%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%%%%%%%%%%%%%%                                    FILTERING                                              %%%%%%%%%%%%%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

@article{hesthaven08b,
Author = {Hesthaven, Jan S. and Kirby, Robert M.},
Title = {{Filtering in Legendre spectral methods}},
Journal = {{Mathematics of Computation}},
Year = {{2008}},
Volume = {{77}},
Number = {{263}},
Pages = {{1425-1452}},
}
	
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%%%%%%%%%%%%%%                          TRACER ADVECTION PAPERS                                          %%%%%%%%%%%%%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

@article{budgell07,
Author = {Budgell, William Paul and Oliveira, Anabela and Skogen, Morten D.},
Title = {{Scalar advection schemes for ocean modelling on unstructured triangular
   grids}},
Journal = {Ocean Dynamics},
Year = {2007},
Volume = {57},
Number = {4-5},
Pages = {339-361},
Month = {OCT},
}


@article{iskandarani05,
Author = {Iskandarani, M and Levin, J C and Choi, B J and Haidvogel, D B},
Title = {{Comparison of advection schemes for high-order h-p finite element and
   finite volume methods}},
Journal = {{Ocean Modelling}},
Year = {2005},
Volume = {10},
Number = {1-2},
Pages = {233-252},
}

@article{ hanert04,
Author = {Hanert, E and Le Roux, D Y and Legat, V and Deleersnijder, E},
Title = {{Advection schemes for unstructured grid ocean modelling}},
Journal = {Ocean Modelling},
Year = {2004},
Volume = {7},
Number = {1-2},
Pages = {39-58},
}

@article{ hect95,
Author = {Hecht, M. W. and Holland, W. R. and Rasch, P. J.},
Title = {{Upwind-Weighted Advection Schemes for Ocean Tracer Transport - an
   Evaluation in a Passive Tracer Context
}},
Journal = {{Journal Of Geophysical Research-Oceans}},
Year = {1995},
Volume = {100},
Number = {C10},
Pages = {20763-20778},
}

@article{levy01,
Author = {Marina L\'evy and Audrey Estublier and Gurvan Madec},
Title = {{Choice of an Advection Scheme for Biogeochemical Models}},
Journal = {{Geophysical Research Letters}},
Year = {{2001}},
Volume = {{28}},
number = {19},
Pages = {{3725-3728}},
}

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%%%%%%%%%%%%%%                      BIOGEOCHEMICAL REACTION EQUATIONS PAPERS                             %%%%%%%%%%%%%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
@article{oschlies00,
Author = {Oschlies, A.},
Title = {{Equatorial nutrient trapping in biogeochemical ocean models: The role of advection numerics}},
Journal = {{Global Biogeochem. Cycles}},
Year = {{2000}},
Volume = {{14}},
Pages = {{655– 667}},
}


@BOOK{fennel04,
   author = "W. Fennel and T. Neumann",
   title = "Introduction to the modelling of marine ecosystems",
   series = "Elsevier Oceanography Series",
   volume = {72},
   month = "jan",
	 publisher = "Elsevier",
   address = "New York, NY",   
   year = "2004",   
}
@BOOK{lalli97,
   author = "Carol Lalli and Timothy Parsons",
   title = {{Biological Oceanography: An Introduction}},
   month = "May",
	 publisher = "Butterworth-Heinemann",
	 edition = {2$^{nd}$},  
   year = "1997",   
}

@BOOK{seav12,
author =  {A. R. Robinson and J. J. McCarthy and B. J. Rothschild}, 
   title = {{Biological-Physical Interactions in the Sea}},
   volume = 12,
   series = "The Sea",
   publisher = "John Wiley \& Sons, Inc.",
   address = "New York, NY",
	 year = 2002
}

@article{flierl02,
author =  {Flierl, G. and D. J. McGillicuddy}, 
title = {{Mesoscale and Submesoscale Physcial-Biological Interactions}},
journal = {The Sea},
volume = {12},
editor = "A. R. Robinson and J. J. McCarthy and B. J. Rothschild",
pages = {1-74},
year = 2002
}

@article{hofmann02,
author =  {Eileen E. Hofmann and Marjorie A. M. Friedrichs}, 
title = {Predictive modeling for marine ecosystems},
journal = {The Sea},
volume = {12},
editor = "A. R. Robinson and J. J. McCarthy and B. J. Rothschild",
pages = {537-565},
year = 2002
}

@article{besiktepe02,
author =  {Besiktepe, S. T. and P. F. J. Lermusiaux and A. R. Robinson}, 
title = {{Coupled physical and biogeochemical data-driven simulations of Massachusetts Bay in late summer: real-time and postcruise data assimilation}},
journal = {Journal of Marine Systems},
volume = {40},
pages = {171-212},
year = 2002
}

