Journal Sciences News
Urologic Oncology: Seminars and Original Investigations
August 2018
Mean circulation of the Mid-Atlantic Bight from a climatological data assimilative model
Publication date: August 2018
Source:Ocean Modelling, Volume 128 Author(s): Julia Levin, John Wilkin, Naomi Fleming, Javier Zavala-Garay The along-shelf momentum balance of the Mid-Atlantic Bight (MAB) coastal ocean includes a significant contribution from the along-shelf gradient in sea level. This sea level tilt, of order 10
July 2018
High resolution tidal model of Canadian Arctic Archipelago, Baffin and Hudson Bay
Publication date: August 2018
Source:Ocean Modelling, Volume 128 Author(s): O. Kleptsova, J.D. Pietrzak Ice induced variability of tides in the Canadian Arctic Archipelago, including Baffin Bay and Hudson Strait/Hudson Bay system, was studied by means of a new high resolution tidal model. Here we show that the seasonal variations of the tidal constants are significant in the major part of the domain. Month to month changes of the tidal phases can reach 180 degrees due to changes in the number and positions of the amphidromic points, whereas the amplitude variations are especially large in the near resonant basins. We also show that the tidal seasonality has undergone dramatic changes in the past decades due the decaying extent of the Arctic sea ice. These seasonal/decadal scale changes not only vary tidal dissipation on the shelf, but also impact tides in the adjacent open ocean and, therefore, cannot be neglected.
July 2018
Editorial Board
Publication date: July 2018
Source:Ocean Modelling, Volume 127

July 2018
Dynamically consistent parameterization of mesoscale eddies. Part III: Deterministic approach
Publication date: July 2018
Source:Ocean Modelling, Volume 127 Author(s): Pavel Berloff This work continues development of dynamically consistent parameterizations for representing mesoscale eddy effects in non-eddy-resolving and eddy-permitting ocean circulation models and focuses on the classical double-gyre problem, in which the main dynamic eddy effects maintain eastward jet extension of the western boundary currents and its adjacent recirculation zones via eddy backscatter mechanism. Despite its fundamental importance, this mechanism remains poorly understood, and in this paper we, first, study it and, then, propose and test its novel parameterization. We start by decomposing the reference eddy-resolving flow solution into the large-scale and eddy components defined by spatial filtering, rather than by the Reynolds decomposition. Next, we find that the eastward jet and its recirculations are robustly present not only in the large-scale flow itself, but also in the rectified time-mean eddies, and in the transient rectified eddy component, which consists of highly anisotropic ribbons of the opposite-sign potential vorticity anomalies straddling the instantaneous eastward jet core and being responsible for its continuous amplification. The transient rectified component is separated from the flow by a novel remapping method. We hypothesize that the above three components of the eastward jet are ultimately driven by the small-scale transient eddy forcing via the eddy backscatter mechanism, rather than by the mean eddy forcing and large-scale nonlinearities. We verify this hypothesis by progressively turning down the backscatter and observing the induced flow anomalies. The backscatter analysis leads us to formulating the key eddy parameterization hypothesis: in an eddy-permitting model at least partially resolved eddy backscatter can be significantly amplified to improve the flow solution. Such amplification is a simple and novel eddy parameterization framework implemented here in terms of local, deterministic flow roughening controlled by single parameter. We test the parameterization skills in an hierarchy of non-eddy-resolving and eddy-permitting modifications of the original model and demonstrate, that indeed it can be highly efficient for restoring the eastward jet extension and its adjacent recirculation zones. The new deterministic parameterization framework not only combines remarkable simplicity with good performance but also is dynamically transparent, therefore, it provides a powerful alternative to the common eddy diffusion and emerging stochastic parameterizations.
July 2018
A 3D unstructured-grid model for Chesapeake Bay: Importance of bathymetry
Publication date: July 2018
Source:Ocean Modelling, Volume 127 Author(s): Fei Ye, Yinglong J. Zhang, Harry V. Wang, Marjorie A.M. Friedrichs, Isaac D. Irby, Eli Alteljevich, Arnoldo Valle-Levinson, Zhengui Wang, Hai Huang, Jian Shen, Jiabi Du We extend the 3D unstructured-grid model previously developed for the Upper Chesapeake Bay to cover the entire Bay and its adjacent shelf, and assess its skill in simulating saltwater intrusion and the coastal plume. Recently developed techniques, including a flexible vertical grid system and a 2nd-order, monotone and implicit transport solver are critical in successfully capturing the baroclinic responses. Most importantly, good accuracy is achieved through an accurate representation of the underlying bathymetry, without any smoothing. The model in general exhibits a good skill for all hydrodynamic variables: the averaged root-mean-square errors (RMSE's) in the Bay are 9
July 2018
Reflection source term for the wave action equation
Publication date: July 2018
Source:Ocean Modelling, Volume 127 Author(s): Yuval Yevnin, Yaron Toledo The wave action equation is a widely used governing equation in wave forecasting models. Whilst it accounts for wave propagation, its analytical derivation neglects various other effects, such as the sea bottom reflection. The present work derives an analytical source term for the bottom reflection of oblique incident waves to be used in numerical forecasting models. This is done by means of a coupled oblique parabolic approximation of the mild-slope equation, which is then decoupled by introducing a perturbation solution. The resulting first two orders produce the wave action equation itself for an on-going wave in the first order and a wave action equation with a reflection source term in the second order for the reflected wave. A method to implement this source term in two-dimensional wave action forecasting models is discussed. Numerical simulations show this new source term to be in excellent agreement with the mild-slope equation for different slopes, wave periods and attack angles.
