Ocean currents transport a variety of natural (e.g. water masses, phytoplankton, zooplankton, sediments, etc.) and man-made materials (e.g. pollutants, floating debris, particulate matter, etc.). Understanding such uncertain Lagrangian transport is imperative for reducing environmental damage due to natural hazards and for allowing rigorous risk analysis and effective search and rescue. While secondary variables and trajectories have classically been used for the analyses of such transports, Lagrangian Coherent Structures (LCSs) provide a robust and objective description of the important material lines. To ensure accurate and useful Lagrangian hazard scenario predictions and prevention, the first goal of this thesis is to obtain accurate probabilistic prediction of the underlying stochastic velocity fields using the Dynamically Orthogonal (DO) approach. The second goal is to merge data from both Eulerian and Lagrangian observations with predictions such that the whole information content of observations is utilized.

In the first part of this thesis, we develop high-order numerical schemes for the DO equations that ensure efficiency, accuracy, stability, and consistency between the Monte Carlo (MC) and DO solutions. We discuss the numerical challenges in applying the DO equations to the unsteady stochastic Navier-Stokes equations. In order to maintain consistent evaluation of advection terms, we utilize linear centered advection schemes with fully explicit and linear Shapiro filters. We then discuss how to combine the semi-implicit projection method with new high order implicit-explicit (IMEX) linear multi-step and multistage IMEX-RK time marching schemes for the coupled DO equations to ensure further stability and accuracy. We also review efficient numerical re-orthonormalization strategies during time marching. We showcase our results with stochastic test cases of stochastic passive tracer advection in a deterministic swirl flow, stochastic flow past a cylinder, and stochastic lid-driven cavity flow. We show that our schemes improve the consistency between reconstructed DO realizations and the corresponding MC realizations, and that we achieve the expected order of accuracy.

In the second part of the work, we first undertake a study of different Lagrangian instruments and outline how the DO methodology can be applied to obtain Lagrangian variables of stochastic flow maps and LCS in uncertain flows. We then review existing methods for Bayesian Lagrangian data assimilation (DA). Disadvantages of earlier methods include the use of approximate measurement models to directly link Lagrangian variables with Eulerian variables, the challenges in respecting the Lagrangian nature of variables, and the assumptions of linearity or of Gaussian statistics during prediction or assimilation. To overcome these, we discuss how the Gaussian Mixture Model (GMM) DO Filter can be extended to fully coupled Eulerian-Lagrangian data assimilation. We define an augmented state vector of the Eulerian and Lagrangian state variables that directly exploits the full mutual information and complete the Bayesian DA in the joint Eulerian-Lagrangian stochastic subspace. Results of such coupled Eulerian-Lagrangian DA are discussed using test cases based on a double gyre flow with random frequency.

The coastal ocean is a prime example of multiscale nonlinear fluid dynamics. Ocean fields in such regions are complex, with multiple spatial and temporal scales and nonstationary heterogeneous statistics. Due to the limited measurements, there are multiple sources of uncertainties, including the initial conditions, boundary conditions, forcing, parameters, and even the model parameterizations and equations themselves. To reduce uncertainties and allow long-duration measurements, the energy consumption of ocean observing platforms need to be optimized. Predicting the distributions of reachable regions, time-optimal paths, and risk-optimal paths in uncertain, strong and dynamic flows is also essential for their optimal and safe operations. Motivated by the above needs, the objectives of this thesis are to develop and apply the theory, schemes, and computational systems for: (i) Dynamically Orthogonal ocean primitive-equations with a nonlinear free-surface, in order to quantify uncertainties and predict probabilities for four-dimensional (time and 3-d in space) coastal ocean states, respecting their nonlinear governing equations and non-Gaussian statistics; (ii) Stochastic Dynamically Orthogonal level-set optimization to rigorously incorporate realistic ocean flow forecasts and plan energy-optimal paths of autonomous agents in coastal regions; (iii) Probabilistic predictions of reachability, time-optimal paths and risk-optimal paths in uncertain, strong and dynamic flows.

For the first objective, we further develop and implement our Dynamically Orthogonal (DO) numerical schemes for idealized and realistic ocean primitive equations with a nonlinear free-surface. The theoretical extensions necessary for the free-surface are completed. DO schemes are researched and DO terms, functions, and operations are implemented, focusing on: state variable choices; DO norms; DO condition for flows with a dynamic free-surface; diagnostic DO equations for pressure, barotropic velocities and density terms; non-polynomial nonlinearities; semi-implicit time-stepping schemes; and re-orthonormalization consistent with leap-frog time marching. We apply the new DO schemes, as well as their theoretical extensions and efficient serial implementation to forecast idealized-to-realistic stochastic
coastal ocean dynamics. For the realistic simulations, probabilistic predictions for the Middle Atlantic Bight region, Northwest Atlantic, and northern Indian ocean are showcased.

