Bibliography
Atkinson, M. J., and Bilger, R. W., 1992. Effects of water velocity
on phosphate uptake in coral reef-flat communities. Limnology
and Oceanography, 37, 273–279.
Atkinson, M. J., Falter, J. L., and Hearn, C. J., 2001. Nutrient
dynamics in the Biosphere 2 coral reef mesocosm: water velocity
controls NH 4 and PO 4 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.
Brock, J., Wright, C., Clayton, T., and Nayegandhi, A., 2004. Lidar
optical rugosity of coral reefs in Biscayne National Park, Florida.
Coral Reefs, 23, 48–59.
Brown, J. H., Gupta, V. K., Li1, B. L., Milne, B. T., Restrepo, C.,
and West, G. B., 2002. The fractal nature of nature: power laws,
ecological complexity and biodiversity. Philosophical Transactions of the Royal Society of London. Series B, 357, 619–626.
Cornelisen, C. D., and Thomas, F. I. M., 2009. Prediction and validation of flow-dependent uptake of ammonium over a seagrass
hardbottom community in Florida Bay. Marine Ecology Progress Series, 386, 71–81.
Hamner, W. M., Colin, P. L., and Hamner, P. P., 2007. Export-import
dynamics of zooplankton on a coral reef in Palau. Marine Ecology Progress Series, 334, 83–92.
Hatcher, B. G., 1997. Coral reef ecosystems: how much greater is
the whole than the sum of the parts? Coral Reefs, 16, S77–S91.
Hatcher, B. G., 1998. Coral reef primary productivity: A beggar’s
banquet. Trends in Ecology and Evolution, 3, 106–111.
Hearn, C. J., 1999. Wave-breaking hydrodynamics within coral reef
systems and the effect of changing relative sealevel. Journal of
Geophysical Research, 104(C12), 30007–30020.
Hearn, C. J., 2001a. The state of knowledge of the hydrodynamics
of coral reefs at the New Millennium. Coral Reefs, 20, 327–329.
Hearn, C. J., 2001b. Roughness and the dynamics of waves, turbulence and currents on nearshore reefs. Eos Transactions of American Geophysical Union, 82, OS12A–0407.
Hearn, C. J., 2006. The great leap forward: particle age in coastal
models. Eos Transactions of American Geophysical Union, 87,
OS33FA–017.
Hearn, C. J., 2008. The Dynamics of Coastal Models. Cambridge:
Cambridge University Press.
Hearn, C. J., 2010. The Methods of Coastal Models. New York:
Taylor and Francis.
Hearn, C. J., and Atkinson, M. J., 2000. Effects of sea-level rise on
the hydrodynamics of a coral reef lagoon: Kaneohe Bay, Hawaii.
In Noye J. (ed.), Sea-Level Changes and Their Effects. Singapore: World Scientific, pp. 25–48.
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, 347–356.
Hearn, C. J., and Parker, I. N., 1988. Hydrodynamic processes on
the ningaloo coral reef, Western Australia. In Proceedings of
6th International Coral Reef Symposium, Coral Reef Symposium
Executive, Vol. 2, pp. 497–502.
Hench, J. L., Leichter, J. J., and Monismith, S. G., 2008. Episodic
circulation and exchange in a wave-driven coral reef and lagoon
system. Limnology and Oceanography, 53, 2681–2694.
Hopley, D., Smithers, S. G., and Parnell, K. E., 2007. The Geomorphology of the Great Barrier Reef; Development, Diversity and
Change. Cambridge: Cambridge University Press.
Johannes, R. E., 1981. Words of the Lagoon: Fishing and Marine
Lore in the Palau District of Micronesia. Berkeley: University
of California Press.
Kaandorp, J. A., and Kübler, J. E., 2001. The Algorithmic Beauty of
Seaweeds, Sponges and Corals. New York: Springer.
Kench, P. S., 1998. Physical processes in an Indian Ocean atoll.
Coral Reefs, 17, 155–168.
Kraines, S. B., Yanagi, T., Isobe, M., and Komiyama, H., 1998.
