View source for SCHISM/SELFE case studies

==OPENCoastS project ==
'''Research Team'''<br/>
Point of Contact: Anabela Oliveira and Alberto Azevedo, LNEC, Portugal

'''Project description'''<br/>
An interactive platform to generate on-demand forecasts based on SCHISM is under development at [http://www.lnec.pt LNEC]. The portal guides the users in the generation of forecast systems and provides the required computational resources. Developments started for the  [http://www.lnec.pt/hidraulica-ambiente/en/estudos/detalhes.php?tipo=0&id=280 Portuguese coast], and a preliminary description is given [http://www.pianc.pt/Jornadas_novembro_2017/22%20_AOliveira.pdf here] (in Portuguese). Starting in January 2018, the platform will be extended to the European coasts in the scope of the project  [https://www.egi.eu/about/newsletters/introducing-the-eosc-hub-project/ EOSC-HUB].

[https://opencoasts.ncg.ingrid.pt/ Project web site]

==North-Baltic Sea study==
'''Research Team'''<br/>
Helmholtz Zentrum Geesthacht, Institute of Coastal Research, Department
of Data Analysis and Data Assimilation: Emil Stanev <br/>
VIMS: Joseph Zhang<br/>
Point of Contact: Emil Stanev

'''Project description'''<br/>
The goal of this project is to understand the dynamics in the two inter-connected basins of North and Baltic Seas, the multiple straits connecting them, and more specifically on the temporal and spatial variability of physical processes. To achieve these goals, we have built a 3D unstructured-grid model SCHISM for this complex system.

The picture below shows the gravity overflow from Danish Strait into Baltic Sea.

[[File:North_Baltic_gravity_flow.PNG]] 

Also here is a [http://ccrm.vims.edu/yinglong/wiki_files/anim_transect_TS_Darss_to_Gotland_new.avi movie] showing the overflow.

[https://www.hzg.de/institutes_platforms/coastal_research/research_topics/windfarms/index.php.en#tab-36 Project web site for an offshore wind energy study]

'''Related publications'''<br/>
<UL>
  <LI>Zhang, Y., Stanev, E.V. and S. Grashorn (2016) Unstructured-grid model for the North Sea and Baltic Sea: validation against observations, Ocean Modelling, 97, 91-108. 
  <LI> Jacob, B., Stanev, E.V., and Zhang, Y. (in press) Local and remote response of the North Sea dynamics to morphodynamic changes in the Wadden Sea, Ocean Dynamics.  
</UL>

==San Francisco Bay and Delta==

'''Project description'''<br/>
Bay-Delta SCHISM is an application of the 3D open source SCHISM hydrodynamic and water quality suite to the San Francisco Bay Delta estuary. The project is a collaboration between the California Department of Water Resources and the Virginia Institute of Marine Sciences (VIMS), College of William & Mary.

The goal of our project is to develop an open-source, cross-scale multidimensional model suitable to answer flow and water quality questions involving large extents of the Bay-Delta system over periods of several years. Target applications include:
<UL>
        <LI> Habitat creation and conveyance options under BDCP;
        <LI> Salinity intrusion changes under drought or sea level rise;
        <LI> Velocity changes following the installation of drought barriers;
        <LI> Fate of mercury produced in the Liberty Island complex;
        <LI> Temperature, flow and food production in the estuary as part of a 3-model full life cycle bioenergetic model of salmon (as participants in the SESAME project).
</UL>


[http://baydeltaoffice.water.ca.gov/modeling/deltamodeling/models/bay_delta_schism/  '''Project web site1''']<br/>
[http://schism.water.ca.gov '''DWR SCHISM site''']<br/>

[[File:Bay-Delta-grid.png|500px|thumb|center|]]

==Forecast of general circulation around Taiwan==
'''Research Team'''<br/>
National Sun Yat-sen Univ (Taiwan): Dan Yu, Jason Yu <br/>
CWB: Marine Meteorology Center <br/>
VIMS: Joseph Zhang<br/>
Point of Contact: Dan Yu (danishyo AT gmail.com) <br/>

A multi-scale Regional Ocean Current Forecast OpeRational System (ROCFORS) is developed at Central Weather Bureau (CWB), Taiwan, since 2008. This system has coupled 4 different model domains, i.e. from the Pacific to the seas around Taiwan. The modeling system has been constructed based on ROMS and SCHISM and implemented for daily operation. Initial field is derived and analyzed from HYCOM and RTOFS daily forecast. Models are driven by meteorological predictions from NCEP GFS and WRF developed at CWB. Daily operational products are presented on CWB website. A cross-scale system based solely on SCHISM will be implemented in the future to replace the existing multi-level nested system.