@MASTERSTHESIS{lisathesis,
   author = "Lisa Janelle Burton",
   title = {{Modeling Coupled Physics and Biology in Ocean Straits with Application to the San Bernardino Strait in the Philippine Archipelago}},
   school = "Massachusetts Institute of Technology",
   type = "$\mathrm{S.M.}$ Thesis",
   address = "Department of Mechanical Engineering",
   month = may,
   year = 2009,
}

@TECHREPORT{robinson99,
	author = {A. R. Robinson and P. F. J. Lermusiaux},
	title = {{Report of a Workshop on the Assimilation of Biological Data in Coupled Physical/Ecosystem Models}},
	number = "3",
	type = {GLOBEC Special Contribution},
	address = "Bologna, Italy",	
	year = {1999}
}

@article{fasham90,
	author = "Fasham, M. J. R. and Ducklow, H. W. and McKelvie, S. M.",
	title = "A nitrogen-based model of plankton dynamics in the oceanic mixed layer",
	journal = "Journal of Marine Research",
	volume = "48",
	year = "1990",
	month ="aug",	
	pages = "591-639(49)",
	}

@article{spitz05,
author = {Y.H. Spitz and J.S. Allen and J. Gan},
title = {Modeling of ecosystem processes on the Oregon shelf during the 2001 summer upwelling},
journal = {Journal of Geophysical Research},
volume = {110},
pages = {C10S17},
year = {2005},
}

@article{ji08,
author = "Rubao Ji and Cabell Davis and Changsheng Chen and Robert Beardsley",
title = {{Influence of local and external processes on the annual nitrogen cycle and primary productivity on Georges Bank: A 3-D biological-physical modeling study}},
journal = "Journal of Marine Systems",
volume = "73",
number = "1-2",
pages = "31 - 47",
year = "2008",
}

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%%%%%%%%%%%%%%                                 Mesh generation                                                 %%%%%%%%%%%%%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

@article{persson04,
author = {Persson, P. O. and G. Strang},
title = {{A Simple Mesh Generator in MATLAB}},
journal = {SIAM Review},
volume = {46},
number = {2},
pages = {329-345},
year = {2004}
}

@article{remacle09,
author = {C. Geuzaine and J. -F. Remacle},
title = {Gmsh: a three-dimensional finite element mesh generator with built-in pre- and post-processing facilities},
journal = {International Journal for Numerical Methods in Engineering},
volume = {79},
number = {11},
pages = {1309-1331},
year = {2009}
}

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%%%%%%%%%%%%%%                                 DG PAPERS                                                 %%%%%%%%%%%%%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%


@misc{lambrechts10,
author = {J. Lambrechts and J.-F. Remacle1 and K. Hillewaert},
title = {Efficient assembly of high order continuous and discontinuous Finite element operators},
year = {2010},
note = {{IMUM2010 - 9th International workshop on Multiscale (Un)-structured mesh
numerical Modeling for coastal, shelf, and global ocean dynamics}},
url = "http://mseas.mit.edu/IMUM2010/",
}

@phdthesis{ueckermann09,
   Author = "Mattheus P. Ueckermann",
   Title = {{Towards Next Generation Ocean Models: Novel Discontinuous Galerkin Schemes for 2$\mathrm {D}$ unsteady biogeochemical models}},
   school = "Massachusetts Institute of Technology",
   type = "$\mathrm{S.M. T}$hesis",
   address = "Department of Mechanical Engineering",
   month = sep,
   year = 2009,
}

@TECHREPORT{reed73,
 	 author = {W. H. Reed and T. R. Hill},
 	 title = {Triangular mesh methods for the neutron transport equations},   
 	 institution = "Fanstord University",
   type = "Los Alamos Scientific Laboratory Report",
   number = "LA-UR-73-479",
   year = 1973,
}
@TECHREPORT{carpenter94,
	author = {M. H. Carpenter and C. Kennedy},
	title = {{Fourth-order 2N-storage Runge-Kutta schemes}},
	number = "TM 109112",
	type = {NASA Report},
	address = "NASA Langley Research Center",	
	year = {1994}
}
@PHDTHESIS{bernardthesis,
   author = "{\'{P}}aul-Emile Bernard",
   title = {{Discontinuous Galerkin methods for geophysical flow modeling}},
   school = "Universit\'e Catholique de Louvain",
   type = "$\mathrm{PhD}$ Thesis",
   address = "Facult\'e des Sciences Appliqu\'es",
   month = oct,
   year = 2008,
}

