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ItemSurface Gravity Waves in Global Climate Models: Development, Evaluation and Optimization(Georgia Institute of Technology, 2023-07-25) Ikuyajolu, Olawale JamesSurface gravity waves play a critical role in several processes at the air-sea interface, including mixing, coastal inundation, and surface fluxes. Yet wind–wave processes are usually excluded from Earth system models partly due to a lack of physical understanding and the high computational costs of spectral wave models. Most wave modeling studies utilize uncoupled short-term simulations and focus on the upper ocean. The impacts of wind-wave processes on coupled climate variability have yet to be thoroughly evaluated. This all underscores the need to advance surface gravity wave modeling frameworks within general circulation models (GCMs). Herein, the first half of this thesis partly addresses the high computational cost of running spectral wave models on a global grid. I identify the wave action source terms as the most computationally intensive part of the spectral wave model WAVEWATCH III (WW3), and then accelerate them on Graphics Processing Units (GPUs) using OpenACC. An average speedup of 1.4x was achieved, resulting in a reduction of 35-40% in runtime and resource usage. In the second half of this thesis, I incorporated a wave-state dependent bulk formula by fully coupling WW3 to the Energy Exascale Earth System Model (E3SM). Current state of the science GCM bulk parameterizations estimate the sea-state roughness as a function of surface wind speed, ignoring wave effects. The newly implemented parameterization includes two primary wave effects: first, a wave-state dependent surface roughness computed by WW3; second, the alteration of momentum flux from the atmosphere to the ocean due to wave growth and dissipation. I conducted numerical experiments with this new parameterization to investigate the sensitivity of the mean climate and Madden-Julian Oscillation (MJO) to different bulk flux parameterizations and the role of waves in air-sea coupling. My results highlight that discrepancies between bulk algorithms have nonnegligible impacts on mean climate such as ocean heat content, sea-ice concentration and a 2℃ difference in sea surface temperature in the North Atlantic. Also, the proper treatment of air-sea coupling via the inclusion of wave-induced effects improves the simulation of MJO. Most importantly, the analysis emphasizes the importance of considering the role of waves in redistributing momentum flux between the atmosphere and the ocean, especially in coastal and high-latitude regions. This work is key to enhancing the capability of future GCMs to simulate coastal changes and extreme events.
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ItemThe impacts of climate variability and change on the physical and social-ecological dynamics of the Kuroshio and North Pacific Transition Zone(Georgia Institute of Technology, 2022-12-08) Navarra, Giangiacomo GiacomoThere is growing recognition that climate change is impacting the ocean's western boundary current system. In the Pacific, the Kuroshio and its offshore Kuroshio-Oyashio Extension (KOE) play a central role in the North Pacific climate and impact the social-ecological dynamics of countries that rely on marine ecosystem services (e.g. fisheries). In the thesis, we have used a combination of observations and modeling approaches to understand how past and projected changes in the physical environment of KOE impact social-ecological dynamics linked to the fish industry of Japan and the North Pacific more widely. The thesis is articulated in 3 Chapters. In Chapter 1 we have introduced the problem and the main motivation that lead us to perform this study. In Chapter 2, we analyze the climate variability and change of the KOE over the historical and future projection period 1920-2100. We perform this task using Coupled Model Intercomparison Project 5 (CMIP5) models and a large ensemble from the Community Earth System Model (CESM-LE) output runs. The reason for considering also the CESM-LE runs is that they give the possibility to explore how the variance of the KOE in one model (e.g. a fixed set of dynamics) responds to anthropogenic forcing when compared to the range of natural variability of the CESM-LE model. In this way, we can perform a scenario which goes beyond the time of the observational data. In Chapter 3, we have used an Empirical Dynamical Model approach to characterize the joint statistics of the physical and social-ecological environmental system (SEES) that is relevant to climate and fisheries. To define the states of the SEES we use three international fish databases, (1) the Large Marine Ecosystem (LME, 9,000 fish stocks), (2) the NOAA fishery database referred to as Restricted Access Management (RAM, 300 fish stock) and the (3) the Food and Agriculture Organization (FAO, 1400 fish stocks). Among the approaches used to explore the relationship between KOE’s climate and the SEES response, we have developed a Linear Inverse Model (LIM) approach that has been very successful to simulate and predict the KOE physical climate and its relation to large-scale Pacific dynamics such as El Niño Southern Oscillation (ENSO), the Pacific Decadal Oscillation (PDO), and others.
