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==<span class="alphabet">A</span>==
==<span class="alphabet">A</span>==
<span id="AllenJS_1995"></span>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.


<span id="AllenSE_2003a"></span>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. ([http://marine.rutgers.edu/po/Papers/Allen_JGR_2001JC000978.pdf PDF])
<span id="AllenSE_2003a"></span>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. ([http://marine.rutgers.edu/po/Papers/Allen_JGR_2001JC000978.pdf PDF])
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<span id="ArakawaA_1977a"></span>Arakawa, A. and V. R. Lamb, 1977: ''Methods of computational physics'', Academic Press, 174-265.
<span id="ArakawaA_1977a"></span>Arakawa, A. and V. R. Lamb, 1977: ''Methods of computational physics'', Academic Press, 174-265.


<span id="ArangoHG_2003a"></span>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. ([http://marine.rutgers.edu/po/Papers/roms_adjoint.pdf PDF])
<span id="ArangoHG_2003a"></span>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. ([http://marine.rutgers.edu/po/Papers/roms_adjoint.pdf PDF])
 
<span id="ArbicBK_2004a"></span>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.
 
<span id="ArbicBK_2018a"></span>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


==<span class="alphabet">B</span>==
==<span class="alphabet">B</span>==
<span id="Batchelor67"></span>Batchelor, G. K., 1967: ''An introduction to fluid dynamics'', Cambridge University Press.


<span id="BissettWP_1999a"></span>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.
<span id="BissettWP_1999a"></span>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.
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<span id="BissettWP_2005a"></span>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.
<span id="BissettWP_2005a"></span>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.
<span id="BooijN_1999a"></span>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.


<span id="BudgellWP_2005a"></span>Budgell, W.P., 2005: Numerical simulation of ice-ocean variability in the Barents Sea region, ''Ocean Dynamics'', DOI 10.1007/s10236-005-0008-3. ([http://marine.rutgers.edu/po/Papers/Budgell_od.pdf PDF])
<span id="BudgellWP_2005a"></span>Budgell, W.P., 2005: Numerical simulation of ice-ocean variability in the Barents Sea region, ''Ocean Dynamics'', DOI 10.1007/s10236-005-0008-3. ([http://marine.rutgers.edu/po/Papers/Budgell_od.pdf PDF])
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<span id="CanutoVM_2001a"></span>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.
<span id="CanutoVM_2001a"></span>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.


<span id="ChapmanSJ_2004a"></span>Chapman, S. J., 2004: ''Fortan 90/95 for Scientists and Engineers''. Second Edition. McGraw-Hill. 814 pp.
<span id="Chapman_1985"></span>Chapman, D. C., 1985: Numerical treatment of cross-shelf open boundaries in a barotropic coastal ocean model, ''J. Phys. Oceanogr.'', '''15''', 1060--1075.
 
<span id="ChapmanSJ_2004a"></span>Chapman, S. J., 2004: ''Fortran 90/95 for Scientists and Engineers''. Second Edition. McGraw-Hill. 814 pp.


<span id="ChassignetEP_2000a"></span>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.  ([http://marine.rutgers.edu/po/Papers/damee_rev.pdf PDF])
<span id="ChassignetEP_2000a"></span>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.  ([http://marine.rutgers.edu/po/Papers/damee_rev.pdf PDF])
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==<span class="alphabet">D</span>==
==<span class="alphabet">D</span>==
<span id="DaleyR_1991a"></span>Daley, R., 1991: Atmospheric Data Analysis, ''Cambridge Atmospheric and Space Science Series'', Cambridge University Press, 457 pages.
<span id="DeanR_1991a"></span>Dean, R. G., and R. A. Dalrymple, 1991: ''Water Wave Mechanics for Engineers and Scientists''.  World Scientific, 353 pp.
<span id="DekshenieksM_1993a"></span>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.
<span id="DekshenieksM_1996a"></span>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.
<span id="DekshenieksM_1997a"></span>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.


