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References to Papers Associated with POM (Including models derived from POM such as ECOM and NCOM, Turbulence schemes, Forecasting Systems, Numerics, etc.) |
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1989 1990 1991 1992 1993 1994 1995 1996 1997 1998 1999 2000 2001 2002 2003 2004 2005 2006 2007 2008 2009 2010 2011 2012 Records found: 1096 Chen C., et al (13 authors), A modeling study of benthic detritus flux's impacts on heterotrophic processes in Lake Michigan. J. Geophys. Res., 109, C10S11, 10.1029/2002JC001689, 2004 Chen C., L. Wang, R. Ji, J. W. Budd, D. J. Schwab, D. Beletsky, G. L. Fahnenstiel, H. Vanderploeg, B. Eadie, J. Cotner, Impacts of suspended sediment on the ecosystem in Lake Michigan: A comparison between the 1998 and 1999 plume events. J. Geophys. Res., 109, C10S05, 10.1029/2002JC001687, 2004 Cirano, M. and J. F. Middleton, Aspects of the Mean Wintertime Circulation along Australia's Southern Shelves: Numerical Studies. J. Phys. Oceanogr., 34(3), 668-684, 2004 Dong, C., H.-W. Ou, D. Chen, and M. Visbeck, Tidally Induced Cross-Frontal Mean Circulation: Analytical Study. J. Phys. Oceanogr., 34(1), 293-305, 2004 Frolov, S. A., G. G. Sutyrin and I. Ginis, Asymmetry of an Equilibrated Gulf Stream–Type Jet over Topographic Slope. J. Phys. Oceanogr., 34(5), 1087-1102, 2004 Haertel, P. T., D. A. Randall and T. G. Jensen, Simulating Upwelling in a Large Lake Using Slippery Sacks. Mon. Wea. Rev., 132(1), 66-77, 2004 Lin, X., L. Oey, and D. Wang, Altimetry and drifter data assimilations of loop current and eddies. J. Geophys. Res., 112, C05046, 10.1029/2006JC003779, 2007 Mitsudera, H., B. Taguchi, Y. Yoshikawa, H. Nakamura, T. Waseda and T. Qu, Numerical Study on the Oyashio Water Pathways in the Kuroshio–Oyashio Confluence. J. Phys. Oceanogr., 34(5), 1174-1196, 2004 Miyazawa, Y., G. Xinyu and T. Yamagata, Roles of Mesoscale Eddies in the Kuroshio Paths. J. Phys. Oceanogr., 34(10), 2203-2222, 2004 Noh Y., H. S. Min and S. Raasch, Large Eddy Simulation of the Ocean Mixed Layer: The Effects of Wave Breaking and Langmuir Circulation. J. Phys. Oceanogr., 34(4), 720735, 2004 Ren, X., W. Perrie, Z. Long and J. Gyakum, Atmosphere–Ocean Coupled Dynamics of Cyclones in the Midlatitudes. Mon. Wea. Rev., 132(10), 2432–2451, 2004 Tilburg, C. E., Across-Shelf Transport on a Continental Shelf: Do Across-Shelf Winds Matter?. J. Phys. Oceanogr., 33(12), 2675–2688, 2003 Wu, Y. S., Tang, C., Sathyendranath, S. and Platt, T., The impact of bio-optical heating on the properties of the upper ocean: a sensitivity study using a 3-D circulation model for the Labrador Sea. Deep Sea Research II, 54, 2630-2642., 2007Ahsan, A. K. M. Q. and A. F. Blumberg, Three-dimensional hydrothermal model of Onondaga Lake, New York. J. Hyd. Eng., 125(9), 912-923, 1999Ahsan, A. K. M. Q., M. S. Bruno, L-Y. Oey, and R. I. Hires, Wind-driven dispersion in New Jersey coastal waters. J. Hyd. Eng., 120(11), 1264-1273, 1994Aiki, H., K. Takahashi and T. Yamagata, The Red Sea outflow regulated by the Indian monsoon. Cont. Shelf Res., 26(12-13), 1448-1468, 2006Aikman, F. III and D. B. Rao, A NOAA Perspective on a coastal ocean forecast system. Coastal Ocean Prediction, Coastal and Estuarine Studies, Vol. 56, C. N. K. Mooers (Ed.), American Geophysical Union, Washington, DC, 467-499, 1999Aikman, F. III and E. Wei, A comparison of model-simulated trajectories and observed drifters in the Middle Atlantic Bight. J. Mar. Env. Eng., 2 (1-2), 123-139, 1995Aikman, F. III, Wei, E.J., and J. R. Schultz, Water level evaluation for the coastal ocean forecast system. Second Conference on Coastal Atmospheric and Oceanic Prediction and Processes, Jan. 11-16, 1998, Phoenix, AZ, American Meteorological Society, Boston, MA, 1-6, 1998Aikman, F., G. L. Mellor and D. B. Rao, A quasi-operational forecast/nowcast assimilation system for the U.S. east coast. Proc., AMS Conf. on Coastal Oceanic and Atmospheric Prediction, Submitted, 1995Aikman, F., G. L. Mellor, T. Ezer, D. Shenin, P. Chen, L. Breaker and D. B. Rao, Toward an operational nowcast/forecast system for the U.S. east coast. Modern Approaches to Data Assimilation in Ocean Modeling, P. Malanotte-Rizzoli Ed., Elsevier Oceanography Ser., 61, 347-376, 1996Aikman, F.III, and O'Connor, W.P., Model-Based Regional Boundary Conditions for Florida Bay. Ocean Community Conference '98 Proceedings of the Marine Technology Society, Vol. I, Nov. 16-19, 1998, Baltimore, MD, Marine Technology Society, Washington, DC, 544-549, 1998Albretsen, J., The impact of freshwater discharges on the ocean circulation in the Skagerrak/northern North Sea area. Part II: energy analysis. Ocean Dynamics, 57(4-5), 287-304, 2007Alford, M. H., M. C. Gregg and M. A. Merrifield, Structure, Propagation, and Mixing of Energetic Baroclinic Tides in Mamala Bay, Oahu, Hawaii. J. Phys. Oceanogr., 36(6), 997-1018, 2006Allen, J. I., P. J. Somerfield and J. Siddorn, Primary and bacterial production in the Mediterranean Sea: a modeling study. J. Mar. Sys., 33-34, 473-495, 2002Allen, J. I., P. J. Somerfield and J. Siddorn, Primary and bacterial production in the Mediterranean Sea:a modelling study. J. Mar.Sys.,33-34,473-495, 2002Allen, J. I., P. J. Somerfield and J. Siddorn, Primary and bacterial production in the Mediterranean Sea:a modelling study. J. Mar.Sys.,33-34,473-495, 2002Allen, J. S. and P. A. Newberger, Downwelling circulation on the Oregon continental shelf. Part I: Response to idealized forcing. J. Phys. Oceanogr., 26, 2011-2035, 1996Allen, J. S. and P. A. Newberger, On symmetric instabilities in oceanic bottom boundary layers. J. Phys. Oceanogr., 28, 1131-1151, 1998Allen, J. S., P. A. Newberger and J. Federiuk, Upwelling circulation on the Oregon Continental Shelf. Part 1: Response to idealized forcing. J. Phys. Oceanogr., 25, 1843-1866, 1995Allen, J. S., P. A. Newberger and R. A. Holman, Nonlinear shear instabilities of alongshore currents on plane beaches. J. Fluid Mech., 310, 181-213, 1996Allen, J., P.J. Somerfield and F.J. Gilbert, Quantifying uncertainty in high-resolution coupled hydrodynamic-ecosystem models. J. Mar. Sys., 64(1-4), 3-14, 2007Andrade, C. A., E. D. Barton and C. N. K. Mooers, Evidence for an eastward flow along the Central and South American Caribbean Coast. J. Geophys. Res., 108(C6), 10.1029/2002JC001549, 2003André, G., P. Garreau, V. Garnier and P. Fraunié, Modelled variability of the sea surface circulation in the North-western Mediterranean Sea and in the Gulf of Lions . Ocean Dynamics, 55(3-4), 294-308, DOI: 10.1007/s10236-005-0013-6, 2005Arango, H. and T. Ezer, Proceedings from the 2001 Terrain-Following Ocean Models Workshop, Boulder, CO, 20-22 August, 2001. Rutgers University,17 pp., 2001Ardhuin, F., A. D. Jenkins, D. Houser, A. Reniers and B. Chapron, Waves and operational oceanography: Toward a coherent description of the upper ocean. EOS Trans., AGU, 86(4), 37-40, 2005Arhonditsis, G., G. Tsirtsis and M. Karydis, The effect of episodic rainfall events to the dynamics of coastal marine ecosystems: applications to a semi-enclosed gulf in the Mediterranean Sea. J. Mar. Sys, 35, 183-205, 2002Arrigo, K. R. and G. L. Van Dijken, Interannual variation in air-sea CO2 flux in the Ross Sea, Antarctica: A model analysis. J. Geophys. Res., 112, C03020, 10.1029/2006JC003492, 2007Arrigo, K. R., D. L. Worthen and D. H. Robinson, A coupled ocean-ecosystem model of the Ross Sea: 2. Iron regulation of phytoplancton taxtonomic variability and primary production. J. Geophys. Res., 108(C7), 10.1029/2001JC000856, 2003As-Salek, J. A. and T. Yasuda, Tide-surge interaction in the Meghna Estuary: Most severe conditions. J. Phys. Oceanogr., 31, 3059-3072, 2001Asplin L., H. Svendsen, and B. Cushman-Roisin, Observations and numerical simulations of freshwater runoff from Maalselva into Malangen. Report at the Geophysical Institute, University of Bergen, Norway. 60 pp., 1994Asplin, L., Simulations of river runoff in a fjord with a three-dimensional numerical model. Report at the Geophysical Institute, University of Bergen, Norway. 109 pp, 1994Asplin, L., The influence of the earth's rotation on flows in fjords and coastal oceans. Thesis at the Geophysical Institute, University of Bergen, Norway. 113 pp, 1994Aucan, J., M. A. Merrifield, D. S. Luther and P. Flament, Tidal mixing events on the deep flanks of Kaena Ridge, Hawaii. J. Phys. Oceanogr., 36(6), 1202-1219, 2006Auclair, F., P. Marsaleix and C. Estournel, Sigma coordinate pressure gradient errors: Evaluation and reduction by an inverse method. J. Atmos. Ocean Tech., 17, 1348-1367, 2000Aukrust, T., Adapting the three-dimensional sigma-coordinate model by Blumberg and Mellor to the Baltic Sea. IBM Bergen Envir. Centre, Report ISBN 82-415-0083-1, Bergen, Norway, 17pp, 1992Austin, J. A. and S. J. Lentz, The inner shelf response to wind-driven upwelling and downwelling. J. Phys. Oceanogr., 32, 2171-2193, 2002Baird, M. E., O. Leth, and J. F. Middleton, Biological response to circulation driven by mean summertime winds off central Chile: A numerical model study. J. Geophys. Res., 112, C07030, 10.1029/2006JC003655, 2007Baird, M. E., P. G. Timko, I. M. Suthers and J. H. Middleton, Coupled physical–biological modelling study of the East Australian Current with idealised wind forcing. Part I: Biological model intercomparison. J. Mar. Sys., 59(3-4), 249-270, 2006Baird, M. E., P. G. Timko, I. M. Suthers and J. H. Middleton, Coupled physical–biological modelling study of the East Australian Current with idealised wind forcing: Part II. Biological dynamical analysis. J. Mar. Sys., 59(3-4), 271-291, 2006Baird, M. E., P. R. Oke, I. M. Suthers and J. H. Middleton, A plankton population model with biomechanical descriptions of biological processes in an idealised 2D ocean basin. J. Mar. Sys., 50(3-4), 199-222, 2004Balotro, R. S. , A. Isobe and M. Shimizu, Seasonal Variability in Circulation Pattern and Residence Time of Suo-Nada. J.Oceanography 59(1) 259-277, 2003Balotro, Rolando S., A.Isobe, M. Shimizu, A. Kaneda, T. Takeuchi, and H. Takeoka, Circulation and Material Transport in Suo-Nada during Spring and Summer. J. Oceanography 58(5), 759-773, 2002Bang I. and C. N. K. Mooers, The Influence of Several Factors Controlling the Interactions between Prince William Sound, Alaska, and the Northern Gulf of Alaska. J. Physical Oceanogr., 33(1), 19-36, 2003Bang, I. and H.-J. Lie, A numerical experiment on the dispersion of the Changjiang River plume. J. Korean Soc. of Oceanogr., 34(4), 185-199, 1999Bang, I. S. L. Vaughan and C. N.K. Mooers, Initial steps toward validation of a seasonal cycle simulation for Prince William Sound circulation (flow and mass) fields. Cont. Shelf Res., 25(7-8), 901-934, 2005Bang, I., J.-K. Choi, L. Kantha, C. Horton, M. Clifford, M.-S. Suk, K.-I. Chang, S.Y. Nam, and H.-J. Lie, A hindcast experiment in the East Sea (Sea of Japan). La mer, 34, 108-130., 1996Bao, X. W., J. Yan and W. X. Sun, A three-dimensional tidal model in boundary-fitted curvilinear grids. Estuarine, Coastal and Shelf Sci., 50, 775-788, 2000Barnes, R.S.K., Coastal lagoons. , 1980Barron, C. N., A. B. Kara, P. J. Martin, R. C. Rhodes and L. F. Smedstad, Formulation, implementation and examination of vertical coordinate choices in the Global Navy Coastal Ocean Model (NCOM). Ocean Modelling, 11 (3-4), 347-375, 2006Barron, C. N., L. F. Smedstad, J. M. Dastugue and O. M. Smedstad, Evaluation of ocean models using observed and simulated drifter trajectories: Impact of sea surface height on synthetic profiles for data assimilation. J. Geophys. Res., 112, C07019, 10.1029/2006JC003982, 2007Barron, C. N., P. I. Martin, A. B. Kara, R. C. Rhodes and L. F. Smedstad, Description and application of the Global Navy Coastal Ocean Model (NCOM), with examination of vertical coordinate system choices. Ocean Modelling, 10, 2005Barron. C. N., A. B. Kara, H. E. Hurlburt, C. Rpwley and L. F Smedstad, Sea surface height predictions from the Global Navy Coastal Ocean Model (NCOM) during 1998-2001. J. Atmos. Ocean. Technol., 21, 1876-1893, 2004Batteen, M. L., A. S. Martinho, H. A. Miller and J. L. McClean, A process-oriented modelling study of the coastal Canary and Iberian Current system. Ocean Modelling, 18(1), 1-36, 2007Batteen, M.L. and H.A. Miller, Process-oriented modeling studies of the 5500-km-long boundary flow off western and southern Australia. Cont. Shelf Res., 29, 702-718, 2009Batteen, M.L., A.S. Martinho, H.A. Miller, and J.L. McClean, A process-oriented modelling study of the coastal Canary and Iberian Current system. Ocean Modelling, 18, 1-36, 2007Batteen, M.L., R.A. Kennedy, and H.A. Miller, A process-oriented numerical study of currents, eddies and meanders in the Leeuwin current system. Deep Sea Res. II, 54(8-10), 859-883, 2007Baumert, H. and H. Peters, Second-moment closures and length scales for weakly stratified turbulent shear flows. J. Geophys. Res., 105(C3), 6453-6468, 2000Baumert, H. Z., J. Simpson and J. Sunderman (Eds.), Marine Turbulence: Theories, Observations and Models, Results of the CARTUM Project. Cambridge University Press, 630 pp., 2005Beckers, J.-M. et al. (24 co-authors), Model intercomparison in the Mediterranean: MEDMEX simulations of the seasonal cycle. J. Mar. Sys., 33-34, 215-251, 2002Bedford, K. and D. Schwab, The Great Lakes Forecasting System - Lake Erie Nowcasts/Forecasts. Marine Technology Society Annual conference (MTS '91), Marine Technology Society, Washington, DC, pp. 260-264, 1991Bedford, K. and D. Schwab, Recent developments in the Great Lakes Forecasting System (HLFS) performance evaluation. Second Conference on Coastal Atmospheric and Oceanic Prediction and Processes, Jan. 11-16, 1998, Phoenix, AZ, American Meteorological Society, Boston, MA, 45-50, 1998Bedford, K., C.-C. Yen, J. Kempf, D. Schwab,R. Marshall and C. Kuan, A 3D- Stereo Graphics Interface for Operational Great Lakes Forecasts. Ed. M. Spaulding, Amer. Soc. of Civil Engrs., New York, NY., pp. 248-257, 1990Beg Paklar, G., A. Bajic, V. Dadic, B. Grbec and M. Orlic, Bora-induced currents corresponding to different synoptic conditions above the Adriatic. Annales Geophysicae, Vol. 23 No. 6, pages 1083-1091, 2005Beg Paklar, G., Isakov, V., Koracin, D., Kourafalou, V., Orlic, M., A case study of bora-driven flow and density changes on the Adriatic Shelf (January 1987). Continental Shelf Research, 21, 1751-1783, 2001Beg Paklar, G., M. Zore-Armanda, V. Dadic, Currents in the Kastela Bay: empirical analysis and results of a numerical model. Acta Adriatica, Vol. 43, 33-64, 2002Beg Paklar, G., N. Zagar, M. Zagar, R. Vellore, D. Koracin, P.-M. Poulain, M. Orlic, I. Vilibic, V. Dadic, Modeling the trajectories of satellite-tracked drifters in the Adriatic Sea during a summertime bora event.. J. Geophys. Res., 113, C11S04, 10.1029/2007JC004536, 2008Beletsky, D. and D. J. Schwab, Modeling circulation and thermal structure in Lake Michigan: Annual cycle and interannual variability. J. Geopys. Res., 106(C9), 19,745-19,771, 2001Beletsky, D., D. Schwab and M. McCormick, Modeling the 1998–2003 summer circulation and thermal structure in Lake Michigan. J. Geophys. Res., 111, C10010, 10.1029/2005JC003222, 2006Beletsky, D., W. P. O'Connor, and D. J. Schwab, Hydrodynamic Modeling for the Lake Michigan Mass Balance Project. G. Delic and M.F. Wheeler (eds.), Next Generation Environmental Models and Computa- tional Methods, Proceedings of the Next Generation Environmental Models Computational Methods (NGEMCOM) Workshop at the National Environmental Supercomputing Center, 1997Beletsky, D., W. P. O'Connor, D. J. Schwab, and D. E. Dietrich, Numerical simulation of internal Kelvin waves and coastal upwelling front. J. Phys. Oceanogr., 27(7), 1197-1215, 1997Bellafiore, D., G. Umgiesser and A. Cucco, Modeling the water exchanges between the Venice Lagoon and the Adriatic Sea. Ocean Dynamics, 58(5-6), 397-413, 2008Bender M.A., and I. Ginis, Real case simulations of hurricane-ocean interaction using a high resolution coupled model: Effect on hurricane intensity. Mon. Wea. Rev. 128, 917-946., 2000Bender, M. A., I. Ginis, R. Tuleya, B. Thomas and T. Marchok, The operational GFDL coupled hurricane-ocean prediction system and a summary of its performance. Mon. Wea. Rev., 135, 3965-3989, 2007Berdeal, I. G., B. M. Hickey and M. Kawase, Influence of wind stress and ambient flow on a high discharge river plume. J. Geophys. Res., 107(C9), 10.1029/2001JC000932, 2002Bergamasco, A. and S. Carniel, Sensitivity analysis of a robust diagnostic general circulation model of the Ross Sea. J. Mar. Sys., 27, 3-36, 2000Bergamasco, A., Carniel, S., & Caldesi Valeri, L., Reconstructing the general circulation of the Ross Sea (Antarctica) by means of a robust numerical model. Oceanography of the Ross Sea (Antarctica), G.C. Spezie & G.M.R. Manzella (Eds), Springer-Verlag, pp. 119-134, 1999Bergamasco, A., Carniel, S., Pastres, R. & Pecenik, G., A unified approach to the modelling of the Venice Lagoon - Adriatic Sea ecosystem. Estuarine Coastal and Shelf Science, 46, pp. 483-492, 1998Bergamasco, A., T. Oguz and P. Malanotte-Rizzoli, Modeling dense water mass formation and winter circulation in the northern and central Adriatic Sea. J. Mar. Sys., 20, 279-300, 1999Bergh J. and J. Berntsen, Numerical studies of wind forced internal waves with a nonhydrostatic model. Ocean Dynamics, 59(6), 1025-1041, doi:10.1007/s10236-009-0226-1, 2009Bergh, J. and J. Berntsen, The surface boundary condition in nonhydrostatic ocean models. Ocean Dynamics, doi: 10.1007/s10236-009-0245-0, 2009Berman, T., N. Paldor, and S. Brenner, Simulation of wind-driven circulation in the Gulf of Elat (Aqaba). J. Mar. Sys., 26, 349-365, 2000Berman, T., N. Paldor, and S. Brenner, The seasonality of the tidal circulation in the Gulf of Elat. Isr. J. Earth Sci., 52, 11-19, 2003Bernier, N. B. and K. R. Thompson, Predicting the frequency of storm surges and extreme sea levels in the northwest Atlantic. J. Geophys. Res., 111, C10009, 10.1029/2005JC003168, 2006Bernier, N. B., and K. R. Thompson, Tide-surge interaction off the east coast of Canada and northeastern United States. J. Geophys. Res., 112, C06008, 10.1029/2006JC003793, 2007Berntsen J. and G. Furnes, Internal pressure errors in sigma-coordinate ocean models—sensitivity of the growth of the flow to the time stepping method and possible non-hydrostatic effects. Cont. Shelf Res., 25(7-8), 829-848, 2005Berntsen, J. and Ø. Thiem, Estimating the internal pressure gradient errors in a σ-coordinate ocean model for the Nordic Seas. Ocean Dynamics, 57(4-5), 417-430, 2007Berntsen, J. and L.-Y. Oey, Estimation of the internal pressure gradient in σ-coordinate ocean models: comparison of second-, fourth-, and sixth-order schemes. Ocean Dynamics, doi: 10.1007/s10236-009-0245-y, 2009Berntsen, J., J. Xing and A. M. Davies, Numerical studies of flow over a sill: sensitivity of the non-hydrostatic effects to the grid size. Ocean Dynamics, 59(6), 1043-1059, doi:10.1007/s10236-009-0227-0, 2009Blaha, Born, Guinasso, Herring, Jacobs, Kelly, Leben, Martin, Mellor, Niiler, Parke, Patchen, Schaudt, Scheffner, Shum, Ohlmann, Sturges, Weatherly, Webb, and White, Gulf of Mexico ocean monitoring System. Oceanography, 13, 10-17, 2000Blain, C. A., Development of a data sampling strategy for semienclosed seas using a shallow water model. J. Atmos. Ocean Tech., 14(5), 1157-1173, 1997Blain, C. A., Development of a data sampling strategy for semienclosed seas using a shallow water model. . J. Atmos. Ocean Tech., 14(5), 1157-1173, 1997, 1997Blumberg A.F., Turbulent mixing processes in lakes, reservoirs and impoundments Physics- based Modeling of Lakes, Reservoirs and Impoundments. Ed.Gray W.G. Amer. Soc. Civ. Eng. New York, 79-104, 1986Blumberg A.F., Galperin B., O'Connor D.J., Modeling vertical structure of open-channel flows. J. Hydraul. Eng. Vol.118, No. 8. 1119-1134, 1992Blumberg, A. F. and D. M. Di Toro, Effects of climate warming on dissolved oxygen concentrations in Lake Erie. Trans. Amer. Fisheries Soc., 119, 210-223, 1990Blumberg, A. F. and D. M. Goodrich, Modeling of wind-induced destratification in Chesapeake Bay. Estuaries, 13, 236-249, 1990Blumberg, A. F. and G. L. Mellor, Diagnostic and prognostic numerical circulation studies of the South Atlantic Bight. J. Geophys. Res., 88, 4579-4592, 1983Blumberg, A. F. and G. L. Mellor, A description of a three-dimensional coastal ocean circulation model. Three-Dimensional Coastal ocean Models, edited by N. Heaps, 208 pp., American Geophysical Union., 1987Blumberg, A.F., Numerical tidal model of Chesapeake Bay. Journal of the Hydraulics Division, ASCE, 103, 1-10, 1997Blumberg, A.F. and D. W. Prichard, Estimates of the transport through the East River, New York. J. Geophys. Res., 102(C3), 5685-5703, 1997Blumberg, A.F., A. L. Khan and J. P. St. John, Three-dimensional hydrodynamic model of New York Harbor region. J. Hyd. Eng., 125(8), 799-816, 1999Blumberg, A.F., and Herring, H.J., Circulation modelling using orthogonal curvilinear coordinates. Three-Dimensional Models of Marine and Estaurine Dynamics, ed Nihoul, J.C.J., and Jamart, B,M., Elsevier Oceanography Series,45, 55-88, 1987Blumberg, A.F., and Kantha, L.H., Open boundary conditions for circulation models. Journal of Hydraulic Engineering, ASCE, 111, 237-255, 1985Blumberg, A.F., and L.-Y. Oey, Models of circulation and mixing in estuaries and coastal oceans. Adv. Geophys., 28A, 525-547, 1985Blumberg, A.F., and Mellor, G.L., A simulation of the circulation in the Gulf of Mexico. Israel Journal of Earth Sciences, 34, 122-144, 1985Blumberg, A.F., E. Gomez-Reyers and L. Munasinghe, 3D hydrodynamic model verification using ADCPS. Hydr. Eng., ASCE, 722-727, 1991Blumberg, A.F., R. P. Signell and H. L. Jenter, Modeling transport processes in the coastal ocean. J. Mar. Envir. Eng., 1, 3-52, 1993Blumberg, A.F., Z.-G. Ji and C. K. Ziegler, Modeling outfall plume behavior using far field circulation model. J. Hyd. Eng., 122, 610-616, 1996Bogden, P. S., P. Malanotte-Rizzoli and R. Signell, Open-ocean boundary conditions from interior data: Local and remote forcing of Massachusetts Bay. J. Geophys. Res., 101(C3), 6487-6500, 1996Book, J. W., P. J. Martin, I. Janeković, M. Kuzmić, and M. Wimbush, Vertical structure of bottom Ekman tidal flows: Observations, theory, and modeling from the northern Adriatic. J. Geophys. Res., 114, C01S06, doi:10.1029/2008JC004736, 2009Bormans, M. and S. A. Condie, Modelling the distribution of Anabaena and Melosira in a stratified river weir pool. Hydrobiologia, 364, 3-13, 1998Bosley, K. T. and K. W. Hess, Comparison of statistical and model-based hindcasts of subtidal water levels in Chesapeake Bay. J. Geophys. Res., 106(C8), 16,869-16,885, 2001Boukas, L. A., N. T. Mimikou, N. M. Missirlis, G. L. Mellor, A. Lascaratos, and G. Korres, The parallelization of the Princeton Ocean Model. Lecture Notes in Computer Sci., Amestoy et al. (Eds.), Springer, 1685, 1395-1402, 1999Bowen, M., M. Geyer, W. Rockwell, Salt transport and the time-dependent salt balance of a partially stratified estuary. J. Geophys. Res., 108(C5), 10.1029/2001JC001231, 2003Bowyer, P. A., Topographically controlled circulation and mixing in a lake. J. Geophys. Res., 106(C4), 7065-7080, 2001Breaker, L. C., D. B. Rao, J. G. W. Kelley, I. Rivin and B. Balasubramaniyan, Development of a real-time regional ocean forecast system with application to a domain off the U.S. east coast. J. Mar. Tech. Soc., 38(1), 61-79, 2004Breaker, L. C., Gemmill, W. H., deWitt, P. W. and Crosby, D. S., A curious relationship between the winds and currents at the western entrance of the Santa Barbara Channel. J. Geophys. Res., 108(C5), 10.1029/2002JC001458, 2003Breaker, L. C., L. D. Burroughs, Y. Y. Chao, D. M. Feit and D. B. Rao, NCEP participation in the coastal marine demonstration project. Third Conf. on Coastal Atmospheric and Oceanic Prediction and Processes, New Orleans, LA, AMS, 195-200, 1999Breivik, O. and O. Satra, Real time assimilation of HF radar currents into a coastal ocean model. J. Mar. Sys., 28, 161-182, 2001Brenner, S., High-resolution nested model simulations of the climatological circulation in the southeastern Mediterranean Sea. Annales Geophysicae, 21, 267-280, 2003Brenner, S., Simulations with a relocatable, nested, high resolution model: the eastern Levantine experience. Oceanography of the Eastern Mediterranean and Black Sea, A. Yilmaz (Editor), Tubitak Publi, 2003Brenner, S.,, High-resolution nested model simulations of the climatological circulation in the southeastern Mediterranean Sea. Annales Geophysicae, 21, 267-280, 2003Brenner, S., I. Gertman and A. Murashkovsky, Preoperational ocean forecasting in the southeastern Mediterranean Sea: Implementation and evaluation of the models and selection of the atmospheric forcing. J. Mar. Sys., doi:10.1016/j.jmarsys.2005.11.018, 2007Briganti, R., R. E. Musumeci, G. Bellotti, M. Brocchini and E. Foti, Boussinesq modeling of breaking waves: Description of turbulence. J. Geophys. Res., 109, C07015, 10.1029/2003JC002065, 2004Brooks, D.A., M.W. Baca and Y.