Initial investigation of Moxtek wire grid polarizers composed of Al and coated with SiO2 - SiX - SiO2 (where SiX is used to indicate a Si rich layer whose complete composition is not to be disclosed for proprietary reasons) showed a growth of 3x in the inner (closest to Al) SiO2 layer after baking. Upon removing the X and varying rib composition and layering composition and geometries in 12 sets of before and after samples, no obvious growth was observed. Even baking the original unbaked sample yielded no growth. Our data suggest that the initial conclusion of buried oxide growth was flawed and that the observed changes in optical properties upon baking are either very sensitive to layer thicknesses (smaller than we can confidently observe) or due to some other mechanism. Here we present our sample preparation and analysis using the Focused Ion Beam (FIB), Scanning Transmission Electron Microscopy (STEM), and Energy Dispersive Xray Spectroscopy (EDXS).

The detrimental influence of humans on the environment is of increasing concern. Humans, their livestock, and their pets have caused fecal contamination of waterways throughout the United States. Understanding the sources of fecal indicator bacteria (FIB) and the environmental processes that affect them can be crucial to reducing the number of impaired streams and limiting the negative impacts on the environment. Antibiotic resistance is an emerging issue facing human health in the United States and across the world. Antibiotic resistant bacteria (ARB) have antibiotic resistance genes (ARGs) that prevent antibiotics from killing them. Limited research has been done on the role of the environment in the propagation of antibiotic resistance. As the use of antibiotics increases, it is critical to examine how this impacts human health through the environment. Models of watersheds in Patillas, Puerto Rico and Christiansburg, Virginia were created using the Soil and Water Assessment Tool (SWAT) to compare how the differences in spatial and temporal sampling of FIB, climate, and population affect FIB movement. The performances of the calibrated bacteria models were comparable to other published studies. A primary challenge faced in this study was the use of grab samples taken months apart as monthly averages of FIB. The high precipitation and constant warm climate made the model for Patillas more difficult to fit because of the high variability in the observed data. While the Patillas watershed had a lower population of people and livestock, the Christiansburg watershed had more available data on wildlife. The lack of spatial variance of data and the use of data from 1993-2018, hindered the ability for the model for Patillas to model FIB. Additionally, the model's performance was limited due to the strong hurricanes that affect land use, soils, and populations of humans and animals in the watershed. Using open-source data needs to be explored further as a faster and more cost-effective way of developing SWAT FIB models. The feasibility to use data collected in the Christiansburg and Patillas watershed to calibrate a SWAT-ARB model was determined based on available ARG data. The results indicate that the bacteria models need to be improved before an effective SWAT-ARB model can be calibrated. One limitation in the available ARG data for the two watersheds was that they were only sampled once. Out of the ARGs sampled, sul1 was the best modeled in both watersheds because it has the highest normalized values and correlated with the amount of developed land. / Master of Science / Humans negatively impact the environment. Humans and animals contribute to the bacteria contamination of waterways. Investigation into where the contamination sources are and environmental processes that contribute can help researchers limit the impact on the environment. Bacteria can build resistance to antibiotics, which can be especially dangerous to humans and livestock when exposed. Little research has been done on how the environment has contributed to the spread of antibiotic resistance in bacteria. The Soil and Water Assessment Tool (SWAT) was used to investigate bacteria in the Patillas, Puerto Rico and Christiansburg, Virginia watershed. These models used data published by the United States Geological Survey (USGS) and Environmental Protection Agency (EPA) to improve performance. When comparing simulated data to observed data, the performances of the models were comparable to other published studies. The Patillas watershed was particularly difficult to model because of the warm climate and high precipitation that caused high variability in bacteria concentrations. Strong weather events including hurricanes and a lack of available data on wildlife were other hinderances to the Patillas model. In comparison, more published data on wildlife was available in the Christiansburg watershed and it had a more temperate climate. The SWAT-ARB model was reviewed and recommendations were made to improve the model. Using the previously collected antibiotic resistance bacteria data in the Christiansburg and Patillas watersheds, it would be impossible to create accurate models. More antibiotic resistance data needs to be taken across as a greater time period before the performance of the models can be assessed.

