High Intensity Focused Ultrasound (HIFU) is a new cancer thermal therapy method which has achieved encouraging results in clinics recently. However, the lack of a temperature monitoring makes it hard to apply widely, safely and efficiently. Conventional ultrasonic temperature estimation based on echo strain suffers from artifacts caused by signal distortion over time, leading to poor estimation and visualization of the 2D temperature map. This thesis presents a novel model-based stochastic framework for ultrasonic temperature estimation, which combines the temperature information from the ultrasound images and a theoretical model of the heat diffusion. Consequently the temperature estimation is more consistent over time and its visualisation is improved. There are 3 main contributions of this thesis related to: improving the conventional echo strain method to estimate temperature, developing and applying approximate heat models to model temperature, and finally combining the estimation and the models. First in the echo strain based temperature estimation, a robust displacement estimator is first introduced to remove displacement outliers caused by the signal distortion over time due to the thermo-acoustic lens effect. To transfer the echo strain to temperature more accurately, an experimental method is designed to model their relationship using polynomials. Experimental results on a gelatine phantom show that the accuracy of the temperature estimation is of the order of 0.1 ◦C. This is better than results reported previously of 0.5 ◦C in a rubber phantom. Second in the temperature modelling, heat models are derived approximately as Gaussian functions which are mathematically simple. Simulated results demonstrate that the approximate heat models are reasonable. The simulated temperature result is analytical and hence computed in much less than 1 second, while the conventional simulation of using finite element methods requires about 25 minutes under the same conditions. Finally, combining the estimation and the heat models is the main contribution of this thesis. A 2D spatial adaptive Kalman filter with the predictive step defined by the shape model from the heat models is applied to the temperature map estimated from ultrasound images. It is shown that use of the temperature shape model enables more reliable temperature estimation in the presence of distorted or blurred strain measurements which are typically found in practice. The experimental results on in-vitro bovine liver show that the visualisation on the temperature map over time is more consistent and the iso-temperature contours are clearly visualised.

L’ablation de cibles d’Al nanocristallines (taille moyenne des cristallites d = 3,1 et 6,2 nm) par impulsions laser ultrabrèves (200 fs) a été étudiée par l’entremise de si- mulations combinant la dynamique moléculaire et le modèle à deux températures (two- temperature model, TTM) pour des fluences absorbées allant de 100 à 1300 J/m2. Nos simulations emploient un potentiel d’interaction de type EAM et les propriétés électro- niques des cibles en lien avec le TTM sont représentées par un modèle réaliste possédant une forme distincte dans le solide monocristallin, le solide nanocristallin et le liquide. Nous avons considéré l’effet de la taille moyenne des cristallites de même que celui de la porosité et nous avons procédé à une comparaison directe avec des cibles mono- cristallines. Nous avons pu montrer que le seuil d’ablation des métaux nanocristallins est significativement plus bas, se situant à 400 J/m2 plutôt qu’à 600 J/m2 dans le cas des cibles monocristallines, l’écart étant principalement dû à l’onde mécanique plus im- portante présente lors de l’ablation. Leur seuil de spallation de la face arrière est aussi significativement plus bas de par la résistance à la tension plus faible (5,40 GPa contre 7,24 GPa) des cibles nanocristallines. Il est aussi apparu que les contraintes résiduelles accompagnant généralement l’ablation laser sont absentes lors de l’ablation de cibles d’aluminium nanocristallines puisque la croissance cristalline leur permet d’abaisser leur volume spécifique. Nos résultats indiquent aussi que le seuil de fusion des cibles nano- cristallines est réduit de façon marquée dans ces cibles ce qui s’explique par la plus faible énergie de cohésion inhérente à ces matériaux. Nos simulations permettent de montrer que les propriétés structurelles et électroniques propres aux métaux nanocristallins ont toutes deux un impact important sur l’ablation. / The ablation of nanocrystalline (mean crystallite size d = 3.1 and 6.2 nm) Al tar- gets by ultrashort (200 fs) laser pulses was studied using hybrid simulations combining molecular-dynamics and the two-temperature model (TTM) for a range of absorbed flu- ence of 100 to 1300 J/m2. Our simulations employ an EAM interatomic potential and the TTM-related electronic properties are modelled using three distinct functions to rep- resent the monocrystalline solid, the nanocrystalline solid, and the liquid in an accurate way. Comparison between targets displaying two mean grain sizes, porous targets, and monocrystalline targets are reported. This study showed a significantly reduced abla- tion threshold of 400 J/m2 instead of the 600 J/m2 obtained for the single crystals, the discrepancy being mainly accounted for by an increase in the magnitude of the pressure wave generated during ablation. The spallation threshold of the back side of the target is also reduced owing to a lower tensile strength (5.40 GPa against 7.24 GPa). This work also allowed to discover that residual stress generally associated with laser ablation is totally absent in nanocrystalline samples as crystal growth provides a mechanism for volume reduction near the melting temperature. Furthermore, our results demonstrate that the melting threshold shows an important decrease and the melting depth an im- portant increase in the nanocrystalline samples which can be explained by their lower cohesion energy. Our simulations shed light on the fact that a realistic modelling of both structural and electronic properties of the nanocrystalline target is important to produce a reliable representation of laser ablation.

