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Item 0-Hecke algebra actions on flags, polynomials, and Stanley-Reisner rings(2013-08) Huang, JiaWe study combinatorial aspects of the representation theory of the 0-Hecke algebra $H_n(0)$, a deformation of the group algebra of the symmetric group $\SS_n$. We study the action of $H_n(0)$ on the polynomial ring in $n$ variables. We show that the coinvariant algebra of this action naturally carries the regular representation of $H_n(0)$, giving an analogue of the well-known result for the symmetric group by Chevalley-Shephard-Todd. By investigating the action of $H_n(0)$ on coinvariants and %finite flag varieties, we interpret the generating functions counting the permutations with fixed inverse descent set by their inversion number and major index. We also study the $H_n(0)$-action on the cohomology rings of the Springer fibers, and similarly interpret the (noncommutative) Hall-Littlewood symmetric functions indexed by hook shapes.We generalize the last result from hooks to all compositions by defining an $H_n(0)$-action on the Stanley-Reisner ring of the Boolean algebra. By studying this action we obtain a family of multivariate noncommutative symmetric functions, which specialize to the noncommutative Hall-Littlewood symmetric functions and their $(q,t)$-analogues introduced by Bergeron and Zabrocki, and to a more general family of noncommutative symmetric functions having parameters associated with paths in binary trees introduced recently by Lascoux, Novelli, and Thibon. We also obtain multivariate quasisymmetric function identities from this $H_n(0)$-action, which specialize to results of Garsia and Gessel on generating functions of multivariate distributions of permutation statistics. More generally, for any finite Coxeter group $W$, we define an action of its Hecke algebra $H_W(q)$ on the Stanley-Reisner ring of its Coxeter complex. We find the invariant algebra of this action, and show that the coinvariant algebra of this action is isomorphic to the regular representation of $H_W(q)$ if $q$ is generic. When $q=0$ we find a decomposition for the coinvariant algebra as a multigraded $H_W(0)$-module.Item 1,3-Butadiene-Induced DNA Damage: Ethnic Differences and Sources of Formation(2022-07) Jokipii Krueger, CaitlinIn the United States, lung cancer is the leading cause of cancer-related deaths. Cigarette smoking is a major risk factor for lung cancer development, with approximately 80% of lung cancer cases directly related to smoking. Up to 1 in 4 smokers will develop lung cancer over the course of their lifetime. This risk varies by racial/ethnic group, with African Americans and Native Hawaiians at greater risk as compared to whites, and Japanese and Latinos at a relatively lower risk than whites. This racial/ethnic difference in risk is not explained by differences in smoking dose, diet, occupation, or socioeconomic status. Cigarette smoke is comprised of over 7000 chemical compounds, more than 70 of which are known human carcinogens. These carcinogens undergo metabolic activation to reactive species which can form adducts with DNA, leading to mutations and eventually lung cancer development. Polymorphisms in metabolic genes responsible for the bioactivation and detoxification of tobacco smoke carcinogens have been hypothesized to play a role in the racial/ethnic differences in lung cancer risk. Among tobacco smoke carcinogens, 1,3-butadiene (butadiene, BD) is one of the most abundant and has the highest cancer risk index. BD is metabolically activated to reactive epoxides 3,4-epoxy-1-butene (EB), 1,2-dihydroxy-3,4-epoxybutane (EBD), and 1,2,3,4-diepoxybutane (DEB) by CYP2E1 and 2A6. These epoxides can be detoxified through glutathione conjugation by GSTT1 to form 2-(N-acetyl-L-cystein-S-yl)-1-hydroxybut-3-ene and 1-(N-acetyl-L-cystein-S-yl)-2-hydroxybut-3-ene (MHBMA) from EB, N-acetyl-S-(3,4-dihydroxybutyl)-L-cysteine (DHBMA) from EB-derived hydroxymethylvinyl ketone (HMVK), 4-(N-acetyl-L-cystein-S-yl)-1,2,3-trihydroxybutane (THBMA) from EBD, and bis-butanediol mercapturic acid (bis-BDMA) from DEB. If not detoxified, these epoxide species can form covalent adducts with DNA such as N7-(1-hydroxy-3-buten-2-yl) guanine (EB-GII) from EB, N7-(2,3,4-trihydroxybut-1-yl) guanine (N7-THBG) from EBD, and 1,4-bis-(guan7-yl)-2,3-butanediol (bis-N7G-BD) from DEB. The first goal of this thesis work was to investigate urinary levels of EB-GII as a biomarker of lung cancer risk in smokers. In Chapter 2 of this thesis, we report the temporal stability and association with smoking of urinary EB-GII. Urinary EB-GII levels were stable over time in smokers, indicating that single adduct measurements provide reliable levels of EB-GII. Additionally, we observed a 34% decrease in the levels of urinary EB-GII upon smoking cessation, indicating that it is associated with smoking status but may also have other sources of formation. In Chapter 3 we quantified urinary EB-GII adducts in smokers and non-smokers belonging to three racial/ethnic groups with differing risks of lung cancer development: Native Hawaiian, white, and Japanese American. We observed higher levels of urinary EB-GII excretion in Japanese Americans as compared to whites and Native Hawaiians and these differences could not be explained by GSTT1 gene deletion or CYP2A6 activity. In Chapter 4 we directly examined the association between urinary EB-GII and lung cancer incidence, revealing that EB-GII levels are elevated in lung cancer cases as compared to smokers without lung cancer (OR = 1.91). In Chapters 2 and 3, we observed that there were low but detectable levels of urinary EB-GII in smokers following smoking cessation and in non-smokers, suggesting additional sources of EB-GII adduct formation. In Chapter 5, we utilized stable isotope tracing to investigate the formation of BD DNA adducts and metabolites from endogenous sources. Laboratory