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  • 1
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    Sears Foundation for Marine Research
    Publication Date: 2017-01-04
    Description: Author Posting. © Sears Foundation for Marine Research, 2006. This article is posted here by permission of Sears Foundation for Marine Research for personal use, not for redistribution. The definitive version was published in Journal of Marine Research 64 (2006): 147-171, doi:10.1357/002224006776412359.
    Description: In intertidal regions with subtidal channels, effects of bathymetry on overlying flow vary greatly with tidal stage. Around low water when mudflats and marsh are exposed, flow is constrained to channels, but when water depths are greater, tidal forcing may not necessarily be aligned with meandering channel axes. Flow across the channel can generate strong shear and turbulence at the elevation of the channel banks and can significantly increase turbulent energy in the middle of the water column. Field observations in a mudflat channel of San Francisco Bay indicate that cross-channel shear regularly occurs there early in ebb tides. With increased freshwater flow, baroclinic forcing can enhance shear by decoupling flow between dense water flooding in the channel and fresher water ebbing above the channel banks. A water column numerical model with κ-ε turbulence closure is modified to represent the cross-channel shear production. Numerical results with uniform density indicate that turbulence production increases with the angle between the barotropic tidal forcing and the channel axis. When a longitudinal salinity gradient is imposed, cross-channel shear production contributes to breakdown of periodic stratification. Turbulence produced at the channel banks locally exceeds dissipation, and the excess energy is either lost to buoyancy or diffuses vertically to lower energy regions near the surface and near the bed. The balance among shear production, buoyancy production, and diffusion of turbulence depends on the flow angle and the strength of the longitudinal salinity gradient.
    Description: This research was funded by National Institutes of Health grant no. P42ES0475 from the National Institute of Environmental Health Sciences.
    Repository Name: Woods Hole Open Access Server
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  • 2
    Publication Date: 2017-01-04
    Description: Author Posting. © Elsevier B.V., 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 Continental Shelf Research 27 (2007): 1510-1527, doi:10.1016/j.csr.2007.01.010.
    Description: Field observations of flow and sediment transport in a tributary channel through intertidal mudflats indicate that suspended sediment was closely linked to advection and dispersion of a tidal salinity front. During calm weather when tidal forcing was dominant, high concentrations of suspended sediment advected up the mudflat channel in the narrow region between salty water from San Francisco Bay and much fresher runoff from the small local watershed. Salinity and suspended sediment dispersed at similar rates through each tidal inundation, such that during receding ebbs the sediment pulse had spread spatially and maximum concentrations had decreased. Net sediment transport was moderately onshore during the calm weather, as asymmetries in stratification due to tidal straining of the salinity front enhanced deposition, particularly during weaker neap tidal forcing. Sediment transport by tidal forcing was periodically altered by winter storms. During storms, strong winds from the south generated wind waves and temporarily increased suspended sediment concentrations. Increased discharge down the tributary channels due to precipitation had more lasting impact on sediment transport, supplying both buoyancy and fine sediment to the system. Net sediment transport depended on the balance between calm weather tidal forcing and perturbations by episodic storms. Net transport in the tributary channel was generally off-shore during storms and during calm weather spring tides, and on-shore during calm weather neap tides.
    Description: The research was funded by National Institutes of Health grant P42ES0475 from the National Institute of Environmental Health Sciences. References
    Keywords: Sediment transport ; Intertidal sedimentation ; Salinity gradients ; Tidal inlets ; Topographic effects ; San Francisco Bay, California, USA
    Repository Name: Woods Hole Open Access Server
    Type: Preprint
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  • 3
    Publication Date: 2017-01-04
    Description: 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): C12006, doi:10.1029/2008JC005014.
    Description: A 3D hydrodynamic model (ROMS) is used to investigate lateral circulation in a partially mixed estuary driven by axial wind events and to explore the associated transport of sediments. The channel is straight with a triangular cross section. The model results suggest that driving mechanisms for lateral circulation during axial wind events are different between stratified and unstratified conditions. When the water column is largely unstratified, rotational effects do not drive significant lateral circulation. Instead, differential advection of the axial salinity gradient by wind-driven axial flow is responsible for regulating the lateral salinity gradients that in turn drive bottom-divergent/convergent lateral circulation during down/up-estuary winds. From the subtidal lateral salt balance, it is found that the development of lateral salinity gradient by wind-induced differential advection is largely counterbalanced by the advection of salt by lateral circulation itself. When the water column is stratified, the lateral flow and salinity structures below the halocline closely resemble those driven by boundary mixing, and rotational effects are important. Lateral sediment flux and the event-integrated sediment transport are from channel to shoals during down-estuary winds but reversed for up-estuary winds. Potential impacts of wind-generated waves on lateral sediment transport are evaluated with two cases representing event conditions typical of upper Chesapeake Bay. Accounting for wind wave effects results in an order of magnitude increase in lateral sediment fluxes because of greater bottom stresses and sediment resuspension.