Wind-wave driven circulation on the coral reef at Bora Bay,
Miyako Island. Coral Reefs, 17, 133–143.
Kuffner, I. B., Brock, J. C., Grober-Dunsmore, R., Bonito, V. E.,
Hickey, T. D., and Wright, C. W., 2007. Relationships between
patch-reef fish communities and remotely sensed rugosity measurements in Biscayne National Park, Florida, U.S.A. Environmental Biology of Fishes, 78, 71–82.
Lacy, J. R., Sherwood, C. R., Wilson, D., Chisholm, T., and
Gelfenbaum, G., 2005. Estimating hydrodynamic roughness in
a wave-dominated environment with a high resolution acoustic
Doppler profiler. Journal of Geophysical Research, 110
(C06014), doi:10.1029/2003JC001814.
Lowe, R. J., Koseff, J. R., and Monismith, S. G., 2005a. Oscillatory
flow through submerged canopies. Part 1. Velocity structure.
Journal Geophysical Research (Oceans), 110, doi:10.1029./
2004.JC002788.
Lowe, R. J., Monismith, S. G., Koseff, J. R., and Falter, J., 2005b.
Oscillatory flow through submerged canopies. Part 2. Canopy
mass transfer. Journal Geophysical. Research (Oceans), 110,
doi: 10.1029./2004.JC002789.
Lowe, R. J., Shavit, U., Falter, J. L., Koseff, J. R., and Monismith,
S. G., 2008. Modeling flow in coral communities with and without waves: A synthesis of porous media and canopy flow
approaches. Limnology and Oceanography, 53, 2668–2680.
Monismith, S. G., 2007. Hydrodynamics of Coral Reefs. Annual
Review of Fluid Mechanics, 39, 37–55.
Monismith, S. G., Reidenbach, M. A., Yahel, G., and Koseff, J. R.,
2006. Thermally driven exchanges between a coral reef and the
adjoining ocean. Journal of Physical Oceanography, 36,
1332–1347.
Munk, W. H., and Sargent, M. C., 1954. Bikini and nearby atolls,
Marshall Islands. U.S. Geological Survey Professional Paper,
260-C, 275–280.
Nepf, H. M., and Vivoni, E. R., 2000. Flow Structure in depthlimited flow. Journal of Geophysical Research (Oceans), 105
(C12), 28547–28557.
Oberdorfer, J. A., and Buddemier, R. W., 1986. Coral reef hydrology: field studies of water movement within a barrier reef. Coral
Reefs, 5, 7–12.
Parnell, K. E., 1986. Water movement within a fringing reef flat,
Orpheus Island, North Queensland, Australia. Coral Reefs, 5, 1–6.
Peterson, E. L., Beger, M., and Pinca, S., 2006. Three-dimensional
model of atoll hydrodynamics. In Proceedings of 10th International Coral Reef Symposium, Japanese Coral Reef Society,
pp. 1434–1439.
Purkis, S. J., and Kohler, K. E., 2008. The role of topography in promoting fractal patchiness in a carbonate shelf landscape. Coral
Reefs, 27, 977–989.
Reidenbach, M. A., Monismith, S. G., Koseff, J. R., Yahel, G., and
Genin, A., 2006. Boundary layer turbulence and flow structure
over a fringing coral reef. Limnology and Oceanography, 51,
1956–1968.
Succi, S., 2001. The Lattice Boltzmann Equation for Fluid Dynamics and Beyond. Oxford: Oxford University Press.
Symonds, G., Black, K. P., and Young, I. R., 1995. Wave driven
flow over shallow reefs. Journal of Geophysical Research, 100
(C2), 2639–2648.
Tait, R. J., 1972. Wave set-up on coral reefs. Journal of Geophysical
Research, 77, 2207–2211.
Tomczak, M., 1988. Island wakes in deep and shallow water. Journal of Geophysical Research, 93, 5153–5154.
von Arx, W. S., 1948. The circulation systems of Bikini and
Rongelap lagoons. Transactions of the American Geophysical
Union, 29, 86–870.
