Land Surface Parameterization (LSP) schemes have evolved from simple tipping-bucket models to fully interactive models, including parameterizations which account for exchanges of momentum, energy, mass, and biogeochemistry. As the demand for greater realism has increased, so has the complexity of LSPs which now includes some parameters that may not be universally relevant to all regions of the globe. The performance of LSP schemes depends on the magnitude of structural, data-related (input and output), and parameter uncertainties in the model. Parameter estimation uncertainty can be reduced by calibrating LSPs against measurements available at field sites. Given the multiple outputs of the models, multi-objective optimization approaches are performed. Some of the parameter values used in LSPs have originally obtained from laboratory studies which analyzed plant behavior under a range of conditions in enclosed chambers. The research described in this dissertation takes advantage of currently available data from several eddy covariance flux towers located mainly in the Brazilian Amazon basin to estimate parameter values of a widely-used LSP scheme, version 3 of the Simple Biosphere model (SiB3). Background climatological data was used to assess the representativeness of the data collection period that might have affected model calibration. Variance-based sensitivity analysis was then used to investigate potential structural deficiencies in SiB3 and to reduce the dimensionality of the subsequent optimization by identifying those model parameters that merit calibration. Finally, some structural and conceptual aspects of SiB3 were tested inside Biosphere 2 Tropical Rain Forest biome (B2-TRF) under meteorological conditions that resemble those predicted in future climate scenarios for the Amazon basin.

No / Three-dimensional (3D) representations of com- plex geometric shapes, especially when they are recon- structed from magnetic resonance imaging (MRI) and com- puted tomography (CT) data, often result in large polygon meshes which require substantial storage for their handling, and normally have only one fixed level of detail (LOD). This can often be an obstacle for efficient data exchange and interactive work with such objects. We propose to re- place such large polygon meshes with a relatively small set of coefficients of the patchwise partial differential equation (PDE) function representation. With this model, the approx- imations of the original shapes can be rendered with any desired resolution at interactive rates. Our approach can di- rectly work with any common 3D reconstruction pipeline, which we demonstrate by applying it to a large reconstructed medical data set with irregular geometry.

La production de dessins animés 2D, qui suit actuellement un schéma mis en place dans les années 1920, fait intervenir un très nombre de compétences humaines et de métiers différents. Par opposition à ce mode de travail traditionnel, la production de films de synthèse 3D, en exploitant les technologies et outils les plus récents de modélisation et d'animation 3D, s'affranchit pour une bonne part de cette composante artisanale et vient concurrencer l'industrie du dessin animé tradtionnel en termes de délais et de coûts de fabrication.<br /><br />Les défis à relever par l'industrie du dessin animé 2D se formulent donc en termes de:<br /><br /> 1. Réutilisation des contenus selon le paradigme Create once, render many,<br /> 2. Facilité d'échange et de transmission des contenus, ce qui nécessite de disposer d'un unique format de représentation,<br /> 3. Production efficace et économique des contenus, requérant une animation automatisée par ordinateur. <br /><br />Dans ce contexte compétitif, ce travail de thèse, réalisé dans le cadre du projet industriel TOON financé par la société Quadraxis avec le support de l' Agence Nationale de Valorisation de la Recherche (Oséo-ANVAR), a pour objectif de contribuer au développement d'une plate-forme de reconstruction, déformation et animation de modèles 3D pour les dessins animés 2D.<br /><br />Un état de l'art des méthodes et outils contribuant à la reconstruction de modèles 3D et à leur animation est présenté et discuté au regard des contraintes spécifiques des règles de création des dessins animés 2D et de la chaîne de fabrication traditionnelle. Ayant identifié les verrous technologiques à lever, nos contributions ont porté sur :<br /><br /> * l'élaboration d'une méthode de reconstruction de personnages virtuels 3D à partir de dessins 2D,<br /> * la mise au point d'une procédure de reconstruction surfacique par NURBS dotée d'une capacité de déformation interactive 2D/3D,<br /> * la conception d'un module de modélisation 3D pour surfaces maillées, compatible avec le standard d'animation MPEG-4/AFX. <br /><br />Les développements réalisés, intégrés dans un prototype de la plate-forme TOON, montrent un gain en temps de 20% sur l'ensemble de la chaîne de production tout en garantissant une complète interopérabilité des applications via le standard MPEG-4.

