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Randomness-Efficient Curve Sampling
Get PDFCurve samplers are sampling algorithms that proceed by viewing the domain as a vector space over a finite field, and randomly picking a low-degree curve in it as the sample. Curve samplers exhibit a nice property besides the sampling property: the restriction of low-degree polynomials over the domain to the sampled curve is still low-degree. This property is often used in combination with the sampling property and has found many applications, including PCP constructions, local decoding of codes, and algebraic PRG constructions.
The randomness complexity of curve samplers is a crucial parameter for its applications. It is known that (non-explicit) curve samplers using O(log N + log(1/δ)) random bits exist, where N is the domain size and δ is the confidence error. The question of explicitly constructing randomness-efficient curve samplers was first raised in [TU06] where they obtained curve samplers with near-optimal randomness complexity.
In this thesis, we present an explicit construction of low-degree curve samplers with optimal randomness complexity (up to a constant factor) that sample curves of degree (m logq(1/δ))O(1) in Fqm. Our construction is a delicate combination of several components, including extractor machinery, limited independence, iterated sampling, and list-recoverable codes.</p
Baryon Number Violation beyond the Standard Model
Get PDFThis thesis describes simple extensions of the standard model with new sources of baryon number violation but no proton decay. The motivation for constructing such theories comes from the shortcomings of the standard model to explain the generation of baryon asymmetry in the universe, and from the absence of experimental evidence for proton decay. However, lack of any direct evidence for baryon number violation in general puts strong bounds on the naturalness of some of those models and favors theories with suppressed baryon number violation below the TeV scale. The initial part of the thesis concentrates on investigating models containing new scalars responsible for baryon number breaking. A model with new color sextet scalars is analyzed in more detail. Apart from generating cosmological baryon number, it gives nontrivial predictions for the neutron-antineutron oscillations, the electric dipole moment of the neutron, and neutral meson mixing. The second model discussed in the thesis contains a new scalar leptoquark. Although this model predicts mainly lepton flavor violation and a nonzero electric dipole moment of the electron, it includes, in its original form, baryon number violating nonrenormalizable dimension-five operators triggering proton decay. Imposing an appropriate discrete symmetry forbids such operators. Finally, a supersymmetric model with gauged baryon and lepton numbers is proposed. It provides a natural explanation for proton stability and predicts lepton number violating processes below the supersymmetry breaking scale, which can be tested at the Large Hadron Collider. The dark matter candidate in this model carries baryon number and can be searched for in direct detection experiments as well. The thesis is completed by constructing and briefly discussing a minimal extension of the standard model with gauged baryon, lepton, and flavor symmetries
Functional Evaluation of Noncovalent Interactions in Neuroreceptors and Progress Toward the Expansion of Unnatural Amino Acid Methodology
Get PDFThis dissertation primarily describes chemical-scale studies of G protein-coupled receptors and Cys-loop ligand-gated ion channels to better understand ligand binding interactions and the mechanism of channel activation using recently published crystal structures as a guide. These studies employ the use of unnatural amino acid mutagenesis and electrophysiology to measure subtle changes in receptor function.
In chapter 2, the role of a conserved aromatic microdomain predicted in the D3 dopamine receptor is probed in the closely related D2 and D4 dopamine receptors. This domain was found to act as a structural unit near the ligand binding site that is important for receptor function. The domain consists of several functionally important noncovalent interactions including hydrogen bond, aromatic-aromatic, and sulfur-π interactions that show strong couplings by mutant cycle analysis. We also assign an alternate interpretation for the linear fluorination plot observed at W6.48, a residue previously thought to participate in a cation-π interaction with dopamine.
Chapter 3 outlines attempts to incorporate chemically synthesized and in vitro acylated unnatural amino acids into mammalian cells. While our attempts were not successful, method optimizations and data for nonsense suppression with an in vivo acylated tRNA are included. This chapter is aimed to aid future researchers attempting unnatural amino acid mutagenesis in mammalian cells.