-T. Lo, Tidal circulation and residence time in a macrotidal estuary: Cobscook Bay, Maine. Estuar. Coast. Shelf Sci., 49, 647-665., 1999Bruno, M. S. and A. F. Blumberg, An urban ocean observatory for the maritime community: Real-time assessment and forecasts of the New York Harbor maritime environment. Sea Technology, 45(8), 27-32, 2004Buranapratheprat, Yanagi, K. Niemann, Matsumura and Sojisuporn, Surface chlorophyll-a dynamics in the upper Gulf of Thailand revealed by a coupled hydrodynamic-ecosystem model. Journal of Oceanography, 64(5), 639-656, 2008Burchard, H and J-M Beckers, Marine turbulence re-revisited — Selected papers from the jointly organised 39th Liège Colloquium and 3rd Warnemünde Turbulence Days. J. Mar. Sys., 77(4), 367-368, 2009Burchard, H., On the q2l equation by Mellor and Yamada (1982). J. Phys. Oceanogr., 31, 1377-1387, 2001Burchard, H., Simulating wave-enhanced layer under breaking surface waves with two-equation turbulence models. J. Phys. Oceanogr., 31, 3133-3145, 2001Burchard, H., Energy-conserving discretisation of turbulent shear and buoyancy production. Ocean Modelling, 4, 347-361, 2002Burchard, H., Applied turbulence modelling in marine waters. Lecture Notes in Earth Sciences, Vol. 100, 229 pp., Springer, Berlin, 2002Burchard, H. and K. Bolding, Comperative analysis of four second- moment turbulence closure models for the oceanic mixed layer. J. Phys. Oceanogr., 31, 1943-1968, 2001Burchard, H. and K. Bolding, GETM, a general estuarine transport model, scientific documentation. Institute for Environment and Sustainability, Ispra, Italy, EUR 20253 EN Report, 157 pp., 2002Burchard, H., O. Peterson and T. P. Rippeth, Comparing the performance of the Mellor-Yamada and k-e two-equation turbulence models. J. Geophys. Res., 103(C5), 10,543-10,554, 1998Burnett, W. H. and V. M. Kamenkovich, On the splitting of main currents in the Indonesian Seas. In: OCEANS 2002, MTS/IEEE, Vol. 1-4, 1522- 1525, 2003Burnett, W. H., V. M. Kamenkovich, A. L. Gordon and G. L. Mellor, The Pacific/Indian Ocean pressure difference and its influence on the Indonesian Sea circulation: Part I- The study with specified total transports. J. Mar. Res., 61, 577-611, 2003Burnett, W. H., V. M. Kamenkovich, D. A. Jaffe, A. L. Gordon and G. L. Mellor, Dynamical balance in the Indonesian Sea circulation. Geophys. Res. Let., 27(17), 2705-2708, 2000Burnett, W. H., V. M. Kamenkovich, G. L. Mellor and A. L. Gordon, The influence of the pressure head on the Indonesian Sea circulation. Geophys. Res. Let., 27(15), 2273-2276, 2000Burnett, W., J. Harding and G. Heburn, Overview of operational forecasting in the U.S. Navy: Past, present and future. Oceanography, 15, 4-12, 2002Byun, D. S., X. H. Wang and P. E. Holloway, Tidal characteristic adjustment due to dyke and seawall construction in the Mokpo Coastal Zone, Korea. Estuar. Coastal and Shelf Sci. 59(2), 185-196, 2004Byun, D.-S. and X. H. Wang, The effect of sediment stratification on tidal dynamics and sediment transport patterns. J. Geophys. Res., 110, C03011, 10.1029/2004JC002459, 2005Byun, D.-S., X. H. Wang, D. E. Hart and Y.-K. Cho, Modeling the effect of freshwater inflows on the development of spring blooms in an estuarine embayment. Est. Coast. Shelf Sci., 65(1-2), 351-360, 2005Calado, L., A. Gangopadhyay, I.C.A. da Silveira, Feature-oriented regional modeling and simulations (FORMS) for the western South Atlantic: Southeastern Brazil region. Ocean Modelling, 25(1-2), 48-64, 2008Camargo, R. and J Harari, Modeling the Paranagua Estuarine Complex, Brazil: tidal circulation and cotidal charts. Brazilian Journal of Oceanography, 51 (1), 23 - 31, 2003Cannaby, H., M. White, and P. Bowyer, Dynamical response to differential rates of temperature change over sloping topography: Lough Corrib, Ireland. J. Geophys. Res., 112, C09009, 10.1029/2006JC003890, 2007Canuto, V. M., A. Howard, Y. Cheng, and M. S. Dubovikov, Ocean turbulence. Part I: One-point closure model-momentum and heat vertical diffusivities. J. Phys. Oceanogr., 31, 1413-1426, 2001Carter, G. S. and M. A. Merrifield, Open boundary conditions for regional tidal simulations. Ocean Modelling, 18(3-4), 194-209, 2007Carter, G. S., M. C. Gregg and M. A. Merrifield, Flow and Mixing around a Small Seamount on Kaena Ridge, Hawaii. J. Phys. Oceanogr., 36(6), 1036–1052., 2006Castelao, R. M. and J. A. Barth,, The Relative Importance of Wind Strength and Along-Shelf Bathymetric Variations on the Separation of a Coastal Upwelling Jet. J. Phys. Oceanogr., 36(3), 412-425, 2006Cerda, C., Intrusoes da Agua Central do Atlantico Sul sobre a plataforma continental situada entre a Ilha de São Sebastiao (SP) e o Cabo de Sao Tomé (RJ)- Brasil. Tese de doutorado, Instituto Oceanografico, Universidade de Sao Paulo, Brasil, 273 pp., 2004Cesarini C., Pinardi N., Struttura e dinamica dello strato di fondo del Mare Adriatico [Structure and dynamics of the Adriatic Sea bottom layer] . IMGA-CNR Techn. Rep. 4/98, 160 pp., 1998Chang, K., S. Ito, C. N.K. Mooers, J. Yoon, Observation and modeling of the ocean circulation and marine ecosystem for CREAMS/PICES. J. Mar. Sys., 78, doi:10.1016/j.jmarsys.2009.03.002, 2009Chang, P. H., Interannual variation of freshwater in the Yellow and East China Seas: Roles of the Changjiang discharge and wind forcing. J. Oceanogr., 61 (5), 817-834, 2005Chang, Pil-Hun, Isobe, Atsuhiko, A numerical study on the Changjiang diluted water in the Yellow and East China Seas. J. Geophys. Res., 108(C9), 10.1029/2002JC001749, 2003Chang, Y.-L., C.-R. Wu and L. Oey, Bimodal behavior of the seasonal upwelling off the northeastern coast of Taiwan. J. Geophys. Res., 114, C03027, 10.1029/2008JC005131, 2009Chao, S.-Y., Hyperpycnal and buoyant plumes from a sediment-laden river. J. Geophys. Res., 103(C2), 3067-3081, 1998Chao, S.-Y., Ocean feedback to wind-driven coastal polynyas. J. Geophys. Res., 104(C8), 18,073-18,085, 1999Chao, S.-Y. and P.-T. Shaw, Initialization, asymmetry, and spindown of Arctic eddies. J. Phys. Oceanogr., 26, 2076-2092, 1996Chao, S.-Y. and P.-T. Shaw, Eddy maintenance and attrition in a vertically sheared current under Arctic ice. J. Phys. Oceanogr., 28, 2427-2443, 1998Chao, S.-Y. and P.-T. Shaw, Close interactions between two pairs of heton- like vortices under sea-ice. J. Geophys. Res., 104(C10), 23,591-23,605, 1999Chapman, D. C., D.-S. Ko and R. H. Preller, A High-Resolution Numerical Modeling Study of Subtidal Circulation in the Northern South China Sea. IEEE J. Oceanic Engineering, 29(4), 1087-1104, 2004Chapman, David C., Dong S. Ko, and Ruth H. Preller, A High-Resolution Numerical Modeling Study of Subtidal Circulation in the Northern South China Sea. IEEE Journal of Oceanic Engineering, Vol. 29, No. 4, pp. 1087-1104, 2004Chassignet, E. P, H. E. Hurlburt, O. M. Smedstad, C. N. Barron, D. S. Ko, Rhodes, Shriver, Walcraft and Arnone, Assesment of data assimilative ocean models in the Gulf of Mexico using ocean color, In: Circulation in the Gulf of Mexico: Observations and Models, W. Sturges and A. Lugo-Fernandez (Eds.). Geophys. Monograph Ser., Vol. 161, pp. 87-100, AGU, Washington, DC, 2005Chassignet, E. P., H. Arango, D. Dietrich, T. Ezer, D. B. Haidvogel, M. Ghil, C. C. Ma, A. Mehra, A. M. Paiva and Z. Sirkes, DAMEE-NAB: The base experiments. Ocean Circulation Model Evaluation Experiments for the North Atlantic Basin, E. P. Chassignet and P. Malanotte-Rizzoli (Eds.), Dyn. Atmos. Ocean, 32, Elsevier Sci. Ltd., 155-184, 2000Chen, C., A modeling study of the episodic cross-frontal water transport over the inner shelf of the South Atlantic Bight. J. Phys. Oceanogr., 30, 1722-1742, 2000Chen, C. and L. Xie, A numerical study of wind-induced, near-inertial oscillations over the Texas-Louisiana shelf. J. Geophys. Res., 102(C7), 15,583-15,593, 1997Chen, C. and R. C. Beardsley, A numerical study of stratified tidal rectification over finite-amplitude banks. Part 1: Symmetric banks. J. Phys. Oceanogr., 25(9), 2090-2110, 1995Chen, C., H. Huang, R. C. Beardsley, H. Liu, Q. Xu, G. Cowles, A finite volume numerical approach for coastal ocean circulation studies: Comparisons with finite difference models. J. Geophys. Res., 112, C03018, 10.1029/2006JC003485, 2007Chen, C., J. Qi, C. Li, R. C. Beardsley, H. Lin, R. Walker, and K. Gates, Complexity of the flooding/drying process in an estuarine tidal-creek salt-marsh system: An application of FVCOM. J. Geophys. Res., 113, C07052, 10.1029/2007JC004328, 2008Chen, C., J. Zhu, E. Ralph, S. A. Green, J. W. Budd and F. Y. Zhang, Prognostic modeling studies of the Keweenaw Current in Lake Superior. Part I: Formation and Evolution. J. Phys. Oceanogr., 31, 379-395, 2001Chen, C., J. Zhu, K. Kang, H. Liu, E. Ralph, S. A. Green and J. W. Budd, Cross-frontal transport along the Keweenaw coast in Lake Superior: a Lagrangian model study. Dyn. Atmos. Ocean, 36, 83-102, 2002Chen, C., L. Zheng and J. O. Blanton, Physical processes controling the formation, evolution, and perturbation of the low-salinity front in the inner shelf off the southeastern United States: A modeling study. J. Geophys. Res., 104(C1), 1259-1288, 1999Chen, C., Q. Xu, E. Ralph, J. W. Budd, and H. Lin, Response of Lake Superior to mesoscale wind forcing: A comparison between currents driven by QuikSCAT and buoy winds. J. Geophys. Res., 109, C10S02, 10.1029/2002JC001692, 2004Chen, C., R. Beardsley and P. J. S. Franks, A 3-D prognostic numerical model study of the Georges Bank ecosystem. Part I: physical model. Deep-Sea Res., II, 48, 419-456, 2001Chen, C., R. C. Beardsley and R. Limeburner, A numerical study of stratified tidal rectification over finite-amplitude banks. Part 2: Georges Bank. J. Phys. Oceanogr., 25(9), 2111-2128, 1995Chen, C., R. C. Beardsley, P. J. S Franks and J. Van Keuren, Influence of diurnal heating on stratification and residual circulation of Georges Bank. J. Geophys. Res., 108(C11), 10.1029/2001JC001245, 2003Chen, C., R. Ji, L. Zheng, M. Zhu and M. Rowson, Influences of physical processes on the ecosystem in Jiaozhou Bay: A coupled physical and biological model experiment. J. Geophys. Res., 104(C12), 29,925-29,949, 1999Chen, C., Xu, Q., Beardsley, R. C. and Franks, P. J. S., Model study of the cross-frontal water exchange on Georges Bank: A three-dimensional Lagrangian experiment. J. Geophys. Res., 108(C5), 10.1029/2000JC00090, 2003Chen, Changsheng; Schlitz, Ronald J.; Lough, R. Gregory; Smith, Keston W.; Beardsley, Robert; Manning, James P., Wind‐induced, cross‐frontal exchange on Georges Bank: A mechanism for early summer on‐bank biological particle transport. J. Geophys. Res., 108(C11), 10.1029/2002JC001358, 2003Chen, D., H.-W. Ou, and C. Dong, A Model Study of Internal Tides in Coastal Frontal Zone. J. Phys. Oceanogr., 33(1), 170187, 2003Chen, H.-X., F.-L. Qiao, T. Ezer and Y.-L. Yuan, Multi-core structure of the Kuroshio in the East China Sea from long-term transect observations. Ocean Dynamics, 59(3), 477-488, 2009Chen, P. and G.L. Mellor, Determination of tidal boundary forcing using tide station data.. Coastal Ocean Prediction, Coastal and Estuarine Studies, Vol. 56, C. N. K. Mooers (Ed.), American Geophysical Union, Washington, DC, 329-351, 1999Chen, X., Dynamic coupling of a three-dimensional hydrodynamic model with a laterally averaged, two-dimensional hydrodynamic model. J. Geophys. Res., 112, C07022, 10.1029/2006JC003805, 2007Chiang, T., C. Wu, and S. Chao, Physical and geographical origins of the South China Sea Warm Current. J. Geophys. Res., 113, C08028, 10.1029/2008JC004794, 2008Chu P. C. and J. Lan, Extremely strong thermohaline sources/sinks generated by diagnostic initialization. Geophys. Res. Let., 30(6), Art. No. 1341, 2003Chu, P. C., High order compact difference schemes for coastal ocean models. Second Conference on Coastal Atmospheric and Oceanic Prediction and Processes, Jan. 11-16, 1998, Phoenix, AZ, American Meteorological Society, Boston, MA, 68-75, 1998Chu, P. C. and C. Fan, Sixth-order difference scheme for sigma coordinate ocean models. J. Phys. Oceanogr., 27(9), 2064-2071, 1997Chu, P. C. and Fan, C., Hydrostatic correction for sigma coordinate ocean models. J. Geophys. Res., 108(C6), 10.1029/2002JC001668, 2003Chu, P. C., C.-L. Fang and C. S. Kim, Japan/East Sea model predictability. Cont. Shelf Res., 2005Chu, P. C., N. L. Edmons and C. Fan, Dynamical mechanisms for the South China Sea seasonal circulation and thermohaline variabilities. J. Phys. Oceanogr., 29, 2971-2989, 1999Chu, P. C., S. Lu and W. T. Liu, Uncertainty of South China Sea prediction using NSCAT and National Centers for Environmental Prediction winds during tropical storm Ernie, 1996. J. Geophys. Res., 104(C5), 11,273- 11,289, 1999Chu, P. C., S. Lu, et al., A numerical simulation of Japan/East Sea (JES) thermohaline structure and circulation . In: Lakhan, V. C. (Editor). Advances in Coastal Modeling. Elsevier Oceanography Ser., 67, 2003Chu, P. C., Y. Chen and S. Lu, On Haney-type surface thermal boundary conditions for ocean circulation models. J. Phys. Oceanogr., 28, 890-901, 1998Chu, P., M. D. Perry, E. L. Gottshall and D. S. Cwalina, Satellite data assimilation for improvement of naval undersea capability. J. Mar. Tech. Soc., 38(1), 12-23, 2004Chu, P.C., J. Lan and C. Fan, Japan Sea thermocline structure and circulation. Part II: A variational P-vector method. J. Phys. Oceanogr., 31, 2886-2902, 2001Chu, P.C., J. M. Veneziano, and C.W. Fan, Response of the South China Sea to tropical cyclone Ernie 1996. J. Geophys. Res., 105(C6), 13,991-14,009, 2000Chu, P.C., S. Lu, and Y. Chen, Evaluation of the Princeton Ocean Model using South China Sea Monsoon Experiment (SCSMEX) data. J. Atm. Ocean Tech., 18, 1521-1539, 2001Chu, P.C., and C.W. Fan, A three-point combined compact difference scheme. Journal of Computational Physics, 140, 370-399, 1998Chu, P.C., and C.W. Fan, Improvement of estuarine and coastal modeling using high-order difference schemes. Estuarine and Coastal Modeling, 5, American Society of Engineering, 28-34, 1998Chu, P.C., and C.W. Fan, A non-uniform three-point combined compact difference scheme. Journal of Computational Physics, 148, 663-674, 1999Chu, P.C., and C.W. Fan, A staggered three-point combined compact difference scheme.. Math. Comp. Mod., 2000Chu, P.C., and N.L. Edmons, A three-dimensional numerical simulation of the South China Sea circulation and thermohaline structure. Chinese Journal of Atmospheric Sciences, 22, 481-503, 1998Chu, P.C., C.W. Fan, and L.L. Ehret, Determination of open boundary conditions from interior observational data. Journal of Atmospheric and Oceanic Technology, 14, 723-734, 1997Chu, P.C., H.-C. Tseng, C. P. Chang and J. M. Chen, South China Sea warm pool detected in spring from the Navy's Master Oceanographic Observational Data Set (MOODS). J. Geophys. Res., 102(C7), 15,761-15,771, 1997Chu, P.C., S. K. Wells, S. D. Haeger, C. Szczechowski and M. Carron, Temporal and spatial scales of the Yellow Sea thermal variability. J. Geophys. Res., 102(C3), 5655-5667, 1997Chu, P.C., S.H. Lu, and Y.C. Chen, Wind-driven South China Sea deep basin warm-core /cool-core eddies. Journal of Oceanography, 54, 347-360, 1998Chu, P.C., S.H. Lu, and Y.C. Chen, A coastal atmosphere-ocean coupled system (CAOCS) evaluated by an airborne expandable bathythermograph survey in the South China Sea, May 1995. Journal of Oceanography, 55, 543-558, 1999Chu, P.C., Y. Qian, C. Fan and Q. Wang, A mixed z-sigma differencescheme in sigma coordinate ocean models. J. Phys. Oceanogr. Submitted, 2001Ciappa, A. C., An operational comparative test of z-levels PGF schemes to reduce pressure gradient errors of the ocean model POM. Ocean Modelling, 12(1-2), 80-100, 2006Ciappa, A. C., A method for reducing pressure gradient errors improving the sigma coordinate stretching function: An idealized flow patterned after the Libyan near-shore region with the POM. Ocean Modelling, 23(1-2), 59-72, 2008Cirano, M., Application of a numerical model in the diagnostic study of the oceanic circulation in the Santos Bight. Msc. Thesis, University of Sao Paulo, 116 pp., 1995Cirano, M. and Edmo J. D. Campos, Numerical diagnostic of the circulation in the Santos Bight with COROAS hydrographic data. Rev. bras. oceanogr. 44(2), 105-121, 1996Clancy, R. M., Operational systems, products, and applications today and tomorrow: The Navy perspective. Coastal Ocean Prediction, Coastal and Estuarine Studies, Vol. 56, C. N. K. Mooers (Ed.), American Geophysical Union, Washington, DC, 501-511, 1999Clancy, R. M., P. W. deWitt, P. W. May and D. S. Ko, Implementation of a coastal ocean circulation model for the west coast of the United States. Proc., AMS Conf. on Coastal Oceanic and Atmospheric Prediction, 1995Clayson, C. N. and L. H. Kantha, Turbulent kinetic energy and its dissipation rate in the equatorial mixed-layer. J. Phys. Oceanogr., 29(9), 2146-2166, 1999Clifford, M., C. Horton, J. Schmitz, and L. H. Kantha, An oceanographic nowcast/forecast system for the Red Sea. J. Geophys. Res., 102(C11), 25,101-25,122, 1997Condie, S. A. and I. T. Webster, Estimating stratification in shallow water bodies from mean meteorological conditions. J. Hyd. Eng., 127(4), 286-292, 2001Condie, S. A. and I. T. Webster, The influence of wind stress, temperature, and humidity gradients on evaporation from reservoirs. Water Resour. Res., 33, 2813-2822, 1997Condie, S. A. and M. Bormans, The influence of density stratification on particle settling, dispersion and population growth. J. Theor. Biol., 187, 65-75, 1997Condie, S., C. Fandry, D. McDonald, J. Parslow and K. Sainsbury, Linking ocean models to coastal management on Australia's North West Shelf. EOS, Transaction, AGU, 84(6), 49-53, 2003Crawford W.R., J.Y. Cherniawsky and P.F. Cummins, Surface currents in British Columbia waters: comparison of observations and model predictions. Atmos.-Ocean, 37, 255-280, 1999Crawford, W. R., J. Y. Chermiawsky, P. F. Cummins and M. G. G. Foreman, Variability of tidal currents in a wide strait: A comparison between drifter observations and numerical simulations. J. Geophys. Res., 103(C6), 12,743-12,760, 1998Cummins, P., Stratified flow over topography: time-dependent comparisons between model solutions and observations. Dyn. Atm. & Oceans, 33, 43-72, 2000Cummins, P. F. and L-Y. Oey, Simulation of barotropic and baroclinic tides off northern British Columbia. J. Phys. Oceanogr., 27, 762-781, 1997Cummins, P. F. and M. G. G. Foreman, A numerical study of circulation driven by mixing over a submarine bank. Deep-Sea Res., 45, 745-769, 1998Cummins, P. F., D. Masson and M. G. G. Foreman, Stratification and mean flow effects on diurnal tidal currents off Vancouver Island. J. Phys. Oceanogr., 30, No. 1, 15-30, 2000D'Alessio, S. J. D., K. Abdella and N. A. McFarlane, A new second-order turbulence closure scheme for modeling the oceanic mixed layer. J. Phys. Oceanogr., 28(8), 1624-1641, 1998D. Beletsky, D. J. Schwab, P. J. Roebber, M. J. McCormick, G. S. Miller and J. H. Saylor, Modeling wind-driven circulation during the March 1998 sediment resuspension event in Lake Michigan. J, Geophys. Res., 108(C2), 10.1029/2001JC001159, 2003D. J. Schwab, D. J. , D. Beletsky and J. Lou, The 1998 Coastal Turbidity Plume in Lake Michigan. Est. Coastal and Shelf Sci.,50, 49-58, 2000da Silveira I. C. A., L. Calado, B. M. Castro, M. Cirano, J. A. M. Lima, A. d. S. Mascarenhas, On the baroclinic structure of the Brazil Current–Intermediate Western Boundary Current system at 22°–23°S. Geophys. Res. Let., 31, L14308, 10.1029/2004GL020036, 2004Dadic, V., M. Bone, G. Beg Paklar, B. Grbec, D. Ivankovic, F. Matic, M. Morovic, Automatic meteo-ocean station (AMOS): real-time data acquision, validation, archiving and numerical modeling. Acta Adriatica, Vol. 47, 133-148., 2006Dai, D., F. Qiao, C. Xia and K. T. Jung, A numerical study on dynamic mechanisms of seasonal temperature variability in the Yellow Sea. J. Geophys. Res., 111, C11S05, 10.1029/2005JC003253, 2006Danielson, S. and Z. Kowalik, Tidal currents in the St. Lawrence Island region. J. Geophys. Res., 110, C10004, 10.1029/2004JC002463, 2005Davidson, F. J. M. and P. Holloway, A study of tropical cyclon influence on the generation of internal tides. J. Geophys. Res., 108(C3), 10.1029/2000JC000783, 2003Davies, A. M. and L.-Y. Oey, Editorial: Recent developments in physical oceanographic modelling: Part III. Cont. Shelf Res., 26(12-13), 1359, 2006Davies, A. M. and L.-Y. Oey, Recent developments in physical oceanographic modelling: Part IV. Cont. Shelf Res., doi: 10.1016/j.csr.2007.01.006, 2007Debreu, L. and E. Blayo, Two-way embedding algorithms: a review. Ocean Dynamics, 58(5-6), 415-428, 2008Deleersnijder, E. and H. Burchard, Reply to Mellor's comments on "Stability of algebraic non-equilibrium second-order closure models" (Ocean Modelling 3 (2001) 3350). Ocean Modelling, 5, 291-293, 2003Deleersnijder, E. and P. Lermusiaux (Eds.), Multi-Scale Modelling: Nested Grid and Unstructured Mesh Approaches, Special Issue. Ocean Dynamics, Vol. 58, 2008Deleersnijder, E., E. Hanert, H. Burchard and H. A. Dijkstra, On the mathematical stability of stratified flow models with local turbulence closure schemes. Ocean Dynamics, 58(3-4), 237-246, 2008Do-Seong Byun and Chang-Woo Cho, Exploring conventional tidal prediction schemes for improved coastal numerical forecast modeling. Ocean Modelling, 28, 193-202, 2009Dobricic, S., Equilibrium surface elevation distribution in a baroclinic ocean with realistic bottom topography. J. Geophys. Res., 108(C10), 10.1029/2002JC001579, 2003Doglioli, A. M., A. Griffa, M. G. Magaldi, Numerical study of a coastal current on a steep slope in presence of a cape: The case of the Promontorio di Portofino. J. Geophys. Res., 109, C12033, 10.1029/2004JC002422, 2004Dong, C. and L.-Y. Oey, Sensitivity of Coastal Currents near Point Conception to Forcing by Three Different Winds: ECMWF, COAMPS, and Blended SSM/I–ECMWF–Buoy Winds. J. Phys. Oceanogr., 35(7), 1229–1244, 2005Dong, C., R. Houghton, H.-W. Ou, D. Chen and T. Ezer, Numerical study of the diapycnal flow through a tidal front with passive tracers. J. Geophys. Res., 109, C05029, 10.1029/2003JC001969, 2004Drakopoulos, P. G. and A. Lascaratos, Modelling the Mediterranean Sea: climatological forcing. J. Mar. Sys., 20, 157-173, 1999Dufau-Julliand, C., P. Marsaleix, A. Petrenko and I. Dekeyser, Three-dimensional modeling of the Gulf of Lion's hydrodynamics (northwest Mediterranean) during January 1999 (MOOGLI3 Experiment) and late winter 1999: Western Mediterranean Intermediate Water's (WIW's) formation and its cascading over the shelf break. J. Geophys. Res., 109, C11002, 10.1029/2003JC002019, 2004Dukhovskoy, D. S., S. L. Morey and J. J. O’Brien, Influence of multi-step topography on barotropic waves and consequences for numerical modeling. Ocean Modelling, 14(1-2), 45-60, 2006Dukhovskoy, D. S., S. L. Morey, P. J. Martin, J. J. O’Brien, C. Cooper, Application of a vanishing, quasi-sigma, vertical coordinate for simulation of high-speed, deep currents over the Sigsbee Escarpment in the Gulf of Mexico. Ocean Modelling, 28(4), 250-265, 2009Dukhovskoy, D.S., S. L. Morey, and J.J. O'Brien, Influence of multi-step topography on barotropic waves and consequences for numerical modeling. Ocean Modelling, 14,45-60, doi:10.1016/j.ocemod.2006.03.002, 2006Dzierzbicka-GImageowacka, L., A numerical investigation of phytoplankton and Pseudocalanus elongatus dynamics in the spring bloom time in the GdaImagesk Gulf. J. Mar. Sys., 53(1-4), 19-36, 2005Eadie, B. J., J. A. Robbins, J. V. Klump, D. J. Schwab and D. N. Edgington, Winter-spring storms and their influence on sediment resuspension, transport, and accumulation patterns in southern Lake Michigan. Oceanography, 21(4), 118-135, 2008Echevin, V. and P. De Mey, Horizontal and vertical structure of the representer functions for sea surface measurements in a coastal circulation model. J. Phys. Oceanogr., 30(10), 2627-2635, 2000Eich, M. L., M. A. Merrifield and M. H. Alford, Structure and variability of semidiurnal internal tides in Mamala Bay, Hawaii. J. Geophys. Res., 109, C05010, 10.1029/2003JC002049, 2004Engedahl, H., Use of the flow relaxation scheme in a three-dimensional baroclinic ocean model with realistic topography. Tellus, 47A, 365-382, 1995Engedahl, H., B. Adlandsvik and E. A. Martinsen, Production of monthly mean climatological archives for the Nordic seas. J. Mar. Sys., 14, 1-26, 1998Erofeeva, S., Y., Egbert, Gary D. and Kosro, P. M., Tidal currents on the central Oregon shelf: Models, data, and assimilation. J. Geophys. Res., 108(C5), 10.1029/2002JC001615, 2003Estouernel, C., X. D. de Madron, P. Marsaleix, F. Auclair, C. Julliand and R. Vehil, Observation and modeling of the winter coastal oceanic circulation in the Gulf of Lion under wind conditions influenced by the continental orography (FETCH experiment). J. Geophys. Res., 108(C3), 10.1029/2001JC000825, 2003Evans, S. and J. F. Middleton, A Regional Model of Shelf Circulation near Bass Strait: A new Upwelling Mechanism. J. Phys. Oceanogr. 