July 2018
An energetically consistent vertical mixing parameterization in CCSM4
Publication date: July 2018
Source:Ocean Modelling, Volume 127 Author(s): S
June 2018
Wind forcing calibration and wave hindcast comparison using multiple reanalysis and merged satellite wind datasets
Publication date: July 2018
Source:Ocean Modelling, Volume 127 Author(s): Justin E. Stopa Wave hindcasts are tools to study climate and are regularly used in offshore and coastal engineering applications. The growing number of wind datasets and reanalysis products create more opportunity for generating wave hindcasts. Each wind dataset or reanalysis product has different resolution, model implementation, and assimilation scheme and if the wave model implementation is not calibrated to the input wind field the resulting wave field can have large biases solely due to the wind. In this work, we calibrate the wind to wave growth parameter within the spectral wave model WAVEWATCH III for 10 reanalysis datasets and 2 datasets composed of merged satellite observations. The calibration is performed globally by minimizing the differences between altimeter wave height observations and the model output for the year of 2001. We place special emphasis on ensuring the largest sea states are well captured and are not underestimated because of the important engineering applications of these data. After the calibration we compare the datasets and find each product reproduces the average sea states similarly, but high sea states have large discrepancies. We demonstrate that the space-time distribution of the extreme waves are very different even after calibration. We summarize by providing recommendations of the most accurate wind datasets to generate wave hindcasts.
June 2018
Editorial Board
Publication date: June 2018
Source:Ocean Modelling, Volume 126

June 2018
Model-based assessment of a Northwestern Tropical Pacific moored array to monitor intraseasonal variability
Publication date: June 2018
Source:Ocean Modelling, Volume 126 Author(s): Danian Liu, Jiang Zhu, Yeqiang Shu, Dongxiao Wang, Weiqiang Wang, Shuqun Cai The Northwestern Tropical Pacific Ocean (NWTPO) moorings observing system, including 15 moorings, was established in 2013 to provide velocity profile data. Observing system simulation experiments (OSSEs) were carried out to assess the ability of the observation system to monitor intraseasonal variability in a pilot study, where ideal “mooring-observed” velocity was assimilated using Ensemble Optimal Interpolation (EnOI) based on the Regional Oceanic Modeling System (ROMS). Because errors between the control and “nature” runs have a mesoscale structure, a random ensemble derived from 20–90-day bandpass-filtered nine-year model outputs is proved to be more appropriate for the NWTPO mooring array assimilation than a random ensemble derived from a 30-day running mean. The simulation of the intraseasonal currents in the North Equatorial Current (NEC), North Equatorial Countercurrent (NECC), and Equatorial Undercurrent (EUC) areas can be improved by assimilating velocity profiles using a 20–90-day bandpass-filtered ensemble. The root mean square errors (RMSEs) of the intraseasonal zonal (U) and meridional velocity (V) above 500
June 2018
Insights on multivariate updates of physical and biogeochemical ocean variables using an Ensemble Kalman Filter and an idealized model of upwelling
Publication date: June 2018
Source:Ocean Modelling, Volume 126 Author(s): Liuqian Yu, Katja Fennel, Laurent Bertino, Mohamad El Gharamti, Keith R. Thompson Effective data assimilation methods for incorporating observations into marine biogeochemical models are required to improve hindcasts, nowcasts and forecasts of the ocean's biogeochemical state. Recent assimilation efforts have shown that updating model physics alone can degrade biogeochemical fields while only updating biogeochemical variables may not improve a model's predictive skill when the physical fields are inaccurate. Here we systematically investigate whether multivariate updates of physical and biogeochemical model states are superior to only updating either physical or biogeochemical variables. We conducted a series of twin experiments in an idealized ocean channel that experiences wind-driven upwelling. The forecast model was forced with biased wind stress and perturbed biogeochemical model parameters compared to the model run representing the “truth”. Taking advantage of the multivariate nature of the deterministic Ensemble Kalman Filter (DEnKF), we assimilated different combinations of synthetic physical (sea surface height, sea surface temperature and temperature profiles) and biogeochemical (surface chlorophyll and nitrate profiles) observations. We show that when biogeochemical and physical properties are highly correlated (e.g., thermocline and nutricline), multivariate updates of both are essential for improving model skill and can be accomplished by assimilating either physical (e.g., temperature profiles) or biogeochemical (e.g., nutrient profiles) observations. In our idealized domain, the improvement is largely due to a better representation of nutrient upwelling, which results in a more accurate nutrient input into the euphotic zone. In contrast, assimilating surface chlorophyll improves the model state only slightly, because surface chlorophyll contains little information about the vertical density structure. We also show that a degradation of the correlation between observed subsurface temperature and nutrient fields, which has been an issue in several previous assimilation studies, can be reduced by multivariate updates of physical and biogeochemical fields.
