo que realmente aprendemos al analizar la variabilidad de conformación del ADN sobre su espacio de secuencia a nivel de los tetrámeros? Está bien establecido que diferentes bps tienen diferentes preferencias con respecto a sus geometrías internas, y hasta cierto punto, el conjunto de reglas heurísticas de Calladine es capaz de dar sentido a estas diferencias. A nivel de bps, algunas secuencias son extremadamente estables, como ApT, y algunas secuencias, como CpG, tienen un equilibrio biestable y convierten entre diferentes disposiciones de sus geometrías internas. Hay casos en que esta frustración puede explicarse por la distribución de cargas, el volumen o la fuerza de sus interacciones de apilamiento y los puentes de hidrógeno, pero en muchos casos requiere una visión más integral, teniendo en cuenta los efectos de secuencia de más alto nivel. En simulaciones de DM de multi-microsegundos, los parámetros de pares intra-base son siempre unimodales ya que los estados alternativos a los que se puede acceder a través de la apertura de la base no se muestrean en esta escala de tiempo. Sin embargo, sus promedios de conjunto muestran diferencias considerables de acuerdo con el cambio en la secuencia. Los parámetros de pares de bases pueden ser bimodales, pero solo en ciertas combinaciones de tetranulceótidos que constituyen aproximadamente el 5% de los casos. Esto puede explicarse teniendo en cuenta que el bps central de una combinación particular de cuatro nucleótidos tiene una preferencia estructural que está en conflicto con la de sus pasos vecinos. Con el fin de minimizar el costo de energía y satisfacer de la mejor manera posible todos los requisitos conformacionales, un bps más flexible poblará varios estados, generalmente un máximo de dos. La optimización de las geometrías entre varios bps generalmente implica reorganizaciones de la red troncal, con el azúcar fosfato actuando como una bisagra que permite la coordinación consecutiva de bps en una coreografía compleja que a menudo involucra otros factores, tales como cambios sutiles en el entorno del solvente. En los ADN-B, la transición principal más importante es BI/BII, que se puede relacionar con la química a través de la fuerza relativa dependiente de la secuencia de puentes de hidrógeno no convencionales que estabilizan las conformaciones BII. En un modelo de tetrámero de ADN-B, las transiciones de la cadena principal de diferentes tetrámeros se traducen en movimientos a lo largo de diferentes grados internos de libertad, dependiendo de la secuencia. Por lo tanto, ahora podemos construir una imagen del espacio conformacional interconectado del ADN como una superposición de secuencias de tetranucleótidos con descriptores estructurales transferibles. Todavía es una cuestión de especulación cómo estas propiedades podrían ser explotadas por proteínas y otras moléculas que se unen al ADN para diferentes funciones biológicas. 3. Transferencia de información a través del ADN. Sin embargo, hay algunos casos especiales en los que el modelo de tetrámero no parece ser suficiente. El CTAG es uno de esos casos que demuestra que, para un tetrámero altamente flexible y polimórfico, la composición de la secuencia de largo alcance puede tener un efecto notable sobre las propiedades estructurales del bps central. Analizar el mecanismo detrás de esta comunicación de largo alcance a través del ADN ha significado más que nada una oportunidad para comprender los raros eventos de modulación de secuencia que podrían ser mucho más generales en casos de distorsiones mayores e inducidas en la hélice. En CTAG pudimos observar la influencia de la secuencia no solo desde el nivel del hexámero, sino incluso más allá, y los datos apuntan a un complejo mecanismo de transferencia de información a través del ADN mediante movimientos coordinados de la cadena principal. En la realización de la función biológica, el ADN a menudo se considera erróneamente como un retículo inerte sobre el cual las proteínas se ensamblan para replicar o transcribir genes. Sin embargo, los experimentos demuestran que la transferencia de información en el ADN puede ocurrir incluso a largas distancias y puede producir efectos alostéricos sobre la unión al ligando. Sin lugar a duda, la unión de proteínas o moléculas pequeñas al ADN puede producir cambios conformacionales acoplados que pueden afectar a un sitio de unión vecino y aumentar su afinidad por la proteína de unión secundaria. Tales cambios no necesitan alterar los promedios del conjunto y solo potencian modificaciones en la forma del pozo de energía en el sitio de unión secundario. Como se ve a partir de la información dinámica proporcionada por una trayectoria de DM, tal vez en más de un caso de parejas de proteínas, el ADN actúa como un cable que transmite pulsos de información originados en el sitio primario de unión que viajan a regiones distantes. Mostramos que los métodos de DM pueden proporcionar explicaciones razonables para los fenómenos de unión cooperativa en el ADN y abren por primera vez la posibilidad de la "alostería sin cambio conformacional" en el reclutamiento de proteínas al ADN. Desde un punto de vista termodinámico, este tipo de enlace cooperativo parece estar impulsado por la entropía. Por lo tanto, el primer evento vinculante congela algunos de los grados de libertad alrededor de su propia región de unión, pero también reduce el costo de entropía asociado al segundo enlace.

Considerable research is being carried out into the parameters that affect catalyst performance in order to meet the latest emission regulations. The conversion efficiency and the durability of automotive catalytic converters are significantly dependent on catalyst flow performance. Related investigations are commonly conducted using CFD techniques which represent an inexpensive and fast alternative to experimental methods. This thesis focuses on the flow performance of automotive catalytic converters using both experimental and computational techniques. The work describes the effects of inlet flow conditions on catalyst performance, the application of radial vanes to catalyst systems and the refinement of the CFD flow model which increases the accuracy of the predicted catalyst flow performance. the effects of inlet flow conditions on the flow maldistribution across the catalyst face and the total pressure loss through the system were assessed using a steady air flow rig. Tests were conducted over a range of Reynolds numbers typically encountered in automotive catalytic converters using a uniform and a fully-developed inlet flow condition. The results showed that the flow maldistribution significantly increases with Reynolds number notably in wide-angled diffusers. The catalyst flow performance is considerably improved when the inlet flow is uniform rather than fully-developed, the non-dimensional total pressure loss is reduced by 8% at Re=60000 and the flow maldistribution across the catalyst face is decreased by 12.5% and 15% respective Reynolds numbers of 30000 and 60000 when using a 60 degree diffuser. The total pressure loss through the system was found to be mostly associated with the monolith brick resistance. When the flow maldistribution is approximately 2, the pressure loss across the monolith brick represents 80% of the system pressure loss. The flow maldistribution across the catalyst face was improved by locating a system of radial splitters in the diffuser. The optimum flow performance was found to be a complex function of the vane design. A maximum improvement in the flow maldistrution indices M and Mi of 25% and 50% respectively was achieved at the expense of an increase in total pressure loss of 13.5% at Re = 60000. Both CFD and flow visualisation techniques were used as an aid to interpreting the flow field in the diffuser. Although a qualitative agreement was obtained using CFD, the flow maldistribution across the catalyst face was underpredected by up to 20%. The accuracy of the flow predictions was significantly improved by investigating the flow field in the monolith channels. Flow recirculation occurs in the channel entry length when the flow approaches the monolith channels at an angle which induces an additional implemented into four models of the flow through axisymmetric catalyst assemblies using various diffuser geometries and inlet flow conditions. By including the flow entrance effects in the porous media approach, the flow maldistribution was predicted within 8% instead of 15% when these effects are neglected. Further investigation of the flow in the monolith channels will be required to accurately model three-dimentional flows (racetrack catalysts) and to include various channel geometries and system flow rates.