@article{bernard09,
Author = {Bernard, P. -E. and Remacle, J. -F. and Legat, V.},
Title = {{Boundary discretization for high-order discontinuous Galerkin
   computations of tidal flows around shallow water islands}},
Journal = {{International Journal For Numerical Methods in Fluids}},
Year = {{2009}},
Volume = {{59}},
Number = {{5}},
Pages = {{535-557}},
Month = {{FEB 20}},
Abstract = {{In this paper some preliminary results concerning the application of
   the high-order discontinuous Galerkin (DG) method for the resolution of
   realistic problems of tidal flows around shallow water islands are
   presented. In particular, tidal flows are computed around the Rattray
   island located in the Great Barrier Reef. This island is a standard
   benchmark problem well documented in the literature providing useful in
   situ measurements for validation of the model. Realistic elements of
   the simulation are a Old flow forcing, a variable bathymetry and a
   non-trivial coastline.
   The computation of tidal flows in shallow water around an island is
   very similar to the simulation of the Eider equations around bluff
   bodies in quasi-steady flows. The main difference lies in the high
   irregularity of islands' shapes and in the fact that, in the framework
   of large-scale ocean models, the number of elements to represent an
   island is drastically limited compared with classical engineering
   computations. We observe that the high-order DG method applied to
   shallow water flows around bluff bodies with poor linear boundary
   representations produces oscillations and spurious eddies. Surprisingly
   those eddies may have the right size and intensity but may be generated
   by numerical diffusion and are not always mathematically relevant.
   Although not interested in solving accurately the boundary layers of an
   island, we show that a high-order boundary representation is mandatory
   to avoid non-physical eddies and spurious oscillations. It is then
   possible to parametrize accurately the subgrid-scale processes to
   introduce the correct amount of diffusion in the model. The DG results
   around the Rattray island are eventually compared with current
   measurements and reveal good agreement. Copyright (C) 2008 John Wiley
   \& Sons, Ltd.}},
Publisher = {{JOHN WILEY \& SONS LTD}},
Address = {{THE ATRIUM, SOUTHERN GATE, CHICHESTER PO19 8SQ, W SUSSEX, ENGLAND}},
Type = {{Article}},
Language = {{English}},}
	

@article{bassi97,
 	author = {F. Bassi and S. Rebay},
 	title = {{A high-order accurate discontinuous Galerkin finite element method for the numerical solution of the compressible Navier-Stokes equations}},  
 	journal = {Journal of Computational Physics},
	volume = {131},
	pages = {267-279},
	year = {1997}	 
}
@article{cockburn89a,
author = {Cockburn, B. and Shu, C. W.},
title = {{TVB Runge-Kutta Local Projection Discontinuous Galerkin Finite-Element Method For Conservation-Laws .2. General Framework}},
journal = {Mathematics of Computation},
volume = {52},
number = {186},
pages = {411-435},
year = {1989}
}
@article{cockburn89b,
author = {Cockburn, B. and Lin, S. Y. and Shu, C. W.},
title = {{TVB Runge-Kutta Local Projection Discontinuous Galerkin Finite-Element Method For Conservation-Laws .3. One-Dimensional Systems}},
journal = {Journal of Computational Physics},
volume = {84},
number = {1},
pages = {90-113},
year = {1989}
}
@article{cockburn90,
author = {Cockburn, B. and Hou, S. C. and Shu, C. W.},
title = {{The Runge-Kutta Local Projection Discontinuous Galerkin Finite-Element Method For Conservation-Laws .4. The Multidimensional Case}},
journal = {Mathematics of Computation},
volume = {54},
number = {190},
pages = {545-581},
year = {1990}
}
@article{cockburn98,
author = {Cockburn, B. and Shu, C. W.},
title = {{The Runge-Kutta discontinuous Galerkin method for conservation laws V - Multidimensional systems}},
journal = {Journal of Computational Physics},
volume = {141},
number = {2},
pages = {199-224},
abstract = {This is the fifth paper in a series in which we construct and study the so-called Runge-Kutta discontinuous Galerkin method for numerically solving hyperbolic conservation laws. In this paper, we extend the method to multidimensional nonlinear systems of conservation laws. The algorithms are described and discussed, including algorithm formulation and practical implementation issues such as the numerical fluxes, quadrature rules, degrees of freedom, and the slope limiters, both in the triangular and the rectangular element cases. Numerical experiments for two-dimensional Euler equations of compressible gas dynamics are presented that show the effect of the (formal) order of accuracy and the use of triangles or rectangles on the quality of the approximation. (C) 1998 Academic Press.},
year = {1998}
}
@article{cockburn98b,
author = {Cockburn, B. and Shu, C. W.},
title = {{The Local Discontinuous Galerkin Method for Time-Dependent Convection-Diffusion Systems.}},
journal = {SIAM Journal of Numerical Analysis},
volume = {35},
number = {6},
pages = {2440-2463},
month = {dec},
year = {1998}
}

