References_all.bib

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@STRING{acc = {Accepted for publication}}

@STRING{ADV = {Advances in Geophysics}}

@STRING{AGU = {American Geophysical Union}}

@STRING{AIAA = {AIAA Journal}}

@STRING{ANM = {Appl. Numer. Math.}}

@STRING{ANNHMM = {Ann. Hydrogr. Marit. Meteorol.}}

@STRING{AnnRev = {Ann. Rev. Fluid Mech.}}

@STRING{APM = {App. Math. Modelling}}

@STRING{AQS = {Aquatic Sciences}}

@STRING{AST = {Journal of Astrophysics}}

@STRING{ASTJ = {The Astrophysical Journal}}

@STRING{AtEn = {Atmospheric Environment}}

@STRING{ATO = {Atmos.-Ocean}}

@STRING{BLM = {Bound. Layer Meteor.}}

@STRING{BMEE = {Beitr. Meereskd.}}

@STRING{CD = {Clim. Dyn.}}

@STRING{CEN = {Coastal Engineering}}

@STRING{CES = {Coastal and Estuarine Studies}}

@STRING{CJP = {Chinese J. Phys.}}

@STRING{CMA = {Computers Math. Appl.}}

@STRING{CMAME = {Comput. Meth. Appl. Mech. Eng.}}

@STRING{CSR = {Cont. Shelf Res.}}

@STRING{DAO = {Dyn. Atmos. Oceans}}

@STRING{DHZ = {Dt. Hydrogr. Z.}}

@STRING{DSR = {Deep-Sea Research}}

@STRING{DSRII = {Deep-Sea Research II}}

@STRING{ECMS = {Estuarine Coastal Mar. Sci.}}

@STRING{ECOMOD = {Ecol. Model.}}

@STRING{ECSS = {Estuarine, Coastal and Shelf Science}}

@STRING{EFM = {Environmental Fluid Mechanics}}

@STRING{EOS = {Eos. Trans. Amer. Geophys. Res.}}

@STRING{ESR = {Earth-Science Reviews}}

@STRING{EST = {Estuaries}}

@STRING{Franzius = {Mitteilungen des Franzius-Institutes}}

@STRING{GBC = {Global Biogeochemical Cycles}}

@STRING{GCA = {Geochimica et Cosmochimica Acta}}

@STRING{GJRAS = {Geophys. J. Roy. Astron. Soc}}

@STRING{IEEE = {IEEE Journal of Oceanic Engineering}}

@STRING{IJNME = {Int. J. Numer. Meth. Engng}}

@STRING{IJNMF = {Int. J. Numer. Meth. Fluids}}

@STRING{JAM = {J. Appl. Meteorol.}}

@STRING{JAOT = {Journal of Atmospheric and Oceanic Technology}}

@STRING{JAS = {Journal of Atmospheric Sciences}}

@STRING{JCP = {J. Computat. Phys.}}

@STRING{JCR = {Journal of Coastal Research}}

@STRING{JFE = {J. Fluids Eng.}}

@STRING{JFM = {J. Fluid Mech.}}

@STRING{JGR = {J. Geophys. Res.}}

@STRING{JHR = {Journal of Hydraulic Research}}

@STRING{JM = {J. Meteorol.}}

@STRING{JMR = {J. Mar. Res.}}

@STRING{JMS = {J. Mar. Sys.}}

@STRING{JPO = {J. Phys. Oceanogr.}}

@STRING{JPR = {Journal of Plankton Research}}

@STRING{LIEGE = {Bulletin de la Soci\'et\'e Royale des Sciences de Li\`ege}}

@STRING{LIM = {Limnol. Oceanogr.}}

@STRING{MAP = {Math. Astron. Phys.}}

@STRING{MARBIO = {Mar. Biol.}}

@STRING{MC = {Math. Comp.}}

@STRING{MCP = {Meth. Comput. Phys.}}

@STRING{MEPS = {Mar. Ecol. Prog. Ser.}}

@STRING{MWR = {Monthly Weather Review}}

@STRING{NJSR = {Neth. J. Sea Res.}}

@STRING{NorHyd = {Nordic Hydrology}}

@STRING{NPG = {Nonlinear Processes in Geophysics}}

@STRING{NSR = {Netherlands Journal of North Sea Research}}

@STRING{OA = {Oceanologica Acta}}

@STRING{OCEANOLOGIA = {Oceanologia}}

@STRING{OD = {Ocean Dynamics}}

@STRING{OMOD = {Ocean Modelling}}

@STRING{PHF = {Phys.\ Fluids}}

@STRING{PhilROYA = {Phil. Trans. R. Soc. Lond. A}}

@STRING{PhilROYB = {Phil. Trans. R. Soc. Lond. B}}

@STRING{prep = {In preparation}}

@STRING{ProcROYA = {Proc. Trans. R. Soc. Lond. A}}

@STRING{prt = {In print}}

@STRING{QAM = {Quart. Applied Math.}}

@STRING{QJR = {Q. J. R. Meteorol. Soc.}}

@STRING{REV = {Rev. Geophys.}}

@STRING{SIAM = {SIAM J. Appl. Math.}}

@STRING{SIAMNum = {SIAM J. Num. Anal.}}

@STRING{SR = {Journal of Sea Research}}

@STRING{sub = {Submitted}}

@STRING{TAN = {The American Naturalist}}

@STRING{UNESCO = {Unesco technical papers in marine sciences}}

@STRING{ZAMM = {Z.\ Angew.\ Math.\ Mech.}}

@STRING{ZfP = {Zeit. f. Phys.}}

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  file = {:../1993-The-Effect-of-Wave-Current-Interaction-Tidally-Forced-Estuarine-Circulation.pdf:PDF},
  issn = {0148-0227},
  publisher = {American Geophysical Union}
}

@ARTICLE{bennis2010comments,
  author = {Bennis, A.C. and Ardhuin, F.},
  title = {Comments on "The Depth-Dependent Current and Wave Interaction Equations:
	A Revision"},
  journal = JPO,
  year = {2011},
  volume = {41},
  pages = {2008--2012},
  doi = {10.1175/JPO-D-11-055.1},
  file = {:../2011-Comments-on-The-Depth-Dependent-Current-and-Wave-Interaction-Bennis_Ardhuin_JPO2011.pdf:PDF}
}

@ARTICLE{bennis2011vertical,
  author = {Bennis, A.C. and Ardhuin, F. and Dumas, F.},
  title = {On the coupling of wave and three-dimensional circulation models:
	Choice of theoretical framework, practical implementation and adiabatic
	tests},
  journal = {Ocean Modelling},
  year = {2011},
  volume = {40},
  pages = {260--272},
  file = {:../2011_Bennis_et_al_OM2011_On-the-coupling-wave-three-dimensional-circulation-models-revised_final_110211.pdf:PDF}
}

@ARTICLE{bennis2014mixing,
  author = {Bennis, Anne-Claire and Dumas, Franck and Ardhuin, Fabrice and Blanke,
	Bruno},
  title = {Mixing parameterization: Impacts on rip currents and wave set-up},
  journal = {Ocean Engineering},
  year = {2014},
  volume = {84},
  pages = {213--227},
  publisher = {Elsevier}
}

@ARTICLE{BerliandBerliand52,
  author = {M. E. Berliand and T. G. Berliand},
  title = {Measurement of the effective radiation of the earth with consideration
	of the effect of cloudiness (in Russian)},
  journal = {Izv. Akad. Nauk SSSR, Ser. Geofiz.},
  year = {1952},
  volume = {1}
}

@ARTICLE{bertin2009modeling,
  author = {Bertin, X. and Fortunato, A.B. and Oliveira, A.},
  title = {{A modeling-based analysis of processes driving wave-dominated inlets}},
  journal = {Continental Shelf Research},
  year = {2009},
  volume = {29},
  pages = {819--834},
  number = {5-6},
  file = {:../2009modeling-based-analysis-of-processes-driving-wave-dominated-inlets_printed.pdf:PDF},
  issn = {0278-4343},
  publisher = {Elsevier}
}

@ARTICLE{Bignamietal95,
  author = {F. Bignami and S. Marullo and R. Santoleri and M. E. Schiano},
  title = {Long-wave radiation budget in the {M}editerranean {S}ea},
  journal = JGR,
  year = {1995},
  volume = {100},
  pages = {2501-2514}
}

@ARTICLE{blaas2007sediment,
  author = {Blaas, M. and Dong, C. and Marchesiello, P. and McWilliams, J.C.
	and Stolzenbach, K.D.},
  title = {{Sediment-transport modeling on Southern Californian shelves: A ROMS
	case study}},
  journal = {Continental shelf research},
  year = {2007},
  volume = {27},
  pages = {832--853},
  number = {6},
  file = {:../2007sediment-transport-modeling-ROMS.pdf:PDF},
  issn = {0278-4343},
  publisher = {Elsevier}
}

@ARTICLE{Blackadar62,
  author = {A.~K. Blackadar},
  title = {The vertical distribution of wind and turbulent exchange in a neutral
	atmosphere},
  journal = JGR,
  year = {1962},
  volume = {67},
  pages = {3095--3102}
}

@ARTICLE{Blumberg99,
  author = {A.~F. Blumberg and L.~A. Khan and J.~P. St.\ John},
  title = {Three-dimensional hydrodynamic model of {N}ew {Y}ork harbor region},
  journal = {J. Hydraul. Eng.},
  year = {1999},
  volume = {125},
  pages = {799--816}
}

@INCOLLECTION{Blumberg87,
  author = {A.~F. Blumberg and G.~L. Mellor},
  title = {A description of a three-dimensional coastal ocean circulation model},
  booktitle = {Three-Dimensional Coastal Ocean Models},
  publisher = {American Geophysical Union},
  year = {1987},
  editor = {N.~S. Heaps},
  volume = {4},
  series = {Coastal and Esturaine Sciences},
  pages = {1--16}
}

@INCOLLECTION{BLUMBERGea87,
  author = {Alan F. Blumberg and George L. Mellor},
  title = {A description of a coastal ocean circulation model},
  booktitle = {Three dimensional ocean models},
  publisher = AGU,
  year = {1987},
  editor = {N. S. Heaps},
  pages = {1-16},
  address = {Washington, D.C.}
}

@ARTICLE{Blumberg90,
  author = {A.~F. Blumberg and D.~M. Di Toro},
  title = {Effects of climate warming on dissolved oxygen concentrations in
	{L}ake {E}rie},
  journal = {Trans. Am. Fish. Soc.},
  year = {1990},
  volume = {119},
  pages = {210--223}
}

@TECHREPORT{boer1996Surfzone,
  author = {Boer, M.},
  title = {Simulation of a surf zone with a barred beach. Report 1. Wave heights
	and wave breaking},
  institution = {Dept. of Civil Engineering, Delft University of Technology},
  year = {1996},
  file = {:../1996-simulation-the-surf-zone-boers-1996-CommHydr9605.PDF:PDF},
  publisher = {Dept. of Civil Engineering, Delft University of Technology}
}

@TECHREPORT{boer1995bedforms,
  author = {Boer, M.},
  title = {Bedforms and undertow in the surf zone; an analysis of the {LIP-11D}-data},
  institution = {Dept. of Civil Engineering, Delft University of Technology},
  year = {1995},
  file = {:../1995-bed-forms-and-undertow-in-the-surf-zone-delft-report-1995-CommHydr9501.PDF:PDF},
  publisher = {Dept. of Civil Engineering, Delft University of Technology}
}

@PHDTHESIS{boers2005surf,
  author = {Boers, M.},
  title = {{Surf Zone Turbulence}},
  school = {Delft University of Technology, Delft},
  year = {2005},
  file = {:../2005-surf-zone-turbulence-ceg_boers_20051122.PDF:PDF},
  publisher = {Delft University of Technology, Delft}
}

@BOOK{boers1996simulation,
  title = {{Simulation of a surf zone with a barred beach. Report 1. Wave heights
	and wave breaking}},
  publisher = {Delft University of Technology, Delft},
  year = {1996},
  author = {Boers, M.}
}

@ARTICLE{bolanos2011three,
  author = {Bolanos-Sanchez, R. and Brown, JM and Souza, A.},
  title = {Three dimensional circulation modeling in the Dee Estuary},
  journal = {Journal of Coastal Research},
  year = {2011},
  pages = {1457--1461},
  number = {64},
  file = {:../est/2011-Three-dimensional-circulation-modeling-in-the-Dee-EstuarySP64_1457-1461_R.Bolanos.pdf:PDF}
}

@ARTICLE{Boldingetal2002,
  author = {Karsten Bolding and Hans Burchard and Thomas Pohlmann and Adolf Stips},
  title = {Turbulent mixing in the {N}orthern {N}orth {S}ea: a numerical model
	study},
  journal = CSR,
  year = {2002},
  volume = {22},
  pages = {2707-2724}
}

@BOOK{Booch99,
  title = {The Unified Modeling Language User Guide},
  publisher = {Addison-Wesley},
  year = {1999},
  author = {G. Booch and J. Rumbaugh and I. Jacobson}
}

@TECHREPORT{booij2004swan,
  author = {Booij, N. and Haagsma, IJG and Holthuijsen, LH and Kieftenburg, A.
	and Ris, RC and Van Der Westhuysen, AJ and Zijlema, M.},
  title = {{SWAN cycle III version 40.41 user manual}},
  institution = {Delft University of Technology},
  year = {2004},
  volume = {115}
}

@ARTICLE{booij1999third,
  author = {Booij, N. and Ris, RC and Holthuijsen, LH},
  title = {A third-generation wave model for coastal regions. {I}- Model description
	and validation},
  journal = JGR,
  year = {1999},
  volume = {104},
  pages = {7649--7666},
  number = {C4},
  file = {:../1999-A third-generation-wave-model-for-coastal-regions-swan1_jgr99.pdf:PDF}
}

@ARTICLE{bowen1969generation,
  author = {Bowen, A.J.},
  title = {The generation of longshore currents on a plane beach},
  journal = {J. Mar. Res.},
  year = {1969},
  volume = {27},
  pages = {206--215}
}

@ARTICLE{Bowen26,
  author = {I.~S. Bowen},
  title = {The ratio of heat losses by conduction and by evaportion from any
	water surface},
  journal = {Phys. Rev.},
  year = {1926},
  volume = {27},
  pages = {779--787},
  number = {2}
}

@BOOK{Bradshaw75,
  title = {An Introduction to Turbulence and its Measurement},
  publisher = {Pergamon},
  year = {1975},
  author = {P. Bradshaw}
}

@ARTICLE{Brickman01,
  author = {D. Brickman and P. C. Smith},
  title = {{Lagrangian Stochastic Modeling in Coastal Oceanography}},
  journal = JAOT,
  year = {2001},
  volume = {19},
  pages = {83--99},
  number = {1},
  abstract = {Lagrangian stochastic (LS) modeling is a common technique in atmospheric
	boundary layer modeling but is relatively new in coastal oceanography.
	This paper presents some fundamental aspects of LS modeling as they
	pertain to oceanography. The theory behind LS modeling is reviewed
	and an introduction to the substantial atmospheric literature on
	the subject is provided. One of the most important properties of
	an LS model is that it maintains an initially uniform distribution
	of particles uniform for all time\&\#8212;the well-mixed condition
	(WMC). Turbulent data for use in an oceanic LS model (LSM) are typically
	output at discrete positions by a general circulation model. Tests
	for the WMC are devised, and it is shown that for inhomogeneous turbulence
	the data output by an oceanic general circulation model is such that
	the WMC cannot be demonstrated. It is hypothesized that this is due
	to data resolution problems. To test this hypothesis analytical turbulence
	data are constructed and output at various resolutions to show that
	the WMC can only be demonstrated if the resolution is high enough
	(the required resolution depending on the inhomogeneity of the turbulence
	data). The output of an LSM represents one trial of possible ensemble
	and this paper seeks to learn the ensemble average properties of
	the dispersion. This relates to the number of particles or trials
	that are performed. Methods for determining the number of particles
	required to have statistical certainty in one\&\#39;s results are
	demonstrated, and two possible errors that can occur when using too
	few particles are shown.},
  url = {http://dx.doi.org/10.1175%2F1520-0426%282002%29019%3C0083%3ALSMICO%3E2.0.CO%3B2}
}

@ARTICLE{Briggsetal98,
  author = {D.~A. Briggs and J.~H. Ferziger and J.~R Koseff and S.~G. Monismith},
  title = {Turbulent mixing in a shear-free stably stratified two-layer fluid},
  journal = {J. Fluid Mech.},
  year = {1998},
  volume = {354},
  pages = {175--208}
}

@ARTICLE{Briggsetal96,
  author = {D.~A. Briggs and J.~H. Ferziger and J.~R Koseff and S.~G. Monismith},
  title = {Entrainment in a shear-free turbulent mixing layer},
  journal = {J. Fluid Mech.},
  year = {1996},
  volume = {310},
  pages = {215--241}
}

@INCOLLECTION{Brockmannetal1983,
  author = {U. H. Brockmann and V. Ittekott and G. Kattner and K. Eberlein and
	K. D. Hammer},
  title = {Release of Dissolved Organic Substances in the Course of Phytoplankton
	Blooms},
  booktitle = {{N}orth {S}ea Dynamics},
  publisher = {Springer},
  year = {1983},
  editor = {J\"urgen S\"undermann and Walter Lenz},
  pages = {530-548}
}

@ARTICLE{brown201011,
  author = {Brown, J.M. and Souza, A.J. and Wolf, J.},
  title = {{An 11-year validation of wave-surge modelling in the Irish Sea,
	using a nested POLCOMS-WAM modelling system}},
  journal = OMOD,
  year = {2010},
  volume = {33},
  pages = {118--128},
  number = {1-2},
  file = {:../2009-An-11-year-validation-wave-surge-modelling.pdf:PDF},
  issn = {1463-5003},
  publisher = {Elsevier}
}

@ARTICLE{brown2009coupled,
  author = {Brown, J.M. and Wolf, J.},
  title = {{Coupled wave and surge modelling for the eastern Irish Sea and implications
	for model wind-stress}},
  journal = {Continental Shelf Research},
  year = {2009},
  volume = {29},
  pages = {1329--1342},
  number = {10},
  file = {:../2009Coupled-wave-surge-modelling-eastern-Irish-Sea-implications.pdf:PDF},
  issn = {0278-4343},
  publisher = {Elsevier}
}

@ARTICLE{Bruggemanetal2005,
  author = {Jorn Bruggeman and Hans Burchard and Bob Kooi and Ben Sommeijer},
  title = {A second-order, unconditionally stable, mass-conserving integration
	scheme for biochemical systems},
  journal = ANM,
  year = {2005},
  note = sub
}

@ARTICLE{BRYAN69,
  author = {Kirk Bryan},
  title = {A numerical model for the study of the world ocean},
  journal = JCP,
  year = {1969},
  volume = {4},
  pages = {347-376}
}

@ARTICLE{buhler2000vorticity,
  author = {Buhler, O.},
  title = {{On the vorticity transport due to dissipating or breaking waves
	in shallow-water flow}},
  journal = JFM,
  year = {2000},
  volume = {407},
  pages = {235--263},
  file = {:../GLM/2000-glm--On-the-vorticity-transport-due-dissipating-breaking-waves_BuhlerJFM00.pdf:PDF},
  issn = {0022-1120},
  publisher = {Cambridge; New York: Cambridge University Press, 1956-}
}

@INCOLLECTION{BURCHARD98,
  author = {Hans Burchard},
  title = {Presentation of a new numerical model for turbulent flow in estuaries},
  booktitle = {Hydroinformatics '98},
  publisher = {Balkema},
  year = {1998},
  editor = {Vladan Babovic and Lars Christian Larsen},
  pages = {41-48},
  address = {Rotterdam},
  note = {{P}roceedings of the third International Conference on Hydroinformatics,
	Copenhagen, Denmark, 24-26 August 1998}
}

@ARTICLE{Burchard09b,
  author = {H. Burchard},
  title = {{Combined Effects of Wind, Tide, and Horizontal Density Gradients
	on Stratification in Estuaries and Coastal Seas}},
  journal = JPO,
  year = {2009},
  volume = {39},
  pages = {2117--2136},
  number = {9},
  month = {September},
  abstract = {The aim of this one-dimensional water column study is to combine modified
	versions of three characteristic parameters for periodic tidal flow
	under the influence of a longitudinal buoyancy gradient\&\#8212;the
	horizontal Richardson number, the inverse Strouhal number, and the
	inverse Ekman number\&\#8212;into a parameter space study, including
	constant wind forcing from various directions. It is shown how the
	underlying dynamical equations can be cast into nondimensional form,
	depending mainly on these three nondimensional parameters plus the
	relative wind speed and the wind direction. Idealized model simulations
	are carried out for the whole realistic range of horizontal Richardson
	and inverse Strouhal numbers for various latitudes, showing the amplitude
	of the tidally induced stratification for a wide range of scenarios.
	It is found that classical threshold values for the horizontal Richardson
	number, indicating the switch from periodic stratification to permanent
	stratification, are valid only for special cases, and that this switch
	also strongly depends on the inverse Strouhal number, the inverse
	Ekman number, and the wind vector. The transverse residual flow is
	close to the thermal wind balance for a variety of parameters, and
	nondimensionalized longitudinal residual flow shows the classical
	estuarine exchange flow pattern with little variation in the near-bed
	onshore component. Wind straining is confirmed as an important estuarine
	and coastal process, enhancing estuarine circulation for offshore
	(down estuary) winds and vice versa. Agreement with field data from
	Liverpool Bay is good, including the explanation of a flood tide
	local maximum of the dissipation rate in the upper half of the water
	column. An equation for the second time derivative of the potential
	energy anomaly is derived for quantifying the dynamical processes
	leading to stratification due to the straining of the horizontal
	density gradient.},
  citeulike-article-id = {5996586},
  citeulike-linkout-0 = {http://dx.doi.org/10.1175/2009JPO4142.1},
  day = {1},
  doi = {10.1175/2009JPO4142.1},
  keywords = {estuarine\_circulation, stratification, tides, wind\_driven\_circulation},
  posted-at = {2009-10-23 07:11:07},
  priority = {2},
  url = {http://dx.doi.org/10.1175/2009JPO4142.1}
}

@ARTICLE{burchard2009combined,
  author = {Burchard, H.},
  title = {Combined effects of wind, tide, and horizontal density gradients
	on stratification in estuaries and coastal seas},
  journal = JPO,
  year = {2009},
  volume = {39},
  pages = {2117--2136},
  number = {9},
  file = {:../est/2009-Combined-Effects-of-Wind-Tide-and-Horizontal-Density-Gradients-on-Stratification-in-Estuaries-and-Coastal-Seas-jpo4142%2E1.pdf:PDF}
}

@ARTICLE{BURCHARD01c,
  author = {Hans Burchard},
  title = {Energy-conserving discretisation of turbulent shear and buoyancy
	production},
  journal = OMOD,
  year = {2002},
  volume = {4},
  pages = {347-361}
}

@BOOK{BURCHARD02,
  title = {Applied turbulence modelling in marine waters},
  publisher = {Springer},
  year = {2002},
  author = {Hans Burchard},
  volume = {100},
  pages = {215 pp.},
  series = {Lecture Notes in Earth Sciences},
  address = {Berlin, Heidelberg, New York}
}

@BOOK{burchard2002applied,
  title = {{Applied turbulence modelling in marine waters}},
  publisher = {Springer},
  year = {2002},
  author = {Burchard, H.},
  file = {:../2002-hans-turbulence-book.pdf:PDF},
  isbn = {3540437959}
}

@ARTICLE{Burchard2001c,
  author = {H. Burchard},
  title = {Note on the $q^2 l$ equation by {M}ellor and {Y}amada [1982]},
  journal = JPO,
  year = {2001},
  volume = {31},
  pages = {1377--1387}
}

@ARTICLE{burchard2001simulating,
  author = {Burchard, H.},
  title = {{Simulating the wave-enhanced layer under breaking surface waves
	with two-equation turbulence models}},
  journal = JPO,
  year = {2001},
  volume = {31},
  pages = {3133--3145},
  file = {:../2001-Simulating-Wave-Enhanced-Layer-under-Breaking-Surface-Waves.pdf:PDF}
}

@ARTICLE{Burchard99,
  author = {Hans Burchard},
  title = {Recalculation of surface slopes as forcing for numerical water column
	models of tidal flow},
  journal = APM,
  year = {1999},
  volume = {23},
  pages = {737-755}
}

@ARTICLE{Burchard99a,
  author = {H. Burchard},
  title = {{Models of turbulence in the marine environment: a comparative study
	of two-equation turbulence models}},
  journal = {Journal of Marine Systems},
  year = {1999},
  volume = {21},
  pages = {29--53},
  number = {1-4},
  month = {June},
  abstract = {This study compares the performance of the most widely used two-equation
	turbulence closures for marine and atmospheric applications, the
	k-- and the Mellor--Yamada level 2.5 (MY) model. For a better understanding,
	the physical equations are given in a joint notation. Stability functions
	originally suggested by Galperin et al. (1988) are used here with
	slight modifications in order to allow for numerically stable computations
	of free convection. For the k-- models, a flux boundary condition
	for the dissipation rate is tested. In contrast to the classical
	Dirichlet condition, its straightforward discretization allows for
	sufficient accuracy also in three-dimensional models with coarse
	vertical resolution. The models are then applied to idealized situations
	including free convection, wind mixing and stratified steady-state
	boundary layer flow. Finally, the spring development of thermal surface
	stratification as measured during the FLEX'76 experiment is simulated.
	For all these different, partially complex situations, the k-- and
	the MY model proved to perform similarly.},
  citeulike-article-id = {6539897},
  citeulike-linkout-0 = {http://dx.doi.org/10.1016/S0924-7963(99)00004-4},
  citeulike-linkout-1 = {http://linkinghub.elsevier.com/retrieve/pii/S0924-7963(99)00004-4},
  doi = {10.1016/S0924-7963(99)00004-4},
  issn = {09247963},
  keywords = {turbulence},
  posted-at = {2010-01-14 12:16:04},
  priority = {2},
  url = {http://dx.doi.org/10.1016/S0924-7963(99)00004-4}
}

@PHDTHESIS{BURCHARD95,
  author = {Hans Burchard},
  title = {Turbulenzmodellierung mit {A}nwendungen auf thermische {D}eck\-schich\-ten
	im {M}eer und {S}tr\"o\-mun\-gen in {W}attengebieten },
  school = {Institut f\"ur Meereskunde, Universit\"at Hamburg},
  year = {1995},
  note = {Published as: Report 95/E/30, GKSS Research Centre}
}

@ARTICLE{BurchardBaumert98,
  author = {Hans Burchard and Helmut Baumert},
  title = {The formation of estuarine turbidity maxima due to density effects
	in the salt wedge. {A} hydrodynamic process study},
  journal = JPO,
  year = {1998},
  volume = {28},
  pages = {309-321}
}

@ARTICLE{BurchardBaumert95,
  author = {H. Burchard and H. Baumert},
  title = {On the performace of a mixed-layer model based on the $k$-$\epsilon$
	turbulence closure},
  journal = JGR,
  year = {1995},
  volume = {100},
  pages = {8523--8540}
}

@ARTICLE{Burchard09,
  author = {H. Burchard and J.-M. Beckers},
  title = {{Marine turbulence re-revisited -- Selected papers from the jointly
	organised 39th Li{\`e}ge Colloquium and 3rd Warnem{\"u}nde Turbulence
	Days}},
  journal = {Journal of Marine Systems},
  year = {2009},
  volume = {77},
  pages = {367--368},
  number = {4},
  issn = {0924-7963},
  risfield_0_t2 = {SPECIAL ISSUE ON MARINE TURBULENCE},
  risfield_1_m3 = {doi: DOI: 10.1016/j.jmarsys.2009.02.001},
  url = {http://www.sciencedirect.com/science/article/B6VF5-4VKXC14-1/2/79966194948f03b4ab0d8bb47fe9233a}
}

@ARTICLE{Burchard04,
  author = {H. Burchard and J.-M. Beckers},
  title = {{Non-uniform adaptive vertical grids in one-dimensional numerical
	ocean models}},
  journal = OMOD,
  year = {2004},
  volume = {6},
  pages = {51--81},
  number = {1},
  doi = {DOI: 10.1016/S1463-5003(02)00060-4},
  issn = {1463-5003},
  url = {http://www.sciencedirect.com/science/article/B6VPS-47C48SM-2/2/60454663b97a7550c442e98353da7414}
}

@TECHREPORT{BURCHARDea02,
  author = {Hans Burchard and Karsten Bolding},
  title = {{GETM} -- a general estuarine transport model. {S}cientific Documentation},
  institution = {European Commission},
  year = {2002},
  number = {EUR 20253 EN},
  pages = {157}
}

@ARTICLE{Burchard01b,
  author = {H. Burchard and K. Bolding},
  title = {{Comparative Analysis of Four Second-Moment Turbulence Closure Models
	for the Oceanic Mixed Layer}},
  journal = JPO,
  year = {2001},
  volume = {31},
  pages = {1943--1968},
  number = {8},
  month = {August},
  abstract = {In this comparative study, four different algebraic second-moment
	turbulence closure models are investigated in detail. These closure
	schemes differ in the number of terms considered for the closure
	of the pressure\&\#8211;strain correlations. These four turbulence
	closures result in the eddy-diffusivity principle such that the closure
	assumptions are contained in dimensionless so-called stability functions.
	Their performance in terms of Prandtl number, Monin\&\#8211;Obukhov
	similarity theory, and length scale ratios are first tested against
	data for simple flows. The turbulence closure is then completed by
	means of a k\&\#8211;\&\#949; two-equation model, but other models
	such as the two-equation model by Mellor and Yamada could also be
	used. The concept of the steady-state Richardson number for homogeneous
	shear layers is exploited for calibrating the sensitivity of the
	four models to shear and stable stratification. Idealized simulations
	of mixed layer entrainment into stably stratified flow due to surface
	stress and due to free convection are carried out. For the latter
	experiment, comparison to recent large eddy simulation data is made.
	Finally, the well-known temperature profile data at OWS Papa are
	simulated for an annual cycle. The main result of this paper is that
	the overall performance of the new second-moment closure model by
	Canuto et al.\&\#8212;expressed as nondimensional stability functions\&\#8212;is
	superior compared to the others in terms of physical soundness, predictability,
	computational economy, and numerical robustness.},
  citeulike-article-id = {6540795},
  citeulike-linkout-0 = {http://dx.doi.org/10.1175/1520-0485(2001)031\%3C1943:CAOFSM\%3E2.0.CO;2},
  day = {1},
  doi = {10.1175/1520-0485(2001)031\%3C1943:CAOFSM\%3E2.0.CO;2},
  keywords = {gotm},
  posted-at = {2010-01-14 16:39:55},
  priority = {2},
  url = {http://dx.doi.org/10.1175/1520-0485(2001)031\%3C1943:CAOFSM\%3E2.0.CO;2}
}

