Sediment Transport
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ArticleA numerical investigation of the mechanisms controlling salt intrusion in the Delaware Bay estuary(Elsevier, 2023-04-05) Cook, Salme E. ; Warner, John C. ; Russell, Kendra L.Salinity intrusion in coastal systems is mainly controlled by freshwater inflows. However, extreme events like drought, low-pressure storms, and longer-term sea level rise can exacerbate the landward salt migration and threaten economic infrastructure and ecological health. Along the eastern seaboard of the United States, approximately 13 million people rely on the water resources of the Delaware River basin. Salinity intrusion is actively managed through river discharge targets to suppress the propagation of the salt front (∼0.52 daily averaged psu line). The purpose of this study is to examine the mechanisms controlling the location of the salt front in the Delaware Bay estuary using a calibrated three-dimensional hydrodynamic model, the Coupled Ocean Atmosphere Wave and Sediment Transport modeling system. This study explored how river discharge, tidal motions, interactions with bathymetric and topographic features, and meteorological events affected the location of the salt front. The model was forced with tides, subtidal water levels, bulk atmospheric conditions, and waves. Compared with the observationally derived location of the salt front line, the model captured the major dynamics throughout the year and performed particularly well during times of low discharge, when salinity intruded up estuary at a constant rate of 0.4 km/day. The daily average salt front moved almost 16 km (10 mi) within a neap-spring tidal cycle, and low-pressure storm systems were found to move the daily averaged salt front by 13–16 km in one event.•A numerical model was developed for Delaware Bay to study salinity intrusion. Key forcing variables in order of importance are river discharge, tides, subtidal motions, winds, and waves.•The salt front position is highly variable until passing a bathymetric control at the Delaware Memorial Bridge.•During constant discharge the salt front propagation speed is steady (∼0.4 km/day) until a storm or discharge event occurs.
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ArticleAccuracy of a pulse-coherent acoustic Doppler profiler in a wave-dominated flow(American Meteorological Society, 2004-09) Lacy, Jessica R. ; Sherwood, Christopher R.The accuracy of velocities measured by a pulse-coherent acoustic Doppler profiler (PCADP) in the bottom boundary layer of a wave-dominated inner-shelf environment is evaluated. The downward-looking PCADP measured velocities in eight 10-cm cells at 1 Hz. Velocities measured by the PCADP are compared to those measured by an acoustic Doppler velocimeter for wave orbital velocities up to 95 cm s−1 and currents up to 40 cm s−1. An algorithm for correcting ambiguity errors using the resolution velocities was developed. Instrument bias, measured as the average error in burst mean speed, is −0.4 cm s−1 (standard deviation = 0.8). The accuracy (root-mean-square error) of instantaneous velocities has a mean of 8.6 cm s−1 (standard deviation = 6.5) for eastward velocities (the predominant direction of waves), 6.5 cm s−1 (standard deviation = 4.4) for northward velocities, and 2.4 cm s−1 (standard deviation = 1.6) for vertical velocities. Both burst mean and root-mean-square errors are greater for bursts with ub ≥ 50 cm s−1. Profiles of burst mean speeds from the bottom five cells were fit to logarithmic curves: 92% of bursts with mean speed ≥ 5 cm s−1 have a correlation coefficient R2 > 0.96. In cells close to the transducer, instantaneous velocities are noisy, burst mean velocities are biased low, and bottom orbital velocities are biased high. With adequate blanking distances for both the profile and resolution velocities, the PCADP provides sufficient accuracy to measure velocities in the bottom boundary layer under moderately energetic inner-shelf conditions.
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PreprintAdvancing coastal ocean modelling, analysis, and prediction for the US Integrated Ocean Observing System( 2017-04-19) Wilkin, John L. ; Rosenfeld, Leslie K. ; Allen, Arthur ; Baltes, Rebecca ; Baptista, Antonio ; He, Ruoying ; Hogan, Patrick ; Kurapov, Alexander ; Mehra, Avichal ; Quintrell, Josie ; Schwab, David ; Signell, Richard P. ; Smith, JaneThis paper outlines strategies that would advance coastal ocean modeling, analysis and prediction as a complement to the observing and data management activities of the coastal components of the U.S. Integrated Ocean Observing System (IOOS®) and the Global Ocean Observing System (GOOS). The views presented are the consensus of a group of U.S. based researchers with a cross-section of coastal oceanography and ocean modeling expertise and community representation drawn from Regional and U.S. Federal partners in IOOS. Priorities for research and development are suggested that would enhance the value of IOOS observations through model-based synthesis, deliver better model-based information products, and assist the design, evaluation and operation of the observing system itself. The proposed priorities are: model coupling, data assimilation, nearshore processes, cyberinfrastructure and model skill assessment, modeling for observing system design, evaluation and operation, ensemble prediction, and fast predictors. Approaches are suggested to accomplish substantial progress in a 3-8 year timeframe. In addition, the group proposes steps to promote collaboration between research and operations groups in Regional Associations, U.S. Federal Agencies, and the international ocean research community in general that would foster coordination on scientific and technical issues, and strengthen federal-academic partnerships benefiting IOOS stakeholders and end users.
