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In ∼1990 a new source of deep water formation in the Eastern Mediterranean was found in the southern part of the Aegean sea. Till then, the only source of deep water formation in the Eastern Mediterranean was in the Adriatic sea; the rate of the deep water formation of the new Aegean source is 1 Sv, three times larger than the Adriatic source. We develop a simple three-box model to study the stability of the thermohaline circulation of the Eastern Mediterranean sea. The three boxes represent the Adriatic sea, Aegean sea, and the Ionian seas. The boxes exchange heat and salinity and may be described by a set of nonlinear differential equations. We analyze these equations and find that the system may have one, two, or four stable flux states. We conjecture that the change in the deep water formation in the Eastern Mediterranean sea is attributed to a switch between the different states on the thermohaline circulation; this switch may result from decreased temperature and/or increased salinity over the Aegean sea.

Based on a fully coupled, high-resolution regional climate model, this study analyzed three-dimensional temperature and momentum changes in the South China Sea (SCS) from 1970 to 2000, during which period the climate shifts from a decadal La Niña-like condition (before 1976/1977) to a decadal El Niño-like condition afterward. With a set of partially coupled experiments, sea surface temperature (SST) and kinetic energy (KE) changes during this period are first decomposed into two components: those induced by lateral boundary forcing and those induced by atmospheric surface fluxes. The results showed that the total SST and KE changes show an increasing trend from 1970 to 2000. The two decomposed components together determined 96 and 89% of the SST and KE changes, respectively, implying their dominant roles on the SCS's surface variability. Spatially, a sandwich pattern of air-sea forcing relationship is revealed in the SCS basin. The increased KE, represented by a cyclonic flow anomaly in the northern SCS, was induced by enhanced cold water intrusion from Pacific into the SCS via the Luzon Strait (boundary forcing). This cold-water inflow, however, resulted in SST cooling along the northern shelf of the SCS. The maximal SST warming occurred in the central SCS and was attributed to the wind-evaporation-SST (WES) positive feedback (surface forcing), in which a southwestward wind anomaly is initialized by SST gradients between the northern and southern SCS. This wind anomaly decelerates the southwestly summer monsoons and in turn increases the SST gradients. Over the shallow Sunda shelf, which is far from the Luzon Strait, the SST/KE variability appeared to be determined primarily by local air-sea interactions. Furthermore, analyses on subsurface components indicated that the subsurface temperature changes are primarily induced by internal ocean mixing, which becomes significantly important below the thermocline. The enhanced subsurface flow is driven by the Luzon Strait

Linear and nonlinear radiating instabilities of an eastern boundary current are studied using a barotropic quasigeostrophic model in an idealized meridional channel. The eastern boundary current is meridionally uniform and produces unstable modes in which long waves are most able to radiate. These long radiating modes are easily suppressed by friction because of their small growth rates. However, the long radiating modes can overcome friction by nonlinear energy input transferred from the more unstable trapped mode and play an important role in the energy budget of the boundary current system. The nonlinearly powered long radiating modes take away part of the perturbation energy from the instability origin to the ocean interior. The radiated instabilities can generate zonal striations in the ocean interior that are comparable to features observed in the ocean. Subharmonic instability is identified to be responsible for the nonlinear resonance between the radiating and trapped modes, but more general nonlinear triad interactions are expected to apply in a highly nonlinear environment., MIT-WHOI Joint Program in Physical Oceanography, MIT Y-S Fellowship, United States. National Aeronautics and Space Administration (Grant NNX12AD47G), Grant OCE-0752346