Heterogeneous electrocatalysis is the usage of solid materials to decrease the amount of energy needed to produce chemicals using electricity. It is of core importance for modern life, as it enables production of chemicals, such as chlorine gas and sodium chlorate, needed for e.g. materials and pharmaceuticals production. Furthermore, as the need to make a transition to usage of renewable energy sources is growing, the importance for electrocatalysis used for electrolytic production of clean fuels, such as hydrogen, is rising. In this thesis, work aimed at understanding and improving electrocatalysts used for these purposes is presented. A main part of the work has been focused on the selectivity between chlorine gas, or sodium chlorate formation, and parasitic oxygen evolution. An activation of anode surface Ti cations by nearby Ru cations is suggested as a reason for the high chlorine selectivity of the “dimensionally stable anode” (DSA), the standard anode used in industrial chlorine and sodium chlorate production. Furthermore, theoretical methods have been used to screen for dopants that can be used to improve the activity and selectivity of DSA, and several promising candidates have been found. Moreover, the connection between the rate of chlorate formation and the rate of parasitic oxygen evolution, as well as the possible catalytic effects of electrolyte contaminants on parasitic oxygen evolution in the chlorate process, have been studied experimentally. Additionally, the properties of a Co-doped DSA have been studied, and it is found that the doping makes the electrode more active for hydrogen evolution. Finally, the hydrogen evolution reaction on both RuO2 and the noble-metal-free electrocatalyst material MoS2 has been studied using a combination of experimental and theoretically calculated X-ray photoelectron chemical shifts. In this way, insight into structural changes accompanying hydrogen evolution on these materials is obtained.
Heterogen elektrokatalys innebär användningen av fasta material för att minska energimängden som krävs för produktion av kemikalier med hjälp av elektricitet. Heterogen elektrokatalys har en central roll i det moderna samhället, eftersom det möjliggör produktionen av kemikalier såsom klorgas och natriumklorat, som i sin tur används för produktion av t ex konstruktionsmaterial och läkemedel. Vikten av användning av elektrokatalys för produktion av förnybara bränslen, såsom vätgas, växer dessutom i takt med att en övergång till användning av förnybar energi blir allt nödvändigare. I denna avhandling presenteras arbete som utförts för att förstå och förbättra sådana elektrokatalysatorer. En stor del av arbetet har varit fokuserat på selektiviteten mellan klorgas och biprodukten syrgas i klor-alkali och kloratprocesserna. Inom ramen för detta arbete har teoretisk modellering av det dominerande anodmaterialet i dessa industriella processer, den så kallade “dimensionsstabila anoden” (DSA), använts för att föreslå en fundamental anledning till att detta material är speciellt klorselektivt. Vi föreslår att klorselektiviteten kan förklaras av en laddningsöverföring från ruteniumkatjoner i materialet till titankatjonerna i anodytan, vilket aktiverar titankatjonerna. Baserat på en bred studie av ett stort antal andra dopämnen föreslår vi dessutom vilka dopämnen som är bäst lämpade för produktion av aktiva och klorselektiva anoder. Med hjälp av experimentella studier föreslår vi dessutom en koppling mellan kloratbildning och oönskad syrgasbildning i kloratprocessen, och vidare har en bred studie av tänkbara elektrolytföroreningar utförts för att öka förståelsen för syrgasbildningen i denna process. Två studier relaterade till elektrokemisk vätgasproduktion har också gjorts. En experimentell studie av Co-dopad DSA har utförts, och detta elektrodmaterial visade sig vara mer aktivt för vätgasutveckling än en standard-DSA. Vidare har en kombination av experimentell och teoretisk röntgenfotoelektronspektroskopi använts för att öka förståelsen för strukturella förändringar som sker i RuO2 och i det ädelmetallfria elektrodmaterialet MoS2 under vätgasutveckling.

QC 20151119

The principal aims of this thesis were to establish whether soluble calcium-phytate complexes inhibit calcium oxalate crystallisation and whether a higher dietary intake of phytate in South African black subjects compared to white subjects may contribute to the relative rarity of urolithiasis in this group. Potentiometric titrations were conducted to determine thermodynamic binding constants of soluble calcium-phytate complexes. Binding constants of seven complexes were identified. These were included in the data base of the Joint Experts Speciation System computer program to model the effect of phytate on the urinary supersaturation of calcium salts. Physiological concentrations of phytate failed to decrease ionized calcium and hence the urinary supersaturation of calcium salts. These theoretical predictions were then tested in an in vitro model. Calcium oxalate crystallisation experiments were conducted in simple salt solutions, artificial urine and real urine of the respective groups. The following parameters were measured: ionized calcium; calcium oxalate metastable limit; calcium oxalate particle volume-size distribution; calcium oxalate crystal nucleation, aggregation and growth kinetics. Deposited crystals were examined by scanning electron microscopy. The results confirmed those of the theoretical modelling. Furthermore, the results demonstrated that the inhibitory capacity of phytate is of a kinetic nature rather than a thermodynamic one. Phytate inhibited calcium oxalate crystal aggregation and the inhibition of calcium oxalate crystal growth was found to be independent of the physiological concentration of phytate. In vivo studies were conducted in which phytate-deficient, phytate-rich diets and a phytate supplement were administered in healthy black and white male volunteers. The baseline intake of phytate was assessed using food frequency questionnaires; urinary phytate was determined using a novel assay; biochemical and physiochemical urinary risk factors were measured. The black group had a significantly higher baseline intake of phytate culminating in a significantly higher urinary phytate excretion. No significant difference in urinary crystallisation kinetics was observed as being due to phytate per se. The findings of this thesis contribute to the pool of knowledge on urolithiasis and provide insight on the relative rarity of this disease in South Africa's black population.

