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Microstructural Effects on Diffusion and Mechanical Properties in Different Material Systems
Get PDFMaterial microstructures is a very broad subject that encompasses most of the field of materials science. Advances in materials characterization and small scale mechanical experiments have brought about progress in the understanding of microstructural features and mechanisms down to the nanometer scale. In contrast to bulk features and properties, the small length scale of these microstructures lead to many interesting properties, and often requires a material-by-material, and even localized region-by-region study. While a thorough understanding of microstructural effects even in one material system is way beyond the scope of this thesis, there are nonetheless many common themes and properties that link together microstructures and their effects on different materials, especially in terms of mechanical properties.
In this thesis, the effects of microstructural features such as grain boundaries, surface modification and structural hierarchy are investigated using two sample material systems: Cu-In-Ga-Se (CIGS) thin films and marine diatom frustules. We find that grain structures (or a lack there of) play a major role in both systems, and lead to differences in material stiffness, strength, and diffusion of species. The latter is also significantly affected by material defects across length scales, exemplified in CIGS by both microscopic voids and pores, and atomic scale like substitutional point defects. On the other hand, in diatoms, a low flaw density combined with an effective hierarchical design can propel the mechanical property of relatively simple ingredients like amorphous silica, to achieve extraordinary mechanical strength. We will conclude by showcasing that we can generalize some of these knowledge on microstructural effects across material systems, to help designing manmade structures that fully capture the material-level and structural-level properties of natural marine diatoms.</p
Eph Receptor Clustering by Chondroitin Sulfate Inhibits Axon Regeneration
Get PDFChondroitin sulfate proteoglycans (CSPGs) play important roles in the developing and mature nervous system, where they guide axons, maintain stable connections, restrict synaptic plasticity, and prevent axon regeneration following CNS injury. The chondroitin sulfate glycosaminoglycan (CS GAG) chains that decorate CSPGs are essential for their functions. Through these sugar chains, CSPGs are able to bind and regulate the activity of a diverse range of proteins and through these interactions can regulate neuronal growth. These CS-protein interactions depend on specific sulfation patterns within the CS GAG chains, and accordingly, particular CS sulfation motifs are upregulated during development, in the mature nervous system, and in response to CNS injury. Thus, spatiotemporal regulation of CS GAG biosynthesis may provide an important mechanism to control the functions of CSPGs and modulate intracellular signaling pathways. Here, we will discuss these sulfation-dependent processes and highlight how the CS sugars on CSPGs contribute to neuronal growth, axon guidance, and plasticity in the nervous system.
Chondroitin sulfate proteoglycans (CSPGs) are a major barrier to regenerating axons in the central nervous system (CNS), exerting their inhibitory effect through their polysaccharide side chains. Chondroitin sulfate (CS) potently inhibits axon regeneration through modulation of inhibitory signaling pathways induced by carbohydrate binding to protein ligands and receptors. Here, we identify a novel carbohydrate-protein interaction between CS and EphA4 that inhibits axon regrowth. We characterize the mechanism of activation and demonstrate how carbohydrate binding induces phosphorylation of the intracellular kinase domain through clustering of cell surface EphA4. Collectively, our studies present a novel mechanism of EphA4 activation by CS independent of the canonical ephrin ligands and uncover the role of this interaction in inhibition of neurite regrowth after injury. Our results underscore a mechanism of action by which carbohydrates can function as direct, activating ligands for protein receptors and provide mechanistic insights into the inhibition of axon growth by CS following injury to the CNS.
