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Particle tracking is widely utilized to study transport features in a range of physical, chemical, and biological processes in oceanography. In this study, a new offline particle-tracking package, Tracker v1.1, is introduced, and its performance is evaluated in comparison to an online Eulerian dye, one online particle-tracking software package, and three offline particle-tracking software packages in a small, high-resolution model domain and a large coarser model domain. It was found that both particle and dye approaches give similar results across different model resolutions and domains when they were tracking the same water mass, as indicated by similar mean advection pathways and spatial distributions of dye and particles. The flexibility of offline particle tracking and its similarity against online dye and online particle tracking make it a useful tool to complement existing ocean circulation models. The new Tracker was shown to be a reliable particle-tracking package to complement the Regional Ocean Modeling System (ROMS) with the advantages of platform independence and speed improvements, especially in large model domains achieved by the nearest-neighbor search algorithm. Lastly, trade-offs of computational efficiency, modifiability, and ease of use that can influence the choice of which package to use are explored. The main value of the present study is that the different particle and dye tracking codes were all run on the same model output or within the model that generated the output. This allows some measure of intercomparison between the different tracking schemes, and we conclude that all choices that make each tracking package unique do not necessarily lead to very different results. [ABSTRACT FROM AUTHOR]

Municipal intakes of surface water have various uses, and their impacts on the aquatic environment and ecosystem, such as the impingement and entrainment of ichthyoplankton, are a major concern. A robust assessment of the intake impacts on ichthyoplankton in a system generally requires modeling efforts that can simulate the transport and dispersal pathways of the ichthyoplankton. However, it is challenging to simulate hydrodynamics with a high-resolution grid at the scale needed for intake screen sizes in a large system. In this study, a 3D unstructured grid model with a fine resolution grid (<1 m) was developed to investigate potential impacts of an intake on aquatic resources in a tidal freshwater estuary. This approach enables us to directly estimate intake-induced mortality. With the use of the coupled particle-tracking model, we evaluated the total and maximum daily removal rates of particles by the intake that can be used to estimate percent mortality of ichthyoplankton. We further investigated how impacts from the intake vary with spawning locations, flow conditions, and vertical migration velocity of ichthyoplankton. A risk assessment was conducted based on designed flow of water withdrawals. This approach is widely applicable and can address impacts of water intakes in other systems. [ABSTRACT FROM AUTHOR]

Accumulation and remineralization of surface‐produced particulate organic matter (POM) in the water column and seabed link closely to hypoxia and the health of aquatic ecosystems. The POM retention time provides a key timescale to interpret biochemical reaction processes. In this study, we investigated the spatiotemporal variations in the vertical particulate age (VPA) of surface‐produced POM, which is the mean time elapsed since the particulates last contact the surface, by incorporating major physical processes including sinking, resuspension, and deposition in the Chesapeake Bay. It was found that the vertical transport time for the particulates (i.e., VPA) is much longer than the dissolved counterparts as the former consists of new material from the surface and the resuspended aged material that has elongated resting on the seabed after deposition. The VPA is sensitive to settling velocity, especially in low‐frequent resuspension environments, and varies over 2 orders of magnitude with settling velocity from 0 to 10 m/day. Slow‐sinking material can remain in suspension and seldom settle to the seabed, thus mainly contribute to pelagic processes, while the fast‐sinking material connects closely with benthic processes. The seasonality of VPA decreases as the settling velocity increases. No significant difference in VPA was found between wet and dry years, yet the episodic strong flood events entrain old materials from the depositional lateral shoals to increase VPA in the channel. The transport age bridges cross disciplinaries by providing the fourth‐dimensional age information as a common currency to compare the physical transport timescale with the timescales for biochemical reactions. Plain Language Summary: The Chesapeake Bay is a highly productive estuary, characterized by spring phytoplankton blooms and subsequent accumulations of particulate organic matter (POM) in the bottom layer, which fuels summertime hypoxia. The retention time of POM provides an important timescale to interpret biochemical reactions in estuaries. In this study, we applied the vertical particulate age (VPA), the average time elapsed since the POM leaving the surface, to estimate the downward‐transport time. The VPA accounts for all possible trajectories, including direct sinking and interactions with the seabed via resuspension and deposition. It was found that the VPA is much longer than the vertical transport time for dissolved material due to the elongated resting of particulates on the seabed and contributions from the resuspended old material. The VPA is sensitive to the settling velocity and increases 2 orders of magnitude with the settling velocity from 0 to 10 m/day in less dynamic environments. The slow‐sinking material can remain in suspension while the fast‐sinking material mostly stays on the seabed. No significant difference in the VPA was found between wet and dry years except during the episodic freshwater pulse, which brought aged materials from the depositional shoals to increase the VPA in the channel. Key Points: The vertical particulate age (VPA) explains the time lag between the springtime algae blooms and the summertime hypoxia in the bayLong resting of particulates on the seabed and resuspension of the aged seabed material largely elongate the VPA in the water columnThe VPA is sensitive to settling velocity and episodic freshwater pulse. The latter entrains old material from shoals to the deep channel [ABSTRACT FROM AUTHOR]

