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  • 1
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    Comparison of physical to numerical mixing with different tracer advection schemes in estuarine environments (2020)
    MDPI
    Details
    Publication Date: 2022-10-27
    Description: © The Author(s), 2019. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Kalra, T. S., Li, X., Warner, J. C., Geyer, W. R., & Wu, H. Comparison of physical to numerical mixing with different tracer advection schemes in estuarine environments. Journal of Marine Science and Engineering, 7(10), (2019): 338, doi: 10.3390/jmse7100338.
    Description: The numerical simulation of estuarine dynamics requires accurate prediction for the transport of tracers, such as temperature and salinity. During the simulation of these processes, all the numerical models introduce two kinds of tracer mixing: (1) by parameterizing the tracer eddy diffusivity through turbulence models leading to a source of physical mixing and (2) discretization of the tracer advection term that leads to numerical mixing. Physical and numerical mixing both vary with the choice of horizontal advection schemes, grid resolution, and time step. By simulating four idealized cases, this study compares the physical and numerical mixing for three different tracer advection schemes. Idealized domains only involving physical and numerical mixing are used to verify the implementation of mixing terms by equating them to total tracer variance. Among the three horizontal advection schemes, the scheme that causes the least numerical mixing while maintaining a sharp front also results in larger physical mixing. Instantaneous spatial comparison of mixing components shows that physical mixing is dominant in regions of large vertical gradients, while numerical mixing dominates at sharp fronts that contain large horizontal tracer gradients. In the case of estuaries, numerical mixing might locally dominate over physical mixing; however, the amount of volume integrated numerical mixing through the domain compared to integrated physical mixing remains relatively small for this particular modeling system.
    Description: This study was funded through the Coastal Model Applications and Field Measurements Project and the Cross-shore and Inlets Project, US Geological Survey Coastal Marine Hazards and Resources Program.
    Keywords: Physical mixing ; Numerical mixing ; Advection schemes ; Estuarine mixing
    Repository Name: Woods Hole Open Access Server
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  • 2
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    Mechanisms of exchange flow in an estuary with a narrow, deep channel and wide, shallow shoals (2021)
    American Geophysical Union
    Details
    Publication Date: 2022-10-20
    Description: © The Author(s), 2020. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Geyer, W. R., Ralston, D. K., & Chen, J. Mechanisms of exchange flow in an estuary with a narrow, deep channel and wide, shallow shoals. Journal of Geophysical Research: Oceans, 125(12), (2020): e2020JC016092, https://doi.org/10.1029/2020JC016092.
    Description: Delaware Bay is a large estuary with a deep, relatively narrow channel and wide, shallow banks, providing a clear example of a “channel‐shoal” estuary. This numerical modeling study addresses the exchange flow in this channel‐shoal estuary, specifically to examine how the lateral geometry affects the strength and mechanisms of exchange flow. We find that the exchange flow is exclusively confined to the channel region during spring tides, when stratification is weak, and it broadens laterally over the shoals during the more stratified neap tides but still occupies a small fraction of the total width of the estuary. Exchange flow is relatively weak during spring tides, resulting from oscillatory shear dispersion in the channel augmented by weak Eulerian exchange flow. During neap tides, stratification and shear increase markedly, resulting in a strong Eulerian residual shear flow driven mainly by the along‐estuary density gradient, with a net exchange flow roughly 5 times that of the spring tide. During both spring and neap tides, lateral salinity gradients generated by differential advection at the edge of the channel drive a tidally oscillating cross‐channel flow, which strongly influences the stratification, along‐estuary salt balance, and momentum balance. The lateral flow also causes the phase variation in salinity that results in oscillatory shear dispersion and is an advective momentum source contributing to the residual circulation. Whereas the shoals make a negligible direct contribution to the exchange flow, they have an indirect influence due to the salinity gradients between the channel and the shoal.
    Description: The ideas in this paper were influenced by discussions with Robert Chant. Funding was provided by National Science Foundation grants OCE‐1325136, OCE‐1634490, and OCE‐1736539.
