We performed large eddy simulation of the flow over a series of two- and three-dimensional dune geometries at laboratory scale using the Lagrangian dynamic eddy-viscosity subgrid-scale model. First, we studied the flow over a standard 2D transverse dune geometry, then bedform three-dimensionality was imposed. Finally, we investigated the turbulent flow over barchan dunes. The results are validated by comparison with simulations and experiments for the 2D dune case, while the results of the 3D dunes are validated qualitatively against experiments. The flow over transverse dunes separates at the dune crest, generating a shear layer that plays a crucial role in the transport of momentum and energy, as well as the generation of coherent structures. Spanwise vortices are generated in the separated shear; as they are advected, they undergo lateral instabilities and develop into horseshoe-like structures and finally reach the surface. The ejection that occurs between the legs of the vortex creates the upwelling and downdrafting events on the free surface known as “boils”. The three-dimensional separation of flow at the crestline alters the distribution of wall pressure, which may cause secondary flow across the stream. The mean flow is characterized by a pair of counter-rotating streamwise vortices, with core radii of the order of the flow depth. Staggering the crestlines alters the secondary motion; two pairs of streamwise vortices appear (a strong one, centred about the lobe, and a weaker one, coming from the previous dune, centred around the saddle). The flow over barchan dunes presents significant differences to that over transverse dunes. The flow near the bed, upstream of the dune, diverges from the centerline plane; the flow close to the centerline plane separates at the crest and reattaches on the bed. Away from the centerline plane and along the horns, flow separation occurs intermittently. The flow in the separation bubble is routed towards the horns and leaves the dune at the tips. Barchan dunes induce two counter-rotating streamwise vortices, along each of the horns, which direct high-momentum fluid toward the symmetry plane and low-momentum fluid near the bed away from the centerline. / Thesis (Ph.D, Mechanical and Materials Engineering) -- Queen's University, 2013-05-27 18:58:48.969

This dissertation includes two fluid dynamics studies that involve fluid flows on vastly different scales, and therefore vastly different physics. The first study is of bacterial swimming using a flagellum for propulsive motion. Because bacteria are only about 10 [micrometers] in length, they swim in a very low Reynolds number (10⁻⁴) world, which is described by the linear set of governing equations known as the Stokes equations, that are a simplified version of the Navier-Stokes equations. The second study is of harmonic generation from nonlinear effects in internal, ocean-like wave beams that reflect from boundaries in a density stratified fluid. Internal wave reflection is an important oceanic process and may help sustain ocean circulation and affect global weather patterns. Such ocean processes have typical Reynold's numbers of 10¹⁰ or more and are only described by the full, nonlinear Navier-Stokes equations. In the low Reynolds number study, I examine theories by Gray et al.(1956) and Lighthill (1975) that describe swimming microorganisms using a helical flagellum for propulsive motion. I determine the resistance matrix, which can fully describe the dynamics of a flagellum, for flagella with different geometries, defined by: filament radius a, helical radius R, helical pitch [lambda], and axial length L. I use laboratory experiments and numerical simulations conducted in collaboration with Dr. Hepeng Zhang. The experiments, conducted with assistance from a fellow graduate student Chih-Hung Chen, use macroscopic scale models of bacterial flagella in a bath of highly viscous silicone oil. Numerical simulations use the Regularized Stokeslet method, which approximates the Stokeslet representation of an immersed body in a low Reynolds number flow. My study covers a biologically relevant parameter regime: 1/10R < a < 1/25R, R < [lambda] < 20R, and 2R< L <40R. I determine the three elements of the resistance