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The following references list follows the the American Meteorological Society (AMS) guidelines for citation style (PDF).




Allen, J. S., P. A. Newberger, and J. Federiuk, 1995: Upwelling circulation on the Oregon continental shelf. Part I: Response to Idealized Forcing, J. Phys. Oceanogr., 25, 1843-1866.

Allen, S. E., M. S. Dinniman, J. M. Klinck, B. M. Hickey, D. D. Gorby, A. J. Hewett, 2003: On vertical advection truncation errors in terrain following numerical models: Comparison to a laboratory model for upwelling over submarine canyons, J. Geophys. Res., 108 (C1), 1-16, doi:10.1029/2001JC000978. (PDF)

Arakawa, A. and V. R. Lamb, 1977: Methods of computational physics, Academic Press, 174-265.

Arango, H. G., A. M. Moore, A. J. Miller, B. D. Cornuelle, E. Di Lorenzo, and D. J. Neilson, 2003: The ROMS Tangent Linear and Adjoint Models: A comprehensive ocean prediction and analysis system, IMCS Technical Reports, Rutgers University, 69pp. (PDF)

Arbic, B.K., Garner, S.T., Hallberg, R.W. and Simmons, H.L., 2004. The accuracy of surface elevations in forward global barotropic and baroclinic tide models. Deep Sea Research Part II: Topical Studies in Oceanography, 51(25-26), pp. 3069-3101.

Arbic, B.K., Alford, M.H., Ansong, J.K., Buijsman, M.C., Ciotti, R.B., Farrar, J.T., Hallberg, R.W., Henze, C.E., Hill, C.N., Luecke, C.A. and Menemenlis, D., 2018. Primer on Global Internal Tide and Internal Gravity Wave Continuum Modeling in HYCOM and MITgcm. In: New Frontiers in Operational Oceanography, E. Chassignet, A. Pascual, J. Tintoré and J. Verron (Eds.), GODAE OceanView, 307-392, doi: 10.17125/gov2018.ch13


Batchelor, G. K., 1967: An introduction to fluid dynamics, Cambridge University Press.

Bissett, W.P., J.J. Walsh, D.A. Dieterle, K.L. Carder, 1999a: Carbon cycling in the upper waters of the Sargasso Sea: I. Numerical simulation of differential carbon and nitrogen fluxes, Deep-Sea Res., 46, 205-269.

Bissett, W. P., K. L. Carder, J. J. Walsh, D. A. Dieterle, 1999b: Carbon cycling in the upper waters of the Sargasso Sea: II. Numerical simulation of apparent and inherent optical properties, Deep-Sea Res., 46, 271-317.

Bissett, W., Arnone, R., DeBra, S., Dieterle, D., Dye, D., Kirkpatrick, G., Schofield, O. and Vargo, G., 2005. Predicting the optical properties of the West Florida Shelf: Resolving the potential impacts of a terrestrial boundary condition on the distribution of colored dissolved and particulate matter. Marine Chemistry, 95(3-4), 199-233.

Booij, N., R. C. Ris, and L. H. Holthuijsen, 1999: A third-generation wave model for coastal regions. Part I - Model description and validation. Journal of Geophysical Research, 104, 7649-7666.

Budgell, W.P., 2005: Numerical simulation of ice-ocean variability in the Barents Sea region, Ocean Dynamics, DOI 10.1007/s10236-005-0008-3. (PDF)

Burchard, H., 2001: Simulating the wave-enhanced layer under breaking surface waves with two-equation turbulence models, J. Phys. Oceanogr., 31, 3133-3145.


Canuto, V. M., A. Howard, Y. Cheng, M. S. Dubovikov, 2001: Ocean turbulence I: one-point closure model. Momentum and heat vertical diffusivities, J. Phys. Oceanogr., 31, 1413-1426.

Chapman, D. C., 1985: Numerical treatment of cross-shelf open boundaries in a barotropic coastal ocean model, J. Phys. Oceanogr., 15, 1060--1075.

Chapman, S. J., 2004: Fortran 90/95 for Scientists and Engineers. Second Edition. McGraw-Hill. 814 pp.

