Turbulent and Electromagnetic Signature of Small- and Fine-scale Biological and Oceanographic Processes

Small- and fine-scale biological and oceanographic processes may have a measurable electromagnetic signature. These types of processes inherently involve turbulence and three-dimensional dynamics. Traditional models of the electromagnetic signature of oceanographic processes are of an analytical nature, do not account for three-dimensional boundary layer dynamics or turbulence, self-inductance, and may not describe the variety of the environmental conditions occurring in the ocean. In order to address this problem, I have implemented magnetohydrodynamic (MHD) computational fluid dynamics (CFD) tools, which has allowed for the evaluation of the electromagnetic signature of a number of small- and fine-scale biological and oceanographic processes in the ocean. The suite of computational tools has included the commercial models ANSYS Fluent, coupled with the MHD module, and ANSYS Maxwell. These computational tools have been well-established in fluid and electromagnetic engineering. The application of CFD and MHD tools in oceanography is new but is undergoing rapid development. In this work, substantial effort was made toward the CFD, MHD, and magnetostatic model verification and identification of model limitations. Verifications of the CFD, MHD, and magnetostatic models were conducted by successfully comparing their results with the field measurements and laboratory experiments. Comparison with the traditional (analytical) models for surface and internal waves, has revealed their limitations related to bottom boundary layer physics, effect of self-inductance, and, to a lesser extent, the magnetic permeability difference at the air-sea interface. These limitations become important for shallow water internal waves. As a result, the traditional models significantly overestimate the magnetic signature of internal waves observed at the Electromagnetic Observatory. After model verification with the field and laboratory data, the computational models were then applied to evaluate the magnetic signature of diel vertical migration (DVM) of zooplankton, surface waves, internal wave solitons, freshwater lens spreading, and Langmuir circulation. The quantitative estimates have been made for typical environmental conditions. In other environmental conditions, their magnetic signature may be somewhat different. The suite of computational models developed in this dissertation work allows for the estimation of the magnetic signature of fine- and small-scale oceanographic processes in virtually any environmental conditions (e.g., in oil emulsions). I anticipate the result of this study will have Naval, environmental, and oil exploration applications

Biophysical Interactions in the Straits of Florida: Turbulent Mixing Due to Diel Vertical Migrations of Zooplankton

Diel vertical migrations (DVM) comprise the largest animal migration on the planet and are a phenomenon present in all bodies of water on Earth. A strong sound scattering layer undergoing DVM was observed in the Straits of Florida via a bottom-mounted Acoustic Doppler current profiler (ADCP) Workhorse Longranger 75 kHz (Teledyne RD Instruments) located at the 244 m isobath. ADCP average backscatter showed a clear periodicity corresponding with sunrise and sunset times indicating the presence of a nocturnal DVM. Analysis of the ADCP backscatter data indicated zooplankton swimming velocities were faster during sunrise than sunset times. In several cases the zooplankton swimming velocity appeared to be faster at the beginning of the descent, after which the swimming velocity decreased. Analysis of ADCP velocity data indicated a measureable decrease in the northward component of the current velocity field during migrations (sunrise and sunset) compared to three hours prior. This was presumably associated with an increase in drag due to turbulent friction associated with DVM. A non-hydrostatic computational fluid dynamics (CFD) model with injection of Lagrangian particles was utilized to simulate the effects of DVM on the velocity field and turbulence signature of the Florida Current. A domain simulating a section of the Florida Current was created and zooplankton were represented by particle injection with a discrete phase model. The model was run with and without particles, holding all other parameters the same, for comparison. Idealized temperature stratification and velocity profiles were set for both summer and winter conditions to observe seasonal differences. For each case, velocity and turbulence with particles were compared to results without particles to confirm the changes in profiles were due to the zooplankton (Lagrangian particles). In several cases there was an observable change in average x-velocity profiles due to the injection of particles into the domain. In all cases there was an observable increase in subgrid turbulent viscosity in the wake of the injected particles. This effect was much stronger in the winter case, most likely due to stratification of the water column which gave a near critical Richardson number. These results indicated that DVM does in fact have an effect on the velocity profile and turbulence signature in a strong current under certain conditions and that there was a seasonal difference due to stratification profiles

