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Understanding the Origin of Glass Forming Ability in Metallic Glasses
Get PDFThe glass forming ability of metallic glasses has been one of their most studied yet least understood properties. Crystal nucleation in a recently development Ni-based metallic glass was studied by undercooling in a DSC under a variety of conditions and showed stochastic very deep undercooling behavior. The glass forming ability of a family of Ni-based alloys was analyzed and was found to depend only on two experimentally accessible factors, the reduced glass transition temperature and the liquid fragility. Neutron scattering experiments showed that in two model glass formers vibrational entropy had essentially no change through the glass transition, demonstrating that the change in entropy through the glass transition is due almost entirely to configurational entropy. The configurational enthalpy of a pair of recently developed Pt-based metallic glasses show almost no change in the undercooled liquid between the liquidus and TTT-nose, demonstrating the inability of current models to explain the thermodynamics of supercooled liquids
Dynamics of Seasonally-Varying Tropical Convergence Zones
Get PDFIn the tropics, rain tends to be organized along concentrated rain bands, with the Intertropical Convergence Zone (ITCZ) over the ocean and monsoonal convergence zones over tropical land masses being particularly prominent features affecting hundreds of millions of people. What fundamentally controls the spatial and temporal distribution of these tropical rainbands remains an outstanding question in the literature. This thesis aims to enhance our understanding of the dynamics of seasonally migrating convergence zones over the ocean and in the South Asian monsoon region.
First, we explore to what extent energetic arguments that have provided insight into the position and shifts of the annual and zonal mean ITCZ can also be applied on shorter timescales. Idealized aquaplanet simulations show that the energy flux equator (EFE) always leads the ITCZ, leading to a breakdown of the commonly assumed anti-correlation between the ITCZ position and the cross-equatorial energy transport. At times during which the EFE and the ITCZ reside on opposite sides of the equator, the required energy transport is in fact achieved by the Hadley cell, in which the ITCZ is embedded, changing its vertical structure into one of negative gross moist stability. One way in which this is accomplished is through the development of a shallow return flow at levels near minimum moist static energy. While the relationship between the EFE and the ITCZ in the observed seasonal cycle is more complex than what is seen in the idealized simulations, the development of bottom-heavy circulations is a common feature both in the zonal mean and in individual longitudinal sectors at times when the EFE and the ITCZ are in opposite hemispheres.
In the last chapter of this thesis, we explore changes in the South Asian monsoon as topography over Africa is removed in the full-physics GFDL AM2.1 GCM. Against expectations, the removal of the African topography is accompanied by a strengthening of the precipitation over India despite a weakening of the Somali jet. This counter-intuitive precipitation increase is associated with the development of a lower-level cyclonic wind anomaly, and associated meridional moisture flux convergence, over the Indian peninsula. Potential vorticity (PV) budget analyses following air parcel trajectories show that this cyclonic anomaly arises because, in the absence of the blocking effect of the African topography, air particles that reach the Arabian Sea originate at higher latitude and hence have a higher background planetary vorticity.</p
Interrogating the Structural Landscape of Malaria Biomarkers with Epitope Targeted Peptide Capture Agents
Get PDFAntibodies have conventionally been used as molecular recognition agents against epitopes, or antigenic regions, for protein capture and detection. The ability of monoclonal and polyclonal antibodies to selectively bind their targets with high affinities makes them excellent agents for specific protein recognition. However, as large proteins themselves (~150 kDa), antibodies are susceptible to changes in pH, temperature, and biochemical environment, particularly proteolytic cleavage. Additionally, epitope binding on antibodies is reliant on their rigid tertiary structure to position key functional groups that facilitation antigen recognition. Retaining the integrity of the protein structure creates rigid limitations against chemical modifications of antibodies to suit unique needs.
Protein-catalyzed capture agents (PCCs) developed within the Heath group at Caltech address the limitation of antibodies as affinity agents. Using epitope-targeted in situ click screening methodology, the Heath group has developed peptidomimetic molecules that offer an alternative solution to antibodies. These PCCs exhibit high affinity and selectivity for their protein targets. As peptide-based molecules, PCCs can be engineered to be biochemically stable and resistant to changes in their chemical environment. Their peptide-based structures are readily amenable to chemical modifications and allow for adaptation to a range of applications.
