Theory: Mathematical Basis of Population models
Continuous population models (Murray, 1.1 to 1.6)
Discrete population models for a single species (Murray, chapter 2)
Continuous models for interacting populations (Murray, 3.1 to3.5)
Modeling Exercises: Predator-Prey Models
The role of higher predation in plankton population models (Edwards and Yool., 2000)
Generic dynamics of a simple plankton population model (Edwards and Bees, 2001)
Theory: Lower Trophic Level Marine Ecosystem Models
Nitrogen Phytoplankton Zooplankton Detritus (NPZD) model (Franks et al., 2002)
Stability analysis of NPZD models (Franks et al., 2002)
Iron limitation with NPZD-Fe (Fiechter et al., 2009)
NPZD with Carbon Cycle (TBD)
Modeling Exercises: 1D vertical NPZD
The Deep Chlorophyll Maxima (Hodges et al., 2004)
Theory: Tracer conservation and Ocean transport
Overview of large-scale ocean circulation: Wind-driven circulation,
Sverdrup balance, Stommel gyre, thermohaline circulation, mixing, geostrophy, circulation of
passive and active tracers, interannual variability (Chapter 2, Sarmiento and Gruber; and Chapter 2 Fasham's
monography)
Modeling Exercises: Eulerian and Lagrangian Transport Equations
Tracer conservation equation for passive tracers (Combes et al., 2007)
Lagrangian transport equation (Schlag et al., 2008, LTRANS)
Review and Midterm Exam
Theory: Continental margin exchange
Recycling and export systems. Costal upwelling systems: the
California current, the Humboldt current and the Benguela current.
Monsoonal systems. The Arctic shelfs. Semi-enclosed marginal seas.
(Chapter 3 Fasham's monography - review article by Williams and
Follows)
Modeling Exercises: 3D Upwelling Ecosystem
Open Ocean Equatorial Upwelling System (TBD)
Eastern Boundary Upwelling Ecosystem (Gruber et al., 2006)
Western Boundary Margin Ecosystem (Fennel et al., 2006)
Spring Break
Theory and Modeling Exercises: Overview of Ocean Ecosystem Models
Regional Ocean Modeling System (ROMS) NPZD (Gruber et al., 2006)
Darwinian Ecosystem Models (Follows et al., 2007)
Individual Based Models (IBMs) (North et al., 2008)
Bayesian Hierarchical Ecosystem Models (BHMs) (Wikle et al. 2007; TBD)
Ecopath with Ecosym, ecosystem modeling and management (http://www.ecopath.org)
Final Exam
Edwards and Yool. The role of higher predation in plankton population models. J Plankton Res (2000) vol. 22 (6) pp. 1085-1112
Fennel et al. Nitrogen cycling in the Middle Atlantic Bight: Results from a three-dimensional model and implications for the North Atlantic nitrogen budget. Global Biogeochem Cy (2006) vol. 20 (3) pp. GB3007
Follows et al. Emergent biogeography of microbial communities in a model ocean. Science (2007) vol. 315 (5820) pp. 1843-1846
Gruber et al. Eddy-resolving simulation of plankton ecosystem dynamics in the California Current System. Deep-Sea Res Pt I (2006) vol. 53 (9) pp. 1483-1516
Haidvogel et al. Ocean forecasting in terrain-following coordinates: Formulation and skill assessment of the Regional Ocean Modeling System. J Comput Phys (2008) vol. 227 (7) pp. 3595-3624
Hodges and Rudnick. Simple models of steady deep maxima in chlorophyll and biomass. Deep-Sea Res Pt I (2004) vol. 51 (8) pp. 999-1015
North et al. Vertical swimming behavior influences the dispersal of simulated oyster larvae in a coupled particle-tracking and hydrodynamic model of Chesapeake Bay. Mar Ecol-Prog Ser (2008) vol. 359 pp. 99-115
Schlag et al. Larval TRANSport Lagrangian model (LTRANS) User’s Guide. University of Maryland Center for Environmental Science, Horn Point Laboratory. Cambridge, MD. (2008) pp. 146
Wikle and Berliner. A Bayesian tutorial for data assimilation. Physica D (2007) vol. 230 (1-2) pp. 1-16
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