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<p>This thesis presents a method for the design of a predictive controller with variable step sizes.Predictive methods such as receding horizon control (or model predictive control) use aa fixed sampling frequency when updating the inputs. In the proposed method, the switchingtimes are incorporated into an optimization problem, thus resulting in anadaptive step-size control process. The controller with variable timesteps is shown to require less tuning and to reduce the number of expensive model evaluations.An alternate solution approach had to be developed to accommodate the new problem formulation.The controller's stability is proven in a context that does not require terminal cost or constraints.The thesis presents examples that compare the performance of the variable switching time controllerwith the receding horizon method with a fixed step size. This research opens many roads for futureextension of the theoretical work and practical applications of the controller.</p> / Doctor of Science (PhD)

Cold-water corals are an important component of deep-sea ecosystems as they establish structurally complex habitats that support benthic biodiversity. These communities face imminent threats from increasing anthropogenic influences in the deep sea. Following the 2010 Deepwater Horizon blowout, several spill-impacted coral communities were discovered in the deep Gulf of Mexico, and subsequent mesophotic regions, although the exact source and extent of this impact is still under investigation, as is the recovery potential of these organisms. At a minimum, impacted octocorals were exposed to flocculant material containing oil and dispersant components, and were visibly stressed. Here the impacts of oil and dispersant exposure are assessed for the octocoral genus Paramuricea. A de novo reference assembly was created to perform gene expression analyses from high-throughput sequencing data. Robust assessments of these data for P. biscaya colonies revealed the underlying expression-level effects resulting from in situ floc exposure. Short-term toxicity studies, exposing the cold-water octocorals Paramuricea type B3 and Callogorgia delta to various fractions and concentrations of oil, dispersant and oil/dispersant mixtures, were also conducted to determine overall toxicity and tease apart the various components of the synergistic exposure effects. Finally, alterations in Paramuricea B3 gene expression profiles were inspected to characterize genome-wide changes induced by each treatment and putative genes under differential regulation. The experimental results provide evidence for a relatively high toxicity of chemical dispersants as compared to oil additions alone, elucidating the implications of applying oil dispersants to future oil spills. My findings revealed signatures of cellular stress in floc-exposed corals associated with xenobiotic metabolism, immune and inflammatory responses as well as transcriptional suppression of vital cellular components like ribosomal proteins. The data also suggests poor recovery potential in our coral samples exposed to floc. In addition, promising biomarker candidates were identified from the differential expression data for use in future spill-impact monitoring. / Biology

This dissertation addresses path planning for an autonomous vehicle navigating in a two dimensional environment for which an a priori map is inaccurate and for which the environment is sensed in real-time. For this class of application, planning decisions must be made in real-time. This work is motivated by the need for fast autonomous vehicles that require planning algorithms to operate as quickly as possible. In this dissertation, we first study the case in which there are only static obstacles in the environment. We propose a hybrid receding horizon control path planning algorithm that is based on level-set methods. The hybrid method uses global or local level sets in the formulation of the receding horizon control problem. The decision to select a new level set is made based on certain matching conditions that guarantee the optimality of the path. We rigorously prove sufficient conditions that guarantee that the vehicle will converge to the goal as long as a path to the goal exists. We then extend the proposed receding horizon formulation to the case when the environment possesses moving obstacles. Since all of the results in this dissertation are based on level-set methods, we rigorously investigate how level sets change in response to new information locally sensed by a vehicle. The result is a dynamic fast marching algorithm that usually requires significantly less computation that would otherwise be the case. We demonstrate the proposed dynamic fast marching method in a successful field trial for which an autonomous surface vehicle navigated four kilometers through a riverine environment. / Ph. D.