This thesis describes the development of PCCs against unique protein biomarkers for the detection of the most lethal species of malaria infection, Plasmodium falciparum. Malaria is a global health epidemic and its eradication is reliant on rapid and accurate diagnostics for prompt treatment. We targeted the P. falciparum specific biomarkers lactate dehydrogenase (LDH) and Histidine-rich protein 2 (HRP2), both of which present unique challenges for protein capture. The LDH biomarker is homologous across malaria species, whereas HRP2 is highly polymorphic and lacks distinct secondary structure. The variation in sensitivity of HRP2 detection by antibody-based tests has been attributed to the genetic polymorphism of the biomarker.
In Chapter 1, we describe the development of high affinity PCCs that bind selectively to the LDH biomarker. We targeted an epitope that was highly homologous across LDH species. This chapter also details the expansion of mono-valent PCC agents into bivalent ligands using the protein architecture to select secondary ligands for binding improvement. For the HRP2 biomarker, we developed a multiple epitope targeting strategy to address protein polymorphism. We targeted for epitopes in HRP2 and developed PCCs that bind in the range of monoclonal antibodies.
Chapter 2 details the expansion of PCC agents developed against HRP2 into multivalent molecules for improved binding. The development of bivalent ligands from combinatorial screening of linker libraries is presented. The optimal linker lengths determined by the screens are described.
In Chapter 3, a general strategy for targeting the protein landscape to inhibit formation of a protein and biomolecule complex with PCCs against HRP2 is demonstrated. Specifically, the inhibition of heme sequestration by HRP2 is shown. A bivalent ligand that targets two epitopes on HRP2 is shown to have enhanced inhibitory potency over any single or cocktail combination of PCCs.
Altogether, the studies herein demonstrate the utility of peptidomimetic molecules as agents for protein capture and detection as well as a generalizable strategy of functional inhibition through epitope-targeting.</p
Characterization and Improvement of the Thermal Stability of TES Bolometers
Get PDFThe successful detection and characterization of the B-modes in the Cosmic Microwave Background (CMB) would dramatically illuminate the physics of the inflationary era. The Observational Cosmology Group is iterating on bolometers in an attempt to detect this signal. The previous detector design became unstable in parts of its transition when adjusted for 220/270 GHz frequencies, limiting its use.
We study the mechanism of instability in these transition edge sensor (TES) bolometers used for ground based observations of the Cosmic Microwave Background (CMB) at 270GHz. The instability limits the range of useful operating resistances of the TES down to ≈50% of the TES normal resistance (R_n), and due to variations in detector properties and optical loading within a column of multiplexed detectors, limits the effective on sky yield to ≈67 %.
Through comparison of 7 new detector thermal capacity designs and measurements of the electrical impedance of the detectors, we show the instability is due to the increased bolometer leg G for higher-frequency detection inducing decoupling of the palladium-gold heat capacity from the thermistor. We demonstrate experimentally that the limiting thermal resistance is due to the small cross sectional area of the silicon nitride bolometer island, and so is easily fixed by layering palladium-gold over an oxide protected TES. The resulting detectors can be biased down to a resistance ≈10% of Rn, improving the effective on-sky yield to ≈93%.
We also investigate a possibly related, unexpected slope in the Aluminum calibration TES transition and determine that it is not due to phase separation, even accounting for the science TES thermal instability.</p
Improving the Speed and Performance of Point-of-Care Diagnostics with Microfluidics
Get PDFMicrofluidic devices play an important role in improving global health because they reduce the study of biological phenomena into physiological scales and lay the foundation for point-of-care (POC) diagnostics. Health is improved and lives are saved because POC diagnostics can enable earlier diagnosis of diseases and therefore more effective treatment. Accurate and available diagnostics also prevent accelerated drug resistance that stems from overtreatment or mistreatment with antibiotics, which is projected to cause up to $100 trillion in lost economic output and 10 million deaths by 2050. This work details new diagnostic assays and theoretical analysis of microfluidic devices that can be implemented at the point-of-care to improve global health
2D and 3D Photonic Crystals: Synthesis, Characterization and Topological Phenomenon
Get PDFTopological photonics has become an increasingly popular research topic in the field of nanophotonics in recent years. Topological phases of light provide opportunities to manipulate light propagation efficiently at the nanoscale volume. Performance of conventional optical elements are limited by back-reflection and bending losses, which hinder their prospect of large scale integration. Topological protection enables unidirectional excitation of edge states or surface states without leaking into the bulk, as well as suppression of scattering when encountering defects and corners. With such advantages, topological photonic elements may surpass conventional photonic
design for future generations of ultra-compact efficient computing, imaging, and sensing applications. Due to limitations of fabrication and characterization techniques, previously experimental efforts on topological photonics have been carried out with 2D micron-scale optical design or at the microwave wavelength.
