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© The Author(s), 2021. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Filippi, M., Hanlon, R., Rypina, I. I., Hodges, B. A., Peacock, T., & Schmale, D. G. Tracking a surrogate hazardous agent (Rhodamine Dye) in a coastal ocean environment using In Situ measurements and concentration estimates derived from drone images. Remote Sensing, 13(21), (2021): 4415, https://doi.org/10.3390/rs13214415., New tools and technology are needed to track hazardous agents such as oil and red tides in our oceans. Rhodamine dye (a surrogate hazardous agent) was released into the Atlantic ocean in August 2018, and experiments were conducted to track the movement of the dye near the water surface within three hours following the release. A DrOne Water Sampling SystEm (DOWSE), consisting of a 3D-printed sampling device tethered to a drone, was used to collect 26 water samples at different locations around the dye plume. Rhodamine concentrations were measured from the drone water samples using a fluorometer and ranged from 1 to 93 ppb. Dye images were taken during the drone-sampling of surface water containing dye and at about 10 m above the sampling point. These images were post-processed to estimate dye concentrations across the sampling domain. A comparison of calibrated heat maps showed that the altitude images yielded dye distributions that were qualitatively similar to those from images taken near the ocean surface. Moreover, the association between red ratios and dye concentrations yielded trendlines explaining up to 67% of the variation. Drones may be used to detect, track and assist in mitigating hazardous agents in the future., This research was supported in part by the U.S. National Science Foundation (NSF) under Grant Numbers AGS 1520825 (Hazards SEES: Advanced Lagrangian Methods for Prediction, Mitigation and Response to Environmental Flow Hazards), and IIS–1637915 (NRI: Coordinated Detection and Tracking of Hazardous Agents with Aerial and Aquatic Robots to Inform Emergency Responders).

In Lagrangian dynamics, the detection of coherent clusters can help understand the organization of transport by identifying regions with coherent trajectory patterns. Many clustering algorithms, however, rely on user-input parameters, requiring a priori knowledge about the flow and making the outcome subjective. Building on the conventional spectral clustering method of Hadjighasem et al. (2016), a new optimized-parameter spectral clustering approach is developed that automatically identifies optimal parameters within pre-defined ranges. A noise-based metric for quantifying the coherence of the resulting coherent clusters is also introduced. The optimized-parameter spectral clustering is applied to two benchmark analytical flows, the Bickley Jet and the asymmetric Duffing oscillator, and to a realistic, numerically generated oceanic coastal flow. In the latter case, the identified model-based clusters are tested using observed trajectories of real drifters. In all examples, our approach succeeded in performing the partition of the domain into coherent clusters with minimal inter-cluster similarity and maximum intra-cluster similarity. For the coastal flow, the resulting coherent clusters are qualitatively similar over the same phase of the tide on different days and even different years, whereas coherent clusters for the opposite tidal phase are qualitatively different.

Submitted in partial fulfillment of the requirements for the degree of Master of Science at the Massachusetts Institute of Technology and the Woods Hole Oceanographic Institution September 2021., This thesis analyzes data from two types of unique drifter experiments in order to characterize two aspects of ocean flows that are often difficult to study. First, vertical velocities and their associated transport processes are often challenging to observe in the real ocean since vertical velocities are typically orders of magnitude smaller than horizontal velocities in mesoscale and submesoscale flows. Second, Lagrangian coherent structures (LCS) are features which categorize ocean flows into regimes of distinct behavior. These structures are also difficult to quantify in the real ocean, since sets of gridded trajectories from real ocean data (rather than model fields) are rarely available. The first experiment uses drifters drogued at multiple depths in the Alboran Sea to observe and characterize the ocean’s vertical structure, particularly near a strong front where vertical velocities are expected to be much stronger than other regions of the Ocean. The second experiment uses a roughly gridded pattern of surface drifters in the Gulf of Mexico to study LCSs as quantified by methods from dynamical systems such as finitetime Lyapunov exponents (FTLEs), trajectory arc-length, correlation dimension, dilation, Lagrangian-averaged vorticity deviation (LAVD), and spectral clustering. This thesis includes the first attempt to apply these dynamical systems techniques to real drifters for LCS detection. Overall, these experiments and the methods used in this paper are shown to be promising new techniques for quantifying both the vertical structure of ocean flows and Lagrangian Coherent Structures of flows using real drifter data. Future work may involve modified versions of the experiments, with denser sets of ocean drifters in the horizontal and/or vertical directions., My Masters studies in the MIT/WHOI Joint Program were funded by the US Navy Civilian Institution Office.