    Description: Financial support from ONR through the Community Sediment Transport Modeling (CSTM) project.
    Keywords: Wind-driven lateral circulation ; Differential advection ; Sediment transport
    Repository Name: Woods Hole Open Access Server
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  • 4
    Publication Date: 2017-01-04
    Description: Author Posting. © American Meteorological Society, 2009. 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 Physical Oceanography 39 (2009): 915-933, doi:10.1175/2008JPO3933.1.
    Description: The temporal response of the length of a partially mixed estuary to changes in freshwater discharge Qf and tidal amplitude UT is studied using a 108-day time series collected along the length of the Hudson River estuary in the spring and summer of 2004 and a long-term (13.4 yr) record of Qf, UT, and near-surface salinity. When Qf was moderately high, the tidally averaged length of the estuary L5, here defined as the distance from the mouth to the up-estuary location where the vertically averaged salinity is 5 psu, fluctuated by more than 47 km over the spring–neap cycle, ranging from 28 to 〉75 km. During low flow periods, L5 varied very little over the spring–neap cycle and approached a steady length. The response is quantified and compared to predictions of a linearized model derived from the global estuarine salt balance. The model is forced by fluctuations in Qf and UT relative to average discharge Qo and tidal amplitude UTo and predicts the linear response time scale τ and the steady-state length Lo for average forcing. Two vertical mixing schemes are considered, in which 1) mixing is proportional to UT and 2) dependence of mixing on stratification is also parameterized. Based on least squares fits between L5 and estuary length predicted by the model, estimated τ varied by an order of magnitude from a period of high average discharge (Qo = 750 m3 s−1, τ = 4.2 days) to a period of low discharge (Qo = 170 m3 s−1, τ = 40.4 days). Over the range of observed discharge, Lo Qo−0.30±0.03, consistent with the theoretical scaling for an estuary whose landward salt flux is driven by vertical estuarine exchange circulation. Estimated τ was proportional to the discharge advection time scale (LoA/Qo, where A is the cross-sectional area of the estuary). However, τ was 3–4 times larger than the theoretical prediction. The model with stratification-dependent mixing predicted variations in L5 with higher skill than the model with mixing proportional to UT. This model provides insight into the time-dependent response of a partially stratified estuary to changes in forcing and explains the strong dependence of the amplitude of the spring–neap response on freshwater discharge. However, the utility of the linear model is limited because it assumes a uniform channel, and because the underlying dynamics are nonlinear, and the forcing Qf and UT can undergo large amplitude variations. River discharge, in particular, can vary by over an order of magnitude over time scales comparable to or shorter than the response time scale of the estuary.
    Description: This study was generously funded by Hudson River Foundation Grant 005/03A and NSF Grant OCE-0452054. Lerczak also received partial support from the Woods Hole Center for Oceans and Human Health, NSF Grant OCE-0430724 and NIEHS Grant 1-P50-ES012742-01.
    Keywords: Estuaries ; Rivers ; Tides ; Stability ; Vertical motion
    Repository Name: Woods Hole Open Access Server
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  • 5
    Publication Date: 2017-01-04
    Description: Author Posting. © American Geophysical Union, 2012. 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 117 (2012): C10013, doi:10.1029/2012JC008124.
    Description: 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.
    Description: This research was funded by a grant from the Hudson River Foundation (#002/07A). D.R. was partially supported by the Office of Naval Research (N00014-08-1-0846).
    Description: 2013-04-17
    Keywords: Estuarine turbidity maximum ; Lateral sediment distribution ; Salinity fronts ; Sediment flux ; Sediment trapping ; Stratification
    Repository Name: Woods Hole Open Access Server
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  • 6
    Publication Date: 2017-01-04
    Description: Author Posting. © The Author(s), 2013. 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 Continental Shelf Research 65 (2013): 1-13, doi:10.1016/j.csr.2013.05.017.