    Description: 2021-04-29
    Keywords: Estuarine circulation ; Tidal dispersion ; Lateral circulation
    Repository Name: Woods Hole Open Access Server
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  • 3
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    Sources, mechanisms, and timescales of sediment delivery to a New England salt marsh (2022)
    American Geophysical Union
    Details
    Publication Date: 2022-10-20
    Description: © The Author(s), 2022. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Baranes, H., Woodruff, J., Geyer, W., Yellen, B., Richardson, J. & Griswold, F. Sources, mechanisms, and timescales of sediment delivery to a New England salt marsh. Journal of Geophysical Research: Earth Surface, 127, (2022): e2021JF006478, https://doi.org/10.1029/2021jf006478.
    Description: he availability and delivery of an external clastic sediment source is a key factor in determining salt marsh resilience to future sea level rise. However, information on sources, mechanisms, and timescales of sediment delivery are lacking, particularly for wave-protected mesotidal estuaries. Here we show that marine sediment mobilized and delivered during coastal storms is a primary source to the North and South Rivers, a mesotidal bar-built estuary in a small river system impacted by frequent, moderate-intensity storms that is typical to New England (United States). On the marsh platform, deposition rates, clastic content, and dilution of fluvially-sourced contaminated sediment by marine material all increase down-estuary toward the inlet, consistent with a predominantly marine-derived sediment source. Marsh clastic deposition rates are also highest in the storm season. We observe that periods of elevated turbidity in channels and over the marsh are concurrent with storm surge and high wave activity offshore, rather than with high river discharge. Flood tide turbidity also exceeds ebb tide turbidity during storm events. Timescales of storm-driven marine sediment delivery range from 2.5 days to 2 weeks, depending on location within the estuary; therefore the phasing of storm surge and waves with the spring-neap cycle determines how effectively post-event suspended sediment is delivered to the marsh platform. This study reveals that sediment supply and the associated resilience of New England mesotidal salt marshes involves the interplay of coastal and estuarine processes, underscoring the importance of looking both up- and downstream to identify key drivers of environmental change.
    Description: The project described in this publication was in part supported by Grant or Cooperative Agreement No. G20AC00071 from the U.S. Geological Survey and a Department of Interior Northeast Climate Adaptation Science Center graduate fellowship awarded to H.E.B (G12AC00001).
    Keywords: Salt marsh ; Sediment ; Estuary ; Tides ; Massachusetts
    Repository Name: Woods Hole Open Access Server
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  • 4
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    Southern Cape Cod Bay hypoxia data (2022)
    Woods Hole Oceanographic Institution
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    Publication Date: 2022-06-14
    Description: This project investigated the distribution of low dissolved oxygen bottom waters (hypoxia) in southern Cape Cod Bay. Hypoxia was documented for the first time in late summer 2019 and 2020 despite extensive monitoring for the past decade. The data include: 1) measurements of bottom dissolved oxygen collected in 2019 by the Massachusetts Division of Marine Fisheries (MDMF) and the Center for Coastal Studies (CCS) ; 2) full water column profiles of temperature, salinity, chlorophyll fluorescence, dissolved oxygen concentration and optical backscatter collected in late summer 2020 by the Woods Hole Oceanographic Institution (WHOI); 3) monthly water quality data including CTD with dissolved oxygen and chlorophyll fluorescence and discrete bottom samples analyzed for dissolved nutrients collected by the CCS for the period 2011-2020; 4) inorganic nutrients from discrete surface and bottom samples collected monthly for the period 2006-2020; 5) bottom temperature data collected the Wreck of Mars location by the MDMF over the period 1991-2021. There are four separate data sets included: 1) MDMF and CCS bottom dissolved oxygn from 2019; 2) CTD and ancillary data collected by WHOI in 2019; 3) CCS monthly survey data from 2011-2020; and 4) bottom temperature data collected by MDMF for 1991-2021. 1) MDMF/CCS dissolved oxygen data was collected from ship-based surveys using an YSI 6920 V2-2 data sonde; 2) WHOI CTD data was collected from vertical casts made from a small research vessel using an RBR CTD; 3) CCS CTD data was collected from vertical casts made from a small research vessel using a SeaBird Electronics CTD; 4) MDMF temperature data was collected from a bottom mounted temperature logger. Related Publications: Scully, M.E., W.R. Geyer, D. Borkman, T.L. Pouch, A. Costa, and O.C. Nichols, in press. Unprecedented summer hypoxia in southern Cape Cod Bay: An ecological response to regional climate change? Biogeosciences.