New tools and technology are needed to track hazardous agents such as oil and red tides in our oceans. Rhodamine dye (a surrogate hazardous agent) was released into the Atlantic ocean in August 2018, and experiments were conducted to track the movement of the dye near the water surface within three hours following the release. A DrOne Water Sampling SystEm (DOWSE), consisting of a 3D-printed sampling device tethered to a drone, was used to collect 26 water samples at different locations around the dye plume. Rhodamine concentrations were measured from the drone water samples using a fluorometer and ranged from 1 to 93 ppb. Dye images were taken during the drone-sampling of surface water containing dye and at about 10 m above the sampling point. These images were post-processed to estimate dye concentrations across the sampling domain. A comparison of calibrated heat maps showed that the altitude images yielded dye distributions that were qualitatively similar to those from images taken near the ocean surface. Moreover, the association between red ratios and dye concentrations yielded trendlines explaining up to 67% of the variation. Drones may be used to detect, track and assist in mitigating hazardous agents in the future.

On Aug 16-17, 2018 a rhodamine dye experiment was conducted in the coastal ocean south of Martha’s Vineyard, MA. One of the experiment’s aims was to investigate the exchanges, or the absence of such, between the mixed layer and the ocean underneath over a time scale of about a day., NSF EAR-1520825

Author Posting. © American Meteorological Society, 2021. This article is posted here by permission of American Meteorological Society for personal use, not for redistribution. The definitive version was published in Journal of Physical Oceanography 51(8),(2021): 2463–2482, https://doi.org/10.1175/JPO-D-20-0291.1., This paper presents analyses of drifters with drogues at different depths—1, 10, 30, and 50 m—that were deployed in the Mediterranean Sea to investigate frontal subduction and upwelling. Drifter trajectories were used to estimate divergence, vorticity, vertical velocity, and finite-size Lyapunov exponents (FTLEs) and to investigate the balance of terms in the vorticity equation. The divergence and vorticity are O(f) and change sign along trajectories. Vertical velocity is O(1 mm s−1), increases with depth, indicates predominant upwelling with isolated downwelling events, and sometimes changes sign between 1 and 50 m. Vortex stretching is one of the significant terms, but not the only one, in the vorticity balance. Two-dimensional FTLEs are 2 × 10−5 s−1 after 1 day, 2 times as large as in a 400-m-resolution numerical model. Three-dimensional FTLEs are 50% larger than 2D FTLEs and are dominated by the vertical shear of horizontal velocity. Bootstrapping suggests uncertainty levels of ~10% of the time-mean absolute values for divergence and vorticity. Analysis of simulated drifters in a model suggests that drifter-based estimates of divergence and vorticity are close to the Eulerian model estimates, except when drifters get aligned into long filaments. Drifter-based vertical velocity is close to the Eulerian model estimates at 1 m but differs at deeper depths. The errors in the vertical velocity are largely due to the lateral separation between drifters at different depths and are partially due to only measuring at four depths. Overall, this paper demonstrates how drifters, heretofore restricted to 2D near-surface observations, can be used to learn about 3D flow properties throughout the upper layer of the water column., Authors Rypina and Pratt were supported by U.S. Office of Naval Research (ONR) Grant N000141812417. Author Getscher acknowledges support from the U.S. Navy Civilian Institution Office with the MIT–WHOI Joint Program. Author Mourre acknowledges support from ONR Grant N00014-16-1-3130. We also thank Eugenio Cutolo for the initial technical support in the implementation of the ultra-high-resolution WMOP simulation. CALYPSO is a Departmental Research Initiative funded by the ONR., 2022-01-16