The first part of this thesis deals with some general aspects of hydrogen transfer reactions.  Based on the idea of similarity between localized orbitals of functional groups in different molecules, an attempt is made to reflect this transferability in segments of the correlation energy belonging to the set of orbitals of a certain functional group.  Various possibilities are examined for such partitioning.  It turns out that localized orbitals are the best choice for this purpose since other transformations delocalize orbitals, and transferability is lost. In the second half, the energetics of terminal and central OH-additions as well as allylic H-abstractions by OH in its reaction with  propene was studied using several single and multireference ab initio techniques. Selection of the localized occupied orbitals forming the active space for multireference methods is discussed.  Initial geometries optimizations and vibrational frequency analysis were carried out at the [5,5]-CASPT2/cc-pVTZ level of theory.  Multireference effects turned out to be negligible and the UCCSD(T)/cc-pVTZ model was chosen for final geometry optimizations and vibrational frequency analysis.  Triples contributions are found to be very important, except for the pi-complex, which has a UCCSD(T)/CBS relative enthalpy of -10.56 kJ/mol compared to infinitely separated propene + OH.  The addition transition states are found to have relative enthalpies of -9.93 kJ/mol for the central and -9.84 kJ/mol for the terminal case.  Allylic abstraction mechanisms, although lying significantly higher, still have only slightly positive barriers a value of 3.21 kJ/mol for the direct and 1.67 kJ/mol for the consecutive case.  Conventional transition state theory was used as a rough estimation for determining rate constants and turned out to agree well with experiment.

This thesis compares theoretical models of ultrasound contrast agents to the acoustic response from single Microbubbles(MBs). The acoustic response was compared using a range of driving parameters. A rigid shelled contrast agent and a lipid shelled contrast agent were used in the comparison. While attempts to model the behaviour of some contrast agents at low mechanical index (MI) have been successful at higher MI the behaviour of MBs is still not well understood. Understanding and predicting the response ofMBs to medical ultrasound can lead to improvements in the clinical use of MBs through improved contrast agent design or improved signal processing. Numerical models were developed to compare to three specific cases; 1) Rigid shelled contrast agents 2) Lipid shelled contrast agents 3) Responses from lipid shelled contrast agents that are hit by subsequent driving pulses. Three models were used to compare to the responses from single rigid shelled contrast agents. Two of these models have been used before and the third was developed based on the optical observations of the responses of these rigid shelled agents at these MI. Two shelled models were used to compare to the response of single lipid shelled MBs. Using statistical methods the parameters defining the shell properties were found. The parameters that gave best agreement with the lipid shelled data was then used with a model to account for the molecular diffusion of gas from a MB and a new model to account for the optically observed shedding of the shell from a MB to compare to the multiple response from single MBs. While the theoretical prediction of an acoustic response of a suspension of MBs or the radial oscillation of single MBs has been compared before to experimental data, the successful comparison of the acoustic response of single MBs to the theoretical prediction is the first of it’s kind known to the author. The new theoretical model of the rigid shelled MB that was developed in this thesis gave better agreement with the experimental data than the other previously used models. The shell parameters of the lipid shelled MB were determined for the lowest driving amplitude and were in agreement with those measured previously from optical observations. Finally, the model for the shedding of the shell was shown to give quantitative agreement with the multiple acoustic responses from single MBs. When shedding of the shell was included the choice of constitutive equation for the shell was shown to strongly affect subsequent responses from the MB.

Replacement of the traditional coil spring with one of more fibre-reinforced plastic sulcated springs is a future possibility. Spring designers of metallic coil springs have design formulae readily available, and software packages specific to coil spring design exist. However, the sulcated spring is at the prototype stage of development, so literature on these springs is very sparse. The thesis contains information on the market for sulcated springs, and their advantages and disadvantages. Literature on other types of fibre reinforced plastic springs has also been reviewed. Design software has been developed for the sulcated spring along similar lines to coil spring design software. In order to develop the software, a theoretical model had to be developed which formed the mathematical basis for the software. The theoretical model is based on a choice of four methods for calculating the flexural rigidity; beam theory, plate theory, and lamination theory assuming isotropic and orthoropic material properties. Experimental results for strain and spring stiffness have been compared with the theoretical model, and were in good agreement. Included in the design software are the results of experimental work on fatigue, and design limiting factors to prevent or warn against impractical designs. Finite element analysis has been used to verify the theoretical model developed, and to find the better approximation to the experimental results. Applications and types of assemblies for the sulcated spring were discussed. Sulcated spring designs for the automotive applications of a suspension, clutch and engine valve spring were found using the design computer software. These sulcated spring designs were within or close to the space of the existing coil spring and yield the same performance. Finally the commercial feasibility of manufacturing the sulcated spring was assessed and compared with the coil spring, to evlauate the plausibility of the sulcated spring replacing the coil spring eventually.

Thesis (S.M.)--Massachusetts Institute of Technology, Dept. of Civil and Environmental Engineering, February 2010.
Cataloged from PDF version of thesis.
Includes bibliographical references (p. 161-163).
Many wave energy devices are currently studied. In this thesis we focus on two specific devices: the Oscillating Water Column (OWC), and the buoys. In the first part of this thesis we examine the effects of coastline geometry on the performance of an OWC. Under the assumption of inviscid irrotationnal flow, we develop a linear theory for the velocity potential for the case of a coastline of arbitrary apex angle. Scattering and radiation problems are solved separately using eigenfunctions expansions, and are then combined to study the energy extraction rate. Numerical simulations for a convex and a concave corner are considered and comparison with an OWC at the tip of a thin breakwater and on a straight coast are discussed. Assuming that the multiple-turbine system can be controlled over a wide range of frequencies, we study the effects of fixed chamber size and air compressibility on the optimal power extraction. A simpler way of optimization is then develop and we show that this simpler scheme can achieve almost as high an efficiency as the idealized many-frequency optimization. In the second part of this thesis, we first model theoretically an array of cylinders and then apply the theory developped to an array of buoys. However, numerical difficulties encountered for the array of cylinders have led to the conclusion that the theory developed is numerically inefficient, although it is accurate.
by Stéphanie Lovas.
S.M.

This thesis deals with the applications of graph theory towards the electrical distribution networks that transmit electricity from the generators that produce it and the consumers that use it. Specifically, we establish the substation and bus network as graph theoretical models for this major piece of electrical infrastructure. We also generate substation and bus networks for a wide range of existing data from both synthetic and real grids and show several properties of these graphs, such as density, degeneracy, and planarity. We also motivate future research into the definition of a graph family containing bus and substation networks and the classification of that family as having polynomial expansion.