<span id="DiLorenzoE_2003a"></span>Di Lorenzo, E., 2003: Seasonal dynamics of the surface circulation in the southern California Current System, ''Deep-Sea Res., Part II'', '''50''', 2371-2388.
<span id="DiLorenzoE_2003a"></span>Di Lorenzo, E., 2003: Seasonal dynamics of the surface circulation in the southern California Current System, ''Deep-Sea Res., Part II'', '''50''', 2371-2388.
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<span id="DinnimanMS_2004a"></span>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. ([http://marine.rutgers.edu/po/Papers/DSRII1415.pdf PDF])
<span id="DinnimanMS_2004a"></span>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. ([http://marine.rutgers.edu/po/Papers/DSRII1415.pdf PDF])
<span id="DoodsonAT_1941a"></span>Doodson, A.T. and Warburg, H.D., 1941. Admiralty Manual of Tides. His Majesty’s Stationery Office, London, UK, 270 pp.
<span id="DoyleJD_2009"></span>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.


<span id="DurskiSM_2004a"></span>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. ([http://marine.rutgers.edu/po/Papers/Durski_JGR04.pdf PDF])
<span id="DurskiSM_2004a"></span>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. ([http://marine.rutgers.edu/po/Papers/Durski_JGR04.pdf PDF])


==<span class="alphabet">E</span>==
==<span class="alphabet">E</span>==
<span id="EgbertGD_2017a"></span>Egbert, G.D. and Ray, R.D., 2017. Tidal prediction. ''Journal of Marine Research'', '''75'''(3), pp.189-237.


<span id="EzerT_2002a"></span>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. ([http://marine.rutgers.edu/po/Papers/ezer_etal_2002.pdf PDF])
<span id="EzerT_2002a"></span>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. ([http://marine.rutgers.edu/po/Papers/ezer_etal_2002.pdf PDF])
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<span id="FairallCW_1996a"></span>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.
<span id="FairallCW_1996a"></span>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.
<span id="FairallCW_2003"></span>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.


<span id="FashamMJR_1990a"></span>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.         
<span id="FashamMJR_1990a"></span>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.         


<span id="FennelK_2006a"></span>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. ([http://marine.rutgers.edu/po/Papers/Fennel_etal_gbc.pdf PDF])  
<span id="Fedorov_1988"></span>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. 
 
<span id="FennelK_2008a"></span>Fennel, K., J. Wilkin, M. Previdi, R. Najjar, 2008: Denitrification effects on air-sea CO<sub>2</sub> flux in the coastal ocean: Simulations for the Northwest North Atlantic, ''Geophys. Res. Let.'', '''35''', L24608. ([http://www.myroms.org/Papers/Fennel_GRL_2008.pdf PDF])
 
<span id="FennelK_2006a"></span>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. ([http://www.myroms.org/Papers/Fennel_etal_gbc.pdf PDF])
 
<span id="FiechterJ_2009a"></span>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. ([http://www.myroms.org/Papers/Fiechter_DSRII_2009.pdf PDF])  
 
<span id="FisherM_1995a"></span>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. [http://www.ecmwf.int/publications/library/ecpublications/_pdf/tm/001-300/tm220.pdf PDF]
 
<span id="FisherM_1997a"></span>Fisher, M., 1997: Efficient minimization of quadratic penalty functions.
Unpublished manuscript.
 
<span id="FisherM_1998a"></span>Fisher, M., 1998: Minimization algorithms for variational data assimilation.
''Recent Developments in Numerical Methods for Atmospheric Modelling'', ECMWF
publication, 364-385.
 
<span id="Flather_1976"></span>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.


<span id="FranksPJS_1986a"></span>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.                                                         
<span id="FranksPJS_1986a"></span>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.                                                         
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<span id="GalperinB_1988a"></span>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.
<span id="GalperinB_1988a"></span>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.
<span id="GolubG_1989a"></span>Golub, G. H. and C. Van Loan, 1989: Matrix Computations, ''Johns Hopkins University Press'', 2nd edition, Baltimore, Maryland.
<span id="GriffiesSM_1998a"></span>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.
<span id="GriffiesSM_2000a"></span>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.


