Atkinson, M. J. and Bilger, R. W. (1992). Effects of water velocity on phosphate uptake on coral reefs. Limnol. Oceanogr. 37, 261–272.
Atkinson, M. J., Falter, J. L., and Hearn, C. J. (2001). Nutrient dynamics in the Biosphere 2 coral reef mesocosm: water velocity controls NH4 and PO4 uptake. Coral Reefs 20, 341–346.
Baird, M. E., Roughan, M., Brander, R. W., Middleton, J. H., and Nippard, G. J. (2004). Mass-transfer-limited nitrate uptake on a coral reef flat, Warraber Island, Torres Strait, Australia. Coral Reefs 23, 386–396.
Bloch, S. C. (2003). Excel for Engineers and Scientists, 2nd edn. New York: John Wiley.
Blumberg, A. F. and G. L. Mellor (1987). A description of a three-dimensional coastal ocean circulation model. In Three-Dimensional Coastal Ocean Models, ed. Heaps, N.. Washington, DC: American Geophysical Union, pp. 1–16.
Brander, R. W., Kench, P. S., and Hart, D. (2004). Spatial and temporal variations in wave characteristics across a reef platform, Warraber Island, Torres Strait, Australia. Marine Geol. 207 (1–4), 169–184.
Courant, R., Friedrichs, K. O., and Levy, H. (1928). Über die partiellen Differenzengleichungen der mathematischen Physik. Math. Annalen 100, 32–74.
Csanady, G. T. (1982). Circulation in the Coastal Ocean (Environmental Fluid Mechanics). New York: Springer.
Dauxois, T. and Peyrard, M. (2006). Physics of Solitons. Cambridge, UK: Cambridge University, Press.
Dean, R. G. and Dalrymple, R. A. (2001). Coastal Processes with Engineering Applications. Cambridge, UK: Cambridge University Press.
DHI (2002). MIKE 21 Coastal Hydraulics and Oceanography, Hydrodynamic Module: Reference Manual. Hørsholm, Denmark: DHI Water and Environment.
Ebbesmeyer, C. C. and Ingraham, W. J. (1994). Shoe spilt in the North Pacific. Eos 73, 361–365.
Forester, C. S. (1953). Hornblower and the Atropos. London: Michael Joseph.
Fredsøe, J. and Diehards, R. (1992). Mechanics of Coastal Sediment Transport, Advanced Series in Ocean Engineering vol. 3. Singapore: World Scientific Publishing Co.
Grant, W. D. and Madsen, O. W. (1979). Combined wave and current interation with a rough bottom. J. Geophys. Res. 84, 1797–1808.
Hatcher, A. (1989). Variation in the components of a benthic community structure in a coastal lagoon as a function of spatial scale. Austr. J. Marine Freshw. Res. 40, 79–96.
Hatcher, B. G. (1990). Coral reef primary productivity: a hierarchy of pattern and process. Trends Ecol. Evol. 5, 149–155.
Hearn, C. J. (1983). Seasonal Aspects of the Oceanography of Koombana Bay, Environmental Dynamics Report ED–83–045. Perth, WA: The University of Western Australia.
Hearn, C. J. (1985). On the value of the mixing efficiency in the Simpson–Hunter h / u3 criterion. Deutsche Hydrogr. Z. 38(3), 133–145.
Hearn, C. J. (1998). Application of the Stommel model to shallow mediterranean estuaries and their characterisation. J. Geophys. Res. 103, 10391–10404.
Hearn, C. J. (1999). Wave-breaking hydrodynamics within coral reef systems and the effect of changing relative sealevel. J. Geophys. Res. 104, 30007–30020.
Hearn, C. J. (2000). The SPECIES simulation software. In Proceedings of the United Nations Conference on Information Management and Decision Support for Marine Biodiversity Protection and Human Welfare: Coral Reefs, pp. 87–100. Townsville, QLD: Australian Institute of Marine Science.
Hearn, C. J. (2006). The great leap forward: particle age in coastal models. Eos Trans. 87(52), Fall Meeting Suppl. Abstract OS33F–01.
Hearn, C. J. and Largier, J. L. (1997). The summer buoyancy dynamics of a shallow mediterranean estuary and some effects of changing bathymetry: Tomales Bay, California. Estuar. Coast. Shelf Sci. 45, 497–506.
Hearn, C. J. and Parker, I. N. (1988). Hydrodynamic processes on the Ningaloo Coral Reef, Western Australia. Proc. 6th Int. Coral Reef Symp. 2, 497–502.
Hearn, C. J. and Prince, G. (1983). A System of Computer Programs for the Acquisition and Analysis of Drogue Data, Environmental Dynamics Report ED-83-052. Perth, WA: The University of Western Australia.
Hearn, C. J. and Robson, B. J. (2001). Inter-annual variability of bottom hypoxia in a shallow mediterranean estuary. Estuar. Coast. Shelf Sci. 52, 643–657.
Hearn, C. J. and E. Schulz (in press). Hydrodynamics of flow across a coral reef. Proc. Roy. Soc. Lond. A.
Hearn, C. J. and Sidhu, H. S. (1999). The Stommel model of shallow coastal basins. Proc. Roy. Soc. Lond. A 455, 3997–4011.
