Modeling Coupled Physics and Biology in Ocean Straits with Application to the San Bernardino Strait in the Philippine Archipelago

In this thesis, we conduct research toward understanding coupled physics-biology processes in ocean straits. Our focus is on new analytical studies and higher-order simulations of idealized dynamics that are relevant to generic biological processes. The details of coupled physics-biology models are reviewed and an in-depth global equilibrium and local stability analysis of a Nutrient-Phytoplankton-Zooplankton (NPZ) model is performed. This analysis includes parameter studies and methods to evaluate parameter sensitivity, especially in the case where some system parameters are unknown. As an initial step toward investigating the interaction between physics and biology in ocean straits, we develop and verify a new coupled physics-biology model for two-dimensional idealized physical processes including tides and apply it to the San Bernardino Strait in the Philippine Archipelago. This two-dimensional numerical model is created on a structured grid using operator splitting and masking. This model is able to accurately represent biology for various physical flows, including advection-dominated flows over discontinuities, by using the Weighted Essentially Non-Oscillatory (WENO) scheme. The numerical model is verified against a Discontinuous-Galerkin (DG) numerical scheme on an unstructured grid. Several simulations of tidal flow are completed using bathymetry and flow magnitudes comparable to those found in the San Bernardino Strait with different sets of parameters, tidal periods, and levels of diffusion. Results are discussed and compared to those of a three-dimensional modeling system. New results include: new methods for analyzing stability, the robust two-dimensional model designed to best represent advection-dominant flows with minimal numerical diffusion and computational time, and a novel technique to initialize three-dimensional biology fields using satellite data. Additionally, application of the two-dimensional model with tidal forcing to the San Bernardino Strait reveals that flow frequencies have strong influence on biology, as very fast oscillations act to stabilize biology in the water column, while slower frequencies provide sufficient transport for increased biological activity. 3 Thesis Supervisor: Pierre Lermusiaux Title: Associate Professor of Mechanical Engineering