Chapter 4 identifies a cation-π interaction between glutamate and a tyrosine residue on loop C in the GluClβ receptor. Using the recently published crystal structure of the homologous GluClα receptor, other ligand-binding and protein-protein interactions are probed to determine the similarity between this invertebrate receptor and other more distantly related vertebrate Cys-loop receptors. We find that many of the interactions previously observed are conserved in the GluCl receptors, however care must be taken when extrapolating structural data.
Chapter 5 examines inherent properties of the GluClα receptor that are responsible for the observed glutamate insensitivity of the receptor. Chimera synthesis and mutagenesis reveal the C-terminal portion of the M4 helix and the C-terminus as contributing to formation of the decoupled state, where ligand binding is incapable of triggering channel gating. Receptor mutagenesis was unable to identify single residue mismatches or impaired protein-protein interactions within this domain. We conclude that M4 helix structure and/or membrane dynamics are likely the cause of ligand insensitivity in this receptor and that the M4 helix has an role important in the activation process.</p
Random Propagation in Complex Systems: Nonlinear Matrix Recursions and Epidemic Spread
Get PDFThis dissertation studies long-term behavior of random Riccati recursions and mathematical epidemic model. Riccati recursions are derived from Kalman filtering. The error covariance matrix of Kalman filtering satisfies Riccati recursions. Convergence condition of time-invariant Riccati recursions are well-studied by researchers. We focus on time-varying case, and assume that regressor matrix is random and identical and independently distributed according to given distribution whose probability distribution function is continuous, supported on whole space, and decaying faster than any polynomial. We study the geometric convergence of the probability distribution. We also study the global dynamics of the epidemic spread over complex networks for various models. For instance, in the discrete-time Markov chain model, each node is either healthy or infected at any given time. In this setting, the number of the state increases exponentially as the size of the network increases. The Markov chain has a unique stationary distribution where all the nodes are healthy with probability 1. Since the probability distribution of Markov chain defined on finite state converges to the stationary distribution, this Markov chain model concludes that epidemic disease dies out after long enough time. To analyze the Markov chain model, we study nonlinear epidemic model whose state at any given time is the vector obtained from the marginal probability of infection of each node in the network at that time. Convergence to the origin in the epidemic map implies the extinction of epidemics. The nonlinear model is upper-bounded by linearizing the model at the origin. As a result, the origin is the globally stable unique fixed point of the nonlinear model if the linear upper bound is stable. The nonlinear model has a second fixed point when the linear upper bound is unstable. We work on stability analysis of the second fixed point for both discrete-time and continuous-time models. Returning back to the Markov chain model, we claim that the stability of linear upper bound for nonlinear model is strongly related with the extinction time of the Markov chain. We show that stable linear upper bound is sufficient condition of fast extinction and the probability of survival is bounded by nonlinear epidemic map
Efficient Methods for Empirical Tests of Behavioral Economics Theories in Laboratory and Field Experiments
Get PDFIn the quest for a descriptive theory of decision-making, the rational actor model in economics imposes rather unrealistic expectations and abilities on human decision makers. The further we move from idealized scenarios, such as perfectly competitive markets, and ambitiously extend the reach of the theory to describe everyday decision making situations, the less sense these assumptions make. Behavioural economics has instead proposed models based on assumptions that are more psychologically realistic, with the aim of gaining more precision and descriptive power. Increased psychological realism, however, comes at the cost of a greater number of parameters and model complexity. Now there are a plethora of models, based on different assumptions, applicable in differing contextual settings, and selecting the right model to use tends to be an ad-hoc process. In this thesis, we develop optimal experimental design methods and evaluate different behavioral theories against evidence from lab and field experiments.