572
HYDRODYNAMICS OF CORAL REEF SYSTEMS
Atkinson, M. J., and Bilger, R. W., 1992. Effects of water velocity
on phosphate uptake in coral reef-flat communities. Limnology
and Oceanography, 37, 273–279.
Atkinson, M. J., Falter, J. L., and Hearn, C. J., 2001. Nutrient
dynamics in the Biosphere 2 coral reef mesocosm: water velocity
controls NH 4 and PO 4 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.
Brock, J., Wright, C., Clayton, T., and Nayegandhi, A., 2004. Lidar
optical rugosity of coral reefs in Biscayne National Park, Florida.
Coral Reefs, 23, 48–59.
Brown, J. H., Gupta, V. K., Li1, B. L., Milne, B. T., Restrepo, C.,
and West, G. B., 2002. The fractal nature of nature: power laws,
ecological complexity and biodiversity. Philosophical Transactions of the Royal Society of London. Series B, 357, 619–626.
Cornelisen, C. D., and Thomas, F. I. M., 2009. Prediction and validation of flow-dependent uptake of ammonium over a seagrass
hardbottom community in Florida Bay. Marine Ecology Progress Series, 386, 71–81.
Hamner, W. M., Colin, P. L., and Hamner, P. P., 2007. Export-import
dynamics of zooplankton on a coral reef in Palau. Marine Ecology Progress Series, 334, 83–92.
Hatcher, B. G., 1997. Coral reef ecosystems: how much greater is
the whole than the sum of the parts? Coral Reefs, 16, S77–S91.
Hatcher, B. G., 1998. Coral reef primary productivity: A beggar’s
banquet. Trends in Ecology and Evolution, 3, 106–111.
Hearn, C. J., 1999. Wave-breaking hydrodynamics within coral reef
systems and the effect of changing relative sealevel. Journal of
Geophysical Research, 104(C12), 30007–30020.
Hearn, C. J., 2001a. The state of knowledge of the hydrodynamics
of coral reefs at the New Millennium. Coral Reefs, 20, 327–329.
Hearn, C. J., 2001b. Roughness and the dynamics of waves, turbulence and currents on nearshore reefs. Eos Transactions of American Geophysical Union, 82, OS12A–0407.
Hearn, C. J., 2006. The great leap forward: particle age in coastal
models. Eos Transactions of American Geophysical Union, 87,
OS33FA–017.
Hearn, C. J., 2008. The Dynamics of Coastal Models. Cambridge:
Cambridge University Press.
Hearn, C. J., 2010. The Methods of Coastal Models. New York:
Taylor and Francis.
Hearn, C. J., and Atkinson, M. J., 2000. Effects of sea-level rise on
the hydrodynamics of a coral reef lagoon: Kaneohe Bay, Hawaii.
In Noye J. (ed.), Sea-Level Changes and Their Effects. Singapore: World Scientific, pp. 25–48.
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, 347–356.
Hearn, C. J., and Parker, I. N., 1988. Hydrodynamic processes on
the ningaloo coral reef, Western Australia. In Proceedings of
6th International Coral Reef Symposium, Coral Reef Symposium
Executive, Vol. 2, pp. 497–502.
Hench, J. L., Leichter, J. J., and Monismith, S. G., 2008. Episodic
circulation and exchange in a wave-driven coral reef and lagoon
system. Limnology and Oceanography, 53, 2681–2694.
Hopley, D., Smithers, S. G., and Parnell, K. E., 2007. The Geomorphology of the Great Barrier Reef; Development, Diversity and
Change. Cambridge: Cambridge University Press.
Johannes, R. E., 1981. Words of the Lagoon: Fishing and Marine
Lore in the Palau District of Micronesia. Berkeley: University
of California Press.
Kaandorp, J. A., and Kübler, J. E., 2001. The Algorithmic Beauty of
Seaweeds, Sponges and Corals. New York: Springer.
Kench, P. S., 1998. Physical processes in an Indian Ocean atoll.
Coral Reefs, 17, 155–168.
Kraines, S. B., Yanagi, T., Isobe, M., and Komiyama, H., 1998.
