Platinum-based catalysts for hydrogen fuel-cell applications have progressed greatly with the addition of a second element in either a mixed-alloy or core-shell structure. Not only do they contain a reduced amount of the more expensive platinum metal but they have been shown to demonstrate a significant improvement in catalytic activity. Further improvement of these systems can only be made by careful investigation of such catalyst panoparticles on an atomic scale. These nanoparticles provide a significant characterisation challenge due to their minute size and beam sensitivity. A new method of quantifying the annular dark-field (ADF) scanning transmission electron microscope (STEM) signal on an absolute scale has been developed to address this problem. Experimental images are scaled to a fraction of the incident beam intensity from a detector map. The integrated intensity of each individual atomic column is multiplied by the pixel area to yield a more robust imaging parameter: a scattering cross section, σ. Using this cross section approach and simulated reference data, I show it is possible to count the number of atoms in individual columns. With some prior knowledge of the sample, this makes it possible to reconstruct the 3-dimensional structures of pure platinum nanoparticles. Such an approach has subsequently been extended to bimetallic particles here the elements are close in atomic number, using the platinum-iridium system as an example. In the same way that the cross section can be calculated from ADF image intensity, it is possible to calculate an energy dispersive x-ray (EDX) partial scattering cross section, beneficial especially because of the simplicity of its implementation. In sufficiently thin samples such that the number of x-ray counts is linearly proportional to sample thickness, we can determine element-specific atom counts. Finally, it is possible to combine EDX and ADF cross sections to provide us with quantitative structural and compositional information.

<p>Human activities represent a significant burden on the global water cycle, with large and increasing demands placed on limited water resources by manufacturing, energy production and domestic water use. In addition to changing the quantity of available water resources, human activities lead to changes in water quality by introducing a large and often poorly-characterized array of chemical pollutants, which may negatively impact biodiversity in aquatic ecosystems, leading to impairment of valuable ecosystem functions and services. Domestic and industrial wastewaters represent a significant source of pollution to the aquatic environment due to inadequate or incomplete removal of chemicals introduced into waters by human activities. Currently, incomplete chemical characterization of treated wastewaters limits comprehensive risk assessment of this ubiquitous impact to water. In particular, a significant fraction of the organic chemical composition of treated industrial and domestic wastewaters remains uncharacterized at the molecular level. Efforts aimed at reducing the impacts of water pollution on aquatic ecosystems critically require knowledge of the composition of wastewaters to develop interventions capable of protecting our precious natural water resources.</p><p>The goal of this dissertation was to develop a robust, extensible and high-throughput framework for the comprehensive characterization of organic micropollutants in wastewaters by high-resolution accurate-mass mass spectrometry. High-resolution mass spectrometry provides the most powerful analytical technique available for assessing the occurrence and fate of organic pollutants in the water cycle. However, significant limitations in data processing, analysis and interpretation have limited this technique in achieving comprehensive characterization of organic pollutants occurring in natural and built environments. My work aimed to address these challenges by development of automated workflows for the structural characterization of organic pollutants in wastewater and wastewater impacted environments by high-resolution mass spectrometry, and to apply these methods in combination with novel data handling routines to conduct detailed fate studies of wastewater-derived organic micropollutants in the aquatic environment. </p><p>In Chapter 2, chemoinformatic tools were implemented along with novel non-targeted mass spectrometric analytical methods to characterize, map, and explore an environmentally-relevant “chemical space” in municipal wastewater. This was accomplished by characterizing the molecular composition of known wastewater-derived organic pollutants and substances that are prioritized as potential wastewater contaminants, using these databases to evaluate the pollutant-likeness of structures postulated for unknown organic compounds that I detected in wastewater extracts using high-resolution mass spectrometry approaches. Results showed that application of multiple computational mass spectrometric tools to structural elucidation of unknown organic pollutants arising in wastewaters improved the efficiency and veracity of screening approaches based on high-resolution mass spectrometry. Furthermore, structural similarity searching was essential for prioritizing substances sharing structural features with known organic pollutants or industrial and consumer chemicals that could enter the environment through use or disposal.</p><p>I then applied this comprehensive methodological and computational non-targeted analysis workflow to micropollutant fate analysis in domestic wastewaters (Chapter 3), surface waters impacted by water reuse activities (Chapter 4) and effluents of wastewater treatment facilities receiving wastewater from oil and gas extraction activities (Chapter 5). In Chapter 3, I showed that application of chemometric tools aided in the prioritization of non-targeted compounds arising at various stages of conventional wastewater treatment by partitioning high dimensional data into rational chemical categories based on knowledge of organic chemical fate processes, resulting in the classification of organic micropollutants based on their occurrence and/or removal during treatment. Similarly, in Chapter 4, high-resolution sampling and broad-spectrum targeted and non-targeted chemical analysis were applied to assess the occurrence and fate of organic micropollutants in a water reuse application, wherein reclaimed wastewater was applied for irrigation of turf grass. Results showed that organic micropollutant composition of surface waters receiving runoff from wastewater irrigated areas appeared to be minimally impacted by wastewater-derived organic micropollutants. Finally, Chapter 5 presents results of the comprehensive organic chemical composition of oil and gas wastewaters treated for surface water discharge. Concurrent analysis of effluent samples by complementary, broad-spectrum analytical techniques, revealed that low-levels of hydrophobic organic contaminants, but elevated concentrations of polymeric surfactants, which may effect the fate and analysis of contaminants of concern in oil and gas wastewaters. </p><p>Taken together, my work represents significant progress in the characterization of polar organic chemical pollutants associated with wastewater-impacted environments by high-resolution mass spectrometry. Application of these comprehensive methods to examine micropollutant fate processes in wastewater treatment systems, water reuse environments, and water applications in oil/gas exploration yielded new insights into the factors that influence transport, transformation, and persistence of organic micropollutants in these systems across an unprecedented breadth of chemical space.</p> / Dissertation