La thèse vise l'application du concept de bioraffinerie (extraction, fractionnement, séparation de composés à partir de biomasse avant transformation ultérieure), via le développement d'étapes de production destinées à être associées en un procédé continu. La complexité du solide nécessite une étape de prétraitement effectuée avec une technologie à faible impact environnemental et l'eau subcritique est déjà utilisée comme solvant d'extraction des produits naturels, en sus de leur hydrolyse. Ces travaux ont porté sur l'hydrolyse de polysaccharides (son de riz) et de triacylglycérols (TAG, huile de tournesol) choisis comme modèles. Les caractéristiques de l'eau subcritique (produit ionique, constante diélectrique) mise en œuvre en réacteurs à circulation construits dans ce but, ont permis l'hydrolyse quasi-totale de l'hémicellulose et des TAG. L'addition de CO2 et donc d'acide carbonique a eu un effet positif sur l'hydrolyse de l'hémicellulose. Les acides gras libres résultant de l'hydrolyse ont été estérifiés en ester éthyliques en présence d'une lipase en réacteur continu en milieu CO2 supercritique, avec un taux de synthèse de 95%. Les cinétiques des réactions ci-dessus d'hydrolyse et d'estérification ont été étudiées. La complexité des interactions entre les nombreux paramètres mis en jeu a conduit à appliquer des méthodes de plans d'expérience. Ces méthodes ont été validées avec succès avec les données expérimentales, montrant ainsi leur utilité dans le développement de procédés. La question importante de la solubilité des extractibles dans l'eau subcritique a été traitée et une méthode de prédiction mise au point et validée avec succès avec les données expérimentales. En conclusion, ce travail montre la possibilité d'appliquer le concept novateur de la Bioraffinerie Intégrée en réacteur continu avec des fluides sub- ou supercritique, contrairement à leur mise en œuvre actuelle en réacteur fermé, pour la production de composés commercialisables. / This work addresses the integrated biorefining concept (extraction, fractionation, separation of compounds from biomass prior to further transformation) by developing discrete units with the ultimate objective of coupling them to enable a continuous flow configuration. Due to the complexity of solid, there is a need for a sustainable and environmentally friendly pre-treatment technology. Sub-critical water has been used as a solvent for extracting natural compounds in addition to hydrolysis. This work investigated the hydrolysis of carbohydrates (rice bran) and triacylglycerols (TAG; sunflower oil) chosen as models. The attribute of subcritical water (ion product and dielectric constant) in continuous flow reactors built for the purpose, allowed almost quantitative hydrolysis of hemicellulose and TAG. The effect of adding CO2 and therefore carbonic acid was positive on the hydrolysis of hemicellulose. Further, free fatty acids were transformed to ethyl esters using lipase within continuous flow super critical CO2 resulting in 95% yield. The hydrolysis and esterification reaction kinetics were studied. To address the complex interplay between multiple processing parameters response surface methodologies (RSM) were developed. Using the empirical data the models were successfully validated, therefore showing the utility of the RSM to assist process development. The important question of solubility of extractible in subcritical water was also addressed, through the development of a prediction method, validated with experimental data. In summary this work shows the possibility of applying the innovative Integrated Biorefining concept under continuous flow conditions -instead of the current application under batch conditions- for producing valuable compounds.