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ArticleAdvantages and limitations to the use of optical measurements to study sediment properties(MDPI, 2018-12-19) Boss, Emmanuel S. ; Sherwood, Christopher R. ; Hill, Paul S. ; Milligan, TimMeasurements of optical properties have been used for decades to study particle distributions in the ocean. They are useful for estimating suspended mass concentration as well as particle-related properties such as size, composition, packing (particle porosity or density), and settling velocity. Measurements of optical properties are, however, biased, as certain particles, because of their size, composition, shape, or packing, contribute to a specific property more than others. Here, we study this issue both theoretically and practically, and we examine different optical properties collected simultaneously in a bottom boundary layer to highlight the utility of such measurements. We show that the biases we are likely to encounter using different optical properties can aid our studies of suspended sediment. In particular, we investigate inferences of settling velocity from vertical profiles of optical measurements, finding that the effects of aggregation dynamics can seldom be ignored.
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PreprintAlexandrium fundyense cysts in the Gulf of Maine : long-term time series of abundance and distribution, and linkages to past and future blooms( 2013-10) Anderson, Donald M. ; Keafer, Bruce A. ; Kleindinst, Judith L. ; McGillicuddy, Dennis J. ; Martin, Jennifer L. ; Norton, Kerry ; Pilskaln, Cynthia H. ; Smith, Juliette L. ; Sherwood, Christopher R. ; Butman, BradfordHere we document Alexandrium fundyense cyst abundance and distribution patterns over nine years (1997 and 2004-2011) in the coastal waters of the Gulf of Maine (GOM) and identify linkages between those patterns and several metrics of the severity or magnitude of blooms occurring before and after each autumn cyst survey. We also explore the relative utility of two measures of cyst abundance and demonstrate that GOM cyst counts can be normalized to sediment volume, revealing meaningful patterns equivalent to those determined with dry weight normalization.Cyst concentrations were highly variable spatially. Two distinct 1 seedbeds (defined here as accumulation zones with > 300 cysts cm-3) are evident, one in the Bay of Fundy (BOF) and one in mid-coast Maine. Overall, seedbed locations remained relatively constant through time, but their area varied 3-4 fold, and total cyst abundance more than 10 fold among years. A major expansion of the mid-coast Maine seedbed occurred in 2009 following an unusually intense A. fundyense bloom with visible red-water conditions, but that feature disappeared by late 2010. The regional system thus has only two seedbeds with the bathymetry, sediment characteristics, currents, biology, and environmental conditions necessary to persist for decades or longer. Strong positive correlations were confirmed between the abundance of cysts in both the 0-1 and the 0-3 cm layers of sediments in autumn and geographic measures of the extent of the bloom that occurred the next year (i.e., cysts → blooms), such as the length of coastline closed due to shellfish toxicity or the southernmost latitude of shellfish closures. In general, these metrics of bloom geographic extent did not correlate with the number of cysts in sediments following the blooms (blooms → cysts). There are, however, significant positive correlations between 0-3 cm cyst abundances and metrics of the preceding bloom that are indicative of bloom intensity or vegetative cell abundance (e.g., cumulative shellfish toxicity, duration of detectable toxicity in shellfish, and bloom termination date). These data suggest that it may be possible to use cyst abundance to empirically forecast the geographic extent of the forthcoming bloom and, conversely, to use other metrics from bloom and toxicity events to forecast the size of the subsequent cyst population as the inoculum for the next year’s bloom. This is an important step towards understanding the excystment/encystment cycle in A. fundyense bloom dynamics while also augmenting our predictive capability for this HAB-forming species in the GOM.