Le contrôle thermique des réactions dans les réacteurs à lits fixes nécessite la maîtrise du transfert thermique en proche paroi. Afin d’optimiser leur conception et en particulier de maintenir un chemin réactionnel le plus proche possible de l’isothermicité, un modèle de transfert thermique pertinent dans un tel milieu est indispensable. Deux premières thèses au Laboratoire d'Energétique et de Mécanique Théorique et Appliquée ont permis de mettre au point un modèle dispersif utilisable à cœur de réacteur. La présente thèse met en évidence un effet de paroi non négligeable causé par la variation de porosité du lit à l’approche de la paroi. Ce travail propose un raccordement du cœur, où le modèle thermique précédent est légitime, à la paroi, par une couche homogénéisée. Cette approche est validée par une caractérisation expérimentale des paramètres du modèle sur un dispositif de laboratoire en utilisant une méthode d’inversion originale reposant sur une approche Bayesienne. Une validation de cette caractérisation dans une géométrie plus proche d’un réacteur industriel est également effectuée / Thermal control for chemical reactions conducted in fixed-bed reactors requires a fine knowledge about heat transfer in the near-wall region of the bed. In order to optimize the process design, to minimize the mass of catalyst that is needed, one must attempt to maintain the operational path of the reactor the closest of the isotherm functioning. A pertinent and reliable heat transfer model is then required. Two thesis were realized in the Laboratoire d'Energétique et de Mécanique Théorique et Appliquée in order to construct a corresponding dispersive model. This model can be used at the core of the reactor, where the porous medium can be homogenized. This thesis shows a wall effect that cannot be neglected. This wall effect is directly caused by the important variation of the porosity distribution near the wall of the bed. This work proposes a junction between a core layer, where the previous model is still valid, and the wall through an homogenized near-wall layer. This approach is validated by the mean of an experimental characterization of the model parameters, using an original inversion technique based on a Bayesian approach. A validation of this characterization in another geometry is also done. This geometry is closer to an industrial reactor

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We discuss the so-called two-temperature model in linear thermoelasticity and provide a Hilbert space framework for proving well-posedness of the equations under consideration. With the abstract perspective of evolutionary equations, the two-temperature model turns out to be a coupled system of the elastic equations and an abstract ordinary differential equation (ODE). Following this line of reasoning, we propose another model which is entirely an abstract ODE.We also highlight an alternative method for a two-temperature model, which might be of independent interest.

Modulation doped heterostructures have revolutionized the operation of field effect devices by increasing the speed of operation. One of the factors that affects the speed of operation of these devices is the mobility of the carriers, which is intrinsic to the material used. Mobility of electrons in silicon based devices has improved drastically over the years, reaching as high as 50.000cm2/Vs at 4.2K and 2600cm2/Vs at room temperature. However, the mobility of holes in p-type silicon devices still remains comparatively lesser than the electron mobility because of large effective masses and complicated valence band structure involved. Germanium is known to have the largest hole mobility of all the known semiconductors and is considered most suitable to fabricate high speed p-type devices. Moreover, it is also possible to integrate germanium and its alloy (Si1_zGex ) into the existing silicon technology. With the use of sophisticated growth techniques it has been possible to grow epitaxial layers of silicon and germanium on Si1_zGex alloy layers grown on silicon substrates. In tills thesis we investigate in detail the electrical properties of p-type germanium and n-type silicon thin films grown by these techniques. It is important to do a comparative study of transport in these two systems not only to understand the physics involved but also to study their compatibility in complementary field effect devices (cMODFET). The studies reported in this thesis lay emphasis both on the low and high field transport properties of these systems. We report experimental data for the maximum room temperature mobility of holes achieved m germanium thin films grown on Si1_zGex layers that is comparable to the mobility of electrons in silicon films. We also report experiments performed to study the high field degradation of carrier mobility due to "carrier heating" in these systems. We also report studies on the effect of lattice heating on mobility of carriers as a function of applied electric field. To understand the physics behind the observed phenomenon, we model our data based on the existing theories for low and high field transport. We report complete numerical calculations based on these theories to explain the observed qualitative difference in the transport properties of p-type germanium and ii-type silicon systems. The consistency between the experimental data and theoretical modeling reported in this work is very satisfactory.

