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Seismic Wavefield Imaging of the Earth: the Regional, the Local, and the Remote
Get PDFIn this thesis, I use seismic wavefield methods to illuminate the interior structure and the dynamics of the Earth across different scales. First, I image the large-scale lithospheric structure at the eastern sector of the Trans-Mexican Volcanic Belt to constrain on the transition from flat to steeper subduction in central Mexico. Then, I move to a regional scale and image the dynamics of the Wallowa Mountain block in northeastern Oregon, where mantle-based stresses appear to have played an essential role in shaping the crustal structure. With the findings of this investigation, I was able to illuminate a deformation mechanism of mantle origin, which I also use here to explain other near-surface processes in different parts of the North America continent. After, I move to a local scale, where I use dense oil-industry instrumentation to image the sub-kilometer crustal structure of Long Beach, California. In the first part of this investigation, I use noise-derived surface waves to create a high-resolution shear wave velocity model of the first kilometer of the crust, which I use to numerically determine the variability in the expected ground shaking intensity of the area. In the second part, I move past the traditional surface wave analysis and use the body wave portion of the noise-derived Green's functions to create a high-resolution compressional wave velocity model beneath one of the surveys. Finally, I present a waveform-based method of analysis that shows great promise as a new way of investigating the seismic behavior and the physical conditions of isolated marine environments.</p
Instabilities in the Flow Over a Spinning Disk at Angle of Attack
Get PDFMicro air vehicles (MAVs) face stability issues, especially as they continue to decrease in size. A spinning disk is inherently robust to external disturbances due to its spin stabilization, and therefore is a potential design for stable MAV flight. However, controlled flight of a spinning disk requires a detailed understanding of the underlying flow structures that determine the aerodynamic behavior. A spinning disk acts to rotate and propel nearby flow tangentially outwards, while drawing in fluid from above. In this way, spin acts as an additional source of both angular and linear momentum from the disk's surface, which can alter the wake structure significantly. In this thesis, we explore how spin affects the aerodynamic forces on a disk and characterize several instabilities that occur. To this end, we use the immersed-boundary Lattice Green's function (IBLGF) method to simulate flow over a spinning disk at angle of attack for Reynolds numbers of O(102) and tip-speed ratios (non-dimensional spin rate) up to 3.
At these Reynolds numbers, the steady flow first undergoes a bifurcation associated with wake instability, giving rise to vortex shedding. Increasing tip-speed ratio leads to monotonic increases in both lift and drag, although the lift-to-drag ratio remains fairly constant. We also identify several distinct wake regimes, including a region of vortex-shedding suppression, and the appearance of a distinct corkscrew-like short-wavelength instability in the advancing tip vortex. To understand the mechanism leading to suppression of vortex shedding, we study the streamlines and vortex lines in the wake. We show that the vorticity produced by the spinning disk strengthens the tip vortices, inducing a spanwise flow in the trailing edge vortex sheet. This helps to dissipate the vorticity, which in turn prevents roll up and thus suppresses vortex shedding. For the short-wavelength instability, we use spectral proper orthogonal decomposition (SPOD) to identify the most energetic modes and compare it to elliptic instabilities seen in counter-rotating vortex pairs with axial flow. The addition of vorticity from the disk rotation significantly alters the circulation and axial velocity in the tip vortices, giving rise to elliptic instability despite its absence in the non-spinning case. We also observe lock-in between the frequency of the elliptic instability and twice the spin frequency, indicating that disk rotation acts as an additional forcing for the elliptic instability. Many of these phenomena are consistent with observations in high Reynolds number studies and for other bluff body geometries. As a result, the mechanisms proposed here may serve as a basis for understanding and predicting the changing wake structures in more complex flow configurations.</p
Development of a Synthetic Strategy Toward Falcatin A. Development of an Asymmetric Diels–Alder Reaction of α-Acyloxy Enones
Get PDFAccessing natural products via de novo synthetic methods is important for the discovery of new medicines, antibiotics, agrochemicals, and more. Design and investigation of efficient strategies is of interest to many pharmaceutical industries.