rats were treated with low ppm (0.3-3.0 ppm) concentrations of BD-d6 to approximate occupational exposure to BD (~1 ppm). Levels of exogenous (deuterated) EB-GII, MHBMA, and DHBMA increased in a dose-dependent manner following BD exposure, while endogenous (unlabeled) adducts and metabolites were unaffected by BD dose. While urinary EB-GII and MHBMA were formed primarily by exogenous exposure, significant amounts of endogenous DHBMA were observed. Additionally, urinary exogenous EB-GII was associated with butadiene-induced genomic EB-GII, suggesting that urinary EB-GII can be used as a non-invasive surrogate measurement for genomic BD-DNA damage. In Chapter 6, formation of a novel BD-DNA adduct, N6-[2-deoxy-D-erythro-pentofuranosyl]-2,6-diamino-3,4-dihydro-4-oxo-5-N-1-(oxiran-2-yl)propan-1-ol-formamidopyrimidine (DEB-FAPy-dG) was investigated. A sensitive isotope dilution nanoLC-ESI+-HRMS/MS methodology was developed and applied to quantitation of DEB-FAPy-dG formation in DEB treated calf thymus DNA. DEB-FAPy-dG formation was dependent on DEB concentration and pH, with higher adduct levels observed at higher pH. Detection of DEB-FAPy-dG in mouse embryonic fibroblast cells and nuclei treated with DEB was unsuccessful, likely due to the adduct forming in low quantities at physiological pH.Item The 13th-century “Constance” tales.(2009-11) Leek, Thomas R.Four texts from the 13th century make up the first attestations of the "Constance" plot, a version of ATU 706 "The Father who Wanted to Marry his Daughter." This dissertation harmonizes a comparative investigation of these tales with an analysis of the cultural milieu of the Middle Ages. The figure of the sexually persecuted and exiled daughter comes to the forefront of popular culture as discourse on repentance centers around the correction of monstrous sins. In the "Constance" tales, the daughter reconciles her repentant father and husband, between whom power is transferred on account of the heroine's suffering. A thematically similar anecdote in the Chronicle of Morea points toward an international motif of an errant daughter benefiting the man she marries against her father's initial wishes.Item A 1D Fluid Model On The Circle, An Algorithm For Simulating Dense Crowds, And Stability For Programs With Seminorm Objective And Linear Constraints(2020-04) Stewart, SamuelIn this thesis, we describe three contributions made to three different fields. First, we prove local stability of solutions to a 1D model equation of the 3D Euler equations. Second, we describe a model of human crowds where people are modeled by ellipses. Finally, we prove local stability of solutions for a family of convex programs.Item 2,5-Cyclohexadienones as a Useful Launching Point for the Synthesis of the Briarane Diterpenoids and A Hypervalent Iodine-Mediated Synthesis of Oxazolines(2015-05) Moon, NicholasThe briarane diterpenoids are a large class of natural products derived from gorgonians and other corals from throughout the world. Despite the extremely large number of briaranes that have been isolated, along with the potent and diverse range of biological activities that have been observed, the total synthesis of the briaranes remains underexplored. A facile synthetic route to the briarane diterpenoids will aid in the further exploration of these molecules. Herein, we will describe a number of synthetic approaches that were evaluated to access a key fragment of the briarane diterpenoids. A key feature of all routes involves the use of 2,5-cyclohexadienone substrates as a diverse platform for the launching of the synthesis. Chapter 1 will provide background information on 2,5-cyclohexadienones. Methods for their synthesis, a survey of their diverse reactivity, and selected examples of their use in natural product synthesis will all be described. Emphasis will be given to reactivity patterns which aided us in our research. Chapter 2 will provide a brief survey of the briarane diterpenoids as well as some of the major biologically active families. Previous synthetic efforts used to access these molecules will also be described. Chapter 3 will describe our efforts to synthesize a key fragment of the briarane diterpenoids (referred to as the briarane stereotetrad) utilizing intermediates containing a bicyclic lactone. Chapter 4 will describe our successful efforts to access the briarane stereotetrad using monocyclic intermediates. The important influence of torsional strain in key steps, as well as a successful route to access the briarane stereotetrad will be described. Chapter 5 will report the results of a separate research project in which an iodine(III) promoted cyclization of N-allylamides to form oxazolines was studied. The development of optimum reaction conditions and the evaluation of the substrate scope will be described. Key results that suggest novel mechanistic details for this electrophilic oxidative cyclization will also be described.Item 21st Century media effects: choice, predispositions, and their impact on agenda setting and priming.