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University of Groningen
Aluminium and manganese in the West Atlantic Ocean
van Hulten, Marco
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Aluminium en Mangaan
in de West-Atlantische Oceaan
een modelstudie
Marco van Hulten
Colofon
Auteurs- en gebruikersrecht:
© 2014 door Marco van Hulten
Dit werk is gelicentieerd onder een Creative Commons
Naamsvermelding-GelijkDelen 3.0 Unported. Bezoek
http://creativecommons.org/licenses/by-sa/3.0/ om een kopie te
zien van de licentie of stuur een brief naar Creative Commons, 444
Castro Street, Suite 900, Mountain View, California, 94041, USA.
Voorzijde:
De afbeelding op de kaft van het boekje is een artistieke doorsnede van
West-Atlantische Oceaan langs het pad van de Nederlandse
Geotraces-cruises. De concentraties opgelost aluminium zijn gemeten
door Dr. Rob Middag; de kleurenschaal is dezelfde als in de
respectievelijke figuren in Hoofdstukken 3 en 4.
Financiëring en projectnummer:
Dit werk is gefinancieerd door de Nederlandse Organisatie voor
Wetenschappelijk Onderzoek (NWO), beursnummer 839.08.414, deel van
het ZKO-programma (Zee- en Kustonderzoek).
Gedrukt door:
Ipskamp Drukkers, Enschede (www.ipskampdrukkers.nl)
Gezet met LATEX2e
ISBN-13 978-90-367-7370-6 paperback
ISBN-13 978-90-367-7369-0 e-boek
Aluminium and Manganese in the
West Atlantic Ocean
A model study
Proefschrift
ter verkrijging van de graad van doctor aan de
Rijksuniversiteit Groningen
op gezag van de
rector magnificus prof. dr. E. Sterken,
en volgens besluit van het College voor Promoties.
De openbare verdediging zal plaatsvinden op
vrijdag 28 november 2014 om 14.30 uur
en gevoerd worden door
Marco Marinus Peter van Hulten
geboren op 23 april 1980
te Elshout
Promotores:
Prof. dr. ir. H.J.W. de Baar
Prof. dr. ir. W. Hazeleger
Copromotores:
Dr. A. Sterl
Dr. A. Tagliabue
Beoordelingscommissie: Prof. dr. M. Roy-Barman
Prof. dr. A.G.J. Buma
Prof. dr. G.J. Reichart
v
For my beautiful wife Jasmijn
vi
“Unfortunately, however, many, and for
the most part those not directly concerned with modelling activity, see in
equations facts rather than ideas.”
– Joel W. Hedgpeth (1977)
“Nothing is impossible. Not if you can
imagine it. That’s what being a scientist
is all about.”
– Hubert J. Farnsworth (3001)
from the Futurama sf animation series
Contents
Nomenclature
xi
1 Introduction
1.1 Rationale . . . . . . . . . .
1.2 Oceans and climate . . . . .
1.2.1 Solubility pump . . .
1.2.2 Biological pump . .
1.2.3 Ocean carbon cycle .
1.3 Nutrients and trace metals .
1.3.1 Silicon . . . . . . . .
1.3.2 Aluminium . . . . .
1.3.3 Manganese . . . . .
1.4 Research questions . . . . .
1.4.1 Aluminium . . . . .
1.4.2 Manganese . . . . .
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2 Methodology
2.1 Philosophical introduction . . . . . . . .
2.1.1 Definition of a model . . . . . . .
2.1.2 Examples of models . . . . . . .
2.1.3 The need for models . . . . . . .
2.2 The model NEMO . . . . . . . . . . . .
2.2.1 Configuration: ORCA2 . . . . .
2.2.2 Dynamical model: OPA . . . . .
2.2.3 Biogeochemical model: PISCES .
2.3 Observational data . . . . . . . . . . . .
2.4 Model-data comparison . . . . . . . . .
2.4.1 Predictive uncertainty and error
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viii
Contents
2.5
2.6
2.4.2 Goodness of fit . . . . . . . . . . . . . . . .
Epilogue . . . . . . . . . . . . . . . . . . . . . . . .