3D Dynamics of Freshwater Lenses in the Near-Surface Layer of the Tropical Ocean

Convective rains in the Intertropical Convergence Zone produce lenses of freshened water on the ocean surface. Due to significant density differences between the freshened and saltier seawater, strong pressure gradients develop, resulting in lateral spreading of freshwater lenses in the form of gravity currents. Gravity currents inherently involve three-dimensional dynamics. As a type of organized structure, gravity currents may also interact with, and be shaped by, the ambient oceanic and atmospheric environment. Among the important environmental factors are background stratification and wind stress. Under certain conditions, a resonant interaction between a propagating freshwater lens and internal waves in the underlying halocline (the barrier layer) may develop, while interaction with the wind stress may produce an asymmetry in the freshwater lens and associated mixing. These two types of interactions working in concert may explain the series of sharp frontal interfaces observed in association with freshwater lenses during the Tropical Ocean Global Atmosphere Coupled Ocean Atmosphere Response Experiment (TOGA COARE). We conducted a series of numerical simulations using computational fluid dynamics tools. These numerical experiments were designed to elucidate the relationship between vertical and horizontal fluxes of salinity under various environmental conditions and the potential impact of these fluxes on the barrier layer and Aquarius and Soil Moisture and Ocean Salinity (SMOS) satellite image formations

Dissipation Rate of Turbulent Kinetic Energy in Diel Vertical Migrations: Comparison of ANSYS Fluent Model to Measurements

Recent studies suggest that diel vertical migrations of zooplankton may have an impact on ocean mixing, though details are not completely clear. A strong sound scattering layer of zooplankton undergoing diel vertical migrations was observed in Saanich Inlet, British Colombia, Canada by Kunze et al. (2006). In this study, a shipboard 200- kHz echosounder was used to track vertical motion of the sound scattering layer, and microstructure profiles were collected to observe turbulence. An increase of dissipation rate of turbulent kinetic energy by four to five orders of magnitude was measured during diel vertical migrations of zooplankton in one case (but not observed during other cases). A strong sound scattering layer undergoing diel vertical migration was also observed in the Straits of Florida via a bottom mounted acoustic Doppler current profiler at 244 m isobath. A 3-D non-hydrostatic computational fluid dynamics model with Lagrangian particle injections (a proxy for migrating zooplankton) via a discrete phase model was used to simulate the effect of diel vertical migrations on the turbulence for both Saanich Inlet and the Straits of Florida. The model was initialized with idealized (but based on observation) density and velocity profiles. Particles, with buoyancy adjusted to serve as a proxy for vertically swimming zooplankton, were injected to simulate diel vertical migration cycles. Results of models run with extreme concentrations of particles showed an increase in dissipation rate of turbulent kinetic energy of approximately five orders of magnitude over background turbulence during migration of particles in both Saanich Inlet and the Straits of Florida cases (though direct relation of the turbulence produced by buoyant particles and swimming organisms isn’t straightforward). This increase was quantitatively consistent, with turbulence measurements by Kunze et al. (2006). When 10 times fewer particles were injected into the model, the effect on dissipation rate of turbulent kinetic energy was an order of magnitude smaller than that from the extreme concentration. At a concentration of particles 100 times smaller than the extreme concentration, there was no longer an observable effect. In the Straits of Florida, direct turbulence measurements were not available to make a quantitative comparison. However, a small, but statistically significant decrease in northward current velocity profiles during migration times were observed after averaging these profiles over 11 months. A small decrease of current velocity connected to the vertical migrations of particles was reproduced in the Straits of Florida model case. The deviations in the velocity profiles can be explained by the increase in turbulent mixing during vertical migration periods