@BOOK{cockburn98c,
   author = "Cockburn, B.",
   title = "An introduction to the discontinuous Galerkin method for convection dominated flows",
   series = "In: Quarteroni, A. (Ed.), Advanced Numerical Approximation of Nonlinear Hyperbolic Equations.",
   publisher = "Springer-Verlag",
   pages = {151–268},
   address = "New York, NY",
   year = "1998",   
}

@article{cockburn03,
Author = {Cockburn, B and Luskin, M and Shu, C W and Suli, E},
Title = {{Enhanced accuracy by post-processing for finite element methods for
   hyperbolic equations}},
Journal = {{Math. Comput.}},
Year = {2003},
Volume = {72},
Number = {242},
Pages = {577-606},
Abstract = {{We consider the enhancement of accuracy, by means of a simple
   post-processing technique, for finite element approximations to
   transient hyperbolic equations. The post-processing is a convolution
   with a kernel whose support has measure of order one in the case of
   arbitrary unstructured meshes; if the mesh is locally translation
   invariant, the support of the kernel is a cube whose edges are of size
   of the order of Deltax only. For example, when polynomials of degree k
   are used in the discontinuous Galerkin (DG) method, and the exact
   solution is globally smooth, the DG method is of order k + 1/2 in the
   L-2-norm, whereas the post-processed approximation is of order 2k + 1;
   if the exact solution is in L-2 only, in which case no order of
   convergence is available for the DG method, the post-processed
   approximation converges with order k + 1/2 in L-2(Omega(0)), where
   Omega(0) is a subdomain over which the exact solution is smooth.
   Numerical results displaying the sharpness of the estimates are
   presented.}},
}

@article{cockburn09,
author = {Cockburn, B. and Gopalakrishnan, J. and Lazarov, R.},
title = {{Unified Hybridization Of Discontinuous Galerkin, Mixed, And Continuous Galerkin Methods For Second Order Elliptic Problems}},
journal = {SIAM Journal on Numerical Analysis},
volume = {47},
number = {2},
pages = {1319-1365},
abstract = {We introduce a unifying framework for hybridization of finite element methods for second order elliptic problems. The methods fitting in the framework are a general class of mixed-dual finite element methods including hybridized mixed, continuous Galerkin, nonconforming, and a new, wide class of hybridizable discontinuous Galerkin methods. The distinctive feature of the methods in this framework is that the only globally coupled degrees of freedom are those of an approximation of the solution defined only on the boundaries of the elements. Since the associated matrix is sparse, symmetric, and positive definite, these methods can be efficiently implemented. Moreover, the framework allows, in a single implementation, the use of different methods in different elements or subdomains of the computational domain, which are then automatically coupled. Finally, the framework brings about a new point of view, thanks to which it is possible to see how to devise novel methods displaying very localized and simple mortaring techniques, as well as methods permitting an even further reduction of the number of globally coupled degrees of freedom.},
year = {2009}
}

@article{qiu05,
author = {J Qiu and C W Shu},
title = {{Runge-Kutta Discontinuous Galerkin Method using WENO Limiters}},
journal = {SIAM Journal of Scientific Computing},
volume = {26},
number = {3},
pages = {907–929},
year = {2005}
}

@techreport{persson06,
	author = {P. O. Persson and J. Peraire},
	title = {{Sub-cell shock capturing for discontinuous Galerkin methods}},
	number = "2006-112",
	type = {{AIAA}},
	month = "jan",	
	year = {2006}
}

@article{krivodonova07,
author = {Krivodonova, L.},
title = {{Limiters for high-order discontinuous Galerkin methods}},
journal = {Journal of Computational Physics},
volume = {226},
number = {1},
pages = {276-296},
year = {2007}
}
@article{hoteit04,
author = {H. Hoteit and Ph. Ackerer and R. Mosé and J. Erhel and B. Philippe},
title = {{New two-dimensional slope limiters for discontinuous Galerkin methods on arbitrary meshes}},
journal = {International Journal for Numerical Methods in Engineering},
volume = {61},
number = {14},
pages = {2566–2593},
year = {2004}
}

@article{kubatko09,
author = {Ethan J. Kubatko and Shintaro Bunya and Clint Dawson and Joannes J. Westerink and Christ Mirabito},
title = {{A Performance Comparison of Continuous and Discontinuous Finite Element Shallow Water Models}},
journal = {Journal of Scientific Computing},
volume = {40},
pages = {315-339},
year = {2009}
}

@article{dawson04,
author = {Clint Dawson and Shuyu Sun and Mary F. Wheeler},
title = {{Compatible algorithms for coupled flow and transport}},
journal = {Comput. Methods Appl. Mech. Engrg.},
volume = {193},
pages = {2565-2580},
year = {2004}
}