Chassignet, E. P., H. G. Arango, D. Dietrich, T. Ezer, M. Ghil, D. B. Haidvogel C.-C. Ma, A. Mehra, A. M. Paiva, Z. Sirkes, 2000: DAMEE-NAB: The Base Experiments, Dyn. Atmos. Oceans, 32, 155-183. (PDF)

Choi, B.-J., and J. L. Wilkin, 2006a: The effect of wind on the dispersal of the Hudson River plume, J. Phys. Oceanogr., 37, 1878-1897. (PDF)

Chua, B. S. and A. F. Bennett, 2001: An inverse ocean modeling system, Ocean Modelling, 3, 137-165. (PDF)


Daley, R., 1991: Atmospheric Data Analysis, Cambridge Atmospheric and Space Science Series, Cambridge University Press, 457 pages.

Dean, R. G., and R. A. Dalrymple, 1991: Water Wave Mechanics for Engineers and Scientists. World Scientific, 353 pp.

Dekshenieks, M.M., E.E. Hofmann, and E.N. Powell, 1993: Environmental effect on the growth and development of Eastern oyster, Crassostrea virginica (Gmelin, 1791), larvae: A modeling study, J. Shelfish Res, 12, 241-254.

Dekshenieks, M.M., E.E. Hofmann, J.M. Klinck, and E.N. Powell, 1996: Modeling the vertical distribution of oyster larvae in response to environmental conditions, Mar. Ecol. Prog. Ser., 136, 97-110.

Dekshenieks, M.M., E.E. Hofmann, J.M. Klinck, and E.N. Powell, 1997: A modeling study of the effect of size- and depth-dependent predation on larval survival, J.Plankton Res., 19, (11), 1583-1598.

Di Lorenzo, E., 2003: Seasonal dynamics of the surface circulation in the southern California Current System, Deep-Sea Res., Part II, 50, 2371-2388.

Di Lorenzo, E., A.M. Moore, H.G. Arango, B.D. Cornuelle, A.J. Miller, B. Powell, B.S. Chua, and A.F. Bennett, 2006: Weak and Strong Constraint Data Assimilation in the inverse Regional Ocean Modeling System (ROMS): development and applications for a baroclinic costal upwelling system, Ocean Modelling, in press.

Dinniman, M. S. and J. M. Klinck, 2002: The influence of open versus periodic alongshore boundaries on circulations near submarine canyons, J. Atmos. Oceanic Tech., 19, 1722-1737 (PDF)

Dinniman, M. S., J. M. Klinck, and W. O. Smith Jr., 2003: Cross shelf exchange in a model of the Ross Sea circulation and biogeochemistry, Deep-Sea Res., Part II, 50, 3103-3120. (PDF)

Dinniman, M. S. and J. M. Klinck, 2004: A model study of circulation and cross shelf exchange on the west Antarctic Peninsula continental shelf, Deep-Sea Res., Part II, 51, 2003-2022. (PDF)

Doodson, A.T. and Warburg, H.D., 1941. Admiralty Manual of Tides. His Majesty’s Stationery Office, London, UK, 270 pp.

Doyle, J. D., Q. Jiang, and J. Farrara, 2009: High-resolution atmospheric modeling over the Monterrey Bay during AOSN II, Deep-Sea Res., Part II, 56, 87-99.

Durski, S. M., S. M. Glenn, D. B. Haidvogel, 2004: Vertical mixing schemes in the coastal ocean: Comparison of the Level 2.5 Mellor-Yamada scheme with an enhanced version of the K-profile parameterization, J. Geophys. Res., 109, C01015, doi:10.1029/2002JC001702. (PDF)


Egbert, G.D. and Ray, R.D., 2017. Tidal prediction. Journal of Marine Research, 75(3), pp.189-237.

Ezer, T., H. G. Arango and A. F. Shchepetkin, 2002: Developments in terrain-following ocean models: intercomparisons of numerical aspects, Ocean Modelling, 4, 249-267. (PDF)


Fairall, C. W., E. F. Bradley, D. P. Rogers, J. B. Edson and G. S. Young, 1996: Bulk parameterization of air-sea fluxes for tropical ocean-global atmosphere Coupled-Ocean Atmosphere Response Experiment, J. Geophys. Res., 101, 3747-3764.

