The National Research Council recently called for a more interdisciplinary approach to drinking water research to address the critical issue of global drinking water supplies. Hypolimnetic oxygenation systems (HOₓ) are being increasingly used to improve water quality in stratified reservoirs by increasing dissolved oxygen (O₂) concentrations and subsequently suppressing the release of soluble species such as iron (Fe) and manganese (Mn) from the sediment into the water. However, while the influence of HOx on the water column has been established, little work has been done on how oxygenation affects sediment O₂ uptake (i.e., sediment oxygen demand) and other sediment-water fluxes. In response to the growing need for alternative approaches for improving water quality, we conducted highly interdisciplinary research to evaluate how O₂, Fe, and Mn cycling at the sediment-water interface is influenced by both natural and HOx-induced variations in water column dynamics, chemical redox processes, and microbial activity within the sediment, all of which may govern sediment-water fluxes. Studies were performed in an alpine lake in Switzerland and in an HOₓ-equipped drinking-water-supply reservoir in Virginia. This research was based on in situ field campaigns paired with laboratory experiments, microbial analyses, and computer simulation to elucidate variable sediment O₂ uptake and corresponding Fe and Mn cycling. This work is unique in that sediment-water fluxes were assessed using in situ data from both sides of the sediment-water interface. Results show that sediment O₂ uptake flux is strongly controlled by both wind- and HOₓ-induced dynamic forcing. Our findings reveal that Fe and Mn fluxes were suppressed from the bulk hypolimnion via biogeochemical cycling in the oxic benthic region. Results also indicate that the sediment microbial community structure may directly respond to HOₓ-induced variation in sediment O₂ availability. Additionally, based on an analysis of the robustness of several commonly used methods for flux calculations, we show that flux estimates are not strongly dependent on the method chosen for analysis. Ultimately, by emphasizing the highly transient nature of sediment O₂ uptake, this research will aid in accurate characterization of various sediment-water fluxes and corresponding water quality. Our results will also directly contribute to the optimization of HOₓ operations and lake and reservoir management. / Ph. D.

De nombreux corps du système solaire possèdent des enveloppes liquides internes, comme par exemple les noyaux métalliques des planètes telluriques et les océans profonds des satellites de glace de Jupiter et Saturne, dans lesquelles se produisent des courants de convection. La modélisation de la dynamique de ces enveloppes est cruciale pour comprendre la génération des champs magnétiques planétaires (pour les noyaux) et pour mieux déterminer l’habitabilité potentielle des satellites joviens. La convection dans ces enveloppes est généralement produite par la combinaison d’au moins deux sources de flottabilité : une source thermique et une source solutale. Une telle situation est plus complexe qu’un régime de convection purement thermique ou purement solutale, d’une part en raison de l’existence d’un couplage thermochimique lorsqu’un processus de fusion ou de cristallisation se produit à l’une des frontières de l’enveloppe, et d’autre part à cause de la forte différence de diffusivité moléculaire entre les champs thermique et compositionnel qui permet potentiellement le développement d’instabilités double-diffusives. Classiquement, ces complexités ont été ignorées dans les simulations numériques de la dynamo terrestre ; les champs thermique et compositionnel ayant été combinés en une seule variable nommée « codensité ». Cette approche est sans doute simpliste mais permet d’esquiver une difficulté technique liée à la description du champ compositionnel dont la très faible diffusivité nécessite de recourir à des méthodes numériques adaptées. Cette thèse présente d’abord l’implémentation d’une méthode semi-Lagrangienne du type « particle-in-cell » dans un code de dynamo pré-existant, permettant ainsi de traiter de manière plus réaliste le champ de composition dans les enveloppes liquides internes des planètes. Les optimisations réalisées sont détaillées ainsi que les résultats de tests sur des cas de benchmark qui valident cet outil. Une comparaison avec des méthodes Eulériennes est également présentée. Une première exploration de la physique de la convection compositionnelle et