CEM Projects

2015

Herzfeld and Gillibrand 2015 Active open boundary forcing using dual relaxation time-scales in downscaled ocean models. Ocean Modelling 89 71-83

Vincent, Dourdet; Robson, Barbara. Prediction of sediment, particulate nutrient and dissolved nutrient concentrations in a dry tropical river to provide input to a mechanistic coastal model. Environmental Modelling & Software. 2015; 63:97-108.

Mariska, Weijerman; Fulton, Beth; Janssen, Annette; Kuiper, Jan; Leemans, Rik; Robson, Barbara 2015 How models can support ecosystem-based management of coral reefs. Progress in Oceanography. http://dx.doi.org/10.1016/j.pocean.2014.12.017

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

Mongin, M., M. E. Baird, B. Tilbrook, R. J. Matear, A. Lenton, M. Herzfeld, K. A. Wild-Allen, J. Skerratt, N. Margvelashvili, B. J. Robson, C. M. Duarte, M. S. M. Gustafsson, P. J. Ralph, A. D. L. Steven. The exposure of the Great Barrier Reef to ocean acidification. (submitted 15 June).

Baird, M. E., M. P. Adams, R. C. Babcock, K. Oubelkheir, M. Mongin, K. A. Wild-Allen, J. Skerratt, B. J. Robson, K. Petrou, P. J. Ralph, K. R. O'Brien, A. B. Carter, J. C. Jarvis, M. A. Rasheed A physical representation of seagrass growth for application in a complex shallow-water biogeochemical model (final preparation).

Baird, M. E., N. Cherukuru, E. Jones, N. Margvelashvili, M. Mongin, K. Oubelkheir, P. J. Ralph, F. Rizwi, B. J. Robson, T. Schroeder, J. Skerratt, A. D. L. Steven and K. A. Wild-Allen (submitted, 8th May 2015) Surface reflectance and true colour produced by a coupled hydrodynamic, optical, sediment, biogeochemical model of the Great Barrier Reef, Australia: comparison with remotely-sensed data. Env. Model. Software.

Everett, J. D., H. Macdonald, M. E. Baird, J. Humphries, M. Roughan, and I. M. Suthers (2015) Cyclonic entrainment of pre-conditioned shelf waters into a frontal eddy. J. Geophy. Res. (Oceans). 120, 677-691.

 

2014

Buchanan, Pearse; Swadling, Kerrie; Eriksen, Ruth; Wild-Allen, Karen. New evidence links changing shelf phytoplankton communities to boundary currents in southeast Tasmania. Reviews in Fish Biology and Fisheries. 2014; 24(2):427-442.

Davies, Claire; Armstrong, Amelia; Baird, Mark; Coman, Frank; Edgar, Steven; Gaughan, Dan; et al. Over 75 years of zooplankton data from Australia. Ecology. 2014; 95(11):3229-3229.

Mongin, Mathieu; Baird, Mark. The impact of photosynthesis, calcification and water circulation on carbon chemistry variability above a coral reef: a modelling study. Ecological Modelling. 2014; 284:19-34.

Gal, Gideon; Hipsey, Matt; Rinke, Karsten; Robson, Barbara. Novel approaches to address challenges in modelling aquatic ecosystems. Environmental Modelling & Software. 2014; 61:246-248.

Harmel, R. Daren; Smith, Patricia; Migliaccio, Katie; Chaubey, Indrajeet; Douglas-Mankin, Kyle; Benham, Brian; et al. Evaluating, interpreting, and communicating performance of hydrologic/water quality models considering intended use: A review and recommendations. Environmental Modelling & Software. 2014; 57:40–51.

Barbara J. Robson; Aurélie Mousquès 2014 Predicting citation counts of environmental modelling papers. International Environmental Modelling and Software Society (iEMSs) 7th Intl. Congress on Env. Modelling and Software, San Diego, CA, USA. Daniel P. Ames, Nigel W.T. Quinn and Andrea E. Rizzoli (Eds.) . http://www.iemss.org/society/index.php/iemss-2014-proceedings

Margvelashvili N., Campbell E., Murray L., Jones E. 2014 Hierarchical Emulation and Data Assimilation into the Sediment Transport Model. Procedia Computer Science, 29, 2121–2126.

Matveev, Vlad; Robson, Barbara. Aquatic food web structure and the flow of carbon. Freshwater Reviews. 2014; 7(1):1-24.

Robson, Barbara; Skerratt, Jenny; Mongin, Mathieu; Wild-Allen, Karen; Baird, Mark. 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. In: 7th International Congress on Environmental Modelling and Software (iEMSs); 15-19 June 2014; San Diego, USA. San Diego, California, USA: iEMSS; 2014. 533-539.