Elastomer seals are widely used in the petroleum industry. Seal failure can be very expensive, due to losses in production and high maintenance costs. Another aspect of this problem is the difficulty in predicting the working life, of a specific elastomeric seal in a specific application, at the design stage. The objective of the present work is to develop the theoretical and computational seal life model to assist reliable prediction of seal life. Seal life computer software has been developed to model fluid ingress into elastomeric seals and the resulting long term material property changes caused by volume swell and chemical reaction between elastomer and ingressed fluid. The approach used is to model diffusion using a finite element method. This permits application to a wide range of seal geometries. The mathematical model of diffusion is coupled with chemical reaction equations of second order to model chemical ageing processes in the seal. To model the effects of swell, volume of absorbed fluid is coupled with Young's modulus. Physical, as opposed to chemical, stress relaxation is not incorporated since the short time scale of this enable direct measurements to be made. The software has been tested against experimental data for a number of elastomer / operating condition combinations. Satisfactory agreement is obtained for ethylene propylene diene (EPDM) and nitrile rubber aged in air or high pressure water; nitrile and hydrogenated nitrile rubber (HNBR) aged in high temperature, high pressure hydrocarbon liquid. The software has also been found useful for calculating required soak time in planning rig tests for the study of explosive decompression caused by absorbed gas in elastomers. Pending further development of the software, long term prediction of retained sealing force of O-rings in high temperature, high pressure water is calculated from compression set by a semi-empirical approach. Results are compared with experimental data.

The prevention of hot gas ingress between rotating and stationary discs in gas turbines is big business, with experimental and computational research being common in the sector. Experimental rigs, operating at a fraction of the engine size and in simulated fluid dynamic conditions, model the engine environment. Computational Fluid Dynamics (CFD) is used in both academia and industry to model the flow and heat transfer in a turbine. CFD is expensive, time consuming and requires detailed experimental validation. The engine designer has a need for simpler, faster mathematical modelling methods, ultimately to be used in 1D design codes. The research in this thesis stems from this need for the industrial engine designers to be able to predict the flow, pressure and temperatures in the secondary-air-system. Momentum-integral equations are known to model flow over rotating and stationary discs in isolation. This thesis shows that the momentum-integral equations can be solved together, to successfully model the flow inside a rotor and stator cavity. New momentum-integral equations are derived, free of the incorrect assumption that swirl ratio inside a rotor-stator cavity does not vary with radius. Two cavity models are described based upon the momentum-integral equations: one for a closed cavity and one for a cavity with sealing flow and no ingress. Both are computationally fast and are shown to give good agreement with experimental measurements and CFD results. Detailed flow structures are given for a range of rotor-stator cavity cases and the results of the models allow conclusions about the flow structure to be drawn. It is found that the outer region, where flow leaves the rotor and is entrained by the stator, is not affected by sealing flow. As well as complete cavity models, two other models for specific rotor-stator phenomenon have been derived. The effect of ingress on the swirl ratio in the cavity has been modelled, using a momentum balance approach. The buffer ratio and buffering effect, which quantify how the rotor is protected from ingress, have been defined, modelled and validated against measurements of adiabatic effectiveness for four different seal geometries. The model has allowed the calculation of Φ′min,r, the sealing flow rate where the effectiveness on the rotor reaches 95%.

The MAPK pathway plays a crucial role in regulating cellular response to external stimuli. Binding of growth factors and other mitogenic signals to cell surface receptors initiates a phosphorylation-dependent relay of protein activation, resulting in altered transcription, ultimately regulating cell proliferation and differentiation. Signalling through this pathway is regulated by the coordinated function of specific protein kinases and protein phosphatases. As perturbation of this signalling system is often associated with diseases such as cancer, modelling is a useful means to help understand the outcomes that may result following changes in component levels or activity. The determination of absolute quantification data, in copies per cell, for proteins of the MAPK pathway will allow the expansion of and improved accuracy within predictive models. The strategy used within this thesis is based on the established technique of stable isotope dilution, generating isotopically labelled peptides using the QconCAT methodology. Recombinant DNA techniques were used to generate artificial concatamers of large numbers of tryptic peptides as quantification standards. A QconCAT, LM1, of 49 KDa (29 tryptic peptides), corresponding to the scaffold proteins was designed and built to encode two peptides per protein. A second QconCAT, LM2, of 58 KDa (34 tryptic peptides), encoded peptides from the dual-specificity phosphatases (DUSPs) and substrates. Quantification was performed using ultra performance liquid chromatography coupled to mass spectrometry. A selected reaction monitoring (SRM) approach was employed where the most intense y-ions per peptide were selected either from experimental data or predictions in silico. Using the ratio of the signal for the light:heavy isotopologues, the amount of light isotopologue can be inferred, allowing copies per cell quantifications to be established. Native peptides were present below the lower limit of quantification, and therefore the upper bounds of copies per cell were obtained for the three cell lines; colon cancer cells HCT 116 (K-Ras mutant) and HT-29 (B-Raf mutant) and a control cell line of HEK-293. Finally, mathematical modelling was undertaken to explore the mass-action kinetics of a three component scaffold signalling molecule. It was found that the optimal scaffold concentration is between the lowest and second lowest concentration of signalling protein.

This thesis aims to provide a basic theoretical explanation for the oscillatory motions observed in solar quiescent prominences. The prominence is treated as a simple plasma slab embedded in a hotter and rarer uniform coronal plasma. Both the slab and its environment are permeated by a uniform magnetic field. The field lines are anchored at rigid walls placed on either side of the plasma slab and representing the photospheric line-tying effect. The magnetohydrodynamic modes of oscillation of the plasma slab are then examined for different orientations of the magnetic field with respect to the long axis of the slab. Particularly interesting in this study is the appearance of the 'string MHD' modes that are analogous to the fundamental vibrations of a mass- loaded stretched elastic string. Such modes appear whenever the magnetic field vector is inclined to the long axis of the slab, thus producing a magnetic field component in the direction transverse to the axis of the slab. Observationally, this inclination of the field is generally small. For realistic values of the angle of inclination of the magnetic field lines, the 'string Alfven' mode and an 'internal slow' mode yield periods in the range 1/2-2 hr. These modes may correspond to the observed long period (40-90 minutes) oscillations in quiescent prominences. Intermediate periodicities, in the range 8-20 min, may be associated with an 'internal Alfven' mode and a 'fast string' mode of the prominence slab. The observed short periodicities, in the range 2-5 min, may correspond to an 'internal fast' mode in prominences. Having thus established a foundation for the theoretical modelling of prominence oscillations in terms of the magnetohydrodynamic modes of oscillation of a non-gravitating plasma slab, we discuss several factors, such as the effects of gravitational stratification, the curvature of the magnetic field lines, and the fine-structures in a prominence, that may complicate a description of its oscillatory modes. Some preliminary investigations of simple magnetohydrostatic equilibrium models suggest that gravity and the curvature of the magnetic field lines play only a secondary role in determining the periods of the oscillatory modes in prominences, the basic structure of the modes being similar to that present in simple slab models.