(2009-12) Holmes, Justin WhitelyIn the past 25 years, we have seen a massive shift to communication technologies that allow increased choice of content for citizens. Using an experiment, this study explores the relationship between individual differences, increased choice, and media effects such as agenda setting and priming. It finds that increased choice greatly attenuates both attention to political news and subsequent priming and framing effects.Item 2D Mott Hopping of Vortices in an Amorphous Indium Oxide Film(2018-07) Percher, IlanaThe electron transport behavior of a thin film of amorphous indium oxide was studied as it was driven across the superconductor-insulator transition by a perpendicular magnetic field. For the range of field values between zero and the critical field of the transition, a positive slope in temperature dependence of the resistance was observed in the data. These data are best described by the form of two dimensional Mott variable range hopping as applied to vortices. The quality of this fit is demonstrated over several orders of magnitude in resistance and over a broad range of fields using several methods of analysis. The observation of variable range hopping of vortices is the main result of this work. Data from a second sample were also found to be consistent with vortex variable range hopping, as were data extracted from a paper within the literature. These examples suggest that this behavior has probably been overlooked in the past. The field-dependence of the characteristic hopping temperature T_0 at very low fields was predicted using a granular model for the thin film. This is consistent with the picture of effective granularity induced in a highly disordered superconductor, which also explains various properties of the film, including the magnetoresistance peak observed at high fields. What was not observed, however, was a crossover from Mott to some other hopping behavior at high fields, where corrections to the hopping exponent due to vortex-vortex interactions were expected. The reason for this is an open question.Item 2D Peskin Problems of an Immersed Elastic Filament in Stokes Flow(2018-05) Rodenberg, AnaliseIn the work that follows we investigate a class of problems where a one dimensional closed elastic structure is immersed in a plane of steady Stokes flow. The dynamics are governed by a boundary integral equation describing the configuration of the immersed structure. Depending on the choice of elasticity law, we break our class into either a semilinear or fully nonlinear system of equations. In the nonlinear setting, we prove that the linearization of the system generates an analytic semigroup and use it to prove local existence and uniqueness in low regularity H\"{o}lder spaces. In the semilinear setting, we remove the principle operator via small scale decomposition and use it to build similar local existence results. Further, we establish spatial smoothness of solutions by careful estimates on a class of commutators. Using these regularity results, we are able to establish that the only equilibria of the system are uniformly parameterized circles which we then prove nonlinear stability about. Finally, we identify a quantity which classifies global-in-time behavior.Item 2D Plasmonics for Gas Sensing and Polarization Optics(2021-12) khaliji, kavehTwo-dimensional (2D) materials emerged in 2004 with the isolation of graphene, a one-atom-thick honeycomb lattice of carbon atoms. The first reports on light interaction with polarizable 2D matter, i.e. 2D polaritons, came out in 2011 wereexperiments confirmed graphene's ability to sustain plasmon polaritons. Today, the 2D family is extended far beyond graphene which can host a full suite of different polaritonic modes with record-high light confinement and optical responses that can be tuned via lattice strain, optical pumping, or electrostatic gating. In this thesis we aim to exploit the optical and plasmonic responses of 2D materials to explore new system designs for selective gas sensing and ubiquitous polarization transformation. Truly robust and selective sensing of gases via remote standard optical spectroscopy, if achieved, has widespread use in key industries, including environmental, semiconductor, healthcare, and security. To date, the impeding challenge hasbeen the weak optical absorption of the gas molecules, which prevents optical read-out of gas traces at minute concentration. To overcome the weak sensitivity of optical techniques, we propose novel strategies, by utilizing plasmons in graphene to enhance light-gas interaction via promoting multiple trapping mechanisms, including surface adsorption, optical tweezing, and electrostatic bias. We discuss the relative strengths of these trapping forces and found gas adsorption in a typical nanoribbon array plasmonic setup produces measurable dips in optical extinction of magnitude 0.1 % for gas concentration of about parts per thousand level. We discuss the dynamic and nonlocal polarizability of two-dimensional electron gas with finite energy bandwidth (FBW-2DEG). This was motivated by recent developments in twisted 2D materials which exhibit isolated electronic bands and finite bandwidths. We show that a FBW allows for plasmon modes of quasi- at dispersion and large momenta to emerge. The FBW-2DEG can also potentially support low-loss plasmon modes immune to elastic or inelastic scattering-assistedLandau damping (dissipation via electron-hole pair excitation). This is of prime significance, since it allows for plasmon modes with concurrent tight spatial confinement and long propagation lengths, the two metrics critical to most branches of plasmonic science, e.g. communication, sensing, lasing, and more. The polarization of scattered light contains vital clues to nature of its light-matter interactions. The ability to control light polarization plays a key role in metrology applications such as stress analysis in glass or plastic, pharmaceutical or food ingredient analysis, biological imaging among others. The recent reports on rich near-field polaritonic-optics of twisted 2D materials with in-plane optical anisotropy, such as twisted Black Phosphorus and -MoO3, motivated us to explore the far-field polarization properties of such setups. We show that a stack of twisted anisotropic 2D materials with electrostatic control can function as arbitrary-birefringent wave-plate or arbitrary polarizer with tunable degree of non-normality. The twisted stack, thus gives access to a plethora of polarization transformers including rotators, pseudo-rotators, symmetric and ambidextrous polarizers. We explore the far-field scattering properties of anisotropic 2D materials in ribbon array configuration. Our study reveals the plasmon-enhanced linear birefringence/dichroism in these ultrathin metasurfaces, where linearly polarized incidentlight can be scattered into its orthogonal polarization or be converted into circular polarized light. We found wide modulation in both amplitude and phase of the scattered light via tuning the operating frequency or material's anisotropy.Item A 3-dimensional analysis of the Cassiopeia a supernova remnant.