Superalloys have performed well as blade and disc materials in turbine engines due to their exceptional elevated temperature strength, high resistance to creep, oxidation and corrosion as well as good fracture toughness. This study explores the use of a relatively new technique of strain measurement, high resolution electron backscatter diffraction (HR-EBSD) to measure local deformation fields. The heart of the HR-EBSD technique lies in comparing regions in EBSD patterns from a strained region of a sample to those in a pattern from an unstrained region. This method was applied to study the elastic strain fields and geometrically necessary dislocation density (GND density) distribution near hard carbide particles in a nickel-based superalloy MAR-M-002. Significant thermal strains were initially induced by thermal treatment, which included a final cooling from the ageing temperature of 870°C. Elastic strains were consistent with a compressive radial strain and tensile hoop strain that was expected as the matrix contracts around the carbide. The mismatch in thermal expansion coefficient of the carbide particles compared to that of the matrix was sufficient to have induced localized plastic deformation in the matrix leading to a GND density of 3 x 10¹³ m^–2 in regions around the carbide. These measured elastic strain and GND densities have been used to help develop a crystal plasticity finite element model in another research group and some comparisons under thermal loading have also been examined. Three-point bending was then used to impose strain levels within the range ±12% across the height of a bend bar sample. GND measurements were then made at both carbide-containing and carbide-free regions at different heights across the bar. The average GND density increases with the magnitude of the imposed strain (both in tension and compression), and is markedly higher near the carbide particles. The higher GND densities near the carbides (order of 10¹⁴ per m²) are generated by the large strain gradients produced around the plastically rigid inclusion during monotonic mechanical deformation with some minor contribution from the pre-existing residual deformation from thermal loading. A method was developed of combining the local EBSD measurements with FE modelling to set the average residual strains within the mapped region even when a good strain free reference point was unavailable. Cyclic loading was then performed under four point loading to impose strain levels of about ±8% across the height of bend bar samples. Similar measurements as in the case of monotonic deformation were made at several interruptions to fatigue loading. Observations from the cyclic loading such as slip features, carbide cracking, GND density accumulation have been explored around carbide particles, at regions away from them and near a grain boundary.