DNA Analysis of Surfactant-Associated Bacteria in a Natural Sea Slick Observed by TerraSAR-X and RADARSAT-2 Over the Gulf of Mexico

The damping of short gravity-capillary waves (Bragg waves) due to surfactant accumulation under low wind speed conditions results in the formation of natural sea slicks. These slicks are detectable visually and in synthetic aperture radar (SAR) imagery. Surfactants are produced by natural life processes of many organisms, such as bacteria, phytoplankton, seaweed, and zooplankton. By using DNA analysis, we are able to determine the relative abundance of surfactant-associated bacteria in the sea surface microlayer and the subsurface water column. A method to reduce contamination of samples during collection, storage, and analysis (Kurata et al., 2016; Hamilton et al., 2015) has been implemented and advanced by increasing the number of successive samples and changing sample storage procedures. In this work, microlayer samples have been collected in the Gulf of Mexico during a research cruise (LASER) on the R/V F.G. Walton Smith during RADARSAT-2 and TerraSAR-X overpasses. We found that in slick areas surfactant-associated bacteria mostly reside in subsurface waters, producing surfactants, which move to the surface, accumulate on and enrich the sea surface microlayer. This is consistent with previous studies (Kurata et al., 2016; Hamilton et al., 2015) and with the experimental results of Cunliffe et al. (2010)

Numerical Simulation of Diel Vertical Migrations of Zooplankton in Oil Emulsions and Freshwater Lenses

Diel vertical migration (DVM) of zooplankton may have an impact on ocean mixing, though details are not completely clear. Zooplankton that undergo DVM can have an impact on oil transport through the water column and oil can have a negative effect on the ability to vertically migrate due to the highly viscous nature of oil emulsions. DVM patterns may also be altered by freshwater inflow, due to convective rains or river runoff, which produces strong anomalies of stratification associated with lenses of freshened water in the near surface layer of the ocean. A computational fluid dynamics model was used to simulate the turbulence signature of DVM in the upper ocean in the presence of oil emulsions and freshwater lenses. The model was initialized with typical vertical density and velocity profiles in the De Soto Canyon (CARTHE GLAD experimental range) located in the northeastern Gulf of Mexico. The effect of oil emulsions on DVM was included by altering the molecular viscosity of water in the upper layer of the ocean. The freshwater lenses were simulated as localized (in space) salinity and temperature anomalies, propagating as gravity currents, eventually mixing with the environment and increasing the vertical stratification. The model results suggest that propulsion speed of some organisms may somewhat change because of buoyancy effects due to varying salinity stratification in the upper layer of the ocean; the presence of oil emulsions, however, can have a more dramatic effect on the DVM of zooplankton (with dire consequences for the marine ecosystem)

3D Dynamics of Freshwater Lenses in the Near-Surface Layer of the Tropical Ocean

Convective rains in the Intertropical Convergence Zone (ITCZ) produce lenses of freshened water on the ocean surface. These lenses are localized in space and typically involve both salinity and temperature anomalies. Due to significant density anomalies, strong pressure gradients develop, which result in lateral spreading of freshwater lenses in a form resembling gravity currents. Gravity currents inherently involve three-dimensional dynamics. As a type of organized structure, gravity currents in the upper layer of the ocean may also interact with, and be shaped by, the ambient oceanic environment and atmospheric conditions. Among the important factors are the background stratification, wind stress, wind/wave mixing and spatially coherent organized motions in the nearsurface layer of the ocean. Under certain conditions, a resonant interaction between a propagating freshwater lens and internal waves in the underlying pycnocline (e.g., barrier layer) may develop, whereas interaction with wind stress may produce an asymmetry in the freshwater lens and associated mixing. These two types of interactions working in concert may explain the series of sharp frontal interfaces, which have been observed in association with freshwater lenses during TOGA COARE. In this work, we have conducted a series of numerical experiments using computational fluid dynamics tools. These numerical simulations were designed to elucidate the relationship between vertical mixing and horizontal advection of salinity under various environmental conditions and potential impact on the Aquarius and SMOS satellite image formation. Available near-surface data from field experiments served as a guidance for numerical simulations. The results of this study indicate that 3D dynamics of freshwater lenses are essential within a certain range of wind/wave conditions and the freshwater influx in the surface layer of the ocean