(2011-10) Isensee, Karl AndrewWe present a multi-wavelength study of the nearby supernova remnant Cassiopeia A (Cas A). Easily resolvable supernova remnants such as Cas A provide a unique opportunity to test supernova explosion models. Additionally, we can observe key processes in the interstellar medium as the ejecta from the initial explosion encounter Cas A’s powerful shocks. In order to accomplish these science goals, we used the Spitzer Space Telescope’s Infrared Spectrograph to create a high resolution spectral map of select regions of Cas A, allowing us to make a Doppler reconstruction of its 3-dimensional structure structure. In the center of the remnant, we find relatively pristine ejecta that have not yet reached Cas A’s reverse shock or interacted with the circumstellar environment. We observe O, Si, and S emission. These ejecta can form both sheet-like structures as well as filaments. Si and O, which come from different nucleosynthetic layers of the star, are observed to be coincident in some regions, and separated by >500 km s−1 in others. Observed ejecta traveling toward us are, on average, #24;800 km s−1 slower than the material traveling away from us. We compare our observations to recent supernova explosion models and find that no single model can simultaneously reproduce all the observed features. However, models of different supernova explosions can collectively produce the observed geometries and structures of the emission interior to Cas A’s reverse shock. We use the results from the models to address the conditions during the supernova explosion, concentrating on asymmetries in the shock structure. We also predict that the back surface of Cassiopeia A will begin brightening in #24;30 years, and the front surface in #24;100 years. We then used similar observations from 3 regions on Cas A’s reverse shock in order to create more 3-dimensional maps. In these regions, we observe supernova ejecta both immediately before and during the shock-ejecta interaction. We determine that the reverse shock of the remnant is spherical to within 7%, although the center of this sphere is offset from the geometric center of the remnant by 810 km s−1. We determine that the velocity width of the nucleosynthetic layers is #24;1000 km s−1 in a given region, although the velocity width of a layer along any given line of sight is <250 km s−1. Si and O are observed to be coincident in some directions, but segregated by up to #24;500 km s−1 in other directions. We again compare these observations of the nucleosynthetic layers to predictions from supernova explosion models in an attempt to constrain such models. Finally, we observe small-scale velocity structures in the recently shocked ejecta. We determine that this corrugation is likely caused during the supernova explosion itself, rather than hundreds of years later at the remnant’s reverse shock. Finally, we present a detailed multi-epoch X-ray analysis of Cas A using Chandra X-ray Observatory exposures from 2000, 2002, and 2004. We identify the most recently shocked X-ray ejecta with ionization timescales of #24;1010 cm−3 s, nearly an order of magnitude smaller than previously identified shocked ejecta. These ejecta are then used to determine if the original nucleosynthetic layers of the star are arriving at Cas A’s reverse shock at different times. We use recent collisional ionization models that allow us to correlate observed changes in spectrum with a rough estimate of when the Mg and Fe layers reached the reverse shock. We find several regions that have a signature consistent with a separation of #24;200 km s−1 between layers, although we find that most regions show no sign of separation greater than 65 km s−1. This method is able to detect substantially smaller separations between layers than earlier X-ray techniques. We test various supernova explosion models against our observations by comparing our observed velocity separation between layers to predictions from the models. We conclude that any mixing between nucleosynthetic layers is most likely caused by Rayleigh-Taylor filamentation and not partial explosive nucleosynthesis in the layers. Our observations of spectral changes provide feedback for future models which will address important physical issues such as the role of cosmic ray production at a supernova remnant’s reverse shock.Item The 340B drug discount program: enrollment and participation among critical access hospitals(2013-06) Wallack, Madeline CarpinelliThe 340B Program is a federal program that provides certain healthcare safety-net providers mandated price reductions on outpatient drugs. In 2010, critical access hospitals (CAHs)--small hospitals in isolated rural communities--became eligible for the program. This project set forth to understand the variables that are important to 340B program enrollment and purchasing through the 340B Prime Vendor Program (PVP), the government's contractor to represent the purchasing volume of all 340B entities. The CAHs with a higher number of total outpatient visits, more staff in the pharmacy department, full implementation of electronic health records, in relatively more urban counties, offer chemotherapy and provide outpatient surgery have higher odds of enrolling in the 340B Program. The CAHs that offer chemotherapy, have a contract pharmacy arrangement and have been enrolled in 340B essentially since program eligibility began are more likely to have made 340B purchases through the PVP. This project has also defined a typology to characterize the spectrum of 340B use by