@article{hesthaven02,
author = {Jan S. Hesthaven and Tim Warburton},
title = {{Nodal High-Order Methods on Unstructured Grids}},
journal = {Journal of Computational Physics},
volume = {181},
pages = {186-221},
year = {2002}
}
@BOOK{hesthaven08a,
   author = "Jan S. Hesthaven and Tim Warburton",
   title = {{Nodal Discontinuous Galerkin Methods}},
   volume = 54,
   series = "Texts in Applied Mathematics",
   publisher = "Springer",
   address = "New York, NY",
   year = "2008",   
}
@article{slimn5,
author = {Bernard, P. E. and Deleersnijder, E. and Legat, V. and Remacle, J. F.},
title = {{Dispersion analysis of discontinuous Galerkin schemes applied to Poincare, Kelvin and Rossby waves}},
journal = {Journal of Scientific Computing},
volume = {34},
pages = {26-47},
year = {2008}
}

@article{nguyen09,
author = {Nguyen, N. C. and Peraire, J. and Cockburn, B.},
title = {{An implicit high-order hybridizable discontinuous Galerkin method for linear convection-diffusion equations}},
journal = {Journal of Computational Physics},
volume = {228},
number = {9},
pages = {3232-3254},
abstract = {We present a hybridizable discontinuous Galerkin method for the numerical solution of steady and time-dependent linear convection-diffusion equations. We devise the method as follows. First, we express the approximate scalar variable and corresponding flux within each element in terms of an approximate trace of the scalar variable along the element boundary. We then define a unique value for the approximate trace by enforcing the continuity of the normal component of the flux across the element boundary; a global equation system solely in terms of the approximate trace is thus obtained. The high number of globally coupled degrees of freedom in the discontinuous Galerkin approximation is therefore significantly reduced. If the problem is time-dependent, we discretize the time derivative by means of backward difference formulae. This results in efficient schemes capable of producing high-order accurate solutions in space and time. Indeed, when the time-marching method is (p + 1)th order accurate and when polynomials of degree p >= 0 are used to represent the scalar variable, the flux and the approximate trace, we observe that the approximations for the scalar variable, the flux and the trace of the scalar variable converge with the optimal order of p + 1 in the L-2-norm. Finally, we introduce a simple element-by-element postprocessing scheme to obtain new approximations of the flux and the scalar variable. The new approximate flux, which has a continuous inter-element normal component, is shown to converge with order p + 1 in the L-2-norm. The new approximate scalar variable is shown to converge with order p + 2 in the L-2-norm. For the time-dependent case, the postprocessing does not need to be applied at each time-step but only at the times for which an enhanced solution is required. Moreover, the postprocessing procedure is less expensive than the solution procedure, since it is performed at the element level. Extensive numerical results are presented to demonstrate the convergence properties of the method. Published by Elsevier Inc.},
year = {2009},
}
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%%%%%%%%%%%%%%                          GENERAL FEM REFS                                                 %%%%%%%%%%%%%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

@BOOK{strang73,
   author = "G. Strang and G. J. Fix",
   title = {{An Analysis of the Finite Element Method}},
   publisher = "Prentice Hall",
   address = "Englewood Cliffs, NJ",
   year = "1973",   
}
@BOOK{solin03,
   author = "P. Solin and K. Segeth and I. Dolezel",
   title = {{Higher-Order Finite Element Methods}},
   publisher = "Chapman \& Hall/CRC Press",
   year = "2003",   
}
@PHDTHESIS{mavriplis89,
   author = "C. A. Mavriplis",
   title = {{Nonconforming Discretization and a Posteriori Error Estimators for Adaptive Spectral Element Techniques}},
   school = "MIT",
   type = "$\mathrm{PhD}$ Thesis",
   month = feb,
   year = 1989,
}
@article{mavriplis94,
author = {C. Mavriplis},
title = {Adaptive mesh strategies for the spectral element method},
journal = {Comput. Methods Appl. Mech. Engrg},
volume = {116},
pages = {77-86},
year = {1994}
}

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%%%%%%%%%%%%%%                                 GFD PAPERS/REFS                                                 %%%%%%%%%%%%%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

@PHDTHESIS{signell89,
   author = "R. Signell",
   title = "Tidal dynamics and dispersion around coastal headlands",
   school = "WHOI/MIT Joint Program",
   type = "$\mathrm{PhD}$ Thesis",
   month = jan,
   year = 1989,
}
@BOOK{pedlosky87,
   author = "Joseph Pedlosky",
   title = {{Geophysical Fluid Dynamics}},
   edition = {2$^{nd}$},
   publisher = "Springer",
   address = "New York, NY",
   year = "1987",   
}
@BOOK{benoit94,
   author = "Benoit Cushman-Roisin",
   title = {{Introduction to Geophysical Fluid Dynamics}},
   month = jan,
   year = "1987",   
}