Robson, Barbara; Gehrke, Peter; Burford, Michele; Webster, Ian; Revill, Andy; Palmer, Duncan. The Ord River estuary: a regulated wet-dry tropical river system. In: Wolanski, Eric, editor/s. Estuaries of Australia in 2050 and beyond. Springer; 2014. 247131–152.

Robson, Barbara. State of the art in modelling of phosphorus cycles in aquatic systems: review, criticisms and commentary. Environmental Modelling & Software. 2014; 61:339-359.

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

Schiller, Andreas; Herzfeld, Mike; Brinkman, Richard; Stuart, Greg. Monitoring, Predicting and Managing one of the Seven Natural Wonders of the World. Bulletin of the American Meteorological Society. 2014; 95(1):23-30.

Wild-Allen, Karen; Rayner, Mark. Continuous nutrient observations capture fine-scale estuarine variability simulated by a 3D biogeochemical model.. Journal of Marine Chemistry. 2014; 167:135-149.

Everett, Jason; Baird, Mark; Roughan, Moninya; Suthers, Iain; Doblin, Martina. Relative impact of seasonal and oceanographic drivers on surface chlorophyll a along a Western Boundary Current. Progress in Oceanography. 2014; 120:340-351

Dowd, Mike; Jones, Emlyn; Parslow, John. A statistical overview and perspectives on data assimilation for marine biogeochemical models. Environmetrics. 2014; 25(4):203-213.

Macreadie, P. I., M.E. Baird, S.M. Trevathan-Tackett, A.W.D. Larkum, P.J. Ralph (2014) Quantifying and modelling the carbon sequestration capacity of seagrass meadows - a critical assessment. Mar. Poll. Bull. 83, 430–439.

Williams, Ray; De Souza Junior, Paulo; Jones, Emlyn. Analysing Coastal Ocean Model Outputs using Competitive-Learning Pattern Recognition Techniques. Environmental Modelling & Software. 2014; 57(. .):165-176

 

2013

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. Journal Env. Modelling and Software, 40, 191-201.

Baird, M. E., P. J. Ralph, F. Rizwi, K. Wild-Allen, and A. D. L. Steven 2013. A dynamic model of the cellular carbon to chlorophyll ratio applied to a batch culture and a continental shelf ecosystem. Limnology and Oceanography 58,4, 1215-1226

Skerratt, J.H., Wild-Allen, K.,  Rizwi, F., Whitehead, J., Coughanowr, C. 2013  Use of a high resolution 3D fully coupled hydrodynamic, sediment and biogeochemical model to understand estuarine nutrient dynamics under various water quality scenarios. Ocean and Coastal Management. http://dx.doi.org/10.1016/j.ocecoaman.2013.05.005.

Wild-Allen K., Skerratt J., Whitehead J., Rizwi F., Parslow J. 2013 Mechanisms driving estuarine water quality: A 3D biogeochemical model for informed management. Estuarine, Coastal and Shelf Science. http://dx.doi.org/10.1016/j.ecss.2013.04.009,

Parslow, J. S., Cressie, N., Campbell, E., Jones. E. M., and Murray, L. 2013. Bayesian learning and predictability in a stochastic nonlinear dynamical model. Ecological Applications 2013 23:4, 679-698 , Ecological Applications

Barbara Robson, Mark Baird and Karen Wild-Allen 2013. A physiological model for the marine cyanobacteria, Trichodesmium. 20th International Congress on Modelling and Simulation, Adelaide, Australia, 1–6 December 2013 www.mssanz.org.au/modsim2013 1652-1658

Barbara Robson and Vincent Dourdet 2013 Incorporating a generalised additive model of river nutrient concentrations into a mechanistic receiving water model. In Piantadosi, J., Anderssen, R.S. and Boland J. (eds) MODSIM2013, 20th International Congress on Modelling and Simulation. Modelling and Simulation Society of Australia and New Zealand, December 2013, pp. 2506–2512. 373-379

Robson Barbara 2013 A systematic review of the treatment of phosphorus in biogeochemical and ecological models. 20th International Congress on Modelling and Simulation, Adelaide, Australia, 1–6 December 2013 www.mssanz.org.au/modsim2013, 1784- 1790

Gustafsson, M. S., Baird, M. E. and Ralph, P. J. (2013) The interchangeability of autotrophic and heterotrophic nitrogen sources in Scleractinian coral symbiotic relationships: a numerical study. Ecol. Model. 250, 183-194.