June 2018
Numerical study of sediment dynamics during hurricane Gustav
Publication date: June 2018
Source:Ocean Modelling, Volume 126 Author(s): Zhengchen Zang, Z. George Xue, Shaowu Bao, Qin Chen, Nan D. Walker, Alaric S. Haag, Qian Ge, Zhigang Yao In this study, the coupled ocean-atmosphere-wave-and-sediment transport (COAWST) modeling system was employed to explore sediment dynamics in the northern Gulf of Mexico during hurricane Gustav in 2008. The performance of the model was evaluated quantitatively and qualitatively against in-situ and remote sensing measurements, respectively. After Gustav's landfall in coastal Louisiana, the maximum significant wave heights reached more than 8
June 2018
Simulation of mesoscale circulation in the Tatar Strait of the Japan Sea
Publication date: June 2018
Source:Ocean Modelling, Volume 126 Author(s): V.I. Ponomarev, P.A. Fayman, S.V. Prants, M.V. Budyansky, M.Yu. Uleysky The eddy-resolved ocean circulation model RIAMOM (Lee et al., 2003) is used to analyze seasonal variability of mesoscale circulation in the Tatar Strait of the Japan Sea. The model domain is a vast area including the northern Japan Sea, Okhotsk Sea and adjacent region in the Pacific Ocean. A numerical experiment with a horizontal 1/18° resolution has been carried out under realistic meteorological conditions from the ECMWF ERA-40 reanalysis with restoring of surface temperature and salinity. The simulated seasonal variability of both the current system and mesoscale eddy dynamics in the Tatar Strait is in a good agreement with temperature and salinity distributions of oceanographic observation data collected during various seasons and years. Two general circulation regimes in the Strait have been found. The circulation regime changes from summer to winter due to seasonal change of the North Asian Monsoon. On a synoptic time scale, the similar change of the circulation regime occurs due to change of the southeastern wind to the northwestern one when the meteorological situation with an anticyclone over the Okhotsk Sea changes to that with a strong cyclone. The Lagrangian maps illustrate seasonal changes in direction of the main currents and in polarity and location of mesoscale eddies in the Strait.
June 2018
The relationship between a deformation-based eddy parameterization and the LANS-
June 2018
On the upper ocean turbulent dissipation rate due to microscale breakers and small whitecaps
Publication date: June 2018
Source:Ocean Modelling, Volume 126 Author(s): Michael L. Banner, Russel P. Morison In ocean wave modelling, accurately computing the evolution of the wind-wave spectrum depends on the source terms and the spectral bandwidth used. The wave dissipation rate source term which spectrally quantifies wave breaking and other dissipative processes remains poorly understood, including the spectral bandwidth needed to capture the essential model physics. The observational study of Sutherland and Melville (2015a) investigated the relative dissipation rate contributions of breaking waves, from large-scale whitecaps to microbreakers. They concluded that a large fraction of wave energy was dissipated by microbreakers. However, in strong contrast with their findings, our analysis of their data and other recent data sets shows that for young seas, microbreakers and small whitecaps contribute only a small fraction of the total breaking wave dissipation rate. For older seas, we find microbreakers and small whitecaps contribute a large fraction of the breaking wave dissipation rate, but this is only a small fraction of the total dissipation rate, which is now dominated by non-breaking contributions. Hence, for all the wave age conditions observed, microbreakers make an insignificant contribution to the total wave dissipation rate in the wave boundary layer. We tested the sensitivity of the results to the SM15a whitecap analysis methodology by transforming the SM15a breaking data using our breaking crest processing methodology. This resulted in the small-scale breaking waves making an even smaller contribution to the total wave dissipation rate, and so the result is independent of the breaker processing methodology. Comparison with other near-surface total TKE dissipation rate observations also support this conclusion. These contributions to the spectral dissipation rate in ocean wave models are small and need not be explicitly resolved.
May 2018
Parameterizing unresolved obstacles with source terms in wave modeling: A real-world application
Publication date: June 2018
Source:Ocean Modelling, Volume 126 Author(s): Lorenzo Mentaschi, Georgia Kakoulaki, Michalis Vousdoukas, Evangelos Voukouvalas, Luc Feyen, Giovanni Besio Parameterizing the dissipative effects of small, unresolved coastal features, is fundamental to improve the skills of wave models. The established technique to deal with this problem consists in reducing the amount of energy advected within the propagation scheme, and is currently available only for regular grids. To find a more general approach, Mentaschi et al., 2015b formulated a technique based on source terms, and validated it on synthetic case studies. This technique separates the parameterization of the unresolved features from the energy advection, and can therefore be applied to any numerical scheme and to any type of mesh. Here we developed an open-source library for the estimation of the transparency coefficients needed by this approach, from bathymetric data and for any type of mesh. The spectral wave model WAVEWATCH III was used to show that in a real-world domain, such as the Caribbean Sea, the proposed approach has skills comparable and sometimes better than the established propagation-based technique.
May 2018
Editorial Board
Publication date: May 2018
Source:Ocean Modelling, Volume 125

May 2018
Intercomparison of the Gulf Stream in ocean reanalyses: 1993
May 2018
The importance of modeling nonhydrostatic processes for dense water reproduction in the Southern Adriatic Sea
Publication date: May 2018
Source:Ocean Modelling, Volume 125 Author(s): Debora Bellafiore, William J. McKiver, Christian Ferrarin, Georg Umgiesser Dense water (DW) formation commonly occurs in the shallow Northern Adriatic Sea during winter outbreaks, when there is a combination of the cooling of surface waters by the winds and high salinity as a result of reduced river inputs. These DWs subsequently propagate southwards over a period of weeks/months, eventually arriving in the Southern Adriatic Sea. The investigation is based on a new nonhydrostatic (NH) formulation of the 3D finite element model SHYFEM that is validated for a number of theoretical test cases. Subsequently this model is used to simulate, through high-resolution numerical simulations, an extreme DW event that occurred in the Adriatic Sea in 2012. We perform both hydrostatic (HY) and NH simulations in order to explicitly see the impact of NH processes on the DW dynamics. The modeled results are compared to observations collected in the field campaign of March–April 2012 in the Southern Adriatic Sea. The NH run correctly reproduces the across isobath bottom-trapped gravity current characterizing the canyon DW pathways. It also more accurately captures the frequency and intensity of dense water cascading pulsing events, as the inclusion of NH processes produces stronger currents with different DW mixing characteristics. Finally, the NH run simulates internal gravity waves (IGW), generated during the cascading at the edge of the canyon, which propagate downslope. This IGW activity is not captured in the HY case.