Appendix: Shipboard methods by Dr. Rob Middag
2.6.1 Sample collection . . . . . . . . . . . . . . .
2.6.2 Analysis of dissolved Al . . . . . . . . . . .
2.6.3 Analysis of dissolved Mn . . . . . . . . . . .
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54
57
58
58
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61
3 Aluminium in an ocean model compared with observations 65
3.1 Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . 66
3.2 Methods . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 70
3.2.1 Model description . . . . . . . . . . . . . . . . . . . 70
3.2.2 Observations . . . . . . . . . . . . . . . . . . . . . . 79
3.3 Results . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 82
3.3.1 Reference simulation . . . . . . . . . . . . . . . . . . 82
3.3.2 Sensitivity simulations . . . . . . . . . . . . . . . . . 88
3.4 Discussion . . . . . . . . . . . . . . . . . . . . . . . . . . . . 97
3.4.1 Comparison with Gehlen et al. (2003) . . . . . . . . 97
3.4.2 Advection versus scavenging . . . . . . . . . . . . . . 98
3.4.3 Ocean sediments source . . . . . . . . . . . . . . . . 103
3.4.4 Internal coefficients . . . . . . . . . . . . . . . . . . . 104
3.4.5 Al versus Si in NADW . . . . . . . . . . . . . . . . . 107
3.5 Conclusions and outlook . . . . . . . . . . . . . . . . . . . . 109
3.6 Appendix: Observational data quality . . . . . . . . . . . . 111
4 Circulation, resuspension and incorporation of Al
4.1 Introduction . . . . . . . . . . . . . . . . . . . . . . .
4.2 Methods . . . . . . . . . . . . . . . . . . . . . . . . .
4.2.1 Model description . . . . . . . . . . . . . . .
4.2.2 Observational datasets . . . . . . . . . . . . .
4.2.3 Data-model comparison . . . . . . . . . . . .
4.3 Results . . . . . . . . . . . . . . . . . . . . . . . . . .
4.3.1 Reference simulation . . . . . . . . . . . . . .
4.3.2 Improved dynamics . . . . . . . . . . . . . . .
4.3.3 Sediment resuspension . . . . . . . . . . . . .
4.3.4 Biological incorporation . . . . . . . . . . . .
4.4 Discussion . . . . . . . . . . . . . . . . . . . . . . . .
4.4.1 General biogeochemistry . . . . . . . . . . . .
4.4.2 Sediment source . . . . . . . . . . . . . . . .
4.4.3 Incorporation . . . . . . . . . . . . . . . . . .
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117
118
125
125
132
133
135
135
138
139
142
145
145
147
149
Contents
4.5
4.6
Conclusion . . . . . . . . . . . . . . . . . . . . . . . . . . . 151
Appendix: Sediment resuspension model . . . . . . . . . . . 153
5 Al as a unique mirror image of the biological cycle?
157
6 Manganese in an ocean general circulation model
6.1 Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . .
6.2 Methods . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
6.2.1 Manganese model . . . . . . . . . . . . . . . . . . .
6.2.2 Simulations . . . . . . . . . . . . . . . . . . . . . . .
6.2.3 Observations . . . . . . . . . . . . . . . . . . . . . .
6.3 Results . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
6.3.1 Reference simulation . . . . . . . . . . . . . . . . . .
6.3.2 Other dust deposition field . . . . . . . . . . . . . .
6.3.3 With biological Mn cycle . . . . . . . . . . . . . . .
6.3.4 Low hydrothermal input and small settling velocity .
6.3.5 Unconstrained settling . . . . . . . . . . . . . . . . .
6.3.6 No aggregation threshold . . . . . . . . . . . . . . .
6.3.7 No oxidation threshold . . . . . . . . . . . . . . . . .
6.4 Discussion . . . . . . . . . . . . . . . . . . . . . . . . . . . .
6.4.1 Manganese sources . . . . . . . . . . . . . . . . . . .
6.4.2 Manganese sinks . . . . . . . . . . . . . . . . . . . .
6.5 Conclusion . . . . . . . . . . . . . . . . . . . . . . . . . . .
167
167
168
168
177
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180
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183
185
186
187
188
191
191
194
199
7 Synthesis and recommendations
7.1 This study . . . . . . . . . . . . .
7.1.1 Aluminium . . . . . . . .
7.1.2 Manganese . . . . . . . .
7.2 Recommendations . . . . . . . .
7.2.1 Aluminium . . . . . . . .
7.2.2 Manganese . . . . . . . .
7.2.3 Trace metals and particles
7.2.4 Modelling in general . . .
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215
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A Sensitivity analysis of the aluminium
A.0 Reference simulation . . . . . . . . .
A.1 Dynamics . . . . . . . . . . . . . . .
A.1.1 Different dynamics . . . . . .
A.1.2 No advection . . . . . . . . .
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ix
x
Contents
A.2 Dust deposition . . . . . . . . . . . . . . .
A.2.1 Other dust deposition field . . . .
A.2.2 Solubility of Al . . . . . . . . . . .
A.2.3 Water column dissolution . . . . .
A.3 Sediment sources . . . . . . . . . . . . . .
A.3.1 Shallow margin sediments . . . . .
A.3.2 Sediment resuspension . . . . . . .
A.3.3 Source from the Arctic Ocean . . .
A.4 Scavenging . . . . . . . . . . . . . . . . .
A.4.1 Partition coefficient . . . . . . . .
A.4.2 First-order rate constant . . . . . .
A.4.3 Settling velocity . . . . . . . . . .
A.4.4 Scavenging by calcium carbonate .
A.5 Biological incorporation . . . . . . . . . .
A.5.1 Simple incorporation . . . . . . . .
A.5.2 Decreased partition coefficient . . .
A.5.3 Decreased first-order rate constant
A.5.4 Increased dust dissolution . . . . .
A.5.5 Moderated incorporation . . . . .
A.5.6 Upper limit of incorporation . . .
A.6 Reduced opal dissolution . . . . . . . . . .
A.6.1 Inhibition by incorporated Al . . .
A.6.2 Inhibition by adsorbed Al . . . . .
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217
217
218
220
221
221
222
227
229
229
230
231
234
236
237
237
238
238
241
241
242
243
245
Bibliography
249
Samenvatting
277
Acknowledgements
285
Biography
289
Index
291
Nomenclature
Symbols
,→
˙
:=
[Tr]
{Tr}
A···
A
B
αTr
βTr
C···
cin
δ
D
Dl
d
∆V
∆zi
e
γ
Γ
F···
FT
“Also see...”; only used in this Nomenclature; look under “Symbols”
for operators, quantities and units; look under “Abbreviations and
terminology” for acronyms, initialisms and technical terms
Time derivative; ẋ := ∂x/∂t
Definition
Concentration of a ,→tracer ,→Tr (mol dm−3 )
Activity of a tracer Tr (mol dm−3 )
Diameter of a ,→particle