Les travaux présentés dans ce manuscrit, sont basés sur l'étude de l'auto-organisation de la matière à l'échelle nanométrique. A cette échelle, les énergies de surfaces jouent un rôle prépondérant dans cette organisation. Pour comprendre au mieux ses mécanismes nous avons étudié plusieurs types de structures à base de Silicium et de Germanium. Nous avons expérimentalement étudié la croissance cristalline ou amorphe sur différents types de substrats (amorphe : SiO2 et cristallins Si ou SOI). Certain de ces substrats furent nano-structurés en utilisant un faisceau d'ions focalisés de type Gallium ou Or-Silicium. De plus nous avons pu utiliser des surfaces différentes telle que le TiO2 ou le Silicium poreux, afin d'étudier l'organisation de la matière sur des pores de petites tailles (inférieurs à 50nm). / The following works are base on the study of self assembly structures at the nanometric scale. At this scale the surface energy have a major impact in this organization. For a better understanding of this mechanism we studied different Silicon-Germanium base structures. We experimentally studied the crystalline or amorphous growth on different types of substrates (amorphous: SiO2, crystalline: Si or SOI). Some of these substrates were nano-structured using a focused ion beam using gallium source or gold-silicon source. In addition, we were able to use different surfaces such as TiO2 or porous silicon to study the organization of the material small size pore(less than 50nm).

Les problématiques liées à la diminution de la taille des dispositifs actuels amènent l’industrie à réfléchir à des techniques de gravure ayant des résolutions à l’échelle de l’atome. Dans ce contexte, les techniques de nanostructuration directes sont très bien adaptées et représentent un potentiel important pour un futur proche dans les laboratoires de recherches. Le projet sur lequel j’ai travaillé avait pour but de coupler dans un environnement Ultra-Vide (UHV), un Dual-Beam, composé d’un FIB (Faisceau d’Ions Focalisé) et d’un MEB (Microscope électronique à balayage) et un bâti d’épitaxie par jet moléculaire (MBE), technique ultime en termes de dépôt. Cet environnement UHV répond à la nécessité de propreté absolue des substrats et constitue un moyen pertinent de rendre fonctionnels les dispositifs ainsi élaborés dans des domaines aussi variés que la micro-nanoélectronique, l’optoélectronique, le photovoltaïque, la spintronique, la plasmonique, etc. La connexion sous UHV de la nanofabrication FIB à la croissance MBE représente une voie unique pour fabriquer des structures 3D en alternant des étapes gravure/dépôt. Parmi les différentes applications, nous avons choisi de nous focaliser sur nanostructures de silicium. Le principal challenge pour l’industrie microélectronique et pour les chercheurs est d’être capable de réaliser une optoélectronique entièrement intégrée à base de Si. Cela nécessite de convertir les matériaux à base de Si en absorbeur/émetteur efficaces de lumière. Une des pistes les plus prometteuses pour obtenir une bande interdite directe est de combiner les effets de la fonctionnalisation chimique et du confinement quantique dans les nano-objets. / The reduction of device sizes represents a major issue in microelectronic industry which motivates several teams of researchers to develop nanopatterning with atomic resolution. In this context, maskless nanostructuration techniques are well-adapted and have an important potential for the nearest future in labs and industry. The aim of the project I worked on is the connection in a Ultra-High-Vacuum (UHV) environment between a Dual-Beam, equipped with a FIB (Focused Ion Beam) and a SEM (Scanning Electron Microscopy) and a MBE (Molecular Beam Epitaxy) cluster, which is the highest-controlled deposition technique. The UHV environment is the solution for an absolute cleanliness and represents a relevant way to fabricate functionalized devices for micro-nanoelectronics, optoelectronics, photovoltaic, spintronic, plasmonic, etc… This UHV connection combining FIB nanostructuration and epitaxy growth technique provides a unique platform to elaborate tridimensional structures with milling/deposition steps. Among different applications, we decided to focus on silicon based nanostructures. Regarding silicon nanostructures. The main challenge for microelectronics industry and for the researchers in this field is the realization of optoelectronics devices fully integrated in silicon systems. This requires to convert silicon based materials into absorber/emitter of light. One of the most promising way to change the electronic structure and to get a direct bandgap is the combination of chemical functionalization and quantum confinement into silicon based nano-objects.