[[File:CWB-pic1.png|600px|thumb|center|]]<br/>

'''Forecast web pages'''<br/>
[http://www.cwb.gov.tw/V7e/forecast/nwp/marine_forecast.htm English] <br/>
[http://www.cwb.gov.tw/V7/forecast/nwp/marine_forecast.htm Chinese]


'''Related publications'''<br/>
<UL>
  <LI>Zhang, Y., Ateljevich, E., Yu, H-C., Wu, C-H., and Yu, J.C.S. (2015) A new vertical coordinate system for a 3D unstructured-grid model, Ocean Modelling, 85, 16-31. 
</UL>

==SESAME==

'''Project description'''<br/>
SESAME will couple stream and estuarine models with a basin-scale ocean model in order to simultaneously model the entire early life history (freshwater, estuarine, and coastal ocean habitats) of the Chinook salmon migrating through the San Francisco Bay estuary system.

SESAME will provide the ecosystem models needed as the basis of the ecosystem-based management and ecological risk assessment framework necessary to improve management of water and fishery resources in California.

[http://oceanview.pfeg.noaa.gov/sesame/ '''Project web site''']<br/>

==Fukushima Daiichi Nuclear Power Plant accident==
'''Research Team'''<br/>
IMMSP (Ukraine): Vladimir Maderich, Igor Brovchenko

'''Project description'''<br/>
This study  evaluates and compares the models used to analyze the transportation and
deposition of radioactive materials that were released in
to the environment after the Tokyo
Electric Power Compan’s
Fukushima Daiichi Nuclear Power Plant (FDNPP) accident on
March 11, 2011. A Working Group for Model Intercomparison was formed in July 2012
under the Subcommittee of Investigation on the Environmental Contamination Caused by the Nuclear Accident in the Sectional Committee on Nuclear Accident, the Committee
Comprehensive Synthetic Engineering, Science Council of Japan (SCJ). The purpose of this
working group (SCJ WG) is to compare existing model results and to assess the uncertainties
in the simulation results. The emerging knowledge will be invaluable for various applications
designed to mitigate environmental contamination in wide areas. The working group solicited
international colleagues and groups to provide their model simulation results for the
intercomparison.


'''Related publications'''<br>
[http://www.jpgu.org/scj/report/20140902scj_report_e.pdf Report from Science Council of Japan]

==Tsunami==
'''Research Team'''<br/>
OHSU & VIMS: Joseph Zhang<br/>
DOGAMI: George Priest, Rob Witter, Laura Stimely<br/>
GeoCanada: Kelin Wang<br/>
Oregon State Univ: Chris Goldfinger<br/>


'''Project description'''<br/>

SCHISM has been certified by National Tsunami Hazard Program (NTHMP, 2012) as a tsunmai inundation model, after passing various benchmarks stipulated by [http://nctr.pmel.noaa.gov/benchmark/ NOAA/PMEL].
It has been used to generate official inundation maps for the state of Oregon, spearheaded by OR Department of Geology ad Mineral Industries  [http://www.oregongeology.org/sub/default.htm (DOGAMI)], under the auspice of NTHMP. <br/>

'''Sample images'''<br/>
Fig. 5 is a sample inundation map for Cannon Beach OR.
[[File:CannonBeachMap-draft.jpg|thumb|center|Fig. 5 Tsunami hazard map for Cannon Beach OR, generated from SCHISM (c/o DOGAMI)]]
<br/>

[http://www.oregongeology.org/tsuclearinghouse/pubs-technical.htm '''Related web site''']<br>