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ItemDeep biosphere microbial protein interactions with clathrates(Georgia Institute of Technology, 2022-05-02) Johnson, Abigail MarieGas clathrates are composed of a latticework of water molecules that trap guest gas molecules and form at high pressure and low temperatures. Methane clathrates along continental margins and in permafrost store thousands of gigatons of carbon in sediments and serve as a habitat for a unique deep subsurface biosphere. Microbes in gas clathrate-bearing sediments may influence clathrate stability and thereby play a role in the release of greenhouse gases to overlying sediments. Gas clathrates also pose a clogging hazard in natural gas pipelines, which has led to a search for environmentally friendly gas clathrate inhibitors. Antifreeze proteins (AFPs) were found to bind to gas clathrates and suppress clathrate growth. This dissertation evaluated whether proteins from methane clathrate-bearing sediment microbes influence clathrate growth and morphology. Bacterial protein sequences with sequence similarity to alpha helical Type I AFPs in cold-water fish were identified in metagenomes from gas clathrate-bearing sediment from Hydrate Ridge, offshore Oregon, and Shimokita Peninsula, offshore Japan. In the search for AFP-like sequences, two Type I AFP amino acid motifs were used as search queries of Hydrate Ridge metagenomes. Homology modeling software and antifreeze prediction software were used to predict antifreeze properties of the resulting sequences. Homologous sequences with predicted antifreeze properties from sediments in Hydrate Ridge were also detected in Shimokita Peninsula sediments. These Clathrate-Binding Protein (CBP) genes (cbpA) and upstream genes (cbpB,C,D) are likely from Dehalococcoidia bacteria, of the phylum Chloroflexi, which are known to occur in methane clathrates. To date, CBPs are unique to gas clathrates. Recombinantly expressed CbpAs were first tested on tetrahydrofuran (THF) clathrate, a structure II clathrate that is stable at atmospheric pressures and 4˚C. In the absence of CbpAs, large (~1 cm diameter) single THF clathrate crystals formed. In the presence of Type I AFPs, CbpA2, and CbpA3, small branching THF clathrate crystals formed. In the presence of CbpA5 and CbpA6, THF clathrates formed a few flat, interconnected sheets with hexagonal growth parallel to the [1 1 1] crystal face. Like Type I AFPs, CbpA, were concentrated in the clathrate crystal compared to the controls and Green Fluorescent Protein labeled CbpAs were observed to bind to THF clathrate. These data show that CbpAs bind to and alter the morphology of THF clathrate and the different morphologies likely represent two distinct binding modes. I then tested the effect of CbpAs on growth of methane clathrate using a high-pressure cell. Methane clathrate shells were synthesized on water droplets at 5 MPa in the presence or absence of CbpAs. Gas consumption was determined after depressurization. Significantly less methane clathrate formed in the presence of CbpAs and the commercial gas clathrate inhibitor, polyvinylpyrrolidone, relative to controls. Type I AFP did not significantly alter methane clathrate formation compared to controls at the high driving force used in this study. Dome-shaped shells formed in treatments with suppressed clathrate growth, whereas treatments with more clathrate formed cratered shells. Overall, I found that CbpAs alter methane clathrate morphology and inhibit methane clathrate formation similarly to the commercial inhibitor, polyvinylpyrrolidone. Discovery of clathrate-binding proteins in gas clathrate-bearing sediments is unprecedented and has many implications: climate change, natural gas pipeline flow assurance and transport, microbial survival strategies, and searching for life on other planetary bodies. CBPs produced by microbes living in clathrate-bearing sediments may be useful as an ecofriendly clathrate inhibitor in natural gas pipelines. CBPs may influence clathrate stability in situ, with important climate impacts. CBPs should be considered in astrobiology as a potential microbial habitat when searching for life on other planetary bodies.
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ItemCrustacean Behavior and Morphology in Low and Intermediate Reynolds Number Environments(Georgia Institute of Technology, 2022-05-02) Ruszczyk, MelissaAn organism’s physical environment can dramatically affect an organisms’ behavior and morphological design. The Reynolds number represents the ratio between inertial and viscous forces in a fluid environment. This study is concerned with the challenges crustaceous plankton face resulting from living in a low- and intermediate-Reynolds number aquatic environment. In the first part of this study, the freshwater copepod Hesperodiaptomus shoshone is exposed to a Burgers vortex- a flow feature meant to mimic turbulent eddies found in an organism’s environment. Male and female copepods were exposed to four vortex intensity levels plus a negative control in either a horizontal or vertical orientation of the vortex axis. Trajectory analysis of H. shoshone swimming behavior shows that this copepod changes its swimming behavior in response to vortex orientation and not vortex level- a notable difference from marine copepods exposed to the same flow feature. These results may be linked to ecological and geographic differences between freshwater and marine copepods. In the second part of this study, the pleopod synchrony in the mysid shrimp Americamysis bahia is quantified. Shrimp and krill beat their pleopods in an adlocomotory sequence, creating a metachronal wave. Usually, pleopod pairs on the same abdominal segment beat in tandem with each other, resulting in one 5-paddle stroke. Americamysis bahia’s pleopods on the same abdominal segment beat independently from each other, resulting in two 5-paddle metachronal cycles that run ipsilaterally along the body, 180° out of phase with each other. High-speed recordings of A. bahia stroke kinematics reveal how this mysid changes its stroke amplitude, beat frequency, and inter-appendage phase lag to achieve high speeds. Trends with Strouhal number and advance ratio suggest that the stroke kinematics of metachrony in A. bahia are tuned to achieve large normalized swimming speeds. In the third part of this study, stroke kinematics in Pacific krill, Euphausia pacifica, are quantified for the first time. Euphaisia pacifica (1-3cm body length) achieve similar swimming modes as the larger E. superba (4-6cm body length) through a different set of stroke kinematics. To better understand the relationship between stroke kinematics, resulting swimming mode, and length scale, these data are used in tandem with previously published stroke kinematics of other 5-paddle metachronal swimmers, including mysid shrimp and stomatopods, to identify broad trends across species and length scale in metachrony. Principle component analysis (PCA) reveals trends in stroke kinematics, Reynolds number, and swimming mode as well as variation among taxonomic order. Additionally, uniform phase lag, i.e. when the timing between power strokes of all adjacent pleopods is equal, in 5-paddles systems is achieved at different Reynolds numbers for each swimming mode, which highlights the importance of taking into consideration stroke kinematics, length scale, and resulting swimming mode in bio-inspired design applications.