Chondroitin sulfate proteoglycans (CSPGs) regulate neuronal plasticity, as well as axon regeneration and guidance through their ability to bind protein ligands and cell surface receptors. In this way, extracellular CSPGs can modulate the activity of intracellular signaling pathways. Here, a computational analysis of EphA4-CS interactions is performed to characterize the importance of key arginine and lysine residues towards CS binding, and to identify structural differences in CS-A, CS-C, CS-D, and CS-E docking to EphA4. Carbohydrate-induced Eph receptor clustering could be a general mechanism of Eph receptor activation. To identify additional Eph receptors that interact with CS, CS-E was docked to all EphA and EphB family members to predict relative binding affinities. The relative strengths of the predicted binding energies are: EphB4 > EphA8 > EphA1 > EphA3 > EphB1 > EphB3 > EphA7 > EphA5 > EphA4 > EphA6 > EphB2 > EphB6 > EphA2. In addition, the arginine and lysine residues that mediate CS binding are identified for each Eph receptor. These computational predictions provide mechanistic insights into Eph receptor activation by chondroitin sulfate and have implications for inhibition of axon regeneration following injury to the nervous system and axon guidance during development.</p
Silicon Revisited: Understanding Pure Phonon Anharmonicity and the Effects on Thermophysical Properties
Get PDFPhonons, quantized lattice vibrations, govern most of the thermophysical properties of solid-state materials such that understanding the temperature dependent lattice dynamics is of great technological importance. I performed inelastic neutron scattering measurements at the Spallation Neutron Source on ARCS, a wide-angular chopper spectrometer, to measure phonon dispersions and density of states over a wide range of temperatures. Large phonon anharmonicities manifested by phonon energy shifts and broadenings were observed in both measured phonon dispersions and phonon density of states. The sources of deviations from the simple harmonic model with temperature were elucidated using experimentally assessed lattice dynamics coupled with ab initio methods. Pure anharmonicity dominates the changes in lattice dynamics with temperature and therefore drive the entropy and thermophysical properties of thermal expansion and thermal conductivity. Crystal structure, anharmonicity, and nuclear quantum effects all play important roles in the thermal expansion of silicon, and a simple mechanical explanation is inappropriate. The quantum effect of nuclear vibrations is also expected to be important for thermal expansion of many materials. My experimental techniques capture the linewidth broadenings from phonon anharmonicity needed to calculate thermal conductivity. The methods developed for data reduction on single crystal inelastic neutron scattering data and predicting macroscopic quantities should also be useful for understanding microscopic mechanisms behind thermophysical properties for materials
The Primordial Origin and Dynamical Sculpting of Close-In Planetary System Architectures
Get PDFFor centuries, planet formation theories were tuned to reproduce the remarkable coplanarity of our Solar System. Specifically, the eight planetary orbital planes exhibit mutual inclinations limited to ~1−2 degrees. Furthermore, the misalignment between the Sun's spin axis and the orbital planes of the planets – the 'spin-orbit misalignment'– is only about 6 degrees. However, observational characterization of close-in extrasolar planetary systems has revealed an abundance of spin-orbit misalignments ranging all the way from 0 to 180 degrees (Winn et al. 2010). Particularly among the hot Jupiters (giant planets with orbital periods shorter than ~1 week), spin-orbit misalignments are more prevalent in systems hosted by stars with effective temperatures exceeding about 6200 K. Previous work has suggested that these misalignments arose from violent dynamical interactions that excited planets onto inclined and eccentric orbits, with subsequent tidal circularization generating the observed population (Albrecht et al. 2012). This hypothesis has had great difficulty explaining misaligned multi-planet systems, and misaligned orbits of planets that are too distant from their host stars for tidal circularization to act over a sufficiently short timescale. A new mechanism is required.
In chapters II-VI, I present a theoretical framework referred to as "disk-torquing," whereby spin-orbit misalignments arise through the tilting of protoplanetary disks themselves (Batygin 2012, Spalding and Batygin 2014, 2015). In this picture, gravitational torques from a companion star lead to the precession of the protoplanetary disk. When the disk is young and massive, gravitational star-disk coupling quenches misalignments between the stellar spin axis and disk plane. However, as the disk dissipates, a secular resonance is encountered that impulsively excites large stellar obliquities, ranging between 0 and 180 degrees, in accordance with the observations. In addition, I computed the magnetic torques between the star and disk, finding that a dipole field strength of ~1 kGauss is sufficiently strong to realign the star and disk within typical disk lifetimes (~3 million years). Magnetic fields of this magnitude are observed to persist throughout the disk-hosting stage only for stars less massive than ~1.2 solar masses (Gregory et al. 2012), corresponding to a main sequence effective temperature of 6200 K, i.e., coincident with the observed break between aligned and misaligned hot Jupiters. Cumulatively, the disk-torquing framework exhibits qualitative consistency with the observed dependence of spin- orbit misalignments upon stellar mass, leaving the theory ripe for a statistical comparison to observations within future work.
