Development of 3D-Coupled hydrodynamics-ecosystem model for Jakarta Bay
Endro Soeyanto* and Akihiko Morimoto***Laboratory for Marine Survey Technology (BTSK)-BPPT, Jakarta Indonesia** Center for Marine Environmental Studies (CMES),Ehime University, Japan
Introduction
Jakarta bay, as one of the entering gate to the Jakarta City, is one of the important waters inIndonesia. According to this function, Jakarta bay has too many changing in hydrodynamics
conditions caused by nature and human activities. The study of current circulation in Jakarta
bay was very important. To study the ocean circulation and physical processes in Jakarta
Bay, a numerical modeling system based on the Princeton Ocean Model (POM Model,Blumberg and Mellor, 1987) has been implemented in the Jakarta Bay.
Although it is clear that Jakarta Bay is heavily impacted by human activities, it is not clear
how the organic inputs interact with physical conditions to inﬂuence the lower trophic levelecosystem. In particular, the physical processes that control the ecosystem are not wellunderstood, so here we examine the interaction between the physical and biologicalprocesses that drive the temporal variation and spatial distribution of nutrients andphytoplankton in Jakarta Bay, using a coupled hydrodynamic–ecosystem model.
A joint collaboation research between Laboratory of Marine Survey Technology(BTSK)-BPPT and Center for Marine and Enviromental Studies (CMES) have beencollected the observation data such as sealevel, temperature-salinity and dissolved oxygen(DO) profiling, ocean current observation, nutrient sampling,etc since December 2015December 2018. These observation data used to perform the above ocean model in JakartaBay.
In this study, we only consider the tidal and wind monsoon as principal forcing to generate
the physical processes in Jakarta Bay waters.
Aims
The aim of this study are,i.e:- to understand the current circulation and to predict the physical processes in Jakarta Bay
using the POM model.
- to predict the distribution of ecosystem parameter such as Dissolved Inorganic Nitrogen(DIN), Dissolved Inorganic Phospate (DIP), phytoplankton type-1 (PHY), zooplankton(ZOO), Detritus (PON) and Dissolved Oxygen (DO)1 / 9Procedures
Numerical Modelling
The Princeton Ocean Model (POM) is a 3-D primitive equations ocean circulation model,
which has been described in detail by Blumberg and Mellor (1987) and Mellor (2004). POM
is a free surface, sigma coordinate model that uses a time-splitting technique to solve
depth-integrated and fully three-dimensional equations with different time steps. The surface
elevation, velocity, temperature, and salinity fields are prognosticated assuming thefundamental hypotheses: (i) that the seawater is incompressible, ii) that the pressure in any
point of the ocean is equal to the weight of the column of water over it (hydrostaticapproximation), and iii) that the density can be expressed in terms of a mean value and asmall fluctuation (Boussinesq’s approximation). Consequently, in a system of orthogonal
Cartesian coordinates, the governing equations are:

𝜕𝑈𝑖
𝜕𝑥𝑖=0

𝜕(𝑈,𝑉)+𝜕𝑡𝜕𝑝𝜕𝑡

𝜕[𝑈𝑖 (𝑈,𝑉)]𝜕𝑥𝑖𝜕𝑝 𝜕𝑝+ 𝑓(−𝑉, 𝑈) = 𝜌0−1 [,𝜕𝑥 𝜕𝑦]+𝜕(𝐾𝑀= −𝜌𝑔𝜕𝑧𝜕𝜃(1)+𝜕𝑆𝜕𝑡𝜕(𝑈𝑖 𝜃)+𝜕𝑥𝑖
𝜕(𝑈𝑖 𝑆)𝜕𝑥𝑖

𝜕(𝑈,𝑉))
𝜕𝑧𝜕𝑧+ (𝐹𝑈, 𝐹𝑉 )

(2)
(3)

==𝜕(𝐾𝐻𝜕𝜃)𝜕𝑧𝜕𝑧
𝜕(𝐾𝐻+𝐹𝜃 +𝜕𝑆)
𝜕𝑧𝜕𝑧

𝜕𝑅(4)

𝜕𝑧+ 𝐹𝑆(5)

Which are KM and KH , are computed according to the Mellor-Yamada 2.5 turbulance closure
scheme (Mellor and Yamada, 1982). This scheme requires progmostic calculations of (q2)and (q2l), where the turbulent kinetic energy is q2/2 and the turbulent macro scale is (l). Theequations that calculate q2 and q2l are similar to those used for temperature and salinity
and include production and dissipation source/sink terms. Horizontal diffusion terms (FU,FV ,F, and FS) are computed using the Smagorinsky (1963) formulation, implemented into POM
according to Mellor and Blumberg (1986). The last term in Eq. (4), is the solar radiation fluxthat penetrates the sea surface. The UNESCO equation of state, as adapted by Mellor(1991) is used. The in situ density is determined as a function of salinity, potential
temperature and pressure; the latter being approximated by the hydrostatic relation andconstant density.