Fairall, C. W., E. F. Bradley, J. E. Hare, A. A. Grachev and J. B. Edson (2003): Bulk parameterization of air-sea fluxes: Updates and verification for the COARE algorithm. J. Clim., 16 (4) 571-591, doi: 10.1175/1520-0442(2003)016<0571:BPOASF>2.0.CO;2.

Fasham, M. J. R., H. W. Ducklow, and S. M. McKelvie, 1990: A nitrogen-based model of plankton dynamics in the oceanic mixed layer, J. Mar. Res., 48, 591-639.

Fedorov, K. N., 1988: Layer thicknesses and effective diffusivities in the diffusive thermocline convection in the ocean, In J.C.J. Nihoul and B.M. Jamart, editors, Small-scale turbulence and mixing in the ocean, pages 471-479, Elsevier, New York.

Fennel, K., J. Wilkin, M. Previdi, R. Najjar, 2008: Denitrification effects on air-sea CO2 flux in the coastal ocean: Simulations for the Northwest North Atlantic, Geophys. Res. Let., 35, L24608. (PDF)

Fennel, K., J. Wilkin, J. Levin, J. Moisan, J. O'Reilly, and D. Haidvogel, 2006: Nitrogen cycling in the Middle Atlantic Bight: Results from a three-dimensional model and implications for the North Atlantic nitrogen budget, Global Biogeochem. Cycles, 20, GB3007, doi:10.1029/2005GB002456. (PDF)

Fiechter, J., A.M. Moore, C.A. Edwards, K.W. Bruland, E. Di Lorenzo, C.V.W. Lewis, T.M. Powell, E. Curchitser, and K. Hedstrom, 2009: Modeling iron limitation of primary production in the coastal Gulf of Alaska, Deep_Sea Res. II, 56(24), 2503-2519. (PDF)

Fisher, M. and P. Courtier, 1995: Estimating the covariance matrices of analysis and forecast error in variational data assimilation, ECMWF Technical Memo N. 220, ECMWF, Reading, UK. PDF

Fisher, M., 1997: Efficient minimization of quadratic penalty functions. Unpublished manuscript.

Fisher, M., 1998: Minimization algorithms for variational data assimilation. Recent Developments in Numerical Methods for Atmospheric Modelling, ECMWF publication, 364-385.

Flather, R. A., 1976: A tidal model of the northwest European continental shelf. "Memoires de la Societe Royale de Sciences de Liege, 6, 141-164.

Franks, P. J. S., J. S. Wroblewski, and G. R. Flierl, 1986: Behavior of simple plankton model with food-level acclimation by herbivores, Mar. Biol., 91, 121-129.

Freeman, N. G., A. M. Hale, and M. B. Danard, 1972: A modified sigma equations' approach to the numerical modeling of great lake hydrodynamics, J. Geophys. Res., 77, 1050-1060.


Galperin, B., L. H. Kantha, S. Hassid, and A. Rosati, 1988: A quasi-equilibrium turbulent energy model for geophysical flows, J. Atmos. Sci., 45, 55-62.

Golub, G. H. and C. Van Loan, 1989: Matrix Computations, Johns Hopkins University Press, 2nd edition, Baltimore, Maryland.

Griffies, S.M., A. Gnanadesikan, R.C. Pacanowski, V. Larichev, J.K. Dukowicz, and R.D. Smith, 1998: Isoneutral diffusion in a z-coordinate ocean model, J. Phys. Oceanogr., 28, 805--830.

Griffies, S.M. and R.W. Hallberg, 2000: Biharmonic friction with a Smagorinsky-like viscosity for use in large-scale eddy-permitting ocean models, Monthly Weather Rev., 128, 8, 2935--2946.


Haidvogel, D. B. and A. Beckmann, 1999: Numerical Ocean Circulation Modeling. Series on Environmental Science and Management, Vol. 2, Imperial College Press, 319 pp.

Haidvogel, D. B., H. G. Arango, K. Hedstrom, A. Beckmann, P. Malanotte-Rizzoli, and A. F. Shchepetkin, 2000: Model evaluation experiments in the North Atlantic Basin: Simulations in nonlinear terrain-following coordinates, Dyn. Atmos. Oceans, 32, 239-281. (PDF)

Hakkinen, S. and G. L. Mellor, 1992: Modeling the seasonal variability of a coupled arctic ice-ocean system, J. Geophys. Res., 97, 20285-20304.