Oil spills have long been recognized as a significant threat to wildlife. Historically, mortality estimates have served as the basis for assessing impact to natural resources. However, these mortality estimates alone neglect the more wide-spread impact of oil spills on wildlife including birds, many of which may not immediately succumb to exposure, but instead suffer sublethal injury that may negatively affect physiological homeostasis, reproduction, and long-term survival. Therefore, there is a need to improve our understanding of the risk of exposure and effect of sublethal oiling during damage assessments. In this dissertation I evaluated the extent of sublethal oil exposure in the immediate aftermath of the Deepwater Horizon spill on American oystercatchers (Haematopus palliatus), black skimmers (Rynchops niger), brown pelicans (Pelecanus occidentalis), clapper rails (Rallus crepitans), and seaside sparrows (Ammodramus maritimus) through both visual evaluation of and under the application of ultraviolet light to individual birds potentially exposed to oil. I found that there were many individual birds with modest oil exposure, demonstrating that more birds are exposed to oil than are accounted for by mortality estimates. Additionally, I developed a field-adapted technique using an in vitro method in brown pelicans that was effective in determining oxidative hematologic injury as measured by a suite of parameters including a reduction in circulating erythrocytes and hemoglobin, formation of Heinz bodies, and an increase in reticulocytes, in birds exposed to oil. I then applied this suite of parameters to individual birds affected in the aftermath of the Deepwater Horizon spill, and found that birds with modest visible or UV-detectible oil exposure suffer hematologic injury, a quantifiable adverse sublethal effect of modest oil exposure. Finally, I used an experimental approach to evaluate the pathologic effects of crude oil exposure in zebra finches (Taeniopygia guttata), evaluating the same suite of hematologic parameters as well as gross pathology, histopathology, and electron microscopy. This controlled study provided evidence that there may be significant variability in the response of birds to oil exposure that may be attributable to species-specific sensitivity and/or other factors such as the use of dispersants after oil spills. Collectively, this body of work demonstrated that many more birds are exposed to oil during spill events than are accounted for by mortality estimates alone, and that these birds can suffer quantifiable sublethal hematologic injury. The ability to accurately assess the extent of exposure and hematologic damage caused by oil spills is critical to determine the appropriate approach to management needed to offset impacts to fisheries, wildlife, habitats, and economic resources impacted by oil spills. / Doctor of Philosophy / Fossil fuels are the world's primary energy source and are an important part of everyday life. Our reliance on petroleum requires extraction, transportation, storage, and refinement of millions of gallons of crude oil each day. As an unintended consequence, some of this oil is inadvertently spilled into the environment, and these oil spills have long been recognized as a threat to wildlife. Assessing the impact of oil spills on wildlife is a major concern to industries, government, and the general public. Historically, mortality estimates have served as the basis for assessing impact to natural resources. However, these mortality estimates alone neglect the more wide-spread impact of oil spills on wildlife including birds, many of which may not immediately succumb to exposure, but instead suffer sublethal physiologic injury that negatively affects physiology, reproduction, and long-term survival. Therefore, there is a need to improve our understanding of the risk of exposure and effects of sublethal oiling during damage assessments. In this dissertation, I evaluated the extent of sublethal exposure to oil from The Deepwater Horizon spill for several species of birds through both visual evaluation of and under the application of ultraviolet light. This demonstrated that many more birds are affected by oil exposure than are accounted for by mortality estimates. Additionally, I developed a field-adapted technique in a controlled setting that is effective in determining oxidative injury to red blood cells in birds exposed to oil, and applied this approach to several species in the field during the aftermath of the Deepwater Horizon spill. Finally, I used an experimental approach to evaluate the extent of pathologic effects of Deepwater Horizon crude oil exposure in individuals under controlled dosages. The ability to accurately assess the extent of damage caused by oil spills is critical to determine the appropriate approach to management needed to offset impacts to fisheries, wildlife, habitats, and economic resources impacted by oil spills.

This work is inspired by robotic search applications where a robot or team of robots is equipped with sensors and tasked to autonomously acquire as much information as possible from a region of interest. To accomplish this task, robots must plan paths through the region of interest that maximize the effectiveness of the sensors they carry. Receding horizon path planning is a popular approach to addressing the computationally expensive task of planning long paths because it allows robotic agents with limited computational resources to iteratively construct a long path by solving for an optimal short path, traversing a portion of the short path, and repeating the process until a receding horizon path of the desired length has been constructed. However, receding horizon paths do not retain the optimality properties of the short paths from which they are constructed and may perform quite poorly in the context of achieving the robotic search objective. The primary contributions of this work address the worst-case performance of receding horizon paths by developing methods of using terminal rewards in the construction of receding horizon paths. We prove that the proposed methods of constructing receding horizon paths provide theoretical worst-case performance guarantees. Our result can be interpreted as ensuring that the receding horizon path performs no worse in expectation than a given sub-optimal search path. This result is especially practical for subsea applications where, due to use of side-scan sonar in search applications, search paths typically consist of parallel straight lines. Thus for subsea search applications, our approach ensures that expected performance is no worse than the usual subsea search path, and it might be much better. The methods proposed in this work provide desirable lower-bound guarantees for a single robot as well as teams of robots. Significantly, we demonstrate that existing planning algorithms may be easily adapted to use our proposed methods. We present our theoretical guarantees in the context of subsea search applications and demonstrate the utility of our proposed methods through simulation experiments and field trials using real autonomous underwater vehicles (AUVs). We show that our worst-case guarantees may be achieved despite non-idealities such as sub-optimal short-paths used to construct the longer receding horizon path and unreliable communication in multi-agent planning. In addition to theoretical guarantees, An important contribution of this work is to describe specific implementation solutions needed to integrate and implement these ideas for real-time operation on AUVs. / Doctor of Philosophy / This work is inspired by robotic search applications where a robot or team of robots is equipped with sensors and tasked to autonomously acquire as much information as possible from a region of interest. To accomplish this task, robots must plan paths through the region of interest that maximize the effectiveness of the sensors they carry. Receding horizon path planning is a popular approach to addressing the computationally expensive task of planning long paths because it allows robotic agents with limited computational resources to iteratively construct a long path by solving for an optimal short path, traversing a portion of the short path, and repeating the process until a receding horizon path of the desired length has been constructed. However, receding horizon paths do not retain the optimality properties of the short paths from which they are constructed and may perform quite poorly in the context of achieving the robotic search objective. The primary contributions of this work address the worst-case performance of receding horizon paths by developing methods of using terminal rewards in the construction of receding horizon paths. The methods proposed in this work provide desirable lower-bound guarantees for a single robot as well as teams of robots. We present our theoretical guarantees in the context of subsea search applications and demonstrate the utility of our proposed methods through simulation experiments and field trials using real autonomous underwater vehicles (AUVs). In addition to theoretical guarantees, An important contribution of this work is to describe specific implementation solutions needed to integrate and implement these ideas for real-time operation on AUVs.

