Stephanie Anderson

Modeling of upwelling/relaxation events with the Navy Coastal Ocean Model

Prediction System (COAMPS TM )(COAMPS is a registered trademark of the Naval Research Laboratory). Issues investigated in this study are: NCOM-based model simulations of upwelling and relaxation events, coupling to COAMPS, use of sigma versus hybrid (sigma-z) vertical grids, and coupling with a larger-scale model on the open boundaries. The NCOM simulations were able to reproduce the observed sequence of the upwelling and relaxation events, which can be attributed, in part, to the good agreement between the observed and COAMPS winds. Comparisons with the mooring observations show that COAMPS overestimates shortwave radiation values, which makes the NCOM modeled SSTs too warm in comparison with observations. The NCOM runs forced with different resolution atmospheric forcing (3 versus 9 km) do not show significant differences in the predicted SSTs and mixed-layer depths at the mooring locations. At the same time, during the extended upwelling event, the model runs forced with 3 and 9 km resolution COAMPS fields show differences in the surface circulation patterns, which are the most distinct in the southern portion of the model domain. The model run with 9-km forcing develops a northward flow along the coast, which is not present in the run with 3-km forcing and in observations (for example, HF radar-derived radials). Comparison of the wind patterns of the 3- and 9-km products shows a weakening of the 9-km wind stress along the southern coast of the NCOM model domain, which is responsible for the development of the artificial northward flow in the NCOM run with 9-km forcing.

Comparisons of upwelling and relaxation events in the Monterey Bay area

[1] Observations show significant differences in circulation patterns of upwelling and relaxation events that occurred in the Monterey Bay during two Autonomous Ocean Sampling Network field experiments in August 2003 and 2006. During the 2003 experiment, circulation exhibited more typical patterns associated with upwelling/relaxation: the development of the southward flowing jet and pair of cyclonic (inside of the bay) and anticyclonic (outside of the bay) circulations during upwelling and the development of the northward flow along the coast during relaxation of winds. During the upwelling event of 2006, the southward flow was weaker and shallower than in 2003. The second relaxation event of 2006 was significantly different from the first relaxation event of 2006 and the relaxation event of 2003: a southward flow was present along the entrance to the bay and this southward flow penetrated into the subsurface up to around 50 m at the mooring location. Two reasons for the observed differences in upwelling and relaxation events of 2003 and 2006 are identified in the paper: weaker winds in August 2006 than in August 2003 and strong positive sea surface height anomalies propagating poleward along the coast during 2006. The 2003 field program included an extensive sampling of the bay and surrounding areas with a fleet of underwater gliders, while during 2006 program, the extensive sampling was conducted in the area of upwelling center to the north of the Monterey Bay. During the 2003 field program, the Monterey Bay model was able to reproduce observed surface and subsurface features with assimilation of glider observations. However, during the 2006 field program, the assimilation of glider data from the upwelling center to the north of the Monterey Bay had minimal impact on model simulations of observed features to the south of the upwelling center.

Development of a Hierarchy of Nested Models to Study the California Current System

The Naval Research Laboratory has developed a hierarch of differing resolution data assimilating models in the Pacific Ocean, which includes global models, regional U.S. West Coast models, and high resolution coastal models such as for the Monterey Bay area. The three regional U.S. West Coast models (from 30 degrees N to 49 degrees N), designed to study the California Current System, are based on the Princeton Ocean Model (POM), the Navy Coastal Ocean Model (MCOM), called NCOM-CCS, and the Hybrid Coordinate Ocean Model (HYCOM), respectively. The NCOM-CCS formulation is a parallel version model capable of running reliably on many computer platforms. The model has nesting capabilities and offers the choice of using the sigma or a hybrid (sigma-z) vertical coordinate. The NCOM-CCS model also includes a coupled ecosystem model based on Chai et al., 2002. A variety of scientific issues related to model initialization, forcing, open boundary conditions, and model sign up are discussed. The focus of this paper is on: the sensitivity of the horizontal resolution of atmospheric forcing on the NCOM-CCs model predictive skills; the impact of open boundary conditions and coupling with global models on reproducing major hydrographic conditions in the California Current System; and the analysis of the model mixed layer predictions and data assimilation issues. Qualitative and quantitative comparisons are made between observations and model predictions for October 2000 - December 2001 period.

Impact of submesoscale processes on dynamics of phytoplankton filaments

In Monterey Bay, CA, during northwesterly, upwelling favorable winds, the development of a southward flowing cold jet along the entrance to the Bay is often observed. This dense cold jet separates warm waters of the anticyclonic circulation offshore from the water masses inside the Bay. Interactions between the cold jet and the offshore anticyclonic circulation generate ageostrophic secondary circulation (ASC) cells due to submesoscale processes as, for example, flow interaction with the development of surface frontogenesis and nonlinear Ekman pumping. Based on observations and modeling studies, we evaluate the impact of these submesoscale processes on the formation of chlorophyll a filaments during late spring-earlier summer, and late summer time frames. We show that during the late summer time frame, ASC leads to the development of filaments with high values of chlorophyll a concentration along the edge of the cold jet–in contrast to the earlier summer time, when the ASC mixes phytoplankton much deeper to the area below of the euphotic depth, and chlorophyll a filaments are 3–4 times weaker.

