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Three kinds of data. 1. Inverted temperature: Time series data of inverted temperatures for four layers from the surface to seafloor 2. CTD temperature: One-time profile data of temperature from the sea surface to seafloor obtained by R. V. Hakuho-maru of JAMSTEC (Japan Marine-Earth Science and Technology Center) on Feb 28, 2019. 3. Time series data of sea surface height (SSH) obtained by the pressure sensor at the periphery of the observation site. Data Time Period: Feb 26-29, 2019 GeoLocation: Worldwide oceanographic data Dataset Progress Status: complete Use Limitations: No limitation Funding Reference: Agency for the Assessment and Application of Technology (BPPT), Indonesian Government. The United States Office of Naval Research-Global (ONR-Global/NICOP Grant N62909-15-1-N055) (non-military fund)

In this article, we present the datasets which are used to estimate the turbulent kinetic energy dissipation rates and vertical diffusivity in the Indonesian seas. An archived CTD (conductivity, temperature, depth) datasets collected between 1990 and 2016 with 1 m vertical resolution is presented and analyzed using an improved Thorpe method. The direct estimates dataset of the dissipation rate from two research expeditions, i.e., INDOMIX Program in 2010 and TOMTOM Program in 2015 were also presented, available to be compared with the indirect estimates from CTD profiles. We also present the dissipation rate output of three recent regional internal tide models in the Indonesian seas for comparison with microstructure measurements and improved Thorpe estimates. The datasets refer to "Spatial structure of turbulent mixing inferred from historical CTD datasets in the Indonesian seas" [1].

Turbulent kinetic energy dissipation rates and vertical diffusivities in the Indonesian seas are inferred from historical CTD measurements gathering for the first time data from Indonesian and international cruises. Dissipation rates are inferred from the CTD using an improved Thorpe scale method, which is validated against microstructure measurements. Elevated dissipation rates ~[10−6–10−7] m2 s−3, were observed in the near field stations, such as in the straits, narrowing passages and shallowing topography where internal tides are generated and Indonesian throughflow (ITF) is intense, while lower dissipation rates ~[10−8–10−10] m2 s−3 were observed in the far field stations and below the pycnocline. The main mixing hot spots are located in the Labani Channel and shallowing topography of the Dewakang waters for the western route of ITF, i.e. the passage that connects the north Pacific source via Sulawesi Sea, Makassar Strait and Flores Sea; in the straits of Halmahera, Lifamatola, and Buru for the eastern route of ITF, i.e. the passage that connects the south Pacific source via Halmahera Sea, Maluku Sea, Seram Sea; and in the ITF exit passages, i.e. the Lombok, Sape and Ombai Straits. The eastern route is more dissipative than the western route, which is consistent with the stronger erosion of the salinity peak of the Pacific waters along the eastern route. We found that tidal variations influence the dissipation rates and diffusivities as has been suggested from the yoyo profiling datasets. The spatial pattern of dissipation rates inferred from the high-resolution 3D hydrodynamics model output of Nagai and Hibiya (2015) shows a general agreement with the observations in the location of the mixing hot spots and suggests that the M2 internal tide is the dominant factor driving the turbulent kinetic energy dissipation rates in the Indonesian seas. Yet the model also shows a bias toward lower dissipation rate in the pycnocline, that we attribute to the lack of representation of the ITF and mesoscale circulation and a bias toward higher dissipation rate in the weak mixing region, suggesting an overestimation of the background dissipation rate in calm waters.

The Indonesian Throughflow (ITF) waters are significantly transformed within the Indonesian Archipelago and consequently influence the large-scale ocean circulation such as Agulhas and Leeuwin Currents. Existing ocean general circulation models (OGCMs) are, however, incapable of reproducing the transformation of the ITF waters, since tidal forcing is neglected in such models. In the present study, we first conduct high-resolution non-hydrostatic three-dimensional numerical experiments focusing on the transformation of the ITF waters in the Halmahera Sea which is thought to be the most important bottleneck in simulating the ITF water-mass properties. It is shown that intensive vertical mixing induced by breaking of internal tides in the shallow regions in the Halmahera Sea dilutes the ITF waters, significantly reducing model biases found in the existing OGCMs. We next evaluate quantitatively the effect of tide-induced vertical mixing on the transformation of the ITF waters. It is shown that tide-induced vertical mixing dominates the transformation of the ITF waters, although some supplementary processes such as horizontal mixing associated with the sub-mesoscale eddies resulting from tidal interaction with land configurations cannot be ignored.

