Cebe 2016 Artigo Water Quality Modelling in Kas Bay

Applied Mathematical Modelling 40 (2016) 18871913
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Applied Mathematical Modelling

journal homepage: www.elsevier.com/locate/apm
Water quality modelling in kas bay

Kagan Cebe, Lale Balas
Civil Engineering Department, Engineering Faculty, Gazi University, Ankara, Turkey
a r t i c l e i n f o a b s t r a c t
Article history: In this study, the physical and chemical parameters at 0.5 m and 10 m water depth (e.g. tem-
Received 14 October 2014 perature, salinity, density, pH, concentration of dissolved oxygen DO, nitrite NO2 , nitrate
Revised 9 June 2015
NO3 turbidity, alkalinity and total dissolved solid TDS) have been monitored by monthly
Accepted 23 September 2015
eld and laboratory measurements for 6 months in Kas Bay, Eastern Mediterranean. The mea-
Available online 5 October 2015
surements for nitrite, nitrate and dissolved oxygen concentrations were compared with the
Keywords: output of the zero dimensional water quality model. The model is a sub model of HYDROTAM-
Water quality 3D, which is an implicit baroclinic three dimensional model developed to simulate the wind
Ecological model driven circulations, hydrodynamics and basic water quality parameters in coastal waters. The
Phytoplankton numerical model has hydrodynamic, transport, turbulence as well as water quality compo-
Zooplankton nents. The water quality component is based on a marine ecological submodel, aiming to sim-
Pelagic bacteria ulate marine ecosystems. By using the general conservation equations, the nitrogen, phospho-
rus and the oxygen cycles were simulated in the ecological submodel as well as the dominant
aquatic life forms, namely phytoplankton, zooplankton and the pelagic bacteria. In this paper,
the model structure and the methods used by HYDROTAM-3D to simulate water quality pa-
rameters are presented together with a comparison of the model results and eld observations
in Kas Bay.
2015 Elsevier Inc. All rights reserved.
1. Introduction
The ecosystems in coastal waters, especially in enclosed or semi-enclosed waters rely upon the complex interaction between
the chemical and physical environment and the organisms that live inside this environment. These ecosystems have very com-
plicated dynamics since the presence of the spatial and seasonal variability of affecting parameters within the water body. It is
possible to dene the ambient conditions by using the basic water quality parameters.
The water quality component of HYDROTAM-3D predicts the water quality parameters by using the formulations representing
physical and biochemical mechanisms that also determine the position and momentum of contaminants in a water body and
thus imitate the complex interrelations between the water quality parameters and the ecosystem.
Most of the marine ecological models aim to simulate the biological and chemical processes in marine environment to predict
water quality parameters. Since the early marine ecosystem models, ecological processes are represented as a series of formulas
driven from data assembled from eld observations [2,10,12,15].
Several models are developed using a dynamic compartment modeling program for surface aquatic systems to investigate 1, 2,
and 3 dimensional systems like WASP5 [1] and QUAL2K [11]. CORMIX [16] uses hydrodynamic mixing zone concept to investigate
the environmental impact of wastewater discharge from point sources. Models like Mohid use a zero-dimensional water-quality

Corresponding author. Tel.: +903125823217.
E-mail addresses: kcebe@nevsehir.edu.tr (K. Cebe), lalebal@gazi.edu.tr (L. Balas).
http://dx.doi.org/10.1016/j.apm.2015.09.037
S0307-904X(15)00571-5/ 2015 Elsevier Inc. All rights reserved.
1888 K. Cebe, L. Balas / Applied Mathematical Modelling 40 (2016) 18871913
model integrated into three-dimensional water modeling system to simulate marine ecology by means of basic water quality
parameters [21].
HYDROTAM-3D, is a three-dimensional, baroclinic numerical model developed to simulate the water quality parameters as
well as the circulation and transport mechanisms in coastal waters. The model is calibrated and tested by eld experiments for
over 15 years. HYDROTAM-3D has been applied successfully to Gulf of Fethiye, Gulf of Izmir, Gksu Lagoon, Gulf of Marmaris,
Gulf of Bodrum, Gulf of ldeniz, Gulf of Mersin, Gulf of Iskenderun, Gulf of Izmit, Gulf of Antalya, Gulf of Gkova [3,68,20,23].
Water quality component of HYDROTAM-3D has been developed since 2011 by a PhD research study and it has been tested and
calibrated through the eld observations in Fethiye Bay and in Kas Bay along the Mediterranean coast of Turkey.
The water quality component of HYDROTAM-3D is based on fundamental biological and chemical cycles of the organic matter
and their relationships with the lower trophic levels in marine environment. In this study, the main theoretical background
will be presented and the comparison of the results of the model applied to Kas Bay, Antalya will be compared with the eld
measurements.
2. Method
The major forces affecting the ow mechanism in coastal waters are the gravity, the tide producing forces due to the Sun and
the Moon, the stress of the wind acting on the sea surface, the Coriolis force, the pressure gradient force and the viscous stresses.
Changes under climatic conditions inuence the movement of surface waters directly by the action of wind stress exerted on
the water surface and indirectly by generating gravitational circulation induced by variations in water density resulting from
differences in temperature and salinity.
2.1. Governing equations
The numerical model has hydrodynamic, transport, turbulence and water quality components. In the hydrodynamic model
component, the NavierStokes equations are solved with Bussinesq approximation. In the transport model component, three-
dimensional convective diffusion equations to simulate pollutant, temperature and salinity transports in water are solved. In
the turbulence model component, k- formulation is solved to calculate the kinetic energy of the turbulence and its rate of
dissipation which is the measure of the vertical turbulent eddy viscosity. Smagorinsky Algebraic Subgrid Scale Turbulence Model
is used to simulate the horizontal eddy viscosity. The water quality component is affected by the key environmental forces such
as currents, transport mechanism, temperature, solar radiation, wind speed and light intensity on the water surface.
The governing model equations in the three-dimensional Cartesian coordinate system are as follows [4,5]:
Continuity equation:
u v w
+ + = 0. (1)
x y z
Momentum equations in horizontal directions (xy):

u u u u 1 p u u v u w
+u +v +w = fv +2 v + v + + v + . (2)
t x y z 0 x x x x y y y x z z z x

v v v v 1 p v u v v w
+u +v +w = fu + v + +2 v + v + . (3)
t x y z 0 y x x x y y y y z z z y
Momentum equation in vertical direction:

w w w w 1 p w u w v w
+u +v +w = + gz + v + + v + +2 v , (4)
t x y z 0 z x x x z y y y z z z z
where x,y are the horizontal coordinates; z is the vertical coordinate,t is time, u, v, w are the velocity components in x, y, z
directions at any grid locations in space, x , y , z are the Eddy viscosity coecients in x, y and z directions respectively, f is the
Coriolis coecient, (x, y, z, t) is the in situ water density, o is the reference density, g is the gravitational acceleration and p is
pressure.
The conservation equation for a pollutant constituent is [4,5]:

C C C C C C C
+u +v +w = + + k pC, (5)
t x y z x Dx x x Dy y z Dz z
where C is the pollutant concentration, kp is the decay rate of the pollutant, Dx , Dy and Dz : are the turbulent diffusion coecient
in x, y and z directions respectively.
In turbulence model component, k- formulation is solved to calculate the kinetic energy of the turbulence and its rate of
dissipation which is the measure of the vertical turbulent eddy viscosity. Smagorinsky Algebraic Subgrid Scale Turbulence Model
is used to simulate the horizontal eddy viscosity.
K. Cebe, L. Balas / Applied Mathematical Modelling 40 (2016) 18871913 1889
The model equations for the kinetic energy and dissipation of the kinetic energy are [4]:

k k k k vz k
+u +v +w = + P + B + Fk , (6)
t x y z z k z

vz 2
+u +v +w = + C1 (P + C3 B) C2 + F , (7)
t x y z z z k k
where k is the kinetic energy, is the rate of dissipation of kinetic energy, z is the vertical eddy viscosity, Fk is the horizontal
diffusion terms for the kinetic energy, F is the horizontal diffusion terms for the dissipation of kinetic energy, P is the stress
production of the kinetic energy, B is the buoyancy production of the kinetic energy.
The buoyancy production of the kinetic energy is dened by [4]:
g vz
B= , (8)
0 Pr z
where Pr is the turbulent Prandtl or Schmidth number. Experiments have shown that, the turbulent Prandtl or Schmidth number,
varies slightly in a ow and from one ow to the other. Therefore, it is considered as a constant, Pr = 0.7.
The horizontal diffusion terms are expressed in the following form, where qi represents k or :

qi qi
Fqi = + . (9)
x Dx x y Dy y
The stress production of the kinetic energy is dened by [4]:
2 2 2 2 2
u v u v u v
P = vh 2 +2 + + + vz + , (10)
x y y x z z
where h is the horizontal eddy viscosity and u, v are the horizontal water particle velocities in x and y directions respectively.
The vertical eddy viscosity is calculated by:
k2
vz = C (11)

The following universal empirical constants are used in diffusion equations: C = 0.09, =1.3, C1 =1.44, C2 =1.92, C3 =1 if
G>0 (unstable stratication) and C3 = 0.2 if G<0 (stable stratication).
To account for large scale turbulence generated by the horizontal shear, horizontal eddy viscosity can be simulated by the
Smagorinsky algebraic subgrid scale turbulence model [4]:
2 2 2 1/2
u v 1 u v
vh = 0, 01xy + + + . (12)
x y 2 y y
In the case of stratied ows the inuence of stratication on turbulence in the horizontal direction is negligible [4]. Hence,
the horizontal eddy diffusivities are approximately equal to the horizontal eddy viscosities. On the other hand, the vertical
diffusivity, Dz , is expressed as:
vz
Dz = , (13)
Pr
where Pr is the turbulent Prandtl or Schmidth number and z is the vertical eddy viscosity coecient.
2.2. Boundary conditions
There are four different boundary conditions dened in the model. These are free surface, sea bed, open sea and coastal land
boundaries [4].
Free Surface Boundary Condition: The wind acting above the free surface changes water velocities just under it. The wind-
induced shear stress at the surface results in a water velocity gradient below the surface.
Sea Bed Boundary Condition: The bottom shear stress at the sea bed is determined by matching velocities with the logarithmic
law of the wall. The gradients of temperature, salinity and the pollutant are taken as zero at the sea bed. This model assumes that
there are no advective and diffusive uxes from the sea bed to the water body.
Open Sea Boundary Condition: The open sea boundary is the lateral boundary through which mass uxes can be occurring.
Coastal Land Boundary Condition: Shorelines in the model are dened in order to simulate the ooding and drying processes,
which can also be seen in nature depending on seasonal variations, and cause some water areas to dry out or land areas to be
ooded. At the end of each step, once the free surface and the new water velocities are computed, the total water depth and
vertical grid spacing are updated before proceeding to the next time step. The water surface slope is calculated at each time step
with the new values of water depth. If the water surface slope is positive at coastal land boundary, the water surface is extended
Fig. 1. Nitrogen Cycle in Marine Environment.
using the calculated slope until it intersects the coastal land boundary. This feature allows the model to redene the shorelines
at each step according to the calculated water depth values.
The normal gradients of temperature, salinity and the pollutant across the shoreline are taken as zero, an assumption that
there are no advective and diffusive uxes across the shoreline boundary.
2.3. Numerical scheme
The model is written in FORTRAN programming language and solves hydrodynamic and transport equations in a composite
nite difference and nite element scheme. Equations are solved numerically by approximating the horizontal gradient terms
using a staggered nite difference scheme. In the vertical plane, however, the Galerkin Weighted Residual Method with linear
shape functions of nite elements is utilized in order to convert the differential equation to a discrete problem. The system of
nonlinear equations is solved implicitly by the Crank Nicholson Method which has second order accuracy in time. Water depths
are divided into the same number of layers following the topography. At all nodal points, the ratio of the length (thickness) of
each element (layer) to the total depth is constant. To increase the vertical resolution wherever necessary, grid clustering can be
applied in the vertical plane. The mesh size in the horizontal plane can be variable.
2.4. Water quality component
The water quality component of HYDROTAM-3D is a zero dimensional ecological model based on the conservation equations
and formulations proposed by the United States Environmental Protection Agency in 1985 [17]. Biochemical cycles simulated in
the model are the cycles of nitrogen, phosphorus, and oxygen. Organisms simulated in the model are the low tropic levels in
aquatic environments i.e. phytoplankton, zooplankton and pelagic bacteria.
The rate of change of the water quality parameters are developed by assuming a homogenous distribution of all properties
throughout the computation cell and can be generalized as follows:
C
+ (aC ) = , (14)
t
where is the sum of the internal sink and sources of the water quality parameter in mg/l/day.
For n number of neighboring computational cells, the formula can be extended as follows:
C C C C
= a1 . + a2 ... + an + Si [K]C, (15)
t x1 x2 xn
where C is the concentration of the water quality parameter in mg/l, ai is the rate of exchange with neighboring computational
cell in m/day, Si is the source of pollution for cell i in mg/l/day, K is the internal rate of change of the water quality parameter.
2.4.1. Nitrogen cycle

Nitrogen cycle in marine environment is one of the important phenomena since it is closely related with primary production
and eutrophication problem. In water quality model nitrogen cycle is demonstrated with basic steps of the cycle which can be
summarized in Fig. 1.
The forms of nitrogen in marine environment demonstrated in the water quality model are ammonia (NH4 ), nitrite (NO2 ),
nitrate (NO3 ), particulate organic nitrogen (PON), non-refractory dissolved organic nitrogen (DONnr) and refractory dissolved
organic nitrogen (DONre).
Ammonia. Main sources of ammonia in marine environment are represented in the model as follows [13]:
a. Inorganic matter from the excretion and respiration of phytoplankton.

b. Excretion of pelagic bacteria.
c. Inorganic matter from the excretion of zooplankton,
d. Inorganic matter from the respiration of zooplankton.
e. Mineralization of the refractory dissolved organic nitrogen.
Main sinks of ammonia in marine environment are represented in the model as follows [13]:
a. Uptake by phytoplankton.
b. Uptake by pelagic bacteria.
c. Nitrication of ammonia.
The rate of change in ammonia concentration can be formulized as follows:

f f

fin e f + r f NH f
f N:C Cf

4

+e NH4 N:C C
b b b b
C NH4
= + finz ez + rz N:C
z
Cz , (16)
t

+Kmin
DONre
C DONre

NH4 NH4
Knit C
where ff in is the fraction of inorganic matter excreted from phytoplankton, fz in is the fraction of inorganic matter excreted from
zooplankton, f NH4 is the ammonia preference factor in phytoplankton uptake, f N:C is the nitrogen to carbon ratio for phyto-
plankton in mgN/mgC, b N:C is the nitrogen to carbon ratio for bacteria in mgN/mgC, z N:C is the nitrogen to carbon ratio for
zooplankton in mgN/mgC, KDONre min is the rate of mineralization in 1/day and KNH4 nit is the nitrication rate in 1/day
Ammonia preference factor in phytoplankton uptake is formulized as a function of the concentrations of the nutrients as
follows [17]:

C NH4 C NO3 C NH4 KNf
NH4
f
= + , (17)
KNf + C NH4 KNf + C NO3 C 4 + C NO3
NH
KNf + C NO3
where Kf N is the nitrogen half-saturation constant for phytoplankton uptake in mgN/l.