The final three chapters change focus from spin-orbit misalignments toward the excitation of mutual inclinations between planetary orbits – orbit-orbit misalignments. Evaluation of the relative numbers of single to multi-transiting planetary systems within the Kepler space telescope’s dataset has revealed a dichotomy whereby there exist two populations of planetary system – one with low orbit-orbit inclination, and a second that either possesses a single planet, or possesses multiple planets with large mutual inclinations, leaving only one detectable via transit (Johansen et al. 2012, Ballard and Johnson 2016). In separate but related observational work, it has become apparent that transiting hot Jupiters often appear without co-transiting, close-in planetary companions, wheres warm Jupiters often do (Steffen et al. 2012, Huang et al. 2016). I showed that both of these observations can naturally arise owing to secular perturbations from the host star (Spalding and Batygin 2016, 2017). Specifically, young stars rotate fast, becoming oblate. If the star’s spin axis is misaligned with respect to the orbits of a multi-planet system, its quadrupole moment can disrupt the coplanarity of the system. Indeed, the stellar perturbations are often sufficient to completely destabilize the system (Chapter VI). In addition to constituting an entirely new mechanism of planetary instability, the origin of the required spin-orbit misalignment relates directly back to the discussion above – spin-orbit misalignments may drive the seemingly unrelated Kepler dichotomy.
Finally, I tied in the observation that hot Jupiters appear lonely by demonstrating that stellar contraction can give rise to a secular resonance that tilts exterior companions of hot Jupiters, taking them out of transit. Crucially, this resonance is encountered at an earlier time in systems hosting warm Jupiters, precisely owing to their slightly increased orbital distance. I found that the demarcation between a system undergoing secular tilting, and one where the disk quenches the tilting, coincides well with the relatively arbitrary dividing line between hot and warm Jupiters, usually set at orbital periods of about a week.
In summary, I showed that spin-orbit misalignments and orbit-orbit misalignments, measured across a range of planetary size classes, can arise primordially owing to interactions with the host star and binary companions. The importance of the central star had most likely been missed in the previous literature owing to our solar system’s peculiarly wide inner edge at ~0.4 AU, as opposed to the more typical ~0.1 AU within a galactic setting. In reality, through the wider lens of our galactic planetary census, a true understanding of planet formation demands a look at star-planet interactions wholly unknown from centuries of solar system exploration.</p
Controls on the Sulfur Isotopic Composition of Carbonate-Associated Sulfate
Get PDFSulfate in the modern ocean has a homogenous concentration and sulfur isotopic composition. It is well-mixed because rivers and mantle degassing deliver small amounts relative to its mass in the ocean. A similar small amount of sulfate is removed as biologic, sedimentary, and hydrothermal processes oxidize and reduce sulfur, carbon, and iron. These sulfur fluxes may have changed along with the carbon and oxygen cycles during ancient evolutionary, extinction, climatic, and tectonic transitions. The changing budget of marine sulfate is therefore key to understanding biogeochemical processes that control Earth’s surface environment. The sulfur isotopic composition of marine sulfate reflects the proportion of sulfur partitioned into reduced minerals, especially pyrite, in marine sediments and weathering rocks.