==<span class="alphabet">H</span>==
==<span class="alphabet">H</span>==
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==<span class="alphabet">L</span>==
==<span class="alphabet">L</span>==
<span id="LaevastuT_1960a"></span>Laevastu, T., 1960: Factors affecting the temperature of the surface layer of the sea, ''Comments Phys. Math.'', '''25''', 1.


<span id="LargeWG_1994a"></span>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.
<span id="LargeWG_1994a"></span>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.


<span id="LaevastuT_1960a"></span>Laevastu, T., 1960: Factors affecting the temperature od the surface layer of the sea, ''Comments Phys. Math.'', '''25''', 1.
<span id="LargeWG_1998"></span>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., 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.
<span id="LargeWG_2008"></span>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.
 
<span id="Ledwell_1993"></span>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.
 
<span id="Lemieux_2015"></span>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.
 
<span id="LeonardBP_1979"></span>Leonard, B. P., 1979: A stable and accurate convective modelling procedure based on quadratic upstream interpolation. ''Comput. Methods Appl. Mech. Eng.'', '''19''', 59-98.
 
<span id="Lesser_2004a"></span>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.


==<span class="alphabet">M</span>==
==<span class="alphabet">M</span>==


<span id="MacCreadyP_2001a"></span>MacCready, P. and W. R. Geyer, 2001: Estuarine salt flux through an isohaline surface, ''J. Geophys. Res.'', '''106''' (C6), 11629-11637. ([http://marine.rutgers.edu/po/Papers/2001JC900006.pdf PDF])
<span id="MacCreadyP_2001a"></span>MacCready, P. and W. R. Geyer, 2001: Estuarine salt flux through an isohaline surface, ''J. Geophys. Res.'', '''106''' (C6), 11629-11637. ([http://marine.rutgers.edu/po/Papers/2001JC900006.pdf PDF])
<span id="Mailhot_1982"></span>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.


<span id="MalanotteRP_2000a"></span>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. ([http://marine.rutgers.edu/po/Papers/damee_roms2.pdf PDF])
<span id="MalanotteRP_2000a"></span>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. ([http://marine.rutgers.edu/po/Papers/damee_roms2.pdf PDF])
Line 149: Line 215:


<span id="MarchesielloP_2003a"></span>Marchesiello, P., J. C. McWilliams, and A. Shchepetkin, 2003: Equilibrium structure and dynamics of the California Current System, ''J. Phys. Oceanogr.'', '''33''', 753-783. ([http://marine.rutgers.edu/po/Papers/CCS_jpo03.pdf PDF])
<span id="MarchesielloP_2003a"></span>Marchesiello, P., J. C. McWilliams, and A. Shchepetkin, 2003: Equilibrium structure and dynamics of the California Current System, ''J. Phys. Oceanogr.'', '''33''', 753-783. ([http://marine.rutgers.edu/po/Papers/CCS_jpo03.pdf PDF])
<span id="Mason_2010"></span>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.
<span id="Maykut_1971"></span>Maykut, G. A. and N. Untersteiner, 1971: Some results from a time-dependent thermodynamic model of sea ice, ''J. Geophys. Res.'', '''76''', 1550-1575.


<span id="MellorGL_1982a"></span>Mellor, G. L. and T. Yamada, 1982: Developement of a turbulence closure model for geophysical fluid problems, ''Rev. Geophys. Space Phys.'', '''20''', 851-875.
<span id="MellorGL_1982a"></span>Mellor, G. L. and T. Yamada, 1982: Developement of a turbulence closure model for geophysical fluid problems, ''Rev. Geophys. Space Phys.'', '''20''', 851-875.
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<span id="MellorGL_1989a"></span>Mellor, G. L. and L. Kantha, 1989: An ice-ocean coupled model, ''J. Geophys. Res.'', '''94''', 10,937-10,954.
<span id="MellorGL_1989a"></span>Mellor, G. L. and L. Kantha, 1989: An ice-ocean coupled model, ''J. Geophys. Res.'', '''94''', 10,937-10,954.


