@string{CTR = {Center for Turbulence Research, NASA Ames-Stanford University}} 
@string{AE = {Atmos. Environ.}}
@string{ARB = {Annual Research Briefs}}
@string{JCP = {J. Comput. Phys.}}
@string{JFM = {J. Fluid Mech.}}
@string{JGR = {J. Geophys. Res.}}
@string{JPO = {J. Phys. Oceanogr.}}
@string{IJNMF = {Int. J. Numer. Methods Fluids}}
@string{DAO = {Dyn. Atmos. Oceans}}
@string{IJHFF = {Int. J. Heat and Fluid Flow}}
@string{GRL = {Geophys. Res. Lett.}}
@string{MWR = {Mon. Wea. Rev.}}
@string{PF = {Phys. Fluids}}
@string{ARFM = {Annu. Rev. Fluid Mech.}}
@string{JAM = {J. Appl. Meteor.}}
@string{BLM = {Boundary-Layer Meteorol.}}

@article{Adcroft97a,
author = {A. Adcroft and C. Hill and J. Marshall},
title = {Representation of topography by shaved cells in a height coordinate ocean model},
journal = MWR,
volume = {125},
number = {9},
pages = {2293--2315},
year = {1997}}

@article{Adcroft97b,
author = {A. J. Adcroft and C. N. Hill and J. Marshall},
title = {A new treatment of the coriolis terms in C-grid models at both high and low resolutions},
journal = MWR,
volume = {127},
number = {8},
pages = {1928--1936},
month = {August},
year = {1999}}

@Article{Albertson99a,
  author = 	 {J. D. Albertson and M. B. Parlange},
  title = 	 {Natural integration of scalar fluxes from compex terrain},
  journal = 	 {Adv. Water Resour.},
  year = 	 {1999},
  volume = 	 {23},
  pages = 	 {239--252}}

@Article{Albertson99b,
  author = 	 {J. D. Albertson and M. B. Parlange},
  title = 	 {Surface length-scales and shear stress: implications
for land-atmosphere interaction over complex terrain},
  journal = 	 {Water Resour. Res.},
  year = 	 {1999},
  volume = 	 {35},
  pages = 	 {2121--2132}}

@ARTICLE{Allen03,
  author = {S. E. Allen and M. S. Dinniman and J. M. Klinck and
D. D. Gorby and A. J. Hewett},
  year = 2003,
  title = {{On vertical advection trunctation errors in terrain-following
numerical models: Comparison to a laboratory model for upwelling over
submarine canyons}},
  journal = JGR,
  volume = 108,
  pages = {Art. No. 3003}}

@ARTICLE{Allen72,
  author = {J. S. Allen},
  year = 1972,
  title = {{Upwelling of a stratified fluid in a rotating annulus: steady
state, part-I, Linear theory}},
  journal = JFM,
  volume = 56,
  pages = {429--445}}

@ARTICLE{Allen95,
  author = {J. S. Allen and P. A. Newberger and J. Federiuk},
  year = 1995,
  title = {{Upwelling circulation of the Oregon continental shelf.
Part I: Response to ideal forcing}},
  journal = JPO,
  volume = 25,
  pages = {1843--1866}}

@ARTICLE{Allwine02,
  author = {K. J. Allwine and J. H. Shinn and G. E. Streit and
  K.L. Clawson and M. Brown},
  year = 2002,
  title = {{Overview of URBAN 2000}:
  a multiscale field study of dispersion through an urban environment},
  journal = {Bull. Amer. Meteor. Soc.},
  volume = 83,
  pages = {521--36}}

@article{Almgren97,
title = {A Cartesian grid projection method for the incompressible {Euler} 
equations in complex geometries},
author = {A. S. Almgren and J. B. Bell and P. Colella and T. Marthaler},
journal = {SIAM J. Sci. Comput.},
volume = {18},
number = {5},
pages = {1289 -- 1309},
month = {},
year = {1997}}

@Article{Aref89,
  author = 	 {H. Aref and S. W. Jones},
  title = 	 {Enhanced separation of diffusing particles by chaotic
advection},
  journal = 	 {Fhys. Fluids},
  year = 	 {1989},
  volume = 	 {A 1},
  pages = 	 {470--474}}

@Article{Asselin72,
  author =       {R. Asselin},
  title =        {Frequency filter for time integrations},
  journal =      MWR,
  year =         {1972},
  volume =       {100},
  pages =        {487--490}}

@TechReport{Bardina83,
  author =      {J. Bardina and J. H. Ferziger and  W. C. Reynolds},
  title =       {Improved turbulence models based on large eddy
simulation of homogeneous, incompressible, turbulent flows},
  institution =  {Thermal sciences
div., Dept. of Mech. Eng., Stanford Univ., Stanford, CA},
  year =        {1983},
  number =   {TF-19}}

@Inproceedings{Baggett97,
  author =       {J.S. Baggett and J. Jimenez and A.G. Kravchenko},
  title =        {Resolution requirements in large-eddy simulations of
shear flows},
  booktitle =      {Annual Research Briefs},
  year =         {1997},
  publisher = {{NASA Ames Research Center/Stanford Univ. Center for
Turbulence Research}},
  address = {Stanford, CA},
  pages =        {51--66}}

@Inproceedings{Baggett00,
  author =       {J.S. Baggett and F. Nicoud and B. Mohammadi and
T. Bewley and J. Gullbrand and O. Botella},
  title =        {{Sub-optimal control based wall models for LES-
including transpiration velocity}},
  booktitle =      {Annual Research Briefs},
  year =         {2000},
  organization = {{NASA Ames Research Center/Stanford Univ. Center for
Turbulence Research}},
  address = {Stanford, CA},
  pages =        {331--342}}
@Article{Baik03,   
  author =       {J. J. Baik and J. J. Kim and H. J. S. Fernando},
  title =        {A {CFD} model for simulating urban flow and dispersion},
  journal =      JAM,
  year =         {2003},
  volume =       {42}, 
  pages =        {1636--1648}}  
  
@Article{Baik99,
  author =       {J. J. Baik and J. J. Kim},
  title =        {A numerical study of flow and pollutant dispersion
  characteristics in urban street canyons},
  journal =      JAM,
  year =         {1999},
  volume =       {38}, 
  pages =        {1576--1589}}  
  
  @Article{Balaras04,   
  author =       {E. Balaras},
  title =        {Modeling complex boundaries using an external force 
field on fixed {Cartesian} grids in large-eddy simulations},
  journal =      {Computers and Fluids},
  year =         {2004},
  volume =       {33}, 
  pages =        {375--404}}  
  
@ARTICLE{Barth89a,
  author = {J. A. Barth},
  year = 1989,
  title = {{Stability of a coastal upwelling front 1. Model development and
a stability theorem}},
  journal = JGR,
  volume = 94,
  pages = {10844--10856}}

@ARTICLE{Barth89b,
  author = {J. A. Barth},
  year = 1989,
  title = {{Stability of a coastal upwelling front 2. Model results and
          comparison with observations}},
  journal = JGR,
  volume = 94,
  pages = {10857--10883}}

@ARTICLE{Barth94,
  author = {J. A. Barth},
  year = 1994,
  title = {Short-wavelength instabilities on coastal jets and fronts},
  journal = JGR,
  volume = 99,
  pages = {16095--16115}}

@ARTICLE{Barth00,
  author = {J. A. Barth and S. D. Pierce and R. L. Smith},
  year = {2000},
  title = {{A seperating coastal upwelling jet at Cape Blanco, Oregon
and its connection to the California Current System}},
  journal = {Deep-Sea Res. II},
  volume = 	 {47},
  pages = 	 {783--810}}

@Article{Batteen97,
  author = 	 {M. L. Batteen},
  title = 	 {Wind-forced modeling studies of currents, meanders,
and eddies in the {California Current} system},
  journal = 	 JGR,
  year = 	 {1997},
  volume = 	 {102},
  pages = 	 {985--1010}}

@Article{Batteen98,
  author = 	 {M. L. Batteen and P. W. Vance},
  title = 	 {Modeling studies of the effects of wind forcing and
thermohaline gradients on the {California Current System}},
  journal = 	 {Deep-Sea Res. II},
  year = 	 {1998},
  volume = 	 {45},
  pages = 	 {1507--1556}}

@Article{Beam76,
  author =       {R. M. Beam and  R. F. Warming},
  title =        {An implicit finite-difference
algorithm for hyperbolic systems in conservation law form},
  journal =      JCP,
  year =         {1976},
  volume =       {22},
  pages =        {87--110}}

@Article{Beckmann97,
  author =       {A. Beckmann and R. Doscher},
  title =        {A method for improved representation
  of dense water spreading over topography in geopotential-coordinate
  models},
  journal =      JPO,
  year =         {1997},
  volume =       {27},
  pages =        {581--591}}

@Article{Benzi99,
  author =       {M. Benzi and W. Joubert and G. Mateescu},
  title =        {{Numerical experiments with parallel orderings
for ILU preconditioners}},
  journal =      {Elec. Trans. Numer. Anal.},
  year =         {1999},
  volume =       {8},
  pages =        {88--114}}
%%Electronic Transactions on Numerical Analysis


@ARTICLE{Bergeron98,
  author = {R. Bergeron},
  year = 1998,
  title = {{Measurement of a scientific workload using the IBM hardware
performance monitor}},
  journal = {Proceedings of the Supercomputing'98 Conference},
  pages = {Orlando, Florida}}

@Book{Beyer81,
author={W. H. Beyer},
title={CRC Standard Mathematical Tables},
publisher={CRC Press},
Edition={26},
address={Boca Raton}, 
year= {1981}}

@Article{Blondeaux91,   
  author =       {P. Blondeaux and G. Vittori},
  title =        {Vorticity dynamics in an oscillatory flow over a
rippled bed},
  journal =      JFM,
  year =         {1991},
  volume =       {226}, 
  pages =        {257--289}}  
  

@InProceedings{Blumberg87,
  author = 	 {A. F. Blumberg and G. L. Mellor},
  title = 	 {A description of a three-dimensional coastal ocean
circulation model},
  booktitle = 	 {Coastal and Estuarine Sciences},
  pages = 	 {1--16},
  year = 	 {1987},
  editor = 	 {N. S. Heaps},
  volume = 	 {4},
  publisher = {Amer. Geophys. Union Geophysical Monograph Board}}

@Article{Boris92,
  author = 	 {J. P. Boris and F. F. Grinstein and E. S. Oran
and R. L. Kolbe},
  title = 	 {New insights into large eddy simulation},
  journal = 	 {Fluid Dyn. Res.},
  year = 	 {1992},
  volume = 	 {10},
  pages = 	 {199--228}}

@Article{Bou04a,
  author = 	 {E. Bou-Zeid and C. Meneveau and M. B. Parlange},
  title = 	 {{Large-eddy simulation of neutral atmospheric boundary
layer flow over heterogeneous surfaces: Blending height and effective surface
roughness}},
  journal = 	 {Water Resour. Res.},
  year = 	 {2004},
  volume = 	 {40},
  pages = 	 {W02505}}

@Article{Bou05,
  author = 	 {E. Bou-Zeid and C. Meneveau and M. B. Parlange},
  title = 	 {A scale-dependent Lagrangian dynamic model for large-eddy
simulation of complex turbulent flow},
  journal = 	 PF,
  year = 	 {2005},
  volume = 	 {17},
  pages = 	 {025105}}

@Article{Bou03,
  author = 	 {E. Bou-Zeid and C. Meneveau and M. B. Parlange},
  title = 	 {Large-eddy simulation of neutral atmospheric boundary layer
flow over heterogeneous surfaces: {Blending height and effective surface
roughness}},
  journal =      {Water Resour. Res.},
  year = 	 {2003},
  volume = 	 {40},
  pages = 	 {W02505}}

@Article{Brandt77,
  author =       {A. Brandt},
  title =        {Multi-level adaptive solutions to boundary-value
problems},
  journal =      {Math. Comp.},
  year =         {1977},
  volume =       {31},
  pages =        {333--390}}

@Article{Breaker94,
  author = 	 {L. C. Breaker and W. W. Broenkow},
  title = 	 {{The circulation of Monterey Bay and related processes}},
  journal = 	 {Oceanogr. and Marine Bio.},
  year = 	 {1994},
  volume = 	 {32},
  pages = 	 {1--64}}


@Article{Breaker86,
  author = 	 {L. C. Breaker and  C. N. K. Mooers},
  title = 	 {{Oceanic variability
off the central California coast}},
  journal = 	 {Progr. Oceanogr.},
  year = 	 {1986},
  volume = 	 {17},
  pages = 	 {61--135}}

@Article{Breidenthal92,
  author = 	 {R. E. Breidenthal},
  title = 	 {Entrainment at thin stratified interfaces: the effects
of Schmidt, Richardson, and Reynolds numbers},
  journal = 	 PF,
  year = 	 {1992},
  volume = 	 {A 4},
  pages = 	 {2141--2144}}

@Article{Briggs98,
  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 = 	 JFM,
  year = 	 {1998},
  volume = 	 {354},
  pages = 	 {175--208}}

@Article{Brien72,
  author = 	 {J. J. O'Brien and H. E. Hurlburt},
  title = 	 {A numerical model of coastal upwelling},
  journal = 	 JPO,
  year = 	 {1972},
  volume = 	 {2},
  pages = 	 {14--26}}

@Article{Brink88,
  author = 	 {K. H. Brink},
  title = 	 {Topographic drag due to barotropic flow over
the continental shelf and slope},
  journal = 	 JPO,
  year = 	 {1988},
  volume = 	 {16},
  pages = 	 {2150--2158}}

@Article{Brink91,
  author = 	 {K. H. Brink and T. J. Cowles},
  title = 	 {The coastal transition zone program},
  journal = 	 JGR,
  year = 	 {1991},
  volume = 	 {96},
  pages = 	 {14637--14647}}

@Article{Broadwell91,
  author = 	 {J. E. Broadwell and M. G. Mungal},
  title = 	 {Large-scale strctures and molecular mixing},
  journal = 	 {Fhys. Fluids},
  year = 	 {1991},
  volume = 	 {A 3},
  pages = 	 {1193--1206}}

@Article{Brooks82,
  author = 	 {A . N. Brooks and T. J. R. Hughes},
  title = 	 {{Streamline upwind Petrov-Galerkin formulations for
convection dominated flows with particular emphasis on the incompressible
Navier-Stokes Equations}},
  journal =      {Comp. Methods Appl. Mech. Engr.},
  year = 	 {1982},
  volume = 	 {32},
  pages = 	 {199--259}}

@Article{Brown00,
  author =       {A. R. Brown and J. M. Hobson and N. Wood},
  title =        {Large-eddy simulation of neutral turbulent flow over
rough sinusoidal ridges},
  journal =      BLM,
  year =         {2000},
  volume =       {98},
  pages =        {411--441}}

@Article{Brown04,
  author = 	 {M. J. Brown},
  title = 	 {Urban dispersion challenges
  for fast response modeling},
  journal = 	 {5th AMS Urban Env. Conf.},
  year = 	 {2004},
  volume = 	 {},
  pages = 	 {Vancouver, B.C., 13 pp.}}

@Article{Browning90,
  author =       {G. L. Browning and W. R. Holland and H. O. Kreiss
and S. J. Worley},
  title =        {An accurate hyperbolic system of approximately
hydrostatic and incompressible oceanographic flows},
  journal =      DAO,
  year =         {1990},
  volume =       {14},
  pages =        {303--332}}

@Article{Buckles84,   
  author =       {J. Buckles and T. J. Hanratty and R. J. Adrian},
  title =        {Turbulent flow over large-amplitude wavy surfaces},
  journal =      JFM,
  year =         {1984},
  volume =       {140}, 
  pages =        {27--44}}  
  
@Article{Cabot00,
  author = 	 {W. Cabot and P. Moin},
  title = 	 {Approximate wall boundary condition in the large-eddy
simulation of high Reynolds number flow},
  journal = 	 {Flow Turb. Combust.},
  year = 	 {2000},
  volume = 	 {63},
  pages = 	 {269--391}}


@Article{Cai89,
  author =       {W. Cai and D. Gottlieb and C. W. Shu},
  title =        {Essentially nonoscillatory spectral {Fourier} 
methods for shock wave calculations},
  journal =      {Math. Comp.},
  year =         {1989},
  volume =       {186},
  pages =        {389--410}}

@article{Calhoun04,
title = {Flow around a complex building: {Comparisons}
between experiments and a {Reynolds-averaged Navier-Stokes} approach},
author = {R. Calhoun and F. Gouveia and J. Shinn and
S. Chan and D. Stevens and R. Lee and J. Leone},
journal = JAM,
volume = {43},
pages = {696--710},
year = {2004}}

@Article{Calhoun01a,
  author = 	 {R. J. Calhoun and R. L. Street},
  title = 	 {{Turbulent flow over a wavy surface: Neutral case}},
  journal = 	 JGR,
  year = 	 {2001},
  volume = 	 {106},
  pages = 	 {9277--9293}}

