We derive conservative time-dependent structured discretizations and two-way embedded (nested) schemes for multiscale ocean dynamics governed by primitive equations (PEs) with a nonlinear free surface. Our multiscale goal is to resolve tidalto- mesoscale processes and interactions over large multiresolution telescoping domains with complex geometries including shallow seas with strong tides, steep shelfbreaks, and deep ocean interactions. We first provide an implicit time-stepping algorithm for the nonlinear free-surface PEs and then derive a consistent time-dependent spatial discretization with a generalized vertical grid. This leads to a novel timedependent finite volume formulation for structured grids on spherical or Cartesian coordinates, second order in time and space, which preserves mass and tracers in the presence of a time-varying free surface. We then introduce the concept of two-way nesting, implicit in space and time, which exchanges all of the updated fields values across grids, as soon as they become available. A class of such powerful nesting schemes applicable to telescoping grids of PE models with a nonlinear free surface is derived. The schemes mainly differ in the fine-to-coarse scale transfers and in the interpolations and numerical filtering, specifically for the barotropic velocity and surface pressure components of the two-way exchanges. Our scheme comparisons show that for nesting with free surfaces, the most accurate scheme has the strongest implicit couplings among grids. We complete a theoretical truncation error analysis to confirm and mathematically explain findings. Results of our discretizations and two-way nesting are presented in realistic multiscale simulations with data assimilation for the middle Atlantic Bight shelfbreak region off the east coast of the USA, the Philippine archipelago, and the Taiwan-Kuroshio region. Multiscale modeling with two-way nesting enables an easy use of different sub-gridscale parameterizations in each nested domain. The new developments drastically enhance the predictive capability and robustness of our predictions, both qualitatively and quantitatively. Without them, our multiscale multiprocess simulations either were not possible or did not match ocean data.