Les illites et les chlorites sont des minéraux ubiquistes dans la plupart des roches diagénétiques. Leurs compositions chimiques dépendent des conditions physiques subies (pression, P ; température, T) et de la composition de l’encaissant (e.g. Vidal et al., 1999 ; Parra et al., 2002a, 2002b). Ces minéraux peuvent donc potentiellement être de très bons marqueurs de l’histoire de l’enfouissement, et sont à la base de nombreuses méthodes empiriques ou thermodynamiques d’estimation des conditions P-T.Une compilation de données naturelles et la comparaison des thermobaromètres existants ont permis d’établir leurs limitations respectives. Pour s’en affranchir, un nouveau modèle ordonné de solution solide pour les chlorites a été développé, qui rend compte des forts contenus en silicium observés dans les chlorites naturelles de basses températures. La calibration de ce nouveau thermobaromètre sur des domaines géologiques variés de BT-BP a été testée sur des analyses de chlorites naturelles de la Gulf Coast (Texas) au pic de température (où les données P-T ont été mesurées in situ) et montre d’excellents résultats. Concernant les illites, le modèle thermodynamique le plus abouti (Dubacq et al., 2010) a également été testé de manière à estimer sa précision. L’étude a été complétée par la quantification de l’influence du fer ferrique. Les analyses chimiques utilisées ont été obtenues grâce à un protocole analytique à haute résolution spatiale. Alliant FIB et MET-EDS, ce protocole a permis une étude microtexturale et chimique fine des chlorites et des illites. Il en ressort que ces minéraux possèdent une diversité intracristalline dans leurs compositions et que la zonation chimique résultante apparaît comme une potentielle source d’erreurs dans la calibration des thermobaromètres, tout en permettant d’envisager la notion d’équilibre à l’échelle locale.Cette approche a été utilisée pour quantifier les trajets P-T d’unités géologiques des Alpes de Glarus. Ces résultats, comparés à ceux obtenus avec des méthodes thermobarométriques conventionnelles, donnent une bonne image des processus d’enfouissement et d’exhumation des roches de basse température. Ainsi, il apparaît que chaque composition enregistre une portion du chemin P-T rétrograde. D’une manière générale, chaque zone d’un même cristal renvoie à une partie de l’histoire de la roche. / Illite and chlorite are ubiquitous in most diagenetic rocks. Their chemical compositions are sensitive to thermobarometric conditions (pressure, P; temperature, T) and the bulk composition (e.g. Vidal et al., 1999; Parra et al., 2002a, 2002b). These minerals can be good indicators of burial history, and are the basis of several empiric or thermodynamic methods to estimate P-T conditions. A compilation of natural data and the comparison of existing thermobarometers allowed to establish their limitations. To circumvent it, an ordered model of solid solution for chlorites was developed which considers Si-rich low-T compositions. The calibration of this new thermobarometer on various LT-LP geologic fields was tested on natural chlorites analysis of Gulf Coast (Texas) at metamorphic peak, and gives accurate results. Concerning illites, the thermodynamic model of Dubacq et al. (2010) was also tested to estimate its precision. The study was completed by the quantification of the Fe3+ effects. Chemical analyses were obtained by an analytical protocol with high spatial resolution. Combining FIB and EDX-TEM, this protocol allowed an accurate microstructural study of chlorites and illites. These minerals have an intracristalline diversity of their chemical composition. The resulting chemical zonation is a potential error in calibration of thermometers, but allowed consideration of local equilibrium.This approach was used to quantify the P-T path of geologic units in Alps (near Glarus). These results, compared to results of conventional thermobarometers, give a good representation of burial and exhumation process for low-T rocks. Thus, the chemistry records a part of retrograde P-T path and each part of a crystal zoning corresponds to a part of rocks history.