Biomixing Due to Diel Vertical Migrations of Zooplankton: Comparison of Computational Fluid Dynamics Model with Observations

Recent studies (Dewar et al., 2006; Wilhelmus and Dabiri, 2014) suggest that diel vertical migrations (DVM) of zooplankton (or other migrating organisms) may have an impact on ocean mixing, though details are not completely clear. Zooplankton that undergo DVM can have an impact on oil transport through the water column, and oil and dispersants can have a negative or even lethal effect on the organisms. Kunze et al. (2006) reported an increase of dissipation rate of turbulent kinetic energy, ε, by four to five orders of magnitude during DVM of zooplankton over background turbulence in Saanich Inlet, British Columbia, Canada. However, the effect was not observed in the same area by Rousseau et al. (2010) and was later reassessed by Kunze (2011). In our work, an 11-month data set obtained in the Straits of Florida with a bottom-mounted acoustic Doppler current profiler revealed strong sound scattering layers undergoing DVM. We used a 3-D non-hydrostatic computational fluid dynamics model with Lagrangian particle injections (a proxy for migrating organisms) via a discrete phase model to simulate the effect of turbulence generation by DVM. We tested a range of organism concentrations from 1000 to 10,000 organisms/m3 based on measurements by Greenlaw (1979) and Mackie and Mills (1983) in Saanich Inlet. At a concentration close to the upper limit, the simulation showed an increase in ε by two to three orders of magnitude during DVM over background turbulence, 10−9 W kg−1. At a concentration of 1000 organisms/m3, almost no turbulence above the background level was produced in the model. These results suggest that the Kunze et al. (2006) observations could have been performed at a larger concentration of migrating zooplankton than those reported by Rousseau et al. (2010). No exact zooplankton concentrations data were provided in either work. The difference between observations and the model can, in part, be explained by the fact that Kunze et al. (2006) measured instantaneous profiles of ε, while the model results on ε were averaged horizontally over the 50 m by 50 m domain. In the Straits of Florida, we observed a small decrease in northward current velocity profiles during migration times after averaging over 11 months of observations. The computational fluid dynamics model reproduced this decrease of current velocity due to turbulence generated by DVM in the Straits of Florida model case. The deviations in the velocity profiles can be explained by the increase in turbulent mixing during vertical migration periods. Comparison of observational data to the model results was complicated by physical factors such as tides, Florida Current meandering, etc., which may have a stronger effect on current velocity profiles than DVM

Diel Vertical Migrations of Zooplankton and Turbulent Mixing: Observations and Numerical Simulation

A strong sound scattering layer undergoing diel vertical migration was observed using a bottom mounted ADCP at 244 m depth in the Straits of Florida. Data collection was a part of the Electromagnetic Observatory funded by the Office of Naval Research and analysis of biophysical interactions is ongoing under the Gulf of Mexico Research Initiative. This project aims to understand biophysical interactions associated with diel vertical migrations in a strong current. A computational fluid dynamics model was used to model the effects of diel vertical migrations on the velocity field and turbulence signature of the Gulf Stream. Zooplankton were represented through a discrete phase model. Temperature stratification was set for both summer and winter conditions to observe seasonal differences. For each season, results from the model with particles were compared to results run in the same conditions without particles to confirm the changes in profiles were due to the zooplankton. Analysis of the ADCP data indicates a distortion to the velocity field at sunrise and sunset, only during winter months, presumably associated with turbulence due to diel vertical migrations