Smokes from biomass burning can contribute substantial amounts of hazardous substances and carbon to the atmosphere. These substances can be transported seaward and deposited on the ocean surface. In this study, Moderate Resolution Imaging Spectroradiometer (MODIS) images are used to map the relative smoke concentration over the ocean between November 8 and 11, 2018 from the recent California fires, with the ultimate goal of developing a generally applicable approach to map smokes over oceans. Because both biomass-burning smokes and clouds can produce strong backscattering signals, two key differences are used to separate them: 1) water-vapor absorption in certain wavelengths only occurs in clouds and 2) cumulus and cirrus clouds occur at different altitudes, therefore, bearing different thermal signatures. Based on these observations, a decision-tree method is developed to separate smokes from clouds. First, MODIS top-of-atmosphere (TOA) reflectance at 936 nm is used to detect both clouds and smokes over oceans. Then, brightness temperature derived from the 9730-nm band is used to separate cirrus from others. Finally, a water absorption depth (WAD) index is used to distinguish cumulus clouds from smokes, whose relative concentration in each image pixel is estimated from the MODIS TOA reflectance at 859 nm. Such derived smoke distribution and concentration are validated using concurrent Cloud-Aerosol Lidar and Infrared Pathfinder Satellite (CALIPSO) data, which provide the fine mode aerosol optical thickness (AOT) of smokes. Test of the approach over the recent Australia fires shows promising results, suggesting that the approach might be implemented by operational agencies to monitor and quantify smokes from biomass burning on a routine basis. [ABSTRACT FROM AUTHOR]

Most estuaries are characterized by non‐uniform axial topography with shallow shoals near the mouth. Previous studies have addressed the impacts of the axial topographic variations on mixing and estuarine circulations yet seldom on material transport and retention. This study investigates the longitudinal structure and mechanisms of exchange flow and material transport of Chesapeake Bay (CB), featuring a shallow sill in the lower bay, by applying total exchange flow (TEF) algorithm, tracer experiments, and partial residence time (PRT) using a validated 32‐years numerical model simulation. A retention coefficient was adopted to quantify the material retention rate using two characteristic PRTs: with and without incorporating water parcels returning to a concerned region. It is found that shoaling from the Rappahannock Shoal to the mouth causes persistent downwelling, strong reflux, and the highest material retention rate in the middle of the bay. The gravitational circulation and the river outflow dominate the transport of salt and riverine dissolved materials (RDMs), whereas the contribution of the tidal oscillatory process is localized near the mouth. The dominance of river outflow over the gravitational circulation for transporting RDMs is confined within the upper bay, where PRTs exhibit distinct seasonality. PRTs show small seasonality in the middle to the lower bay controlled by the exchange flow. The present analysis combining TEF, efflux/reflux theory, and PRT is applicable to other coastal aquatic ecosystems to characterize the water exchange and renewal efficiency along the salinity gradient and understand the contributions of transport to biogeochemical processes. Plain Language Summary: Chesapeake Bay (CB) is the largest estuary in the United States, with a major deep channel indented by a shallow sill in the lower bay. The longitudinal topography of CB can be characterized as "Shallow‐Deep‐Shallow." Previous studies in other estuaries addressed the impact of the axial topographic variations on estuarine hydrodynamics yet seldom on material transport and retention, such as the retention time of organic matter, an important indicator for hypoxia issue. This study examines how the particular longitudinal topography affects the transport of salt (from the coastal ocean) and riverine dissolved materials (RDMs, from the river) by using a 32‐years numerical model simulation. We find that the shallow sill will obviously increase the retention time of RDMs upstream of the shoal, mainly because the abrupt shoaling near the shoal results in strong mixing and reflux of the surface outflow, associated with the surface velocity convergence and resultant downwelling. Exchange flow (i.e., surface outflow and bottom inflow) and river outflow dominate the transports of salt and RDMs in CB, whereas the contribution from the tidal process is localized near the mouth. It is also found the shallow sill will not block the exchange flow, which increases monotonically toward downstream. Key Points: Density‐driven exchange flow and river outflow dominate the salt and riverine dissolved material transport in Chesapeake BayRiver outflow dominates the transport of riverine dissolved materials upstream, while exchange flow dominates the transport downstreamRapid seaward shoaling causes strong reflux that increases material retention in the middle of the bay [ABSTRACT FROM AUTHOR]

