Flow Separation on the β-plane

In non-rotating fluids, boundary-layer separation occurs when the nearly inviscid flow just outside a viscous boundary-layer experiences an appreciable deceleration due to a region of adverse pressure gradient. The fluid ceases to flow along the boundary due to a flow recirculation region close to the boundary. The flow is then said to be "detached." In recent decades, attention has shifted to the study of boundary-layer separation in a rotating reference frame due to its significance in Geophysical Fluid Dynamics (GFD). Since the Earth is a rotating sphere, the so-called β-plane approximation f = f0 + βy is often used to account for the inherent meridional variation of the Coriolis parameter, f, while still solving the governing equations on a plane. Numerical simulations of currents on the β-plane have been useful in understanding ocean currents such as the Gulf Stream, the Brazil Current, and the Antarctic Circumpolar Current to name a few. In this thesis, we first consider the problem of prograde flow past a cylindrical obstacle on the β-plane. The problem is governed by the barotropic vorticity equation and is solved using a numerical method that is a combination of a finite difference method and a spectral method. A modified form of the β-plane approximation is proposed to avoid computational difficulties. Results are given and discussed for flow past a circular cylinder at selected Reynolds numbers (Re) and non-dimensional β-parameters (β^). Results are then given and discussed for flow past an elliptic cylinder of a fixed aspect ratio (r = 0.2) and at two angles of inclination (90°, 15°) at selected Re and β^. In general, it is found that the β-effect acts to suppress boundary-layer separation and to allow Rossby waves to form in the exterior flow field. In the asymmetrical case of an inclined elliptic cylinder, the β-effect was found to constrain the region of vortex shedding to a small region near the trailing edge of the cylinder. The shed vortices were found to propagate around the trailing edge instead of in the expected downstream direction, as observed in the non-rotating case. The second problem considered in this thesis is the separation of western boundary currents from a curved coastline. This problem is also governed by the barotropic vorticity equation, and it is solved on an idealized model domain suitable for investigating the effects that boundary curvature has on the tendency of a boundary current to separate. The numerical method employed is a two-dimensional Chebyshev spectral collocation method and yields high order accuracy that helps to better resolve the boundary-layer dynamics in comparison to low-order methods. Results are given for a selection of boundary curvatures, non-dimensional β-parameters (β^), Reynolds numbers (Re), and Munk Numbers (Mu). In general, it is found than an increase in β^ will act to suppress boundary-layer separation. However, a sufficiently sharp obstacle can overcome the β-effect and force the boundary current to separate regardless of the value of β^. It is also found that in the inertial limit (small Mu, large Re) the flow region to the east of the primary boundary current is dominated by strong wave interactions and large eddies which form as a result of shear instabilities. In an interesting case of the inertial limit, strong waves were found to interact with the separation region, causing it to expand and propagate to the east as a large eddy. This idealized the mechanism by which western boundary currents such as the Gulf Stream generate eddies in the world's oceans

The characterization of checkpoint kinase 2 in Oncorhynchus mykiss: Tissue specific expression suggests biomarker potential

Chk2 is a cell cycle checkpoint kinase that is essential for initiating the DNA damage response in the presence of genetic damage. Its role is highly conserved from budding yeast (where it is named Rad53) to humans. Very few cell cycle checkpoint proteins have ever been studied in fish and the role of Chk2 has never been characterized. Oncorhynchus mykiss (Rainbow trout) was chosen for this project due to its importance in the commercial aquaculture industry and the availability of rainbow trout cell cultures at the University of Waterloo. This study was the first to clone the CHK2 gene in a teleost species, verified through both genomic and cDNA cloning. A section of the CHK2 gene, specifically the forkhead associated domain (FHA), was used to express recombinant Chk2 protein and generate polyclonal anti-Chk2 antibodies. A southern blot was performed and CHK2 was found to exist as a single copy number in the rainbow trout genome. The tissue specificity of Chk2 was also examined both at the mRNA transcript and protein level. Interesting tissue specific differences were discovered with transcript levels moderately low in gill and higher in brain, while protein levels were extremely high in gill and lower in brain tissues. Protein levels were verified in both whole fish tissue samples and in cell culture suggesting that cell cultures accurately reflect the state of checkpoint proteins in vivo. These tissue specific differences suggest that in gill, Chk2 is maintained at a high protein level to combat any toxins in the water attempting to transverse this barrier tissue and gain access to the fish’s circulatory system. Meanwhile, the blood brain barrier offers protection to the highly sensitive brain tissue, suggesting that high levels of Chk2 protein are not constitutively required, but instead remain in a transcript reservoir able to be quickly translated in the event of DNA damage. To determine whether Chk2’s checkpoint role is conserved in O. mykiss, both gill and brain cell cultures were treated with low and high doses of bleocin (a commercially available form of bleomycin) known to cause high levels of double-strand breaks, the most deleterious type of DNA damage and a specific activator of the Chk2 DNA damage response (DSB). Results showed that bleocin had no effect on levels of Chk2 in gill cells, confirming that the protein is constitutively active in this tissue always on alert against potential genetic insult. In contrast, brain cells were able to upregulate Chk2 in a dose-dependent manner to bleocin induced DNA damage demonstrating that Chk2 can act as a biomarker for genetic damage in brain cells. In conclusion, the tissue specific expression of Chk2 and its ability to respond to DNA damage suggests that checkpoint proteins may serve as suitable biomarkers for DNA damage in O. mykiss and other fish species