Hearn, C. J. and Sidhu, H. S. (2003). Stommel transitions in shallow coastal basins. Continent. Shelf Res. 23, 1071–1085.
Hearn, C. J., Hunter, J. R., Imberger, J., and Senden, D. (1985). Tidally induced jet in Koombana Bay, Western Australia. Austr. J. Marine Freshw. Res. 36(4), 453–479.
Hearn, C. J., Atkinson, M. J., and Falter, J. L. (2001). A physical derivation of nutrient uptake rates in coral reefs: effects of roughness and waves. Coral Reefs 20(4), 347–356.
Kantha, H. and Clayson, C. A. (2000). Numerical Models of Oceans and Oceanic Processes, International Geophysics Series vol. 66. New York: Academic Press.
Kato, H. and Phillips, O. M. (1969). On the penetration of a turbulent layer into a stratified fluid. J. Fluid Mech. 37, 643–655.
Longuet-Higgins, M. S. and Stewart, R. W. (1964). Radiation stress in water waves: a physical discussion with applications. Deep Sea Res. 11, 529–562.
Luketina, D. A. and Imberger, J. (1987). Characteristics of a surface buoyant jet. J. Geophys. Res. 92, 5435–5447.
Mangor, K. (2004). Shoreline Management Guidelines. Hørshølm, Denmark: DHI Water and Environment.
Mann, K. H. and Lazier, J. R. (2005). Dynamics of Marine Ecosystems: Biological–Physical Interactions in the Oceans. Oxford, UK: Blackwell.
Mellor, G. L. and Yamada, T. (1982). Development of a turbulence closure model for geophysical fluid problems. Rev. Geophys. Space Phys. 20, 851–875.
Minorsky, N. (1974). Introduction to Nonlinear Oscillations. Malabar, FL: Krieger.
Munk, W. H. and Anderson, E. R. (1948). Notes on a theory of the thermocline. J. Marine Res. 3, 276–295.
Officer, C. B. (1976). Physical Oceanography of Estuaries and Associated Coastal Waters. New York: John Wiley.
Paterson, J. C., Hamblin, P. F., and Imberger, J. (1984). Classification and dynamic simulation of the vertical structure of lakes. Limnol. Oceangr. 29, 845–861.
Pope, S. B. (2000). Turbulent Flows. Cambridge, UK: Cambridge University Press.
Rahmstorf, S. (1995). Bifurcations of the Atlantic thermohaline circulation in response to changes in the hydrological cycle. Nature 378, 145–149.
Rahmstorf, S. and Ganopolski, A.. (1999). Simple theoretical model may explain apparent climate instability. J. Climate 12, 1349–1352.
Simpson, J. H. and Hunter, J. R. (1974). Fronts in the Irish Sea. Nature 250, 404–406.
Simpson, J. H., Brown, J., Matthews, J., and Allen, G. (1990). Tidal strain, density currents and stirring in the control of estuarine stratification. Estuaries 13, 125–132.
Smith, S. V., Kimmerer, W. J., Laws, E. A., Brock, R. E., and Walsh, T. W. (1981). Kaneohe Bay sewage diversion experiment: perspectives on ecosystem responses to nutritional perturbation. Pacif. Sci. 35, 279–395.
Smith, S. V., Hollibaugh, J. T., Dollar, S. J., and Vink, S. (1991a). Tomales Bay Metabolism: C–N–P stoichiometry and ecosystem heterotrophy at the land–sea interface. Estuar. Coast. Shelf Sci. 33, 223–257.
Smith, S. V., Hollibaugh, J. T., Dollar, S. J., and Vink, S. (1991b). Tomales Bay, California: a case for carbon controlled nitrogen cycling. Limnol. Oceanogr. 34, 37–52.
Stocker, T. F. and Wright, D. G. (1991). Rapid transitions of the ocean's deep circulation induced by changes in surface water fluxes. Nature 351, 729–732.
Stommel, H. (1961). Thermohaline convection with two stable regimes of flow. Tellus 13 (2), 224–230.
Stommel, H. (1963). Varieties of oceanographic experience: the ocean can be investigated as a hydrodynamical phenomenon as well as explored geographically. Science 15, 572–576.
Tait, R. J. (1972). Wave set-up on coral reefs. J. Geophys. Res. 77, 2207–2211.
Taylor, G. I. (1953). Dispersion of soluble matter in solvent flowing through a tube. Proc. Roy. Soc. Lond. A 219, 186–203.
Thorpe, S. A. (2005). The Turbulent Ocean. Cambridge, UK: Cambridge University Press.
Thurman, H. V. and Trujillo, A. P. (2003). Introductory Oceanography, 10th edn. New York: Prentice Hall.
Whitehead, J. A. (1995). Thermohaline ocean processes and models. Ann. Rev. Fluid Mech. 27, 89–113.
Whitehead, J. A. (1998). Multiple T–S states for estuaries, shelves, and marginal seas. Estuaries 21, 281–293.
Wolanski, E. and Spagnol, S. (2000). Sticky waters in the Great Barrier Reef. Estuar. Coast. Shelf Sci. 50, 27–32.
Zeidberg, L. D. and Hamner, W. M. (2002). Distribution of squid paralarvae, Loligo opalescens (Cephalopoda: Myopsida), in the Southern California Bight in the three years following the 1997–1998 El Niño. Marine Biol. 141, 111–122.