@Article{Calhoun01b,
  author = 	 {R. J. Calhoun and R. L. Street},
  title = 	 {{Turbulent flow over a wavy surface: Stratified case}},
  journal = 	 JGR,
  year = 	 {2001},
  volume = 	 {106},
  pages = 	 {9295--9310}}

@article{Calhoun00,
title = {A Cartesian grid finite-volume method for the advection-diffusion 
equation in irregular geometries},
author = {D. Calhoun and R. J. LeVeque},
journal = JCP,
volume = {157},
number = {1},
pages = {143 -- 180},
year = {2000}}

@article{Calhoun02,
title = {A Cartesian grid method for solving the two-dimensional 
streamfunction-vorticity equations in irregular regions},
author = {D. Calhoun},
journal = JCP,
volume = {176},
number = {2},
pages = {231 -- 275},
year = {2002},}

@PhdThesis{Calhoun99,
  author = 	 {D. Calhoun},
  title = 	 {{A Cartesian grid method for solving the streamfunction
vorticity equations in irregular geometries}},
  school = 	 {University of Washington},
  year = 	 {1999}
}

@PhdThesis{Calhoun98,
  author = 	 {R. J. Calhoun},
  title = 	 {Numerical investigations of turbulent flow
over complex terrain},
  school = 	 {Stanford University},
  year = 	 {1998}}

@Article{Camarri02,
  author = 	 {S. Camarri and M. V. Salvetti and B. Koobus and A. Dervieux},
  title = 	 {Large-eddy simulation of a bluff-body flow on unstructured
grid},
  journal = 	 IJNMF,
  year = 	 {2002},
  volume = 	 {40},
  pages = 	 {1431--1460}}

@Article{Camerlengo80,
  author =       {A. L. Camerlengo and J. J. O'Brien},
  title =        {Open boundary conditions in rotating fluids
algorithm for hyperbolic systems in conservation law form},
  journal =      JCP,
  year =         {1980},
  volume =       {35},
  pages =        {12--35}}

@Article{Casulli99,
  author = 	 {V. Casulli},
  title = 	 {A semi-implicit finite difference method for non-hydrostatic,
free-surface flows},
  journal = 	 IJNMF,
  year = 	 {1999},
  volume = 	 {30},
  pages = 	 {425--440}}

@Article{Casulli98,
  author = 	 {V. Casulli and G. S. Stelling},
  title = 	 {Numerical simulation of {3D} quasi-hydrostatic,
free-surface flow},
  journal = 	 {J. Hydrau. Eng.},
  year = 	 {1998},
  volume = 	 {124},
  pages = 	 {678--686}}

@Article{Casulli97,
  author = 	 {V. Casulli},
  title = 	 {Numerical simulation of three-dimensional free surface
flow in isopycnal coordinates},
  journal = 	 IJNMF,
  year = 	 {1997},
  volume = 	 {25},
  pages = 	 {645--658}}

@Article{Cenedese04,
  author = 	 {C. Cenedese and J. A. Whitehead and T. Ascarelli
and M. Ohiwa},
  title = 	 {A dense current flowing down a sloping bottom in a
rotating fluid},
  journal = 	 JPO,
  year = 	 {2004},
  volume = 	 {34},
  pages =        {188-203}}

@Article{Chan70,
  author = 	 {R. K.-C. Chan and R. L. Street},
  title = 	 {A computer study of finite-amplitude water waves},
  journal = 	 JCP,
  year = 	 {1970},
  volume = 	 {6},
  pages = 	 {68--94}}

@Article{Chao02,
  author = 	 {S. Y. Chao and P. T. Shaw},
  title = 	 {Nonhydrostatic aspects of coastal upwelling meanders and
filaments off eastern ocean boundaries},
  journal = 	 {Tellus},
  year = 	 {2002},
  volume = 	 {54(A)},
  pages = 	 {63--75}}

@Article{Chao02a,
  author = 	 {Y. Chao and Z. Li and P. Marchesiello and J. C. McWilliams
and F. Chavez},
  title = 	 {Modeling the mean circulation and seasonal cycle of Monterey
Bay, California},
  journal = 	 {Ocean Sciences Meeting},
  year = 	 {2002},
  volume = 	 {},
  pages = 	 {Honolulu, Hawaii}}

@Article{Chan04,
  author = 	 {S. Chan and T. Humphries and R. Lee},
  title = 	 {A simplified CFD approach for modeling urban dispersion},
  journal = 	 {Symp. on the Urban Zone, 84th Annual AMS Meeting},
  year = 	 {2004},
  volume = 	 {},
  pages = 	 {Seattle,WA}}

@Article{Charney47,
  author = 	 {J. G. Charney},
  title = 	 {The dynamics of long waves in a baroclinic westerly current},
  journal = 	 {J. Meteorol.},
  year = 	 {1947},
  volume = 	 {4},
  pages = 	 {135--163}}

@Article{Chavez99,
  author =       {F. P. Chavez and R.P. Michisaki and G.E. Friederich and 
J.T. Pennington and B. Schlining and C. Fayos and P. Walz and C. Sakamoto
and  R. Hopcroft and R. Kudela and C. Castro and E. Mauri and K.R. Buck},
  title =        { A ten-year time series for Monterey    
Bay, California: Seasonal, interannual and long-term patterns},
  journal =      {TOS},
  year =         {1999},
  volume =       {Reno, Nevada},
  pages =        {}}

@Article{Chelton84,
  author = 	 {D. B. Chelton},
  title = 	 {Seasonal variability of alongshore geostrophic velocity
off central {California}},
  journal = 	 JGR,
  year = 	 {1984},
  volume = 	 {89},
  pages = 	 {3473--3486}}

 @Article{Chereskin00,
  author = 	 {T. K. Chereskin and M. Y. Morris and P. P. Niiler and
P. M. Kosro and R. L. Smith and S. R. Ramp and C. A. Collins
and D. L. Musgrave},
  title = 	 {Spatial and temporal characteristics of the mesoscale
circulation of the California Current from eddy-resolving moored and
shipboard measurements},
  journal = 	 JGR,
  year = 	 {2000},
  volume = 	 {105},
  pages = 	 {1245--1269}}

@Article{Collins00,
  author = 	 {C. A. Collins and N. Garfield and T. A. Rago and

F. W. Rischmiller and E. Carter},
  title = 	 {{Mean structure of the inshore countercurrent and
California undercurrent off Point Sur, California}},
  journal = 	 {Deep-Sea Res. II},
  year = 	 {2000},
  volume = 	 {47},
  pages = 	 {765--782}}

@Article{Crawford86,
  author = 	 {W. R. Crawford},
  title = 	 {A comparison of length scales and decay times of
turbulence in stably stratified flows},
  journal = 	 JPO,
  year = 	 {1986},
  volume = 	 {16},
  pages = 	 {1847--1854},
}

@PhdThesis{Cui99,
  author = 	 {A. Cui},
  title = 	 {On the parallel computation of turbulent, rotating,
stratified flows},
  school = 	 {Stanford University},
  year = 	 {1999}
}

@Article{Cui00,
  author = 	 {A. Cui and R. L. Street},
  title = 	 {Frontal instabilities and coherent structures in
large eddy simulations of coastal upwelling},
  journal = 	 {Proceedings of the 5th International Symposium on
Stratified Flow, International Association of Hydraulic Research},
  year = 	 {2000},
  volume = 	 {},
  pages = 	 {Vancouver, Canada},
}

@Article{Cui01,
  author = 	 {A. Cui and R. L. Street},
  title = 	 {Large-eddy simulation of turbulent rotating convective
flow development},
  journal = 	 JFM,
  year = 	 {2001},
  volume = 	 {447},
  pages = 	 {53--84},}

@Article{Cui03a,
  author = 	 {A. Cui and R. L. Street},
  title = 	 {Large-eddy simulation of coastal upwelling flow},
  journal = 	 {Environmental Fluid Mechanics (accepted)},
  year = 	 {2003},
  volume = 	 {},
  pages = 	 {},}

@article{Cui03,
title = {Prediction of turbulent flow over rough surfaces using a force field 
in large eddy simulation},
author = {J. Cui and V. C. Patel and C. L. Lin},
journal = {ASME J. Fluids Eng.},
volume = {125},
number = {1},
pages = {2 -- 9},
month = {},
year = {2003}}

@article{Cushman-Roisin07,
title = {Simulation and characterization of the {Adriatic Sea} mesoscale variability},  
author = {B. Cushman-Roisin and K. A. Korotenko and C. E. Galos and D. 
E. Dietrich},
journal = JGR,
volume = {112},
number = {C03S14},
pages = {doi:10.1029/2006JC003515},
year = {2007}}

@MastersThesis{Daily95,
  author = 	 {C. Daily},
  title = 	 {{Numerical modeling of upwelling, relaxation,
and downwelling in Monterey Bay, California}},
  school = 	 {Princeton University},
  year = 	 {1995}}

@Article{Davidson95,
author = {M. J. Davidson and K. R. Mylne and C. D. Jones and
J. C. Phillips and R. J. Perkins and J. C. H. Fung and J. C. R. Hunt},
title={Plume dispersion through large groups of obstacles
- a field investigation},
journal=AE,
volume=29, pages={3245--3256},
year= 1995        }

@Article{Davis83b,
author = {G. de Vahl Davis},
title={Natural convection of air in a
square cavity: a bench mark numerical solution},
journal=IJNMF,
volume=3, pages={249--264},
year= 1983        }

@Article{Davis83a,
author = {G. de Vahl Davis and I. P. Jones},
title={Natural convection of air in a
square cavity: a comparison exercise},
journal=IJNMF,
volume=3, pages={227--248},
year= 1983        }

@Article{Dawson91,
author = {D. Dawson and D. E. Stock and B. Lamb},
title={The numerical simulation of airflow and dispersion in
three-dimensional atmospheric recirculation zones},
journal=JAM,
volume=30, pages={1005--1024},
year= 1991}

@Article{DeAngelis97,
author = {V. {De Angelis} and P. Lombardi and S. Banerjee},
title={Direct numerical simulation of turbulent flow over a wavy wall},
journal=PF,
volume={3}, pages={2429--2442},
year= 1997        }

@Inproceedings{DeCroix02,
  author = 	 {D. S. DeCroix},
  title = 	 {Large-eddy simulation of urban dispersion during the
{URBAN2000} field program {IOP}-10},
  booktitle = 	 {Fourth Symposium on the Urban Environment},
  publisher = {American Meteorological Society},
  address = {Norfolk, VA},
  year = 	 {2002},
  volume = 	 {},
  pages = 	 {J30--J31}}

@InCollection{Dengg96,
  author = 	 {J. Dengg and A. Beckmann and R. Gerdes},
  title = 	 {{The Gulf Stream separation problem}},
  editor = 	 {W. Krauss},
  booktitle = {The warmwatersphere of the North Atlantic Ocean},
  publisher = 	 {Gebr. Borntraeger},
  address = 	 {Berlin},
  year = 	 {1996},
  pages = 	 {253--290},}


@TechReport{Dias01,
  author =      {A. Dias and S. Majumdar},
  title =       {Numerical computation of flow around a circular
cylinder},
  institution =  {PS II Report, BITS Pilani, India},
  year =        {2001},
  number =   {}}

@Article{Dietrich06,
  author = 	 {D. E. Dietrich and Y. H. Tseng and R. Medina
and M. Liste and M. Olabarriet and S. Piacsek and M. Bowman
and A. Mehra},
  title = 	 {MOW and density current simulation using a nested
high resolution Gibraltar grid in a purely z-level model of the
coupled Mediterranean Sea and North Atlantic Oean running on a
personal computer},
  journal = 	 JGR,
  year = 	 {2006},
  volume = 	 {},
  pages = 	 {submitted}}

@Article{Dietrich04a,
  author = 	 {D. E. Dietrich and A. Mehra and R. L. Haney
and M. J. Bowman and Y. H. Tseng},
  title = 	 {Dissipation effects in modeling the North Atlantic ocean},
  journal = 	 GRL,
  year = 	 {2004},
  volume = 	 {31},
  pages = 	 {L05302}}

@Article{Dietrich04b,
  author = 	 {D. E. Dietrich and R. L. Haney and V. Fernandez and
S. Josey and J. Tintore},
  title = 	 {Air-sea fluxes based on observed annual cycle
surfce climatology and ocean model internal dynamics:
{A} precise, non-damping zero-phase-lag approach
applied to the {Mediterranean Sea}},
  journal = 	{J. Mar. Systems},
  year = 	 {2004},
  volume = 	 {52},
  pages = 	 {145--165}}

@Article{Dietrich02,
  author = 	 {D. E. Dietrich and C. A. Lin},
  title = 	 {Effects of hydrostatic approximation and resolution
on the simulation of convective adjustment},
  journal = 	{Tellus},
  year = 	 {2002},
  volume = 	 {54(A)},
  pages = 	 {34--43}}

@Article{Dietrich96,
  author = 	 {D. E. Dietrich and M. J. Bowman and C. A. Lin
and A. Mestas-Nunez},
  title = 	 {Numerical studies of small island wakes in
the ocean},
  journal = 	{Geophys. Astrophys. Fluid Dyn.},
  year = 	 {1996},
  volume = 	 {83},
  pages = 	 {195--231}}

@Article{Dietrich97a,
  author = 	 {D. E. Dietrich},
  title = 	 {{Application of a modified `a' grid ocean model 
having reduced numerical dispersion to the gulf of Mexico
circulation}},
  journal = 	 DAO,
  year = 	 {1997},
  volume = 	 {27},
  pages = 	 {201--217}}

@Article{Dietrich97b,
  author = 	 {D. E. Dietrich and C. A. Lin and A. Mestas-Nunez
and D. S. Ko},
  title = 	 {{A high resolution numerical study of gulf of
Mexico fronts and eddies}},
  journal = 	{Meteorol. Atmos. Phys.},
  year = 	 {1997},
  volume = 	 {64},
  pages = 	 {187--201}}

@Article{Dietrich94,
  author = 	 {D. E. Dietrich and D. S. Ko},
  title = 	 {{A semi-collocated ocean model-based on the SOMS approach}},
  journal = 	IJNMF,
  year = 	 {1994},
  volume = 	 {19},
  pages = 	 {1103-1113}}

@Article{Dietrich87,
  author = 	 {D. E. Dietrich and M. G. Marietta and P. J. Roache},
  title = 	 {{An ocean modeling system with turbulent boundary
layers and topography: Part 1. Numerical studies of small island wakes
in the ocean}},
  journal = 	IJNMF,
  year = 	 {1987},
  volume = 	 {7},
  pages = 	 {833--855}}

@Article{Dietrich77,
  author = 	 {D. E. Dietrich},
  title = 	 {Direct simulation of convective adjustment and other
ensemble effects},
  journal = 	 {Atmosphere},
  year = 	 {1977},
  volume = 	 {15},
  pages = 	 {1--18}}

@Article{Dillon87,
  author = 	 {T. M. Dillon and M. M. Park},
  title = 	 {The available potential energy of overturns as an
indicator of mixing in the seasonal thermocline},
  journal = 	 JGR,
  year = 	 {1987},
  volume = 	 {92},
  pages = 	 {5345--5353}}

@Article{Dillon82,
  author = 	 {T. M. Dillon},
  title = 	 {Vertical overturns: A comparison of Thorpe
and Ozmidov length scales},
  journal = 	 JGR,
  year = 	 {1982},
  volume = 	 {87},
  pages = 	 {9601-9613}}

@Book{Dongarra98,
author={J. J. Dongarra and I. S. Duff and D. C. Sorensen and
H. A. van der Vorst},
title={Numerical Linear Algebra for High-Performance Computers},
publisher={Society for Industrial and Applied Mathematics},
address={Philadelphia}, 
year= {1998}}

@Article{Dukowicz93,
  author =       {J. K. Dukowicz and R. D. Smith and R. C. Malone},
  title =        {{A reformulation and implementation of the
Bryan-Cox-Semtner ocean model on the connection machine}},
  journal =      {J. Atmos. Oceanic Technol.},
  year =         {1993},
  volume =       {10},
  pages =        {195--208}}

@Article{Ellison57,
  author = 	 {T. H. Ellison},
  title = 	 {Turbulent transport of heat and momentum from 
an infinite rough plane},
  journal = 	 JFM,
  year = 	 {1957},
  volume = 	 {2},
  pages = 	 {456--466} }

@Article{Ezer04a,
  author = 	 {T. Ezer and G.L. Mellor},
  title = 	 {A generalized coordinate ocean model and
  a comparison of the bottom boundary layer dynamics in terrain-following
  and in z-level grid},
  journal = 	 {Ocean Modelling},
  year = 	 {2004},
  volume = 	 {6},
  pages = 	 {379--403} }