High-Order Numerical Methods in Lake Modelling

The physical processes in lakes remain only partially understood despite successful data collection from a variety of sources spanning several decades. Although numerical models are already frequently employed to simulate the physics of lakes, especially in the context of water quality management, improved methods are necessary to better capture the wide array of dynamically important physical processes, spanning length scales from ~ 10 km (basin-scale oscillations) - 1 m (short internal waves). In this thesis, high-order numerical methods are explored for specialized model equations of lakes, so that their use can be taken into consideration in the next generation of more sophisticated models that will better capture important small scale features than their present day counterparts. The full three-dimensional incompressible density-stratified Navier-Stokes equations remain too computationally expensive to be solved for situations that involve both complicated geometries and require resolution of features at length-scales spanning four orders of magnitude. The main source of computational expense lay with the requirement of having to solve a three-dimensional Poisson equation for pressure at every time-step. Simplified model equations are thus the only way that numerical lake modelling can be carried out at present time, and progress can be made by seeking intelligent parameterizations as a means of capturing more physics within the framework of such simplified equation sets. In this thesis, we employ the long-accepted practice of sub-dividing the lake into vertical layers of different constant densities as an approximation to continuous vertical stratification. We build on this approach by including weakly non-hydrostatic dispersive correction terms in the model equations in order to parameterize the effects of small vertical accelerations that are often disregarded by operational models. Favouring the inclusion of weakly non-hydrostatic effects over the more popular hydrostatic approximation allows these models to capture the emergence of small-scale internal wave phenomena, such as internal solitary waves and undular bores, that are missed by purely hydrostatic models. The Fourier and Chebyshev pseudospectral methods are employed for these weakly non-hydrostatic layered models in simple idealized lake geometries, e.g., doubly periodic domains, periodic channels, and annular domains, for a set of test problems relevant to lake dynamics since they offer excellent resolution characteristics at minimal memory costs. This feature makes them an excellent benchmark to compare other methods against. The Discontinuous Galerkin Finite Element Method (DG-FEM) is then explored as a mid- to high-order method that can be used in arbitrary lake geometries. The DG-FEM can be interpreted as a domain-decomposition extension of a polynomial pseudospectral method and shares many of the same attractive features, such as fast convergence rates and the ability to resolve small-scale features with a relatively low number of grid points when compared to a low-order method. The DG-FEM is further complemented by certain desirable attributes it shares with the finite volume method, such as the freedom to specify upwind-biased numerical flux functions for advection-dominated flows, the flexibility to deal with complicated geometries, and the notion that each element (or cell) can be regarded as a control volume for conserved fluid quantities. Practical implementation details of the numerical methods used in this thesis are discussed, and the various modelling and methodology choices that have been made in the course of this work are justified as the difficulties that these choices address are revealed to the reader. Theoretical calculations are intermittently carried out throughout the thesis to help improve intuition in situations where numerical methods alone fall short of giving complete explanations of the physical processes under consideration. The utility of the DG-FEM method beyond purely hyperbolic systems is also a recurring theme in this thesis. The DG-FEM method is applied to dispersive shallow water type systems as well as incompressible flow situations. Furthermore, it is employed for eigenvalue problems where orthogonal bases must be constructed from the eigenspaces of elliptic operators. The technique is applied to the problem calculating the free modes of oscillation in rotating basins with irregular geometries where the corresponding linear operator is not self-adjoint

A matrix-free high-order discontinuous Galerkin compressible Navier-Stokes solver: A performance comparison of compressible and incompressible formulations for turbulent incompressible flows

Both compressible and incompressible Navier-Stokes solvers can be used and are used to solve incompressible turbulent flow problems. In the compressible case, the Mach number is then considered as a solver parameter that is set to a small value, $\mathrm{M}\approx 0.1$, in order to mimic incompressible flows. This strategy is widely used for high-order discontinuous Galerkin discretizations of the compressible Navier-Stokes equations. The present work raises the question regarding the computational efficiency of compressible DG solvers as compared to a genuinely incompressible formulation. Our contributions to the state-of-the-art are twofold: Firstly, we present a high-performance discontinuous Galerkin solver for the compressible Navier-Stokes equations based on a highly efficient matrix-free implementation that targets modern cache-based multicore architectures. The performance results presented in this work focus on the node-level performance and our results suggest that there is great potential for further performance improvements for current state-of-the-art discontinuous Galerkin implementations of the compressible Navier-Stokes equations. Secondly, this compressible Navier-Stokes solver is put into perspective by comparing it to an incompressible DG solver that uses the same matrix-free implementation. We discuss algorithmic differences between both solution strategies and present an in-depth numerical investigation of the performance. The considered benchmark test cases are the three-dimensional Taylor-Green vortex problem as a representative of transitional flows and the turbulent channel flow problem as a representative of wall-bounded turbulent flows