28, 1439-1457, 1998Ezer, Sensitivity studies with the North Atlantic Princeton Ocean Model.. Dyn. Atmos. Ocean., 32, 2000Ezer, T., On the interaction between the Gulf Stream and the New England Seamount Chain. J. Phys. Oceanogr., 24, 191-204, 1994Ezer, T., On the seasonal mixed-layer simulated by a basin-scale ocean model and the Mellor-Yamada turbulence scheme. J. Geophys. Res., 105(C7), 16,843-16,855, 2000Ezer, T., Simulations of past and future climatic variability of the Atlantic Ocean and the coastal zone, In: Climate Variations, the Oceans, and Social Impacts. Amer. Met. Soc., Boston, MA, 82-86, 2001Ezer, T., On the response of the Atlantic Ocean to climatic changes in high latitudes: Sensitivity studies with a sigma coordinate ocean model, In: The Oceans and Rapid Climate Change: Past, Present and Future, D. Seidov, B. J. Haupt and M. Maslin (Eds.). American Geophysical Union, 199-215, 2001Ezer, T., Can long-term variability in the Gulf Stream transport be inferred from sea level?. Geophys. Res. Let., 28(6), 1031-1034, 2001Ezer, T., Entrainment, diapycnal mixing and transport in three-dimensional bottom gravity current simulations using the Mellor-Yamada turbulence scheme. Ocean Modelling, 9(2), 151-168, 2005Ezer, T., Topographic influence on overflow dynamics: Idealized numerical simulations and the Faroe Bank Channel overflow. J. Geophys. Res., 111, C02002, 10.1029/2005JC003195, 2006Ezer, T., Hydrodynamic numerical ocean models support environmental studies and conservation efforts: From an arctic estuary to a Caribbean coral reef. CCPO Circulation, Spring 2008, Vol. 15, No. 1, 1-3, 2008Ezer, T. (Ed.), The Princeton Ocean Model (POM) Users Meeting, Abstracts Princeton , June 10-12, 1996. Program in Atmospheric and Oceanic Sciences, Princeton University, 58pp, 1996Ezer, T. and G. L. Mellor, A numerical study of the variability and the separation of the Gulf Stream, induced by surface atmospheric forcing and lateral boundary flows. J. Phys. Oceanogr., 22, 660-682, 1992Ezer, T. and G. L. Mellor, Continuous assimilation of Geosat altimeter data into a three-dimensional primitive equation Gulf Stream model. J. Phys. Oceanogr., 24, 832-847, 1994Ezer, T. and G. L. Mellor, Diagnostic and prognostic calculations of the North Atlantic circulation and sea level using a sigma coordinate ocean model. J. Geophys. Res., 99(C7), 14,159-14,171, 1994Ezer, T. and G. L. Mellor, A generalized coordinate ocean model and a comparison of the bottom boundary layer dynamics in terrain following and in z-level grids. Ocean Modelling, 6, 379-403, 2004Ezer, T. and G. L. Mellor (Eds.) and the CFS group, A Coastal Forecast System: A collection of enabling information. Program in Atmospheric and Oceanic Sciences Report, Princeton University, 47pp, 1994Ezer, T. and G. L. Weatherly, On eddy diffusion profiles in oceanic bottom boundary layers associated with cold eddies and filaments. Bound. Layers Met., 48, 83-97, 1989Ezer, T. and G. L. Weatherly, A numerical study of the interaction between a deep cold jet and the bottom boundary layer of the ocean. J. Phys. Oceanogr.,20, 801-816, 1990Ezer, T. and L.-Y. Oey, The role of the Alaskan Stream in modulating the Bering Sea climate. J. Geophys. Res., doi:10.1029/2009JC005830, 2009Ezer, T. and Mellor, Sensitivity studies with the North Atlantic Princeton Ocean Model. Ocean Circulation Model Evaluation Experiments for the North Atlantic Basin, E. P. Chassignet and P. Malanotte-Rizzoli (Eds.) Dyn. Atmos. Ocean, 32, Elsevier Sci. Ltd., 185-208, 2000Ezer, T., and H. Liu, Combining remote sensing data and an inundation model to map tidal mudflat regions and improve flood predictions: A proof of concept demonstration in Cook Inlet, Alaska. Geophys. Res. Let., 36, L04605, doi:10.1029/2008GL036873., 2009Ezer, T., D. S. Ko and G. L. Mellor, Modeling and forecasting the Gulf Stream Oceanic and Atmospheric Nowcasting and Forecasting, edited by D. L. Durham and J. K. Lewis. Mar. Tech. Soc. Journal, 26(2), 5-14, 1992Ezer, T., D. V. Thattai, B. Kjerfve and W. D. Heyman, On the variability of the flow along the Meso-American Barrier Reef System: A numerical model study of the influence of the Caribbean Current and eddies. Ocean Dynamics, 55, 458-475, doi: 10.1007/s10236-005-0033-2, 2005Ezer, T., G. L. Mellor, and R. J. Greatbatch, On the interpentadal variability of the North Atlantic ocean: Model simulated changes in transport, meridional heat flux and coastal sea level between 1955-1959 and 1970-1974. J. Geophys. Res., 100(C6), 10,559-10,566, 1995Ezer, T., G. L. Mellor, D. S. Ko and Z. Sirkes, A comparison of Gulf Stream sea surface height fields derived from Geosat altimeter data and those derived from sea surface temperature data.. J. Atmos. Oceanic. Technol., 10, 76-87, 1993Ezer, T., G. L. Mellor, J. Jungclaus, Atlantic ocean climate studies with the Princeton Ocean Model. The Atlantic Climate Change Program, Proc. from the PI meeting, 111-114, 1995Ezer, T., G. L. Mellor, S. Hakkinen, and C. Mauritzen, Simulations of the Arctic and the North Atlantic oceans, The Atlantic Climate Change Program. Proc. from the PI meeting, 115-119, 1994Ezer, T., H. Arango and A. F. Shchepetkin, Developments in terrain-following ocean models: Intercomparisons of numerical aspects. Ocean Modelling, 4, 249-267, 2002Ezer, T., H. Arango and A. Herman (Eds.), Proceedings, 2003 Terrain-Following Ocean Models Users Workshop. Program in Atm. & Oceanic Sci., Princeton University, 19pp, 2003Ezer, T., L.-Y. Oey, H.-C. Lee, and W. Sturges, The variability of currents in the Yucatan Channel: Analysis of results from a numerical model. J. Geophys. Res., 10.1029/2002JC001509, 2002Ezer, T., L.-Y. Oey. and H.-C. Lee, Simulation of velocities in the Yucatan Channel. In: Proc., Oceans 2002, MTS/IEEE Publ., 1467-1471, 2002Ezer, T., R. Hobbs and L.-Y. Oey, On the movement of Beluga whales in Cook Inlet, Alaska: Simulations of tidal and environmental impacts using a hydrodynamic inundation model. Oceanography, 21(4), 186-195, 2008Ezer,T., Decadal variabilities of the upper layers of the subtropical North Atlantic: An ocean model study. J. Phys. Oceanogr., 29(12), 3111-3124, 1999Ezer,T. and G. L. Mellor, Simulations of seasonal, interannual and interdecadal Atlantic Ocean variabilities associated with variations in observed surface temperatures and winds. The Atlantic Climate Change Program, Proc. from the PI meeting, 41-43, 1996Ezer,T. and G. L. Mellor, Simulations of the Atlantic Ocean with a free surface sigma coordinate ocean model. J. Geophys. Res., 102(C7), 15,647-15,657, 1997Ezer,T. and G. L. Mellor, Data assimilation experiments in the Gulf Stream region: How useful are satellite-derived surface data for nowcasting the subsurface fields?. J. Atmos. Ocean Tech., Special issue on Data Assimilation and Model Evaluation Experiments, Vol. 16, No. 6, 1379-1391, 1997Ezer,T., and G. L. Mellor, Studies of the Atlantic Ocean climate with a sigma coordinate coastal ocean model. ACCP Notes, Vol. II, No. 1, 4-6, 1995Fan, S., L.-Y. Oey and P. Hamilton, Assimilation of drifter and satellite data in a model of the Northeastern Gulf of Mexico . Cont. Shelf Res., 24(9), 1001-1013, 2004Feddersen, F. and J. H. Trowbridge, The Effect of Wave Breaking on Surf-Zone Turbulence and Alongshore Currents: A Modeling Study. J. Phys. Oceanogr., 35(11), 2187-2203, 2005Federiuk, J. and J. S. Allen, Upwelling circulation on the Oregon Continental Shelf. Part 2: Simulations and comparisons with observations. J. Phys. Oceanogr., 25, 1867-1889, 1995Federiuk, J. and J. S. Allen, Model Studies of near-inertial waves in flow over the Oregon Continental Shelf. J. Phys. Oceanogr., 26, 2050-2075, 1996Fiechter, J., and C. N. K. Mooers, Primary production associated with the Florida Current along the East Florida Shelf: Weekly to seasonal variability from mesoscale-resolution biophysical simulations. J. Geophys. Res., 112, C12002, 10.1029/2006JC003576, 2007First, A., B. Second and C. Third, physical model of the polynya. Journal, Vol. No., pages, 2003Flexas, M. M., G. J. F. van Heijst, G. Jorda and A. Sanchez-Arcilla, Numerical simulation of barotropic jets over a sloping bottom: Comparison to a laboratory model of the Northern Current. J. Geophys. Res., 109, C12039, 10.1029/2004JC002286, 2004Fong, D. A. and W. R. Geyer, Response of a river plume during an upwelling favorable wind event. J. Geophys. Res., 106(C1), 1067-1084, 2001Fontes, R. F. C., B. M. Castro and R. C. Beardsley, Numerical study of circulation on the inner Amazon Shelf. Ocean Dynamics, 58(3-4), 187-198, 2008Fossum, I, Analysis of instability and mesoscale motion off southern Norway. J. Geophys. Res., 111, C08006, 10.1029/2006JC003228, 2006Fox, D. N., C. N. Barron, M. R. Carnes, M. Booda, G. Peggion and J. Van Gurley, The modular ocean data assimilation system. Oceanography, 15, 22-28, 2002Fragoso, M. D. A. R. Torres, N. Mehdi, et al., Oil spill fate forecast system for Ilha Grande Bay, Rio de Janeiro, Brasil. Wat. Stud. Ser., 11, 47- 56, 2003Fragoso, M.R., Estudo Numrico da Circulao Marinha da Regio das Baas de Sepetiba e Ilha Grande (RJ) (Numerical Study od the Marine Circulation at Ilha Grande Bay- Rio de Janeiro - Brazil). MSc. dissertation, Oceanographic Institute - University So Paulo, Brasil, 1999Fragoso, M.R.; Torres, A.R. and Neto, A.C.L., Modelling Ballast Water Discharges. Ballast Water News,8, 2002Franks, P. J. S. and C. Chen, A 3-D prognostic numerical model study of the Georges Bank ecosystem. Part II: biological-physical model. Deep-Sea Res., II, 48, 457-482, 2001Furuichi, N., T. Hibiya., and Y. Niwa, Model-predicted distribution of wind-induced internal wave energy in the world's oceans. J. Geophys. Res., 113, C09034, 10.1029/2008JC004768, 2008Galperin, B. and G. L. Mellor, A time-dependent, three-dimensional model of the Delaware Bay and River. Part 1: Description of the model and tidal analysis. Estuarine, Coastal and Shelf Sci., 31, 231-253, 1990Galperin, B. and G. L. Mellor, A time-dependent, three-dimensional model of the Delaware Bay and River. Part 2: Three-dimensional flow fields and residual circulation. Estuarine, Coastal and Shelf Sci., 31, 255-281, 1990Galperin, B., A. F. Blumberg and R. H. Weisberg, The importance of density driven circulation in well mixed estuaries: The Tampa Bay experience. Estuarine and Coastal Modeling, ASCE, 332-341, 1992Galperin, B., L. H. Kantha, S. Hasid, and A. Rosati, A Quasi-equilibrium turbulent energy model for geophysical flows. J. Atmos. Sci., 45, 55-62, 1988Gan, J. and J. S. Allen, A modeling study of shelf circulation off northern California in the region of the Coastal Ocean Dynamics Experiment: Response to relaxation of upwelling winds. J. Geophys. Res., 107(C9), 10.1029/200JC000768, 2002Gan, J. and J. S. Allen, On open boundary conditions for a limited-area coastal model off Oregon. Part 1: Response to idealized wind forcing. Ocean Modelling, 8(1-2), 115-133, 2005Gan, J. and J. S. Allen, Modeling upwelling circulation off the Oregon coast. J. Geophys. Res., 110, C10S07, 10.1029/2004JC002692, 2005Gan, J., and J. S. Allen, A modeling study of shelf circulation off northern California in the region of the Coastal Ocean Dynamics Experiments, 2, Simulations and comparisons with observations. J. Geophys. Res., 107, 10.1029/2001JC001190, 2002Gan, J., H. Li, E. N. Curchitser and D. B. Haidvogel, Modeling South China Sea circulation: Response to seasonal forcing regimes. J. Geophys. Res., 111, C06034, 10.1029/2005JC003298, 2006Gan, J., J. S. Allen and R. M. Samelson, On open boundary conditions for a limited-area coastal model off Oregon. Part 2: Response to wind forcing from a regional mesoscale atmospheric model. Ocean Modelling, 8(1-2), 155-173, 2005Gan, J., L. A. Mysak and D. N. Strub, Simulation of the South Atlantic Ocean circulation and its seasonal variability. J. Geophys. Res., 103(C5), 10,241-10,251, 1998Garvine, R. W., Penetration of buoyant coastal discharge onto the continental shelf: A numerical model experiment. J. Phys. Oceanogr., 29(8), Part 2, 1892-1909, 1999Gastgifvars, M, S. M. Navarra, L. Funkquist and V. Huess, Performance of operational systems with respect to water level forecasts in the Gulf of Finland. Ocean Dynamics, 58(2), 139-153, 2008Genin, A., B. Lazar, and S. Brenner, Vertical mixing and coral death in the Red Sea following the eruption of Mt. Pinatubo. Nature, 377, 507-510, 1995Ghelfibbs, M. T., J. H. Middleton and P. Marchesiello, Baroclinic response of Sydney shelf waters to local wind and deep ocean forcing. J. Phys. Oceanogr., 28, 178-190, 1998Ghisolfi, R. D. and W. D. McKee, The effects of the alongshore wind stress on the top-to-bottom front along the Southern Brazilian coast: a two-dimensional modelling approach. Cont. Shelf Res., 23(14-15), 1401-1424, 2003Ghisolfi, R. D.,, Oceanic fronts off the Southern Brazilian coast. PhD thesis, The University of New South Wales, 188 pages, 2001Gillibrand, P. A. and T. L. Amundrud, A numerical study of the tidal circulation and buoyancy effects in a Scottish fjord: Loch Torridon. J. Geophys. Res., 112, C05030, 10.1029/2006JC003806, 2007Gillibrand, P. A., W. R. Turrell and A. J. Elliot, Deep-water renewal in the upper basin Loch Sunart, a Scottish Fjord. J. Phys. Oceanog., 25, 1488-1503, 1995Greatbatch, R. J. and G. L. Mellor, An overview of coastal ocean models, In: Coastal Ocean Prediction. Coastal and Estuarine Studies, Vol. 56, C. N. K. Mooers (Ed.), American Geophysical Union, Washington, DC, 31-57, 1999Greatbatch, R. J. and Y. Lu, Relaxing the Boussinesq approximation in ocean circulation models. J. Atm. Ocean. Tech., 18, 1911-1923, 2001Grieco, L., L.-B. Tremblay and E. Zambianchi, A hybrid approach to transport processes in the Gulf of Naples: an application to phytoplankton and zooplankton population dynamics. Cont. Shelf Res., 25(5-6), 711-728, 2005Grieco, L., L.-B. Tremblay and E. Zambianchi, A hybrid approach to transport processes in the Gulf of Naples: an application to phytoplankton and zooplankton population dynamics. Cont. Shelf Res., 25(5-6), 711-728, 2005Griffies, S. M., C. Boning, F. O. Bryan, E. P. Chassignet, R. Gerdes, H. Hasumi, A. Hirst, A.-M., Treguier and D. Webb, Developments in ocean climate modelling. Ocean Modelling, 2 (3-4), 123-192, 2000Guo, X. and A. Valle-Levinson, Tidal effects on estuarine circulation and outflow plume in the Chesapeake Bay. Cont. Shelf Res., 27(1), 20-42, 2007Guo, X., A. Futamura and H. Takeoka, Residual currents in a semi-enclosed bay of the Seto Inland Sea, Japan. J. Geophys. Res., 109, C12008, 10.1029/2003JC002203, 2004Guo, X., H. Hukuda, Y. Miyazawa, and T. Yamagata, A Triply Nested Ocean Model for Simulating the KuroshioRoles of Horizontal Resolution on JEBAR. J. Phys. Oceanogr., 33(1), 146-169, 2003Haidvogel, D. B. and A. Beckmann, Numerical models of the coastal ocean. The Sea, K. H. Brink and A. R. Robinson (Eds.), Vol. 10, John Wileyand Sons, 457-482, 1998Haidvogel, D. B., J. Blanton, J. C. Kindle, and D. R. Lynch, Coastal ocean modeling: Processes and real-time systems. Oceanography, 13(1), 35-46, 2000Hakkinen, S., Models and their applications in polar oceanography. Polar Oceanography (ed. W.O. Smith), Pergamon Press, 1991Hakkinen, S., An Arctic source for the great salinity anomaly: a simulation of the Arctic ice-ocean system. J. Geophys. Res., 98, 16,379-16,410, 1993Hakkinen, S., Simulated interannual variability of the Greenland Sea deep water formation and its connection to surface forcing. J. Geophys. Res., 100, 4761-4770, 1995Hakkinen, S., Seasonal simulation of the Southern Ocean coupled ice- ocean system. J. Geophys. Res., 100(C11), 22,733-22,748, 1995Hakkinen, S., A simulation of thermohaline effects of a Great Salinity Anomaly. J. Clim., 12(6), 1781-1795, 1999Hakkinen, S., Variability of the simulated meridional heat transport in the North Atlantic for the period 1951-1993. J. Geophys. Res., 104(C5), 10,991-11,007, 1999Hakkinen, S., Decadal air-sea interaction in the North Atlantic based on observations and modeling results. J. Clim., 13(6), 1195-1219, 2000Hakkinen, S., Variability in sea surface height: A qualitative measure for the meridional overturning in the North Atlantic. J. Geophys. Res., 106(C7), 13,837-13,848, 2001Hakkinen, S., Freshening of the Labrador Sea surface waters in the 1990s: Another great salinity anomaly?. Geophys. Res. Lett., 29(24), 2232, 10.1029/2002GL015243, 2002Hakkinen, S., Surface salinity variability in the northern North Atlantic during recent decades. J. Geophys. Res., 107(C12), 10.1029/2001JC000812, 2002Hakkinen, S. and C. A. Geiger, Simulated low-frequency modes of circulation in the Arctic Ocean. J. Geophys. Res., 105(C3), 6549-6564, 2000Hakkinen, S. and C. Mauritzen, Modeling of the seasonal variability of the Arctic-North Atlantic system. The Atlantic Climate Change Program, Proc. from the PI meeting, 125-127, 1995Hakkinen, S. and G. L. Mellor, One hundred years of arctic ice cover variations as simulated by a one-dimensional coupled ice-ocean model. J. Geophys. Res., 95, 15,959-15,969, 1990Hakkinen, S. and G. L. Mellor, Modeling the seasonal variability of a coupled arctic ice-ocean system. J. Geophys. Res., 97, 20,285-20,304, 1992Hakkinen, S. and P. R. Rhines, Shifting surface currents in the northern North Atlantic. J. Geophys. Res., 114, C04005, doi: 10.1029/2008JC004883, 2009Hakkinen, S., G. L. Mellor and L. H. Kantha, Modeling deep convection. J. Geophys. Res., 97, 5389-5408, 1992Han, G., Three-dimensional modeling of tidal current and mixing quantities over the Newfoundland shelf. J. Geophys. Res., 105(C5), 11,407-11,422, 2000Harari, J. and M. Gordon, Numerical simulations of substances dispersion in the Port and Bay of Santos, under the influence of tides and winds. Review of Hydric Resources, 6(4), 115 - 131, 2001Harari, J. and R. de Camargo, Numerical simulation of the tidal propagation in the coastal region of Santos (Brazil, 24°S 46°W. Cont. Shelf Res., 23(16), 1597-1613, 2003Harari, J., R. Camargo, and M. Gordon, Numerical simulations of the hydrodynamics and the dispersion of substances in the coastal area of Santos (Brazil). ICECE 2000 - International Conference on Engineering and Computer Education, So Paulo, Brasil, September 2000, 4p (published in digital form), 2000Harari, J., R. Camargo, and P. L. Cacciari, Numerical modeling of tidal circulation in coastal areas of Southern Brazil. Afro-America Gloss News, publication of the Global Sea Level Observing System (GLOSS), sponsored by the International Oceanographic Commission (IOC), vol. 3 (1), 7-9, 1998Harding, J., R. Preller and R. Rhodes, Coastal ocean prediction at the Naval research Laboratory. Second Conference on Coastal Atmospheric and Oceanic Prediction and Processes, Jan. 11-16, 1998, Phoenix, AZ, American Meteorological Society, Boston, MA, 108-114, 1998Hareesh Kumar PV, Madhu Joshi, KV Sanilkumar, P Anand, AD Rao, K Anilkumar & CVK Prasada Rao, Growth and decay of the Arabian Sea mini warmpool during May 2000:Observations and simulations. Deep Sea Res., 10.1016/j.dsr.2008.12.004, 2009Haza,A. C., L. I. Piterbarg, P. Martin, T. M. Özgökmen and A. Griffa, A Lagrangian subgridscale model for particle transport improvement and application in the Adriatic Sea using the Navy Coastal Ocean Model. Ocean Modelling, 17(1), 68-91, 2007Häkkinen, S., Upper ocean T-S variations in the Greenland Sea and their association to climatic conditions. J. Geophys. Res., 112, C07004, 10.1029/2006JC003498, 2007Häkkinen, S., F. Dupont, M. Karcher, F. Kauker, D. Worthen, and J. Zhang, Model simulation of Greenland Sea upper-ocean variability. J. Geophys. Res., 112, C06S90, 10.1029/2006JC003687, 2007He, R. and R. H. Weisberg, West Florida Shelf Circulation and Temperature Budget for the 1999 Spring Transition. Continental Shelf Research,22, 719-748, 2002He, R. and R. H. Weisberg, Tides on the west Florida shelf. J. Phys. Oceanogr., 32(12), 3455-3473, 2002He, R. and R. H. Weisberg, A Loop Current intrusion case study on the West Florida Shelf. J. Phys. Oceanogr., 33, 465-477, 2003He, R. Y. and R. H. Weisberg, West Florida shelf circulation and temperature budget for the 1998 fall transition. Cont. Shelf Res., 23, 777-800, 2003He, R. Y., Y. G. Liu and R. H. Weisberg, Coastal ocean wind fields gauged against the performance of an ocean circulation model. Geophys. Res. Let., 31(14), L14303, 2004Hellweger, F. L., A. F. Blumberg, P. Schlosser, D. T. Ho, T. Caplow, U. Lall and H. H. Li, Transport in the Hudson estuary: A modeling study of estuarine circulation and tidal trapping. Estuaries, 27 (3), 527-538, 2004Henderson, S. M., J. S. Allen and P. A. Newberger, Toward modeling turbulent suspension of sand in the nearshore. J. Geophys. Res., 109, C06024, 10.1029/2003JC002240, 2004Herman A. and A. Jankowski, Wind- and density-driven water circulation in the Southern Baltic Sea - a numerical analysis. TASK Quarterly, vol. 5, No. 1, 29 - 58, 2001Herrington, T.O., M.S. Bruno and K.L. Rankin, The New Jersey Coastal Monitoring Network: A Real-Time Coastal Observation System. J. Mar. Env. Eng., 6, 69-82, 2000Herrmann, M., S. Somot, F. Sevault, C. Estournel and M. Deque, Modeling the deep convection in the northwest Mediterranean Sea using an eddy-permitting and an eddy-resolving model: case study of winter 1986-1987. J. Geophys. Res., 113, C04011, 10.1029/2006JC003991, 2008Herzfeld, M, Improving stability of regional numerical ocean models. Ocean Dynamics, 59(1), 21-46, 2009Hess, K. W., Orthogonal curvilinear grid generation. NOAA Technical Report, NOS OES, 48 pp., National Ocean Service, Coastal & Estuarine Oceanography Branch, Silver Spring, MD, 1995Heyman, W., B. Kjerfve and T. Ezer, Mesoamerican reef spawning aggregations help maintain fish population: A review of connectivity research and priorities for science and management. pp. 150-169. In: Grober-Dunsmore, R., and B.D. Keller, (Eds.), Caribbean connectivity: Implications for marine protected area management. Marine Sanctuaries Conservation Series ONMS-08-07, NOAA, Silver Spring, MD, 2008Hisaki, Y., and C. Imadu, Southward recirculation of the East China Sea Kuroshio west of Okinawa Island. J. Geophys. Res., 114, C06013, doi:10.1029/2008JC004943, 2009Hjøllo, S. S., M. D. Skogen and Svendsen, Exploring currents and heat within the North Sea using a numerical model. J. Mar. Sys., 78(1), 180-192, 2009Hodur, R. M., J. Pullen, J. Cummings, X. Hong, J. D. Doyle, P. Martin and M. A. Rennick, The coupled ocean/atmosphere mesoscale prediction system (COAMPS). Oceanography, 15, 88-98, 2002Holloway, Dupont, Golubeva, Hakkinen, et al (17 authors), Water properties and circulation in Arctic Ocean models. J. Geophys. Res., 112, C04S03, 10.1029/2006JC003642, 2007Holloway, P., A numerical model of internal tides with application to the Australian north west shelf. J. Phys. Oceanogr., 26, 21-37, 1996Holloway, P., A regional model of the semidiurnal internal tide on the Australian North West shelf. J. Geophys. Res., 106(C9), 19,625-19,638, 2001Holloway, P. E. and M. A. Merrifield,, On the Spring-neap variability and age of the internal tide at the Hawaiian Ridge. J. Geophys. Res., 108(C4), 10.1029/2002JC001486, 2003Hong, C. H., Simulation of sea water response in Deukryang Bay to Typhoon using the Princeton Ocean Model. J. Korean Soc. Oceanogr., 33, 53-63, 1998Hong, C. H., A three-dimensional numerical study of effects of typhoons on oceanographic condition in the Korea Strait. J. Korean Soc. Oceanogr., 34(2), 73-85, 1999Hong, C. H. and Y.Q. Choi, The response of temperature and velocity fields to M2 tide in Deukryang Bay in the southern sea of Korea. J. Korean Fisher. Soc. 30, 667-678, 1997Hong, C.-H. and J.-H. Yoon, A three-dimensional numerical simulation of Typhoon Holly in the northwestern Pacific Ocean. J. Geophys. Res., 108(C8), 10.1029/2002JC001563, 2003Hong, C.H., On the circulation in the Jinhae Bay using the Princeton Ocean Model. I. Characteristics in vertical-tidal motion. J. Korean Fisher. Soc. J. Fish. Sci. Tech. 1(2), 168-179, 1998Hong, X., P. J. Martin, S. Wang, C. Rowley, High SST variability south of Martha's Vineyard: Observation and modeling study. J. Mar. Sys., 78, 59-76, 2009Hordoir, R., K. D. Nguyen and J. Polcher, Simulating tropical river plumes, a set of parameterizations based on macroscale data: A test case in the Mekong Delta region. J. Geophys. Res., 111, C09036, 10.1029/2005JC003392, 2006Horsburgh K. J. and A. E. Hill, A three-dimensional model of density-driven circulation in the Irish Sea. J. Phys. Oceanogr., 33, 343-365, 2003Horton, C. W. and M. A. Clifford, A shallow water analysis and forecast system. Coastal Ocean Prediction, Coastal and Estuarine Studies, Vol. 56, C. N. K. Mooers (Ed.), American Geophysical Union, Washington, DC, 223-276, 1999Horton, C., M. Clifford, J. Schmitz, and B. Hester, SWAFS: A shallow water analysis and forecast system overview and status report. Naval Oceanogr. Office, Ocean Modeling Devision, Stennis Space Center, MS, 53pp, 1994Horton, C., M. Clifford, J. Schmitz, and L. H. Kantha, A real-time oceanographic nowcast/forecast system for the Mediterranean Sea. J. Geophys. Res., 102(C11), 25,123-25,156, 1997Hoteit, I., G. Korres and G. Triantafyllou, Comparison of extended and ensemble based Kalman filters with low and high resolution primitive equation ocean models. Nonlinear Proc. Geophys., 12 (5), 755-765, 2005Hoteit, I., G. Triantafyllou and G. Petihakis, Towards a data assimilation system for the Cretan Sea ecosystem using a simplified Kalman filter. J. Mar. Sys., 45, 3-4, 159-171, 2004Hsin, Y.-C., C.-R. Wu and P.-T. Shaw, Spatial and temporal variations of the Kuroshio east of Taiwan, 1982-2005: A numerical study. J. Geophys. Res., 113, C04002, 10.1029/2007JC004485, 2008Hsu, H.-M., L.