The dynamics of oscillating flows past roughness elements often are dominated by coherent vortical structures. These vortices contribute significantly to the dispersion, mixing and transport of sediments, nutrients and pollutants at a wide range of space and time scales. The focus of this dissertation is in the three-dimensional (3D) structure and dynamics of these vortices, and how the vortex mechanics influence the flow.;The 3D dynamics of coherent vortices and their interactions in an oscillatory flow past an obstacle are examined experimentally. A periodic, unidirectional vortex pairing regime is observed, in which the direction of propagation of the vortex pairs is set by the initial conditions of the oscillations. A single vortex pair is formed in each cycle, which then propagates away from the boundary under mutual advection, at an angle to the free-stream velocity. Once the direction of vortex propagation is established, it remains stable for all subsequent cycles. Vortex pairs are observed to be short-lived relative to the oscillation timescale, which limits their propagation distance from the boundary. An elliptical instability of the strained vortex cores is found to dominate the vortex breakdown process. Velocity measurements are used to identify the spatial structure of the perturbations associated with the elliptical instability. A mean flow is generated as a result of the vortex pairing mechanics. This residual flow is composed of an asymmetric outward jet which is inclined with respect to the free-stream velocity.;The structure of baroclinic vortices generated by oscillatory flow separation past a sloping headland in deep, stably stratified waters is then investigated via field observations and the analysis of numerical data. The most distinctive feature of these eddies is that their cores are strongly tilted with respect to the stratification, yet their velocity field remains mostly horizontal. It is found that vortex tilt results in a fundamental asymmetry of the density field. As the vortices release from the boundary, adjust and decay, their tilt, as well as the associated density perturbation, decreases and loses coherence, suggesting a conversion of potential energy into kinetic energy.;Finally, the centrifugal instability of the boundary layer on an oscillating cylinder is examined qualitatively using flow visualizations. Detailed dye experiments reveal the onset of the centrifugal instability, which is manifested as growing Gortler vortices on the cylinder surface. These vortices are observed to break down after several cycles, leading to flow separation at the locations at which these vortices were initially present.
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