'''Related publications'''<br>
<UL>
  <LI>NTHMP (2012) Proceedings and results of the 2011 NTHMP model benchmarking workshop. Boulder: US Depart. of Commerce/NOAA/NTHMP, NOAA Special
Report 436p.
  <LI>Horrillo,H., Grilli, S.T., Nicolsky, D., Roeber, V. and Zhang, Y. (2014) Performance Benchmarking Tsunami Models for NTHMP's Inundation Mapping Activities, Pure and Applied Geophysics, DOI 10.1007/s00024-014-0891-y.
  <LI>Priest, G.R., Goldfinger, C., Wang, K., Witter, R.C., Zhang, Y., Baptista, A.M. (2010) Confidence levels for tsunami-inundation limits in northern Oregon inferred from a 10,000-year history of great earthquakes at the Cascadia subduction zone. Natural Hazards, 54(1), 27-73.
  <LI>Witter, R.C, Zhang, Y., Wang, K., Goldfinger, C., Priest, G.R., Allan, J.C. (2012) Coseismic slip on the Cascadia megathrust implied by tsunami deposits in an Oregon lake. Journal of Geophysical Research-Solid Earth, 117, B10303, doi:10.1029/2012JB009404. 
  <LI>Witter, R.C., Jaffe, B., Zhang, Y. and Priest, G.R. (2011) Reconstructing hydrodynamic flow parameters of the 1700 tsunami at Cannon Beach, Oregon, USA., Natural Hazards, DOI 10.1007/s11069-011-9912-7.
  <LI>Zhang, Y., Witter, R.W. and Priest, G.P. (2011) Tsunami-Tide Interaction in 1964 Prince William Sound Tsunami, Ocean Modelling, 40, 246-259.   
  <LI>Zhang, Y.L., and Baptista, A.M. (2008) Benchmarking a new finite-element tsunami model on unstructured grids. Pure and Applied Geophysics: Topical issue on Tsunamis, vol. 165, pp. 2229-2248. pdf . 
</UL>

<br/>

==SURA==

'''Research Team'''<br/>
VIMS: Harry Wang, Yi-Cheng Teng, Yan-qiu Meng, Joseph Zhang<br/>
OHSU: Joseph Zhang<br/>


'''Project description'''<br/>

SELFE/SCHISM was used in an IOOS sponsored super-regional testbed for coastal inundation, led by Dr. Rick Luettich (UNC). The testbed focuses on two coastal regions that are prone to inundation hazard: Gulf of Mexico and Gulf of Maine.<br/>



[http://testbed.sura.org/node/554 '''Project web site''']<br>
'''Related publications'''<br>
<UL>
  <LI> Teng, Y.C., Wang, H.V., Zhang, Y., Roland, A. (to be submitted) The effect of bottom boundary layer dynamics on the forerunner simulation during Hurricane Ike in the Gulf of Mexico.
  <LI>Roland, A., Zhang, Y., Wang, H.V., Meng, Y., Teng, Y., Maderich, V., Brovchenko, I., Dutour-Sikiric, M. and Zanke, U. (2012) A fully coupled wave-current model on unstructured grids, Journal of Geophysical Research- Oceans, 117,C00J33,doi:10.1029/2012JC007952.
  <LI>Cho, K.H. Wang, H.V., Shen, J., Valle-Levinson, A. and Teng, Y.C. (2012) A modeling study on the response of the Chesapeake Bay to Hurricane Events of Floyd and Isabel. Ocean Modeling, vol. 49-50, pp. 22-46.
</UL>
'''Sample images'''<br/>
Fig. 2 shows an example application of the fully coupled SELFE-WWM and a simple sediment model to hurricane Ike (2008) in Gulf of Mexico. The full results are being published (Teng et al. 2012).
[[File:SURA-Ike-YC.jpg|thumb|center|Fig. 2 Domain used to simulate hurricane Ike in Gulf of Mexico. The comparison plot shows the primary surge and forerunner simulated with different physical formulations (c/o Y.C. Teng)]]
<br/>

==Columbia River estuary and plume==
'''Research Team'''<br/>
OHSU: Antonio Baptista, Joseph Zhang, Nate Hyde, Paul J. Turner, Charles Seaton<br/>
 
'''Project description'''<br/>
Columbia River estuary and plume circulation presents a formidable challenge for hydrodynamic models due to the interaction between strong tides, meteorological forcing, high river discharge, and strong stratification. SELFE was originally developed to address these challenges and some details can be found in the SELFE paper.

