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  • 1
    Publication Date: 2017-01-04
    Description: This paper is not subject to U.S. copyright. The definitive version was published in Journal of Atmospheric and Oceanic Technology 21 (2004): 1448–1461, doi:10.1175/1520-0426(2004)021〈1448:AOAPAD〉2.0.CO;2.
    Description: 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.
    Description: This work was funded by the U.S. Geological Survey as part of the Southwest Washington Coastal Erosion Study
    Repository Name: Woods Hole Open Access Server
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  • 2
    Publication Date: 2017-01-04
    Description: Author Posting. © The Author(s), 2007. This is the author's version of the work. It is posted here by permission of Elsevier B.V. for personal use, not for redistribution. The definitive version was published in Journal of Marine Systems 69 (2008): 154-161, doi:10.1016/j.jmarsys.2007.02.013.
    Description: 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.
    Description: S. Carniel was partially supported by the Office of Naval Research (ONR grant number N00014-05-1-0730). I. Janekovic was supported by the Croatian Ministry of Science, Education and Sport (grant number 0098113).
    Keywords: Data collections ; Information systems ; Modelling ; Adriatic Sea
    Repository Name: Woods Hole Open Access Server
    Type: Preprint
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  • 3
    Publication Date: 2016-12-21
    Description: This paper is not subject to U.S. copyright. The definitive version was published in Ocean Modelling 33 (2010): 299-313, doi:10.1016/j.ocemod.2010.03.003.
    Description: A variety of algorithms are available for parameterizing the hydrodynamic bottom roughness associated with grain size, saltation, bedforms, and wave–current interaction in coastal ocean models. These parameterizations give rise to spatially and temporally variable bottom-drag coefficients that ostensibly provide better representations of physical processes than uniform and constant coefficients. However, few studies have been performed to determine whether improved representation of these variable bottom roughness components translates into measurable improvements in model skill. We test the hypothesis that improved representation of variable bottom roughness improves performance with respect to near-bed circulation, bottom stresses, or turbulence dissipation. The inner shelf south of Martha’s Vineyard, Massachusetts, is the site of sorted grain-size features which exhibit sharp alongshore variations in grain size and ripple geometry over gentle bathymetric relief; this area provides a suitable testing ground for roughness parameterizations. We first establish the skill of a nested regional model for currents, waves, stresses, and turbulent quantities using a uniform and constant roughness; we then gauge model skill with various parameterization of roughness, which account for the influence of the wave-boundary layer, grain size, saltation, and rippled bedforms. We find that commonly used representations of ripple-induced roughness, when combined with a wave–current interaction routine, do not significantly improve skill for circulation, and significantly decrease skill with respect to stresses and turbulence dissipation. Ripple orientation with respect to dominant currents and ripple shape may be responsible for complicating a straightforward estimate of the roughness contribution from ripples. In addition, sediment-induced stratification may be responsible for lower stresses than predicted by the wave–current interaction model.
    Description: Funding was provided through the Office of Naval Research Ripples DRI and U.S. Geological Survey Coastal and Marine Geology Program.
    Keywords: Sediment transport ; Roughness ; Bottom-boundary layer ; Model skill
    Repository Name: Woods Hole Open Access Server
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  • 4
    Publication Date: 2017-01-04
    Description: Author Posting. © American Geophysical Union, 2011. This article is posted here by permission of American Geophysical Union for personal use, not for redistribution. The definitive version was published in Geophysical Research Letters 38 (2011): L09602, doi:10.1029/2011GL047174.
    Description: Hydrocarbons released following the Deepwater Horizon (DH) blowout were found in deep, subsurface horizontal intrusions, yet there has been little discussion about how these intrusions formed. We have combined measured (or estimated) observations from the DH release with empirical relationships developed from previous lab experiments to identify the mechanisms responsible for intrusion formation and to characterize the DH plume. Results indicate that the intrusions originate from a stratification-dominated multiphase plume characterized by multiple subsurface intrusions containing dissolved gas and oil along with small droplets of liquid oil. Unlike earlier lab measurements, where the potential density in ambient water decreased linearly with elevation, at the DH site it varied quadratically. We have modified our method for estimating intrusion elevation under these conditions and the resulting estimates agree with observations that the majority of the hydrocarbons were found between 800 and 1200 m.
    Description: Funding for this project was supported by the National Science Foundation under RAPID grants CBET‐1045831, CBET‐1046890, and OCE‐1048976, and by the U. S. Geological Survey, Coastal and Marine Geology Program.