CAHs. The 340B typology is a systematic approach to understanding the differences in how the program may or may not be used and includes categories that range from CAHs never enrolling in the 340B Program to CAHs that are purchasing drugs using the PVP.Item 3D Bioprinting Pediatric Trachea(2022-02) Galliger, ZacharyTracheal failures due to trauma, disease, or congenital anomalies, if not fatal, severely decrease quality of life. While small defects can be resolved surgically with resection and anastomosis, defects exceeding a critical length of trachea require graft material. This critical length varies from 50% in adults to 30% in children. Current silicone grafts pose further challenges for pediatric patients, who require yearly follow up surgeries to adjust the implant to their growing bodies. To assuage these challenges, the work in this thesis seeks to develop biologically derived grafts with the potential to grow and respond to the needs of pediatric patients. First, this work focuses on incorporating extracellular matrix (ECM) into bioinks for 3D bioprinting patient specific, tissue engineered constructs. The results discussed in this dissertation show while ECM is a powerful mediator of cell behavior, its efficacy can be inhibited by chemical modification. Lastly, this work investigates an in vivo rabbit model for evaluating tracheal transplants and poses further questions concerning the regenerative capabilities of tracheal cartilage.Item 3D Computer Vision Algorithms for Semantic Reconstruction of Agricultural Environments(2020-06) Dong, WenboVision sensors mounted on mobile robotic platforms hold great promise in automated agriculture management. However, established computer vision techniques often fail to perform well in agricultural environments due to the environmental complexity, which makes automation difficult. To address this problem, we have designed and developed three-dimensional (3D) computer vision algorithms that improve the accuracy of imaging devices, suppress the undesirable environmental interferences, and generate accurate and precise 3D models of plants with detailed information automatically extracted for farmers. This dissertation is roughly separated into three main parts. In the first part of the thesis, we study the problem of extrinsic calibration of a 2D laser rangefinder and a camera. We present a novel method for extrinsically calibrating a camera and a 2D laser rangefinder whose beams are invisible from the camera image. We show that the point-to-plane constraints from a single observation of a V-shaped calibration pattern composed of two non-coplanar triangles suffice to uniquely constrain the relative pose between two sensors. We propose an approach to obtain analytical solutions using point-to-plane constraints from single or multiple observations. Along the way, we also show that the previous solutions, in contrast to our method, have inherent ambiguities and therefore must rely on a good initial estimate from a large number of observations. In the second part of the thesis, we study the problem of building coherent 3D reconstructions of orchard rows to improve the accuracy of measuring semantic traits for phenotyping and to automate such measurements. Even though 3D reconstructions of side views can be obtained using standard mapping techniques, merging the two side-views is difficult due to the lack of overlap between the two partial reconstructions. We propose a novel method that utilizes global features and semantic information to obtain an initial solution aligning the two sides. Our merging technique then refines the 3D model of the entire tree row by integrating semantic information common to both sides, and extracted using our novel robust detection and fitting algorithms. The proposed vision system automatically measures the semantic traits (i.e., canopy volume, trunk diameter, tree height, and fruit count) of the optimized 3D model that is built from the RGB or RGB-D data in real orchard environments. In the third part of the thesis, we study two problems of suppressing undesirable environmental interferences during sensing and mapping. In the first problem, we present a novel method to estimate the linear velocity of an unmanned aerial vehicle (UAV) from a downward-facing stereo camera even in the presence of disorderly motion of image features. In the second problem, I study the problem of detecting and localizing each elliptical object in clustered and occluded scenarios, such as fruit clusters in trees. We propose the first convolutional neural network (CNN)-based ellipse detector, called Ellipse R-CNN, to represent and infer occluded objects as ellipses. We first design a robust and compact ellipse regression that is able to infer the parameters of multiple elliptical objects even they are occluded by other neighboring objects. For better occlusion handling, we exploit refined feature regions for the regression stage, and integrate the encoder-decoder structure to learn different occlusion patterns. To further boost the accuracy of 3D object estimation, we propose a novel ellipse regression loss to learn the uncertainties of regressed parameters and predict the geometric quality for each detection in 2D. Such multi-view detections and geometric uncertainties are integrated into our probabilistic framework to accurately localize the enclosing ellipsoid of each occluded object in 3D. This dissertation makes progress towards achieving automated agricultural practices by building 3D semantic maps of farmlands, crops fields, and orchards, and advances the state-of-the-art automation techniques for precision agriculture. We also demonstrate the feasibility and applicability of our methods through system implementation and with results from synthetic and extensive real experiments.Item 3D Orientation of Alpha Helix in Muscle Myosin Regulatory Light Chain Using Bifunctional Electron