<p>The fluid dynamics of blood in the systemic circulation modulates production of nitric oxide (NO), a potent vasodilator. Non-invasive techniques such as the flow-mediated dilation (FMD) test and physiologic phenomena associated with autonomic stress induce hyperemia and subsequently higher levels of wall shear stress (WSS), stimulating endothelial nitric oxide synthase (eNOS) expression. In the current clinical practice, WSS–a key regulator of endothelial function–is commonly estimated assuming a parabolic velocity distribution, despite the evidence that the temporal changes of pulsatile blood flow over the cardiac cycle modulate vasodilation in mammals. This work investigates the effect of cardiovascular stress on local WSS distributions and the potential for near-wall accumulation of nitrite, the vasoactive storage form of NO in the bloodstream. The specific aims of the project are therefore as follows: 1) develop a reduced-order model of the major systemic vasculature at rest, during a flight-or-flight response, and under moderate levels of aerobic exercise; 2) derive a velocity-driven Womersley solution for pulsatile flow to support accurate estimation of pulsatile WSS in the clinical setting; and 3) quantify cumulative transport of nitrite in a multiscale model of bifurcating vasculature utilizing computational fluid dynamics (CFD). Development of these open-source, translatable methods enable accurate quantification of hemodynamics and species transport during cardiovascular stress. Results detailed herein extend our knowledge about regulation of regional blood flow during autonomic stress, suggest a convergent evolutionary theory for having a complete circle of Willis, and potentially clarify reproducibility concerns associated with the FMD test. </p>

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Ultrasound acoustic energy transfer (UAET) is an emerging contactless technology that offers the capability to safely and efficiently power sensors and devices while eliminating the need to replace batteries, which is of interest in many applications. It has been proposed to recharge and communicate with implanted medical devices, thereby eliminating the need for invasive and expensive surgery and also to charge sensors inside enclosed metal containers typically found in automobiles, nuclear power plants, space stations, and aircraft engines. In UAET, energy is transferred through the reception of acoustic waves by a piezoelectric receiver that converts the energy of acoustic waves to electrical voltage. It has been shown that UAET outperforms the conventional CET technologies that use electromagnetic waves to transfer energy, including inductive coupling and capacitative coupling. To date, the majority of research on UAET systems has been limited to modeling and proof-of-concept experiments, mostly in the linear regime, i.e., under small levels of acoustic pressure that result in small amplitude longitudinal vibrations and linearized piezoelectricity. Moreover, existing models are based on the "piston-like" deformation assumption of the transmitter and receiver, which is only accurate for thin disks and does not accurately account for radiation effects. The linear models neglect nonlinear effects associated with the nonlinear acoustic wave propagation as well as the receiver's electroelastic nonlinearities on the energy transfer characteristics, which become significant at high source strengths. In this dissertation, we present experimentally-validated analytical and numerical multiphysics modeling approaches aimed at filling a knowledge gap in terms of considering resonant acoustic-piezoelectric structure interactions and nonlinear effects associated with high excitation levels in UAET systems. In particular, we develop a reduced-order model that can accurately account for the radiation effects and validate it by performing experiments on four piezoelectric disks with different aspect ratios. Next, we study the role of individual sources of nonlinearity on the output power characteristics. First, we consider the effects of electroelastic nonlinearities. We show that these nonlinearities can shift the optimum load resistance when the acoustic medium is fluid. Next, we consider the nonlinear wave propagation and note that the shock formation is associated with the dissipation of energy, and as such, shock formation distance is an essential design parameter for high-intensity UAET systems. We then present an analytical approach capable of predicting the shock formation distance and validate it by comparing its prediction with finite element simulations and experimental results published in the literature. Finally, we experimentally investigate the effects of both the nonlinearity sources on the output power characteristics of the UAET system by considering a high intensity focused ultrasound source and a piezoelectric disk receiver. We determine that the system's efficiency decreases, and the maximum voltage output position drifts towards the source as the source strength is increased. / Doctor of Philosophy / Advancements in electronics that underpinned the development of low power sensors and devices have transformed many fields. For instance, it has led to the innovation of implanted medical devices (IMDs) such as pacemakers and neurostimulators that perform life-saving functions. They also find applications in condition monitoring and wireless sensing in nuclear power plants, space stations, automobiles and aircraft engines, where the sensors are enclosed within sealed metal containers, vacuum/pressure vessels or located in a position isolated from the operator by metal walls. In all these applications, it is desired to communicate with and recharge the sensors wirelessly. Such a mechanism can eliminate the need for invasive and expensive surgeries to replace batteries of IMDs and preserve the structural integrity of metal containers by eliminating the need for feed through wires. It has been shown that ultrasound acoustic energy transfer (UAET) outperforms conventional wireless power transfer techniques. However, existing models are based on several assumptions that limit their potential and do not account for effects that become dominant when a higher output power is desired. In this dissertation, we present experimentally validated numerical and theoretical investigations to fill those knowledge gaps. We also provide crucial design recommendations based on our findings for the efficient implementation of UAET technology.