This thesis contributes to the experimental development of topological photonics in two aspects: first, how to fabricate and characterize 3D photonic crystals and therefore extend topological protection into the 3D (Chapters 2-3); and second, how to realize nanoscale topological protection in the visible frequencies (chapters 4-6). Specifically, Chapter 2 reports fabrication of 3D single gyroid structures composed of a-Si and FTIR characterization of a photonic bandgap at the mid-infrared wavelength. This is the foundation to investigate more complex morphologies to introduce topologically nontrivial photonic states. Chapter 3 describe properties of
double gyroid photonic crystals, followed by angle resolved characterization method in the mid-infrared. Double gyroid photonic crystals can be designed to possess quadratic degeneracy points, Weyl points, and line nodes. Since Weyl points have non-zero Chern numbers, surface states are topologically protected in double gyroid photonic crystals with parity breaking symmetry. The angle resolved characterization method could be utilize to resolve both Weyl points and surface states. Chapter 4 depicts design, fabrication, and characterization of Dirac-like surface plasmon dispersions in metallic nano-pillars. Chapter 5 presents experimental investigation
of coupled silicon Mie resonators, which is the first step towards topological design based on inter-lattice sites coupling in the next chapter. Chapter 6 details photonic bandstructure from angle-resolved cathodoluminescence measurements. We analyze bandstructures collected from the bulk of trivially and topologically gapped lattices, as well as zigzag and arm-chaired edges of domain boundaries. Chapter 7 outlines a method to optically enhance dissociation of hydrazine molecules using ultraviolet plasmons, and attempts to use this method for low temperature GaN growth.</p
Transition Metals as Catalysts for Cross-Coupling and Dinitrogen Fixation
Get PDFTransition metals are used as catalysts in the laboratory and by nature to facilitate difficult chemical transformations. Herein, three different metal containing catalysts are discussed: Pd and Ni catalysts towards the formation of carbon-carbon (C-C) bonds and Fe catalysts towards the reduction of N2 to NH3.
In Chapter 2, mechanistic studies of Pd- and Ni-catalyzed cross-coupling reactions are discussed. The mechanism of transmetalation of a Pd-catalyzed Suzuki cross-coupling reaction is studied using a stereochemical probe, revealing that transmetalation occurs with retention of configuration, consistent with transmetalation occurring through a frontside-attack mechanism. Next, to explore the viability of a transmetalation first pathway in an asymmetric Negishi cross-coupling reaction, S = 1/2 NiIBr and NiI–alkyl complexes were synthesized, crystallographically characterized, and their reactivities explored. Based on these reactivity studies, evidence against a transmetalation first pathway is provided using a variety of spectroscopic methods.
In Chapter 3, new Fe(N2)(H)x complexes are synthesized. These complexes catalyze the reduction of N2 to NH3 and the yields for NH3 are improved if the reactions are performed in the presence of Hg lamp photolysis. Preliminary mechanistic studies exploring the role of light are discussed. In the final chapter, new ligand scaffolds are developed that can bind a Lewis acidic and Lewis basic metal center. These ligand frameworks support one- and two-atom bridges between the two metal sites. Finally, we discovered that some of the new complexes are catalysts for N2 to NH3 reduction and olefin hydrogenation.</p
Graph Clustering: Algorithms, Analysis and Query Design
Get PDFA wide range of applications in engineering as well as the natural and social sciences have datasets that are unlabeled. Clustering plays a major role in exploring structure in such unlabeled datasets. Owing to the heterogeneity in the applications and the types of datasets available, there are plenty of clustering objectives and algorithms. In this thesis we focus on two such clustering problems: Graph Clustering and Crowdsourced Clustering.
In the first part, we consider the problem of graph clustering and study convex-optimization-based clustering algorithms. Datasets are often messy -- ridden with noise, outliers (items that do not belong to any clusters), and missing data. Therefore, we are interested in algorithms that are robust to such discrepancies. We present and analyze convex-optimization-based clustering algorithms which aim to recover the low-rank matrix that encodes the underlying cluster structure for two clustering objectives: clustering partially observed graphs and clustering similarity matrices with outliers. Using block models as generative models, we characterize the performance of these convex clustering algorithms. In particular, we provide explicit bounds, without any large unknown constants, on the problem parameters that determine the success and failure of these convex approaches.