-Y. Oey, W. Johnson, C. Dorman and R. Hodour, Model wind over the central and southern California coastal ocean. Mon. Wea. Rev., 135, 1931-1944., 2007Hu, J. and S. Li, Modeling the mass fluxes and transformations of nutrients in the Pearl River Delta, China. J. Mar. Sys., 78(1), 146-167, 2009Huang, C.-J. and F. Qiao, Wave-turbulence interaction and its induced mixing in the upper ocean. J. Geophys. Res., in press, 2009Huang, H., C. Chen, G. W. Cowles, C. D. Winant, R. C. Beardsley, K. S. Hedstrom, and D. B. Haidvogel, FVCOM validation experiments: Comparisons with ROMS for three idealized barotropic test problems. J. Geophys. Res., 113, C07042, 10.1029/2007JC004557, 2008Hkkinen, S. and A. Proshutinsky, Freshwater content variability in the Arctic Ocean. J. Geophys. Res., 109(C3), 10.1029/2003JC001940, 2004Ingvaldsen, R. B., L. Asplin and L. Harald, Velocity field of the western entrance to the Barents Sea. J. Geophys. Res., 109(C3), 10.1029/2003JC001811, 2004Ioualalen, M,, Y. Wakata, Y. Kawahara, et al., Variability of the sea surface salinity (SSS) in the western tropical Pacific: On the ability of an OGCM to simulate the SSS, and on the sampling of an operating merchant ship SSS network. J. Oceanogr., 59(1), 105-111, 2003Isachsen, P. E., J. H. LaCasce, C. Mauritzen and S. Hkkinen, Wind-Driven Variability of the Large-Scale Recirculating Flow in the Nordic Seas and Arctic Ocean. J. Phys. Oceanogr., 33(12), 25342550, 2003Isobe, A., Ballooning of River-Plume Bulge and Its Stabilization by Tidal Currents.. J. Phys. Oceanogr., 35(12), 2337–2351, 2005Isobe, A. and R. C. Beardsley, An estimate of the cross-frontal transport at the shelf break of the East China Sea with the Finite Volume Coastal Ocean Model. J. Geophys. Res., 111, C03012, 10.1029/2005JC003290, 2006Itoh, S. and T. Sugimoto, Numerical experiments on the movement of a warm-core ring with the bottom slope of a western boundary. J. Geophys. Res., 106(C11), 26,851-26,862, 2001Ives, D. C., and R. M. Zacharias, Conformal mapping and orthogonal grid generation. AIAA/SAE/ASME/ASEE 23rd Joint Propulsion Conf., June 29- July 2, 1987, San Diego, Paper No. AIAA-87-2057, 11pp, 1987Jacobs, G. A., Sea surface height variations in the Yellow and East China Seas, 1, Linear response to local wind stress. J. Geophys. Res., 103(C9), 18,459-18,477, 1998Jacobs, G. A., H. B. Hur and S. K. Riedlinger, Yellow and East China Seas response to winds and currents. J. Geophys. Res., 105(C9), 21,947-21,968, 2000Jacobs, G. A., W. J. Teague, S. K. Riedlinger, R. H. Preller and J. P. Blaha, Sea surface height variations in the Yellow and East China Seas, 2, SSH variability in the weekly and semiweekly bands. J. Geophys. Res., 103(C9), 18,479-18,496, 1998Jahnke, R. and D. Jahnke (Eds.), Coastal Ocean Processes, Special issue. Oceanography, Vol. 21, No. 4, December, 2008Jan, S. and C.-T. Chen, Potential biogeochemical effects from vigorous internal tides generated in Luzon Strait: A case study at the southernmost coast of Taiwan. J. Geophys. Res., 114, C04021, doi:10.1029/2008JC004887, 2009Jan, S., C. Chern, J. Wang, and S. Chao, Generation of diurnal K1 internal tide in the Luzon Strait and its influence on surface tide in the South China Sea. J. Geophys. Res., 112, C06019, 10.1029/2006JC004003, 2007Jankowski , A., Variability of coastal water hydrodynamics in the southern Baltic - hindcast modelling of an upwelling event along the Polish coast . Oceanologia, 44(4), 395-418, 2002Jankowski, A., Wind-induced variability of hydrological parameters in the coastal zone of the Southern Baltic Sea - a numerical study. Oceanol. Stud., 29(3), 5-34, 2000Jankowski, A., Application of a sigma-coordinate baroclinic model to the Baltic Sea. Oceanologia, 44(1), 59-80, 2002Jankowski, A., Variability in the saline water exchange between the Baltic and the Gulf of Gdansk by the sigma-coordinate model. OCEANOLOGIA, 45, 81-105, 2003Jensen, T. G., Computational benchmarks of IPRC ocean models. International Pacific Research Center Report SOEST 99-03, Univ. of Hawaii at Manoa, 15pp., 1999Jewell, P. W., R. F. Stallard, and G. L. Mellor, Numerical studies of bottom shear stress and sediment distribution on the Amazon continental shelf. J. Sediment Petrology, 63, 734-745, 1993Jiang, L. and R. W. Garwood, A numerical study of three-dimensional dense water plumes on a Southern Ocean continental slope. J. Geophys. Res., 100(C9), 18,471-18,488, 1995Jiang, L. and R. W. Garwood, Three-dimensional simulations of overflows on continental slopes. J. Phys. Oceanogr., 26, 1214-1233, 1996Jiang, L. and R. W. Garwood, Effects of topographic steering and ambient stratification on overflows on continental slopes: A model study. J. Geophys. Res., 103(C3), 5459-5476, 1998Jin, H., S. Raman and L. Xie, A numerical study of shelf ocean responses in the Gulf Strean region. Second Conference on Coastal Atmospheric and Oceanic Prediction and Processes, Jan. 11-16, 1998, Phoenix, AZ, American Meteorological Society, Boston, MA, 267-270, 1998Jin, H., S. Raman and L. Xie, A coupled regional ocean-atmosphere prediction system (ROAPS) and its application to coastal land-air-sea interaction in the Gulf Strean region. Second Conference on Coastal Atmospheric and Oceanic Prediction and Processes, Jan. 11-16, 1998, Phoenix, AZ, American Meteorological Society, Boston, MA, 271-274, 1998Jin, M, C. Deal, J. Wang and C. P. McRoy, Response of lower trophic level production to long-term climate change in the southeastern Bering Sea. J. Geophys. Res., 114, C04010, doi:10.1029/2008JC005105, 2009Jin, M. and J. Wang, Interannual variability and sensitivity study of the ocean circulation and thermohaline structure in Prince William Sound, Alaska. Cont. Shelf Res., 24(3), 393-411, 2004Jin, M., C. Deal, J. Wang, N. Tanaka and M. Ikeda, Vertical mixing effects on the phytoplankton bloom in the southeastern Bering Sea midshelf. J. Geophys. Res., 111, C03002, 10.1029/2005JC002994, 2006Johns, N. L. and S. G. Monismith, Modeling the influence of wave-enhanced turbulence in a shallow tide- and wind-driven water column. J. Geophys. Res., 113, C03009, doi:10.1029/2007JC004246, 2008Johnson, M., S. Gaffigan, E. Hunke, and R. Gerdes, A comparison of Arctic Ocean sea ice concentration among the coordinated AOMIP model experiments. J. Geophys. Res., 112, C04S11, 10.1029/2006JC003690, 2007Johnston, T. M. S. and Merrifield, M. A., Internal tide scattering at seamounts, ridges, and islands. J. Geophys. Res., 108(C6), 10.1029/2002JC001528, 2003Johnston, T. M. Shaun; Merrifield, Mark A.; Holloway, Peter E., Internal tide scattering at the Line Islands Ridge. J. Geophys. Res., 108(C11), 10.1029/2003JC001844, 2003Jones, N. L. and S. G. Monismith, Modeling the influence of wave-enhanced turbulence in a shallow tide- and wind-driven water column. J. Geophys. Res., 113, C03009, 10.1029/2007JC004246, 2008Jungclaus, J. H., A three dimensional simulation of the formation of anticyclonic lenses (meddies) by the instability of an intermediate depth boundary current. J. Phys. Oceanogr., 29, 1579-1598, 1999Jungclaus, J. H. and G. L. Mellor, A three dimensional model study of the Mediterranean outflow. J. Mar. Sys., 24, 41-66, 2000Jungclaus, J. H. and M. Vanicek, Frictionally modified flow in a deep ocean channel: Application to the Vema Channel. J. Geophys. Res., 104(C9), 21,123-21,136, 1999Jungclaus, J. H., J. Hauser and R. H. Kase, Cyclogenesis in the Denmark Strait overflow plume. J. Phys. Oceanogr., 31, 3214-3229, 2001Kabbara, N, R. Sorgente, S. Natale, D. R. Hayes, and G. Zodiatis, High-resolution nested model for the Lebanese coastal area, Eastern Mediterranean: implementation and climatological runs. Ocean Sci. Discussions, 3, 373-396, 2006Kagimoto, T. and T. Yamagata, Seasonal transport variations of the Kuroshio: An OGCM simulation. J. Phys. Oceanogr., 27, 403-418, 1997Kamenkovich, V. M., On the divergence-free finite-difference approximation to the momentum advection in curvilinear orthogonal coordinates. Ocean Modeling, 1, 95-99, 1999Kamenkovich, V. M., W. H. Burnett, A. L. Gordon and G. L. Mellor, The Pacific/Indian Ocean pressure difference and its influence on the Indonesian Sea circulation: Part II- The study with specified sea surface heights. J. Mar. Res., 61, 613-634, 2003Kanarska Y., Maderich V., A non-hydrostatic numerical model for calculating free-surface stratified flows. Ocean Dynamics 53, 176–185, 2003Kanarska Y., Maderich V., Modelling of seasonal exchange flows through the Dardanelles Strait. Est. Coast. Shelf Sci., 79, 449-458, 2008Kaneko A., Remedies for artificial diapycnal mixing in a sigma co-ordinated model of Tokyo bay. Inter. J. Numer. Methods Fluids, 36, 329-349, 2001Kang, H.-S. and C. N.K. Mooers, Diagnoses of simulated water-mass subduction/formation/transformation in the Japan/East Sea (JES). Deep Sea Res., 52(11-13), 1505-1524, 2005Kanth, L. H., Comments on “Oscillatory Bottom Boundary Layers". J. Phys. Oceanogr., 35(7), 1297–1300, 2005Kantha, L., A note on the decay rate of swell. Ocean Modelling, 11(1-2), 167-173, 2006Kantha, L., Barotropic tides in the Gulf of Mexico, In: Circulation in the Gulf of Mexico: Observations and Models, W. Sturges and A. Lugo-Fernandez (Eds.). Geophys. Monograph Ser., Vol. 161, pp. 159-164, AGU, Washington, DC, 2005Kantha, L. H., Barotropic tides in the global oceans from a nonlinear tidal model assimilating altimetric tides, 1, Model description and results. J. Geophys. Res., 100(C12), 25,283-25,308, 1995Kantha, L. H., A general ecosystem model for applications to primary productivity and carbon cycle studies in the global oceans. Ocean Modelling, 6(3-4), 285-334, 2004Kantha, L. H. and C. A. Clayson, On the effect of surface gravity waves on mixing in the oceanic mixed layer. Ocean Modelling, 6(2), 101-124, 2004Kantha, L. H., and C. A. Clayson, An improved mixed layer model for geophysical applications. J. Geophys. Res., 99(C12), 25,235-25,266, 1994Kantha, L. H., and C. A. Clayson, Numerical Models of Oceans and Oceanic Processes. Academic Press, 940 pp., 2000Kantha, L. H., and C. A. Clayson, Small Scale Processes in Geophysical Fluid Flows. Academic Press, 888 pp., 2000Kantha, L. H., C. Tierney, J. W. Lopez, S. D. Desai, M. E. Parke and L. Drexler, Barotropic tides in the global oceans from a nonlinear tidal model assimilating altimetric tides, 2, Altimetric and geophysical implications. J. Geophys. Res., 100(C12), 25,309-25,317, 1995Kantha, L., J.-K. Choi, K. J. Schaudt and C. K. Cooper, A Regional Data-Assimilative Model for Operational Use in the Gulf of Mexico, In: Circulation in the Gulf of Mexico: Observations and Models, W. Sturges and A. Lugo-Fernandez (Eds.).. Geophys. Monograph Ser., Vol. 161, pp. 165-180, AGU, Washington, DC, 2005Kantha, L.H., A. Rosati, and B. Galperin, Effect of rotation on vertical mixing and associated turbulence in stratified fluids. J. Geophys. Res., 94(C4), 4843-4854, 1989Kantha, L.H., and A. Rosati, The effect of curvature on turbulence in stratified fluids. J. Geophys. Res., 95(C11), 20313-20330, 1990Kantha, L.H., and Mellor, A two-dimensional coupled ocean-ice model to the Bering sea marginal ice zone. J. Geophys. Res., 94(C8), 10921-10935, 1989Kara, A. B., C. N. Barron, P. J. Martin, L. F. Smedstad and R. C. Rhodes, Validation of interannual simulations from the 1/8° global Navy Coastal Ocean Model (NCOM) . Ocean Modelling, 10, 2005Kara, A. B., C. N. Barron, P. J. Martin, L. F. Smedstad and R. C. Rhodes, Validation of interannual simulations from the 1/8° global Navy Coastal Ocean Model (NCOM). Ocean Modelling, 11(3-4), 376-398, 2006Kara, Wallcraft, Martin and Chassignet, Performance of mixed layer models in simulating SST in the equatorial Pacific Ocean. J. Geophys. Res., 113, C02020, 10.1029/2007JC004250, 2008Kawaguchi, Y. and H. Mitsudera, Effects of along-shore winds on DSW formation beneath coastal polynyas: Application to the Sea of Okhotsk. J. Geophys. Res., 114, C10013, doi:10.1029/2008JC005041, 2009Keen, T. R. and S. E. Allen, The generation of internal waves on the continental shelf by Hurricane Andrew. J. Geophys. Res., 105(C11), 26,203-26,224, 2000Keen, T. R. and S. M. Glenn, Factors influencing model skill for hindcasting shallow water currents during Hurricane Andrew. J. Atmos. & Ocean Tech. 15, 221-236, 1998Keen, T. R., R. W. Gould, J.-F. Cayula, W. E. McBride, J. P. Blaha, and C. Rowley, A simple method of deriving three-dimensional temperature fields using remotely sensed and in situ data for application to numerical hydrodynamic models of estuaries and bays. J. Atmos. Ocean. Technol., 21(7), 1044-1058, 2004Keen, T. R., S. J. Bentley, W. C. Vaughan and C. A. Blain, The generation and preservation of multiple hurricane beds in the northern Gulf of Mexico. Marine Geol., 210(1-4), 79-105, 2004Kelley, J. G. W., H. J. Thiebaux, D. Chalikov, D. W. Behringer and B.Balasubramaniyan, Impact of data assimilation in the coastal ocean forecast system. Second Conference on Coastal Atmospheric and Oceanic Prediction and Processes, Jan. 11-16, 1998, Phoenix, AZ, American Meteorological Society, Boston, MA, 7-10, 1998Kelley, J. G. W., D. W. Behringer and H. J. Thiebaux, Description of the SST data assimilation system used in the NOAA Coastal Ocean Forecast System (COFS) for the U.S. east coast Version 3.2. NOAA/NCEP Technical Note, OMB Cont. No. 174, 49 pp.,, 1999Kelley, J. G. W., D. W. Behringer, H. J. Thiebaux and B. Balasubramaniyan, Assimilation of SST data into a real-time coastal ocean forecast system for the U.S. east coast. Weather and Forecasting, 17, 670-690, 2002Kelley, J. G. W., F. Aikman, L. C. Breaker and G. L. Mellor, Coastal ocean forecasts. Sea Technol., Vol. 38, No. 5, 10-17, 1997Kelley, J. G. W., J. S. Hobgood, K. W. Bedford, and D. Schwab, Generation of three-dimensional lake model forecasts for Lake Erie. Weather & Forecasting, 13, 659-687, 1998Kelley, J. G. W., L. C. Breaker, B. Balasubramaniyan, J. L. Miller and J. B. Zaitzeff, The importance of salinity in estimating the circulation in coastal areas such as the shelf region off Chesapeake Bay. Second Conference on Coastal Atmospheric and Oceanic Prediction and Processes, Jan. 11-16, 1998, Phoenix, AZ, American Meteorological Society, Boston, MA, 30-33, 1998Kelley, J., C.-C. Yen, K. Bedford, J. Hobgood and D. Schwab, Coupled Lake Erie Air-Sea, Storm Resolving Forecasts and Predictions, the Vien to Project. Proc. of the 3rd International Conference of Estuarine and Coastal Modeling, Oak Brook, Illinois, September 8-10, 1993, Amer. Soc. of Civil Engrs., New York, NY. pp. 202-215, 1993Kettle, A. J., and S. M. Turner, Upper ocean response to a summer gale south of Iceland: Importance of sea spray in the heat and freshwater budgets of storms. J. Geophys. Res., 112, C08011, 10.1029/2006JC004011, 2007Kikuchi, T., M. Wakatsuchi and M. Ikeda, A numerical investigation of the transport process of dense shelf water from a continental shelf to a slope. J. Geophys. Res., 104(C1), 1197-1210, 1999Kim, D.-M., N. Nakada, T. Horiguchi, H. Takada, H. Shiraishi and O. Nakasugi, Numerical simulation of organic chemicals in a marine environment using a coupled 3D hydrodynamic and ecotoxicological model. Mar. Pol. Bul., 48(7-8), 671-678, 2004Kim, K. O. and T. Yamashita, Storm surge simulation using wind-wave-surge coupling model. Journal of Oceanography, 64(4), 621-630, 2008Kim, K. O., H. S. Lee, T. Yamashita and B. H. Choi, Wave and storm surge simulations for Hurricane Katrina using coupled process based models. J. Civ. Eng., 12(1), 1-8, 2008Klein, P., A simulation of the effects of air-sea transfer variability on the structure of marine upper layers. J. Phys. Oceanogr., 10, 1824-1841, 1980Klein, P., A simulation of the effects of air-sea transfer variability on the structure of marine upper layers. J. Phys. Oceanogr., 10, 1824-1841, 1980Kliem, N. and J. D. Pietrzak, On the pressure gradient error in sigma coordinate ocean models: A comparison with laboratory experiment. J. Geophys. Res., 104(C12), 29,781-29,799, 1999Knutson, T.R., R.E. Tuleya, and I. Ginis,, Impact of CO2-warming on hurricane intensities as simulated in a hurricane ocean with ocean coupling. J. Climate, 14, p. 2458-2468, 2001Ko, D.S., R.H. Preller, G.A. Jacobs, T.Y. Tang and S.F. Lin, Transport reversals at Taiwan Strait during October and November 1999,. J. Geophys. Res., 108(C11), 10.1029/2003JC001836, 2003Kobayashi, S., J. H. Simpson, T. Fujiwarab and J. Kevin, idal stirring and its impact on water column stability and property distributions in a semi-enclosed shelf sea (Seto Inland Sea, Japan). Cont. Shelf Res., 26(11), 1295-1306, 2006Kontoyiannis, H., V. H. Kourafalou and V. Papadopoulos, Seasonal characteristics of the hydrology and circulation in the northwest Aegean Sea (eastern Mediterranean): Observations and modeling. J. Geophys. Res., 108(C9), 10.1029/2001JC001132, 2003Koropitan, A. F. and M. Ikeda, Three-dimensional modeling of tidal circulation and mixing over the Java Sea. Journal of Oceanography, Vol. 64, No. 1, 61-80, 2008Koropitan, A. F., Ikeda, M., Damar, A., and Yamanaka, Y, Influences of physical processes on the ecosystem of Jakarta Bay: a coupled physical – ecosystem model experiment. ICES Journal of Marine Science, 66: 336 – 348, 2009Korotenko, K. A., Chemical warfare munitions dumped in the Baltic Sea: Modeling of pollutant transport due to possible leakage. Oceanology, 43(1), 16-29, 2003Korotenko, K. A., Chemical warfare munitions dumped in the Baltic Sea: Modeling of pollutant transport due to possible leakage. Ocean Modelling, 13(3-4), 379-403, 2003Korotenko, K. A., Chemical warfare munitions dumped in the Baltic Sea: Modeling of pollutant transport due to possible leakage. Ocean Modelling, 13(3-4), 379-403, 2003Korotenko, K. A., R. M. Mamedov, A. E. Kontar and L. A. Korotenko, Particle tracking method in the approach for prediction of oil slick transport in the sea: modelling oil pollution resulting from river input. J. Mar. Sys., 48(1-4), 159-170, 2004Korotenko, K.A. and A.V. Sentchev, 2004 To the Formation of Ichthyoplankton Assemblages Along the Eastern English Channel French Coast: Numerical Approach . Oceanology, 44(5). 729-741., 2004Korotenko, K.A. and P.M. Mamedov, Modeling oil spill transport processes in sea coastal waters of the Caspian Sea. Oceanology (Engl. Edition by AGU), 40(1), 34-45. , 2001Korotenko, K.A. and R.M. Mamedov, Modeling formation of a thermal plume in the sea coastal zone. Oceanology (Engl. Edition by AGU), 40(4),15-26, 2000Korotenko, K.A. R.M. Mamedov and C.N.K. Mooers, Prediction of the Transport and Dispersal of Oil in the South Caspian Sea Resulting from Blowouts. Journal of Environmental Fluid Mechanics, 1 (4): 383-414, 2001Korotenko, K.A., R.M. Mamedov and C.N.K. Mooers, Prediction of the Dispersal of Oil Transport in the Caspian Sea Resulting from a Continuous Release . Spill Sci. Technol. Bull., 6 (5/6), pp.323-329, 2001Korres, G, K. Nittis, I. Hoteit and G. Triantafyllou, A high resolution data assimilation system for the Aegean Sea hydrodynamics. J. Mar. Sys., 77(3), 325-340, 2009Korres, G., I Hoteit and G. Triantafyllou, Data assimilation into a Princeton Ocean Model of the Mediterranean Sea using advanced Kalman filters. J. Mar. Sys., 64, doi:10.1016/j.jmarsys.2006.09.005, 2007Kourafalou, V. H., L.-Y. Oey, J. D. Wang, and T. N. Lee, The fate of river discharge on the continental shelf, 1, Modeling the river plume and the inner shelf coastal current. J. Geophys. Res., 101(C2), 3415-3434, 1996Kourafalou, V. H., L.-Y. Oey, J. D. Wang, and T. N. Lee, The fate of river discharge on the continental shelf, 1, Modeling the river plume and the inner shelf coastal current. . Geophys. Res., 101(C2), 3415-3434, 1996, 1996Kourafalou, V. H., T. N. Lee, L.-Y. Oey, and J. D. Wang, The fate of river discharge on the continental shelf, 2, Transport of coastal low-salinity water under realistic wind and tidal forcing. J. Geophys. Res., 101(C2), 3415-3434, 1996Kourafalou, V. H., Y. G. Savvidisb, Y. N. Krestenitisb and C. G. Koutitasb, Modelling studies on the processes that influence matter transfer on the Gulf of Thermaikos (NW Aegean Sea). Cont. Shelf Res., 24(2), 203-222, 2004Kourafalou, V.H., Process studies on the Po River plume, North Adriatic Sea. J. Geophys. Res., 104(C12), 29,963-29,985, 1999Kourafalou, V.H., A 3-D model of the Po River plume. Ecosystems Research Report, the Adriatic Sea. EU/Environment Series, Brussels, 1998Kourafalou, V.H., River plume development in semi-enclosed Mediterranean regions: North Adriatic Sea and Northwestern Aegean Sea. J. Mar. Sys., 30, 181-205, 2001Kourafalou, V.H. and M. Zavatarelli, Shelf - open sea exchanges in the Adriatic Sea. 36 pp. IMGA - CNR Techn. Report 10-97, 1997Kowalewska-Kalkowska H. Kowalewski M., Hydrological forecasting in the Oder Estuary using a three-dimensional hydrodynamic model. Hydrobiologia 554(1): 47 – 55, 2006Kowalewska-Kalkowska H. Kowalewski M.,, Operational hydrodynamic model for forecasting of extreme Hydrological events in the Oder Estuary. Nordic Hydrology 36(4) 411-422, 2005Kowalewski M, The influence of the Hel upwelling (the Baltic Sea) on nutrient concentration and primary production – the results of an ecohydrodynamic model. Oceanologia, 47 (4), 567–590, 2005Kowalewski M., A three-dimensional, hydrodynamic model of the Gulf of Gdansk. Oceanol. Stud., 26 (4), 77–98, 1997Kowalewski M., Ostrowski M, Coastal up- and downwelling in the southern Baltic. Oceanologia, 47 (4), 453–475, 2005Kurapov, A. L., J. S. Allen, G. D. Egbert, and R. N. Miller, Modeling bottom mixed layer variability on the mid-Oregon shelf during summer upwelling.. J. Phys. Oceanogr., 35(9), 1629–1649., 2005Kurapov, A. L., G. D. Egbert, J. S. Allen, R. N. Miller, S. Y. Erofeeva, and P. M. Kosro, The M2 Internal Tide off Oregon: Inferences from Data Assimilation. J.Phys. Oceanogr., 33(8), 1733<96>1757, 2003Kurapov, A. L., J. S. Allen, G. D. Egbert, R. N. Miller, P. M. Kosro, M. D. Levine, T. Boyd, and J. A. Barth, Assimilation of moored velocity data in a model of coastal wind-driven circulation off Oregon: Multivariate capabilities. J. Geophys. Res., 110, C10S08, doi:10.1029/2004JC002493, 2005Kurapov, A. L., J. S. Allen, G. D. Egbert, R. N. Niiler, P. M. Korso, M. D. Levine, T. Boyd and J. A. Barth, Assimilation of moored velocity data in a model of coastal wind-driven circulation off Oregon: Multivariate capabilities. J. Geophys. Res., 110, C10S08, 10.1029/2004JC002493, 2005Kurapov, L. A., J. S. Allen, G. D. Egbert, R. N. Miller, P. M. Korso, M. Levine and T. Boyd, Distant effect of assimilation of moored currents into a model of the coastal wind-driven circulation off Oregon. J. Geophys. Res., 110, C02022, 10.1029/2003JC002195, 2005Kuzmic, M., I. Janekovic, J. W. Book, P. J. Martin and J. D. Doyle, Modeling the northern Adriatic double-gyre response to intense bora wind: A revisit. J. Geophys. Res., 112, C03S13, 10.1029/2005JC003377, 2007Kuzmić, M., I. Janeković, W. Jeffrey, P. Martin and J. D. Doyle, Modeling the northern Adriatic double-gyre response to intense bora wind: A revisit. J. Geophys. Res., 111, C03S13, 10.1029/2005JC003377, 2006LaCasce, J. H. and H. Engedahl, Statistics of low frequency currents over the western Norwegian shelf and slope II: Model. Ocean Dynamics, 55(3-4), 222-237, 2005Lakhan, V. C. (Editor), Advances in Coastal Modeling. Elsevier Oceanography Ser., 67, Elsevier, 616 pp., 2003Large, W.G., and G.B. Crawford, Observations and simulations of upper-ocean response to wind events during the Ocean Storms Experiment. J. Phys. Oceanogr., 25 (11), 2831-2852, 1995Larson, M., R. Bellanca, L. Jonsson, et al., A model of the 3D circulation, salinity distribution, and transport pattern in the pearl river estuary, China. J. Coastal Res., 21 (5), 896-908, 2005Lascaratos A., K.Nittis and L.Perivoliotis, LIW formation and spreading : a 3-D numerical study. Rapp. Comm. int. Mer Medit., 34, 1995Lascaratos, A. and K. Nittis, A high-resolution three-dimensional numerical study of intermediate water formation in the Levantine Sea. J. Geophys. Res., 103(C9), 18,497-18,511, 1998Lascaratos, A., W. Roether, K. Nittis and B. Klein, Recent changes in deep water formation and spreading in the eastern Mediterranean Sea: a review. Prog. Oceanogr., 44, 5-36, 1999Lü, X. and F. Qiao, Distribution of sunken macroalgae against the background of tidal circulation in the coastal waters of Qingdao, China, in summer 2008.. Geophys. Res. Let., 35, L23614, doi:10.1029/2008GL036084, 2008Lü, X., F. Qiao, C. Xia, J. Zhu and Y. Yuan, Upwelling off Yangtze River estuary in summer. J. Geophys. Res., 111, C11S08, 10.1029/2005JC003250, 2006Le Hénaff, M., P. De Mey and P. Marsaleix, Assessment of observational networks with the Representer Matrix Spectra method—application to a 3D coastal model of the Bay of Biscay. Ocean Dynamics, 59(1), 3-20, 2009Lee, C. M. et al. (19 authors), Northern Adriatic response to a wintertime Bora wind event. EOS, Trans., 86(16), 157-165, 2005Lee, C., D. J. Schwab and N. Howley, Sensitivity analisis of sediment resuspension parameters in coastal area of southern Lake Michigan. J. Geophys. Res., 110, C03004, 10.1029/2004JC002326, 2005Lee, C., D. Schwab, D. Belesky, J. Stroud and B. Lesht, Numerical modeling of mixed sediment resuspension, transport, and deposition during the March 1998 episodic events in southern Lake Michigan. J. Geophys. Res., 112, C02018, 10.1029/2005JC003419, 2007Lee, Hyun-Chul and G. L. Mellor, Numerical simulation of the Gulf Stream System.: the Loop Current and the deep circulation. J. Geophysical Res., 108, C2, 3043,dol:10.1029/2001JC001074, 2003Lee, Hyun-Chul and G. L. Mellor, Numerical simulation of the Gulf Stream and the deep circulation. J. Oceanography, A-0201, 2003Lee, Hyun-Chul and G. L. Mellor, Numerical simulation of the Gulf Stream system: the Gulf Stream and the deep circulation. AGU Ocean Science, Eos, 80290, 2000Lee, S.