thermochimique en rotation dans la limite d’un nombre de Prandtl compositionnel infini est ensuite conduite dans le contexte du noyau liquide terrestre. Il est montré que la dynamique convective est très différente de celle de la convection thermique pure. Notamment, les matériaux légers injectés à la frontière graine/noyau liquide sont capables d’atteindre la frontière noyau/manteau et de s’y accumuler pour former une couche chimiquement stratifiée, dont l’existence a été évoquée théoriquement mais qui n’a jamais pu être produite dans de précédentes simulations. Enfin, la dynamique double-diffusive des couches stratifiées est également discutée, et de premières simulations de « salt fingers » sont présentées. / Numerous planetary bodies contain internal liquid layers in which convective currents are generated by the combination of buoyancy sources of thermal and compositional origin. The strong difference between the thermal and chemical molecular diffusivities and the possibility of thermo-chemical coupling at melting or freezing boundaries create a convective regime that is much more complex than pure thermal convection, partly due to the potential occurrence of double-diffusive instabilities. Traditionally, numerical simulations have modeled the dynamics of the liquid part of planetary cores in a more simplistic way by neglecting the diffusivity difference and combining both fields into one single variable, an approximation that is convenient but maybe not relevant. However, distinguishing both fields and dealing with a large or infinite diffusivity ratio makes it compulsory to use numerical methods that minimize numerical diffusion as much as possible. In this thesis, I adapted a semi-Lagrangian particle-in-cell method into a pre-existing dynamo code to describe the weakly diffusive compositional field. I optimized the code for massively parallel computing and validated it on two different benchmarks. I compared the particle-in-cell method to Eulerian schemes and showed that its advantages extend beyond its lower numerical dissipation. Using this new tool, I performed first numerical simulations of rotating pure compositional and thermochemical convection in the limit of null chemical diffusivity. I explored the physics of pure compositional convection and addressed questions related to the existence and the dynamics of a stratified layer below the Earth’s core mantle boundary. In particular, I showed that the stratification could potentially be of chemical origin and proposed some mechanisms to explain its formation. In the case of a thermally stratified layer, I performed a scaling analysis of fingering instabilities, wrote the first steps of a linear stability analysis and ran a few simulations of fingering instabilities in the rotating case. The potential effects of the magnetic field and the coupling of thermochemical boundary conditions in planetary cores are finally discussed in this thesis.

Le contrôle de la température d'un milieu thermique reste d'une grande importance en raison du coût économique qu'il peut engendrer. Ainsi, un moyen efficace de réduire les coûts de chauffage/refroidissement est de fournir un bon système de contrôle qui limite l'énergie nécessaire pour exécuter ces tâches. À cette fin, nous étudierons le contrôle d'une interface diffusive homogène finie utilisant le contrôleur CRONE de trois générations et contrôlons leurs comportements. La nouveauté de ce travail existe dans l'utilisation d'un contrôleur de commande fractionnaire (le contrôleur CRONE) appliqué à une unité d'ordre fractionnaire et l'utilisation d'un contrôleur complexe (la troisième génération) qui n'est pas si familier dans le domaine des contrôleurs. Les résultats montrent le comportement et la robustesse des contrôleurs CRONE de trois générations. / Controlling thermal medium’s temperature remains of a great importance, because of the economic cost that it may engender. Thus, one effective way to reduce heating/cooling cost is by providing a good control system that limits power needed to run these tasks. For this purpose, we will study the control of a finite homogeneous diffusive interface using the three generations CRONE controller and control their behaviors. The novelty of this work exists in the use of a fractional order controller (the CRONE controller) applied to a fractional order plant and the use of a complex controller (the third generation) which is not so familiar in the controllers domain. The results show the behavior and the robustness of the three generations CRONE controllers.