In this thesis, I examine how the sulfur isotopic compositions of ancient oceans is recorded in the sedimentary rock record and examine local and global effects on the sulfur isotopic composition of Paleozoic and the Mesoproterozoic sedimentary rocks. Carbonate minerals form in many depositional environments throughout Earth history and their chemical compositions relate to that of the fluid in which they formed. Much of my thesis focuses on the sulfur isotopic composition of minor amounts of sulfate incorporated into calcite, dolomite, and aragonite called carbonate-associated sulfate. Unpacking the local biogeochemical processes and global budgets affecting the sulfur isotopic composition of ancient carbonates enriches and clarifies the paleoenvironmental information preserved in the sedimentary record.
Chapter 1 is a compilation and critical comparison of proxy records of the sulfur isotopic composition of Phanerozoic seawater sulfate. I compared data from marine evaporites, barite, and carbonate-associated sulfate and showed where each record is prone to biases and which processes create variance. Only carbonate-associated sulfate data fills critical periods of biogeochemical change, but it is the most susceptible to sources of variance other than passively recording the composition of ancient oceans. However, this additional variance reflects changes in the biogeochemical processes during early diagenesis in penecontemporaneous sediments, which are the locus of the pyrite burial and sulfide reoxidation fluxes pulling on the global sulfur budget.
Chapter 2 utilizes a recently-developed analytical technique to compare the carbonate-associated sulfate of diagenetic carbonates and primary marine biogenic carbonates from latest Ordovician and earliest Silurian strata on Anticosti Island, Quebec. These samples span the duration of the Hirnantian Stage glaciation of Gondwana, which coincided with and possibly caused the Late Ordovician Mass Extinction. Much of the variance observed in bulk carbonate-associated sulfate is imparted during early diagenesis and burial diagenesis, and the best-preserved calcite from ancient brachiopods faithfully reflects seawater’s sulfur isotopic composition. Seawater sulfate’s isotopic composition did not change during the glaciation and extinction, supporting prior constraints on the mass of the marine sulfate reservoir and the magnitude of sulfur flux changes.
In Chapter 3, we extended the record of seawater sulfate’s sulfur isotopic composition from well-preserved brachiopod calcite from the Cincinnati Arch, Indiana-Ohio-Kentucky and Gotland, Sweden. We demonstrated that marine sulfate likely remained globally well-mixed with a constant isotopic composition for at least 30 Myr, from the earliest Late Ordovician through the late Silurian. The ocean’s sulfur isotope composition likely changed little during multiple biotic crises, periods of basin restriction, oceanographic circulation changes, and sea level and climate changes. However, the first replicate carbonate-associated sulfate measurements of individual brachiopods indicate that even the best-preserved calcite is prone to diagenetic alteration that may obscure small changes in the ocean sulfate budget.
Exquisitely-preserved biogenic calcite is rare in the rock record and absent in Precambrian strata, but bulk limestones and dolomites may record changes in the composition of ancient oceans. Chapter 4 compares the sulfur isotopic composition of carbonate-associated sulfate from limestones and dolostone deposited in peritidal to basinal environments on the Capitan Reef carbonate platform in the Guadalupe Mountains, west Texas. Rocks formed in different environments at the same time have carbonate-associated sulfate with different sulfur isotope compositions. Carbonate-associated sulfate is incorporated into bulk limestone and dolostone during early marine diagenesis, and its sulfur isotopic composition reflects the diagenetic and depositional environment. Carbonates recrystallizing in low-energy environments may incorporate marine pore fluids whose sulfur isotopic compositions evolved by the action of microbial sulfate reducing organisms. The sulfur isotopic composition of rocks deposited in high-energy environments, however, reflects that of seawater sulfate because the diagenetic fluid is open to the ocean and has the same sulfur isotopic composition of seawater. Later meteoric and burial diagenetic processes to which other geochemical tracers, such as carbon and oxygen isotopes, are sensitive do not greatly affect carbonate-associated sulfate. Thus, a record of the evolution of the sulfur, carbon, and oxygen isotopic composition of ancient oceans cannot come from the same sedimentary archives.