Shallow groundwater flow in the critical zone of steep headwater mountain catchments is often assumed to mimic surface topography. However, groundwater flow is influenced by other variables, such as the elevation of the water table and subsurface hydraulic conductivity, which can result in temporal variations in both magnitude and direction of flow. In this study, I investigated the temporal variability of groundwater flow in the soil zone (solum) within the critical zone of a headwater catchment at the Hubbard Brook Experimental Forest in North Woodstock, NH. Groundwater levels were continuously monitored throughout several seasons (March 2019 to Jan 2020) in a network of wells comprising three hillslope transects within the upper hillslopes of the catchment. Five clusters of three wells per cluster were screened from 0.18 – 1.1 m depth at the base of the solum. Water levels were also monitored in five deeper wells, screened from 2.4 - 6.9 m depth within glacial sediments of the C horizon. I conducted 47 slug tests across the well network to determine hydraulic properties of the aquifer materials surrounding each well. In addition, our team conducted a large-scale auger investigation mapping soil horizon depths and thicknesses. Results show that the magnitude of hydraulic gradients and subsurface hydrologic fluxes varied at each site with respect to changing water-table elevation, having a maximum range of 0.12 m/m and 9.19 x 10-6 m/s, respectively. The direction of groundwater flow had an arithmetic mean deviating from surface topography by 2-10 degrees, and a total range that deviated from surface topography by as much as 51 degrees. During lower water table regimes, groundwater flow direction deviated from the ground surface, but under higher water table regimes, in response to recharge events, flow direction mimicked surface topography. Within most of the well clusters, there is an observable connection between the slope direction of the top of the C horizon and the direction of groundwater flow during lower water table regimes. Slug test results show the interquartile range of saturated hydraulic conductivity (Ksat) within the C horizon (1.5×10-7 to 9.8×10-7 m/s) is two orders of magnitude lower than the interquartile range of Ksat values within the solum (2.9×10-5 to 5.2×10-5 m/s). Thus, the C horizon is on average a confining unit relative to the solum that may constrict groundwater flow below the solum. Additionally, results from the larger scale auger investigation suggest that deviations in subsurface topography of the C horizon may be generalizable at the larger hillslope scale. Overall, these results indicate that 1) shallow groundwater flow direction and magnitude within this headwater catchment are dynamic and can deviate from surface topography, and 2) the subsurface topography of the C horizon can influence groundwater flow direction. These results imply that temporal dynamics of groundwater flow direction and magnitude should be considered when characterizing subsurface flow in critical zone studies. Additionally, knowledge of subsurface topography of confining units may provide constraints on the temporal variability of groundwater flow direction. / M.S. / Streams that originate at higher elevations (defined as headwater streams) are important drinking water sources and deliver water and nutrients to maintain freshwater ecosystems. Groundwater is a major source of water to these streams, but little is known about how groundwater flows in these areas. Scientists delineate watersheds (areas of land that drain water to the same point) using surface topography. This approach works well for surface water, but not as well for groundwater, as groundwater may not flow in the same direction as surface water. Thus, assuming that the ground-watershed is the same as the surface watershed can lead to errors in hydrologic studies. To obtain more accurate information about groundwater flow in headwater areas, I continuously measured groundwater levels in forest soils at the Hubbard Brook Experimental Forest in North Woodstock, NH. My main objective was to determine if there is variability in the direction and amount of groundwater flow. I also measured the characteristics of the soils to identify the thicknesses of soil units and the permeability of those units. I used these data to evaluate the relationship between groundwater flow direction, surface topography, and the permeability of soil units. Overall, I found that groundwater flow direction can differ significantly from surface topography, and groundwater flow direction was influenced by the groundwater levels. When groundwater levels were high (closer to the land surface), groundwater flow was generally in the same direction as surface topography. However, when groundwater levels were lower, flow direction typically followed the slope of the lowest permeability soil unit. These results suggest that scientists should not assume that groundwater flow follows the land surface topography and should directly measure groundwater levels to determine flow direction. In addition, results from this study show that characterizing soil permeability can help scientists make more accurate measurements of groundwater flow.

This thesis studies the relationship between the internal characteristics of the site, based on an existing set of artifacts, abandoned concrete railroad trestles, and external views of them. The project establishes orthogonal and non-orthogonal geometries in re-developing this urban site creating buildings that relate to the site, surroundings, and themselves. The physical, structural connections and spatial relationships reconcile the superimposition of geometries. Ultimately every decision in the project returns to the analysis of the site allowing for different buildings, people, and environments to interact as a single entity. / Master of Architecture