Cette thèse est consacrée à l’étude des modèles microscopiques pour la dérivation de la conduction de la chaleur. Démontrer rigoureusement une équation diffusive macroscopique à partir d’une description microscopique du système est à aujourd’hui encore un problème ouvert. On étudie un système décrit par l’équation de Schrödinger linéaire discrète (DLS) en dim 1, perturbé par une dynamique stochastique conservative. On peut montrer que le système a une limite hydrodynamique donnée par la solution de l’équation de la chaleur. Quand le système est rattaché aux bords à deux réservoirs de Langevin à deux différents potentiels chimiques, on peut montrer que l’état stationnaire, dans la limite vers l'infinie, satisfait la loi de Fourier. On étudie une chaine des oscillateurs anharmonique immergée en un réservoir de chaleur avec un gradient de température. On exerce une tension, variable dans le temps, à une des deux extrémités de la chaine, et l’autre reste fixe. On montre que sous un changement d’échelle diffusive dans l’espace et dans le temps, la distribution d’étirement de la chaine évolue selon un équation diffusive non-linéaire. On développe des estimations qui reposent sur l’hypocoercitivité entropique. La limite macroscopique peut être utilisée pour modéliser les transformations thermodynamique isothermiques entre états stationnaire de non-équilibre. / The object of research of this thesis is the derivation of heat equation from the underlying microscopic dynamics of the system. Two main models have been studied: a microscopic system described by the discrete Schrödinger equation and an anharmonic chain of oscillators in presence of a gradient of temperature. The first model considered is the one-dimensional discrete linear Schrödinger (DLS) equation perturbed by a conservative stochastic dynamics, that changes the phase of each particles, conserving the total norm (or number of particles). The resulting total dynamics is a degenerate hypoelliptic diffusion with a smooth stationary state. It has been shown that the system has a hydrodynamical limit given by the solution of the heat equation. When it is coupled at the boundaries to two Langevin thermostats at two different chemical potentials, it has been proven that the stationary state, in the limit to infinity, satisfies the Fourier’s law. The second model considered is a chain of anharmonic oscillators immersed in a heat bath with a temperature gradient and a time varying tension applied to one end of the chain while the other side is fixed to a point. We prove that under diffusive space-time rescaling the volume strain distribution of the chain evolves following a non-linear diffusive equation. The stationary states of the dynamics are of non-equilibrium and have a positive entropy production, so the classical relative entropy methods cannot be used. We develop new estimates based on entropic hypocoercivity, that allows to control the distribution of the positions configurations of the chain. The macroscopic limit can be used to model isothermal thermodynamic transformations between non-equilibrium stationary states. CEMRACS project on simulating Rayleigh- Taylor and Richtmyer-Meshkov turbulent mixing zones with a probability density function method at last.

Capillarity and dynamic wetting of non-Newtonian fluids are important in many natural and industrial processes, examples cover from a daily phenomenon as splashing of a cup of yogurt to advanced technologies such as additive manufacturing. The applicable non-Newtonian fluids are usually viscoelastic compounds of polymers and solvents. Previous experiments observed diverse interesting behaviors of a polymeric droplet on a wetted substrate or in a microfluidic device. However, our understanding of how viscoelasticity affects droplet dynamics remains very limited. This work intends to shed light on viscoelastic effect on two small scale processes, i.e., the motion of a wetting contact line and droplet splitting at a bifurcation tip.   Numerical simulation is employed to reveal detailed information such as elastic stresses and interfacial flow field. A numerical model is built, combining the phase field method, computational rheology techniques and computational fluid dynamics. The system is capable for calculation of realistic circumstances such as a droplet made of aqueous solution of polymers with moderate relaxation time, impacting a partially wetting surface in ambient air.   The work is divided into three flow cases. For the flow case of bifurcation tube, the evolution of the interface and droplet dynamics are compared between viscoelastic fluids and Newtonian fluids. The splitting or non-splitting behavior influenced by elastic stresses is analyzed. For the flow case of dynamic wetting, the flow field and rheological details such as effective viscosity and normal stress difference near a moving contact line are presented. The effects of shear-thinning and elasticity on droplet spreading and receding are analyzed, under inertial and inertialess circumstances. In the last part, droplet impact of both Newtonian and viscoelastic fluids are demonstrated. For Newtonian droplets, a phase diagram is drawn to visualize different impact regions for spreading, splashing and gas entrapment. For viscoelastic droplets, the viscoelastic effects on droplet deformation, spreading radius and contact line motion are revealed and discussed. / <p>QC 20160329</p>