Chapter 5 considers the range of hydrothermal and sedimentary reactions that fractionate sulfur isotopes to understand the origin of unusual millimeter-scale pyrite tubes associated with a Mesoproterozoic massive sulfide deposit in the Newland Formation, Belt Supergroup, Meagher County, Montana. The petrography and sedimentology of the tubes indicates that they formed on the seafloor or in the uppermost unlithified sediments from the effluence of metalliferous fluids into euxinic seawater. The texture-specific sulfur isotopic compositions of diagenetic barite, carbonate-associated sulfate, and diagenetic and hydrothermal pyrite indicates that there was an active microbial sulfate reducing community in the sediments and possibly colonizing the vents. A dynamic set of oxidation and reduction interactions between hydrothermal fluids and seawater were controlled by this community, leading to the novel morphology and texture of vent structures.
This work indicates that combining sedimentological and petrographic observations with sulfur isotope data can constrain a wide range of biogeochemical processes. It guides future sulfur geochemical examination of parts of the rock record, especially the Precambrian, with few traditional archives of ancient seawater sulfate’s chemistry. Information on both local and global controls on the sulfur isotopic composition of carbonate-associated sulfate, barite, and pyrite helps to resolve paleoenvironmental change.</p
Inclusive Searches for Supersymmetry at √s = 13 TeV Using Razor Kinematic Variables, and Data Scouting Using the CMS Trigger System
Get PDFWe present two searches for supersymmetric particles using proton-proton collision data collected by the CMS experiment at √s = 13 TeV. The searches use razor kinematic variables for signal discrimination and target the pair production of heavy gluinos and squarks in R-parity conserving supersymmetry. The first search is performed on 2.3 fb−1 of data collected by CMS in 2015. Two complete, independent background predictions are made: one based on fits using a parameterized functional form, and the other based on Monte Carlo simulation corrected via control samples in data. The second search is an expanded version of the first search, and is performed using the Monte Carlo-based background prediction method on 35.9 fb−1 of data collected in 2016. Both searches obtain results compatible with standard model background expectations. The null results are interpreted as limits on the masses and cross sections of gluinos, squarks, and higgsinos in the context of simplified models of supersymmetry. We discuss the outlook for the fit-based search strategy and explore how the technique of gaussian process regression may be useful as a tool to combat the challenges of this analysis methodology.
We also describe a new paradigm for trigger-level collider data analysis, which we refer to as data scouting. In this paradigm, searches for new physics are performed using event information reconstructed within the experiment’s trigger software. This circumvents traditional event rate constraints, such as disk space and the latency of offline reconstruction. We provide details on the implementation of a framework for data scouting in the CMS High-Level Trigger system and its successful use in Run II of the LHC. We discuss the impact of scouting on the physics program of CMS and demonstrate that it enables searches for new physics that would not otherwise be possible due to trigger constraints, such as hadronic resonance searches at low mass and searches for leptonic decays of dark photons.</p
Exploiting Structure for Scalable and Robust Deep Learning
Get PDFDeep learning has seen great success training deep neural networks for complex prediction problems, such as large-scale image recognition, short-term time-series forecasting, and learning behavioral models for games with simple dynamics. However, neural networks have a number of weaknesses: 1) they are not sample-efficient and 2) they are often not robust against (adversarial) input perturbations. Hence, it is challenging to train neural networks for problems with exponential complexity, such as multi-agent games, complex long-term spatiotemporal dynamics, or noisy high-resolution image data.
This thesis contributes methods to improve the sample efficiency, expressive power, and robustness of neural networks, by exploiting various forms of low-dimensional structure, such as spatiotemporal hierarchy and multi-agent coordination. We show the effectiveness of this approach in multiple learning paradigms: in both the supervised learning (e.g., imitation learning) and reinforcement learning settings.
First, we introduce hierarchical neural networks that model both short-term actions and long-term goals from data, and can learn human-level behavioral models for spatiotemporal multi-agent games, such as basketball, using imitation learning.
Second, in reinforcement learning, we show that behavioral policies with a hierarchical latent structure can efficiently learn forms of multi-agent coordination, which enables a form of structured exploration for faster learning.
