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Characterization and Optimization of a Fully Passive Flapping Foil in an Unsteady Environment for Power Production and Propulsion
Get PDFThis thesis provides an experimental window into the duality between thrust production and energy harvesting by a flapping foil subject to unsteadiness in an oncoming flow. In particular, an airfoil is placed downstream of a circular cylinder, and allowed to interact with the vorticity shed in its wake to produce motions in both the transverse and streamwise directions. It is confirmed that under the right conditions, passive fluid-structure interactions arising from such a configuration give rise to simultaneous extraction of energy from the flow, coupled with net thrust larger than net drag experienced by the airfoil.
Measurements of forces acting on the airfoil and the motion that arises are presented, for cases where the flapping motion is both active (the foil is driven through a pre-planned trajectory) and fully passive (the foil is allowed to react to the fluid forcing it experiences). These are coupled with simultaneous Particle Image Velocimetry (PIV) measurements of the flow field in the region of the airfoil. These measurements allow for direct observation of fluid-structure interactions which give rise to both thrust production and power extraction potential, illuminating the mechanisms driving each. The dynamics of a fully passive flapping foil are largely determined by the mounting system used to facilitate its motion. It is shown that by leveraging Cyber-Physical Fluid Dynamics (CPFD) capabilities to tune these mounting parameters, the behaviour of a fully passive flapping foil can be made similar to that of a representative driven system. A framework based on a simplified linear model for mounting system dynamics is presented, to allow for the optimization of such a system for power extraction potential subject to relevant engineering constraints. The effects of nonlinearity on airfoil behaviour, particularly those due to friction in the mechanism(s) permitting passive flapping, are also explored. Finally, two-dimensional motion of a fully passive flapping foil is demonstrated, allowing for the foil to travel upstream against the oncoming flow solely due to forces induced by interactions with oncoming unsteadiness.</p
Three Essays on Survey Methods and their Applications to Measuring Political Behavior and Attitudes
Get PDFIn this thesis, I develop survey methods and apply them to measure political behavior or attitudes more accurately. Two of the challenges to researchers in measuring political behavior or attitudes are respondents’ reluctance to respond to sensitive questions truthfully and respondents' inattention to providing accurate responses. I contribute to advancing survey methodology to tackle these challenges.
Eliciting truthful answers from respondents on sensitive issues is a difficult problem in surveys, and list experiments emerge as the most popular indirect questioning technique to do so among political scientists and sociologists. The analysis of list experiments depends on two assumptions, known as "no design effect" and "no liars." The no liars assumption is strong and may fail in many list experiments. In Chapter II (published in Political Analysis), I relax the no liars assumption and develop a method to provide bounds for the prevalence of sensitive behaviors or attitudes under a weaker behavioral assumption. I apply the method to a list experiment on the anti-immigration attitudes of California residents and a broad set of existing list experiment datasets. My results indicate that the bounds tend to be narrower when the list consists of items of the same category, such as multiple groups or organizations, different corporate activities, and various considerations for politician decision-making. The contribution of my paper is to illustrate when the full power of the no liars assumption is most needed to pin down the prevalence of the sensitive behavior or attitudes, and to facilitate analysis of list experiments robust to violations of the no liars assumption.
Over the past two decades, the environment in which respondents participate in surveys and polls has changed, with shifts from interviewer-driven to respondent-driven surveying, and from probability to nonprobability sampling. One consequence of these technological changes is that survey respondents in these environments may be less attentive to survey questions. In Chapter III (published in Political Analysis), co-authored with R. Michael Alvarez, Lonna Atkeson, and Ines Levin, we study respondent attention and its implications using data from a self-completion online survey that identified inattentive respondents using instructed-response items (IRIs), a simple attention check that received little scholarly attention. Our results demonstrate that ignoring attentiveness provides a biased portrait of the distribution of critical political attitudes and behavior of both sensitive and more prosaic nature, and results in violations of key assumptions underlying experimental designs. We discuss four approaches to dealing with inattentiveness in surveys and when these approaches are appropriate.