Impact of errors in short wave radiation and its attenuation on modeled upper ocean heat content

Abstract. Photosynthetically available radiation (PAR) and its attenuation with the depth represent a forcing (source) term in the governing equation for the temperature in the oceanic dynamical models. PAR usually comes from the atmospheric model predictions, whereas PAR’s attenuation schemes are internally prescribed (estimated) inside the oceanic dynamical model. We perform sensitivity analyses to investigate the impact that errors in model surface PAR and vertical attenuation of PAR have on the upper ocean model heat content. In the Monterey Bay area, we show that with a decrease in water clarity, the relative error in surface PAR introduces a larger error in the modeled upper 25 m ocean heat content than the same magnitude relative error in the attenuation coefficient. For Jerlov’s type “IA” water (attenuation coefficient is 0.049  m−1), the relative error in surface PAR introduces an error twice as large into the model heat content as the same magnitude relative error in the attenuation coefficient. For the more turbid water Jerlov’s type “III” (attenuation coefficient is 0.127  m−1), the relative error in surface PAR introduces error seven times as large into the model heat content than the same magnitude relative error in the attenuation coefficient. We present how the upper ocean heat content sensitivities to errors in PAR and its attenuation change in space and time. While the sensitivities to the errors in surface PAR are all positive, sensitivities to the errors in attenuation coefficient have positive and negative values, depending on location. They are positive in shallower water for locations on the shelf in the northern part of the bay and negative in deeper offshore waters. Sensitivities derived provide a capability to understand and control the impact of errors in PAR and its attenuation on the upper ocean model heat content predictions.

Bio‐Optical Data Assimilation With Observational Error Covariance Derived From an Ensemble of Satellite Images

An ensemble-based approach to specify observational error covariance in the data assimilation of satellite bio-optical properties is proposed. The observational error covariance is derived from statistical properties of the generated ensemble of satellite MODIS-Aqua chlorophyll (Chl) images. The proposed observational error covariance is used in the Optimal Interpolation scheme for the assimilation of MODIS-Aqua Chl observations. The forecast error covariance is specified in the subspace of the multivariate (bio-optical, physical) empirical orthogonal functions (EOFs) estimated from a month-long model run. The assimilation of surface MODIS-Aqua Chl improved surface and subsurface model Chl predictions. Comparisons with surface and subsurface water samples demonstrate that data assimilation run with the proposed observational error covariance has higher RMSE than the data assimilation run with ‘‘optimistic’’ assumption about observational errors (10% of the ensemble mean), but has smaller or comparable RMSE than data assimilation run with an assumption that observational errors equal to 35% of the ensemble mean (the target error for satellite data product for chlorophyll). Also, with the assimilation of the MODIS-Aqua Chl data, the RMSE between observed and model-predicted fractions of diatoms to the total phytoplankton is reduced by a factor of two in comparison to the nonassimilative run.

Sensitivity of modeled ocean heat content to errors in short wave radiation and its attenuation with depth

Short wave radiation (SWR) and its attenuation with depth have a major impact on the vertical distribution of the oceanic water temperature, dynamical processes, and ocean-atmosphere interactions. In numerical modeling of oceanic processes, the SWR usually comes from the atmospheric model predictions, while the short wave attenuation schemes are internally prescribed (estimated) inside the oceanic dynamical model. It has been reported that atmospheric models show a tendency to overestimate the shortwave radiation due to underestimation of predicted low-level clouds. Most existing schemes to specify the attenuation of SWR with depth in numerical models are based on: the Jerlov (1976) water-types classification; climatological estimates of attenuation coefficients or from the biological model predictions of light-absorbing and scattering water constituents. All of the above attenuation schemes are prone to introducing errors in the attenuation of short wave radiation with depth. As a result, we have to deal with two types of errors in the oceanic modeling: those due to the incorrect specification of the magnitude of SWR at the surface (from the atmospheric model), and those due to inaccurate vertical attenuation of SWR (prescribed in the oceanic model). We have developed an approach for estimating errors in the oceanic model heat budget due to errors in surface values of SWR and in its attenuation with depth. Based on this approach, we present examples illustrating sensitivities of the heat budget of the water column to the changes in specification of surface SWR and its attenuation.

Are the satellite-observed narrow, streaky chlorophyll filaments locally intensified by the submesoscale processes?

Based on observations and modeling studies we have evaluated the impact of submesoscale processes on the development and intensification of offshore narrow (5-10km wide) phytoplankton filaments during summer time in the Monterey Bay, CA. We have demonstrated that, submesoscale processes (surface frontogenesis and nonlinear Ekman transport) lead to the development of very productive phytoplankton patches along the edges between the cold jet and warm anticyclonic eddy. Our results illustrate that during persistent upwelling favorable winds, submesoscale processes can modulate the development and intensification of offshore narrow (5-10km wide) phytoplankton filaments. These processes can incubate the phytoplankton population offshore (as for example, bioluminescent dinoflagellates during August 2003). These offshore phytoplankton filaments can migrate onshore during relaxed winds following the upwelling, and be an additional source of phytoplankton bloom development in and around Monterey Bay. Therefore, the discussed offshore phytoplankton filaments may be a factor in the Bay ecosystem health, as for example, in the development of such events as harmful algae blooms (HABs). All these emphasize the importance of further observational and modeling studies of these submesoscale processes which impact the development and intensification of offshore phytoplankton filaments.

Assimilation of bio-optical properties into coupled physical, bio-optical coastal model

Data assimilation experiments with the coupled physical, bio-optical model of Monterey Bay are presented. The approach is based on the representation of the error covariances in the subspace of the multivariate (bio-optical, physical) empirical orthogonal functions (EOFs) estimated from the model run. Estimated coupled bio-optical, physical error covariances are used in the Kalman gain update providing updates of coupled bio-optical properties in accord with the model dynamics and available observations. With the assimilation of satellite-derived bio-optical properties (chlorophyll-a and absorption due to phytoplankton), the model was able to reproduce intensity and tendencies in subsurface chlorophyll distributions observed at water samples locations in the Monterey Bay, CA. Data assimilation also improved agreement between the observed and model-predicted ratios between diatoms and small phytoplankton populations.