Mathematical notation for ,→Al concentrations (M); subscript denotes phase
Horizontal ,→eddy diffusion coefficient (m2 s−1 )
Vertical ,→eddy diffusion coefficient (m2 s−1 )
Dissolution fraction of ,→Tr from deposited ,→dust
Dissolution fraction of ,→Tr from sediment source
Mathematical notation for ,→C concentrations (M); subscript denotes
phase
Weight factor for the Al/Si incorporation ratio
Excretion fraction of ,→DOC
Root Mean Square Deviation
Root Mean Square Deviation, vertical distribution homogenised
Day
Gridbox volume (m3 )
Thickness of ,→model layer i
Unit vector
Activity coefficient, the factor accounting for mixture effects;
{Tr} = γ [Tr]
‘Dynamical operator’; this is the full derivative plus eddy diffusion
Mathematical notation for ,→Fe concentrations (M); subscript denotes phase
,→Forcing field of dynamical or biogeochemical tracers at one of the
ocean interfaces (amount time−1 per length, area or volume)
xii
Nomenclature
fT
f
fTr
fT1:T2
Φ
g
gzoo
G
Gmol
I
K
L
log
µ
µphyt
mphyt
mi
mTr
mol
Mmol
M···
M
µM
nM
O
P
p
p
pM
r
rmax
RT1:T2
R
rl
ρ
S
S···
Sv
T
T
Factor to convert forcing FT to a concentration change
Coriolis parameter (rad s−1 )
Mass fraction of an element Tr
Molar ratio T1/T2 of a source term
Flux of a tracer into the ocean (amount surface−2 time−1 )
Gravity of the Earth, approximately 9.8 m s−2
Grazing rate (s−1 )
Gravitational constant (G ≈ 6.673 × 10−11 N m2 kg−2 )
Gigamole, 109 mol
Flow of a tracer (mol s−1 )
Half-saturation constant; at this concentration the concerning process
occurs at half the rate
Limitation term for phytoplankton growth
Natural logarithm
Viscosity (Pa s = kg m−1 s−1 )
Rate of photosynthesis (s−1 )
Phytoplankton mortality rate (s−1 )
Mass of body i (kg)
Atomic mass of Tr (g mol−1 )
Mole, about 6.022 · 1023 elementary entities of a substance
Megamole, 106 mol
Mathematical notation for ,→Mn concentrations (M); subscript denotes phase
Molar, mol dm−3
Micromolar, 10−6 M
Nanomolar, 10−9 M
Measured value of a ,→tracer (Observation)
Modelled value of a tracer (Prediction)
Pressure (Pa = kg m−1 s−2 )
Classical momentum (kg m s−1 ), p = mv
Picomolar, 10−12 M
Radius of a ,→particle (m)
Maximum Al/Si incorporated into living ,→diatom ,→frustules
Reaction stoichiometry between reactants ,→T1 and T2
Distance between two bodies (m)
Correlation coefficient, vertically adjusted
Density (kg m−3 )
Salinity (‰)
Mathematical notation for ,→Si concentrations (M); subscript denotes
phase
Sverdrup, 106 m3 s−1
Temperature (◦ C) (Chapter 1)
True value of a tracer (in practice its reference value) (Section 2.4)
Nomenclature
T
Tmol
Tr,T1,T2
U, V , W
v
VP
waggr
ws
x̄
x
Mathematical notation for (the concentration of) an arbitrary tracer
Teramole, 1012 mol
Any ocean tracer, e.g. Al, Mn, Si, C; only used in this Nomenclature
Zonal, meridional and vertical component of the ,→velocity (m s−1 )
,→Velocity (m s−1 )
Phytoplankton growth rate (M d−1 )
Phytoplankton aggregation rate (M−1 d−1 )
,→Settling ,→speed (often referred to as ‘velocity’) of ,→particles
(m s−1 ); −ws ẑ is the ,→settling ,→velocity
Average value of a quantity x
Vectorial location, (x, y, z)
Abbreviations and terminology
1-D
3-D
AABW
AAIW
ADP
adsorption
Al
Alads
Albiog
Aldiat
Aldiss
Alpart
aluminosilicate
AMOC
aphotic zone
ATP
BATS
BEC
biogenic
Boussinesq
approximation
C
CaCO3
clay
One-dimensional
Three-dimensional
AntArctic Bottom Water
AntArctic Intermediate Water
Adenosine diphosphate
The adhesion of a substance onto a surface of a ,→particle
Aluminium, member of the boron group with atomic number 13,