    Description: An unstructured grid, phase-averaged wave model forced with winds from a high resolution atmospheric model is used to evaluate wind wave conditions in the Red Sea over an approximately 2-year period. The Red Sea lies in a narrow rift valley, and the steep topography surrounding the basin steers the dominant wind patterns and consequently the wave climate. At large scales, the model results indicated that the primary seasonal variability in waves was due to the monsoonal wind reversal. During the winter, monsoon winds from the southeast generated waves with mean significant wave heights in excess of 2 m and mean periods of 8 s in the southern Red Sea, while in the northern part of the basin waves were smaller, shorter period, and from northwest. The zone of convergence of winds and waves typically occurred around 19-20˚N, but the location varied between 15 to 21.5˚N. During the summer, waves were generally smaller and from the northwest over most of the basin. While the seasonal winds oriented along the axis of the Red Sea drove much of the variability in the waves, the maximum wave heights in the simulations were not due to the monsoonal winds but instead were generated by localized mountain wind jets oriented across the basin (roughly east-west). During the summer, a mountain wind jet from the Tokar Gap enhanced the waves in the region of 18 and 20˚N, with monthly mean wave heights exceeding 2 m and maximum wave heights of 14 m during a period when the rest of the Red Sea was relatively calm. Smaller mountain gap wind jets along the northeast coast created large waves during the fall and winter, with a series of jets providing a dominant source of wave energy during these periods. Evaluation of the wave model results against observations from a buoy and satellites found that the spatial resolution of the wind model significantly affected the quality of the wave model results. Wind forcing from a 10-km grid produced higher skills for waves than winds from a 30-km grid, largely due to under-prediction of the mean wind speed and wave height with the coarser grid. The 30-km grid did not resolve the mountain gap wind jets, and thus predicted lower wave heights in the central Red Sea during the summer and along the northeast coast in the winter.
    Description: This research is based on work supported by Award No. USA00001, USA00002, KSA00011, made by the King Abdullah University of Science and Technology (KAUST) in Saudi Arabia.
    Repository Name: Woods Hole Open Access Server
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  • 7
    Publication Date: 2017-01-04
    Description: Author Posting. © American Geophysical Union, 2013. 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 40 (2013): 5451–5455, doi:10.1002/2013GL057906.
    Description: Tropical Storms Irene and Lee in 2011 produced intense precipitation and flooding in the U.S. Northeast, including the Hudson River watershed. Sediment input to the Hudson River was approximately 2.7 megaton, about 5 times the long-term annual average. Rather than the common assumption that sediment is predominantly trapped in the estuary, observations and model results indicate that approximately two thirds of the new sediment remained trapped in the tidal freshwater river more than 1 month after the storms and only about one fifth of the new sediment reached the saline estuary. High sediment concentrations were observed in the estuary, but the model results suggest that this was predominantly due to remobilization of bed sediment. Spatially localized deposits of new and remobilized sediment were consistent with longer term depositional records. The results indicate that tidal rivers can intercept (at least temporarily) delivery of terrigenous sediment to the marine environment during major flow events.
    Description: This research was supported by grants from the Hudson Research Foundation (002/07A) and the National Science Foundation (1232928).
    Description: 2014-04-18
    Keywords: Sediment transport ; Tidal river ; Estuary ; Sediment trapping
    Repository Name: Woods Hole Open Access Server
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  • 8
    Publication Date: 2016-09-22
    Description: © The Author(s), 2015. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Estuaries and Coasts 39 (2016): 311-332, doi:10.1007/s12237-015-0011-y.
    Description: Numerical modeling has emerged over the last several decades as a widely accepted tool for investigations in environmental sciences. In estuarine research, hydrodynamic and ecological models have moved along parallel tracks with regard to complexity, refinement, computational power, and incorporation of uncertainty. Coupled hydrodynamic-ecological models have been used to assess ecosystem processes and interactions, simulate future scenarios, and evaluate remedial actions in response to eutrophication, habitat loss, and freshwater diversion. The need to couple hydrodynamic and ecological models to address research and management questions is clear because dynamic feedbacks between biotic and physical processes are critical interactions within ecosystems. In this review, we present historical and modern perspectives on estuarine hydrodynamic and ecological modeling, consider model limitations, and address aspects of model linkage, skill assessment, and complexity. We discuss the balance between spatial and temporal resolution and present examples using different spatiotemporal scales. Finally, we recommend future lines of inquiry, approaches to balance complexity and uncertainty, and model transparency and utility. It is idealistic to think we can pursue a “theory of everything” for estuarine models, but recent advances suggest that models for both scientific investigations and management applications will continue to improve in terms of realism, precision, and accuracy.