Paramagnetic Resonance(2021-06) Savich, YahorMuscle contraction is a coordinated work of nanometer-sized force generators, myosin molecules. These molecules are out of equilibrium: they use the energy stored in the form of ATP to move collectively along the track protein actin. The myosin molecules transfer their work via lever arms that connect force generators to their cargo. Orientation of these lever arms has been studied thoroughly since 1) their structural dynamics is fundamental for understanding the muscle contraction and 2) their particular orientations are associated with disease states of cardiac and skeletal muscle. Electron microscopy, fluorescence polarization, and X-ray diffraction have provided insight into the structure of muscle, but there is still no high-resolution data of the vertebrate lever arm orientation available at ambient (not vitrified or crystallized) conditions. The present work establishes a method of measuring the orientation of the alpha helices in three dimensions using electron paramagnetic resonance (EPR). Chapter 3 introduces the use of EPR with bifunctional spin labels attached to different helices of the myosin regulatory light chain (RLC) protein with and without ATP. Demembranated skeletal muscle fibers were aligned with the slowly-varying magnetic field; RLC was chemically substituted by labeled RLC; axial orientational dynamics of the probe with respect to the muscle axis was determined. Chapter 4 utilizes 1) directional statistics that replaces the previous use of a Gaussian distribution and provides new insights into the degree of disorder and 2) a new bifunctional probe that adds an azimuthal dimension to the orientational data. Together, these techniques allow determination of the tilt and roll angles of the alpha helix without relying on the myosin structure.Item 3D Printed Functional Materials and Devices and Applications in AI-powered 3D Printing on Moving Freeform Surfaces(2020-08) Zhu, ZhijieThe capability of 3D printing a diverse palette of functional inks will enable the mass democratization of manufactured patient-specific wearable devices and smart biomedical implants for applications such as health monitoring and regenerative biomedicines. These personalized wearables could be fabricated via in situ printing --- direct printing of 3D constructs on the target surfaces --- at ease of the conventional fabricate-then-transfer procedure. This new 3D printing technology requires functional (e.g., conductive and viscoelastic) inks and devices (e.g., wearable and implantable sensors) that are compatible with in situ printing, as well as the assistance of artificial intelligence (AI) to sense, adapt, and predict the state of the printing environment, such as a moving hand and a dynamically morphing organ. To advance this in situ printing technology, this thesis work is focused on (1) the development of functional materials and devices for 3D printing, and (2) the AI-assisted 3D printing system. To extend the palette of 3D printable materials and devices, on-skin printable silver conductive inks, hydrogel-based deformable sensors, and transparent electrocorticography sensors were developed. As with the AI for in situ 3D printing, solutions for four types of scenarios were studied (with complexity from low to high): (1) printing on static, planar substrates without AI intervention, with a demonstration of fully printed electrocorticography sensors for implantation in mice; (2) printing on static, non-planar parts with open-loop AI, with a demonstration of printing viscoelastic dampers on hard drives to eliminate specific modes of vibration; (3) printing on moving targets with closed-loop and predictive AI, with demonstrations of printing wearable electronics on a human hand and depositing cell-laden bio-inks on live mice; (4) printing on deformable targets with closed-loop and predictive AI, with demonstrations of printing a hydrogel sensor on a breathing lung and multi-material printing on a phantom face. We anticipate that this convergence of AI, 3D printing, functional materials, and personalized biomedical devices will lead to a compelling future for on-the-scene autonomous medical care and smart manufacturing.Item 3D Printing Multifunctional Optoelectronic and Microfluidic Devices(2020-10) Su, RuitaoFunctional materials encompass different classes of materials possessing intrinsic or synthetic properties that are responsive to external stimuli. A few examples include semiconducting polymers/crystals, electroluminescent polymers, polymers with controlled cross-linking mechanisms and printable metallic inks with tunable sintering mechanisms and conductivity. The technology of additive manufacturing, or 3D printing, has been extensively investigated with structural plastics and metals to realize rapid prototyping of irregular/customized geometries, demonstrating a few successful examples of commercialization. Yet, a further systematic study is demanded to investigate the methodologies to incorporate multiple functional materials in the 3D printed multifunctional devices. This will lay important foundations for the fabrication of a range of devices under ambient conditions that were conventionally accessible exclusively to the cleanroom-based microfabrication. More importantly, the capability of 3D printing to integrate materials in a freeform manner will facilitate novel device form-factors and functionalities that are challenging to realize with microfabrication. In this work, the methodologies of 3D printing optoelectronic and microfluidic devices were investigated with an emphasis on material selection, device configuration, alignment, performance optimization and scalable fabrication. To this end, a custom-built 3D printing system was utilized to accurately pattern functional materials that possess varying rheological properties. Over the past several decades, 3D printing has demonstrated an array