This thesis presents four research papers. In the first three papers we have derived analytical results for the transport properties in unconventional superconductors and ferromagnetic systems with multiple broken symmetries. In Paper I and parts of Paper II we have studied tunneling transport between two non-unitary ferromagnetic spin-triplet superconductors, and found a novel interplay between ferromagnetism and superconductivity manifested in the Josephson effect as a spin- and charge-current in the absence of an applied voltage across the junction. The critical amplitudes of these currents can be adjusted by the relative magnetization direction on each side of the junction. Furthermore, in Paper II, we have found a way of controlling a spin-current between two ferromagnets with spin-orbit coupling. Paper III considers a junction consisting of a ferromagnet and a non-unitary ferromagnetic superconductor, and we show that the conductance spectra contains detailed information about the superconducting gaps and pairing symmetry of the Cooper-pairs.

In the last paper we present a Monte Carlo study of an effective Hamiltonian describing orbital currents in the CuO2 layers of high-temperature superconductive cuprates. The model features two intrinsically anisotropic Ising models, coupled through an anisotropic next-nearest neighbor interaction, and an Ashkin–Teller nearest neighbor fourth order coupling. We have studied the specific heat anomaly, as well as the anomaly in the staggered magnetization associated with the orbital currents and its susceptibility. We have found that in a limited parameter regime, the specific heat anomaly is substantially suppressed, while the susceptibility has a non-analytical peak across the order-disorder transition. The model is therefore a candidate for describing the breakup of hidden order when crossing the pseudo-gap line on the under-doped side in the phase diagram of high-temperature superconductors.

Different theoretical approaches have been presented in this thesis to study the Raman scattering effect. The first one is response theory applied up to third order of polarization, where the determination of α, β and γ is used to calculate linear Raman scattering (resonance Raman scattering (RRS) and normal Raman scattering (NRS)), hyper Raman scattering (HRS) and coherent anti-Stokes Raman scattering (CARS), respectively. The response theory refers to adiabatic time-dependent density functional theory in the complex domain with applications on RRS and NRS, and to a recently developed methodology (Thorvaldsen et al. [105, 106]) for the analytic calculation of frequency-dependentpolarizability gradients of arbitrary order, here with applications on CARSand HRS. Various systems have been studied with the response theory, such as explosive substances (DNT, TNT, RDX and H2O2), optical power limiting materials (platinum(II) acetylide molecules), DNA bases (methylguanine-methylcytosine) and other systems (Trans-1,3,5-hexatriene and Pyridine). We have explored the dependency of the calculated spectra on parametrization in terms of exchange-correlation functionals and basis sets, and on geometrica loptimization. The second approach refers to time-dependent wave packet methodology for RRS and its time-independent counterpart in the Kramers-Heisenberg equation for the scattering cross section, which reduces the calculation of the RRS amplitude to computation of matrix elements of transition dipole moments between vibrational wave functions. The time-dependent theory has been used to examine RRS as a dynamical process where particular attention is paid to the notion of fast scattering in which the choice of photon frequency controls the scattering time and the nuclear dynamics. It is shown that a detuning from resonance causes a depletion of the RRS spectrum from overtones and combination bands, a situation which is verified in experimental spectra. The cross section of NRS has been predicted for the studied molecules to be in the order of 10−30 cm2/sr. A further increase in sensitivity with a signal enhancement up to 104 to 105 is predicted for the RRS technique, while CARS conditions imply an overall increase of the intensity by several orders of magnitude over NRS. In contrast to RRS and CARS, the HRS intensity is predicted to be considerably weaker than NRS, by about four orders of magnitude. However, silent modes in NRS can be detected by HRS which in turncan provide essential spectroscopic information and become complementary to NRS scattering. With the above mention methodological development for NRS, RRS, CARS and HRS, we have at our disposal a powerful set of modelling tools for the four different Raman techniques. They have complementary merits and limitations which facilitate the use of these spectroscopes in applications of Raman scattering for practical applications, for instance stand-off detection of foreign substances.
QC 20110112

A general method of analysis of a variety of stochastic processes in terms of probability density functions (PDFs) is developed and applied to several model as well as physically realistic systems. A model for diffusion in a bistable potential is the first system considered. The time dependence of the PDF for this system is described by a Fokker-Planck equation with non-linear coefficients. A numerical procedure is developed for finding the solution of this class of Fokker-Planck equations. The solution of the Fokker-Planck equation is obtained in terms of an eigenfunction expansion. The numerical procedure provides an efficient method of determining the eigenfunctions and eigenvalues of Fokker-Planck operators. The methods developed in the study of the model system are then applied to the trans-gauche isomerization of n-butane in CC1₄. This system is studied with the use of Kramers equation to describe the time evolution of the PDF. It is found that at room temperature the isomerization rate obeys a first order rate law. The rate constant for this system is sensitive to the collision frequency between the the n-butane and CC1₄ as has been previously suggested. It is also found that transition state theory underestimates the rate constant at all collision frequencies. However, the activation energy given by transition state theory is consistent with the activation energy obtained in this work. The problem of the escape of light constituents from planetary atmospheres is also considered. Here, the primary objective is to construct a collisional kinetic theory of planetary exospheres based on a rigorous solution of the Boltzmann equation. It is shown that this problem has many physical and mathematical similarities with the problems previously considered. The temperature and density profiles of light gases in the exosphere as well as their escape fluxes are calculated. In the present work, only a thermal escape mechanism was considered, although it is shown how non-thermal escape mechanisms may be included. In addition, these results are compared with various Monte-Carlo calculations of escape fluxes.
Science, Faculty of
Chemistry, Department of
Graduate

This thesis involves the computational study of uranium, neptunium, plutonium, and americium complexes in aqueous and non-aqueous solution. It seeks answers to specific experimental questions, to provide additional information to experiments, and to make predictions that experimentalists can use to design or abstain from new experiments. The work mainly uses density functional theory, as this method shows good scaling with system size. This is important because actinides have a large number of electrons, and the ligands in this work are often very large. The family of compounds with the formula U02(H2O) (OH)m 2 ,7 ( +w=5) are studied, to investigate how the changing equatorial ligand field affects the uranyl ion as hydroxide ligands replace water ligands. The investigation involves uranyl stretching vibrations, orbital analysis, charge analysis, and bond orders. I evaluate how solvent models affect the geometry and uranyl stretching vibrations. The cis and trans isomers of the U02Cl2(Cy3PNH)2 and U02Cl2(Cy3PO)2 (Cy = cyclohexyl) exist in equilibrium, even though one expects the bulky phosphinimine and phosphine oxide ligands to show large repulsion in a cis configuration. It is unknown experimentally whether the trans or the cis isomer is the major species. N-donor ligands displace O-donor ligands, when added to solution of U02Cl2(Cy3PO)2, i.e. the N-donor ligands form stronger bonds to uranium than the O-donor ligands. I investigate which isomer is the major species, and explain why the cis isomer exists at all. The origin of the stronger N-donor ligand bonds is studied by orbital analysis, energy decomposition, and electron densities. This study is extended to include all halide ligands, and uranium is substituted by neptunium, plutonium, and americium. I use the concepts of electron localisation and electron density differences on the systems above, to further study the actinyl axial and equatorial bonding in greater detail. I compare this analysis with the results from more traditional methods, e.g. charge analysis. I also investigate if it is possible to form stable c/s-uranyl compounds and neptunyl complexes with cation-cation interactions.