    Description: National Science Foundation - OCE- 2053240 NOAA Seagrant - NA20OAR4170506
    Keywords: Hypoxia ; Harmful Algal Blooms ; Climate Change ; Thermal stratification
    Repository Name: Woods Hole Open Access Server
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  • 5
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    North River estuary 2017 dataset (2021)
    Woods Hole Oceanographic Institution
    Details
    Publication Date: 2022-05-26
    Description: These are the observational data collected in 2017 from the North River estuary. Data files include the long-term (LT) CTD and Aquadopp measurements from April to July, the short-term (STI from April to May and STII in late July) CTD measurements, eight shipboard CTD and ADCP surveys in April, May and July, the ADV measurements in late July, the North River mid-estuary region bathymetry, and the North River discharge (from USGS measurements).
    Description: National Science Foundation#1634480
    Repository Name: Woods Hole Open Access Server
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  • 6
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    Unprecedented summer hypoxia in southern Cape Cod Bay: an ecological response to regional climate change? (2022)
    European Geosciences Union
    Details
    Publication Date: 2022-12-22
    Description: © The Author(s), 2022. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Scully, M. E., Geyer, W. R., Borkman, D., Pugh, T. L., Costa, A., & Nichols, O. C. Unprecedented summer hypoxia in southern Cape Cod Bay: an ecological response to regional climate change? Biogeosciences, 19(14), (2022): 3523–3536, https://doi.org/10.5194/bg-19-3523-2022.
    Description: In late summer 2019 and 2020 bottom waters in southern Cape Cod Bay (CCB) became depleted of dissolved oxygen (DO), with documented benthic mortality in both years. Hypoxic conditions formed in relatively shallow water where the strong seasonal thermocline intersected the sea floor, both limiting vertical mixing and concentrating biological oxygen demand (BOD) over a very thin bottom boundary layer. In both 2019 and 2020, anomalously high sub-surface phytoplankton blooms were observed, and the biomass from these blooms provided the fuel to deplete sub-pycnocline waters of DO. The increased chlorophyll fluorescence was accompanied by a corresponding decrease in sub-pycnocline nutrients, suggesting that prior to 2019 physical conditions were unfavorable for the utilization of these deep nutrients by the late-summer phytoplankton community. It is hypothesized that significant alteration of physical conditions in CCB during late summer, which is the result of regional climate change, has favored the recent increase in sub-surface phytoplankton production. These changes include rapidly warming waters and significant shifts in summer wind direction, both of which impact the intensity and vertical distribution of thermal stratification and vertical mixing within the water column. These changes in water column structure are not only more susceptible to hypoxia but also have significant implications for phytoplankton dynamics, potentially allowing for intense late-summer blooms of Karenia mikimotoi, a species new to the area. K. mikimotoi had not been detected in CCB or adjacent waters prior to 2017; however, increasing cell densities have been reported in subsequent years, consistent with a rapidly changing ecosystem.
    Description: This research has been supported by the National Science Foundation (grant no. OCE-2053240) and the National Oceanic and Atmospheric Administration (grant no. NA20OAR4170506).