@ARTICLE{burchard2001comparative,
  author = {Burchard, H. and Bolding, K.},
  title = {{Comparative analysis of four second-moment turbulence closure models
	for the oceanic mixed layer}},
  journal = JPO,
  year = {2001},
  volume = {31},
  pages = {1943--1968},
  number = {8},
  file = {:../2001-Comparative-Analysis-Four-Second-Moment-Turbulence-Closure-Models-Oceanic-Mixed-Layer.pdf:PDF},
  issn = {1520-0485}
}

@MISC{BurchardBolding2000,
  author = {Hans Burchard and Karsten Bolding},
  title = {Implementation of the {V}erduin and {B}ackhaus seagrass-current interaction
	into the {G}eneral {O}cean {T}urbulence {M}odel ({GOTM}). {A} short
	feasability study},
  year = {2000},
  note = {Unpublished manuscript}
}

@ARTICLE{Burchard06,
  author = {H. Burchard and K. Bolding and W. K{\"u}hn and A. Meister and T.
	Neumann and L. Umlauf},
  title = {{Description of a flexible and extendable physical-biogeochemical
	model system for the water column}},
  journal = {Journal of Marine Systems},
  year = {2006},
  volume = {61},
  pages = {180--211},
  number = {3-4},
  issn = {0924-7963},
  keywords = {Baltic Sea, Ecosystem modelling, North Sea, Numerical modelling, ODE
	solvers, Physical-biological interaction, Plankton bloom},
  risfield_0_t2 = {Workshop on Future Directions in Modelling Physical-Biological Interactions
	(WKFDPBI)},
  risfield_1_m3 = {doi: DOI: 10.1016/j.jmarsys.2005.04.011},
  url = {http://www.sciencedirect.com/science/article/B6VF5-4JHMFG5-1/2/2c3dab87bc9933059813f96349c54f2e}
}

@ARTICLE{Burchardetal2002,
  author = {Hans Burchard and Karsten Bolding and Tom P. Rippeth and Adolf Stips
	and John H. Simpson and J\"urgen S\"undermann},
  title = {Microstructure of turbulence in the {N}orthern {N}orth {S}ea: {A}
	comparative study of observations and model simulations},
  journal = SR,
  year = {2002},
  volume = {47},
  pages = {223-238}
}

@ARTICLE{BURCHARDea03a,
  author = {Hans Burchard and Karsten Bolding and Manuel Ruiz Villarreal},
  title = {Three-dimensional modelling of estuarine turbidity maxima in a tidal
	estuary},
  journal = OD,
  year = {2004},
  volume = {54},
  pages = {250-265}
}

@TECHREPORT{Burchardetal99,
  author = {Hans Burchard and Karsten Bolding and Manuel Ruiz Villarreal},
  title = {{GOTM} -- a general ocean turbulence model. {T}heory, applications
	and test cases},
  institution = {European Commission},
  year = {1999},
  number = {EUR 18745 EN},
  pages = {103 pp.}
}

@ARTICLE{BurchardDeleersnijder2001,
  author = {H. Burchard and E. Deleersnijder},
  title = {Stability of algebraic non-equilibrium second-order closure models},
  journal = OMOD,
  year = {2001},
  volume = {3},
  pages = {33--50}
}

@ARTICLE{Burchardetal2005b,
  author = {Hans Burchard and Eric Deleersnijder and Andreas Meister},
  title = {Application of {M}odified {P}atankar schemes to stiff biogeochemical
	models for the water column},
  journal = OD,
  year = {2005},
  volume = {55},
  pages = {326-337}
}

@ARTICLE{Burchardetal2003b,
  author = {Hans Burchard and Eric Deleersnijder and Andreas Meister},
  title = {A high-order conservative {P}atankar-type discretisation for stiff
	systems of production-destruction equations},
  journal = ANM,
  year = {2003},
  volume = {47},
  pages = {1-30}
}

@ARTICLE{burchard2011drivers,
  author = {Burchard, H. and Hetland, R.D. and Schulz, E. and Schuttelaars, H.M.},
  title = {Drivers of Residual Estuarine Circulation in Tidally Energetic Estuaries:
	Straight and Irrotational Channels with Parabolic Cross Section},
  journal = JPO,
  year = {2011},
  volume = {41},
  pages = {548--570},
  file = {:../est/2010-Drivers-of-Residual-Estuarine-Circulation-in-Tidally-Energetic-Estuariesjpo4453%2E1.pdf:PDF}
}

@ARTICLE{Burchard08a,
  author = {H. Burchard and R. Hofmeister},
  title = {{A dynamic equation for the potential energy anomaly for analysing
	mixing and stratification in estuaries and coastal seas}},
  journal = {Estuarine, Coastal and Shelf Science},
  year = {2008},
  volume = {77},
  pages = {679--687},
  number = {4},
  abstract = { In this paper, a time-dependent dynamic equation for the potential
	energy anomaly, [phi], is rigorously derived from dynamic equations
	for potential temperature and salinity, the continuity equation and
	the equation of state for sea water. The terms locally changing [phi]
	are (A) the [phi]-advection, (B) the depth-mean straining, (C) the
	non-mean straining, (D) the vertical advection, (E) the vertical
	mixing, (F) surface and bottom density fluxes, (G) inner sources
	of density e.g. due to absorption of solar radiation and the non-linearity
	of the equation of state, and (H) horizontal divergence of horizontal
	turbulent density fluxes. In order to derive the equation in concise
	form, a vertical velocity (linearly varying with depth) with respect
	to depth-proportional vertical coordinates had to be defined. The
	evaluation of the terms in the [phi]-equation is then carried out
	for a one-dimensional tidal straining study and a two-dimensional
	estuarine circulation study. Comparisons to empirical estimates for
	these terms are made for the one-dimensional study. It is concluded
	that the [phi]-equation provides a general reference for empirical
	bulk parameterisations of stratification and mixing processes in
	estuaries and coastal seas and that it is a tool for complete analysis
	of the relevant terms from numerical models.},
  doi = {DOI: 10.1016/j.ecss.2007.10.025},
  issn = {0272-7714},
  keywords = {mixing},
  keywords1 = {stratification},
  keywords2 = {estuaries},
  keywords3 = {potential energy anomaly},
  keywords4 = {tidal straining},
  keywords5 = {differential advection},
  url = {http://www.sciencedirect.com/science/article/B6WDV-4R2RN6T-1/2/ee4abdc066c63671de73ab859971cbe8}
}

@ARTICLE{Burchard09a,
  author = {H. Burchard and F. Janssen and K. Bolding and L. Umlauf and H. Rennau},
  title = {{Model simulations of dense bottom currents in the Western Baltic
	Sea}},
  journal = {Continental Shelf Research},
  year = {2009},
  volume = {29},
  pages = {205--220},
  number = {1},
  issn = {0278-4343},
  keywords = {Dense bottom currents, Entrainment, Mixing, Three-dimensional numerical
	modelling, Turbulence modelling, Western Baltic Sea},
  risfield_0_t2 = {Physics of Estuaries and Coastal Seas: Papers from the PECS 2006 Conference},
  risfield_1_m3 = {doi: DOI: 10.1016/j.csr.2007.09.010},
  url = {http://www.sciencedirect.com/science/article/B6VBJ-4PW5XRG-1/2/7d2ac276b491066ae796353632cb620a}
}

@ARTICLE{BURCHARDea09,
  author = {Hans Burchard and Frank Janssen and Karsten Bolding and Lars Umlauf
	and Hannes Rennau},
  title = {Model simulations of dense bottom currents in the {W}estern {B}altic
	{S}ea},
  journal = CSR,
  year = {2009},
  volume = {29},
  pages = {205-220}
}

@ARTICLE{BurchardPetersen99,
  author = {H. Burchard and O. Petersen},
  title = {Models of turbulence in the marine enviroment - a comparative study
	of two-equation turbulence models},
  journal = JMS,
  year = {1999},
  volume = {21},
  pages = {29--53}
}

@ARTICLE{BURCHARDea97,
  author = {Hans Burchard and Ole Petersen},
  title = {Hybridisation between $\sigma$ and $z$ coordinates for improving
	the internal pressure gradient calculation in marine models with
	steep bottom slopes},
  journal = IJNMF,
  year = {1997},
  volume = {25},
  pages = {1003-1023}
}

@ARTICLE{Burchard98,
  author = {H. Burchard and O. Petersen and T. P. Rippeth},
  title = {{Comparing the performance of the k-$\epsilon$ and the Mellor-Yamada
	two-equation turbulence models.}},
  journal = JGR,
  year = {1998},
  volume = {103},
  pages = {10543--10554}
}

@ARTICLE{Burchardetal98,
  author = {H. Burchard and O. Petersen and T.~P. Rippeth},
  title = {Comparing the performance of the {M}ellor-{Y}amada and the $k-\epsilon$
	two-equation turbulence models},
  journal = JGR,
  year = {1998},
  volume = {103},
  pages = {10,543--10,554}
}

@ARTICLE{Burchard08,
  author = {H. Burchard and H. Rennau},
  title = {{Comparative quantification of physically and numerically induced
	mixing in ocean models}},
  journal = OMOD,
  year = {2008},
  volume = {20},
  pages = {293--311},
  number = {3},
  doi = {DOI: 10.1016/j.ocemod.2007.10.003},
  issn = {1463-5003},
  keywords = {Numerical mixing},
  keywords1 = {Advection schemes},
  keywords2 = {Variance decay},
  url = {http://www.sciencedirect.com/science/article/B6VPS-4PYYV1T-1/2/624007940b6d39455567c7bdb21b66dc}
}

@ARTICLE{BURCHARDea08b,
  author = {Hans Burchard and Hannes Rennau},
  title = {Comparative quantification of physically and numerically induced
	mixing in ocean models},
  journal = OMOD,
  year = {2008},
  volume = {20},
  pages = {293-311}
}

@INCOLLECTION{Burchardetal2000,
  author = {Hans Burchard and Adolf Stips and Walter Eifler and Karsten Bolding
	and Manuel Ruiz Villarreal},
  title = {Numerical simulation of dissipation measurements in non-stratified
	and strongly stratified estuaries},
  booktitle = {Interactions between estuaries, coastal seas and shelf seas},
  publisher = {Terra Scientific Publishing},
  year = {2000},
  editor = {Tetsuo Yanagi},
  pages = {1-18},
  address = {Tokyo}
}

@ARTICLE{Burrage03,
  author = {K. Burrage and T. Tian},
  title = {{Predictor-Corrector Methods of Runge-Kutta Type for Stochastic Differential
	Equations}},
  journal = {SIAM Journal on Numerical Analysis},
  year = {2003},
  volume = {40},
  pages = {1516--1537},
  number = {4},
  abstract = {In this paper we construct predictor-corrector (PC) methods based
	on the trivial predictor and stochastic implicit Runge-Kutta (RK)
	correctors for solving stochastic differential equations. Using the
	colored rooted tree theory and stochastic B-series, the order condition
	theorem is derived for constructing stochastic RK methods based on
	PC implementations. We also present detailed order conditions of
	the PC methods using stochastic implicit RK correctors with strong
	global order 1.0 and 1.5. A two-stage implicit RK method with strong
	global order 1.0 and a four-stage implicit RK method with strong
	global order 1.5 used as the correctors are constructed in this paper.
	The mean-square stability properties and numerical results of the
	PC methods based on these two implicit RK correctors are reported.},
  copyright = {Copyright © 2003 Society for Industrial and Applied Mathematics},
  issn = {00361429},
  jstor_articletype = {primary\_article},
  jstor_formatteddate = {2003},
  publisher = {Society for Industrial and Applied Mathematics},
  url = {http://www.jstor.org/stable/4101016}
}

@ARTICLE{Busingeretal71,
  author = {J. A. Businger and others},
  title = {Flux-profile relationships in the atmospheric surface layer},
  journal = {J. Atmos. Sci.},
  year = {1971},
  volume = {28},
  pages = {181--189}
}

@ARTICLE{Baeuerle94,
  author = {E. B{\"a}uerle},
  title = {Tranverse baroclinic oscillations in {L}ake {{\"U}}berlingen},
  journal = {Aquat. Sci.},
  year = {1994},
  volume = {56},
  pages = {145--160},
  number = {2}
}

@ARTICLE{Baeuerle98,
  author = {E. B{\"a}uerle and D. Ollinger and J. Ilmberger},
  title = {Some meteorological, hydrological and hydrodynamical aspects of {U}pper
	{L}ake {C}onstance},
  journal = {Arch. Hydrobiol. Spec. Issues Advanc. Limnol.},
  year = {1998},
  volume = {53},
  pages = {31--83}
}

@ARTICLE{Buehrer75,
  author = {H. B{\"u}hrer and A. H. Amb{\"u}hl},
  title = {Die {E}inleitung von gereingtem {A}bwasser in {S}een},
  journal = {Z. Hydrol.},
  year = {1975},
  volume = {37},
  pages = {347--369}
}

@ARTICLE{Caldwell79,
  author = {D.~R. Caldwell and T.~M Chriss},
  title = {The viscous sublayer at the sea floor},
  journal = {Science},
  year = {1979},
  volume = {205},
  pages = {1131--1132}
}

@ARTICLE{Cambon99,
  author = {C. Cambon and J.~F. Scott},
  title = {Linear and nonlinear models of anisotropic turbulence},
  journal = {Ann. Rev. Fluid Mech.},
  year = {1999},
  volume = {31},
  pages = {1--53}
}

@ARTICLE{Canuto94,
  author = {V.~M. Canuto},
  title = {Large eddy simulation of turbulence: {A} subgrid scale model including
	shear, vorticity, rotation, and buoyancy},
  journal = {Astrophys. J.},
  year = {1994},
  volume = {428},
  pages = {729--752}
}

@ARTICLE{Canuto93,
  author = {V.~M. Canuto},
  title = {Turbulent convection with overshooting: {R}eynolds stress approach.
	{II}},
  journal = {Astrophys. J.},
  year = {1993},
  volume = {416},
  pages = {331--354}
}

@ARTICLE{Canuto92,
  author = {V.~M. Canuto},
  title = {Turbulent convection with overshooting: {R}eynolds stress approach},
  journal = {Astrophys. J.},
  year = {1992},
  volume = {392},
  pages = {218--232}
}

@ARTICLE{Canutoetal2001a,
  author = {V.~M. Canuto and A. Howard and Y. Cheng and M.~S. Dubovikov},
  title = {Ocean turbulence. {P}art {I}: {O}ne-point closure model---Momentum
	and heat vertical diffusivities},
  journal = JPO,
  year = {2001},
  volume = {31},
  pages = {1413--1426},
  number = {6}
}

@ARTICLE{CanutoMinotti93,
  author = {V.~M. Canuto and F. Minotti},
  title = {Stratified turbulence in the atmosphere and oceans: {A} new subgrid
	model},
  journal = {J. Atmos. Sci.},
  year = {1993},
  volume = {50},
  pages = {1925--1935},
  number = {13}
}

@ARTICLE{Canutoetal94,
  author = {V.~M. Canuto and F. Minotti and C. Ronchi and M. Ypma and O. Zeman},
  title = {Second-order closure {PBL} model with new third-order moments: {C}omparison
	with {LES} data},
  journal = {J. Atmos. Sci.},
  year = {1994},
  volume = {51},
  pages = {1605--1618}
}

@INCOLLECTION{Capblancq94,
  author = {J. Capblancq and J. Catalan},
  title = {Phytoplankton: {W}ich and how much},
  booktitle = {Limnology now: {A} paradigm of planetary problems},
  publisher = {Elsevier},
  year = {1994},
  editor = {R. Margalef},
  pages = {9--36}
}

@ARTICLE{carniel2009investigating,
  author = {S. Carniel and John C. Warner and J. Chiggiato and Mauro Sclavo},
  title = {{Investigating the impact of surface wave breaking on modeling the
	trajectories of drifters in the northern Adriatic Sea during a wind-storm
	event}},
  journal = OMOD,
  year = {2009},
  volume = {30},
  pages = {225--239},
  number = {2-3},
  abstract = { An accurate numerical prediction of the oceanic upper layer velocity
	is a demanding requirement for many applications at sea and is a
	function of several near-surface processes that need to be incorporated
	in a numerical model. Among them, we assess the effects of vertical
	resolution, different vertical mixing parameterization (the so-called
	Generic Length Scale -GLS- set of k-[epsilon], k-[omega], gen, and
	the Mellor-Yamada), and surface roughness values on turbulent kinetic
	energy (k) injection from breaking waves. First, we modified the
	GLS turbulence closure formulation in the Regional Ocean Modeling
	System (ROMS) to incorporate the surface flux of turbulent kinetic
	energy due to wave breaking. Then, we applied the model to idealized
	test cases, exploring the sensitivity to the above mentioned factors.
	Last, the model was applied to a realistic situation in the Adriatic
	Sea driven by numerical meteorological forcings and river discharges.
	In this case, numerical drifters were released during an intense
	episode of Bora winds that occurred in mid-February 2003, and their
	trajectories compared to the displacement of satellite-tracked drifters
	deployed during the ADRIA02-03 sea-truth campaign. Results indicted
	that the inclusion of the wave breaking process helps improve the
	accuracy of the numerical simulations, subject to an increase in
	the typical value of the surface roughness z0. Specifically, the
	best performance was obtained using [alpha]CH = 56,000 in the Charnok
	formula, the wave breaking parameterization activated, k-[epsilon]
	as the turbulence closure model. With these options, the relative
	error with respect to the average distance of the drifter was about
	25% (5.5 km/day). The most sensitive factors in the model were found
	to be the value of [alpha]CH enhanced with respect to a standard
	value, followed by the adoption of wave breaking parameterization
	and the particular turbulence closure model selected.},
  doi = {DOI: 10.1016/j.ocemod.2009.07.001},
  file = {:../wave-turb/2009-impact-surface-wave-breaking-on-modelingCarniel-warnner_OM_09.pdf:PDF},
  issn = {1463-5003},
  keywords = {Wave breaking},
  keywords1 = {Turbulence},
  keywords2 = {Drifter},
  url = {http://www.sciencedirect.com/science/article/B6VPS-4WTHSBG-1/2/620bcea5ccd89a2de6deef8a663ef799}
}

@ARTICLE{carniello2011modeling,
  author = {Carniello, L. and D'Alpaos, A. and Defina, A.},
  title = {Modeling wind waves and tidal flows in shallow micro-tidal basins},
  journal = {Estuarine, Coastal and Shelf Science},
  year = {2011},
  volume = {92},
  pages = {263--276},
  number = {2},
  file = {:../est/2011-Modeling-wind-waves-and-tidal-flows-in-shallow-micro-tidal-basins.pdf:PDF},
  publisher = {Elsevier}
}

@ARTICLE{castelle2006dynamics,
  author = {Castelle, B. and Bonneton, P. and Senechal, N. and Dupuis, H. and
	Butel, R. and Michel, D.},
  title = {{Dynamics of wave-induced currents over an alongshore non-uniform
	multiple-barred sandy beach on the Aquitanian Coast, France}},
  journal = {Continental shelf research},
  year = {2006},
  volume = {26},
  pages = {113--131},
  number = {1},
  file = {:../2006Dynamics-wave-induced-currents-alongshore.pdf:PDF},
  issn = {0278-4343},
  publisher = {Elsevier}
}

@ARTICLE{castelle2010laboratory,
  author = {Castelle, B. and Michallet, H. and Marieu, V. and Leckler, F. and
	Dubardier, B. and Lambert, A. and Berni, C. and Bonneton, P. and
	Barth{\'e}lemy, E. and Bouchette, F.},
  title = {{Laboratory experiment on rip current circulations over a moveable
	bed: Drifter measurements}},
  journal = JGR,
  year = {2010},
  volume = {115},
  file = {:../undertow/2010-undertow-Laboratory-experiment-rip-current-circulations.pdf:PDF}
}

@ARTICLE{Casulli94,
  author = {V. Casulli and E. Cattani},
  title = {Stability, Accuracy and Efficiency of a Semi-Implicit Method for
	Three-Dimensional Shallow Water Flow},
  journal = {Computers Math. Applic.},
  year = {1994},
  volume = {27},
  pages = {99--112},
  number = {4}
}

@ARTICLE{CASULLIea94,
  author = {V. Casulli and E. Cattani},
  title = {Stability, accuracy and efficiency of a semi-implicit method for
	three-dimensional shallow water flow},
  journal = CMA,
  year = {1994},
  volume = {27},
  pages = {99-112}
}

@ARTICLE{Casulli92,
  author = {V. Casulli and R.~T. Cheng},
  title = {Semi-Implicit Finite Difference Methods for Three-Dimensional Shallow
	Water Flow},
  journal = {Int. J. Numer. Methods Fluids},
  year = {1992},
  volume = {15},
  pages = {629--648}
}

@ARTICLE{catalan2011optical,
  author = {Catal{\'a}n, Patricio A and Haller, Merrick C and Holman, Robert
	A and Plant, William J},
  title = {Optical and microwave detection of wave breaking in the surf zone},
  journal = {Geoscience and Remote Sensing, IEEE Transactions on},
  year = {2011},
  volume = {49},
  pages = {1879--1893},
  number = {6},
  publisher = {IEEE}
}

@ARTICLE{catalan2008remote,
  author = {Cat{\'a}lan, Patricio A and Haller, Merrick C},
  title = {Remote sensing of breaking wave phase speeds with application to
	non-linear depth inversions},
  journal = {Coastal Engineering},
  year = {2008},
  volume = {55},
  pages = {93--111},
  number = {1},
  publisher = {Elsevier}
}

@ARTICLE{cavaleri2012wind,
  author = {Cavaleri, L and Fox-Kemper, B and Hemer, Mark},
  title = {Wind waves in the coupled climate system},
  journal = {Bulletin of the American Meteorological Society},
  year = {2012},
  volume = {93},
  pages = {1651--1661},
  number = {11},
  publisher = {American Meteorological Society}
}

@ARTICLE{Celik84,
  author = {I. Celik and W. Rodi},
  title = {Simulation of free-surface effects in turbulent channel flows},
  journal = {PhysicoChemical Hydrodynamics},
  year = {1984},
  volume = {5},
  pages = {217--227},
  number = {3/4}
}

@ARTICLE{Cencini07,
  author = {M. Cencini and J. Bec and L. Biferale and G. Boffetta and A. Celani
	and A. S. Lanotte and S. Musacchio and F. Toschi},
  title = {{Dynamics and statistics of heavy particles in turbulent flows}},
  journal = {Journal of Turbulence},
  year = {2006},
  volume = {7},
  pages = {N36+},
  abstract = {We present the results of direct numerical simulations (DNS) of turbulent
	flows seeded with millions of passive inertial particles. The maximum
	Reynolds number is <i>Re</i><sub>\&b.lambda;</sub>\&sim; 200. We
	consider particles much heavier than the carrier flow in the limit
	when the Stokes drag force dominates their dynamical evolution. We
	discuss both the <i>transient</i> and the <i>stationary</i> regimes.
	In the transient regime, we study the growth of inhomogeneities in
	the particle spatial distribution driven by the preferential concentration
	out of intense vortex filaments. In the stationary regime, we study
	the acceleration fluctuations as a function of the Stokes number
	in the range <i>St</i> \&isin; [0.16:3.3]. We also compare our results
	with those of pure fluid tracers (<i>St</i> = 0) and we find a critical
	behavior of inertia for small Stokes values. Starting from the pure
	monodisperse statistics we also characterize polydisperse suspensions
	with a given mean Stokes, .},
  citeulike-article-id = {2484564},
  citeulike-linkout-0 = {http://dx.doi.org/10.1080/14685240600675727},
  doi = {10.1080/14685240600675727},
  keywords = {dns, inertial, lagrangian, particles},
  posted-at = {2008-11-07 11:39:26},
  priority = {2},
  publisher = {Taylor \&amp; Francis},
  url = {http://dx.doi.org/10.1080/14685240600675727}
}

@ARTICLE{chapman1985bou,
  author = {Chapman, David C},
  title = {Numerical treatment of cross-shelf open boundaries in a barotropic
	coastal ocean model},
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@ARTICLE{Chapman92b,
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@ARTICLE{Charles09,
  author = {W.M. Charles and E. {van den Berg} and H. X. Lin and A.W. Heemink},
  title = {{Adaptive stochastic numerical scheme in parallel random walk models
	for transport problems in shallow water}},
  journal = {Mathematical and Computer Modelling},
  year = {2009},
  volume = {50},
  pages = {1177--1187},
  number = {7-8},
  doi = {DOI: 10.1016/j.mcm.2009.05.034},
  issn = {0895-7177},
  keywords = {Wiener processes},
  keywords1 = {Stochastic differential equation},
  keywords2 = {Random walk model},
  keywords3 = {Variable step size},
  keywords4 = {Parallel processing},
  keywords5 = {Speed up},
  keywords6 = {Efficiency},
  url = {http://www.sciencedirect.com/science/article/B6V0V-4WR1B1T-6/2/efbc02aea2dc5a0174507d201cb7549f}
}

@ARTICLE{Charles08,
  author = {W.M. Charles and E. {van den Berg} and H. X. Lin and A.W. Heemink
	and M. Verlaan},
  title = {{Parallel and distributed simulation of sediment dynamics in shallow
	water using particle decomposition approach}},
  journal = {Journal of Parallel and Distributed Computing},
  year = {2008},
  volume = {68},
  pages = {717--728},
  number = {6},
  abstract = { This paper describes the parallel simulation of sediment dynamics
	in shallow water. By using a Lagrangian model, the problem is transformed
	to one in which a large number of independent particles must be tracked.
	This results in a technique that can be parallelised with high efficiency.
	We have developed a sediment transport model using three different
	sediment suspension methods. The first method uses a modified mean
	for the Poisson distribution function to determine the expected number
	of the suspended particles in each particular grid cell of the domain
	over all available processors. The second method determines the number
	of particles to suspend with the aid of the Poisson distribution
	function only in those grid cells which are assigned to that processor.
	The third method is based on the technique of using a synchronised
	pseudo-random-number generator to generate identical numbers of suspended
	particles in all valid grid cells for each processor. Parallel simulation
	experiments are performed in order to investigate the efficiency
	of these three methods. Also the parallel performance of the implementations
	is analysed. We conclude that the second method is the best method
	on distributed computing systems (e.g., a Beowulf cluster), whereas
	the third maintains the best load distribution.},
  doi = {DOI: 10.1016/j.jpdc.2007.09.007},
  issn = {0743-7315},
  keywords = {Lagrangian particle model},
  keywords1 = {Stochastic differential equation},
  keywords2 = {Sediment transport},
  keywords3 = {Parallel processing},
  keywords4 = {Speed up},
  keywords5 = {Load balance},
  keywords6 = {Efficiency},
  url = {http://www.sciencedirect.com/science/article/B6WKJ-4S0YXMB-2/2/ef6cfa4d0f29b8c2fe93c9ad7346677a}
}

@ARTICLE{Charles09b,
  author = {W.M. Charles and A.W. Heemink and E. {van den Berg}},
  title = {{Coloured noise for dispersion of contaminants in shallow waters}},
  journal = {Applied Mathematical Modelling},
  year = {2009},
  volume = {33},
  pages = {1158--1172},
  number = {2},
  abstract = { In this article, we explore the application of a set of stochastic
	differential equations called particle model in simulating the advection
	and diffusion of pollutants in shallow waters. The Fokker-Planck
	equation associated with this set of stochastic differential equations
	is interpreted as an advection-diffusion equation. This enables us
	to derive an underlying particle model that is exactly consistent
	with the advection-diffusion equation. Still, neither the advection-diffusion
	equation nor the related traditional particle model accurately takes
	into account the short-term spreading behaviour of particles. To
	improve the behaviour of the model shortly after the deployment of
	contaminants, a particle model forced by a coloured noise process
	is developed in this article. The use of coloured noise as a driving
	force unlike Brownian motion, enables to us to take into account
	the short-term correlated turbulent fluid flow velocity of the particles.
	Furthermore, it is shown that for long-term simulations of the dispersion
	of particles, both the particle due to Brownian motion and the particle
	model due to coloured noise are consistent with the advection-diffusion
	equation.},
  doi = {DOI: 10.1016/j.apm.2008.01.008},
  issn = {0307-904X},
  keywords = {Brownian motion},
  keywords1 = {Stochastic differential equations},
  keywords2 = {Traditional particle models},
  keywords3 = {Coloured noise force},
  keywords4 = {Advection-diffusion equation},
  keywords5 = {Fokker-Planck equation},
  url = {http://www.sciencedirect.com/science/article/B6TYC-4RM7N3Y-1/2/21b9d558652af376a1ac07e5e2bcd250}
}

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@TECHREPORT{chen2012unified,
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	Rick and Campbell, Tim and Smith, Travis and Chen, Sue and Jin, Hao
	and Wang, Shouping and Doyle, James},
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	Models for Improving Intensity Prediction of Tropical Cyclones},
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@ARTICLE{chen2013directional,
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@OTHER{chen2010coupling,
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  publisher = {University of Delaware},
  title = {{Coupling of Wave and Circulation Models for Predicting Storm-Induced
	Waves, Surges, and Coastal Inundation}},
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@INPROCEEDINGS{chen:10,
  author = {Yunfeng Chen and Fengyan Shi and Wenting Qin and James T. Kirby},
  title = {Coupling of Meteorology, Ocean and Nearshore Models for Predicting
	Coastal Inundation along Delaware's Coast},
  booktitle = {Estuarine and Coastal Modeling (2007)},
  year = {2007},
  editor = {Malcolm L. Spaulding},
  volume = {324},
  number = {40990},
  pages = {10-10},
  publisher = {ASCE},
  doi = {10.1061/40990(324)10},
  keywords = {Coupling; Meteorology; Oceans; Delaware; Coastal environment; Predictions},
  location = {Newport, Rhode Island, USA},
  url = {http://link.aip.org/link/?ASC/324/10/1}
}

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  publisher = {Elsevier}
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  pages = {169--198},
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  publisher = {Elsevier}
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@ARTICLE{CHUea03,
  author = {Peter C. Chu and Chenwu Fan},
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@BOOK{Chung02,
  title = {{Computational Fluid Dynamics}},
  publisher = {Cambridge University Press, Cambridge},
  year = {2002},
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@TECHREPORT{cialone2002coupling,
  author = {Cialone, M.A.},
  title = {{Coupling of wave and circulation numerical models at Grays Harbor
	Entrance, Washington, USA}},
  institution = {ENGINEER RESEARCH AND DEVELOPMENT CENTER VICKSBURG MS COASTAL AND
	HYDRAULICS LAB},
  year = {2002},
  file = {:../2002COUPLING-WAVE-CIRCULATION-NUMERICAL-MODELS.pdf:PDF}
}

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	T. Saur},
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	{P}acific for 1961-1971},
  institution = {NOAA, U.S. Dept. of Commerce},
  year = {1974},
  number = {NMFS SSRF-682},
  address = {Washington, D.C.}
}

@TECHREPORT{COX84,
  author = {M. D. Cox},
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  institution = {Geophysical Fluid Dynamics Laboratory, University of Princeton},
  year = {1984},
  number = {1},
  address = {Princeton, N. J.},
  note = {75 pp.}
}