matrix by measuring propulsive force and torque generated by a rotating, non-translating flagellum, and the drag force on a translating, non-rotating flagellum. I investigate the dependences of the resistance matrix elements on both the flagellum's axial length and its wavelength. The experimental and numerical results are in excellent agreement, but they compare poorly with the predictions of resistive force theory. The theory's neglect of hydrodynamic interactions is the source of the discrepancies in both the length dependence and wavelength dependence studies. I show that the experimental and simulation data scale as L/ln(L/r), a scaling analytically derived from slender body theory by my other collaborator Dr. Bin Liu. This logarithmic scaling is new and missing from the widely used resistive force theory. Dr. Zhang's work also includes a new parameterized version of resistive force theory. The second part of the dissertation is a study of harmonic generation by internal waves reflected from boundaries. I conduct laboratory experiments and two-dimensional numerical simulations of the Navier-Stokes equations to determine the value of the topographic slope that gives the most intense generation of second harmonic waves in the reflection process. The results from my experiments and simulations agree well but differ markedly from theoretical predictions by Thorpe (1987) and by Tabaei et al. (2005), except for nearly inviscid, weakly nonlinear flow. However, even for weakly nonlinear flow (where the dimensionless Dauxois-Young amplitude parameter value is only 0.01), I find that the ratio of the reflected wavenumber to the incoming wavenumber is very different from the prediction of weakly nonlinear theory. Further, I observe that for incident beams with a wide range of angles, frequencies, and intensities, the second harmonic beam produced in reflection has a maximum intensity when its width is the same as the width of the incident beam. This observation yields a prediction for the angle corresponding to the maximum in second harmonic intensity that is in excellent accord with my results from experiments and numerical simulations. / text

The accurate and efficient numerical simulation of geophysical flows is of great interest in numerical weather prediction and climate modeling as well as in numerous critical areas and industries, such as agriculture, construction, tourism, transportation, weather-related disaster management, and sustainable energy technologies. Oceanic and atmospheric flows display an enormous range of temporal and spatial scales, from seconds to decades and from centimeters to thousands of kilometers, respectively. Scale interactions, both spatial and temporal, are the dominant feature of all aspects of general circulation models in geophysical fluid dynamics. In this thesis, to decrease the cost for these geophysical flow computations, several types of multiscale methods were systematically developed and tested for a variety of physical settings including barotropic and stratified wind-driven large scale ocean circulation models, decaying and forced two-dimensional turbulence simulations, as well as several benchmark incompressible flow problems in two and three dimensions. The new models proposed here are based on two classes of modern multiscale methods: (i) interpolation based approaches in the context of the multigrid/multiresolution methodologies, and (ii) deconvolution based spatial filtering approaches in the context of large eddy simulation techniques. In the first case, we developed a coarse-grid projection method that uses simple interpolation schemes to go between the two components of the problem, in which the solution algorithms have different levels of complexity. In the second case, the use of approximate deconvolution closure modeling strategies was implemented for large eddy simulations of large-scale turbulent geophysical flows. The numerical assessment of these approaches showed that both the coarse-grid projection and approximate deconvolution methods could represent viable tools for computing more realistic turbulent geophysical flows that provide significant increases in accuracy and computational efficiency over conventional methods. / Ph. D.