@article{lermusiaux08,
author = {Deleersnijder, E. and P. F. J. Lermusiaux},
title = {Multi-scale modeling: nested grid and unstructured grid approaches},
journal = {Ocean Dynamics},
volume = {58},
pages = {335-336},
year = {2008}
}

@BOOK{haidvogel99,
   author = "Dale B. Haidvogel and Aike Beckmann",
   title = "Numerical ocean circulation modeling",
   publisher = "London : Imperial College Press",
   address = "River Edge, NJ : Distributed by World Scientific Pub.",
   year = "1999",   
}

@article{bourgault04,
author = {D. Bourgault and D. E. Kelley},
title = {A Laterally Averaged Nonhydrostatic Ocean Model},
journal = {Journal of Atmospheric and Oceanic Technology},
volume = {21},
pages = {1910-1924},
year = {2004}
}

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%%%%%%%%%%%%%%                          GENERAL NUMERICS REFS                                            %%%%%%%%%%%%%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

@BOOK{karniadakis05,
   author = "G. E. Karniadakis and S. J. Sherwin",
   title = {{Spectral/hp Element Methods for CFD}},
   edition = {2$^{nd}$},
   publisher = "Oxford University Press",
   address = "New York, NY",
   year = "2005",   
}
@BOOK{chapra06,
   author = "S. C. Chapra and R. P. Canale",
   title = {{Numerical Methods for Engineers}},
   edition = {5$^{th}$},
   publisher = "McGraw-Hill Higher Education",
   address = "Boston, MA",
   year = "2006",   
}
@BOOK{chung02,
   author = "T. J. Chung",
   title = {{Computational Fluid Dynamics}},
   publisher = "Cambridge University Press",
   address = "New York, NY",
   year = "2002",   
}

@BOOK{ferziger02,
   author = "J. H. Ferziger and M. Peric",
   title = {{Computational Methods for Fluid Dynamics}},
   edition = {3$^{rd}$},
   publisher = "Springer",
   address = "New York, NY",
   year = "2002",   
}

@BOOK{cebeci05,
   author = "T. Cebeci and J. P. Shao and F. Kafyeke and E. Laurendeau",
   title = {{Computational Fluid Dynamics for Engineers}},
   publisher = "Springer",
   address = "New York, NY",
   year = "2005",   
}

@BOOK{lomax03,
   author = "H. Lomax and T. H. Pulliam and D. W. Zingg",
   title = {{Fundamentals of Computational Fluid Dynamics (Scientific Computation)}},
   publisher = "Springer",
   address = "New York, NY",
   year = "2003",   
}

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%%%%%%%%%%%%%%                          INTRODUCTORY REFERENCES                                          %%%%%%%%%%%%%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

@article{logutov08,
author = {Logutov, O. G. and P. F. J. Lermusiaux},
title = {{Inverse Barotropic Tidal Estimation for Regional Ocean Applications }},
journal = {Ocean Modelling},
volume = {25},
pages = {17-34},
year = {2008}
}

@article{lermusiaux06,
author = {Lermusiaux, P. F. J.},
title = {{Uncertainty Estimation and Prediction for Interdisciplinary Ocean Dynamics}},
journal = {{Journal of Computational Physics}},
note = {{Special issue on ``Uncertainty Quantification.'' J. Glimm and G. Karniadakis, Eds.}},
pages = {176-199},
year = {2006},
}

@article{sapsis09,
author = {Sapsis, T.P. and P.F.J. Lermusiaux},
title = {{Dynamically orthogonal field equations for continuous stochastic dynamical systems}},
journal = {{Physica D}},
volume = {238},
pages = {2347-2360},
year = {2009}
}

@article{lermusiaux07,
author = {P. F. J. Lermusiaux},
title = {{Adaptive Modeling, Adaptive Data Assimilation and Adaptive Sampling}},
journal = {{Physica D}},
note = {{Special issue on ``Mathematical Issues and Challenges in Data Assimilation for Geophysical Systems: Interdisciplinary Perspectives.'' C.K.R.T. Jones and K. Ide, Eds.}}, 
volume = {230},
pages = {172-196},
year = {2007}
}

@techreport{mseas,
      AUTHOR = "MSEAS-Group",
      TITLE = {{Multidisciplinary Simulation, Estimation, and Assimilation Systems ( http://mseas.mit.edu/ , http://mseas.mit.edu/codes )}},
      type = {{Reports in Ocean Science and Engineering}},
      number = 6,
      MONTH = "June",
      YEAR = {2010},
      institution = {{Department of Mechanical Engineering, Massachusetts Institute of Technology}},
      address = {{Cambridge, Massachusetts}}
}
@MISC{philex,
      AUTHOR = "P. F. J. Lermusiaux and Haley, Jr.,P. J. and W. G. Leslie and O. G. Logutov",
      TITLE = {{Philippines Strait Dynamics Experiment - $\mathrm{MSEAS}$ Home Page}},
      YEAR = {2009},
      NOTE = "{\em http://mseas.mit.edu/Research/Straits/}"
}