The SELFE-enabled virtual Columbia River is a skill-assessed 4D (space-time) simulation environment that offers multiple representations of circulation processes, variability and change across river-to-shelf scales. Circulation includes water levels, salinity, temperature, and velocities. <br/>



[http://www.stccmop.org/datamart/virtualcolumbiariver '''Project web site''']<br/>
[http://tidesandcurrents.noaa.gov/ofs/creofs/creofs.html '''SELFE-enabled Columbia River forecast system at NOAA''']<br/> 

'''Related publications'''<br>
<UL>
  <LI>Burla, M., Baptista, A.M. Zhang, Y., and Frolov, S. (2010) Seasonal and inter-annual variability of the Columbia River plume: a perspective enabled by multi-year simulation databases. Journal of Geophysical Research: special issue on NSF RISE project, 115, C00B16. 
  <LI>Frolov, S., Baptista, A.M., Zhang, Y., and Seaton, C. (2009) Estimation of Ecologically Significant Circulation Features of the Columbia River Estuary and Plume Using a Reduced-Dimension Kalman Filter. Continental Shelf Research, 29(2), 456-466. 
  <LI>Frolov, S., A.M. Baptista, M. Wilkin, (2008). Optimizing Placement of Fixed Observational Sensors in a Coastal Observatory, Continental Shelf Research, 28(19) 2644-2659. 
  <LI>Zhang, Y. and Baptista, A.M. (2008) "SELFE: A semi-implicit Eulerian-Lagrangian finite-element model for cross-scale ocean circulation", Ocean Modelling, 21(3-4), 71-96. 
</UL>


'''Sample images'''<br/>

Fig. 1 shows the Columbia River plume in 3D view forecasted by SELFE.
[[File:Virtual-CR.png|thumb|center|Fig. 1 3D view of the Columbia River plume]]<br/>



==Marine Submersion (Xynthia Storm Surge)==
'''Research Team'''<br/>
DPL: Xavier Bertin, Kai Li, Aron Roland, Nicolas Bruneau, Jean-François Breilh et al.<br/>
<br/>
'''Project description'''<br/>
In February 2010, the storm Xynthia hit the central part of the Bay of Biscay severely. The storm surge locally exceeded 1.5m (Bertin et al., 2011) and peaked at the same time as a high spring tide, causing the flooding of large areas of the low-lying coast. Analysis results show the wave processes are important in the storm surge. The 2DH SCHISM with WWM coupled model was applied in the research. And a highly refined flooding multiscale grid was developed to catch the pysical processes of flooding.<br/>


'''Related publications'''<br>
*Bertin, X., Li, K., Roland, A., Zhang, Y., Breilh, J.F. and Chaumillon, E. (2014) A modeling-based analysis of the flooding associated with Xynthia, central Bay of Biscay, Ocean Eng, 94,80-89. 
*Bertin, X., Bruneau, N., Breilh, J., Fortunato, A. and Karpytchev, M., (2011) [http://www.sciencedirect.com/science/article/pii/S1463500311001776 Importance of wave age and resonance in storm surges: The case Xynthia, Bay of Biscay]. ''Ocean Modelling'', 42:16-30.
<br/>


'''Sample images'''<br/>

Fig. 3 shows the simulated water depth in North of La Rochelle during Xynthia of preliminary result.
[[File:Xynthia flooding.png|thumb|center|Fig. 3 Simulated water depth in North of La Rochelle during Xynthia (red line: observed flooding boundary]]<br/>

==Portuguese coastal systems==

There are 3 related projects for this system.

<OL>
 <LI> ''A nowcast-forecast system for for Portuguese coastal systems''<br/>
'''Research Team'''<br/>

LNEC: Anabela Oliveira, André Fortunato, Marta Rodrigues, Alberto Azevedo, João Palha Fernandes<br/>
OHSU: António Melo Baptista, Joseph Zhang, Bill Howe, Paul J. Turner, Charles Seaton<br/>
VIMS: Joseph Zhang

'''Project description'''<br/>

The goal of this project is to integrate complementary research strengths at the two institutions towards the development of a nowcast-forecast system for 
water quality prediction in estuarine and coastal waters. The Portuguese partners will provide the water quality models and 
the American institution will provide the innovative nowcast-forecast technology.<br/>


[http://www.lnec.pt/organization/dha/nec/estudos_id/nowcast '''Project web site''']<br/>
[http://ariel.lnec.pt/node/40 '''Nowcast-forecast web''']

  <LI>''Improvement of a morphodynamic model applied to tidal inlet environments'' <br/>
'''Research Team'''<br/>

LNEC: André Fortunato, Anabela Oliveira, Xavier Bertin<br/>
'''Project description'''<br/>