In recent years, magnetic separation has attracted considerable attention as a technique for the separation of paramagnetic particles from the media carrying them. Equipment may be at least approximately specified by theoretical formulae, or by analysis of the results of laboratory experiments. In general, and neglecting experimental errors, the two methods of predicting separator performance will not agree due to the physical approximations which are necessary to achieve analytical solutions of the resulting equations.

This Thesis describes some theoretical studies on ligated and bare clusters. Chapter 1 gives a review of the two theoretical models, Tensor Surface Harmonic Theory (TSH) and Jellium Model, accounting for the electronic structures of ligated and bare clusters. The Polyhedral Skeletal Electron Pair Theory (PSEPT), which correlates the structures and electron counts (total number of valence electrons) of main group and transition metal ligated clusters, is briefly described. A structural jellium model is developed in Chapter 2 which accounts for the electronic structures of clusters using a crystal-field perturbation. The zero-order potential we derive is of central-field form, depends on the geometry of the cluster, and has a well-defined relationship to the full nuclear-electron potential. Qualitative arguments suggest that this potential produces different energy level orderings for clusters with a nucleus with large positive charge at the centre of the cluster, enabling the spherical jellium model to be applied to alkali metal clusters seeded with magnesium and zinc. Analysis of the effects of the non-spherical perturbation on the spherical jellium shell structures leads to the conclusion that for a cluster with a closed shell electronic structure a high symmetry arrangement which is approximately or precisely close packed will be preferred. It also provides a basis for rationalising those structures, which have been predicted using ab initio calculations, of clusters with incomplete shell electronic configurations In Chapter 3, the geometric conclusions derived in the structural jellium model are developed in more detail. Alkali metal clusters with closed shell electronic configurations according to the jellium model adopt geometries of high symmetry and based on the T_d , O_h and I_h point groups. For high nuclearity clusters alternative high symmetry structures can occur and those which are either the most close packed or spherical are predicted to be the most stable. When the jellium closed shell "magic numbers" coincides with one of these high symmetry structures then the cluster will be particularly stable. The group theoretical consequences of the Tensor Surface Harmonic Theory are developed in Chapter 4 for[ML₂]_n, [ML₄]_n and [ML₅]_n clusters where either the xz and yz or x²-y² and xy components to L^π_d and L^δ_d do not contribute equally to the bonding. The closed shell requirements for such clusters are defined and the orbital symmetry constraints pertaining to the interconversion of conformers of these clusters are described. In Chapter 5 Stone's Tensor Surface Harmonic methodology is applied to high nuclearity transition metal carbonyl cluster compounds with 13-44 metal atoms. Two limiting bonding situations are identified and represented in terms of general electron counting rules. If the radial bonding effects predominate the clusters are characterised by 12n_s+Δ_i valence electrons, where Δ_i is the characteristic electron count of the interstitial moiety. If radial and tangential bonding effects are important then the total number of valence electrons is 12n_s+2(s_s+s_i-l), where s_s and s_i are the number of skeletal bonding molecular orbitals associated with surface (s_s) and interstitial (s_i) moieties. Chapter 6 develops a new theoretical framework to account for the bonding in the high nuclearity ligated clusters with columnar topologies. The wave functions of columnar metal clusters can be expressed as an expansion based on the particle on the cylinder problem. This bonding analysis is applied to clusters containing columns of triangles and squares. In Chapter 7 the origin of non-bonding orbitals in molecular compounds is reviewed and analysed using general quantum mechanical considerations. A combination of the pairing theorem and a group theoretical analysis leads to a definition of the number of the non-bonding molecular orbitals in co-ordination, polyene and cluster compounds. The non-bonding molecular orbitals have been generated by defining the nodal characteristics of the relevant orbitals and evaluating the solutions under the appropriate boundary conditions. The stereochemical role of nonbonding molecular orbitals in co-ordination compounds is also discussed.

Optical metamaterials are artificial media that exhibit new properties from structuring on the nanometric scale. One of the main researches in metamaterials investigates materials with negative refractive index, which can allow the development of perfect lens and other exciting potential applications. In this thesis, we theoretically study the properties of negative-index optical fishnet metamaterials, especially the origin of their negative-valued refractive index, and also associated theoretical problems. The thesis can be divided into 4 parts. In the first part we study the light scattering at an interface between air and a semi-infinite fishnet metamaterial. With a fully-vectorial numerical method, we calculate the scattering coefficients of the interface and find that the energy transport inside the fishnet is due to a single Bloch mode, the fundamental one. Based on the single-interface scattering coefficients and the effective index of this Bloch mode we propose a new algorithm for retrieving effective optical parameters of the metamaterial. The approach emphasizes the key role played by the fundamental Bloch mode and provides retrieved parameters that are more accurate or stable than those obtained by classical methods based only on light reflection and transmission through finite-thickness metamaterial slabs. Due to the importance of the fundamental Bloch mode in the light transport in metamaterials, in the second part, based on the Bloch mode orthogonality we derive closed-form expressions for the scattering coefficients at an interface between two periodic media with slightly different geometrical parameters, which is a computationally demanding electromagnetic problem. We show that the analytical expressions are very accurate for various geometries, including dielectric waveguides and metallic metamaterials. Thus they can be useful for designing and engineering stacks of periodic structures. As shown in the first part, the fundamental Bloch mode is central to explain the negative refraction phenomenon in fishnet metamaterials. In the third part, we derive an accurate semi-analytical model for the complex propagation constant of the fishnet fundamental Bloch mode. This is achieved by analyzing light propagation and scattering inside the fishnet. The model shows that the origin of broad-band negative index of fishnets can be mainly understood as a plasmon resonance in the transversal metal-insulator-metal (MIM) channels. The plasmon resonance enhances the 'magnetic' response of fishnet and the losses associated to this resonance can be compensated by including gain in the dielectric layers of the fishnet. Furthermore, the model allows an easy and precise geometrical tailoring of fishnet metamaterials. As shown in the third part, it is the plasmon resonance in metal-insulator-metal (MIM) structures that induces the negative index of fishnet metamaterials. In the last part, we study the asymptotic behavior of 3D MIM nanoresonators, as the resonator size is shrunk below the diffraction limit. In particular we show that the quality factor increases from 10 to 100 when the resonator volume is scaled down from (λ/2n)3 to (λ/50)3. We provide a comprehensive study with a semi-analytical Fabry-Perot model. The model remains accurate over the whole size scale even in the quasi-static regime for which retardation effects are not expected. This important and counterintuitive result indicates that both localized plasmon resonances in nanoparticles and delocalized resonance in elongated plasmonic nanowires can be possibly understood as a wave-retardation based antenna problem.