@Article{Ezer04b,
  author = 	 {T. Ezer},
  title = 	 {Entrainment, diapycnal mixing and transport in
three-dimensional bottom gravity current simulations using the Mellor-Yamada
turbulence scheme},
  journal = 	 {Ocean Modelling},
  year = 	 {2004},
  volume = 	 {},
  pages = 	 {in press} }


@Article{Ezer92,
  author = 	 {T. Ezer and G. L. Mellor},
  title = 	 {A numerical study of the variability
  and the separation of the {Gulf Stream}, induced by surface atmospheric
  forcing and lateral boundary flows},
  journal = 	 JPO,
  year = 	 {1992},
  volume = 	 {22},
  pages = 	 {660--682} }


@Article{Ezer90,
  author = 	 {T. Ezer},
  title = 	 {A numerical study of the interaction between a deep cold
  jet and the bottom boundary layer of the ocean},
  journal = 	 JPO,
  year = 	 {1990},
  volume = 	 {20},
  pages = 	 {801--816} }

@Article{Fadlun00,
  author = 	 {E. A. Fadlun and R. Verzicco and P. Orlandi and
J. Mohd-Yusof},
  title = 	 {Combined immersed-boundary finite-difference methods
for three-dimensional complex flow simulations},
  journal = 	 JCP,
  year = 	 {2000},
  volume = 	 {161},
  pages = 	 {30--60} }


@Article{Fedkiw02,
  author = 	 {R. P. Fedkiw},
  title = 	 {{Coupling an Eulerian fluid calculation to a Lagrangian
solid calculation with the ghost fluid method}},
  journal = 	 JCP,
  year = 	 {2002},
  volume = 	 {175},
  pages = 	 {200--224} }

@Article{Fedkiw99,
  author = 	 {R. P. Fedkiw and T. Aslam and B. Merriman and S. Osher},
  title = 	 {{A non-oscillatory Eulerian approach to interfaces in
multimaterial flows (the ghost fluid method)}},
  journal = 	 JCP,
  year = 	 {1999},
  volume = 	 {152},
  pages = 	 {457--492}}

@Article{Fernandez05,
  author = 	 {V. Fernandez and D. E. Dietrich and R. L. Haney
and J. Tintore},
  title = 	 {Mesoscale, seasonal and interannual variability in the
{Mediterranean Sea} using the DieCAST Ocean Model},
  journal = 	{J. Mar. Systems},
  year = 	 {2005},
  volume = 	 {},
  pages = 	 {(in press)}}

@Article{Fernando96,
  author = 	 {H. J. S. Fernando and J. C. R. Hunt},
  title = 	 {Some aspects of turbulence and mixing in stably stratified
layers},
  journal = 	 {Dyn. Atmos. Oceans.},
  year = 	 {1996},
  volume = 	 {23},
  pages = 	 {35--62}}

@Article{Fernando91,
  author = 	 {H. J. S. Fernando},
  title = 	 {Turbulent mixing in stratified fluids},
  journal = 	 ARFM,
  year = 	 {1991},
  volume = 	 {23},
  pages = 	 {455--493}}

@Book{Ferziger96,
author={J. H. Ferziger and M. Peri\'{c}},
title={Computational methods for fluid dynamics},
publisher={Springer Verlag},
Edition={1},
address={Berlin Heidelberg}, year= 1996}

@Inproceedings{Ferziger97,
  author = 	 {J. H. Ferziger},
  title = 	 {Introduction to the physics and simulation of turbulence},
  booktitle = 	 {Introduction to the modelling of turbulence-Lecture series},
  publisher = 	 {von Karman Institute for Fluid Dynamics},
  year = 	 {1997},
  volume = 	 {},
  pages = 	 {}}

@InBook{Ferziger98i,
  author = 	 {J. H. Ferziger},
  title = 	 {Direct and arge eddy simulation of turbulence},
  booktitle = 	 {CRM Proceedings and Lecture Notes},
  publisher = 	 {American Mathematical Society},
  year = 	 {1998},
  volume = 	 {16},
  pages = 	 {53--97}}

@Book{Ferziger99,
author={J. H. Ferziger and M. Peri\'{c}},
title={Computational methods for fluid dynamics},
publisher={Springer Verlag},
Edition={2},
address={Berlin Heidelberg}, year= 1999}}

@Book{Ferziger01,
author={J. H. Ferziger and M. Peri\'{c}},
title={Computational Methods for Fluid Dynamics},
publisher={Springer Verlag},
Edition={3},
address={Berlin Heidelberg}, year= 2001}}

@Article{Ferziger04,
  author = 	 {J. H. Ferziger and Y. H. Tseng},
  title = 	 {A coordinate system independent streamwise upwind method
for fluid flow computation},
  journal = 	 {Int. J. Numer. Methods Fluids},
  year = 	 {2004},
  volume = 	 {45},
  pages = 	 {1235--1247}}

@ARTICLE{Flament85,
  author = {P. Flament and L. Armi and L. Washburn},
  year = {1985},
  title = {The evolving structure of an upwelling filament},
  journal = JGR,
  volume = {90},
  pages = {1765--1985}}

@Manual{Fogelson98,
  title = 	 {A software system for immersed boundary and
software simulations},
  author = 	 {A. Fogelson and J. Keener},
  organization = {Available on the web at
\emph{http:/www.math.utah.edu/IBIS}},
  year = 	 {1998}}

@Article{Forrer98,
  author =       {H. Forrer and R. Jeltsch},
  title =        {{A higher-order boundary treatment for Cartesian-grid
method}},
  journal =      JCP,
  year =         {1998},
  volume =       {140},
  pages =        {259--277}}


@Article{Franke82,
  author = 	 {R. Franke},
  title = 	 {{Scattered data interpolation: Tests of some methods}},
  journal = 	 {Math. Comput.},
  year = 	 {1982},
  volume = {38},
  pages = {181--200}}

@Article{Fredsoe99,
  author = 	 {J. Fredsoe and K. Andersen and B. Sumer},
  title = 	 {Wave plus current over a ripple covered bed},
  journal = 	 {Coastal Eng.},
  year = 	 {1999},
  volume = {38},
  pages = {177--221}}

@Inproceedings{Fringer00,
title={Direct numerical simulation of unstable finite amplitude
progressive intefacial waves},
author={O. B. Fringer and S. W. Armfield and R. L. Street},
pages={},
booktitle={The Proceedings of 5th Int. Symp. on Stratified Flows,
Vancouver, 10-13 July},
year = 	 {2000}}

@PhdThesis{Fringer01,
  author = 	 {O. B. Fringer},
  title = 	 {Numerical simulation of breaking interfacial
waves},
  school = 	 {Stanford University},
  year = 	 {2001}}


@Inproceedings{Fringer03a,
title={A nonstaggered curvilinear grid pressure correction method
applied to interfacial waves},
author={O. B. Fringer and S. W. Armfield and R. L. Street},
pages={},
booktitle={The Proceedings of 2nd Int. Conf. on Heat Transfer, Fluid
Mechanics and Thermodynamics, Victoria Falls, Zambia, 24-26 June},
year = 	 {2003}}

@ARTICLE{Fringer03,
  author = {O. B. Fringer and R. L. Street},
  year = {2003},
  title = {The dynamics of breaking progressive interfacial waves},
  journal = JFM,
  volume = {494},
  pages = {319--353}}

@ARTICLE{Fringer05,
  author = {O. B. Fringer and S. W. Armfield and R. L. Street},
  year = {2005},
  title = {Reducing numerical diffusion in interfacial gravity wave simulations},
  journal = IJNMF,
  volume = {49},
  pages = {301--329}}

@Book{Wong01,
author={F. L. Wong and S. E. Eittreim},
title={{Continental Shelf GIS for the Monterey Bay National Marine 
Sanctuary: U.S. Geological Survey Open-File Report 01-179}},
publisher={U. S. Geological Survey},
address={Menlo Park, CA},
year= {2001}}
  
@Article{Fureby96,
  author = 	 {C. Fureby},
  title = 	 {On subgrid scale modeling in large eddy simulations of
compressible fluid flow},
  journal = 	 PF,
  year = 	 {1996},
  volume = 	 {8},
  pages = 	 {1301--1311}}

@Article{Fureby00,
  author =       {C. Fureby and G. Tabor and H. Weller and A. Gosman},
  title =        {Large eddy simulation of the flow around a square prism},
  journal =      {AIAA Journal},
  year =         {2000},
  volume = {38},
  pages =        {442--452}}

@Article{Garnier99,
  author =       {E. Garnier and M. Mossi and P. Sagaut and P. Comte and
M. Deville},
  title =        {On the use of shock-capturing schemes for large-eddy
simulation},
  journal =      JCP,
  year =         {1999},
  volume =       {153},
  pages =        {273--311}}

@Article{Garfield99,
  author =       {N. Garfield and C. A. Collins and R. G. Paquette
and E. Carter},
  title =        {{Lagrangian exploration of the California undercurrent}},
  journal =      JPO,
  year =         {1999},
  volume =       {29},
  pages =        {560--583}}

@Article{Geer97,
  author =       {J. Geer and N. S. Banerjee},
  title =        {Exponentially accurate approximations to piece-wise
smooth periodic functions},
  journal =      {J. Sci. Comput.},
  year =         {1997},
  volume =       {12},
  pages =        {253--287}}

@Article{Germano92,
  author =       {M. Germano},
  title =        {Turbulence: the filtering approach},
  journal =      JFM,
  year =         {1992},
  volume =       {238},
  pages =        {325--336}}

@Article{Germano91,
  author =       {M. Germano and U. Piomelli and P. Moin and  W. H.
Cabot},
  title =        {A dynamic sub-grid scale eddy viscosity model},
  journal =      PF,
  year =         {1991},
  volume =       {A(3)},
  pages =        {1760--1765}}

@Article{Ghosal96,
  author =       {S. Ghosal},
  title =        {An analysis of numerical errors in large-eddy simulations
of turbulence},
  journal =      JCP,
  year =         {1996},
  volume =       {125},
  pages =        {187--206}}

@Article{Ghosal95,
  author =       {S. Ghosal and T. S. Lund and P. Moin and K. Akselvoll},
  title =        {A dynamic localization model for large-eddy simulation of
turbulent flows},
  journal =      JFM,
  year =         {1995},
  volume =       {286},
  pages =        {229--255}}

@Article{Gibou02,
  author =       {F. Gibou and R. P. Fedkiw and L. T. Cheng and M. Kang},
  title =        {{A second-order-accurate symmetric discretization of
the Poisson equation on irregular domains}},
  journal =      JCP,
  year =         {2002},
  volume =       {176},
  pages =        {205--227}}

@Book{Gill82,
author={A. E. Gill},
title={Atmosphere-Ocean Dynamics},
publisher={Academic Press},
address={New York}, 
year= {1982}}

@Article{Girton03,
  author =       {J. B. Girton and T. B. Sanford},
  title =        {{Descent and modification of the overflow plume
in the Denmark Strait}},
  journal =      JPO,
  year =         {2003},
  volume =       {33},
  pages =        {1351--1364}}

@Article{Goldstein93,
  author =       {D. Goldstein and R. Handler and L. Sirovich},
  title =        {Modeling a no-slip flow boundary with an external force
field},
  journal =      JCP,
  year =         {1993},
  volume =       {105},
  pages =        {354--366}}

@Book{Golub96,
author={G. H. Golub and C. F. van Loan},
title={Matrix Computations},
publisher={The Johns Hopkins University Press},
Edition={3},
address={Baltimore}, 
year= {1996}}


@Article{Gore90,
  author = 	 {R. Gore},
  title = 	 {{Between Monterey tides}},
  journal = 	 {National Geographic},
  year = 	 {1990},
  volume = 	 {177},
  pages = 	 {2--43}}


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

@Article{Gresho84,
  author = 	 {P. M. Gresho and R. Chan and C. Upson and R. Lee},
  title = 	 {{A modified finite element method for solving the
time-dependent, incompressible Navier-Stokes equations. 2. Applications}},
  journal = 	 IJNMF,
  year = 	 {1984},
  volume = 	 {4},
  pages = 	 {619--640}}

@Article{Gresho81,
  author = 	 {P. M. Gresho and R. L. Lee},
  title = 	 {Don't suppress the wiggles-they're telling you something},
  journal = 	 {Computers and Fluids},
  year = 	 {1981},
  volume = 	 {9},
  pages = 	 {223--253}}

@Article{Griffiths82,
  author = 	 {R. W. Griffiths and  P. F. Linden},
  title = 	 {Laboratory experiments on fronts. Part1.
Density driven boundary currents},
  journal = 	 {Geophys. Astrophysc. Fluid Dyn.},
  year = 	 {1982},
  volume = 	 {19},
  pages = 	 {159--187}}

@Article{Griffiths81a,
  author =       {R. W. Griffiths and  P. F. Linden},
  title =        {The stability of vortices in a rotating, stratified fluid},
  journal =      JFM,
  year =         {1981},
  volume =       {105},
  pages =        {283--316}}

@Article{Griffiths81b,
  author =       {R. W. Griffiths and  P. F. Linden},
  title =        {The  stability of buoyancy-driven coastal currents},
  journal =      DAO,
  year =         {1981},
  volume =       {5},
  pages =        {281--306}}

@Article{Griffies00,
  author = 	 {S. M. Griffies and R. C. Pacanowski and R. W. Hallberg},
  title = 	 {Spurious diapycnal mixing associated with advection in a z-coordinate ocean model},
  journal = 	 MWR,
  year = 	 {2000},
  volume = 	 {128},
  pages = 	 {538--564}}

@Article{Grinstein02,
  author = 	 {F. F. Grinstein and C. Fureby},
  title = 	 {Recent progress on MILES for high Reynolds number flows},
  journal = 	 {ASME J. Fluids Eng.},
  year = 	 {2002},
  volume = 	 {124},
  pages = 	 {848-861}}

@article{Gullbrand01,
title = {High-order Cartesian grid method for calculation of incompressible 
turbulent flows},
author = {J. Gullbrand and X. S. Bai and L. Fuchs},
journal = IJNMF,
volume = {36},
number = {6},
pages = {687 -- 709},
month = {},
year = {2001}}

@Article{Gutknecht93,
  author = 	 {M. H. Gutknecht},
  title = 	 {{Variants of BICGSTAB for matrices with complex spectrum}},
  journal = 	 {SIAM J. Sci. Comput.},
  year = 	 {1993},
  volume = 	 {14},
  pages = 	 {1020--1033}}
%SIAM Journal of Scientific Computing

@Article{Haidvogel91,
  author =       {W. R. Holland and D. B. Haidvogel},
  title =        {A parameter study of the mixed instability of idealized
 ocean currents},
  journal =      DAO,
  year =         {1980},
  volume =       {4},
  pages =        {185--215}}

@ARTICLE{Hall01,
  author = {D. J. Hall and A. M. Spanton and I. H.Griffiths
and J. M. Hargrave and S. Walker and C. John},
  year = {2001},
  title = {The {UDM: A} puff model for estimating dispersion in urban areas},
  journal = {7th Int. Conf. on Harmonisation within
Atmospheric Dispersion Modelling for Regulatory Purposes},
  pages = {256--260}}

@Article{Haney01,
  author = 	 {R. L. Haney and R. A. Hale and D. E. Dietrich},
  title = 	 {{Offshore propagation of eddy kinetic energy in the
California Current}},
  journal = 	 JGR,
  year = 	 {2001},
  volume = 	 {106},
  pages = 	 {11709--11717}}

@Article{Haney91,
  author = 	 {R. L. Haney},
  title = 	 {On the pressure gradient force over steep topography
in sigma coordinate ocean models},
  journal = 	 JPO,
  year = 	 {1991},
  volume = 	 {21},
  pages = 	 {610--619}}

@Article{Haney71,
  author = 	 {R. L. Haney},
  title = 	 {Surface thermal boundary condition for ocean
circulation modes},
  journal = 	 JPO,
  year = 	 {1971},
  volume = 	 {1},
  pages = 	 {241--248}}

@Article{Hanna03,
  author = 	 {S. R. Hanna and R. Britter and P. Franzese},
  title = 	 {A baseline urban dispersion model evaluated
  with {Salt Lake City} and {Los Angeles} tracer data},
  journal = 	 AE,
  year = 	 {2003},
  volume = 	 {37},
  pages = 	 {5069--5082}}

@Article{Hanna02,
  author = 	 {S. R. Hanna and S. Tehranian and B. Carissimo
  and R. W. Macdonald and R. Lohner},
  title = 	 {Comparisons of model simulations with observations
  of mean flow and turbulence within simple obstacle arrays},
  journal = 	 AE,
  year = 	 {2002},
  volume = 	 {36},
  pages = 	 {5067--5079}}

 
@Article{Hannoun88,
  author = 	 {I. A. Hannoun and E. J. List},
  title = 	 {Turbulent mixing at a shear-free density interface},
  journal = 	 JFM,
  year = 	 {1988},
  volume = 	 {189},
  pages = 	 {211--234}}

