Marine Ecosystem Modeling

EAS 8803 Spring 2010

Norway Bloom
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Prof. Emanuele Di Lorenzo
phone 404-894-3994, web
office ES&T 3252
Prof. Annalisa Bracco
phone 404-894-1749, web
office ES&T 3256
ES&T L1116, TuTh 12.05- 1:25 PM

Ocean Biogeochemical Dynamics by Jorge Sarmiento and Nicolas Gruber
Ocean Biogeochemistry: The role of the ocean carbon cycle in global change; edited by M. J. R. Fasham
Mathematical Biology, by J. D. Murray

WEEK 1-3
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
Introduction to Numerical Methods
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)
WEEK 5-6
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)
WEEK 7 (Feb 23 and 25)
Review and Midterm Exam

WEEK 8-9
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

Week 11-15
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 (
Week 16
Final Exam

Edwards and Yool. The role of higher predation in plankton population models. J Plankton Res (2000) vol. 22 (6) pp. 1085-1112

Edwards and Bees. Generic dynamics of a simple plankton population model with a non-integer exponent of closure. Chaos, Solitons and Fractals 12 (2001) pp .289-300

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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