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A particle tracking model, based on output from the Princeton Ocean Model (POM), is established to study the year-to-year variation of the gathering of giant jellyfish Nemopilema nomurai in early autumn in the Yellow Sea. Particles standing for scyphistoma adhered to the bottom are put initially along the coast from the Changjiang River estuary to Haizhou Bay. The triggering temperature for scyphistoma strobilation is set to 13 degrees C. The simulated N. nomurai distribution is in good agreement with observations in August 2009. Model results suggest that more jellyfish gathered near tidal front in August September of 2008 than during the same period of 2009. Using a set of sensitivity experiments, the influences of temperature and circulation on N. nomurai gathering are discussed. Model results suggest the modeled difference in fall gathering of jellyfish between 2008 and 2009 can be attributed more to changes in circulation than the triggering of strobilation by spring bottom temperature. (C) 2014 Elsevier B.V. All rights reserved.

Pagasitikos gulf is a semi-enclosed basin highly influenced both by anthropogenic activities (inflow of nutrients at the north and west parts) as well as by water exchange between the gulf and the Aegean Sea at its south part (Trikeri channel) resulting in the development of functional sub-areas within the gulf. Thus the inner part is characterised by eutrophic conditions with sporadic formation of harmful algal blooms whilst the central part acts as a buffer with mesotrophic characteristics influenced by the outer area. In a companion paper, the circulation fields and the development of water masses in the Pagasitikos gulf were explored. The aim of this study is to investigate the interactions between the physical and biogeochemical systems in the Pagasitikos gulf by coupling advanced hydrodynamic and ecological models. The simulation system comprises two on-line coupled sub-models: a three-dimensional hydrodynamic model based on the Princeton Ocean Model (POM) and an ecological model adapted from the European Regional Seas Ecosystem Model (ERSEM) for this specific ecosystem. After a model spin up period of 10 years, the results from an annual simulation are presented. Emphasis is given to the description of the spatial and temporal variability of the ecosystem parameters as well as to the relationship between physical forcing and the evolution of the ecosystem along with other factors affecting the nutrient cycling and primary production. A cost function is used for the validation of model results with field data. Simulation results are in good agreement with in-situ data illustrating the role of the physical processes in determining the evolution and variability of the ecosystem, as well as highlighting the potential usefulness of the model as an operational tool to support environmental management decisions.

Within the framework of the European INSEA project, an advanced assimilation system has been implemented for the Pagasitikos Gulf ecosystem. The system is based on a multivariate sequential data assimilation scheme that combines satellite ocean sea color (chlorophyll-a) data with the predictions of a three-dimensional coupled physical–biochemical model of the Pagasitikos Gulf ecosystem presented in a companion paper. The hydrodynamics are solved with a very high resolution (1/100°) implementation of the Princeton Ocean Model (POM). This model is nested within a coarser resolution model of the Aegean Sea which is part of the Greek POSEIDON forecasting system. The forecast of the Aegean Sea model, itself nested and initialized from a Mediterranean implementation of POM, is also used to periodically re-initalize the Pagatisikos hydrodynamics model using variational initialization techniques. The ecosystem dynamics of Pagasitikos are tackled with a stand-alone implementation of the European Seas Ecosystem Model (ERSEM). The assimilation scheme is based on the Singular Evolutive Extended Kalman (SEEK) filter, in which the error statistics are parameterized by means of a suitable set of Empirical Orthogonal Functions (EOFs). The assimilation experiments were performed for year 2003 and additionally for a 9-month period over 2006 during which the physical model was forced with the POSEIDON-ETA 6-hour atmospheric fields. The assimilation system is validated by assessing the relevance of the system in fitting the data, the impact of the assimilation on non-observed biochemical processes and the overall quality of the forecasts. Assimilation of either GlobColour in 2003 or SeaWiFS in 2006 chlorophyll-a data enhances the identification of the ecological state of the Pagasitikos Gulf. Results, however, suggest that subsurface ecological observations are needed to improve the controllability of the ecosystem in the deep layers.