Tidal inlets are among the most dynamic environments along the world coastlines while social-economic activities are there concentrated. These problems are particularly relevant in Portugal due to its extensive coastline and the existence of many tidal inlets of social, environmental and economic importance. In the perspective of a sustainable development, it is essential to understand and to be able to predict the long-term evolution of these systems. To achieve these goals, one of the most promising avenues is the development of morphodynamic models, which consist of a set of modules to simulate tidal hydrodynamics, wave propagation, sediment transport and bottom evolution. This project aims at contributing to the advance of an existing morphodynamic modeling system (MORSYS2D) that is under development at the host institution (LNEC). <br/>

[http://www.lnec.pt/organization/dha/nec/estudos_id/immatie '''Project web site''']
  <LI>''Towards operational forecasting of ecosystem dynamics: Benchmarking and Grid-enabling of an ecological model (BGEM)'' 
'''Research Team'''<br/>
LNEC: Anabela Oliveira, André Fortunato, Marta Rodrigues and  João Palha Fernandes<br/>
CMOP: António Melo Baptista, Joseph Zhang, Bill Howe, Charles Seaton,  Paul J. Turner<br/>


'''Project description'''<br/>
This proposal aims to integrate complementary research strengths at the two institutions to improve and validate a sophisticated ecological modeling system for operational forecasting of ecosystem dynamics based on grid computing resources. The Portuguese partner will provide the ecological model and the expertise on grid-enabling of numerical models. The American partner will provide the expertise on parallel computing and the benchmark for validation and inter-model comparison.<br/>
[[File:model-ecoselfe.jpg|thumb|center|Fig. 4 An overview of the ecological model ECOSELFE (Rodrigues, 2008)]]<br/>


[http://www.lnec.pt/organization/dha/nec/estudos_id/bgem '''Project web site''']
</OL>

'''Related publications'''<br/>
*Azevedo, A., Oliveira, A., Fortunato, A.B., Zhang, Y. and Baptista, A.M. (2014) A cross-scale numerical modeling system for management support of oil spill accidents, Marine Pollution Bulletin, 80, 132-147.
*Dodet, G., X. Bertin, N. Bruneau, A. B. Fortunato, A. Nahon, and A. Roland (2013), Wave-current interactions in a wave-dominated tidal inlet, J. Geophys. Res. Oceans, 118, 15871605, doi: 10.1002/jgrc.20146.
*A.B. Fortunato, M. Rodrigues, J.M. Dias, C. Lopes, A. Oliveira (2013) Generating inundation maps for a coastal lagoon: A case study in the Ria de Aveiro (Portugal), Ocean Engineering, Volume 64, 60-71.
*Pinto, L., Fortunato, A.B., Zhang, Y., Oliveira, A. and Sancho, F.E.P. (2012) Development and validation of a three-dimensional morphodynamic modelling system, Ocean Modelling, Volumes 57-58, 1-14.

*Rodrigues, M., Oliveira, A., Queiroga, H., Brotas, V. (in press). Seasonal and diurnal water quality modelling along a salinity gradient (Mira channel, Aveiro lagoon, Portugal), Procedia Environmental Science.

