The broad absorption spectrum of Protoporphyrin IX (PpIX) allows being activated by a source with an emission spectrum in the visible region. Also, PpIX can be activated simultaneously by two or more sources whose emission spectrum overlaps with its absorption spectrum. Sources with a wide spectrum of illumination, such as lamps and Sun, have a different light-tissue interaction, and the constant monitoring of the dose of light and the total damage caused by photodynamic therapy (PDT) becomes difficult. The main objectives of this study were to simulate the distribution of light in the tissue for a multi-wavelength source and determine the total theoretical photodynamic dose. This study is composed of three parts. First, photobleaching experiments of PpIX using different light sources and the development of a mathematical model was used to explain the change in PpIX concentration. Second, Monte Carlo simulation using MCX (Monte Carlo eXtreme) was performed to know the light distribution through in a human skin model. Finally, the theoretical photodynamic dose was determined using the two steps mentioned previously. The experimental results show that the decrease in the concentration of PpIX is mainly dependent on the dose of photons absorbed. Therefore, for a multi-wavelength source, the total damage is calculated by partial damages caused by each wavelength that active the PpIX. The simulation of the light distribution in the human skin phantom demonstrated that the energy fluence rate decrease as a function of the depth. The mathematical model estimates that the efficacy of PDT, where it is guaranteed there is necrosis, has a diameter and depth of about 0.3 and 0.2 mm respectively. This model can be expanded to other biological media, other photosensitizers and even to any source of illumination. / O amplo espectro de absorção da Protoporfirina IX (PpIX) permite sua ativação por uma fonte com um espectro de emissão amplo na região visível. Além disso, a PpIX pode ser ativada simultaneamente por duas ou mais fontes de luz, cujo espectro de emissão se sobrepõe ao seu espectro de absorção. Fontes com um amplo espectro de emissão, como lâmpadas e Sol, têm uma interação luz-tecido biológico diferente, e o monitoramento constante da dose de luz e o dano total causado pela Terapia Fotodinâmica (TFD) se tornam difíceis. Os principais objetivos deste trabalho foram simular a distribuição de luz no tecido para uma fonte de múltiplos comprimentos de onda e determinar a dose fotodinâmica teórica total. Este trabalho é composto de três partes. Primeiro, experimentos de fotodegradação da PpIX usando diferentes fontes de luz e o desenvolvimento de um modelo matemático foram usados para explicar a mudança na concentração de PpIX. Em segundo lugar, uma simulação de Monte Carlo usando MCX (Monte Carlo eXtreme) foi realizada para obter a distribuição de luz, de múltiplos comprimetos de onda, em um modelo de pele humana. Finalmente, a dose fotodinâmica teórica foi determinada usando as duas etapas mencionadas anteriormente. Os resultados experimentais mostram que a diminuição na concentração de PpIX é principalmente dependente da dose de fótons absorvidos. Portanto, para uma fonte de multi-comprimentos de onda, o dano total é calculado por danos parciais causados por cada comprimento de onda que ativa a PpIX. A simulação da distribuição de luz na pele humana demonstrou que a taxa de fluência de energia diminui em função da profundidade. O modelo matemático estima que a eficácia da TFD, onde é garantida a existência de necrose, tenha diâmetro e profundidade de aproximadamente 0.3 e 0.2 mm respectivamente. Este modelo pode ser expandido para outros meios biológicos, outros fotossensibilizadores e até mesmo para qualquer fonte de iluminação.

Over the past decade vehicle judder caused by Disc Thickness Variation (DTV) has become of major concern to automobile manufacturers worldwide. Judder is usually perceived by the driver as minor to severe vibrations transferred through the chassis during braking [1-9]. In this research, DTV is investigated via the use of a Smart Brake Pad (SBP). The SBP is a tool that will enable engineers to better understand the processes which occur in the harsh and confined environment that exists between the brake pad and disc whilst braking. It is also a tool that will enable engineers to better understand the causes of DTV and stick-slip the initiators of low and high frequency vibration in motor vehicle brakes. Furthermore, the technology can equally be used to solve many other still remaining mysteries in automotive, aerospace, rail or anywhere where two surfaces may come in contact. The SBP consists of sensors embedded into an automotive brake pad enabling it to measure pressure between the brake pad and disc whilst braking. The two sensor technologies investigated were Thick Film (TF) and Fibre Optic (FO) technologies. Each type was tested individually using a Material Testing System (MTS) at room and elevated temperatures. The chosen SBP was then successfully tested in simulated driving conditions. A preliminary mathematical model was developed and tested for the TF sensor and a novel Finite Element Analysis (FEA) model for the FO sensor. A new method called the Total Expected Error (TEE) method was also developed to simplify the sensor specification process to ensure consistent comparisons are made between sensors. Most importantly, our achievement will lead to improved comfort levels for the motorist.