 

 

2012

Margvelashvili, N., Campbell, E., 2012. Sequential data assimilation in fine resolution models using error-subspace emulators: theory and preliminary evaluation. Journal of Marine Systems, 90, 13-22.

Jones, E. M., Oke, P.R., Rizwi, F. and Murray, L. (2012) Assimilation of glider and mooring data into a coastal ocean model. Ocean Modelling, 47, 1-13

Herzfeld, M., Andrewartha, J.R. (2012) A simple, stable and accurate Dirichlet open boundary condition for ocean model downscaling. Ocean Modelling, 43-44, 1-21.

Herzfeld, M., Schmidt, M., Griffies, S.M., Liang, Z. (2011) Realistic test cases for limited area ocean modelling. Ocean Modelling, 37, 1 – 34.

Wild-Allen, K., Thompson, P., Volkman, J., Parslow, J. (2011) Use of a coastal biogeochemical model to select environmental monitoring sites, Journal of Marine Systems, doi: 10.1016/j.jmarsys.2011.02.017

Herzfeld, M., Andrewartha, J.A. (2010) Modelling the physical oceanography of D’Entrecasteaux Channel and the Huon Estuary, south-eastern Tasmania. Marine and Freshwater Research, 61, 568-586.

Herzfeld, M., Andrewartha, J., Sakov. P. (2010) Modelling the physical oceanography of the D'Entrecasteaux Channel and the Huon Estuary, south-eastern Tasmania. Marine and Freshwater Research 61, 568–586. 

Jones, E. M., Parslow, J. S. and Murray, L. (2010). A Bayesian approach to state and parameter estimation in a Phytoplankton-Zooplankton model. Australian Meteorological and Oceanographic Journal, (59), 7-16.

Wild-Allen, K., Herzfeld, M., Thompson, P.A., Rosebrock, U., Parslow, J., Volkman, J.K. (2010) Applied coastal biogeochemical modelling to quantify the environmental impact of fish farm nutrients and inform managers. Journal of Marine Systems 81, 134–147.

Condie, S. A., M. Herzfeld, N. Margvelashvili, and J. R. Andrewartha (2009) Modeling the physical and biogeochemical response of a marine shelf system to a tropical cyclone, Geophys. Res. Lett., 36, L22603, doi:10.1029/2009GL039563.

Herzfeld, M. (2009) The role of numerical implementation on open boundary behaviour in limited area ocean models. Ocean Modelling, 27, 18-32.

Herzfeld, M. (2009) Improving stability of regional numerical ocean models. Ocean Dynamics 59(1): 21.

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

Margvelashvili, N. (2008) Stretched Eulerian Coordinate Model of Coastal Sediment Transport. Computers and Geosciences, 35, 1167-1176.

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

 

Baird, M. E., S. J. Walker, B. B. Wallace, I. T. Webster and J. S. Parslow (2003) The use of mechanistic descriptions of algal growth and zooplankton grazing in an estuarine eutrophication model. Estuarine, Coastal and Shelf Science 56, 685-695.

 

Technical Reports:

Gillibrand, P.A., Andrewartha, J.R., Herzfeld, M. (2012) Numerical hydrodynamic modelling of the Leschenault Estuary. CSIRO Technical Report, October 2012, 79 pp.

Herzfeld, M., Middleton, J., Andrewartha, J.R., Luik, J., Leeying, W. (2008) Numerical hydrodynamic modelling of Boston Bay, Spencer Gulf. Hobart, Tas.: CSIRO Marine and Atmospheric Research. (Aquafin CRC technical report).

Herzfeld, M. (2006). ROAM : Task 5 Model Description and Assessment / prepared for the Royal Australian Navy as part of the BLUElink project. Hobart, Tas.: CSIRO Marine and Atmospheric Research. 

Herzfeld, M., and Cahill, M. L. (2006). ROAM: Task 6 ROAM ocean model evaluation / prepared for the Royal Australian Navy as part of the BLUElink project. Hobart, Tas.: CSIRO Marine and Atmospheric Research.

Herzfeld, M., Andrewartha, J. R., Sakov, P. V., and Webster, I. T.  (2006). Numerical hydrodynamic modelling of the Fitzroy Estuary. CRC for Coastal Zone, Estuary and Waterway Management Technical Report 38. 93 p. 

Robson, B., Webster, I., Margvelashvili, N. Y., Herzfeld, M.  (2006). Scenario modelling: simulating the downstream effects of changes in catchment land use. CRC for Coastal Zone, Estuary and Waterway Management Technical Report 41. 26 p.