The glyoxalase enzyme system catalyses the conversion of methylglyoxal to D-lactic acid. The first of the two component enzymes, glyoxalase I, is responsible for the transfer of two protons in an iscmerisation reaction. This enzyme has been ascribed a role in tumorigenesis in the past and some of its inhibitors are known to be carcinostatic. This thesis describes quantum chemical calculations on the enzyme mechanism and on some enzyme inhibitors. The calculations on the mechanism of the enzyme take the form of studies of model reaction schemes, with minimal and split-valence basis sets. The calculation of the energies of various intermediates has led to the evaluation of different pathways as models of the enzyme mechanism. The comparison of different substituted compounds has led to further conclusions on the part played by the sulphur atom in the enzyme-catalysed reaction. Two main groups of inhibitor molecules are discussed; these are flavone and coumarin derivatives. The molecular electrostatic potential of these molecules has been calculated on various surfaces, using a minimal basis set, to attempt to correlate this property with the compounds' inhibitory power. A FORTRAN program is presented which depicts calculated properties on the surfaces. This program allowed the identification of various regions which seemed to be indicative of the inhibitory strength of the compounds.

Dans le contexte de transition énergétique mondial actuel, lathermoélectricité peut prendre une part importante parmi lesnouvelles sources d’énergie en tant que technologie applicable àde multiples échelles et à de nombreux domaines, de l’habitat àl’automobile, de la climatisation à la production d’électricité. Afinde développer l’utilisation de la thermoélectricité, il est nécessairede mieux comprendre les interactions chimiques qui régissentces matériaux et d’identifier de nouveaux matériaux à fortspotentiels applicatifs. Ainsi, la modélisation atomique peut aider àcomprendre les propriétés structurales, physico-chimiques et detransport de ces matériaux et suggérer de nouvelles pistes demodifications ou de nouvelles synthèses pour identifier lesmatériaux de demain. Ce travail de thèse s’inscrit dans ce cadre. Le premier chapitre de ce manuscrit porte sur la description desméthodes de chimie quantique utilisées dans cette étude. Lesecond chapitre rappelle les fondements de thermoélectricitéainsi que les principales familles de matériaux étudiées. Letroisième chapitre est dédié à l’analyse topologique de la densitéélectronique des composés de formule TM3 avec T = métal detransition des groupes 7 à 9 et M = Ga, In, afin de mieuxcomprendre d’une part, la liaison chimique dans ces matériaux,et d’autre part, les propriétés semi-conductrices de certainsd’entre eux, présentant des propriétés thermoélectriques. Lechapitre suivant est dédié à l’étude des propriétés structurales etde transport de composés hypothétiques de formule TM3 où Test un métal de transition du groupe 6. Nos calculs suggèrent unpotentiel thermoélectrique exceptionnel pour le composé WGa3en particulier. Les deux derniers chapitres sont dédiés à l’étude de composésclusters de molybdène. Dans un premier temps, les propriétés detransport des composés AgxMo9Se11 (3,4 ≤ x ≤ 3,9),Ag2Tl2Mo9Se11, et Ag3In2Mo9Se11, dont la structurecristallographique est basée sur le cluster bioctaédrique Mo9,sont étudiées dans le cadre d’une approche semi-classique. L’accent est porté sur l’étude de l’influence de la structure et desparamètres de calcul. Dans la dernière partie, nous mettons àprofit les résultats obtenus dans la partie précédente pour prédireles propriétés de transport de composés à clusters demolybdène
In the context of worldwide energetic transition, thermoelectricitycan significantly play a part among the new sources of renewableenergy that can be used at different scales and applied to severaldomains, from houses to cars, from air-conditioning to electricityproduction. In order to develop the use of thermoelectricity, thereis a need to better understand the chemical interactions thatgovern these materials and identify new thermoelectric materials. Hence, atomic modeling can help in understanding the structuraland physical properties of these materials as well as theirtransport properties, and suggest new candidates with interestingproperties. With this aim, this thesis work is based on the use ofquantum chemical tools. The first chapter of this manuscript deals with the quantumchemistry methods used. The second chapter reminds somebasics of thermoelectricity and the main class of thermoelectricmaterials. The third chapter focuses on the topological analysis ofthe electronic density of compounds with general formula TM3with T = transition metal of Group-7 to 9 and M = Ga, In, in orderto better understand on one hand the chemical bonding in thethese materials, and on the other hand the semi-conductingproperties of some of them that exhibit thermoelectric properties. The next chapter deals with the structural and transportproperties of some hypothetical materials of general formula TM3,(T = group-6 transition metal, M = Ga, In). Our calculationssuggest an exceptional thermoelectric potential for WGa3. The last two chapters are devoted to molybdenum cluster-basedcompounds. The penultimate part tackles the modeling of thetransport properties of AgxMo9Se11 (3. 4 ≤ x ≤ 3. 9), Ag2Tl2Mo9Se11and Ag3In2Mo9Se11 that contain bi-octahedral Mo9 clusters. Aspecial attention has been paid to the influence of the structuraland computational details. In the last part, we used the resultsobtained for Mo9-based selenides to predict the transportproperties of few molybdenum cluster compounds