<span id="MooreAM_2004a"></span>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. ([http://marine.rutgers.edu/po/Papers/Moore_2004_om.pdf PDF])
<span id]"Meyer-PeterE_1948a"></span>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.
 
<span id="MooreAM_2011a"></span>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.
 
<span id="MooreAM_2011b"></span>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.
 
<span id="MooreAM_2011c"></span>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.


<span id="MooreAM_2006a"></span>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.
<span id="MooreAM_2006a"></span>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.
<span id="MooreAM_2004a"></span>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. ([http://marine.rutgers.edu/po/Papers/Moore_2004_om.pdf PDF])


<span id="MuccinoJC_2006a"></span>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.
<span id="MuccinoJC_2006a"></span>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.
Line 163: Line 241:


==<span class="alphabet">O</span>==
==<span class="alphabet">O</span>==
<span id="Orlanski_1976"></span>Orlanski, I., 1976: A simple boundary condition for unbounded hyperbolic flows.
''J. Comp. Sci.'', '''21'''(3), 251-269.
<span id="Overland_1988"></span>Overland, J. E. and C. H. Pease, 1988: Modeling ice dynamics of coastal seas.
''J. Geophys. Res.'', '''93'''(C12), 15,619-15,637.


==<span class="alphabet">P</span>==
==<span class="alphabet">P</span>==


<span id="ParkinsonCL_1979a"></span>Parkinson, C. L. and W. M. Washington, 1979: A large-scale numerical model of sea ice, ''J. Geophys. Res.'', '''84''', 311-337.
<span id="ParkinsonCL_1979a"></span>Parkinson, C. L. and W. M. Washington, 1979: A large-scale numerical model of sea ice, ''J. Geophys. Res.'', '''84''', 311-337.
<span id="PaulsonCA_1977a"></span>Paulson, C. A., and J. J. Simpson, 1977: Irradiance measurements in the upper ocean, ''J. Phys. Oceanogr.'', '''7''', 952-956.


<span id="PelizA_2003a"></span>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. ([http://marine.rutgers.edu/po/Papers/Peliz_jpo03.pdf PDF])
<span id="PelizA_2003a"></span>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. ([http://marine.rutgers.edu/po/Papers/Peliz_jpo03.pdf PDF])
Line 177: Line 263:


<span id="PenvenP_2001b"></span>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. ([http://marine.rutgers.edu/po/Papers/grl_2001_28_6.pdf PDF])
<span id="PenvenP_2001b"></span>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. ([http://marine.rutgers.edu/po/Papers/grl_2001_28_6.pdf PDF])
<span id="Peters_1988"></span>Peters, H., M. C. Gregg and J. M. Toole, 1988: On the parameterization of equatorial turbulence, ''J. Geophys. Res.'', '''93''', 1199-1218.


<span id="PhillipsNA_1957a"></span>Phillips, N. A., 1957: A coordinate system having some special advantages for numerical forecasting, ''J. Meteorology'', '''14''', 184-185.
<span id="PhillipsNA_1957a"></span>Phillips, N. A., 1957: A coordinate system having some special advantages for numerical forecasting, ''J. Meteorology'', '''14''', 184-185.
<span id="PowellBS_2008a"></span>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.


<span id="PowellTP_2006a"></span>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.
<span id="PowellTP_2006a"></span>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.
Line 185: Line 275:


==<span class="alphabet">R</span>==
==<span class="alphabet">R</span>==
<span id="RaschP_1994"></span>Rasch, P.J., 1994: Conservative shape-preserving two-dimensional transport on a spherical reduced grid, ''Mon. Wea. Rev'', '''122''', 1337-1350.
<span id="Raymond_Kuo_1984"></span>Raymond, W. H. and H. L. Kuo, 1984: A radiation boundary condition for multi-dimensional flows, ''Quart. J. R. Met. Soc.'', '''110''', 535-551.