An understanding of the dynamics and behaviors of suspended sediments is vital in analysis of morphological, environmental, and ecological processes occurring in coastal marine environments. To study the mechanisms of maintaining high suspended sediment concentrations (SSCs) on a tide-dominated offshore shoal, we measured water depths, current velocities, SSCs, wave parameters and bottom sediment compositions in the southern Yellow Sea. These data were then used to calculate bottom shear stresses generated by currents ( τ c ), waves ( τ w ), and wave–current interactions ( τ cw ). SSCs time series exhibited strong quarter-diurnal peaks during spring tides, in contrast to the semidiurnal signal during neap tides. A Fourier analysis showed that suspended sediment variations within tidal cycles was mainly controlled by resuspension in most stations. There existed relatively stable background SSCs (maintaining high SSCs among tidal cycles) values at all four stations during both windy (wind speed > 9.0 m/s) and normal weather conditions (wind speed < 3.0 m/s). The background SSCs had strong relationship with spring/neap-averaged τ cw , indicating background SSCs were mainly controlled by mean bottom shear stress, with a minimum value of 0.21 N/m 2 . On account of the strong tidal currents, background SSCs of spring tides were greater than that of neap tides. In addition, on the base of wavelet, statistics analyses and turbulence dissipation parameter, background SSCs during slack tide in the study area may be maintained by intermittent turbulence events induced by a combined tidal current and wave action. [ABSTRACT FROM AUTHOR]

Water exchange, featured by bottom inflow and surface outflow in a typical estuary, determines the transport and redistribution of salt, nutrients, pollutants, and suspended sediments and organisms. Water exchange in Chesapeake Bay, the largest estuary in the US, has been extensively studied, yet its long-term interannual variability and its relationship with the external forcings are not fully understood. Based on a long-term (1980–2011) numerical model simulation, this study examines the water exchanges between Chesapeake Bay and the adjacent coastal shelf, between different regions within the bay, as well as their relationships with river discharge, wind, and residence time. Through an EOF analysis of the bottom inflow and surface outflow at seven selected cross-bay sections, we found that over 90% of the spatiotemporal variations of water exchange can be explained by the first two EOF modes, which are highly correlated with the freshwater discharge and northwesterly wind, respectively. Unlike the outflow that increases linearly with river discharge as commonly expected, the inflow responds non-monotonically to river discharge. The relationship between the river discharge and inflow can be described by a combination of the Michaelis–Menten/Monod equation and a linearly decreasing function, i.e., the inflow initially increases with river discharge due to enhanced gravitational circulation and then levels, and gradually declines due to overwhelming seaward barotropic current. We found a locally enhanced water exchange in the lower-middle bay, which can be attributed to the persistent reflux of surface outflow due to the irregular geometry and rapid shoaling in the channel bathymetry. The water exchange and the mean residence time can be connected reciprocally through the bay volume, yet the validation of this relationship depends on the timescale to be considered since the residence time at a given time is controlled by the future hydrodynamics. A delay effect should be considered when using the relationship to estimate outflow interchangeably with the direct computation of the outflow. • Reflux contributes significantly to the water exchange in the lower bay. • River discharge and down-estuary wind dominate the water exchange in the bay. • Bottom inflow responds non-monotonically to the river discharge. • Water exchanges in the lower/upper bay respond oppositely to the down-estuary wind. • The time-lag effect should be considered to estimate the residence time by V/ Q out. [ABSTRACT FROM AUTHOR]

