References and Publications

References

Andrews, J.C. and Furnas, M.J., 1986.  Subsurface intrusions of Coral Sea water into the central Great Barrier Reef – I. Structures and shelf-scale dynamics.  Continental Shelf Res., 6(4):491-514.

Ariathurai, R. & Krone, R. B. 1976. Finite element model for cohesive sediment transport. Journal of the Hydraulics Division, ASCE, 104, HY2, 323–328.

Beaman, R. 2010. Project 3DGBR: a high-resolution depth model for the Great Barrier Reef and Coral Sea. Final Report to Marine and Tropical Sciences Research Facility Final Report, June 2010.

Blumberg, A.F., Herring, J., 1987. Circulation modelling using orthogonal curvilinear coordinates, in Three-Dimensional Models of marine and Estuarine Dynamics, Ed. J.C.J. Nihoul and B.M. Jamart, Elsevier.

Brodie, J., Furnas, M., 2001. Status of nutrient and sediment inputs from Great Barrier Reef catchments and impacts on the Reef.  Proceedings of the 2^nd National Conference on Aquatic Environments: Sustaining Our Aquatic Environments – Implementing Solutions. 20-23 November, 2001, Townsville, 14 p.

Brodie J., Kroon F., Schaffelke B., Wolanski E., Lewis S., Devlin M., Bohnet I., Bainbridge Z., Waterhouse J., Davis A. 2012. Terrestrial pollutant runoff to the Great Barrier Reef: An update of issues, priorities and management responses. Marine Pollution Bulletin 65, 81–100

Brodie J., Waterhouse J.,Schaffelke B., Kroon F., Thorburn P., Rolfe J., Johnson J., Fabricius K., Lewis S., Devlin M., Warne M., McKenzie L. 2013. Scientific Consensus Statement Land use impacts on Great Barrier Reef water quality and ecosystem condition. The State of Queensland 2013. Published by the Reef Water Quality Protection Plan Secretariat, July 2013

Burrage, D.M., C. R. Steinberg, W. J. Skirving and J. A. Kleypas, 1996. Mesoscale circulation features of the Great Barrier Reef lagoon inferred from NOAA satellite imagery. Remote Sens. Environ., 56, 21 – 41.

Darnell R., Henderson B., Kroon F., Kuhnert P. 2012. Statistical power of detecting trends in total suspended sediment loads to the Great Barrier Reef Marine Pollution Bulletin 65, 203–209

Debreu, L., Vouland, C., Blayo, E., 2008. AGRIF: adaptive grid refinement in Fortran. Comput. Geosci. 34 (1), 8–13.

Fabricius K., De’ath George, Humphrey C., Zagorskis I., Schaffelke B. 2013. Intra-annual variation in turbidity in response to terrestrial runoff on near-shore coral reefs of the Great Barrier Reef Estuarine, Coastal and Shelf Science 116, 57-65.

Fabricius K., Logan M., Weeks S., Brodie J. 2014. The effects of river run-off on water clarity across the central Great Barrier Reef Marine Pollution Bulletin 84, 191–200

Furnas, M.J., (1991). Net in situ growth rates of phytoplankton in an oligotrophic, tropical shelf ecosystem. Limnol. Oceanogr., 36(1): 13-29.

Furnas, M.  2003. Catchments and corals: terrestrial runoff to the Great Barrier Ref. Australian Institute of Marine Science, Queen land., 334 p.

Furnas, M., Mitchell, A., Skuza, M. and Brodie, J., (2005).  In the other 90%: phytoplankton responses to enhanced nutrient availability in the Great Barrier Reef Lagoon.  Mar. Poll. Bull., 51: 253-265.

Furnas, M and Mitchell, A.W., (1986). Phytoplankton dynamics in the central Great Barrier Reef – I. Seasonal changes in biomass and community structure and therir relation to intrusive activity. Continental Shelf Res., 6(3): 363-384.

Grant, D., Madsen, O., 1982. Movable bed roughness in unsteady oscillatory flow. J. of Geophysical Research, V. 87, N C1, pp. 469-481.

Griffin, D. A. and J. H. Middleton, 1986. Coastal trapped waves behind a large continental shelf island, southern Great Barrier Reef. J. Phys. Oceanogr., 16, 1651 – 1664.

Griffin, D. A., J. H. Middleton and L. Bode, 1987. The tidal and longer-period circulation of Capricornia, souther Great Barrier Reef. Aust. J. Mar. Freshw. Res., 38, 461 – 474.

Harris, P.T., Hughes, M.G., Baker, E.K., Dalrymple, R.W., Keene, J.B., 2004. Sediment transport in distributary channels and its export to the pro-deltaic environment in a tidally-dominated delta: Fly River, Papua New Guinea. Continental Shelf Research, 24, 2431-2454.

Herzfeld, M., 2006. An alternative coordinate system for solving finite difference ocean models. Ocean Modelling, 14, 174 – 196.

