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Host-Microbe Interactions Impacting and Mediated by Nervous Systems
Get PDFAnimals and microbes coevolved, and thus it is not surprising that the trillions of microorganisms that harmoniously inhabit the mammalian gastrointestinal tract (GIT), collectively termed the gut microbiome, continue to be implicated in healthy and disease states. However, less is known about the mechanisms by which these states are maintained, and how deviations from homeostasis (i.e., dysbiosis) occurr. This thesis explores the relationship between host-microbe interactions and the central and peripheral nervous systems. Specifically, the first chapter of this thesis explores how the microbiome differs is patients with multiple sclerosis and how these differences alter diseases outcomes in a mouse model of the disease. Next, we introduce the enteric nervous system (ENS), the intrinsic nervous system of the GI tract which is supposed as a major conduit of the bidirectional communication between the gut and the brain. Lastly, by adopting biotechnologies in gene delivery and genetically encoded tools for neuroscience, we introduce a molecular toolkit to characterize the ENS in a robust and efficient manner and modulate the ENS to uncover novel mechanisms by which innervation of the GI mediates host-microbe interactions
Using DNA Origami to Create Hybrid Nanophotonic Architectures for Single-Photon Emitters
Get PDFThe limitations in physical dimensions of silicon transistors give us a stimulus to explore alternative systems for better computational performance. The most promising system that received a lot of attention in the past few years is a quantum computer. Ideally, a nanophotonic quantum computer would consist of hundreds of single-photon emitters, optical or plasmonic resonators, optical waveguides and interconnects. The main difficulty in large-scale production of such quantum photonic networks is the integration and deterministic coupling of single-photon sources to photonic elements.
In the first part of this thesis, we utilize spontaneous parametric down-conversion to create correlated pairs of indistinguishable photons. These photons are generated by bismuth borate nonlinear crystal and then are coupled to a photonic chip where they interfere at directional couplers to produce a path-entangled state. Our photonic chip consists of waveguides, directional couplers, and a single Mach-Zender interferometer with a thermo-optic phase shifter. When a part of the waveguide connecting directional couplers is replace with a plasmonic waveguide, quantum state of photons is converted to plasmonic state. Here we report a measurement of path entanglement between surface plasmons with 95% contrast, confirming that a path-entangled state can indeed survive without measurable decoherence. Our measurement suggests that elastic scattering mechanisms of the type that might cause pure dephasing in plasmonic systems must be weak enough not to significantly perturb the state of the metal under the experimental conditions we investigated.
The second part of this work is dedicated to the study of a novel DNA origami self-assembly technique for creating hybrid nanophotonic architectures to create single-photon emitters. DNA origami is a modular platform for the combination of molecular and colloidal components to create optical, electronic, and biological devices. We present a DNA origami molecule that can be deterministically positioned on a silicon chip within 3.2° alignment. Orientation is absolute (all degrees of freedom are specified) and arbitrary (every molecule’s orientation is independently specified). The use of orientation to optimize device performance is shown by aligning fluorescent emission dipoles within microfabricated optical cavities. Large-scale integration is demonstrated via an array of 3,456 DNA origami with 12 distinct orientations, which indicates the polarization of the excitation light. Following this experiment, we explore how many molecular emitters can be coupled to this DNA origami shape and discover interesting interactions between ssDNA extensions that can cause origami to fold along its seam. Finally, we examine DNA origami self-assembly methods that can be used to deterministically couple single-photon emitters to resonators in order to decrease pure-dephasing rates and increase indistinguishability of emitted photons.</p
Towards Next Generation of Optoelectronics: from Quantum Plasmonics and 2D Materials to Advanced Optimization Techniques of Nanophotonic Devices
Get PDFIn this thesis, we explore different novel concepts and materials for the next-generation of nanophotonic and optoelectronic devices that could be used both in classical and quantum settings.