May 2018
A parameterization of the passive layer of a quasigeostrophic flow in a continuously-stratified ocean
Publication date: May 2018
Source:Ocean Modelling, Volume 125 Author(s): E.S. Benilov This paper examines quasigeostrophic flows in an ocean that can be subdivided into an upper active layer (AL) and a lower passive layer (PL), with the flow and density stratification mainly confined to the former. Under this assumption, an asymptotic model is derived parameterizing the effect of the PL on the AL. The model depends only on the PL’s depth, whereas its V
May 2018
Representing grounding line migration in synchronous coupling between a marine ice sheet model and a z-coordinate ocean model
Publication date: May 2018
Source:Ocean Modelling, Volume 125 Author(s): D.N. Goldberg, K. Snow, P. Holland, J.R. Jordan, J.-M. Campin, P. Heimbach, R. Arthern, A. Jenkins Synchronous coupling is developed between an ice sheet model and a z-coordinate ocean model (the MITgcm). A previously-developed scheme to allow continuous vertical movement of the ice-ocean interface of a floating ice shelf (“vertical coupling”) is built upon to allow continuous movement of the grounding line, or point of floatation of the ice sheet (“horizontal coupling”). Horizontal coupling is implemented through the maintenance of a thin layer of ocean (
May 2018
A discontinuous Galerkin approach for conservative modeling of fully nonlinear and weakly dispersive wave transformations
Publication date: May 2018
Source:Ocean Modelling, Volume 125 Author(s): Mohammad Kazem Sharifian, Georges Kesserwani, Yousef Hassanzadeh This work extends a robust second-order Runge–Kutta Discontinuous Galerkin (RKDG2) method to solve the fully nonlinear and weakly dispersive flows, within a scope to simultaneously address accuracy, conservativeness, cost-efficiency and practical needs. The mathematical model governing such flows is based on a variant form of the Green–Naghdi (GN) equations decomposed as a hyperbolic shallow water system with an elliptic source term. Practical features of relevance (i.e. conservative modeling over irregular terrain with wetting and drying and local slope limiting) have been restored from an RKDG2 solver to the Nonlinear Shallow Water (NSW) equations, alongside new considerations to integrate elliptic source terms (i.e. via a fourth-order local discretization of the topography) and to enable local capturing of breaking waves (i.e. via adding a detector for switching off the dispersive terms). Numerical results are presented, demonstrating the overall capability of the proposed approach in achieving realistic prediction of nearshore wave processes involving both nonlinearity and dispersion effects within a single model.
May 2018
The numerics of hydrostatic structured-grid coastal ocean models: State of the art and future perspectives
Publication date: May 2018
Source:Ocean Modelling, Volume 125 Author(s): Knut Klingbeil, Florian Lemari
April 2018
Some effects of horizontal discretization on linear baroclinic and symmetric instabilities
Publication date: May 2018
Source:Ocean Modelling, Volume 125 Author(s): William Barham, Scott Bachman, Ian Grooms The effects of horizontal discretization on linear baroclinic and symmetric instabilities are investigated by analyzing the behavior of the hydrostatic Eady problem in ocean models on the B and C grids. On the C grid a spurious baroclinic instability appears at small wavelengths. This instability does not disappear as the grid scale decreases; instead, it simply moves to smaller horizontal scales. The peak growth rate of the spurious instability is independent of the grid scale as the latter decreases. It is equal to c f / Ri where Ri is the balanced Richardson number, f is the Coriolis parameter, and c is a nondimensional constant that depends on the Richardson number. As the Richardson number increases c increases towards an upper bound of approximately 1/2; for large Richardson numbers the spurious instability is faster than the Eady instability. To suppress the spurious instability it is recommended to use fourth-order centered tracer advection along with biharmonic viscosity and diffusion with coefficients (
April 2018
Editorial Board
Publication date: April 2018
Source:Ocean Modelling, Volume 124

April 2018
Parameterized and resolved Southern Ocean eddy compensation
Publication date: April 2018
Source:Ocean Modelling, Volume 124 Author(s): Mads B. Poulsen, Markus Jochum, Roman Nuterman The ability to parameterize Southern Ocean eddy effects in a forced coarse resolution ocean general circulation model is assessed. The transient model response to a suite of different Southern Ocean wind stress forcing perturbations is presented and compared to identical experiments performed with the same model in 0.1° eddy-resolving resolution. With forcing of present-day wind stress magnitude and a thickness diffusivity formulated in terms of the local stratification, it is shown that the Southern Ocean residual meridional overturning circulation in the two models is different in structure and magnitude. It is found that the difference in the upper overturning cell is primarily explained by an overly strong subsurface flow in the parameterized eddy-induced circulation while the difference in the lower cell is mainly ascribed to the mean-flow overturning. With a zonally constant decrease of the zonal wind stress by 50% we show that the absolute decrease in the overturning circulation is insensitive to model resolution, and that the meridional isopycnal slope is relaxed in both models. The agreement between the models is not reproduced by a 50% wind stress increase, where the high resolution overturning decreases by 20%, but increases by 100% in the coarse resolution model. It is demonstrated that this difference is explained by changes in surface buoyancy forcing due to a reduced Antarctic sea ice cover, which strongly modulate the overturning response and ocean stratification. We conclude that the parameterized eddies are able to mimic the transient response to altered wind stress in the high resolution model, but partly misrepresent the unperturbed Southern Ocean meridional overturning circulation and associated heat transports.