In this thesis, control and guidance algorithms for unmanned sea surface vehicles are studied. To design control algorithms of different complexity, first a mathematical model for an unmanned sea surface vehicle is derived. The dynamical and kinematical equations for a sea surface vehicle are obtained, and they are adapted to real life conditions with necessary additions and simplifications. The forces and torques effecting on the vehicle are investigated in detail. Control algorithms for under-actuated six degrees-of-freedom model are designed. PID and LQR controllers are implemented to attain desired surge speed and yaw position. The autopilots are designed and their performances are compared. Based on the autopilots, a guidance algorithm is implemented to achieve desired motions of the vehicle. An obstacle avoidance algorithm is proposed for safe motion among the obstacles. A next-point generation algorithm is designed to direct the vehicle to the most appropriate next way-point if the one ahead is missed. The effects of disturbances on the motion of the vehicle are studied thoroughly on simulation results. PID controller for an unmanned sea surface vehicle is implemented on ArduPilot Mega v1.4 cart controlling a Traxxas Spartan model boat. The performance of the controller is validated. Simulations and experimental results are provided.

Car exhaust catalysts were introduced in the early 1980’s, to limit the release of pollutants such as hydrocarbons, carbon monoxide and nitrogen oxides. These catalysts contain noble metals such as palladium (Pd), platinum (Pt) and rhodium (Rh) and are able to simultaneously abate all three of the above-mentioned pollutants, hence the name three-way catalyst (TWC). The exposure to high temperatures (800-1000 °C) during operation and the presence of additives in gasoline and lubricants will, after a certain time, lower the activity of the TWC. High temperatures reduce the active area by causing the noble metals to agglomerate and sinter, whereas the additives alter the activity either by fouling the pores of the support material or by interacting with the metals. The main objective of this work was to develop a method which allows for the removal of contaminants (additives) from the washcoat and enables the redispersion of the active sites (noble metals), in an effort to recover lost catalyst activity. For this purpose, regeneration experiments were carried out on a wide spectrum of different commercial car exhaust catalysts. The influence of a thermal treatment in a controlled gas atmosphere, such as oxygen or hydrogen, and a redispersing agent, e.g. chlorine, on the activity of TWC was investigated by means of laboratory-scale activity measurements. Several complementary characterization methods such as SEM/TEM, XRD, BET, LA, XPS and TPR were employed to verify the effects of the regeneration treatments on the catalyst morphology (Papers I, II). The results show that partial regeneration of catalyst activity and noble metal dispersion was achieved after thermal treatment in an oxygen-chlorine rich atmosphere at temperatures below 500 °C. A wet-chemical regeneration treatment with dilute oxalic and citric acid solutions is evaluated in Paper III. These acidic solutions are able to dissolve and remove contaminants from the washcoat, thus partly restoring the catalyst activity. An investigation of the effects of an oxy-chlorine thermal treatment for regeneration of a ‘full-scale’ commercial automotive three-way catalyst was carried out (Paper IV). Improved catalyst activity for a high mileage catalyst could be observed, with emissions lowered by approximately 30 to 40 vol.% over the EC2000 driving cycle. The properties of fresh, aged and regenerated catalysts were then studied by means of labscale experiments, on a local as well as a global level using a mathematical model (Paper V). The model allows for comparison of the intrinsic properties of the active surface by deriving and tuning parameters of a fresh catalyst and verifying the activity of a regenerated or aged catalyst. / QC 20100812

The aim of this thesis work is to increase the knowledge of inclusion behavior at the steel-slag interface by mathematical modeling and in-situ Confocal Scanning Laser Microscope experiments. Mathematical models based on the equation of motion predicting liquid and solid inclusion behavior was first investigated. Four main forces, the buoyancy force, the added mass force, the rebound force and the drag force, act on the inclusion as it crosses the interface. There are three types of behavior an inclusion at the steel-slag interface can adopt. These are a) pass, which means that the inclusion is separated to the slag, b) remain, where the inclusion stays at the interface without being fully transferred to the slag or c) oscillate, and the inclusion rises and descends at the interface until the motion is dampened out by the interfacial forces. The studies showed the importance of accurate experimental physical property data. Application of the models to industrial conditions illustrated that useful plots could be made showing the industry how to optimize their interfacial properties in the ladle and tundish to obtain maximum inclusion separation. In-situ Confocal Scanning Laser Microscope (CSLM) experiments were carried out in order to study agglomeration of liquid and semi liquid inclusions at the steel-gas and steel-slag interfaces and in the slag. Liquid-liquid inclusion agglomeration at steel-gas and steel-slag interfaces was seen to not occur without using force. However, when already transferred to the slag the inclusions agglomerated freely due to a higher free energy force. Comparison of experimental and theoretical agglomeration force showed good agreement between experiments and theory. The main conclusion of this work is that inclusion separation is a complex field of study and there exist no model that takes everything into account. Here the tendency for inclusion transfer and how to manipulate the physical properties for inclusion separation together with agglomeration experiments have been studied. For the future maybe coupling of models for computational fluid dynamics, agglomeration, inclusion separation, dissolution and slag entrainment in addition with experimental physical property data can provide a better overview and understanding. / QC 20100823