Climatological high resolution coupled climate model simulations for the maritime continent have been carried out using the regional climate model (RegCM) version 3 and the finite volume coastal ocean model (FVCOM) specifically designed to resolve regions characterized by complex geometry and bathymetry. The RegCM3 boundary forcing is provided by the EMCWF-ERA40 re-analysis. FVCOM is embedded in the Global MITgcm which provides boundary forcing. The domain of the coupled regional model covers the entire South China Sea with its through-flow, the entire Indonesian archipelago with the Indonesian through-flow (ITF) and includes a large region in the western Pacific and eastern Indian oceans. The coupled model is able to provide stable and realistic climatological simulations for a specific decade of atmospheric–oceanic variables without flux correction. The major focus of this work is on oceanic properties. First, the coupled simulation is assessed against ocean-only simulations carried out under two different sets of air–sea heat fluxes. The first set, provided by the MITgcm, is proved to be grossly deficient as the heat fluxes are evaluated by a two-dimensional, zonally averaged atmosphere and the simulated SST have anomalous cold biases. Hence the MITgcm fluxes are discarded. The second set, the NCEP re-analysis heat fluxes, produces a climatological evolution of the SST with an average cold bias of ~−0.8 °C. The coupling eliminates the cold bias and the coupled SST evolution is in excellent agreement with the analogous evolution in the SODA re-analysis data. The detailed comparison of oceanic circulation properties with the International Nusantara Stratification and Transport observations shows that the coupled simulation produces the best estimate of the total ITF transport through the Makassar strait while the transports of three ocean-only simulations are all underestimated. The annual cycle of the transport is also very well reproduced. The coupling also consi, Singapore. National Research Foundation (Center for Environmental Sensing and Monitoring (CENSAM)), Singapore-MIT Alliance for Research and Technology (SMART) program, National Natural Science Foundation (China) (NSFC, No. 41106003)

This paper is the outcome of a workshop held in Rome in November 2011 on the occasion of the 25th anniversary of the POEM (Physical Oceanography of the Eastern Mediterranean) program. In the workshop discussions, a number of unresolved issues were identified for the physical and biogeochemical properties of the Mediterranean Sea as a whole, i.e., comprising the Western and Eastern sub-basins. Over the successive two years, the related ideas were discussed among the group of scientists who participated in the workshop and who have contributed to the writing of this paper. Three major topics were identified, each of them being the object of a section divided into a number of different sub-sections, each addressing a specific physical, chemical or biological issue: 1. Assessment of basin-wide physical/biochemical properties, of their variability and interactions. 2. Relative importance of external forcing functions (wind stress, heat/moisture fluxes, forcing through straits) vs. internal variability. 3. Shelf/deep sea interactions and exchanges of physical/biogeochemical properties and how they affect the sub-basin circulation and property distribution. Furthermore, a number of unresolved scientific/methodological issues were also identified and are reported in each sub-section after a short discussion of the present knowledge. They represent the collegial consensus of the scientists contributing to the paper. Naturally, the unresolved issues presented here constitute the choice of the authors and therefore they may not be exhaustive and/or complete. The overall goal is to stimulate a broader interdisciplinary discussion among the scientists of the Mediterranean oceanographic community, leading to enhanced collaborative efforts and exciting future discoveries.

Non-tidal sea level anomalies (SLAs) can be produced by many different dynamical phenomena over many time scales, and they can induce serious damages in coastal regions especially during extreme events. In this work, we focus on the SLAs in the South China Sea (SCS) to understand whether and how they can be related to the large-scale, seasonal monsoon system which dominates the SCS circulation and dynamics. We have two major objectives. The first one is to understand whether the NE (winter) and SW (summer) monsoons can be responsible for the persistent SLAs, both positive and negative, observed at the SCS ends along the main monsoon path. The second objective is to understand the SCS response as a free system upon onset/relaxation or sudden changes in the forcing wind. It is well known that sudden changes in the forcing mechanism induce free oscillations, or seiches, in closed, semi-enclosed basins and harbors, and we want to identify the possible seiche modes of the SCS. To our knowledge, these two objectives have not been previously addressed. We address these objectives both through observational analysis and modeling simulations. Multi-year tide-gauge data from stations along the coastal regions of the SCS are analyzed examining their spatial correlations. Strong negative correlations are found between the northeast and southwest stations at the two ends of the SCS under the path of the NE/SW monsoons. They correspond to wind-induced positive/negative sea level set-ups lasting for the entire monsoon season and changing sign from winter to summer. Short periods of negative correlations are also found between the SLAs at eastern and western stations during El Niño years in which the monsoons are weaker and have an enhanced E/W component inducing corresponding sea level set-ups. The tide-gauge station at Tanjong Pagar at the southwest SCS end near Singapore is chosen to study four extreme SLAs events in the observational record during 1999. Modeling simulations are, Singapore-MIT Alliance for Research and Technology (Center for Environmental Sensing and Modeling (CENSAM))