Mineralization and nitrication are formulized as half-saturation functions as shown below [17]:
(T Tre f ) Cf
DONre
Kmin DONre
= Kmin (Tre f ) Qmin
DONre
, (18)
Krf +Cf
(T Tre f ) CO
NH4
Knit NH4
= Knit (Tre f ) Qnit
NH4
, (19)
sat
Knit +Cf
where KDONre min (Tref ) is the mineralization rate for refractory dissolved organic nitrogen at reference temperature (Tref ) in 1/day,
KNH4 nit (Tref ) is the nitrication rate for ammonia at reference temperature (Tref ) in 1/day, QDONre min is the temperature constant
for mineralization of refractory dissolved organic nitrogen, Kf r is the half-saturation rate for mineralization in mgC/l, QNH4 nit is the
temperature constant for nitrication of ammonia, CO is the concentration of oxygen in mgO2 /l and Ksat nit is the half-saturation
constant for nitrication in mgO2 /l.
Nitrite. The rate of change in nitrite concentration is formulated as follows:
C NO2 NH4 NO2

= Knit C NH4 Knit C NO2 , (20)
t
NO
where Knit 2 is the nitrication rate of nitrite in 1/day.
Similar to the nitrication rate for ammonia, nitrication rate for nitrite can be expressed as follows:
(T Tre f ) CO
NO2
Knit NO2
= Knit (Tre f ) Qnit
NO2
, (21)
sat
Knit + CO
NO
where Knit 2 (Tre f ) is the nitrication rate for nitrite at reference temperature (Tref ) in 1/day, QNO2 nit is the temperature coecient
for nitrication of nitrite.
Nitrate. The rate of change in nitrite concentration is formulated as follows:
C NO3 f f
= 1 NH
f
N:C C f + Knit
NO2
C NO2 Kdnit C NO3 (22)
t 4
where Kdnit is the rate of denitrication in 1/day.

Similar to the nitrication rates, the denitrication rate is calculated as an half-saturation function as follows :
(T Tre f ) sat

Kdnit
Kdnit = Kdnit (Tre f ) Qdnit (23)
Kdnit + C O
sat
where Kdnit (Tref ) is the denitrication rate at reference temperature in 1/day, Qdnit is the temperature coecient for denitrication
and Ksat dnit is the half saturation constant for denitrication in mgO2 /l.
Particulate Organic Nitrogen (PON). The sources for particulate organic nitrogen in marine environment are [13]:
a. Particulate organic fraction of matter produced by excretion.

b. Respiration and mortality of the phytoplankton.
c. Particulate matter produced by mortality of the pelagic bacteria.
d. Particulate fraction of the matter that cannot be assimilated through grazing of phytoplankton and bacteria by zooplankton
and the stoichiometric losses.
e. Particulate organic fraction of matter produced by excretion, mortality and grazing of the zooplankton.
The sinks for particulate organic nitrogen can be summarized as follows [13]:
a. Uptake by pelagic bacteria.

b. Degradation to dissolved organic nitrogen.
The rate of change in particulate organic nitrogen concentration can be formulized as follows:
f f

1 finf 1 forgD
f
e + r f + m f N:C Cf
b

C PON PON mb N:C b
Cb
= z z (24)
t
+ 1 finz 1 forgD z
e + mz + pz N:C C z + Nz + Nz C z

(1 forgp ) Kdec
PON
C PON
where z N is the rate of production of the particulate fraction of the matter that cannot be assimilated by grazing of phyto-
plankton and bacteria by zooplankton in 1/day, z N is the rate of the stoichiometric losses in 1/day, forgP is the fraction of the
particulate organic nitrogen available for mineralization and KPON dec is the rate of degradation of the particulate organic nitrogen
in 1/day.
The rate of production of the particulate fraction of the matter that cannot be assimilated by grazing of phytoplankton and
bacteria by zooplankton is formulated as follows [22]:
f b
Nz = 1 E f N:C Czf + 1 E b N:C Czb (25)
where Cf z is the assimilation rate of the phytoplankton by zooplankton in 1/day, Cb z is the assimilation rate of the bacteria by
zooplankton in1/day, Ef is the assimilation eciency of the phytoplankton by zooplankton and Eb is the assimilation eciency
of the bacteria by zooplankton.
The rate of the stoichiometric losses are formulated as follow [22]:
f f f b b b
Nz = N:C N:C
z
E Cz + N:C N:C
z
E Cz , (26)
where f N:C is the ratio of nitrogen to carbon for phytoplankton in mgN/mgC, b N:C is the ratio of nitrogen to carbon for bacteria
in mgN/mgC and z N:C is the ratio of nitrogen to carbon for zooplankton in mgN/mgC.
The rate of degradation of particulate organic nitrogen is dened as a temperature limiting function and formulated as
follows [17]:
(T Tre f )
PON
Kdec PON
= Kdec (Tre f ) Qdec (27)
where KPON dec (Tref ) is the degradation rate of PON at reference temperature (Tref ) in 1/day, Qdec is the temperature constant for
degradation.
Non-refractory Dissolved Organic Nitrogen (DONnr). Sources of the non-refractory dissolved organic nitrogen (DONnr) are the
dissolved fraction of the organic matter produced by the excretion and the respiration of the phytoplankton. The sink of the
non-refractory dissolved organic nitrogen is the bacterial uptake. The rate of the change in the non-refractory dissolved organic
Fig. 2. Phosphorus Cycle in Marine Environment.
nitrogen is formulated as follows:

f

1 fin forgD (e + r ) N:C C
f f f f f
C DONnr
= DONnr C
b b
(28)
t + 1 f z f z ez z C z

in orgD N:C
where bDONnr is the uptake rat of the non-refractory dissolved organic nitrogen by bacteria 1/day.
Refractory Dissolved Organic Nitrogen (DONre). The refractory dissolved organic nitrogen (DONre) is produced by the degrada-
tion of the particulate organic nitrogen and decreases by mineralization to ammonia. The rate of change in refractory dissolved
organic nitrogen is dened as follows:
C DONre
= (1 forgP ) Kdec
PON
C PON Kmin
DONre
C DONre (29)
t
where KPON dec is the rate of degradation of the particulate organic nitrogen in 1/day, KDONre min is the rate of mineralization of the
refractory dissolved organic nitrogen in 1/day.
2.4.2. Phosphorus cycle

Phosphorus cycle is demonstrated in the water quality model in basic steps of the cycle which can be summarized in Fig. 2.
The forms of phosphorus in marine environment demonstrated in the water quality model are inorganic phosphorus (IP),
particulate organic phosphorus (POP), non-refractory dissolved organic phosphorus (DOPnr), and refractory dissolved organic
phosphorus (DOPre).
Inorganic Phosphorus (IP). The sources for inorganic phosphorus are [13]:
a. Inorganic fraction of matter produced by excretion and respiration of phytoplankton.