We present the development and validation of an eddy-resolving sequential data assimilation system for the Aegean Sea hydrodynamics that has been developed as part of the Poseidon operational system. The assimilation scheme is based on the Singular Evolutive Extended Kalman (SEEK) filter which is an error subspace Extended Kalman filter that operates with low-rank error covariance matrices as a way to reduce the computational burden. The filter was used to correct the forecast state of a 1/20° Princeton Ocean Model (POM) of the Aegean Sea every time new observations were available. The model is forced with hourly fluxes from a 1/10° ETA regional atmospheric model and is one-way nested to a 1/10° POM model of the Eastern Mediterranean Sea. The assimilated data set is multivariate including weekly AVISO sea level anomalies, weekly AVHRR sea surface temperature, and daily Ferrybox sea surface salinity (SSS) along the ferry boat route from Piraeus to Heraklion. Data assimilation experiments are performed to validate the system over a 6-month period (January–June, 2004). In one of the assimilation experiments, where the Ferrybox SSS data were not assimilated and used as independent observations, the multivariate assimilation system was able to reduce the error on the SSS prediction. Additional assimilation of the Ferrybox data on a daily basis shows their positive impact on other predicted variables of the system and their significant local effect on the SSS prediction within the southern Aegean Sea.

This study investigates the effectiveness of the Singular Evolutive Extended Kalman filter (SEEK) and its variants (SEIK and SFEK filters) for data assimilation into a Princeton Ocean Model (POM) of the Mediterranean Sea. The SEEK filters are sub-optimal Kalman filters based on the approximation of the filter's error covariance matrices by singular low-rank matrices, reducing in this way extensive computational burden. At the initialization, the filters error covariance matrix is parameterized by a set of multivariate empirical orthogonal functions (EOFs) which describe the dominant modes of the system's variability. The Mediterranean model is implemented on a 1/4° × 1/4° horizontal grid with 25 sigma levels and is forced with 6-hour ECMWF re-analysis atmospheric data. Several twin experiments, in which pseudo-observations of altimetric data and/or data profiles were assimilated, were first performed to evaluate the filters performances and to study their sensitivities to different parameters and setups. The results of these experiments were very encouraging and helped in setting up an effective configuration for the assimilation of real data in near-real time situation. In the hindcast experiments, Topex/Poseidon and ERS weekly sea level anomaly data were first assimilated during 1993 and the filters solution was evaluated against independent Reynolds sea surface temperature (SST) analysis. The assimilation system was able to significantly enhance the consistency between the model and the assimilated data, although the improvement with respect to independent SST data was significantly less pronounced. The model SST was only improved after including SST data in the assimilation system.

Within the framework of several local and international programs, a quasi-operational ocean-forecasting system for the Southeastern Mediterranean Sea has been established and evaluated through a series of preoperational tests. The Princeton Ocean Model (POM) is used for simulating and predicting the hydrodynamics while the Wave Model (WAM) is used for predicting surface waves. Both models were set up to allow varying resolution and multiple nesting. In addition, POM was set up to be easily relocatable to allow rapid deployment of the model for any region of interest within the Mediterranean Sea. A common requirement for both models is the need for atmospheric forcing. Both models require time varying wind or wind stress. In addition, the hydrodynamic model requires initial conditions as well as time dependent surface heat fluxes, fresh water flux, and lateral boundary conditions at the open boundaries. Several sources of atmospheric forcing have been assessed based on their availability and their impact on the quality of the ocean models' forecasts. The various sources include operational forecast centers, other research centers, as well as running an in-house regional atmospheric model. For surface waves, higher spatial and temporal resolution of the winds plays a central role in improving the forecasts in terms of significant wave height and the timing of various high wave events. For the hydrodynamics, using the predicted wind stress and heat fluxes directly from an atmospheric model can potentially produce short range ocean forecasts that are nearly as good as hindcasts forced with gridded atmospheric analyses. Finally, a high-resolution, nested version of the model has shown to be stable under a variety of forcing conditions and time scales, thus indicating the robustness of the selected nesting strategy. For the southeastern corner of the Mediterranean, at forecast lead times of up to 4 days the high-resolution model shows improved skill over the coarser resolution driving model when compared to satellite derived sea surface temperatures. Most of the error appears to be due to the analysis error inherent in the initial conditions.

