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).

Description: Measurement of suspended particulate matter concentration (SPMC) spanning large time and geographical scales have become a matter of growing importance in recent decades. At many places worldwide, complex observation platforms have been installed to capture temporal and spatial variability over scales ranging from cm (turbulent regimes) to whole basins. Long-term in situ measurements of SPMC involve one or more optical and acoustical sensors and, as the ground truth reference, gravimetric measurements of filtered water samples. The estimation of SPMC from optical and acoustical proxies generally results from the combination of a number of independent calibration measurements, as well as regression or inverse models. Direct or indirect measurements of SPMC are inherently associated with a number of uncertainties along the whole operation chain, the autonomous field deployment, to the analyses necessary for converting the observed proxy values of optical and acoustical signals to SPMC. Controlling uncertainties will become an important issue when the observational input comprises systems of sensors spanning large spatial and temporal scales. This will be especially relevant for detecting trends in the data with unambiguous statistical significance, separating anthropogenic impact from natural variations, or evaluating numerical models over a broad ensemble of different conditions using validated field data. The aim of the study is to present and discuss the benefits and limitations of using optical and acoustical backscatter sensors to acquire long-term observations of SPMC. Additionally, this study will formulate recommendations on how to best acquire quality-assured SPMC data sets, based on the challenges and uncertainties associated with those long-term observations. The main sources of error as well as the means to quantify and reduce the uncertainties associated with SPMC measurements are also illustrated.