@Article{Haworth00,
  author = 	 {D. C. Haworth and K. Jansen},
  title = 	 {{Large-eddy simulation on unstructured deforming meshes:
Towards reciprocating IC engines}},
  journal = 	 {Computers and Fluids},
  year = 	 {2000},
  volume = 	 {29},
  pages = 	 {493--524}}

@ARTICLE{Haynes93,
  author = {R. Haynes and E. D. Barton and I. Pilling},
  year = 1993,
  title = {{Development, persistence, and variability of upwelling
filaments off the Atlantic coast of the Iberian Peninsula}},
  journal = JGR,
  volume = 98,
  pages = {22681--22692}}

@Article{He05,
  author = 	 {Y. He and C. H. Q. Ding},
  title = 	 {Coupling multi-component models with MPH on
distributed memory computer architectures},
  journal = 	 {Int. J. High Perform. Comput. Appl.},
  year = 	 {2005},
  volume = 	 {19},
  pages = 	 {329-340}}

@Article{Hellerman83,
  author = 	 {S. Hellerman and M. Rosenstein},
  title = 	 {Normal monthly wind stress over the world ocean with
error estimates},
  journal = 	 JPO,
  year = 	 {1983},
  volume = 	 {13},
  pages = 	 {1093--1104}}

@ARTICLE{Henn99,
  author = {D. Henn and I. Sykes},
  year = 1999,
  title = {Large-eddy simulation of flow over wavy surfaces},
  journal = JFM,
  volume = 383,
  pages = {75--112}}

@ARTICLE{Hickey97,
  author = {B. M. Hickey},
  year = 1997,
  title = {The response of s steep-sided narrow canyon to strong
wind forcing},
  journal = JPO,
  volume = 27,
  pages = {697--726}}

@ARTICLE{Hickey79,
  author = {B. M. Hickey},
  year = 1979,
  title = {{The California Current System}-hypotheses and facts},
  journal = {Progr. Oceanogr.},
  volume = 8,
  pages = {191--279}}

@Book{Hirsch88,
author={C. Hirsch},
title={Numerical Computation of internal and external flows},
publisher={Wiley},
address={New York}, year= 1988}


@Article{Holland80,
  author =       {W. R. Holland and D. B. Haidvogel},
  title =        {A parameter study of the mixed instability of idealized
 ocean currents},
  journal =      DAO,
  year =         {1980},
  volume =       {4},
  pages =        {185--215}}

@Article{Holt92, 
author = {S. E. Holt and J. R. Koseff and J. H. Ferziger},
title={A numerical study of the evolution and structure of homogeneous
stably straatified sheared turbulence},
journal=JFM,
volume=237, pages={499--539},
year= 1992	}

@Article{Hortmann90,
author = {M. Hortmann and M. Peri\'{c} and G. Scheuerer},
title={Finite volume multigrid prediction of natural convection: bench-mark
solutions},
journal=IJNMF,
volume=11, pages={189--207},
year= 1990        }

@Article{Hoskins75,
  author =       {B. J. Hoskins},
  title =        {The geostrophic momentum approximation and the
semi-geostrophic equations},
  journal =      {J. Atmos. Sci.},
  year =         {1975},
  volume =       {32},
  pages =        {233--242}}

@Article{Huang98,
author = {R. X. Huang},
title={Mixing and available potential
energy in a Boussinesq ocean},
journal=JPO,
volume=28, pages={669--678},
year= 1998        }

@Article{Hudson96,
author = {J. Hudson and L. Dykhno and T. Hanratty},
title={Turbulent production in flow over wavy wall},
journal={Exp. Fluids},
volume=20, pages={257--265},
year= 1996        }

@Article{Hurley01,
author = {P. J. Hurley and A. Blockley and K. Rayner},
title={Verification of a prognostic meteorological and
air pollution model for year-long predictions in the {Kwinana}
industrial region of Western Australia},
journal=AE,
volume={35}, pages={1871--1880},
year= 2001}


@ARTICLE{Huyer83,
  author = {A. Huyer},
  year = 1983,
  title = {{Coastal upwelling in the California current system}},
  journal = {Prog. Oceanogr.},
  volume = 12,
  pages = {259--284}}

@Article{Iaccarino03,
  author =       {G. Iaccarino and R. Verzicco},
  title =        {Immersed boundary technique for turbulent flow simulations},
  journal =      {Applied Mech. Rev.},
  year =         {2003},
  volume =       {56},
  pages =        {331--347}}

@Article{Ikeda84a,
  author = 	 {M. Ikeda and  W. J. Emery},
  title = 	 {{Satellite observation and modelling of meanders
in the california current system off Oregon and Northern California}},
  journal = 	 JPO,
  year = 	 {1984},
  volume = 	 {14},
  pages = 	 {1434--1450}
}

@Article{Ikeda84b,
  author = 	 {M. Ikeda and L. A. Mysak and W. J. Emery},
  title = 	 {{Observation and modeling of satellite-sensed meanders and
eddies off Vancouver island}},
  journal = 	 JPO,
  year = 	 {1984},
  volume = 	 {14},
  pages = 	 {3--21}}

@Article{Itsweire93,
author = {E. C. Itsweire and J. R. Koseff and D. A. Briggs
and J. H. Ferziger},
title={Turbulent in stratified shear flows: Impplications for
interpreting shear-induced mixing in the ocean},
journal=JPO,
volume=28, pages={1508--1522},
year= 1993        }

@Article{Itsweire84,
  author = 	 {E. C. Itsweire},
  title = 	 {Measurements of vertical overturns in a stably
turbulent flow},
  journal = 	 PF,
  year = 	 {1984},
  volume = 	 {27},
  pages = 	 {764--767}
}

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

@Article{Jameson95a,
  author = 	 {A. Jameson},
  title = 	 {Analysis and design of numerical schemes for gas dynamics
1, artificial diffusion, upwind biasing, limiters and their effect on
multigrid convergence},
  journal = 	 {Int. J. Comp. Fluid Dyn.},
  year = 	 {1995},
  volume = 	 {4},
  pages = {171-218}}

@Article{Jameson95b,
  author = 	 {A. Jameson},
  title = 	 {Analysis and design of numerical schemes for gas dynamics
2. artificial diffusion and discrete shock structure},
  journal = 	 {Int. J. Comp. Fluid Dyn.},
  year = 	 {1995},
  volume = 	 {5},
  pages =        {1-38}}

@Article{Jameson81,
  author = 	 {A. Jameson and W. Schmidt and E. Turkel},
  title = 	 {Numerical solutions of the {Euler} equations by
finite volume methods with {Runge-Kutta} time stepping schemes},
  journal = 	 {AIAA paper},
  year = 	 {1981},
  volume = 	 {81-1259}}

@Article{Jeong95,
  author = 	 {J. Jeong and F. Hussain},
  title = 	 {On the identification of a vortex},
  journal = 	 JFM,
  year = 	 {1995},
  volume = 	 {285},
  pages =        {69-94}}

@Article{Jiang96,
  author = 	 {L. Jiang and R. W. Garwood},
  title = 	 {Three-dimensional simulations of overflows on
continental slopes},
  journal = 	 JPO,
  year = 	 {1996},
  volume = 	 {26},
  pages =        {1214-1233}}

@article{Johansen98,
title = {A Cartesian grid embedded boundary method for Poisson's equation on 
irregular domains},
author = {H. Johansen and P. Colella},
journal = JCP,
volume = {147},
number = {1},
pages = {60 -- 85},
month = {},
year = {1998},}

@Inproceedings{Jones79,
title={A comparison problem for numerical
methods in fluid dynamics: The double-glazing problem},
author={I. P. Jones},
pages={338--348},
booktitle={Numerical
Methods in Thermal Problems},
editor={R. W. Lewis and K. Morgan},
organization={Pinerdge
Press},
year={1979},
address={Swansea}        }

@Article{Kanda04,
author = {M. Kanda and R. Moriwaki and F. Kasamatsu},
title={Large-eddy simulation of turbulent organized
structures within and above explicitly resolved cube arrays},
journal= BLM,
volume=112, pages={343--368},
year= 2004}

@Article{Karageorghis93,
author = {A. Karageorghis and S. Sivaloganathan},
title={A Chebyshev spectral collocation method for the computation 
of buoyancy-induced flows},
journal={Appl. Math. Comput.},
volume=55, pages={297--308},
year= 1993        }

@Article{Kastner-Klein99,
author = {P. Kastner-Klein and E. J. Plate},
title={Wind-tunnel study of concentration in street canyons},
journal= AE,
volume=33,
pages={3973-3979},
year= 1999}

@Article{Kelly98,
  author =       {K. A. Kelly and R. C. Beardsley and R. Limeburner
and K. H. Brink and J. D. Paduan and T. K. Chereskin},
  title =        {{Variability of the near-surface eddy kinetic energy in
the California Current based on altimetric, drifter, and moored current data}},
  journal =      JGR,
  year =         {1998},
  volume =       {103},
  pages =        {13067--13083}}

@Article{Kelly80,
  author =       {D. W. Kelly and S. Nakazawa and O. C. Zienkiewicz and
J. C. Heinrich},
  title =        {A note on upwinding and anisotropic balancing dissipation in
finite element approximations to convective diffusion problems},
  journal =      {Int. J. Numer. Methods Eng.},
  year =         {1980},
  volume =       {15},
  pages =        {1705--1711}}

@Article{Khadra00,
author = {K. Khadra and P. Angot and S. Parneix and J. P. Caltagirone},
title={Fictitious domain approach for numerical modelling of
Navier-Stokes equations},
journal=IJNMF,
volume=34, pages={651--684},
year= 2000        }

@Article{Killworth01,
  author =       {P. Killworth},
  title =        {On the rate of descent of overflows},
  journal =      JGR,
  year =         {2001},
  volume =       {106},
  pages =        {22267--22275}}

@ARTICLE{Killworth99,
  author = {P. D. Killworth and N. R. Edwards},
  year = 1999,
  title = {A turbulent bottom boundary layer code for use in numerical
ocean models},
  journal = JPO,
  volume = 29,
  pages = {1221--1238}}

@ARTICLE{Killworth84,
  author = {P. D. Killworth and N. Paldor and M. E. Stern},
  year = 1984,
  title = {Wave propagation and growth on a surface front on a two-layer
          geostrophic current},
  journal = {J. Mar. Res.},
  volume = 42,
  pages = {761-785}
}

@ARTICLE{Killworth80,
  author = {P. D. Killworth},
  year = 1980,
  title = {Barotropic and baroclinic instability in rotating stratified
fluids},
  journal = DAO,
  volume = 4,
  pages = {143-184}}

@Article{Kim85,
  author =       {J. Kim and  P. Moin},
  title =        {Application of a fractional-step method
to incompressible Navier-Stokes equations},
  journal =      JCP,
  year =         {1985},
  volume =       {59},
  pages =        {308--323}
}

@Article{Kim01,
  author =       {J. Kim and  D. Kim and H. Choi},
  title =        {An immersed-boundary finite-volume method for simulations
of flow in complex geometries},
  journal =      JCP,
  year =         {2001},
  volume =       {171},
  pages =        {132--150}}

@article{Kirkpatrick03,
title = {A representation of curved boundaries for the solution of the 
Navier-Stokes equations on a staggered three-dimensional Cartesian 
grid},
author = {M. P. Kirkpatrick and S. W. Armfield and J. H. Kent},
journal = JCP,
volume = {184},
number = {1},
pages = {1 -- 36},
month = {},
year = {2003}}

@Article{Kleissl04,
  author =       {J. Kleissl and C. Meneveau and M. B. Parlange},
  title =        {Field experimental study of dynamic {Smagorinsky}
models in the atmospheric surface layers},
  journal =      {J. Atmos. Sci.},
  year =         {2004},
  volume =       {61},
  pages =        {2296--2307}}

@Article{Kleissl05,
  author =       {J. Kleissl and V. Kumar and C. Meneveau and M. B. Parlange},
  title =        {Numerical study of dynamic {Smagorinsky} models in
{Large Eddy Simulation} of the atmospheric boundary layer:
validation in stable and unstable conditions},
  journal =      {Water Resour. Res.},
  year =         {2005},
  volume =       {},
  pages =        {submitted}}

@Article{Kliem99,
  author =       {N. Kliem and J. D. Pietrzak},
  title =        {{On the pressure gradient error in sigma coordinate
ocean models: A comparison with a laboratory experiment}},
  journal =      JGR,
  year =         {1999},
  volume =       {104},
  pages =        {29781--29799}}

@Article{Kosro87,
  author =       {P. M. Kosro},
  title =        {Structure of the coastal current field off northern
Callifornia during the coastal ocean dynamics experiment},
  journal =      JGR,
  year =         {1987},
  volume =       {92},
  pages =        {1637--1654}}

@Article{Kravchenko00,
  author = 	 {A. G. Kravchenko and P. Moin},
  title = 	 {Numerical studies of flow over a circular cylinder ar
$Re_D=3900$},
  journal = 	 PF,
  year = 	 {2000},
  volume = 	 {12},
  pages = 	 {403--417}}

@Article{Kreiss79,
  author =       {H. O. Kreiss and J. Oliger},
  title =        {{Stability of the Fourier method}},
  journal =      {SIAM J. Num. Anal.},
  year =         {1979},
  volume =       {16},
  pages =        {421--433}}

@Article{Kunze96,
  author =       {E. Kunze and T. B. Sandford},
  title =        {{Abyssal mixing: Where it is not}},
  journal =      JPO,
  year =         {1996},
  volume =       {26},
  pages =        {2286--2296}}

@Article{Kuo78,
  author =       {H. L. Kuo},
  title =        {2-layer model study of combined barotropic and baroclinic
instability in tropics},
  journal =      {J. Atmos. Sci.},
  year =         {1978},
  volume =       {35},
  pages =        {1840--1860}}

@Article{Lai00,
author = {M.C. Lai and C. S. Peskin},
title={An immersed boundary method with formal second-order accuracy
and reduced numerical viscosity},
journal=JCP,
volume={160}, pages={705--719},
year= {2000}        }

@Article{Lai04,
author = {C. A. Lai and D. E. Dietrich and M.L. Bowman},
title={Global Warming and Mining of Oceanic Methane Hydrate},
journal={Submitted to},
volume={}, pages={},
year={2004}         }

@Article{Large01,
author = {W. G. Large and G. Danabasoglu and J. C. McWilliams and P. R. Gent and F. O. Bryan},
title={Equatorial circulation of a global ocean climate model with anisotropic horizontal viscosity},
journal=JPO,
volume=31, pages={518--536},
year= 2001        }
  
@Article{Large94,
author = {W. G. Large and J. C. McWilliams and S. C. Doney},
title={{Oceanic vertical mixing: A review and a model with a nonlocal 
boundary layer parameterization}},
journal={Rev. Geophys.},
volume=32, pages={363--403},
year= 1994        }

@Article{Legg03,
author = {S. Legg and A. Adcroft},
title={Internal wave breaking at concave and convex continental slopes},
journal=JPO,
volume={33}, pages={2224--2246},
year= {2003}}

@Article{Legg06,
author = {S. Legg and R. W. Hallberg and J. B. Girton},
title={Comparison of entrainment in overflows simulated by z-coordinate,
isopycnal and nonhydrostatic models},
journal={Ocean Modelling},
volume={11}, pages={69--97},
year= {2006}}

@Article{Leister94,
  author =       {H. J. Leister and M. Peric},
  title =        {Vectorized strongly implicit solving procedure for seven
diagonal coefficient matrix},
  journal =      IJHFF,
  year =         {1994},
  volume = {4},
  pages =        {159--172}}


@Article{Lentz95,
  author =       {S. J. Lentz},
  title =        {{U.S. contributions to the physical oceanography
of continental shelves in the early 1990's}},
  journal =      {Rev. Geophys.},
  year =         {1995},
  volume = {33},
  pages =        {1225--1236}}

@Article{Leonard90,
  author =       {B. P. Leonard},
  title =        {Beyond first-order upwinding: the {ULTRA-SHARP} alternative
for non-oscillatory steady-state simulation of convection},
  journal =      {Int. J. Numer. Methods Eng.},
  year =         {1990},
  volume = {30},
  pages =        {729--766}}

@Article{Leonard88,
  author =       {B. P. Leonard},
  title =        {Simple high-accuracy resolution program for convective
modelling of discontinuities},
  journal =      IJNMF,
  year =         {1988},
  vol = {8},
  pages =        {1291--1318}}

@Article{Leonard79,
  author =       {B. P. Leonard},
  title =        {A stable and accurate convective
 modeling procedure based on quadratic upstream interpolation},
  journal =      {Comp. Methods Appl. Mech. Engr.},
  year =         {1979},
  volume =       {19},
  pages =        {58--98}}