Reduced-order models are frequently used in the simulation of complex flows to overcome the high computational cost of direct numerical simulations, especially for three-dimensional nonlinear problems. Proper orthogonal decomposition, as one of the most commonly used tools to generate reduced-order models, has been utilized in many engineering and scientific applications. Its original promise of computationally efficient, yet accurate approximation of coherent structures in high Reynolds number turbulent flows, however, still remains to be fulfilled. To balance the low computational cost required by reduced-order modeling and the complexity of the targeted flows, appropriate closure modeling strategies need to be employed. In this dissertation, we put forth two new closure models for the proper orthogonal decomposition reduced-order modeling of structurally dominated turbulent flows: the dynamic subgrid-scale model and the variational multiscale model. These models, which are considered state-of-the-art in large eddy simulation, are carefully derived and numerically investigated. Since modern closure models for turbulent flows generally have non-polynomial nonlinearities, their efficient numerical discretization within a proper orthogonal decomposition framework is challenging. This dissertation proposes a two-level method for an efficient and accurate numerical discretization of general nonlinear proper orthogonal decomposition closure models. This method computes the nonlinear terms of the reduced-order model on a coarse mesh. Compared with a brute force computational approach in which the nonlinear terms are evaluated on the fine mesh at each time step, the two-level method attains the same level of accuracy while dramatically reducing the computational cost. We numerically illustrate these improvements in the two-level method by using it in three settings: the one-dimensional Burgers equation with a small diffusion parameter, a two-dimensional flow past a cylinder at Reynolds number Re = 200, and a three-dimensional flow past a cylinder at Reynolds number Re = 1000. With the help of the two-level algorithm, the new nonlinear proper orthogonal decomposition closure models (i.e., the dynamic subgrid-scale model and the variational multiscale model), together with the mixing length and the Smagorinsky closure models, are tested in the numerical simulation of a three-dimensional turbulent flow past a cylinder at Re = 1000. Five criteria are used to judge the performance of the proper orthogonal decomposition reduced-order models: the kinetic energy spectrum, the mean velocity, the Reynolds stresses, the root mean square values of the velocity fluctuations, and the time evolution of the proper orthogonal decomposition basis coefficients. All the numerical results are benchmarked against a direct numerical simulation. Based on these numerical results, we conclude that the dynamic subgrid-scale and the variational multiscale models are the most accurate. We present a rigorous numerical analysis for the discretization of the new models. As a first step, we derive an error estimate for the time discretization of the Smagorinsky proper orthogonal decomposition reduced-order model for the Burgers equation with a small diffusion parameter. The theoretical analysis is numerically verified by two tests on problems displaying shock-like phenomena. We then present a thorough numerical analysis for the finite element discretization of the variational multiscale proper orthogonal decomposition reduced-order model for convection-dominated convection-diffusion-reaction equations. Numerical tests show the increased numerical accuracy over the standard reduced-order model and illustrate the theoretical convergence rates. We also discuss the use of the new reduced-order models in realistic applications such as airflow simulation in energy efficient building design and control problems as well as numerical simulation of large-scale ocean motions in climate modeling. Several research directions that we plan to pursue in the future are outlined. / Ph. D.