Third, we showcase tensor-train recurrent neural networks that can model high-order mutliplicative structure in dynamical systems (e.g., Lorenz dynamics). We show that this model class gives state-of-the-art long-term forecasting performance with very long time horizons for both simulation and real-world traffic and climate data.
Finally, we demonstrate two methods for neural network robustness: 1) stability training, a form of stochastic data augmentation to make neural networks more robust, and 2) neural fingerprinting, a method that detects adversarial examples by validating the network’s behavior in the neighborhood of any given input.
In sum, this thesis takes a step to enable machine learning for the next scale of problem complexity, such as rich spatiotemporal multi-agent games and large-scale robust predictions.</p
Gravity Informed
Get PDFFormulating a universally satisfactory theory of quantum gravity is a long-standing open problem in theoretical physics. Relatively recently, the use of techniques from quantum information has emerged as a powerful tool for analyzing phenomena that lie at the intersection of quantum theory and gravitation. This thesis describes several advances and novel proposals that were made regarding information theoretic aspects of quantum gravity in three broad areas: holography, cosmology, and the black hole information problem.
Regarding holography, we first assess the differences between typical holographic states and fully random states. Next, we show that determining Ryu-Takayanagi surfaces in AdS3/CFT2 is computationally easy from a complexity-theoretic standpoint. Finally, we identify precise consistency conditions that constrain the validity of an early tensor network model for the AdS/CFT correspondence that uses the Multiscale Entanglement Renormalization Ansatz (MERA).
Regarding cosmology, we propose an alternative interpretation of the MERA as a discretization of de Sitter spacetime. Next, we return to holographic ideas and show that an appropriately-defined Generalized Second Law implies a cosmic no-hair theorem for certain classes of cosmological spacetimes. Finally, we advance an information-theoretic proposal for calculating the signature of a quantum gravity-motivated, fully covariant, natural ultraviolet cutoff in the spectrum of inflationary perturbations.
Regarding the black hole information problem, we begin by exhibiting a simple protocol which, under highly specific circumstances, allows one to retrieve a single qubit from a black hole. Next, we propose an operational resolution of the black hole information problem in which observers who enter the black hole could never detect an inconsistency between their experiences and quantum mechanics due to the finite amount of time available before reaching the central singularity. Finally, we discuss a proposal to understand the emergence of an ensemble of definite geometries during the process of black hole evaporation as a decoherence process, as well as its implications for the black hole information problem.</p
Advancing the Protein-Catalyzed Capture Agent Technology to New Frontiers
Get PDFProtein-catalyzed capture (PCC) agents are a nascent synthetic aptamer technology that was first disclosed in 2009. In addition to reviewing the different classes of peptide-based aptamers in chapter 1, this thesis records efforts to advance the PCC technology in two ways. First, in chapter 2 the development of a barcoded-rapid assay platform (B-RAP) technology enables the parallel analysis of up to fifteen PCC agents at once as well as dramatically shortening the time required to characterize the binding affinity for a pool of ligands from weeks to a couple of days. Secondly, the capture agent technology was utilized to target difficult proteins. Kirsten rat sarcoma (KRas) protein is a GTPase that acts as a light switch for several important cellular signaling pathways. Oncogenic variants of KRas are responsible for driving roughly 20-25% of all cancers, but KRas is considered “undruggable” from a small molecule targeting point of view. We report the identification of PCC ligands that bind to conserved allosteric switches on KRas and inhibit the protein’s GTPase enzymatic activity. The biomarker Plasmodium falciparum Histidine Rich Protein II (HRP2) presents an unusual challenge as it is a highly variable, unstructured and sticky protein. In chapter 3 we report on efforts to develop low nM binding capture agents against highly prevalent epitopes of HRP2, and the use of medicinal chemistry optimization to prepare structurally related variants of the lead capture agent for probing the structure-activity relationship and how it affects binding to HRP2
The Spectral Theory of Multiboundary Wormholes
Get PDFThis thesis introduces a new phase transitions in three dimensional quantum gravity. The main technical tools comes from the spectral theory of hyperbolic manifolds