@Article{Lesieur00,
  author =       {M. Lesieur and O. Metais and E. Garnier},
  title =        {Baroclinic instability and severe storms},
  journal =      {J. Turbulence},
  year =         {2000},
  volume =       {1},
  pages =        {002}}

@Article{LeVeque83,
  author =       {R. J. LeVeque and J. Oliger},
  title =        {Numerical-methods based on additive splittings for hyperbolic
partial-differential equations},
  journal =      {Math. Comp.},
  year =         {1983},
  volume =       {40},
  pages =        {469--497}}

@Inproceedings{Levitus82,
  author =       {S. Levitus},
  title =        {Climatological atlas of the world oceans},
  booktitle =      {NOAA Prof. Pap.},
  year =         {1982},
  organization = {{U.S. Govt. Print Off.}},
  address = {Washington, D. C.},
  pages =        {173}}

@Article{Lewis98,
  author =       {J. K. Lewis and I. Shulman and F. Blumberg},
  title =        {Assimilation of Doppler radar current data into
numerical ocean models},
  journal =      {Cont. Shelf Res.},
  year =         {1998},
  volume =       {18},
  pages =        {541--559}}

@Article{Lien04,
  author =       {F. S. Lien and E. Yee},
  title =        {Numerical modelling of the turbulent flow
  developing within and over a 3-D building array, {Part I:
  a high-resolution Reynolds-Averaged Navier-Stokes approach}},
  journal =      BLM,
  year =         {2004},
  volume =       {112},
  pages =        {427--466}}

@Article{Lilly92,
  author =       {D. K.  Lilly},
  title =        {{A proposed modification of the Germano subgrid
scale closure method}},
  journal =      PF,
  year =         {1992},
  volume =       {A(4)},
  pages =        {633--635}}


@InProceedings{Lilly67,
  author = 	 {D. K. Lilly},
  title = 	 {The representation of small scale turbulence in
numerical simulation experiments},
  booktitle = 	 {Proceedings of IBM Scientific Computing Symposium of
Environmental Sciences},
  pages = 	 {195},
  publisher = {IBM Data Process. Div.},
  address = {Whiteplains, N. Y.},
  year = 	 {1967}}

@Article{Lilly65,
  author = 	 {D. K. Lilly},
  title = 	 {On the computational stability of numerical solutions of time-dependent non-linear geophysical fluid dynamics problems},
  journal = 	 MWR,
  year = 	 {1967},
  volume = 	 {93},
  pages = 	 {11--26}}

@Article{Linden84,
  author =       {P. F. Linden and  J. F. Van Heijst},
  title =        {Two-layer spin-up and frontogenesis},
  journal =      JFM,
  year =         {1984},
  volume =       {143},
  pages =        {69--94}}

@article{Liu00,
title = {A boundary condition capturing method for {Poisson's} equation on 
irregular domains},
author = {X. D. Liu and R. P. Fedkiw and M. J. Kang},
journal = JCP,
volume = {160},
number = {1},
pages = {151 -- 178},
month = {MAY},
year = {2000}}

@Article{Lorenz55,
author = {E. N. Lorenz},
title={ Available potential energy and the
maintenance of the general circulation},
journal={Tellus},
volume=7, pages={157--167},
year= 1955        }

@Article{Lozej03,
  author = 	 {C. Lozej},
  title = 	 {Personal communication},
  year = 	 {2003}}

@Article{Lu01,
  author =       {Y. Y. Lu and D. G. Wright and D. Brickman},
  title =        {{Internal tide generation over topography: Experiments with a free-surface z-level ocean model}},
  journal =      {J. Atmos. Oceanic Technol.},
  year =         {2001},
  volume =       {18},
  pages =        {1076--1091}}

@Article{Luther85,
  author =       {M. E. Luther and J. M. Bane},
  title =        {{Mixed instabilities in the Gulf-stream over the continental
slope}},
  journal =      JPO,
  year =         {1985},
  volume =       {15},
  pages =        {3--23}}


@Article{Ly97,
  author =       {L. N. Ly and P. A. Luong},
  title =        {A mathematical coastal ocean circulation system with breaking
waves and numerical grid generation},
  journal =      {Appl. Math. Modelling},
  year =         {1997},
  volume =       {21},
  pages =        {633--641}}

@Article{Ly99a,
  author =       {L. N. Ly and P. A. Luong},
  title = {Numerical grid used in a coastal ocean model with breaking
wave effects},
  journal =      {J. Comput. Appl. Math},
  year =         {1999},
  volume =       {103},
  pages =        {125--137}}

@Article{Ly99b,
  author =       {L. N. Ly and P. A. Luong},
  title = {Numerical multi-block grids in coastal ocean circulation modeling},
  journal =      {Appl. Math. Modelling},
  year =         {1999},
  volume =       {23},
  pages =        {865--879}}

@Article{Lyn94,
  author =       {D. A. Lyn and W. Rodi},
  title =        {The flapping shear layer formed by flow separation from the
forward corner of a square cylinder},
  journal =      JFM,
  year =         {1994},
  volume =       {267},
  pages =        {353--376}}

@Article{Lyn95,
  author =       {D. A. Lyn and S. Einav and W. Rodi and J. H. Park},
  title =        {A {laser-Dopper} velocimetry study of ensemble-averaged
characteristics of the turbulent near wake of a square cylinder},
  journal =      JFM,
  year =         {1995},
  volume =       {304},
  pages =        {285--319}}

@Article{Lynn87,
  author =       {R. J. Lynn and J. J. Simpson},
  title =        {The {California Current System}: the seasonal variability
of its physical characteristics},
  journal =      JGR,
  year =         {1987},
  volume =       {92},
  pages =        {12947--12966}}

@Article{Macdonald00,
  author = 	 {R. W. Macdonald},
  title = 	 {Modeling the mean velocity profile in the urban canopy layer},
  journal = 	 BLM,
  year = 	 {2000},
  volume = 	 {97},
  pages = 	 {25--45}}

@Article{Mahadevan96a,
  author = 	 {A. Mahadevan and J. Oliger and R. Street},
  title = 	 {{A nonhydrostatic mesoscale ocean model. Part I:
Well-posedness and scaling}},
  journal = 	 JPO,
  year = 	 {1996},
  volume = 	 {26},
  pages = 	 {1868--1880}}

@Article{Mahadevan96b,
  author = 	 {A. Mahadevan and J. Oliger and R. Street},
  title = 	 {{A nonhydrostatic mesoscale ocean model. Part II:
Numerical implementation}},
  journal = 	 JPO,
  year = 	 {1996},
  volume = 	 {26},
  pages = 	 {1881--1900}}

@Inproceedings{Majumdar01,
  author =       {S. Majumdar and G. Iaccarino and P. Durbin},
  title =        {{RANS} solvers with adaptive structured boundary
non-conforming grids},
  booktitle =      {Annual Research Briefs},
  year =         {2001},
  organization = {{NASA Ames Research Center/Stanford Univ. Center for
Turbulence Research}},
  address = {Stanford, CA},
  pages =        {353--366}}

@Article{Majumdar05,
  author =       {S. J. Majumdar and C. H. Bishop and Z. Li and Y. Chao and J.K. Choi and P. F. J. Lermusiaux},
  title =        {Ensemble forecasting and adaptive observations in Monterey Bay},
  journal =      {6th Conference on Coastal Atmospheric and Oceanic Prediction and Processes},
  year =         {2005},
  volume =       {},
  pages =        {San Diego, California}}
 

@article{Marchesiello01,
author = {P. Marchesiello and J. C. McWilliams and A. Shchepetkin},
title = {Open boundary conditions for long-term integration of regional
oceanic models},
journal = {Ocean Modelling},
volume = {3},
pages = {1--20},
year = {2001}}

@article{Marchesiello03,
author = {P. Marchesiello and J. C. {McWilliams} and A. Shchepetkin},
title = {Equilibrium structure and dynamics of the {California} current
system},
journal = JPO,
volume = {32},
number = {},
pages = {753--783},
year = {2003}}

@article{Marshall97a,
author = {J. Marshall and C. Hill and L. Perelman and A. Adcroft},
title = {Hydrostatic ; quasi-hydrostatic ; and nonhydrostatic ocean modeling},
journal = JGR,
volume = {102},
number = {C3},
pages = {5733--5752},
year = {1997}}

@article{Marshall97b,
author = {J. Marshall and A. Adcroft and C. Hill and L. Perelman
and C. Heisey},
title = {A finite-volume ; incompressible Navier Stokes model for studies of
the ocean on parallel computers},
journal = JGR,
volume = {102},
number = {C3},
pages = {5753--5766},
year = {1997}}

@article{Martinuzzi93,
author = {R. Martinuzzi and C. Tropea},
title = {The flow around a surface mounted prismatic obstacle placed in
a fully developed channel flow},
journal = {ASME J. Fluids Eng.},
volume = {115},
pages = {85--92},
year = {1993}}

@article{Martinuzzi00,
author = {R. Martinuzzi and B. Havel},
title = {Turbulent flow around two interfering surface-mounted cubic
obstacles in tandem arrangement},
journal = {ASME J. Fluids Eng.},
volume = {122},
pages = {24--31},
year = {2000}}

@Article{Mason92,
  author = 	 {P. J. Mason and D. J. Thomson},
  title = 	 {Stochastic backscatter in large-eddy simulations
boundary layers},
  journal = 	 JFM,
  year = 	 {1992},
  volume = 	 {242},
  pages = 	 {51--78}}

@Article{Mason94,
  author = 	 {P. J. Mason},
  title = 	 {Large-eddy simulation-{A} critical review of the technique},
  journal = 	 {Q. J. R. Meteorol. Soc.},
  year = 	 {1994},
  volume = 	 {120},
  pages = 	 {1--26}}

@article{McCorquodale01,
title = {A cartesian grid embedded boundary method for the heat equation on 
irregular domains},
author = {P. McCorquodale and P. Colella and H. Johansen},
journal = JCP,
volume = {173},
number = {2},
pages = {620 -- 635},
month = {},
year = {2001},}

@Article{McCreary91,
  author = 	 {J. P. McCreary and Y. Fukamachi and P. Kundu},
  title = 	 {A numerical investigation of jets and eddies
near an eastern ocean boundary},
  journal = 	 JGR,
  year = 	 {1991},
  volume = 	 {96},
  pages = 	 {2515--2534}}

@Article{McDonald89,
  author = 	 {B. E. McDonald},
  title = 	 {Flux-corrected pseudospectral method for scalar hyperbolic
conservation laws},
  journal = 	 JCP,
  year = 	 {1989},
  volume = 	 {82},
  pages = 	 {413--428}}

@Article{McElroy97,
  author = 	 {J. L. McElroy},
  title = 	 {Diffusion from low-level urban sources:
  reexamination using recently available experimental data},
  journal = 	 JAM,
  year = 	 {1997},
  volume = 	 {36},
  pages = 	 {1027--1030}}

@article{McKenney95,
title = {{A fast Poisson solver for complex geometries}},
author = {A. McKenney and L. Greengard and A. Mayo},
journal = JCP,
volume = {118},
number = {2},
pages = {348 -- 355},
month = {},
year = {1995}}

@Article{McQueen97,
  author = 	 {D. M. McQueen and C. S. Peskin},
  title = 	 {Shared-memory parallel vector implementation of the immersed
boundary method for the computation of blood flow in the beating
mammalian heart},
  journal = 	 {J. Supercomput.},
  year = 	 {1997},
  volume = 	 {11},
  pages = 	 {213-236}}


@Article{McWilliams97,
  author = 	 {J. C. McWilliams and P. P. Sullivan and C. H. Moeng},
  title = 	 {{Langmuir turbulence in the ocean}},
  journal = 	 JFM,
  year = 	 {1997},
  volume = 	 {334},
  pages = 	 {1--30}}

@Article{McWilliams94,
  author = 	 {J. C. McWilliams and J. B. Weiss and I. Yavneh},
  title = 	 {{Anisotrophy and coherent structures in planetary
turbulence}},
  journal = 	 {Science},
  year = 	 {1994},
  volume = 	 {264},
  pages = 	 {410--413}}

@InProceedings{McWilliams93,
  author = 	 {J. C. McWilliams and P.C. Gallacher, C. H. Moeng and
J. C. Wyngaard},
  title = 	 {Modeling the oceanic planetary boundary layer},
  booktitle = 	 {Large Eddy Simulation of Complex Engineering and
Geophysical Flows},
  pages = 	 {441-454},
  publisher = {Cambridge Univ. Press, New York},
  year = 	 {1993}}


@article{Meinders99,
title = {Vortex structure and heat transfer in turbulent flow over a
wall-mounted matrix of cubes},
author = {E. R. Meinders and K. Hanjali\'c},
journal = {J. Heat and Fluid Flow},
volume = {20},
pages = {255--267},
year = {1999}}


@PhdThesis{Meinders98,
  author = 	 {E. R. Meinders},
  title = 	 {Experimental study of heat transfer in thrbulent flows
over wall-mounted cubes},
  school = 	 {Delft University of Technology, Delft, The Netherlands},
  year = 	 {1998}}


@article{Melander94,
title = {Topological vortex dynamics in axisymmetrical viscous flows},
author = {M. V. Melander and F. Hussain},
journal = JFM,
volume = {260},
pages = {57--80},
year = {1994}}

@Article{Mellor82,
  author =       {G. L. Mellor and T. Yamada},
  title =        {Development of a turbulence closure model for
geophysical fluid problems},
  journal =      {Rev. Geophys.},
  year =         {1982},
  volume = {20},
  pages =        {851--879}}

@article{Meneveau00,
author = {C. Meneveau and J. Katz},
title = {Scale-invariance and turbulence models for large-eddy simulation},
journal = ARFM,
volume = {32},
pages = {1--32},
year = {2000}}

@article{Meneveau97,
author = {C. Meneveau and T. S. Lund},
title = {The dynamic {Smagorinsky} model and scale-dependent coefficients
in the viscous range of turbulence},
journal = PF,
volume = {9},
pages = {3932--3934},
year = {1997}}

@article{Meneveau96,
author = {C. Meneveau and T. S. Lund and W. H. Cabot},
title = {A {Lagrangian} dynamic subgrid-scale model of turbulence},
journal = JFM,
volume = {319},
pages = {353--385},
year = {1996}}

@article{Meroney99,
author = {},
title = {Wind-tunnel and numerical modeling of flow and dispersion
about several building shapes},
journal = {J. Wind Eng. Ind. Aerodyn.},
volume = {81},
pages = {333-345},
year = {1999}}

@Article{Mittal97,
  author =       {R. Mittal and P. Moin},
  title =        {Suitability of upwind-biased finite difference schemes
for large-eddy simulation of turbulent flows},
  journal =      {AIAA Journal},
  year =         {1997},
  volume = {35},
  pages =        {1415--1417}}

@Inproceedings{Mohd97,
  author =       {J. Mohd-Yusof},
  title =        {Combined immersed boundary/{B}-{Spline} methods
for simulations of flows in complex geometries},
  booktitle =      {Annual Research Briefs},
  year =         {1997},
  organization = {{NASA Ames Research Center/Stanford Univ. Center for
Turbulence Research}},
  address = {Stanford, CA},
  pages =        {317--327}}

@Article{Morinishi98,
author   =  {Y. Morinishi and T. Lund and O. Vasilyev and P. Moin},
title    =  {Fully conservative higher order finite difference schemes for Incompressible Flow},
journal  = JCP,
volume   = {143}, 
pages    = {90-104},
year     = {1998}}	

@Article{Mulder92,
author   =  {W. Mulder and S. Osher and J. A. Sethian},
title    =  {Computing Interface Motion in Compressible Gas Dynamics},
journal  = JCP,
volume   = {100}, 
pages    = {209-228},
year     = {1992}}	

@Article{Moeng84,
  author =       {C. H. Moeng},
  title =        {A large-eddy simulation model for the study of planetary
boundary-layer turbulence},
  journal =      {J. Atmos. Sci.},
  year =         {1984},
  volume =       {41},
  pages =        {2052--2062}}

@Article{Moin91,
  author =       {P. Moin and K. Squires and W. Cabot and S. Lee},
  title =        {A dynamic subgrid-scale model for compressible
turbulence and scalar transport},
  journal =      PF,
  year =         {1991},
  volume =       {A3},
  pages =        {2746--2757}}

@Article{Monismith86,
  author = 	 {S. Monismith},
  title = 	 {An experimental study of the upwelling response
of stratified reservoirs to surface shear stress},
  journal = 	 JFM,
  year = 	 {1986},
  volume = 	 {171},
  pages = 	 {407--439}}

@Article{Mooers84,
  author = 	 {C. N. K. Mooers and A. R. Robinson},
  title = 	 {{Turbulent jets and eddies in the
California current and inferred cross-shore transport}},
  journal = 	 {Science},
  year = 	 {1984},
  volume = 	 {223},
  pages = 	 {51--53}}