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  year = {1996},
  volume = {23},
  pages = {99--114}
}

@ARTICLE{Craftetal96b,
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  year = {1996},
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  pages = {108--115}
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  publisher = {American Geophysical Union}
}

@ARTICLE{craig1994modeling,
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  pages = {2546--2559},
  number = {12},
  file = {:../wave-turb/1994-craig-and-banner-turbulance.pdf:PDF},
  publisher = {American Meteorological Society}
}

@ARTICLE{Craig96,
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@ARTICLE{davies2000determining,
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	upon computed storm driven currents}},
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@ARTICLE{deigaard1991modelling,
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@ARTICLE{Deleersnijder92,
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@ARTICLE{DeleersnijderBurchard2003,
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@ARTICLE{Deleersnijder07,
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	of complex marine models},
  risfield_1_m3 = {doi: DOI: 10.1016/j.ecss.2007.05.007},
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@ARTICLE{Deleersnijder94,
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@ARTICLE{DELEERSNIJDERea92,
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@ARTICLE{Delhez10,
  author = {E. J. M. Delhez and E. Deleersnijder},
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	euphotic layer}},
  journal = {Journal of Theoretical Biology},
  year = {2010},
  volume = {262},
  pages = {505--516},
  number = {3},
  issn = {0022-5193},
  keywords = {Exposure time, Light exposure, Mixed layer, Residence time},
  risfield_0_m3 = {doi: DOI: 10.1016/j.jtbi.2009.10.004},
  url = {http://www.sciencedirect.com/science/article/B6WMD-4XFFJVW-3/2/4d7cabc07dd77ba20f2fda80c37367ed}
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@ARTICLE{Delhez08,
  author = {E. J. M. Delhez and E. Deleersnijder},
  title = {{Age and the time lag method}},
  journal = {Continental Shelf Research},
  year = {2008},
  volume = {28},
  pages = {1057--1067},
  number = {8},
  issn = {0278-4343},
  keywords = {Age, Age of seawater, Time lag, Tracer},
  risfield_0_m3 = {doi: DOI: 10.1016/j.csr.2008.02.003},
  url = {http://www.sciencedirect.com/science/article/B6VBJ-4RW43C2-1/2/6e91958fe234711157a060d9fa4e4f2d}
}

@ARTICLE{Delhez07,
  author = {E. J. M. Delhez and E. Deleersnijder},
  title = {{Overshootings and spurious oscillations caused by biharmonic mixing}},
  journal = OMOD,
  year = {2007},
  volume = {17},
  pages = {183--198},
  number = {3},
  issn = {1463-5003},
  keywords = {Biharmonic mixing, Monotonicity, Numerical model, Ocean dynamics,
	Positiveness},
  risfield_0_m3 = {doi: DOI: 10.1016/j.ocemod.2007.01.002},
  url = {http://www.sciencedirect.com/science/article/B6VPS-4MY6GG9-2/2/f0d1ac8cbb4f072c0b955599735a99bd}
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@ARTICLE{delworth2012simulated,
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@ARTICLE{Ezer2000,
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@ARTICLE{fan2014impacts,
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@ARTICLE{farquharson2004pod,
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	Frasier, Stephen J and Tessier, Russell and McLaughlin, David J and
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@ARTICLE{Federiuk95,
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@ARTICLE{FEISTEL03,
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@ARTICLE{Fennel92,
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  title = {{Dynamics of the western Baltic}},
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  year = {1992},
  volume = {3},
  pages = {183--205},
  number = {1-2},
  abstract = { The western Baltic is the southernmost part of the transition area
	between North Sea and Baltic Proper. The relatively shallow, strongly
	stratified region is subject to three kinds of external forcing:
	(i) local winds, (ii) barotropic pressure gradient due to sea level
	differences between Baltic and North Sea and (iii) baroclinic pressure
	gradients sustained by freshwater outflow at the sea surface and
	inflow of saline water near the bottom. Owing to the time scale of
	the weather patterns (2 to 4 days) the circulation is mostly governed
	by transients rather than by permanent currents. In order to elucidate
	the dynamics of the area four expeditions have been carried out in
	summer 1983, 1987, 1989 and in autumn 1984 where dense grids of CTD
	stations were worked in the area of the Mecklenburg Bight and Darss
	sill. The experimental findings reveal that easterly winds force
	coastal jets off the german coast associated with coastal upwelling.
	This response can be amplified substantially by pressure gradient
	forcing. Westerly winds generate eddy patterns rather than coastal
	jets. This can be explained by the fact that the cross-circulation
	forced by westerly winds is diminished by the opposite cross-circulation
	driven by pressure gradients, implying only a weak resulting coastal
	up- or downwelling. There are indications that the eddies are generated
	by vortex shedding at topographical features and eddy detachment
	at coastal irregularities.},
  doi = {DOI: 10.1016/0924-7963(92)90038-A},
  issn = {0924-7963},
  url = {http://www.sciencedirect.com/science/article/B6VF5-48B0CMX-R/2/04b5c42b3be5dd7e6f2b4f11f8e77fb6}
}

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  author = {J.~H. Ferziger and M. Peri{\'c}},
  edition = {2nd}
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@ARTICLE{Finlayson66,
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  number = {6}
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@ARTICLE{Fischer96,
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  title = {{The importance of the Drogden Sill in the Sound for major Baltic
	inflows}},
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  year = {1996},
  volume = {9},
  pages = {137--157},
  number = {3-4},
  abstract = { Saline water from the North Sea, which is able to enter the deep
	water of the central parts of the Baltic Sea, must unavoidably pass
	two shallow sill areas: the Darss Sill in the Belt Sea area and the
	Drogden Sill in the Sound. Both sills restrict considerably the inflow
	of highly saline and oxygen-rich water known as major Baltic inflows.
	Long-term observations of salinity and current made at light vessels
	Gedser Rev and Drogden in the sill areas are used to evaluate the
	role of the Drogden Sill in major inflow of events. The different
	contributions of the two passages are documented on the basis of
	90 events that took place between 1897 and 1976. Based on the volume
	and salt transports across the two sills the intensity of major inflows
	is re-assessed. The significance of each sill varies considerably
	from event to event. The volume crossing the Drogden Sill during
	major events is, on average, one third of that crossing the Darss
	Sill and usually far more salt enters the Baltic across the latter.
	However, in some cases, the amounts of salt transported across the
	sills are equal (e.g. January 1993) or the amount crossing the Drogden
	Sill is even the larger fraction (e.g. January 1925, January 1908).
	The re-assessed intensity of the 1993 event showed that the inflow
	in January 1993 must be characterized as very strong owing to the
	considerable salt transport across the Drogden Sill.},
  doi = {DOI: 10.1016/S0924-7963(96)00046-2},
  issn = {0924-7963},
  keywords = {Baltic Sea},
  keywords1 = {Sound},
  keywords2 = {entrance sills},
  keywords3 = {major inflow},
  keywords4 = {salinity},
  keywords5 = {sali transport},
  url = {http://www.sciencedirect.com/science/article/B6VF5-3SVPVKB-C/2/c390fef33581c1a965092f6d3e0c353c}
}

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  author = {C.~A.~J. Fletcher}
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}

@ARTICLE{FREEMANea72,
  author = {N. G. Freeman and A. M. Hale and M. B. Danard},
  title = {A modified sigma equations' approach to the numerical modeling of
	{G}reat {L}akes hydrodynamics},
  journal = JGR,
  year = {1972},
  volume = {77},
  pages = {1050-1060}
}

@ARTICLE{Frey91,
  author = {H. Frey},
  title = {A three-dimensional, baroclinic shelf sea circulation model --- 1.
	{T}he turbulence closure scheme and the one-dimensional test model},
  journal = {Cont. Shelf Res.},
  year = {1991},
  volume = {11},
  pages = {365--395},
  number = {4}
}

@INCOLLECTION{Friedrich83,
  author = {Hans Friedrich},
  title = {Simulation of the thermal stratification at the {FLEX} central station
	with a one-dimensional integral model},
  booktitle = {{N}orth {S}ea Dynamics},
  publisher = {Springer},
  year = {1983},
  editor = {J\"urgen S\"undermann and Walter Lenz},
  pages = {396-411}
}

@ARTICLE{Fukumori92,
  author = {I. Fukumori and J. Benveniste, C. Wunsch and D.B. Haidvogel},
  title = {Assimilation of sea surface topography into an ocean circulation
	model using a steady-state smoother},
  journal = JPO,
  year = {1992},
  notes = {submitted}
}

@ARTICLE{funakoshi:321,
  author = {Yuji Funakoshi and Scott C. Hagen and Peter Bacopoulos},
  title = {Coupling of Hydrodynamic and Wave Models: Case Study for Hurricane
	Floyd (1999) Hindcast},
  journal = {Journal of Waterway, Port, Coastal, and Ocean Engineering},
  year = {2008},
  volume = {134},
  pages = {321-335},
  number = {6},
  doi = {10.1061/(ASCE)0733-950X(2008)134:6(321)},
  keywords = {Storm surges; Two-dimensional models; Hydrodynamics; Hurricanes; Computer
	aided simulation; Coupling; Coastal processing; Wave action; Estuaries},
  publisher = {ASCE},
  url = {http://link.aip.org/link/?QWW/134/321/1}
}

@ARTICLE{Gal-Chen75a,
  author = {T. Gal-Chen and R.~C.~J. Sommerville},
  title = {On the Use of a Coordinate Transform for the {N}avier-{S}tokes Equations},
  journal = {J. Comput. Phys.},
  year = {1975},
  volume = {17},
  pages = {209--228}
}

@ARTICLE{Gal-Chen75b,
  author = {T. Gal-Chen and R.~C.~J. Sommerville},
  title = {Numerical Solution of the {N}avier-{S}tokes Equations with Topography},
  journal = {J. Comp. Phys.},
  year = {1975},
  volume = {17},
  pages = {276--310}
}

@ARTICLE{Galperinetal88,
  author = {B. Galperin and L.~H. Kantha and S. Hassid and A. Rosati},
  title = {A quasi-equilibrium turbulent energy model for geophysical flows},
  journal = {J. Atmos. Sci.},
  year = {1988},
  volume = {45},
  pages = {55--62},
  number = {1}
}

@ARTICLE{Galperinetal89,
  author = {B. Galperin and A. Rosati and L.~H. Kantha and G.~L. Mellor},
  title = {Modeling rotating stratified turbulent flows with an application
	to the oceanic mixed layer},
  journal = JPO,
  year = {1989},
  volume = {19},
  pages = {901--916}
}

@ARTICLE{Ganju2010,
  author = {Neil K. Ganju and Christopher R. Sherwood},
  title = {{Effect of roughness formulation on the performance of a coupled
	wave, hydrodynamic, and sediment transport model}},
  journal = OMOD,
  year = {2010},
  volume = {In Press, Accepted Manuscript},
  pages = {--},
  abstract = { A variety of algorithms are available for parameterizing the hydrodynamic
	bottom roughness associated with grain size, saltation, bedforms,
	and wave-current interaction in coastal ocean models. These parameterizations
	give rise to spatially and temporally variable bottom-drag coefficients
	that ostensibly provide better representations of physical processes
	than uniform and constant coefficients. However, few studies have
	been performed to determine whether improved representation of these
	variable bottom roughness components translates into measurable improvements
	in model skill. We test the hypothesis that improved representation
	of variable bottom roughness improves performance with respect to
	near-bed circulation, bottom stresses, or turbulence dissipation.
	The inner shelf south of Martha's Vineyard, Massachusetts, is the
	site of sorted grain-size features which exhibit sharp alongshore
	variations in grain size and ripple geometry over gentle bathymetric
	relief; this area provides a suitable testing ground for roughness
	parameterizations. We first establish the skill of a nested regional
	model for currents, waves, stresses, and turbulent quantities using
	a uniform and constant roughness; we then gauge model skill with
	various parameterization of roughness, which account for the influence
	of the wave-boundary layer, grain size, saltation, and rippled bedforms.
	We find that commonly used representations of ripple-induced roughness,
	when combined with a wave-current interaction routine, do not significantly
	improve skill for circulation, and significantly decrease skill with
	respect to stresses and turbulence dissipation. Ripple orientation
	with respect to dominant currents and ripple shape may be responsible
	for complicating a straightforward estimate of the roughness contribution
	from ripples. In addition, sediment-induced stratification may be
	responsible for lower stresses than predicted by the wave-current
	interaction model.},
  doi = {DOI: 10.1016/j.ocemod.2010.03.003},
  issn = {1463-5003},
  keywords = {sediment transport},
  keywords1 = {roughness},
  keywords2 = {bottom boundary layer},
  keywords3 = {model skill},
  url = {http://www.sciencedirect.com/science/article/B6VPS-4YPT1XR-1/2/c97cdb79746b25e28993642794da0ddc}
}

@ARTICLE{faria2000undertow,
  author = {Garcez Faria, A.F and Thornton, EB and Lippmann, TC and Stanton,
	TP},
  title = {Undertow over a barred beach},
  journal = JGR,
  year = {2000},
  volume = {105},
  pages = {16--17},
  number = {C7},
  publisher = {American Geophysical Union}
}

@ARTICLE{faria1998vertical,
  author = {Garcez Faria, A.F. and Thornton, EB and Stanton, TP and Soares, CV
	and Lippmann, TC},
  title = {Vertical profiles of longshore currents and related bed shear stress
	and bottom roughness},
  journal = JGR,
  year = {1998},
  volume = {103},
  pages = {3217--3232},
  number = {C2},
  publisher = {American Geophysical Union}
}

@ARTICLE{Garrett91,
  author = {C. Garrett},
  title = {Marginal mixing theories},
  journal = {Atmosphere-Ocean},
  year = {1991},
  volume = {29},
  pages = {313--339},
  number = {2}
}

@ARTICLE{Garrett90,
  author = {C. Garrett},
  title = {The role of secondary circulation in boundary mixing},
  journal = JGR,
  year = {1990},
  volume = {95},
  pages = {3181--3188},
  number = {C3}
}

@ARTICLE{garrett1976generation,
  author = {Garrett, C.},
  title = {Generation of {Langmuir} circulations by surface waves-a feedback
	mechanism},
  journal = {J. Mar. Res.},
  year = {1976},
  volume = {34},
  pages = {117--130}
}

@ARTICLE{Garrett72,
  author = {C. Garrett and W. Munk},
  title = {Space-timescales of internal waves},
  journal = {Geophys. Fluid Dyn.},
  year = {1972},
  volume = {2},
  pages = {225--264}
}

@ARTICLE{Gasparetal90,
  author = {P. Gaspar and Y. Gregoris and J. Lefevre},
  title = {A simple eddy kinetic energy model for simulations of the oceanic
	vertical mixing: {T}ests at station {P}apa and long-term upper ocean
	study site},
  journal = JGR,
  year = {1990},
  volume = {95},
  pages = {16179-16193}
}

@ARTICLE{Gatski93,
  author = {T.~B. Gatski and C.~G. Speziale},
  title = {On explicit algebraic stress models},
  journal = {J. Fluid Mech.},
  year = {1993},
  volume = {254},
  pages = {59--78}
}

@ARTICLE{gemmrich1994energy,
  author = {Gemmrich, JR and Mudge, TD and Polonichko, VD},
  title = {On the energy input from wind to surface waves},
  journal = JPO,
  year = {1994},
  volume = {24},
  pages = {2413--2417},
  number = {11}
}

@ARTICLE{gemmrich2008spectrally,
  author = {Gemmrich, Johannes R and Banner, Michael L and Garrett, Chris},
  title = {Spectrally resolved energy dissipation rate and momentum flux of
	breaking waves},
  journal = JPO,
  year = {2008},
  volume = {38},
  pages = {1296--1312},
  number = {6}
}

@ARTICLE{gemmrich2004near,
  author = {Gemmrich, Johannes R and Farmer, David M},
  title = {Near-surface turbulence in the presence of breaking waves},
  journal = JPO,
  year = {2004},
  volume = {34},
  pages = {1067--1086},
  number = {5}
}

@ARTICLE{GemmrichFarmer99,
  author = {J.~R. Gemmrich and D.~M. Farmer},
  title = {Near-surface turbulence and thermal structure in a wind-driven sea},
  journal = JPO,
  year = {1999},
  volume = {29},
  pages = {480-499}
}

@ARTICLE{gerbi2013breaking,
  author = {Gerbi, Gregory P and Chant, Robert J and Wilkin, John L},
  title = {Breaking Surface Wave Effects on River Plume Dynamics during Upwelling-Favorable
	Winds},
  journal = JPO,
  year = {2013},
  volume = {43},
  pages = {1959--1980},
  number = {9}
}

@ARTICLE{GERDES93,
  author = {R. Gerdes},
  title = {A primitive equation ocean circulation model using a general vertical
	coordinate transformation. 1.\ {D}escription and testing of the model},
  journal = JGR,
  year = {1993},
  volume = {98},
  pages = {14683-14701}
}

@ARTICLE{Gerzetal89,
  author = {T. Gerz and U. Schumann and S.~E. Elghobashi},
  title = {Direct numerical simulation of stratified homogeneous turbulent shear
	flows},
  journal = {J. Fluid Mech.},
  year = {1989},
  volume = {200},
  pages = {563--594}
}

@ARTICLE{Geyer93,
  author = {W. R. Geyer},
  title = {The importance of suppression of turbulence by stratification on
	the estuarine turbidity maximum},
  journal = EST,
  year = {1993},
  volume = {16},
  pages = {113-125}
}

@ARTICLE{gfdl_ww3,
  author = {GFDL},
  title = {Wave Atmosphere Coupled System},
  journal = {\url {http://www-gfdl-noaa-gov/wave-atmosphere-coupled-system}},
  year = {2014},
  urldate = {2014-04-30}
}

@ARTICLE{GibsonLaunder78,
  author = {M.~M. Gibson and B.~E. Launder},
  title = {Ground effects on pressure fluctuations in the atmospheric boundary
	layer},
  journal = {J. Fluid Mech.},
  year = {1978},
  volume = {86},
  pages = {491--511}
}

@ARTICLE{GibsonLaunder76,
  author = {M.~M. Gibson and B.~E. Launder},
  title = {On the calculation of horizontal, turbulent, free shear flows under
	gravitational influence},
  journal = {J. Heat Transfer},
  year = {1976},
  volume = {98C},
  pages = {81--87}
}

@PHDTHESIS{Gloor95,
  author = {E.~U. Gloor},
  title = {Methode der Temperaturmikrostruktur und deren Anwendung auf die Bodengrenzschicht
	in geschichteten Wasserk{\"o}rpern},
  school = {Eidgen{\"o}ssische Technische Hochschule (ETH) Z{\"u}rich, Switzerland},
  year = {1995},
  note = {Nr. 11336}
}

@ARTICLE{Gloor2000,
  author = {M. Gloor and A. W{\"u}est and D.~M. Imboden},
  title = {Dynamics of mixed bottom layers and its implications for diapycnal
	transport in a stratified, natural water basin},
  journal = JGR,
  year = {2000},
  volume = {105},
  pages = {8629--8646},
  number = {C5}
}

@ARTICLE{Gloor94,
  author = {M. Gloor and A. W{\"u}est and M. M{\"u}nnich},
  title = {Benthic boundary mixing and resuspension induced by internal seiches},
  journal = {Hydrobiologica},
  year = {1994},
  volume = {284},
  pages = {59--68}
}

@BOOK{Gottlieb77,
  title = {Numerical analysis of spectral methods: Theory and applications},
  publisher = {Society for Industrial and Applied Mathematics},
  year = {1977},
  author = {D. Gottlieb and S.~A. Orszag}
}

@ARTICLE{Goudsmit97,
  author = {G.-H. Goudsmit and F. Peeters and M. Gloor and A. W{\"u}est},
  title = {Boundary versus internal diapycnal mixing in stratified natural waters},
  journal = JGR,
  year = {1997},
  volume = {102},
  pages = {27903--27914},
  number = {C13}
}

@ARTICLE{govender2004dissipation,
  author = {Govender, K and Mocke, GP and Alport, MJ},
  title = {Dissipation of isotropic turbulence and length-scale measurements
	through the wave roller in laboratory spilling waves},
  journal = JGR,
  year = {2004},
  volume = {109},
  number = {C8}
}

@ARTICLE{govender2002video,
  author = {Govender, K and Mocke, GP and Alport, MJ},
  title = {Video-imaged surf zone wave and roller structures and flow fields},
  journal = JGR,
  year = {2002},
  volume = {107},
  pages = {9--1},
  number = {C7},
  publisher = {Wiley Online Library}
}

@ARTICLE{grasso2012turbulence,
  author = {Grasso, F and Castelle, B and Ruessink, BG},
  title = {Turbulence dissipation under breaking waves and bores in a natural
	surf zone},
  journal = {Continental Shelf Research},
  year = {2012},
  volume = {43},
  pages = {133--141},
  publisher = {Elsevier}
}

@ARTICLE{greenan2001estimates,
  author = {Greenan, Blair JW and Oakey, Neil S and Dobson, Fred W},
  title = {Estimates of dissipation in the ocean mixed layer using a quasi-horizontal
	microstructure profiler.},
  journal = JPO,
  year = {2001},
  volume = {31},
  number = {4}
}

@ARTICLE{greenwood1990vertical,
  author = {Greenwood, B. and Osborne, P.D.},
  title = {{Vertical and horizontal structure in cross-shore flows: an example
	of undertow and wave set-up on a barred beach}},
  journal = {Coastal Engineering},
  year = {1990},
  volume = {14},
  pages = {543--580},
  number = {6},
  file = {:../undertow/1990-undertow-Vertical-horizontal-structure-cross-shore-flows.pdf:PDF},
  issn = {0378-3839},
  publisher = {Elsevier}
}

@ARTICLE{Gregg89,
  author = {M.~C. Gregg},
  title = {Scaling turbulent dissipation in the thermocline},
  journal = JGR,
  year = {1989},
  volume = {94},
  pages = {9686--9698},
  number = {C7}
}

@ARTICLE{Gregg87,
  author = {M.~C. Gregg},
  title = {Diapycnal mixing in the thermocline: {A} review},
  journal = JGR,
  year = {1987},
  volume = {92},
  pages = {5249--5286},
  number = {C5}
}

@ARTICLE{grimshaw1984wave,
  author = {Grimshaw, R.},
  title = {{Wave action and wave-mean flow interaction, with application to
	stratified shear flows}},
  journal = {Annual Review of Fluid Mechanics},
  year = {1984},
  volume = {16},
  pages = {11--44},
  number = {1},
  file = {:../GLM/1984-glm-WAVE-ACTION-AND-WAVE-MEAN-FLOW-INTERACTION.pdf:PDF},
  issn = {0066-4189},
  publisher = {Annual Reviews 4139 El Camino Way, PO Box 10139, Palo Alto, CA 94303-0139,
	USA}
}

@ARTICLE{groeneweg1998changes,
  author = {Groeneweg, J. and Klopman, G.},
  title = {{Changes of the mean velocity profiles in the combined wave--current
	motion described in a GLM formulation}},
  journal = JFM,
  year = {1998},
  volume = {370},
  pages = {271--296},
  number = {-1},
  file = {:../GLM/1980-glm-changes-on-mean-velocity-profile-due-waves-using-GLM-approach-Gr_Kl_1998.pdf:PDF},
  issn = {1469-7645},
  publisher = {Cambridge Univ Press}
}

@ARTICLE{gross2010three,
  author = {Gross, E.S. and MacWilliams, M.L. and Kimmerer, W.J.},
  title = {Three-dimensional modeling of tidal hydrodynamics in the San Francisco
	Estuary},
  journal = {San Francisco Estuary and Watershed Science},
  year = {2010},
  volume = {7},
  number = {2},
  file = {:../est/2010-Three-dimensional-modeling-of-tidal-hydrodynamics-in-the-San-Francisco-Estuary.pdf:PDF}
}

@ARTICLE{Grawe09b,
  author = {U. Gr{\"a}we and J.-O. Wolff},
  title = {{Suspended particulate matter dynamics in a particle framework}},
  journal = {Environmental Fluid Mechanics},
  year = {2009},
  volume = {10},
  pages = {21--39},
  number = {1},
  abstract = {Suspended particulate matter (SPM) dynamics in ocean models are usually
	treated with an advection--diffusion equation for one or more sediment
	size classes coupled to the hydrodynamical part of the model. Numerical
	solution of these additional partial differential equations unavoidably
	introduces numerical diffusion, i.e. in the case of sharp gradients
	the possible occurrence of artificial oscillations and non-positivity.
	A Lagrangian particle-tracking model has been developed to simulate
	short-term SPM dynamics. Modelling individual sediment particles
	allows a straightforward physical interpretation of the processes.
	The tracking of large numbers of individual and independent particles
	(up to 25 million in total in a single sediment class) can be achieved
	on high performance computer clusters, due to efficient parallelisation
	of particle tracking. The movement of the particles is described
	by a stochastic differential equation, which is consistent with the
	advection--diffusion equation. Here, the concentration profile is
	represented by a set of independent moving particles, which are advected
	according to the 3D velocity field, while the diffusive displacements
	of the particles are sampled from a random distribution, which is
	related to the eddy diffusivity field. To account for erosion a new
	parameterisation is proposed. Three numerical particle tracking schemes
	(EULER, MILSTEIN and HEUN) are presented and validated in idealised
	test cases. Finally, the particle tracking algorithms are applied
	to a realistic scenario, a severe winter storm in the East Frisian
	Wadden Sea (southern North Sea). The comparison with observations
	and an Eulerian SPM transport model seems to indicate a somewhat
	better fidelity of the Lagrangian approach.},
  doi = {10.1007/s10652-009-9141-8},
  url = {http://dx.doi.org/10.1007/s10652-009-9141-8}
}

@ARTICLE{Grawe10,
  author = {U. Gr{\"a}we and J.-O. Wolff and J. Ribbe},
  title = {{Impact of climate variability on an east Australian bay}},
  journal = {Estuarine, Coastal and Shelf Science},
  year = {2010},
  volume = {86},
  pages = {247--257},
  number = {2},
  issn = {0272-7714},
  keywords = {climate variability, drying trend, floods, hypersalinity, inverse
	circulation},
  risfield_0_m3 = {doi: DOI: 10.1016/j.ecss.2009.11.020},
  url = {http://www.sciencedirect.com/science/article/B6WDV-4XSJVTB-1/2/b9c2cdd85e6f1db7bdd2846caa0987db}
}

@ARTICLE{Grawe09a,
  author = {U. Gr{\"a}we and J.-O. Wolff and J. Ribbe},
  title = {{Mixing, hypersalinity and gradients in Hervey Bay, Australia}},
  journal = {Ocean Dynamics},
  year = {2009},
  volume = {59},
  pages = {643--658},
  number = {5},
  doi = {10.1007/s10236-009-0195-4},
  url = {http://www.springerlink.com/content/mq53j473k4g347m7}
}

@ARTICLE{guo2008wind,
  author = {Guo, X. and Valle-Levinson, A.},
  title = {Wind effects on the lateral structure of density-driven circulation
	in Chesapeake Bay},
  journal = {Continental Shelf Research},
  year = {2008},
  volume = {28},
  pages = {2450--2471},
  number = {17},
  file = {:../est/2008-Wind-effects-on-the-lateral-structure-of-density-driven-circulation-in-Chesapeake-Bay.pdf:PDF},
  publisher = {Elsevier}
}

@ARTICLE{Gust85,
  author = {G. Gust and G.~L. Weatherly},
  title = {Velocities, turbulence, and skin friction in a deep-sea logarithmic
	layer},
  journal = JGR,
  year = {1985},
  volume = {90},
  pages = {4779--4792},
  number = {C3}
}

@ARTICLE{Gaestgifvars06,
  author = {M. G{\"a}stgifvars and H. Lauri and A. Sarkanen and Kai Myrberg and
	O. Andrejev and C. Ambj{\"o}rn},
  title = {{Modelling surface drifting of buoys during a rapidly-moving weather
	front in the Gulf of Finland, Baltic Sea}},
  journal = {Estuarine, Coastal and Shelf Science},
  year = {2006},
  volume = {70},
  pages = {567--576},
  number = {4},
  note = {Merging Engineering and Science in Marine Environmental Model Applications},
  abstract = { The Gulf of Finland is an elongated estuary located in the north-eastern
	extremity of the Baltic Sea. This semi-enclosed sea-area is subject
	to heavy sea traffic, and is one of the main risk areas for oil accidents
	in the Baltic. The continuous development and validation of operational
	particle drift and oil-spill forecasting systems is thus seen to
	be essential for this sea-area. Here, the results of a three-day
	drift experiment in May 2003 are discussed. The field studies were
	performed using GPS-positioned surface floating buoys. The aim of
	this paper is to evaluate how well models can reproduce the drift
	of these buoys. Model simulations, both in forecast and hindcast
	modes, were carried out by three different 3D hydrodynamic models,
	the results of which are evaluated by comparing the calculated drifts
	with observations. These models were forced by HIRLAM (High Resolution
	Limited Area Model) and ECMWF (European Centre for Medium-Range Weather
	Forecasts) meteorological forecast fields. The simulated drift of
	the buoys showed a good agreement with observations even when, during
	the study period, a rapidly-changing wind situation was observed
	to affect the investigation area; in this situation the winds turned
	about 100 degrees in half an hour. In such a case it is a very complicated
	task to forecast the drifters' routes: there is a need to regularly
	update the meteorological forcing fields and to use these regularly-updated
	fields throughout the simulations. It is furthermore recommended
	that forecasts should be made using several circulation models and
	several meteorological forecasts, in order to get an overview of
	the accuracy of the forecasted drifts and related differences in
	between the forecasts.},
  doi = {DOI: 10.1016/j.ecss.2006.06.010},
  issn = {0272-7714},
  keywords = {Lagrangian current measurement},
  keywords1 = {surface drifters},
  keywords2 = {surface currents},
  keywords3 = {modelling},
  keywords4 = {atmospheric forcing},
  keywords5 = {Baltic Sea},
  url = {http://www.sciencedirect.com/science/article/B6WDV-4KGX8DS-1/2/10ee19ed6780816370607059969de683}
}

@PHDTHESIS{Gueting98a,
  author = {P. G{\"u}ting},
  title = {Dreidimensionale {B}erechnung windgetriebener {S}tr{\"o}mungen mit
	einem k-$\epsilon$ {M}odell in idealisierten {B}ecken und im {B}odensee},
  school = {University of Technology at Darmstadt, FB6},
  year = {1998}
}

@MASTERSTHESIS{Gueting94,
  author = {P. G{\"u}ting},
  title = {Windgetriebene {S}tr{\"o}mungen und {D}iffusion eines {T}racers},
  school = {Technische Hochschule Darmstadt, FB6},
  year = {1994}
}

@ARTICLE{Gueting98b,
  author = {P. G{\"u}ting and K. Hutter},
  title = {Modelling wind-induced circulation in the homogeneous {L}ake {C}onstance
	using a $k$-$\epsilon$-closure},
  journal = {Aquatic Sciences},
  year = {1998},
  volume = {60},
  pages = {266--277}
}