For the second objective, we integrate data-driven ocean modeling with our stochastic DO level-set optimization to compute and study energy-optimal paths, speeds, and headings for ocean vehicles in the Middle Atlantic Bight region. We compute the energy-optimal paths from among exact time-optimal paths. For ocean currents, we utilize a data-assimilative multiscale re-analysis, combining observations with implicit two-way nested multi-resolution primitive-equation simulations of the tidal-to-mesoscale dynamics in the region. We solve the reduced-order stochastic DO level-set partial differential equations (PDEs) to compute the joint probability of minimum arrival-time, vehicle-speed time-series, and total energy utilized. For each arrival time, we then select the vehicle-speed time-series that minimize the total energy utilization from the marginal probability of vehicle-speed and total energy. The corresponding energy-optimal path and headings be obtained through a particle backtracking equation. For the missions considered, we analyze the effects of the regional tidal currents, strong wind events, coastal jets, shelfbreak front, and other local circulations on the energyoptimal paths.

For the third objective, we develop and apply stochastic level-set PDEs that govern the stochastic time-optimal reachability fronts and paths for vehicles in uncertain, strong, and dynamic flow fields. To solve these equations efficiently, we again employ their dynamically orthogonal reduced-order projections. We develop the theory and schemes for risk-optimal planning by combining decision theory with our stochastic time-optimal planning equations. The risk-optimal planning proceeds in three steps: (i) obtain predictions of the probability distribution of environmental flows, (ii) obtain predictions of the distribution of exact timeoptimal paths for the forecast flow distribution, and (iii) compute and minimize the risk of following these uncertain time-optimal paths. We utilize the new equations to complete stochastic reachability, time-optimal and risk-optimal path planning in varied stochastic quasi-geostrophic flows. The effects of the flow uncertainty on the reachability fronts and time-optimal paths is explained. The risks of following each exact time-optimal path is evaluated and risk-optimal paths are computed for different risk tolerance measures. Key properties of the risk-optimal planning are finally discussed.

Theoretically, the present methodologies are PDE-based and compute stochastic ocean fields, and optimal path predictions without heuristics. Computationally, they are several orders of magnitude faster than direct Monte Carlo.

Such technologies have several commercial and societal applications. Specifically, the probabilistic ocean predictions can be input to a technical decision aide for a sustainable fisheries co-management program in India, which has the potential to provide environment friendly livelihoods to millions of marginal fishermen. The risk-optimal path planning equations can be employed in real-time for efficient ship routing to reduce greenhouse gas emissions and save operational costs.

The sensitivity of the Bay of Bengal (BoB) upper ocean circulation and thermohaline structure to varying wind strengths and river salinity conditions is investigated using a set of long-term mesoscale simulations. The Regional Ocean Modeling System (ROMS) simulations differ in their forcing fields for winds (strong vs. weak) and in their representations of river input salinity conditions (seasonally varying estuarine salinity vs. zero salinity). The sensitivities are analyzed in terms of the responses of the surface circulation, thermohaline structure, freshwater plume dispersion, and the coastal upwelling along the western boundary. All the simulations reproduce the main broad-scale features of the Bay, while their magnitudes and variabilities depend on the forcing conditions. The impact of stronger wind is felt at greater depths for temperature than for salinity throughout the domain; however, the impact is realized with vertical distributions that are different in the northern than in the southern Bay.

As expected, the stronger wind-induced enhanced mixing lowers (enhances) the upper ocean temperature (salinity) by 0.2C (0.3 psu), and weakens the near-surface stratification. Moreover, stronger wind enhances eddy activity, strengthens the springtime Western Boundary Current (WBC) and enhances coastal upwelling during spring and summer along the east coast of India. The fresher river input reduces the surface salinity and hence enhances the spreading and intensity of the freshwater plume, stratification, and barrier layer thickness. The lower salinity simulation leads to an eddy-dominant springtime WBC, and enhances the freshness, strength, and southward extent of the autumn East India Coastal Current (EICC). The stronger wind simulations appear to prevent the spreading of the freshwater plume during the summer monsoon due to enhanced mixing. Fresher river input reduces the overall surface salinity by ~0.4 psu; however, it significantly underestimates the salinity near the river mouths, whereas the estuarine salinity river input simulations are closer to reality. These results highlight the importance of river input salinity and realistic strong winds in reducing model biases of high-resolution simulations for the Bay of Bengal.