He, R., and J. L. Wilkin, 2006a: Barotropic tides on the southeast New England shelf: A view from a hybrid data assimilative modeling approach, J. Geophys. Res., 111, C08002, doi:10.1029/2005JC003254. (PDF)

Hibler, III, W. D., 1979: A dynamic thermodynamic sea ice model, J. Phys. Oceanogr., 9, 815-846.

Hunke, E. C., 2001: Viscous-plastic sea ice dynamics with the EVP model: linearization issues, J. Comp. Phys., 170, 18-38.

Hunke, E. C. and J. K. Dukowicz, 1997: An elastic-viscous-plastic model for sea ice dynamics, J. Phys. Oceanogr., 27, 1849-1868.



Jackett, D. R. and T. J. McDougall, 1995: Minimal Adjustment of Hydrostatic Profiles to Achieve Static Stability, J. Atmos. Oceanic Techn., 12, 381-389.


Kantha, L.H., C.A. Clayson, 1994: Nermerical Models of Oceans and Oceanic Processes. In: International Geophysics Series, Vol. 66. Academic Press, San Diego. 940 pp.

Keeling, R. F., B. B. Stephens, R. G. Najjar, S. C. Doney, D. Archer, and M. Heimann, 1998: Seasonal variations in the atmospheric O2/N2 ratio in relation to the kinetics of air-sea gas exchange, Global Biogeochem. Cycles, 12(1), 141-163.

Kishi, M. J., et al., 2007: Nemuro - a lower trophic level model for the North Pacific marine ecosystem, Ecological Modelling, 202, 12-25.

Kosters, F., 2004: Denmark Strait overflow: Comparing model results and hydraulic transport estimates, J. Geophys. Res., 109, C10011, doi:10.1029/2004JC002297. (PDF)


Laevastu, T., 1960: Factors affecting the temperature of the surface layer of the sea, Comments Phys. Math., 25, 1.

Large, W. G., J. C. McWilliams, and S. C. Doney, 1994: Oceanic vertical mixing: a review and a model with a nonlocal boundary layer parameterization, Rev. Geophys., 32, 363-403.

Large, W. G., 1998: Modeling and parameterization ocean planetary boundary layers, In Ocean Modeling and Parameterization, E. P. Chassignet and J. Verron editors, pages 81-120, Kluwer Academic Publishers.

Large, W. G. and S. G. Yeager, 2009: The global climatology of an interannually varying air-sea flux data set, Clim. Dyn., 33, 341-364, DOI 10.1007/s00382-0008-0441-3.

Ledwell, J. R., A. J. Wilson, and C. S. Low, 1993: Evidence for slow mixing across the pycnocline from an open-ocean tracer-release experiment, Nature, 364, 701-703.

Lemieux, J.-F., L. B. Tremblay, F. Dupont, M. Plante, G. C. Smith, and D. Dumont (2015), A basal stress parameterization for modeling landfast ice, J. Geophys. Res. Oceans, 120, 3157–3173, doi:10.1002/2014JC010678.

Leonard, B. P., 1979: A stable and accurate convective modelling procedure based on quadratic upstream interpolation. Comput. Methods Appl. Mech. Eng., 19, 59-98.

Lesser, G. R., J. A. Roelvink, J. A. T. M. van Kester, and G. S. Stelling, 2004: Development and validation of a three-dimensional morphological model. Coastal Engineering, 51, 883-915.


MacCready, P. and W. R. Geyer, 2001: Estuarine salt flux through an isohaline surface, J. Geophys. Res., 106 (C6), 11629-11637. (PDF)

Mailhôt, J. and R. Benoit, 1982: A finite-element model of the atmospheric boundary layer suitable for use with numerical weather prediction models, J. Atmos. Sci., 39, 2249-2266.

