In the present doctoral work we have developed and tested a model for dissolved oxygen (DO) transfer from water to underlying flat and cohesive sediment beds populated with DO-absorbing bacteria. The model couples Large-Eddy Simulation (LES) of turbulent transport in the water-column, a biogeochemical model for DO transport and consumption in the sediment, and Darcy’s Law for the pore water-driven solute dispersion and advection. The model’s predictions compare well against experimental data for low friction-Reynolds numbers (Re). The disagreement for higher Re is investigated by progressively increasing the complexity of the model. A sensitivity analysis shows that the sediment-oxygen uptake (or demand, SOD) is approximately proportional to the bacterial content of the sediment layer, and varies with respect to fluid dynamics conditions, in accordance to classic high-Schmidt-number mass-transfer laws. The non- linear transport dynamics responsible for sustaining a statistically steady SOD are investigated by temporal- and-spatial correlations and with the aid of instantaneous visualizations: the near-wall coherent structures modulate the diffusive sublayer, which exhibits complex spatial and temporal filtering behaviours; its slow and quasi-periodic regeneration cycle determines the streaky structure of the DO field at the sediment-water interface (SWI), retained in the deeper layers of the porous medium. Oxygen depletion dynamics are then simulated by preventing surface re-areation with turbulent mixing driven by an oscillating low-speed current — an idealization of hypolimnetic DO depletion in the presence of a non-equilibrium periodic forcing. The oxygen distribution exhibits a self-similar pattern of decay with, during the deceleration phase, oscillations modulated by the periodic ejection of peaks of high turbulent mass flux (pumping oxygen towards the SWI), generated at the edge of the diffusive sublayer at the end of the acceleration phase. These fronts of highly turbulent mixing propagate away from the SWI, at approximately constant speed, in layers of below-average oxygen concentration. Finally, the model has been tested in a real geophysical framework, reproducing published in-situ DO measurements of a transitional flow in the bottom boundary layer of lake Alpnach. A simple model for the SOD is then derived for eventual inclusion in RANSE biogeochemical management-type models for similar applications. / Thesis (Ph.D, Mechanical and Materials Engineering) -- Queen's University, 2012-07-04 11:13:24.936