Fine-grained sediments suspended in coastal waters play an important role in submarine topography evolution and associated environment changes. The convergence of suspended sediments concentrated near the seabed results in high sediment concentration, and contributes significantly to sediment transport. In order to investigate the mechanism triggering high suspended sediment concentration (SSC), we deployed a tripod to the seabed to obtain in situ bottom boundary layer measurements of sediment dynamics and a buoy to the sea surface to collect meteorological and wave data at the northern Changjiang River mouth from December 20, 2015 to January 20, 2016. The high SSC (e.g. >3 g/L) events were observed together with fluid mud (thicknesses of 4–16 cm) near the seabed during neap tides when cold air intrusion generated winter storms and strong waves. Further, we found that the high SSC event was mainly resulted from wind waves and sediment resuspension supported by local benthic fluid mud, which was associated with three stages. At the setting up stage, the winter storm brought long duration of strong-waves (e.g. significant wave height >1.5 m) more than 15 h, resulting in a maximum wave-current combined bottom shear stress of 3.2 Pa and the increase of SSC to >1 g/L. At the reinforcement stage, the strong waves and bottom shear stress lasted for several hours, and further increased the SSC to >3 g/L. At the final decay stage, wind waves and the maximum wave-current shear stresses decreased significantly, with the disappearance of high SSC. Thus, there was no high SSC event observed even with strong wind waves during spring tides because strong wave duration was too short for the reinforcement process. The sediment source for the high SSC events was mainly from bottom fluid mud resuspension, as well as the advection transport from the adjacent subaqueous Changjiang River delta. • Tripod deployment obtains bottom sediment dynamics under winter storm conditions. • Resuspension SSC peaks supported by wind waves and local benthic fluid mud. • High SSC events formed through the setting up to reinforcement and decay stages. • Reinforcement determined by winter storm induced long duration of strong waves. [ABSTRACT FROM AUTHOR]

The definition of the threshold of sediment motion is critical for continental shelf sediment dynamics. The work by A. Shields laid the foundation for this research direction, leading to the well-known Shields curve. Here we review the most widely used threshold curves that have followed from the original Shields curve over the last 80 years, and propose that in terms of physical processes the threshold (critical Shields parameter) is a function of at least six variables, i.e. grain Reynolds number, grain size distribution, sphericity, roundness, particle cohesiveness and the scale effects of turbulence. Identifying these key factors, we paid a special attention to the role of the scale effects of turbulence. Turbulence was thought to be a random process, but the improvement of measurement techniques revealed that it has both temporal and spatial structures: the magnitude of instantaneous velocity fluctuations varies in time and in location, which can cause the deviation between in situ measurements and flume experiments. In coastal and shelf waters, in situ measurements of tidal currents and suspended sediment concentrations have revealed that resuspension takes place even though the bed shear stress is well below the Shields curve. Further process and mechanism studies are required to improve the theoretical framework regarding the turbulence structures and their interplay with sediment threshold. The scientific problems for future studies include the establishment of laboratory experiments, in situ measurements and process-based modelling under different water depths and hydrodynamic conditions to quantify the scale effects of turbulence; the development of new observation techniques for higher resolution and for extreme environments; development of new data processing methods, including big data methods to analyse turbulence structures; and the quantification of the effects of biological contributions and non-particle components on the family of Shields curves. • Measured threshold for initial sediment motion is well below the Shields curve. • The scale effects of turbulence cause the deviation between in situ measurements and flume experiments. • The threshold (critical Shields parameter) is now a function of at least six variables. [ABSTRACT FROM AUTHOR]