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ArticleAlong-shelf current variability on the Catalan inner-shelf (NW Mediterranean)(American Geophysical Union, 2012-09-22) Grifoll, Manel ; Aretxabaleta, Alfredo L. ; Espino, Manuel ; Warner, John C.We examine the circulation over the inner-shelf of the Catalan Sea using observations of currents obtained from three Acoustic Doppler Current Profilers (two at 24 m and one at 50 m) during March–April 2011. The along-shelf current fluctuations during that period are mainly controlled by local wind stress on short time scales and by remote pressure gradients on synoptic time scales. Different forcing mechanisms are involved in the along-shelf momentum balance. During storm conditions, wind stress, sea level gradients and the nonlinear terms dominate the balance. During weak wind conditions, the momentum balance is controlled by the pressure gradient, while during periods of moderate wind in the presence of considerable stratification, the balance is established between the Coriolis and wind stress terms. Vertical variations of velocity are affected by the strong observed density gradient. The increased vertical shear is accompanied by the development of stratified conditions due to local heating when the wind is not able to counteract (and break) stratification. The occasional influence of the Besòs River plume is observed in time scales of hours to days in a limited area in near the city of Barcelona. The area affected by the plume depends on the vertical extent of the fresher layer, the fast river discharge peak, and the relaxation of cross-shore velocities after northeast storm events. This contribution provides a first interpretation of the inner-shelf dynamics in the Catalan Sea.
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ArticleAlongshore momentum balance analysis on a cuspate foreland(John Wiley & Sons, 2013-10-15) Kumar, Nirnimesh ; Voulgaris, George ; List, Jeffrey H. ; Warner, John C.Nearshore measurements of waves and currents off Cape Hatteras, North Carolina, U.S.A, are used to investigate depth-averaged subtidal circulation and alongshore momentum balances in the surf and inner shelf region around a cuspate foreland. Data were collected on both sides of the cape representing shorefaces with contrasting shoreline orientation (north-south vs. northwest-southeast) subjected to the same wind forcing. In the nearshore, the subtidal flow is aligned with the local coastline orientation while at the cape point the flow is along the existing submerged shoal, suggesting that cape associated shoals may act as an extension of the coastline. Alongshore momentum balance analysis incorporating wave-current interaction by including vortex and Stokes-Coriolis forces reveals that in deep waters surface and bottom stress are almost in balance. In shallower waters, the balance is complex as nonlinear advection and vortex force become important. Furthermore, linearized momentum balance analysis suggests that the vortex force can be of the same order as wind and wave forcing. Farther southwest of Cape Hatteras point, wind and wave forcing alone fail to fully explain subtidal flow variability and it is shown that alongshore pressure gradient as a response to the wind forcing can close the momentum balance. Adjacent tide gauge data suggest that the magnitude of pressure gradient depends on the relative orientation of local coastline to the wind vector, and in a depth-averaged sense the pressure gradient generation due to change in coastline orientation even at km length scale is analogous to the effect of alongshore variable winds on a straight coastline.
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ArticleAnalysis and visualization of coastal ocean model data in the cloud.(MDPI, 2019-04-19) Signell, Richard P. ; Pothina, DharhasThe traditional flow of coastal ocean model data is from High-Performance Computing (HPC) centers to the local desktop, or to a file server where just the needed data can be extracted via services such as OPeNDAP. Analysis and visualization are then conducted using local hardware and software. This requires moving large amounts of data across the internet as well as acquiring and maintaining local hardware, software, and support personnel. Further, as data sets increase in size, the traditional workflow may not be scalable. Alternatively, recent advances make it possible to move data from HPC to the Cloud and perform interactive, scalable, data-proximate analysis and visualization, with simply a web browser user interface. We use the framework advanced by the NSF-funded Pangeo project, a free, open-source Python system which provides multi-user login via JupyterHub and parallel analysis via Dask, both running in Docker containers orchestrated by Kubernetes. Data are stored in the Zarr format, a Cloud-friendly n-dimensional array format that allows performant extraction of data by anyone without relying on data services like OPeNDAP. Interactive visual exploration of data on complex, large model grids is made possible by new tools in the Python PyViz ecosystem, which can render maps at screen resolution, dynamically updating on pan and zoom operations. Two examples are given: (1) Calculating the maximum water level at each grid cell from a 53-GB, 720-time-step, 9-million-node triangular mesh ADCIRC simulation of Hurricane Ike; (2) Creating a dashboard for visualizing data from a curvilinear orthogonal COAWST/ROMS forecast model.