@article{haley10,
author = {Haley, Jr.,P. J. and Pierre F. J. Lermusiaux},
title = {{Multiscale two-way embedding schemes for free-surface primitive-equations in the “Multidisciplinary Simulation, Estimation and Assimilation System” ($\mathrm{MSEAS}$)}},
journal = {Ocean Dynamics},
volume = {Accepted},
year = {2010},
}

@article{agarwal10,
author = {Agarwal, A. and Pierre F. J. Lermusiaux},
title = {{Statistical Field Estimation for Complex Coastal
Regions and Archipelagos}},
journal = {Ocean Modeling},
volume = {In prep.},
year = {2010},
}

@MASTERSTHESIS{arpitthesis,
   author = "Agarwal, A.",
   title = {{Statistical Field Estimation and Scale Estimation for Complex Coastal Regions and Archipelagos}},
   school = "Massachusetts Institute of Technology",
   type = "$\mathrm{S.M.}$ Thesis",
   address = "Department of Mechanical Engineering",
   month = may,
   year = 2009,
}

@article{lermusiaux99,
author =  {Lermusiaux, P.F.J.}, 
title = {{Data Assimilation via Error Subspace Statistical Estimation, Part II: Mid-Atlantic Bight Shelfbreak Front Simulations, and ESSE Validation}},
journal = {Monthly Weather Review},
volume = {127},
number = {{8}},
pages = {1408-1432},
year = {1999},
}

@article{haley09,
author =  {Haley, P.J. Jr. and Lermusiaux, P.F.J. and A.R. Robinson and W.G. Leslie and O. Logutov and G. Cossarini and
X.S. Liang and P. Moreno and S.R. Ramp and J.D. Doyle and J. Bellingham and F. Chavez and S. Johnston},
title = {{Forecasting and Reanalysis in the Monterey Bay/California Current Region for the Autonomous Ocean Sampling Network-II Experiment}},
journal = {Special issue on AOSN-II, Deep Sea Research Part II: Topical Studies in Oceanography},
volume = {56},
pages = {127-148},
year = {2009},
}

@article{lermusiaux10,
author = {Lermusiaux, P.F.J. and J. Xu},
title = {{Coupled Ocean-Acoustic prediction of transmission loss in a continental shelfbreak region: predictive skill, uncertainty quantification and dynamical sensitivities}},
journal = {IEEE Transactions, Journal of Oceanic Engineering},
volume = {In press},
year = {2010},
}

@article{doney09,
Author = {Doney, S C and Ivan Lima and J. Keith Moore and Keith Lindsay and Michael J. Behrenfeld and Toby K. Westberryand Natalie Mahowald and David M. Glovera and Taro Takahashi},
Title = {{Skill metrics for confronting global upper ocean ecosystem-biogeochemistry models against field and remote sensing data
}},
Journal = {{Journal of Marine Systems}},
pages = {{95-112}},
Year = {{2009}},
Volume = {{76}},
Number = {{1-2}},
Month = {{February}},
}

@article{doney04,
Author = {Doney, S C and Lindsay, K and Caldeira, K and Campin, J M and Drange, H
   and Dutay, J C and Follows, M and Gao, Y and Gnanadesikan, A and Gruber,
   N and Ishida, A and Joos, F and Madec, G and Maier-Reimer, E and
   Marshall, J C and Matear, R J and Monfray, P and Mouchet, A and Najjar, R
   and Orr, J C and Plattner, G K and Sarmiento, J and Schlitzer, R and
   Slater, R and Totterdell, I J and Weirig, M F and Yamanaka, Y and Yool, A},
Title = {{Evaluating global ocean carbon models: The importance of realistic
   physics}},
Journal = {{GLOBAL BIOGEOCHEMICAL CYCLES}},
Year = {{2004}},
Volume = {{18}},
Number = {{3}},
Month = {{SEP 15}},
Abstract = {{A suite of standard ocean hydrographic and circulation metrics are
   applied to the equilibrium physical solutions from 13 global carbon
   models participating in phase 2 of the Ocean Carbon-cycle Model
   Intercomparison Project (OCMIP-2). Model-data comparisons are presented
   for sea surface temperature and salinity, seasonal mixed layer depth,
   meridional heat and freshwater transport, 3-D hydrographic fields, and
   meridional overturning. Considerable variation exists among the OCMIP-2
   simulations, with some of the solutions falling noticeably outside
   available observational constraints. For some cases, model-model and
   model-data differences can be related to variations in surface forcing,
   subgrid-scale parameterizations, and model architecture. These errors
   in the physical metrics point to significant problems in the underlying
   model representations of ocean transport and dynamics, problems that
   directly affect the OCMIP predicted ocean tracer and carbon cycle
   variables (e.g., air-sea CO2 flux, chlorofluorocarbon and anthropogenic
   CO2 uptake, and export production). A substantial fraction of the large
   model-model ranges in OCMIP-2 biogeochemical fields (+/-25-40\%)
   represents the propagation of known errors in model physics. Therefore
   the model-model spread likely overstates the uncertainty in our current
   understanding of the ocean carbon system, particularly for
   transport-dominated fields such as the historical uptake of
   anthropogenic CO2. A full error assessment, however, would need to
   account for additional sources of uncertainty such as more complex
   biological-chemical-physical interactions, biases arising from poorly
   resolved or neglected physical processes, and climate change.}},
Publisher = {{AMER GEOPHYSICAL UNION}},
}