-H. and R. C. Beardsley, Influence of stratification on residual tidal currents in the Yellow Sea. J. Geophys. Res., 104(C7), 15,679-15,701, 1999Legg, Chang, Chassignet, Danabasoglu, Ezer, et al. (10 authors), Improving oceanic overflow representation in climate models: the Gravity Current Entrainment Climate Process Team. Bull. Amer. Met. Soc., 90(5), 657-670., 2009Leth, O. and G. Shaffer, A numerical study of the seasonal variability in the circulation off central Chile. J. Geophys. Res., 106(C10), 22,229-22,248, 2001Leth, O. and J. F. Middleton, A mechanism for enhanced upwelling off central Chile: Eddy advection. J. Geophys. Res., C12020, 10.1029/2003JC002129, 2004Leth, O. and J. F. Middleton, A numerical study of the upwelling circulation off central Chile: Effects of remote oceanic forcing. J. Geophys. Res., 111, C12003, 10.1029/2005JC003070, 2006Leth, O. and J. F. Middleton, A numerical study of the upwelling circulation off central Chile: Effects of remote oceanic forcing. J. Geophys. Res., 111, C12003, 10.1029/2005JC003070, 2006Leth, O. K., Ocean circulation in the eastern south Pacific: An observational and numerical modelling study. Ph.D Dissertation, Niels Bohr Institute for Astronomy, Physics and Geophysics,University of Copenhagen, 184pp., 2000Li, C., F. Qiao, Z. Pan, W. Zhao and Z. Wan, Investigation of wind, wave, current extreme parameter of the Wenchang area in the west of the South China Sea, analysis of conditional extreme values. Proceedings of the international conference on Marine Disasters Forecast and Reduction, China Ocean Press, 66-76, 1998Li, L. and R. Wu, Comment on “Circulation in the South China Sea during summer 2000 as obtained from observations and a generalized topography-following ocean model” by H. Wang et al.. J. Geophys. Res., 111, C03007, 10.1029/2004JC002751, 2006Li, Y., H. Xue, and J. M. Bane, Air-Sea Interactions during the Passage of a Winter Storm over the Gulf Stream: A 3D Coupled Atmosphere-Ocean Model Study. J. Geophys. Res., 107, C11, 3200, doi:10.1029/2001JC001161, 2002Li, Z. and R. H. Weisberg, West Florida Shelf response to upwelling favorable wind forcing: Kinematics. J. Geophys. Res., 104(C6), 13,507-13,527, 1999Li, Z. and R. H. Weisberg, West Florida continental shelf response to upwelling favorable wind forcing, 2, Dynamics. J. Geophys. Res., 104(C10), 23,427-23,442, 1999Lima, I. D.; D. B. Olson, S. C. Doney, Biological response to frontal dynamics and mesoscale variability in oligotrophic environments: Biological production and community structure. 107(C8), 10.1029/2000JC000393, 2002Lima, J.A.M; Torres, A.R.T.; Fragoso, M.R.; Mehdi, N., OIL SPILL STUDY AT BAIA DE GUANABARA, BRAZIL. Proceedings of OMAE 2001 20th International Conference on Offshore Mechanics and Arctic Engineering 3rd -8th June, 2001 Rio de Janeiro, Brazil , 2001Lima,J.A.M., Oceanic Circulation on the Brazilian Shelf Break and Continental Slope at 22S. Ph.D. dissertation, University of New South Wales, Australia, 1998Lin, Xiaopei, S.-P. Xie, X. Chen and L. Xu, A well mixed warm water column in the central Bohai Sea in summer: Effects of tidal and surface wave mixing. J. Geophys. Res., 111, C11017, 10.1029/2006JC003504, 2006Liu Hao, Yin Baoshu, Annual cycle of carbon, nitrogen and phosphorus in the Bohai Sea: A model study.. Cont. Shelf Res., 2007, doi: 10.1016/j.csr.2007.01.015, 2007Liu, H, Yin, BS, Xu, YQ, et al., Numerical simulation of tides and tidal currents in Liaodong Bay with POM. Prog. Nat. Sci., 15 (1), 47-55, 2005Liu, H. and T. Ezer, Integration of Landsat imagery and an inundation model in flood assessment and predictions: A case study in Cook Inlet, Alaska. The 17th International Conference on Geoinformatics, IEEE Xplore Publ., 2009Liu, H., B. S. Yin, Y. Q. Xu and D. Z. Yang, Numerical simulation of tides and tidal currents in Liaodong Bay with POM. Prog. Natural Sci., 15 (1), 47-55, 2005Liu, J. T., S. Chao and R. T. Hsu, Numerical modeling study of sediment dispersal by a river plume. Cont. Shelf Res., 22(11-13), 1745-1773, 2002Liu, Y., R. H. Weisberg and C. N. K. Mooers, Performance evaluation of the self-organizing map for feature extraction. J. Geophys. Res., 111, C05018, 10.1029/2005JC003117, 2006Liu, Z., H. Wei, G. Liu and J. Zhang, Simulation of water exchange in Jiaozhou Bay by average residence time approach. Est. Coast. Shelf Sci., 61(1), 25-35, 2004Liu, Z., H. Yang and Q. Liu, Regional dynamics of seasonal variability in the South China Sea. J. Phys. Oceanogr., 31, 272-284, 2001Lou, J., D. J. Schwab, D. Belsky and N. Hawley, A model of sediment resuspension and transport dynamics in southern Lake Michigan. J. Geophys. Res., 105(C3), 6591-6610, 2000Lu, X., F. Qiao and C. Xia, Numerical simulation of tides and three dimensional tidal currents in Jiaozhou Bay by a movable land-sea boundary model. Acta Oceanol. Sinica, 30(4), 21-29, 2008Lu, X., F. Qiao, C. Xia and Y. Yuan, Tidally induced upwelling off Yangtze River estuary and in Zhejiang coastal waters in summer. Sci. China Ser. D- Earth Sci., 50(3), 462-473, doi: 10.1007/s11430-007-2050-0, 2007Lu, X., F. Qiao, C. Xia, G. Wang, Y. Yuan, Upwelling and surface cold patches in the Yellow Sea in summer:Effects of tidal mixing on the vertical circulation. Cont. Shelf Res., in press, 2009Luis, A. J. and H. Kawamura,, Dynamics and mechanism for sea surface cooling near the Indian tip during May 1997. J. Geophys. Res., 107(C11), 10.1029/2000JC000778, 2002Luong, P. V., C. P. Breshears, L. N. Ly, et al., Dual-level parallelism and multiblock grids in coastal ocean circulation modeling. In: PARALLEL AND DISTRIBUTED COMPUTING SYSTEMS, 361- 366, 2003Luong, P., C. P. Breshears, and L. N. Ly, Application of Multi-Block Grid and Dual-Level Parallelism in Coastal Ocean Circulation Modeling. SIAM J.on Scientific Computing}. (Submitted), 2000Luong, P., C. P. Breshears, and L. N. Ly, Dual-Level Parallelism and Multi-Block Grids. Thirteen International Conference on Parallel and Distributed Computing Systems. Proceedings, 361-366, 2000Luong, P., C. P. Breshears, and L. N. Ly, Dual-Level Parallelism Improves Load-Balance in Coastal Ocean Circulation Modeling. ERDC MSRC PET. Technical Report, Vicksburg, MS, 23 pp., 2000L X., F. Qiao, C. Xia, Y. Yuan, Tidally induced upwelling off Yangtze River estuary and in Zhejiang coastal waters in summer.. Sci. China Ser. D - Earth Sci., 50(3), 462-473, doi: 10.1007/s11430-007-2050-0., 2007Ly, L.N, and C.-S. Chiu, Coastal Acoustic Tomography Data Constraints Applied to A Coastal Ocean CirculationModel. Technical Report, Naval Postgraduate School, Monterey, CA, 1994Ly, L.N, P. Luong, T. Ezer and G.L. Mellor, Grid Sensitivity Study for the Mediterrainean Sea Using Grid Generation Techniques. Princeton University, 1994Ly, L.N., The Gulf of Mexico Response to Hurricane Frederic Simulated with the Princeton Numerical Ocean Circulation Model. Technical Report, Institute for Naval Oceanography, 42 pp., 1992Ly, L.N., A Numerical Study of Sea Level and Current Responses to Hurricane Frederic Using a Coastal Ocean Model for the Gulf of Mexico. Japan J. Phys. Oceanogr, 1994Ly, L.N. and L.H. Kantha, Hurricane Camille Shelf Wave Simulation Using a Numerical Ocean Circulation Model. Proceedings: Estuarine and Coastal Modeling, Second Int'l Conference/WE Div., Amer. Soc, of Civil Engineers, 586-593, 1991Ly, L.N. and L.H. Kantha, A Numerical Study of the Nonlinear Interaction of Hurricane Camille with the Gulf of Mexico Loop Current. Oceanologica Acta, Vol. 4, 341--348, 1993Ly, L.N., and O'Connor, W.P., Gulf Coast Hurricane Surge Simulations Using a Numerical Ocean Circulation Model. Proceedings of the Marine Technology Society Conference, Vol. II, Nov. 10-14, New Orleans, LA., 1236-1241, 1991Ly, L.N., O'Connor, W.P., and Paduan, J.D., A Barotropic Simulation of Semi-Diurnal and Diurnal Tides for the Monterey Bay Region, in: W.R. Blain and C.A. Brebbia (eds.). Hydraulic Engineering Software VIII, Hydrosoft 2000, Eighth International Conference Hydraulic Engineering Software, June 12-14, 2000, Lisbon, Portugal, WIT Press, Boston, MA, 155-169, 2000L, X., F. Qiao, C. Xia, J. Zhu, and Y. Yuan, Upwelling off Yangtze River estuary in summer. J. Geophys. Res., 111,C11S08, doi:10.1029/2005JC003250., 2006L, X., F. Qiao, G. Wang,C. Xia, and Y. Yuan, Upwelling off the west coast of Hainan Island in summer: Its detection and mechanisms.. Geophys. Res. Let., 35, L02604, doi:10.1029/2007GL032440., 2008M. A. Ahumada and A. Cruzado, Modeling of the circulation in the Northwestern Mediterranean Sea with the Princeton Ocean Model. Ocean Sci., 3, 77-89, 2007Ma, J. and F. Qiao, Simulation and analysis on the seasonal variability of salinity in the Yellow Sea. Chinese Journal of Oceanology and Limnology, 22 (3): 306-313, 2004Ma, J., F. Qiao, C. Xia and Y. Yang, Tidal effects on the temperature front in the Yellow Sea. Chinese Journal of Oceanology and Limnology, 22 (3): 314-321, 2004Ma, J., F. Qiao, C. Xia, and C. S. Kim, Effects of the Yellow Sea Warm Current on the winter temperature distribution in a numerical model. J. Geophys. Res., 111, C11S04, 10.1029/2005JC003171, 2006Macdonald, H. S., M. E. Baird, and J. H. Middleton, Effect of wind on continental shelf carbon fluxes off southeast Australia: A numerical model. J. Geophys. Res., 114, C05016, doi:10.1029/2008JC004946, 2009Maderich V., Talipova T., Grimshaw R., Pelinovsky E., Choi B.H., Brovchenko I., Terletska K., Kim D.C., Transformation of an interfacial solitary wave of elevation at a bottom step. Nonlinear Processes in Geophysics , 16, 33-42., 2009Maggiore A., Pinardi N., Zavatarelli M., Studio della variabilita' stagionale della circolazione Adriatica tramite simulazioni numeriche.[A numerical study of the Adriatic Sea circulation seasonal variability]. IMGA-CNR, Techn. Rep. 3/1998, 170 pp., 1998Malačič, V., and B. Petelin, Climatic circulation in the Gulf of Trieste (northern Adriatic). J. Geophys. Res., 114, C07002, doi:10.1029/2008JC004904, 2009Manda, A. and K. Matsuoka, Changes in Tidal Currents in the Ariake Sound Due to Reclamation. Estuaries and Coasts, 29(4), 645-652, 2006Manning, J. P., L-Y. Oey, D. Packer, J. Vitaliano, T. W. Finneran, K. W. You, and S. Fromm, Observations of bottom currents and estimates of resuspended sediment transport at the New York Bight 12-mile dumpsite. J. Geoph. Res., 99 (C5), 10,221-10,239, 1994Mantziafou A., Lascaratos A., An eddy resolving numerical study of the general circulation and deep-water formation in the Adriatic Sea. Deep Sea Res. I, Vol 51, 7, 251-292, 2004Mantziafou, A. and A. Lascaratos, An eddy resolving numerical study of the general circulation and deep-water formation in the Adriatic Sea. Deep Sea Res., Part I, 51(7), 921-952, 2004Marchesiello, P. and J. H. Middleton, Modeling the East Australia Current in the western Tasman Sea. J. Phys. Oceanogr., 30, 2956-2971, 2000Marie-Aude Pradal, Bertrand Millet, Spatial heterogeneity of wind forcing: application to artificial reef functioning influenced by the circulation in the Bay of Marseilles, France. Comptes Rendus Biologies, Volume 329, Issue 7, Pages 541-550, 2006Marsaleix, P., C. Estournel, V. Kondrachoff and R. Vehil, A numerical study of the formation of the Rhone River plume. J. Mar. Sys., 14, 99-115, 1998Martínez, J. A. and J. S. Allen, A Modeling Study of Coastal-Trapped Wave Propagation in the Gulf of California. Part I: Response to Remote Forcing. J. Phys. Oceanogr., 34(6), 1313–1331, 2004Martínez, J. A. and J. S. Allen, A Modeling Study of Coastal-Trapped Wave Propagation in the Gulf of California. Part II: Response to Idealized Forcing. J. Phys. Oceanogr., 34(6), 1332–1349, 2004Martin, P. J., Simulation of the mixed layer at OWS November and Papa with several models. J. Geoph. Res., 90 (C1), 903-916, 1985Martin, P. J., An ocean model applied to the Chesapeake Bay plome. In: Est. Coast. Mod.. Proc., 6th International Conf., 1055-1067, 1999Martin, P. J., G. Peggion and K. J. Yip, A comparison of several coastal ocean models. Naval research Laboratory, NRL/FR/7322-97-9672, 96pp, 1998Martin, P. J., J. W. Book, D. M. Burrage, C. D. Rowley, and M. Tudor, Comparison of model-simulated and observed currents in the central Adriatic during DART. J. Geophys. Res., 114, C01S05, doi:10.1029/2008JC004842, 2009Martin, P., J. W. Book and J. D. Doyle, Simulation of the northern Adriatic circulation during winter 2003. J. Geophys. Res., 111, C03S12, 10.1029/2006JC003511, 2006Martin, P., J. W. Book and J. D. Doyle, Simulation of the northern Adriatic circulation during winter 2003. J. Geophys. Res., 112, C03S12, 10.1029/2006JC003511, 2007Martin, T., and R. Gerdes, Sea ice drift variability in Arctic Ocean Model Intercomparison Project models and observations. J. Geophys. Res., 112, C04S10, 10.1029/2006JC003617, 2007Martinho, A. S. and M. L. Batteen, On reducing the slope parameter in terrain-following numerical ocean models. Ocean Modelling, 13(2), 166-175, 2006Martinho, A.S., and M.L.Batteen, On reducing the slope parameter in terrain-flollowing numerical ocean models. Ocean Modelling, 13, 166-175, 2006Marullo, S., E. Napolitano, R. Santoleri, B. Manca, and R. Evans, Variability of Rhodes and Ierapetra Gyres during Levantine Intermediate Water Experiment: Observations and model result. J. Geophys. Res., 108, (C9), 10.1029/2002JC001393, 2003Mask A. C. and R. H. Preller, A numerical simulation of the East Asian Seas in March 2002: Effect of vertical grid choice. Ocean Modelling, 18(2), 81-96, 2007Mask, A. C., J. J. O'Brien and R. Preller, Wind-driven effects on the Yellow Sea warm current. J. Geoph. Res., 103 (C13), 30,713-30,730, 1998Masson, D. and P.F. Cummins, Numerical simulations of a buoyancy-driven coastal countercurrent off Vancouver Island. J. Phys. Oceanog., Vol. 29, No. 3, 418-435, 1999Masson, D. and P.F. Cummins, Fortnightly modulation of the estuarine circulation in Juan de Fuca Strait. J. Mar. Res., 58, 439-463, 2000Masumoto, Y., T. Kagimoto, T. Yamagata, M. Yoshida, M. Fukuda and N. Hirose, Simulated circulation in the Indonesian Archipelago from a high resolution global ocean general circulation model on the Numerical Wind Tunnel,(Ext. Abs.). Super Computing '99, Portland, Oregon, 1999Matano, R. P., A numerical study of the Agulhas retroflection: The role of bottom topography. J. Phys. Oceanogr., 26, 2267-2279, 1996Matano, R. P., and E. D. Palma, On the upwelling of downwelling currents. J. Phys. Oceanogr., doi: 10.1175/2008JPO3783.1, 2008Mauritzen, C. and S. Hakkinen, Water mass formation in a model of the Arctic-North ocean and ice system. The Atlantic Climate Change Program,Proc. from the PI meeting, 115-120, 1996Mauritzen, C. and S. Hakkinen, Influence of sea ice on the meridional overturning cell in the North Atlantic. ACCP Notes, Vol. IV, No. 2, 6-10, 1997Mauritzen, C. and S. Hakkinen, Sensitivity of thermohaline circulation to sea-ice forcing in an Arctic-North Atlantic model. Geoph. Res. Let., 24, 3257-3260, 1997McClimans, T. A., J. D. Pietrzak , V. Huess, N. Kliem, J. H. Nilsen and B. O. Johannessen, Laboratory and numerical simulation of the Skagerrak circulation . Cont. Shelf Res., 20(9), 941-974, 2004Meier, H. E. M., On the parameterization of mixing in three-dimensional Baltic Sea models. J. Geophys. Res., 106, 30,997-31,016, 2001Mellor, Ocen modelling. J. Atmos. Ocean. Technol., 23(5), 100-110, 2006Mellor G.L., Durbin P.A., The structure and dynamics of the ocean surface mixed layer. J. Phys. Oceanogr. Vol.5. 718-728, 1975Mellor G.L., Mechoso C.R., Keto E., A diagnostic calculation of the general circulation of the Atlantic Ocean. Deep-Sea Res. Vol.29, 1171-1192, 1982Mellor GL, Users guide for a three-dimensional, primitive equation, numerical ocean model. Ocean Modelling, 13(3-4), 379-403, 1996Mellor, Donelan, Oey, A Surface Wave Model for Coupling with Numerical Ocean Circulation Models. J. Atmos. Ocean. Technol.,25, 1785–1807., 2008Mellor, G. L., Numerical simulation and analysis of the mean coastal circulation offCalifornia. Continental Shelf Res., 6, 689-713, 1986Mellor, G. L., Retrospect on oceanic boundary layer modeling and second moment closure. Parameterization of Small-Scale Processes, P. Muller and D. Henderson (Eds.), Proc. Aha Hulika'o Hawaiian Winter Workshop, University of Hawaii, 251-272, 1989Mellor, G. L., An equation of state for numerical models of ocean and estuaries. J. Atmos. Oceanic Technol., 8, 609-611, 1991Mellor, G. L., User's guide for a three-dimensional, primitive equation, numerical ocean model. 35 pp., Prog. in Atmos. and Ocean. Sci, Princeton University, 1992Mellor, G. L., Users guide for a three-dimensional, primitive equation, numerical ocean model (June 1996version). 38 pp., Prog. in Atmos. and Ocean. Sci, Princeton University, 1996Mellor, G. L., Introduction to Physical Oceanography. AIP Press, Woodbury,New York, 260pp, 1996Mellor, G. L., A coastal ocean forecasting system. Second Conference on Coastal Atmospheric and Oceanic Prediction and Processes, Jan. 11-16, 1998, Phoenix, AZ, American Meteorological Society, Boston, MA, J19-J20, 1998Mellor, G. L., Comments on 'On the utility and disutility of JEBAR'. J. Phys. Oceanogr., 29(8), Part 2, 2117-2118, 1999Mellor, G. L., One-dimensional, ocean surface layer modeling, a problem and a solution. J. Phys. Oceanogr., 31(3), 790-809, 2001Mellor, G. L., Oscillatory Bottom Boundary Layers. J. Phys. Oceanogr., 32(11), 3075-3088, 2002Mellor, G. L., Comments on "Stability of algebric non-equilibrium second-order closure models" by H. Burchard and E. Deleersnjder [Ocean Modelling 3 (2001) 33-50]. Ocean Modelling, 5, 193-194, 2003Mellor, G. L., The three-dimensional current and wave equations. J. Phys. Oceanogr., 33(9), 1978-1989, 2003Mellor, G. L., Some Consequences of the Three-Dimensional Current and Surface Wave Equations. J. Phys. Oceanogr., 35(11), 2291–2298, 2005Mellor, G. L., Reply (to Kanth, 2005). J. Phys. Oceanogr., 35(7), 1301-1301, 2005Mellor, G. L., Users guide for a three-dimensional. primitive equation, numerical ocean model. POM, 2003Mellor, G. L., The three dimensional, current and surface wave equations: a revision. J. Phys. Oceanogr., 38, 2587-2596.. J. Phys. Oceanogr., 38, 2587-2596, 2008Mellor, G. L. and A. F. Blumberg, Modeling vertical and horizontal diffusivities with the sigma coordinate system. Mon. Wea. Rev., 113, 1380-1383, 1985Mellor, G. L. and A. F. Blumberg, Wave breaking and ocean surface layer thermal response. J. Phys. Oceanogr., 34, 693-698, 2004Mellor, G. L. and S. Hakkinen, A review of coupled ice-ocean models. The Polar Oceans and Their Role in Shaping the Global Environment, O. M. Johannessen, R. D. Muench and J. E. Overland Eds., Geophysical Monograph 85, 21-32, Americam Geophysical Union, 1994Mellor, G. L. and T. Ezer, A Gulf Stream model and an altimetry assimilation scheme. J. Geophys. Res, 96, 8779-8795, 1991Mellor, G. L. and T. Ezer, Sea level variations induced by heating and cooling: An evaluation of the Boussinesq approximation in ocean models. J. Geophys. Res., 100(C10), 20,565-20,577, 1995Mellor, G. L. and T. Yamada, A hierarchy of turbulence closure models for planetary boundary layers. J. Atmos. Sci., 13, 1791-1806, 1974Mellor, G. L. and T. Yamada, Development of a turbulent closure model for geophysical fluid problems. Rev. Geophys., 20, 851-875, 1982Mellor, G. L. and X. H. Wang, Pressure compensation and the bottom boundary layer. J. Phys. Oceanogr., 26(10), 2214-2222, 1996Mellor, G. L., L. Y. Oey and T. Ezer, Sigma coordinate pressure gradient errors and the seamount problem. J. Atmos. Oceanic. Technol., 15(5), 1122-1131, 1998Mellor, G. L., S. Hakkinen, T. Ezer and R. Patchen, A generalization of a sigma coordinate ocean model and an intercomparison of model vertical grids. Ocean Forecasting: Conceptual Basis and Applications, N. Pinardi and J. D. Woods (Eds.), Springer, 55-72, 2002Mellor, G. L., T. Ezer and L. Y. Oey, The pressure gradient conundrum of sigma coordinate ocean models. J. Atmos. Oceanic. Technol., Vol. 11, No. 4, Part 2, 1126-1134, 1994Melsom, A., Realistic near-surface momentum mixing in the Princeton Ocean Model. Norwegian Met. Ins., Rep. 41, 22pp, 1996Melsom, A. and O. Saetra, Effects of Wave Breaking on the Near-Surface Profiles of Velocity and Turbulent Kinetic Energy. J. Phys. Oceanogr., 34(2), 490504, 2004Merrifield, M. A. and P. E. Holloway, Model estimates of M2 internal tide energetics at the Hawaiian Ridge. 107(C8), 10.1029/2001JC000996, 2002Merrifield, M. A., P. E. Holloway and T. M. S. Johnson, The generation of internal tides at the Hawaiian Ridge. Geophys. Res. Lett., 28, 559-562, 2001Mesias, J. M., R. P. Matano, and P. T. Strub, A numerical study of the upwelling circulation off central Chile. J. Geophys. Res., 106(C9), 19,611-19,623, 2001Mesias, J. M., R. P. Matano, and P. T. Strub, Dynamical analysis of the upwelling circulation off central Chile. J. Geophys. Res., 108(C3), 10.1029/2001JC001135, 2003Middleton, J. F., Wind-Forced Upwelling: The role of the surface mixed layer. J. Phys. Oceanogr., 30, 745-763, 2000Middleton, J. F., The coastal-trapped wave paddle and open boundary conditions. Ocean Modelling, 12(1-2), 224-236, 2006Middleton, J. F. and G. Platov, The mean summertime circulation along Australia's southern shelves: A numerical study. J. Phys. Oceanogr., 33 (11), 2270-2287, 2003Middleton, J. F. and M. Cirano, Wind-Forced Downwelling Slope Currents: A numerical study. J. Phys. Oceanogr., 29(8), Part 1, 1723-1743, 1999Middleton, J. F. and M. Cirano, A northern boundary current along Australia's southern shelves: The Flinders Current. J. Geophys. Res., 107(C9), 10.1029/2000JC000701, 2002Middleton, J. F. and M. Cirano, Wintertime circulation off southeast Australia: Strong forcing by the East Australian Current. J. Geophys. Res., 110, C12012, 10.1029/2004JC002855, 2005Middleton, J. F. and O. Leth, Wind-forced setup of upwelling, geographical origins, and numerical models: The role of bottom drag. J. Geophys. Res., C12019, 10.1029/2003JC002126, 2004Miller, J.L. and T.N. Lee, Gulf Stream meanders in the South Atlantic Bight, Part I: Scaling and Energetics. J. Geophys. Res., 100, 6687-6704, 1995Miller, J.L. and T.N. Lee, Gulf Stream meanders in the South Atlantic Bight, Part II: Momentum Balances. J. Geophys. Res., 100, 6705-6723, 1995Minato, S., Numerical simulation of tide and storm surge along the coast of Japan using Blumberg and Mellor model. Proc. International Workshop on Wind and Earthquake Engineering for Offshore and Coastal Facilities, University of California at Berkeley, 391-396, 1995Minato, S., Storm surge simulation using POM and a revisitation of dynamics of sea surface elevation short-term variation,. Papers in Met. and Geophys.,Vol. 48, No. 3, 79-88, 1998Miyazawa, I, T. Kagimoto, X. Guo and S. Sakuma, The Koroshio large meander formation in 2004 analyzed by an eddy-resolving ocean forecast system. J. Geophys. Res., 113, C10015, 10.1029/2007JC004226, 2008Miyazawa, Y. and S. Minato, POM and two-way nesting POM study of Kuroshio damping phenomenon caused by a strong wind. J. Oceanogr., 56, 275-294, 2000Miyazawa, Y. and S. Minato, POM and two-way nesting POM study of Kuroshio damping phenomenon caused by a strong wind.. , 2000Miyazawa, Y., R. Zhang, X. Guo, H. Tamura, D. Ambe, J.-S. Lee, A. Okuno, H. Yoshinari, T. Setou, and K. Komatsu, Water mass variability in the western North Pacific detected in a 15-year eddy resolving ocean reanalysis. Journal of Oceanography, 65, 737-756, 2009Miyazawa, Y., S. Yamani, X. Guo and T. Yamagata, Ensemble forecast of the Kuroshio meandering. J. Geophys. Res., 110, C10026, 10.1029/2004JC002426, 2005Miyazawa, Y., X. Guo and T. Yamagata, Roles of meso-scale eddies in the Kuroshio paths. J. Phys. Oceanogr., 34(10), 2203-2222, 2004Mizobata, K., J. Wang and S. Saitoh, Eddy-induced cross-slope exchange maintaining summer high productivity of the Bering Sea shelf break. J. Geophys. Res., 111, C10017, 10.1029/2005JC003335, 2006Mizoguchi, K., S. L. Morey, J. Zavala-Hidalgo, N. Suginohara, S. Hkkinen and J. J. O'Brien, Convective activity in the Labrador Sea: Preconditioning associated with decadal variability in subsurface ocean stratification. J. Geophys. Res., 108(C10), 10.1029/2002JC001735, 2003Montecinos, A., O. Leth, and O. Pizarro, Wind-driven interdecadal variability in the eastern tropical and South Pacific. J. Geophys. Res., 112, C04019, 10.1029/2006JC003571, 2007Monterey, G. I, L. deWitt and F. B. Schwing, Seasonal to interdecadal variability of the North Pacific circulation based on the climatological observed data and the Princeton Ocean Model. Pacific Fisheries Enviromental Laboratory, Report PG-99-01, 1999Mooers, C. N. K., Introduction to coastal ocean prediction. Coastal Ocean Prediction, Coastal and Estuarine Studies, Vol. 56, C. N. K. Mooers (Ed.) American Geophysical Union, Washington, DC, 1-5, 1999Mooers, C. N. K. (Ed), Proceedings from the Princeton Ocean Model Users Meeting (POM98), RSMAS, University of Miami, 17-19 Feb. 1998. 