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ArticleAre elevation and open-water conversion of salt marshes connected?(American Geophysical Union, 2020-01-29) Ganju, Neil K. ; Defne, Zafer ; Fagherazzi, SergioSalt marsh assessments focus on vertical metrics such as accretion or lateral metrics such as open‐water conversion, without exploration of how the dimensions are related. We exploited a novel geospatial data set to explore how elevation is related to the unvegetated‐vegetated marsh ratio (UVVR), a lateral metric, across individual marsh “units” within four estuarine‐marsh systems. We find that elevation scales consistently with the UVVR across systems, with lower elevation units demonstrating more open‐water conversion and higher UVVRs. A normalized elevation‐UVVR relationship converges across systems near the system‐mean elevation and a UVVR of 0.1, a critical threshold identified by prior studies. This indicates that open‐water conversion becomes a dominant lateral instability process at a relatively conservative elevation threshold. We then integrate the UVVR and elevation to yield lifespan estimates, which demonstrate that higher elevation marshes are more resilient to internal deterioration, with an order‐of‐magnitude longer lifespan than predicted for lower elevation marshes.
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ArticleBarrier island breach evolution : alongshore transport and bay-ocean pressure gradient interactions(John Wiley & Sons, 2016-12-16) Safak, Ilgar ; Warner, John C. ; List, Jeffrey H.Physical processes controlling repeated openings and closures of a barrier island breach between a bay and the open ocean are studied using aerial photographs and atmospheric and hydrodynamic observations. The breach site is located on Pea Island along the Outer Banks, separating Pamlico Sound from the Atlantic Ocean. Wind direction was a major control on the pressure gradients between the bay and the ocean to drive flows that initiate or maintain the breach opening. Alongshore sediment flux was found to be a major contributor to breach closure. During the analysis period from 2011 to 2016, three hurricanes had major impacts on the breach. First, Hurricane Irene opened the breach with wind-driven flow from bay to ocean in August 2011. Hurricane Sandy in October 2012 quadrupled the channel width from pressure gradient flows due to water levels that were first higher on the ocean side and then higher on the bay side. The breach closed sometime in Spring 2013, most likely due to an event associated with strong alongshore sediment flux but minimal ocean-bay pressure gradients. Then, in July 2014, Hurricane Arthur briefly opened the breach again from the bay side, in a similar fashion to Irene. In summary, opening and closure of breaches are shown to follow a dynamic and episodic balance between along-channel pressure gradient driven flows and alongshore sediment fluxes.
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ArticleBathymetric controls on sediment transport in the Hudson River estuary : lateral asymmetry and frontal trapping(American Geophysical Union, 2012-10-17) Ralston, David K. ; Geyer, W. Rockwell ; Warner, John C.Analyses of field observations and numerical model results have identified that sediment transport in the Hudson River estuary is laterally segregated between channel and shoals, features frontal trapping at multiple locations along the estuary, and varies significantly over the spring-neap tidal cycle. Lateral gradients in depth, and therefore baroclinic pressure gradient and stratification, control the lateral distribution of sediment transport. Within the saline estuary, sediment fluxes are strongly landward in the channel and seaward on the shoals. At multiple locations, bottom salinity fronts form at bathymetric transitions in width or depth. Sediment convergences near the fronts create local maxima in suspended-sediment concentration and deposition, providing a general mechanism for creation of secondary estuarine turbidity maxima at bathymetric transitions. The lateral bathymetry also affects the spring-neap cycle of sediment suspension and deposition. In regions with broad, shallow shoals, the shoals are erosional and the channel is depositional during neap tides, with the opposite pattern during spring tides. Narrower, deeper shoals are depositional during neaps and erosional during springs. In each case, the lateral transfer is from regions of higher to lower bed stress, and depends on the elevation of the pycnocline relative to the bed. Collectively, the results indicate that lateral and along-channel gradients in bathymetry and thus stratification, bed stress, and sediment flux lead to an unsteady, heterogeneous distribution of sediment transport and trapping along the estuary rather than trapping solely at a turbidity maximum at the limit of the salinity intrusion.