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  • 7
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    High and variable drag in a sinuous estuary with intermittent stratification (2022)
    American Geophysical Union
    Details
    Publication Date: 2022-05-27
    Description: © The Author(s), 2021. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Bo, T., Ralston, D. K., Kranenburg, W. M., Geyer, W. R., & Traykovski, P. High and variable drag in a sinuous estuary with intermittent stratification. Journal of Geophysical Research: Oceans, 126(10), (2021): e2021JC017327, https://doi.org/10.1029/2021JC017327
    Description: In field observations from a sinuous estuary, the drag coefficient C based on the momentum balance was in the range of 5-20 X10-3, much greater than expected from bottom friction alone. C also varied at tidal and seasonal timescales. CD was greater during flood tides than ebbs, most notably during spring tides. The ebb tide CD was negatively correlated with river discharge, while the flood tide CD showed no dependence on discharge. The large values of CD are explained by form drag from flow separation at sharp channel bends. Greater water depths during flood tides corresponded with increased values of CD, consistent with the expected depth dependence for flow separation, as flow separation becomes stronger in deeper water. Additionally, the strength of the adverse pressure gradient downstream of the bend apex, which is indicative of flow separation, correlated with CD during flood tides. While CD generally increased with water depth, CD decreased for the highest water levels that corresponded with overbank flow. The decrease in CD may be due to the inhibition of flow separation with flow over the vegetated marsh. The dependence of CD during ebbs on discharge corresponds with the inhibition of flow separation by a favoring baroclinic pressure gradient that is locally generated at the bend apex due to curvature-induced secondary circulation. This effect increases with stratification, which increases with discharge. Additional factors may contribute to the high drag, including secondary circulation, multiple scales of bedforms, and shallow shoals, but the observations suggest that flow separation is the primary source.
    Description: The research leading to these results was funded by NSF awards OCE-1634480, OCE-1634481, and OCE-2123002.
    Description: 2022-03-29
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  • 8
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    Tidal dispersion in short estuaries (2022)
    Woods Hole Oceanographic Institution
    Details
    Publication Date: 2022-10-21
    Description: The salinity distribution of an estuary depends on the balance between the river outflow, which is seaward, and a dispersive salt flux, which is landward. The dispersive salt flux at a fixed cross-section can be divided into shear dispersion, which is caused by spatial correlations of the cross-sectionally varying velocity and salinity, and the tidal oscillatory salt flux, which results from the tidal correlation between the cross-section averaged, tidally varying components of velocity and salinity. The theoretical moving plane analysis of Dronkers and van de Kreeke (1986) indicates that the oscillatory salt flux is exactly equal to the difference between the “local” shear dispersion at a fixed location and the shear dispersion which occurred elsewhere within a tidal excursion – therefore, they refer to the oscillatory salt flux as “nonlocal” dispersion. We apply their moving plane analysis to a numerical model of a short, tidally dominated estuary and provide the first quantitative confirmation of the theoretical result that the spatiotemporal variability of shear dispersion accounts for the oscillatory salt flux. Shear dispersion is localized in space and time and is most pronounced near regions of flow separation. Notably, we find that dispersive processes near the mouth contribute significantly to the overall salt balance, especially under strong river and tidal forcing. Furthermore, while mechanisms of vertical shear dispersion produce the majority of the dispersive salt flux during neap tide and high river flow, lateral mechanisms associated with flow separation provide the dominant mode of dispersion during spring tide and low flow. Dataset used in support of manuscript "Tidal dispersion in short estuaries". The dataset includes the model output from the idealized estuary for 16 different forcing conditions, corresponding to 4 tidal conditions (weak〈neap〈intm〈spring) and 4 river flow conditions (q01〈q03〈q10〈q30), as well as along-channel salinity measurements in the North River (Marshfield, MA, USA) during a 2017 field campaign.