*A. Nahon; X. Bertin, A.B. Fortunato, A. Oliveira (2012). A modeling-based assessment of tidal inlet classification, Marine Geology, vol. 291-294, pp. 1 - 11.
*C.L. Lopes, P.A. Silva, J.M. Dias, A. Rocha, A.T. Picado, S. Plecha, A.B. Fortunato, 2011. Local sea level rise scenarios for the end of the 21st century and potential physical impacts in the lower Ria de Aveiro (Portugal), Continental Shelf Research, 31/14: 1515-1526
*Picado, P. A. Silva, A. B. Fortunato and J. M. Dias. 2011. Particle tracking-modeling of morphologic changes in the Ria de Aveiro, J. Coastal Res., SI64, 1560-1564.Zhang, Y., Witter, R.W. and Priest, G.P. (2011) 
*A.B. Fortunato, N. Bruneau, A. Azevedo, M.A.V.C. AraÃƒÂºnd A. Oliveira. 2011. Automatic improvement of unstructured grids for coastal simulations J. Coastal Res., SI64, 1028-1032.
*A. Nahon, A. B. Fortunato, X. Bertin, A. R. Pires, A. Oliveira, M.C. Freitas, C. Andrade. 2011. Numerical modelling of opening and closure of an artificial inlet (Santo AndrÃƒÂ©agoon, Portugal). Revista GestÃƒÂ£Costeira Integrada, 11/3: 341-353
*J. Rosa, D. GonÃƒÂ§ves, P.A. Silva, L.M. Pinheiro, L. RebÃƒÂª, A.B. Fortunato, X Bertin. 2011. Sand Extraction Evolution Area offshore Vale do Lobo (Algarve, Portugal) - comparison between numerical results and bathymetric data, Revista GestÃƒÂ£Costeira Integrada, 11/3: 369-377.
*N. Bruneau, A.B Fortunato, G. Dodet, P. Freire, A. Oliveira, X. Bertin, 2011. Future evolution of a tidal inlet due to changes in wave climate, sea level and lagoon morphology (ÃƒÂ“idos Lagoon, Portugal), Continental Shelf Research, 31/18: 1915-1930
*N. Bruneau, G. Dodet, X. Bertin and A. B. Fortunato. 2011. Development of a three-dimensional coupled wave-current model for coastal environments, J. Coastal Res., SI64, 986-990.
*J. Rosa, P. A. Silva, X. Bertin and A. B. Fortunato.2011. Waves, wind and tidal forcing on a sandpit morphodynamics, J. Coastal Res., SI64, 1070-1074.
*M. Rodrigues, A. Oliveira, M. Guerreiro, A.B. Fortunato, J. Menaia, L.M. David & A. Cravo. 2011. Modeling fecal contamination in the Aljezur coastal stream (Portugal), Ocean Dynamics, 61:841.856.
*Oliveira, M. Rodrigues, A.B. Fortunato and M. Guerreiro. 2011. Impact of seasonal bathymetric changes and inlet morphology on the 3D water renewal and residence times of a small coastal stream, J. Coastal Res., SI64, 1555-1559.
*Picado, A., Dias, J.M. and Fortunato, A.B. 2010. Tidal changes in estuarine systems induced by local geomorphologic modifications, Continental Shelf Res., 30/17: 1854-1864.
*Plecha, S., P.A. Silva, N. Vaz, X. Bertin, A. Oliveira, A.B. Fortunato and J.M. Dias. 2010. Sensitivity analysis of a morphodynamic modelling system applied to a coastal lagoon inlet, Ocean Dynamics, 60/2: 275-284.
*Bertin, X., A. Oliveira and A.B. Fortunato (2009). Simulating morphodynamics with unstructured grids: description and validation of an operational model for coastal applications, Ocean Modelling, 28(1-3): 75-87.

*Fortunato, A.B., X. Bertin and A. Oliveira (2009) Space and time variability of uncertainty in morphodynamic simulations, Coastal Engineering, 56(8): 886-894 .
*Azevedo, A., A. Oliveira, A.B. Fortunato and X. Bertin (2009) Application of an Eulerian-Lagrangian oil spill modeling system to the Prestige accident: trajectory analysis, J. Coastal Research, SI56: 777-781.
*Bertin, X., A.B. Fortunato and A. Oliveira (2009) A modeling-based analysis of processes driving wave-dominated inlets, Continental Shelf Research, 29(5-6): 819-834.
*Bertin, X., A.B. Fortunato and A. Oliveira (2009) Morphodynamic modeling of the AncÃƒÂ£o Inlet, South Portugal, J. Coastal Research, SI56: 10-14.
*Dias, J.M., M.C. Sousa, X. Bertin, A.B. Fortunato and A. Oliveira (2009) Numerical modeling of the impact of the AncÃƒÂ£o Inlet relocation (Ria Formosa, Portugal), Environmental Modeling and Software, 24: 711-725.
*Lopes, V., P.A. Silva, X. Bertin, A.B. Fortunato and A. Oliveira (2009) Impact of a dredged sandpit on tidal and wave hydrodynamics, J. Coastal Research, SI56: 529-533.
*Picado, A., J.M. Dias, A.B. Fortunato (2009) Effect of flooding the salt pans in the Ria de Aveiro, J. of Coastal Research, SI56, 1395-1399.
*Rodrigues, M., A. Oliveira, M. Costa, A.B. Fortunato and Y.J. Zhang (2009) Sensitivity analysis of an ecological model applied to the Ria de Aveiro, J. Coastal Research, SI56, 448-452.
*Rodrigues, M., A. Oliveira, H. Queiroga, A.B. Fortunato and Y.J. Zhang (2009) Three-Dimensional Modeling of the Lower Trophic Levels in the Ria de Aveiro (Portugal), Ecological Modelling, 220, 1274-1290.
*Oliveira, A., A.B. Fortunato and L. Pinto, 2006. Modeling the Hydrodynamics and the Fate of Passive and Active Tracers in the Guadiana Estuary, Estuarine, Coastal and Shelf Science, 70, 76-84.
*Oliveira, A., A.B. Fortunato and J. Rego, (2006). Effect of Morphological Changes on the Hydrodynamics and Flushing Properties of the ÃƒÂ“bidos lagoon, Continental Shelf Research, 26, 917-942.
*Pinto, L.L., A.B. Fortunato, A. Oliveira and A.M. Baptista, 2004. Haline stratification in the Guadiana estuary. II ? Numerical modeling, Recursos HÃƒÂdricos, 25/2: 99-110. (in Portuguese)
*A.B. Fortunato and A. Oliveira. 2007. Case study: Promoting the stability of the Obidos Lagoon Inlet. J. Hydraulic Eng., 133(7): 816-824. pdf
*Fortunato, A.B. and A. Oliveira (2007) Improving the stability of a morphodynamic modeling system, Journal of Coastal Research, SI50: 486-490.
*Oliveira, A., A.B. Fortunato, M. Rodrigues and A. Azevedo (2007) Integration of physical and water quality models, Houille Blanche, 4: 40-46. 