First, we study quantum coherence properties of surface plasmon polaritons (SPPs) in the regime of extreme dispersion. Most experiments to date, that tested quantum coherence properties of SPPs, used essentially weakly-confined plasmons, which experience limited light-matter hybridization, thus restricting the potential for decoherence. Our setup is based on a hole-array chip supporting SPPs near the surface plasma frequency, where plasmonic dispersion and confinement is much stronger than in previous experiments, making the plasmons much more susceptible for decoherence processes. We generated polarization-entangled pairs of photons and transmitted one of the photons through this plasmonic hole array. Our results show that the quality of photon entanglement after the highly-dispersive plasmonic channel is unperturbed. Our findings provide a lower bound of 100 femtoseconds for the pure dephasing time of dispersive plasmons in our materials, and show that even in a highly dispersive regime, surface plasmons preserve quantum mechanical correlations, making possible harnessing the power of extreme light confinement for integrated quantum photonics.
Second, we systematically study different passivation schemes of sulfur vacancies in 2D molybdenum disulfide using first-principles calculations based on density functional theory. We aim at building a microscopic understanding of passivation mechanisms of treatment with TFSI superacid - a popular approach of to improve optical properties. Since superacids have a strong ability to donate protons, we consider hydrogenation and protonation of sulfur vacancies as a possible passivation scheme. Our calculations show that effects of protonation and hydrogenation on properties of 2D molybdenum disulfide are very similar. Moreover, we find that four hydrogen atoms can fully "heal" sulfur vacancies in this material. Our results are an important step towards controllable defects design in 2D transition metal dichalcogenides.
And third, we study applications of advanced methods of optimization and machine learning to the design of different nanophotonic devices. We explore feasibility of using novel multi-fidelity Gaussian processes optimization technique to optimize plasmonic mirror filters for hyperspectral imaging. We compare our results with other common optimization approaches. Then we apply deep-learning inspired techniques to optimize control voltages of individual pixels of active metasurfaces to achieve dynamic beamsteering. We obtain interesting results that pave the way for future experiments both in nanophotonics and machine learning fields.</p
Investigation of Past Habitable Environments through Remote Sensing of Planetary Surfaces
Get PDFPlanetary surfaces record a history of potentially habitable environments throughout the solar system. This dissertation focuses on the characterization of three planetary surfaces to inform their evolution and past habitability: Earth (Chapter 2), Mars (Chapters 3-4), and Ceres (Chapters 5-6). In chapter 1, we introduce major questions driving the work presented in this thesis. In Chapter 2, we use a combination of UAV-based images and in-situ observations to characterize the processes that control the texture and distribution of modern microbial mats in the Turks and Caicos. We find that the surface texture and distribution of the mats is controlled primarily by subtle differences in elevation that drive significant changes in subaerial exposure time. Sedimentation and mechanical weathering from storm events also play a key role in controlling the distribution of mats. In Chapter 3, we apply a PCA-based regression method to stereo Curiosity Mastcam images to measure the structural orientation of the Murray formation. We constrain the dip to be effectively horizontal, which indicates that the Murray formation predates the creation of Aeolis Mons and is consistent with flat strata being deposited on an equipotential surface in a lacustrine setting. In Chapter 4, we summarize the investigation of networks of reticulate ridges on the surface of several rock slabs in the Murray formation using data from the Curiosity rover. We find that the features are preserved mudcracks that were likely deposited during a lowstand in a lake ~3.2-3.6 Ga. The mudcracks are one of few definitive textural markers of drying in the Murray formation and suggest a history of oscillating lake levels that led to intermittent exposure. In Chapter 5, we catalog bright spots on Ceres and propose mechanisms for their formation. We identify hundreds of Na-carbonate-bearing regions on Ceres. We show with a Monte Carlo impact model that these deposits must have been exposed within the last few hundred Ma. In Chapter 6, we investigate the source of shallow subsurface Na-carbonate deposits. We show that the deposits must have been emplaced in the last ~1 Ga and that the solid-state mobilization of water ice and hydrated Na-carbonates could simultaneously explain the formation of domes and large crater rim Na-carbonate exposures. Chapter 7 synthesizes the major results of this thesis and avenues for future exploration
