A global algorithm for estimating Absolute Salinity

The International Thermodynamic Equation of Seawater – 2010 has defined the thermodynamic properties of seawater in terms of a new salinity variable, Absolute Salinity, which takes into account the spatial variation of the composition of seawater. Absolute Salinity more accurately reflects the effects of the dissolved material in seawater on the thermodynamic properties (particularly density) than does Practical Salinity. <br><br> When a seawater sample has standard composition (i.e. the ratios of the constituents of sea salt are the same as those of surface water of the North Atlantic), Practical Salinity can be used to accurately evaluate the thermodynamic properties of seawater. When seawater is not of standard composition, Practical Salinity alone is not sufficient and the Absolute Salinity Anomaly needs to be estimated; this anomaly is as large as 0.025 g kg<sup>−1</sup> in the northernmost North Pacific. Here we provide an algorithm for estimating Absolute Salinity Anomaly for any location (<i>x, y, p</i>) in the world ocean. <br><br> To develop this algorithm, we used the Absolute Salinity Anomaly that is found by comparing the density calculated from Practical Salinity to the density measured in the laboratory. These estimates of Absolute Salinity Anomaly however are limited to the number of available observations (namely 811). In order to provide a practical method that can be used at any location in the world ocean, we take advantage of approximate relationships between Absolute Salinity Anomaly and silicate concentrations (which are available globally)

Eddy heat fluxes from direct current measurements of the Antarctic Polar Front in Shag Rocks Passage

Determining meridional heat flux in the Southern Ocean is critical to the accurate understanding and model simulation of the global ocean. Mesoscale eddies provide a significant but poorly-defined contribution to this transport. An eighteen-month deep-water current meter array deployment in Shag Rocks Passage (53°S, 48°W) between May 2003 and November 2004 provides estimates of the eddy flux of heat across the Polar Front. We calculate a statistically nonzero (99% level), vertically coherent local poleward heat flux of 12.0 ± 5.8 kW m-2 within the eddy frequency band at ~2750 m depth. Exceeding previous deep-water estimates by up to an order of magnitude, this highlights the large spatial variation in flux estimates and illustrates that constriction of circumpolar fronts facilitates large eddy transfers of heat southwards

Calculating Reynolds stresses from ADCP measurements in the presence of surface gravity waves using the cospectra-fit method

Author Posting. © American Meteorological Society, 2010. This article is posted here by permission of American Meteorological Society for personal use, not for redistribution. The definitive version was published in Journal of Atmospheric and Oceanic Technology 27 (2010): 889-907, doi:10.1175/2009JTECHO682.1.Recently, the velocity observations of acoustic Doppler current profilers (ADCPs) have been successfully used to estimate turbulent Reynolds stresses in estuaries and tidal channels. However, the presence of surface gravity waves can significantly bias stress estimates, limiting application of the technique in the coastal ocean. This work describes a new approach to estimate Reynolds stresses from ADCP velocities obtained in the presence of waves. The method fits an established semiempirical model of boundary layer turbulence to the measured turbulent cospectra at frequencies below those of surface gravity waves to estimate the stress. Applied to ADCP observations made in weakly stratified waters and variable significant wave heights, estimated near-bottom and near-surface stresses using this method compared well with independent estimates of the boundary stresses in contrast to previous methods. Additionally, the vertical structure of tidal stress estimated using the new approach matched that inferred from a linear momentum balance at stress levels below the estimated stress uncertainties. Because the method makes an estimate of the horizontal turbulent length scales present as part of the model fit, these results can also enable a direct correction for the mean bias errors resulting from instrument tilt, if these scales are long relative to the beam separation.AK acknowledges support from the WHOI Coastal Ocean Institute, and SL acknowledges support from NSF Ocean Science Grant OCE-0548961

Storm-driven sediment transport in Massachusetts Bay

This paper is not subject to U.S. copyright. The definitive version was published in Continental Shelf Research 28 (2008): 257-282, doi:10.1016/j.csr.2007.08.008.Massachusetts Bay is a semi-enclosed embayment in the western Gulf of Maine about 50 km wide and 100 km long. Bottom sediment resuspension is controlled predominately by storm-induced surface waves and transport by the tidal- and wind-driven circulation. Because the Bay is open to the northeast, winds from the northeast (‘Northeasters’) generate the largest surface waves and are thus the most effective in resuspending sediments. The three-dimensional oceanographic circulation model Regional Ocean Modeling System (ROMS) is used to explore the resuspension, transport, and deposition of sediment caused by Northeasters. The model transports multiple sediment classes and tracks the evolution of a multilevel sediment bed. The surficial sediment characteristics of the bed are coupled to one of several bottom-boundary layer modules that calculate enhanced bottom roughness due to wave–current interaction. The wave field is calculated from the model Simulating WAves Nearshore (SWAN). Two idealized simulations were carried out to explore the effects of Northeasters on the transport and fate of sediments. In one simulation, an initially spatially uniform bed of mixed sediments exposed to a series of Northeasters evolved to a pattern similar to the existing surficial sediment distribution. A second set of simulations explored sediment-transport pathways caused by storms with winds from the northeast quadrant by simulating release of sediment at selected locations. Storms with winds from the north cause transport southward along the western shore of Massachusetts Bay, while storms with winds from the east and southeast drive northerly nearshore flow. The simulations show that Northeasters can effectively transport sediments from Boston Harbor and the area offshore of the harbor to the southeast into Cape Cod Bay and offshore into Stellwagen Basin. This transport pattern is consistent with Boston Harbor as the source of silver found in the surficial sediments of Cape Cod Bay and Stellwagen Basin.We gratefully acknowledge support from the USGS Mendenhall Post-Doctoral Research Program for John C. Warner