Density functional theory (DFT) has become the most widely used first-principles computational method to simulate different atomic, molecular, and solid phase systems based on electron density assumptions. The complexity of describing a many-body system has been significantly reduced in DFT. However, it also brings in potential error when dealing with a system that involves the interactions between metallic and non-metallic species. DFT tends to overly-delocalize the electrons in metallic species and sometimes results in the overestimation of reaction energy, metallic properties in insulators, and predicts relative surface stabilities incorrectly in some instances. There are two approaches to overcoming the failure of DFT using standard exchange-correlation functionals: One can either use a higher level of theory (and thus incur a greater computational cost) or one can apply an efficient correction scheme. However, inaccurate corrections and improper calculation models can also lead to more errors. In the beginning of this dissertation, we introduce the correction methods we developed to accurately model the structure and electron density in material surfaces; then we apply the new methods in surface reactivity studies under experimental conditions to rationalize and solve real life problems. We first investigate the post-DFT correction method in predicting the chemisorption energy (Echem) of a NO molecule on transition metal surfaces. We show that DFT systematically enhances back-donation in NO/metal chemistorption from the metal d-band to NO 2π* orbital, and relate the back-donation charge transfer to the promotion of an electron from the 5σ orbital to the 2π* orbital in the gas-phase NO G2Σ-←X2Π excitation. We establish linear relationships between Echem and ΔEG←X and formulate an Echem correction scheme to the (111) surfaces of Pt, Pd, Rh and Ir. As a precursor to further optimization of DFT corrections on transition metal oxide surfaces, we systematically compare the alumina (α-Al2O3) and hematite (α-Fe2O3) (0001) surfaces to study how the atomic positions treatment during geometry optimizations would affect the electronic structure and modeled reactivity, since they are often reported to have a minimal effect. Our results suggest that both can vary significantly in quantitative and qualitative ways between partially constrained or fully relaxed slab models. We continue to use the α-Fe2O3 (0001) surfaces to optimize the Hubbard U method implemented in DFT that determines the Coulomb repulsion correction (Ud) to localize Fe d-electrons. It successfully restores the insulating properties of bulk hematite, but underestimates the stability of the oxygen-terminated surface. It is mainly due to the fact that all the chemically distinct surface Fe atoms were treated the same way. Here we develop a linear response technique to derive specific Ud values for all Fe atoms in several slab geometries. We also find that in a strongly correlated system, the O p-orbitals also need the Hubbard correction (Up) to accurately predict the structural and electronic properties of bulk hematite. Our results show that the site-specific Ud, combined with Up as Ud+p, is crucial in obtaining theoretical results for surface stability that are congruent with the experimental literature results of α-Fe2O3 (0001) surface structure. Besides methodology development, we continue to apply our specific Ud+p method in the engineered application of the Chemical Looping Combustion (CLC) process in which transition metal oxides play the role of oxidizing fuel molecules for full CO2 capture. Current molecular dynamic studies use partially constrained surface models to simulate the CH4 reaction on hematite surfaces without the detailed comparison of the early stage adsorption products. Here we use hematite (α-Fe2O3) and magnetite (Fe3O4) surfaces as analogous to systematically study the early adsorption products of CH4. Our results show that the reaction favors the homolytic pathway on O-terminated surface, and that as a reduced form of hematite, the magnetite surface also shows excellent reactivity on CH4 dissociation. Knowing how to simulate DFT surface model properly we continue to enrich our theoretical methods for more complicated systems under aqueous conditions. We focus on various structures of the lithium-ion battery material, LiCoO2 (LCO) (001) surface, involving hydroxyl groups. We assess the relative stabilities of different surface configurations using a thermodynamic framework, and a second approach using a surface-solvent ion exchange model. We find that for both models the –CoO–H1/2 surface is the most stable structure near the O-rich limit, which corresponds to ambient conditions. We also found that this surface has nonequivalent surface geometry with the stoichiometric –CoO–Li1/2 surface, leading to distinct band structures and surface charge distributions. We go on to probe how those differences affect the surface reactivity in phosphate anion adsorption. All of the work presented in this dissertation reveals the importance of accurately modeled material structures in theoretical studies to achieve correct physical properties and surface reactivity predictions. We hope our DFT correction schemes can continue to contribute to future surface studies and experimental measurements, and to enlighten new ideas in future DFT methodology improvements.

The work presented in this dissertation informs on river network modeling at large scales using geographic information systems, parallel computing and the latest advancements of atmospheric and land surface modeling. This work is motivated by the availability of a vector-based Geographic Information System dataset that describes the networks of streams and rivers in the United States, and how they are connected. A land surface model called Noah-distributed is used to provide lateral inflow to an NHDPlus river network in the Guadalupe River Basin in Texas. Challenges related to the projection of gridded hydrographic data from a coordinate system to another are investigated. The different representations of the shape of the Earth used in atmospheric science (spherical) and hydrology (spheroidal) can lead to a significant North-South shift on the order of 20 km at mid latitudes. A river network model called RAPID is developed and applied in a four-year study of the Guadalupe and San Antonio River Basins in Texas using the river network of NHDPlus. Gage measurements are used to estimate flow wave celerities in a river network and to assess the quality of RAPID flow computations. The performance of RAPID in a massively-parallel computing environment is tested and further investigation of its scalability is needed before using RAPID at the state or federal level. The replacement by RAPID of the river routing scheme used in SIM-France -- a hydro-meteorological model -- is investigated in a ten-year study of river flow in France. While the formulation of RAPID improves the functionality of SIM-France, the flow simulations are comparable in accuracy to those previously obtained by SIM-France. Sub-basin parameterization was found to improve model results. A single criterion for quantifying the quality of river flow simulations using several river gages globally in a river network is developed that normalizes the square error of modeled flow to allow equal treatment of all gaging stations regardless of the magnitude of flow. The use of this criterion as the cost function for parameter estimation in RAPID allows better results than by increasing the degree of spatial variability in model parameters. / text