Malanotte-Rizzoli, P., K. Hedstrom, H.G. Arango, and D.B. Haidvogel, 2000: Water mass pathways between the subtropical and tropical ocean in a climatological simulation of the North Atlantic ocean circulation, Dyn. Atmos. Oceans, 32, 331-371. (PDF)

Marchesiello, P., J. C. McWilliams, A. F. Shchepetkin, 2001: Open boundary conditions for long-term integration of regional ocean models, Ocean Modelling, 3, 1-20. (PDF)

Marchesiello, P., J. C. McWilliams, and A. Shchepetkin, 2003: Equilibrium structure and dynamics of the California Current System, J. Phys. Oceanogr., 33, 753-783. (PDF)

Mason, E., J. Molemaker, A. F. Shcheptkin, F. Colas, J. C. McWilliams and P. Sangrà, 2010: Procedures for offline grid nesting in regional ocean models, Ocean Modelling, 35, 1-15.

Maykut, G. A. and N. Untersteiner, 1971: Some results from a time-dependent thermodynamic model of sea ice, J. Geophys. Res., 76, 1550-1575.

Mellor, G. L. and T. Yamada, 1982: Developement of a turbulence closure model for geophysical fluid problems, Rev. Geophys. Space Phys., 20, 851-875.

Mellor, G. L. and L. Kantha, 1989: An ice-ocean coupled model, J. Geophys. Res., 94, 10,937-10,954.

Meyer-Peter, E., and R. Mueller, 1948: Formulas for bedload transport. In: Report on the Second Meeting of the International Association Hydraulic Structure Research, Stockholm, Sweden, 39-64.

Moore, A.M., H.G. Arango, G. Broquet, B.S. Powell, A.T. Weaver, and J. Zavala-Garay, 2011: The Regional Ocean Modeling System (ROMS) 4-dimensional variational data assimilation systems, Part I - System overview and formulation, Progress in Oceanography, 91, 34-49.

Moore, A.M., H.G. Arango, and G. Broquet, C. Edwards, M. Veneziani, B.S. Powell, D. Foley, J. Doyle, D. Costa, and P. Robinson, 2011: The Regional Ocean Modeling System (ROMS) 4-dimensional variational data assimilation systems, Part II: Performance and application to the California Current System, Progress in Oceanography, 91, 50-73.

Moore, A.M., H.G. Arango, and G. Broquet, C. Edwards, M. Veneziani, B.S. Powell, D. Foley, J. Doyle, D. Costa, and P. Robinson, 2011: The Regional Ocean Modeling System (ROMS) 4-dimensional variational data assimilation systems, Part III: Observation Impact and Observation Sensitivity in the California Current System, Ocean Modelling, 91, 74-94.

Moore, A.M., H.G. Arango, E. Di Lorenzo, A.J. Miller and B.D. Cornuelle, 2006: An adjoint sensitivity analysis of the southern portion of the California Current circulation and ecosystem, Part I: The physical circulation, J. Phys. Oceanogr., submitted.

Moore, A. M., H. G. Arango, A. J. Miller, B. D. Cornuelle, E. Di Lorenzo and D. J. Neilson, 2004: A Comprehensive Ocean Prediction and Analysis System Based on the Tangent Linear and Adjoint Components of a Regional Ocean Model, Ocean Modelling, 7, 227-258. (PDF)

Muccino, J. C., H. G. Arango, A. B. Bennett, B. S. chua, B. D. Cornuelle, E. Di Lorenzo, G. D. Egbert, D. B. Haidvogel, L. Hao, J. C. Levin, A. J. Miller, A. M. Moore, and E. D. Zaron, 2006: The Inverse Ocean Modeling System. II: Applications, J. Atmos. Oceanic Tech., submitted.



Orlanski, I., 1976: A simple boundary condition for unbounded hyperbolic flows. J. Comp. Sci., 21(3), 251-269.

Overland, J. E. and C. H. Pease, 1988: Modeling ice dynamics of coastal seas. J. Geophys. Res., 93(C12), 15,619-15,637.


Parkinson, C. L. and W. M. Washington, 1979: A large-scale numerical model of sea ice, J. Geophys. Res., 84, 311-337.

Paulson, C. A., and J. J. Simpson, 1977: Irradiance measurements in the upper ocean, J. Phys. Oceanogr., 7, 952-956.