b. Inorganic fraction of matter produced by excretion and respiration of zooplankton.
c. Mineralization of refractory and non-refractory dissolved organic phosphorus,
d. Degradation of particulate organic phosphorus.
The rate of change in concentration of the inorganic phosphorus is formulized as follows:

f f

fin (e f + r f ) f P:C Cf

+ finz ez + rz P:C
z
Cz
C IP
= +Kmin
DO Pr e
C DO Pr e (30)
t

+K DOP nr
C DOPnr

min
+ forgP Kdec
POP
C POP
where. ff in is the inorganic fraction of matter produced by phytoplankton, fz in is the inorganic faction of the matter produced
by zooplankton, f P:C is the ratio of phosphorus to carbon for phytoplankton in mgP/mgC, z P:C is the ratio of phosphorus to
carbon for zooplankton in mgP/mgC, KDOPre min is the rate of mineralization of refractory dissolved organic phosphorus in 1/day,
KDOPnr min is the rate of mineralization of non-refractory dissolved organic phosphorus in 1/day, KPOP dec is the rate of degradation
of particulate organic phosphorus in 1/day.
The rate of mineralization of refractory dissolved organic phosphorus is formulized in the model as follows [17]:
(T Tre f ) Cf
DOPre
Kmin DOPre
DOPre
(31)
Krf + C f
where KDOPre min (Tref ) is the rate of mineralization of refractory dissolved organic phosphorus at reference temperature (Tref )
in1/day, Qmin DOPre is the temperature coecient for mineralization of DOPre, Kf r is the half saturation constant for in mgC/l
The rate of mineralization of non-refractory dissolved organic phosphorus is as follows [17]:
(T Tre f ) Cf
DOPnr
Kmin DOPnr
DOPnr
, (32)
Krf +Cf
where KDOPnr min (Tref ) is the rate of the mineralization of non-refractory dissolved organic phosphorus at reference temperature
(Tref ) in 1/day, Qmin DOPnr is the temperature constant for mineralization of DOPnr.
The rate of degradation of the particulate organic phosphorus is formulated as follows [17]:
(T Tre f )
POP
Kdec POP
= Kdec (Tre f ) Qdec
POP
, (33)
where KPOP dec (Tref ) is the rate of the degradation of particulate organic phosphorus at reference temperature (Tref ) in 1/day,
QPOP dec is the temperature coecient for degradation of POP.
Particulate Organic Phosphorus (POP). The sources of particulate organic phosphorus in marine environment are [13]:
a. Organic particulate fraction of the matter produced by excretion and respiration of phytoplankton
b. Mortality of phytoplankton.
c. Particulate fraction of the matter that cannot be assimilated through grazing of phytoplankton and bacteria by zooplankton
and the stoichiometric losses.
d. Organic particulate fraction of the matter produced by excretion of zooplankton.
e. Grazing and mortality of zooplankton.
POP is decreased by degradation to dissolved organic phosphorus.

The rate of change in concentration of the POP can be formulized as follows:
f f
1 finf 1 forgD
f
e + r f + m f P:C Cf
C POP
= + 1 finz 1 forgD z
ez + mz + pz P:C
z
C z + Pz + Pz C z (34)
t
forgP Kdec C
POP POP
,
where z P is the rate production of the matter that cannot be assimilated by zooplankton during the grazing of phytoplankton
and bacteria in 1/day, z P is the rate of the stoichiometric losses in 1/day, forgP is the fraction of particulate organic phosphorus
available for mineralization.
The rate production of the matter that cannot be assimilated by zooplankton during the grazing of phytoplankton and bacteria
is dened as [22]:
Pz = (1 E f ) P:C
f
Czf + (1 E b ) P:C
b
Czb , (35)
where Cf z is the assimilation rate of phytoplankton by zooplankton in 1/day, Cb z is the assimilation rate of bacteria by zooplankton
in 1/day, Ef assimilation eciency of phytoplankton by zooplankton, Eb is the assimilation eciency of bacteria by zooplankton.
The rate of the stoichiometric losses for grazing of phytoplankton and bacteria by zooplankton are as follows [22]:
f f f b b b
Pz = P:C P:C
z
E Cz + P:C P:C
z
E Cz , (36)
where f P:C is the ratio of phosphorus to carbon for phytoplankton in mgP/mgC, b P:C is the ratio of phosphorus to carbon for
pelagic bacteria in mgP/mgC, z P:C is the ratio of phosphorus to carbon for zooplankton in mgP/mgC.
Non-refractory Dissolved Organic Phosphorus (DOPnr). The sources of the non-refractory dissolved organic phosphorus (DONnr)
are [13]:
a. The dissolved organic faction of the matter produced by excretion and respiration of the phytoplankton.
b. The dissolved organic faction of the matter produced by excretion of zooplankton.
Non-refractory dissolved organic phosphorus decreases by mineralization to inorganic phosphorus.

Fig. 3. Oxygen Cycle in Marine Environment.
The rate of change in concentration of the non-refractory dissolved organic phosphorus (DONnr) can be formulized as follows:
f f
1 fin forgD e f + r f P:C C f
f
C DOPnr
= + 1 f z forgD
z
ez P:C
z
Cz (37)
t DOPnr in DOPnr
Kmin C
Refractory Dissolved Organic Phosphorus (DONre). The refractory dissolved organic phosphorus increases by the degradation of
the particulate organic phosphorus (POP) and decreases by mineralization to inorganic phosphorus.
The rate of change in the concentration of the refractory dissolved organic phosphorus is formulated as follows:
C DO Pr e
= (1 forgP ) Kdec
POP
C POP Kmin
DPO Pr e
C DO Pr e (38)
t
2.4.3. Oxygen cycle
Oxygen cycle is demonstrated in the water quality model in basic steps of the cycle which can be summarized in Fig. 3.
Dissolved oxygen plays an important role throughout the nitrogen and phosphorus cycle as well as in the aquatic life. The
sources of the dissolved oxygen in the marine environment are [13]:
a. Photosynthesis of the phytoplankton.

b. Oxygen transfer across the water surface
c. Denitrication of the nitrate.
The sinks of the dissolved oxygen are [13]:
a. The respiration of the aquatic life forms.

b. Degradation of the particulate organic materials.
c. Mineralization of the inorganic nitrogen forms.
The rate of change in the concentration of the dissolved oxygen can be formulated as follows:
f ph f
O:C + 1 NH4 f f O:N NO3
N:C
f
C

f IP f

+ O:P P:C r O:C C
f f f

r z O:C
z
Cz
b
C DO Pr e
= b + b
DONnr O:C C
b (39)
t

PON

Kmin O:N C
DONre min DONre

K POP min C ,POP Kmin
DOPre
O:P
min
C DOPre Kmin
DOPnr
O:P
min
C DOPnr

dec O:P
Knit
O
C NH4 + Kdnit
O
C NO3
where min O:N oxygen consumption ratio for nitrogen mineralization in mgO/mgN/day, min O:P oxygen consumption ratio for
phosphorus mineralization in mgO/mgP/day, KO nit oxygen consumption rate in nitrication in 1/day, KO dnit oxygen consumption
rate in denitrication 1/day.
The oxygen consumption rate for nitrogen mineralization can be formulated as follows [19]:
1 CO
O:N
min
= O:C
CO2
(40)
OM
N:C
0, 5 + C O
Similarly, the oxygen consumption ratio for phosphorus mineralization can be formulated as follows [19]:
1 CO
O:P
min
= O:C
CO2
(41)
OM
P:C
0, 5 + C O
Oxygen consumption rate in nitrication can be calculated as follows [19]:
O
Knit = Knit O:N
NO3
, (42)
where Knit is the rate of nitrication in 1/day.
Oxygen consumption rate in denitrication can be calculated as follows:
O
Kdnit = Kdnit O:N
NO3
, (43)
where Kdnit is the rate of denitrication in 1/day.
2.4.4. Phytoplankton
The change in the concentration of the phytoplankton is modelled as it is proposed by EPA [17] and dened as follows:
C f f
= rf ef sf mf C f Gf , (44)
t
where Cf is the phytoplankton concentration in mgC/l, f is the phytoplankton gross grow, rf is the respiration rate, ef is the
excretion rate, sf is the settling rate, mf is the mortality rate in 1/day, Gf is the phytoplankton grazing rate in mgC/l/day.
Gross Growth Rate. The growth rate of the phytoplankton is limited by temperature, light intensity and nutrients available in
the ambient water, namely phosphorus and nitrogen. The gross growth rate of the phytoplankton is described as:
f = max
f
(Tre f ) f f (T ) f f (L) min[, f f (P), f f (N)], (45)
f
where max (Tref ) is maximum gross growth rate at reference temperature in 1/day, Tref is the reference temperature in C, ff (T)
is
the growth limiting function for temperature, ff (L) is the growth limiting function for light, ff (N) is the growth limiting function
for nitrogen, ff (P) is the growth limiting function for phosphorus.
The Growth Limiting Factor for Temperature. The growth limiting factor for temperature is based on the temperature-optimum
curve and temperature tolerance limits of the organism, proposed by Thornton and Lessem [30] as follows:
f f (T ) = KAf (T ) KBf (T ), (46)
where KA f (T) and KB f (T) are raising limb and falling limb of the temperature curve and can be formulated as follows:
K1f e1 (T Tmin )
f f
KAf (T ) = , (47)
1 + K1f e1 (T Tmin ) 1
f f
K4f e2 (Tmax T )
f f
KBf (T ) = , (48)
1 + K4f e2 (Tmax T ) 1
f f
where Kf 1 , Kf 2 , Kf 3 , Kf 4 are rate multipliers for temperature limits, Tf min is the minimum temperature for phytoplankton, Tf max is
the maximum temperature for phytoplankton in C, f 1 , f 2 are rate coecients for temperature curve.
Rate coecients for temperature curve 1 f and 2 f are as follows:

K2f 1K 1f
ln f f

K1 1K2
1f = f f
, (49)
Topt. min
Tmin

K3f 1K4f
ln f f

K4 1K3
2f = f f
, (50)
Tmax Topt. max
where Tf opt.min is the minimum optimum temperature for phytoplankton growth and Tf opt.max is the maximum optimum temper-
ature for phytoplankton growth in C.
The Growth Limiting Factor for Light. The relationship between the growth of phytoplankton and the ambient light intensity is
formulated by using the growth limiting function for light as proposed by Steele [28].

I(z) 1 II(z)
f f (L) = e opt
, (51)
Iopt
where Iopt is the optimum light intensity for phytoplankton growth in W/m2 , I(z) is the light intensity at the depth z in W/m2 .
The light intensity in the ambient water is calculated according to Beer-Lambert Law as:
I(z) = Io ekz , (52)
where Io is the light intensity at the water surface in W/m2 , k is the light extinction coecient in 1/m which also varies according
to the turbidity of the ambient water.
Light extinction coecient k can be limited as a function of chlorophyll, a concentration as Parson et al. [25] proposes:
k = 0.04 + 0.0088Kla + 0.054Kla2/3 , (53)
where Kla is the chlorophyll -a concentration in g Kla /l. In order to calculate chlorophyll-a concentration following formula
can be used:
Kla = C f Kla:C 1000, (54)
where Kla:C is the chlorophyll-a to carbon rate in g Kla /g C.
The Growth Limiting Factor for Nitrogen. The growth limiting factor for nitrogen is based on conventional Michealis and Menten
Kinetics and formulated as follows:
C NH4 + C NO3
f f (N) = , (55)
KNf + C NH4 + C NO3
where C NH4 is the concentration of ammonium in mg N/l, C NO3 is the concentration of nitrate in mg N/l, Kf N is the nitrogen
half-saturation constant for phytoplankton in mg N/l.
The Growth Limiting Factor for Phosphorus. The growth limiting factor for phosphorus is similar to the growth limiting factor
for nitrogen.
C IP
f f (P ) = , (56)
KPf + C IP
where CIP is the concentration of the inorganic phosphorus in mg P/l, Kf P is the phosphorus half-saturation constant for phyto-
plankton in mg N/l.
Respiration Rate. Respiration rate of the phytoplankton can be described as proposed by Groden [18] and Park et al. [24].
r f = re f + r f f , (57)
rf
where e is the endogenous respiration rate, rf f is the photorespiration rate in 1/day. Endogenous and photorespiration respira-
tion rate formulized as follows [17]:
re f = Kef e(0,069T ) , (58)
r f f = Kpf f , (59)
where Kf e is the endogenous respiration constant, Kf p is the photorespiration constant.

Excretion Rate. Excretion rate of the phytoplankton is formulized according Collins [14] as follows:
e f = Ke f (1 f (L)), (60)
where Ke is the fraction of photosynthesis excreted.
Mortality Rate. A modied Michealis-Menten type saturation function for phytoplankton mortality is used as proposed by
Rodgers and Salisbury [26].

C f / f
m(Tre f ) = mmax (Tre f ) , (61)
Kmf + C f / f
where Kf m is the half-saturation rate for phytoplankton mortality in mg C/l.day.
Settling Rate. Phytoplankton settling rate is directly related with the density, size and physiologic condition of the cells, as
well as the density, current velocity and the turbulence of the ambient water. Scavia [27] has dened a modied Stoke law for
the settling velocity for non-spherical shaped phytoplankton cells as follows:
2 g R2 ( p w )
Vs = , (62)
9 Fs
where Vs is the settling velocity of the particle in m/day, g is the gravitational acceleration in m/day2 , R is the equivalent radius
in m, p is the density of the cell in kg/m3 , w is the density of the ambient water in kg/m3 , is the kinematic viscosity, Fs is the
shape factor.
Changes in the settling velocity can be expressed according to formula below [29]:
Vs (Tre f )
sf = fs (T ), (63)
d
where Vs,max (Tref ) is the maximum settling velocity at reference temperature in m/day, Tref is the reference temperature and fs(T)
is the temperature adjustment function for settling velocity.
Also the temperature adjustment factor is described as follows [29]:
157, 5
f s (T ) = . (64)
0, 069 T 2 5, 3 T + 177, 6
Grazing Rate. Phytoplankton grazing is dened as a function of temperature, predator population density (i.e. zooplankton
concentration), and phytoplankton concentration as proposed by EPA [17] as follows:
G f = pzf Azmax fzf (A) f z (T ) C z . (65)
pf Az
where z is the phytoplankton proportion in zooplankton ingestion, max is the maximum ingestion rate of zooplankton in
1/day, ff z (A) is the limiting factor for prey concentration, fz (T) is the limiting factor for temperature and Cz is the concentration
of zooplankton in mgC/l.
2.4.5. Pelagic bacteria

The rate of change in heterotrophic pelagic bacteria concentrations in the model is dened as it is proposed by Bernardes [9].
Cb
= [b eb mb ] C b Gb , (66)
t
where Cb is the concentration of bacteria in mgC/l, b is the total bacterial uptake in 1/day, eb is the excretion rate in 1/day, mb is
the mortality rate in 1/day, Gb is the grazing rate of the bacteria in mgC/l/day.
Total Bacterial Uptake. Total bacterial uptake is related directly to the availability of nutrients and the temperature of the
ambient water and can be formulated as follows [22]:
b = bNH4 + bPON + bDONnr (67)
where b NH4 is the ammonia uptake in 1/day, b PON is the particulate organic nitrogen uptake in 1/day, b DONnr is the nonre-
fractory dissolved organic nitrogen uptake in 1/day.
Similar to the phytoplankton growth, bacterial uptake function can be modied by limitation factor for temperature as follows
[22]:
bmax (Tre f ) f b (T ) f bNH4 (N)

bNH4 = (68)
N:C
b
bmax (Tre f ) f b (T ) f bPON (N)

bPON = (69)
N:C
b
bmax (Tre f ) f b (T ) f bDONnr (N)

bDONnr = (70)
N:C
b
where fb NH4 (N), fb PON (N), fb DONnr (N) are bacterial uptake limiting functions for ammonia, particulate organic nitrogen and non-
refractory dissolved organic nitrogen, b max (Tref ) is the maximum bacterial uptake in reference temperature in mgN/mgC/day,
fb (T) is the bacterial uptake limiting function for temperature according to Thornton and Lessem [30], b N:C nitrogen carbon ratio
for bacteria in mgN/mgC.
Bacterial uptake limiting functions for ammonia, particulate organic nitrogen and nonrefractory dissolved organic nitrogen
are dened as Michealis-Menten Half-Saturation Function as follows:

C NH4 b,N
i f, C NH4 > Cmin

b
fNH (N) = KNb + C NH4 , (71)
4
b,N
0 i f, C NH4 Cmin

C PON
i f, C PON
> b,N
Cmin

b
fPON (N) = KNb + C PON , (72)
b,N
0 i f, C PON Cmin

C DONnr
i f, C DONnr
> b,N
Cmin

b
fDONnr (N) = KNb + C DONnr , (73)
b,N
0 i f, C DONnr Cmin
where Kb N is the half saturation rate for bacterial uptake in mgN/l, Cb,N min is the minimum concentration of nutrients for bacterial
uptake in mgN/l.
Grazing Rate. Grazing rate of heterotrophic pelagic bacteria is formulated similar to the grazing of phytoplankton by zooplank-
ton as follows:
Gb = pbz Azmax fzb (A) f z (T ) C z , (74)
where pb z is the fraction of bacteria in zooplankton grazing.
Limiting factor for prey concentration can be dened also similar to the phytoplankton grazing [22]:

czb C b Czmin,b
i f, czb C b Czmin,b > 0
fzb (A) = KAz + czb C b Cz min,b
, (75)

0 i f, czb C b
Czmin,b 0
where z is the assimilation eciency of bacteria by zooplankton, Cmin,b z is the minimum concentration of zooplankton for
cb
bacteria grazing in mgC/l, Kz A is the half-saturation constant for bacteria grazing by zooplankton in mgC/l.
2.4.6. Zooplankton
The rate of change in the zooplankton concentration is dened as follows [17]:
Cz
= [z rz mz ] C z Gz , (76)
t
where Cz is the concentration of zooplankton in mgC/l, z is the gross growth rate of zooplankton in 1/day, rz is the respiration
rate in 1/day, mz mortality in 1/day, Gz is the grazing in mgC/l/day.
Gross Growth. Gross growth of zooplankton is dened as follows [17]:
z = Czf E f + Czb E b , (77)

where z is grazing rate of phytoplankton by zooplankton in 1/day, z is the grazing rate of bacteria by zooplankton in 1/day, Ef
Cf Cb
is the assimilation coecient of phytoplankton by zooplankton, Eb is the assimilation coecient of bacteria by zooplankton.
Grazing rates of phytoplankton and bacteria are directly related to the concentration of zooplankton and can be formulized
as follows:
Gf
Czf = , (78)
Cz
Gb
Czb = , (79)
Cz
where Cz is the concentration of zooplankton, Gf and Gz are grazing rates of phytoplankton and bacteria.
Respiration Rate. Respiration rate of zooplankton is formulated as follows [17]:
rz = rz (Tre f ) f z (T ), (80)
where rz (Tref ) is the respiration rate of zooplankton at reference temperature in 1/day, fz (T) is the limiting factor for zooplankton
respiration calculated similar to phytoplankton.
Mortality Rate. Mortality rate of the zooplankton is limited according to a limiting function for temperature and formulated
as follows [17]:
mz = mz (Tre f ) f z (T ), (81)
Fig. 4. Location of Kas Region and Field Measurement Points (K).
where mz (Tref ) is the mortality rate of zooplankton at reference temperature in 1/day and f(T) is the mortality limiting function
for temperature.
Grazing Rate. Grazing rate of zooplankton by higher trophic levels are proportional to the zooplankton concentration and
formulated as follows [17]:
Gz = pz C z , (82)
where pz is the zooplankton grazing rate in 1/day.
3. Study site
Kas Region is located at the Mediterranean coast of Antalya (Fig. 4). At the north of the region lies the touristic district, which
has a dense population and yacht trac in summer season. The coast is divided into three marine subregions namely Kas, Bucak
and Limanagz Bays according to their geographical properties. Kas Bay and Limanagz Bay are connected to each other with an
opening of 793 m long and 50 m deep maximum. A marina with a 472 berthing capacity has been operating since 2011 in Bucak
Bay, which is a shallow and sheltered water body. A waste water treatment facility with a capacity of 5400 m3 /day is installed
in 2006, which discharges its outfall water to Kas Bay. HYDROTAM-3D water quality component is adapted to Kas Region with
three interrelated computational subregions to simulate the water quality properties (Fig. 5).
3.1. Kas subregion
Kas Bay is a deep water body which is fully open to wind driven currents from the Mediterranean. The simulation area has
a 2490 m long border along the open sea through 1-1 section and 793 m long border along Limanagz bay through 2-2 section.
The cross-sectional area at 1-1 is 235,370 m2 , and at 2-2, 23,520 m2 . The simulated water body has a surface area of 6514,300 m2
and a water volume of 2274,00,000 m3 .
The main sources that affect the water quality parameters in Kas Bay are the outfall water discharged from the waste water
treatment plant and the waste water produced by the boats berthing at Kas Port.
3.2. Limanagz subregion
Limanagz Bay is a sheltered area and connected only to Kas Bay through an opening with a length of 793 m and 50 m
depth maximum. It is less subjected to open sea circulations, and there are fewer facilities discharging their waste water to the
Fig. 5. Computational Subregions of Kas Region.
Table 1
Waste water and water exchange budget for Kas Subregion (m3 /day).
September 2013 October 2013 November 2013 December 2013 January 2014 February 2014
Discharge water from Kas waste water 2450 2450 2450 1900 1900 1900
treatment facility
Waste water produced by the boats 68 68 68 8 8 8
berthing at Kas Port
Water exchange with open sea through 30119.040 30119.040 64540.800 64540.800 64540.800 64540.800
1-1 cross section
Water exchange with Limanagz 2730.240 2730.240 4095.360 4095.360 4095.360 4095.360
Subregion through the 2-2 cross
section
bay without a treatment. On the other hand, the bay is visited by numerous tour boats in summer which generate considerable
pollution during tourist season. The simulated water body has a surface area of 972,910 m2 and a water volume of 150,68,000 m3 .
3.3. Bucak subregion
Bucak Bay has a connection to open sea through the 3-3 section with a length of 300 m and 23 m depth maximum. The main
pollution sources in Bucak Bay are the marina facility and the boats berthing there. The cross-sectional area at 3-3 is 5100 m2 .
The simulated water body has a surface area of 697,800 m2 and water volume of 17445,200 m3 .
4. Field measurements
In order to investigate the water quality parameters, 10 measurement points are selected from the regions that can represent
the characteristics of the marine environment. The physical and chemical parameters at 0.5 m and 10 m depth (i.e. temperature,
salinity, density, pH, concentration of the dissolved oxygen DO, nitrite NO2 , nitrate NO3 , turbidity, alkalinity and total dissolved
solid TDS) are monitored monthly by eld and laboratory measurements for 6 months. In order to investigate the currents and
water exchange between the computational regions the current velocities are also measured for each eld measurement point.
The mean water ow through 1-1, 2-2 and 3-3 sections are calculated based on the current velocities observed for 6 months.
The mean water quality parameters of the discharged water from the treatment facility are observed to investigate the sources of
pollution. The waste water budget and the mean water exchange values used in the model are presented in the following tables
(Table 13):
Table 2
Waste water and water exchange budget for Limanagz Subregion (m3 /day).