Bed topography identification in open channel and glacier flows is of paramount importance for the study of the respective flows. In the former, the knowledge of the channel bed topography is required for modelling the hydrodynamics of open channel flows, fluvial hydraulics, flood propagation, and river flow monitoring. Indeed, flow models based on the Shallow Water Approximation require prior information on the channel bed topography to accurately capture the flow features. While in the latter, usable bedrock topographic information is very important for glacier flow modellers to accurately predict the flow characteristics. Experimental techniques to infer the bed topography are usually used but are mostly time consuming, costly, and sometimes not possible due to geographical restrictions. However, the measurement of free surface elevation is relatively easy. Alternative to experimental techniques, it is therefore important to develop fast, easy-to-implement, and cost-effective numerical methods. The inverse of the classical hydrodynamic problem corresponds to the determination of hydraulic parameters from measurable quantities. The forward problem uses model parameters to determine measurable quantities. New one-shot and direct pseudo-analytical and numerical approaches for reconstructing the channel bed topography from known free surface elevation data is developed for one-dimensional shallow water flows. It is shown in this work that instead of treating this inverse problem in the traditional partial differential equation (PDE)-constrained optimization framework, the governing equations of the direct problem can be conveniently rearranged to obtain an explicit PDE for the inverse problem. This leads to a direct solution of the inverse problem which is successfully tested on a range of benchmark problems and experimental data for noisy and noiseless free surface data. It was found that this solution approach creates very little amplification of noise. A numerical technique which uses the measured free surface velocity to infer the channel bed topography is also developed. The one-dimensional shallow water equations along with an empirical relationship between the free surface and the depth averaged velocities are used for the inverse problem analysis. It is shown that after a series of algebraic manipulation and integration, the equation governing the inverse problem simplifies to a simple integral equation. The proposed method is tested on a range of analytical and experimental benchmark test cases and the results confirm that, it is possible to reconstruct the channel bed topography from a known free surface velocity distribution of one-dimensional open channel flows. Following the analysis of the case of one-dimensional shallow water flows, a numerical technique for reconstructing the channel bed topography from known free surface elevation data for steep open channel flows is developed using a modified set of equations for which the zero-inertia shallow water approximation holds. In this context, the shallow water equations are modified by neglecting inertia terms while retaining the effects of the bed slope and friction terms. The governing equations are recast into a single first-order partial differential equation which describes the inverse problem. Interestingly, the analysis shows that the inverse problem does not require the knowledge of the bed roughness. The forward problem is solved using MacCormack’s explicit numerical scheme by considering unsteady modified shallow water equations. However, the inverse problem is solved using the method of characteristics. The results of the inverse and the forward problem are successfully tested against each other. In the framework of full two-dimensional shallow water equations, an easy-to-implement and fast to solve direct numerical technique is developed to solve the inverse problem of shallow open channel flows. The main underlying idea is analogous to the idea implemented for the case of one-dimensional reconstruction. The technique described is a “one-shot technique” in the sense that the solution of the partial differential equation provides the solution to the inverse problem directly. The idea is tested on a set of artificial data obtained by first solving the forward problem. Glaciers are very important as an indicator of future climate change or to trace past climate. They respond quickly compared to the Antarctica and Greenland ice sheets which make them ideal to predict climate changes. Glacier bedrock topography is an important parameter in glacier flow modelling to accurately capture its flow dynamics. Thus, a mathematical technique to infer this parameter from measured free surface data is invaluable. Analogous to the approaches implemented for open channel flows, easy-to-implement direct numerical and analytical algorithms are developed to infer the bedrock topography from the knowledge of the free surface elevation in one space dimension. The numerical and analytical methods are both based on the Shallow Ice Approximation and require the time series of the ablation/accumulation rate distribution. Moreover, the analytical method requires the knowledge of a non-zero glacier thickness at an arbitrary location. Numerical benchmark test cases are used to verify the suitability and applicability of the algorithms.