Peliz, A., J. Dubert, D. B. Haidvogel, 2003: Subinertial Response of a Density-Driven Eastern Boundary Poleward Current to Wind Forcing, J. Phys. Oceanogr., 33, 1633-1650. (PDF)

Peliz, A., J. Dubert, D. B. Haidvogel, and B. Le Cann, 2003: Generation and unstable evolution of a density-driven Eastern Poleward Current: The Iberian Poleward Current, J. Geophys. Res., 108 (C8), 3268, doi:10.1029/2002JC001443. (PDF)

Penven, P., C. Roy, A. Colin de Verdiere and J. Largier, 2000: Simulation of a coastal jet retention process using a barotropic model, Oceanology Acta, 23(5), 615-634. (PDF)

Penven, P., C. Roy, J.R.E. Lutjeharms, A. Colin de Verdiere, A. Johnson, F. Shillington, P. Freon and G. Brundrit, 2001: A regional hydrodynamic model of the Southern Benguela, S. Afr. J. Sci. Res. Letters, 97, 1-4. (PDF)

Penven, P., J. R. E. Lutjeharms, P. Marchesiello, C. Roy and S. J. Weeks, 2001: Generation of cyclonic eddies by the Agulhas Current in the lee of the Agulhas Bank, Geophys. Res. Letters, 27, 1055-1058. (PDF)

Peters, H., M. C. Gregg and J. M. Toole, 1988: On the parameterization of equatorial turbulence, J. Geophys. Res., 93, 1199-1218.

Phillips, N. A., 1957: A coordinate system having some special advantages for numerical forecasting, J. Meteorology, 14, 184-185.

Powell, B.S., H.G. Arango, A.M. Moore, E. DiLorenzo, R.F. Milliff and D. Foley, 2008: 4DVAR Data Assimilation in the Intra-Americas Sea with the Regional Ocean Modeling System (ROMS). Ocean Modelling, 25, 173-188.

Powell T. P., C. V. W. Lewis, E. N. Curchitser, D. B. Haidvogel, A. J. Hermann, E. L. Dobbins (2006), Results from a three-dimensional, nested biological-physical model of the California Current System and comparisons with statistics from satellite imagery, J. Geophys. Res., 111, C07018, doi:10.1029/2004JC002506.



Rasch, P.J., 1994: Conservative shape-preserving two-dimensional transport on a spherical reduced grid, Mon. Wea. Rev, 122, 1337-1350.

Raymond, W. H. and H. L. Kuo, 1984: A radiation boundary condition for multi-dimensional flows, Quart. J. R. Met. Soc., 110, 535-551.

Robertson, R., 2006: Modeling internal tides over Fieberling Guyot: resolution, parameterization, performance, Ocean Dynamics, doi:10.1007/s10236-006-0062-5. (PDF)


Sadourny, R. and K. Maynard, 1997: Formulations of lateral diffusion in geophysical fluid dynamics models, In Numerical Methods of Atmospheric and Oceanic Modelling, C.A. Lin, R. Laprise, and H. Ritchie, Eds., NRC Research Press, 547--556.

Semtner, Jr., A. J., 1976: A model for the thermodynamic growth of sea ice in numerical investigations of climate, J. Phys. Oceanogr., 6, 379-389.

Shchepetkin, A. F., and J. C. McWilliams, 1998: Quasi-monotone advection schemes based on explicit locally adaptive dissipation, Monthly Weather Rev., 126, 1541-1580. (PDF)

Shchepetkin, A. F., and J. C. McWilliams, 2003: A method for computing horizontal pressure-gradient force in an oceanic model with a nonaligned vertical coordinate, J. Geophys. Res., 108 (C3), 3090, doi:10.1029/2001JC001047. (PDF)

Shchepetkin, A. F., and J. C. McWilliams, 2005: The Regional Ocean Modeling System: A split-explicit, free-surface, topography following coordinates ocean model, Ocean Modelling, 9, 347-404. (PDF)

Shchepetkin, A. F., and J. C. McWilliams, 2009: Correction and Commentary for "Ocean forecasting in terrain-following coordinates: formulation and skill assessment of the Regional Ocean Modeling System" by Haidvogel et al., J. Comp. Phys., 228, 8985-9000.