A simple barotropic quasi-geostrophic model is used to demonstrate that instabilities radiated from an unstable eastern boundary current can generate zonal striations in the ocean interior with realistic wavelengths and amplitudes. Nonlinear transfer of energy from the more unstable trapped modes is important for radiating modes to overcome friction. The dynamics shown here are generic enough to point to the eastern boundary current as a likely source of the observed striations extending from oceanic eastern boundaries., United States. National Aeronautics and Space Administration (Grant NNX12AD47G), National Science Foundation (U.S.) (Grant OCE-0752346), Massachusetts Institute of Technology (Y-S Fellowship), Joint Program in Oceanography/Applied Ocean Science and Engineering. Education Office

URL to conference page. Scroll down to 2009 conference (June 21-26), click "Paper and session list," and search under Patrikalakis' name., Oceanographic features such as jets and vortices are often found downstream of obstacles and landforms such as islands or peninsulas. Such features have high spatial and temporal variability and are, hence, interesting but difficult to measure and quantify. This paper discusses an experiment to identify and resolve such oceanographic features in Selat Pauh, in the Straits of Singapore. The deployment formation for multiple robotic vehicles (Autonomous Surface Craft - ASC), the measurement instruments, and the algorithms developed in extracting oceanographic field variables are described. These were based on two ocean field predictions from well-known geophysical flow dynamic models. Field experiments were carried out and comparison of the forecasts with measurements was attempted. To investigate an unexpected behaviour of one ASC, hindcasts with wind effects and simulation with vortex feature extraction on a larger domain with more involved bathymetry were also partially carried out., Singapore-MIT Alliance for Research and Technology, Singapore. National Research Foundation (SMART/CENSAM initiative)

In June of 2009, a sea trial was carried out around Singapore to study and monitor physical, biological and chemical oceanographic parameters. Temperature, salinity and velocities were collected from multiple vehicles. The extensive data set collected in the Serangoon Harbour provides an opportunity to study barotropic and baroclinic circulation in the harbour and to apply data assimilation methods in the estuarine area. In this study, a three-dimensional, primitive equation coastal ocean model (FVCOM) with a number of vertical layers is used to simulate barotropic and baroclinic flows and reconstruct the vertical velocity structures. The model results are validated with in situ ADCP observations to assess the realism of the model simulations. EnKF data assimilation method is successively implemented to assimilate all the available ADCP data, and thus correct for the model forecast deficiencies., Singapore. National Research Foundation, Singapore-MIT Alliance, Singapore-MIT Alliance. Center for Environmental Sensing and Monitoring