Wind-wave driven circulation on the coral reef at Bora Bay,
Miyako Island. Coral Reefs, 17, 133–143.
Kuffner, I. B., Brock, J. C., Grober-Dunsmore, R., Bonito, V. E.,
Hickey, T. D., and Wright, C. W., 2007. Relationships between
patch-reef fish communities and remotely sensed rugosity measurements in Biscayne National Park, Florida, U.S.A. Environmental Biology of Fishes, 78, 71–82.
Lacy, J. R., Sherwood, C. R., Wilson, D., Chisholm, T., and
Gelfenbaum, G., 2005. Estimating hydrodynamic roughness in
a wave-dominated environment with a high resolution acoustic
Doppler profiler. Journal of Geophysical Research, 110
(C06014), doi:10.1029/2003JC001814.
Lowe, R. J., Koseff, J. R., and Monismith, S. G., 2005a. Oscillatory
flow through submerged canopies. Part 1. Velocity structure.
Journal Geophysical Research (Oceans), 110, doi:10.1029./
2004.JC002788.
Lowe, R. J., Monismith, S. G., Koseff, J. R., and Falter, J., 2005b.
Oscillatory flow through submerged canopies. Part 2. Canopy
mass transfer. Journal Geophysical. Research (Oceans), 110,
doi: 10.1029./2004.JC002789.
Lowe, R. J., Shavit, U., Falter, J. L., Koseff, J. R., and Monismith,
S. G., 2008. Modeling flow in coral communities with and without waves: A synthesis of porous media and canopy flow
approaches. Limnology and Oceanography, 53, 2668–2680.
Monismith, S. G., 2007. Hydrodynamics of Coral Reefs. Annual
Review of Fluid Mechanics, 39, 37–55.
Monismith, S. G., Reidenbach, M. A., Yahel, G., and Koseff, J. R.,
2006. Thermally driven exchanges between a coral reef and the
adjoining ocean. Journal of Physical Oceanography, 36,
1332–1347.
Munk, W. H., and Sargent, M. C., 1954. Bikini and nearby atolls,
Marshall Islands. U.S. Geological Survey Professional Paper,
260-C, 275–280.
Nepf, H. M., and Vivoni, E. R., 2000. Flow Structure in depthlimited flow. Journal of Geophysical Research (Oceans), 105
(C12), 28547–28557.
Oberdorfer, J. A., and Buddemier, R. W., 1986. Coral reef hydrology: field studies of water movement within a barrier reef. Coral
Reefs, 5, 7–12.
Parnell, K. E., 1986. Water movement within a fringing reef flat,
Orpheus Island, North Queensland, Australia. Coral Reefs, 5, 1–6.
Peterson, E. L., Beger, M., and Pinca, S., 2006. Three-dimensional
model of atoll hydrodynamics. In Proceedings of 10th International Coral Reef Symposium, Japanese Coral Reef Society,
pp. 1434–1439.
Purkis, S. J., and Kohler, K. E., 2008. The role of topography in promoting fractal patchiness in a carbonate shelf landscape. Coral
Reefs, 27, 977–989.
Reidenbach, M. A., Monismith, S. G., Koseff, J. R., Yahel, G., and
Genin, A., 2006. Boundary layer turbulence and flow structure
over a fringing coral reef. Limnology and Oceanography, 51,
1956–1968.
Succi, S., 2001. The Lattice Boltzmann Equation for Fluid Dynamics and Beyond. Oxford: Oxford University Press.
Symonds, G., Black, K. P., and Young, I. R., 1995. Wave driven
flow over shallow reefs. Journal of Geophysical Research, 100
(C2), 2639–2648.
Tait, R. J., 1972. Wave set-up on coral reefs. Journal of Geophysical
Research, 77, 2207–2211.
Tomczak, M., 1988. Island wakes in deep and shallow water. Journal of Geophysical Research, 93, 5153–5154.
von Arx, W. S., 1948. The circulation systems of Bikini and
Rongelap lagoons. Transactions of the American Geophysical
Union, 29, 86–870.
572
HYDRODYNAMICS OF CORAL REEF SYSTEMS