L’étude réalisée porte sur l’évaluation du niveau de contamination par les éléments traces métalliques (ETM) des sédiments de la rade de Toulon, une rade semi-fermée soumise à un fort impact anthropique. Le prélèvement de carottes d’interface en 52 points répartis sur l’intégralité de la Rade a permis d’établir une cartographie précise des caractéristiques sédimentaires et des teneurs en métaux/métalloïdes. Les résultats obtenus sur les sédiments de surface ont montré l’état de contamination significatif de la rade (en particulier en Cu, Hg, Pb, et Zn), notamment dans les zones les plus enclavées de la petite rade, où les teneurs peuvent dépasser de plusieurs ordres de grandeur les limites définies par la législation en vue d’opérations de dragage. La distribution de la contamination observée a clairement indiqué un export de la petite vers la grande rade (normalement moins exposée), probablement gouverné par des processus hydrodynamiques responsables de la remise en suspension du sédiment contaminé. Les profils sédimentaires de carottes d’interface prélevées dans des zones de contamination contrastée ont révélé la présence systématique de pics de contamination dans les 20 premiers cm. Compte tenu des taux de sédimentation déterminés, ceci démontrerait que la rade a été soumise à un épisode de multi-contaminations majeur, probablement lié aux conséquences de la 2nde guerre mondiale. L’analyse des eaux interstitielles et surnageantes (paramètres physico-chimiques, majeurs, traceurs diagénétiques et ETM) de ces carottes d’interface a permis d’étudier la mobilité des ETM dans le sédiment. Les profils obtenus apparaissent essentiellement contrôlés par des mécanismes diagénétiques et démontrent le rôle exercé par les principales phases porteuses présentes dans le sédiment (oxy-hydroxydes de Fe et de Mn, sulfures) sur la mobilité des ETM. La modélisation de ces profils a permis d’évaluer les flux diffusifs à l’interface eau sédiment, afin de déterminer l’action du sédiment, en tant que puits ou source de contamination pour la colonne d’eau. Les flux diffusifs sortant calculés apparaissent relativement faibles en comparaison des teneurs totales mesurées dans le sédiment, démontrant que la majorité des ETM est fortement immobilisée dans le sédiment.Enfin, ce travail a été complété par des expériences de remise en suspension en laboratoire et sur le terrain, visant à simuler différents scénarios possibles (tempête,trafic maritime, dragage). Dans les conditions étudiées, si pour certains ETM la remobilisation en solution est faible (ex. As, Hg), elle peut au contraire être très significative pour d’autres (ex. Cd, Cu, Pb) conduisant à une contamination non négligeable de la colonne d’eau. / This study deals with the assessment of sediment contamination levels by trace metals in the Toulon bay, a semi-closed Mediterranean area submitted to heavy anthropogenic inputs. The sampling of interface cores in 52 points located in thewhole bay allowed establishing a precise mapping of the sedimentary characteristics and the metals/metalloids contents. The obtained results from the surface sediments revealed a significant contamination of the bay (especially for Cu, Hg, Pb and Zn), mainly in the most enclosed parts of the small bay. There, the levels may exceed by several orders of magnitude the limits concerning dredging operations defined by the French legislation. The observed contamination distribution clearly indicated an export from the small to the large bay (normally less exposed) probably governed by hydrodynamic processes, responsible for the contaminated sediment resuspension. The sedimentary profiles of interface cores sampled in contrasted contamination areas revealed the presence of systematic contamination peaks in the first 20 cm. Taking into account the calculated sedimentation rate, this would demonstrate that the Toulon bay was submitted to a strong multi-contamination, probably linked to the 2nd world war. The analysis of interstitial waters (physico-chemical parameters,major, trace metals, and diagenetic tracers) allowed studying trace metals mobility. The obtained profiles appeared mainly controlled by diagenetic mechanisms and showed the major role of the main carrier phases present in the sediments (oxyhydroxides of Fe and Mn, sulphides). The modeling of these profiles led to the determination of the diffusive fluxes at the sediment/water interface, and so, to the action of the sediment as a sink or a source of contamination for the water column.The calculated outgoing diffusive fluxes appeared relatively low in comparison to the total contents measured in the sediment, proving that the main part of the studied trace metals remains in the sediment. Finally, resuspension experiments in lab and on field were performed with the aim to simulate different possible scenarios (storm,nautical traffic, dredging). Under the studied conditions, the remobilization can be low for some trace metals (e.g. As, Hg), but it may contrariwise be quite important for others (e.g. Cd, Cu, Pb) leading to a non-negligible contamination of the water column.