April 2018
Tidal downscaling from the open ocean to the coast: a new approach applied to the Bay of Biscay
Publication date: April 2018
Source:Ocean Modelling, Volume 124 Author(s): F. Toublanc, N.K. Ayoub, F. Lyard, P. Marsaleix, D.J. Allain Downscaling physical processes from a large scale to a regional scale 3D model is a recurrent issue in coastal processes studies. The choice of boundary conditions will often greatly influence the solution within the 3D circulation model. In some regions, tides play a key role in coastal dynamics and must be accurately represented. The Bay of Biscay is one of these regions, with highly energetic tides influencing coastal circulation and river plume dynamics. In this study, three strategies are tested to force with barotropic tides a 3D circulation model with a variable horizontal resolution. The tidal forcings, as well as the tidal elevations and currents resulting from the 3D simulations, are compared to tidal harmonics extracted from satellite altimetry and tidal gauges, and tidal currents harmonics obtained from ADCP data. The results show a strong improvement of the M2 solution within the 3D model with a ”tailored” tidal forcing generated on the same grid and bathymetry as the 3D configuration, compared to a global tidal atlas forcing. Tidal harmonics obtained from satellite altimetry data are particularly valuable to assess the performance of each simulation. Comparisons between sea surface height time series, a sea surface salinity database, and daily averaged 2D currents also show a better agreement with this tailored forcing.
April 2018
Nonhydrostatic simulation of hyperpycnal river plumes on sloping continental shelves: Flow structures and nonhydrostatic effect
Publication date: April 2018
Source:Ocean Modelling, Volume 124 Author(s): Chien-Yung Tseng, Yi-Ju Chou A three-dimensional nonhydrostatic coastal model SUNTANS is used to study hyperpycnal plumes on sloping continental shelves with idealized domain setup. The study aims to examine the nonhydrostatic effect of the plunging hyperpycnal plume and the associated flow structures on different shelf slopes. The unstructured triangular grid in SUNTANS allows for local refinement of the grid size for regions in which the flow varies abruptly, while retaining low-cost computation using the coarse grid resolution for regions in which the flow is more uniform. These nonhydrostatic simulations reveal detailed three-dimensional flow structures in both transient and steady states. Via comparison with the hydrostatic simulation, we show that the nonhydrostatic effect is particularly important before plunging, when the plume is subject to significant changes in both the along-shore and vertical directions. After plunging, where the plume becomes an undercurrent that is more spatially uniform, little difference is found between the hydrostatic and nonhydrostatic simulations in the present gentle- and mild-slope cases. A grid-dependence study shows that the nonhydrostatic effect can be seen only when the grid resolution is sufficiently fine that the calculation is not overly diffusive. A depth-integrated momentum budget analysis is then conducted to show that the flow convergence due to plunging is an important factor in the three-dimensional flow structures. Moreover, it shows that the nonhydrostatic effect becomes more important as the slope increases, and in the steep-slope case, neglect of transport of the vertical momentum during plunging in the hydrostatic case further leads to an erroneous prediction for the undercurrent.
April 2018
Bottom boundary layer forced by finite amplitude long and short surface waves motions
Publication date: April 2018
Source:Ocean Modelling, Volume 124 Author(s): H. Elsafty, P. Lynett A multiple-scale perturbation approach is implemented to solve the Navier–Stokes equations while including bottom boundary layer effects under a single wave and under two interacting waves. In this approach, fluid velocities and the pressure field are decomposed into two components: a potential component and a rotational component. In this study, the two components are exist throughout the entire water column and each is scaled with appropriate length and time scales. A one-way coupling between the two components is implemented. The potential component is assumed to be known analytically or numerically a prior, and the rotational component is forced by the potential component. Through order of magnitude analysis, it is found that the leading-order coupling between the two components occurs through the vertical convective acceleration. It is shown that this coupling plays an important role in the bottom boundary layer behavior. Its effect on the results is discussed for different wave-forcing conditions: purely harmonic forcing and impurely harmonic forcing. The approach is then applied to derive the governing equations for the bottom boundary layer developed under two interacting wave motions. Both motions—the shorter and the longer wave—are decomposed into two components, potential and rotational, as it is done in the single wave. Test cases are presented wherein two different wave forcings are simulated: (1) two periodic oscillatory motions and (2) short waves interacting with a solitary wave. The analysis of the two periodic motions indicates that nonlinear effects in the rotational solution may be significant even though nonlinear effects are negligible in the potential forcing. The local differences in the rotational velocity due to the nonlinear vertical convection coupling term are found to be on the order of 30% of the maximum boundary layer velocity for the cases simulated in this paper. This difference is expected to increase with the increase in wave nonlinearity.
April 2018
Amplification of drawdown and runup over Hawaii's insular shelves by tsunami N-waves from mega Aleutian earthquakes
Publication date: April 2018
Source:Ocean Modelling, Volume 124 Author(s): Yefei Bai, Yoshiki Yamazaki, Kwok Fai Cheung The latest tsunami evacuation maps of Hawaii include an extreme scenario triggered by an Mw 9.3 Aleutian earthquake with large near-trench rupture. The tectonic plate motion produces concentrated seafloor uplift toward the deepest part of the trench generating a tsunami with strong non-hydrostatic characters. A parametric study shows the skewed seafloor uplift produces a dispersive leading crest followed by a prominent trough in the form of an N-wave. The trough maintains its depth across the ocean in the absence of side lobes and dispersion. Shifting of the uplift toward the trench tends to deepen the trough, but has diminishing effects on the wave crest away from the source. While the attenuated leading crest produces relatively moderate runup on north-facing shores of the Hawaiian Islands, with matching of the N-wave and shelf resonance periods, the trough produces an impulsive drawdown followed by an energetic upswing with unprecedented runup for a far-field tsunami. A set of control computations without dispersion reaffirms that a non-hydrostatic model is essential to account for these complex wave processes from the source to the shore. This case study highlights the unique tsunami hazards posed by the Aleutians to Hawaii and the role of wave troughs in delineating the impacts for hazard assessment and engineering design.