This dissertation uses spatial filtering to develop a large eddy simulation reduced order model (LES-ROM) framework for fluid flows. Proper orthogonal decomposition is utilized to extract the dominant spatial structures of the system. Within the general LES-ROM framework, two approaches are proposed to address the celebrated ROM closure problem. No phenomenological arguments (e.g., of eddy viscosity type) are used to develop these new ROM closure models. The first novel model is the approximate deconvolution ROM (AD-ROM), which uses methods from image processing and inverse problems to solve the ROM closure problem. The AD-ROM is investigated in the numerical simulation of a 3D flow past a circular cylinder at a Reynolds number $Re=1000$. The AD-ROM generates accurate results without any numerical dissipation mechanism. It also decreases the CPU time of the standard ROM by orders of magnitude. The second new model is the calibrated-filtered ROM (CF-ROM), which is a data-driven ROM. The available full order model results are used offline in an optimization problem to calibrate the ROM subfilter-scale stress tensor. The resulting CF-ROM is tested numerically in the simulation of the 1D Burgers equation with a small diffusion parameter. The numerical results show that the CF-ROM is more efficient than and as accurate as state-of-the-art ROM closure models. / Ph. D.

Les moteurs de fusées à ergols solides (SRMs) sont sensibles aux instabilités hydrodynamiques qui peuvent déclencher des oscillations auto-entretenues de pression de grandes amplitudes lorsqu’elles se couplent à l’un des modes acoustiques du système. Le moteur de ces instabilités est la formation de structures tourbillonnaires cohérentes synchronisées par des ondes acoustiques longitudinales. Pour certaines conditions de fonctionnement, les ondes acoustiques générées par l’interaction de ces tourbillons avec la tuyère amorcée du moteur renforcent l’oscillation acoustique. L’objectif des travaux menés dans cette thèse est de déterminer l’amplitude et la fréquence des oscillations de pression au cycle limite des instabilités. Celui-ci est atteint par saturation non linéaire des sources, qui est la conséquence de la formation de grosses structures cohérentes. Dans ce cas l’interaction tourbillon tuyère devient insensible à l’amplitude de l’onde du mode acoustique établi dans le foyer. Dans ces conditions, on peut se concentrer sur l’interaction d’un tourbillon avec la tuyère dans le mécanisme de production sonore. En considérant un écoulement incompressible et l’absence de frottement, un premier modèle analytique est développé permettant de déterminer la production sonore d’un tourbillon ingéré par une tuyère bidimensionnelle plane, lorsque le tourbillon est traité comme une ligne vorticité. Des expériences précédentes indiquent que le volume de la cavité autour de l’entrée d’une tuyère intégrée a une grande influence sur l’amplitude des oscillations de pression dans les grands SRMs. On montre que ceci est dû au champ de vitesse acoustique induit par la compressibilité du gaz dans la cavité qui produit une fluctuation de vitesse transverse à la trajectoire du tourbillon. Une seconde alternative au modèle analytique incompressible est développée en considérant toujours l’absence de frottement, mais un modèle compressible de l’interaction tourbillon-tuyère. Celui-ci repose sur un code aéroacoustique pour les écoulements internes basé sur les équations d’Euler (EIA) qui est utilisé ici pour la simulation de l’interaction tourbillon-tuyère. Une étude systématique de cette interaction a été menée pour une tuyère amorcée. Les résultats ont permis de proposer un modèle de sources localisées pour des ondes planes basé sur une analyse théorique des lois d’échelles de ces phénomènes. Les simulations de ces interactions tourbillons-tuyères ont été réalisées pour différents types de tuyères. En employant un bilan énergétique, un modèle avec un seul paramètre de contrôle est formulé, qui permet de reproduire qualitativement le comportement du cycle limite d’oscillations de pression observées dans des expériences réalisées avec des gaz froids