@Article{Mooers76,
  author =       {C. N. K. Mooers and C. A. Collins and R. L. Smith},
  title =        {{Dynamic structure of frontal zone in coastal upwelling region off Oregon}},
  journal =      JPO,
  year =         {1976},
  volume =       {6},
  pages =        {3--21}}


@Inproceedings{Nakayama02,
  author =       {A. Nakayama and K. Sakio},
  title =        {Simulation of flows over wavy rough boundaries},
  booktitle =      {Annual Research Briefs},
  year =         {2002},
  organization = {{NASA Ames Research Center/Stanford Univ. Center for
Turbulence Research}},
  address = {Stanford, CA},
  pages =        {313--324}}

@Article{Nakayama02a,
  author = 	 {A. Nakayama and S. N. Vengadesan},
  title = 	 {On the influence of numerical schemes and subgrid-stress
models on large eddy simulation of turbulent flow past a square cylinder},
  journal = 	 IJNMF,
  year = 	 {2002},
  volume = 	 {38},
  pages = 	 {227--253}}

@Article{Narimousa91,
  author = 	 {S. Narimousa and  T. Maxworthy},
  title = 	 {Experiments on the structure and dynamics of forced,
quasi-two-dimensional turbulence},
  journal = 	 JFM,
  year = 	 {1991},
  volume = 	 {223},
  pages = 	 {113--133}}

@Article{Narimousa89,
  author = 	 {S. Narimousa and  T. Maxworthy},
  title = 	 {Application of a laboratory model to the interpretation
of satellite and field observations of coastal upwelling},
  journal = 	 DAO,
  year = 	 {1989},
  volume = 	 {13},
  pages = 	 {1--46}
}
@Article{Narimousa87a,
  author = 	 {S. Narimousa and  T. Maxworthy},
  title = 	 {Coastal upwelling on a sloping bottom: 
the formation of plumes, jets and pinched--off cyclones},
  journal = 	 {J. of Fluid Mech.},
  year = 	 {1987},
  volume = 	 {176},
  pages = 	 {169--190}
}
@Article{Narimousa87b,
  author = 	 {S. Narimousa and  T. Maxworthy},
  title = 	 {On the effects of coastline 
perturbations on coastal currents and fronts},
  journal = 	 JPO,
  year = 	 {1987},
  volume = 	 {17},
  pages = 	 {1296--1303}
}
@Article{Narimousa86,
  author = 	 {S. Narimousa and  T. Maxworthy},
  title = 	 {Effects of a discontinuous surface 
stress on a model of coastal upwelling},
  journal = 	 JPO,
  year = 	 {1986},
  volume = 	 {16},
  pages = 	 {2071--2083}
}

@Article{Narimousa85,
  author = 	 {S. Narimousa and  T. Maxworthy},
  title = 	 {Two-layer model
of shear-driven coastal upwelling in the presence of bottom topography},
  journal = 	 JFM,
  year = 	 {1985},
  volume = 	 {159},
  pages = 	 {503--531}}

@Inproceedings{Nicoud99,
  author =       {F. Nicoud and J. S. Baggett},
  title =        {On the use of optimal control theory for deriving wall
models for {LES}},
  booktitle =      {Annual Research Briefs},
  year =         {1999},
  organization = {{NASA Ames Research Center/Stanford Univ. Center for
Turbulence Research}},
  address = {Stanford, CA},
  pages =        {329--341}}

@article{Nicoud01,
Author={F. Nicoud and J. S. Baggett and P. Moin and Cabot},
Title={{LES wall-modeling based on optimal control theory}},
Year={2001},
  journal = 	 {submitted to Phys. Fluids}}

@article{Nikitin00,
Author={N. V. Nikitin and F. Nicoud and B. Wasistho and K. D. Squires
and P. R. Spalart},
title={An approach to wall modeling in large-eddy simulations},
Year={2000},
journal = PF,
volume = 	 {12},
pages = 	 {1629-1632}}


@Article{Noh95,
  author = 	 {Y. Noh and H. J. S. Fernando},
  title = 	 {Onset of stratification in a mixed layer subjected to
a stabilizing buoyancy flux},
  journal = 	 JFM,
  year = 	 {1995},
  volume = 	 {304},
  pages = 	 {27-46}}

@Article{Noh93,
  author = 	 {Y. Noh and H. J. S. Fernando},
  title = 	 {The role of molecular diffusion in 
the deepening of the mixed layer},
  journal = 	 DAO,
  year = 	 {1993},
  volume = 	 {17},
  pages = 	 {187-215}}

@Book{Oke87,
author={T. Oke},
title={Boundary Layer Climates},
publisher={Halsted},
Edition={2nd},
address={New York}, year= 1987}

@Article{Oliger78,
  author =       {J. Oliger and A. Sundstrom},
  title =        {Theoretical and practical aspects of some initial boundary
value problems in fluid dynamics},
  journal =      {SIAM J. Appl. Math.},
  year =         {1978},
  volume =       {35},
  pages =        {419--446}}

@Article{Oort89,
  author = 	 {A. H. Oort and S. C. Ascher and S. Levitus 
and J. P. Peix\'{o}to},
  title = 	 {New estimates of the available potential energy in
the world ocean},
  journal = 	 JGR,
  year = 	 {1989},
  volume = 	 {94},
  pages = 	 {3187--3200}}

@Article{Orlanski76,
  author = 	 {I. Orlanski},
  title = 	 {A simple boundary condition for unbounded hyperbolic flows},
  journal = 	 JCP,
  year = 	 {1976},
  volume = 	 {21},
  pages = 	 {251--269}}

@Article{Orszag70,
  author = 	 {S. A. Orszag},
  title = 	 {Transform method for calculation of vector coupled sums:
{Application} to the spectral form of the vorticity equation},
  journal = 	 {J. Atmos. Sci.},
  year = 	 {1970},
  volume = 	 {27},
  pages = 	 {890--895}}

@Article{Orszag74,
  author = 	 {S. A. Orszag},
  title = 	 {Numerical computation of turbulent shear flows},
  journal = 	 {Adv. Geophys.},
  year = 	 {1974},
  volume = 	 {18},
  pages = 	 {224--236}}

@Article{Osborne96,
  author = 	 {P. D. Osborne and C. E. Vincent},
  title = 	 {Vertical and horizontal structure in suspended sand
concentrations and wave-induced fluxes over bedforms},
  journal = 	 {Marine Geology},
  year = 	 {1996},
  volume = 	 {131(3-4)},
  pages = 	 {195--608}}


@Article{Ozmidov65,
  author = 	 {R. V. Ozmidov},
  title = 	 {On the turbulent exchange in a stably stratified
ocean},
  journal = 	 {Izv. Atmos. Oceanic Phys.},
  year = 	 {1965},
  volume = 	 {1},
  pages = 	 {853--860}
}

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

@Article{Pacanowski98,
  author = 	 {R. C. Pacanowski and A. Gnanadesikan},
  title = 	 {Transient response in a z-level ocean model that resolves
topography with partial cells},
  journal = 	 MWR,
  year = 	 {1998},
  volume = 	 {126},
  pages = 	 {3248--3270}}

@Article{Paduan96,
  author = 	 {J. D. Paduan and L. K. Rosenfeld},
  title = 	 {Remotely sensed surface currents in Monterey Bay
from shore-based HF radar (Coastal Ocean Dynamics Application Radar)},
  journal = 	 JGR,
  year = 	 {1996},
  volume = 	 {101},
  pages = 	 {20669--20686}}


@Article{Paduan04,
  author = 	 {J. D. Paduan and I. Shulman},
  title = 	 {{HF radar data assimilation in the Monterey Bay area}},
  journal = 	 JGR,
  year = 	 {2004},
  volume = 	 {109},
  pages = 	 {C07S09}}

@Article{Palma00,
  author = 	 {E. D. Palma and R. P. Matano},
  title = 	 {On the implementation of open boundary condition for a
general circulation model: {The} three-dimensional case},
  journal = 	 JGR,
  year = 	 {2000},
  volume = 	 {105},
  pages = 	 {8605--8627}}

@Article{Park04,
  author = 	 {I.S. Park and S.J. Lee and C. H. Kim and C. Yoo and Y.H. Lee},
  title = 	 {Simulating urban-scale air pollutants and
  their predicting capabilities over the {Seoul} metropolitan area},
  journal = 	 {J. Air \& Waste Manage. Assoc.},
  year = 	 {2004},
  volume = 	 {54},
  pages = 	 {695--710}}

@Article{Patankar72,
author = {S. V. Patankar and D. B. Spalding},
title={A calculation procedure for heat, mass and momentum transfer in
three-dimensional parabolic flows},
journal={Int. J. Heat. Mass Transfer},
volume=15, pages={1787--1806},
year= 1972    }


@Inproceedings{Patnaik04,
  author =       {G. Patnaik and J. P. Boris and F. F. Grinstein and J. P. Iselin},
  title =        {Large scale urban simulations with {FCT}},
  booktitle =    {High-resolution schemes for convection-dominated flows: 30 years of FCT},
  publisher =    {Springer},
  year =         {2005},
  volume =       {},
  address=       {},
  pages =        {105--130}}

@Article{Pavageau99,
  author = 	 {M. Pavageau and M. Schatzmann},
  title = 	 {Wind tunnel measurements of concentration
  in an urban street canyon},
  journal = 	 AE,
  year = 	 {1999},
  volume = 	 {33},
  pages = 	 {3961--3971}}

@Article{Pelegri93,
  author =       {J. L. Pelegri and J. G. Richman},
  title =        {{On the role of shear mixing during transient coastal
upwelling}},
  journal =      {Cont. Shelf Res.},
  year =         {1993},
  volume =       {13},
  pages =        {1363--1400}}

@article{Pember95,
title = {An adaptive {Cartesian} grid method for unsteady compressible
flow in irregular regions},
author = {R. B. Pember and J. B. Bell and P. Colella and W. Y. Crutchfield and 
M. L. Welcome},
journal = JCP,
volume = {120},
number = {2},
pages = {278 -- 304},
month = {},
year = {1995}}

@Article{Penduff02,
  author =       {T. Penduff and B. Barnier and M.-A. Kerbiriou and
J. Verron},
  title =        {How topographic smoothing contributes to differences
between the eddy flows simulated by sigma- and geopotential-coordinate
system},
  journal =      JPO,
  year =         {2002},
  volume =       {32},
  pages =        {122--137}}

@Article{Peric88,
  author = 	 {M. Peri\'c and R. Kessler and  G. Scheuerer},
  title = 	 {Comparison of finite-volume numerical methods with
staggered and colocated grids},
  journal = 	 {Computers and Fluids},
  year = 	 {1988},
  volume = 	 {16},
  pages = 	 {389--403}}

@Article{Perng89,
author = {C. Y. Perng and R. L. Street},
title={Three-dimensional unsteady flow simulation:
alternative strategies for a volume averaged calculation},
journal=IJNMF,
volume=9, pages={341--362},
year= 1989        }

@Article{Peskin72,
  author =       {C. S. Peskin},
  title =        {Flow patterns around heart valves: a numerical method},
  journal =      JCP,
  year =         {1972},
  volume =       {10},
  pages =        {252--271}}

@Article{Peskin77,
  author =       {C. S. Peskin},
  title =        {Numerical analysis of blood flow in the heart},
  journal =      JCP,
  year =         {1977},
  volume =       {25},
  pages =        {220--252}}


@Article{Peters05a,
  author = 	 {H. Peters and W. E. Johns and A. S. Bower and D. M. Fratantoni},
  title = 	 {{Mixing and entrainment in the Red Sea outflow plume. Part II:
Plume structure}},
  journal = 	 JPO,
  year = 	 {2005},
  volume = 	 {35},
  pages = 	 {569--583}}

@Article{Peters05b,
  author = 	 {H. Peters and W. E. Johns},
  title = 	 {{Mixing and entrainment in the Red Sea outflow plume. Part II:
Turbulence characteristics}},
  journal = 	 JPO,
  year = 	 {2005},
  volume = 	 {35},
  pages = 	 {584--600}}

@Article{Petitjeans96,
  author = 	 {P. Petitjeans and J-E Wesfreid},
  title = 	 {Spatial evolution of G\"ortler instability in a curved duct
of high curvature},
  journal = 	 {AIAA Journal},
  year = 	 {1996},
  volume = 	 {34},
  pages = 	 {1793--1800}}

@Article{Petrie87,
  author = 	 {B. Petrie and B. J. Topliss and D. G. Wright},
  title = 	 {{Coastal upwelling and eddy development off
Nova Scotia}},
  journal = 	 JGR,
  year = 	 {1987},
  volume = 	 {29},
  pages = 	 {12979--12991}}

@Article{Petruncio02,
  author = 	 {E. T. Petruncio and J. D. Paduan and L. K. Rosenfeld},
  title = 	 {Numerical simulations of the internal tide in
a submarine canyon},
  journal = 	 {Ocean Modelling},
  year = 	 {2002},
  volume = 	 {4},
  pages = 	 {221--249}}

@PhdThesis{Petruncio96,
  author = 	 {E. T. Petruncio},
  title = 	 {Observation and modeling of the internal tide in a submarine
canyon},
  school = 	 {Naval Postgraduate School},
  year = 	 {1996}}

@Article{Phillips54,
  author = 	 {N. A. Phillips},
  title = 	 {Energy transformations and meridional 
circulations associated with simple baroclinic waves in
a two-level, quasi-geostrophic model},
  journal = 	 {Tellus},
  year = 	 {1954},
  volume = 	 {6},
  pages = 	 {273--286}}

@ARTICLE{Pierce00,
  author = {S. D. Pierce and R. L. Smith and P. M. Kosro and J. A. Barth
and C. D. Wilson},
  year = {2000},
  title = {{Continuity of the poleward undercurrent along the eastern boundary
of the mid-latitude Pacific}},
  journal = {Deep-Sea Res. II},
  volume = 	 {47},
  pages = 	 {811--829}}

@Article{Pierrehumbert95,
  author = 	 {R. T. Pierrehumbert and K. L. Swanson},
  title = 	 {Baroclinic instability},
  journal = 	 ARFM,
  year = 	 {1995},
  volume = 	 {27},
  pages = 	 {419--467}}


@Article{Piomelli90,
  author =       {U. Piomelli and T. A. Zang and C. G. Speziale and
M. Y. Hussiani},
  title =        {On the large-eddy simulation of transitional
wall-bounded flows},
  journal =      PF,
  year =         {1990},
  volume =       {A(2)},
  pages =        {257--265}}

@Article{Piomelli02,
  author =       {U. Piomelli and E. Balaras},
  title =        {Wall-layer models for large-eddy simulations},
  journal =      ARFM,
  year =         {2002},
  volume =       {34},
  pages =        {349--374}}

@Article{Pope85,
  author = 	 {S. B. Pope},
  title = 	 {Pdf methods for Turbulent reactive flows},
  journal = 	 {Prog. Energy Combust. Sci},
  year = 	 {1985},
  volume = 	 {11},
  pages = 	 {119-192}}

@Article{Porte00,
  author = 	 {F. Port\'e-Agel and C. Meneveau and M. B. Parlange},
  title = 	 {A scale-dependent dynamic model for large-eddy simulation:
application to a neutral atmospheric boundary layer},
  journal = 	 JFM,
  year = 	 {2000},
  volume = 	 {415},
  pages = 	 {261-284}}

@Article{Porte04,
  author = 	 {F. Port\'e-Agel},
  title = 	 {A scale-dependent dynamic model for scalar transport in
large-eddy simulations of the atmospheric boundary layer},
  journal = 	 BLM,
  year = 	 {2004},
  volume = 	 {112},
  pages = 	 {81-105}}

@Article{Pratt04,
  author = 	 {G. C. Pratt and C. Y. Wu and D. Bock and J. L. Adgate
and G. Ramachandran and T. H. Stock and M. Morandi and K. Sexton},
  title = 	 {Comparing air dispersion model predictions with
measured concentrations of {VOCs} in urban communities},
  journal = 	 {Environ. Sci. Technol.},
  year = 	 {2004},
  volume = 	 {38},
  pages = 	 {1949--1959}}

@Article{Preller80,
  author = 	 {R. Preller and J. J. O'Brien},
  title = 	 {{The influence of bottom topography on upwelling
off Peru}},
  journal = 	 JPO,
  year = 	 {80},
  volume = 	 {10},
  pages = 	 {1377--1398}}

@Article{Pouquet83,
  author = 	 {A. Pouquet and U. Frisch and J. P. Chollet},
  title = 	 {Turbulence with a spectral gap},
  journal = 	 PF,
  year = 	 {1983},
  volume = 	 {26},
  pages = 	 {877-880}}

@Article{Rafailidis97,
  author = 	 {S. Rafailidis},
  title = 	 {Influence of building areal density and
  roof shape on the wind characteristics above a town},
  journal = 	 BLM,
  year = 	 {1997},
  volume = 	 {85},
  pages = 	 {255--271}}