The upper layer, wind-driven circulation of the South China Sea (SCS), its through-flow (SCSTF) and the Indonesian through flow (ITF) are simulated using a high resolution model, FVCOM (finite volume coastal ocean model) in a regional domain comprising the Maritime Continent. The regional model is embedded in the MIT global ocean general circulation model (ogcm) which provides surface forcing and boundary conditions of all the oceanographic variables at the lateral open boundaries in the Pacific and Indian oceans. A five decade long simulation is available from the MITgcm and we choose to investigate and compare the climatologies of two decades, 1960–1969 and 1990–1999. The seasonal variability of the wind-driven circulation produced by the monsoon system is realistically simulated. In the SCS the dominant driving force is the monsoon wind and the surface circulation reverses accordingly, with a net cyclonic tendency in winter and anticyclonic in summer. The SCS circulation in the 90s is weaker than in the 60s because of the weaker monsoon system in the 90s. In the upper 50 m the interaction between the SCSTF and ITF is very important. The southward ITF can be blocked by the SCSTF at the Makassar Strait during winter. In summer, part of the ITF feeds the SCSTF flowing into the SCS through the Karimata Strait. Differently from the SCS, the ITF is primarily controlled by the sea level difference between the western Pacific and eastern Indian Ocean. The ITF flow, consistently southwestward below the surface layer, is stronger in the 90s. The volume transports for winter, summer and yearly are estimated from the simulation through all the interocean straits. On the annual average, there is a ∼5.6 Sv of western Pacific water entering the SCS through the Luzon Strait and ∼1.4 Sv exiting through the Karimata Strait into the Java Sea. Also, ∼2 Sv of SCS water enters the Sulu Sea through the Mindoro Strait, while ∼2.9 Sv flow southwards through the Sibutu Strait merging into, Singapore. National Research Foundation (Singapore-MIT Alliance for Research and Technology Center. Center of Environment Sensing and Modeling Program)

Based on a high-resolution (0.1° × 0.1°) regional ocean model covering the entire northern Pacific, this study investigated the seasonal and interannual variability of the Indonesian Throughflow (ITF) and the South China Sea Throughflow (SCSTF) as well as their interactions in the Sulawesi Sea. The model efficiency in simulating the general circulations of the western Pacific boundary currents and the ITF/SCSTF through the major Indonesian seas/straits was first validated against the International Nusantara Stratification and Transport (INSTANT) data, the OFES reanalysis, and results from previous studies. The model simulations of 2004–12 were then analyzed, corresponding to the period of the INSTANT program. The results showed that, derived from the North Equatorial Current (NEC)–Mindanao Current (MC)–Kuroshio variability, the Luzon–Mindoro–Sibutu flow and the Mindanao–Sulawesi flow demonstrate opposite variability before flowing into the Sulawesi Sea. Although the total transport of the Mindanao–Sulawesi flow is much larger than that of the Luzon–Mindoro–Sibutu flow, their variability amplitudes are comparable but out of phase and therefore counteract each other in the Sulawesi Sea. Budget analysis of the two major inflows revealed that the Luzon–Mindoro–Sibutu flow is enhanced southward during winter months and El Niño years, when more Kuroshio water intrudes into the SCS. This flow brings more buoyant SCS water into the western Sulawesi Sea through the Sibutu Strait, building up a west-to-east pressure head anomaly against the Mindanao–Sulawesi inflow and therefore resulting in a reduced outflow into the Makassar Strait. The situation is reversed in the summer months and La Niña years, and this process is shown to be more crucially important to modulate the Makassar ITF’s interannual variability than the Luzon–Karimata flow that is primarily driven by seasonal monsoons.

Decadal variability of the South China Sea (SCS) sea surface temperature (SST) during 1982–2014 is investigated using observations and ocean reanalysis datasets. The SCS SST shows an abrupt transition from a cold-to-warm regime in the late 1990s. Based on the long-term SST variability two epochs are defined, 1982–1996 and 2000–2014 as cold and warm regimes respectively, spanning on either side of the 1997–1999 SCS warming. Despite the occurrence of strong El Nino induced warming events, the SST anomalies tend to be negative in the cold regime. Conversely during the warm regime, the positive SST anomalies have dominated over the La Nina driven cooling events. The cold (warm) SST regime is marked by net heat gain (loss) by the SCS. The long-term variations of net surface heat flux are mainly driven by the latent heat flux anomalies while the short wave flux plays a secondary role. Low-frequency variability of the South China Sea throughflow (SCSTF) appears to be closely related to the SCS SST regime shift. The SCSTF shows reversing trends during the cold and warm epochs. The weakened SCSTF in the warm regime has promoted the SCS warming by limiting the outward flow of warm water from the SCS. Meanwhile, enhanced SCSTF during the cold regime acts as a cooling mechanism and lead to persistent negative SST anomalies. The change in trend of the SCSTF and SST regime shift coincides with the switching of pacific decadal oscillation from a warm to cold phase in the late 1990s., Singapore. National Research Foundation (Singapore MIT Alliance for Research and Technology’s Centre for Environmental Sensing and Modeling interdisciplinary research program)