We look at evidence from controlled laboratory experiments. Subjects are presented with choices between monetary gambles or lotteries. Different decision-making theories evaluate the choices differently and would make distinct predictions about the subjects' choices. Theories whose predictions are inconsistent with the actual choices can be systematically eliminated. Behavioural theories can have multiple parameters requiring complex experimental designs with a very large number of possible choice tests. This imposes computational and economic constraints on using classical experimental design methods. We develop a methodology of adaptive tests: Bayesian Rapid Optimal Adaptive Designs (BROAD) that sequentially chooses the "most informative" test at each stage, and based on the response updates its posterior beliefs over the theories, which informs the next most informative test to run. BROAD utilizes the Equivalent Class Edge Cutting (EC2) criteria to select tests. We prove that the EC2 criteria is adaptively submodular, which allows us to prove theoretical guarantees against the Bayes-optimal testing sequence even in the presence of noisy responses. In simulated ground-truth experiments, we find that the EC2 criteria recovers the true hypotheses with significantly fewer tests than more widely used criteria such as Information Gain and Generalized Binary Search. We show, theoretically as well as experimentally, that surprisingly these popular criteria can perform poorly in the presence of noise, or subject errors. Furthermore, we use the adaptive submodular property of EC2 to implement an accelerated greedy version of BROAD which leads to orders of magnitude speedup over other methods.
We use BROAD to perform two experiments. First, we compare the main classes of theories for decision-making under risk, namely: expected value, prospect theory, constant relative risk aversion (CRRA) and moments models. Subjects are given an initial endowment, and sequentially presented choices between two lotteries, with the possibility of losses. The lotteries are selected using BROAD, and 57 subjects from Caltech and UCLA are incentivized by randomly realizing one of the lotteries chosen. Aggregate posterior probabilities over the theories show limited evidence in favour of CRRA and moments' models. Classifying the subjects into types showed that most subjects are described by prospect theory, followed by expected value. Adaptive experimental design raises the possibility that subjects could engage in strategic manipulation, i.e. subjects could mask their true preferences and choose differently in order to obtain more favourable tests in later rounds thereby increasing their payoffs. We pay close attention to this problem; strategic manipulation is ruled out since it is infeasible in practice, and also since we do not find any signatures of it in our data.
In the second experiment, we compare the main theories of time preference: exponential discounting, hyperbolic discounting, "present bias" models: quasi-hyperbolic (α, β) discounting and fixed cost discounting, and generalized-hyperbolic discounting. 40 subjects from UCLA were given choices between 2 options: a smaller but more immediate payoff versus a larger but later payoff. We found very limited evidence for present bias models and hyperbolic discounting, and most subjects were classified as generalized hyperbolic discounting types, followed by exponential discounting.
In these models the passage of time is linear. We instead consider a psychological model where the perception of time is subjective. We prove that when the biological (subjective) time is positively dependent, it gives rise to hyperbolic discounting and temporal choice inconsistency.
We also test the predictions of behavioral theories in the "wild". We pay attention to prospect theory, which emerged as the dominant theory in our lab experiments of risky choice. Loss aversion and reference dependence predicts that consumers will behave in a uniquely distinct way than the standard rational model predicts. Specifically, loss aversion predicts that when an item is being offered at a discount, the demand for it will be greater than that explained by its price elasticity. Even more importantly, when the item is no longer discounted, demand for its close substitute would increase excessively. We tested this prediction using a discrete choice model with loss-averse utility function on data from a large eCommerce retailer. Not only did we identify loss aversion, but we also found that the effect decreased with consumers' experience. We outline the policy implications that consumer loss aversion entails, and strategies for competitive pricing.
In future work, BROAD can be widely applicable for testing different behavioural models, e.g. in social preference and game theory, and in different contextual settings. Additional measurements beyond choice data, including biological measurements such as skin conductance, can be used to more rapidly eliminate hypothesis and speed up model comparison. Discrete choice models also provide a framework for testing behavioural models with field data, and encourage combined lab-field experiments.</p
High Fidelity Probe and Mitigation of Mirror Thermal Fluctuations
Get PDFThermal noise arising from mechanical loss in high reflective dielectric coatings is a significant source of noise in precision optical measurements. In particular, Advanced LIGO, a large scale interferometer aiming to observed gravitational wave, is expected to be limited by coating thermal noise in the most sensitive region around 30–300 Hz. Various theoretical calculations for predicting coating Brownian noise have been proposed. However, due to the relatively limited knowledge of the coating material properties, an accurate approximation of the noise cannot be achieved. A testbed that can directly observed coating thermal noise close to Advanced LIGO band will serve as an indispensable tool to verify the calculations, study material properties of the coating, and estimate the detector’s performance.