<span id="RobertsonR_2006a"></span>Robertson, R., 2006: Modeling internal tides over Fieberling Guyot: resolution, parameterization, performance, ''Ocean Dynamics'', doi:10.1007/s10236-006-0062-5. ([http://marine.rutgers.edu/po/Papers/Robertson_OceanDynamics-06.pdf PDF])
<span id="RobertsonR_2006a"></span>Robertson, R., 2006: Modeling internal tides over Fieberling Guyot: resolution, parameterization, performance, ''Ocean Dynamics'', doi:10.1007/s10236-006-0062-5. ([http://marine.rutgers.edu/po/Papers/Robertson_OceanDynamics-06.pdf PDF])


==<span class="alphabet">S</span>==
==<span class="alphabet">S</span>==
<span id="SadournyR_1997a"></span>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.


<span id="SemtnerAJ_1976a"></span>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.
<span id="SemtnerAJ_1976a"></span>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.
Line 197: Line 293:


<span id="ShchepetkinAF_2005a"></span>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. ([http://marine.rutgers.edu/po/Papers/Shchepetkin_om05.pdf PDF])
<span id="ShchepetkinAF_2005a"></span>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. ([http://marine.rutgers.edu/po/Papers/Shchepetkin_om05.pdf PDF])
<span id="ShchepetkinAF_2008a"></span>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.
<span id="ShchepetkinAF_2008b"></span>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.
<span id="ShchepetkinAF_2008c"></span>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. ([http://www.atmos.ucla.edu/~alex/ROMS/EOSArticle2011.pdf preprint PDF])


<span id="SheJ_2000a"></span>She, J. and J. M. Klinck, 2000: Flow near submarine canyons driven by constant winds, ''J. Geophys. Res.'', '''105'''(C12), 28671-28694. ([http://marine.rutgers.edu/po/Papers/2000JC900126.pdf PDF])
<span id="SheJ_2000a"></span>She, J. and J. M. Klinck, 2000: Flow near submarine canyons driven by constant winds, ''J. Geophys. Res.'', '''105'''(C12), 28671-28694. ([http://marine.rutgers.edu/po/Papers/2000JC900126.pdf PDF])
Line 205: Line 307:


<span id="SmithWO_2003a"></span>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. ([http://marine.rutgers.edu/po/Papers/DSRII1414.pdf PDF])
<span id="SmithWO_2003a"></span>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. ([http://marine.rutgers.edu/po/Papers/DSRII1414.pdf PDF])
<span id="SmolarkiewiczPK_1998a"></span>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.


<span id="SongY_1994a"></span>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. ([http://marine.rutgers.edu/po/Papers/scrum.pdf PDF])
<span id="SongY_1994a"></span>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. ([http://marine.rutgers.edu/po/Papers/scrum.pdf PDF])
<span id="SoulsbyR_2005b"></span>Soulsby, R. L. and Damgaard, J. S. 2005: Bedload sediment transport in coastal waters. ''Coastal Engineering'', '''52''', 673-689.
<span id="SoulsbyR_2005a"></span>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.
<span id="SoulsbyR_2006a"></span>Soulsby, R. L., 2006: ''Simplified calculation of wave-orbital velocities''. Report TR 155, HR Wallingford, Wallingford, UK.
<span id="Steele_89"></span>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.
<span id="SouzaJ_2015"></span>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.


<span id="StylesR_2000a"></span>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. ([http://marine.rutgers.edu/po/Papers/styles00.pdf PDF])
<span id="StylesR_2000a"></span>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. ([http://marine.rutgers.edu/po/Papers/styles00.pdf PDF])


==<span class="alphabet">T</span>==
==<span class="alphabet">T</span>==
<span id="ThuburnJ_1995"></span>Thuburn, J., 1995: Dissipation and cascade to small scales in numerical models using a shape-preserving advection scheme. ''Mon. Wea. Rev.'', '''123''', 1888-1903.
<span id="Troen_1986"></span>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.
<span id="TshimangaJ_2007a"></span>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.
<span id="TshimangaJ_2008a"></span>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.


