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Schistosomiasis, a debilitating parasitic disease of poverty affecting more than 250 million people worldwide, is contracted upon contact with the larval form of the parasite, known as cercaria, emerging from infected freshwater snails, the obligate intermediate host of the parasite. Understanding how infectious larvae can be transported in rivers and irrigation canals is crucial to fine-tune environmental interventions targeting the parasite and its intermediate host. Specifically, lateral cavities along many tropical rivers act as water access points but can also entrap parasitic larvae and provide low-velocity environments for snail-supporting vegetation to flourish, creating potential areas of high schistosomiasis infection. In this paper, the circulation of larvae in a typical transmission site along the Lampsar River in Senegal is modeled under a range of wind and vegetation conditions to better understand how such environmental factors affect their transport. We found that wind direction has a large influence on the distribution and abundance of parasitic larvae at the water access point, whereas increasing wind speed scales velocities but does not affect flow patterns. The area of coverage of vegetation can significantly alter flow magnitudes and circulation patterns for the same wind speed and direction. Increasing vegetation coverage generally leads to an increase in larvae residence time in the side pond, but the relationship is non-monotonic with five regimes of residence time behavior based on vegetation patch radius. The results suggest that there is an optimal patch radius at which larvae residence time and velocity deviations within the side pond are maximized. 

We present direct numerical simulation results of a wave-current boundary layer in a current-dominated flow regime (wave driven to steady current ratio of 0.34) over bumpy walls for hydraulically smooth flow conditions (wave orbital excursion to roughness ratio of 10). The turbulent, wave-current channel flow has a friction Reynolds number of $350$ and a wave Reynolds number of $351$ . At the lower boundary, a bumpy wall is introduced with a direct forcing immersed boundary method, while the top wall has a free-slip boundary condition. Despite the hydraulically smooth nature of the wave-driven flow, the phase variations of the turbulent statistics for the bumpy wall case were found to vary substantially when compared with the flat wall case. Results show that the addition of weak waves to a steady current over flat walls has a negligible effect on the turbulence or bottom drag. However, the addition of weak waves to a steady current over bumpy walls has a significant effect through enhancement of the Reynolds stress (RS) accompanied by a drag coefficient increase of $$11\,\%$$ relative to the steady current case. This enhancement occurs just below the top of the roughness elements during the acceleration portion of the wave cycle: Turbulent kinetic energy (TKE) is subsequently transported above the roughness elements to a maximum height of roughly twice the turbulent Stokes length. We analyse the TKE and RS budgets to understand the mechanisms behind the alterations in the turbulence properties due to the bumpy wall. The results provide a mechanistic picture of the differences between bumpy and flat walls in wave-current turbulent boundary layers and illustrate the importance of bumpy features even in weakly energetic wave conditions. 

Abstract We conducted field work in South San Francisco Bay to examine cohesive sediment flocculation dynamics in a shallow, wave‐ and current‐driven estuarine environment. Drawing on data collected using a suite of acoustic and optical instrumentation over three distinct seasons, we found that the factors driving floc size variability differed substantially when comparing locally sourced sediment (i.e., through wave‐driven resuspension) to suspended sediment advected from upstream. Statistical analysis of our extensive field data revealed additional seasonal variability in these trends, with wave stress promoting floc breakup during the summer and winter months, and biological processes encouraging floc growth during the spring productive period. Combining these data with fractal dimension estimates, we found that seasonally varying floc composition can lead to differences in floc settling velocity by a factor of approximately two to five for a given floc size. Finally, by analyzing co‐located turbulence and sediment flux measurements from the bottom boundary layer, we present evidence that the relationship between floc size and the inverse turbulent Schmidt number varies with floc structure. These results can be used to inform sediment transport modeling parameterizations in estuarine environments. 

Abstract Over the course of a year, we conducted three field deployments in South San Francisco Bay to examine seasonal variability in bottom drag. Our data consisted of turbulence measurements both within and outside the bottom boundary layer and benthic characterization surveys adjacent to our study site. Our results suggest that canopies of benthic worm and amphipod feeding tubes, which were denser during summer, can increase the drag coefficient by up to a factor of three relative to the smoother beds found in winter and spring. The extent of the drag increase varied depending on the measurement device, with the greatest increase inferred by measurements taken further from the bed. The small scale and temporally varying population densities of these living roughness elements pose significant challenges for hydrodynamic models, and future work is needed to begin incorporating benthic biology statistics into drag coefficient parameterizations.