Herein, we discuss several strategies geared towards the synthesis of the natural product falcatin A. First, a general discussion of the class of natural products is discussed. Secondly, we discuss our first generation photoredox cascade cyclization approach toward the synthesis of falcatin A. This strategy allows for the efficient and convergent synthesis of two halves of falcatin. Next, a transition metal-catalyzed cascade cyclization approach is discussed in which we were able to successfully synthesize the core of the natural product on a model system. Efforts are ongoing to elaborate to more advanced fragments for the synthesis of falcatin A. Lasty, we discuss our work on the yttrium-catalyzed asymmetric Diels–Alder reaction of α-acyloxy enone dienophiles, performed in collaboration with BASF. We demonstrate that this methodology can be utilized to access enantioenriched natural product T-4-ol.</p
Random Quantum Circuits and Their Simulation Complexity: an Analysis with Statistical Mechanics
Get PDFRandom circuit simulation, the task of replicating the output of a randomly chosen noiseless quantum computation, has been proposed as a path toward achieving quantum advantage: it is believed to be easy for quantum devices, but hard for classical ones. This thesis scrutinizes both sides of this belief. On the one hand, we investigate whether the task is classically hard—we find that, in certain non-trivial cases, it can actually be easy, complicating a potential general proof of hardness. On the other hand, we investigate whether the task can be easily accomplished on realistic quantum devices, which are subject to substantial noise rates—we find that, indeed, a version of the circuit simulation task can be salvaged even on a noisy quantum device performing the computation with low fidelity, as long as the noise meets certain conditions. Thus, this thesis emphasizes that, to construct a strong argument of quantum advantage via random circuit simulation on noisy quantum hardware, the core theoretical challenge remains proving lower bounds on the classical complexity of the task; doing so will require new ideas to circumvent the barriers presented by our work.
A key analytical technique we utilize for each of our results is the statistical mechanics method for random quantum circuits, which maps random quantum circuits made from local Haar-random gates to partition functions of classical statistical mechanical systems. This thesis demonstrates the utility of this method by applying it in several new ways. In some cases, we use it for heuristic reasoning about the behavior of random quantum circuits. In others, we go further and perform rigorous calculations of the resulting partition function, leading to precise technical conclusions about random quantum circuits, such as sharp bounds on the number of random gates needed to achieve the anti-concentration property.</p
Understanding Exoplanet Atmospheres
Get PDFThe study of exoplanet atmospheres is a blossoming field. Over the past two decades, dozens of hot gas giant atmospheres have been observed using a variety of techniques with both space and ground telescopes, revealing the presence of water, the ubiquity of clouds, the presence of equatorial jets, the existence of photoevaporation, and much more. For the far more abundant planets smaller than ~3 R⊕, which potentially have a wide variety of exotic atmospheric compositions, observations are more challenging. We are just beginning to characterize their atmospheres.
This thesis consists of 6 papers on the topic of exoplanet atmospheres. In paper 1, we use Spitzer observations to make rudimentary 1D maps of two hot giant planets, allowing us to infer atmospheric circulation properties and compare them to models and to similar observations of other giant planets. In paper 2, we present PLATON, a fast, open source, easy to use, and easy to understand Python package that calculates transmission spectra for exoplanets and retrieves atmospheric characteristics based on observed spectra. PLATON supports the most common atmospheric parameters, in addition to less commonly included features such as a Mie scattering cloud model and unocculted starspot corrections. In paper 3, we add significant improvements to PLATON, including updated molecular opacities and emission spectra capability. In addition, we perform the most comprehensive retrieval on published HST and Spitzer transmission and emission spectra of the archetypal hot Jupiter HD 189733b, finding that they are well-matched by a moderately metal-enhanced atmosphere with a solar C/O ratio where the terminator is dominated by extended nm-sized hazes.
Papers 4-6 cover mass loss from sub-Neptunes. In paper 4, we present a tight upper limit on the amount of escaping helium from the the archetypal super Earth 55 Cnc e, suggesting that it has no primordial (H/He) atmosphere. In paper 5, we obtain the first detection of an escaping atmosphere from a young mini Neptune by measuring Lyα absorption from HD 63433c. We do not detect absorption from the inner planet, suggesting that the inner planet may have lost its primordial atmosphere while the outer one has not. In paper 6, we detect escaping helium from a young mini Neptune for the first time. The inferred mass loss rate is high enough to strip a significant portion of the atmosphere within the planet's lifetime; combined with the previous paper, these observations support the canonical explanation of mini Neptunes as rocky planets with a substantial primordial H/He atmosphere and validate models predicting that mini Neptunes can transform into super Earths.</p
Charge and Heat Transport in Non-Metallic Crystals Using First-Principles Boltzmann Transport Theory
Get PDFPhonon-phonon and electron-phonon interactions underlie many fundamental transport properties like thermal conductivity and electrical mobility, and models of these properties provide information about the underlying microscopic interactions present in the materials. Many of these models use the Boltzmann transport equation where the choice of the expression for the collision integral is the most important and challenging aspect since it should capture all of the relevant interactions. In the past the expressions were semi-empirical, but in recent decades first principles models with no fitting parameters have become more commonplace, leading to discovery of new materials or providing deeper insights into the relevant mechanisms governing transport. This thesis presents first-principles calculations of thermal conductivity in polymer crystals, and charge transport at high electric fields in semiconductors in the Boltzmann transport framework.