<div>The interactions of femtosecond lasers with gold targets were investigated with a numerical method combining molecular dynamics (MD) and the two-temperature model (TTM). Previous works using MD-TTM method did not consider all the thermodynamic parameters and the interatomic potential dependent of the electron temperature simultaneously. Therefore, we developed a LAMMPS function to achieve this. To accurately capture the physics behind the interactions, we also included the electron blast force from free electron pressure and the modified Fourier law with steep electron temperature gradient in our model. For bulk materials, a stress non-reflecting and heat conducting boundary is added between the atomistic and the continuum parts. The modified boundary force in our study greatly reduces the reflectivity of the atomistic-continuum boundary compared with its original form. Our model is the first to consider all these factors simultaneously and manage to predict four femtosecond laser ablation phenomena observed in the experiments. </div><div><br></div><div>In this dissertation, the thermodynamic parameters in the two-temperature model were extensively explored. We considered three different approaches to calculate these parameters: namely interpolation, <i>ab initio</i> calculation, and analytical expression. We found that simple interpolation between solid state and plasma state could lead to high level of inaccuracy, especially for electron thermal conductivity. Therefore, <i>ab initio</i> calculation and analytical expression were used for the calculation of the thermodynamic parameters in more advanced studies. The effects of electron thermal conductivity and electron-phonon coupling factor on electron and lattice temperatures were analyzed.</div><div><br></div><div>Our studies considered electron temperature dependent (ETD) and electron temperature independent (ETI) interatomic potentials. The ETI interatomic potential is easier to implement and therefore it is used in our phase change study to investigate the effects of target thickness on melting. Homogeneous melting occurred for thin films, while melting can be observed through the movement of the solid-liquid interface in thick or bulk materials. However, the ETI potential overestimated the bond strength at high temperatures. Therefore, ablation process was studied with the ETD potential. Three ablation mechanisms were found in our simulations at different laser fluences. Short nonthermal ablation was only observed at the ablation threshold. With increasing laser fluence, spallation was then seen. In high laser fluence regime, phase explosion occurred on the surface and coexisted with spallation.</div><div><br></div><div>Lastly, we researched on the effects of the delay time between two femtosecond laser pulses. Various delay times did not have much influence on melting depth. In low laser fluence regime, with increasing delay time, the target went through nonthermal ablation, to spallation and to no ablation. In high laser fluence regime, longer delay time encouraged phase explosion while suppressed spallation.</div>

Many communities are currently seeking to balance urban water needs with preservation of sensitive fish habitat. As part of that effort, CE-QUAL-W2, a hydrodynamic and temperature model, was developed for Chester Morse Lake and the lower Cedar River, WA. Chester Morse Lake is approximately 10 km long with a maximum depth at full pool of 40 m. The Cedar River model started immediately downstream of the Chester Morse dam and ended 21 km downstream at Landsburg, where drinking water is diverted for the City of Seattle. This water quality model was coupled with a fish habitat and bioenergetics model for bull trout and was calibrated to temperature data between 2005 and 2008. Bull trout fish bioenergetics parameters were provided by the USGS. The CE-QUAL-W2 model was found to be highly accurate in modeling temperature variation in the lake - at most locations having an average absolute mean error of between 0.5 and 0.8 oC. The Cedar River model had an average absolute mean error of 0.7oC. This tool is designed to allow managers and operators to estimate the impact to fish habitat and growth potential from various management decisions including extent of drawdown, timing/volume of flows, and various pumping operations. Future studies could include incorporating further water quality parameters such as nutrients, algae, and zooplankton as they relate to fish productivity.

The Middle Fork John Day Basin in Northeastern Oregon is prime habitat for spring Chinook salmon and Steelhead trout. In 2008, a major tributary supporting rearing habitat, Big Boulder Creek, was restored to its historic mid-valley channel along a 1 km stretch of stream 800 m upstream of the mouth. Reduction of peak summer stream temperatures was among the goals of the restoration. Using Distributed Temperature Sensing (DTS) Fiber Optic Technology, stream temperature was monitored prior to restoration in June 2008, and after restoration in September 2008, July 2009, and August 2009. Data gathered was used to determine locations of groundwater and hyporheic inflow and to form a stream temperature model of the system. The model was used both to develop an evaluation method to interpret components of model performance, and to better understand the physical processes important to the study reach. A very clear decreasing trend in surface temperature was seen throughout each of the DTS stream temperature datasets in the downstream 500 m of the study reach. Observed reduction in temperature was 0.5°C (±0.10) in June 2008, 0.3°C (±0.37) in September 2008, 0.6°C (±0.25) in July 2009, and 0.2°C (±0.08) in August 2009. Groundwater inflow was calculated to be 3% of the streamflow for July 2009 and 1% during the August 2009 installation. Statistically significant locations of groundwater and hyporheic inflow were also determined. July 2009 data was used to model stream temperature of the 1 km (RMSE 0.28°C). The developed model performance evaluation method measures timelag, offset, and amplitude at a downstream observed or simulated point compared with the boundary condition, rather than evaluating the model based on error. These measures are particularly relevant to small scale models in which error may not be a true reflection of the ability of a model to correctly predict temperature. Breaking down model performance into these three predictive measures was a simple and graphic method to show the model's predictive capability without sorting through large amounts of data. To better understand the model and the stream system, a sensitivity analysis was conducted showing high sensitivity to streamflow, air temperature, groundwater inflow, and relative humidity. Somewhat surprisingly, solar radiation was among the lowest sensitivity. Furthermore, three model scenarios were run: a 25% reduction in water velocity, a 5°C increase in air temperature, and no groundwater inflow. Simulations of removal of groundwater inflows resulted in a 0.5°C increase in average temperature over the modeled time period at the downstream end, further illustrating the importance of groundwater in this stream system to reduce temperatures. / Graduation date: 2012