April 2018
Extreme wind-wave modeling and analysis in the south Atlantic ocean
Publication date: April 2018
Source:Ocean Modelling, Volume 124 Author(s): R.M. Campos, J.H.G.M. Alves, C. Guedes Soares, L.G. Guimaraes, C.E. Parente A set of wave hindcasts is constructed using two different types of wind calibration, followed by an additional test retuning the input source term Sin in the wave model. The goal is to improve the simulation in extreme wave events in the South Atlantic Ocean without compromising average conditions. Wind fields are based on Climate Forecast System Reanalysis (CFSR/NCEP). The first wind calibration applies a simple linear regression model, with coefficients obtained from the comparison of CFSR against buoy data. The second is a method where deficiencies of the CFSR associated with severe sea state events are remedied, whereby “defective” winds are replaced with satellite data within cyclones. A total of six wind datasets forced WAVEWATCH-III and additional three tests with modified Sin in WAVEWATCH III lead to a total of nine wave hindcasts that are evaluated against satellite and buoy data for ambient and extreme conditions. The target variable considered is the significant wave height (Hs). The increase of sea-state severity shows a progressive increase of the hindcast underestimation which could be calculated as a function of percentiles. The wind calibration using a linear regression function shows similar results to the adjustments to Sin term (increase of
April 2018
FVCOM one-way and two-way nesting using ESMF: Development and validation
Publication date: April 2018
Source:Ocean Modelling, Volume 124 Author(s): Jianhua Qi, Changsheng Chen, Robert C. Beardsley Built on the Earth System Modeling Framework (ESMF), the one-way and two-way nesting methods were implemented into the unstructured-grid Finite-Volume Community Ocean Model (FVCOM). These methods help utilize the unstructured-grid multi-domain nesting of FVCOM with an aim at resolving the multi-scale physical and ecosystem processes. A detail of procedures on implementing FVCOM into ESMF was described. The experiments were made to validate and evaluate the performance of the nested-grid FVCOM system. The first was made for a wave-current interaction case with a two-domain nesting with an emphasis on qualifying a critical need of nesting to resolve a high-resolution feature near the coast and harbor with little loss in computational efficiency. The second was conducted for the pseudo river plume cases to examine the differences in the model-simulated salinity between one-way and two-way nesting approaches and evaluate the performance of mass conservative two-way nesting method. The third was carried out for the river plume case in the realistic geometric domain in Mass Bay, supporting the importance for having the two-way nesting for coastal-estuarine integrated modeling. The nesting method described in this paper has been used in the Northeast Coastal Ocean Forecast System (NECOFS)-a global-regional-coastal nesting FVCOM system that has been placed into the end-to-end forecast and hindcast operations since 2007.
March 2018
Discontinuous Galerkin modeling of the Columbia River’s coupled estuary-plume dynamics
Publication date: April 2018
Source:Ocean Modelling, Volume 124 Author(s): Valentin Vallaeys, Tuomas K
March 2018
Editorial Board
Publication date: March 2018
Source:Ocean Modelling, Volume 123

March 2018
Sub-seasonal prediction of significant wave heights over the Western Pacific and Indian Oceans, part II: The impact of ENSO and MJO
Publication date: March 2018
Source:Ocean Modelling, Volume 123 Author(s): Ravi P Shukla, James L. Kinter, Chul-Su Shin This study evaluates the effect of El Ni
March 2018
On wave breaking for Boussinesq-type models
Publication date: March 2018
Source:Ocean Modelling, Volume 123 Author(s): M. Kazolea, M. Ricchiuto We consider the issue of wave breaking closure for Boussinesq type models, and attempt at providing some more understanding of the sensitivity of some closure approaches to the numerical set-up, and in particular to mesh size. For relatively classical choices of weakly dispersive propagation models, we compare two closure strategies. The first is the hybrid method consisting in suppressing the dispersive terms in breaking regions, as initially suggested by Tonelli and Petti in 2009. The second is an eddy viscosity approach based on the solution of a a turbulent kinetic energy. The formulation follows early work by O. Nwogu in the 90’s, and some more recent developments by Zhang and co-workers (Ocean Mod. 2014), adapting it to be consistent with the wave breaking detection used here. We perform a study of the behaviour of the two closures for different mesh sizes, with attention to the possibility of obtaining grid independent results. Based on a classical shallow water theory, we also suggest some monitors to quantify the different contributions to the dissipation mechanism, differentiating those associated to the scheme from those of the partial differential equation. These quantities are used to analyze the dynamics of dissipation in some classical benchmarks, and its dependence on the mesh size. Our main results show that numerical dissipation contributes very little to the the results obtained when using eddy viscosity method. This closure shows little sensitivity to the grid, and may lend itself to the development and use of non-dissipative/energy conserving numerical methods. The opposite is observed for the hybrid approach, for which numerical dissipation plays a key role, and unfortunately is sensitive to the size of the mesh. In particular, when working, the two approaches investigated provide results which are in the same ball range and which agree with what is usually reported in literature. With the hybrid method, however, the inception of instabilities is observed at mesh sizes which vary from case to case, and depend on the propagation model. These results are comforted by numerical computations on a large number of classical benchmarks.