3rd most abundant element in the Earth’s crust
,→Adsorbed ,→Al
Incorporated biogenic Al
Incorporated diatom Al
Dissolved Al: Al3+ , Al OH2+ and ,→colloids with < 0.2 µM
,→Particulate Al: either Alads or Albiog , lithogenic Al not included
Lithogenic minerals mostly composed of aluminium, silicon, and
oxygen
Atlantic Meridional Overturning Circulation
The deep ocean where there is no light; includes the ,→disphotic
zone in this thesis
Adenosine triphosphate
Bermuda Atlantic Time-series Study (1988–)
Biogeochemical Elemental Cycling (ocean biogeochemistry
model; previously: biogeochemistry/ecosystem/circulation)
Created by organisms
The assumption that density differences are sufficiently small to
be neglected, except for ,→ g-dependent terms
Elemental carbon
Calcium carbonate: calcite and aragonite
,→Aluminosilicates with < 2 µm
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xiv
Nomenclature
CLIVAR
CO2
conceptual
model
colloid
desorption
diagenesis
diatom
DFS3
DIC
disphotic zone
DOC
DSOW
dust
ECMWF
eddy diffusion
eddy viscosity
empiricism
ERA-40
ERS
euphotic zone
ENSO
Fe
Fediss
fluid
forcing
frustule
GCM
Climate Variability and Predictability (2010–), project of the
World Climate Programme
Carbon dioxide
Composition of concepts to clarify the working of certain phenomena, usually presented as a schematic diagram
,→Particle with 1 nm < < 1 µm; however, in observational
oceanography particles with < 0.2 µm are often considered
‘dissolved’
The release of a substance from a surface of a particle
The change of sediments after ,→sedimentation
Functional type of phytoplankton with a silica frustule
Third version of the Drakkar Forcing Set (Brodeau et al. 2010)
Dissolved Inorganic Carbon
The layer of the ocean below the ,→euphotic zone where there is
still some light but not enough for net photosynthesis
Dissolved Organic Carbon
Denmark Strait Overflow Water
Atmospheric ,→particles, mainly coming from desserts; deposited
again on land and in the ocean
European Centre for Medium Range Weather Forecasting
Parameterisation for subgrid advection
Parameterisation for subgrid transport and dissipation of energy
The view that regards observations and experiments as the main
source and test of knowledge
,→ECMWF Re-Analysis of 40 yr (sic), a 45-year re-analysis of
the atmosphere and surface conditions from September 1957 to
August 2002
European Remote Sensing; refers to the ERS-1 and ERS-2 satellites
The surface layer of the ocean that is well-lit, i.e. more than 1%
of sunlight penetration
El Niño–Southern Oscillation, a 2–7 year internal climate oscillation at the Pacific Ocean
Iron, a metal with atomic number 26, 4th most abundant element
in the Earth’s crust
Dissolved Fe: Fe3+ , ligands and colloids with < 0.2 µm
Liquid or gas; in case of geophysical fluids the ocean and atmosphere, respectively
An external source of a tracer, typically located at the boundary
of the model domain
Cell wall made of ,→biogenic ,→silica
General Circulation Model, a model of general circulation based
on the primitive equations
Nomenclature
GEOSECS
Geotraces
HAMOCC
HOT
hydrothermal
vent
IMAU
INCA
instrumentalism
IPY
isopycnal
JGOFS
light
reactions
lithogenic
LMDzT
LSCE
LSG
mixed layer
Mn
Mnads
Mndiss
Mnox
MOC
MOW
model
N
NADP+
NADPH
NADW
Navier-Stokes
equations
NEMO
GEochemical Ocean SECtions Study (1972–1978)
Programme aiming to improve our understanding of ocean biogeochemical cycles and large-scale distribution of trace elements
and their isotopes in the marine environment (www.geotraces.