Lignin polymers provide natural rigidity to plant cell walls by forming complex molecular networks with polysaccharides such as cellulose and hemicellulose. This evolved strategy equips plants with recalcitrance to biological and chemical degradation. While naturally beneficial, recalcitrance complicates the use of inedible plant materials as feedstocks for biofuel production. Genetically modifying lignin biosynthesis is an effective way to generate varieties of bioenergy crops with reduced recalcitrance, but certain lignin-modified plants display undesirable phenotypes and/or unexplained effects on lignin composition, suggesting that the process and regulation of lignin biosynthesis is not fully understood. Given the intrinsic complexities of metabolic pathways in plants and the technical hurdles in understanding them purely with experimental methods, the objective of this dissertation is to develop novel computational tools combining static, constraint-based, and dynamic, kinetics-based modeling approaches for a systematic analysis of lignin biosynthesis in wild-type and genetically engineered plants. Pathway models are constructed and analyzed, yielding insights that are difficult to obtain with traditional molecular and biochemical approaches and allowing the formulation of new, testable hypotheses with respect to pathway regulation. These model-based insights, once they are verified experimentally, will form a solid foundation for the rational design of genetic modification strategies towards the generation of lignin-modified crops with reduced recalcitrance. More generically, the methods developed in this dissertation are likely to have wide applicability in similar studies of complex, ill-characterized pathways where regulation occurring at the metabolic level is not entirely known.

Type 1 diabetes (T1D) is an auto-immune disease characterized by insulin-deficiency. Insulin is a metabolic hormone that is involved in lowering blood glucose (BG) levels in order to control BG level to a tight range. In T1D this glycemic control is lost, causing chronic hyperglycemia (excess glucose in blood stream). Chronic hyperglycemia damages vital tissues. Therefore, glycemic control must be restored. A common therapy for restoring glycemic control is intensive insulin therapy, where the missing insulin is replaced with regular insulin injections. When dosing this compensatory insulin many factors that affect glucose metabolism must be considered. Linkura is a company that has developed tools for monitoring the most important factors, which are meals and exercise. In the Linkura meal and exercise tools, the nutrition content in meals and the calorie consumption during exercise are estimated. Another tool designed to aid control of BG is the bolus calculator. Bolus calculators use input of BG level, carbohydrate intake, and insulin history to estimate insulin need. The accuracy of these insulin bolus calculations suffer from two problems. First, errors occur when users inaccurately estimate the carbohydrate content in meals. Second, exercise is not included in bolus calculations. To reduce these problems, it was suggested that the Linkura web tools could be utilized in combination with a bolus calculator. For this purpose, a bolus calculator was developed. The bolus calculator was based on existing models that utilize clinical parameters to relate changes in BG levels to meals, insulin, and exercise stimulations. The bolus calculator was evaluated using data collected from Linkura's web tools. The collected data showed some inconsistencies which cannot be explained by any model.  The performance of the bolus calculator in predicting BG levels using general equations to derive the clinical parameters was inadequate. Performance was increased by adopting an update-algorithm where the clinical parameters were updated daily using previous data. Still, better model performance is prefered for use in a bolus calculator.   The results show potential in developing bolus calculator tools combined with the Linkura tools. For such bolus calculator, further evaluation on modeling long-term exercise and additional safety features minimizing risk of hypoglycemia are required.

Proteins carry out an almost innumerable amount of biological processes that are absolutely necessary to life and as a result proteins and their structures are very often the objects of study in research. As such, this thesis will begin with a description of protein function and structure, followed by brief discussions of the two major experimental structure determination methods. Another problem that often arises in molecular modeling is referred to as the Molecular Distance Geometry Problem (MDGP). This problem seeks to find coordinates for the atoms of a protein or molecule when given only a set of pair-wise distances between atoms. To introduce the complexities of the MDGP we begin at its origins in distance geometry and progress to the specific sub-problems and some of the solutions that have been developed. This is all in preparation for a discussion of what is known as the Geometric Build-up (GBU) Solution. This solution has lead to the development of several algorithms and continues to be modified to account for more and different complexities. The culmination of this thesis, then, is a new algorithm, the Revised Updated Geometric Build-up, that is faster than previous GBU’s while maintaining the accuracy of the resulting structure.

