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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 noncohesive 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.

© The Author(s), 2014. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Journal of Marine Science and Engineering 2 (2014): 413-436, doi:10.3390/jmse2020413., The Community Sediment Transport Modeling System (CSTMS) cohesive bed sub-model that accounts for erosion, deposition, consolidation, and swelling was implemented in a three-dimensional domain to represent the York River estuary, Virginia. The objectives of this paper are to (1) describe the application of the three-dimensional hydrodynamic York Cohesive Bed Model, (2) compare calculations to observations, and (3) investigate sensitivities of the cohesive bed sub-model to user-defined parameters. Model results for summer 2007 showed good agreement with tidal-phase averaged estimates of sediment concentration, bed stress, and current velocity derived from Acoustic Doppler Velocimeter (ADV) field measurements. An important step in implementing the cohesive bed model was specification of both the initial and equilibrium critical shear stress profiles, in addition to choosing other parameters like the consolidation and swelling timescales. This model promises to be a useful tool for investigating the fundamental controls on bed erodibility and settling velocity in the York River, a classical muddy estuary, provided that appropriate data exists to inform the choice of model parameters., Funding by the National Science Foundation (OCE-1061781 and OCE-0536572) supported Fall, Harris, Friedrichs, and Rinehimer.