March 2018
The inclusion of ocean-current effects in a tidal-current model as forcing in the convection term and its application to the mesoscale fate of CO2 seeping from the seafloor
Publication date: March 2018
Source:Ocean Modelling, Volume 123 Author(s): Ryosuke Sakaizawa, Takaya Kawai, Toru Sato, Hiroyuki Oyama, Daisuke Tsumune, Takaki Tsubono, Koichi Goto The target seas of tidal-current models are usually semi-closed bays, minimally affected by ocean currents. For these models, tidal currents are simulated in computational domains with a spatial scale of a couple hundred kilometers or less, by setting tidal elevations at their open boundaries. However, when ocean currents cannot be ignored in the sea areas of interest, such as in open seas near coastlines, it is necessary to include ocean-current effects in these tidal-current models. In this study, we developed a numerical method to analyze tidal currents near coasts by incorporating pre-calculated ocean-current velocities. First, a large regional-scale simulation with a spatial scale of several thousand kilometers was conducted and temporal changes in the ocean-current velocity at each grid point were stored. Next, the spatially and temporally interpolated ocean-current velocity was incorporated as forcing into the cross terms of the convection term of a tidal-current model having computational domains with spatial scales of hundreds of kilometers or less. Then, we applied this method to the diffusion of dissolved CO2 in a sea area off Tomakomai, Japan, and compared the numerical results and measurements to validate the proposed method.
March 2018
Atmosphere-ocean feedbacks in a coastal upwelling system
Publication date: March 2018
Source:Ocean Modelling, Volume 123 Author(s): J.M.R. Alves, A. Peliz, R.M.A. Caldeira, P.M.A. Miranda The COAWST (Coupled Ocean-Atmosphere-Wave-Sediment Transport) modelling system is used in different configurations to simulate the Iberian upwelling during the 2012 summer, aiming to assess the atmosphere-ocean feedbacks in the upwelling dynamics. When model results are compared with satellite measurements and in-situ data, two-way coupling is found to have a moderate impact in data-model statistics. A significant reinforcement of atmosphere-ocean coupling coefficients is, however, observed in the two-way coupled run, and in the WRF and ROMS runs forced by previously simulated SST and wind fields, respectively. The increasing in the coupling coefficient is associated with slight, but potentially important changes in the low-level coastal jet in the atmospheric marine boundary layer. While these results do not imply the need for fully coupled simulations in many applications, they show that in seasonal numerical studies such simulations do not degrade the overall model performance, and contribute to produce better dynamical fields.
March 2018
CMIP5-based global wave climate projections including the entire Arctic Ocean
Publication date: March 2018
Source:Ocean Modelling, Volume 123 Author(s): M. Casas-Prat, X.L. Wang, N. Swart This study presents simulations of the global ocean wave climate corresponding to the surface winds and sea ice concentrations as simulated by five CMIP5 (Coupled Model Intercomparison Project Phase 5) climate models for the historical (1979–2005) and RCP8.5 scenario future (2081–2100) periods. To tackle the numerical complexities associated with the inclusion of the North Pole, the WAVEWATCH III (WW3) wave model was used with a customized unstructured Spherical Multi-Cell grid of
March 2018
Impacts of wave-induced circulation in the surf zone on wave setup
Publication date: March 2018
Source:Ocean Modelling, Volume 123 Author(s): Thomas Gu
February 2018
Understanding variability of the Southern Ocean overturning circulation in CORE-II models
Publication date: March 2018
Source:Ocean Modelling, Volume 123 Author(s): S.M. Downes, P. Spence, A.M. Hogg The current generation of climate models exhibit a large spread in the steady-state and projected Southern Ocean upper and lower overturning circulation, with mechanisms for deep ocean variability remaining less well understood. Here, common Southern Ocean metrics in twelve models from the Coordinated Ocean-ice Reference Experiment Phase II (CORE-II) are assessed over a 60 year period. Specifically, stratification, surface buoyancy fluxes, and eddies are linked to the magnitude of the strengthening trend in the upper overturning circulation, and a decreasing trend in the lower overturning circulation across the CORE-II models. The models evolve similarly in the upper 1 km and the deep ocean, with an almost equivalent poleward intensification trend in the Southern Hemisphere westerly winds. However, the models differ substantially in their eddy parameterisation and surface buoyancy fluxes. In general, models with a larger heat-driven water mass transformation where deep waters upwell at the surface (
February 2018
Editorial Board
Publication date: February 2018
Source:Ocean Modelling, Volume 122

February 2018
Frontal dynamics at the edge of the Columbia River plume
Publication date: February 2018
Source:Ocean Modelling, Volume 122 Author(s):
February 2018
Vertical and horizontal resolution dependency in the model representation of tracer dispersion along the continental slope in the northern Gulf of Mexico
Publication date: February 2018
Source:Ocean Modelling, Volume 122 Author(s): Annalisa Bracco, Jun Choi, Jaison Kurian, Ping Chang A set of nine regional ocean model simulations at various horizontal (from 1 to 9
February 2018
Idealised modelling of ocean circulation driven by conductive and hydrothermal fluxes at the seabed
Publication date: February 2018
Source:Ocean Modelling, Volume 122 Author(s): Jowan M. Barnes, Miguel A. Morales Maqueda, Jeff A. Polton, Alex P. Megann Geothermal heating is increasingly recognised as an important factor affecting ocean circulation, with modelling studies suggesting that this heat source could lead to first-order changes in the formation rate of Antarctic Bottom Water, as well as a significant warming effect in the abyssal ocean. Where it has been represented in numerical models, however, the geothermal heat flux into the ocean is generally treated as an entirely conductive flux, despite an estimated one third of the global geothermal flux being introduced to the ocean via hydrothermal sources. A modelling study is presented which investigates the sensitivity of the geothermally forced circulation to the way heat is supplied to the abyssal ocean. An analytical two-dimensional model of the circulation is described, which demonstrates the effects of a volume flux through the ocean bed. A simulation using the NEMO numerical general circulation model in an idealised domain is then used to partition a heat flux between conductive and hydrothermal sources and explicitly test the sensitivity of the circulation to the formulation of the abyssal heat flux. Our simulations suggest that representing the hydrothermal flux as a mass exchange indeed changes the heat distribution in the abyssal ocean, increasing the advective heat transport from the abyss by up to 35% compared to conductive heat sources. Consequently, we suggest that the inclusion of hydrothermal fluxes can be an important addition to course-resolution ocean models.