    Keywords: Deepwater Horizon ; Fluid dynamics ; Intrusion ; Multiphase flow ; Oil well blowout ; Plume
    Repository Name: Woods Hole Open Access Server
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  • 5
    Publication Date: 2016-09-22
    Description: © The Author(s), 2013. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Deep Sea Research Part II: Topical Studies in Oceanography 103 (2014): 79–95, doi:10.1016/j.dsr2.2013.10.011.
    Description: Cysts of Alexandrium fundyense, a dinoflagellate that causes toxic algal blooms in the Gulf of Maine, spend the winter as dormant cells in the upper layer of bottom sediment or the bottom nepheloid layer and germinate in spring to initiate new blooms. Erosion measurements were made on sediment cores collected at seven stations in the Gulf of Maine in the autumn of 2011 to explore if resuspension (by waves and currents) could change the distribution of over-wintering cysts from patterns observed in the previous autumn; or if resuspension could contribute cysts to the water column during spring when cysts are viable. The mass of sediment eroded from the core surface at 0.4 Pa ranged from 0.05 kg m−2 near Grand Manan Island, to 0.35 kg m−2 in northern Wilkinson Basin. The depth of sediment eroded ranged from about 0.05 mm at a station with sandy sediment at 70 m water depth on the western Maine shelf, to about 1.2 mm in clayey–silt sediment at 250 m water depth in northern Wilkinson Basin. The sediment erodibility measurements were used in a sediment-transport model forced with modeled waves and currents for the period October 1, 2010 to May 31, 2011 to predict resuspension and bed erosion. The simulated spatial distribution and variation of bottom shear stress was controlled by the strength of the semi-diurnal tidal currents, which decrease from east to west along the Maine coast, and oscillatory wave-induced currents, which are strongest in shallow water. Simulations showed occasional sediment resuspension along the central and western Maine coast associated with storms, steady resuspension on the eastern Maine shelf and in the Bay of Fundy associated with tidal currents, no resuspension in northern Wilkinson Basin, and very small resuspension in western Jordan Basin. The sediment response in the model depended primarily on the profile of sediment erodibility, strength and time history of bottom stress, consolidation time scale, and the current in the water column. Based on analysis of wave data from offshore buoys from 1996 to 2012, the number of wave events inducing a bottom shear stress large enough to resuspend sediment at 80 m ranged from 0 to 2 in spring (April and May) and 0 to 10 in winter (October through March). Wave-induced resuspension is unlikely in water greater than about 100 m deep. The observations and model results suggest that a millimeter or so of sediment and associated cysts may be mobilized in both winter and spring, and that the frequency of resuspension will vary interannually. Depending on cyst concentration in the sediment and the vertical distribution in the water column, these events could result in a concentration in the water column of at least 104 cysts m−3. In some years, resuspension events could episodically introduce cysts into the water column in spring, where germination is likely to be facilitated at the time of bloom formation. An assessment of the quantitative effects of cyst resuspension on bloom dynamics in any particular year requires more detailed investigation.
    Description: Research support to Donald M. Anderson and Bruce A. Keafer provided through the Woods Hole Center for Oceans and Human Health; National Science Foundation Grants OCE-0430724 and OCE-0911031; and National Institute of Environmental Health Sciences Grant 1-P50-ES012742-01; the ECOHAB Grant program through NOAA Grants NA06NOS4780245 and A09NOS4780193; the MERHAB Grant program through NOAA Grant NA11NOS4780025; and the PCMHAB Grant program through NOAA Grant NA11NOS4780023. Research support to all other authors was provided by U.S. Geological Survey.
    Keywords: Sediment transport ; Bottom stress ; Sediment resuspension ; Harmful algal blooms ; Gulf of Maine ; Alexandrium fundyense ; HAB
    Repository Name: Woods Hole Open Access Server
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  • 6
    Publication Date: 2017-01-04
    Description: 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.
    Description: 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.
    Description: P.S. Dalyander was supported by the U.S. Geological Survey Mendenhall Research Fellowship Program.
    Keywords: Bottom stress ; Wave stress ; Current stress ; Sea floor disturbance ; Middle Atlantic Bight
    Repository Name: Woods Hole Open Access Server
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  • 7
    Publication Date: 2018-05-31
    Description: © The Author(s), 2018. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Geoscientific Model Development 11 (2018): 1849-1871, doi:10.5194/gmd-11-1849-2018.