@ARTICLE{haas2002laboratory,
  author = {Haas, K.A. and Svendsen, I.A.},
  title = {Laboratory measurements of the vertical structure of rip currents},
  journal = JGR,
  year = {2002},
  volume = {107},
  pages = {3047},
  number = {C5},
  file = {:../2001-Laboratory-measurements-of-the-vertical-structure-of-rip-currentsJC000911.pdf:PDF},
  publisher = {American Geophysical Union}
}

@ARTICLE{haas2003quasi,
  author = {Haas, K.A. and Svendsen, IA and Haller, M.C. and Zhao, Q.},
  title = {Quasi-three-dimensional modeling of rip current systems},
  journal = JGR,
  year = {2003},
  volume = {108},
  pages = {3217},
  number = {C7},
  file = {:../2003-Quasi-three-dimensional-modeling-of-rip-Haas_et_al_JGR_2003.pdf:PDF},
  publisher = {American Geophysical Union}
}

@ARTICLE{Haidvogel91b,
  author = {D. Haidvogel and J. Wilkin and R. Young},
  title = {A semi-spectral primitive equation ocean circulation model using
	vertical sigma and orthogonal curvilinear horizontal coordinates},
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}

@BOOK{HAIDVOGELea99,
  title = {Numerical Ocean Circulation Modelling},
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  volume = {2},
  pages = {318 pp.},
  series = {Series on Environmental Science and Management},
  address = {London}
}

@ARTICLE{Haidvogel93,
  author = {D.~B. Haidvogel and A. Beckmann and D.~C. Chapman and R.-Q. Lin},
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	II: Resonant Generation of Trapped Waves},
  journal = JPO,
  year = {1993},
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  pages = {2373-2391}
}

@ARTICLE{Haidvogel91a,
  author = {D.~B. Haidvogel and A. Beckmann and K.~S. Hedstrom},
  title = {Dynamical Simulations of filament formation and evolution in the
	coastal transition zone},
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  year = {1991},
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}

@BOOK{Hairer93,
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  publisher = {Springer},
  year = {1993},
  author = {E. Hairer and S. N{{\o}}rsett and G. Wanner},
  series = {{Springer Series in Computational Mathematics, Vol. 8}},
  edition = {2nd},
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@ARTICLE{haller2007waves,
  author = {Haller, MC and {\"O}zkan-Haller, HT},
  title = {{Waves on unsteady currents (12 pages)}},
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  publisher = {AMERICAN INSTITUTE OF PHYSICS}
}

@ARTICLE{hamill2001distance,
  author = {Hamill, Thomas M and Whitaker, Jeffrey S and Snyder, Chris},
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	in an ensemble Kalman filter},
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}

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@ARTICLE{Haney99,
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}

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  year = {1972},
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@ARTICLE{Hannounetal88,
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  year = {1988},
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}

@ARTICLE{HannounList88,
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  year = {1988},
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  pages = {211--234}
}

@ARTICLE{vanHaren94,
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}

@ARTICLE{Harris78,
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	of phytoplankton},
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  year = {1978}
}

@ARTICLE{Harrisonetal1996,
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}

@ARTICLE{hasselmann1971mass,
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	larger-scale motions}},
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  year = {1971},
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  pages = {189--205},
  file = {:../1971-On-mass-momentum-transfer-between-short-gravity-waves-larger-scale-motions-hasselmann-jfm71.pdf:PDF},
  issn = {1469-7645},
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}

@ARTICLE{hasselmann1973measurements,
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	Cartwright, DE and Enke, K. and Ewing, JA and Gienapp, H. and Hasselmann,
	DE and Kruseman, P. and others},
  title = {Measurements of wind-wave growth and swell decay during the Joint
	North Sea Wave Project (JONSWAP)},
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  year = {1973},
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}

@ARTICLE{Hassid83,
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}

@TECHREPORT{HastenrathLamb78,
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	{O}ceans},
  institution = {University of Wisconsin},
  year = {1978},
  address = {Madison},
  pages = {90 pp.}
}

@TECHREPORT{Hedstrom90,
  author = {K.~S. Hedstrom},
  title = {User's Manual for a Semi-spectral Primitive Equation Regional Ocean-Circulation
	Model},
  institution = {Institute for Naval Oceanography},
  year = {1990},
  number = {SR-1},
  month = {July}
}

@ARTICLE{Heemink90,
  author = {A.W. Heemink},
  title = {{Stochastic modelling of dispersion in shallow water}},
  journal = {Stochastic Hydrology and Hydraulics},
  year = {1990},
  volume = {4},
  pages = {161--174},
  number = {2},
  abstract = {A random walk model to describe the dispersion of pollutants in shallow
	water is developed. By deriving the Fokker-Planck equation, the model
	is shown to be consistent with the two-dimensional advection-diffusion
	equation with space-varying dispersion coefficient and water depth.
	To improve the behaviour of the model shortly after the deployment
	of the pollutant, a random flight model is developed too. It is shown
	that over long simulation periods, this model is again consistent
	with the advection-diffusion equation. The various numerical aspects
	of the implementation of the stochastic models are discussed and
	finally a realistic application to predict the dispersion of a pollutant
	in the Eastern Scheldt estuary is described.},
  doi = {10.1007/BF01543289},
  url = {http://www.springerlink.com/content/g1058u0855hp401n}
}

@ARTICLE{henderson2004nearshore,
  author = {Henderson, S.M. and Allen, JS and Newberger, PA},
  title = {{Nearshore sandbar migration predicted by an eddy-diffusive boundary
	layer model}},
  journal = JGR,
  year = {2004},
  volume = {109},
  pages = {06024},
  number = {C18},
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}

@BOOK{Henderson-Sellers84,
  title = {Engineering Limnology},
  publisher = {Pitman Publishing},
  year = {1984},
  author = {B. Henderson-Sellers},
  address = {Boston, London, Melbourne}
}

@OTHER{henrotte2008implementation,
  author = {Henrotte, J.},
  file = {:../2008Implementation-validation-evaluation-Quasi-3D-model-Delft3D.pdf:PDF},
  title = {{Implementation, validation and evaluation of a Quasi-3D model in
	Delft3D.}},
  year = {2008}
}

@ARTICLE{Hense10,
  author = {I. Hense and H. Burchard},
  title = {{Modelling cyanobacteria in shallow coastal seas}},
  journal = {Ecological Modelling},
  year = {2010},
  volume = {221},
  pages = {238--244},
  number = {2},
  issn = {0304-3800},
  keywords = {Baltic Sea, Cyanobacteria, Life cycle, Minimum value, Phosphorus,
	Phytoplankton, Seed population},
  risfield_0_m3 = {doi: DOI: 10.1016/j.ecolmodel.2009.09.006},
  url = {http://www.sciencedirect.com/science/article/B6VBS-4XDFXYN-2/2/df31263654a7b6f27ceb569b206be0d4}
}

@ARTICLE{Hermann93c,
  author = {A.~J. Hermann},
  title = {An eddy resolving model of wind and buoyancy-forced circulation in
	the western Gulf of Alaska},
  journal = JGR,
  year = {1993},
  notes = {submitted}
}

@ARTICLE{Hermann93a,
  author = {A.~J. Hermann and H.-M. Hsu},
  title = {A vertical coordinate mapping technique for semi-spectral primitive
	equation models of ocean circulation},
  journal = {J. Atmos. Ocean. Tech.},
  year = {1993},
  volume = {10},
  pages = {381--396}
}

@INCOLLECTION{Hermann91,
  author = {A.~J. Hermann and W.~B. Owens},
  title = {Modeling the geostrophic adjustment and spreading of waters formed
	by deep convection},
  booktitle = {Deep Convection and Deep Water Formation},
  publisher = {Elsevier Oceanography Series},
  year = {1991},
  editor = {J.~C. Gascard and P.~C. Chu}
}

@ARTICLE{Hermann93b,
  author = {A. J. Hermann and W. B. Owens},
  title = {Energetics of gravitational adjustment for mesoscale chimneys},
  journal = JPO,
  year = {1993},
  volume = {23},
  pages = {346--371}
}

@ARTICLE{Higham03,
  author = {D.J. Higham and X. Mao and A. M. Stuart},
  title = {{Strong Convergence of Euler-Type Methods for Nonlinear Stochastic
	Differential Equations}},
  journal = {SIAM Journal on Numerical Analysis},
  year = {2003},
  volume = {40},
  pages = {1041--1063},
  number = {3},
  abstract = {Traditional finite-time convergence theory for numerical methods applied
	to stochastic differential equations (SDEs) requires a global Lipschitz
	assumption on the drift and diffusion coefficients. In practice,
	many important SDE models satisfy only a local Lipschitz property
	and, since Brownian paths can make arbitrarily large excursions,
	the global Lipschitz-based theory is not directly relevant. In this
	work we prove strong convergence results under less restrictive conditions.
	First, we give a convergence result for Euler-Maruyama requiring
	only that the SDE is locally Lipschitz and that the pth moments of
	the exact and numerical solution are bounded for some p > 2. As an
	application of this general theory we show that an implicit variant
	of Euler-Maruyama converges if the diffusion coefficient is globally
	Lipschitz, but the drift coefficient satisfies only a one-sided Lipschitz
	condition; this is achieved by showing that the implicit method has
	bounded moments and may be viewed as an Euler-Maruyama approximation
	to a perturbed SDE of the same form. Second, we show that the optimal
	rate of convergence can be recovered if the drift coefficient is
	also assumed to behave like a polynomial.},
  copyright = {Copyright © 2003 Society for Industrial and Applied Mathematics},
  issn = {00361429},
  jstor_articletype = {primary\_article},
  jstor_formatteddate = {2003},
  publisher = {Society for Industrial and Applied Mathematics},
  url = {http://www.jstor.org/stable/4100914}
}

@ARTICLE{Hinrichsen02,
  author = {H. -H. Hinrichsen and M. St.John and A. Lehmann and B. R. MacKenzie
	and F. W. K{\"o}ster},
  title = {{Resolving the impact of short-term variations in physical processes
	impacting on the spawning environment of eastern Baltic cod: application
	of a 3-D hydrodynamic model}},
  journal = {Journal of Marine Systems},
  year = {2002},
  volume = {32},
  pages = {281--294},
  number = {4},
  abstract = { Variations in oxygen conditions below the permanent halocline influence
	the ecosystem of the Baltic Sea through a number of mechanisms. In
	this study, we examine the effects of physical forcing on variations
	in the volume of deep oxygenated water suitable for reproductive
	success of central Baltic cod. Recent research has identified the
	importance of inflows of saline and oxygenated North Sea water into
	the Baltic Sea for the recruitment of Baltic cod. However, other
	processes have been suggested to modify this reproduction volume
	including variations in timing and volume of terrestrial runoff,
	variability of the solubility of oxygen due to variations in sea
	surface temperature as well as the influence of variations in wind
	stress. In order to examine the latter three mechanisms, we have
	performed simulations utilizing the Kiel Baltic Sea model for a period
	of a weak to moderate inflow of North Sea water into the Baltic,
	modifying wind stress, freshwater runoff and thermal inputs. The
	model is started from three-dimensional fields of temperature, salinity
	and oxygen obtained from a previous model run and forced by realistic
	atmospheric conditions. Results of this realistic reference run were
	compared to runs with modified meteorological forcing conditions
	and river runoff. From these simulations, it is apparent that processes
	other than major Baltic inflows have the potential to alter the reproduction
	volume of Baltic cod. Low near-surface air temperatures in the North
	Sea, the Skagerrak/Kattegat area and in the western Baltic influence
	the water mass properties (high oxygen solubility). Eastward oriented
	transports of these well-oxygenated highly saline water masses may
	have a significant positive impact on the Baltic cod reproduction
	volume in the Bornholm Basin. Finally, we analysed how large scale
	and local atmospheric forcing conditions are related to the identified
	major processes affecting the reproduction volume.},
  doi = {DOI: 10.1016/S0924-7963(02)00040-4},
  issn = {0924-7963},
  keywords = {Baltic cod spawning},
  keywords1 = {Reproduction volume},
  keywords2 = {Physical forcing variation},
  url = {http://www.sciencedirect.com/science/article/B6VF5-451S9FC-1/2/8169d0ab5cf150e3b9c2e5c0d69b3ed8}
}

@BOOK{Hinze59,
  title = {Turbulence},
  publisher = {McGraw-Hill Book Company, Inc.},
  year = {1959},
  author = {J. O. Hinze}
}

@BOOK{Hirsch88/2,
  title = {Numerical Computation of Internal and External Flows},
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  year = {1988},
  author = {C. Hirsch},
  volume = {2}
}

@ARTICLE{Hodges2000,
  author = {B.~R. Hodges and J. Imberger and A. Saggio},
  title = {Modeling basin-scale internal waves in a stratified lake},
  journal = {Limnol. Oceanogr.},
  year = {2000},
  note = {in press}
}

@ARTICLE{Hofmann91,
  author = {E.~E. Hofmann and K. S. Hedstrom and J. R. Moisan and D. B. Haidvogel
	and D. L. Mackas},
  title = {Use of simulated drifter tracks to investigate general transport
	patterns and residence times in the coastal transition zone},
  journal = JGR,
  year = {1991},
  volume = {96},
  pages = {15041--15052}
}

@ARTICLE{Hofmeister10,
  author = {R. Hofmeister and H. Burchard and J.-M. Beckers},
  title = {{Non-uniform adaptive vertical grids for 3D numerical ocean models}},
  journal = OMOD,
  year = {2010},
  volume = {33},
  pages = {70--86},
  number = {1-2},
  issn = {1463-5003},
  keywords = {3D ocean modelling, Adaptive non-uniform grid, Numerical mixing}
}

@ARTICLE{Hofmeister09,
  author = {R. Hofmeister and H. Burchard and K. Bolding},
  title = {{A three-dimensional model study on processes of stratification and
	de-stratification in the Limfjord}},
  journal = {Continental Shelf Research},
  year = {2009},
  volume = {29},
  pages = {1515--1524},
  number = {11-12},
  issn = {0278-4343},
  keywords = {Differential advection, Limfjord, Potential energy anomaly, Stratification},
  risfield_0_m3 = {doi: DOI: 10.1016/j.csr.2009.04.004},
  url = {http://www.sciencedirect.com/science/article/B6VBJ-4W38RMG-2/2/e0b4227e1ea2093c0ab35f9048ae2bc1}
}

@ARTICLE{holman2013cbathy,
  author = {Holman, Rob and Plant, Nathaniel and Holland, Todd},
  title = {cBathy: A robust algorithm for estimating nearshore bathymetry},
  journal = JGR,
  year = {2013},
  volume = {118},
  pages = {2595--2609},
  number = {5},
  publisher = {Wiley Online Library}
}

@ARTICLE{Holt08,
  author = {Jason Holt and L. Umlauf},
  title = {{Modelling the tidal mixing fronts and seasonal stratification of
	the Northwest European Continental shelf}},
  journal = {Continental Shelf Research},
  year = {2008},
  volume = {28},
  pages = {887--903},
  number = {7},
  issn = {0278-4343},
  keywords = {Coastal-ocean modelling, Fronts, GOTM, Mixing, Northwest European
	shelf, POLCOMS, Stratification},
  risfield_0_m3 = {doi: DOI: 10.1016/j.csr.2008.01.012},
  url = {http://www.sciencedirect.com/science/article/B6VBJ-4RR1NX1-1/2/87a2bcd3f21593fd6e12982e7943ac9b}
}

@ARTICLE{Holtetal92,
  author = {S.~E. Holt and J.~R. Koseff and J.~H. Ferziger},
  title = {A numerical study of the evolution and structure of homogeneous stably
	stratified sheared turbulence},
  journal = {J. Fluid Mech.},
  year = {1991},
  volume = {237},
  pages = {499-539}
}

@ARTICLE{honnorat2010identification,
  author = {Honnorat, Marc and Monnier, J{\'e}r{\^o}me and Rivi{\`e}re, Nicolas
	and Huot, {\'E}tienne and Le Dimet, Fran{\c{c}}ois-Xavier},
  title = {Identification of equivalent topography in an open channel flow using
	Lagrangian data assimilation},
  journal = {Computing and visualization in science},
  year = {2010},
  volume = {13},
  pages = {111--119},
  number = {3},
  publisher = {Springer}
}

@ARTICLE{Hopfinger87,
  author = {E.~J. Hopfinger},
  title = {Turbulence in stratified fluids: {A} review},
  journal = JGR,
  year = {1987},
  volume = {92},
  pages = {5287--5303},
  number = {C5}
}

@ARTICLE{HopfingerToly76,
  author = {E.~J. Hopfinger and J.~A. Toly},
  title = {Spatially decaying turbulence and its relation to mixing across density
	interfaces},
  journal = {J. Fluid Mech.},
  year = {1976},
  volume = {78},
  pages = {155--175}
}

@PHDTHESIS{Hossain80,
  author = {M. S. Hossain},
  title = {Mathematische {M}odellierung von turbulenten {A}uftriebsstr\"omungen},
  school = {Universit\"at Karlsruhe},
  year = {1980},
  pages = {145 pp.}
}

@ARTICLE{hsu2006wave,
  author = {Hsu, T.J. and Elgar, S. and Guza, RT},
  title = {{Wave-induced sediment transport and onshore sandbar migration}},
  journal = {Coastal engineering},
  year = {2006},
  volume = {53},
  pages = {817--824},
  number = {10},
  file = {:../2006Wave-induced-sediment-transport-onshore-sandbar-migration.pdf:PDF},
  issn = {0378-3839},
  publisher = {Elsevier}
}

@ARTICLE{huang2010wave,
  author = {Huang, C.J. and Qiao, F.},
  title = {{Wave-turbulence interaction and its induced mixing in the upper
	ocean}},
  journal = JGR,
  year = {2010},
  volume = {115},
  file = {:../GLM/2010-glm-Wave‐turbulence-interaction-and-its-induced-mixing-in-the-upper-ocean-Chuan-Jiang-Huang1.pdf:PDF}
}

@ARTICLE{huang2011improving,
  author = {Huang, C.J. and Qiao, F. and Song, Z. and Ezer, T.},
  title = {Improving simulations of the upper ocean by inclusion of surface
	waves in the Mellor-Yamada turbulence scheme},
  journal = JGR,
  year = {2011},
  volume = {116},
  pages = {01007},
  number = {C15},
  file = {:../wave-turb/2011-improving-simulations-upper-ocean-inclusion-surface-waves.pdf:PDF}
}

@ARTICLE{huang2009turbulence,
  author = {Huang, Zhi-Cheng and Hsiao, Shih-Chun and Hwung, Hwung-Hweng and
	Chang, Kuang-An},
  title = {Turbulence and energy dissipations of surf-zone spilling breakers},
  journal = {Coastal Engineering},
  year = {2009},
  volume = {56},
  pages = {733--746},
  number = {7},
  publisher = {Elsevier}
}

@ARTICLE{Hunter93,
  author = {J. R. Hunter and P.D. Craig and H. E. Phillips},
  title = {{On the use of random walk models with spatially variable diffusivity}},
  journal = {Journal of Computational Physics},
  year = {1993},
  volume = {106},
  pages = {366--376}
}

@ARTICLE{Hussain72,
  author = {K.~M.~F. Hussain and W.~C. Reynolds},
  title = {The mechanics of an organized wave in turbulent shear flow. {P}art
	2. {E}xperimental results},
  journal = {J. Fluid Mech.},
  year = {1972},
  volume = {54},
  pages = {241--261}
}

@ARTICLE{Hussain70,
  author = {K.~M.~F. Hussain and W.~C. Reynolds},
  title = {The mechanics of an organized wave in turbulent shear flow},
  journal = {J. Fluid Mech.},
  year = {1970},
  volume = {41},
  pages = {241--258}
}

@INCOLLECTION{Hutter93,
  author = {K. Hutter},
  title = {Waves and Oscillations in the Ocean and in Lakes},
  booktitle = {Continuum Mechanics in Enviromental Sciences and Geophysics},
  publisher = {Springer-Verlag, Berlin/Heidelberg/New York},
  year = {1993},
  editor = {K. Hutter}
}

@BOOK{Hutter95,
  title = {Fluid- und Thermodynamik},
  publisher = {Springer-Verlag Berlin},
  year = {1995},
  author = {K. Hutter}
}

@ARTICLE{hwang2006duration,
  author = {Hwang, P.A.},
  title = {Duration-and fetch-limited growth functions of wind-generated waves
	parameterized with three different scaling wind velocities},
  journal = JGR,
  year = {2006},
  volume = {111},
  pages = {C02005},
  number = {C2},
  file = {:../wave-turb/2006-Duration-fetch-limited-growth-functions-wind-generated-waves.pdf:PDF},
  publisher = {American Geophysical Union}
}

@ARTICLE{hwang2004influence,
  author = {Hwang, P.A.},
  title = {Influence of wavelength on the parameterization of drag coefficient
	and surface roughness},
  journal = JPO,
  year = {2004},
  volume = {60},
  pages = {835--841},
  number = {5},
  file = {:../wave-turb/2004-Influence-Wavelength-Parameterization--Drag-coefficient-Surface0835.pdf:PDF},
  publisher = {Springer}
}

@PHDTHESIS{Haese96,
  author = {C. H{\"a}se},
  title = {Die Vorhersage der Produktivit{\"a}t des Phytoplanktons im Bodensee
	unter Ber{\"u}cksichtigung der Temperatur sowie der spektralen Zusammensetzung
	des Unterwasser-Strahlungsfeldes},
  school = {University of Konstanz},
  year = {1996},
  type = {Konstanzer {D}issertationen, {V}ol.\ 514},
  note = {Hartung-Gorre Verlag}
}

@INCOLLECTION{Imberger98,
  author = {J. Imberger},
  title = {Flux paths in a stratified lake: {A} review},
  booktitle = {Physical Processes in Lakes and Oceans},
  publisher = {American Geophysical Union},
  year = {1998},
  editor = {J. Imberger},
  series = {Coastal and Esturaine Studies},
  pages = {1--17}
}

@ARTICLE{Imberger85,
  author = {J. Imberger},
  title = {The diurnal mixed layer},
  journal = {Limnol. Oceanogr.},
  year = {1985},
  volume = {30},
  pages = {737--770},
  number = {4}
}

@ARTICLE{Imberger82,
  author = {J. Imberger and P.~F. Hamblin},
  title = {Dynamics of lakes, reservoirs, and cooling ponds},
  journal = {Ann. Rev. Fluid Mech.},
  year = {1982},
  volume = {14},
  pages = {153--187}
}

@ARTICLE{Imberger93,
  author = {J. Imberger and G.~N. Ivey},
  title = {Boundary mixing in stratified reservoirs},
  journal = {J. Fluid. Mech.},
  year = {1993},
  volume = {248},
  pages = {477--491}
}

@ARTICLE{Imberger91,
  author = {J. Imberger and G.~N. Ivey},
  title = {On the nature of turbulence in a stratified fluid. {P}art {II}: Application
	to lakes},
  journal = JPO,
  year = {1991},
  volume = {21},
  pages = {659--680}
}

@INPROCEEDINGS{Imberger81,
  author = {J. Imberger and J.~C. Patterson},
  title = {A dynamic reservoir simulation model - {DYRESM}:5},
  booktitle = {Transport models for inland and coastal waters},
  year = {1981},
  editor = {H. Fischer},
  pages = {310--361}
}

@ARTICLE{Imboden78,
  author = {D.~M. Imboden and S. Emerson},
  title = {Natural radon and phosphorous as limnological tracers},
  journal = {Limnol. Oceanogr.},
  year = {1978},
  volume = {23},
  pages = {77--90}
}

@INCOLLECTION{Imboden94,
  author = {D.~M. Imboden and A. W{\"u}est},
  title = {Mixing mechanisms in lakes},
  booktitle = {Lakes},
  publisher = {Springer, New York},
  year = {1994},
  editor = {A. Lerman},
  pages = {83--138}
}

@INPROCEEDINGS{Inanc04,
  author = {T. Inanc and S. C. Shadden and J. E. Marsden},
  title = {{Optimal trajectory generation in ocean flows}},
  booktitle = {American Control Conference, 2005. Proceedings of the 2005},
  year = {2004},
  abstract = {Abstract — In this paper it is shown that Lagrangian Coherent Structures
	(LCS) are useful in determining near optimal trajectories for autonomous
	underwater gliders in a dynamic ocean environment. This opens the
	opportunity for optimal path planning of autonomous underwater vehicles
	by studying the global flow geometry via dynamical systems methods.
	Optimal glider paths were computed for a 2-dimensional kinematic
	model of an end-point glider problem. Numerical solutions to the
	optimal control problem were obtained using Nonlinear Trajectory
	Generation (NTG) software. The resulting solution is compared to
	corresponding results on LCS obtained using the Direct Lyapunov Exponent
	method. The velocity data used for these computations was obtained
	from measurements taken in August, 2000, by HF-Radar stations located
	around Monterey Bay, CA. I.}
}

@ARTICLE{Iskandarani95,
  author = {M. Iskandarani and D.~B. Haidvogel and J.~P. Boyd},
  title = {A staggered spectral element model with application to the ocean
	shallow water equations},
  journal = {Int. J. Numer. Methods Fluids},
  year = {1995},
  volume = {20},
  pages = {393--414}
}

@ARTICLE{Itsweire86,
  author = {E.~C. Itseire and K.~N. Helland and C.~W. van Atta},
  title = {The evolution of grid-generated turbulence in a stably stratfied
	fluid},
  journal = {J. Fluid Mech.},
  year = {1986},
  volume = {162},
  pages = {299--338}
}

@ARTICLE{Itsweire93,
  author = {E.~C. Itsweire and J.~R. Koseff and D.~A. Briggs and J.~H. Ferziger},
  title = {Turbulence in stratified shear flows: {I}mplications for interpreting
	shear-induced mixing in the ocean},
  journal = JPO,
  year = {1995},
  volume = {23},
  pages = {1508--1522}
}

@INPROCEEDINGS{Ives87,
  author = {D. C. Ives and R. M. Zacharias},
  title = {Conformal mapping and orthogonal grid generation},
  booktitle = {AIAA'87},
  year = {1987},
  organisation = {AIAA/SAE/ASME/ASEE 23rd Joint Propulsion Conference}
}

@ARTICLE{Ivey91,
  author = {G.~N. Ivey and J. Imberger},
  title = {On the nature of turbulence in a stratified fluid. {P}art {I}: The
	energetics of mixing},
  journal = JPO,
  year = {1991},
  volume = {21},
  pages = {650--658}
}

@ARTICLE{JACKETTea05,
  author = {David R. Jackett and Trevor J. McDougall and Rainer Feistel and Daniel
	G. Wright and Stephen M. Griffies},
  title = {Updated algorithms for density, potential temperature, conservative
	temperature and freezing temperature of seawater},
  journal = JAOT,
  year = {2005},
  note = sub
}

@ARTICLE{jacob2005m,
  author = {Jacob, R. and Larson, J. and Ong, E.},
  title = {{M$\times$ N communication and parallel interpolation in Community
	Climate System Model version 3 using the Model Coupling Toolkit}},
  journal = {International Journal of High Performance Computing Applications},
  year = {2005},
  volume = {19},
  pages = {293--307},
  publisher = {SAGE Publications}
}

@ARTICLE{Jacobitzetal97,
  author = {F.~C. Jacobitz and S. Sarkar and C.~W. van Atta},
  title = {Direct numerical simulations of the turbulence evolution in a uniformly
	sheared and stably stratifed flow},
  journal = {J. Fluid Mech.},
  year = {1997},
  volume = {342},
  pages = {231--261}
}

@PHDTHESIS{Jakirlic97,
  author = {S. Jakarli{\'c}},
  title = {Reynolds-Spannungs-Modellierung komplexer turbulenter Str{\"o}mungen},
  school = {University of Erlangen-N{\"u}rnberg, Technische Fakult{\"a}t, Germany},
  year = {1997},
  publisher = {Herbert Utz Verlag Wissenschaft, Munich, Germany}
}

@ARTICLE{Jakobsen95,
  author = {F. Jakobsen},
  title = {{The major inflow to the Baltic Sea during January 1993}},
  journal = {Journal of Marine Systems},
  year = {1995},
  volume = {6},
  pages = {227--240},
  number = {3},
  abstract = { The volume of highly saline water transported through the Great Belt
	(Storeb{\ae}lt) and the Sound ({\O}resund) to the Baltic Sea is quantified
	directly from data measured in the Great Belt and the Sound. The
	measurements include current velocity, temperature and conductivity.
	The inflow through the Little Belt (Lilleb{\ae}lt) is estimated from
	the volume transported through the Great Belt. The volume of highly
	saline water, transported into the Baltic Sea in the period January
	5 to January 26, 1993, is calculated to be 154 km3. The mean water
	mass temperature was approximately 4 °C and the mean concentration
	of oxygen approximately 8 ml/l (11 mg/l). During the major inflow,
	the volume of water with a high salinity (more than 17 PSU) transported
	through the Great Belt was in a ratio of 7:6 with the volume of highly
	saline water transported through the Sound. Data from a survey in
	the Bornholm Basin with R / V Dana during the period from February
	27, 1993 to March 14, 1993 are investigated to study the inflow through
	the western part of the Baltic.},
  doi = {DOI: 10.1016/0924-7963(94)00025-7},
  issn = {0924-7963},
  url = {http://www.sciencedirect.com/science/article/B6VF5-3YYTMJ7-T/2/601edfe7f213106d93e0c1248845075c}
}

@ARTICLE{janssen1991quasi,
  author = {Janssen, Peter AEM},
  title = {Quasi-linear theory of wind-wave generation applied to wave forecasting},
  journal = JPO,
  year = {1991},
  volume = {21},
  pages = {1631--1642},
  number = {11}
}

@ARTICLE{janssen1989wave,
  author = {Janssen, Peter AEM},
  title = {Wave-induced stress and the drag of air flow over sea waves},
  journal = JPO,
  year = {1989},
  volume = {19},
  pages = {745--754},
  number = {6}
}

@ARTICLE{janssen2007note,
  author = {Janssen, TT and Battjes, JA},
  title = {A note on wave energy dissipation over steep beaches},
  journal = {Coastal Engineering},
  year = {2007},
  volume = {54},
  pages = {711--716},
  number = {9},
  publisher = {Elsevier}
}

@ARTICLE{Jassby76,
  author = {A.~D. Jassby and T. Platt},
  title = {Mathematical formulation of the relationship between photosynthesis
	and light of phytoplankton},
  journal = {Limnol. Oceanogr.},
  year = {1976},
  volume = {21},
  pages = {540--547}
}

@ARTICLE{jenkins1989use,
  author = {Jenkins, A.D.},
  title = {The use of a wave prediction model for driving a near-surface current
	model},
  journal = {Ocean Dynamics},
  year = {1989},
  volume = {42},
  pages = {133--149},
  number = {3},
  file = {:../GLM/1989-The-use-of-a-Wave-Surface-Current-Model.pdf:PDF},
  publisher = {Springer}
}