Logistics and results of a real-time modeling effort, which took place in fall 2000 in the waters between Corsica and Italy in the Mediterranean Sea, are presented. The major objective was to nest a high-resolution local version of the Harvard Ocean Prediction System (HOPS) into a coarse resolution Colorado University Princeton Ocean Model (CUPOM) covering the northern part of the Western Mediterranean. Due to the different designs of CUPOM and HOPS, traditional nesting methods were not successful. Therefore, a new method was developed that assimilated the CUPOM prognostic fields into HOPS instead of prescribing them only along the open boundaries. Another objective of the effort was to set up and test a data distribution system, providing Internet-based rapid data transfer among the project partners being partly at sea and partly on land in different continents. It is shown that such a system works, enabling turnaround times of less than a day from the time when measurements are taken to the release of the model forecast.

The long-term changes in the thermohaline circulation and water mass characteristics of the Mediterranean Sea caused by the damming of the Nile in 1964 are investigated using a 3-D primitive equation model (Princeton Ocean Model, POM). The model is first integrated for 65 years under climatological forcing and without taking into account the Nile runoff to obtain an initial steady state. Then the model is integrated for 75 years with the Nile outflow included until it reaches a steady state representative of that existing in the Mediterranean prior to the damming. Finally, the model is integrated for another 75 years eliminating the Nile runoff to reach a new steady state. The model results show that the absence of the Nile freshwater input induces a saltier surface layer in the vicinity of the Rhodes Gyre thus favoring the preconditioning for the formation of the Levantine Intermediate Water (LIW). This results in about 30% increase of the LIW formation rate. Intermediate waters become saltier, and as they are transported westward they reduce the stability of the water column in the deep-water formation sites, namely the South Adriatic and the Gulf of Lions. Thus saltier and larger amounts of dense waters are formed filling the deep parts of the Mediterranean Sea. According to the model, the Nile damming explains about 45% of the observed salinity increasing trend occurring over the last 40 years in the Western Mediterranean Deep Water (WMDW). Furthermore, model results demonstrate that the Nile damming played a crucial role in the long-term salt preconditioning of the surface/intermediate layers of the Cretan Sea, thus contributing in triggering the Eastern Mediterranean climatic transient in the late 1980s.

With the aim of using data assimilation techniques for state estimation in marine ecosystem models, a singular evolutive extended Kalman (SEEK) filter was used to assimilate real in situ data in a water column marine coupled physical-biogeochemical model describing the Cretan sea ecosystem. The biogeochemistry of the ecosystem is described by the European Regional Sea Ecosystem Model (ERSEM), while the Princeton Ocean Model (POM) describes the physical forcing. In the SEEK filter, the error statistics are parameterised by means of a suitable set of empirical orthogonal functions (EOFs). Numerical experiments were conducted to evaluate the performance of this assimilation system. In this context, sensitivity studies to the observations are also presented and discussed.

A modelling procedure of hourly time discretisation is developed in order to study the effects of episodic rainfall events to the dynamics of coastal marine environments. This methodology was applied on the gulf of Gera, Island of Lesvos, Greece, a semi-enclosed and shallow ecosystem surrounded by an intensively cultivated watershed. The simulation of biological and chemical processes in the water column was focused on the interactions of inorganic nutrients, primary producers and organic matter. The hydrodynamic behaviour of the area was estimated by the combination of the Princeton Ocean Model and a multiple-box mass balance approach in order to describe the tidal hydraulic regime. The estimation of nutrient fluxes due to non-point sources was based on a modification of the unit-mass response functions. The results have shown that nutrient loading from agricultural runoff could be considerable after episodic rainfall events, resulting in an increase of the nutrient stock from 40% to 60%. The responses of the primary producers are regulated from weather conditions of the following period and the residence time of excessive nutrient loads within the gulf that ranges from a time span of less than 10 days to 1 month period. The good fit between simulated and experimental data supports the view that this integrated modelling approach should be considered as a realistic reproduction of the dynamics of coastal marine ecosystems and be used for testing various scenarios concerning their sustainability.