    Description: NKG, ALA, and RPS acknowledge support from the USGS Coastal and Marine Geology Program. DKR gratefully acknowledges support from NSF (OCE-1314642) and NIEHS (1P50-ES021923-01). MJB and JMPV gratefully acknowledge support from NOAA NOS NCCOS (NA05NOS4781201 and NA11NOS4780043). MJB and SJL gratefully acknowledge support from the Strategic Environmental Research and Development Program—Defense Coastal/Estuarine Research Program (RC-1413 and RC-2245).
    Keywords: Numerical modeling ; Hydrodynamics ; Ecological modeling ; Ecosystem modeling ; Skill assessment
    Repository Name: Woods Hole Open Access Server
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  • 9
    Publication Date: 2018-07-02
    Description: © The Author(s), 2016. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in PeerJ 4 (2016): e1770, doi:10.7717/peerj.1770.
    Description: A research cruise to Hannibal Bank, a seamount and an ecological hotspot in the coastal eastern tropical Pacific Ocean off Panama, explored the zonation, biodiversity, and the ecological processes that contribute to the seamount’s elevated biomass. Here we describe the spatial structure of a benthic anomuran red crab population, using submarine video and autonomous underwater vehicle (AUV) photographs. High density aggregations and a swarm of red crabs were associated with a dense turbid layer 4–10 m above the bottom. The high density aggregations were constrained to 355–385 m water depth over the Northwest flank of the seamount, although the crabs also occurred at lower densities in shallower waters (∼280 m) and in another location of the seamount. The crab aggregations occurred in hypoxic water, with oxygen levels of 0.04 ml/l. Barcoding of Hannibal red crabs, and pelagic red crabs sampled in a mass stranding event in 2015 at a beach in San Diego, California, USA, revealed that the Panamanian and the Californian crabs are likely the same species, Pleuroncodes planipes, and these findings represent an extension of the southern endrange of this species. Measurements along a 1.6 km transect revealed three high density aggregations, with the highest density up to 78 crabs/m2, and that the crabs were patchily distributed. Crab density peaked in the middle of the patch, a density structure similar to that of swarming insects.
    Description: This work was sponsored by a grant from the Dalio Foundation, Inc, through the Woods Hole Oceanographic Institution.
    Keywords: Swarms ; Ecological hotspot ; Patchiness ; Panama ; Eastern Pacific ; Seamount ; Pleuroncodes planipes ; Hypoxic environment ; Anomuran crabs
    Repository Name: Woods Hole Open Access Server
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  • 10
    Publication Date: 2017-07-28
    Description: Author Posting. © American Geophysical Union, 2017. 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: Oceans 122 (2017): 692–712, doi:10.1002/2016JC011738.
    Description: The Connecticut River is a tidal salt wedge estuary, where advection of sharp salinity gradients through channel constrictions and over steeply sloping bathymetry leads to spatially heterogeneous stratification and mixing. A 3-D unstructured grid finite-volume hydrodynamic model (FVCOM) was evaluated against shipboard and moored observations, and mixing by both the turbulent closure and numerical diffusion were calculated. Excessive numerical mixing in regions with strong velocities, sharp salinity gradients, and steep bathymetry reduced model skill for salinity. Model calibration was improved by optimizing both the bottom roughness (z0), based on comparison with the barotropic tidal propagation, and the mixing threshold in the turbulence closure (steady state Richardson number, Rist), based on comparison with salinity. Whereas a large body of evidence supports a value of Rist ∼ 0.25, model skill for salinity improved with Rist ∼ 0.1. With Rist = 0.25, numerical mixing contributed about 1/2 the total mixing, while with Rist = 0.10 it accounted for ∼2/3, but salinity structure was more accurately reproduced. The combined contributions of numerical and turbulent mixing were quantitatively consistent with high-resolution measurements of turbulent mixing. A coarser grid had increased numerical mixing, requiring further reductions in turbulent mixing and greater bed friction to optimize skill. The optimal Rist for the fine grid case was closer to 0.25 than for the coarse grid, suggesting that additional grid refinement might correspond with Rist approaching the theoretical limit. Numerical mixing is rarely assessed in realistic models, but comparisons with high-resolution observations in this study suggest it is an important factor.
    Description: NSF Grant Number: OCE 0926427; ONR Grant Number: N00014-08-1-1115
    Description: 2017-07-28
    Keywords: Estuary ; Salt wedge ; Numerical mixing ; Turbulence closure ; Numerical model
    Repository Name: Woods Hole Open Access Server
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