Polymers are thermally insulating in their typical amorphous form, but it is known that their thermal conductivity can be enhanced through drawing and aligning of their polymer chains. With perfect chain alignment, the structures can be described as polymer crystals, which tend to contain many atoms per unit cell. However, the conventional understanding of thermal transport in crystals predicts low thermal conductivity for complex, many atom unit cells. It is known from simple models that phonon focusing redirects the heat flow into the polymer chain direction, but the extent to which phonon focusing plays a role in setting the intrinsic upper limits of polymer thermal conductivity has not been assessed from a first principles standpoint. We calculate the ab initio lattice conductivity of polythiophene, a complex molecular crystal with 28 atoms per unit cell, using the temperature dependent effective potential (TDEP) method to obtain finite temperature phonon properties taking into account the large quantum nuclear motion of hydrogen atoms present in polymers. We find a high thermal conductivity due to phonon focusing and stiff branches that overcome the expected low phonon lifetimes. The phonon focusing aligns group velocities along the chain axis throughout the Brillouin zone, even for states with wave vector almost orthogonal to the chain axis.
For charge transport, ab initio calculations focus almost exclusively on low field mobility, but technologically relevant phenomena like negative differential resistance manifest only at high fields far from equilibrium. Further, there are no ab initio calculations of non-equilibrium electronic noise, which differs qualitatively from transport observables at high fields. We report a methodological advance that obtains both the high-field transport properties and the non-equilibrium noise using an ab initio Boltzmann transport approach. Our method extends the collision integral to high fields by making physically motivated approximations to account for the non-linearities at high fields.
Using our method, we calculate the high-field noise and transport properties in GaAs and find that the 1ph level of theory is inadequate. Thus, we implement an approximate form of higher order interactions where electrons are scattered consecutively by two phonons (2ph) and find that these 2ph processes qualitatively alter the energy relaxation of the electron system compared to 1ph scattering, resolving a long-standing discrepancy in the strength of intervalley scattering inferred from different experiments. We also calculate non-equilibrium electronic noise from first principles for the first time. However, we are not able to reproduce experimental trends, and we suggest that 2ph processes beyond our approximation may be necessary to obtain experimental agreement. Our calculation shows how noise provides a new observable against which the accuracy of first-principles methods can be measured.</p
Gut Microbiome Modulates Microglia Physiology in Homeostatic and Disease States
Get PDFThe gastrointestinal tract (GI) harbors a complex community of ~100 trillion bacteria, fungi, and viruses collectively referred to as the gut microbiome. Through direct and indirect signaling mechanisms, the gut microbiome exerts its effects on almost every organ system, including the brain. Constant, bi-directional communication along the gut-brain axis is required for the normal and healthy development of the host Central Nervous System (CNS). One of the cells in the CNS shaped by microbial-derived cues is microglia, the resident immune cells in the brain. Aberrant microglia activity is a driving force of several neurological diseases in which the gut microbiome plays a role, including Parkinson’s disease (PD).