Les méta-matériaux offrent la possibilité d'obtenir des propriétés physiques nettement améliorées en comparaison avec celles des matériaux naturels. Dans ce travail, nous explorons une nouvelle variété de métamatériaux thermoélectriques à base de micro-et nano-structuration du silicium, sous la forme de super-réseaux verticaux, avec comme visée applicative la récupération d'énergie thermique ainsi que le refroidissement. En outre, nous focalisons nos efforts sur une méthodologie expérimentale permettant la réalisation de ces matériaux par des moyens simples et peu coûteux. La première partie de cette thèse sert d'introduction aux phénomènes thermiques qui constituent la base de la conduction électrique et de la dissipation de chaleur dans les nanostructures, respectivement par émission thermo-ionique et par la diffusion de phonons. Cette partie détaille également les principes et résultats de caractérisation thermique à l'aide des méthodes 3ω et 2ω. La deuxième partie de cette thèse décrit les approches de micro- nanostructuration descendante « top-down » et ascendante « bottom-up », en vue de la fabrication de super-réseaux nanométriques sur du silicium mono-cristallin. La nouvelle architecture verticale proposée soulève des défis technologiques qui sont traités à travers l'exploration de techniques expérimentales originales pour produire, d'une manière efficace et sur de grandes surfaces, des structures submicroniques à fort facteur de forme. Ces techniques comprennent l'utilisation de motifs résultant de lithographie traditionnelle combinée à l'extrusion pour en produire des structures volumiques. En outre, l'utilisation de nanofibres et de diblocs copolymères comme nano-motifs géométriques sont également présentés pour nous rapprocher davantage de l'objectif ultime du projet / Metamaterials offer the benefit of obtaining improved physical properties over natural materials. In this work, we explore a new variety of thermoelectric metamaterials based on silicon micro- and nano- structuration, in the form of vertical superlattices for use in energy-related applications. Additionally, we focus on a route towards fabricating these materials using simple and low-cost means compared to prior attempts. The first part of this thesis serves as an introduction to the thermal phenomena which form the basis for electrical conduction and heat dissipation by thermionic emission and phonon scattering at the nanoscale. These principles forms the crux of the device. This section also details the characterization principles and results using the 3ω and 2ω methods for thermal measurement. The second part of this thesis describes both top-down and bottom-up approaches towards fabricating nanoscale superlattices from single-crystalline silicon. The novel proposed vertical architecture raised technological challenges that were tackled through the exploration of original experimental techniques for producing high aspect ratio (HAR) structures in an effective manner and over large surface areas. These techniques include the use of traditional lithography patterning and subsequent extrusion of volumic structures. Additionally, the use of nanofibers and diblock copolymers as templates for further etching of HAR silicon nanostructures are also presented to bring us closer to the ultimate goal of the project

Graphene and other two-dimensional materials can be stacked together to form vander Waals heterostructures: synthetic crystals composed of different atomically thin layers with a bespoke electronic band structure. Structural characterisation of vander Waals heterostructures is difficult using conventional methods as the properties are almost entirely defined by the nature of the buried interfaces between dissimilar crystals. These methods also fall short of resolving the atomic structure of buried defects in van der Waals materials such as graphite. This work demonstrates the refinement and successful application of ion beam specimen preparation to produce cross sectional slices through these unique crystals so that they can be characterised by high resolution scanning transmission electron microscopy (STEM). Cross sectional specimen were prepared using in situ lift-out in a focused ion beam (FIB) dual-beam instrument. The fine polishing steps were optimised to prevent damage to the core of the specimen. High resolution STEM imaging of twin defects in graphene, hexagonal boron ni-tride and MoSe2 revealed that the boundaries are not atomically sharp but extended across many atoms. Advanced processing and analysis of these images uncovered fundamental mechanics which govern their geometry. This technique was further applied to complex transition metal dichalcogenide heterostructures to quantitatively determine the properties of buried interfaces between atomically thin crystals.