@ARTICLE{jenkins1987wind,
  author = {Jenkins, A.D.},
  title = {Wind and wave induced currents in a rotating sea with depth-varying
	eddy viscosity},
  journal = {J. Phys. Oceanogr},
  year = {1987},
  volume = {17},
  pages = {938--951},
  number = {7},
  file = {:../GLM/1987-wind-wave-induced-current-Jenkins19871-AMS.pdf:PDF}
}

@ARTICLE{jenkins1interaction,
  author = {Jenkins, A.D. and Ardhuin, F.},
  title = {{Interaction of Ocean Waves and Currents: How Different Approaches
	may be Reconciled.}},
  journal = {continuity},
  year = {2006},
  volume = {1},
  pages = {14},
  number = {2},
  file = {:../2006-Interaction-OceanWaves-Currents-How-Different-Approaches-Reconciled-JenkinsArdhuinISOPE2004.pdf:PDF}
}

@ARTICLE{jenkins1987lagrangian,
  author = {Jenkins, Alastair D},
  title = {A Lagrangian model for wind-and wave-induced near-surface currents},
  journal = {Coastal engineering},
  year = {1987},
  volume = {11},
  pages = {513--526},
  number = {5},
  publisher = {Elsevier}
}

@ARTICLE{jenkins1986theory,
  author = {Jenkins, Alastair D},
  title = {A theory for steady and variable wind-and wave-induced currents},
  journal = {Journal of Physical Oceanography},
  year = {1986},
  volume = {16},
  pages = {1370--1377},
  number = {8}
}

@BOOK{JERLOV68,
  title = {Optical oceanography},
  publisher = {Elsevier},
  year = {1968},
  author = {N. G. Jerlov}
}

@TECHREPORT{jessup2011darla,
  author = {Jessup, Andrew T and Chickadel, Chris and Farquharson, Gordon and
	Thomson, Jim and Holman, Robert A and Haller, Merrick and Kuropov,
	Alexander and {\"O}zkan-Haller, Tuba and Elgar, Steve and Raubenheimer,
	Britt},
  title = {DARLA: Data Assimilation and Remote Sensing for Littoral Applications},
  institution = {DTIC Document},
  year = {2011}
}

@ARTICLE{Jinetal2003,
  author = {L.~H. Jin and R.~M.~C. So and T.~B. Gatski},
  title = {Equilibrium states of turbulent homogeneous buoyant flows},
  journal = {J. Fluid Mech.},
  year = {2003},
  volume = {482},
  pages = {207--233}
}

@PHDTHESIS{Jo92,
  author = {Jin-Hoon Jo},
  title = {Simulations num\'{e}riques des circulations oc\'{e}aniques dans la
	r\'{e}gion de confluence des courants du Br\'{e}sil et des Malouines},
  school = {l'Universit\'{e} Joseph Fourier de Grenoble},
  year = {1992},
  month = {september}
}

@ARTICLE{Joehnk2001a,
  author = {K. Joehnk and L. Umlauf},
  title = {Modelling the metalimnetic oxygen minimum in a medium sized alpine
	lake},
  journal = {Ecol. Model.},
  year = {2001},
  volume = {136},
  pages = {67--80}
}

@ARTICLE{johnson1998dependence,
  author = {Johnson, HK and H{\o}jstrup, J. and Vested, HJ and Larsen, SE},
  title = {On the dependence of sea surface roughness on wind waves},
  journal = JPO,
  year = {1998},
  volume = {28},
  pages = {1702--1716},
  number = {9},
  file = {:../wave-turb/1998-On-the-Dependence-of-Sea-Surface-Roughness-on-Wind-Waves.pdf:PDF}
}

@ARTICLE{jones2001influence,
  author = {Jones, JE and Davies, AM},
  title = {{Influence of wave-current interaction, and high frequency forcing
	upon storm induced currents and elevations}},
  journal = {Estuarine, Coastal and Shelf Science},
  year = {2001},
  volume = {53},
  pages = {397--413},
  number = {4},
  file = {:../2001Influence-of-Wave-current-Interaction.pdf:PDF},
  issn = {0272-7714},
  publisher = {Elsevier}
}

@ARTICLE{Jones93,
  author = {M. C. Jones},
  title = {{Simple boundary correction for kernel density estimation}},
  journal = {Statistics and Computing},
  year = {1993},
  volume = {3},
  pages = {135--146},
  number = {3},
  abstract = {If a probability density function has bounded support, kernel density
	estimates often overspill the boundaries and are consequently especially
	biased at and near these edges. In this paper, we consider the alleviation
	of this boundary problem. A simple unified framework is provided
	which covers a number of straightforward methods and allows for their
	comparison: lsquogeneralized jackknifingrsquo generates a variety
	of simple boundary kernel formulae. A well-known method of Rice (1984)
	is a special case. A popular linear correction method is another:
	it has close connections with the boundary properties of local linear
	fitting (Fan and Gijbels, 1992). Links with the lsquooptimalrsquo
	boundary kernels of M{\"u}ller (1991) are investigated. Novel boundary
	kernels involving kernel derivatives and generalized reflection arise
	too. In comparisons, various generalized jackknifing methods perform
	rather similarly, so this, together with its existing popularity,
	make linear correction as good a method as any. In an as yet unsuccessful
	attempt to improve on generalized jackknifing, a variety of alternative
	approaches is considered. A further contribution is to consider generalized
	jackknife boundary correction for density derivative estimation.
	En route to all this, a natural analogue of local polynomial regression
	for density estimation is defined and discussed.},
  doi = {10.1007/BF00147776},
  url = {http://www.springerlink.com/content/nr4711m6330152u8}
}

@ARTICLE{jones2008influence,
  author = {Jones, N.L. and Monismith, S.G.},
  title = {The influence of whitecapping waves on the vertical structure of
	turbulence in a shallow estuarine embayment},
  journal = JPO,
  year = {2008},
  volume = {38},
  pages = {1563--1580},
  file = {:../wave-turb/2007-The-Influence-Whitecapping-Waves-Vertical-Structure-TurbulenceJPO3766.pdf:PDF}
}

@ARTICLE{jones2008modeling,
  author = {Jones, N.L. and Monismith, S.G.},
  title = {Modeling the influence of wave-enhanced turbulence in a shallow tide-and
	wind-driven water column},
  journal = JGR,
  year = {2008},
  volume = {113},
  pages = {C03009},
  number = {C3},
  file = {:../wave-turb/2007-Modeling-influence-wave-enhanced-turbulenceJC004246.pdf:PDF},
  publisher = {American Geophysical Union}
}

@ARTICLE{jones2008note,
  author = {Jones, N.L. and Thompson, J.K. and Monismith, S.G.},
  title = {A Note on the Effect of Wind Waves on Vertical Mixing in Franks Tract,
	Sacramento-San Joaquin Delta, California},
  journal = {San Francisco Estuary and Watershed Science},
  year = {2008},
  volume = {6},
  number = {2},
  file = {:../wave-turb/2008-Effect-Wind-waves-on-Vertical-Mixing.pdf:PDF}
}

@ARTICLE{Jones72,
  author = {W.~P. Jones and B.~E. Launder},
  title = {The prediction of laminarization with a two-equation model of turbulence},
  journal = {Int. J. Heat Mass Transfer},
  year = {1972},
  volume = {15},
  pages = {301--314}
}

@ARTICLE{Jonsson1990,
  author = {I.G. Jonsson},
  title = {Wave current interactions},
  journal = {The Sea},
  year = {1990},
  volume = {9A},
  pages = {65--120},
  owner = {moghimi}
}

@ARTICLE{jordü2007assessment,
  author = {Jord{\\"u}, G. and Bola{\~n}os, R. and Espino, M. and S{\'a}nchez-Arcilla,A.},
  title = {Assessment of the importance of the current-wave coupling in the
	shelf ocean forecasts},
  journal = {Ocean Science},
  year = {2007},
  volume = {3},
  pages = {345--362},
  number = {3},
  file = {:../2007Assessment-importance-current-wave-coupling.pdf:PDF}
}

@TECHREPORT{Joehnk2000a,
  author = {K. J{\"o}hnk},
  title = {{1D Hydrodynamische Modelle in der Limnophysik. Turbulenz-Meromixis-Sauerstoff.}},
  institution = {Department of Mechanics, Technical University at Darmstadt, Germany},
  year = {2000},
  type = {Habilitation Thesis},
  note = {in German}
}

@TECHREPORT{Joehnk98,
  author = {K. J{\"o}hnk and K. Hutter},
  title = {Simulation der {S}chichtung und des {S}auerstoffgehaltes im {A}mmersee},
  institution = {Institut zur {E}rforschung und zum {S}chutz der {G}ew{\"a}sser, {K}onstanz,
	{G}ermany},
  year = {1998},
  type = {Final Report},
  note = {in German}
}

@BOOK{Joehnk97,
  title = {lecture notes``Mechanik umweltrelevanter Systeme'' an der TH-Darmstadt},
  publisher = {available the department of mechanics, TH-Darmstadt},
  year = {1997},
  author = {K. J{\"o}hnk and K. Hutter}
}

@ARTICLE{Jorgensen95,
  author = {S.~E. J{\o}rgensen},
  title = {State of the art of ecological modelling in limnology},
  journal = {Ecol. Model.},
  year = {1995},
  volume = {78},
  pages = {101--115}
}

@ARTICLE{KuehnRadach1997,
  author = {Wilfried K\"uhn and G\"unther Radach},
  title = {A one-dimensional physical-biological model study of the pelagic
	nitrogen cycling during the spring bloom in the northern {N}orth
	{S}ea ({FLEX}'76)},
  journal = JMR,
  year = {1997},
  volume = {55},
  pages = {687-734}
}

@BOOK{KAGAN95,
  title = {Ocean-atmosphere interaction and climate modelling},
  publisher = {Cambridge University Press},
  year = {1995},
  author = {Boris Abramovich Kagan},
  address = {Cambridge}
}

@ARTICLE{kalnay2010accelerating,
  author = {Kalnay, Eugenia and Yang, Shu-Chih},
  title = {Accelerating the spin-up of Ensemble Kalman Filtering},
  journal = {Quarterly Journal of the Royal Meteorological Society},
  year = {2010},
  volume = {136},
  pages = {1644--1651},
  number = {651},
  publisher = {Wiley Online Library}
}

@ARTICLE{Kaltenbachetal94,
  author = {H.-J. Kaltenbach and T. Gerz and U. Schumann},
  title = {Large-{E}ddy simulation of homogeneous turbulence and diffusion in
	stably stratified shear flow},
  journal = {J. Fluid Mech.},
  year = {1994},
  volume = {280},
  pages = {1--40}
}

@ARTICLE{kang2006depth,
  author = {Kang, K.R. and Di Iorio, D.},
  title = {Depth-and current-induced effects on wave propagation into the Altamaha
	River Estuary, Georgia},
  journal = {Estuarine, Coastal and Shelf Science},
  year = {2006},
  volume = {66},
  pages = {395--408},
  number = {3-4},
  file = {:../est/2006-Depth-and-current-induced-effects-on-waveECSS_Ref_SK-124-4.pdf:PDF},
  publisher = {Elsevier}
}

@ARTICLE{kantha2004effect,
  author = {Kantha, L.H. and Clayson, A. C.},
  title = {On the effect of surface gravity waves on mixing in the oceanic mixed
	layer},
  journal = OMOD,
  year = {2004},
  volume = {6},
  pages = {101--124},
  number = {2},
  publisher = {Elsevier}
}

@ARTICLE{kantha2010note,
  author = {Kantha, L. and Lass, H.U. and Prandke, H.},
  title = {{A note on Stokes production of turbulence kinetic energy in the
	oceanic mixed layer: observations in the Baltic Sea}},
  journal = {Ocean Dynamics},
  year = {2010},
  volume = {60},
  pages = {171--180},
  number = {1},
  file = {:../2010-A-note-Stokes-production-turbulence-kinetic-energy-the-oceanic.pdf:PDF},
  issn = {1616-7341},
  publisher = {Springer}
}

@ARTICLE{Kantha2003,
  author = {L.~H. Kantha},
  title = {On an improved model for the turbulent PBL},
  journal = {J. Atmos. Sci.},
  year = {2003},
  volume = {60},
  pages = {2239--2246},
  number = {17}
}

@ARTICLE{KanthaClayson2001,
  author = {L.~H. Kantha and C.~A. Clayson},
  title = {On the effect of surface gravity waves on mixing in an oceanic mixed
	layer model},
  journal = OMOD,
  year = {2001},
  note = {(submitted)}
}

@BOOK{KANTHAea00b,
  title = {Numerical models of oceans and oceanic processes},
  publisher = {Academic Press},
  year = {2000},
  author = {Lakshmi H. Kantha and Carol Anne Clayson},
  volume = {66},
  series = {International Geophysics Series}
}

@ARTICLE{KanthaClayson94,
  author = {L.~H. Kantha and C.~A. Clayson},
  title = {An improved mixed layer model for geophysical applications},
  journal = JGR,
  year = {1994},
  volume = {99},
  pages = {25235--25266},
  number = {C12}
}

@ARTICLE{Kantha77,
  author = {L.~H. Kantha and O.~M. Phillips and R.~S. Azad},
  title = {On turbulent entrainment at a stable density interface},
  journal = {J. Fluid Mech.},
  year = {1977},
  volume = {79},
  pages = {753--768},
  number = {4}
}

@ARTICLE{Kasahara74,
  author = {A. Kasahara},
  title = {Various vertical coordinate systems used for numerical weather prediction},
  journal = {Mon. Weather Rev.},
  year = {1974},
  volume = {102},
  pages = {509}
}

@ARTICLE{KatoPhillips69,
  author = {H. Kato and O.~M. Phillips},
  title = {On the penetration of a turbulent layer into stratified fluid},
  journal = {J. Fluid Mech.},
  year = {1969},
  volume = {37},
  pages = {643--655},
  number = {4}
}

@BOOK{Kay,
  title = {Tensor Calculus},
  publisher = {McGraw-Hill Book Company, Inc.},
  year = {1988},
  author = {D.~C. Kay},
  series = {Schaum's Outline Series }
}

@CONFERENCE{Khosronejad2008qual,
  author = {Khosronejad, A. and Moghimi, S.},
  title = {Qualitative Analysis of Sediment Entering into Power Tunnels Using
	a Sophisticated 3D Numerical Model; Case Study: Dez Dam},
  booktitle = {8th International Conference on Hydro-Science and Engineering, ICHE2008
	, Nagoya, JAPAN},
  year = {2008},
  pages = {95-96},
  owner = {moghimi},
  timestamp = {2014.01.24}
}

@ARTICLE{khosronejad20073d,
  author = {Khosronejad, A. and Rennie, C.D. and Moghimi, S},
  title = {3D Numerical Modeling of Flow field and Sediment Transport in Laboratory
	Reservoir Flushing Process},
  journal = {PROCEEDINGS OF THE CONGRESS-INTERNATIONAL ASSOCIATION FOR HYDRAULIC
	RESEARCH},
  year = {2007},
  volume = {32},
  pages = {432},
  number = {1}
}

@CONFERENCE{Khosronejad2007app,
  author = {Khosronejad, A. and Renny, C. and Moghimi, S.},
  title = {Application of Intelligent system of ANN to predict the scour process
	in coastal engineering},
  booktitle = {RCEM 2007, University of Twente, Neatherland},
  year = {2007},
  owner = {moghimi},
  timestamp = {2014.01.24}
}

@ARTICLE{killworth1999turbulent,
  author = {Killworth, P.D. and Edwards, N.R.},
  title = {{A turbulent bottom boundary layer code for use in numerical ocean
	models}},
  journal = JPO,
  year = {1999},
  volume = {29},
  pages = {1221--1238},
  number = {6},
  file = {:../1999-Inclusion-Bottom-Boundary-Layer-in-Ocean-Models-Killworth.pdf:PDF},
  issn = {1520-0485}
}

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	for vanishing drift the algorithm yields a martingale independent
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	A discussion of errors shows that sample size can be as important
	as truncation.},
  copyright = {Copyright © 1985 Society for Industrial and Applied Mathematics},
  issn = {00361429},
  jstor_articletype = {primary\_article},
  jstor_formatteddate = {Dec., 1985},
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  edition = {Corrected},
  month = {July},
  abstract = {The numerical analysis of stochastic differential equations differs
	significantly from that of ordinary differential equations, due to
	the peculiarities of stochastic calculus. The book proposes to the
	reader whose background knowledge is limited to undergraduate level
	methods for engineering and physics, and easily accessible introductions
	to SDE and then applications as well as the numerical methods for
	dealing with them. To help the reader develop an intuitive understanding
	and hand-on numerical skills, numerous exercises including PC-exercises
	are included.},
  day = {01},
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  isbn = {3540540628},
  keywords = {numerical, sde},
  posted-at = {2007-04-11 16:31:01},
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	Utah, Department of Mathematics, 110 LCB, 155 S 1400 E RM 233, Salt
	Lake City, UT 84112-0090, USA, Tel: +1 801 581 5254, FAX: +1 801
	581 4148, e-mail: \path|beebe@math.utah.edu|, \path|beebe@acm.org|,
	\path|beebe@computer.org|, \path|beebe@ieee.org| (Internet), URL:
	\path|http://www.math.utah.edu/~beebe/|},
  bibdate = {Mon Jan 20 15:27:00 MST 1997},
  coden = {SJNAAM},
  issn = {0036-1429 (print), 1095-7170 (electronic)},
  mrclass = {60H10 (65L99 65U05 93E25)},
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  mrnumber-url = {http://www.ams.org/mathscinet-getitem?mr=96h%3a60094},
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}

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  author={Kumar, Nirnimesh and Voulgaris, George and Warner, John C and Olabarrieta, Maitane},
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@INPROCEEDINGS{kurapov2012correction,
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  booktitle = {AGU Fall Meeting Abstracts},
  year = {2012},
  volume = {1},
  pages = {06}
}

@ARTICLE{kurapov2013bathymetry,
  author = {Kurapov, Alexander L and {\"O}zkan-Haller, H},
  title = {Bathymetry correction using an adjoint component of a coupled nearshore
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@ARTICLE{Kuznetsov08,
  author = {I. Kuznetsov and T. Neumann and H. Burchard},
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	cyanobacteria in the Baltic Proper}},
  journal = {Ecological Modelling},
  year = {2008},
  volume = {219},
  pages = {107--114},
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  issn = {0304-3800},
  keywords = {Anoxic conditions, Baltic Sea, Biogeochemical modeling, Non-Redfield
	stoichiometry},
  risfield_0_m3 = {doi: DOI: 10.1016/j.ecolmodel.2008.08.002},
  url = {http://www.sciencedirect.com/science/article/B6VBS-4TKSNKH-1/2/0b2e4698c05626d2fed49d8a449500f0}
}

@INCOLLECTION{LEcuyer04,
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  year = {2004},
  editor = {James E. Gentle and Wolfgang Hardle and Yuichi Mori}
}

@ARTICLE{LEcuyer96,
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  title = {{Maximally equidistributed combined {Tausworthe} generators}},
  journal = {Mathematics of Computation},
  year = {1996},
  volume = {65},
  pages = {203--213},
  number = {213},
  month = jan,
  acknowledgement = {Nelson H. F. Beebe, University of Utah, Department of Mathematics,
	110 LCB, 155 S 1400 E RM 233, Salt Lake City, UT 84112-0090, USA,
	Tel: +1 801 581 5254, FAX: +1 801 581 4148, e-mail: \path|beebe@math.utah.edu|,
	\path|beebe@acm.org|, \path|beebe@computer.org| (Internet), URL:
	\path|http://www.math.utah.edu/~beebe/|},
  bibdate = {Fri Jul 16 10:38:30 MDT 1999},
  bibsource = {http://www.ams.org/mcom/1996-65-213},
  classcodes = {C5230 (Digital arithmetic methods); C1160 (Combinatorial mathematics);
	C7310 (Mathematics computing)},
  coden = {MCMPAF},
  issn = {0025-5718},
  keywords = {maximally equidistributed, number theory, primitive, random number
	generation, random number generators, statistical properties, Tausworthe
	generators, trinomial},
  mrclass = {65C10},
  mrnumber = {96d:65017},
  mrnumber-url = {http://www.ams.org/mathscinet-getitem?mr=96d%3a65017},
  mrreviewer = {Henri Faure},
  treatment = {T Theoretical or Mathematical},
  url = {http://www.ams.org/jourcgi/jour-pbprocess?fn=110&amp;arg1=S0025-5718-96-00696-5&amp;u=/mcom/1996-65-213/}
}

@INPROCEEDINGS{LEcuyer92,
  author = {P. L'Ecuyer},
  title = {{Testing Random Number Generators}},
  booktitle = {{Proceedings of the 1992 Winter Simulation Conference}},
  year = {1992},
  volume = {Proceedings of the 1992 Winter Simulation Conference },
  pages = {305--313},
  publisher = {IEEE Press}
}

@ARTICLE{LEcuyer90,
  author = {P. L'Ecuyer},
  title = {{Random Numbers for Simulation}},
  journal = {Communications of the ACM},
  year = {1990},
  volume = {33}
}

@ARTICLE{LEcuyer88,
  author = {P. L'Ecuyer},
  title = {{Efficient and Portable Combined Random Number Generators}},
  journal = {CACM: Communications of the ACM},
  year = {1988},
  volume = {31}
}

@ARTICLE{Lalescu09,
  author = {C.C. Lalescu and B. Teaca and D. Carati},
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	test particles in discretized fields}},
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  year = {2009},
  volume = {In Press, Accepted Manuscript},
  doi = {10.1016/j.jcp.2009.10.046},
  issn = {0021-9991},
  keywords = {Numerical optimization, Spline interpolation, Test particle},
  risfield_0_m3 = {doi: DOI: 10.1016/j.jcp.2009.10.046},
  url = {http://www.sciencedirect.com/science/article/B6WHY-4XKHDFB-4/2/617bccbaa896c188c524cdba3d75c097}
}

@ARTICLE{Lambrechts08,
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	and V. Legat and J.-F. Remacle and E. Wolanski},
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	Reef}},
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  year = {2008},
  volume = {79},
  pages = {143--151},
  number = {1},
  issn = {0272-7714},
  keywords = {East Australian Current, finite elements, Great Barrier Reef, hydrodynamics,
	shelf dynamics, unstructured mesh},
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  url = {http://www.sciencedirect.com/science/article/B6WDV-4S62RRP-1/2/1484494d6f60644751d10fbd064fd633}
}

@BOOK{Lampert97,
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  publisher = {Oxford University Press, Inc.},
  year = {1997},
  author = {W. Lampert and U. Sommer}
}

@TECHREPORT{LANDERea94,
  author = {J. W. M. Lander and P. A. Blokland and Johan M. de Kok},
  title = {The three-dimensional shallow water model {TRIWAQ} with a flexible
	vertical grid definition},
  institution = {National Institute for Coastal and Marine Management / RIKZ},
  year = {1994},
  number = {RIKZ/OS-96.104x, SIMONA report 96-01},
  address = {The Hague, The Netherlands}
}

@ARTICLE{landon2012ensemble,
  author = {Landon, Kyle C and Wilson, Greg W and {\"O}zkan-Haller, H Tuba and
	MacMahan, Jamie H},
  title = {Bathymetry Estimation Using Drifter-Based Velocity Measurements on
	the Kootenai River, Idaho},
  journal = JAOT,
  year = {2014},
  volume = {31},
  pages = {503--514},
  number = {2}
}

@ARTICLE{Lane07,
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	Vortex-Force Representations}},
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  year = {2007},
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}

@ARTICLE{Large95,
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	during the ocean storms experiment},
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  year = {1974},
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}

@ARTICLE{LARGEea94,
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@ARTICLE{Largeetal94,
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}

@ARTICLE{Launder75,
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  year = {1975},
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@ARTICLE{Launderetal75,
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@ARTICLE{LaunderSpalding74,
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  year = {1974},
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}

@ARTICLE{lee2012symmetric,
  author = {Lee, Chia-Ying and Chen, Shuyi S},
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	coupled atmosphere--wave--ocean models and observations},
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}

@ARTICLE{lee2007wave,
  author = {Lee, K. and Mizutani, N.},
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  journal = {INTERNATIONAL JOURNAL OF OFFSHORE AND POLAR ENGINEERING},
  year = {2007},
  volume = {17},
  pages = {259},
  number = {4},
  file = {:../2007-ABS-Wave-current-Interaction-Waves-Propagating-Against-Currents.pdf:PDF},
  issn = {1053-5381},
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}

@ARTICLE{VANLEER79,
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  pages = {101-136}
}

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  title = {{On wave-current interaction theories of Langmuir circulations}},
  journal = JFM,
  year = {1980},
  volume = {99},
  pages = {715--724},
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}

@ARTICLE{leibovich1977cio,
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  title = {{Convective instability of stably stratified water in the ocean}},
  journal = JFM,
  year = {1977},
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@ARTICLE{Lekien05,
  author = {F. Lekien and C. Coulliette and A. J. Mariano and E. H. Ryan and
	Lynn K. Shay and G. Haller and J. E. Marsden},
  title = {{Pollution release tied to invariant manifolds: A case study for
	the coast of Florida}},
  journal = {Physica D: Nonlinear Phenomena},
  year = {2005},
  volume = {210},
  pages = {1--20},
  number = {1-2},
  issn = {0167-2789},
  keywords = {Finite-time Lyapunov exponents, Lagrangian coherent structures, Pollution
	control},
  risfield_0_m3 = {doi: DOI: 10.1016/j.physd.2005.06.023},
  url = {http://www.sciencedirect.com/science/article/B6TVK-4GSTP5X-1/2/71661e54256c0c74cd705645162abe0a}
}

@ARTICLE{Lekien05b,
  author = {F. Lekien and J. Madsen},
  title = {{Tricubic Interpolation in Three Dimensions}},
  journal = {Journal of Numerical Methods and Engineering},
  year = {2005},
  volume = {63},
  pages = {455--471},
  number = {3},
  abstract = {The purpose of this paper is to give a local tricubic interpolation
	scheme in three dimensions that is both C 1 and isotropic. The algorithm
	is based on a specific 64 × 64 matrix that gives the relationship
	between the derivatives at the corners of the elements and the coefficients
	of the tricubic interpolant for this element. In contrast with global
	interpolation where the interpolated function usually depends on
	the whole data set, our tricubic local interpolation only uses data
	in a neighbourhood of an element. We show that the resulting interpolated
	function and its three first derivatives are continuous if one uses
	cubic interpolants. The implementation of the interpolator can be
	downloaded as a static and dynamic library for most platforms. The
	major difference between this work and current local interpolation
	schemes is that we do not separate the problem into three one-dimensional
	problems. This allows for a much easier and accurate computation
	of higher derivatives of the extrapolated field. Applications to
	the computation of Lagrangian coherent structures in ocean data are
	briefly discussed.}
}

@ARTICLE{Lemmin87,
  author = {U. Lemmin},
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@INPROCEEDINGS{Liberati04,
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  title = {{On the Efficiency of Simplified Weak Taylor Schemes for Monte Carlo
	Simulation in Finance}},
  booktitle = {{International Conference on Computational Science}},
  year = {2004},
  editor = {Marian Bubak and G. Dick {van Albada} and Peter M. A. Sloot and Jack
	Dongarra},
  volume = {3039},
  series = {{Lecture Notes in Computer Science}},
  pages = {771--778},
  publisher = {Springer},
  bibdate = {2004-11-26},
  bibsource = {DBLP, http://dblp.uni-trier.de/db/conf/iccS/iccS2004-4.html\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\#LiberatiP04},
  booktitle1 = {Computational Science - {ICCS} 2004, 4th International Conference,
	Krak{\'o}w, Poland, June 6-9, 2004, Proceedings, Part {IV}},
  isbn = {3-540-22129-8},
  url = {http://springerlink.metapress.com/openurl.asp?genre=article&amp;amp;issn=0302-9743&amp;amp;volume=3039&amp;amp;spage=771}
}

@ARTICLE{Lienhard90,
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@ARTICLE{Lintrup99,
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	Flinten and Drogden Channels, this paper assesses the relative importance
	of major Baltic inflows on [`]everyday' flow conditions of highly
	saline water (S>17 PSU) through the {\"O}resund for a period of 43
	months. During years with no major Baltic inflows, 1994-1996, it
	is found that the {\"O}resund on average supplies 1.2 Peta-grams
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	in the order of 2.3 to 4.0 Pg/year. Sixty percent of this inflow
	is in the salinity range 17-23 PSU; the remainder has a higher salinity.
	It is, thus, concluded that normal and regularly occurring flow in
	the {\"O}resund plays a much larger role in supplying salt to the
	Baltic than is usually assumed.},
  doi = {DOI: 10.1016/S0924-7963(98)00018-9},
  issn = {0924-7963},
  keywords = {{\"O}resund},
  keywords1 = {Drodgen Sill},
  keywords2 = {Baltic},
  url = {http://www.sciencedirect.com/science/article/B6VF5-3V8THRM-3/2/8ba3b7411ba23f0ecf0bc3e697da642b}
}

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@ARTICLE{liu2011coupled,
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@PHDTHESIS{liu2007analysis,
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@INPROCEEDINGS{longuet1964radiation,
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}

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	to ‘surf beats’},
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  year = {1962},
  volume = {13},
  pages = {481-504},
  abstract = {This paper studies the second-order currents and changes in mean surface
	level which are caused by gravity waves of non-uniform amplitude.
	The effects are interpreted in terms of the radiation stresses in
	the waves. The first example is of wave groups propagated in water
	of uniform mean depth. The problem is solved first by a perturbation
	analysis. In two special cases the second-order currents are found
	to be proportional simply to the square of the local wave amplitude:
	(a) when the lengths of the groups are large compared to the mean
	depth, and (b) when the groups are all of equal length. Then the
	surface is found to be depressed under a high group of waves and
	the mass-transport is relatively negative there. In case (a) the
	result can be simply related to the radiation stresses, which tend
	to expel fluid from beneath the higher waves. The second example
	considered is the propagation of waves of steady amplitude in water
	of gradually varying depth. Assuming no loss of energy by friction
	or reflexion, the wave amplitude must vary horizontally, to maintain
	the flux of energy constant; it is shown that this produces a negative
	tilt in the mean surface level as the depth diminishes. However,
	if the wave height is limited by breaking, the tilt is positive.
	The results are in agreement with some observations by Fairchild.
	
	
	Lastly, the propagation of groups of waves from deep to shallow water
	is studied. As the mean depth decreases, so the response of the fluid
	to the radiation stresses tends to increase. The long waves thus
	generated may be reflected as free waves, and so account for the
	'surf beats’ observed by Munk and Tucker.
	
	
	Generalle speaking, the changes in mean sea level produced by ocean
	waves are comparable with those due to horizontal wind stress. It
	may be necessary to allow for the wave stresses in calculating wind
	stress coefficients.
	