"On Lily Bart's Specializations and Survival in the Upper Class": What Women Want: Desire and the Modern American Novel
No full text[Introduction] Lily Bart, the queen of easy elegance and perfectly-timed blushes, experiences a dramatic fall in status in Edith Wharton’s The House of Mirth. Once a socialite whose presence hosts vied for, Lily progressively falls into more and more dishonorable positions until she ultimately perishes. What factors are at play in such a drastic change? For one, Lily’s love of risk does not serve her well in the competitive game of the elite class, where women are “capable of sacrificing all…old friends” (Wharton 263) for the chance at improving their social standing. Lily’s initial footing in the elite, already unstable without a reliable income or wealthy husband, is shaken by her inaccurate judgments of risks, and she eventually finds herself unable to survive in her new environment. Unlike her malicious cohorts who are willing to ruin others to maintain their own footings in the upper class, Lily has a sense of morality, which becomes a hindrance to her fight for survival. Nature-inspired imagery of Lily’s situation pervades the novel and is reminiscent of social Darwinism, where only the wealthy and well-endowed can thrive—one woman’s gain is another woman’s loss. Interestingly, this zero sum game does not apply for upper class men. Seldon, for example, is able to aspire towards morality and engage in sentimental risks because, as a man, his reputation is not as easily damaged as Lily’s. Like Darwin’s finches, whose modified bills fit them for certain foods but not others, Lily’s specialization in forms and manners makes her only suitable for life in the upper class, where her decorative nature is appreciated; unfortunately, she is unable to regain entry into the elite after she is kicked out due to her risky behavior and personal moral code, and she faces her mortality when she is unable to adapt
Probing the Progression, Properties, and Progenies of Magnetic Reconnection
Get PDFMagnetic reconnection is a plasma phenomenon in which opposing magnetic fields annihilate and release their magnetic energy into other forms of energy. In this thesis, various aspects of collisionless magnetic reconnection are studied analytically and numerically, and an experimental diagnostic for magnetic fields in a plasma is described.
The progression of magnetic reconnection is first illustrated through the formulation of a framework that revolves around canonical vorticity flux, which is ideally a conserved quantity. The reconnection instability, electron acceleration, and whistler wave generation are explained in an intuitive manner by analyzing the dynamics of canonical vorticity flux tubes. The validity of the framework is then extended down to first principles by the inclusion of the electron canonical battery effect. The importance of this effect during reconnection determines the overall structure and evolution of the process.
A crucial property of magnetic reconnection is its accompaniment by anomalous ion heating much faster than conventional collisional heating. Stochastic heating is a mechanism in which, under a sufficiently strong electric field, particles undergo chaotic motion in phase space and heat up dramatically. Using the previously established canonical vorticity framework, it is demonstrated that the Hall electric fields that develop during reconnection satisfy the stochastic ion heating criterion and that the ions involved indeed undergo chaotic motion. This mechanism is then kinetically verified via exact analyses and particle simulations and is thus ultimately established as the main ion heating mechanism in magnetic reconnection.
An important progeny of magnetic reconnection is whistler waves. These waves interact with energetic particles and scatter their pitch-angles, triggering losses of magnetic confinement. A previous study demonstrated via exact relativistic analyses that if a particle undergoes a "two-valley" motion, it undergoes drastic changes in its pitch-angle. This analysis is extended to a relativistic thermal distribution of particles. The condition for two-valley motion is first derived; it is then shown that a significant fraction of the particle distribution meets this condition and thus undergoes large pitch-angle scatterings. The scaling of this fraction with the wave amplitude suggests that relativistic microburst events may be explained by the two-valley mechanism. It is also found that the widely-used second-order trapping theory is an inaccurate approximation of the theory presented.