La thèse est consacrée à l'étude des membranes sous contrainte en mettant l'accent sur les structures biologiques telles que les tissus en croissance et la membrane cellulaire. Elle combine des approches analytiques et numériques pour étudier le lien entre la géométrie et la mécanique. Elle contient également quelques résultats expérimentaux mais ce ne sont que peu nombreux et à petite échelle. Après un chapitre d'introduction, nous explorons trois modèles physiques abordés dans trois chapitres différents. Dans le premier modèle, les déformations des tissus mous lors de la croissance sont traitées comme des singularités ponctuelles gaussiennes dans les surfaces bidimensionnelles. Les formes d'équilibre sont calculées pour deux défauts qui forment un dipôle. Les prédictions du modèle sont par ailleurs comparées aux résultats des expériences. Le chapitre suivant étudie les invaginations des membranes fluides auto-évitantes dans des espaces confinés. À cette fin, nous avons développé un code basé sur la méthode des éléments finis et effectué des simulations afin de construire un diagramme de phase (volume/surface) pour des membranes piégées à l'intérieur d'une sphère. Nous analysons également les effets de la courbure spontanée de la membrane et les déformations de la paroi extérieure sur la forme de l'invagination. Enfin, dans le quatrième chapitre de la thèse, en vue de modéliser des tiges biologiques, nous construisons une membrane tubulaire à partir d'éléments caractérisés par deux états géométriques. Cette approche nous a permis d'examiner, par le biais des simulations du type dynamique brownienne, comment la forme globale émerge des interactions locales
The present thesis is devoted to the study of constrained membranes with a focus on biological structures such as growing tissues and the cell membrane. It combines analytical and numerical approaches to investigate the interplay of geometry and mechanics. It also includes some experimental results albeit they are few in number and modest in size. After an introductory chapter, we explore three physical models addressed in three distinct chapters. In the first model, the deformations of growing soft tissues are treated as Gaussian point singularities in two dimensional surfaces. The equilibrium shapes are evaluated for two such defects forming a dipole. The predictions of the theory are also compared to tabletop experiments. The next chapter studies the invaginations of self-avoiding fluid membranes in constrained spaces. To this end, we developed a Finite Element code and performed extensive simulations to construct a geometric phase diagram for a fluid membrane vesicle in a spherical confinement. We also investigate the effects of the membrane's spontaneous curvature and the deformations of the container on the geometry of the invagination. In the fourth chapter of the manuscript, a tubular membrane composed of switchable components is proposed as a model to study conformations of intrinsically curved biological rods. We translated this system to a computational framework based on the Brownian Dynamics method and inquired how global shape emerges from local interactions

En esta tesis se utiliza la aproximación de masa efectiva y función envolvente para estudiar teóricamente las propiedades optoelectrónicas de una gran variedad de nanoestructuras semiconductoras, muchas de las cuales son obtenibles en un laboratorio a día de hoy. El primer capítulo de la tesis se centra en el estudio de los efectos derivados de aplicar campos magnéticos externos sobre varias nanoestructuras formadas por anillos cuánticos: dos anillos acoplados lateralmente y verticalmente, y una red periódica bidimensional de anillos. El segundo capítulo constituye la parte más extensa e importante de la tesis y estudia la influencia del entorno dieléctrico sobre las propiedades optoelectrónicas de nanocristales sintetizados mediante técnicas de química coloidal con forma esférica y alargada. Mediante cálculos multipartícula basados en las metodologías DFT y CI, se estudia el efecto del confinamiento dieléctrico sobre nanocristales poblados con un alto número de electrones o con pares electrón hueco. Finalmente, el último capítulo de la tesis se centra en el estudio de los estados multipartícula y las transiciones de fase a lo largo de un proceso en el que un nanocristal esférico es alargado hasta formar una estructura casi unidimensional.

The thesis deals with the deformation problem of segmental, cast-in-place concrete cantilever bridges. This type of bridge has shown some propensity to develop larger deflections than those were predicted in the design calculation. Excessive deflections may lead to deterioration of aesthetics, serviceability problems and eventually early reconstruction of the bridge. Also in the construction stages the deflections have to be properly compensated to achieve the smooth camber in the completed bridge deck.

Deformation prediction in concrete cantilever bridges is not as reliable as it would be necessary due to several factors. The high degree of uncertainty in creep and shrinkage prediction in concrete constitutes the major difficulty. Other factors are the complex segmental construction procedure and the sensitivity of the deformations to variations in the construction schedule, the uncertainty in estimating the frictional loss of prestress and relaxation in the prestressing tendons and uncertainty in estimating model parameters such as temperature and relative humidity.

The doctoral study was initiated with the objective to improve deformation prediction in segmentally cast concrete cantilever bridges and to establish guidelines for deformation analysis based on advanced numerical methods.

A database on observed deformations in three modern long span concrete cantilever bridges in Norway has been established. Two of the bridges were partly constructed from lightweight aggregate concrete. The deformations have been monitored since the construction stages up to the present time. The measurements cover the construction stages and the service life of 14, 8 and 3 years, respectively for the three bridges. The measured deformations are deflections in the superstructure and in one of the bridges, also strain measurements in the piers and the superstructure.

A sophisticated numerical model was created for deformation analysis. The numerical model realistically simulates the segmental construction procedure and the entire life span of the bridge. The effects of the segmental construction method, temporarily supports and constraints and changes in the structure system during construction are taken into account. The model considers the different concrete age from segment to segment, the sequential application of permanent loads and prestressing and the effect of temporary loads. The prestressing tendons are individually modelled with their true profile taking into account the variation of the effective prestressing force along the length of the tendon and with time.

The finite element model consists of beam elements which are based on an advanced beam element formulation. The beam model was verified against a robust two-and-a-half dimensional shell model concerning its general performance and some specific issues. The comparison confirmed the accuracy of the beam model. Existing experimental data on creep and shrinkage in lightweight aggregate concrete and high strength concrete were evaluated in comparison with theoretical models. The main focus was on the CEB-FIP Model Code 1990 and its subsequent extensions. The findings were considered in the numerical studies.

Deformations of the three bridges were computed. The CEB-FIP Model Code 1990 material model was used for concrete for the most part. The elastic moduli were taken from test results where they were available. The creep coefficient and the shrinkage strain of the lightweight aggregate concrete were assumed equal to those of normal density concrete of the same strength. The agreement between the calculated and the measured deformations were satisfactory in view of the large uncertainty involved in theoretical prediction. While moderate differences were observed in most cases, no clear overall tendency toward underor overestimation was found. In subsequent numerical studies, the sensitivity of the deformations to variations in various model parameters was investigated. The B3 model was compared to the CEB-FIP Model Code 1990 in the analysis of one of the bridges, where the latter model showed somewhat better agreement with the measurements.

The last part of the work concerned a robust probabilistic analysis which was based on a Monte Carlo simulation. The objective of the probabilistic analysis was to estimate the statistical properties of the deformation responses. With the distribution function of a given deformation response being known, the confidence limit for the deformation can be determined. It is recommended to design the bridge for the long-time deflection which represents a certain confidence limit (e.g. the 95 % confidence limit) of the response rather than its mean. Such way the risk that the bridge will suffer intolerable deflection over its life span can be minimised.