Attention checks, in the form of instructional manipulation checks (IMCs) or instructed response items (IRIs), are useful tools for survey quality control. However, due to the lack of ground truth information, these previous works rely on various post hoc measures to evaluate the performance of attention filters. For the same reason, it has also been impossible to evaluate the performance of different statistical approaches to dealing with inattentive respondents. In Chapter IV, co-authored with R. Michael Alvarez, we conduct a first validation study by analyzing a large-scale post-election survey following the November 2018 General Election and validating survey responses at the individual level using administrative records. Our results show that for each type of attention check, respondents failing the check provided responses with lower accuracy than respondents passing it. We compare the performance of different approaches to dealing with inattentive respondents in the study of turnout and voting method, two variables of substantive interest that are available from the administrative record, and conclude that the best strategy depends on a bias-variance trade-off that also accounts for the correlation between respondent attention and the outcome variables of interest.</p
A Bubble Is Born: Nucleation and Early Growth of CO₂ Bubbles in Polymer Foams
Get PDFGas bubble nucleation is a fundamental phenomenon both throughout the natural sciences and in the production of foams for lightweight, functional materials; it is also the basis for many a bubbly beverage. Enhancing bubble nucleation in polyurethane insulating foams used for refrigeration can further reduce their low thermal conductivity without resorting to hazardous blowing agents used in the past. Experimental challenges of measuring the kinetics of the rapid, multiscale process of bubble nucleation pose a roadblock to investigation of suitable processing conditions, as well as the development of theoretical models of bubbles and foams.
Here, using a microfluidic flow-focusing technique developed for measurement of protein and chemical kinetics, we built a microfluidic cell to probe gas bubble nucleation of CO₂ in polyol, a model system for polyurethane insulating foams, at controlled pressure with millisecond resolution over acquisition times sufficient for optical, IR, and X-ray measurements. This technique allows for repeated measurements of bubble nucleation at any degree of supersaturation without the interference of heterogeneous nucleation from surfaces. By extrapolating a model fit to high-speed optical microscopy measurements of bubble growth backward in time, we estimated the degree of supersaturation at nucleation for thousands of bubbles. Estimates of the nucleation rate based on Poisson statistics were consistent with predictions by a string method model based on density functional theory and G-ADSA measurements. This model predicted that the addition of cyclopentane (a common physical blowing agent in polyurethane foams) can dramatically reduce the nucleation energy barrier due to the formation of a liquid-like layer of cyclopentane and CO₂ along the surface of the bubble that reduces the interfacial tension, which previous models have only predicted at significantly higher saturation pressures. This prediction was supported by thermodynamic measurement of a three-phase coexistence under similar conditions, which is a known fingerprint for such nucleation pathways, and measurement of significantly higher bubble nucleation rates upon the addition of cyclopentane. These findings shed light on the possibility of a previously unappreciated role of physical blowing agents like cyclopentane in enhancing bubble nucleation by opening up a qualitatively distinct and more favorable nucleation pathway.</p
Axial Descent of Multirotor Configurations -- Experimental Studies for Terrestrial and Extraterrestrial Applications
Get PDFAxial descent, specifically the vortex ring state (VRS), poses great challenges for rotorcraft operation as this flight stage is typically accompanied by severe aerodynamic losses and excessive vibrational loads due to the re-ingestion of rotor downwash. Given the hazardous nature of this flight stage, its fluid dynamic properties in regards to single, large-scale rotors have been extensively investigated since the early stages of manned helicopter flight. In light of the rapidly expanding use of small-scale multirotor systems, the field of VRS research has recently received increased interest, with a shifted focus towards small-scale rotors, as the thrust generation and stability of these aerial systems have also been shown to be adversely affected by complex descent aerodynamics. While experimental studies have started examining low Reynolds number rotor aerodynamics in steep or vertical descent, the influence of small-scale rotor geometry and aerodynamic coupling between neighboring rotors have not yet been sufficiently explored.
The objective of this work is, therefore, to extend the current understanding of rotorcraft vortex ring state aerodynamics to low Reynolds number multirotor systems. A series of experimental studies employing various wind tunnel setups and flow visualization techniques is presented with the aim of identifying the underlying fluid-structure interactions, and quantifying rotor performance losses during multirotor axial descent. The work is divided into two fundamental experimental approaches, one utilizing statically mounted rotor systems and one utilizing free-flight testing.
The first part of this work (Chapters 4 and 5) presents the results of wind-tunnel tested statically-mounted rotors for precise aerodynamic identification of rotor performance under simulated descent conditions. Chapter 4 covers a parametric analysis to comprehensively assess the extent to which relevant geometric parameters of a small-scale rotor influence its descent characteristic. Chapter 5 then explores the influence of separation between rotors and identifies potential rotor-rotor interactions in the VRS. The studies in this part of the thesis also make use of PIV setups for visualizing the flow field around small-scale rotors in the axial descent regime, subject to changing geometric parameters and rotor separation.