In the second part, we consider the problem of crowdsourced clustering -- the task of clustering items using answers from non-expert crowd workers who can answer similarity comparison queries. Since the workers are not experts, they provide noisy answers. Further, due to budget constraints, we cannot make all possible comparisons between items in the dataset. Thus, it is important to design queries that can reduce the noise in the responses and design algorithms that can work with noisy and partial data. We demonstrate that random triangle queries (where three items are compared per query) provide less noisy data as well as greater quantity of data, for a fixed query budget, as compared to random edge queries (where two items are compared per query). We extend the analysis of convex clustering algorithms to show that the exact recovery guarantees hold for triangle queries despite involving dependent edges. In addition to random querying strategies, we also present a novel active querying algorithm that is guaranteed to find all the clusters regardless of their sizes and without the knowledge of any parameters as long as the workers are better than random guessers. We also provide a tight upper bound on the number of queries made by the proposed active querying algorithm. Apart from providing theoretical guarantees for the clustering algorithms we also apply our algorithms to real datasets.</p
Frequency Noise Control of Heterogeneous Si/III-V Lasers
Get PDFNarrow-linewidth lasers have many applications including optical telecommunication, laser spectroscopy, atomic clocks, and light detection and ranging. Conventionally, narrow linewidth lasers have been realized in the form of fiber-based or solid-state lasers. These lasers are bulky and relatively expensive, limiting their usage as bench-top systems in laboratory environments. Historically, semiconductor lasers, also known as laser diodes, have served applications where size and cost are important factors, including fiber optic communications. The linewidth of the semiconductor lasers, however, has been limited to the MHz-level, due to high loss in laser cavities and small size.
Recently, reduction of the frequency fluctuations in the semiconductor lasers has been achieved, obtaining tens of kHz linewidth, using the heterogeneous Silicon/III-V platform with a new design strategy. In this design, the majority of the optical energy is stored in the low-loss high-Q silicon resonator away from the high-loss III-V active region, requiring the minimal gain from the active region to overcome the reduced modal loss.
This work explores the new design strategy further, and demonstrates theoretically and experimentally that the strategy eliminates the frequency fluctuations arising from the amplitude-phase coupling by placing a relaxation resonance frequency at frequencies of a few hundred MHz. Consequently, it becomes possible to obtain a semiconductor laser device possessing sub-kHz quantum-limited linewidths at frequencies of a few GHz (the frequencies of interest in optical telecommunication).
In addition to the frequency noise reduction, the strategy turns out to have the additional benefit of accomplishing a coherent and stable lasing operation, even under external reflections. Thus, the new design strategy has the potential to replace the costly, but currently indispensable external optical isolators, which have been traditionally used to maintain the consistent performance of semiconductor lasers in the presence of external reflection.
This work paves the way for the design of narrow-linewidth and stable semiconductor lasers that can function without the use of the bulky and costly external components, such as external cavities or optical isolators.</p
Egospace Motion Planning Representations for Micro Air Vehicles
Get PDFNavigation of micro air vehicles (MAVs) in unknown environments is a complex sensing and trajectory generation task, particularly at high velocities. In this work, we introduce an efficient sense-and-avoid pipeline that compactly represents range measurements from multiple sensors, trajectory generation, and motion planning in a 2.5–dimensional projective data structure called an egospace representation. Egospace coordinates generalize depth image obstacle representations and are a particularly convenient choice for configuration flat mobile robots, which are differentially flat in their configuration variables and include a number of commonly used MAV plant models. After characterizing egospace obstacle avoidance for robots with trivial dynamics and establishing limits on applicability and performance, we generalize to motion planning over full configuration flat dynamics using motion primitives expressed directly in egospace coordinates. In comparison to approaches based on world coordinates, egospace uses the natural sensor geometry to combine the benefits of a multi-resolution and multi-sensor representation architecture into a single simple and efficient layer.
We also present an experimental implementation, based on perception with stereo vision and an egocylinder obstacle representation, that demonstrates the specialization of our theoretical results to particular mission scenarios. The natural pixel parameterization of the egocylinder is used to quickly identify dynamically feasible maneuvers onto radial paths, expressed directly in egocylinder coordinates, that enable finely detailed planning at extreme ranges within milliseconds. We have implemented our obstacle avoidance pipeline with an Asctec Pelican quadcopter, and demonstrate the efficiency of our approach experimentally with a set of challenging field scenarios. The scalability potential of our system is discussed in terms of sensor horizon, actuation, and computational limitations and the speed limits that each imposes, and its generality to more challenging environments with multiple moving obstacles is developed as an immediate extension to the static framework