Shchepetkin, A. F., and J. C. McWilliams, 2008: Computational kernel algorithms for fine-scale, multi-process, long-time oceanic simulations. In: Handbook of Numerical Analysis: Computational Methods for the Ocean and the Atmosphere, eds. R. Temam & J. Tribbia, Elsevier Science, ISBN-10: 0444518932, ISBN-13: 978-0444518934.

Shchepetkin, A. F., and J. C. McWilliams, 2011: An Accurate Boussinesq oceanic model with a practical, "Stiffened" equation of state. Ocean Modeling, 38, pp. 41-70, doi:10.1016/j.ocemod.2011.01.010. (preprint PDF)

She, J. and J. M. Klinck, 2000: Flow near submarine canyons driven by constant winds, J. Geophys. Res., 105(C12), 28671-28694. (PDF)

Signell, R. P., R. C. Beardsley, H. C. Graber, and A. Capotondi, 1990: Effect of Wave-Current Interaction on Steady Wind-Driven Circulation in Narrow, Shallow Embayments, J. Geophys. Res., 95(C6), 9671-9678.

Signell, R. P., W. R. Geyer, 1991: Transient Eddy Formation Around Headlands, J. Geophys. Res., 96(C2), 2561-2575.

Smith, W.O., Jr., M.S. Dinniman, J.M. Klinck and E.E. Hofmann, 2003: Biogeochemical Climatologies of the Ross Sea, Antarctica: Seasonal Patterns of Nutrients and Biomass, Deep-Sea Res., Part II, 50, 3083-3101. (PDF)

Smolarkiewicz, P.K. and L.G. Margolin, 1998: MPDATA: A Finite-Difference Solver for Geophysical Flows, Journal of Computational Physics, 140(2), 459-480, doi: 10.1006/jcph.1998.5901.

Song, Y. and D. B. Haidvogel, 1994: A semi-implicit ocean circulation model using a generalized topography-following coordinate system, J. Comp. Phys., 115 (1), 228-244. (PDF)

Soulsby, R. L. and Damgaard, J. S. 2005: Bedload sediment transport in coastal waters. Coastal Engineering, 52, 673-689.

Soulsby, R. L. and Whitehouse, R. J. S., 2005: Prediction of Ripple Properties in Shelf Seas; Mark 2 Predictor for Time Evolution. Report TR 154, HR Wallingford, Wallingford, UK.

Soulsby, R. L., 2006: Simplified calculation of wave-orbital velocities. Report TR 155, HR Wallingford, Wallingford, UK. Steele, M., G. L. Mellor and M. G. McPhee, 1989: Role of the molecular sublayer in the melting or freezing of sea ice, J. Phys. Oceanogr., 19, 139-147.

Souza, J. M., B. Powell, A. C. Castillo-Trujillo, and P. Flament, 2015: The Vorticity Balance of the Ocean Surface in Hawaii fron a Regional Reanalysis, J. Phys. Oceanogr., 45, 424-440, doi:10.1175/JPO-D-14-0074.1.

Styles, R. and S. M. Glenn, 2000: Modeling stratified wave and current bottom boundary layers in the continental shelf, J. Geophys. Res., 105, 24119-24139. (PDF)


Thuburn, J., 1995: Dissipation and cascade to small scales in numerical models using a shape-preserving advection scheme. Mon. Wea. Rev., 123, 1888-1903.

Troen, I.B. and L. Mahrt, 1986: A simple model of the atmospheric boundary layer; sensitivity to surface evaporation. Boundary-Layer Meteor., 37, 129-148.

Tshimanga, J., 2007: On a class of limited memory preconditioners for large-scale nonlinear least-squares problems. PhD thesis, Facultes Universitaires Notre-Dame de la Paix, Namur, Belgium.

Tshimanga, J., S. Gratton, A.T. Weaver and A. Sartenaer, 2008: Limited-memory preconditioners with application to incremental variational data assimilation. Q. J. R. Meteorol. Soc., 134, 751-769.


Umlauf, L., H. Burchard, 2003: A generic length-scale equation for geophysical turbulence models, J. Marine Res., 61, 235-265.



Wajsowicz, R.C, 1993: A consistent formulation of the anisotropic stress tensor for use in models of the large-scale ocean circulation, J. Comput. Phys., 105, 333-338.

Wanninkhof, R., 1992: Relationship between wind speed and gas exchange over the ocean, J. Geophys. Res., 97(C5), 7373-7382.