In this thesis, we explore the interplay between gut microbiota signaling and microglia physiology during homeostatic and disease states. We first detail how microbial signaling along the gut-brain axis shapes microglial development and function. Next, we explore how the gut microbiome composition influences microglial activation states in the context of disease. Leveraging a preclinical mouse model of PD, we show that dietary-driven changes to the gut microbiome through the use of prebiotics attenuates motor deficits and α-synuclein aggregation. These effects result from changes in microglial gene expression and activation status. Collectively, these findings have broad implications for the gut microbiome research community and highlight potential for development of microbiome-based therapies for diseases of the brain
Path Space Markov Chain Monte Carlo Methods for Molecular Simulation
Get PDFPath space Markov-chain Monte Carlo (McMC) provides a versatile framework for simulating the structure and dynamics of condensed-phase systems aptly described by classical and quantum Boltzmann statistics. This thesis comprises our efforts to design, analyze and improve path space McMC algorithms to achieve numerically advantageous, and physically accurate, simulation of molecular processes across a range of scales. To improve molecular dynamics (MD) simulations of atomically resolved systems exhibiting pronounced nuclear quantum effects, we introduce a family of integrators for non-preconditioned path-integral MD exhibiting dimension-free statistical accuracy and efficiency, and enabling a many-fold increase in time-step stability relative to conventional approaches at no additional computational cost or implementation complexity. The integrators come with robust performance guarantees that are borne out in thermostatted ring-polymer MD simulations of realistic condensed-phase models. Concurrently, toward extending the range of accessible timescales in stochastic MD simulations of mesoscale coarse-grained molecular systems, we introduce a parallel-in-time integrator for the overdamped Langevin equation based on McMC evaluation of a path-integral representation of the many time-step stochastic MD transition kernel. The parallel-in-time integrator achieves simultaneous integration of multiple stochastic MD time-steps at no greater wall-time cost and with no lesser accuracy than a standard Euler--Maruyama integrator does in serial, and thus instantiates new opportunities to accelerate stochastic dynamics simulations on massively parallel computer architectures. Our work along these two methodological avenues extends the utility of path space McMC across applications in molecular simulation and has broader implications in other disciplines that require accurate and efficient simulations of Markov diffusion processes in state spaces or path spaces.</p
Development of Nickel-Catalyzed Asymmetric Cross-Coupling Reactions
Get PDFAsymmetric cross-coupling reactions have emerged in recent decades as powerful tools for the formation of valuable carbon–carbon bonds in the synthesis of enantioenriched small molecules. Nickel catalysis in particular has proven to be an especially powerful tool for the formation of C(sp²)–C(sp³) bonds in part due to the propensity of nickel catalysts to access odd oxidation states and interact with radical intermediates. Application of asymmetric nickel catalysis to a variety of radical precursors has resulted in the development of a broad range of stereoconvergent reductive and redox-neutral cross coupling reactions, allowing for the highly enantioselective formation of many synthetically useful and biologically relevant molecules.
Herein we describe our recent efforts in the development of new nickel-catalyzed enantioselective cross-coupling reactions. First, an enantioselective reductive cross- coupling of alkenyl and benzyl halides was rendered electroreductive. Careful electrochemical cell design proved critical for this reaction, which represents the first report of an enantioselective nickel-catalyzed electroreductive cross coupling reaction. We next discuss our development of an enantioselective reductive cross coupling of ⍺-chloroesters with aryl iodides. This reaction proceeds with especially high ee when β-branched substrates are employed, prompting the development of a multivariate linear regression model to probe the origin of the observed enantioselectivity trends. Finally, a redox-neutral nickel/photoredox co-catalyzed coupling of ⍺-N-heterocyclic potassium alkyl trifluoroborates and aryl bromides is reported. This reaction, developed in collaboration with researchers at Merck, provides rapid enantioselective access to motifs commonly found in bioactive molecules.</p
Detecting Small Signals: Near-Infrared Studies of Substellar Companions
Get PDFAs the number of known exoplanets, or planets in other solar systems, grows, we have become empowered to ask deeper and more specific questions about the possibilities presented by our universe. A group of giant gaseous planets called "hot Jupiters" spurred us to think in new ways about giant planet formation. The diversity of solar system architectures, exoplanet sizes, atmospheric composition and dynamics expands our perspective on the many possible outcomes resulting from the same primordial ingredients in different amounts and in different environments. To fully answer these questions, we need to look directly into exoplanet atmospheres. Infrared spectra can reveal atmospheres' molecular content and certain physical processes, such as winds and rotation effects. From spectoscopic measurements, we can test theories of planet formation, evolution, and habitability. Unfortunately, most current direct exoplanet characterization techniques are limited to certain populations, whether planets with specific orbital geometries or planets either very far from or very near their host stars. These well-established methods miss a key population of exoplanets, specifically those that are non-transiting and with orbital separations between roughly 0.15 and 5 AU. This group contains around 19% of the exoplanets known today (a percentage which will only increase in the coming extreme precision radial velocity era) and will almost certainly include the nearest potentially habitable world. This dissertation presents two projects. In the first, we work to further a direct exoplanet characterization approach that will be sensitive to these elusive planets by identifying and reducing an insidious source of structured noise - in the process, making it easier to directly detect planetary emission. With advancements promised by the simulation framework presented in this dissertation, our multi-epoch direct detection approach, in combination with planet-to-star contrast gains enabled by high-contrast imaging technology, will be uniquely capable of characterizing ever smaller, cooler, and more complex planetary atmospheres. In the second project, we apply the direct detection method to a particularly interesting substellar object, a brown dwarf in a very close (<2 hour) orbit around a white dwarf, in order to understand how gaseous atmospheres behave in exotic irradiation environments. Together, these projects demonstrate the capacity of multi-epoch spectroscopic observations to serve as a window into gaseous atmospheres and a pathway to potentially habitable worlds