58pp, 1998Mooers, C. N. K. (Ed), Coastal Ocean Prediction. Coastal and Estuarine Studies, Vol. 56, American Geophysical Union, Washington, DC, 526pp, 1999Mooers, C. N. K. and D. S. Ko, Nowcast system development for the Straits of Florida. Proceedings of the 3rd International Estuarine and Coastal Modeling, ASCE, Oak Brook, IL, 1993Mooers, C. N. K. and H. S. Kang, Initial spinup of a Sea of Japan numerical circulation model. In: Advanced Mathematics: Computations and Apploications, NCC Publ. Russia, 350-357pp, 1995Mooers, C. N. K. and J. Fiechter, Numerical simulations of mesoscale variability in the Straits of Florida . Ocean Dynamics, 55(3-4), 309-325, doi: 10.1007/s10236-005-0019-0, 2005Mooers, C. N. K., C. S. Meinen, M. O. Baringer, I. Bang, R. Rhodes, C. N. Barron and F. Pub, Cross validating ocean prediction and monitoring systems. EOS, Trans., 86(29), 269-273, 2005Mooers, C. N. K., H. S. Kang, I. Bang and D. P. Snowden, Some lessons learned from comparisons of numerical simulations and observations of the JES circulation. Oceanography, 19(3), 86-95, 2006Mooers, C. N. K., I. Bang and F. J. Sandoval, Comparisons between observations and numerical simulations of Japan (East) Sea flow and mass fields in 1999 through 2001. Deep Sea Res., 52(11-13), 1639-1661, 2005Moon, I.-J., Impact of a coupled ocean wave-tide-circulation system on coastal modeling. Ocean Modelling, 8(3), 203-300, 2005Morey, S. L. and J. J. O'Brien, The spring transition from horizontal to vertical stratification on a mid-latitude continental shelf. J. Geophys. Res., 107(C8), 10.1029/2001JC000826, 2002Morey, S. L., J. Zavala-Hidalgo and J. J. O’Brien, The Seasonal Variability of Continental Shelf Circulation in the Northern and Western Gulf of Mexico From a High-Resolution Numerical Model, In: Circulation in the Gulf of Mexico: Observations and Models, W. Sturges and A. Lugo-Fernandez (Eds.). Geophys. Monograph Ser., Vol. 161, pp. 203-218, AGU, Washington, DC, 2005Morey, S. L., M. A. Bourassa, D. S. Dukhovskoy and J. J. O’Brien, Modeling studies of the upper ocean response to a tropical cyclone. Ocean Dynamics, DOI: 10.1007/s10236-006-0085-y, 2006Morey, S. L., M. A. Bourassa, X. J. Davis, J. J. O'Brien and J. Zavala-Hidalgo, Remotely sensed winds for episodic forcing of ocean models. J. Geophys. Res., 110, C10024, 10.1029/2004JC002338, 2005Morey, S. L., P. Martin, J. J. O'Brien, A. Wallcraft, J. Zavala-Hidalgo, Export pathways for river discharged fresh water in the northern Gulf of Mexico. J. Geophys. Res., 108(C10), 10.1029/2002JC001674, 2003Morey, S. L., W. W. Schroeder, J. J. O'Brien and J. Zavala-Hidalgo, The annual cycle of riverine influence in the eastern Gulf of Mexico basin. Geophys. Res. Let., 30(16), 10.1029/2003GL017348, 2003Morey, S. L.; J. J. O'Brien, The spring transition from horizontal to vertical thermal stratification on a midlatitude continental shelf. 107(C8), 10.1029/2001JC000826, 2002Moum, J. N., J. D. Nash and J. M. Klymak, Small-scale processes in the coastal ocean. Oceanography, 21(4), 22-33, 2008Munroe, J. R. and K. G. Lamb, Topographic amplitude dependence of internal wave generation by tidal forcing over idealized three-dimensional topography. J. Geophys. Res., 110, C02001, 10.1029/2004JC002537, 2005Nakamura, H., Numerical study on the Kuroshio path states in the northern Okinawa Trough of the East China Sea. J. Geophys. Res., 110, C04003, 10.1029/2004JC002656, 2005Nakamura, H., H. Ichikawa, and A. Nishina, Numerical study of the dynamics of the Ryukyu Current system. J. Geophys. Res., 112, C04016, 10.1029/2006JC003595, 2007Napolitano, E, G. Sannino, V. Artale and S. Marullo, Modeling the baroclinic circulation in the area of the Sicily channel: the role of stratification and energy diagnostics. J. Geophys. Res., vol 108, 10.1029/2002jc001502, 2003Napolitano, E., T. Oguz, P. Malanotte-Rizzoli, A. Yilmaz and E. Sansone, Simulations of biological production in the Rhodes and Ionian basins of the eastern Mediterranean. J. Mar. Sys., 24, 277-298, 2000Newberger, P. A., and J. S. Allen, Forcing a three-dimensional, hydrostatic, primitive-equation model for application in the surf zone: 1. Formulation. J. Geophys. Res., 112, C08018, 10.1029/2006JC003472, 2007Newberger, P. A., and J. S. Allen, Forcing a three-dimensional, hydrostatic, primitive-equation model for application in the surf zone: 2. Application to DUCK94. J. Geophys. Res., 112, C08019, 10.1029/2006JC003474, 2007Newberger, P.A., Y.H. Spitz and J.S. Allen, Analysis and comparison of three ecosystem models. J. Geophys. Res., 108 (C3), 3061 doi:10.1029/2001JC001182, 2003Nittis K. and A.Lascaratos, Intermediate Water Formation in the Levantine Sea : The Response to Interannual variabilitry of Atmospheric Forcing. P.Malanotte-Rizzoli and V.N.Eremeev (eds.), The Eastern Mediterranean as a Laboratory Basin for the Assessment of Contrasting Ecosystems, Kluwer Academic Publ., 2-51, 441-446, 1999Nittis K. and A.Lascaratos, Diagnostic and Prognostic Numerical Studies of LIW Formation. J. Mar. Systems, 18, 179-195, 1998Nittis K. and A.Lascaratos, Interannual Variability of Intermediate Water Formation in the Levantine. Annales Geophysicae, 14(II), C401, 1996Nittis K. and A.Lascaratos, Variability of Water Mass Formation Processes in the Eastern Mediterranean : A Numerical Study. European Commission Report EUR 19302 (International Conference Oceanography of the Eastern Mediterranean and Black Sea), ISBN 92-828-9019-8, pp. 238-239, 1999Nittis K., A. Lascaratos and L.Perivoliotis, A numerical study of the Aegean Sea General Circulation. Rapp. Comm. int. Mer Medit., 34, 1995Nittis K., V. Zervakis, L. Perivoliotis, A. Papadopoulos and G. Chronis, Operational Monitoring and Forecasting in the Aegean Sea: System Limitations and Forecasting Skill Evaluation. Marine Pollution Bulletin,43/7-12,154-163, 2001Nittis, K., A. Lascaratos and A., Theocharis: Dense water formation in the Aegean Sea: Numerical simulations during the Eastern Mediterranean Transient. J. Geophys. Res., 108, (C9), 10.1029/2002JC001352, 2003Niwa, Y. and T. Hibiya, Numerical study of the spatial distribution of the M2 internal tide in the Pacific Ocean. J. Geophys. Res., 106(C10), 22,441-22,449, 2001Niwa, Y. and T. Hibiya, Three-dimensional numerical simulation of M2 internal tide in the East China Sea. J. Geophys. Res., 109, C04027, 10.1029/2003JC001923, 2004Noh, Y., Dynamics of diurnal thermocline formation in the oceanic mixed layer. J. Phys. Oceanogr., 26, 2183-2195, 1996Noh, Y. and H. J. Kim, Simulations of temperature and turbulence structure of the oceanic boundary layer with the improved near-surface processes. J. Geophys. Res., 104(C7), 15,621-15,634, 1999North, E. W., R. R. Hood, S. Y. Chao, et al., The influence of episodic events on transport of striped bass eggs to the estuarine turbidity maximum nursery area. Estuaries, 28 (1), 108-123, 2005Nycander, J. and Das, K., Open boundary conditions for barotropic waves. J. Geophys. Res., 108(C5), 10.1029/2002JC001529, 2003O'Connor, W.P., A User's Manual for the Princeton Numerical Ocean Model. Special Report SP-5, Institute for Naval Oceanography, Stennis Space Center, MS, 69 p., 1991O'Connor, W.P., A Numerical Model of Tides and Storm Surges in the Rio de la Plata Estuary. Continental Shelf Res., 11, 1491- 1508, 1991O'Connor, W.P., Aikman, F. III, Wei, E.J., and Richardson, P.H.,, Comparison of Observed and Forecasted Sea Levels for the Texas Coast near Galveston Bay. Second Conference on Coastal Atmospheric and Oceanic Prediction and Processes, Jan. 11-16, 1998, Phoenix, AZ, American Meteorological Society, Boston, MA, 23-29, 1998O'Connor, W.P., Aikman, F. III, Wei, E.J., and Richardson, P.H.,, Comparison of Observed and Forecasted Sea Levels along the West Florida Coast M.L. Spaulding and A.F. Blumberg (eds.), Estuarine and Coastal Modeling. Proceedings of the Fifth InternationalConference, Oct. 22-24, 1997, Alexandria, VA, American Society of Civil Engineers, Reston, VA,601-612, 1998O'Connor, W.P., and Schwab, D.J., Sensitivity of Great Lakes Forecasting System Nowcasts to Meteorological Fields and Model Parameters, in: M.L. Spaulding, K. Bedford, A. Blumberg, R. Cheng, and C. Swanson (eds.), Estaurine and Coastal Modeling III. Proceedings of the 3rd International Conference, ASCE, Sep. 8-10, 1993, Oak Brook, IL, 149-157, 1994O'Connor, W.P., Chao, B.F., Zheng, D., and Au, A.Y., Wind stress forcing of the North Sea 'pole tide'. Geophysical Journal International, 142, 620-630, 2000O'Connor, W.P., Schwab, D.J., and Lang, G.A., Forecast Verification for Eta Model Winds Using Lake Erie Storm Surge Water Levels. Weather and Forecasting, 14(1), 119-133, 1999Oberpriller, W. D., A. Sawdey, M. T. O'Keefe and S. Gao, Parallelizing the Princeton Ocean Model using TOPAZ. Parallel Computer Sys. Lab., Dept. Elec. Comp. Eng., University of Minnesota, Tech. Report, 21pp., 1999Oddo, P., N. Pinardi and M. Zavatarelli, A numerical study of the interannual variability of the Adriatic Sea (2000–2002). Science of The Total Envir., 353(1-3), 39-56, 2005Oey, Inoue, Lai, Lin, Welsh & Rouse Jr., Stalling of near-inertial waves in a cyclone. Geophys. Res. Let., 35, L12604, doi:10.1029/2008GL034273., 2008Oey, Inoue, Lai, Lin, Welsh and Rouse Jr, Stalling of near-inertial waves in a cyclone. GRL, 35, L12604, doi:10.1029/2008GL034273.. Geophys. Res. Let., 35, L12604, 10.1029/2008GL034273, 2008Oey, L-Y, Y-L Chang, Z Sun, and X-H Lin, June, Topocaustics. Ocean Modelling, 29(4), doi:10.1016/j.ocemod.2009.05.006., 2009Oey, L-Y., On steady salinity distribution and circulation in partially mixed and well mixed estuaries. J. Phys. Oceanogr., 14(3), 629-645, 1984Oey, L.-Y., Eddy- and wind-forced shelf circulation. J. Geophys. Res.,100, 8621-8637, 1995Oey, L.-Y., Flow around a coastal bend: A model of the Santa Barbara Channel eddy. J. Geophys. Res., 101(C7), 16,667-16,682, 1996Oey, L.-Y., Simulation of mesoscale variability in the Gulf of Mexico: Sensitivity studies, comparison with observations, and trapped wave propagation. J. Phys. Oceanogr., 26, 145-175, 1996Oey, L.-Y., Eddy energetics in the Faroe-Shetland Channel: A model resolution study. Cont. Shelf Res., 17(15), 1929-1944, 1998Oey, L.-Y., Subtidal energetics in the Faroe-Shetland Channel: Coarse-grid model experiments. J. Geophys. Res., 103(C6), 12,689-12,708, 1998Oey, L.-Y., A forcing mechanism for the poleward flow off the southern California coast. J. Geophys. Res., 104(C6), 13,529-13,539, 1999Oey, L.-Y., A wetting and drying scheme for POM. Ocean Modelling, 9(2), 133-150, 2005Oey, L.-Y., Vorticity flux through the Yucatan Channel and Loop Current variability in the Gulf of Mexico. J. Geophys. Res., 109, C1004, 10.1029/2004JC002400, 2004Oey, L.-Y., An OGCM with movable land–sea boundaries. Ocean Modelling, 13(2), 176-195, 2006Oey, L.-Y., Loop Current and Deep Eddies. J. Phys. Oceanogr., 38, 1426-1449, 2008Oey, L.-Y. and G. L. Mellor, Subtidal variability of estuarine outflow, plume, and coastal current: a model study. J. Phys. Oceanogr., 23, 164-171, 1993Oey, L.-Y. and H. C. Zhang, The generation of subsurface cyclons and jets through eddy-slope interaction. Cont. Shelf Res., 24, 2109-2131, 2004Oey, L.-Y. and H.-C. Lee, Deep eddy energy and topographic Rossby waves in the Gulf of Mexico. J. Phys. Oceanogr., 32(12), 3499-3527, 2002Oey, L.-Y. and Hyun-Chul Lee, Deep eddy energy and topographic Rossby waves in the Gulf of Mexico. J. Phys. Oceanogr. 32(12), 3499-3527, 2002Oey, L.-Y. and P. Chen, A model simulation of circulation in the northeast Atlantic shelves and seas. J. Geophys. Res., 97, 20,087-20,115, 1992Oey, L.-Y. and P. Chen, A nested-grid ocean model: with application to the simulation of meanders and eddies in the Norwegian coastal current. J. Geophys. Res., 97, 20,063-20,086, 1992Oey, L.-Y., C. Winant, E. Dever, W. R. Johnson and D.-P. Wang, A Model of the Near-Surface Circulation of the Santa Barbara Channel: Comparison with Observations and Dynamical Interpretations. J. Phys. Oceanogr., 34(1), 2343, 2004Oey, L.-Y., D.-P. Wang, T. Hayward, C. Winant and M. Hendershott, 'Upwelling' and 'cyclonic' regimes of the near-surface circulation in the Santa Barbara Channel. J. Geophys. Res., 106(C5), 9213-9222, 2001Oey, L.-Y., G. L. Mellor and R. I. Hires, A three-dimensional simulation of the Hudson-Raritan estuary. Part I: Description of the model and model simulations. J. Phys. Oceanogr., 15, 1676-1692, 1985Oey, L.-Y., G. L. Mellor and R. I. Hires, A three-dimensional simulation of the Hudson-Raritan estuary. Part II: Comparison with observation. J. Phys. Oceanogr., 15, 1693-1709, 1985Oey, L.-Y., H.-C. Lee and W. J. Schmitz Jr., Effects of wind and Caribbean eddies on the frequency of Loop Current eddy shedding: A numerical model study. J. Geophys. Res, 108(C10), 10.1029/2002JC001698, 2003Oey, L.-Y., T. Ezer and H.-C. Lee, Loop Current, rings and related circulation in the Gulf of Mexico: A review of numerical models and future challenges, In: Circulation in the Gulf of Mexico: Observations and Models, W. Sturges and A. Lugo-Fernandez (Eds.). Geophys. Monograph Ser., Vol. 161, pp. 31-56, AGU, Washington, DC, 2005Oey, L.-Y., T. Ezer and W. Sturges, Modeled and observed Empirical Orthogonal Functions of currents in the Yucatan Channel, Gulf of Mexico. J. Geophys. Res., 109, C08011, 10.1029/2004JC002345, 2004Oey, L.-Y., T. Ezer, C. Hu and F. E. Muller-Karger, Baroclinic tidal flows and nundation processes in Cook Inlet, Alaska: Numerical modeling and satellite observations. Ocean Dynamics, 57, 205-221, 2007Oey, L.-Y., T. Ezer, D.-P. Wang, S.-J. Fan and X.-Q. Yin, Loop Current warming by Hurricane Wilma. Geophys. Res. Let., 33(8), L08613, 10.1029/2006GL025873, 2006Oey, L.-Y., T. Ezer, D.-P. Wang, X.-Q. Yin and S.-J. Fan, Hurricane-induced motions and interaction with ocean currents. Cont. Shelf Res., 27, 1249-1263, 2007Oey, L.-Y., T. Ezer, G. Forristall, C. Cooper, S. DiMarco and S. Fan, An exersise in forecasting loop current and eddy frontal positions in the Gulf of Mexico. Geophys. Res. Let., 32, L12611, 10.1029/2005GL023253, 2005Oey, L.-Y., T. Ezer, G. L. Mellor and P. Chen, A model study of 'bump' induced western boundary current variabilities. J. Mar. Sys., 3, 321-342, 1992OGUZ T.P., WIND AND THERMOHALINE CIRCULATION. Geophys. Res. Let., 31, L11303, 10.1029/2004GL019824, 1995Oguz, T. and A. Merico, Factors controlling the summer Emiliania huxleyi bloom in the Black Sea: A modeling study. J. Mar. Sys., 59(3-4), 173-188, 2006Oguz, T. and P. Malanotte-Rizzoli, Seasonal variability of wind and thermohaline driven circulation in the Black Sea . J. Geophys. Res., 101(C7), 16,551-16,569, 1996Oguz, T., H. Ducklow, P. Malanotte-Rizzoli, S. Tugrul, N. Nezlin, U. Unluata, Simulation of annual plankton productivity cycle in the Black Sea by a one-dimensional physical-biological model. J. Geophyhs. Res., 101(C7), 16,585-16,599, 1996Oguz, T., H. W. Ducklow, J. E. Purcell and P. Malanotte-Rizzoli, Modelling and response of tot-down control exerted by gelatinous carnivores on the Black Sea pelagic food web.. J. Geophyhs. Res., 106(C3), 4543-4564, 2001Oguz, T., P. Malanotte-Rizzoli, and D. Aubrey, Wind and thermohaline circulation of the Black Sea driven by yearly mean climatological forcing. J. Geophys. Res., 100, 6845-6863, 1995Ohashi, K, J. Sheng, K. R. Thompson, C. G. Hannah and H. Ritchie, Effect of stratification on tidal circulation over the Scotian Shelf and Gulf of St. Lawrence: a numerical study- using a three-dimensional shelf circulation model. Ocean Dynamics, 59(6), 809-826, 2009Ohashi, K. and D.-P. Wang, Circulation in the Santa Maria Basin, California, during 1998. J. Geophys. Res., 109, C11012, 10.1029/2004JC002362, 2004Ohshima K. I. and D. Simizu, Particle tracking experiments on a model of the Okhotsk Sea: Toward oil spill simulation. Journal of Oceanography, 64(1), 103-114, 2008Oke, P. R. and J. H. Middleton, Topographically Induced Upwelling off Eastern Australia. J. Phys. Oceanogr., 30(3), 512-530, 2000Oke, P. R. and J. H. Middleton, Nutrient enrichment off Port Stephens: the Role of the East Australian Current. Cont. Shelf Res., 21, 587-606, 2001Oke, P. R., J. S. Allen, R. N. Miller and G. D. Egbert, A modeling study of the three-dimensional continental shelf circulation off Oregon. Part II: Dynamical Analysis. J. Phys. Oceanogr., 32, 1383-1403, 2002Oke, P. R., J. S. Allen, R. N. Miller and G. D. Egbert and P. M. Kosro, Assimilation of surface velocity data into a primitive equation coastal ocean model. J. Geophys. Res., 107(C9), 10.1029/2000JC000511, 2002Oke, P. R., J. S. Allen, R. N. Miller, G. D. Egbert, J. A. Austin, J. A. Barth, T. J. Boyd, P. M. Korso and M. D. Levine, A modeling study of the three-dimensional continental shelf circulation off Oregon. Part I: Model-data comparisons. J. Phys. Oceanogr., 32, 1360-1382, 2002Onken, R., A. R. Robinson, L. Kantha, C. J. Lozano, P. J. Haley and S. Carniel, A rapid response nowcast/forecast system using multiply nested ocean models and distributed data systems. J. Mar. Sys., 56(1-2), 45-66, 2005Orlic, M. et al (11 coauthors), Wintertime buoyancy forcing changing seawater properties, and two different circulation systems produced in the Adriatic. J. Geophys. Res., 112, C03S07, 10.1029/2005JC003271, 2007Orlic, M. Et al (12 authors), Wintertime buoyancy forcing, changing seawater properties, and two different circulation systems produced in the Adriatic. J. Geophys. Res., 111, C03S07, 10.1029/2005JC003271, 2006Orlic, M., G. Beg Paklar, Z. Pasaric, B. Grbec, M. Pasaric, Nested modeling of the east Adriatic coastal waters. Acta Adriatica, Vol. 47, 219-245, 2006Orlic, M., V. Dadic, B. Grbec, N. Leder, A. Marki, F. Matic, H. Mihanovic, G. Beg Paklar, M. Pasaric, Z. Pasaric, Wintertime buoyancy forcing, changing seawater properties, and two different circulation systems produced in the Adriatic. J. Geophys. Res., 111, C03S07, 10.1029/2005JC003271, 2006Ou, H.-W., C. Dong and D. Chen, Tidal Diffusivity: A Mechanism for Frontogenesis. J. Phys. Oceanogr., 33(4), 840847, 2003Paduan, J. D. and I. Shulman, HF radar data assimilation in the Monterey Bay area. J. Geophys. Res., 109, C07S09, 10.1029/2003JC001949, 2004Paklar, G. B., N. Zagar, M. Zagar, Vellor, Koracin, Paulin, Orlic, Vilibic and Dadic, Modeling the trajectories of satellite-tracked drifters in the Adriatic Sea during a summertime bora event. J. Geophys. Res., 113, C11S04, 10.1029/2007JC004536, 2008Paklar, G. B., V. Isakov, D. Koracin, V. Kourafalou and M. Orlic, A case study of bora-driven flow and density changes on the Adriatic Shelf (January 1987). Cont. Shelf Res., 21, 1751-1783, 2001Palma, E. D., and R. P. Matano, On the implementation of passive open boundary conditions for a general circulation Model: The barotropic mode. J. Geophys. Res., 103(C1), 1319-1341, 1998Palma, E. D., and R. P. Matano, On the implementation of open boundary conditions for a general circulation Model: The three-dimensional case. J. Geophys. Res., 105(C4), 8605-8627, 2000Palma, E. D., and R. P. Matano, Disentangling the upwelling mechanisms of the South Brazil Bight. Cont. Shelf Res., 29(11-12), 1525-1534, 2009Palma, E. D., R. P. Matano and A. R. Piola, A numerical study of the Southwestern Atlantic Shelf circulation: Barotropic response to tidal and wind forcing. J. Geophys. Res., 109, C08014, 10.1029/2004JC002315, 2004Palma, E. D., R. P. Matano and A. R. Piola, A numerical study of the southwestern Atlantic shelf circulation: Stratified ocean response to local and offshore forcing. J. Geophys. Res., 113, C11010, 10.1029/2007JC004720, 2008Pandey A.C., IML Das, S Rai, A.P. Mishra, Vivek. Kumar. Pandey, S. Dwivedi, A. Mitra, K.C. Tripathi and B.P. Kirtman, Mathematical Modelling of Atmosphere and Ocean Processes around Antarctica, Review paper. edited by NCAOR, Goa, HeadLland Sada, Vasco-da-Gama, 2007Pandey, Vivek Kumar and A. C. Pandey, ITF and Heat Poleward Heat Transport of Indian Ocean. Mar. Geodesy, 31(3), 2008Pandey, Vivek Kumar and Avinash Chandra Pandey, Heat Transport through Indonesian Throughflow. J. Ind. Geophys. Union, 10 (4), 223-227, 2006Pandey, Vivek Kumar and Avinash Chandra Pandey, Turbulent kinetic energy and its dissipation rate of the Indonesian throughflow region via Lombok and Savu Straits. J. Ind. Geophys, 11 (2), 85-90, 2007Pandey, Vivek Kumar, Vihang Bhatt, A C Pandey and I M L Das, Impact of Indonesian throughflow Blockage on Southern Indian Ocean, Current Science. Current Science, Vol. 93 (3), 399-406, 2007Park, J-H and A. Kaneko, Assimilation of coastal acoustic tomography data into a barotropic ocean model. Geophys. Res. Letters, 27(20), 3373-3376, 2000Patchen, R., Establishment of a Delaware Bay model evaluation environment.. Est. and Coast. Mod., Amer. Soc. Civ. Eng., Proc. 10th Intern. Conf., 783-818, 2008Patchen, R. and J. Blaha, Implementation of an infrastructure to support operation and evaluation of Gulf of Mexico models. In: OCEANS 2002, MTS/IEEE, Vol. 1-4, 803- 809, 2003Peggion, G, D. Fox and C. Barron, A rapidly relocatable prediction system: Operational implementation and validation. In: OCEANS 2002, MTS/IEEE, V. 1-4, 841- 846, 2003Peng, M., L. Xie and L. J. Pietrafesa, A numerical study of storm surge and inundation in the CroatanAlbemarlePamlico Estuary System. Estuar. Coastal and Shelf Sci., 59(1), 121-137, 2004Peng, M., L. Xie and L. J. Pietrafesa, Tropical cyclone induced asymmetry of sea level surge and fall and its presentation in a storm surge model with parametric wind fields. Ocean Modelling, 14(1-2), 81-101, 2006Peng, M., L. Xie and L. J. Pietrafesa, A numerical study of hurricane-induced storm surge and inundation in Charleston Harbor, South Carolina. J. Geophys. Res., 111, C08017, 10.1029/2004JC002755, 2006Peng, S.-Q. and L. Xie, Effect of determining initial conditions by four-dimensional variational data assimilation on storm surge forecasting. Ocean Modelling, 14(1-2), 1-18, 2006Peng, S.