Kroon F., Kuhnert P., Henderson B., Wilkinson S., Kinsey-Henderson A., Abbott B., Brodie J., Turner R. 2012. River loads of suspended solids, nitrogen, phosphorus and herbicides delivered to the Great Barrier Reef lagoon Marine Pollution Bulletin 65, 167–181

Kuhnert P., Henderson B., Lewis S., Bainbridge Z., Wilkinson S., Brodie J. 2012. Quantifying total suspended sediment export from the Burdekin River catchment using the loads regression estimator tool. Water Resour. Res., 48, W04533, doi:10.1029/2011WR011080.

Larcombe, P., Woolfe, K. 1999. Increased sediment supply to the Great Barrier Reef will not increase sediment accumulation at most coral reefs. Coral Reefs 18, 163-169

Larcombe, P., Carter, R. 2004. Cyclone pumping,sediment partitioning and the development of the Great Barrier Reef shelf system: a review. Quaternary Science Reviews 23, 107–135

Lewis S., Olley J., Furuichi T., Sharma A., Burton J. 2014. Complex sediment deposition history on a wide continental shelf: Implications for the calculation of accumulation rates on the Great Barrier Reef. Earth and Planetary Science Letters 393, 146–158

Madsen, O.S., 1994. Spectral wave-current bottom boundary layer flows, in Coastal Engineering 1994 Proceedings, 24^th International Conference Coastal Engineering Research Council/ASCE, pp. 384-398.

Margvelashvili, N., Saint-Cast, F., Condie, S., 2008. Numerical modelling of the suspended sediment transport in Torres Strait. Continental Shelf Research 28, 2241-2256.

Neil D., Orpin, A., Ridd, P., Yu, B. 2002. Sediment yield and impacts from river catchments to the Great Barrier Reef lagoon. Mar. Freshwater Res. 53, 733-752.

Orpin , A.R., Ridd, P.V. and Stewart, L.K. (1999) Assessment of the relative importance of major sediment-transport mechanisms in the central Great Barrier Reef lagoon. Australian Journal of Earth Science 46: 883 – 896.

Steinberg, C., 2007. Impacts of climate change on the physical oceanography of the Great Barrier Reef. Chapter 3, Climate Change and the Great Barrier Reef, eds. Johnson J.E. and Marshall P.A. Great Barrier Reef Marine Park Authority & Australian Greenhouse Office, pp 51-74.

Thompson A., Schroeder T., Brando V., Schaffelke B. 2014. Coral community responses to declining water quality: Whitsunday Islands, Great Barrier Reef, Australia. Coral Reefs DOI 10.1007/s00338-014-1201-y

Webster I., Brinkman R., Parslow J., Prange J., Steven A., Waterhouse J. 2008. Review and gap analysis of receiving-water water quality modelling in the Great Barrier Reef. CSIRO Report to Department of Environment, Water, Heritage and the Arts, 150 p.

Wolanski, E., Spagnol, S. (2000). Sticky waters in the Great Barrier Reef. Estuarine, Coastal and Shelf Science 50, 27-32

Wolanski, E., Fabricius, K., Cooper, T., Humphrey, C. 2008 Wet season fine sediment dynamics on the inner shelf of the Great Barrier Reef. Estuarine, Coastal and Shelf Science

Publications

BAIRD, M. E., ADAMS, M. P., BABCOCK, R. C., OUBELKHEIR, K., MONGIN, M., WILD-ALLEN, K. A., SKERRATT, J., ROBSON, B., PETROU, K., RALPH, P. J., O’BRIEN, K. R., CARTER, A. B., JARVIS, J. C. & RASHEED, M. A. minor revisions-a. A physical representation of seagrass growth for application in a complex shallow-water biogeochemical model Ecological Modelling.

BAIRD, M. E., CHERUKURU, N., JONES, E. M., MARGVELASHVILI, N., MONGIN, M., OUBELKHEIR, K., RALPH, P. J., RIZWI, F., ROBSON, B., SCHROEDER, T., SKERRATT, J., STEVEN, A. D. L. & WILD-ALLEN, K. A. minor revisions-b. Remote-sensing reflectance and true colour produced by acoupled hydrodynamic, optical, sediment, biogeochemical model of the Great Barrier Reef, Australia: comparison with remotely-sensed data Environmental Modelling and Software Journal.

GILLIBRAND, P. A. & HERZFELD, M. minor revisions. A mass-conserving advection scheme for offline simulation of tracer transport in coastal ocean models. Ocean Modelling.

HERZFELD, M. 2015. Methods for freshwater riverine input into regional ocean models. Ocean Modelling, 90, 1-15.

HERZFELD, M. & GILLIBRAND, P. A. 2015. Active open boundary forcing using dual relaxation time-scales in downscaled ocean models. Ocean Modelling, 89, 71-83.