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February 2018
Impacts of sea-surface salinity in an eddy-resolving semi-global OGCM
Publication date: February 2018
Source:Ocean Modelling, Volume 122 Author(s): Ryo Furue, Kohei Takatama, Hideharu Sasaki, Niklas Schneider, Masami Nonaka, Bunmei Taguchi To explore the impacts of sea-surface salinity (SSS) on the interannual variability of upper-ocean state, we compare two 10-year runs of an eddy-resolving ocean general circulation model (OGCM): in one, SSS is strongly restored toward a monthly climatology (World Ocean Atlas ’98) and in the other, toward the SSS of a monthly gridded Argo product. The inclusion of the Argo SSS generally improves the interannual variability of the mixed layer depth; particularly so in the western tropical Pacific, where so-called “barrier layers” are reproduced when the Argo SSS is included. The upper-ocean subsurface salinity variability is also improved in the tropics and subtropics even below the mixed layer. To understand the reason for the latter improvement, we separate the salinity difference between the two runs into its “dynamical” and “spiciness” components. The dynamical component is dominated by small-scale noise due to the chaotic nature of mesoscale eddies. The spiciness difference indicates that as expected from the upper-ocean general circulation, SSS variability in the mixed layer is subducted into the thermocline in subtropics; this signal is generally advected downward, equatorward, and westward in the equator-side of the subtropical gyre. The SSS signal subducted in the subtropical North Pacific appears to enter the Indian Ocean through the Indonesian Throughflow, although this signal is weak and probably insignificant in our model.
February 2018
A commentary on the Atlantic meridional overturning circulation stability in climate models
Publication date: February 2018
Source:Ocean Modelling, Volume 122 Author(s): Peter R. Gent The stability of the Atlantic meridional overturning circulation (AMOC) in ocean models depends quite strongly on the model formulation, especially the vertical mixing, and whether it is coupled to an atmosphere model. A hysteresis loop in AMOC strength with respect to freshwater forcing has been found in several intermediate complexity climate models and in one fully coupled climate model that has very coarse resolution. Over 40% of modern climate models are in a bistable AMOC state according to the very frequently used simple stability criterion which is based solely on the sign of the AMOC freshwater transport across 33°
February 2018
Resolving high-frequency internal waves generated at an isolated coral atoll using an unstructured grid ocean model
Publication date: February 2018
Source:Ocean Modelling, Volume 122 Author(s): Matthew D. Rayson, Gregory N. Ivey, Nicole L. Jones, Oliver B. Fringer We apply the unstructured grid hydrodynamic model SUNTANS to investigate the internal wave dynamics around Scott Reef, Western Australia, an isolated coral reef atoll located on the edge of the continental shelf in water depths of 500,m and more. The atoll is subject to strong semi-diurnal tidal forcing and consists of two relatively shallow lagoons separated by a 500 m deep, 2 km wide and 15 km long channel. We focus on the dynamics in this channel as the internal tide-driven flow and resulting mixing is thought to be a key mechanism controlling heat and nutrient fluxes into the reef lagoons. We use an unstructured grid to discretise the domain and capture both the complex topography and the range of internal wave length scales in the channel flow. The model internal wave field shows super-tidal frequency lee waves generated by the combination of the steep channel topography and strong tidal flow. We evaluate the model performance using observations of velocity and temperature from two through water-column moorings in the channel separating the two reefs. Three different global ocean state estimate datasets (global HYCOM, CSIRO Bluelink, CSIRO climatology atlas) were used to provide the model initial and boundary conditions, and the model outputs from each were evaluated against the field observations. The scenario incorporating the CSIRO Bluelink data performed best in terms of through-water column Murphy skill scores of water temperature and eastward velocity variability in the channel. The model captures the observed vertical structure of the tidal (M 2) and super-tidal (M 4) frequency temperature and velocity oscillations. The model also predicts the direction and magnitude of the M 2 internal tide energy flux. An energy analysis reveals a net convergence of the M 2 energy flux and a divergence of the M 4 energy flux in the channel, indicating the channel is a region of either energy transfer to higher frequencies or energy loss to dissipation. This conclusion is supported by the mooring observations that reveal high frequency lee waves breaking on the turning phase of the tide.
January 2018
Dynamically adaptive data-driven simulation of extreme hydrological flows
Publication date: February 2018
Source:Ocean Modelling, Volume 122 Author(s): Pushkar Kumar Jain, Kyle Mandli, Ibrahim Hoteit, Omar Knio, Clint Dawson Hydrological hazards such as storm surges, tsunamis, and rainfall-induced flooding are physically complex events that are costly in loss of human life and economic productivity. Many such disasters could be mitigated through improved emergency evacuation in real-time and through the development of resilient infrastructure based on knowledge of how systems respond to extreme events. Data-driven computational modeling is a critical technology underpinning these efforts. This investigation focuses on the novel combination of methodologies in forward simulation and data assimilation. The forward geophysical model utilizes adaptive mesh refinement (AMR), a process by which a computational mesh can adapt in time and space based on the current state of a simulation. The forward solution is combined with ensemble based data assimilation methods, whereby observations from an event are assimilated into the forward simulation to improve the veracity of the solution, or used to invert for uncertain physical parameters. The novelty in our approach is the tight two-way coupling of AMR and ensemble filtering techniques. The technology is tested using actual data from the Chile tsunami event of February 27, 2010. These advances offer the promise of significantly transforming data-driven, real-time modeling of hydrological hazards, with potentially broader applications in other science domains.

Editorial Board
Publication date: January 2018
Source:Ocean Modelling, Volume 121


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