	(Published Online March 28 2006)
	
	(Received September 1 1961)
	
	(Revised April 10 1962)},
  owner = {moghimi}
}

@PHDTHESIS{Lorke98,
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  year = {1998}
}

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@ARTICLE{ly2002ocean,
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@ARTICLE{Mackerle2000,
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@ARTICLE{Mackie92,
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@ARTICLE{macmahan2014fortnightly,
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	Steve and Raubenheimer, Britt and Thornton, Ed and Weltmer, Micah
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@ARTICLE{macmahan2006rip,
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@ARTICLE{MADALAea77,
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@ARTICLE{mahdipaper2002caspian,
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	D and MOGHIMI, S},
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@ARTICLE{MaierReimer82,
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  year = {1982},
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}

@ARTICLE{Maiss94,
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@ARTICLE{malarkey1998modelling,
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@ARTICLE{malhadas2009effect,
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@BOOK{Mandelbrot83,
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@ARTICLE{marin2004eddy,
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  number = {3},
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  publisher = {Elsevier}
}

@ARTICLE{Marsaglia03,
  author = {G. Marsaglia},
  title = {{Xorshift RNGs}},
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  pages = {1--6},
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  month = {7},
  accepted = {2003-07-04},
  bibdate = {2003-07-04},
  coden = {JSSOBK},
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  issn = {1548-7660},
  submitted = {2003-05-06},
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}

@INCOLLECTION{Marsaglia03a,
  author = {G. Marsaglia},
  title = {{Random number generation}},
  booktitle = {{Encyclopedia of Computer Science}},
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  year = {2003},
  pages = {1499--1503},
  address = {Chichester, UK},
  isbn = {0-470-86412-5}
}

@ARTICLE{Marsaglia02,
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  year = {2002},
  volume = {7},
  pages = {1--9},
  number = {3},
  month = {1},
  accepted = {2002-01-27},
  bibdate = {2002-01-27},
  coden = {JSSOBK},
  day = {27},
  issn = {1548-7660},
  submitted = {2001-11-30},
  url = {http://www.jstatsoft.org/v07/i03}
}

@ARTICLE{Marsaglia00,
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  year = {2000},
  volume = {5},
  pages = {1--7},
  number = {8},
  month = {10},
  accepted = {2000-10-02},
  bibdate = {2000-10-02},
  coden = {JSSOBK},
  day = {2},
  issn = {1548-7660},
  submitted = {2000-04-15},
  url = {http://www.jstatsoft.org/v05/i08}
}

@TECHREPORT{Marsaglia87,
  author = {G. Marsaglia and A. Zaman},
  title = {{Toward a Universal Random Number Generator.}},
  institution = {Florida State University},
  year = {1987},
  number = {FSU-SCRI-87-50}
}

@ARTICLE{Marti86,
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}

@TECHREPORT{Martin86,
  author = {Paul J. Martin},
  title = {Testing and comparison of several mixed-layer models},
  institution = {Naval Oceanographic Research and Development Agency (NORDA), Stennis
	Space Center},
  year = {1986},
  number = {143},
  address = {Mississippi}
}

@ARTICLE{Martin85,
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	several models},
  journal = JGR,
  year = {1985},
  volume = {90},
  pages = {903--916},
  number = {C1}
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@ARTICLE{MARTINSENea87,
  author = {E. A. Martinsen and H. Engedahl},
  title = {Implementation and testing of a lateral boundary scheme as an open
	boundary condition in a barotropic ocean model},
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  year = {1987},
  volume = {11},
  pages = {603-627}
}

@ARTICLE{mashhadi2013numerical,
  author = {Mashhadi, Leila and Hadjizadeh Zaker, Nasser and Soltanpour, Mohsen
	and Moghimi, Saeed},
  title = {Numerical simulation of waves and storm surge induced by the Gonu
	tropical cyclone in the Chahbahar Bay area},
  journal = {International Journal of Maritime Technology},
  year = {2013},
  volume = {9},
  pages = {37--50},
  number = {17},
  publisher = {International Journal of Maritime Technology}
}

@ARTICLE{mashhadi2013study,
  author = {Mashhadi, Leila and Zaker, Nasser Hadjizadeh and Soltanpour, Mohsen
	and Moghimi, Saeed},
  title = {Study of the Gonu Tropical Cyclone in the Arabian Sea},
  journal = {Journal of Coastal Research},
  year = {2013},
  pages = {In-Press},
  publisher = {The Coastal Education and Research Foundation}
}

@ARTICLE{mastenbroek1993dynamical,
  author = {Mastenbroek, C. and Burgers, G. and Janssen, P.},
  title = {{The dynamical coupling of a wave model and a storm surge model through
	the atmospheric boundary layer}},
  journal = JPO,
  year = {1993},
  volume = {23},
  pages = {1856--1866},
  number = {8},
  issn = {0022-3670},
  publisher = {American Meteorological Society}
}

@ARTICLE{MATHIEUea01,
  author = {Pierre-Philiipe Mathieu and Eric Deleersnijder and Ben\^oit Cushman-Roisin
	and Jean-Marie Beckers and Karsten Bolding},
  title = {The role of topography in small well-mixed bays, with application
	to the lagoon of {M}ururoa},
  journal = CSR,
  year = {2002},
  volume = {22},
  pages = {1379-1395}
}

@ARTICLE{Matsumoto98,
  author = {M. Matsumoto and Takuji Nishimura},
  title = {{Mersenne twister: a 623-dimensionally equidistributed uniform pseudo-random
	number generator}},
  journal = {ACM Trans. Model. Comput. Simul.},
  year = {1998},
  volume = {8},
  pages = {3--30},
  number = {1},
  address = {New York, NY, USA},
  doi = {http://doi.acm.org/10.1145/272991.272995},
  issn = {1049-3301},
  publisher = {ACM}
}

@ARTICLE{McCalpin93,
  author = {J.~D. McCalpin},
  title = {A comparison of second-order and fourth-order pressure gradient algorithms
	in a $\sigma$-coordinate ocean model},
  journal = {Int. J. Numer. Methods Fluids},
  year = {1994},
  volume = {18},
  pages = {361-383}
}

@ARTICLE{mcintyre1980introduction,
  author = {McIntyre, ME},
  title = {{An introduction to the generalized Lagrangian-mean description of
	wave, mean-flow interaction}},
  journal = {Pure and Applied Geophysics},
  year = {1980},
  volume = {118},
  pages = {152--176},
  number = {1},
  file = {:../GLM/1980-glm-Introduction-Generalized-Lagrangian-Mean-Description-of-Wave-Mean-Flow-Interaction.pdf:PDF},
  issn = {0033-4553},
  publisher = {Springer}
}

@TECHREPORT{McMillan73,
  author = {W. McMillan},
  title = {Cooling from open water surfaces: {P}art 1: {L}ake {T}rawsfynydd
	cooling investigation},
  institution = {Scientific Services Department, CEGB Manchester},
  year = {1973},
  type = {Final Report},
  number = {NW/SSD/RR/1204/73}
}

@ARTICLE{mcwilliams2004asymptotic,
  author = {McWilliams, J.C. and Restrepo, J.M. and Lane, E.M.},
  title = {An asymptotic theory for the interaction of waves and currents in
	coastal waters},
  journal = JFM,
  year = {2004},
  volume = {511},
  pages = {135--178},
  file = {:../2004-An-Asymptotic-Theory-for-Wave-Effects-on-Currentswcjfm.pdf:PDF},
  publisher = {Cambridge Univ Press}
}

@ARTICLE{mcwilliams1997langmuir,
  author = {McWilliams, James C and Sullivan, Peter P and Moeng, Chin Hoh},
  title = {Langmuir turbulence in the ocean},
  journal = {Journal of Fluid Mechanics},
  year = {1997},
  volume = {334},
  pages = {1--30},
  publisher = {Cambridge Univ Press}
}

@ARTICLE{Megard84,
  author = {R.~O. Megard and D.~W. Tonkyn and W.~H. Senft},
  title = {Kinetics of oxygenic photosynthesis in planktonic algae},
  journal = {J. Plankt. Res.},
  year = {1984},
  volume = {6},
  pages = {325--337},
  number = {2}
}

@ARTICLE{Meier07,
  author = {H.E. M. Meier},
  title = {{Modeling the pathways and ages of inflowing salt- and freshwater
	in the Baltic Sea}},
  journal = {Estuarine, Coastal and Shelf Science},
  year = {2007},
  volume = {74},
  pages = {610--627},
  number = {4},
  note = {Timescale- and tracer-based methods for understanding the results
	of complex marine models},
  abstract = { A three-dimensional, eddy-permitting ocean circulation model with
	implemented bottom boundary layer model and flux-corrected transport
	scheme is used to calculate the pathways and ages of various water
	masses in the Baltic Sea. The agreement between simulated and observed
	temperature and salinity profiles of the period 1980-2004 is satisfactory.
	Especially the renewal of the deep water in the Baltic proper by
	gravity-driven dense bottom flows is better simulated than in previous
	versions of the model. Based upon these model results details of
	the mean circulation are analyzed. For instance, it is found that
	after the major Baltic inflow in January 2003 saline water passing
	the Slupsk Furrow flows directly towards northeast along the eastern
	slope of the Hoburg Channel. However, after the baroclinic summer
	inflow in August/September 2002 the deep water flow spreads along
	the southwestern slope of the Gdansk Basin. Further, the model results
	show that the patterns of mean vertical advective fluxes across the
	halocline that close the large-scale vertical circulation are rather
	patchy. Mainly within distinct areas are particles of the saline
	inflow water advected vertically from the deep water into the surface
	layer. To analyze the time scales of the circulation mean ages of
	various water masses are calculated. It is found that at the sea
	surface of the Bornholm Basin, Gotland Basin, Bothnian Sea, and Bothnian
	Bay the mean ages associated to inflowing water from Kattegat amount
	to 26-30, 28-34, 34-38, and 38-42 years, respectively. Largest mean
	sea surface ages of more than 30 years associated to the freshwater
	of the rivers are found in the central Gotland Basin and Belt Sea.
	At the bottom the mean ages are largest in the western Gotland Basin
	and amount to more than 36 years. In the Baltic proper vertical gradients
	of ages associated to the freshwater inflow are smaller than in the
	case of inflowing saltwater from Kattegat indicating an efficient
	recirculation of freshwater in the Baltic Sea.},
  doi = {DOI: 10.1016/j.ecss.2007.05.019},
  issn = {0272-7714},
  keywords = {Baltic Sea},
  keywords1 = {numerical modeling},
  keywords2 = {circulation},
  keywords3 = {passive tracer},
  keywords4 = {age of water masses},
  url = {http://www.sciencedirect.com/science/article/B6WDV-4P6MH16-3/2/cfeb935cc693849b585ca4e849ddcfa2}
}

@ARTICLE{mellor2015combined,
  author = {Mellor, George},
  title = {A Combined Derivation of the Integrated and Vertically Resolved,
	Coupled Wave-Current Equations},
  journal = {Journal of Physical Oceanography},
  year = {2015},
  number = {In Press}
}

@ARTICLE{mellor2011CORRIGENDA,
  author = {Mellor, G.L.},
  title = {{CORRIGENDUM}},
  journal = JPO,
  year = {2011},
  volume = {41},
  pages = {1417--1418},
  file = {:../2011-CORRIGENDA-The-Three-Dimensional-Current-and-Surface-Wave-Equations.doc:DOC}
}

@ARTICLE{mellor2011radiation,
  author = {Mellor, G.L.},
  title = {{Wave radiation stress}},
  journal = {Ocean Dynamics},
  year = {2011},
  volume = {61},
  pages = {563--568},
  file = {:../2011-Wave-radiation-stress.pdf:PDF}
}

@ARTICLE{mellor2011reply,
  author = {Mellor, G.L.},
  title = {{Reply to Comments by Bennis,A.C. and Ardhuin,F.}},
  journal = JPO,
  year = {2011},
  volume = {41},
  pages = {2013--2015},
  file = {:../2011-Reply-to-Comments-by-A-C-Bennis-and-F-Ardhuin-jpo-d-11-071-2E1.pdf:PDF},
  url = {http://dx.doi.org/10.1175/JPO-D-11-071.1}
}

@ARTICLE{mellor2008depth,
  author = {Mellor, G.L.},
  title = {{The depth-dependent current and wave interaction equations: A revision}},
  journal = JPO,
  year = {2008},
  volume = {38},
  pages = {2587--2596}
}

@ARTICLE{mellor2005some,
  author = {Mellor, G.L.},
  title = {{Some Consequences of the Three-Dimensional Current and Surface Wave
	Equations}},
  journal = JPO,
  year = {2005},
  volume = {35},
  pages = {2291--2298}
}

@ARTICLE{mellor2003,
  author = {Mellor, G.},
  title = {{The three-dimensional current and surface wave equations}},
  journal = JPO,
  year = {2003},
  volume = {33},
  pages = {1978--1989}
}

@ARTICLE{mellor2004wave,
  author = {Mellor, G. and Blumberg, A.},
  title = {Wave breaking and ocean surface layer thermal response},
  journal = JPO,
  year = {2004},
  volume = {34},
  pages = {693--698},
  file = {:../wave-turb/2004-Wave-Breaking-Ocean-Surface-Layer-Thermal-Response.pdf:PDF}
}

@INPROCEEDINGS{Mellor89,
  author = {G.~L. Mellor},
  title = {Retrospect on oceanic boundary layer modeling and second moment closure},
  booktitle = {Parameterization of Small--Scale Processes; Proc. of the Aha Hulikoa
	Hawaiian Winter Workshop},
  year = {1989},
  editor = {P. Mueller and D. Henderson},
  pages = {251--271},
  address = {University of Hawaii at Manoa, Honolulu}
}

@ARTICLE{Mellor2001,
  author = {G.~L. Mellor},
  title = {One-dimensional ocean surface layer modeling, a problem and a solution},
  journal = JPO,
  year = {2001},
  volume = {31},
  pages = {790--809},
  number = {3}
}

@ARTICLE{Mellor73,
  author = {G.~L. Mellor},
  title = {Analytic prediction of the properties of planetary surface layers},
  journal = {J. Atmos. Sci.},
  year = {1973},
  volume = {30},
  pages = {1061--1069}
}

@ARTICLE{MellorDurbin75,
  author = {G.~L. Mellor and P.~A. Durbin},
  title = {The structure and dynamics of the ocean surface mixed layer},
  journal = JPO,
  year = {1975},
  volume = {3},
  pages = {718--728}
}

@ARTICLE{MELLORea94,
  author = {George L. Mellor and Tal Ezer and L.-Y. Oey},
  title = {The pressure gradient conundrum of sigma coordinate ocean models},
  journal = JAOT,
  year = {1994},
  volume = {11},
  pages = {1126-1134}
}

@ARTICLE{MellorHerring73,
  author = {G.~L. Mellor and H. J. Herring},
  title = {A survey of the mean turbulent field closure models},
  journal = {AIAA J.},
  year = {1973},
  volume = {11},
  pages = {590--599},
  number = {5}
}

@ARTICLE{MellorStrub80,
  author = {G.~L. Mellor and P.~T. Strub},
  title = {Similarity solutions for the stratified turbulent {R}ayleigh problem},
  journal = JPO,
  year = {1980},
  volume = {10},
  pages = {455--460}
}

@ARTICLE{MellorYamada82,
  author = {G.~L. Mellor and T. Yamada},
  title = {Development of a Tubulence Closure Model for Geophysical Fluid Problems},
  journal = {Reviews of Geophysics and Space Physics},
  year = {1982},
  volume = {20},
  pages = {851--875}
}

@ARTICLE{MellorYamada74,
  author = {G.~L. Mellor and T. Yamada},
  title = {A hierarchy of turbulence closure models for planetary boundary layers},
  journal = {J. Atmos. Sci.},
  year = {1974},
  volume = {31},
  pages = {1791--1806}
}

@ARTICLE{melville1985momentum,
  author = {Melville, WK and Rapp, Ronald J},
  title = {Momentum flux in breaking waves},
  journal = {Nature},
  year = {1985},
  volume = {317},
  pages = {514--516},
  number = {6037}
}

@ARTICLE{Menter92,
  author = {F.~R. Menter},
  title = {Influence of freestream values on $k$-$\omega$ turbulence model predictions},
  journal = {AIAA J.},
  year = {1992},
  volume = {30},
  pages = {1657--1659},
  number = {6}
}

@ARTICLE{Mercier10,
  author = {Ch. Mercier and E. J. M. Delhez},
  title = {{Really TVD advection schemes for the depth-integrated transport
	equation}},
  journal = OMOD,
  year = {2010},
  volume = {33},
  pages = {10--19},
  number = {1-2},
  issn = {1463-5003},
  keywords = {Depth-integrated models, Finite volume, Flux limiters, TVD advection
	schemes},
  risfield_0_m3 = {doi: DOI: 10.1016/j.ocemod.2009.11.004},
  url = {http://www.sciencedirect.com/science/article/B6VPS-4XV0712-1/2/79d7eb17d8c84682c75f77255b373ee6}
}

@ARTICLE{Meyer08,
  author = {Michael Meyer and Jan Harff and M. Gogina and A. Barthel},
  title = {{Coastline changes of the Darss-Zingst Peninsula -- A modelling approach}},
  journal = {Journal of Marine Systems},
  year = {2008},
  volume = {74},
  pages = {S147--S154},
  number = {Supplement 1},
  note = {Baltic Sea Science Congress 2007, Baltic Sea Science Congress 2007},
  abstract = { Coastline development is a function of eustasy and isostasy. On a
	regional scale, the precision of models based on these two components
	is sufficient for the investigation of coastline scenarios. However,
	on a local scale sediment dynamic is responsible for the evolution
	of coastal structures that alter the coastline in detail considerably.
	The Darss-Zingst Peninsula at the southern coast of the Baltic Sea
	serves as a example for a case study of such a structure. Longshore
	sediment transport driven by waves and responsible for the formation
	of this barrier during the Holocene is simulated for the next 840
	years with the sediment transport modelling software package SEDSIM.
	The main objectives are to test if SEDSIM is a viable tool for the
	modelling of such structures and if the available data basis is suitable
	for this task. Basic data used for the modelling are a recent digital
	elevation model, measured wave time series, a map of sediment distribution,
	and a modelled eustatic scenario. In result, SEDSIM proved to be
	a stable and highly configurable program that can handle the requested
	simulations. Input data have to be improved and must include event
	data like storm surges.},
  doi = {DOI: 10.1016/j.jmarsys.2008.03.023},
  issn = {0924-7963},
  keywords = {Coastline change},
  keywords1 = {Baltic Sea},
  keywords2 = {Darss-Zingst Peninsula},
  keywords3 = {Sediment dynamic},
  keywords4 = {SEDSIM},
  url = {http://www.sciencedirect.com/science/article/B6VF5-4TP49M6-1/2/6b598d0130fb5160e18c98ca1bdb20dc}
}

@ARTICLE{Milstein79,
  author = {G. N. Milstein},
  title = {{A Method of Second-Order Accuracy Integration of Stochastic Differential
	Equations}},
  journal = {Theory of Probability and its Applications},
  year = {1979},
  volume = {23},
  pages = {396--401},
  number = {2},
  doi = {10.1137/1123045},
  publisher = {SIAM},
  url = {http://link.aip.org/link/?TPR/23/396/1}
}

@ARTICLE{Mironov2000,
  author = {D.~V. Mironov and V.~M. Gryanik and C.-H. Moeng and D.~J. Olbers
	and T.~H. Warncke},
  title = {Vertical turbulence structure and second-moment budgets in convection
	with rotation: {A} large-eddy simulation},
  journal = {Quart. J. Roy. Meteor. Soc.},
  year = {2000},
  volume = {126},
  pages = {477--516}
}

@TECHREPORT{moghimi-meighan,
  author = {Saeed Moghimi},
  title = {An Investigation on Environment Impact of Arak City Wastewater
	
	 Treatment Plant Outfall on Water Body of Meighan Wetland},
  institution = {Department of the Environment of Markazi Province, Arak,
	
	 Iran},
  year = {2009},
  owner = {moghimi},
  timestamp = {2015.02.20}
}

@TECHREPORT{moghimi-mpi,
  author = {Saeed Moghimi},
  title = {Operational wave forecasting system using parallel processing technology},
  institution = {Iran Meteorology Organization, Tehran, Iran},
  year = {2009},
  owner = {moghimi},
  timestamp = {2015.02.20}
}

@TECHREPORT{moghimi-permit,
  author = {Saeed Moghimi},
  title = {Shoreline construction permitting procedure},
  institution = {Research Deputy, Arak University, Arak, Iran},
  year = {2008},
  owner = {moghimi},
  timestamp = {2015.02.20}
}

@PHDTHESIS{moghimi-phd-thesis,
  author = {Saeed Moghimi},
  title = {Dynamical Coupling of a Spectral Wave Model and A Storm Surge Model
	in Shallow Waters},
  school = {Tarbiat Modarres University, Tehran, Iran},
  year = {2005},
  owner = {moghimi},
  timestamp = {2015.02.20}
}

@TECHREPORT{shafiee-mobin,
  author = {Saeed Moghimi},
  title = {East and West outfall thermal diffusion studies - Mobin Petrochemical
	complex},
  institution = {Iran Marine Industrial Company (SADRA), Tehran, Iran},
  year = {2003},
  owner = {moghimi},
  timestamp = {2015.02.20}
}

@CONFERENCE{moghimi2000iczm,
  author = {Moghimi, S.},
  title = {An investigation on National Regulation of Coastal Area Management
	and Planning},
  booktitle = {The First National conference on Integrated Coastal Zone Management
	of Iranian Coasts, Port \& Shipping Organization, Tehran, Iran},
  year = {2000},
  pages = {42--53},
  owner = {moghimi},
  timestamp = {2014.01.24}
}

@OTHER{moghimi-master,
  author = {Saeed Moghimi},
  owner = {moghimi},
  school = {Tarbiat Modarres University, Tehran, Iran},
  timestamp = {2015.02.20},
  title = {Diffraction of Regular Waves in ports and Investigation of the Effect
	of Waves Irregularity},
  year = {1998}
}

@CONFERENCE{moghimi2012three,
  author = {Moghimi, S. and klingbeil, K. and Graewe, U. and Burchard, H.,},
  title = {Three dimensional wave current interaction in nearshore regions},
  booktitle = {JONSMOD2012 , Brest, France.},
  year = {2012},
  owner = {moghimi},
  timestamp = {2014.01.24}
}

@CONFERENCE{Moghimi1998msc,
  author = {Moghimi, S. and Aghakoochak, A.},
  title = {Numerical Solution of the Diffraction of Regular Waves and Investigation
	of the Effects of Wave Irregularity},
  booktitle = {International Conference of Coasts , Ports and Marine Structure ,
	Amir Kabir Univ. , Tehran, Iran,},
  year = {1998},
  pages = {221--229},
  owner = {moghimi},
  timestamp = {2014.01.24}
}

@CONFERENCE{moghimi2010met,
  author = {Moghimi, S. and Alemi, O. and Dalvandi, B.},
  title = {Met-ocean forecasting system: Developing Operational Wind and Wave
	Prediction System for Iranian Coastal Areas.},
  booktitle = {CLIMA2010, Humboldt University, Berlin, Germany.},
  year = {2010},
  owner = {moghimi},
  timestamp = {2014.01.24}
}

@CONFERENCE{moghimi2008openmp,
  author = {Moghimi, S. and Doustar, M.F. and Behrens, A.,},
  title = {Evaluation of Different OpenMP-Oriented Implementations for the Wave
	Model WAM Cycle 4.5},
  booktitle = {The Sixth International Conference on Engineering Computational Technology,
	Athens, Greece},
  year = {2008},
  number = {ISBN: 978-1-905088-25-6},
  owner = {moghimi},
  timestamp = {2014.01.24}
}

@CONFERENCE{moghimi2005effects,
  author = {Moghimi, S. and Gayer, G. and Guenther, H. and Shafieefar, M.},
  title = {Effects of different wave conditions on SPM distribution patterns
	in highly variable tidal environments},
  booktitle = {Coastal Dynamics2005, Barcelona, Spain},
  year = {2005},
  pages = {108--109},
  owner = {moghimi},
  timestamp = {2014.01.24}
}

@ARTICLE{moghimi2005application,
  author = {Moghimi, S. and Gayer, G. and G{\"u}nther, H. and Shafieefar, M.},
  title = {Application of third generation shallow water wave models in a tidal
	environment},
  journal = {Ocean Dynamics},
  year = {2005},
  volume = {55},
  pages = {10--27},
  number = {1},
  publisher = {Springer-Verlag}
}

@CONFERENCE{moghimi2010investig,
  author = {Moghimi, S. and Graewe, U. and Burchard, H.,},
  title = {An investigation of three dimensional hydrodynamics of semi-enclosed
	tidal basin including wind waves effects},
  booktitle = {15th Physics of Estuaries and Coastal Seas (PECS) conference, Colombo,
	Sri Lanka.},
  year = {2010},
  owner = {moghimi},
  timestamp = {2014.01.24}
}

@CONFERENCE{moghimi2008effects,
  author = {Moghimi, S. and Guenther, H. and Khosronejad, A.},
  title = {Effects of Presence of Waves on Shallow Estuaries Hydrodynamics},
  booktitle = {8th International Conference on Hydro-Science and Engineering, ICHE2008,
	NAGOYA, JAPAN},
  year = {2008},
  pages = {579--580},
  owner = {moghimi},
  timestamp = {2014.01.24}
}

@CONFERENCE{moghimi2001sealevel,
  author = {Moghimi, S. and Hamedi, A. and Mirmousavi, B. M.},
  title = {Sea level evaluation using joint probability method to combine Wave,
	surge and tide effects},
  booktitle = {The first conference of lake Urmia sustainable development, University
	of Urmia, Urmia, Iran},
  year = {2001},
  pages = {66},
  owner = {moghimi},
  timestamp = {2014.01.24}
}

@ARTICLE{moghimi2013direct,
  author = {Saeed Moghimi and Knut Klingbeil and Ulf Gräwe and Hans Burchard},
  title = {A direct comparison of a depth-dependent Radiation stress formulation
	and a Vortex force formulation within a three-dimensional coastal
	ocean model },
  journal = {Ocean Modelling },
  year = {2013},
  volume = {70},
  pages = {132 - 144},
  number = {0},
  doi = {http://dx.doi.org/10.1016/j.ocemod.2012.10.002},
  issn = {1463-5003},
  url = {http://www.sciencedirect.com/science/article/pii/S1463500312001473}
}

@CONFERENCE{moghimi2003gis,
  author = {Moghimi, S. and Montaseri, H. and Shafieefar, M.},
  title = {Application of a 3rd generation wave model in Caspian Sea managed
	using GIS platform},
  booktitle = {the 4th Iranian Hydraulic Conference, Shiraz, Iran},
  year = {2003},
  pages = {703--711},
  owner = {moghimi},
  timestamp = {2014.01.24}
}

@CONFERENCE{moghimi2008data,
  author = {Moghimi, S. and Najafi, A.},
  title = {Needs for Establishment of Caspian Sea International Data Center},
  booktitle = {International Conference of Marine Data and Information Systems-
	IMDIS2008, Athens, Greece},
  year = {2008},
  owner = {moghimi},
  timestamp = {2014.01.24}
}

@ARTICLE{moghimi2015assim_syn,
  author = {Saeed Moghimi and H. Tuba {\"O}zkan-Haller and Greg Wilson and Alexander
	Kurapov},
  title = {Data assimilation for bathymetry estimation at a tidal inlet},
  journal = {Journal of Atmospheric and Oceanic Technology },
  year = {2014},
  pages = {In Review}
}

@ARTICLE{moghimi2015assim_real,
  author = {Moghimi, S. and {\"O}zkan-Haller, T. and Wilson, G. and Kurapov, A. and
	Farquharson, G. and Haller, M. and Honegger, D. and Thomson, J.
	