JONES, E. M., DOBLIN, M. A., MATEAR, R. & KING, E. 2015. Assessing and evaluating the ocean-colour footprint of a regional observing system. Journal of Marine Systems, 143, 49-61.

JONES, E. M., HERZFELD, M. & OKE, P. R. To be submitted Dec2015. Efficient estimation of coastal hydrodynamic model parameters. Ocean Science Discussion.

MARGVELASHVILI, N., ANDREWARTHA, J., HERZFELD, M., ROBSON, B. & BRANDO, V. 2013. Satellite data assimilation and estimation of a 3d coastal sediment transport model using error-subspace emulators. Environmental Modelling and Software Journal 40, 191-201.

MARGVELASHVILI, N., CAMPBELL, E., MURRAY, L. & JONES, E. M. 2014. Hierarchical emulation and data assimilation into the sediment transport model. Procedia Computer Science, 29, 2121-2126.

MARGVELASHVILI, N., HERZFELD, M., F. RIZWI, M. M., M. E. BAIRD, E. JONES, , E. KING, T. SCHROEDE, RIZWI, F., MONGIN, M., BAIRD, M. E., JONES, E. M., SCHAFFELKE, B., KING, E. & SCHROEDER, T. Submitted. Emulator-assisted data assimilation in complex models. . Ocean Dynamics (under review).

MONGIN, M. & BAIRD, M. 2014. The impact of photosynthesis, calcification and water circulation on carbon chemistry variability above a coral reef: a modelling study. Ecological Modelling, 284, 19-34.

MONGIN, M., BAIRD, M. E., TILBROOK, B., MATEAR, R., LENTON, A., HERZFELD, M., WILD-ALLEN, K. A., SKERRATT, J., MARGVELASHVILI, N., ROBSON, B., DUARTE, C. M., GUSTAFSSON, M. S. M., RALPH, P. J. & STEVEN, A. D. L. minor revisions. The exposure of the Great Barrier Reef to ocean acidification. Nature Communications (in press).

OKE, P. R., LARNICOL, G., JONES, E. M., KOURAFALOU, V., SPERREVIK, A. K., CARSE, F., TANAJURA, C. A. S., MOURRE, B., TONANI, M., BRASSINGTON, G. B., LE HENAFF, M., HALLIWELL, J., GEORGE R., ATLAS, R., MOORE, A. M., EDWARDS, C. A., MARTIN, M. J., SELLAR, A. A., ALVAREZ, A., DE MEY, P. & ISKANDARANI, M. 2014. Assessing the impact of observations on ocean forecasts and reanalyses: Part 2, Regional applications. Journal of Operational Oceanography, issue?

ROBSON, B. 2014. When do aquatic systems models provide useful predictions, what is changing, and what is next? Environmental Modelling & Software, 61, 287-296.

ROBSON, B. J., BAIRD, M. & WILD-ALLEN, K. 2013. A physiological model for the marine cyanobacteria, Trichodesmium. MODSIM2013, 20th International Congress on Modelling and Simulation, Modelling and Simulation Society of Australia and New Zealand, 1652-1658.

ROBSON, B. J. & DOURDET, V. 2015. Prediction of sediment, particulate nutrient and dissolved nutrient concentrations in a dry tropical river to provide input to a mechanistic coastal water quality model. Environmental Modelling & Software, 63, 97-108.

ROBSON, B. J., SKERRATT, J., MONGIN, M., WILD-ALLEN, K. A. & BAIRD, M. E. 2014. Varying the temporal resolution of river nutrient boundary conditions to a coupled hydrodynamic-biogeochemical model of a coastal system has surprisingly little impact on model results. Proceedings – 7th International Congress on Environmental Modelling and Software: Bold Visions for Environmental Modeling, iEMSs Vol 1, 533-539.

SCHILLER, A., HERZFELD, M., BRINKMAN, R., RIZWI, F. & ANDREWARTHA, J. 2015. Cross-shelf exchanges between the Coral Sea and the Great Barrier Reef lagoon determined from a regional-scale numerical model. Continental Shelf Research, 109, 150-163.

SCHILLER, A., HERZFELD, M., BRINKMAN, R. & STUART, G. 2014. Monitoring, Predicting, and Managing One of the Seven Natural Wonders of the World. Bulletin of the American Meteorological Society, 95, 23-30.

STEVEN, A. D. L., HODGE, J., CANNARD, T., CARLIN, G., FRANKLIN, H., MCJANNET, D., MOESENEDER, C. & SEARLE, R. 2015. Continuous Water Quality Monitoring on the Great Barrier Reef. CSIRO Final Report to Great Barrier Reef Foundation. CSIRO, 159pp.

WEIJERMAN, M., FULTON, E. A., JANSSEN, A. B. G., KUIPER, J. J., LEEMANS, R., ROBSON, B. J., VAN DE LEEMPUT, I. A. & MOOIJ, W. M. 2015. How models can support ecosystem-based management of coral reefs. Progress in Oceanography.