Hossain, Md monir2022-01-222022-01-222020-07-30vt_gsexam:26901http://hdl.handle.net/10919/107847Knowledge of the detailed flow dynamics at the interior of branching corals is critical for a full understanding of nutrient uptake, mass transport, wave dissipation, and other essential processes. These physiological processes depend on the local velocity field, local concentration gradients of nutrients and waste, and the turbulent stresses developed on and above the coral surface. Though the large-scale hydrodynamics over coral reefs are well studied, the interior hydrodynamics, between the branches, remains uncharacterized due to limited optical and acoustic access to the interior. In the current thesis, a three-dimensional immersed boundary method in the large eddy simulation framework was used to compute the flow inside several branching coral colony geometries in order to study the effects of branch density and surface structure on the flow fields in the coral interiors. Two different Pocillopora colony species were studied at different Reynolds numbers. A ray-tracing algorithm was used for capturing the arbitrary branches of these complex geometries to obtain the three-dimensional flow fields within these colonies for the first time. The analysis showed the formation of vortices at the colony interior that stir the water column and thus passively enhance mass transport, compensating for the reduced mean velocity magnitude compared to the free stream value, within the densely branched Pocillopora meandrina colony. Further analysis showed that the mean streamwise velocity profile changes shape along the streamwise direction inside P. meandrina, whereas the mean velocity profile did not change shape from the front to the back for the loosely branched Pocillopora colony, Pocillopora eydouxi. Moreover, turbulent flow field quantities were computed for both these structures, and for two almost identical Montipora capitata colony geometries, one with, and one without roughness elements called verrucae. The analyses demonstrated significant differences in the mean velocity profiles, Reynolds stress, and other flow quantities with changes in colony branch density and surface structure.ETDIn CopyrightCoral hydrodynamicsimmersed boundary methodlarge eddy simulationmass transportturbulent stressDissertation