Among the semi-enclosed basins of the world ocean, the South China Sea (SCS) is unique in its configuration as it lies under the main southwest-northeast pathway of the seasonal monsoons. The northeast (NE) monsoon (November–February) and southwest (SW) monsoon (June–August) dominate the large-scale sea level dynamics of the SCS. Sunda Shelf at the southwest part of SCS tends to amplify Sea Level Anomalies (SLAs) generated by winds over the sea. The entire region, bounded by Gulf of Thailand on the north, Karimata Strait on the south, east cost of Peninsular Malaysia on the west, and break of Sunda Shelf on the east, could experience positive or negative SLAs depending on the wind direction and speed. Strong sea level surges during NE monsoon, if coincide with spring tide, usually lead to coastal floods in the region. To understand the phenomena, we analyzed the wind-driven sea level anomalies focusing on Singapore Strait (SS), laying at the most southwest point of the region. An analysis of Tanjong Pagar tide gauge data in the SS, as well as satellite altimetry and reanalyzed wind in the region, reveals that the wind over central part of SCS is arguably the most important factor determining the observed variability of SLAs at hourly to monthly scales. Climatological SLAs in SS are found to be positive, and of the order of 30 cm during NE monsoon, but negative, and of the order of 20 cm during SW monsoon. The largest anomalies are associated with intensified winds during NE monsoon, with historical highs exceeding 50 cm. At the hourly and daily time-scales, SLA magnitude is correlated with the NE wind speed over central part of SCS with an average time lag of 36–42 h. An exact solution is derived by approximating the elongated SCS shape with one-dimensional two-step channel. The solution is utilized to derive simple model connecting SLAs in SS with the wind speeds over central part of SCS. Due to delay of sea level anomaly in SS with respect to the remote source at, Singapore. National Research Foundation (Singapore MIT Alliance for Research and Technology), Singapore-MIT Alliance for Research and Technology. Center for Environmental Sensing and Modeling

Spatial distribution of the South China Sea (SCS) surface temperature shows strong cold anomalies over the Sunda Shelf during the boreal winter season. The band of low sea surface temperature (SST) region located south/southeast of Vietnam is called as the winter cold tongue (CT) in the SCS. Using observational and re-analysis datasets a comprehensive investigation of the dynamical and thermodynamical processes associated with the evolution of SCS CT is performed in this study. The role and relative importance of wind-driven ocean transports, air–sea heat fluxes and oceanic processes are explored. The north-south Sverdrup transport demonstrates strong southward transport during the northeast monsoon period aiding the SST cooling by bringing relatively cold water from the north. The zonal and meridional Ekman transports exhibit relatively weak westward and northward transports to the CT region during this period. The study suggests that wind-driven ocean transports have a significant role in regulating the shape and spatial extent of the CT. The heat budget analysis revealed that net surface heat flux decrease during the northeast monsoon acts as the primary cooling mechanism responsible for the development of the SCS CT, while the horizontal advection of cold water by the western boundary current along the coast of Vietnam plays a secondary role. The wintertime SST anomalies over the CT region are significantly linked to the Nino3 index. Most of the warming/cooling events in the SST anomalies coincide with the El Nino/La Nina phenomena in the Pacific Ocean., Singapore-MIT Alliance for Research and Technology. Center for Environmental Sensing and Modeling