Ce mémoire de thèse a pour but de présenter un modèle de prédiction du transport des algues en mer le long des côtes. La méthode choisie a été d'utiliser un code industriel eulérien pour prédire l'écoulement moyen sur une grande surface, et d'ensuite ajouter un modèle lagrangien pour prédire le mouvement des particules individuelles. Ce modèle lagrangien comporte trois étapes. Premièrement, les caractéristiques moyennes du fluide trouvées avec le modèle eulérien sont utilisées pour alimenter un modèle stochastique pour trouver les vitesses turbulentes du fluide à l'emplacement des particules modélisant les algues. Ensuite ces vitesses turbulentes sont utilisées à travers les composantes de la force de traînée, de l'inertie, de la force de Basset et de la poussée d'Archimède pour trouver les vitesses des corps. La dernière étape consiste à utiliser ces vitesses des corps pour calculer leurs trajectoires. Une méthode avec un intégrateur exact a été développée pour résoudre ces équations. Ce modèle a ensuite été validé grâce à deux expériences. Dans la première expérience, des sphères de tailles différentes ont été lâchées dans deux fluides avec des densités différentes, où une turbulence stationnaire quasi-homogène a été générée en utilisant une paire de grilles oscillantes. Dans la deuxième expérience des particules sphériques ont été lâchées dans un écoulement non homogène. Cet écoulement a été obtenu en obstruant partiellement un canal, afin qu'une zone de recirculation soit générée. Le modèle de transport des particules a ensuite été testé sur des simulations d'un écoulement réel le long des côtes normandes, dans lequel des particules numériques représentant des algues ont été lâchées / The aim of this PhD thesis was to develop a model to predict the motion of algae in sea waters along a coastline. The method chosen was to use a large Eulerian industrial code to model the mean flow, and add Lagrangian model to predict the motion of individual particles. This Lagrangian modelis a three-step model. In the first modelling step, the mean flow characteristics at the location of the particles (solid bodies modelling the algae) are extracted from the Eulerian model and imputed into a stochastic model to find the turbulent fluid velocities. These fluid velocities are used in the second step to solve for the solid body velocities, by solving for the drag, momentum, buoyant and Basset history forces. The final modelling step is to use these solid body velocities to calculate the trajectories of particles. An exact integrator method was then developed to solve for these equations. The model was then validated using two experiments. Firstly sphere of different size were released in fluids of different densities, where a stationary quasi-homogeneous turbulence. This turbulence was generated by oscillating a pair of grids. In the second experiment spherical particles were released in anon-homogeneous turbulent flow. This flow was achieved by partially obstructing a channel, so that a recirculation zone was generated. The particle transport model was then tested numerically using the simulations of a real flow along the coasts of Normandy where numerical particles representing algae were released

The aim of this PhD thesis was to develop a model to predict the motion of algae in sea waters along a coastline. The method chosen was to use a large Eulerian industrial code to model the mean flow, and add Lagrangian model to predict the motion of individual particles. This Lagrangian modelis a three-step model. In the first modelling step, the mean flow characteristics at the location of the particles (solid bodies modelling the algae) are extracted from the Eulerian model and imputed into a stochastic model to find the turbulent fluid velocities. These fluid velocities are used in the second step to solve for the solid body velocities, by solving for the drag, momentum, buoyant and Basset history forces. The final modelling step is to use these solid body velocities to calculate the trajectories of particles. An exact integrator method was then developed to solve for these equations. The model was then validated using two experiments. Firstly sphere of different size were released in fluids of different densities, where a stationary quasi-homogeneous turbulence. This turbulence was generated by oscillating a pair of grids. In the second experiment spherical particles were released in anon-homogeneous turbulent flow. This flow was achieved by partially obstructing a channel, so that a recirculation zone was generated. The particle transport model was then tested numerically using the simulations of a real flow along the coasts of Normandy where numerical particles representing algae were released