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Model Configuration
The model domain comprises the Jakarta Bay, Indonesia, from 106o 33’ 00”-107o 01’ 30”Eand from 6 o 12’ 00’’ – 5o 49’ 30”S. The bottom topography used the Shuttle RadarTopography

Mission(SRTM)

with30secondgrids(https://topex.ucsd.edu/WWW_html/srtm30_plus.html ). Grid resolution model constructed fromthe topogarphy data for 1/400o x 1/400o degree. In this model version (afterward JB model),there are three open lateral boundaries; at 106.555 oE, at 107.025 oE and 5.825 oN. The JB
model has been configured with a horizontal resolution of 1/400o in latitude by 1/400o inlongitude. In the vertical , the grid has 11 sigma layers with logaritmic distributions at thesurface and the bottom and a linear distribution in between. Other significant model
parameters are given in Table-1.
Table-1. Model Parameter used in The Jakarta Bay (JB) model.
Parameter

Description
Value

C

Non-dimensional constant used in calculating
0.2
the horizontal viscosity for momentum

tprni

Inverse horizontal Prandtl Number0.2

M

Background viscosity
0.00002

ZoBottom roughness length
0.01

text

External mode time step
3 sec

tint

Internal mode time step
60 secOpen lateral boundaries conditions which are derived from FES2016 Global Tide Model aremodified, e.g. tidal amplitude of FES2016 + 0.008m. Therefore, open lateral boundary ofbarotropic tidal currents which are derived 2-D tidal model are applied to the 3-D tidal model.
Surface boundary applied in this model are only the wind data collected from Meteorological
Maritime Station at Tanjung Priok Port, Jakarta (106° 52' 49.7”E, 06° 06' 28.3” S). Timesimulation period for the model is started from June 1, 2015 untill December 31, 2016 (1.5years).
Ecosystem ModelThe ecosystem model (Figure 2) has five compartments, namely nitrate (NO3), ammonium(NH4), phytoplankton (F), zooplankton (Z), and benthic detritus.

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Results
In the following paragraph, the harmonic analyses for four constituents (M2,S2, K1 and O1)
from model results compare to the tide observations as reported by Koropitan and Ikeda(2008) on a tidal station at in Jakarta Port (106.89083oE, 6.10667oS). Table-2 show themodel is very close to the observation. Some small differences of phase is considered as
mixing process of water masses in the Jakarta Bay.
After the wind forcing considered in the JB’s 3D-Tide model, we did the monthly-mean ofsurface horizontal distributions of sea level and current velocity fields from the daily modelresults. The analysis started from August 2015 to December 2016 due to neglect the spin-up
time period (~about 2 months).
In August-September 2015 the vector fields flows from the east to west side of Jakarta Bay.
Vector field on September 2015 tends to increase due to the moonsoon winds change fromeast to east-west transition monsoon winds. Sea surface tends to increase on western sideof Jakarta Bay on August-September 2015. But, starting in October-December 2015 theincreasing of sea surface propagates to the center and eastern side of Jakarta Bay(Figure-1).

Table-2. Comparison of observed and modelled M2,S2,K1 & O1 tidal elevations at thecoastal tide-gauge station at Jakarta (106° 52' 49.7”E, 06° 06' 28.3” S).
________________________________________________________________________
Constituents

Observed*ModelAmplitude (cm)Phase (oG)________________________________________________________________________
M2
S2
K1
O1

5.41

5.45

140.85134.06

5.04

5.08

78.08

73.69

25.17

24.92

34.73

32.69

13.75

13.70

25.32

22.84

________________________________________________________________________*Koropitan and Ikeda,2008

Again, the surface currents tends to flow from west to east side Jakarta Bay

duringDecember 2015 to February 2016. But in this period, there are three positions of highsealevel in Jakarta Bay, i.e. east side (December 2015), west side (January 2016) andeast side (February 2016). It means the model results shows the anomaly sea surface in4 / 9

January 2016.
From March-May 2016 the surface velocity fields shows changing from southward towestward. This conditioo is similar to the propagation of high sea surfaces (the transitionmonsoon period). The easterly monsoon wind looks dominant in period May to August 2016.
In this period the surface current propagate from east to west side of Jakarta Bay (westwardcurrents). This situation confirmed to the existence of high sea surface in west side ofJakarta Bay.
The westward surface current fields increase from September to December 2016. Thissituation is also coinciding to the presence of high sea surface in east side of Jakarta Bay.
Perspective in the future
To complete this physical-ecosystem model in Jakarta bay, we still find the good riverdischarges data surronding the bay, at least between June 2015 to 2016.

5 / 9Figure-1. Monthly mean of Surface Current and Sealevel from June 2015 to December2016(to be continued)

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Figure-1. Monthly mean of Surface Current and Sealevel from June 2015 to December
2016(to be continued)

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Figure-1. Monthly mean of Surface Current and Sealevel from June 2015 to December
2016
References
Blumberg, A. and Mellor, G., 1987: A Description of a Three-Dimensional Coastal Ocean
Circulation Model, in: Three-Dimensional Coastal Ocean Models, Coastal Estuarine Science,edited by: Heaps, N. S., American Geophysical Union, 1–16.
Mellor, G.: An equation of state for numerical models of oceans and estuaries, J. Atmos.
Oceanic Tech., 8, 609–611, 1991.
Mellor, G. and Blumberg, A. F.: Modeling Vertical and Horizontal Diffusivities with the Sigma
Coordinate System, Mon. Weather Rev., 113, 1279–1383, 1986.
Mellor, G. and Yamada, T.: Development of a turbulence closure sub-model for geophysicalfluid problems, Rev. Geophys., 20, 851–875, 1982
Mellor, G. 2004 User’s Guide for a Three-Dimensional Primitive Equation, Numerical Ocean
Model. Princeton University, Princeton,N.J., 1–56.
Koropitan, A.F,

Ikeda,

Damar A. and Yamanaka, Y., 2009. Influences of physicalprocesses on the ecosystem of Jakarta Bay: a coupled physical–ecosystem modelexperiment. ICES Journal of Marine Science, Volume 66, Issue 2, 1 March 2009, Pages
336–348
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Koropitan, A. F., and Ikeda, M. 2008. Three-dimensional modelling of tidal circulation andmixing over the Java Sea. Journal of Oceanography, 64: 61–80.

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