This study is focused on the technique for fabrication of high aspect ratio nanostructures by combining both the advantages of maskless patterning of focused ion beam (FIB) and anisotropic etching of inductively coupled plasma etcher (ICP) in CF4 atmosphere. The materials contain p-type (100) single crystal silicon and thermal silicon dioxide. The study details include¡G (1) The reliability of AFM when scanning isotropic and anisotropic nanostructures with high aspect ratio tip in tapping mode. (2) FIB direct writing test. (3) The influences of ICP parameters including ICP power, bias power, content of oxygen, and process pressure. After completion of above-mentioned items, an optimized condition is used to get the anisotropic Si-based high aspect ratio nanostructures of holes array, gratings and cylinder under 100nm. The smallest line width of single crystal silicon gratings is 48nm, and aspect ratio up to 2.36. The smallest line width of silicon dioxide gratings is about 100nm, height is 410nm and aspect ratio up to 2.36 measured by SEM. By combining both advantages of different systems, we can provide another simple and rapid method for nanofabrication.

This work is studying the layers of cerium oxide (doped with platinum) prepa- red by magnetron sputtering on different types of substrates. Attention is focused mainly on modes of growth and morfology of (Pt−)CeO2 layers. The study was carried out by scanning electron microscopy (SEM) and transmission electron microscopy (TEM). The specimens (lamellas) were created by using focused ion beam (FIB) with respect to transparency for electron beam and material contrast. The emphasis was on elimination of redeposition and minimize the amorphous layer of lamella. Representation of elements was determined by energy-dispersive spectroscopy (EDX) and electron-energy loss spectroscopy (EELS). 1

The goal of this work is to understand the relationships between electrode microstructure and mass transport resistances. One can use this information to predict cell performance from fundamental principles. This work includes new types of particle-scale 3D models for correlating and predicting the effects of electrode microstructure on both ionic and electronic transport. The 3D models imitate the sub-micrometer-scale arrangement of active material particles, carbon, binder, and pores and use FIB/SEM images as a basis for parameterization. The 3D models are based respectively on the statistical mechanics techniques of molecular dynamics and Monte Carlo. The approach closely related to molecular dynamics, named the dynamic particle packing (DPP) model, uses aggregates of spheres to recreate electrode microstructures. The other approach, named the stochastic grid (SG) model, is closely related to Monte Carlo techniques in which a small set of fundamental interdomain and bulk energy parameters are used to generate structures.In order to predict electrode microstructures we correlated the fundamental interdomain and bulk energy parameters for the SG model to electrode mass composition and porosity. We used the revised computer program, known as predict SG, to estimate structures of which there are no experimental measurements of electrode structure. From these predicted electrode structures we obtained electronic and ionic transport properties. This allowed us to estimate the trade-offs between ionic and electronic transport for different porosities and carbon fractions. We found from experimental measurements of electrode structure that carbon and binder formed distinct agglomerates. From the 3D models we determined at commercial fractions of carbon and binder that the conductivity of these carbon agglomerates plays a large role in determining both the electronic and ionic pathways. So in order to better understand the role that these carbon/binder agglomerates play, we explored and developed several experimental methods to find the electronic and ionic conductivity of both simulated carbon domains and complete electrode films. The goal was not only to elucidate the role carbon agglomerates play, but also to develop a non-destructive method of determining overall film properties. Although we found that a non-destructive method is extremely challenging due to probe contact resistances, we did find success in determining carbon domain properties using a delamination method.