Ce travail de thèse cherche à caractériser, à l'aide d’expériences de laboratoire, le mouvement d'un fluide stratifié à la fois tournant et cisaillé. Dans ce contexte on a considéré trois problèmes qui sont issus des observations géophysiques et astrophysiques où ces écoulements sont très communs. En premier nous avons observé expérimentalement et modélisé l'évolution en temps d'un anticyclone en milieu stratifié tournant, dans le but de comprendre la longévité des meddies, des vortex qui se forment à la sortie de la Méditerranée et peuvent perdurer pendant des années. Nos anticyclones modèles montrent une relaxation visqueuse anormale en raison de l’interaction entre stratification et cisaillement. Nos résultats expérimentaux ont été confirmés à l'aide d'un modèle géostrophique et de simulations numériques qui montrent aussi le rôle majeur joué par les circulations secondaires. Dans un deuxième temps nous avons considéré la stabilité linéaire de l'écoulement de Couette Plan, un des plus simple des écoulement plans cisaillés. On montre que cet écoulement devient instable lorsque l'on ajoute de la stratification verticale. Nous remarquons aussi que la structure spatiale de l'instabilité ressemble à celle de certains jets océaniques que l'on observe près de l'équateur. Enfin nous avons caractérisé une instabilité non linéaire dite des zombie vortex qui a été récemment découverte et pourrait jouer un rôle fondamental dans la déstabilisation des disques d'accrétion, une étape fondamentale de la formation des planétaire. Nous avons construit le diagramme de stabilité de la ZVI dans l'espace de trois fréquences caractéristiques et quantifié la dissipation visqueuse. / The present PhD work comes with the scope of characterizing, analysing and modelling some laboratory flows in the simultaneous presence of rotation, stratification and shear. To this aim we address three specific questions inspired by geophysics and astrophysics where these three ambient features are commonly relevant. First we characterize and model the time evolution of a compact anticyclone in a rotating and stratified laboratory flow. We aim to understand the longevity of analogous vortices known as meddies which populate the Atlantic ocean at the exit of the Mediterranean sea. We observe that viscous relaxation happens in an unusual way because of the balance between rotation and stratification. The results are confirmed by a quasi-geostrophic model and numerical simulations which show the crucial role played by secondary circulations. Secondly we consider the linear stability of one of the simplest parallel shear flow, namely the plane Couette Flow, and show that it becomes unstable when adding a vertical stratification. Interestingly the unstable pattern reminds of deep oceanic jets observed close to the equator. The signature of this instability is observed in an ad-hoc experimental flow and interpreted with the support of direct numerical simulations. Finally we characterize the behaviour of a recently disclosed finite amplitude instability, namely the zombie vortex instability or ZVI. This instability appears when rotation, stratification and shear are of the same order and may may destabilize proto-planetary disks. We construct a stability diagram for ZVI in the space of the three ambient frequencies and analyse the effect of viscous dissipation.

abstract: The tools developed for the use of investigating dynamical systems have provided critical understanding to a wide range of physical phenomena. Here these tools are used to gain further insight into scalar transport, and how it is affected by mixing. The aim of this research is to investigate the efficiency of several different partitioning methods which demarcate flow fields into dynamically distinct regions, and the correlation of finite-time statistics from the advection-diffusion equation to these regions. For autonomous systems, invariant manifold theory can be used to separate the system into dynamically distinct regions. Despite there being no equivalent method for nonautonomous systems, a similar analysis can be done. Systems with general time dependencies must resort to using finite-time transport barriers for partitioning; these barriers are the edges of Lagrangian coherent structures (LCS), the analog to the stable and unstable manifolds of invariant manifold theory. Using the coherent structures of a flow to analyze the statistics of trapping, flight, and residence times, the signature of anomalous diffusion are obtained. This research also investigates the use of linear models for approximating the elements of the covariance matrix of nonlinear flows, and then applying the covariance matrix approximation over coherent regions. The first and second-order moments can be used to fully describe an ensemble evolution in linear systems, however there is no direct method for nonlinear systems. The problem is only compounded by the fact that the moments for nonlinear flows typically don't have analytic representations, therefore direct numerical simulations would be needed to obtain the moments throughout the domain. To circumvent these many computations, the nonlinear system is approximated as many linear systems for which analytic expressions for the moments exist. The parameters introduced in the linear models are obtained locally from the nonlinear deformation tensor. / Dissertation/Thesis / Doctoral Dissertation Applied Mathematics 2018

It is often desirable to study simulated turbulent flows at steady state even if the flow has no inherent source of turbulence kinetic energy. Doing so requires a numerical forcing scheme and various methods have been studied extensively for turbulence that is isotropic and homogeneous in three dimensions. A review of these existing schemes is used to form a framework for more general forcing methods. In this framework, the problem of developing a forcing scheme in Fourier space is abstracted into the two problems of (1) prescribing the spectrum of the input power and (2) specifying a force that has the desired characteristics and that adds energy to the flow with the correct spectrum. The framework is used to construct three forcing schemes for horizontally homogeneous and isotropic, vertically stratified turbulence. These schemes are implemented in large-eddy simulations and their characteristics analyzed. Which method is “best” depends on the purpose of the simulations, but the framework for specifying forcing schemes enables a systematic approach for identifying a method appropriate for a particular application.