In the second part (Chapters 6 and 7), a series of free-flight investigations is described for realistically simulated axial descent scenarios. Chapter 6 introduces the methodology for quantifying thrust generation of a multirotor in free-flight without rigid attachment to a load cell, and presents the results of exploratory axial flight studies. Chapter 7 discusses a study on axial descent of variable-pitch multirotor configurations, which was carried out to evaluate the feasibility of deploying a future Mars helicopter in mid air. Findings from this study helped to inform the entry descent and landing (EDL) strategy for JPL's future Martian rotorcraft missions.</p
Engineering the Tryptophan Synthase β-Subunit for Synthesis of Noncanonical Amino Acids
Get PDFThe tryptophan synthase β-subunit (TrpB) naturally catalyzes a pyridoxal phosphate cofactor-mediated β-substitution reaction between indole and serine to form L-tryptophan. Almost half a century ago, it was realized that TrpB could accept nucleophiles other than indole to synthesize noncanonical amino acids (ncAAs), which are highly useful small-molecule building blocks that are found in many bioactive molecules. Since then, TrpB has been applied to synthesize a wide range of ncAAs. This thesis details the engineering of TrpB for synthesis of new and useful ncAAs and the application of TrpB as a model to study the principles that govern intra-protein interactions. Chapter I chronicles the history of tryptophan synthase, provides useful information about the enzyme’s catalytic cycle, and describes how TrpB has been used to synthesize ncAAs in works preceding this thesis. Chapter II describes the evolution, application, and characterization of TrpB for the synthesis of a blue, fluorescent noncanonical amino acid β-(1-azulenyl)-L-alanine (AzAla). Chapter III details the engineering and mechanistic characterization of TrpB to asymmetrically catalyze C–C bond formation with an entirely new class of nucleophile: ketones. Chapter IV describes the in vivo continuous evolution of TrpB which resulted in sequence-diverse TrpB orthologs that have been adapted to function at lower temperatures and display a range of substrate-selectivity profiles. Chapter V describes the development of a deep mutational scanning experiment of combinatorial site-saturation mutagenesis (SSM) libraries for generating a large dataset that maps enzyme sequence to function for the purpose of studying epistasis with machine learning. Overall, the work presented in this thesis expands the repertoire of ncAAs that can be synthesized by TrpB and demonstrates unique applications of TrpB as a model enzyme for continuous in vivo directed evolution and for generating a dataset that will be useful to the protein machine learning community.</p
Neural Crest and Placodal Cells Contributions to Cranial Sensory Development
Get PDFThe sensory system of vertebrates is incredibly complex. Many important components of the sensory system are located within the cranial region, including the sense organs and cranial sensory ganglia. Early in development two progenitor populations, the neural crest and the cranial placodes, arise at the neural plate border and throughout vertebrate development contribute to the developing vertebrate peripheral sensory system. The interactions and contributions of both of these cell populations to the development of the pituitary system, the eyes, the nose, the ears, and the cranial ganglia of the head and neck are vital for the appropriate development of an embryo’s nervous system.
In this dissertation we explore the contributions of both the neural crest and placodal cells to the sensory system of the developing embryo. In Chapter 1 we review the origin of these two cell populations at the neural plate border and give an overview of the development of the various cranial peripheral sensory systems and their placode and neural crest contributions.
In Chapter 2 we use replication incompetent avian retroviruses to lineage trace both the olfactory placode and the neural crest to their respective cellular contributions in the olfactory system. We confirm previous studies which showed that GnRH neurons of the nose receive contributions from both the olfactory placode and the neural crest and we show that both the olfactory placode and the neural crest contribute to the olfactory neurons of the olfactory epithelium. However, neural crest alone gives rise to the olfactory ensheathing cells which are critical for neuronal migration from the olfactory epithelium to the forebrain. We also show for the first time that the neural crest gives rise to the p63 positive horizontal basal stem cell population of the olfactory epithelium.
In Chapter 3, along with collaborators from SUNY Buffalo, we show that multipotent and functional NC cells can be derived by induction with a growth factor cocktail containing FGF2 and IGF1 from cultures of human inter-follicular keratinocytes (KC) isolated from elderly donors. They also maintained their multipotency, as evidenced by their ability to differentiate into all NC-specific lineages including neurons, Schwann cells, melanocytes, and smooth muscle cells (SMC). Notably, upon implantation into chick embryos, adult NC cells behaved similar to their embryonic counterparts, migrated along stereotypical pathways, and contributed to multiple NC derivatives in ovo. These results suggest that KC-derived NC cells may provide an easily accessible, autologous source of stem cells that can be used for treatment of neurodegenerative diseases or as a model system for studying disease pathophysiology and drug development.