Based on 10 year climatological data and simulations from a regional atmosphere–ocean coupled model (FVCOM-RegCM3), this study examined the coupled seasonal and intraseasonal variability of atmospheric–oceanic variables [sea surface temperature (SST), winds, rainfall and heat fluxes] and important roles of coupling in the South China Sea. It is showed that even though both coupled and uncoupled models in general are able to capture observed seasonal and intraseasonal variability, the coupled model demonstrates stronger coupling relationship than the uncoupled model. For seasonal variability, the atmosphere–ocean relationship is presented as SST forcing atmosphere. Atmospheric variables are significantly influenced by strong seasonally-varied SST. The coupled model very accurately reproduced the observed SST variation with a stable equilibrium state, while SST from the uncoupled model gradually drifted away from the equilibrium state lacking of the so-called negative SST-heat flux feedback. Lead-lag analysis showed that the coupled variables demonstrated stronger SST-atmosphere relationship than the uncoupled and even observed variables. For intraseasonal variability, the atmosphere–ocean relationship is presented as atmosphere forcing SST. Wind becomes a dominant forcing and demonstrates robust negative relationship with SST and positive relationship with rainfall/LHF. Both coupled and uncoupled models are able to reproduce this observed relationship. In wind-SST relationship, compared to uncoupled and observed variables, the coupled model produced the smallest SST variances and therefore the strongest negative coupling feedback. Sensitivity experiments were also carried out to examine the roles of coupling by directly comparing differences between the coupled and uncoupled experiments with initial temperature perturbations. It is showed that the differences can be up to 50 % of the standard deviations of the variables. Root-mean-square errors of the uncoupled model, National Natural Science Foundation (China) (No. 41106003), Chinese Academy of Sciences. Strategic Priority Research Program (No. XDA11010303), Singapore. National Research Foundation (Center for Environmental Sensing and Monitoring (CENSAM) under the Singapore-MIT Alliance for Research and Technology (SMART) program)

The linkage between physical and biological processes is studied by applying a one-dimensional physical-biological coupled model to the Sargasso Sea. The physical model is the Princeton Ocean Model and the biological model is a five-component system including phytoplankton, zooplankton, nitrate, ammonium, and detritus. The coupling between the physical and biological model is accomplished through vertical mixing which is parameterized by the level 2.5 Mellor and Yamada turbulence closure scheme. The coupled model investigates the annual cycle of ecosystem production and the response to external forcing, such as heat flux, wind stress, and surface salinity, and the relative importance of physical processes in affecting the ecosystem. Sensitivity experiments are also carried out, which provide information on how the model bio-chemical parameters affect the biological system. The computed seasonal cycles compare reasonably well with the observations of the Bermuda Atlantic Time-series Study (BATS). The spring bloom of phytoplankton occurs in March and April, right after the weakening of the winter mixing and before the establishment of the summer stratification. The bloom of zooplankton occurs about two weeks after the bloom of phytoplankton. The sensitivity experiments show that zooplankton is more sensitive to the variations of biochemical parameters than phytoplankton., Shandong Sheng (China) (Shandong Young Scientists Research Award, grant BS2011HZ021)

The linkage between physical and biological processes, particularly the effect of the circulation field on the distribution of phytoplankton, is studied by applying a two-dimensional model and an adjoint data assimilation approach to the Gulf of Maine-Georges Bank region. The model results, comparing well with observation data, reveal seasonal and geographic variations of phytoplankton concentration and verify that the seasonal cycles of phytoplankton are controlled by both biological sources and advection processes which are functions of space and time and counterbalance each other. Although advective flux divergences have greater magnitudes on Georges Bank than in the coastal region of the western Gulf of Maine, advection control over phytoplankton concentration is more significant in the coastal region of the western Gulf of Maine. The model results also suggest that the two separated populations in the coastal regions of the western Gulf of Maine and on Georges Bank are self-sustaining., Shandong Sheng (China) (Shandong Young and Middle-Aged Scientists Research Award, grant BS2011HZ021)