In this study we investigate the interactions between two co-rotating vortices. These vortices are subject to rapid rotation and stable stratification such as are found in planetary atmospheres and oceans. By conducting a large number of simulations of vortex interactions, we intend to provide an overview of the interactions that could occur in geophysical turbulence. We consider a wide parameter space covering the vortices height-to-width aspect-ratios, their volume ratios and the vertical offset between them. The vortices are initially separated in the horizontal so that they reside at an estimated margin of stability. The vortices are then allowed to evolve for a period of approximately 20 vortex revolutions. We find that the most commonly observed interaction under the quasi-geostrophic (QG) regime is partial-merger, where only part of the smaller vortex is incorporated into the larger, stronger vortex. On the other hand, a large number of filamentary and small scale structures are generated during the interaction. We find that, despite the proliferation of small-scale structures, the self-induced vortex energy exhibits a mean `inverse-cascade' to larger scale structures. Interestingly we observe a range of intermediate-scale structures that are preferentially sheared out during the interactions, leaving two vortex populations, one of large-scale vortices and one of small-scale vortices. We take a subset of the parameter space used for the QG study and perform simulations using a non-hydrostatic model. This system, free of the layer-wise two-dimensional constraints and geostrophic balance of the QG model, allows for the generation of inertia-gravity waves and ageostrophic advection. The study of the interactions between two co-rotating, non-hydrostatic vortices is performed over four different Rossby numbers, two positive and two negative, allowing for the comparison of cyclonic and anti-cyclonic interactions. It is found that a greater amount of wave-like activity is generated during the interactions in anticyclonic situations. We also see distinct qualitative differences between the interactions for cyclonic and anti-cyclonic regimes.

The effect of rotation on the stability of multiple jets in planetary atmospheres is system- atically investigated. Typically in Jovian planetary atmospheres, multiple zonal jets have been observed and their morphology has been systematically studied. The formation of jets has always been viewed as a nonlinear problem where most work has followed from the ideas of potential vorticity (PV) homogenization or turbulent mixing on a β-plane. In our present work, we have aimed to look at the linear stability of multiple jets in a geophysical fluid, and hope to add further insight into the observed jet profiles in β-plane turbulence. In addition, we also study the evolution and life-cycle of these jets as they interact with each other in a non linear fashion. We begin with the linear stability of the \Bickley jet" using the linearized shallow water quasigeostrophic (QG) equations. We have included a finite deformation radius in our calculations to partially mimic the effects of compressibility. A family of synthetically generated velocity profiles with east-west jets are then studied. In particular, a variety of flow configurations with two jets have been considered with a parameter sweep across jet separation, relative jet strength and thickness. As a broad observation, it is noted that an asymmetric east-west jet profile with a stronger and sharper eastward jet is the most stable of all the profiles considered, and a finite deformation radius further stabilizes such profiles. More realistic jet profiles have also been considered and the role of a finite deformation radius in stabilizing such jets is elucidated. We also examined the nonlinear evolution of multiple jets in a periodic domain and in a channel geometry, as we undertake freely decaying long time simulations of the governing QG equation. As per the \Selective Decay" principle we observe that arbitrary initial conditions approach the flow configuration of the prescribed \suitable end states". In addition, we have shown how a finite deformation length scale modifies these \suitable end states". As a broad observation, we have noted that a linearly unstable jet flow configuration, in the presence of β, breaks down into turbulence and reforms into a more asymmetric jet profile with a stronger and sharper eastward jet. The inclusion of a finite deformation length scale in our calculations, is observed to suppress such jet formation. Similar numerical experiments have been performed in a channel and the results have been compared. Chiefly, for the end states, the nature of the observed jet asymmetry is reversed, i.e., the westward jets are observed to be stronger in a channel.