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@article{lynch09,
author =  {Lynch, D. R. and McGillicuddy, D. J. and F. E. Werner}, 
title = {Skill assessment for coupled biological/physical models of marine systems},
journal = {Journal of Marine Systems},
volume = {76(1-2)},
pages = {1-3},
year = 2009,
}

@article{stow09,
author =  {Stow, C. A. and Jolliff,  J. and McGillicuddy, D. J. and Doney, S. C. and Allen, J. I. and Friedrichs, M. A. M. and Rose, K. A. and P. Wallhead}, 
title = {{Skill Assessment for Coupled Biological/Physical Models of Marine Systems}},
journal = {Journal of Marine Systems},
volume = {76},
number = {1-2},
pages = {4-15},
year = 2009,
}

@article{anderson05,
Author = {Anderson, D and McGillicuddy, D and Townsend, D and Turner, J},
Title = {{The ecology and oceanography of toxic Alexandrium fundyense blooms in
   the Gulf of Maine - Preface}},
Journal = {{Deep-Sea Research Part II-Topical Studies in Oceanography}},
Year = {{2005}},
Volume = {{52}},
Number = {{19-21}},
Pages = {{2365-2368}},
}

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Author = {Oschlies, A. and V. Garcon},
Title = {{Eddy-induced enhancement of primary production in a model of the North Atlantic Ocean}},
Journal = {{Nature}},
Year = {{1998}},
Volume = {{394}},
Pages = {{266-269}},
}



@article{rothstein06,
Author = {Rothstein, L. M. and Cullen, J. J. and Abbott, M. and Chassignet, E. P. and Denman, K. and Doney, S. C. and Ducklow, H. and Fennel, K. and Follows, M. and Haidvogel, D. and Hoffman, E. and Karl, D. M. and Kindle, J. and Lima, I. and Maltrud, M. and McClain, C. and McGillicuddy, D. J. and Olascoaga, M. J. and Spitz, Y. and Wiggert, J. and J. Yoder},
Title = {{Modeling Ocean Ecosystems: The Paradigm Program}},
Journal = {{Oceanography}},
Year = {{2006}},
Volume = {{19}},
number = {1},
Pages = {{22-51}},
}

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% Misc


@article{chen03,
Author = {Changsheng Chen and Hedong Liu and R. C. Beardsley},
Title = {{An Unstructured Grid, Finite-Volume, Three-Dimensional, Primitive Equations Ocean Model: Application to Coastal Ocean and Estuaries}},
Journal = {{J. Atmos. Oceanic Technol.}},
Year = {{2003}},
Volume = {{20}},
Pages = {{159–186}},
}

@article{burchard05,
Author = {Hans Burchard and Eric Deleersnijder and Andreas Meister},
Title = {{Application of modified Patankar schemes to stiff biogeochemical models for the water column}},
Journal = {{Ocean Dynamics}},
Year = {{2005}},
Volume = {{55}},
Pages = {{326-337}},
}

@article{pain05,
author = {Pain, C. C. and Piggott, M. D. and Goddard, A. J. H. and Fang, F. and Gorman, G. J. and Marshall, D. P. and Eaton, M. D. and Power, P. W. and de Oliveira, C. R. E.},
title = {Three-dimensional unstructured mesh ocean modelling},
journal = {Ocean Modelling},
volume = {10},
number = {1-2},
pages = {5-33},
year = {2005}
}

@article{slingo09,
author = {Slingo, J. and Bates, K. and Nikiforakis, N. and Piggott, M. and Roberts, M. and Shaffrey, L. and Stevens, I. and Vidale, P. L. and Weller, H.},
title = {Developing the next-generation climate system models: challenges and achievements},
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number = {1890},
pages = {815-831},
year = {2009},
}