The uniquely predictable and controllable binding mechanism of DNA strands has been exploited to construct a vast range of synthetic nanodevices, capable of autonomous motion and computation. This thesis proposes novel ideas for the control and observation of such devices. The first of these proposals hinges on introducing mismatched base pairs into toehold-mediated strand displacement – a fundamental primitive in most dynamic DNA devices and reaction networks. Previous findings that such mismatches can impede strand displacement are extended insofar as it is shown that this impediment is highly dependent on mismatch position. This discovery is examined in detail, both experimentally and through simulations created with a coarse-grained model of DNA. It is shown that this effect allows for kinetic control of strand displacement decoupled from reaction thermodynamics. The second proposal improves upon a previously presented strand displacement scheme, in which two strands perform displacement cooperatively. This scheme is extended to be cascadable, so that the output of one such reaction serves as input to the next. This scheme is implemented in reaction networks capable of performing fundamental calculations on directed graphs. The third proposal is exclusively concerned with a novel observation methodology. This method is based on single-molecule fluorescence microscopy, and uses quantum dots, a fluorescent type of semiconductor nanocrystal, as a label. These quantum dots display a set of characteristics particularly promising for single-molecule studies on the time- and length scales most commonly encountered in DNA nanotechnology. This method is shown to allow for highly precise measurements on static DNA devices. Preliminary data for the observation of a complex dynamic device is also presented.

The primary purpose of newborn screening is to quickly identify children that are at risk of having a specific disorder in order to start treatment, prevent early death and reduce the chances of permanent physical or mental damage. The current and widely accepted approach used for identification of metabolism disorders involves a flow injection analysis with mass spectrometry detection of acylcarnitines and amino acids. Although this approach is widely accepted and has shown to be sufficient for identification of multiple metabolism disorders the method is not fully quantitative and results often have to be confirmed by second-tier tests. The primary focus of this research was to improve the accuracy and selectivity of this screening method by employing a high resolution chromatographic separation for the combined analysis of twelve acylcarnitines and seven amino acids. This method is an improvement over the current methodology allowing for separation of key isomers that are diagnostic for different metabolism disorders, reducing the need for multiple second-tier tests to confirm results and shortening the time to diagnosis. In order to further improve the efficiency of newborn screening we developed an in-line desorption device, which allows for direct analysis of DBS eliminating the need for punching disks from the filter paper cards. Our device was the first published paper that demonstrated the ability to directly analyze dried blood spots, without the need for any offline sample processing. Using this device, we validated a method to quantify biomarkers related to Maple Syrup Urine Disease, a disorder that requires a second-tier test for confirmation. To further improve the accuracy of dried blood spot analysis we evaluated a technique to correct the sample volume in low and high hematocrit samples. The level of hematocrit in blood spotted on filter paper cards affects the volume of sample analyzed, leading to errors in accuracy. Diffuse reflectance was used to relate differences in sample hematocrit on dried blood spots. We validated our technique with eighteen donor samples at various levels of hematocrit. Correcting sample volume for hematocrit showed improved precision and accuracy over the standard approach, ultimately reducing the potential to misidentify samples.