    Description: This work was funded under NSF Grant OCE-1634490 and NSF Graduate Research Fellowship, Grant No. #1122374
    Keywords: Shear dispersion ; Estuary
    Repository Name: Woods Hole Open Access Server
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  • 9
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    Mechanisms of exchange flow in an estuary with a narrow, deep channel and wide, shallow shoals (2020)
    Woods Hole Oceanographic Institution
    Details
    Publication Date: 2022-10-21
    Description: Delaware Bay is a large estuary with a deep, relatively narrow channel and wide, shallow banks, providing a clear example of a “channel-shoal” estuary. This numerical modeling study addresses the exchange flow in this channel-shoal estuary, specifically to examine how the lateral geometry affects the strength and mechanisms of exchange flow. We find that the exchange flow is exclusively confined to the channel region during spring tides, when stratification is weak, and it broadens laterally over the shoals during the more stratified neap tides, but still occupies a small fraction of the total width of the estuary. Exchange flow is relatively weak during spring tides, resulting from oscillatory shear dispersion in the channel augmented by weak Eulerian exchange flow. During neap tides, stratification and shear increase markedly, resulting in a strong Eulerian residual shear flow, with a net exchange flow roughly 5 times that of the spring tide. During both spring and neap tides, lateral salinity gradients generated by differential advection at the edge of the channel drive a tidally oscillating cross-channel flow, which strongly influences the stratification, along-estuary salt balance and momentum balance. The lateral flow also causes the phase variation in salinity that results in oscillatory shear dispersion during both spring and neap tides and is a significant advective momentum source driving the residual circulation. Thus, although the shoals make a negligible direct contribution to the exchange flow, the salinity gradients between the channel and the shoal are critical to the stratification and exchange flow within the estuarine channel.
    Description: National Science Foundation (NSF): OCE-1325136; National Science Foundation (NSF): OCE-1634490; National Science Foundation (NSF): Jia-Lin Chen OCE-1736539
    Keywords: Estuarine circulation ; Tidal dispersion ; Lateral circulation
    Repository Name: Woods Hole Open Access Server
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  • 10
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    Using tracer variance decay to quantify variability of salinity mixing in the Hudson River Estuary (2021)
    American Geophysical Union
    Details
    Publication Date: 2022-10-21
    Description: © The Author(s), 2020. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Warner, J. C., Geyer, W. R., Ralston, D. K., & Kalra, T. Using tracer variance decay to quantify variability of salinity mixing in the Hudson River Estuary. Journal of Geophysical Research: Oceans, 125(12), (2020): e2020JC016096, https://doi.org/10.1029/2020JC016096.
    Description: The salinity structure in an estuary is controlled by time‐dependent mixing processes. However, the locations and temporal variability of where significant mixing occurs is not well‐understood. Here we utilize a tracer variance approach to demonstrate the spatial and temporal structure of salinity mixing in the Hudson River Estuary. We run a 4‐month hydrodynamic simulation of the tides, currents, and salinity that captures the spring‐neap tidal variability as well as wind‐driven and freshwater flow events. On a spring‐neap time scale, salinity variance dissipation (mixing) occurs predominantly during the transition from neap to spring tides. On a tidal time scale, 60% of the salinity variance dissipation occurs during ebb tides and 40% during flood tides. Spatially, mixing during ebbs occurs primarily where lateral bottom salinity fronts intersect the bed at the transition from the main channel to adjacent shoals. During ebbs, these lateral fronts form seaward of constrictions located at multiple locations along the estuary. During floods, mixing is generated by a shear layer elevated in the water column at the top of the mixed bottom boundary layer, where variations in the along channel density gradients locally enhance the baroclinic pressure gradient leading to stronger vertical shear and more mixing. For both ebb and flood, the mixing occurs at the location of overlap of strong vertical stratification and eddy diffusivity, not at the maximum of either of those quantities. This understanding lends a new insight to the spatial and time dependence of the estuarine salinity structure.
    Description: This study was funded through the Coastal Model Applications and Field Measurements Project and the Cross‐shore and Inlets Project, US Geological Survey Coastal Marine Hazards and Resources Program. Any use of trade, firm, or product names is for descriptive purposes only and does not imply endorsement by the US Government.
    Keywords: Hudson River Estuary ; Mixing ; Numerical modeling ; Tracer variance
    Repository Name: Woods Hole Open Access Server
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