Author Posting. © American Meteorological Society, 2020. This article is posted here by permission of American Meteorological Society for personal use, not for redistribution. The definitive version was published in Journal of Physical Oceanography 50(7), (2020): 1839-1852, https://doi.org/10.1175/JPO-D-19-0209.1., The Lagrangian characteristics of the surface flow field arising when an idealized, anticyclonic, mesoscale, isolated deep-ocean eddy collides with continental slope and shelf topography are explored. In addition to fluid parcel trajectories, we consider the trajectories of biological organisms that are able to navigate and swim, and for which shallow water is a destination. Of particular interest is the movement of organisms initially located in the offshore eddy, the manner in which the eddy influences the ability of the organisms to reach the shelf break, and the spatial and temporal distributions of organisms that do so. For nonswimmers or very slow swimmers, the organisms arrive at the shelf break in distinct pulses, with different pulses occurring at different locations along the shelf break. This phenomenon is closely related to the episodic formation of trailing vortices that are formed after the eddy collides with the continental slope, turns, and travels parallel to the coast. Analysis based on finite-time Lyapunov exponents reveals initial locations of all successful trajectories reaching the shoreline, and provides maps of the transport pathways showing that much of the cross-shelf-break transport occurs in the lee of the eddy as it moves parallel to the shore. The same analysis shows that the onshore transport is interrupted after a trailing vortex detaches. As the swimming speeds are increased, the organisms are influenced less by the eddy and tend to show up en mass and in a single pulse., IR and LP were supported by National Science Foundation (NSF) Grant OCE-1558806. DC was supported by NSF U.S. National Science Foundation’s Physical Oceanography program through Grants OCE-1059632 and OCE-1433953 as well as the Academic Programs Office, Woods Hole Oceanographic Institution. We acknowledge high-performance computing support from Yellowstone (http://n2t.net/ark:/85065/d7wd3xhc) provided by NCAR’s Computational and Information Systems Laboratory, sponsored by the National Science Foundation.

Author Posting. © American Meteorological Society, 2020. This article is posted here by permission of American Meteorological Society for personal use, not for redistribution. The definitive version was published in Journal of Physical Oceanography 50(12), (2020): 3379-3402, https://do.org/10.1175/JPO-D-20-0028.1., One of the largest and most persistent features in the Alboran Sea is the Western Alboran Gyre (WAG), an anticyclonic recirculation bounded by the Atlantic Jet (AJ) to the north and the Moroccan coast to the south. Eulerian budgets from several months of a high-resolution model run are used to examine the exchange of water across the Eulerian WAG’s boundary and the processes affecting the salinity, temperature, and vorticity of the WAG. The volume transport across the sides of the WAG is found to be related to vertical isopycnal movement at the base of the gyre. Advection is found to drive a decay in the salinity minimum and anticyclonic vorticity of the Eulerian WAG. Given the large contributions of advection, a Lagrangian analysis is performed, revealing geometric aspects of the exchange that are hidden in an Eulerian view. In particular, stable and unstable manifolds identify a stirring region around the outer reaches of the gyre where water is exchanged with the WAG on a time scale of weeks. Its complement is an inner core that expands with depth and exchanges water with its surroundings on much longer time scales. The 3D evolution of one parcel, or lobe, of water as it enters the WAG is also described, identifying a general Lagrangian subduction pathway., This work was supported on DOD (MURI) Grant N000141110087, ONR Grant N000141812417, and NSF Grant OCE-1558806., 2021-05-18

In Lagrangian dynamics, the detection of coherent clusters can help understand the organization of transport by identifying regions with coherent trajectory patterns. Many clustering algorithms, however, rely on user-input parameters, requiring a priori knowledge about the flow and making the outcome subjective. Building on the conventional spectral clustering method of Hadjighasem et al. (2016), a new optimized-parameter spectral clustering approach is developed that automatically identifies optimal parameters within pre-defined ranges. A noise-based metric for quantifying the coherence of the resulting coherent clusters is also introduced. The optimized-parameter spectral clustering is applied to two benchmark analytical flows, the Bickley Jet and the asymmetric Duffing oscillator, and to a realistic, numerically generated oceanic coastal flow. In the latter case, the identified model-based clusters are tested using observed trajectories of real drifters. In all examples, our approach succeeded in performing the partition of the domain into coherent clusters with minimal inter-cluster similarity and maximum intra-cluster similarity. For the coastal flow, the resulting coherent clusters are qualitatively similar over the same phase of the tide on different days and even different years, whereas coherent clusters for the opposite tidal phase are qualitatively different.