-Q., L. Xie and L. J. Pietrafesa, Correcting the errors in the initial conditions and wind stress in storm surge simulation using an adjoint optimal technique. Ocean Modelling, 18(3-4), 175-193, 2007Pereira, A. F., B. M. Castro, L. Calado, and I. C. A. da Silveira, Numerical simulation of M2 internal tides in the South Brazil Bight and their interaction with the Brazil Current. J. Geophys. Res., 112, C04009, 10.1029/2006JC003673, 2007Petihakis G., Triantafyllou G., Allen J.I, Hoteit I and Dounas C, Modelling the Spatial and Temporal Variability of the Cretan Sea Ecosystem. Journal of Marine Systems vol 36/3-4 pp 173-196, 2002Petihakis, G., G. Triantafyllou, J. Allen, et al., Modelling the spatial and temporal variability of the Cretan Sea ecosystem. J. Mar. Sys., 36(3-4), 173-196, 2002Petrenko, A., Y. Leredde and P. Marsaleix, Circulation in a stratified and wind-forced Gulf of Lions, NW Mediterranean Sea: in situ and modeling data. Cont. Shelf Res., 25(1), 7-27, 2005Petruncio, E. T., Observations and modeling of the internal tide in a submarine canyon. PhD. Dissertation, Naval Postgraduate School, Monterey, CA, 181 pp, 1996Petruncio, E. T., J. D. Paduan and L. K. Rosenfeld, Numerical simulations of the internal tide in a submarine canyon. Ocean Modelling, 4, 221-248, 2002Pietrafesa, L. J., L. Xie and E. Bohm, Atmospheric forcing of an estuary- coastal coupled system. Second Conference on Coastal Atmospheric and Oceanic Prediction and Processes, Jan. 11-16, 1998, Phoenix, AZ, American Meteorological Society, Boston, MA, 275-278, 1998Pietrzak, J. D., A comparison of advection schemes for ocean modeling. Scientific Report, 95-8, Danish Meteorological Institute, 45 pp., 1995Pietrzak, J. D., On the use of TVD limiters for forward-in-time upstream biased advection schemes in ocean modeling. Mon. Wea. Rev., 126, 812-830, 1998Pietrzak, J. D. and K. Bolding, Towards a coastal ocean prediction system for the Danish domestic waters. Coastal Ocean Prediction, Coastal and Estuarine Studies, Vol. 56, C. N. K. Mooers (Ed.), American Geophysical Union, Washington, DC, 195-222, 1999Pinardi et al. (6 co-authors), Very Large Ensemble Ocean Forecasting Experiment Using the Grid Computing Infrastructure. Bul. Am. Met, Soc., 89(6), 799-804, 2008Pinardi, N., F. Auclair, C. Cesarini, E. Demirov, S. F. Umani, M. Giani, G. Montanari, P. Oddo, M. Tonani and M.Zavatarelli, Toward marine environmental predictions in the Mediterranean Sea coastal areas: Monitoring approach. Ocean Forecasting: Conceptual Basis and Applications, N. Pinardi and J. D. Woods (Eds.), Springer, 339-376, 2002Pinho, J. L. S., J. M. P. Vieira and J. S. A. Carmo, Hydroinformatic environment for coastal waters hydrodynamics and water quality modelling. Adv. Eng. Software, 35(3-4), 205-222, 2004Pinkel, R. et al. (and HOME group), Ocean mixing studies near Hawaiian Ridge. EOS, 81(46), 545, 553, 2000Piola, A. R., R. P. Matano, E. D. Palma, O. O. Moller, and E. J. Campos, The influence of the Plata River discharge on the western South Atlantic shelf. Geophys. Res. Let., 32, L01603, 10.1029/2004GL021638, 2005Polimene L., N. Pinardi, M. Zavatarelli, J. I. Allen, M. Giani, M. Vichi, A numerical simulation study of dissolved organic carbon accumulation in the northern Adriatic Sea. J. Geophys. Res., 112, C03S20, 10.1029/2006JC003529, 2007Polimene, L. N. Pinardi, M. Zavatarelli and S. Colella, The Adriatic Sea ecosystem seasonal cycle: Validation of a three-dimensional numerical model. J. Geophys. Res., 111, C03S19, 10.1029/2005JC003260, 2006Polimene, L., N. Pinardi, M. Zavatarelli, S. Collella, The Adriatic Sea ecosystem seasonal cycle: Validation of a three-dimensiona numerical model. J. Geophys. Res., 112, C03S19, 10.1029/2005JC003260, 2007Pollani A., G.Triantafyllou, G.Petihakis , K.Nittis, K.Dounas and C.Koutitas, The POSEIDON Operational Tool for the Prediction of Floating Pollutant Transport. Marine Pollution Bulletin, 43/7-12, 270-278, 2001Powers, J. G., M. T. Stoelinga and W. S. Boyd, Distributed numerical weather prediction via satellite. Bull. Amer. Met. Soc., 78(12), 2755-2770, 1997Prasad, T. G., A comparison of mixed-layer dynamics between the Arabian Sea and Bay of Bengal: One-dimensional model results. J. Geophys. Res., 109(C3), 10.1029/2003JC002000, 2004Prasad, T. G. and M. Ikeda, The wintertime water mass formation in the northern Arabian Sea: A model study. J. Phys. Oceanogr., 32, 1028-1040, 2002Prasad, T., G. and Ikeda, M, A numerical study of the seasonal variability of Arabian Sea high-salinity water. J. Geophys. Res., 107, C3197, 10.1029/2001JC001139, 2002Preller, R. H., Prediction in ice-covered shallow seas. Coastal Ocean Prediction, Coastal and Estuarine Studies, Vol. 56, C. N. K. Mooers (Ed.), American Geophysical Union, Washington, DC, 405-441, 1999Proshutinsky et al., Multinational effort studies differences among Arctic ocean models. EOS, AGU, Washington, DC, 82(51), 637-644, 2001Proshutinsky, A., and Z. Kowalik, Preface to special section on Arctic Ocean Model Intercomparison Project (AOMIP) Studies and Results. J. Geophys. Res., 112, C04S01, 10.1029/2006JC004017, 2007Proshutinsky, A., I. Ashik, S. Häkkinen, E. Hunke, R. Krishfield, M. Maltrud, Maslowski, and Zhang, Sea level variability in the Arctic Ocean from AOMIP models. J. Geophys. Res., 112, C04S08, 10.1029/2006JC003616, 2007Proshutinsky, A., I. M. Ashik, E. N. Dvorkin, S. Hkkinen, R. A. Krishfield, W. R. Peltier, Secular sea level change in the Russian sector of the Arctic Ocean. J. Geophys. Res., 109(C3), 10.1029/2003JC002007, 2004Pullen, J. D. and J. S. Allen, Modeling studies of the coastal circulation off Northern California: shelf response to a major Eel river floodevent. Continental Shelf Res., 20(16), 2213-2238, 2000Pullen, J. D. and J. S. Allen, Modeling studies of the coastal circulation off Northern California: Statistics and patterns of wintertime flow. J. Geophys. Res., 106(C11), 26,959-26,984, 2001Pullen, J., J. D. Doyle, R. Hodur, A. Ogston, J. W. Book, H. Perkins, R. Signell, Coupled ocean-atmosphere nested modeling of the Adriatic Sea during winter and spring 2001. J. Geophys. Res., 108(C10), 10.1029/2003JC001780, 2003Pullen, J.D. and J.S. Allen, Modeling studies of the coastal circulation off northern California: shelf response to a major Eel River flood event. Continental Shelf Res., 20, 2213-2238, 2000Pullen, J.D. and J.S. Allen, Modeling studies of the coastal circulation off northern California: statistics and patterns of wintertime flow. J. Geophys. Res., 106, 26,959-26,984, 2001Qiao, F. and S. Chen et al, The study of wind, wave, current extreme parameters and climatic characters of the South China Sea. Marine Technology Society, 33(1), 61-68, 1999Qiao, F., D. Dai, J. Simpson and H. Svendsen, Banded structure of drifting macroalgae. Mar. Pol. Bull., 58, 1792-1795, 2009Qiao, F., J. Ma, C. Xia, Y. Yang and Y. Yuan, Influence of the wave-induced mixing and tidal mixing on the vertical temperature structure in the Yellow Sea and the East China Sea in summer. Advances in Natural Science, 14 (12): 1434-1441, 2004Qiao, F., J. Ma, Y. Yang and Y. Yuan, 2004, Simulation of the temperature and salinity along 36°N in the Yellow Sea with a wave-current coupled model. Journal of Korean Society of Oceanography, 39 (1): 35-45, 2004Qiao, F., M. Watanabe, Y. Yuan, and Z. Wan, Simulation of general circulation in the East China Sea and the Yellow Sea. J. Hydrodynamics, Ser. B, 3, 91-100, 1998Qiao, F., T. Ezer and Y. Yuan, The zonal distribution features of high frequency planetary waves in the oceans derived from satellite altimeter data. Acta Oceanol. Sinica, 23(1), 91-96, 2004Qiao, F., Y. Yang, X. Lü, C. Xia, X. Chen, B. Wang and Y. Yuan, Coastal upwelling in the East China Sea in winter. J. Geophys. Res., 111, C11S06, 10.1029/2005JC003264, 2006Qiao, F., Y. Yuan, W. Zhao and Z. Wan, Eddy-resolving hydrodynamic numerical model of the East China Sea and Yellow Sea. Sino-US Marine Science and Technology Collaboration Workshop, Qingdao, 46, August, 58-59, 1998Qiao, F., Y. Yuan, Y. Yang, Q. Zheng, C. Xia and J. Ma, Waves-induced mixing in the upper ocean: Distribution and application to a global ocean circulation model. Geophys. Res. Let., 31, L11303, 10.1029/2004GL019824, 2004Radhakrishnan, S. and U. Piomelli, Large-eddy simulation of oscillating boundary layers: Model comparison and validation. J. Geophys. Res., 113, C03029, 10.1029/2007JC004518, 2008Rai, Shailendra, A. P. Mishra and A. C. Pandey, Simulation of Southern Indian Ocean Currents with σ and z Coordinate Ocean Models. Western Indian Ocean . Mar. Sci, 5(1), 89-94, 2005Rajkovic, B., and G. L. Mellor, Coastal ocean response to atmospheric forcing. Small-Scale Turbulence and Mixing in the Ocean, J. C. J. Nihoul and B. M. Jamart, Eds., Elsevier Oceanogr. Ser., 46, 141-149, 1988Rao, R. A., M. Joshi and M. Ravichandran, Oceanic upwelling and downwelling processes in waters off the west coast of India. Ocean Dynamics, 58(3-4), 213-226, 2008Rascle, N., F. Ardhuin and E. A. Terray, Drift and mixing under the ocean surface: A coherent one-dimensional description with application to unstratified conditions. J. Geophys. Res., 111, C03016, 10.1029/2005JC003004, 2006Raudsepp, U., D. Beletsky and D. J. Schwab, Basin-scale topographic waves in the Gulf of Riga. J. Phys. Oceanogr., 33(5), 1129-1140, 2003Røed, L. P. and J. Albretsen, The impact of freshwater discharges on the ocean circulation in the Skagerrak/northern North Sea area Part I: model validation. Ocean Dynamics, 57(4-5), 269-285, 2007Reffray, G., P. Fraunie and P. Marsaleix, Secondary flows induced by wind forcing in the Rhone region of freshwater influence. Ocean Dynamics, 54(2), 179-196, 2004Ren, X. J. and Y. F. Qian, A coupled regional air-sea model, its performance and climate drift in simulation of the east Asian summer Monsoon in 1998. Int. J. Climatol., 25 (5), 679-692, 2005Rennau, H. and H. Burchard, Quantitative analysis of numerically induced mixing in a coastal model application. Ocean Dynamics, 59(5), 671-687, 2009Rhodes, Navy real-time global Modeling systems. Oceanography, 17(2), 68-75, 2002Rhodes, R. C., H. E. Hurlburt, A. J. Wallcraft, C. N. Barron, P. J. Martin, E. J. Metzger, J. F. Shriver, D. S. Ko, O. M. Smedstad, S. L. Cross and A. B. cara, Navy real-time global modeling system. Oceanography, 15, 29-43, 2002Ribbe, J., Holloway, P. E., Modelling Sediment Transport By Internal Tides. Cont. Shelf Res., 26(5), 1001-1013, 2001Richardson, R. A., G. G. Sutyrin, D. Hebert and L. M. Rothstein, Universality of the modeled small-scale response of the upper tropical ocean to squall wind forcing. J. Phys. Oceanogr., 29, 519-529, 1999Richtmeyer and Morton, Difference Methods for Initeial-Value Problem. Journal, Vol. No., pages, 2004Riedlinger, S. K. and G. A. Jacobs, Study of the dynamics of wind-driven transports into the Yellow Sea during winter. J. Geophys. Res., 105(C12), 28,695-28,708, 2000Righi, D. D. and T. Strub, The use of simulated drifters to estimate vorticity. J. Mar. Sys., 29, 125-140, 2001Robertson, R., Mixing and heat flux mechanisms in the upper ocean in the Weddell Sea. Ph.D. thesis, Oregon State University, 173 pp., 1999Robertson, R., Internal tides and baroclinicity in the southern Weddell Sea. 1, Model description. J. Geophys. Res., 106(C11), 27,001-27,016, 2001Robertson, R., Internal tides and baroclinicity in the southern Weddell Sea.2, Effects of the critical latitude and stratification. J. Geophys. Res., 106(C11), 27,017-27,034, 2001Robertson, R., L. Padman, and G. D. Egbert, Tides in the Weddell Sea. Ocean, Ice and Atmosphere: Interactions at the Antarctic Continental Margin, Antarctic Res. Ser., 75, AGU, 341-369., 1999Robertson, R., L. Padman, and M. D. Levine, A correction to the baroclinic pressure gradient term in the Princeton Ocean Model. J. Atm. Ocean Tech., 18, 1068-1075, 2001Roed, L. P. and I. Fossum, Mean and eddy motion in the Skagerrak/northern North Sea: Insight from a numerical model. Ocean Dynamics, 54(2), 197-220, 2004Rolando S. Balotro, Diagnostic and Prognostic Models of Circulation and Material Transport in Suo-Nada, Japan. Phd Thesis Interdiscplinary Graduate School of Engineering Sciences Kyushu University, 2002Rosentraub, Z. and S. Brenner, Circulation over the southeastern continental shelf and slope of the Mediterranean Sea: Direct current measurements, winds, and numerical model simulations. J. Geophys. Res., 112, C11001, 10.1029/2006JC003775, 2007Roughan, M., P. R. Oke and J. H. Middleton, A Modeling Study of the Climatological Current Field and the Trajectories of Upwelled Particles in the East Australian Current. J. Phy. Oceanogr., 33(12), 25512564, 2003Rygg, K., L. I. Enstad and G. Alendal, Simulating CO2 transport into the ocean from a CO2 lake at the seafloor using a z- and a σ-coordinate model. Ocean Dynamics, 59(6), doi:10.1007/s10236-009-0211-8, 2009Sakamoto, T. and T Yamagata, Seasonal transport variation of the wind-driven ocean circulation in a two-layer planetary geostrophic model with continental slope. J. Mar. Res., 54, 261-284, 1996Samelson, R. M., J. S. Allen and P. MacCready, Progress in coastal ocean modeling during CoOP. Oceanography, 21(4), 136-147, 2008Sannino, G., A. Bargagli and V. Artale, Numerical modeling of the mean exchange through the Strait of Gibraltar. J. Geophys. Res., 107(C8), 10.1029/2001JC000929, 2002Sannino, G., A. Bargagli and V. Artale, Numerical modeling of the semidiurnal tidal exchange through the Strait of Gibraltar. J. Geophys. Res., 109, C05011, 10.1029/2003JC002057, 2004Sannino, G., A.Carillo and V. Artale, Three-layer view of transports and hydraulics in the Strait of Gibraltar: A three-dimensional model study. J. Geophys. Res., 112, C03010, 10.1029/2006JC003717, 2007Sannino, G., V. Artale and P. Lanucara, An Hybrid openMP-MPI parallelization of the Princeton Ocean Model. Proceedings to ParCo2001, 2001Santoleri, R., V. Banzon, S. Marullo, E. Napolitano, F. D'Ortenzio and R. Evans, Year-to-year variability of the phytoplankton bloom in the southern Adriatic Sea (1998<96>2000): Sea-viewing Wide Field-of-view Sensor observations and modeling study. J. Geophys. Res., 108(C9), 10.1029/2002JC001636, 2003Saramul, S. and T. Ezer, Tidal-driven dynamics and mixing processes in a coastal ocean model with wetting and drying. Ocean Dynamics, doi:10.1007/s10236-009-0250-1, 2009Saucier, F. J. and J. Dionne, A 3-D coupled ice-ocean model applied to Hudson Bay, Canada: The seasonal cycle and time-dependent climate response to atmospheric forcing and runoff. J. Geophys. Res., 103(C12), 27,689-27,706, 1998Sánchez-Román, A., G. Sannino, J. García-Lafuente, A. Carillo, and F. Criado-Aldeanueva, Transport estimates at the western section of the Strait of Gibraltar: A combined experimental and numerical modeling study. J. Geophys. Res., 114, C06002, doi:10.1029/2008JC005023, 2009Schmalz, R. A., Design of a nowcast/forecast system for Galveston Bay,. Second Conference on Coastal Atmospheric and Oceanic Prediction and Processes, Jan. 11-16, 1998, Phoenix, AZ, American Meteorological Society, Boston, MA, 15-22, 1998Schwab, D. J. and D. Beletsky, Relative effects of wind stress curl, topography and stratification on large-scale circulation in Lake Michigan. J. Geophys. Res., 108(C2), 10.1029/2001JC001066, 2003Schwab, D. J., D. Beletsky, W. P. O'Connor and D. E. Dietrich, Numerical simulation of internal Kelvin waves with Z-level and Sigma level models. M.L. Spaulding and R.T. Cheng (eds.), Estuarine and Coastal Modeling IV, Proc. of the 4th International Conf., Oct. 26-28, 1995, San Diego, CA, J. Amer. Soc. of Civ. Eng., NY, 298-312, 1996Schwab, D. J., W. P. O'Connor and G. L. Mellor, On the net cyclonic circulation in large stratified lakes. J. Phys. Oceanogr., Vol. 25, No. 6, Part II, 1516-1520, 1995Schwab, D.J. and K.W. Bedford, Initial Implementation of the Great Lakes Forecasting System: A Real-Time System for Predicting Lake Circulation and Thermal Structure. Can. J. Water Poll. Control., 1994Schwab,D. J. and K. W. Bedford, The Great Lakes forecasting system. Coastal Ocean Prediction, Coastal and Estuarine Studies, Vol. 56, C. N. K. Mooers (Ed.), American Geophysical Union, Washington, DC, 157-173, 1999Seim, H. E., M. Fletcher, C.N.K. Mooers, J.R. Nelson and R.H. Weisberg, Towards a regional coastal ocean observing system: An initial design for the Southeast Coastal Ocean Observing Regional Association. J. Mar. Sys., 77(3), 261-277, 2009Seim, H. et al. (15 co-authors), SEA-COOS: A model for a multi-states, multi-institutional regional observation system. J. Mar. Tech. Soc., 37(3), 92-101, 2003Sentchev, A. and K. Korotenko, Stratification and tidal current effects on larval transport in the eastern English Channel: Observations and 3D modeling . Environ. Fluid Mech. 4, 305-331., 2004Shchepetkin, A. F. and J. C. McWilliams, A method for computing horizontal pressure gradient force in an oceanic model with nonaligned vertical coordinate. J. Geophys. Res., 108(C3), 10.1029/2001JC001047, 2003Shen, W. and I. Ginis, The impact of ocean coupling on hurricanes during landfall. Geophys. Res. Let. Vol. 28 , No. 14, 2839-2842, 2001Sheng, J., Dynamics of a buoyancy-driven coastal jet: The Gaspe Current. J. Phys. Oceanogr., 31, 3146-3162, 2001Sheng, J. and K. R. Thompson, A robust method for diagnosting regional shelf circulation from scattered density profiles. J. Geophys. Res., 101(C11), 25,647-25,659, 1996Sheng, J., L. Wang, S. Andréfouët, C. Hu, B. G. Hatcher, F. E. Muller-Karger, B. Kjerfve, W. D. Heyman, and B. Yang, Upper ocean response of the Mesoamerican Barrier Reef System to Hurricane Mitch and coastal freshwater inputs: A study using Sea-viewing Wide Field-of-view Sensor (SeaWiFS) ocean color data and a nested-grid ocean circulation model. J. Geophys. Res., 112, C07016, 10.1029/2006JC003900, 2007Shi, C., and S.-Y. Chao, Eastward jets over diverging isobaths, with applications to the Gulf Stream past the Grand Banks. J. Geophys. Res., 99(C11), 22,689-22,706, 1994Shi, C., and S.-Y. Chao, The bifurcation of eastward jets induced by mid-ocean ridges and diverging isobaths. Tellus, 47A, 1032-1046, 1995Shulman, Geore L.Mellor, and J. K. Lewis, Optimization approach to the treatment of open boundary conditions. J. Phys. Oceanogr. 25, 1006-1011, 1995Shulman, I., Local data assimilation in specification of open boundary conditions. J. Atmos. Ocean Tech., 14(6), 1409-1419, 1997Shulman, I., Local data assimilation in the estimation of barotropic and baroclinic open boundary conditions. J. Geophys. Res., 104(C6), 13,667-13,680, 1999Shulman, I., C. -R. Wu, J. D. Paduan, J. K. Lewis, L. K. Rosenfeld, S. R. Ramp, High Frequency Radar Data Assimilation in the Monterey Bay.. In Spaulding, M. L. (Ed.). Estuarine and Coastal Modeling, 434-446, 2002Shulman, I., C. -R. Wu, J. K. Lewis, J. D. Paduan, L. K. Rosenfeld, J. C. Kindle, S. R. Ramp, C.A. Collins, High resolution modeling and data assimilation in the Monterey Bay Area. Continental Shelf Research, 22, 1129 -1151, 2002Shulman, I., and J. K. Lewis, Optimization approach to the treatment of open boundary conditions. J. Phys. Oceanogr., 25, 1006-1011, 1995Shulman, I., and J. K. Lewis, Optimized boundary conditions for coastal modeling. Proc. Estuarine and Coastal Modeling ASCE, October 26-28, 1995, San Diego, CA, 268-282, 1996Shulman, I., J. Kindle, P. Martin, S. deRada, J. Doyle, B. Penta, S. Anderson, F. Chavez, J. Paduan, and S. Ramp, Modeling of upwelling/relaxation events with the Navy Coastal Ocean Model. J. Geophys. Res., 112, C06023, 10.1029/2006JC003946, 2007Shulman, I., S. H. D. Haddock, D. J. McGillicuddy, J. D. Paduan and W. P. Bissett, Numerical modeling of bioluminescence distributions in the coastal ocean. J. Atm. Ocean Tech., 20(7), 1060-1068, 2003Signell, R. P., H. L. Jenter and A.F. Blumberg, Modeling the seasonal circulation in Massachusetts Bay, Est. Coast. Mod.. ASCE, 578-590, 1994Sikiric, M. D., M. Janekovic and M. Kusmic, A new approach to bathymetry smoothing in sigma-coordinate ocean models. Ocean Modelling, doi:10.1016/j.ocemod.2009.03.009, 2009Simizu, D. and K. L. Ohshima, A model simulation on the circulation in the Sea of Okhotsk and the East Sakhalin Current. J. Geophys. Res., 111, C05016, 10.1029/2005JC002980, 2006Skliris N, Lascaratos A, River discharge into the Mediterranean Sea: Climatology and aspects of the observed variability. J. Atmos. Ocean. Technol., 23(5), 100-110, 2004Skliris, N. and A. Lascaratos, Impacts of the Nile River damming on the thermohaline circulation and water mass characteristics of the Mediterranean Sea. J. Mar. Sys., 52(1-4), 121-143., 2004Skliris, N., S. Sofianos and A. Lascaratos, Hydrological changes in the Mediterranean Sea in relation to changes in the freshwater budget: A numerical modelling study. J. Mar. Sys., 64, doi:10.1016/j.jmarsys.2006.01.015, 2007Slordal, L. H. and J. E. Weber, Adjustment to JEBAR forcing in a rotating ocean. J. Phys. Oceanogr. 26, 657-670, 1996Slordal, L. H., E. A. Martinsen, and A. F. Blumberg, Modeling the response of an idealized coastal ocean to a traveling storm and to flow over bottom topography. J. Phys. Oceanogr., 24, 1689-1705, 1994Sl\o rdal, Leiv Harvard, The pressure gradient force in sigma-co-ordinate ocean models.. Int. J. Numer. Methods Fluids 24, No. 10, 987-1017 (1997), 1997Soares, I. D., V. Kourafalou, and T. N. Lee, Circulation on the western South Atlantic continental shelf: 1. Numerical process studies on buoyancy. J. Geophys. Res., 112, C04002, 10.1029/2006JC003618, 2007Soares, I. D., V. Kourafalou, and T. N. Lee, Circulation on the western South Atlantic continental shelf: 2. Spring and autumn realistic simulations. J. Geophys. Res., 112, C04003, 10.1029/2006JC003620, 2007Song, Y. T., A general pressure gradient formulation for ocean models. Part I: Scheme design and diagnostic analysis. Mon. Weath. Rev., 126, 3213-3230, 1998Song, Y. T. and D. G. Wright, A general pressure gradient formulation for ocean models. Part II: Energy, momentum, and bottom torque consistency. Mon. Weath. Rev., 126, 3231-3247, 1998Spitz, Y. H., J. S. Allen and J. Gan, Modeling of ecosystem processes on the Oregon Shelf during the 2001 summer upwelling. J. Geophys. Res., 110, C10S17, 10.1029/2005JC002870, 2005Spitz, Y.H., P.A. Newberger and J.S. Allen, Ecosystem response to upwelling off the Oregon coast: Behavior of three nitrogen-based models. J. Geophys. Res., 108(C3),3062, doi:10.1029/2001JC001181, 2003Stacey, M. T., J. P. Fram, and F. K. Chow, Role of tidally periodic density stratification in the creation of estuarine subtidal circulation. J. Geophys. Res., 113, C08016, 10.1029/2007JC004581, 2008Stacey, M. W. and S. Pond, On the Mellor-Yamada turbulence closure scheme: The surface boundary condition for q2. J. Phys. Oceanogr., 27, 2081-2086, 1997Stacey, M. W. and Y. Gratton, The energetics and tidally induced reverserenewal in a two-silled Fjord. J. Phys. Oceanogr., 31, 1599-1615, 2001Stacey, M. W., S. Pond and Z. P. Nowak, A numerical model of the circulation in Knight Inlet, British Columbia, Canada. J. Phys. Oceanigr., 25, 1037-1062, 1995Stacy, M. W. and S. Pond, Dependence of current and density on the Spring-Neap cycle and the diurnal inequality in Burrard Inlet, British Columbia: Simulations and observations. J. Phys. Oceanogr., 33(11), 2366-2374, 2003Stanev, E. V., G. Brink-Spalink, and J. Wolff, Sediment dynamics in tidally dominated environments controlled by transport and turbulence: A case study for the East Frisian Wadden Sea. J. Geophys. Res., 112, C04018, 10.1029/2005JC003045, 2007Steiner, N., G. Holloway, R. Gerdes, S. Hakkinen, et al. (7 more authors), Comparing modeled streamfunction, heat and freshwater content in the Arctic Ocean. Ocean Modelling, 6(3-4), 265-284, 2004Sturges, W. and A. Lugo-Fernandez (Eds.), Circulation in the Gulf of Mexico: Observations and Models. Geophys. Monograph Ser., Vol. 161, AGU Publ., Washington, D.C., 360 pp., 2005Su, J, Wu, HD, Zhang, YF, et al., A coupled ice-ocean model for the Bohai Sea - I. Study on model and parameter. Acta Oceanol. Sin., 23 (4), 597-608, 2005Sutyrin, G. G., I. Ginis and S. A. Frolov, Equilibration of baroclinic meanders and deep eddies in a Gulf Stream-type jet over a sloping bottom. J. Phys. Oceanogr., 31, 2049-2065, 2001Svendsen, E., J. Bernsten, M. Skogen, B. Adlandsvik and E. Martinsen, Model simulation of the Skagerrak circulation and hydrography during Skaglex. J. Mar. Sys., 8, 219-236, 1996Szilagyi, G. J.(Ed.), Science and Engineering of the Coastal Marine Demonstration Project. NOAA, National Ocean Servise, Office of Coastal Survey, 236 pp., 2000Szilagyi, G. J., F. Aikman and L. C. Breaker, Evaluation of the Coastal Marine Demonstration. NOAA, National Ocean Servise, Office of Coastal Survey, 53 pp., 2000Taguchi, K., and K. Nakata, Analysis of water quality in Lake Hamana using a coupled physical and biochemical model. J. Mar. Sys., 16, 107-132, 1998Tanaka, Y., T. Hibiya and Y. Niwa, Estimates of tidal energy dissipation and diapycnal diffusivity in the Kuril Straits using TOPEX/POSEIDON altimeter data. J. Geophys. Res., 112, C10021, 10.1029/2007JC004172, 2007Tang, C. C. L, Q. Gui, and I. K. Peterson, Modeling the mean circulation of the Labrador Sea and the adjacent shelves. J. Phys. Oceanogr., 26, 1989-2010, 1996Tang, C. L., W. Perrie, A. D. Jenkins, B. M. DeTracey, Y. Hu, B. Toulany and P. Smith, Observation and modeling of surface currents on the Grand Banks: A study of the wave effects on surface currents. J. Geophys. Res., 112, C10025, 10.1029/2006JC004028, 2007Tang, C.L., Q. Gui and B.M. DeTracey, Barotropic response of the Labrador/Newfoundland shelf to a moving storm. Journal of Physical Oceangraphy, 28, 1152-1172, 1998Tang, L., J. Sheng, X. Ji, W. Cao and D. Liu, Investigation of three-dimensional circulation and hydrography over the Pearl River Estuary of China using a nested-grid coastal circulation model. Ocean Dynamics, 59(6), 899-919, doi:10.1007/s10236-009-0218-1, 2009Teague, W. J., D. S. Ko, Jacobs, Perkins, Book, Smith, Chang, Suk, Kim, Lyu and Tang, Currents through the Korea/Tsushima Strait: A review of LINKS observations. Oceanography, 19(3), 50-63, 2006Thiebaux, J., B. Katz, J. Kelly, L. Breaker and B. Balasubramaniyan, National Ocean Partnership Project advances real-time coastal ocean forecasting. EOS, Trans., American Geophysical Union, Vol. 81, No. 14, 145, 150, 2000Thiem, O. and J. Berntsen, Internal pressure errors in sigma-coordinate ocean models due to anisotropy. Ocean Modelling, 12(1-2), 140-156, 2006Thiem, O. and J. Berntsen, Numerical studies of large-amplitude internal waves shoaling and breaking at shelf slopes. Ocean Dynamics, 59(6), 937-952, doi:10.1007/s10236-009-0220-7, 2009Thiem, O., J. Berntsen and B. Gjevik, Development of eddies in an idealised shelf slope area due to an along slope barotropic jet. Cont. Shelf Res., 26(12-13), 1481-1495, 2006Thompson, K. R., K. Ohashi and J. Sheng, Suppressing bias and drift of coastal circulation models through the assimilation of seasonal climatologies of temperature and salinity. Cont. Shelf Res., doi:10.1016/j.csr.2006.10.011, 2007Thompson, R. E., M. M. Sabbotina and M. V. Anisimov, Numerical simulation of hydrothermal vent-induced circulation at Endeavour Ridge. J. Geophys. Res., 110, C01004, 10.1029/2004JC002337, 2005Thomson, R. E., M. M. Subbotina and M. V. Anisimov, Numerical simulations of mean currents and water property anomalies at Endeavour Ridge: Hydrothermal versus topographic forcing. J. Geophys. Res., 114, C09020, doi:10.1029/2008JC005249, 2009Thomson, R. E., Subbotina, M. M., Anisimov, M. V., Numerical simulation of hydrothermal vent-induced circulation at Endeavour Ridge. J. Geophys. Res., 110 (C01004), 2005Tierney, C. C., L. H. Kantha and G. H. Born, Shallow and deep water global ocean tides from altimetry and numerical modeling. J. Geophys. Res., 105(C5), 11,259-11,277, 2000Tilburg, C. E., R. W. Houghton, and R. W. Garvine, Mixing of a dye tracer in the Delaware plume: Comparison of observations and simulations. J. Geophys. Res., 112, C12004, 10.1029/2006JC003928, 2007Toner, M., A. D. Kirwan Jr., A. C. Poje, L. H. Kantha, F. E. Muller-Karger and C. K. R. T. Jones, Chlorophyll dispersal by eddy-eddy interactions in the Gulf of Mexico. J. Geophys. Res., 108(C4), 10.1029/2002JC001499, 2003Toner, M., A. D. Kirwan, L. H. Kantha, and J. K. Choi, Can general circulation models be assessed and their output enhanced with drifter