Bibliography

Bibliography

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

A

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 Univeristy, 69pp. (PDF)

B

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.

C

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)

D

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)

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)

E

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)

F

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.

G

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.

H

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.

J

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

K

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)

L

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.

M

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.

O

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.

P

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.

R

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)

S

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)

T

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.

U

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

W

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.

Y

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.

Z

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.