La cristallographie des rayons-X à ultra-haute résolution permet d'analyser la distribution de charge des molécules et d'étudier les interactions intermoléculaires avec précision. Des études structurales de plusieurs composés à base de thiophène ont été menées à bien, et le phénomène de désordre a été discuté. Des analyses expérimentales et théoriques de la densité de charge de deux molécules importantes ont été réalisées en utilisant le modèle d'atome multipolaire. Un nouveau modèle d'atomes virtuels est également testé : il permet le calcul rapide des propriétés électrostatiques. La liaison hydrogène avec l'oxygène comme accepteur est étudiée par l'analyse extensive de plus de 500.000 structures cristallines. Les résultats de stéréochimie sont comparés avec la densité électronique des atomes d'oxygène dans différents environnement chimiques, ce qui permet de montrer la dépendance directionnelle des liaisons hydrogène et des formes et orientations des paires d'électrons libres. Finalement, il est montré qu'en l'absence de données de diffraction des rayons X à haute résolution, le principe de transférabilité des paramètres de la densité électronique peut être exploité pour étudier les propriétés électrostatiques et les interactions intermoléculaires. Ce principe a été utilisé avec succès sur une petite molécule à base de thiophène et sur la protéine FAD-dépendante Cholestérol oxydase / Ultra high resolution X-ray crystallography allows for analyzing the charge distribution in the molecules and provides methods to study the intermolecular interactions at a deeper level. Structural studies of several thiophene based compounds have been carried out and the phenomenon of disorder has been discussed. Experimental and theoretical charge density analysis of two important molecules was performed using a multipolar atom model. A new virtual atom model is also tested which allows for a rapid calculation of the electrostatic properties. The hydrogen bonding with oxygen atom acceptor is studied through an extensive survey of more than 500,000 crystal structures. The stereo chemical results are compared with the electron density of the oxygen atoms in different chemical environments which give conclusive evidences for the dependence of directionality of hydrogen bonds on the shape and orientation of the electrons lone pairs. Finally, it has been shown that how in the absence of high resolution X-rays data, principle of transferability of electron density parameters between molecules can be used to study the electrostatic properties and the intermolecular interactions. This principle has been successfully applied to a small thiophene based molecule and the large FAD binding protein Cholesterol oxidase

Classification of road network from airborne laser scanning data and from remote sensing images with high resolution Abstract Object classification of land cover is currently one of the methods of remote Earth exploration. Road network classification only is unique because it is covered with anthropogenic material and has different characteristics than other elements of the landscape. This work deals with the possibility of using a combination of data from airborne laser scanning and high resolution optical data for detection of the road network in the specific area. The premise is that the use of two different types of data could provide better results, because airborne laser scanning data provide very precise information about the position and height of the point, while satellite data of very high resolution represent the real landscape. Searching for suitable features and classification rules for unambiguous determination of the road network is one of the objectives of the work. Segmentation parameters will also be important for object classification. Another objective is to verify the transferability of classification schemes into the other scene. The results should present a response on whether a procedure can be applied over a different location and also that the use of two types of data can bring...

The research investigated whether a Latent Semantic Analysis (LSA)-based approach to image retrieval can map pixel intensity into a smaller concept space with good accuracy and reasonable computational cost. From a large set of computed tomography (CT) images, a retrieval query found all images for a particular patient based on semantic similarity. The effectiveness of the LSA retrieval was evaluated based on precision, recall, and F-score. This work extended the application of LSA to high-resolution CT radiology images. The images were chosen for their unique characteristics and their importance in medicine. Because CT images are intensity-only, they carry less information than color images. They typically have greater noise, higher intensity, greater contrast, and fewer colors than a raw RGB image. The study targeted level of intensity for image features extraction. The focus of this work was a formal evaluation of the LSA method in the context of large number of high-resolution radiology images. The study reported on preprocessing and retrieval time and discussed how reduction of the feature set size affected the results. LSA is an information retrieval technique that is based on the vector-space model. It works by reducing the dimensionality of the vector space, bringing similar terms and documents closer together. Matlab software was used to report on retrieval and preprocessing time. In determining the minimum size of concept space, it was found that the best combination of precision, recall, and F-score was achieved with 250 concepts (k = 250). This research reported precision of 100% on 100% of the queries and recall close to 90% on 100% of the queries with k=250. Selecting a higher number of concepts did not improve recall and resulted in significantly increased computational cost.

Abstract Charge density studies have been conducted on ten CB1 cannabinoid receptor antagonists via high resolution x-ray crystallography. Bond critical point values and various other properties derived from these studies including the electrostatic potential were analyzed in correlation to the affinity of each compound with the CB1 receptor. Correlation/anti-correlation was found between several properties and Ki. The data was also interpreted by principal component analysis with three principal components accounting for 85% of the data variation. Data mining was limit due to the low sample count and the requirements set for the inclusion of correlated/anti-correlated variables left fewer variables to analyze. The model presented is left for future interpretation.

