I successfully defended my doctoral thesis on August 5th, 2013. You can download a PDF copy here or get the "official" copy from the JILA web database.
My thesis included the results from my previously published papers as well as chapters on the validation of the dynamic Smagorinsky subgrid-scale model and a new upper boundary condition which applies small-scale plumes on the top of the simulation in order to mimc the effects of near-surface convection.