    Description: We 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.
    Description: This work was supported by the US Geological Survey, Coastal and Marine Geology Program and the National Ocean Partnership Program. Courtney K. Harris was supported by the NSF (OCE-1459708, OCE-1061781, and OCE-0536572).
    Repository Name: Woods Hole Open Access Server
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  • 8
    Publication Date: 2019-02-07
    Description: Author Posting. © American Meteorological Society, 2018. 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 Marine Science and Engineering 6(4), (2018): 144. doi:10.3390/jmse6040144.
    Description: Geochronologies derived from sediment cores in coastal locations are often used to infer event bed characteristics such as deposit thicknesses and accumulation rates. Such studies commonly use naturally occurring, short-lived radioisotopes, such as Beryllium-7 (7Be) and Thorium-234 (234Th), to study depositional and post-depositional processes. These radioisotope activities, however, are not generally represented in sediment transport models that characterize coastal flood and storm deposition with grain size patterns and deposit thicknesses. We modified the Community Sediment Transport Modeling System (CSTMS) to account for reactive tracers and used this capability to represent the behavior of these short-lived radioisotopes on the sediment bed. This paper describes the model and presents results from a set of idealized, one-dimensional (vertical) test cases. The model configuration represented fluvial deposition followed by periods of episodic storm resuspension. Sensitivity tests explored the influence on seabed radioisotope profiles by the intensities of bioturbation and wave resuspension and the thickness of fluvial deposits. The intensity of biodiffusion affected the persistence of fluvial event beds as evidenced by 7Be. Both resuspension and biodiffusion increased the modeled seabed inventory of 234Th. A thick fluvial deposit increased the seabed inventory of 7Be and 234Th but mixing over time greatly reduced the difference in inventory of 234Th in fluvial deposits of different thicknesses.
    Description: The Bureau of Ocean Energy Management (BOEM) provided funding for Birchler, Harris, and Kniskern. During his M.S. program Birchler received additional funds from VIMS’ Office of Academic Studies. This work was partially supported by the U.S. Geological Survey, Coastal and Marine Geology Program.
    Keywords: numerical model ; sediment transport ; marine ; short-lived radioisotopes
    Repository Name: Woods Hole Open Access Server
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  • 9
    Publication Date: 2019-02-22
    Description: © The Author(s), 2018. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Boss, E., Sherwood, C. R., Hill, P., & Milligan, T. Advantages and limitations to the use of optical measurements to study sediment properties. Applied Sciences-Basel, 8(12), (2018):2692, doi:10.3390/app8122692.
    Description: Measurements 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.
    Description: This work was supported by the Office of Naval Research and the United States Geological Survey Coastal and Marine Geology Program. The unique instrument platform and data acquisition system was designed and built by technical staff lead by Marinna Martini at the United States Geological Survey Woods Hole Coastal and Marine Science Center. This team was also responsible for deployment and recovery of the instrumentation. We thank the Woods Hole Oceanographic Institution (WHOI) MVCO staff for support during this experiment, and we thank the captains and crews of the R/V Connecticut and the R/V Tioga. Any use of trade, product, or firm names is for descriptive purposes only and does not imply endorsement by the United States Government. This paper has benefited significantly from insightful comments from D. Stramski, A. Aretxabaleta and two anonymous reviewers.
    Keywords: particle dynamics ; optical properties ; suspended sediment
    Repository Name: Woods Hole Open Access Server
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  • 10
    Publication Date: 2017-01-04
    Description: This paper is not subject to U.S. copyright. The definitive version was published in Sedimentary Geology 202 (2007): 402-408, doi:10.1016/j.sedgeo.2007.03.020.
    Description: For more than a century, studies of sedimentology and sediment transport have measured bed-sediment grain size by collecting samples and transporting them back to the laboratory for grain-size analysis. This process is slow and expensive. Moreover, most sampling systems are not selective enough to sample only the surficial grains that interact with the flow; samples typically include sediment from at least a few centimeters beneath the bed surface. New hardware and software are available for in situ measurement of grain size. The new technology permits rapid measurement of surficial bed sediment. Here we describe several systems we have deployed by boat, by hand, and by tripod in rivers, oceans, and on beaches.
    Keywords: Underwater microscope ; Bed sediment ; Grain size ; In situ measurement ; Colorado River ; Adriatic Sea
    Repository Name: Woods Hole Open Access Server
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