Les crayons combustibles au sein des Réacteurs à Eau Pressurisée (REP) sont constitués de pastilles de céramique (UO2 ou (U-Pu)O2) empilées dans des gaines en alliage de zirconium, le Zircaloy. Avant l'irradiation, il existe un jeu de fabrication entre les pastilles et la gaine de l'ordre d'une centaine de microns. Au cours de l'irradiation, ce jeu est rapidement réduit ou totalement rattrapé du fait des différentes déformations que subissent les pastilles et la gaine. La connaissance de la nature de ce contact pastille-gaine à chaud, nécessaire pour comprendre les phénomènes et valider les modélisations de l'évolution de l'état de l’interface en fonction du taux de combustion, est accessible aujourd’hui exclusivement à partir de mesures destructives effectuées en laboratoire de haute activité, après retour à froid des combustibles. Pour obtenir un plus grand nombre d’informations sur des zones d’intérêt étendues, ou sur un tronçon de crayon avant refabrication pour ré-irradiation en réacteur expérimental, un moyen de caractérisation non destructif de l’interface pastille-gaine est nécessaire. C'est dans ce contexte que l'Institut d'Electronique et des Systèmes UMR CNRS 5214 de l'Université de Montpellier développe, dans le cadre d'une collaboration avec le Commissariat à l'Energie Atomique et aux Energies Alternatives, et en partenariat avec EDF et Framatome, un microscope acoustique adapté aux géométries cylindriques. Le travail mené au cours de cette thèse inclut la conception et l’adaptation d’une tête de mesure sur un banc prototype et la démonstration de la faisabilité de l’acquisition d’images haute résolution (quelques dizaines de microns) sur tubes de gaine, l’enjeu étant de conserver la focalisation sur l’ensemble des zones imagées sur un même tube de diamètre externe de l’ordre de 10 mm et de longueur de 100 à 500 mm. La difficulté à reproduire les conditions de contact pastille-gaine en laboratoire ont orienté le choix des échantillons simulants, élaborés à partir de tubes de gaine avec ou sans zircone et chargés localement de colle. Les acquisitions réalisées sur ces échantillons simulants montrent la capacité de la méthode à détecter les changements de structure de la surface interne de la gaine. La mesure est ainsi sensible à la présence d’une couche de zircone interne d’épaisseur de 10 $mu$m, et à la présence de matériau adhérent à l’intérieur du tube. Ces résultats montrent l’intérêt de poursuivre ces études, pour améliorer grâce à du traitement du signal l’interprétation des images avec pour objectif final l’adaptation de la méthode et sa qualification sur un banc sur crayon irradié. / Pressurized Water Reactor (PWR) fuel rods are made of ceramic pellets (UO2,(U,Pu)O2 or gadolinium fuel) assembled in a zirconium alloy cladding tube. By design, an initial gap, filled with helium, exists between these two elements. However during irradiation this gap decreases gradually, on the one hand, owing to a variation in cladding diameter, due to creepdown caused by pressure from the coolant, and, on the other hand, increased pellet diameter, due to thermal expansion, and swelling. In hot conditions, during the second or third cycle of irradiation, the pellet/cladding gap is closed. However, during the return to cooler conditions, the gap can reopen. At a high burnup (generally beyond the 3rd cycle of irradiation) an inner zirconia layer of the order of 10 to 15 $mu$m is developed by oxidation leading to a chemical bonding between the pellet and the cladding. This bonding layer may contribute to a non-reopening of the pellet-cladding gap.Currently, only destructive examinations, after cutting fuel rods, allow the visualization of this area, however, they require a preliminary preparation of the samples in a hot cell. This limits the number of tests and measurements on the fuel rods. In this context, the Institute of Electronic and Systems of Montpellier University (IES - UMR CNRS 5214), in collaboration with the Alternative Energies and Atomic Energy Commission (CEA), Electricité de France (EDF) and Framatome, is developing a high frequency acoustic microscope adapted to the control and imaging of the pellet/cladding interface by taking into account the complexity of the structure's cladding which has a tubular form. Because the geometrical, chemical and mechanical nature of the contact interface is neither axially nor radially homogeneous, the ultrasonic system must allow the acquisition of 2D images of this interface by means of controlled displacements of the sample rod along both its axis and its circumference. The final objective of the designed acoustic microscope is to be introduced in hot cells.