Tidal mixing in the Indonesian Archipelago contributes to regulation of the tropical atmospheric circulation and water-mass transformation in the Indonesian Throughflow. The present study quantifies the vertical diffusivity in the Indonesian Archipelago by driving a high-resolution three-dimensional numerical model and investigates the processes of internal tide generation, propagation, and dissipation. The numerical experiment shows that M2 internal tides are effectively generated over prominent subsurface ridges. The conversion rate from M2 barotropic to baroclinic energy over the whole analyzed model domain is estimated to be 85.5 GW. The generated internal tides dissipate 50–100% of their energy in close proximity to the generation sites (“near-field”), and the remaining baroclinic energy propagates away causing relatively large energy dissipation far from the generation sites (“far-field”). The local dissipation efficiency q, therefore, has an extremely nonuniform spatial distribution, although it has been assumed to be constant in the existing tidal mixing parameterization for the Indonesian Archipelago. Compared with the model-predicted values, the existing parameterization yields the same order of vertical diffusivity averaged within the Indonesian Archipelago, but significantly overestimated (or underestimated) vertical diffusivity in the near-field (or the far-field). This discrepancy is attributable to the fact that the effects of internal wave propagation are completely omitted in the existing parameterization, suggesting the potential danger of using such parameterized vertical mixing in predicting the distribution of SST as well as water-mass transformation in the Indonesian Seas.

The sudden intrusion of Kuroshio warm water into the Bungo Channel (kyucho) occurs mainly at neap tides during summer, suggesting that tidal mixing is one of the essential factors regulating kyucho. In order to clarify the physical mechanisms responsible for the regulation of kyucho, we carry out non-hydrostatic three-dimensional numerical experiments allowing Kuroshio warm water to intrude into a strong tidal mixing region. It is shown that the Kuroshio warm water can (or cannot) pass through the tidal mixing regions off the east coast of the Bungo Channel during neap (or spring) tides. The analysis of the dynamic balance off the east coast of the Bungo Channel shows that tidal residual currents generated by tidal flow interaction with complicated land configurations off the east coast of the Bungo Channel can also play an important role in regulating kyucho. In order to assess separately the effects of tidal mixing and tidal residual currents on kyucho, we incorporate the parameterized vertical mixing and tidal stresses into the numerical model instead of tidal currents. It is demonstrated that tidal mixing cannot by itself block the northward intrusion of Kuroshio warm water, and that an additional effect induced by tidal residual eddies equivalent to horizontal mixing is needed to regulate kyucho. This strongly suggests that the basin–ocean water exchange processes in areas with complicated land configurations can only be reproduced by taking into account the effects of tidal residual eddies on a 1-km scale in addition to tidal mixing effects evaluated by microstructure measurements.

It is well known that the sudden intrusion of Kuroshio warm water into the Bungo Channel (kyucho) is regulated by spring–neap tidal forcing. In order to clarify the physical background behind this regulation, numerical experiments are carried out using a high-resolution non-hydrostatic three-dimensional model. We first reproduce the strong mixing region off the east coast of the Bungo Channel resulting from tidal flow interaction with complicated land configurations during spring tides; behind islands and headlands, small-scale eddies satisfying an approximate cyclostrophic balance are generated. As a result, averaged over the whole model domain, the tidal-mean energy dissipation rate reaches ≈1.6 × 10−6 W kg−1. The model predicted energy dissipation rates at the location and times of direct microstructure measurements in the Bungo Channel are comparable to the observed values. We next examine whether or not strong tidal mixing thus reproduced can inhibit the northward intrusion of Kuroshio warm water in the Bungo Channel. It is shown that the Kuroshio warm water can (or cannot) pass through the tidal mixing regions off the east coast of the Bungo Channel during periods of weakened (or enhanced) tidal mixing at neap (or spring) tides. This indicates that taking into account the realistic spring–neap modulation of tidal mixing intensity is indispensable to further increase the ability of the existing forecast system for kyucho in the Bungo Channel.

To assess each of the two possible mechanisms responsible for the fortnightly modulation of semi-enclosed basin–ocean water exchange (‘density tides’), a set of numerical experiments is carried out using a vertically two-dimensional numerical model with realistic situations in Puget Sound in mind. It is found that, although the localized vertical viscosity (or the localized vertical diffusivity) enhanced in the entrance sill region primarily controls the bottom-water transport (or the bottom-water density) during spring tides, it does not lead to any appreciable variations of bottom-water density (or bottom-water transport). This indicates that the fortnightly modulation of vertical viscosity and that of vertical diffusivity both play important roles in creating density tides. In the real ocean, the vertical viscosity and diffusivity are enhanced simultaneously during spring tides, so that it is difficult to discriminate between both effects on density tides. This causes the widespread misunderstanding that density tides are mainly caused by the decreased advection of dense bottom-water from outside due to the enhanced vertical viscosity during spring tides.