	},
  title = {Data fusion and bathymetry inversion in New River Inlet using remotly
	sensed data},
  journal = JGR,
  year = {2015},
  pages = {In Review}
}

@CONFERENCE{moghimi2009devel,
  author = {Moghimi, S. and Qaeeni, H. and Alemi, O.},
  title = {Developing wave forecasting system for Caspian Sea using Parrallel
	processing technology},
  booktitle = {International workshop on integrated coastal zone management, Izmir,
	Turkey.},
  year = {2009},
  owner = {moghimi},
  timestamp = {2014.01.24}
}

@CONFERENCE{moghimi2006linear,
  author = {Moghimi, S. and Shafieefar, M. and Gayer, G.},
  title = {Linear wind input activation rule on wave generation process in semi
	enclosed basins},
  booktitle = {7th International Conference on Coasts, Ports and Marine Structures,
	Tehran, Iran},
  year = {2006},
  pages = {17},
  owner = {moghimi},
  timestamp = {2014.01.24}
}

@CONFERENCE{moghimi2010dyn,
  author = {Moghimi, S. and Shafieefar, M. and Guenther, H.},
  title = {Dynamical Coupling of a Spectral Wave Model and a 3D Hydrodynamic
	Model in Highly Variable Tidal Environment},
  booktitle = {Jonsmod2010, Deltares, Delft, The Netherlands.},
  year = {2010},
  owner = {moghimi},
  timestamp = {2014.01.24}
}

@ARTICLE{moghimi2007evaluation,
  author = {Moghimi, S and Shafieefar, M and Khosronejad, A},
  title = {Evaluation of the effects of causeway construction on Urmia Lake
	fresh water circulation},
  journal = {Proceedings of the congress-international association for hydraulic
	research, 32nd IAHR World Congress, Venice, Italy},
  year = {2007}
}

@article{moghimi2016modeling,
  title={On the modeling of wave-enhanced turbulence nearshore},
  author={Moghimi, Saeed and Thomson, Jim and {\"O}zkan-Haller, Tuba and Umlauf, Lars and Zippel, Seth},
  journal={Ocean Modelling},
  volume={103},
  pages={118--132},
  year={2016},
  publisher={Elsevier}
}

@CONFERENCE{moghimi2012assim_agu,
  author = {Moghimi, S. and Wilson, G. and Akan, {\c{C}}i{\u{g}}dem and {\"O}zkan-Haller, T.},
  title = {Data assimilation for bathymetry inversion of a natural tidal inlet},
  booktitle = {AGU fall meeting 2012, San Francisco, US.},
  year = {2012},
  owner = {moghimi},
  timestamp = {2014.01.24}
}

@ARTICLE{Mohamed90,
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}

@BOOK{Mohammadi94,
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}

@ARTICLE{Moisan96a,
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@ARTICLE{Moisan96b,
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@ARTICLE{Molot97,
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}

@ARTICLE{monbaliu2000spectral,
  author = {Monbaliu, J. and Padilla-Hernandez, R. and Hargreaves, J.C. and Albiach,
	J.C.C. and Luo, W. and Sclavo, M. and Guenther, H.},
  title = {{The spectral wave model, WAM, adapted for applications with high
	spatial resolution}},
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  year = {2000},
  volume = {41},
  pages = {41--62},
  number = {1-3},
  issn = {0378-3839},
  publisher = {Elsevier}
}

@ARTICLE{Monin54,
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@ARTICLE{monismith2007laboratory,
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  publisher = {Cambridge Univ Press}
}

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@ARTICLE{moon2005impact,
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	modeling}},
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  number = {3},
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  issn = {1463-5003},
  publisher = {Elsevier}
}

@ARTICLE{Moore71,
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}

@ARTICLE{Mortimer81,
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}

@ARTICLE{Mortimer74,
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}

@ARTICLE{Moum96,
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@ARTICLE{mulligan2008whitecapping,
  author = {Mulligan, RP and Bowen, AJ and Hay, AE and Van der Westhuysen, AJ
	and Battjes, JA},
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  pages = {C03008},
  number = {C3},
  publisher = {American Geophysical Union}
}

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  year = {1950}
}

@ARTICLE{MunkAnderson48,
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@ARTICLE{myrhaug2005bottom,
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	waves for laminar and smooth turbulent flow}},
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  issn = {0029-8018},
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}

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	closure},
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}

@ARTICLE{neshaei2009effect,
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  year = {2009},
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  issn = {1028-6284},
  publisher = {Shiraz University,}
}

@ARTICLE{Neumann10,
  author = {T. Neumann},
  title = {{Climate-change effects on the Baltic Sea ecosystem: A model study}},
  journal = {Journal of Marine Systems},
  year = {2010},
  volume = {81},
  pages = {213--224},
  number = {3},
  abstract = { The expected climate change is of growing interest on the regional
	scale, including the Baltic Sea. However, simulations with global
	models do not sufficiently resolve the regional impact. Consequently,
	dynamic downscaling methods are being used to convert the results
	obtained in global models to the regional scale. In the present study,
	two regional data sets for greenhouse gas emission scenarios, A1B
	and B1, for the period 1960 to 2100, were used to force transient
	simulations with a 3D ecosystem model of the Baltic Sea. The results
	showed that the expected warming of the Baltic Sea is 1-4 K, with
	a decrease in salinity and a much reduced sea-ice cover in winter.
	In addition, the season favoring cyanobacterial blooms is prolonged,
	with the spring bloom in the Northern Baltic Sea beginning earlier
	in the season, while the oxygen conditions in deep water are expected
	to improve slightly.},
  doi = {DOI: 10.1016/j.jmarsys.2009.12.001},
  issn = {0924-7963},
  keywords = {Baltic Sea},
  keywords1 = {Climate change},
  keywords2 = {Modeling},
  keywords3 = {Ecosystem},
  url = {http://www.sciencedirect.com/science/article/B6VF5-4XY4GHF-1/2/7c679377803b539daf048be551646f49}
}

@ARTICLE{Neumann00,
  author = {T. Neumann},
  title = {{Towards a 3D-ecosystem model of the Baltic Sea}},
  journal = {Journal of Marine Systems},
  year = {2000},
  volume = {25},
  pages = {405--419},
  number = {3-4},
  abstract = { The paper describes briefly the preliminary results of a coupled
	chemical-biological and circulation model of the Baltic Sea. The
	chemical-biological model involves nine state variables to simulate
	the nitrogen cycle. A 1-year simulation shows how the model could
	be used to estimate budgets and nitrogen transports. The importance
	of shallow coastal areas for the removal of riverborne nitrogen is
	demonstrated on the Pomeranian Bight area. Within the simulation
	period, only 15% of the Oder river nitrogen load have left the Pomeranian
	Bight into the Baltic Sea.},
  doi = {DOI: 10.1016/S0924-7963(00)00030-0},
  issn = {0924-7963},
  keywords = {Baltic Sea},
  keywords1 = {ecosystem},
  keywords2 = {modelling},
  keywords3 = {nitrogen cycle},
  url = {http://www.sciencedirect.com/science/article/B6VF5-40X8G24-J/2/0cbfab0688f68067a9ee01cf174ebaf6}
}

@ARTICLE{Neumannetal2002,
  author = {Thomas Neumann and Wolfgang Fennel and Christine Kremp},
  title = {Experimental simulations with an ecosystem model of the {B}altic
	{S}ea: {A} nutrient load reduction experiment},
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  year = {2002},
  volume = {16},
  pages = {10.1029/2001GB001450}
}

@ARTICLE{newberger2007forcing,
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  pages = {C08018},
  number = {C8},
  file = {:../2007-Forcing-three-dimensional-hydrostatic-primitive-equation-surf-zone.pdf:PDF},
  issn = {0148-0227},
  publisher = {American Geophysical Union}
}

@ARTICLE{newberger2007forcing2,
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	for application in the surf zone: 2. Application to DUCK94},
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  pages = {C08019},
  number = {C8},
  file = {:../2007-Forcing-three-dimensional-hydrostatic-primitive-equation-model-Newberger_Allen_JGR_2007_2.pdf:PDF},
  publisher = {American Geophysical Union}
}

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}

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}

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}

@ARTICLE{noh2010estimation,
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  title = {{Estimation of the particle flux from the convective mixed layer
	by large eddy simulation}},
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  year = {2010},
  volume = {115},
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}

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  title = {On the entrainment rate across a density interface},
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  year = {1988},
  volume = {188},
  pages = {185--204}
}

@ARTICLE{North06,
  author = {E.W. North and R.R. Hood and S.-Y. Chao and L.P. Sanford},
  title = {{Using a random displacement model to simulate turbulent particle
	motion in a baroclinic frontal zone: A new implementation scheme
	and model performance tests}},
  journal = {Journal of Marine Systems},
  year = {2006},
  volume = {60},
  pages = {365--380},
  number = {3-4},
  doi = {DOI: 10.1016/j.jmarsys.2005.08.003},
  issn = {0924-7963},
  keywords = {Lagrangian particle-tracking modeling},
  keywords1 = {Fronts},
  keywords2 = {Mathematical models},
  keywords3 = {Biological-physical interactions},
  url = {http://www.sciencedirect.com/science/article/B6VF5-4JN2NT2-2/2/46ff44a9fbde65f7dc7cf99c80faf7c3}
}

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}

@ARTICLE{Obukhov46*,
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}

@ARTICLE{oke2007impacts,
  author = {Oke, Peter R and Sakov, Pavel and Corney, Stuart P},
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	small model},
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  pages = {32--45},
  number = {1},
  publisher = {Springer}
}

@ARTICLE{olabarrieta2012ocean,
  author = {Olabarrieta, Maitane and Warner, John C and Armstrong, Brandy and
	Zambon, Joseph B and He, Ruoying},
  title = {Ocean--atmosphere dynamics during Hurricane Ida and Norida: an application
	of the coupled ocean--atmosphere--wave--sediment transport (COAWST)
	modeling system},
  journal = {Ocean Modelling},
  year = {2012},
  volume = {43},
  pages = {112--137},
  publisher = {Elsevier}
}

@ARTICLE{Omstedt83,
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}

@PHDTHESIS{orton2011estuary,
  author = {Orton, P.M.},
  title = {Estuary Turbulence and Air-Water Carbon Dioxide Exchange},
  school = {COLUMBIA UNIVERSITY},
  year = {2011},
  file = {:../est/2009-Variability-of-internally-generated-turbulence-in-an-estuary-Orton_Visbeck_CSR09.pdf:PDF}
}

@ARTICLE{orton2010sea,
  author = {Orton, P.M. and McGillis, W.R. and Zappa, C.J.},
  title = {Sea breeze forcing of estuary turbulence and air-water CO 2 exchange},
  journal = {Geophysical Research Letters},
  year = {2010},
  volume = {37},
  number = {13},
  file = {:../est/2010-Sea-breeze-forcing-of-estuary-turbulence-and-air‐water-CO2Orton_etal_GRL10_2010GL043159.pdf:PDF},
  publisher = {American Geophysical Union, 2000 Florida Ave., N. W. Washington DC
	20009 United States of America}
}

@ARTICLE{orton2009variability,
  author = {Orton, P.M. and Visbeck, M.},
  title = {Variability of internally generated turbulence in an estuary, from
	100 days of continuous observations},
  journal = {Continental Shelf Research},
  year = {2009},
  volume = {29},
  pages = {61--77},
  number = {1},
  file = {:../est/2009-Variability-of-internally-generated-turbulence-in-an-estuary-Orton_Visbeck_CSR09.pdf:PDF},
  publisher = {Elsevier}
}

@ARTICLE{orton2010tidal,
  author = {Orton, P.M. and Zappa, C.J. and McGillis, W.R.},
  title = {Tidal and atmospheric influences on near-surface turbulence in an
	estuary},
  journal = JGR,
  year = {2010},
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  pages = {C12029},
  file = {:../est/2010-Tidal-and-atmospheric-influences-on-near‐surface-turbulence-Orton_etal_JGR10_2010JC006312.pdf:PDF}
}

@ARTICLE{Osbornetal92,
  author = {T.~R. Osborn and D.~M. Farmer and S. Vagle and S.~A. Thorpe and M.
	Cure},
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  pages = {419-440}
}

@ARTICLE{Ostrovsky96,
  author = {I. Ostrovsky and Y.~Z. Yacobi and P. Walline and I. Kalikhman},
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  year = {1996},
  volume = {41},
  pages = {323--332},
  number = {2}
}

@ARTICLE{osuna2004wave,
  author = {Osuna, P. and Monbaliu, J.},
  title = {{Wave-current interaction in the Southern North Sea}},
  journal = {Journal of Marine Systems},
  year = {2004},
  volume = {52},
  pages = {65--87},
  number = {1-4},
  file = {:../2004-Wave–current-interaction-Southern-North-Sea.pdf:PDF},
  issn = {0924-7963},
  publisher = {Elsevier}
}

@ARTICLE{ozer2000coupling,
  author = {Ozer, J. and Padilla-Hernandez, R. and Monbaliu, J. and Alvarez Fanjul,
	E. and Carretero Albiach, J.C. and Osuna, P. and Yu, J. and Wolf,
	J.},
  title = {{A coupling module for tides, surges and waves}},
  journal = {Coastal engineering},
  year = {2000},
  volume = {41},
  pages = {95--124},
  number = {1-3},
  file = {:../2000-Acoupling-module-for-tides-surges-waves.pdf:PDF},
  issn = {0378-3839},
  publisher = {Elsevier}
}

@ARTICLE{ozkan2003effects,
  author = {{\"O}zkan-Haller, H.T. and Li, Y.},
  title = {Effects of wave-current interaction on shear instabilities of longshore
	currents},
  journal = JGR,
  year = {2003},
  volume = {108},
  pages = {3139},
  number = {C5},
  file = {:../2003-Effects-wave-current-interaction-Ozkan-Haller_and_Li_JGR_2003.pdf:PDF},
  publisher = {American Geophysical Union}
}

@ARTICLE{Ozmidov65,
  author = {R.~V. Ozmidov},
  title = {On the turbulent exchange in a stably stratified ocean},
  journal = { Akad. Nauk USSR Izv. Atmos. Ocean Phys.},
  year = {1965},
  volume = {1},
  pages = {853--860},
  number = {8}
}

@BOOK{Meyberg90/2,
  title = {H{\"o}here Mathematik},
  publisher = {Springer-Verlag, Berlin},
  year = {1990},
  author = {K. Meyberg und P. Vachenauer},
  volume = {2}
}

@ARTICLE{Pacanowski81,
  author = {R.~C. Pacanowsci and S.~G.~H. Philander},
  title = {Parameterization of vertical mixing in numerical models of tropical
	oceans},
  journal = JPO,
  year = {1981},
  volume = {11},
  pages = {1443--1451}
}

@ARTICLE{Paizis75,
  author = {S.~T. Paizis and W.~H. Schwarz},
  title = {Entrainment rates in turbulent shear flows},
  journal = {J. Fluid Mech.},
  year = {1975},
  volume = {68},
  pages = {297--308},
  number = {2}
}

@ARTICLE{Parker91,
  author = {R.~A. Parker},
  title = {Eddy diffusion of phytoplankton and nutrients: estimating coefficients
	from simulated and observed vertical distributions},
  journal = {J. Plankton. Res},
  year = {1991},
  volume = {13},
  pages = {815--830}
}

@BOOK{Patankar80,
  title = {Numerical Heat Transfer and Fluid Flow},
  publisher = {Taylor \& Francis},
  year = {1980},
  author = {S.~V. Patankar}
}

@INPROCEEDINGS{patricola2012effect,
  author = {Patricola, CM and Chang, P and Saravanan, R and Montuoro, R},
  title = {The effect of atmosphere-ocean-wave interactions and model resolution
	on Hurricane Katrina in a coupled regional climate model},
  booktitle = {EGU General Assembly Conference Abstracts},
  year = {2012},
  volume = {14},
  pages = {11855}
}

@ARTICLE{Patterson85,
  author = {J.~C. Patterson and B.~R. Allenson and G.~N. Ivey},
  title = {A dissolved oxygen budget model for {L}ake {E}rie in summer},
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  year = {1985},
  volume = {15},
  pages = {683--694}
}

@ARTICLE{PaulsonSimpson77,
  author = {C. A. Paulson and J. J. Simpson},
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  journal = JPO,
  year = {1977},
  volume = {7},
  pages = {952-956}
}

@ARTICLE{Payne72,
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  title = {Albedo of the sea surface},
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  volume = {9},
  pages = {959-970}
}

@BOOK{PEDLOSKY87,
  title = {Geophysical fluid mechanics},
  publisher = {Springer},
  year = {1987},
  author = {Joseph Pedlosky},
  address = {New York},
  edition = {2.}
}

@ARTICLE{Peeters96,
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  year = {1994},
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}

@ARTICLE{perrie2003impact,
  author = {Perrie, W. and Tang, CL and Hu, Y. and DeTracy, BM},
  title = {The impact of waves on surface currents},
  journal = JPO,
  year = {2003},
  volume = {33},
  pages = {2126--2140},
  number = {10},
  file = {:../2003-The-Impact-of-Waves-on-Surface-Currents.pdf:PDF}
}

@ARTICLE{PHILLIPS57,
  author = {N. A. Phillips},
  title = {A coordinate system having some special advantages for numerical
	forecasting},
  journal = JM,
  year = {1957},
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  pages = {184-185}
}

@BOOK{phillips1977dynamics,
  title = {The dynamics of the upper ocean},
  publisher = {Cambridge university press},
  year = {1977},
  author = {Phillips, O.M.}
}

@ARTICLE{PiccarilloVanAtta97,
  author = {P.~S. Piccarillo and C.~W. van Atta},
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	flow},
  journal = {J. Fluid Mech.},
  year = {1997},
  volume = {334},
  pages = {61--68}
}

@ARTICLE{Pietrzak98,
  author = {Julie Pietrzak},
  title = {The use of {TVD} limiters for forward-in-time upstream-biased advection
	schemes in ocean modeling},
  journal = MWR,
  year = {1998},
  volume = {126},
  pages = {812-830}
}

@ARTICLE{plant1982relationship,
  author = {Plant, William J},
  title = {A relationship between wind stress and wave slope},
  journal = JGR,
  year = {1982},
  volume = {87},
  pages = {1961--1967},
  number = {C3},
  publisher = {Wiley Online Library}
}

@TECHREPORT{Platen99,
  author = {E. Platen},
  title = {{An Introduction to Numerical Methods for Stochastic Differential
	Equations}},
  institution = {Quantitative Finance Research Centre, University of Technology, Sydney},
  year = {1999},
  type = {Research Paper Series},
  number = {6},
  url = {http://ideas.repec.org/p/uts/rpaper/6.html}
}

@ARTICLE{Platen82,
  author = {E. Platen and W. Wagner},
  title = {{On a Taylor formula for a class of Ito process}},
  journal = {Prob. Math. Stat.},
  year = {1982},
  volume = {3},
  pages = {37--51}
}

@ARTICLE{Pohlmann97,
  author = {Thomas Pohlmann},
  title = {Estimating the influence of advection during {FLEX'76} by means of
	a three-dimensional shelf sea circulation model},
  journal = DHZ,
  year = {1997},
  volume = {49},
  pages = {215-226}
}

@ARTICLE{Pohlmann96,
  author = {Thomas Pohlmann},
  title = {Predicting the thermocline in a circulation model of the {N}orth
	{S}ea -- {P}art {I}: {M}odel description, calibration and verification},
  journal = CSR,
  year = {1996},
  volume = {16},
  pages = {131-146}
}

@ARTICLE{Pollard73,
  author = {R.~T. Pollard and P.~B. Rhines and R.~O.~R.~Y. Thompson},
  title = {The deepening of the wind mixed layer},
  journal = {Geophys. Fluid Dyn.},
  year = {1973},
  volume = {3},
  pages = {381--404}
}

@TECHREPORT{Prandkeetal2000,
  author = {Hartmut Prandke and Kurt Holtsch and Adolf Stips},
  title = {{MITEC} technology development: {T}he microstructure/turbulence measuring
	system MSS},
  institution = {European Commission, Joint Research Centre, Ispra, Italy},
  year = {2000},
  number = {EUR 19733 EN}
}

@ARTICLE{prandle2000tide,
  author = {Prandle, D. and Hargreaves, J.C. and McManus, J.P. and Campbell,
	A.R. and Duwe, K. and Lane, A. and Mahnke, P. and Shimwell, S. and
	Wolf, J.},
  title = {{Tide, wave and suspended sediment modelling on an open coast--Holderness}},
  journal = {Coastal Engineering},
  year = {2000},
  volume = {41},
  pages = {237--267},
  number = {1-3},
  issn = {0378-3839},
  publisher = {Elsevier}
}

@ARTICLE{Prandtl45,
  author = {L. Prandtl},
  title = {{\"U}ber ein neues {F}ormelsystem f{\"u}r die ausgebildete {Turbulenz}},
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  year = {1945},
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}

@ARTICLE{Prandtl25,
  author = {L. Prandtl},
  title = {Bericht {\"u}ber {U}ntersuchungen zur ausgebildeten {T}urbulenz},
  journal = {Zeitschrift f{\"u}r angewandte Mathematik und Mechanik},
  year = {1925},
  volume = {5},
  pages = {136},
  number = {2}
}

@ARTICLE{Price79,
  author = {J.~F. Price},
  title = {On the scaling of stress driven entrainment experiments},
  journal = {J. Fluid Mech.},
  year = {1979},
  volume = {90},
  pages = {509--529},
  number = {3}
}

@ARTICLE{Price78,
  author = {J.~F. Price and C.~N.~K. Mooers and J.~C. van Leer},
  title = {Observation and simulation of storm-induced mixed-layer deepening},
  journal = JPO,
  year = {1978},
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  pages = {582--599}
}

@ARTICLE{prince1990bubble,
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  title = {Bubble coalescence and break-up in air-sparged bubble columns},
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  volume = {36},
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}

@ARTICLE{Proehl05,
  author = {J. A. Proehl and D. R. Lynch and D. J. McGillicuddy and J. R. Ledwell},
  title = {{Modeling turbulent dispersion on the North Flank of Georges Bank
	using Lagrangian Particle Methods}},
  journal = {Continental Shelf Research},
  year = {2005},
  volume = {25},
  pages = {875--900},
  number = {7-8},
  note = {Recent Developments in Physical Oceanographic Modelling: Part II},
  abstract = { Circulation and transport at the North Flank of Georges Bank are
	studied using a data-assimilative 3-D model of frontal dynamics under
	stratified, tidally energetic conditions over steep topography. The
	circulation model was used in real-time during a cross-frontal transport
	study. Skill is evaluated retrospectively, relative to CTD, ADCP,
	drifter, and fluorescent dye observations. Hydrographic skill is
	shown to be retained for periods of weeks, requiring only initialization
	from routine surveys and proper atmospheric heating subsequently.
	Transport skill was limited by the wind stress input; real-time forecast
	winds taken from an operational meteorological model produced cross-isobath
	Ekman transport which was not observed locally. Retrospective use
	of observed local wind stress removed this cross-frontal bias. The
	contribution of tidal-time motion to the dispersion of a passive
	tracer is assessed using an ensemble of passive particles. The particle
	release simulates an at-sea dye injection in the pycnocline, which
	is followed for four days. Non-advective vertical tracer transport
	is represented as a random walk process sensitive to the local eddy
	diffusivity and its gradient, as computed from the turbulence closure.
	Non-advective horizontal tracer transport is zero for these ensembles.
	Computations of ensemble variance growth support estimates of (Lagrangian)
	horizontal dispersion. Off-bank, ensembles are essentially non-diffusive.
	As an ensemble engages the mixing front, its vertical diffusivity
	rises by 3 orders of magnitude, and horizontal spreading occurs in
	the complex front. The resultant horizontal dispersion is estimated
	from the ensemble variance growth, in along-bank and cross-bank directions.
	It is partitioned, roughly, between that contributed by 3-D advection
	alone, and that initiated by vertical diffusion. Engagement in the
	mixing front occurred in the forecast ensemble as a result of Ekman
	drift produced by an erroneous wind prediction. In the hindcast,
	observed wind left the ensemble non-diffusive and compact, advecting
	parallel to the mixing front and experiencing some advective shear
	dispersion. Lagrangian dispersion is event-specific and both simulations
	here represent credible events with dramatically different ecological
	outcomes. The skill metrics used are less sensitive, indicating that
	metrics tailored to surface-layer phenomena would be more appropriate
	in a data-assimilative context. The hindcast is closer to truth,
	based on first principles (better information). The level 2.5 closure
	used is realistic in the ocean interior; the near-surface processes
	need further refinement, especially as both surface- and bottom-generated
	turbulence affect these events strongly.},
  doi = {DOI: 10.1016/j.csr.2004.09.022},
  issn = {0278-4343},
  keywords = {Dispersion},
  keywords1 = {Georges Bank},
  keywords2 = {Langrangian Ensemble},
  keywords3 = {Hindcast},
  keywords4 = {Forecast},
  keywords5 = {Mixing},
  keywords6 = {Diffusion},
  url = {http://www.sciencedirect.com/science/article/B6VBJ-4FHJYH0-2/2/7da67d397e88aed0ca704b572617fd1b}
}

@ARTICLE{putrevu1999three,
  author = {Putrevu, U. and Svendsen, I.A.},
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	currents},
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  year = {1999},
  volume = {18},
  pages = {409--427},
  number = {3},
  publisher = {Elsevier}
}

@ARTICLE{putrevu1998vertical,
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  year = {1993},
  volume = {98},
  pages = {22707--22},
  number = {C12},
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  publisher = {American Geophysical Union}
}

@ARTICLE{qi2009unstructured,
  author = {Qi, Jianhua and Chen, Changsheng and Beardsley, Robert C and Perrie,
	Will and Cowles, Geoffrey W and Lai, Zhigang},
  title = {An unstructured-grid finite-volume surface wave model (FVCOM-SWAVE):
	implementation, validations and applications},
  journal = {Ocean Modelling},
  year = {2009},
  volume = {28},
  pages = {153--166},
  number = {1},
  publisher = {Elsevier}
}

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  title = {On the relation of primary production to grazing during the {F}ladenground
	{E}xperiment 1976 ({FLEX} '76)},
  booktitle = {Flows of Engergy and Materials in Marine Ecosystems},
  year = {1984},
  editor = {M. J. R. Fasham},
  pages = {597-625},
  address = {New York},
  organization = {NATO Conf. Ser. IV: Marine Sciences 13}
}

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@ARTICLE{Rahmstorf10,
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}

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}

@PHDTHESIS{rascleimpact2007,
  author = {Rascle, N.},
  title = {Impact of waves on the ocean circulation},
  school = {Universit ́ de Bretagne Occiedentale},
  year = {2007},
  file = {:../2007-rascle_thesis.pdf:PDF},
  url = {http://tel.archives-ouvertes.fr/tel-00182250/}
}

@ARTICLE{rascle2008global,
  author = {Rascle, N. and Ardhuin, F. and Queffeulou, P. and Croiz{\'e}-Fillon,
	D.},
  title = {{A global wave parameter database for geophysical applications. part
	1: wave-current-turbulence interaction parameters for the open ocean
	based on traditional parameterizations}},
  journal = OMOD,
  year = {2008},
  volume = {25},
  pages = {154--171},
  number = {3-4},
  file = {:../GLM/2008-glm-global-wave-parameter-database-geophysical-applications.pdf:PDF},
  issn = {1463-5003},
  publisher = {Elsevier}
}

@ARTICLE{rascle2012note,
  author = {Rascle, Nicolas and Chapron, Bertrand and Ardhuin, Fabrice and Soloviev,
	Alexander},
  title = {A note on the Direct Injection of Turbulence by Breaking Waves},
  journal = {Ocean Modelling},
  year = {2012},
  publisher = {Elsevier}
}

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  title = {An Introduction to the Finite Element Method},
  publisher = {McGraw-Hill, Inc., New York},
  year = {1993},
  author = {J.~N. Reddy},
  edition = {2nd}
}

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}

@ARTICLE{Reissmann09,
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	U. Lass and Volker Mohrholz and G{\"u}nther Nausch and L. Umlauf
	and G. Wieczorek},
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	- A review}},
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  number = {1},
  issn = {0079-6611},
  risfield_0_m3 = {doi: DOI: 10.1016/j.pocean.2007.10.004},
  url = {http://www.sciencedirect.com/science/article/B6V7B-4VV2NFP-1/2/f67a70de7799a8b576f14bed07c1fc23}
}

@ARTICLE{reniers2004morphodynamic,
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  pages = {C01030},
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}

@ARTICLE{reniers2002linear,
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  year = {2002},
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  pages = {3137},
  number = {C10},
  file = {:../2002-Linear-modeling-of-infragravity-waves-during-Delilah2001JC001083.pdf:PDF},
  publisher = {American Geophysical Union}
}

@ARTICLE{Rennau09,
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  title = {{Quantitative analysis of numerically induced mixing in a coastal
	model application}},
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  pages = {671--687},
  number = {5},
  doi = {10.1007/s10236-009-0201-x},
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}

@ARTICLE{restrepo2001wave,
  author = {Restrepo, J.M.},
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	ridges}},
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  year = {2001},
  volume = {21},
  pages = {1331--1360},
  number = {13-14},
  file = {:../2001Wave-current-interactions-in-shallow-waters.pdf:PDF},
  issn = {0278-4343},
  publisher = {Elsevier}
}

@INCOLLECTION{Reynolds98,
  author = {C.~S. Reynolds},
  title = {Plants in {M}otion: Physical-{B}iological {I}nteraction in the {P}lankton},
  booktitle = {Physical Processes in Lakes and Oceans},
  publisher = {American Geophysical Union},
  year = {1998},
  editor = {J. Imberger},
  series = {Coastal and Esturaine Studies},
  pages = {535--560}
}

@ARTICLE{Ribbe06,
  author = {J. Ribbe},
  title = {{A study into the export of saline water from Hervey Bay, Australia}},
  journal = {Estuarine, Coastal and Shelf Science},
  year = {2006},
  volume = {66},
  pages = {550--558},
  number = {3-4},
  doi = {DOI: 10.1016/j.ecss.2005.10.012},
  issn = {0272-7714},
  keywords = {estuaries},
  keywords1 = {estuarine dynamics},
  keywords2 = {water masses},
  keywords3 = {CTD observations},
  keywords4 = {box model},
  keywords5 = {climate change},
  keywords6 = {Australia},
  keywords7 = {East Australia Current},
  keywords8 = {Hervey Bay Water},
  url = {http://www.sciencedirect.com/science/article/B6WDV-4HWX9X2-1/2/30cdf76135927fe2c197d069897c85c4}
}

@ARTICLE{Ribbe01,
  author = {J. Ribbe and P.E. Holloway},
  title = {{A model of suspended sediment transport by internal tides}},
  journal = {Continental Shelf Research},
  year = {2001},
  volume = {21},
  pages = {395--422},
  number = {4},
  doi = {DOI: 10.1016/S0278-4343(00)00081-9},
  issn = {0278-4343},
  keywords = {Internal tides},
  keywords1 = {Sediment transport},
  url = {http://www.sciencedirect.com/science/article/B6VBJ-429XTC9-4/2/f25f35a335fbb98b21b1043daa8f65d9}
}

@ARTICLE{Ribbe08,
  author = {J. Ribbe and J.-O. Wolff and J. V. Staneva and U. Gr{\"a}we},
  title = {{Assessing water renewal time scales for marine environments from
	three-dimensional modelling: A case study for Hervey Bay, Australia}},
  journal = {Environmental Modelling \& Software},
  year = {2008},
  volume = {23},
  pages = {1217--1228},
  number = {10-11},
  issn = {1364-8152},
  keywords = {Coastal management, COHERENS, Estuaries, Flushing, Hervey Bay, Impact
	assessment, Ocean modelling, Residence time, Sustainability, Water
	quality, Water renewal},
  risfield_0_m3 = {doi: DOI: 10.1016/j.envsoft.2008.02.007},
  url = {http://www.sciencedirect.com/science/article/B6VHC-4S56425-1/2/4d2fb19bc8ef32967f94a426def8d0e8}
}

@ARTICLE{Richards82,
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  journal = JPO,
  year = {1982},
  volume = {12},
  pages = {428--439}
}

@ARTICLE{Richardson20,
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  year = {1920},
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  pages = {354--373}
}

@ARTICLE{Richardsonetal99,
  author = {R.~A. Richardson and G.~G. Sutyrin and D. Hebert and L.~M. Rothstein},
  title = {Universality of the modeled small-scale response of the upper tropical
	ocean to squall wind forcing},
  journal = JPO,
  year = {1999},
  volume = {29},
  pages = {519--529},
  number = {3}
}

@ARTICLE{Riley88,
  author = {M.~J. Riley and H.~G. Stefan},
  title = {{MINLAKE}: A dynamic lake water quality simulation model},
  journal = {Ecol. Model.},
  year = {1988},
  volume = {43},
  pages = {155--182}
}

@ARTICLE{Rippethetal2001A,
  author = {Tom P. Rippeth and Neil Fisher and John H. Simpson},
  title = {The semi-diurnal cycle of turbulent dissipation in the presence of
	tidal straining},
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  year = {2001},
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  pages = {2458-2471}
}

@ARTICLE{Rippethetal2001,
  author = {T.~P. Rippeth and E.~W. Williams and J.~H. Simpson},
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  journal = JPO,
  year = {2002},
  volume = {32},
  pages = {1242-1251}
}

@ARTICLE{ris1999third,
  author = {Ris, RC and Holthuijsen, LH and Booij, N.},
  title = {A third-generation wave model for coastal regions 2. Verification},
  journal = JGR,
  year = {1999},
  volume = {104},
  pages = {7667--7681},
  number = {C4},
  file = {:../1999-A third-generation-wave-model-for-coastal-regions-swan2_jgr99.pdf:PDF}
}