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ArticleBora event variability and the role of air-sea feedback(American Geophysical Union, 2007-02-13) Pullen, Julie ; Doyle, James D. ; Haack, Tracy ; Dorman, Clive E. ; Signell, Richard P. ; Lee, Craig M.A two-way interacting high resolution numerical simulation of the Adriatic Sea using the Navy Coastal Ocean Model (NCOM) and Coupled Ocean/Atmosphere Mesoscale Prediction System (COAMPS®) was conducted to improve forecast momentum and heat flux fields, and to evaluate surface flux field differences for two consecutive bora events during February 2003. (COAMPS® is a registered trademark of the Naval Research Laboratory.) The strength, mean positions and extensions of the bora jets, and the atmospheric conditions driving them varied considerably between the two events. Bora 1 had 62% stronger heat flux and 51% larger momentum flux than bora 2. The latter displayed much greater diurnal variability characterized by inertial oscillations and the early morning strengthening of a west Adriatic barrier jet, beneath which a stronger west Adriatic ocean current developed. Elsewhere, surface ocean current differences between the two events were directly related to differences in wind stress curl generated by the position and strength of the individual bora jets. The mean heat flux bias was reduced by 72%, and heat flux RMSE reduced by 30% on average at four instrumented over-water sites in the two-way coupled simulation relative to the uncoupled control. Largest reductions in wind stress were found in the bora jets, while the biggest reductions in heat flux were found along the north and west coasts of the Adriatic. In bora 2, SST gradients impacted the wind stress curl along the north and west coasts, and in bora 1 wind stress curl was sensitive to the Istrian front position and strength. The two-way coupled simulation produced diminished surface current speeds of ∼12% over the northern Adriatic during both bora compared with a one-way coupled simulation.
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ArticleA catastrophic meltwater flood event and the formation of the Hudson Shelf Valley(Elsevier B.V., 2007-01-04) Thieler, E. Robert ; Butman, Bradford ; Schwab, William C. ; Allison, Mead A. ; Driscoll, Neal W. ; Donnelly, Jeffrey P. ; Uchupi, ElazarThe Hudson Shelf Valley (HSV) is the largest physiographic feature on the U.S. mid-Atlantic continental shelf. The 150-km long valley is the submerged extension of the ancestral Hudson River Valley that connects to the Hudson Canyon. Unlike other incised valleys on the mid-Atlantic shelf, it has not been infilled with sediment during the Holocene. Analyses of multibeam bathymetry, acoustic backscatter intensity, and high-resolution seismic reflection profiles reveal morphologic and stratigraphic evidence for a catastrophic meltwater flood event that formed the modern HSV. The valley and its distal deposits record a discrete flood event that carved 15-m high banks, formed a 120-km2 field of 3- to 6-m high bedforms, and deposited a subaqueous delta on the outer shelf. The HSV is inferred to have been carved initially by precipitation and meltwater runoff during the advance of the Laurentide Ice Sheet, and later by the drainage of early proglacial lakes through stable spillways. A flood resulting from the failure of the terminal moraine dam at the Narrows between Staten Island and Long Island, New York, allowed glacial lakes in the Hudson and Ontario basins to drain across the continental shelf. Water level changes in the Hudson River basin associated with the catastrophic drainage of glacial lakes Iroquois, Vermont, and Albany around 11,450 14C year BP (~ 13,350 cal BP) may have precipitated dam failure at the Narrows. This 3200 km3 discharge of freshwater entered the North Atlantic proximal to the Gulf Stream and may have affected thermohaline circulation at the onset of the Intra-Allerød Cold Period. Based on bedform characteristics and fluvial morphology in the HSV, the maximum freshwater flux during the flood event is estimated to be ~ 0.46 Sv for a duration of ~ 80 days.
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ArticleCharacteristics of storms driving wave-induced seafloor mobility on the U.S. East Coast continental shelf(Elsevier, 2015-05-12) Dalyander, P. Soupy ; Butman, BradfordThis study investigates the relationship between spatial and temporal patterns of wave-driven sediment mobility events on the U.S. East Coast continental shelf and the characteristics of the storms responsible for them. Mobility events, defined as seafloor wave stress exceedance of the critical stress of 0.35 mm diameter sand (0.2160 Pa) for 12 or more hours, were identified from surface wave observations at National Data Buoy Center buoys in the Middle Atlantic Bight (MAB) and South Atlantic Bight (SAB) over the period of 1997–2007. In water depths ranging from 36–48 m, there were 4–9 mobility events/year of 1–2 days duration. Integrated wave stress during events (IWAVES) was used as a combined metric of wave-driven mobility intensity and duration. In the MAB, over 67% of IWAVES was caused by extratropical storms, while in the SAB, greater than 66% of IWAVES was caused by tropical storms. On average, mobility events were caused by waves generated by storms located 800+ km away. Far-field hurricanes generated swell 2–4 days before the waves caused mobility on the shelf. Throughout most of the SAB, mobility events were driven by storms to the south, east, and west. In the MAB and near Cape Hatteras, winds from more northerly storms and low-pressure extratropical systems in the mid-western U.S. also drove mobility events. Waves generated by storms off the SAB generated mobility events along the entire U.S. East Coast shelf north to Cape Cod, while Cape Hatteras shielded the SAB area from swell originating to the north offshore of the MAB.
