Oceanography is evolving from a ship-based expeditionary science to a distributed, observatory- based approach in which scientists continuously interact with instruments in the field. These new capabilities will facilitate the collection of long- term time series while also providing an interactive capability to conduct experiments using data streaming in real time. The U.S. National Science Foundation has funded the Ocean Observatories Initiative (OOI), which over the next 5 years will deploy infrastructure to expand scientists’ ability to remotely study the ocean. The OOI is deploying infrastructure that spans global, regional, and coastal scales. A global component will address planetary- scale problems using a new network of moored buoys linked to shore via satellite telecommunications. A regional cabled observatory will “wire” a single region in the northeastern Pacific Ocean with a high-speed optical and power grid. The coastal component will expand existing coastal observing assets to study the importance of high-frequency forcing on the coastal environment. These components will be linked by a robust cyberinfrastructure (CI) that will integrate marine observatories into a coherent system of systems. This CI infrastructure will also provide a Web- based social network enabled by real- time visualization and access to numerical model information, to provide the foundation for adaptive sampling science. Thus, oceanographers will have access to automated machine-to-machine sensor networks that can be scalable to increase in size and incorporate new technology for decades to come. A case study of this CI in action shows how a community of ocean scientists and engineers located throughout the United States at 12 different institutions used the automated ocean observatory to address daily adaptive science priorities in real time.

Accurate numerical modeling of biogeochemical ocean dynamics is essential for numerous applications, including coastal ecosystem science, environmental management and energy, and climate dynamics. Evaluating computational requirements for such often highly nonlinear and multiscale dynamics is critical. To do so, we complete comprehensive numerical analyses, comparing low- to high-order discretization schemes, both in time and space, employing standard and hybrid discontinuous Galerkin finite element methods, on both straight and new curved elements. Our analyses and syntheses focus on nutrient-phytoplankton-zooplankton dynamics under advection and diffusion within an ocean strait or sill, in an idealized 2D geometry. For the dynamics, we investigate three biological regimes, one with single stable points at all depths and two with stable limit cycles. We also examine interactions that are dominated by the biology, by the advection, or that are balanced. For these regimes and interactions, we study the sensitivity to multiple numerical parameters including quadrature-free and quadrature-based discretizations of the source terms, order of the spatial discretizations of advection and diffusion operators, order of the temporal discretization in explicit schemes, and resolution of the spatial mesh, with and without curved elements. A first finding is that both quadrature-based and quadrature-free discretizations give accurate results in well-resolved regions, but the quadrature-based scheme has smaller errors in underresolved regions. We show that low-order temporal discretizations allow rapidly growing numerical errors in biological fields. We find that if a spatial discretization (mesh resolution and polynomial degree) does not resolve the solution, oscillations due to discontinuities in tracer fields can be locally significant for both lowand high-order discretizations. When the solution is sufficiently resolved, higher-order schemes on coarser grids perform better (higher accuracy, less dissipative) for the same cost than lower-order scheme on finer grids. This result applies to both passive and reactive tracers and is confirmed by quantitative analyses of truncation errors and smoothness of solution fields. To reduce oscillations in un-resolved regions, we develop a numerical filter that is active only when and where the solution is not smooth locally. Finally, we consider idealized simulations of biological patchiness. Results reveal that higher-order numerical schemes can maintain patches for long-term integrations while lowerorder schemes are much too dissipative and cannot, even at very high resolutions. Implications for the use of simulations to better understand biological blooms, patchiness, and other nonlinear reactive dynamics in coastal regions with complex bathymetric features are considerable.

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.