This cruise aimed to identify transport pathways from the surface into the interior ocean during the late winter in the Alborán sea between the Strait of Gibraltar (5°40’W) and the prime meridian. Theory and previous observations indicated that these pathways likely originated at strong fronts, such as the one that separates salty Mediterranean water and the fresher water in owing from the Atlantic. Our goal was to map such pathways and quantify their transport. Since the outcropping isopycnals at the front extend to the deepest depths during the late winter, we planned the cruise at the end of the Spring, prior to the onset of thermal stratification of the surface mixed layer., Funding was provided by the Office of Naval Research under Contract No. N000141613130.

© The Author(s), 2020. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Serra, M., Sathe, P., Rypina, I., Kirincich, A., Ross, S. D., Lermusiaux, P., Allen, A., Peacock, T., & Haller, G. Search and rescue at sea aided by hidden flow structures. Nature Communications, 11(1), (2020): 2525, doi:10.1038/s41467-020-16281-x., Every year, hundreds of people die at sea because of vessel and airplane accidents. A key challenge in reducing the number of these fatalities is to make Search and Rescue (SAR) algorithms more efficient. Here, we address this challenge by uncovering hidden TRansient Attracting Profiles (TRAPs) in ocean-surface velocity data. Computable from a single velocity-field snapshot, TRAPs act as short-term attractors for all floating objects. In three different ocean field experiments, we show that TRAPs computed from measured as well as modeled velocities attract deployed drifters and manikins emulating people fallen in the water. TRAPs, which remain hidden to prior flow diagnostics, thus provide critical information for hazard responses, such as SAR and oil spill containment, and hence have the potential to save lives and limit environmental disasters., We are grateful to Margaux Filippi, Michael Allshouse, Javier González-Rocha, Peter Nolan, Siavash Ameli, Patrick Haley Jr., and the MSEAS team for their contribution in the field experiments. We also acknowledge the NSF Hazard funding grant no. 1520825. S.D.R. acknowledges support from NSF grant no. 1821145. M.S. would like to acknowledge support from the Schmidt Science Fellowship (https://schmidtsciencefellows.org/). G.H. acknowledges support from the Turbulent Superstructures Program of the German National Science Foundation (DFG).

© The Author(s), 2019. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Brett, G. J., Pratt, L., Rypina, I., & Wang, P. Competition between chaotic advection and diffusion: Stirring and mixing in a 3-D eddy model. Nonlinear Processes in Geophysics, 26(2), (2019):37-60, doi:10.5194/npg-26-37-2019., The importance of chaotic advection relative to turbulent diffusion is investigated in an idealized model of a 3-D swirling and overturning ocean eddy. Various measures of stirring and mixing are examined in order to determine when and where chaotic advection is relevant. Turbulent diffusion is alternatively represented by (1) an explicit, observation-based, scale-dependent diffusivity, (2) stochastic noise, added to a deterministic velocity field, or (3) explicit and implicit diffusion in a spectral numerical model of the Navier–Stokes equations. Lagrangian chaos in our model occurs only within distinct regions of the eddy, including a large chaotic “sea” that fills much of the volume near the perimeter and central axis of the eddy and much smaller “resonant” bands. The size and distribution of these regions depend on factors such as the degree of axial asymmetry of the eddy and the Ekman number. The relative importance of chaotic advection and turbulent diffusion within the chaotic regions is quantified using three measures: the Lagrangian Batchelor scale, the rate of dispersal of closely spaced fluid parcels, and the Nakamura effective diffusivity. The role of chaotic advection in the stirring of a passive tracer is generally found to be most important within the larger chaotic seas, at intermediate times, with small diffusivities, and for eddies with strong asymmetry. In contrast, in thin chaotic regions, turbulent diffusion at oceanographically relevant rates is at least as important as chaotic advection. Future work should address anisotropic and spatially varying representations of turbulent diffusion for more realistic models., This work was supported by DOD (MURI) grant no. N0004110087 as well as the US National Science Foundation grants OCE-1154641 and OCE-1558806 and the National Aeronautics and Space Administration (NASA) grant no. NNX14AH29G. Genevieve Jay Brett received additional support from the Woods Hole Oceanographic Institution Academic Programs Office. We also thank Marianna Linz, Dan Collura, and four anonymous reviewers for their constructive input on how to present this material.