A new method of probing the magnetic field in a plasma is described and developed to some extent. It utilizes the two-photon Doppler-free laser-induced fluorescence technique, where two counter-propagating laser beams effectively cancel out the Doppler effect and excite electron populations. The fluorescence resulting from the subsequent de-excitation is then measured, enabling the resolution of Zeeman splitting of the spectral lines from which the magnetic field information can be inferred. A high-power, repetitively-pulsed radio-frequency plasma source was developed as the subject of diagnosis, and preliminary results are presented.</p
Aspects of Reduced-Order Modeling of Turbulent Channel Flows: From Linear Mechanisms to Data-Driven Approaches
Get PDFThis thesis concerns three key aspects of reduced-order modeling for turbulent shear flows. They are linear mechanisms, nonlinear interactions, and data-driven techniques. Each aspect is explored by way of example through analysis of three different problems relevant to the broad area of turbulent channel flow.
First, linear analyses are used to both describe and better understand the dominant flow structures in elastoinertial turbulence of dilute polymer solutions. It is demonstrated that the most-amplified mode predicted by resolvent analysis (McKeon and Sharma, 2010) strongly resembles these features. Then, the origin of these
structures is investigated, and it is shown that they are likely linked to the classical Tollmien-Schichting waves.
Second, resolvent analysis is again utilized to investigate nonlinear interactions in Newtonian turbulence. An alternative decomposition of the resolvent operator into Orr-Sommerfeld and Squire families (Rosenberg and McKeon, 2019b) enables a highly accurate low-order representation of the second-order turbulence statistics. The reason for its excellent performance is argued to result from the fact that the decomposition enables a competition mechanism between the Orr-Sommerfeld and Squire vorticity responses. This insight is then leveraged to make predictions about how resolvent mode weights belonging to several special classes scale with increasing Reynolds number.
The final application concerns special solutions of the Navier-Stokes equations known as exact coherent states. Specifically, we detail a proof of concept for a data-driven method centered around a neural network to generate good initial guesses for upper-branch equilibria in Couette flow. It is demonstrated that the neural network is capable of producing upper-branch solution predictions that successfully converge to numerical solutions of the governing equations over a limited range of Reynolds numbers. These converged solutions are then analyzed, with a particular emphasis on symmetries. Interestingly, they do not share any symmetries with the known equilibria used to train the network. The implications of this finding, as well as broader outlook for the scope of the proposed method, are discussed.</p
Towards High Solar to Fuel Efficiency: From Photonic Design, Interface Study, to Device Integration
Get PDFEfficient unassisted solar fuel generation, a pathway to storable renewable energy in the form of chemical bonds, requires optimization of a photoelectrochemical device based on photonic design and interface study. We first focused on enhancing absorption via nanophotonic design of light absorbers. Near-unity, broadband absorption in sparse InP nanowire arrays with multi-radii and tapered nanowire array designs are simulated and experimentally demonstrated. Later, a few strategies are introduced to achieved high solar-to-fuel efficiency.
Optically, photoelectrochemical device would require the catalyst ensembles to be highly transparent. We report a record solar-to-hydrogen efficiency by integrating Rh nanoparticle catalysts onto photocathodes with minimal parasitic absorption and reflection losses in the visible range. The other two light management strategies have been developed and experimentally verified to create highly active and effectively transparent catalyst structures: i) arrays of mesophotonic dielectric cone structures that serve as tapered waveguide light couplers to efficiently guide incident light through apertures in an opaque catalyst into the light absorber, and ii) an effectively transparent catalyst consisting of arrays of micron-scale triangular cross-sectional metal grid fingers, which are capable of redirecting the incoming light to the open areas of the PEC cell without shadow loss.