The effectiveness of an ensemble Kalman filter (EnKF) is assessed in the Selat Pauh of Singapore using observing system simulation experiment. Perfect model experiments are first considered. The perfect model experiments examine the EnKF in reducing the initial perturbations with no further errors than those in the initial conditions. Current velocity at 15 observational sites from the true ocean is assimilated every hour into the false ocean. While EnKF reduces the initial velocity error during the first few hours, it fails after one tidal cycle (approximately 12 h) due to the rapid convergence of the ensemble members. Successively, errors are introduced in the surface wind forcing. A random perturbation ε [epsilon] is applied independently to each ensemble member to maintain the ensemble spread. The assimilation results showed that the success of EnKF depends critically on the presence of ε [epsilon], yet it is not sensitive to the magnitude of ε [epsilon], at least in the range of weak to moderate perturbations. Although all experiments were made with EnKF only, the results could be applicable in general to all other ensemble-based data assimilation methods., United States. Office of Naval Research, Singapore. National Research Foundation, Singapore-MIT Alliance for Research and Technology Center, Singapore-MIT Alliance. Center for Environmental Sensing and Monitoring

To obtain a better understanding of environment-related physical oceanography in Singapore Strait Region, numerical experiments are implemented to study the circulation in SSR. The three important components, tidal, wind and eddy-driven circulations are identified. It is shown that the tidal circulation is dominant in the region. Even though the wind and eddy circulations are relatively small, they may have significant effect on the local circulation and material transport., Singapore-MIT Alliance. Center for Environmental Sensing and Monitoring, Singapore. National Research Foundation

Twin experiments were made to compare the reduced rank Kalman filter (RRKF), ensemble Kalman filter (EnKF), and ensemble square-root Kalman filter (EnSKF) for coastal ocean problems in three idealized regimes: a flat bottom circular shelf driven by tidal forcing at the open boundary; an linear slope continental shelf with river discharge; and a rectangular estuary with tidal flushing intertidal zones and freshwater discharge. The hydrodynamics model used in this study is the unstructured grid Finite-Volume Coastal Ocean Model (FVCOM). Comparison results show that the success of the data assimilation method depends on sampling location, assimilation methods (univariate or multivariate covariance approaches), and the nature of the dynamical system. In general, for these applications, EnKF and EnSKF work better than RRKF, especially for time-dependent cases with large perturbations. In EnKF and EnSKF, multivariate covariance approaches should be used in assimilation to avoid the appearance of unrealistic numerical oscillations. Because the coastal ocean features multiscale dynamics in time and space, a case-by-case approach should be used to determine the most effective and most reliable data assimilation method for different dynamical systems., United States. Office of Naval Research (grant N00014-06-1-0290), National Science Foundation (U.S.) (grant OCE-0234545), National Science Foundation (U.S.) (grant OCE-0227679), National Science Foundation (U.S.) (grant OCE-0606928), National Science Foundation (U.S.) (grant OCE-0712903), National Science Foundation (U.S.) (grant OCE-0726851), National Science Foundation (U.S.) (grant OCE-0814505), United States. National Oceanic and Atmospheric Administration (grant NA-16OP2323), National Science Foundation (U.S.) (grant ARC0712903), National Science Foundation (U.S.) (grant ARC0732084), National Science Foundation (U.S.) (grant ARC0804029), URI Sea Grant (R/P-061), Massachusetts Institute of Technology. Sea Grant College Program (2006-RC-103), Massachusetts Marine Fisheries Institute (NOAA grant NA05NMF4721131), Massachusetts Marine Fisheries Institute (NOAA grant NA04NMF4720332), National Science Foundation (U.S.) (grant OCE-02227679), Massachusetts Institute of Technology. Sea Grant College Program (NA06OAR1700019)