Methods for widening the range of resolved scales (i.e. performing multi-scale simulations) in ocean sciences and engineering are developing rapidly, now allowing multiscale ocean dynamics studies. Having recourse to grid nesting has been and still is a popular method for increasing marine models’ resolution when and where needed and for easily allowing the use of different dynamics at different resolution. However, this is not the only way to achieve this goal. Various techniques for modifying locally the grid resolution or dealing with complex-geometry domains are available. For instance, composite, structured grids and unstructured meshes offer an almost infinite geometrical flexibility. This special issue focuses on multi-scale modelling of coastal, shelf and global ocean dynamics, including the development of new methodologies and schemes and their applications to ocean process studies. Several articles focus on numerical aspects of unstructured mesh space discretisation. Danilov (2010) shows that the noise developing on triangular meshes on which the location of the variables is inspired by Arakawa’s C-grid is the largest for regimes close to geostrophic balance. The noise can be reduced by specific operators but cannot be entirely suppressed, “making the triangular C-grid a suboptimal choice for large-scale ocean modelling”. Then, the companion articles of Blaise et al. (2010) and Comblen et al. (2010) describe the space and time discretisation of a three-dimensional, baroclinic, finite element model based on the discontinuous Galerkin (DG) technique. This is a significant step forward in the field of finite element ocean modelling, though this model cannot yet be regarded as suitable for tackling realistic applications. Ueckermann and Lermusiaux (2010) also consider DG finite element techniques, focusing on biological-physical dynamics in regions with complex bathymetric features. They compare low- to high-order discretisations, both in time and space, for regimes in which biology dominates, advection dominates or terms are balanced. They find that higher-order schemes on relatively coarse grids generally perform better than low-order schemes on fine grids. Kleptsova et al. (2010) assess various advection schemes for z-coordinate, threedimensional models in which flooding and drying is taken into account. In this study, the ability to conserve momentum is regarded as the main criterion for selecting a suitable method. On the other hand, Massmann (2010) assesses automatic differentiation for obtaining the adjoint of an unstructured mesh, tidal model of the European continental shelf. Two articles deal with grid nesting. Nash and Hartnett (2010) introduce a flooding and drying method that can be used in structured, nested grid systems. This can be regarded as an alternative to flooding and drying techniques that are being developed for unstructured mesh models (e.g. Karna et al. 2010). Then, Haley and Lermusiaux (2010) derive conservative time-dependent structured finite volume discretisations and implicit two-way embedded schemes for primitive equations with the intent to resolve tidal-to-mesoscale processes over large multi-resolution telescoping domains with complex geometries including shallow seas with strong tides, steep shelf breaks and deep ocean interactions. The authors present realistic simulations with data assimilation in three regions with diverse dynamics and show that their developments enhance the predictive capability, leading to better match with ocean data. Various multi-scale, realistic simulations are presented. Using a finite element ice model and a slab ocean as in Lietaer et al. (2008), Terwisscha van Scheltinga et al. (2010) model the Canadian Arctic Archipelago, focusing on the pathways for freshwater and sea-ice transport from the Arctic Ocean to the Labrador Sea and the Atlantic Ocean. The unstructured mesh can represent the complex geometry and narrow straits at high resolution and allows improving transports of water masses and sea ice. Walters et al. (2010) have recourse to an unstructured mesh model to study tides and current in Greater Cook Strait (New Zealand). They identify the mechanisms causing residual currents. By means of the unstructured mesh Finite Volume Coastal Ocean Model (FVCOM), Wang et al. (2010) study the hydrodynamics of the Bohai Sea. Xu et al. (2010) simulate coastal and urban inundation due to storm surges along US East and Gulf Coasts. A sensitivity analysis reveals the importance of precise topographic data and the need for a bottom drag coefficient accounting for the presence of mangroves. Finally, Yang and Khangaonkar (2010) resort to FVCOM to simulate the three-dimensional circulation of Puget Sound, a large complex estuary system in the Pacific Northwest coastal ocean, including variable forcing from tides, the atmosphere and river inflows. Comparisons of model estimates with measurements for tidal elevation, velocity, temperature and salinity are deemed to be promising, from larger-scale circulation features to nearshore tide flats. This special issue suggests that numerical techniques for multi-scale space discretisation are progressively becoming mature. One direction for future progress lies in the improvement of time discretisation methods for the new generation models, so that they can successfully compete with finite difference, structured mesh models based on (almost) constant resolution grids that have been developed and used over the past 40 years (e.g. Griffies et al. 2009).

The Autonomous Ocean Sampling Network Phase Two (AOSN-II) experiment was conducted in and offshore from the Monterey Bay on the central California coast during July 23-September 6, 2003. The objective of the experiment was to learn how to apply new tools, technologies, and analysis techniques to adaptively sample the coastal ocean in a manner demonstrably superior to traditional methodologies, and to use the information gathered to improve predictive skill for quantities of interest to end-users. The scientific goal was to study the upwelling/relaxation cycle near an open coastal bay in an eastern boundary current region, particularly as it developed and spread from a coastal headland. The suite of observational tools used included a low-flying aircraft, a fleet of underwater gliders, including several under adaptive autonomous control, and propeller-driven AUVs in addition to moorings, ships, and other more traditional hardware. The data were delivered in real time and assimilated into the Harvard Ocean Prediction System (HOPS), the Navy Coastal Ocean Model (NCOM), and the Jet Propulsion Laboratory implementation of the Regional Ocean Modeling System (JPL/ROMS).

Two upwelling events and one relaxation event were sampled during the experiment. The upwelling in both cases began when a pool of cold water less than 13^oC appeared near Cape Ano Nuevo and subsequently spread offshore and southward across the bay as the equatorward wind stress continued. The primary difference between the events was that the first event spread offshore and southward, while the second event spread only southward and not offshore. The difference is attributed to the position and strength of meanders and eddies of the California Current System offshore, which blocked or steered the cold upwelled water. The space and time scales of the mesoscale variability were much shorter than have been previously observed in deep-water eddies offshore. Additional process studies are needed to elucidate the dynamics of the flow.