décrites dans la littérature. Finalement le modèle Euler est utilisé pour comparer la production de son par interaction tourbillon-tuyère avec celle due à l’ingestion d’une onde d’entropie, appelée aussi tache d’entropie. Contrairement au cas des tourbillons, le bruit produit par ingestion de taches d’entropie n’est pas sensible au volume de la cavité d’une tuyère intégrée. Ces résultats indiquent que le bruit produit par les tourbillons est dominant dans le cas des SRMs étudiés. L’ensemble de ces travaux permet d’améliorer la compréhension des phénomènes d’interaction entre des non-homogénéités de l’écoulement et la tuyère. Elle permet surtout de déterminer quels sont les facteurs de l’écoulement et les éléments géométriques importants qui pilotent le niveau sonore produit par ces interactions. Les modèles développés dans ces travaux, avec divers degrés d’approximation et de complexité permettent d’enrichir la gamme des outils de conception des SRMs. / Solid Rocket Motors (SRMs) can display self-sustained acoustic oscillations driven by coupling between hydrodynamic instabilities of the internal flow and longitudinal acoustic standing waves. The hydrodynamic instabilities are triggered by the acoustic standing wave and results in the formation of coherent vortical structures. For nominal ranges of flow conditions the sound waves generated by the interaction between these vortices and the choked nozzle at the end of the combustion chamber reinforces the acoustic oscillation. Most available literature on this subject focuses on the threshold of instability using a linear model. The focus of this work is on the prediction of the limit-cycle amplitude. The limit-cycle is reached due to nonlinear saturation of the source, as a consequence of the formation of large coherent vortical structures. In this case the vortex-nozzle interaction becomes insensitive to the amplitude of the acoustic standing wave. Hence, one can focus on the sound generation of a vortex with the nozzle. Sound production can be predicted from an analytical two-dimensional planar incompressible frictionless model using the so-called Vortex Sound Theory. In this model the vorticity is assumed to be concentrated in a line vortex. Experiments indicate that the volume of cavities around so-called “integrated nozzles” have a large influence on the pulsation amplitude for large SRMs. This is due to the acoustical field normal to the vortex trajectory, induced by the compressibility of the gas in this cavity. As an alternative to the incompressible analytical model a compressible frictionless model with an internal Euler Aeroacoustic (EIA) flow solver is used for simulations of vortex-nozzle interaction. A dedicated numerical simulation study focusing on elementary processes such as vortex-nozzle and entropy spot-nozzle interaction allows a systematic variation of relevant parameters and yields insight which would be difficult by means of limit cycle studies of the full engine. A systematic study of the vortex-nozzle interaction in the case of a choked nozzle has been undertaken. The results are summarized by using a lumped element model for plane wave propagation, which is based on theoretical scaling laws. From EIA simulations it appears that sound due to vortex-nozzle interaction is mainly generated during the approach phase and that for the relevant parameter range there is no impingement of the vortex on the nozzle wall as has been suggested in the literature. Using an energy balance approach, a single fit-parameter model is formulated which qualitatively predicts limit-cycle observations in cold gas-scale experiments reported in the literature. Finally the Euler model is used to compare the sound production by vortex-nozzle interaction with that due to the ingestion of an entropy non-uniformity also called entropy spot. In addition to insight, this study provides a systematic procedure to develop a lumped element model for the sound source due to non-homogeneous flow-nozzle interactions in SRMs. Such lumped models based on experimental data or a limited number of flow simulations can be used to ease the design of SRMs.