@Article{Raithby76,
  author = 	 {G. D. Raithby},
  title = 	 {Skew upstream differencing schemes for problems
involving fluid flow},
  journal = 	 {Comp. Methods Appl. Mech. Engr.},
  year = 	 {1976},
  volume = 	 {9},
  pages = 	 {153--164}}

@Article{Ramp97,
  author = 	 {S. R. Ramp and L. K. Rosenfeld and T. D. Tisch and
M. R. Hicks},
  title = 	 {{Moored observations of the current and temperature
structure over the continental slop off central California, 1, A basic
description of the variability}},
  journal = 	 JGR,
  year = 	 {1997},
  volume = 	 {102},
  pages = 	 {22877--22902}}

@Article{Reid81,
author = {R. O. Reid and B. A. Elliott and D. B. Olson},
title={Available potential energy: A clarification},
journal=JPO,
volume=11, pages={15--29},
year= 1981        }

@Article{Redondo96,
author = {J. M. Redondo and M. A. Sanchez and I. R. Cantalapiedra},
title={Turbulent mechanisms in stratified fluids},
journal={Dyn. Atmos. Oceans},
volume=24, pages={107--115},
year= 1996        }


@PhdThesis{Rehmann95,
  author = 	 {C. R. Rehmann},
  title = 	 {Effects of stratification and molecular diffusivity
on the mixing efficiency of decaying grid turbulence},
  school = 	 {Stanford University},
  year = 	 {1995}}


@Article{Rhie83,
  author = 	 {C. M. Rhie and  W. L. Chow},
  title = 	 {Numerical study
of the turbulent flow past an airfoil with trailing edge separation},
  journal = 	 {AIAA Journal},
  year = 	 {1983},
  volume = 	 {21},
  pages = 	 {1525--1532}}

@Book{Roache98,
author={P. J. Roache},
title={Verification and validation in computational science and Engineering},
publisher={Hermosa Publishers},
Edition={},
address={}, year= 1998}

@Book{Roache95,
author={P. J. Roache},
title={Elliptic marching methods and domain decomposition},
publisher={CRC Press},
Edition={},
address={}, year= 1995}

@Article{Roache88,
  author =       {P. J. Roache and D. E. Dietrich},
  title =        {Evaluation of the filtered
  {Leapfrog-Trapezoidal} time integration method},
  journal =      {Num. Heat Transfer},
  year =         {1988},
  volume =       {14},
  pages =        {149--164}}

@Article{Robins01,
  author = 	 {A. Robins and C. McHugh},
  title = 	 {Development and evaluation of the {ADMS} building effects module},
  journal = 	 {Int. J. Env. and Poll.},
  year = 	 {2001},
  volume = 	 {16},
  pages = 	 {161--174}}

@Article{Rodi89,
  author = 	 {W. Rodi and S. Majumdar and B. Sch$\ddot{o}$nung},
  title = 	 {Finite volume methods for two-dimensional
incompressible flows with complex boundaries},
  journal = 	 {Comp. Methods Appl. Mech. Engr.},
  year = 	 {1989},
  volume = 	 {75},
  pages = 	 {369--392}}

@Article{Rodi97,
  author = 	 {W. Rodi and J. H. Ferziger and M. Breuer and M. Pourquie},
  title = 	 {Status of large eddy simulation results of a workshop},
  journal = 	 {ASME J. Fluids Eng.},
  year = 	 {1997},
  volume = 	 {119},
  pages = 	 {248--262}}


@Inproceedings{Rosenfeld99,
  author = 	 {L. K. Rosenfeld and J. D. Paduan and E. T. Petruncio
and J. E. Gocalves},
  title = 	 {Numerical simulations and observations of the internal tide
in a submarine canyon},
  booktitle = 	 {The Proceedings of 11th 'Aha Huliko'a Hawaiian Winter
Workshop.  Honolulu, HI, January 19-22},
  year = 	 {1999},
  volume = 	 {},
  pages = 	 {63-71}}

@Article{Rosenfeld95,
  author = 	 {L. K. Rosenfeld and T. Anderson and
G. Hatcher and J. Roughgarden and Y. Shkedy},
  title = 	 {{Upwelling fronts and barnacle recruitment in central 
California}},
  journal = 	 {MBARI tech. report},
  year = 	 {1995},
  volume = 	 {95-19}}

@Article{Rosenfeld94,
  author =       {L. K. Rosenfeld and F. B. Schwing and N. Garfield
and D. E. Tracy},
  title =        {{Bifurcated flow from an upwelling center: A cold
water source for Monterey Bay}},
  journal =      {Cont. Shelf Res.},
  year =         {1994},
  volume =       {14},
  pages =        {931--964}}


@Article{Rosenfeld91,
  author =       {M. Rosenfeld and D. Kwak and  M. Vinokur},
  title =        {{A fractional step solution method for the unsteady
incompressible Navier-Stokes equations in generalized coordinate systems}},
  journal =      JCP,
  year =         {1991},
  volume =       {94},
  pages =        {102--137}}

@Article{Roshko76,
  author =       {A. Roshko},
  title =        {Structure of turbulent shear flows: A new look},
  journal =      {AIAA Journal},
  year =         {1976},
  volume =       {14},
  pages =        {1349-1357}}

@Article{Rueda03,
  author =       {F. J. Rueda and S. Geoffrey and S. G. Schladow},
  title =        {{Dynamics of large polymictic lake. II: numerical
simulations}},
  journal =      {J. Hydrau. Eng.},
  year =         {2003},
  volume =       {129},
  pages =        {92--101}}

@PhdThesis{Rueda01,
  author = 	 {F. J. Rueda},
  title = 	 {A three-dimensional hydrodynamics and transport model for
lake environments},
  school = 	 {Univ. of California, Davis},
  year = 	 {2001}}

@Article{Ryther69,
  author = 	 {J. H. Ryther},
  title = 	 {Photosynthesis and fish production in the sea},
  journal = 	 {Science},
  year = 	 {1969},
  volume = 	 {166},
  pages = 	 {72--76}}

@ARTICLE{Reszka99,
  author = {M. K. Reszka and G. E. Swaters},
  year = 1999,
  title = {Eddy formation and interaction in a baroclinic frontal geostrophic
          model},
  journal = JPO,
  volume = 29,
  pages = {3025--3042}}

@Book{Saad96,
author={Y. Saad},
title={Iterative methods for sparse linear systems},
publisher={PWS Publishing Company},
Edition={},
address={Boston}, year= 1996}

@Article{Saiki96,
  author =       {E. M. Saiki and S. Biringen},
  title =        {Numerical simulation of a cylinder in uniform flow:
application of a virtual boundary method},
  journal =      JCP,
  year =         {1996},
  volume =       {123},
  pages =        {450--465}}

@Book{Salmon98,
author={R. Salmon},
title={Lectures on Geophysical Fluid Dynamics},
publisher={Oxford Univ. Press},
Edition={},
pages ={378},
address={New York}, year= 1998}

@Article{Salvetti97,
  author =       {M. Salvetti and Y. Zang and R. Street and S. Banerjee},
  title =        {Large eddy simulation of free-surface decaying turbulence
with dynamic subgrid-scale models},
  journal =      PF,
  year =         {1997},
  volume =       {9},
  pages =        {2405--2419}}


@Article{Sanderson98a,
  author =       {B. G. Sanderson},
  title =        {Order and resolution for computational
ocean dynamics},
  journal =      JPO,
  year =         {1998},
  volume =       {28},
  pages =        {1271--1286}}

@Article{Sanderson98b,
  author =       {B. G. Sanderson and G. Brassington},
  title =        {Accuracy in the context of a control-volume model},
  journal =      {Atmos.-Ocean},
  year =         {1998},
  volume =       {36},
  pages =        {355--384}}

@Article{Sanderson98c,
  author =       {B. G. Sanderson and G. Brassington},
  title =        {Fourth- and fifth order finite difference methods applied
to a control volume ocean model},
  journal =      {J. Atmos. Oceanic Technol.},
  year =         {1998},
  volume =       {19},
  pages =        {1424--1441}}

@Article{Saric94,
  author = 	 {W. S. Saric},
  title = 	 {G\"ortler vortices},
  journal = 	 ARFM,
  year = 	 {1994},
  volume = 	 {26},
  pages = 	 {379--409}}

@Article{Saric91,
  author = 	 {W. S. Saric and A. Benmalek},
  title = 	 {G\"ortler vortices with periodic curvature},
  journal = 	 {Boundary Layer Stability and Transition to Turbulence, ASME-FED},
  year = 	 {1991},
  volume = 	 {114},
  pages = 	 {37--42}}

@article{Scandura00,
title = {Three-dimensional oscillatory flow over steep ripples},
author = {P. Scandura and G. Vittori and P. Blondeaux},
journal = JFM,
volume = {412},
pages = {355 -- 378},
month = {},
year = {2000}}

@Article{Schulman00,
  author =       {L. L. Schulman and D. G. Strimaitis and J. S. Scire},
  title =        {Development and evaluation of the {PRIME Plume Rise}
  and building downwash model},
  journal =      {J. Air \& Waste Manage. Assoc.},
  year =         {2000},
  volume =       {50},
  pages =        {378--390}}

@Article{Shearman99,
  author = 	 {R. K. Shearman and J. A. Barth and P. M. Kosro},
  title = 	 {{Diagnosis of the three-dimensional circulation associated
with mesoscale motion in the California Current}},
  journal = 	 JPO,
  year = 	 {1999},
  volume = 	 {29},
  pages = 	 {651--670}}

@Article{Sheng98,
  author = 	 {J. Y. Sheng and D. G. Wright and R. J. Greatbatch
and D. E. Dietrich},
  title = 	 {{CANDIE: A new version of the DieCAST ocean circulation model}},
  journal = 	 {J. Atmos. Oceanic Technol.},
  year = 	 {1998},
  volume = 	 {15},
  pages = 	 {1414--1432}}

@ARTICLE{Shih00,
  author = {L. H. Shih and J. R. Koseff and J. H. Ferziger and C. R. Rehmann},
  year = 2000,
  title = {Scaling and parameterization of stratified homogeneous turbulent
shear flow},
  journal = JFM,
  volume = 412,
  pages = {1--20}}

@Article{Shyy91,
  author = 	 {W. Shyy and  T. C. Vu},
  title = 	 {On the adoption of velocity variable and grid system
for fluid flow computation in curvilinear coordinates},
  journal = 	 JCP,
  year = 	 {1991},
  volume = 	 {92},
  pages = 	 {82--105}}

@Article{Shulman01,
  author = 	 {I. Shulman},
  title = 	 {Personal communication},
  year = 	 {2001}}

@ARTICLE{Shulman02,
  author = {I. Shulman and C. R. Wu and J. K. Lewis and J. D. Paduan
L. K. Rosenfeld and J. C. Kindle and S. R. Ramp and C. A. Collins},
  year = 2002,
  title = {High resolution modeling and data assimilation in the
{Monterey Bay} area},
  journal = {Cont. Shelf Res.},
  volume = 22,
  pages = {1129--1151}}

@ARTICLE{Skyllingstad95,
  author = {E. D. Skyllingstad and D. W. Denbo},
  year = 1995,
  title = {{An ocean large-eddy simulation of Langmuir circulations
and convection in the surface mixed layer}},
  journal = JGR,
  volume = 100,
  pages = {8501--8522}}

@ARTICLE{Skyllingstad00,
  author = {E. D. Skyllingstad and W. D. Smyth and G. B. Crawford},
  year = {2000},
  title = {Resonant wind-driven mixing in the ocean boundary layer},
  journal = JPO,
  volume = 30,
  pages = {1866--1890}}

@ARTICLE{Sleijpen96,
  author = {G. L. G. Sleijpen and H. A. van der Vorst},
  year = {1996},
  title = {{Reliable updated residuals in hybrid Bi-CG methods}},
  journal = {Comput.},
  volume = 56,
  pages = {141--163}}

@Article{Smagorinsky63,
  author =       {J. Smagorinsky},
  title =        {{General circulation experiments with the
primitive equations, I. The basic experiment}},
  journal =      MWR,
  year =         {1963},
  volume =       {91},
  pages =        {99--164}}

@Article{Smith01,
  author = 	 {W. S. Smith and J. M. Reisner and C.Y.J. Kao},
  title = 	 {Simulations of flow around a cubical building:
  comparison with towing-tank data and assessment of radiatively
  induced thermal effects},
  journal = 	 AE,
  year = 	 {2001},
  volume = 	 {35},
  pages = 	 {3811--3821}}

@Article{Smith92,
  author = 	 {R. D. Smith and J. K. Dukowicz and R. C. Malone},
  title = 	 {Parallel ocean general circulation modeling},
  journal = 	 {Physica D.},
  year = 	 {1992},
  volume = 	 {60},
  pages = 	 {38--61}}

@Article{Smyth00,
  author = 	 {W. D. Smyth and J. N. Moum},
  title = 	 {Length scales of turbulence in stably stratified
mixing layer},
  journal = 	 PF,
  year = 	 {2000},
  volume = 	 {12},
  pages = 	 {1327--1342}}

@Inproceedings{Smith02,
  author = 	 {W. S. Smith and M. J. Brown},
  title = 	 {A {CFD}-generated wind field library feasibility study:
{Maximum} wind direction interval},
  booktitle = 	 {Fourth Symposium on the Urban Environment},
  publisher = {American Meteorological Society},
  address = {Norfolk, VA},
  year = 	 {2002},
  volume = 	 {},
  pages = 	 {196--197}}

@Article{Sohankar00,
  author = 	 {A. Sohankar and L. Davidson and C. Norberg},
  title = 	 {Large eddy simulation of flow past a square cylinder:
{Comparison} of different subgrid scale models},
  journal = 	 {ASME J. Fluids Eng.},
  year = 	 {2000},
  volume = 	 {122},
  pages = 	 {39--47}}


@Article{Solomon93,
  author =       {T. H. Solomon and W. J. Holloway and H. L. Swinney},
  title =        {Shear-flow instabilities and Rossby waves in barotropic flow
in a rotating annulus},
  journal =      {Phys. Fluids A},
  year =         {1993},
  volume =       {5},
  pages =        {1971--1982}}

@Article{Song00,
  author =       {Y. T. Song and Y. Chao},
  title =        {An embedded bottom boundary layer formulation for
z-coordinate ocean models},
  journal =      {J. Atmos. Oceanic Technol.},
  year =         {2000},
  volume =       {17},
  pages =        {546--560}}

@Article{Song94,
  author =       {Y. H. Song and D. B. Haidvogel},
  title =        {{A semi-implicit ocean circulation model using a generalized
topography-following coordinate system}},
  journal =      JCP,
  year =         {1994},
  volume =       {115},
  pages =        {228--244}}

@Article{Spalart00,
  author =       {P. R. Spalart},
  title =        {Strategies for turbulence modelling and simulations},
  journal =      IJHFF,
  year =         {2000},
  volume =       {21},
  pages =        {252--263}}

@Article{Staneva01, 
author = {J. V. Staneva and D.E. Dietrich and E.V. Stanev and M.J. Bowman},
title={{Rim current and coastal eddy mechanisms in an eddy-resolving Black Sea
general circulation model}},
journal= {J. Marine Systems},
volume=31, pages={137--157},
year= 2001	}


@Article{Stillinger83, 
author = {D. C. Stillinger and K. N. Helland and C. W. Van Atta},
title={Experiments on the transition of homogeneous turbulence to
internal waves in a stratified fluid},
journal=JFM,
volume=131, pages={91--122},
year= 1983	}

@Article{Stone68, 
author = {H. L. Stone},
title={Iterative solution of implicit approximations of multidimensional partial differential equations},
journal={SIAM J. Num. Anal.},
volume=5, pages={530--558},
year= 1968	}

@Article{Strub00, 
author = {P. T. Strub and C. James},
title={Altimeter-derived variability of surface velocities in the {California}
current system, 2, Seasonal circulation and eddy statistics},
journal={Deep Sea Res., Part II},
volume={47}, pages={831--870},
year= 2000	}

@Article{Strub91,
author = {P. T. Strub and P. M. Kosro and A. Huyer},
title={The nature of the cold filaments in the {California Current} system},
journal=JGR,
volume={96}, pages={14743--14768},
year= 1991	}

@PhdThesis{Tadepalli97,
  author = 	 {S. Tadepalli},
  title = 	 {Numerical simulation and prediction of upwelling flow},
  school = 	 {Stanford University},
  year = 	 {1997}}

@Article{Tadepalli02a,
  author = 	 {S. Tadepalli and J. H. Ferziger and Y. H. Tseng},
  title = 	 {Simulation of coastal upwelling. I. Linear stability and 
the early turbulent regime},
  journal = 	 {Submitted to J. Phy. Oceanogr.},
  year = 	 {2002}}

