Cohesive and mixed sediment in the Regional Ocean Modeling System (ROMS v3.6) implemented in the Coupled Ocean-Atmosphere-Wave-Sediment Transport Modeling System (COAWST r1234)

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

Progress and Challenges in Coupled Hydrodynamic-Ecological Estuarine Modeling

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

Modeling winter circulation and particle retention in the Magdalena-Almejas Bay lagoon system (Baja California Sur, Mexico)

Se describe la circulación y el transporte pasivo de partículas en las inmediaciones del sistema lagunar Bahía Magdalena- Almejas mediante un modelo lineal de circulación en el dominio de la frecuencia con el que se obtuvieron los campos básicos de flujo. El modelo está forzado por mareas, marea residual, viento medio, viento periódico para simular el efecto de la brisa marina y una simulación aproximada del efecto de la Corriente de California. Se realizaron dos experimentos principales, uno enfocado a detectar zonas de retención en el interior del sistema lagunar, y el segundo para observar el intercambio de partículas entre el sistema y el océano abierto adyacente. Se encontró que las partículas sembradas en el sistema tienden a quedarse dentro y concentrarse en regiones particulares que se correspondieron con la distribución real de bancos pesqueros de recursos bentónicos y, en segundo término, que durante condiciones poco comunes de viento se pueden presentar intrusiones importantes de partículas de la plataforma continental al interior del sistema lagunar. Los resultados son de importancia para el estudio de la zona en general, y particularmente para la modelación y desarrollo de pronósticos de procesos de deriva larval de recursos pesqueros importantes. We describe circulation and passive particle transport in the Magdalena-Almejas Bay lagoon system through a linear circulation model in the frequency domain to obtain basic flux fields. The model is forced by tides, residual tides, mean wind speed, periodic winds (to simulate sea breeze), and an approximation of advection in the California Current. Two main experiments were performed: one to detect retention zones within the lagoon system and another to evaluate particle exchange between the lagoon system and the open ocean. We found that particles seeded within the system tend to remain inside and concentrate in restricted areas that correspond to the real distribution of benthic fish and that, under rare wind conditions, masses of particles seeded on the continental shelf could enter the lagoon system. The results are relevant for the general study of the system and for modeling and developing forecasts of the larval drift of important fish resources