of electronic devices such as batteries, capacitors, sensors, wireless transmitters etc. This progress renders an expectation for fully 3D printed integrated circuits that can be rapidly prototyped and adopt more complicated spatial architectures. However, fully 3D printed optoelectronic devices are still a relatively unexplored paradigm. One major challenge of 3D printed optoelectronics is to optimize the device performance by controlling the thickness and uniformity of the solution-processed layers. An optimized layer thickness maintains the balance between charge injection and light extraction for light emitting diodes (LEDs) or light absorption and charge separation for photodetectors. Layer uniformity affects the contact between adjacent layers and therefore the charge carrier transport. In this work, electroluminescent semiconductors, including silicon nanocrystals (SiNCs) and conjugated polymers, were 3D printed as the active layers of LEDs and photodetectors. The effect of printed layer thickness on the device performance was investigated for the extrusion-based printing. A spray printing method was integrated in the 3D printing system and an improved device performance was observed. Significantly, for the 3D printed polymer photodetectors, an external quantum efficiency (EQE) of 25.3%, comparable to that of spin-coated devices, was achieved by controlling the concentration of the active ink. For the device integration, photodetector arrays were printed on flexible and spherical substrates for a freeform and wide field-of-view image sensing. Novel multifunctional optoelectronic devices consisting of integrated LEDs and photodetectors in a side-by-side layout was printed on the same platform, demonstrating potential applications of wearable physiological sensors. Next, for the 3D printed microfluidic devices, this work demonstrates that yield-stress fluids, such as viscoelastic gels, can be extruded to construct self-supporting hollow microstructures that are highly flexible and stretchable. Several additive manufacturing methods, such as stereolithography and multi-jet printing, have demonstrated 3D printed microfluidic devices with improved automation compared to the conventional soft lithography. However, it remains a challenge to directly incorporate electrical and biological sensing elements in the microfluidic devices. In this study, because of the yield strength of the viscoelastic ink, mechanical equilibrium states were found to exist for the inclined standing walls. Self-supporting microfluidic channels and chambers were 3D printed by stacking silicone filaments according to prescribed toolpaths. Since no sacrificial material was demanded to realize the hollow structures, the microfluidic structures can be directly aligned and printed onto microfabricated circuits without contaminating the electrodes. The high modeling precision of this method was demonstrated via fully 3D printed chemical species mixers that were embedded with herringbone ridges. In addition, automation components, including microfluidic valves and peristaltic pumps, were also 3D printed with overlapping silicone channels that were encapsulated by UV-curable resins. Most compellingly, microfluidic networks integrated with valves transcended the conventional planar form-factors and were directly printed on 3D surfaces. The 3D microfluidics suggests a potential application of microfluidics-based physiological sensors that can be directly printed onto freeform surfaces such as human bodies. Lastly, this work demonstrates that the above two distinct systems can be seamlessly integrated together via 3D printing, yielding fully encapsulated and flexible LED matrices. Liquid metals such as eutectic GaIn are promising candidates for soft and stretchable electronics. As the cathode material of 3D printed optoelectronic devices, it has the desired work function and a high mechanical compliance. However, current challenge of patterning liquid metals lies in the design of a robust encapsulation for the cathodes and simultaneously creating an effective interface with interconnects. To this end, self-supporting microfluidic networks that are highly adaptable and aligned to the layout of LED matrices were printed to encapsulate the liquid metal. The 3D printed liquid metal microfluidics enabled the scalable fabrication of flexible and individually addressable LED matrices. In summary, this research expanded the scope of ink composition for 3D printed multifunctional devices. Transferring these materials from microfabrication to 3D printing significantly improves the manufacturability of optoelectronic and microfluidic devices. The intrinsic capabilities of 3D printing to pattern 3D structures in a freeform manner facilitated novel functionalities for both types of devices, including spherical image sensors, 3D microfluidic networks, flexible organic LED matrices etc.Item 3D Printing of Soft Electromechanical Transducers and Their Application in Development of Patient-Specific Organ Models(2020-01) Haghiashtiani, GhazalehThe ability to mimic nature and biological systems has revolutionized various fields and has inspired a plethora of scientific discoveries to solve human problems. Medicine is among the areas that has vastly benefited from bio-inspired innovations, such as the gecko-inspired adhesive and parasitic worm-inspired microneedle. Driven by the fact that medical errors are among the leading causes of death, several efforts have been focused to create phantoms that mimic the actual patients’ organ with the main purpose of enhancing preoperational planning and surgical outcomes, as well as reducing the risk of intraoperative errors and postoperative complications. Over the past decade, 3D printing technologies have played an important role in fabrication of patient-specific organ phantoms, however, despite being anatomically correct, these 3D printed organ models