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ArticleCharacterizing wave- and current- induced bottom shear stress : U.S. middle Atlantic continental shelf(Elsevier B.V., 2012-11-05) Dalyander, P. Soupy ; Butman, Bradford ; Sherwood, Christopher R. ; Signell, Richard P. ; Wilkin, John L.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.
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ArticleCoastalImageLib: an open- source Python package for creating common coastal image products(Elsevier, 2022-10-19) McCann, Maile P. ; Anderson, Dylan L. ; Sherwood, Christopher R. ; Bruder, Brittany ; Bak, A. Spicer ; Brodie, Katherine L.CoastalImageLib is a Python library that produces common coastal image products intended for quantitative analysis of coastal environments. This library contains functions to georectify and merge multiple oblique camera views, produce statistical image products for a given set of images, and create subsampled pixel instruments for use in bathymetric inversion, surface current estimation, run-up calculations, and other quantitative analyses. This package intends to be an open-source broadly generalizable front end to future coastal imaging applications, ultimately expanding user accessibility to optical remote sensing of coastal environments. This package was developed and tested on data collected from the Argus Tower, a 43 m tall observation structure in Duck, North Carolina at the US Army Engineer Research and Development Center’s Field Research Facility that holds six stationary cameras which collect twice-hourly coastal image products. Thus, CoastalImageLib also contains functions designed to interface with the file storage and collection system implemented at the Argus Tower.
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ArticleCohesive and mixed sediment in the Regional Ocean Modeling System (ROMS v3.6) implemented in the Coupled Ocean–Atmosphere–Wave–Sediment Transport Modeling System (COAWST r1234)(Copernicus Publications on behalf of the European Geosciences Union, 2018-05-14) Sherwood, Christopher R. ; Aretxabaleta, Alfredo L. ; Harris, Courtney K. ; Rinehimer, J. Paul ; Verney, Romaric ; Ferré, BénédicteWe describe and demonstrate algorithms for treating cohesive and mixed sediment that have been added to the Regional Ocean Modeling System (ROMS version 3.6), as implemented in the Coupled Ocean–Atmosphere–Wave–Sediment Transport Modeling System (COAWST Subversion repository revision 1234). These include the following: floc dynamics (aggregation and disaggregation in the water column); changes in floc characteristics in the seabed; erosion and deposition of cohesive and mixed (combination of cohesive and non-cohesive) sediment; and biodiffusive mixing of bed sediment. These routines supplement existing non-cohesive sediment modules, thereby increasing our ability to model fine-grained and mixed-sediment environments. Additionally, we describe changes to the sediment bed layering scheme that improve the fidelity of the modeled stratigraphic record. Finally, we provide examples of these modules implemented in idealized test cases and a realistic application.
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ArticleCohesive sediment modeling in a shallow estuary: model and environmental implications of sediment parameter variation(American Geophysical Union, 2021-08-20) Allen, Rachel M. ; Lacy, Jessica R. ; Stevens, Andrew W.Numerical models of sediment transport in estuarine systems rely on parameter values that are often poorly constrained and can vary on timescales relevant to model processes. The selection of parameter values can affect the accuracy of model predictions, while environmental variation of these parameters can impact the temporal and spatial ranges of sediment fluxes, erosion, and deposition in the real world. We implemented a numerical model of San Pablo Bay, an embayment within San Francisco Bay, California, for November–December 2014, and compared model outputs to observations of water level, velocity, wave parameters, salinity, and suspended sediment concentration (SSC) in the shallow regions. Idealized model runs show that wind timing relative to the phase of the tides is the strongest control on sediment fluxes and bed erosion. We varied sediment erodibility in the outflow of the Petaluma River; while this causes erosion and deposition to vary strongly through the shallows system, total export from the shallows does not change. Model runs with realistic winds show that wind likely resuspends faster settling particles or allows for more particle flocculation; particle settling velocity controls system-wide sediment accumulation. At the margins of the system, the magnitude of SSC is closely tied to wind direction when winds occur during flood tide, but sediment deposition is less connected: Both bed evolution and SSC need to be considered in the prediction of marsh fate. Spatial patterns of light attenuation due to SSC is strongly tied to assumed settling velocity.