org) (2006–)
HAmburg Model for the Ocean Carbon Cycle
Hawaii Ocean Time-series (1988–)
A fissure in the Earth’s crust, typically found at spreading regions
like the Mid-Atlantic Ridge
Institute for Marine and Atmospheric research Utrecht
INteraction with Chemistry and Aerosols (atmospheric dust
model)
The view that a scientific theory is a useful instrument in understanding the world (agnostic about realism)
3rd International Polar Year (2007–2009)
A surface of constant density
Joint Global Ocean Flux Study (1989–2005)
The first of two parts of photosynthesis where light energy is
stored in ,→ATP and ,→NADPH
Originating from the lithosphere; not ,→biogenic
Laboratoire de Météorologie Dynamique (atmospheric model)
Laboratoire des Sciences du Climat et l’Environnement
Hamburg Large-Scale Geostrophic ,→OGCM
Ocean layer where properties are mixed by turbulence; between
the air-sea interface and the ,→thermocline
Manganese, transition metal with atomic number 25, 12th most
abundant element in the Earth’s crust
,→Adsorbed Mn
Dissolved Mn: Mn2+ and ,→colloids with < 0.2 µm
Oxidised Mn: MnOx or colloids thereof with ≥ 0.2 µm
Meridional Overturning Circulation
Mediterranean Overflow Water
Structure for which at least some sentences of a theory, hypotheses or observations are satisfied; ,→conceptual, ,→numerical
model
Elemental nitrogen
Nicotinamide adenine dinucleotide phosphate
Reduced form of ,→NADP+
North Atlantic Deep Water
Main equations for the description of the motion of fluids: basically conservation of momentum (based on Newton’s second law)
for a viscous flow
Nucleus for European Modelling of the Ocean
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Nomenclature
numerical
model
O
OGCM
OPA
opal
ORCA
ORCA2
OSF
P
particle
Pisces
plankter
plankton
POC
POM
primary
production
PS I
PS II
rationalism
RMSD
ROS
SAAMW
SAFe
sand
scavenging
sedimentation
settling
Mathematical model for which no analytical solution exists and
hence is typically solved, by approximation, on a computer
Elemental oxygen, a highly reactive non-metal with atomic number 8, 1st most abundant element in the Earth’s crust
Ocean General Circulation Model
Océan PArallélisé, ocean dynamics component of NEMO
Biogenic Si (dead ,→diatoms)
Any of five meshes based on the conformal mapping of Madec
and Imbard (1996)
Model configuration based on the 2◦ resolution ,→ORCA mesh,
used in ,→NEMO
Overturning Stream Function, measure for the ,→MOC in ,→Sv
Phosphorus, a non-metallic essential nutrient with atomic number 15
A localised object, typically larger and heavier than ,→colloids
Biogeochemical model developed by ,→LSCE and community,
component of ,→NEMO-TOP
Single member of ,→plankton: a floater
Organisms in the water column that cannot swim but move with
the currents
Particulate Organic Carbon
Particulate Organic Matter
The storage of chemical energy in organic compounds by living
organisms
Photosystem I, a protein complex used in the ,→light-dependent
reactions
Photosystem II, the first protein complex used in the ,→lightdependent reactions
The view that regards reason as the chief source and test of knowledge
Root Mean Square Deviation
Reactive Oxygen Species, chemically reactive molecules among
which oxygen ions and peroxides
SubAntArctic Mode Water
Sampling and Analysis of Fe (an international standard for sampling and cross-validation)
,→Aluminosilicates with > 63 µm
The combination of adsorption onto the solid surface of a particle, followed by ,→settling due to insufficient buoyancy of the
,→particle in seawater
The last step of particle ,→settling where ,→particles in seawater
become part of the sediment
The process of sinking of heavy particles through the seawater
Nomenclature
Si
silica
Sibiog
Sidiss
Sidiat
silt
speed
SOD
structural
realism
thermocline
TOP
tracer
velocity
WOCE
Silicon, a metalloid with atomic number 14, 2nd most abundant
element in the Earth’s crust
Hydrated silicon dioxide: SiO2 · nH2 O
Biogenic Si (dead ,→diatoms)
Dissolved Si or silicic acid: Si(OH)4
Si incorporated into the ,→frustules of living diatoms
,→Aluminosilicates with 2 µm < < 63 µm
The magnitude of the ,→velocity, ||v||; in the context of sinking of
particles through the water column usually named the ,→settling
velocity ,→ ws
SuperOxide Dismutase
The view that regards only structures or relationships as real (as
opposed to concrete objects)
Layer with a large vertical temperature gradient; between upper
,→mixed layer and deep ocean
Tracer in the Ocean Paradigm, biogeochemistry and transport
components of NEMO
Any property of seawater, e.g. temperature, salinity, iron concentration
The rate of change of the position, denoted by the vector v
(m s−1 )
World Ocean Circulation Experiment (1990–2002)
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xviii Nomenclature