<br/>

==Water Quality in the Chesapeake Bay Region==

'''Research Team'''

Virginia Institute of Marine Science: Junzheng Zhu and  [http://www.vims.edu/people/wang_hv/index.php Harry Wang]

'''Project description'''

The Chesapeake Bay and the Coastal Bays of the Maryland/Virginia Atlantic shore are highly valuable and productive ecosystems that are increasingly threatened by degraded water quality and loss of habitat due to both anthropogenic and natural disturbances.

In an effort to reverse this trend, federal and state governments have implemented a Total Maximum Daily Load (TMDL) program to control point source and non-point source pollution in each watershed.

In order to quantify these controls and better understand cause and effect relationships, the Virginia Institute of Marine Science is developing numerical hydrodynamic and water quality models and linking them together as a tool for predicting and measuring success of the TMDL effort.


Virginia Institute of Marine Science is involved in two TMDL projects in the Chesapeake Bay region:

<OL>
 <LI>TMDL scenario development and implementation for the Maryland and Virginia Coastal Bays system.
 <LI>Impact on localized water quality resulting from allocation of nutrient loads to dredged material contaminant facilities in Baltimore Harbor.
</OL>

Both projects involve coupling SCHISM and ICM (Integrated Compartment Model). 

'''Sample images'''

Fig. 6 shows some sample results.
[[File:MDcoast-image.jpg|thumb|center|Fig. 6 SCHISM-ICM for Maryland coast and bay]]

<br/>

==Aquaculture and coastal pollutants modelling (New Zealand)==

'''Research Team'''<br/>
[http://www.cawthron.org.nz Cawthron Institute]: Ben Knight<br/>
[http://www.metocean.co.nz/ MetOcean Solutions Limited]: Brett Beamsley<br/>
 
'''Application description'''<br/>
Aquaculture and other coastal developments in New Zealand have the potential to place increasing pressures on coastal environments.  The Cawthron Institute and MetOcean Solutions Limited have been collaborating to produce open-source community models for coastal environments around New Zealand to aid in coastal effects assessments. We are presently utilising and building upon SCHISM community modelling tools associated with Lagrangian and Eularian transport for a range of coastal transport applications (e.g. faecal indicator bacteria, nutrients, oil spills).<br/><br/>
We have a number of collaborative projects under-way, but are currently working towards simplifying the set up and analysis of tracers for modelling a range of chemical and biological constituents in aquaculture and coastal discharge assessments.<br/> 

'''Sample images'''<br/>

Fig. 7 shows SCHISM Matlab GUI (currently under development) with a bathymetric map of the Marlborough Sounds, New Zealand.
[[File:SELFE_GUI.PNG|thumb|center|Fig. 7 SCHISM Matlab GUI showing bathymetric map of the Marlborough Sounds, New Zealand]]<br/>