Northern Monterey Bay upwelling shadow front : observations of a coastally and surface-trapped buoyant plume

Author Posting. © American Geophysical Union, 2009. This article is posted here by permission of American Geophysical Union for personal use, not for redistribution. The definitive version was published in Journal of Geophysical Research 114 (2009): C12013, doi:10.1029/2009JC005623.During the upwelling season in central California, northwesterly winds along the coast produce a strong upwelling jet that originates at Point Año Nuevo and flows southward across the mouth of Monterey Bay. A convergent front with a mean temperature change of 3.77 ± 0.29°C develops between the warm interior waters and the cold offshore upwelling jet. To examine the forcing mechanisms driving the location and movement of the upwelling shadow front and its effects on biological communities in northern Monterey Bay, oceanographic conditions were monitored using cross-shelf mooring arrays, drifters, and hydrographic surveys along a 20 km stretch of coast extending northwestward from Santa Cruz, California, during the upwelling season of 2007 (May–September). The alongshore location of the upwelling shadow front at the northern edge of the bay was driven by: regional wind forcing, through an alongshore pressure gradient; buoyancy forces due to the temperature change across the front; and local wind forcing (the diurnal sea breeze). The upwelling shadow front behaved as a surface-trapped buoyant current, which is superimposed on a poleward barotropic current, moving up and down the coast up to several kilometers each day. We surmise that the front is advected poleward by a preexisting northward barotropic current of 0.10 m s−1 that arises due to an alongshore pressure gradient caused by focused upwelling at Point Año Nuevo. The frontal circulation (onshore surface currents) breaks the typical two-dimensional wind-driven, cross-shelf circulation (offshore surface currents) and introduces another way for water, and the material it contains (e.g., pollutants, larvae), to go across the shelf toward shore.Funded primarily by the Gordon and Betty Moore Foundation and the David and Lucile Packard Foundation

Tidal and groundwater fluxes to a shallow, microtidal estuary : constraining inputs through field observations and hydrodynamic modeling

This paper is not subject to U.S. copyright. The definitive version was published in Estuaries and Coasts 35 (2012): 1285-1298, doi:10.1007/s12237-012-9515-x.Increased nutrient loading to estuaries has led to eutrophication, degraded water quality, and ecological transformations. Quantifying nutrient loads in systems with significant groundwater input can be difficult due to the challenge of measuring groundwater fluxes. We quantified tidal and freshwater fluxes over an 8-week period at the entrance of West Falmouth Harbor, Massachusetts, a eutrophic, groundwater-fed estuary. Fluxes were estimated from velocity and salinity measurements and a total exchange flow (TEF) methodology. Intermittent cross-sectional measurements of velocity and salinity were used to convert point measurements to cross-sectionally averaged values over the entire deployment (index relationships). The estimated mean freshwater flux (0.19 m3/s) for the 8-week period was mainly due to groundwater input (0.21 m3/s) with contributions from precipitation to the estuary surface (0.026 m3/s) and removal by evaporation (0.048 m3/s). Spring–neap variations in freshwater export that appeared in shorter-term averages were mostly artifacts of the index relationships. Hydrodynamic modeling with steady groundwater input demonstrated that while the TEF methodology resolves the freshwater flux signal, calibration of the index– salinity relationships during spring tide conditions only was responsible for most of the spring–neap signal. The mean freshwater flux over the entire period estimated from the combination of the index-velocity, index–salinity, and TEF calculations were consistent with the model, suggesting that this methodology is a reliable way of estimating freshwater fluxes in the estuary over timescales greater than the spring– neap cycle. Combining this type of field campaign with hydrodynamic modeling provides guidance for estimating both magnitude of groundwater input and estuarine storage of freshwater and sets the stage for robust estimation of the nutrient load in groundwater.Funding was provided by the USGS Coastal and Marine Geology Program and by National Science Foundation Award #0420575 from the Biocomplexity/Coupled Biogeochemical Cycles Program

Vigorous lateral export of the meltwater outflow from beneath an Antarctic ice shelf