Water is essential to life on Earth. Since water exists in all three phases (solid, liquid, and gas) on Earth, it exists in various reservoirs throughout the planet that compose the hydrologic cycle, and its movement through these reservoirs requires energy. Thus, water is a key component of the energy balance of the Earth. Despite its importance, its representation in modeling and dataset generation is problematic. Here, the depiction of three phenomena, ocean surface turbulent fluxes, humidity inversions, and groundwater, are assessed, and suggestions for improvements of their representations are made. First, ocean surface turbulent fluxes, including those of moisture (latent heat flux), heat (sensible heat flux), and momentum (wind stress), from reanalysis, satellite-derived, and combined products which are commonly used to produce climatologies and to evaluate global climate models are compared to in situ observations from ship cruises to ascertain which products are the least problematic. The National Aeronautics and Space Administration’s reanalysis, the Modern Era Retrospective Analysis for Research and Applications, is the least problematic for all three fluxes, while a couple of others are the least problematic for only one of the three fluxes. Also, the product biases are disaggregated into uncertainties from the grid cell mean quantities, or bulk variables, used plus the residual uncertainties which includes the algorithm uncertainties due to the parameterization used to relate the small-scale turbulent processes to the large-scale bulk variables. The latter contribute the most to the majority of product latent heat fluxes, while both uncertainties can contribute the most to product sensible heat fluxes and wind stress. Thus, both algorithms and bulk variables need to be improved in ocean surface flux datasets. Second, humidity inversion climatologies in five reanalyses are evaluated. Humidity inversions, similar to its thermal counterpart, are layers in which specific humidity increases with height rather than the usual decrease with height. These are especially persistent in the polar regions in autumn and winter. However, Arctic inversions are the strongest in summer corresponding to the time of year that low cloud cover is the highest. Comparing the reanalysis inversions to radiosonde observations reveals some problems with the realization of humidity inversions in reanalyses including the misrepresentation of the diurnal cycle and of the overproduction of inversions in areas outside the polar regions. Finally, the simulation of groundwater in the Community Land Model (CLM) as used in the Community Earth System Model is made more realistic by including variable soil thickness. Because the bottom of the model soil column is placed at effectively bedrock, the unconfined aquifer model currently used in CLM is removed and a zero bottom water flux is put in place. The removal of the unconfined aquifer allows the simulation of groundwater to not be treated separately from soil moisture. The model is most affected where the number of soil layers is reduced from the original constant 10 layers and largely unaffected where the number of soil layers is increased except for baseflow where the mean annual range in rainfall is large.

The ability of fast and accurate acquiring of large 3D spatial data is the main benefit for consideration of a terrestrial laser scanner in deformation monitoring. The objective of this paper is to discuss this technique with support of practical experiments performed inside a laboratory. It also includes measuring changes from millimetre to sub millimetre level and a comparison of measurements from a terrestrial laser scanner with measurements of other instruments. Various areas of applications are reviewed. The report discusses a surface modeling method to estimate deformation parameters of objects, such as planar, spherical and cylindrical surface representations. Illustrative numerical examples are performed by simulating randomly generated sample point coordinates for estimation of changes of modeled planar and cylindrical surfaces. The practical experiments were performed using a scan of a carton box, a ball and a rounded paper holder, which correspond to the planar, spherical and cylindrical surfaces, respectively. Independent measurements were performed using a total station and a measuring tape to make a comparison with the scanner measurements. A statistical test was performed independently for the changes obtained from each type of modeled surface in order to check whether the movement is real or due to measurement noises.  A significant change of the normal of a plane was detected between epochs, and similar results were obtained from both scanner and total station measurements. The normal of the plane was rotated by  between scan epochs. A translation of 3.2 and 3.7 millimetres were detected between scan epochs for the center of the sphere and axis of the cylinder, respectively. Only the scanner data was used in this case. From the scanner measurement changes in radii of the sphere and the cylinder were obtained as 1.6 and 3.1 millimetres, respectively between scan epochs. The measurement of the scanner was verified by performing independent measurements using measuring tape. And hence the change in radii of the sphere and the cylinder were obtained as 2.5 and 4 millimetres, respectively.

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