@ARTICLE{Rixen08,
  author = {M. Rixen and E. Ferreira-Coelho and Richard Signell},
  title = {{Surface drift prediction in the Adriatic Sea using hyper-ensemble
	statistics on atmospheric, ocean and wave models: Uncertainties and
	probability distribution areas}},
  journal = {Journal of Marine Systems},
  year = {2008},
  volume = {69},
  pages = {86--98},
  number = {1-2},
  note = {Maritime Rapid Environmental Assessment - New Trends in Operational
	Oceanography},
  abstract = { Despite numerous and regular improvements in underlying models, surface
	drift prediction in the ocean remains a challenging task because
	of our yet limited understanding of all processes involved. Hence,
	deterministic approaches to the problem are often limited by empirical
	assumptions on underlying physics. Multi-model hyper-ensemble forecasts,
	which exploit the power of an optimal local combination of available
	information including ocean, atmospheric and wave models, may show
	superior forecasting skills when compared to individual models because
	they allow for local correction and/or bias removal. In this work,
	we explore in greater detail the potential and limitations of the
	hyper-ensemble method in the Adriatic Sea, using a comprehensive
	surface drifter database. The performance of the hyper-ensembles
	and the individual models are discussed by analyzing associated uncertainties
	and probability distribution maps. Results suggest that the stochastic
	method may reduce position errors significantly for 12 to 72 h forecasts
	and hence compete with pure deterministic approaches.},
  doi = {DOI: 10.1016/j.jmarsys.2007.02.015},
  issn = {0924-7963},
  keywords = {Forecast},
  keywords1 = {Surface drift},
  keywords2 = {Multi-model super-ensembles},
  keywords3 = {Linear regression},
  keywords4 = {Ocean models},
  keywords5 = {Atmospheric models},
  keywords6 = {Wave models},
  url = {http://www.sciencedirect.com/science/article/B6VF5-4N3GFG2-1/2/abaa17474d4c15bc1b1b0182b6c2714c}
}

@ARTICLE{Robarts78,
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	{Mc}{I}llwaine, {R}hodesia},
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  year = {1978},
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  pages = {213--221}
}

@INCOLLECTION{RobertOuellet87,
  author = {J.~L. Robert and Y. Ouellet},
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	and non--steady natural flows},
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  publisher = {Elsevier},
  year = {1987},
  editor = {J.~C. Nihoul and B.~M. Jamart},
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}

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	the changes in dissolved oxygen},
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  year = {1994},
  volume = {79},
  pages = {159--176},
  number = {2}
}

@ARTICLE{Robinson96,
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  year = {1996},
  volume = {10},
  pages = {458--462},
  number = {5}
}

@ARTICLE{robinson2002data,
  author = {Robinson, ALLAN R and Lermusiaux, PIERRE FJ},
  title = {Data assimilation for modeling and predicting coupled physical--biological
	interactions in the sea},
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  year = {2002},
  volume = {12},
  pages = {475--536}
}

@BOOK{Rodi93,
  title = {Tubulence Models and Their Application to Hydraulics},
  publisher = {A.~A. Balkema},
  year = {1993},
  author = {W. Rodi},
  series = {IAHR Monograph Series},
  address = {Rotterdam/Brookfield}
}

@ARTICLE{Rodi87,
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@TECHREPORT{Rodi80,
  author = {Wolfgang Rodi},
  title = {Turbulence models and their application in hydraulics},
  institution = {Int. Assoc. for Hydraul. Res.},
  year = {1980},
  address = {Delft, The Netherlands}
}

@ARTICLE{Rodi76,
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@ARTICLE{Rodi70,
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  pages = {85--95},
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}

@ARTICLE{ROE85,
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@ARTICLE{roelvink1993cross,
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  journal = {Coastal Engineering},
  year = {1993},
  volume = {21},
  pages = {163--191},
  number = {1-3},
  file = {:../1993-Cross-shore-profile-models.pdf:PDF},
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  publisher = {Elsevier}
}

@TECHREPORT{roelvink1995lip,
  author = {Roelvink, JA and Reniers, A. and WL/Delft Hydraulics},
  title = {LIP 11D Delta Flume Experiments: A Dataset for Profile Model Validation},
  institution = {WL/Delft Hydraulics},
  year = {1995},
  publisher = {WL/Delft Hydraulics}
}

@ARTICLE{roelvink1989bar,
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  title = {{Bar-generating cross-shore flow mechanisms on a beach}},
  journal = {J. Geophys. Res},
  year = {1989},
  volume = {94},
  pages = {4785--4800},
  number = {C4},
  file = {:../1989-cross_shore_flow_on_beach_1989.pdf:PDF}
}

@ARTICLE{Rohretal88,
  author = {J.~J. Rohr and E.~C. Itsweire and K.~N. Helland and C.~W. van Atta},
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  journal = {J. Fluid Mech.},
  year = {1988},
  volume = {195},
  pages = {77--111}
}

@ARTICLE{Rolinski05,
  author = {S. Rolinski and G. Umgiesser},
  title = {{Modelling short-term dynamics of suspended particulate matter in
	Venice Lagoon, Italy}},
  journal = {Estuarine, Coastal and Shelf Science},
  year = {2005},
  volume = {63},
  pages = {561--576},
  number = {4},
  doi = {DOI: 10.1016/j.ecss.2005.01.002},
  issn = {0272-7714},
  keywords = {suspended particulate matter},
  keywords1 = {numerical modelling},
  keywords2 = {sediment stabilization},
  keywords3 = {erosion},
  keywords4 = {Bora event},
  keywords5 = {Venice Lagoon},
  url = {http://www.sciencedirect.com/science/article/B6WDV-4FNW4W6-5/2/0b5ed24a222f2cd40c6391d38d48c1d7}
}

@ARTICLE{romeiser2005current,
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  title = {Current measurements by airborne along-track InSAR: Measuring technique
	and experimental results},
  journal = {Oceanic Engineering, IEEE Journal of},
  year = {2005},
  volume = {30},
  pages = {552--569},
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  publisher = {IEEE}
}

@ARTICLE{rosales2008wave,
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	and Padilla-Hernandez, R.},
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	stress}},
  journal = {Journal of Marine Systems},
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  pages = {131--148},
  number = {1-2},
  file = {:../2008Wave-current-interaction-coastal-waters-Effects-on--bottom-shear-stress.pdf:PDF},
  issn = {0924-7963},
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}

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  institution = {Aerodynamische Versuchsanstalt G{\"ottingen}},
  year = {1968},
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}

@ARTICLE{Rotta51a,
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@ARTICLE{Rotta51b,
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@ARTICLE{ruessink2001modeling,
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}

@ARTICLE{Rumelin82,
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  number = {3},
  copyright = {Copyright © 1982 Society for Industrial and Applied Mathematics},
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@ARTICLE{ryu2003fully,
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	numerical wave tank}},
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  pages = {336--346},
  number = {4},
  file = {:../2003-Fully-nonlinear-wave-current-interactions-kinematics-BEM-based-numerical-wave.pdf:PDF},
  issn = {0178-7675},
  publisher = {Springer}
}

@ARTICLE{Sadiki2000a,
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@ARTICLE{Sadiki2000b,
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@ARTICLE{SadikiHutter96,
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@ARTICLE{Saggio98,
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@ARTICLE{sanay2005wind,
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@ARTICLE{Sander98a,
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@ARTICLE{Sander98b,
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@ARTICLE{SantalaTerray91,
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@ARTICLE{Schernewski05,
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	study}},
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  year = {2005},
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  pages = {109--124},
  number = {1-4},
  abstract = { We apply a 3-D circulation model with a biogeochemical module (ERGOM)
	for the simulation of trophic conditions in the Baltic Sea a century
	ago. One aim is to provide reference or background data for nitrogen,
	phosphorus and chlorophyll, which is required for the implementation
	of the European Water Framework Directive (WFD). We assume that the
	situation a century ago serves this purpose well. Model input for
	this long-term simulation study are the regionally differentiated
	riverine and atmospheric nutrient loads to the Baltic Sea, which
	were compiled and calculated for a situation 100 years ago on the
	basis of various literature sources. For the mixed surface layer
	of the open Baltic Sea, we suggest maximum winter concentrations
	for dissolved phosphorus (dissolved inorganic nitrogen) of 0.23-0.35
	(2.7-3.7) mmol/m3. Maximum chlorophyll-a concentrations are between
	1.8 and 2.4 mg/m3. The concentrations of all parameters for different
	coastal waters vary in a wide range, depending on exposure to nutrient
	sources. Our nutrient concentrations for the situation a century
	ago are close to early measured data (1950-1960) and suggest that
	this data is suitable as reference data, as well.},
  doi = {DOI: 10.1016/j.jmarsys.2004.03.007},
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  keywords2 = {Nitrogen},
  keywords3 = {Phosphorus},
  keywords4 = {Chlorophyll},
  keywords5 = {River loads},
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@ARTICLE{Schladow97,
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@BOOK{Schlichting2000,
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@ARTICLE{Schumann91,
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@ARTICLE{Schumann87,
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@ARTICLE{SchumannGerz95,
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@CONFERENCE{scott2004estimates,
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@ARTICLE{Seifert09,
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  title = {{High resolution model studies of transport of sedimentary material
	in the south-western Baltic}},
  journal = {Journal of Marine Systems},
  year = {2009},
  volume = {75},
  pages = {382--396},
  number = {3-4},
  note = {Dynamics of Natural and Anthropogenic Sedimentation (DYNAS)},
  abstract = { The paper presents high resolution model simulations of transport,
	deposition and resuspension of sedimentary material in the south-western
	Baltic, based on an upgrade of the sediment transport model described
	in the work of Kuhrts et al. [Kuhrts, C., Fennel, W., Seifert, T.,
	2004. Model studies of transport of sedimentary material in the Western
	Baltic. Journal of Marine Systems 52, 167.]. In the western Baltic,
	a grid spacing of at least 1 nautical mile is required to resolve
	the shallow and narrow bathymetry and the associated current patterns.
	A series of experimental model simulations is carried out with forcing
	data for the year 1993, which include a sequence of storms in January.
	Compared to earlier model versions, a more detailed description of
	potential deposition areas can be provided. The study quantifies
	the influence of enhanced bottom roughness caused by biological structures,
	like mussels and worm holes, provides estimates of the regional erosion
	risks for fine grained sediments, and analyses scenarios of the settling
	and spreading of material at dumping sites. Although the effects
	of changed bottom roughness, as derived from more detailed, re-classified
	sea floor data, are relatively small, the sediment transport and
	deposition patterns are clearly affected by the variation of the
	sea bed properties.},
  doi = {DOI: 10.1016/j.jmarsys.2007.01.017},
  issn = {0924-7963},
  keywords = {Numerical model},
  keywords1 = {Sediment transport},
  keywords2 = {Resuspension},
  keywords3 = {Accumulation},
  keywords4 = {Dumping},
  keywords5 = {Bed roughness},
  keywords6 = {Baltic Sea},
  url = {http://www.sciencedirect.com/science/article/B6VF5-4SBY4SH-5/2/106a84d2b68bcc5570502e91b8c67818}
}

@ARTICLE{Shadden05,
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	finite-time Lyapunov exponents in two-dimensional aperiodic flows}},
  journal = {Physica D: Nonlinear Phenomena},
  year = {2005},
  volume = {212},
  pages = {271--304},
  number = {3-4},
  issn = {0167-2789},
  keywords = {Coherent structures, Direct and finite-time Lyapunov exponents, Mixing,
	Transport barriers},
  risfield_0_m3 = {doi: DOI: 10.1016/j.physd.2005.10.007},
  url = {http://www.sciencedirect.com/science/article/B6TVK-4HNS9VK-1/2/8ef21b2aec4f3c853487a54e9a152808}
}

@ARTICLE{Shadden09,
  author = {S. C. Shadden and F. Lekien and J. D. Paduan and F. P. Chavez and
	J. E. Marsden},
  title = {{The correlation between surface drifters and coherent structures
	based on high-frequency radar data in Monterey Bay}},
  journal = {Deep Sea Research Part II: Topical Studies in Oceanography},
  year = {2009},
  volume = {56},
  pages = {161--172},
  number = {3-5},
  issn = {0967-0645},
  keywords = {Aperiodic flows, Chaotic transport, Coastal radar, Drifters, Lagrangian
	coherent structures, Lyapunov exponents},
  risfield_0_t2 = {AOSN II: The Science and Technology of an Autonomous Ocean Sampling
	Network},
  risfield_1_m3 = {doi: DOI: 10.1016/j.dsr2.2008.08.008},
  url = {http://www.sciencedirect.com/science/article/B6VGC-4TJ1HH1-3/2/9f098e9e2684e5cd8f53e69ab3c59c26}
}

@TECHREPORT{shafiee-urmia,
  author = {Shafieefar, M. and Moghimi, S.},
  title = {Hydrodynamic, hydraulic and environmental of Urmia Lake investigation
	report},
  institution = {Iran Marine Industrial Company (SADRA), Tehran, Iran},
  year = {2004},
  owner = {moghimi},
  timestamp = {2015.02.20}
}

@ARTICLE{Shao95,
  author = {Y. -P. Shao},
  title = {{A Lagrangian stochastic model for nonpassive particle diffusion
	in turbulent flows}},
  journal = {Mathematical and Computer Modelling},
  year = {1995},
  volume = {21},
  pages = {31--37},
  number = {9},
  note = {Meteorological and Air Quality Modelling},
  abstract = { In this paper, we present a Lagrangian stochastic model for heavy
	particle dispersion in turbulence. The model includes the equation
	of motion for a heavy particle and a stochastic approach to predicting
	the velocity of fluid elements along the heavy particle trajectory.
	The trajectory crossing effect of heavy particles is described by
	using an Ito type stochastic differential equation combined with
	a fractional Langevin equation. The comparison of the predicted dispersion
	of four heavy particles with the observations shows that the model
	is potentially useful but requires further development.},
  doi = {DOI: 10.1016/0895-7177(95)00049-8},
  issn = {0895-7177},
  keywords = {Lagrangian stochastic modelling},
  keywords1 = {Turbulent dispersion},
  keywords2 = {Heavy particles},
  keywords3 = {Fractional Brownian motion},
  keywords4 = {Wind erosion},
  url = {http://www.sciencedirect.com/science/article/B6V0V-3YCKKCC-1G/2/d9bd5e071b1f20dfbfa54aaa02affcfc}
}

@ARTICLE{Sharma98,
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	simulation model}},
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  year = {1998},
  volume = {12},
  pages = {33--52},
  number = {1},
  doi = {10.1007/s004770050008},
  url = {http://www.springerlink.com/content/fcebxy8hk88ce6ex}
}

@PHDTHESIS{Sharples92,
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  title = {Time-dependent stratification in regions of large horizontal density
	gradient},
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}

@ARTICLE{Shaw91,
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@ARTICLE{shchepetkin2005regional,
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  journal = OMOD,
  year = {2005},
  volume = {9},
  pages = {347--404},
  publisher = {Elsevier}
}

@ARTICLE{SHCHEPETKINea03,
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  journal = JGR,
  year = {2003},
  volume = {108},
  pages = {10.1029/2001JC001047}
}

@ARTICLE{sheng2011three,
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  year = {2011},
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  pages = {C05021},
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  publisher = {American Geophysical Union}
}

@ARTICLE{Sherman78,
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@ARTICLE{Shihetal2000,
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@INCOLLECTION{ShihShabbir92,
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@ARTICLE{Shihetal95,
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@ARTICLE{Shima93,
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@ARTICLE{Shir73,
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@ARTICLE{Siek99,
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@ARTICLE{Spivakovskaya05,
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@ARTICLE{Stefan95,
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  school = {University of Darmstadt, Germany},
  year = {2001},
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@MASTERSTHESIS{Umlauf97,
  author = {L. Umlauf},
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  school = {Technical University of Darmstadt, Department of Mechanics III},
  year = {1997},
  type = {Diploma-Thesis},
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@ARTICLE{UmlaufBurchard2005a,
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@ARTICLE{Umlauf03a,
  author = {L. Umlauf and H. Burchard},
  title = {{A generic length-scale equation for geophysical turbulence models}},
  journal = {Journal of Marine Research},
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  pages = {235--265},
  month = {March},
  abstract = {A generalization of a class of differential length-scale equations
	typically used in second-order turbulence models for oceanic flows
	is suggested. Commonly used models, like the k- model and the Mellor-Yamada
	model, can be recovered as special cases of this generic model, and
	thus can be rationally compared. In addition, a method is proposed
	that yields a generalized framework for the calibration of the most
	frequently used class of differential length-scale equations. The
	generic model, calibrated with this method, exhibits a greater range
	of applicability than any of the traditional models. Stratified flows,
	plane mixing layers, and turbulence introduced by breaking surface
	waves are considered besides some classical test cases.},
  citeulike-article-id = {6664631},
  citeulike-linkout-0 = {http://dx.doi.org/10.1357/002224003322005087},
  citeulike-linkout-1 = {http://www.ingentaconnect.com/content/jmr/jmr/2003/00000061/00000002/art00004},
  doi = {10.1357/002224003322005087},
  file = {:../wave-turb/2003-A-generic-length-scale-equation-for-geophysical-turbulence-models-umlauf.pdf:PDF},
  issn = {0022-2402},
  keywords = {gls, numerical\_simulation, tke, turbulence, turbulence\_models},
  posted-at = {2010-02-15 16:06:19},
  priority = {4},
  publisher = {Sears Foundation for Marine Research},
  url = {http://dx.doi.org/10.1357/002224003322005087}
}

@ARTICLE{UmlaufBurchard2003,
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  pages = {235--265}
}

@TECHREPORT{Umlauf2005gotm,
  author = {Lars Umlauf and Hans Burchard and Karsten Bolding},
  title = {The {G}eneral {O}cean {T}urbulence {M}odel ({GOTM}) – Scientific
	Documentation. Version 3.2.},
  institution = {Leibniz-Institute for Baltic Sea Research, Warnemünde, Germany},
  year = {2005},
  number = {63}
}

@TECHREPORT{UMLAUFea05,
  author = {Lars Umlauf and Hans Burchard and Karsten Bolding},
  title = {General {O}cean {T}urbulence {M}odel. {S}ource code documentation},
  institution = {Baltic Sea Research Institute Warnem\"unde},
  year = {2005},
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  address = {Warnem\"unde, Germany},
  pages = {274 pp},
  series = {Marine Science Reports}
}

@ARTICLE{Umlaufetal2003,
  author = {L. Umlauf and H. Burchard and K. Hutter},
  title = {Extending the $k$-$\omega$ turbulence model towards oceanic applications},
  journal = OMOD,
  year = {2003},
  volume = {5},
  pages = {195-218}
}

@INPROCEEDINGS{Umlauf99b,
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@CONFERENCE{valizadeh2003urmia,
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	turbidity plume}},
  school = {THE OHIO STATE UNIVERSITY},
  year = {2009},
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  year = {2000}
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@ARTICLE{Visser08,
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  year = {2008},
  volume = {70},
  pages = {287--299},
  number = {3-4},
  note = {Impact of Small-scale Physics on Marine Biology - Selected papers
	from the 2nd Warnem{\"u}nde Turbulence Days, 2nd Warnem{\"u}nde Turbulence
	Days},
  doi = {DOI: 10.1016/j.jmarsys.2006.07.007},
  issn = {0924-7963},
  keywords = {Organism aggregations},
  keywords1 = {Plankton},
  keywords2 = {Swimming},
  keywords3 = {Turbulent diffusion},
  keywords4 = {Stochastic process},
  keywords5 = {Foraging behaviour},
  url = {http://www.sciencedirect.com/science/article/B6VF5-4P192G6-4/2/e88f25062b916285a56ebfef1bbdb2e9}
}

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@ARTICLE{walsh2014hurricanes,
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	Anne Sophie and Elsner, James and Emanuel, Kerry and Horn, Michael
	and Lim, Young-Kwon and Roberts, Malcolm and Patricola, Christina
	and others},
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@ARTICLE{walsh2012climate,
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  pages = {149--164},
  publisher = {Elsevier}
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@INPROCEEDINGS{walstra2001calculation,
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  booktitle = {COASTAL ENGINEERING CONFERENCE},
  year = {2001},
  volume = {2},
  pages = {1050--1063},
  organization = {ASCE AMERICAN SOCIETY OF CIVIL ENGINEERS},
  file = {:../2000-Calculation-of-Wave-Driven-Currents-in-a-3D-Mean-Flow-Mod-icce2000-walstra.pdf:PDF},
  issn = {0893-8717}
}

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	under the Wind Wave Surface},
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  year = {2013},
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  pages = {1494--1510}
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@ARTICLE{wang2010development,
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  title = {Development and validation of a three-dimensional, wave-current coupled
	model on unstructured meshes},
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  file = {:../2010-Development-and-validation-of-a-three-dimensional-wave-current. pdf:PDF},
  publisher = {Springer}
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@ARTICLE{wang2007sediment,
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	2001: A numerical modelling study}},
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  number = {5},
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  issn = {0278-4343},
  publisher = {Elsevier}
}

@PHDTHESIS{Wang95,
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@ARTICLE{Wang98a,
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@ARTICLE{Wang98b,
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@INPROCEEDINGS{Wannikhof91,
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@ARTICLE{warner2010development,
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  title = {Development of a Coupled Ocean--Atmosphere--Wave--Sediment Transport
	(COAWST) Modeling System},
  journal = OMOD,
  year = {2010},
  volume = {35},
  pages = {230--244},
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}

@ARTICLE{warner2008using,
  author = {Warner, J.C. and Perlin, N. and Skyllingstad, E.D.},
  title = {{Using the Model Coupling Toolkit to couple earth system models}},
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  year = {2008},
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  issn = {1364-8152},
  publisher = {Elsevier}
}

@ARTICLE{warner2008development,
  author = {Warner, J.C. and Sherwood, C.R. and Signell, R.P. and Harris, C.K.
	and Arango, H.G.},
  title = {{Development of a three-dimensional, regional, coupled wave, current,
	and sediment-transport model}},
  journal = {Computers \& Geosciences},
  year = {2008},
  volume = {34},
  pages = {1284--1306},
  file = {:../2008Development-three-dimensional-regional-coupled-wave-current.pdf:PDF},
  issn = {0098-3004},
  publisher = {Elsevier}
}

@ARTICLE{Warner05,
  author = {J. C. Warner and C. R. Sherwood and H. G. Arango and R. P. Signell},
  title = {{Performance of four turbulence closure models implemented using
	a generic length scale method}},
  journal = OMOD,
  year = {2005},
  volume = {8},
  pages = {81--113},
  number = {1-2},
  doi = {DOI: 10.1016/j.ocemod.2003.12.003},
  issn = {1463-5003},
  keywords = {Turbulence closure},
  keywords1 = {Ocean modeling},
  keywords2 = {Sediment transport},
  url = {http://www.sciencedirect.com/science/article/B6VPS-4BD5GGX-1/2/e50480de5d8207d9ed1ebdb8ce1af57d}
}

@ARTICLE{Warner08,
  author = {John C. Warner and Christopher R. Sherwood and Richard P. Signell
	and C. K. Harris and H. G. Arango},
  title = {{Development of a three-dimensional, regional, coupled wave, current,
	and sediment-transport model}},
  journal = {Computers \& Geosciences},
  year = {2008},
  volume = {34},
  pages = {1284--1306},
  note = {Predictive Modeling in Sediment Transport and Stratigraphy},
  abstract = { We are developing a three-dimensional numerical model that implements
	algorithms for sediment transport and evolution of bottom morphology
	in the coastal-circulation model Regional Ocean Modeling System (ROMS
	v3.0), and provides a two-way link between ROMS and the wave model
	Simulating Waves in the Nearshore (SWAN) via the Model-Coupling Toolkit.
	The coupled model is applicable for fluvial, estuarine, shelf, and
	nearshore (surfzone) environments. Three-dimensional radiation-stress
	terms have been included in the momentum equations, along with effects
	of a surface wave roller model. The sediment-transport algorithms
	are implemented for an unlimited number of user-defined non-cohesive
	sediment classes. Each class has attributes of grain diameter, density,
	settling velocity, critical stress threshold for erosion, and erodibility
	constant. Suspended-sediment transport in the water column is computed
	with the same advection-diffusion algorithm used for all passive
	tracers and an additional algorithm for vertical settling that is
	not limited by the CFL criterion. Erosion and deposition are based
	on flux formulations. A multi-level bed framework tracks the distribution
	of every size class in each layer and stores bulk properties including
	layer thickness, porosity, and mass, allowing computation of bed
	morphology and stratigraphy. Also tracked are bed-surface properties
	including active-layer thickness, ripple geometry, and bed roughness.
	Bedload transport is calculated for mobile sediment classes in the
	top layer. Bottom-boundary layer submodels parameterize wave-current
	interactions that enhance bottom stresses and thereby facilitate
	sediment transport and increase bottom drag, creating a feedback
	to the circulation. The model is demonstrated in a series of simple
	test cases and a realistic application in Massachusetts Bay.},
  doi = {DOI: 10.1016/j.cageo.2008.02.012},
  issn = {0098-3004},
  keywords = {Sediment transport},
  keywords1 = {Nearshore modeling},
  keywords2 = {Three-dimensional numerical model},
  keywords3 = {Model coupling},
  url = {http://www.sciencedirect.com/science/article/B6V7D-4S21TN6-4/2/52d3a2265dd04e80f20475b8a09cad82}
}

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  file = {:../GLM/2006-glm-Eulerian-versus-Lagrangian-Approaches-the-Wave-Induced-Transport-in-the-Upper-Ocean.pdf:PDF},
  url = {http://journals.ametsoc.org/doi/abs/10.1175/JPO2951.1}
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@ARTICLE{wehner2014effect,
  author = {Wehner, Michael F and Reed, Kevin A and Li, Fuyu and Bacmeister,
	Julio and Chen, Cheng-Ta and Paciorek, Christopher and Gleckler,
	Peter J and Sperber, Kenneth R and Collins, William D and Gettelman,
	Andrew and others},
  title = {The effect of horizontal resolution on simulation quality in the
	Community Atmospheric Model, CAM5. 1},
  journal = {Journal of Advances in Modeling Earth Systems},
  year = {2014},
  publisher = {Wiley Online Library}
}

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  number = {C5},
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  publisher = {American Geophysical Union}
}

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@INPROCEEDINGS{weisse2000approach,
  author = {Weisse, R. and Gayer, G. and others},
  title = {An approach towards a 40-year high-resolution wave hindcast for the
	Southern North Sea},
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	and Forecast, Monterey, USA},
  year = {2000},
  organization = {Citeseer},
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}

@INPROCEEDINGS{welsh:135,
  author = {D. Welsh and K. Bedford and Y. Guo and P. Sadayappan},
  title = {A Coupled Wave, Current, and Sediment Transport Modeling System},
  booktitle = {Ocean Wave Measurement and Analysis (2001)},
  year = {2001},
  editor = {Billy L. Edge and J. Michael Hemsley},
  volume = {273},
  pages = {135-135},
  publisher = {ASCE},
  abstract = {A Coupled Wave, Current, and Sediment Transport Modeling System
	
	Ocean Wave Measurement and Analysis
	
	Proceedings of the Fourth International Symposium
	
	ABSTRACT
	
	David J. S. Welsh,1 Keith W. Bedford,2 M. ASCE; Yong Guo,3 and Ponnuswamy
	Sadayappan4
	
	1Senior Research Engineer, Dept. of Civil Engineering, Ohio State
	University, Columbus, Ohio 43210. welsh.3@osu.edu
	
	2Professor, Dept. of Civil Engineering, OSU. bedford.1@osu.edu
	
	3Research Associate, Dept. of Civil Engineering, OSU. yguo@superior.ceegs.ohio-state.edu
	
	4Professor, Dept. of Computer and Information Science, OSU. sadayappan.1@osu.edu
	
	
	The impact of inter-model coupling on regional scale numerical predictions
	of wind-waves, marine circulation, and sediment transport is investigated.
	This is done using the COupled MArine Prediction System (COMAPS),
	which consists of parallel-processing versions of the CH3D-SED circulation
	and sediment transport model, the WAM wind-wave model, and the WCBL
	bottom boundary layer model. COMAPS includes physics couplings between
	wave and current motions at the water surface and wave, current,
	and sediment motions at the marine bed. Adriatic Sea hindcasts are
	discussed. These indicate that the coupling mechanisms have significant
	impacts on coastal water levels, currents, and wave heights, as well
	as basin-wide sediment transport.}
}

@ARTICLE{welsh1999coupling,
  author = {Welsh, DJS and Wang, R. and Sadayappan, P. and Bedford, KW},
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  journal = {CEWES MSRC PET TR/99-22, CESES Major Shared Resource Center},
  year = {1999},
  volume = {1},
  pages = {25},
  file = {:../1999-Coupling-Marine-Circulation-Wind-Wave-Models-Parallel-Platforms.pdf:PDF},
  publisher = {Citeseer}
}

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  author = {van der Westhuysen, Andr{\'e} J and Zijlema, Marcel and Battjes,
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	and shallow water},
  journal = {Coastal Engineering},
  year = {2007},
  volume = {54},
  pages = {151--170},
  number = {2},
  publisher = {Elsevier}
}

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@BOOK{Wilcox98,
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}

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@TECHREPORT{Wilcox80,
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@INPROCEEDINGS{wilson2012assimilation,
  author = {Wilson, G and {\"O}zkan-Haller, HT and Holman, RA},
  title = {Assimilation of Remote Sensing Observations to Estimate Surf Zone
	Bathymetry},
  booktitle = {AGU Fall Meeting Abstracts},
  year = {2012},
  volume = {1},
  pages = {0103}
}

@ARTICLE{wilson2010data,
  author = {Wilson, GW and {\"O}zkan-Haller, HT and Holman, RA},
  title = {Data assimilation and bathymetric inversion in a two-dimensional
	horizontal surf zone model},
  journal = JGR,
  year = {2010},
  volume = {115},
  number = {C12}
}

@ARTICLE{wilson2014surf,
  author = {Wilson, GW and {\"O}zkan-Haller, HT and Holman, RA and Haller, MC
	and Honegger, DA and Chickadel, CC},
  title = {Surf zone bathymetry and circulation predictions via data assimilation
	of remote sensing observations},
  journal = JGR,
  year = {2014},
  volume = {119},
  pages = {1993--2016},
  number = {3},
  publisher = {Wiley Online Library}
}

@ARTICLE{wilson2012ensemble,
  author = {Wilson, Greg and {\"O}zkan-Haller, H Tuba},
  title = {Ensemble-based data assimilation for estimation of river depths},
  journal = JAOT,
  year = {2012},
  volume = {29},
  pages = {1558--1568},
  number = {10},
  file = {:../assim/2012-Ensemble-Based-Data-Assimilation-for-Estimation-of-River-Depths.pdf:PDF}
}

@INPROCEEDINGS{wilson2010bathymetric,
  author = {Wilson, G and {\"O}zkan-Haller, HT},
  title = {Bathymetric Sensitivity/Inversion in a River Model},
  booktitle = {AGU Fall Meeting Abstracts},
  year = {2010},
  volume = {1},
  pages = {1395}
}

@ARTICLE{wilson2013quantifying,
  author = {Wilson, Greg W and {\"O}zkan-Haller, H and Holman, Robert A},
  title = {Quantifying the length-scale dependence of surf zone advection},
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