Os processos de conversão de energia tendem a considerar cada vez mais restrições econômicas e ambientais, tornando-se necessário o entendimento da interação entre combustão e turbulência. Este trabalho tem como objetivo o desenvolvimento de soluções analíticas para a fração de mistura de uma chama difusiva, sob forma de um jato turbulento axissimétrico. Foi desenvolvida, também, uma metodologia analíticonumérica para a determinação das frações mássicas dos componentes, considerando uma reação de combustão de dois passos. Os resultados foram comparados com dados experimentais encontrados na literatura para uma chama de hidrogênio H2=N2 (50/50% em volume). De modo geral, os resultados obtidos foram satisfatórios frente aos dados experimentais, sendo a principal limitação o fato das expressões analíticas obtidas não serem capazes de representar o jato próximo à saída do bocal, sendo válidas a partir de, aproximadamente, x=d > 10, onde x é a coordenada ao longo do comprimento do jato. A principal vantagem do método empregado neste trabalho é a diminuição da complexidade do sistema de equações a ser resolvido numericamente. / The energy conversion processes tend to consider even more economical and environmental constraints, making it necessary to understand the interaction between combustion and turbulence. This study aims at the development of analytical solutions for the mixture fraction of a diffusive flame in the form of an axisymmetric turbulent jet. It was also considered an analytical-numerical approach for the determination of the mass fractions of the compounds, for a two-step reaction. The results were compared with data found in literature for a hydrogen flame H2=N2 (50/50 % by volume). Overall, the results were satisfactory when compared with the experimental data, however the principal limitation was the fact that the analytical expressions were not able to represent the jet near the nozzle exit, being the solution valid from, approximately, x=d > 10, where x is the coordinate along the jet length. The main advantage of the method employed in this work is the decrease in the complexity of the equations system to be solved numerically.

xii, 122 p. : ill. (some col.) A print copy of this thesis is available through the UO Libraries. Search the library catalog for the location and call number. / Biological molecular motors achieve directed motion and perform work in an environment dominated by thermal noise and in most cases incorporate thermally driven motion into the motor process. Inspired by bio-molecular motors, many other motor systems that incorporate thermal motion have been developed and studied. These motors are broadly referred to as Brownian motors. This dissertation presents simulation studies of two particular Brownian motors, the feedback-controlled flashing ratchet and an artificial molecular motor concept, the results of which not only drive experimental considerations but also illuminate physical behaviors that may be applicable to other Brownian motors. A flashing ratchet rectifies the motion of diffusive particles using a time dependent, asymmetric potential energy landscape, and the transport speed of the ratchet can be increased if information about the particle distribution is incorporated as feedback in the time dependency of the landscape. Using a Langevin Dynamics simulation, we compare two implementations of feedback control, a discrete algorithm and a continuous algorithm, and find that the discrete algorithm is less sensitive to fluctuations in the particle distribution. We also model an experimental system with time delay and find that the continuous algorithm can be improved by adjusting the feedback criteria to react to the expected state of the system after the delay time rather than the real-time state of the system. Motivated by the desire to understand bio-molecular linear stepping motors, we present a bottom-up approach of designing an artificial molecular motor. We develop a coarse-grained Molecular Dynamics model that is used to understand physical contributions to the diffusive stepping time of the motor and discover that partially reducing the diffusional space from 3D to 1D can dramatically increase motor speed. We also develop a stochastic model based on the classical Master equation for the system and explore the sensitivity of the motor to currently undetermined experimental parameters. We find that a reduced diffusional stepping time is critical to maintain motor attachment for many successive steps and explore an experimental design effect that leads to motor misstepping. / Committee in charge: Stephen Kevan, Chairperson, Physics; Heiner Linke, Member, Physics; John Toner, Member, Physics; Raghuveer Parthasarathy, Member, Physics; Marina Guenza, Outside Member, Chemistry