Suppliers in competitive electricity markets regularly respond to prices that change hour by hour or even more frequently, but most consumers respond to price changes on a very different time scale, i. e. they observe and respond to changes in price as reflected on their monthly bills. This thesis examines mixed complementarity programming models of equilibrium that can bridge the speed of response gap between suppliers and consumers, yet adhere to the principle of marginal cost pricing of electricity. It develops a computable equilibrium model to estimate the time-of-use (TOU) prices that can be used in retail electricity markets. An optimization model for the supply side of the electricity market, combined with a price-responsive geometric distributed lagged demand function, computes the TOU prices that satisfy the equilibrium conditions. Monthly load duration curves are approximated and discretized in the context of the supplier's optimization model. The models are formulated and solved by the mixed complementarity problem approach. It is intended that the models will be useful (a) in the regular exercise of setting consumer prices (i. e. , TOU prices that reflect the marginal cost of electricity) by a regulatory body (e. g. , Ontario Energy Board) for jurisdictions (e. g. , Ontario) where consumers' prices are regulated, but suppliers offer into a competitive market, (b) for forecasting in markets without price regulation, but where consumers pay a weighted average of wholesale price, (c) in evaluation of the policies regarding time-of-use pricing compared to the single pricing, and (d) in assessment of the welfare changes due to the implementation of TOU prices.

Solid oxide fuel cells (SOFCs) are solid-state ceramic cells, typically operating between 1073 K and 1273 K. Because of high operating temperature, SOFCs are mostly applicable in stationary power generation. Among various configurations in which SOFCs exist, the planar configuration of solid oxide fuel cell (SOFC) has the potential to offer high power density due to shorter current path. Moreover, the planar configuration of SOFC is simple to stack and closely resemble the stacking arrangement of polymer electrolyte membrane (PEM) fuel cells. However, due to high operating temperature, there are problems associated with the development and commercialization of planar SOFCs, such as requirement of high temperature gas seals, internal stresses in cell components, and high material and manufacturing costs. Mathematical modeling is an essential tool for the advancement of SOFC technology. Mathematical models can help in gaining insights on the processes occurring inside the fuel cell, and can also aid in the design and optimization of fuel cells by examining the effect of various operating and design conditions on performance. A multi-component and multi-dimensional mathematical model of SOFCs has been developed in this thesis research. One of the novelties of the present model is its treatment of electrodes. An electrode in the present model is treated as two distinct layers referred to as the backing layer and the reaction zone layer. Reaction zone layers are thin layers in the vicinity of the electrolyte layer where electrochemical reactions occur to produce oxide ions, electrons and water vapor. The other important feature of the present model is its flexibility in fuel choice, which implies not only pure hydrogen but also any reformate composition can be used as a fuel. The modified Stefan-Maxwell equations incorporating Knudsen diffusion are used to model multi-component diffusion in the porous backing and reaction zone layers. The coupled governing equations of species, charge and energy along with the constitutive equations in different layers of the cell are solved for numerical solution using the finite volume method and developed code written in the computer language of C++. In addition, the developed numerical model is validated with various experimental data sets published in the open literature. Moreover, it is verified that the electrode in an SOFC can be treated as two distinct layers referred to as the backing layer and the reaction zone layer. The numerical model not only predicts SOFC performance at different operating and design conditions but also provides insight on the phenomena occurring within the fuel cell. In an anode-supported SOFC, the ohmic overpotential is the single largest contributor to the cell potential loss. Also, the cathode and electrolyte overpotentials are not negligible even though their thicknesses are negligible relative to the anode thickness. Moreover, methane reforming and water-gas shift reactions aid in significantly reducing the anode concentration overpotential in the thick anode of an anode-supported SOFC. A worthwhile comparison of performance between anode-supported and self-supported SOFCs reveals that anode-supported design of SOFCs is the potential design for operating at reduced temperatures. A parametric study has also been carried out to investigate the effect of various key operating and design parameters on the performance of an anode-supported SOFC. Reducing the operating temperature below 1073 K results in a significant drop in the performance of an anode-supported SOFC; hence ionic conductivity of the ion-conducting particles in the reaction zone layers and electrolyte needs to be enhanced to operate anode-supported SOFCs below 1073 K. Further, increasing the anode reaction zone layer beyond certain thickness has no significant effect on the performance of an anode-supported SOFC. Moreover, there is a spatial limitation to the transport of oxide ions in the reaction zone layer, thereby reflecting the influence of reaction zone thickness on cell performance.