An ensemble data assimilation scheme, Error Subspace Statistical Estimation (ESSE), is utilized to investigate the seasonal ecosystem dynamics of the Lagoon of Venice and provide guidance on the monitoring and management of the Lagoon, combining a rich data set with a physical-biogeochemical numerical estuary-coastal model. Novel stochastic ecosystem modeling components are developed to represent prior uncertainties in the Lagoon dynamics model, measurement model, and boundary forcing by rivers, open-sea inlets, and industrial discharges. The formulation and parameters of these additive and multiplicative stochastic error models are optimized based on data-model forecast misfits. The sensitivity to initial and boundary conditions is quantified and analyzed. Half-decay characteristic times are estimated for key ecosystem variables, and their spatial and temporal variability are studied. General results of our uncertainty analyses are that boundary forcing and internal mixing have a significant control on the Lagoon dynamics and that data assimilation is needed to reduce prior uncertainties. The error models are used in the ESSE scheme for ensemble uncertainty predictions and data assimilation, and an optimal ensemble dimension is estimated. Overall, higher prior uncertainties are predicted in the central and northern regions of the Lagoon. On the basis of the dominant singular vectors of the ESSE ensemble, the two major northern rivers are the biggest sources of dissolved inorganic nitrogen (DIN) uncertainty in the Lagoon. Other boundary sources such as the southern rivers and industrial discharges can dominate uncertainty modes on certain months. For dissolved inorganic phosphorus (DIP) and phytoplankton, dominant modes are also linked to external boundaries, but internal dynamics effects are more significant than those for DIN. Our posterior estimates of the seasonal biogeochemical fields and of their uncertainties in 2001 cover the whole Lagoon. They provide the means to describe the ecosystem and guide local environmental policies. Specifically, our findings and results based on these fields include the temporal and spatial variability of nutrient and plankton gradients in the Lagoon; dynamical connections among ecosystem fields and their variability; strengths, gradients and mechanisms of the plankton blooms in late spring, summer, and fall; reductions of uncertainties by data assimilation and thus a quantification of data impacts and data needs; and, finally, an assessment of the water quality in the Lagoon in light of the local environmental legislation.

During the August-September 2003 Autonomous Ocean Sampling Network-II experiment, the Harvard Ocean Prediction System (HOPS) and Error Subspace Statistical Estimation (ESSE) system were utilized in real-time to forecast physical fields and uncertainties, assimilate various ocean measurements (CTD, AUVs, gliders and SST data), provide suggestions for adaptive sampling, and guide dynamical investigations. The qualitative evaluations of the forecasts showed that many of the surface ocean features were predicted, but that their detailed positions and shapes were less accurate. The root-mean-square errors of the real-time forecasts showed that the forecasts had skill out to two days. Mean one-day forecast temperature RMS error was 0.26^oC less than persistence RMS error. Mean two-day forecast temperature RMS error was 0.13^oC less than persistence RMS error. Mean one- or two-day salinity RMS error was 0.036 PSU less than persistence RMS error. The real-time skill in the surface was found to be greater than the skill at depth. Pattern correlation coefficient comparisons showed, on average, greater skill than the RMS errors. For simulations lasting 10 or more days, uncertainties in the boundaries could lead to errors in the Monterey Bay region.

Following the real-time experiment, a reanalysis was performed in which improvements were made in the selection of model parameters and in the open-boundary conditions. The result of the reanalysis was improved long-term stability of the simulations and improved quantitative skill, especially the skill in the main thermocline (RMS simulation error 1^oC less than persistence RMS error out to five days). This allowed for an improved description of the ocean features. During the experiment there were two-week to 10-day long upwelling events. Two types of upwelling events were observed: one with plumes extending westward at point Ano Nuevo (AN) and Point Sur (PS); the other with a thinner band of upwelled water parallel to the coast and across Monterey Bay. During strong upwelling events the flows in the upper 10-20 m had scales similar to atmospheric scales. During relaxation, kinetic energy becomes available and leads to the development of mesoscale features. At 100-300 m depths, broad northward flows were observed, sometimes with a coastal branch following topographic features. An anticyclone was often observed in the subsurface fields in the mouth of Monterey Bay.