The electronic properties of the surface films exposed to the electrolyte are also critical. The anatase TiO₂ protection layer on the photocathode creates a favorable internal band alignment for hydrogen evolution, promoting the transport of the excess electrons and inhibiting voltage drops. The interfacial conduction mechanism between the defected TiO₂ and metal catalysts is investigated. A combinatorial approach of electrochemistry, X-ray photoelectron spectroscopy, and resonant X-ray spectroscopy reveals the correlation between the interfacial quasi-metal phase with TiO₂ properties. By careful control of gas diffusion electrode assembling to maintain appropriate wetted catalyst interface, another record solar-to-CO efficiency with extended stability can be realized.</p
Elemental Abundances in the Local Group: Tracing the Formation History of the Great Andromeda Galaxy
Get PDFThe Local Group (LG) is an environment accessible to detailed studies of galaxy formation, providing a complement to the early universe. In particular, spectroscopy of resolved stellar populations in the LG provides kinematical and chemical information for individual stars that can be used to infer the history of L★ galaxies like the Milky Way (MW) and Andromeda (M31).
The Gaia revolution in the MW, combined with spectroscopy from APOGEE and other surveys, has enabled comprehensive observational studies of the MW's formation history. In addition, comparisons to simulations can be leveraged to maximally utilize such observational data to probe the hierarchical assembly of galaxies. Toward this goal, I have analyzed simulations of chemical evolution in LG dwarf galaxies to assess their ability to match observations.
The exquisite detail in which the MW has been studied is currently not achievable in any other L★ galaxy. For this reason, the MW is a template for our understanding of galaxy formation. M31 is the only external galaxy that we can currently hope study in a level of detail approaching the MW. Studies of M31 have recently taken on greater significance, given the growing body of evidence that its formation history differs substantially from that of the MW.
In an era of limited information about elemental abundances in M31, I have developed a technique to apply spectral synthesis to low-resolution stellar spectroscopy in order to measure abundances for individual giant stars in distant LG galaxies. Through undertaking the largest deep, spectroscopic survey of M31 to date with my collaborators, this has resulted in the first measurements of the elemental abundances in the inner stellar halo and stellar disk of M31, and the largest homogeneous catalog of elemental abundances in M31. With this foundational work, we have opened the doors to detailed studies of the chemical composition of M31.
Now, we can begin to ask--and answer--what differences in the elemental abundances of the M31 and the MW imply for our knowledge of galaxy formation in the broader universe. At the cusp of next-generation observational facilities and theoretical simulations, we can only advance toward this goal.</p
Functional Autonomy Techniques for Manipulation in Uncertain Environments
Get PDFAs robotic platforms are put to work in an ever more diverse array of environments, their ability to deploy visuomotor capabilities without supervision is complicated by the potential for unforeseen operating conditions. This is a particular challenge within the domain of manipulation, where significant geometric, semantic, and kinetic understanding across the space of possible manipulands is necessary to allow effective interaction. To facilitate adoption of robotic platforms in such environments, this work investigates the application of functional, or behavior level, autonomy to the task of manipulation in uncertain environments. Three functional autonomy techniques are presented to address subproblems within the domain.
The task of reactive selection between a set of actions that incur a probabilistic cost to advance the same goal metric in the presence of an operator action preference is formulated as the Obedient Multi-Armed Bandit (OMAB) problem, under the purview of Reinforcement Learning. A policy for the problem is presented and evaluated against a novel performance metric, disappointment (analogous to prototypical MAB's regret), in comparison to adaptations of existing MAB policies. This is posed for both stationary and non-stationary cost distributions, within the context of two example planetary exploration applications of multi-modal mobility, and surface excavation.
Second, a computational model that derives semantic meaning from the outcome of manipulation tasks is developed, which leverages physics simulation and clustering to learn symbolic failure modes. A deep network extracts visual signatures for each mode that may then guide failure recovery. The model is demonstrated through application to the archetypal manipulation task of placing objects into a container, as well as stacking of cuboids, and evaluated against both synthetic verification sets and real depth images.
Third, an approach is presented for visual estimation of the minimum magnitude grasping wrench necessary to extract massive objects from an unstructured pile, subject to a given end effector's grasping limits, that is formulated for each object as a "wrench space stiction manifold". Properties are estimated from segmented RGBD point clouds, and a geometric adjacency graph used to infer incident wrenches upon each object, allowing candidate extraction object/force-vector pairs to be selected from the pile that are likely to be within the system's capability.</p