L'objective de la thèse est de comprendre s'il est envisageable d'utiliser les modèles qui décrivent la croissance tumorale (systèmes d'EDP) pour des applications médicales. En particulier, les modèles paramétriques sont calibrés en utilisant les données d'imagerie médicale d'un patient. Une fois calibré, le modèle donne une représentation de la croissance tumorale. Des techniques différentes sont proposées. Un approche classique basé sur la sensibilité est comparé à un approche réduit basé sur la Proper Orthogonal Decomposition. Des cas réalistes concernants l'étude des métastases dans les poumons ont été mis à point en collaboration avec l'Institut Bergonié. Des exigence pratique de traitement de l'image ont motivé l'étude des méthodes de recalage non-rigide des images et parmi ceux là, le transport optimale. Un étude de la numérique du problème de Monge-Kantorovich est décrit, avec des cas test numérique. Des applications concernants l'application de la distance de Wasserstein à la réduction de modèle sont envisagées. / The main purpose of this work was to understand if and wether PDE based modeling of tumor growth may be used in realistic applications. Models proposed in the literature are parametric. The goal is to identify parameters in such a way that the pathology evolution of a given patient is recovered. The identification is performed by means of inverse problems, taking medical images as data.Different techniques were tested: a classical Sensitivity approach is compared to a reduced one, based on Proper Orthogonal Decomposition. Realistic cases were set up in collaboration with Institut Bergonié, concerning lung metastasis evolution.Practical needs when dealing with medical images pushed us to interest to Optimal transport theory and Monge-Kantorovich problem. A numerical study was carried out and a family of lagrangian methods proposed. A perspective on the using of Wasserstein distance in model reduction concludes this work.

Les structures soumises à des vibrations sont rencontrées dans diverses applications. Dans denombreux cas, elles sont de nature linéaires, mais quand les amplitudes des oscillations deviennentimportantes, cela provoque un comportement non-linéaire. Par ailleurs, les oscillations desstructures dans un milieu fluide entrainent une interaction fluide-structure. Cette thèse porte surla modélisation du problème fluide-structure non-linéaire. Les cas de non-linéarités étudiés sont lanon-linéarité grands-déplacements caractéristique des structures minces, la non-linéarité localiséegéométrique décrivant une liaison non-linéaire entre deux structures et la non-linéarité acoustiqueparticularité des très hauts niveaux de pression.Pour la modélisation de ces problèmes, il se peut que le calcul en réponse demeure infaisable enraison du temps de calcul. D’une part, on est amené à résoudre des systèmes matriciels (symétriquesou non) de grandes tailles générés par la méthode des éléments finis et d’autre part, cetterésolution demande une évaluation de la force non-linéaire à chaque itération. Afin de diminuer lecoût de calcul, la réduction de modèle par des bases de réductions couplées avec un algorithmeparallélisant l’évaluation de la force non-linéaire, est une alternative à la résolution du systèmecomplet. La construction des bases de réduction doit s’adapter au mieux à chaque problème traité.La base modale du problème linéaire est une première approximation puis elle est enrichie par desinformations qui proviennent à la fois de la nature du couplage et du comportement non-linéaire / Structures subjected to vibrations are found in various applications. In many cases, they behave ina linear way, but when the amplitudes of the oscillations become important, it causes a nonlinearbehavior. Moreover, the oscillations of structures in a fluid field lead to a fluid-structureinteraction. This thesis focuses on the modeling of nonlinear fluid-structure problem. Differentkind of nonlinearities are studied in this work including the large-displacement nonlinearitycharacteristic of thin structures, the localized geometrical nonlinearity describing a nonlinear linkbetween two structures, and the acoustic nonlinearity characteristic of very high levels ofpressure.Modeling such problems are time and memory consuming, that may lead to a limitations of themodel. Therefore, it is necessary to solve a large matrix system (either symmetric or not)generated by the finite element method and the resolution needs an evaluation of the nonlinearforce at each iteration. In order to reduce the computational cost, model reduction with reducedbases combined with parallelization of the nonlinear force evolution is proposed as an alternative tothe resolution of complete systems. Building reduction bases must be adapted to each concernedproblem. The eigenmode of the linear problem is a first approximation and it is enriched withinformation coming from both coupling and nonlinear behaviors.