Finally, in Chapter 4 we discuss future directions and experiments that I plan to pursue post-graduation. I propose to conduct a closer examination of the variants of GnRH neurons across developmental time in various representative taxa of cartilaginous fish and reptiles. Furthermore, I intend to identify and experimentally confirm a molecular regulatory region for GnRH2, the most highly conserved variant across vertebrates, within the chicken embryo. Once this regulatory region is identified, the sequence can also be used to probe the genomes of other non-model taxa. Finally, I would like to perform lineage analysis using DiI in a non-model system to probe the embryonic origins (neural crest vs. placode) of the GnRH neurons in more ancient taxa.</p
Developing Technologies for Real-Time Whole-Organism Imaging via FTIR Spectromicroscopy
Get PDFFTIR spectromicroscopy heavily resides in the domain of cell-based and tissue-based studies when focusing on its direct application to biological systems. The goal of the reported graduate research is to extend FTIR spectromicroscopy to multicellular whole-organism imaging, ideally for non-invasive, non-destructive, and label-free spatiochemical imaging of biological model Caenorhabditis elegans (C. elegans). With modern optics, detector, and light source technologies implemented at synchrotron facilities, this thesis focuses on exploring the feasibility of multicellular whole-organism imaging while identifying challenges and presenting working solutions for them.</p
Investigation of the Roles of Hopanoids in the Lifecycle of Bradyrhizobium diazoefficiens in the Context of Climate Change
Get PDFRhizobia are a group of bacteria that participate in plant-growth promoting symbioses with legumes, where the bacteria supply the plant with a source of useable nitrogen. In agriculture, crop rotation capitalizes on this symbiosis by planting legumes to restore the nitrogen content of depleted soils. The effects of climate change, such as increased temperature and changing precipitation patterns, threaten the future viability of agriculture. Rhizobia exemplify the role bacteria can play to improve agriculture’s resilience to climate change and prevent land degradation and food insecurity. However, in order for bacteria to realize this potential, they need to survive the challenges of climate change. In my thesis, I detail the environments that rhizobia experience throughout their lifecycle and how the soil environment will likely change as the climate changes. Then, I connect these environmental parameters, especially hypo and hyperosmolarity, to the outer membrane. The outer membrane is the first line of defense for bacteria against external assaults. Rhizobia make many changes to their outer membrane compared to commonly studied enteric bacteria. For example, the ability to synthesize hopanoids, steroid-like lipids, is overrepresented in rhizobia.
Hopanoids are known to help protect bacteria against a wide range of stresses – but, surprisingly, we found that the extended hopanoid class is not required for a moderately successful symbiosis between rhizobia strain Bradyrhizobium diazoefficiens and the tropical legume Aeschynomene afraspera. The main defect was in the initiation of the symbiosis, perhaps due to motility defects in the extended hopanoid—deficient mutant. As we investigated this paradox, we discovered that hopanoids are conditionally essential in B. diazoefficiens depending on the medium in which the organism is grown. Specifically, we investigated the role of hypoosmolarity and divalent cation concentration, discovering that extended hopanoids confer robustness to the physicochemical environment. This property indicates that extended hopanoids may be important in the soil environment, which is prone to osmotic variability, especially as the climate changes. This work increases our understanding of the role of the outer membrane and hopanoids in bacterial resilience which may help with engineering or selection of better crop additives in the future.</p
Koopman-based Learning and Control of Agile Robotic Systems
Get PDFLearning methods to enable high performance control systems have recently shown promising results in selected environments and applications. These advances promote the next generation of autonomous robots capable of significantly improving efficiency, cost, and safety in their respective domains. Importantly, these systems are safety-critical and operate in proximity to humans in diverse and uncertain environments. As a result, operational failures may cause significant material and societal losses. Additionally, robot learning and control are further complicated by requiring fast controller update rates and operational constraint satisfaction.
To address these challenges, this thesis presents multiple methods based on Koopman operator theory. The first approach develops algorithms to learn lifted-dimensional models of nonlinear systems and leverages the models in model predictive control (MPC) design. Koopman-based methods typically employ hand-crafted observable functions to "lift" the state variables to the higher dimensional space. For most systems, this leads to poor prediction performance and inefficient use of data and computational resources. Instead, I present methods that generate observable functions from data, both based on underlying theory and by incorporating the observable functions and model structure in a neural network model. This allows lower dimensional models, important for real-time control, and enables the nonlinearities of control-affine dynamics to be captured, crucial to describing many robotic systems. I use quadrotor drones to experimentally demonstrate that the learned models combined with MPC can achieve close to optimal behavior while respecting important operational constraints.
The last part of the thesis is concerned with endowing systems with an arbitrary nominal control policy with safety guarantees. Control barrier functions (CBFs) are a powerful tool to achieve this, yet they rely on the computation of control invariant sets, which is notoriously difficult. To avoid this, a backup strategy can be used to implicitly define a control invariant set. However, this requires forward integration of the system dynamics under a backup controller, which is prohibitively expensive for realistic systems. I present a method that replaces the expensive integration using learned Koopman operators of the closed-loop dynamics. As a result, the online computation time required to evaluate the controller is drastically reduced, enabling real-time use. I also derive an error bound on the unmodeled dynamics in order to robustify the CBF controller and demonstrate the method on multi-agent collision avoidance for wheeled robots and quadrotors.</p