==<span class="alphabet">U</span>==
==<span class="alphabet">U</span>==
Line 224: Line 345:
<span id="Wanninkhof_1992a"></span>Wanninkhof, R., 1992: Relationship between wind speed and gas exchange over the ocean, ''J. Geophys. Res.'', '''97'''(C5), 7373-7382.
<span id="Wanninkhof_1992a"></span>Wanninkhof, R., 1992: Relationship between wind speed and gas exchange over the ocean, ''J. Geophys. Res.'', '''97'''(C5), 7373-7382.


<span id="WarnerJC_2005a"></span>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. ([http://marine.rutgers.edu/po/Papers/Warner_2004_om.pdf PDF])
<span id="WarnerJC_2005a"></span>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. ([http://marine.rutgers.edu/po/Papers/Warner_2004_om.pdf PDF])


<span id="WarnerJC_2005b"></span>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. ([http://marine.rutgers.edu/po/Papers/Warner_2005_jgr.pdf PDF])
<span id="WarnerJC_2005b"></span>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. ([http://marine.rutgers.edu/po/Papers/Warner_2005_jgr.pdf PDF])


<span id="WarnerJC_2006a"></span>Warner, J. C., C. R. Sherwood, R. P. Signell, C. Harris, and H. G. Arango, 2006: Development of a three-dimensional, regional, coupled wave-, current-, and sediment-transport model, submitted.
<span id="WarnerJC_2006a"></span>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.
 
<span id="WarnerJC_2008a"></span>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.
 
<span id="WibergP_1994a"></span>Wiberg, P. L. and C. K. Harris, 1994: Ripple geometry in wave-dominated environments. ''Journal of Geophysical Research'', '''99'''(C1), 775-789.
 
<span id="WibergP_2008a"></span>Wiberg, P. L. and C. R. Sherwood, 2008: Calculating wave-generated bottom orbital velocity from surfacewave parameters. ''Computers & Geosciences'', '''34''', 1243-1262.
 
<span id="WeaverAT_2005a"></span>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.
 
<span id="WeaverAT_2003a"></span>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.
 
<span id="WeaverAT_2001a"></span>Weaver, A. and P. Courtier, 2001: Correlation modeling on the sphere using a generalized diffusion equation, ''Q.J.R. Meteo. Soc'', '''127''', 1815-1846.


<span id="WilkinJL_2005a"></span>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. ([http://marine.rutgers.edu/po/Papers/Wilkin_2005_jgr.pdf PDF])
<span id="WilkinJL_2005a"></span>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. ([http://marine.rutgers.edu/po/Papers/Wilkin_2005_jgr.pdf PDF])
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<span id="WinsorP_2004a"></span>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. ([http://marine.rutgers.edu/po/Papers/winsor2004_jgr.pdf PDF])
<span id="WinsorP_2004a"></span>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. ([http://marine.rutgers.edu/po/Papers/winsor2004_jgr.pdf PDF])
<span id="WuH_2010a"></span>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.
<span id="WunschC_2007"></span>Wunsch, C. and P. Heimbach, 2007: Practical global ocean state estimation, ''Physica D'', '''230''', 197-208.


==<span class="alphabet">X</span>==
==<span class="alphabet">X</span>==


==<span class="alphabet">Y</span>==
==<span class="alphabet">Y</span>==
<span id="Yaglom_1974"></span>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.


==<span class="alphabet">Z</span>==
==<span class="alphabet">Z</span>==

Latest revision as of 22:31, 9 September 2021

Bibliography

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

Contents

A B C D E F G H I J K L M N O P Q R S T U V W X Y Z

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 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

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)

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)

E

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)

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.

I

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.

N

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.

Q

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.

V

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.

X

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.