data?. J. Geophys. Res., 106(C9), 19,563-19,579, 2001Triantafyllou, G., I. Hoteit and G. Petihakis, A singular evolutive interpolated Kalman filter for efficient data assimilation in a 3-D complex physical-biogeochemical model of the Cretan Sea. J. Mar. Sys., 40-41, 213-231, 2003Triantafyllou, G., I. Hoteit and G. Petihakis, A singular evolutive interpolated Kalman filter for efficient data assimilation in a 3-D complex physical–biogeochemical model of the Cretan Sea. J. Mar. Sys., 40-41, 213-231, 2003Tsiaras, K. P., V. H. Kourafalou, A. Davidov, and J. Staneva, A three-dimensional coupled model of the western Black Sea plankton dynamics: Seasonal variability and comparison to SeaWiFS data. J. Geophys. Res., 113, C07007, 10.1029/2006JC003959, 2008ueda, F. J., S. G. Schladow and S. O. Palmarson, Basin-scale internal wave dynamics during a winter cooling in a large lake. J. Geophys. Res., 108(C3), 10.1029/2001JC000942, 2003Ulses, C., C. Estournel, J. Bonning, X. D. Madron and P. Marsaleix, Impact of storm and dense water cascading on shelf-slope exchanges in the Gulf of Lion (NW Mediterranean). J. Geophys. Res., 113, C02010, 10.1029/2006JC003795, 2008Umlauf, L. and H. Burchard, Second-order turbulence closure models for geophysical boundary layers. A review of recent work. Cont. Shelf Res., 25(7-8), 795-827, 2005Uotila, P., D. M. Holland, M. A. M. Maqueda, S. Häkkinen, et al (7 more authors), An energy-diagnostics intercomparison of coupled ice-ocean Arctic models. Ocean Modelling, 11(1-2), 1-27, 2006Valle-Levinson, A. and K. M. M. Lwiza, The effect of channels and shoals on exchange between the Chesapeake Bay and the adjacent ocean. J. Geophys. Res., 100(C9), 18,551-18,565, 1995Vichi M., Oddo P., Zavatarelli M., Coluccelli A., Coppini G., Celio M., Fonda Umani S., Pinardi N., Calibration and Validation of a one-dimensional complex marine biogeochemical fluxes model in different areas of the northern Adriatic Sea. Annales Geophysicae, 21(1) 413-436, 2003Vichi M., Pinardi N., Zavatarelli M., Frascari F., Interazione fra forzante idrodinamico e cicli biogeochimici nel Mare Adriatico settentrionale: esperimenti numerici. [Interactions between hydrodynamical forcing and biogeochemical cycles in the northern Adriatic Sea: numerical experiments]. IMGA-CNR, Techn. Rep. 5/98, 218 pp., 1998Vichi M., Pinardi N., Zavatarelli M., Matteucci G., Marcaccio M., Bergamini M.C., Frascari F., One-dimensional ecosystem model tests in the Po prodelta area (northern Adriatic Sea). Environmental Modelling &Software, 13, 471-481, 1998Vichi M., Zavatarelli M., Pinardi N., Seasonal modulation of microbially mediated carbon fluxes in the northern Adriatic Sea - a model study. Fisheries Oceanography, 7, 182-190, 1998Vilibic, I., G. Beg Paklar, N. Zagar, H. Mihanovic, N. Supic, M. Zagar, N. Domijan, M. Pasaric, Summer breakout of trapped bottom dense water from the northern Adriatic. J. Geophys. Res., 113, C11S02, 10.1029/2007JC004535, 2008Vinogradova, N., S. Vinogradov, D. Nechaev, V. Kamenkovich, A. Blumberg and Q. Ashan, Evaluation of the Northern Gulf of Mexico Littoral Initiative model based on the observed temperature and salinity in the Mississippi Bight. Mar. Tech. Soc. Journal, 39(2), 25-38, 2005Wakelin, S. L., J. T. Holt and R. Proctor, The influence of initial conditions and open boundary conditions on shelf circulation in a 3D ocean-shelf model of the North East Atlantic. Ocean Dynamics, 59(1), 67-81, 2009Walsh, J. J., R. H. Weisberg, D. A. Dieterle, R. He, et al. (16 authors), Phytoplankton response to intrusions of slope water on the West Florida Shelf: Models and observations. J. Geophys. Res., 108(C6), 10.1029/2002JC001406, 2003Walstad, L. J., and D. J. McGillicuddy, Data assimilation for coastal observing systems. Oceanography, 13(1), 47-53, 2000Wan, Z., Y. Yuan and F. Qiao, Numerical simulation of tidal wave in the East China Sea. J. of Hydrodynamics, Ser. A, 14(4B), 82-91 (in chinese), 1999Wang and L.-Y. Oey, Hindcast of Waves and Currents in Hurricane Katrina.. Bul. Am. Met. Soc.. DOI:10.1175/BAMS-89-4-487., 2008Wang, D.-P., Tidally generated internal waves in partially mixed estuaries. Cont. Shelf Res., 26(12-13), 1001-1013, 2006Wang, D.-P., L.-Y. Oey, T. Ezer and P. Hamilton, Nearsurface Currents in DeSoto Canyon (1997-1999): Comparison of Current Meters, Satellite Observation, and Model Simulation. J. Phys. Oceanogr., 33(1), 313-326, 2003Wang, H., Y. Yuan, W. Guan, C. Liang, R. Lou, G. Liao and K. Wang, Reply to comment by L. Li and R. Wu on “Circulation in the South China Sea during summer 2000 as obtained from observations and a generalized topography-following ocean model". J. Geophys. Res., 111, C03008, 10.1029/2005JC002932, 2006Wang, H., Y. Yuan, W. Guan, R. Lou, and K. Wang, Circulation in the South China Sea during summer 2000 as obtained from observations and a generalized topography-following ocean model. J. Geophys. Res., 109, C07007, 10.1029/2003JC002134 , 2004Wang, J., Global linear stability of the two-dimensional shallow water equations: An application of the distributive theorem of roots for polynomials on the unit circle. Mon. Weather Rev., 124, 1301-1310, 1996wang, J., A two-channel laterally aceraged estuarine circulation model (LAECIM). J. Geophys. Res., 103(C9), 18,381-18,391, 1998wang, J. and C. N. K. Mooers, Three-dimensional perspectives of the Florida Current: transport, potential vorticity, and related dynamical properties. Dyn. of Atmos. and Oceans, 27, 135-149, 1997Wang, J. and M. Ikeda, Diagnosing ocean unstable baroclinic waves and meanders using the quasigeostrophic equations and Q-vector method. J. Phys. Oceanogr., 27, 1158-1172, 1997Wang, J., H. Hu, K. Mizobata and S. Saitoh, Seasonal variations of sea ice and ocean circulation in the Bering Sea: A model-data fusion study. J. Geophys. Res., 114, C02011, 10.1029/2008JC004727, 2009Wang, J., L. A. Mysak, and R. G. Ingram, A three-dimensional numerical simulation of Hudson Bay summer ocean circulation: Topographic gyres, separations, and coastal jets. J. Phys. Oceanogr., 24, 2496-2514, 1994Wang, J., L. A. Mysak, and R. G. Ingram, A numerical simulation of sea ice cover in Hudson Bay. J. Phys. Oceanogr., 24, 2515-2533, 1994Wang, J., Q. Z. Liu, M. B. Jin, M. Ikeda and F. J. Saucier, A coupled ice-ocean model in the pan-Arctic and North Atlantic Ocean: Simulation of seasonal cycles. J. Oceanography, 61(2), 213-233, 2005Wang, Q., S. Danilov, and J. Schrter, Finite element ocean circulation model based on triangular prismatic elements, with application in studying the effect of topography representation. J. Geophys. Res., 113, C05015, doi:10.1029/2007JC004482, 2008Wang, Q., S. Danilov, J. Schrter, Comparison of overflow simulations on different vertical grids using the Finite Element Ocean circulation Model. Ocean Modelling, 20(4), 313-335, 2008Wang, Q., X. Guo, and H. Takeoka, Seasonal variations of the Yellow River plume in the Bohai Sea: A model study. J. Geophys. Res., 113, C08046, 10.1029/2007JC004555, 2008Wang, X. H., Tide-induced sediment resuspension and the bottom boundary layer in an idealized estuary with a muddy bed. J. Phys. Oceanogr., 32(11), 3113-3131, 2002Wang, X. H., A numerical study of sediment transport in a coastal embayment during a winter storm.. Journal of Coastal Research,34, Special Issue, 414-427, 2001Wang, X. H., Circulation and heat budget of the northern Adriatic Sea (Italy) due to a Bora event in January 2001: a numerical model study. Ocean Modelling, 10(3-4), 253-271, 2005Wang, X. H. and G. Symonds, Coastal embayment circulation due to atmospheric cooling. J. Geophys. Res., 104(C12), 29,801-29,816, 1999Wang, X. H. and J. H. Jungclaus, Open boundary conditions in a three dimensional coastal ocean model. Working Paper 1996/1, School of Geography and Oceanography, University College, Australian Defence Academy, Canberra, 29pp, 1996Wang, X. H. P. Oddo and N. Pinardi, On the bottom density plume on coastal zone off Gargano (Italy) in the southern Adriatic Sea and its interannual variability. J. Geophys. Res., 111, C03S17, 10.1029/2005JC003110, 2006Wang, X. H., D.S. Byun, X.L. Wang and Y.K. Cho, Modelling tidal currents in a sediment stratified idealized estuary. Cont. Shelf Res., 25(5-6), 655-665, 2005Wang, X. H., P. Oddo and N. Pinardi, On the bottom density plume on coastal zone off Gargano (Italy) in the southern Adriatic Sea and its interannual variability. J. Geophys. Res., 112, C03S17, 10.1029/2005JC003110, 2007Wang, X.H. and N. Pinardi, Modeling the dynamics of sediment transport and resuspension in the northern Adriatic Sea. J. Geophys. Res., 107 (C12), 10.1029/2001JC001303, 2002Warner, J. C., C. R. Sherwood, H. G. Arango and R. P. Signell, Performance of four turbulence closure models implemented using a generic length scale method. Ocean Modelling, 8(1-2), 81-113, 2005Warrach, K., Modelling the thermal stratification in the North Sea. J. Mar. Sys., 14, 151-165, 1998Warrior, H., and K. Carder, An optical model for heat and salt budget estimation for shallow seas. J. Geophys. Res., 112, C12021, 10.1029/2006JC003866, 2007Waseda, T., H. Mitsudera, B. Taguchi, and Y. Yoshikawa, On the eddy-Kuroshio interaction: Evolution of the mesoscale eddy. 107(C8), 10.1029/2000JC000756, 2002Waseda, T., H. Mitsudera, B. Taguchi, and Y. Yoshikawa, On the eddy-Kuroshio interaction: Meander formation process. J. Geophys. Res., 108(C7), 10.1029/2002JC001583, 2003Wei, E. J. and C. L. Sun, Development of a New York/New Jersey harbor water level and current nowcast/forecast system. Second Conference on Coastal Atmospheric and Oceanic Prediction and Processes, Jan. 11-16, 1998, Phoenix, AZ, American Meteorological Society, Boston, MA, 11-14, 1998Weisberg, R. H. and L. Zheng, Hurricane storm surge simulations comparing three-dimensional with two-dimensional formulations based on Ivan-like storm over the Tampa Bay, Florida region. J. Geophys. Res., 113, C12001, 10.1029/2008JC005115, 2008Weisberg, R. H. and R. He, Local and deep-ocean forcing contributions to anomalous water properties on the West Florida Shelf. J. Geophys. Res., 108(C6), 10.1029/2002JC001407, 2003Weisberg, R. H., B. D. Black and Z. Li, An upwelling case study on Florida's west coast. J. Geophys. Res., 105(C5), 11,459-11,469, 2000Weisberg, R. H., R. He, G. Kirkpatrick, F. Muller-Karger and J. J. Walsh, Coastal ocean circulation influences on remotely sensed optical properties: A West Florida Shelf case study. Oceanography, 17(2), 68-75, 2004Weisberg, R. H., R. He, Y. Liu and J. I. Virmani, West Florida Shelf Circulation on Synoptic, Seasonal, and Interannual Time Scales, In: Circulation in the Gulf of Mexico: Observations and Models, W. Sturges and A. Lugo-Fernandez (Eds.). Geophys. Monograph Ser., Vol. 161, p. 325, AGU, Washington, DC, 2005Weisberg, R. H., Z. Li and F. Muller-Karger, West Florida shelf response to local wind forcing: April 1998. J. Geophys. Res., 106, 31,239-31,262, 2001Wheless, G. H. and A. Valle-Levinson, `A Walk Through Chesapeake Bay-Numerical Model Results in a Virtual Environment'. NSF MetaCenter Display, Supercomputing 94, 1994Wheless, G. H. and A. Valle-Levinson, A modeling study of tidally driven estuarine exchange through a narrow inlet onto a sloping shelf. J. Geophys. Res., 101(C11), 25,675-25,687, 1996Wheless, G. H., A. Valle-Levinson and W. Sherman, Virtual reality in oceanography. Oceanography, Vol. 8, No. 2, 52-58, 1995Whitehouse, B. G., P. Hines, D. Ellis and C. N. Barron, Rapid environmental assessment within NATO. Sea Techlology, 45(11), 10-14, 2004Whitney, M. M. and R. W. Garvine, Wind influence on a coastal buoyant outflow. J. Geophys. Res., 110, C03014, 10.1029/2003JC002261, 2005Whitney, M. M. and R. W. Garvine, Simulating the Delaware Bay Buoyant Outflow: Comparison with Observations. J. Phys. Oceanogr., 36(1), 3-21, 2006Wijesekera, H.W., J.S. Allen and P.A. Newberger,, Modeling study of turbulent mixing over the continental shelf: comparison of turbulent closure schemes. J. Geophys. Res., 108 (c3) 3103,doi:10.1029/2001JC001234, 2003Wilkin, J. L., A computer program for generating two-dimensional orthogonal curvilinear coordinate grids. Woods Hole Oceanographic Institution, Unpublished Report, 1988WILKIN, J.L., A COMPUTER PROGRAM FOR GENERATING TWO-DIMENSIONAL ORTHOGONAL CURVILINEAR COORDINATE GRIDS. UNPUBLISHED REPORT,1987, 1995Willems, R. C., S. M. Glenn, M. F. Crowley, P. Malanotte-Rizzoli, R. E. Young, T. Ezer, G. L. Mellor, H. G. Arango, A. R. Robinson, and C.-C. Lai, Experiment evaluates ocean models and data assimilation in the Gulf Stream. EOS, Transactions, American Geophysical Union, 75(34), 385-394, 1994Williams, B., Hydrobiological Modelling. 708 pp, 2006Wong, L. A., Chen, J. C., Xue, H., Dong, L. X., Guan, W. B. and Su, J. L., A model study of the circulation in the Pearl River Estuary (PRE) and its adjacent coastal waters: 2. Sensitivity experiments. J. Geophys. Res., 108(C5), 10.1029/2002JC001452, 2003Wong, L. A., Chen, J. C., Xue, H., Dong, L. X., Su, J. L. and Heinke, G., A model study of the circulation in the Pearl River Estuary (PRE) and its adjacent coastal waters: 1. Simulations and comparison with observations. J. Geophys. Res., 108(C5), 10.1029/2002JC001451, 2003Wong, L. A., J. C. Chen and L. X. Dong, A model of the plume front of the Pearl River Estuary, China and adjacent coastal waters in the winter dry season. Cont. Shelf Res., 24(16), 1737-1987, 2004Wu, C., H. Lu, and S. Chao, A numerical study on the formation of upwelling off northeast Taiwan. J. Geophys. Res., 113, C08025, 10.1029/2007JC004697, 2008Wu, Chang, Oey, Chang & Hsin, Air-sea interaction between tropical cyclone Nari and Kuroshio. Geophys. Res. Let., 31, L12605, 10.1029/2008GL033942, 2008Xia, C., F. Qiao, Y. Yang, J. Ma and Y. Yuan, Three-dimensional structure of the summertime circulation in the Yellow Sea from a wave-tide-circulation coupled model. J. Geophys. Res., 111, C11S03, 10.1029/2005JC003218, 2006Xie, L. and D. B. Eggleston, Computer Simulations of Wind-induced Estuarine Circulation Patterns and Estuary-shelf Exchange Processes: The Potential Role of Wind Forcing on Larval Transport. Est. Coast. Shelf Sci., 49(2), 221-234, 1999Xie, L. and L.J. Pietrafesa, Systemwide Modeling of wind and density driven circulation in the Croatan-Albemarle-Pamlico Estuary System. Part I: Model configuration and testing. J. Coastal Res., 15 (4), 1163-1177, 1999Xie, L., H. Liu and M. Peng, The effect of wavecurrent interactions on the storm surge and inundation in Charleston Harbor during Hurricane Hugo 1989. Ocean Modelling, 20(3), 252-269, 2008Xie, L., K. Wu, L. Pietrafesa, and C. Zhang, A numerical study of wave-current interaction through surface and bottom stresses: Wind-driven circulation in the South Atlantic Bight under uniform winds. J. Geophys. Res., 106(C8), 16,841-16,855, 2001Xie, L., L. J. Pietrafesa and K. Wu, A numerical study of wave-current interaction through surface and bottom stresses: Coastal ocean response to Huricane Fran of 1996. J, Geophys. Res., 108(C2), 10.1029/2001JC001078, 2003Xie, L., L. J. Pietrafesa and M. Peng, Incorporation of a mass-conserving inundation scheme into a three dimensional storm surge model. J. Coastal Res., 1-17, 2003Xie, L., L. J. Pietrafesa, E. Bohm, C. Zhang and X. Li, Interaction of Hurricane Fran and a cold-core Gulf Stream trough off the southeast U.S. coast. Second Conference on Coastal Atmospheric and Oceanic Prediction and Processes, Jan. 11-16, 1998, Phoenix, AZ, American Meteorological Society, Boston, MA, 279-284, 1998Xie, L., L.J. Pietrafesa E. Bohn, C. Zhang, and X. Li, Evidence and mechanism of hurricane Fran-induced ocean cooling in the Charleston trough. Geophysical Res. Letters, 25, 769-772, 1998Xie, L., L.J. Pietrafesa, and C. Zhang, Subinertial response of the Gulf Stream system to Hurricane Fran of 1996. Geophysical Research Letters, 26, 3457-3460, 1999Xue, H. (Ed.), Sigma Coordinate Ocean Model Users Meeting '99 Proceedings,Bar Harbor, ME, 20-22 September 1999. School of Marine Sciences, University of Maine, Orono, 52 pp., 1999Xue, H. and J. M. Bane, A numerical investigation of the Gulf Stream and its meanders in response to cold air outbreaks. J. Phys. Oceanogr.,27, 2606-2629, 1997Xue, H., and G. L. Mellor, Instability of the Gulf Stream front in the South Atlantic Bight. J. Phys. Oceanogr., 23, 2326-2350, 1993Xue, H., F. Chai and N. R. Pettigrew, A model study of the seasonal circulation in the Gulf of Maine. J. Phys. Oceanogr., 30, 1111-1135, 2000Xue, H., F. Chai, N. Pettigrew, D. Xu, M. Shi and J. Xu, Kuroshio intrusion and the circulation in the South China Sea. J. Geophys. Res., 109(C2), 10.1029/2002JC001724, 2004Xue, H., J. M. Bane, and L. M. Goodman, Modification of the Gulf Stream through strong air-sea interaction in winter: observations and numericalsimulations. J. Phys. Oceanogr., 25, 533-557, 1995Xue, H., Z. Pan and J. M. Bane, A 2D coupled atmosphere-ocean model study of air-sea interactions during a cold air outbreak over the Gulf Stream. Mon. Weather Rev., 128, 973-996, 2000Y. Luo, H.-M. Zhang, M. D. Prater and L. M. Rothstein, Warm water pathways, transports, and transformations in the northwestern North Atlantic and their modification by cold air outbreaks. J. Geophys. Res., 108(C4), 10.1029/2002JC001442, 2003Yamaguchi, S. and H. Kawamura, Influence of orographically steered winds on Mutsu Bay surface currents. J. Geophys. Res., 110, C09010, 10.1029/2004JC002462, 2005Yang, B. and J. Sheng, Process study of coastal circulation over the inner Scotian Shelf using a nested-grid ocean circulation model, with a special emphasis on the storm-induced circulation during tropical storm Alberto in 2006 . Ocean Dynamics, 58(5-6), 375-396, 2008Yang, H. and R. H. Weisberg, Response of the West Florida Shelf circulation to climatological wind stress forcing. J. Geophys. Res., 104(C3), 5301-5320, 1999Yang, H., Q. Liu, Z. Liu, D. Wang and X Liu, A general circulation model study of the dynamics of the upper ocean circulation of the South China Sea. J. Geophys. Res., 107(C7), 10.1029/2001JC001084, 2002Yang, Z., A. Baptista and J. Darland, Numerical modeling of flow characteristics in a rotating annular flume. Dyn. Atmos. Oceans, 31, 271-294, 2000Yao, T. and C.L. Tang, The formation and maintenance of the North Water Polynya. Atmosphere-Ocean, 41, 187-201, 2003Yao, T., C. L. Tang and I. K. Peterson, Modeling the seasonal variation of sea ice in the Labrador Sea with a coupled multicategory ice model and the Princeton Ocean Model. J. Geophys. Res., 105(C1), 1153-1165, 2000Yin X.-Q. and L.-Y. Oey, Bred-ensemble ocean forecast of loop current and rings. Ocean Modelling, 17(4), 300-326, 2007You, S. H. and J. W. Seo, Numerical study of storm surges and tide around Korea using operational ocean model. Marine Geodesy, 32, 243-263., 2009Young, E. F., J. Brown, J. N. Aldridge, K. J. Horsburgh and L. Fernand, Development and application of a three-dimensional baroclinic model to the study of the seasonal circulation in the Celtic Sea. Cont. Shelf Res., 24(1), 13-36, 2004Zavala-Hidalgo, J., A. Gallegos-García, B. Martínez-López, S. L. Morey and J. J. O’Brien, Seasonal upwelling on the Western and Southern Shelves of the Gulf of Mexico. Ocean Dynamics, DOI: 10.1007/s10236-006-0072-3, 2006Zavala-Hidalgo, J., S. L. Morey and J. J. O'Brien, Seasonal circulation on the western shelf of the Gulf of Mexico using a high-resolution numerical model. J. Geophys. Res., 108(C12), 10.1029/2003JC001879, 2003Zavatarelli, Mediterranean Sea multiscale variability and environmental management issues: a scientific perspective. Prog. Oceanogr., 44, 401-409, 1999Zavatarelli M., Pinardi N., The Adriatic Modelling System: a nested approach. Annales Geophysicae, 21(1), 345-364, 2003Zavatarelli M., Pinardi N., Maggiore A., Winter density compensation in the northern Adriatic Sea. A numerical model process study. Ecosystems Research Report, 32, 141-156, 1999Zavatarelli, M. and G. L. Mellor, A numerical study of the Mediterranean Sea circulation. J. Phys. Oceanogr., Vol. 25, No. 6, Part II, 1384-1414, 1995Zavatarelli, M., F. Raicich, A. Artegiani, D. Bregant and A. Russo, Climatological biogeochemical characteristics of the Adriatic Sea. J. Mar. Sys., 18, 227-263, 1998Zavatarelli, M., J. W. Baretta, J. G. Baretta-Bekker and N. Pinardi, The dynamics of the Adriatic Sea ecosystem: an idealized model study. Deep-Sea Res., 47, 937-970, 2000Zavatarelli, M., N. Pinardi, V. H. Kourafalou and A. Maggiore, Diagnostic and prognostic model studies of the Adriatic Sea general circulation: Seasonal variability. J. Geophys. Res., 107(C1), 4-1 - 4-20, 2002Zedler, S. E., Observations and modeling of the ocean's response to hurricane Felix at the Bermuda testbed mooring, M.A. Thesis,. Univ. of Cal. at Santa Barbara, 129 pp., 1999Zedler, S. E., T. D. Dickey, S. C. Doney, J. F. Price, X. Yu and G. L. Mellor, Analysis and simulations of the upper ocean's response to Hurricane Felix at the Bermuda Testbed Mooring site: 13-23 August 1995. J. Geophys. Res., 107(C12), 10.1029/2001JC000969, 2002Zhang, A., B. B. Parker and E. Wei, Assimilation of water level data into a coastal hydrodynamic model by an adjoint optimal technique. Cont. Shelf Res., 22(14), 1909-1934, 2002Zhang, A., E. Wei and B. B. Parker, Optimal estimation of tidal open boundary conditions using predicted tides and adjoint data assimilation technique. Cont. Shelf Res., 23, 1055-1070, 2003Zhang, H., O. S. Madsen, S.A. Sannasiraj and E. S. Chan, Hydrodynamic model with wave–current interaction in coastal regions. Est. Coast. Shelf Sci., 61(2), 317-324, 2004Zhang, K. Q. and L. M. Rothstein, Local mixed layer response to wind and buoyancy forcing in the western equatorial Pacific. J. Geophys. Res., 104(C1), 1301-1324, 1999Zhang, Q. Y., Comparison of two three-dimensional hydrodynamic modeling systems for coastal tidal motion. Ocean Engineering, 2005Zhang, Q. Y., Comparison oof three-dimensional hydrodynamic modeling systems for coastal tidal motion. Ocean Engineering, 33(2), 2006Zhang, Q. Y., Comparison of three-dimensional hydrodynamic modeling systems for coastal tidal motion. Oceanography, 19(2), 68-75, 2006Zheng, L. and R. H. Weisberg, Tide, buoyancy, and wind-driven circulation of the Charlotte Harbor estuary: A model study. J. Geophys. Res., 109, C06011, 10.1029/2003JC001996, 2004Zheng, Q, G. Fang and T. Song, Introduction to special section: Dynamics and circulation of the Yellow, East, and South China Seas. J. Geophys. Res., 111, C11S01, 10.1029/2005JC003261, 2006Zhu, J., Chen, C., E. Ralph, S. A. Green, J. W. Budd and F. Y. Zhang, Prognostic modeling studies of the Keweenaw Current in Lake Superior. Part II: Simlation. J. Phys. Oceanogr., 31, 396-410, 2001Zhurbas, V. M., I. S. Oh and V. T. Paka, Generation of cyclonic eddies in the Eastern Gotland Basin of the Baltic Sea following dense water inflows: numerical experiments. J. Mar. Sys., 38(3-4), 323-336, 2003Zhurbas, V. M., J. Laanemets, N. P. Kuzmina, S. S. Muraviev and J. Elken, Direct estimates of the lateral eddy diffusivity in the gulf of finland of the Baltic Sea (based on the results of numerical experiments with an eddy resolving model). Oceanology, 48(2), 175-181, 2008Zhurbas, V., I. S. Oh and T. Park, Formation and decay of a longshore baroclinic jet associated with transient coastal upwelling and downwelling: A numerical study with applications to the Baltic Sea. J. Geophys. Res., 111, C04014, 10.1029/2005JC003080, 2006Zhurbas, V., I. S. Oh and T. Park, Formation and decay of a longshore baroclinic jet associated with transient coastal upwelling and downwelling: A numerical study with applications to the Baltic Sea.. J. Geophys. Res., 111, C04014, 10.1029/2005JC003080, 2006Zhurbas, V., J. Laanemet and E. Vehtera, Modeling of the mesoscale structure of coupled upwelling/downwelling events and the related input of nutrients to the upper mixed layer in the Gulf of Finland, Baltic Sea. J. Geophys. Res., 113, C05004, 10.1029/2007JC004280, 2008Zhurbas, V., J. Laanemets, and E. Vahtera, Modeling of the mesoscale structure of coupled upwelling/downwelling events and the related input of nutrients to the upper mixed layer in the Gulf of Finland, Baltic Sea. J. Geophys. Res., 113, C05004, 10.1029/2007JC004280, 2008Zhurbas, V., T. Stipa, P. Malkki, V. Paka, N. Golenko, I. Hense and V. Sklyarov, Generation of subsurface cyclonic eddies in the southeast Baltic Sea: Observations and numerical experiments. J. Geophys. Res., 109, C05033, 10.1029/2003JC002074, 2004ziegler and nisbet, . Journal, Vol. No., pages, 1995Zodiatis G., R. Lardner, A. Lascaratos, G. Georgiou, G. Korres and M. Syrimis, High resolution nested model for the Cyprus, NE Levantine Basin, Eastern Mediterranean Sea: implementation and climatological runs. Annales Geophysicae, 21,221-236, 2003Zodiatis G., R. Lardner, G. Georgiou, E. Demirov, N. Pinardi and G. Manzella, The Cyprus coastal ocean forecasting and observing system. Sea Technology, 44(10), 10-15, 2003Zodiatis, G., R. Lardner, G. Georgiou, E. Demitrov, G. Manzella and N. Pinardi, An operational European global ocean observation system for the easterm Mediterranean basin: The Cyprus coastal ocean forecasting and observing system. J. Mar. Tech. Soc., 37(3), 115-123, 2003 |
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