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As brackish turbid waters exit San Francisco Bay, one of the largest estuaries in the U.S. West Coast, they form the San Francisco Bay Plume (SFBP), which spreads offshore and influences the Gulf of the Farallones (GoF), an ecologically significant region in the California Current System that is also home to three National Marine Sanctuaries. This paper provides the first observationally based investigation of the spatio-temporal variability of the SFBP, using a plume tracking algorithm applied to more than two decades (2002-2023) of ocean color data from the Moderate Resolution Imaging Spectroradiometer (MODIS) sensor onboard satellites Aqua and Terra. The turbid SFBP spreads radially, extending 10-20 km offshore around 50% of the time, and during extreme discharge events (<1% of the time), the plume can reach nearly 60 km offshore to the shelf break. The greatest variability in frequency of plume occurrence was observed 10-20 km offshore and it was largely explained by the seasonal cycle (80% of total variance), linked primarily to seasonal changes in river discharge. Largest plume areas (determined by summing up all pixel areas weighted by their respective fraction of plume occurrence) were observed during winter and smallest during summer, occupying on average 24% and 1.5% of GoF area, respectively. Beyond 20-30 km offshore, variability in frequency of plume occurrence was dominated by the intraseasonal band (50-80% of total variance), attributed to plume response to synoptic wind-forcing and/or filaments and eddies, while the interannual band played a secondary role in the plume variability (<20% of total variance). Finally, a multivariable linear regression model of the turbid SFBP area was created to explore the potential predictability of the plume’s influence in the GoF. The model included the annual and semi-annual cycles and discharge anomalies (deseasoned and detrended), and despite its simplicity, it explained over 78% of total variance of the turbid SFBP area. Therefore, it could be a useful tool for scientists and stakeholders to better understand how management actions on freshwater supply can have consequences offshore beyond the Golden Gate and help guide future management decisions in this ecologically important region. 

{"Abstract":["This is an archive of model output from the Regional Ocean Modeling System (ROMS) with two grids and two-way nesting. The parent grid resolution (referred to as Doppio) is 7 km and spans the Atlantic Ocean off the northeast United States from Cape Hatteras to Nova Scotia. The refinement grid (referred to as Snaildel) focuses on Delaware Bay and the adjacent coastal ocean at 1 km resolution. This ROMS configuration uses turbulence kinetic energy flux and significant wave height from Simulating Waves Nearshore (SWAN) as surface boundary conditions for turbulence closure.Ocean state variables computed are sea level, velocity, temperature, and salinity. Also inclued are surface and bottom stresses, as well as vertical diffusivity of tracer and momentum. \nThe files uploaded here are examples of one time record from each of this dataset. Outputs for the full reanalysis, which comprises 14 Terabytes of data, are made available for download via a THREDDS (Thematic Real-time Environmental Distributed Data Services) web service to facilitate user geospatial or temporal sub-setting.\nThe THREDDS catalog URLs and example filenames available here, for the respective collections, are:\n\t- 12 minute snapshots of the Doppio domain 2009-2015:\nhttps://tds.marine.rutgers.edu/thredds/roms/snaildel/catalog.html?dataset=snaildel_doppio_history\n\t- 12 minute snapshots of the Snaildel domain 2009-2015:\nhttps://tds.marine.rutgers.edu/thredds/roms/snaildel/catalog.html?dataset=snaildel_snaildel_history\n \nGarwood, J. C., H. L. Fuchs, G. P. Gerbi, E. J. Hunter, R. J. Chant and J. L. Wilkin (2022). "Estuarine retention of larvae: Contrasting effects of behavioral responses to turbulence and waves." Limnol. Oceanogr. 67: 992-1005.\nHunter, E. J., H. L. Fuchs, J. L. Wilkin, G. P. Gerbi, R. J. Chant and J. C. Garwood (2022). "ROMSPath v1.0: Offline Particle Tracking for the Regional Ocean Modeling System (ROMS)." Geosci. Model Dev. 15: 4297-4311."]} 

Abstract. Offline particle tracking (OPT) is a widely used tool for theanalysis of data in oceanographic research. Given the output of ahydrodynamic model, OPT can provide answers to a wide variety of researchquestions involving fluid kinematics, zooplankton transport, the dispersionof pollutants, and the fate of chemical tracers, among others. In thispaper, we introduce ROMSPath, an OPT model designed to complement theRegional Ocean Modeling System (ROMS). Based on the Lagrangian TRANSport(LTRANS) model (North et al., 2008), ROMSPath is written in Fortran90 and provides advancements in functionality and efficiency compared toLTRANS. First, ROMSPath calculates particle trajectories using the ROMSnative grid, which provides advantages in interpolation, masking, andboundary interaction while improving accuracy. Second, ROMSPath enablessimulated particles to pass between nested ROMS grids, which is anincreasingly popular scheme to simulate the ocean over multiple scales.Third, the ROMSPath vertical turbulence module enables the turbulent(diffusion) time step and advection time step to be specified separately,adding flexibility and improving computational efficiency. Lastly, ROMSPathincludes new infrastructure which enables inputting of auxiliary parameters for addedfunctionality. In particular, Stokes drift can be input and added toparticle advection. Here we describe the details of these updates andperformance improvements.