The instability and accelerated melting of the Antarctic Ice Sheet are among the foremost elements of contemporary global climate change1, 2. The increased freshwater output from Antarctica is important in determining sea level rise1, the fate of Antarctic sea ice and its effect on the Earth’s albedo4, 5, ongoing changes in global deep-ocean ventilation6, and the evolution of Southern Ocean ecosystems and carbon cycling7, 8. A key uncertainty in assessing and predicting the impacts of Antarctic Ice Sheet melting concerns the vertical distribution of the exported meltwater. This is usually represented by climate-scale models3–5, 9 as a near-surface freshwater input to the ocean, yet measurements around Antarctica reveal the meltwater to be concentrated at deeper levels10, 11, 12, 13, 14. Here we use observations of the turbulent properties of the meltwater outflows from beneath a rapidly melting Antarctic ice shelf to identify the mechanism responsible for the depth of the meltwater. We show that the initial ascent of the meltwater outflow from the ice shelf cavity triggers a centrifugal overturning instability that grows by extracting kinetic energy from the lateral shear of the background oceanic flow. The instability promotes vigorous lateral export, rapid dilution by turbulent mixing, and finally settling of meltwater at depth. We use an idealized ocean circulation model to show that this mechanism is relevant to a broad spectrum of Antarctic ice shelves. Our findings demonstrate that the mechanism producing meltwater at depth is a dynamically robust feature of Antarctic melting that should be incorporated into climate-scale models

Identification of the first steps in charge separation in bacterial photosynthetic reaction centers of Rhodobacter sphaeroides by ultrafast mid-infrared spectroscopy: Electron transfer and protein dynamics

AbstractTime-resolved visible pump/mid-infrared (mid-IR) probe spectroscopy in the region between 1600 and 1800cm−1 was used to investigate electron transfer, radical pair relaxation, and protein relaxation at room temperature in the Rhodobacter sphaeroides reaction center (RC). Wild-type RCs both with and without the quinone electron acceptor QA, were excited at 600nm (nonselective excitation), 800nm (direct excitation of the monomeric bacteriochlorophyll (BChl) cofactors), and 860nm (direct excitation of the dimer of primary donor (P) BChls (PL/PM)). The region between 1600 and 1800cm−1 encompasses absorption changes associated with carbonyl (CO) stretch vibrational modes of the cofactors and protein. After photoexcitation of the RC the primary electron donor P excited singlet state (P*) decayed on a timescale of 3.7ps to the state P+BL− (where BL is the accessory BChl electron acceptor). This is the first report of the mid-IR absorption spectrum of P+BL−; the difference spectrum indicates that the 9-keto CO stretch of BL is located around 1670–1680cm−1. After subsequent electron transfer to the bacteriopheophytin HL in ∼1ps, the state P+HL− was formed. A sequential analysis and simultaneous target analysis of the data showed a relaxation of the P+HL− radical pair on the ∼20ps timescale, accompanied by a change in the relative ratio of the PL+ and PM+ bands and by a minor change in the band amplitude at 1640cm−1 that may be tentatively ascribed to the response of an amide CO to the radical pair formation. We conclude that the drop in free energy associated with the relaxation of P+HL−, is due to an increased localization of the electron hole on the PL half of the dimer and a further consequence is a reduction in the electrical field causing the Stark shift of one or more amide CO oscillators

Characterizing wave- and current- induced bottom shear stress : U.S. middle Atlantic continental shelf

This paper is not subject to U.S. copyright. The definitive version was published in Continental Shelf Research 52 (2013): 73-86, doi:10.1016/j.csr.2012.10.012.Waves and currents create bottom shear stress, a force at the seabed that influences sediment texture distribution, micro-topography, habitat, and anthropogenic use. This paper presents a methodology for assessing the magnitude, variability, and driving mechanisms of bottom stress and resultant sediment mobility on regional scales using numerical model output. The analysis was applied to the Middle Atlantic Bight (MAB), off the U.S. East Coast, and identified a tidally-dominated shallow region with relatively high stress southeast of Massachusetts over Nantucket Shoals, where sediment mobility thresholds are exceeded over 50% of the time; a coastal band extending offshore to about 30 m water depth dominated by waves, where mobility occurs more than 20% of the time; and a quiescent low stress region southeast of Long Island, approximately coincident with an area of fine-grained sediments called the “Mud Patch”. The regional high in stress and mobility over Nantucket Shoals supports the hypothesis that fine grain sediment winnowed away in this region maintains the Mud Patch to the southwest. The analysis identified waves as the driving mechanism for stress throughout most of the MAB, excluding Nantucket Shoals and sheltered coastal bays where tides dominate; however, the relative dominance of low-frequency events varied regionally, and increased southward toward Cape Hatteras. The correlation between wave stress and local wind stress was lowest in the central MAB, indicating a relatively high contribution of swell to bottom stress in this area, rather than locally generated waves. Accurate prediction of the wave energy spectrum was critical to produce good estimates of bottom shear stress, which was sensitive to energy in the long period waves.P.S. Dalyander was supported by the U.S. Geological Survey Mendenhall Research Fellowship Program