berthing at Limanagz Bay
Waste water produced by the facilities 150 150 150 10 10 10
located at Limanagz Bay
Water exchange with Kas Subregion 2730240 2730.240 4095.360 4095.360 4095.360 4095.360
through the 2-2 cross section
Table 3
Waste water and water exchange budget for Bucak Subregion (m3 /day).
berthing at Kas Marina
Water exchange with open sea through 1036.800 1036.800 1036.800 1036.800 1036.800 1036.800
the 2-2 cross section
0.048
0.044
0.04
0.036
0.032
0.028
0.024
0.02
0.016
0.012
0.008
Fig. 6. Distribution of Nitrite Concentration (mg N/l) in January 2014 at 0.5 m Depth.
4.1. Nitrite
The distribution of the nitrite concentrations for January and February 2014 at 0.5 m depth are presented in Figs. 6 and 7
respectively.
Figs. 6 and 7 show the variation of nitrite concentrations measured in the labotary by analyzing the water samples taken at
0.5 m depth from the sea surface in January and February 2014. Measured values of nitrite concentration, which is one of the
parameters indicating the signicance of nitrogen nutrient in water, varies between 0.008 and 0.048 mg N/l. Although the nitrite
concentrations in the region are generally below the critical values of pollution, measurements reveal higher concentration
values for Nitrite in K8 at the Marina in Bucak Bay, in K6 at the wastewater discharge and in K3 by the shore of the touristic
district, where the main pollution sources in the region are located. At the stations K1 and K10, representing offshore water
charactistics, minimum values for nitrite concentration are observed.
4.2. Nitrate
The distribution of the nitrate concentrations for January and February 2014 at 0.5 m depth are presented in Figs. 8 and 9
respectively.
0.048
0.044
0.04
0.036
0.032
0.028
0.024
0.02
0.016
0.012
0.008
Fig. 7. Distribution of Nitrite Concentration (mg N/l) in February 2014 at 0.5 m Depth.
1.3
1.2
1.1
0.9
0.8
0.7
0.6
0.5
0.4
0.3
0.2
0.1
Fig. 8. Distribution of Nitrate Concentration (mg N/l) in January 2014 at 0.5 m Depth.
The nitrate concentration varies from 0 to 1.3 mg N/l for January and February 2014 as its distributions show in Figs. 8 and
9. Nitrate is another signicant parameter for nitrogen nutrient in water and is only mildly toxic for the marine environment in
comparison with the other nitrogen involving pollutants. In most cases higher levels of nitrate are thought to result from human
activities since the reasons of having nitrate in water are mainly the breakdown of fertilizers, manures, plants, animals or other
organic residues by microorganisms. Similar to the distribution of the nitrite concentrations, nitrate concentrations indicate
higher levels in K8, K6, K3 as well as in K4, which are the stations near main pollution sources. Since the region is open to strong
currents from offshore water, no signicant pollution level is observed at any station.
1.3
1.2
1.1
0.9
0.8
0.7
0.6
0.5
0.4
0.3
0.2
0.1
Fig. 9. Distribution of Nitrate Concentration (mg N/l) in February 2014 at 0.5 m Depth.
7.6
7.4
7.2
6.8
6.6
6.4
6.2
5.8
5.6
Fig. 10. Distribution of Dissolved Oxygen Concentration (mg O/l) in September 2013 at 0.5m Depth.
4.3. Dissolved oxygen
The distribution of dissolved oxygen concentrations for September, October 2013 and January, February 2014 at 0.5 m and
10m depth are presented in Figs. 1017.
The concentration of dissolved oxygen measurements at the site varies from 5.6 to 7.6 mg O/l between September and Febru-
ary. The concentration of dissolved oxygen is inversely related to water temperature and the presence of other solutes in water. It
is clearly observed in Figs. 1017 that the concentration increases as the ambient water temperature and salinity decreases from
September to February. The concentration values in K8 and K9 also appear to be less than in other stations because of weaker
7.6
7.4
7.2
6.8
6.6
6.4
6.2
5.8
5.6
Fig. 11. Distribution of Dissolved Oxygen Concentration (mg O/l) in September 2013 at 10m Depth.
7.6
7.4
7.2
6.8
6.6
6.4
6.2
5.8
5.6
Fig. 12. Distribution of Dissolved Oxygen Concentration (mg O/l) in October 2013 at 0.5m Depth.
currents inside Bucak Bay. Similar to that, due to wind and wave actions higher concentration values are observed at 0.5 m below
the surface rather than at 10 m depth, for all that the measurements are within the standart ranges of the Mediterranean.
5. Results
The measured values for nitrite, nitrate and dissolved oxygen concentrations are compared with the simulation outputs for
each computational region.
7.6
7.4
7.2
6.8
6.6
6.4
6.2
5.8
5.6
Fig. 13. Distribution of Dissolved Oxygen Concentration (mg O/l) in October 2013 at 10m Depth.
7.6
7.4
7.2
6.8
6.6
6.4
6.2
5.8
5.6
Fig. 14. Distribution of Dissolved Oxygen Concentration (mg O/l) in January 2014 at 0.5m Depth.
5.1. Kas subregion
Figs. 1820 display the comparison of the mean concentration values for nitrite, nitrate and dissolved oxygene obtained
through the water quality model in comparison with the eld measurements at stations K3, K4, K5, K6 and for Kas Subregion.
According to the model estimations for the Kas Subregion in Fig. 18, the mean nitrite concentration is around 0.035 mg N/l
in autumn and decreases to the level of approximately 0.010 mg N/l in the winter months of January and February. Comparing
the estimations with the nitrite concentrations measured in January, an overestimation of 0.001 to 0.015 mg N/l is observed. For
7.6
7.4
7.2
6.8
6.6
6.4
6.2
5.8
5.6
Fig. 15. Distribution of Dissolved Oxygen Concentration (mg O/l) in January 2014 at 10m Depth.
7.6
7.4
7.2
6.8
6.6
6.4
6.2
5.8
5.6
Fig. 16. Distribution of Dissolved Oxygen Concentration (mg O/l) in February 2014 at 0.5m Depth.
February, all of the eld measurement values except the one at K5 show higher values than the model estimations. The deviation
varies between 0.007 and 0.016 mg N/l.
The comparison of the mean nitrate concentrations obtained through the water quality model and the eld measurements
is given in Fig. 19. According to the model estimations the mean nitrate concentration, which is around 0.238 mg N/l in autumn
remains almost at the same levels during the whole period of the study. However, comparing with the the nitrate concentrations
from the eld measurements, it is observed that the model underestimates the concentration values in February while result
is almost stays at the average in January. Despite that, the model estimates are found to be close to the order of the measured
values. The deviation between model results and eld measurements varies between 0.12 and 0.75 mg N/l.
7.6
7.4
7.2
6.8
6.6
6.4
6.2
5.8
5.6
Fig. 17. Distribution of Dissolved Oxygen Concentration (mg O/l) in February 2014 at 10m Depth.
Fig. 18. Nitrite Concentration Values for Kas Subregion (mg N/l).
In Fig. 20, it is observed that the estimated concentration of the mean dissolved oxygen is around 5.3 mg O/l at the end of the
summer season and it is slightly underestimated as the measured values are in between 5.7 and 6.5 mg O/l. For the following
months, with the decrease in sea water temperature, the estimations increase to the level of 7.6 mg O/l. The model estimations
for dissolved oxygen are in general quite consistent with the measurements in terms of both the level of concentrations and the
temporal variation. A slight underestimation for autumn and an underestimation for winter, however, is apparent. The deviation
between model results and eld measurements varies from 0.2 to 1.2 mg O/l.
5.2. Limanagz subregion
Figs. 2123 display the comparison of the mean concentration values for nitrite, nitrate and dissolved oxygene, obtained
through the water quality model with the eld measurements at stations K2 and for Limanagz Subregion.
Fig. 19. Nitrate Concentration Values for Kas Subregion (mg N/l).
Fig. 20. Dissolved Oxygen Concentration Values for Kas Subregion (mg O/l).
According to the model estimations for the Limanagz Subregion in Fig. 21, the mean nitrite concentration is increased to
0.0245 mg N/l level at the beginning of the winter and continued to increase to the levels of approximately 0.0295 mg N/l in
the winter month of February. Comparing the estimations with the nitrite concentrations measured in January, a deviation of
0.0015 mg N/l is observed. The deviation in February is more signicant with a level of 0.0015 mg N/l.
In Fig. 22, the comparison of the mean nitrate concentrations obtained through the water quality model and the eld mea-
surements is presented. The model estimates the mean nitrate concentration around 0.23 mg N/l through the end of autumn and
winter. The nitrate concentration in K2 station almost matches the model estimation with a slight overestimation in January. A
small deviation of 0.03 mg N/l is observed. However, in February, estimated nitrate concentrations show a large deviation from
the eld measurements with a difference of approximately 0.75 mg N/l.
The comparison of the eld measurements and the model results for the mean dissolved oxygen concentration in Limanagz
subregion is given in Fig. 23. At the end of summer season, the estimated concentration of the mean dissolved oxygen is around
5.9 mg O/l, and it is slightly overestimating the measured average values of 5.7 to 6.9 mg O/l. Similar to Kas Subregion with
the decrease in the sea water temperature, the estimations increase to the level of approximately 8.1 mg O/l in winter season.
Fig. 21. Nitrite Concentration Values for Limanagz Subregion (mg N/l).
Fig. 22. Nitrate Concentration Values for Limanagz Subregion (mg N/l).
The model estimations for dissolved oxygen match in general with the measurements in autumn season with a 0.30.5 mg O/l
deviation. However, in the measurements in winter season, especially in February, a large deviation between model estimations
and eld measurements with a difference of 2.54 mg O/l is observed. The reason of this large deviation, which is also observed
in nitrite and nitrate concentration values, is thought to be the momentary regional conditions affecting the eld measurement
in Limanagz Subregon, i.e. unusual discharges and excess surface runoff after rainy weather in February.
5.3. Bucak subregion
Figs. 2426 display the comparison of the mean concentration values for nitrite, nitrate and dissolved oxygen, obtained
through the water quality model with the eld measurements at stations K8 and K9 for Bucak Subregion.
The water quality model estimated the nitrite concentration above 0.05 mg N/l in autumn and 0.04 mg N/l in winter with a
gradual decrease for Bucak subregion. Although the model estimations in January is consistent to the eld measurements with a
Fig. 23. Dissolved Oxygen Concentration Values for Limanagz Subregion (mg O/l).
Fig. 24. Nitrite Concentration Values for Bucak Subregion (mg N/l).
small underestimation of about 0.004 mg N/l, the estimations show respectively a large deviation from the eld measurements
which is approximately 0.010.02 mg N/l.
The nitrate concentrations obtained through the water quality model and the eld measurements for Bucak subregion are
compared in Fig. 25. The model estimation shows stable results around 0.62 mg N/l during the whole period of the study. Field
measurement results almost stay at the average in January; however, there is a signicant underestimation of the model results
for Bucak subregion in February with a deviation of 0.78 mg N/l.
The comparison of the eld measurements and model results for the mean dissolved oxygen concentration in Bucak sub-
region is given in Fig. 26. Similar to Figs. 20 and 23 a gradual increase in model estimations is observed as the ambient water
temperature decreases in winter. For Bucak subregion the model shows a slight overestimation in comparison to the eld mea-
surements with a difference between 0.2 and 0.9 mg O/l. The deviation is more apparent in winter. Despite that the model esti-
mations for dissolved oxygen can be considered quite consistent with the measurements in general, in terms of both levels of the
concentrations.
Fig. 25. Nitrate Concentration Values for Bucak Subregion (mg N/l).
Fig. 26. Dissolved Oxygen Concentration Values for Bucak Subregion (mg O/l).
6. Conclusion
Except an indistinct deviation from the measured values for nitrate concentration in February 2014, the model displays almost
overlapping results for all three parameters in Kas Subregion. Measured values for nitrite concentration in Limanagz Subregion
show a similar distribution whereas the eld measurements of nitrate concentration in February 2014 and of dissolved oxygen
concentration in January and February 2014 deviate distinctly from the model output. It must, however, be stressed that the
January measurements are closer to the model output than February. The Bucak Subregion measurements display a similar
graphic only with a difference of nitrate concentration in eld measurement in February 2014.
These results show that the model demonstrates the changes in nitrite and dissolved oxygen concentration in a fairly real-
istic way. It can also be observed that the model displays close results to the eld measurements of nitrate concentration. For
measurements where the two values derivate, the reason of the derivation is believed to depend on momentary regional condi-
tions in the eld, which can be an unusual discharges, excess surface runoff after rainy weather, or any factor affecting the eld
measurement in February.
In conclusion, it is proved that the water quality model with three computational subregions in Kas Region shows accurate
outputs and has tandem results with the eld measurements.
The eld measurements presented in this study provides a rich data for calibrating the water quality model of HYDROTAM
in marine environment. Future work on the water quality model will develop it according to regional dynamics. The model can
easily be extended to multiple computational zones and simulation periods, and can work coupled with the hydrodynamic and
transport models of HYDROTAM-3D interactively.
As it is demonstrated, HYDROTAM uses a comprehensive method with a 3-dimensional numerical solution scheme for hy-
drodynamics, which provides very precise predictions for the wind and tidal forced circulations in coastal waters. Besides its
precision in coastal hydrodynamics, it stands for a useful water quality tool providing a set of basic ecological simulations for
coastal waters.
Acknowledgments
This study is a part of the governmentally nanced Southwestern Development Agency Support Project called Protection,
Development and Management of Marine and Coastal Areas of Kas, which is nalized in 2014. The output of the model has been
considered in detail and the results are served to the use of coastal management in Kas Region.
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Applied Mathematical Modelling 40 (2016) 18871913