@Article{Tamamidis93,
  author = 	 {P. Tamamidis and D. N. Assanis},
  title = 	 {Evaluation of various high-order-accuracy
schemes with and without flux limmiters},
  journal = 	 IJNMF,
  year = 	 {1993},
  volume = {16},
  pages = {931--948}}

@Article{Tansley01,
  author =       {C. E. Tansley and D. P. Marshall},
  title =        {Flow past a cylinder on a beta-plane, with application 
to Gulf Stream separation and the Antarctic Circumpolar Current},
  journal =      JPO,
  year =         {2001},
  volume = {31},
  pages = {3274--3283}}

@Article{Theurer96,
  author =       {W. Theurer and E. J. Plate and K. Hoeschele},
  title =        {Semi-empirical models as a combination of
  wind tunnel and numerical dispersion modelling},
  journal =      AE,
  year =         {1996},
  volume = {30},
  pages = {3583--3597}}

@Article{Thompson89,
  author = 	 {J. D. Thompson and W.J. Schmitz},
  title = 	 {A limited-area model of the {Gulf
  Stream: Design}, initial experiments and model-data intercomparison},
  journal = 	 JPO,
  year = 	 {1989},
  volume = 	 {19},
  pages = 	 {791--814}}

@Article{Thorpe77,
  author = 	 {S. A. Thorpe},
  title = 	 {Turbulence and mixing in a Scottish loch},
  journal = 	 {Trans. Roy. Soc. London.},
  year = 	 {1977},
  volume = 	 {A 286},
  pages = 	 {125--181}}

@Article{Thorpe68,
  author = 	 {S. A. Thorpe},
  title = 	 {On standing internal gravity waves of finite amplitude},
  journal = 	 JFM,
  year = 	 {1968},
  volume = 	 {32},
  pages = 	 {693--704}}

@Article{Tisch97,
  author = 	 {T. D. Tisch and S. R. Ramp},
  title = 	 {{Moored observations of the current and temperature
structure over the continental slop off central California, 2, The
energetics of the flow off Point Sur}},
  journal = 	 JGR,
  year = 	 {1997},
  volume = 	 {102},
  pages = 	 {22903--22920}}

@Article{Tisch92,
  author = 	 {T. D. Tisch and S. R. Ramp and C. A. Collins},
  title = 	 {{Observations of the geostrophic current
and water mass charcacteristics off Point Sur California, from
May 1988 through November 1989}},
  journal = 	 JGR,
  year = 	 {1992},
  volume = 	 {97},
  pages = 	 {12535--12555}}

@Article{Townsend00,
  author = 	 {T. L. Townsend and H.E. Hurlburt and P.J. Hogan},
  title = 	 {{Modeled Sverdrup flow in the North Atlantic
from 11 different wind stress climatologies}},
  journal = 	 {Dyn. Atmos. Oceans.},
  year = 	 {2000},
  volume = 	 {32},
  pages = 	 {373--417}}

@Article{Traganza80,
  author =       {E. D. Traganza and D. A. Nestor and A. K. McDonald},
  title =        {Satellite observations of a nutrient upwelling off
the coast of {California}},
  journal =      JGR,
  year =         {1980},
  volume = {85},
  pages = {4101--4106}}

@ARTICLE{Tritton59,
  author = {D. J. Tritton},
  year = 1959,
  title = {Experiments on the flow past a circular cylinder at low
Reynolds number},
  journal = JFM,
  volume = 6,
  pages = {547--567}}

@Article{Tseng01,
  author = 	 {Y. H. Tseng and J. H. Ferziger},
  title = 	 {Mixing and available potential energy in
stratified flows},
  journal = 	 PF,
  year = 	 {2001},
  volume = 	 {13},
  pages = 	 {1281--1293}}

@Article{Tseng01a,
  author = 	 {Y. H. Tseng and J. H. Ferziger and A. Jameson},
  title = 	 {Using high order local extremum diminishing schemes
to study density interface in upwelling simulation},
  journal = 	 {J. Compu. Phys.(in preparation)},
  year = 	 {2001},
  volume = 	 {},
  pages = 	 {}}

@Inproceedings{Tseng01b,
  author = 	 {Y. H. Tseng and J. H. Ferziger},
  title = 	 {The effects of coastal geometry on turbulent mixing
in upwelling flows},
  booktitle = 	 {The Proceedings of 2nd Int. Symp. of Turbulence and
Shear Flow Phenomena, Stockholm, Sweden, 27-29 June},
  year = 	 {2001},
  volume = 	 {},
  pages = 	 {}}

@Article{Tseng01c,
  author = 	 {Y. H. Tseng and J. H. Ferziger},
  title = 	 {Effects of coastal geometry and the formation
of cyclonic/anti-cyclonic eddies on turbulent mixing in upwelling simulation},
  journal = 	 {J. Turbulence},
  year = 	 {2001},
  volume = 	 {2},
  pages = 	 {014}}

@Article{Tseng03,
  author = 	 {Y. H. Tseng and J. H. Ferziger},
  title = 	 {A ghost-cell immersed boundary method
for flow in complex geometry},
  journal = 	 JCP,
  year = 	 {2003},
  volume = 	 {192},
  pages = 	 {593-623}}

@PhdThesis{Tseng03t,
  author = 	 {Y. H. Tseng},
  title = 	 {On the development of a ghost-cell immersed boundary
method and its application to large eddy simulation and geophysical fluid
dynamics},
  school = 	 {Stanford University},
  year = 	 {2003}}

@Article{Tseng03a,
  author = 	 {Y. H. Tseng and D. E. Dietrich and J. H. Ferziger},
  title = 	 {Numerical simulation of regional circulation in the
Monterey Bay region},
  journal = 	{Center for Turbulent Research, Stanford/Annual Research Brief},
  year = 	 {2003},
  pages = 	 {115-126}}


@Article{Tseng05a,
  author = 	 {Y. H. Tseng and D. E. Dietrich and J. H. Ferziger},
  title = 	 {Regional circulation of the {Monterey Bay} region-
{Hydrostatic} versus {Non-hydrostatic} modeling},
  journal = 	 JGR,
  year = 	 {2005},
  volume = 	 {110},
  pages = 	 {doi:10.1029/2003JC002153}}

@Article{Tseng04b,
  author = 	 {Y. H. Tseng and D. E. Dietrich},
  title = 	 {Guide for the DieCAST Ocean Model},
  journal = 	 {http://fluid.stanford.edu/~yhtseng/research/DIECAST},
  year = 	 {2005}}

@Article{Tseng04c,
  author = 	 {Y. H. Tseng and J. H. Ferziger},
  title = 	 {Large-eddy simulation of turbulent wavy boundary flow -
illustration of vortex dynamics},
  journal = 	 {J. Turbulence},
  year = 	 {2004},
  volume = 	 {5},
  pages = 	 {34}}

@Article{Tseng06b,
  author = 	 {Y. H. Tseng and D. E. Dietrich},
  title = 	 {Entrainment and transport in idealized three-dimensional
gravity current simulation},
  journal = 	 {J. Atmos. Oceanic Technol.},
  year = 	 {2006},
  volume = 	 {23},
  pages = 	 {1249-1269}}

@Article{Tseng06a,
  author = 	 {Y. H. Tseng and C. Meneveau and M. B. Parlange},
  title = 	 {Modelling flow around bluff bodies and urban dispersion
using large eddy simulation},
  journal = 	 {Environ. Sci. Tech. },
  year = 	 {2006},
  volume = 	 {40},
  pages = 	 {2653-2662}}


@Article{Tseng04f,
  author = 	 {Y. H. Tseng and C. Meneveau and M. B. Parlange},
  title = 	 {Modelling flow around bluff bodies and urban dispersion
using large eddy simulation. {Part II: Application}},
  journal = 	 {in preparation},
  year = 	 {2004},
  volume = 	 {},
  pages = 	 {}}

@Article{Udaykumar01,
  author =       {H. S. Udaykumar and R. Mittal and
P. Rampunggoon and A. Khanna},
  title =        {{A sharp interface Cartesian grid method
for simulating flows with complex moving boundaries}},
  journal =      JCP,
  year =         {2001},
  volume =       {174},
  pages =        {345--380}}


@Article{Van92,
  author = 	 {H. A. {Van der Vorst}},
  title = 	 {{Bi-CGSTAB: A fast and smoothly converging variant
of Bi-CG for the solution of non-symmetric linear systems}},
  journal = 	 {SIAM J. Sci. Stat. Comput.},
  year = 	 {1992},
  volume = 	 {13},
  pages = 	 {631--644}}
%SIAM Jounral of Scientific and Statistical Computin

@Article{Van57,
  author = 	 {I. {Van der Hoven}},
  title = 	 {Power spectrum of horizontal wind speed
in the frequency range from 0.0007 to 900 cycles per hour},
  journal = 	 {J. Meteor.},
  year = 	 {1957},
  volume = 	 {14},
  pages = 	 {160--164}}

@Article{Venayagamoorthy06,
  author = 	 {S. K. Venayagamoorthy and O. B. Fringer},
  title = 	 {Numerical simulations of the interaction of internal waves with a shelf break},
  journal = 	 PF,
  year = 	 {2006},
  volume = 	 {18},
  pages = 	 {doi:10.1063/1.2221863}}

@Article{Verzicco00a,
  author = 	 {R. Verzicco and J. Mohd-Yusof and P. Orlandi and D. Haworth},
  title = 	 {Large eddy simulation in complex geometry configurations
using boundary body forces},
  journal = 	 {AIAA Journal},
  year = 	 {2000},
  volume = 	 {38},
  pages = 	 {427--433}}

@Inproceedings{Verzicco00b,
  author =       {R. Verzicco and G. Iaccarino and M. Fatica and P. Orlandi},
  title =        {Flow in an impeller stirred tank using an
immersed boundary method},
  booktitle =      {Annual Research Briefs},
  year =         {2000},
  organization = {{NASA Ames Research Center/Stanford Univ. Center for
Turbulence Research}},
  address = {Stanford, CA},
  pages =        {251--261}}

@ARTICLE{Walton02,
  author = {A. Walton and A.Y.S. Cheng},
  year = {2002},
  title = {Large-eddy simulation of pollution dispersion in an urban street canyon:
  {Part II: Idealised canyon simulation}},
  journal = AE,
  volume = {36},
  pages = {3615--3627}}

@ARTICLE{Wang98,
  author = {D. Wang and J. C. McWilliams and W. G. Large},
  year = 1998,
  title = {Large eddy simulation of the diurnal cycle of deep equatorial
turbulence},
  journal = JPO,
  volume = 28,
  pages = {129--148}}

@ARTICLE{Warner04,
  author = {S. Warner and N. Platt and J. F. Heagy},
  year = 2004,
  title = {Comparisons of transport and dispersion model
  predictions of the URBAN 2000 field experiment },
  journal = {J. Appl. Me},
  volume = 46,
  pages = {829--846}}

@Article{Wiin-Nielsen62,
  author = 	 {A. Wiin-Nielson},
  title = 	 { On the transformation of kinetic energy between
  vertical shear flow and the vertical mean flow in the atmosphere},
  journal = 	 MWR,
  year = 	 {1962},
  volume = 	 {90},
  pages = 	 {311--323}}

@Article{Williams04,
  author = 	 {M. D. Williams and M. J. Brown and
  D. Boswell and B. Singh and E. Pardyjak},
  title = 	 {Testing of the {QUIC-PLUME} model with
  wind-tunnel measurements for a high-rise building},
  journal = 	 {5th AMS Urban Env. Conf.},
  year = 	 {2004},
  volume = 	 {},
  pages = 	 {Vancouver, B.C.}}


@Article{Winters94,
  author = 	 {K. B. Winters and E. A. D'Asaro},
  title = 	 {Three-dimensional wave breaking near a critical level},
  journal = 	 JFM,
  year = 	 {1994},
  volume = 	 {272},
  pages = 	 {255--284}}

@Article{Winters95, 
author = {Kraig B. Winters and Peter N. Lombard and James J. Riley and
Eric A. D'Asaro},
title={Available potential energy and mixing in density-stratified
fluids},
journal=JFM,
volume=289, pages={115--128},
year= 1995	}

@Article{Winters96, 
author = {Kraig B. Winters and Eric A. D'Asaro},
title={Diascalar flux and the rate of fluid mixing},
journal=JFM,
volume=317, pages={179--193},
year= 1996	}


@Article{Winton98,
  author = 	 {M. Winton and R. Hallberg and A. Gnanadesikan},
  title = 	 {Simulation of density driven frictional downslope flow
in z-coordinate ocean models},
  journal = 	 JPO,
  year = 	 {1998},
  volume = 	 {28},
  pages = 	 {2163--2174}}

@article{Xu97,
title = {High resolution numerical simulation of ideal and non-ideal 
compressible reacting flows with embedded internal boundaries},
author = {S. J. Xu and T. Aslam and D. S. Stewart},
journal = {Combustion Theory and Modelling},
volume = {1},
number = {1},
pages = {113 -- 142},
month = {},
year = {1997}}
@Article{Yanase93,
  author = 	 {S. Yanase and C. Flores and O. M\'etais and  J. J. Riley},
  title = 	 {{Rotating free-shear flows. 1. Linear-stability analysis}},
  journal = 	 {Phys. Fluids A},
  year = 	 {1993},
  volume = 	 {5},
  pages = 	 {2725--2737}}

@Article{Ye99,
  author =       {T. Ye and  R. Mittal and H. S. Udaykumar and W. Shyy},
  title =        {An accurate {Cartesian} grid method for viscous
incompressible flows with complex immersed boundaries},
  journal =      JCP,
  year =         {1999},
  volume =       {156},
  pages =        {209--240}}


@Article{Zang95a,
  author = 	 {Y. Zang and  R. L. Street},
  title = 	 {Numerical simulation
of coastal upwelling and interfacial instability of a rotating and
stratified fluid},
  journal = 	 JFM,
  year = 	 {1995},
  volume = 	 {305},
  pages = 	 {47--75}
}

@Article{Zang95b,
  author =       {Y. Zang and  R. L. Street},
  title =        {A composite multigrid method for calculating unsteady
incompressible flows in geometrically complex domains},
  journal =      IJNMF,
  year =         {1995},
  volume =       {20},
  pages =        {341--361}}

@Article{Zang94,
  author =       {Y. Zang and  R. L. Street and J. R. Koseff},
  title =        {{A non-staggered grid, fractional step method for
time-dependent incompressible Navier-stokes equations in curvilinear
coordinates}},
  journal =      JCP,
  year =         {1994},
  volume =       {114},
  pages =        {18--33}}

@PhdThesis{Zang93t,
  author = 	 {Y. Zang},
  title = 	 {On the development of tools for the
simulation of geophysical flows},
  school = 	 {Stanford University},
  year = 	 {1993}}

@Article{Zang93,
  author = 	 {Y. Zang and  R. L. Street and J. R. Koseff},
  title = 	 {A dynamic mixed subgrid-scale model and 
its application to turbulent recirculating flows},
  journal = 	 PF,
  year = 	 {1993},
  volume = 	 {A(5)},
  pages = 	 {3186--3196}
}

@Article{Zajic02,
  author =       {D. Zajic and H. J. S. Fernando and M. Brown and M. Nelson},
  title =        {A field study of flow around a building},
  journal =      {Bull. Amer. Phys. Soc.},
  year =         {2002},
  volume =       {47},
  pages =        {166}}

@Article{Zedler01b,
  author =       {E. A. Zedler and R. L. Street},
  title =        {{Large-eddy simulation of sediment transport:
Currents over ripples}},
  journal =      {J. Hydrau. Eng.},
  year =         {2001},
  volume =       {127},
  pages =        {444--452}}

@Inproceedings{Zedler01a,
  author = 	 {E. A. Zedler and R. L. Street},
  title = 	 {{Large eddy simulations: Sediment transport in waves
over ripples}},
  booktitle = 	 {The Proceedings of 3rd Int. Symp. on Environmental
Hydraulics, Tempe, USA, 5-8 December},
  year = 	 {2001},
  volume = 	 {},
  pages = 	 {}}

@PhdThesis{Zedler02,
  author = 	 {E. A. Zedler},
  title = 	 {Large eddy simulation of sediment transport in oscillatory
flow over wavy terrain},
  school = 	 {Stanford University},
  year = 	 {2002}}


@Book{Zilitinkevich91,
author={S. S. Zilitinkevich},
title={Turbulent Penetrative Convection},
publisher={Aldershot},
address={Brookfield, USA},
year= 1991}

@PhdThesis{Zhou99,
  author = 	 {H. Zhou},
  title = 	 {{Numerical simulation of langmuir circulations in a wavy
domain and its comparison with the Craik-Leibovich theory}},
  school = 	 {Stanford University},
  year = 	 {1999}
}


@phdthesis{Tseng02,
author={Y. H. Tseng},
year=2003,
school={Stanford University},
title={{Data assimilation}}}