Volkman, J. K., Parslow, J. S., Thompson, P. A., Herzfeld, M., Wild-Allen, K., Blackburn, S. I., Crawford, C., Bonham, P., Holdsworth, D. G., Sakov, P. V., Andrewartha, J. R., and Revill, A. T. (2006). System-wide environmental issues for sustainable salmonid aquaculture: interim report. Hobart, Tas.: CSIRO Marine and Atmospheric Research. (Aquafin CRC project (FRDC project); 4.2 (2001/097)). 94 p. 

Herzfeld, M., Parslow, J. S., Sakov, P. V., and Andrewartha, J. R. (2005). Numerical hydrodynamic modelling of the D’Entrecasteaux Channel and Huon Estuary . In: System-wide environmental issues for sustainable salmonid aquaculture: interim report, J. K. Volkman, J. S. Parslow, P. A. Thompson, M. Herzfeld, K. Wild-Allen, S. I. Blackburn, C. Crawford, P. Bonham, D. G. Holdsworth, P. V. Sakov, J. R. Andrewartha, and A. T. Revill. Hobart, Tas.: CSIRO Marine and Atmospheric Research. (Aquafin CRC technical report).

Herzfeld, M., Parslow, J. S., Margvelashvili, N. Y., Andrewartha, J. R., Sakov, P. V., (2005) Numerical hydrodynamic modelling of the Derwent Estuary. Report prepared for Derwent estuary WQIP. CSIRO Marine Research. 91 p.

Herzfeld, M. (2005). Chloramine T : tracer release scenarios. Unpublished report for the Tasmanian Salmonid Growers Association. 7 p. 

Wild-Allen, K., Parslow, J. S., Herzfeld, M., Sakov, P. V., Andrewartha, J. R., and Rosebrock, U. (2005). Biogeochemical Modelling of the D’Entrecasteaux Channel and Huon Estuary . In: System-wide environmental issues for sustainable salmonid aquaculture: interim report, J. K. Volkman, J. S. Parslow, P. A. Thompson, M. Herzfeld, K. Wild-Allen, S. I. Blackburn, C. Crawford, P. Bonham, D. G. Holdsworth, P. V. Sakov, J. R. Andrewartha, and A. T. Revill. Hobart, Tas.: CSIRO Marine and Atmospheric Research. (Aquafin CRC technical report).

Herzfeld, M., Parslow, J. S., Andrewartha, J. R., Sakov, P. V., and Webster, I. T. (2004). Hydrodynamic modelling of the Port Curtis region, Project CM2.11. Indooroopilly. Qld.: Cooperative Research Centre for Coastal Zone, Estuary and Waterway Management. (Cooperative Research Centre for Coastal Zone, Estuary and Waterway Management. Technical report ; no. 7). 51 p. 

Herzfeld, M., Parslow, J. S., Sakov, P. V., Andrewartha, J. R. (2003). North West Shelf Joint Environmental Management Study. Milestone Report 2.5 Biogeochemical Modelling of the North West Shelf of Australia. NWSJEMS Technical Report No. 8, 58 p.

Margvelashvili, N., Robson, B., Sakov, P. V., Webster, I. T., Parslow, J. S., Herzfeld, M., and Andrewartha, J. R. (2003). Numerical modelling of hydrodynamics, sediment transport and biogeochemistry in the Fitzroy Estuary. Coastal CRC final report CSIRO Marine Research ; CSIRO Land and Water. (; 9). 47 p. 

Herzfeld, M., Andrewartha, J. R., Sakov, P. V., and Parslow, J. S. (2002). North West Bay numerical tracer analysis . Appendix 1 to: Assessment and monitoring of nutrients and habitats in North West Bay: supporting sustainable management. A. Jordan, J. Doole, L. Archer, M. Lawler, V. Halley, and C. Sanderson Kingston, Tas.: Kingborough Council//Tasmanian Aquaculture and Fisheries Institute, University of Tasmania, Marine Research Laboratories. 1 CD (6 p.).

Parslow, J. S., Herzfeld, Sakov, P. V., Andrewartha, J. R. (2002). Environmental effects of Derwent River flow on the upper Derwent Estuary: predictions from integrated biophysical models. Final report. Hobart, Tas.: CSIRO Div. of Marine Research. 87 p. 

Parslow, J. S., Herzfeld, M., Hunter, J. R., Andrewartha, J. R., Sakov, P. V., and Waring, J. R. (2001). Mathematical modelling of the dispersal and fate of CES discharge from the Boyer Mill in the upper Derwent Estuary. Results of part B. Final report. Hobart, Tas.: CSIRO Div. of Marine Research. 189 p.

 
 








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