Contents lists available at ScienceDirect

Applied Mathematical Modelling

Water quality modelling in kas bay

2.1. Governing equations

2.2. Boundary conditions

Fig. 1. Nitrogen Cycle in Marine Environment.

2.3. Numerical scheme

2.4. Water quality component

2.4.1. Nitrogen cycle

a. Inorganic matter from the excretion and respiration of phytoplankton.

The rate of change in ammonia concentration can be formulized as follows:

where Kf N is the nitrogen half-saturation constant for phytoplankton uptake in mgN/l.

C NO2 NH4 NO2

Nitrate. The rate of change in nitrite concentration is formulated as follows:

where Kdnit is the rate of denitrication in 1/day.

(T Tre f ) sat

a. Particulate organic fraction of matter produced by excretion.

a. Uptake by pelagic bacteria.

Fig. 2. Phosphorus Cycle in Marine Environment.

nitrogen is formulated as follows:

2.4.2. Phosphorus cycle

a. Inorganic fraction of matter produced by excretion and respiration of phytoplankton.

The rate of change in concentration of the inorganic phosphorus is formulized as follows:

POP is decreased by degradation to dissolved organic phosphorus.

Non-refractory dissolved organic phosphorus decreases by mineralization to inorganic phosphorus.

Fig. 3. Oxygen Cycle in Marine Environment.

a. Photosynthesis of the phytoplankton.

The sinks of the dissolved oxygen are [13]:

a. The respiration of the aquatic life forms.

f f (T ) = KAf (T ) KBf (T ), (46)

Rate coecients for temperature curve 1 f and 2 f are as follows:

re f = Kef e(0,069T ) , (58)

where Kf e is the endogenous respiration constant, Kf p is the photorespiration constant.

G f = pzf Azmax fzf (A) f z (T ) C z . (65)

2.4.5. Pelagic bacteria

b = bNH4 + bPON + bDONnr (67)

bmax (Tre f ) f b (T ) f bNH4 (N)

bmax (Tre f ) f b (T ) f bPON (N)

bmax (Tre f ) f b (T ) f bDONnr (N)

z = Czf E f + Czb E b , (77)

Fig. 4. Location of Kas Region and Field Measurement Points (K).

3.1. Kas subregion

3.2. Limanagz subregion

Fig. 5. Computational Subregions of Kas Region.

3.3. Bucak subregion

Waste water produced by the boats 68 68 68 8 8 8

4.3. Dissolved oxygen

5.1. Kas subregion

5.2. Limanagz subregion

5.3. Bucak subregion

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(T Tre f ) sat