Warner, J. C., C. R. Sherwood, H. G. Arango, and R. P. Signell, 2005a: Performance of four turbulence closure methods implemented using a generic length scale method, Ocean Modelling, 8, 81-113. (PDF)

Warner, J. C., W. R. Geyer, and J. A. Lerczak, 2005b: Numerical modeling of an estuary: a comprehensive skill assessment, J. Geophys. Res., 110, C05001, doi:10.1029/2004JC002691. (PDF)

Warner, J. C., C. R. Sherwood, R. P. Signell, C. K. Harris, and H. G. Arango, 2008: Development of a three-dimensional, regional, coupled wave, current, and sediment-transport model, Computers & Geosciences, 34, 1284-1306.

Warner, J. C., N. Perlin, E. D. Skyllingstad, 2008: Using the Model Coupling Toolkit to couple earth system models, Environmental Modelling & Software, 23, 1240-1249.

Wiberg, P. L. and C. K. Harris, 1994: Ripple geometry in wave-dominated environments. Journal of Geophysical Research, 99(C1), 775-789.

Wiberg, P. L. and C. R. Sherwood, 2008: Calculating wave-generated bottom orbital velocity from surfacewave parameters. Computers & Geosciences, 34, 1243-1262.

Weaver, A.T., C. Deltel, E. Machu, S. Ricci, and N. Daget, 2005: A multivariate balance operator for variational data assimilation, Q. J. R. Meteorol. Soc., 131, 3605-3625.

Weaver, A.T., J. Vialard and D.L.T. Anderson, 2003: Three and four-dimensional variational data assimilation with a general circulation model of the tropical Pacific Ocean. Part I: Formulation, internal diagnostics, and consistency checks. Mon. Wea. Rev., 131, 1360-1378.

Weaver, A. and P. Courtier, 2001: Correlation modeling on the sphere using a generalized diffusion equation, Q.J.R. Meteo. Soc, 127, 1815-1846.

Wilkin, J. L., H. G. Arango, D. B. Haidvogel, C. S. Lichtenwalner, S. M. Durski, and K. S. Hedstrom, 2005: A regional Ocean Modeling System for the Long-term Ecosystem Observatory, J. Geophys. Res., 110, C06S91, doi:10.1029/2003JC002218. (PDF)

Wilkin, J. L., and L. Lanerolle, 2005: Ocean Forecast and Analysis Models for Coastal Observatories, in: Ocean Weather Forecasting, An Integrated View of Oceanography, Springer, 577p., ISBN: 978-1-4020-3981-2. (Publisher)

Wilkin, J. L., 2006: The summer time heat budget and circulation of southeast New England shelf, J. Phys. Oceanog., 36, 1997-2011. (PDF)

Wilkin, J. L., and W. Zhang, 2006: Modes of mesoscale sea surface height and temperature variability in the East Australian Current, J. Geophys. Res., 112, C01013, doi:10.1029/2006JC003590. (PDF)

Winsor, P. and D. C. Chapman, 2004: Pathways of Pacific water across the Chukchi Sea: A numerical model study, J. Geophys. Res., 109, C03002, doi: 10.1029/2003JC001962. (PDF)

Wu, Hui and Jianrong Zhu, 2010: Advection scheme with 3rd high-order spatial interpolation at the middle temporal level and its application to saltwater intrusion in the Changjiang Estuary, Ocean Modelling 33, 33-51, doi:10.1016/j.ocemod.2009.12.001.

Wunsch, C. and P. Heimbach, 2007: Practical global ocean state estimation, Physica D, 230, 197-208.



Yaglom, A. M. and B. A. Kader, 1974: Heat and mass transfer between a rough wall and turbulent fluid at high Reynolds and Peclet numbers, J. Fluid Mech., 62, 601-623.


Zillman, J. W., 1972: A study of some aspects of radiation and heat budgets of southern hemisphere oceans, Meteorological Studies, 26, 562-575.

Zhu, Y. and R. Gelaro, 2008: Observation Sensitivity Calculations Using the Adjoint of the Gridpoint Statistical Interpolation (GSI) Analysis System, Monthly Weather Review, 136, 335-351.