The Mediterranean Sea has many coastal regions with complex topography. The study concentrates on semi-enclosed regions that receive freshwater input from rivers. The development of the river plumes under the influence of the important circulation forcing mechanisms and under the guidance of the topographic controls is examined. The study rivers are the Po (North Adriatic) and the Axios (North Aegean). They both provide important inputs of low-salinity waters and land-drained materials for their respected shelf regimes. The rivers are parameterised as sources of zero salinity in the three-dimensional, primitive equation Princeton Ocean Model (POM). The river plumes are studied in the presence of realistic topography and idealised winds. The influence of the general basin circulation on the plume structure is also examined. The development and evolution of the two river plumes exhibit the following common characteristics. The buoyancy-driven flow is characterised by an anticyclonic bulge seaward of the river mouth and a coastal current south of the discharge site contained within a narrow strip along the coast. The coastal current has a southward direction, as both rivers discharge at the west side of the basin. The “meandering” along this dynamic region is due to a baroclinic instability process. Downwelling-favorable winds enhance the buoyancy-driven coastal current and restrict offshore removal of low-salinity waters, while the opposite holds for upwelling-favorable winds. The circulation is influenced by the presence of three coastal boundaries. Differences in the modeled phenomena for the two study regions arise from (a) interaction with ambient flow, which may substantially influence the behavior of the plumes, and (b) the topography and geometry of each basin. For instance, the presence of strong neighboring rivers influences the Po River plume. On the other hand, the narrowness of the basin near the discharge site of the Axios River allows for offshore expansion of the plume all the way to the east coast and the establishment of anticyclonic flow over a large part of the shelf, regardless of wind conditions.

Evaporation over the Mediterranean basin produces a salty water mass that overflows the relatively narrow and shallow Strait of Gibraltar. The outflow is investigated with the three-dimensional Princeton Ocean Model. The model makes use of a bottom-following, sigma-coordinate system and an imbedded turbulence closure scheme to simulate the bottom boundary layer. Starting as a channel flow confined by the sidewalls of the trench of the westernmost part of the Strait, the bottom boundary current descends the steep continental slope of the eastern Gulf of Cadiz. The flow is controlled by a balance of the pressure gradient and the Coriolis acceleration, entrainment and bottom friction. Downslope Ekman fluxes are largest at the shelf break near the entrance of the Strait where we observe the most pronounced entrainment of North Atlantic Central Water. Profiles of modeled horizontal velocity, as well as scalar and turbulent quantities, show a remarkable resemblance to observed features. The model reproduces the “nose” shape of the velocity profile that is typical for a density current; below the velocity maximum, there is a well-mixed layer and a stratified shear layer exists above the nose. The evolution of water mass properties along the path of the outflow agrees favorably with observations and the sensitivity of the Mediterranean outflow (MO) to varying source water properties is investigated. The combined effect of initial stratification, differential entrainment, and routing by the topography leads to the evolution of the well-known two-core structure of the bottom layer. Whereas the upper part of the outflow continues to follow the continental slope northward in the form of a bottom boundary current after it passes Cape St. Vincent, the lower core separates from the slope and there is a lateral spreading of the saline and warm outflow water in the depth range of the lower salinity maximum (centered at about 1200 m). The outflow becomes hydrodynamically unstable and lenses of saline water shed from the core, carrying their water mass characteristic into the Atlantic. The model results confirm that the area of Cape St. Vincent is a prominent formation area for Mediterranean water (MW) eddies (Meddies).

Within the framework of a Mediterranean model evaluation experiment, a Princeton Ocean Model (POM) of the Mediterranean has been developed in University of Athens. In this paper, the results of the coarse resolution version (1/4°×1/4°) are presented. SST and SSS were restored to monthly climatology with a time constant of 1 m day−1. The seasonal variability of the general circulation was found to be in a good agreement with the observed patterns and some known features have been modelled for the first time. The implied surface fluxes (heat loss and salt gain) were too weak and resulted in absence of deep water formation.