mostly lack the precise mimicry of the sense and mechanical properties of the biological tissue of interest. In addition, they lack advanced functionalities, such as tactile sensing, to provide quantitative feedback during organ handling which can be a valuable metric in different surgical interventions or for training purposes. This dissertation aims at addressing these two limitations by conducting an investigation at the intersection of soft biomimicking electroactive, and tissue-like material systems and electromechanical transducer design coupled with multi-material, extrusion-based 3D printing process, for primary applications in development of smart, patient-specific organ models. Specifically, the design and development of (i) a tunable silicone-based material system with tissue-like mechanical properties compatible with direct ink writing 3D printing process, (ii) soft electromechanical actuators and sensors based on the biomimicking hydrogel-elastomer hybrid material system, and (iii) coalescence of these concepts for fabrication of patient-specific organ models with integrated functionalities were presented. It is envisioned that these organ models can augment the current practices in a gamut of medical applications, including preoperative planning, clinical training, patient education, and development of next-generation medical devices with the end goal of enhancing surgical outcomes, reducing medical errors, and improving patient safety. In addition, on a long-term basis, the outcomes of this work could contribute to the incorporation of cell-seeded structures into the organ models, thus setting the stage for development of dynamic bionic organs.Item 3D Printing to Recapitulate Cardiac Tissue Development, Structure, and Function(2019-09) Kupfer, MollyHeart disease is the leading cause of death worldwide, due in large part to the low regenerative capacity of the heart. With recent advances in stem cell biology, cardiac tissue engineering with human cells has emerged as an avenue to replace lost muscle after a cardiac event and to produce in vitro, human models for drug and medical device testing. However, efforts in this realm are still limited in their ability to recapitulate the complex, microscale interactions that enable macroscale function of cardiac muscle. 3D printing is a technology that is poised to meet this challenge, as it enables precise deposition of cues that are critical for cells to connect with each other and engage with their environment. Here we present three studies that capitalize on the replicative power of 3D printing as tool to advance the functionality of engineered cardiac tissues by promoting connections between cardiomyocytes, supporting cells of the heart, and the extracellular matrix. The foundation of this work lies in our view that the generation of physiologically relevant tissue mimics requires a robust mechanistic understanding of how these systems develop in vivo, and how the vital interactions that occur between differentiating cells and their environment can be recapitulated in vitro. Doing so will enable us to address critical gaps in field of cardiac tissue engineering while advancing clinical models and therapeutics.Item 45 Minutes For 128 Musicians(2015-06) Bergmann, Andrew45 Minutes for 128 Musicians has demonstrated a wide range of possibilities regarding the sincere incorporation of improvisational and improvisationally-derived procedures in orchestral composition. Huge groupings of people have made music together almost exclusively in traditional settings. I finish this project expecting that the methods and technologies of modern studio production, as well as the eternal artistic migration towards new forms and new textures, will hasten the development of new orchestral textures. This production of this piece provides one such example.Item 4d and 5d compounds as the new frontier of the anisotropic spin physics(2017-07) Sizyuk, YuriyI perform a series of studies of the magnetism of 4d and 5d transition metal compounds. In particular I concentrate on the realization of anisotropic magnetic Hamiltonians by use of the spin-orbit coupling to tie together the real space geometry and spin space magnetism. In the first part, I derive the magnetic Hamiltonians of Sr2IrO4 and Na2IrO3 from microscopic parameters. The difficulty of these calculation arises from the fact that many microscopic parameters, such as Hund's coupling, spin-orbit coupling, and crystal field distortions are all of the same order and thus have to be treated on an equal footing. The competition and cooperation of these interactions leads to a rich magnetic Hamiltonians with many different anisotropic interactions. My calculations provide a clear dependence of these interactions on the microscopic parameters. This in turn can be used experimentally to single out and enhance given anisotropies by changing the microscopic parameters. In the second part I propose experimental measurements for the anisotropic interactions. In particular I study how different anisotropic interactions contribute to the anisotropy in the Curie-Weiss temperatures of these compounds. I show that the difference of Curie-Weiss temperatures along particular axes gives a way to measure the strength of the anisotropic interactions in the compounds. In the last part, I study how the multitude of the magnetic anisotropies determine the magnetic ground state in 4d and 5d compounds. We have developed a new method to calculate the fluctuational contribution to the free energy in anisotropic Hamiltonians at any temperature within the magnetically ordered phase. The calculation can be done for both classical (which includes only thermal fluctuations) and quantum (quantum and thermal fluctuations) systems. I also study the effects of external magnetic field applied to the nearest neighbor Kitaev-Heisenberg model, a model of particular interest for alpha-RuCl3.