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PreprintCollaboration tools and techniques for large model datasets( 2006-08-08) Signell, Richard P. ; Carniel, Sandro ; Chiggiato, Jacopo ; Janekovic, Ivica ; Pullen, Julie ; Sherwood, Christopher R.In MREA and many other marine applications, it is common to have multiple models running with different grids, run by different institutions. Techniques and tools are described for low-bandwidth delivery of data from large multidimensional data sets, such as those from meteorological and oceanographic models, directly into generic analysis and visualization tools. Output is stored using the NetCDF CF Metadata Conventions, and then delivered to collaborators over the web via OPeNDAP. OPeNDAP datasets served by different institutions are then organized via THREDDS catalogs. Tools and procedures are then used which enable scientists to explore data on the original model grids using tools they are familiar with. It is also low-bandwidth, enabling users to extract just the data they require, an important feature for access from ship or remote areas. The entire implementation is simple enough to be handled by modelers working with their webmasters – no advanced programming support is necessary.
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ArticleColored dissolved organic matter in shallow estuaries : relationships between carbon sources and light attenuation(Copernicus Publications on behalf of the European Geosciences Union, 2016-02-02) Oestreich, William K. ; Ganju, Neil K. ; Pohlman, John W. ; Suttles, Steven E.Light availability is of primary importance to the ecological function of shallow estuaries. For example, benthic primary production by submerged aquatic vegetation is contingent upon light penetration to the seabed. A major component that attenuates light in estuaries is colored dissolved organic matter (CDOM). CDOM is often measured via a proxy, fluorescing dissolved organic matter (fDOM), due to the ease of in situ fDOM sensor measurements. Fluorescence must be converted to CDOM absorbance for use in light attenuation calculations. However, this CDOM–fDOM relationship varies among and within estuaries. We quantified the variability in this relationship within three estuaries along the mid-Atlantic margin of the eastern United States: West Falmouth Harbor (MA), Barnegat Bay (NJ), and Chincoteague Bay (MD/VA). Land use surrounding these estuaries ranges from urban to developed, with varying sources of nutrients and organic matter. Measurements of fDOM (excitation and emission wavelengths of 365 nm (±5 nm) and 460 nm (±40 nm), respectively) and CDOM absorbance were taken along a terrestrial-to-marine gradient in all three estuaries. The ratio of the absorption coefficient at 340 nm (m−1) to fDOM (QSU) was higher in West Falmouth Harbor (1.22) than in Barnegat Bay (0.22) and Chincoteague Bay (0.17). The CDOM : fDOM absorption ratio was variable between sites within West Falmouth Harbor and Barnegat Bay, but consistent between sites within Chincoteague Bay. Stable carbon isotope analysis for constraining the source of dissolved organic matter (DOM) in West Falmouth Harbor and Barnegat Bay yielded δ13C values ranging from −19.7 to −26.1 ‰ and −20.8 to −26.7 ‰, respectively. Concentration and stable carbon isotope mixing models of DOC (dissolved organic carbon) indicate a contribution of 13C-enriched DOC in the estuaries. The most likely source of 13C-enriched DOC for the systems we investigated is Spartina cordgrass. Comparison of DOC source to CDOM : fDOM absorption ratios at each site demonstrates the relationship between source and optical properties. Samples with 13C-enriched carbon isotope values, indicating a greater contribution from marsh organic material, had higher CDOM : fDOM absorption ratios than samples with greater contribution from terrestrial organic material. Applying a uniform CDOM : fDOM absorption ratio and spectral slope within a given estuary yields errors in modeled light attenuation ranging from 11 to 33 % depending on estuary. The application of a uniform absorption ratio across all estuaries doubles this error. This study demonstrates that light attenuation coefficients for CDOM based on continuous fDOM records are highly dependent on the source of DOM present in the estuary. Thus, light attenuation models for estuaries would be improved by quantification of CDOM absorption and DOM source identification.