This dissertation reports a setup that has sensitivity to observe wide band (10Hz to 1kHz) thermal noise from fused silica/tantala coating at room temperature from fixed-spacer Fabry–Perot cavities. Important fundamental noises and technical noises associated with the setup are discussed. The coating loss obtained from the measurement agrees with results reported in the literature.
The setup serves as a testbed to study thermal noise in high reflective mirrors from different materials. One example is a heterostructure of AlxGa1−xAs (AlGaAs). An optimized design to minimize thermo–optic noise in the coating is proposed and discussed in this work.</p
Direct Simulation of Quantum Dynamics in Complex Systems
Get PDFAccurate simulation of quantum dynamics in complex systems poses a fundamental theoretical challenge with immediate application to problems in biological catalysis, charge transfer, and solar energy conversion. The varied length- and timescales that characterize these kinds of processes necessitate development of novel simulation methodology that can both accurately evolve the coupled quantum and classical degrees of freedom and also be easily applicable to large, complex systems. In the following dissertation, the problems of quantum dynamics in complex systems are explored through direct simulation using path-integral methods as well as application of state-of-the-art analytical rate theories
Strength of Tantalum at High Pressures through Richtmyer-Meshkov Laser Compression Experiments and Simulations
Get PDFStrength at extreme pressures (>1 Mbar or 100 GPa) and high strain rates (106-108 s-1) of materials is not well characterized. The goal of the research outlined in this thesis is to study the strength of tantalum (Ta) at these conditions. The Omega Laser in the Laboratory for Laser Energetics in Rochester, New York is used to create such extreme conditions. Targets are designed with ripples or waves on the surface, and these samples are subjected to high pressures using Omega’s high energy laser beams. In these experiments, the observational parameter is the Richtmyer-Meshkov (RM) instability in the form of ripple growth on single-mode ripples. The experimental platform used for these experiments is the “ride-along” laser compression recovery experiments, which provide a way to recover the specimens having been subjected to high pressures. Six different experiments are performed on the Omega laser using single-mode tantalum targets at different laser energies. The energy indicates the amount of laser energy that impinges the target. For each target, values for growth factor are obtained by comparing the profile of ripples before and after the experiment. With increasing energy, the growth factor increased.
Engineering simulations are used to interpret and correlate the measurements of growth factor to a measure of strength. In order to validate the engineering constitutive model for tantalum, a series of simulations are performed using the code Eureka, based on the Optimal Transportation Meshfree (OTM) method. Two different configurations are studied in the simulations: RM instabilities in single and multimode ripples. Six different simulations are performed for the single ripple configuration of the RM instability experiment, with drives corresponding to laser energies used in the experiments. Each successive simulation is performed at higher drive energy, and it is observed that with increasing energy, the growth factor increases. Overall, there is favorable agreement between the data from the simulations and the experiments. The peak growth factors from the simulations and the experiments are within 10% agreement. For the multimode simulations, the goal is to assist in the design of the laser driven experiments using the Omega laser. A series of three-mode and four-mode patterns are simulated at various energies and the resulting growth of the RM instability is computed. Based on the results of the simulations, a configuration is selected for the multimode experiments. These simulations also serve as validation for the constitutive model and the material parameters for tantalum that are used in the simulations.
By designing samples with initial perturbations in the form of single-mode and multimode ripples and subjecting these samples to high pressures, the Richtmyer-Meshkov instability is investigated in both laser compression experiments and simulations. By correlating the growth of these ripples to measures of strength, a better understanding of the strength of tantalum at high pressures is achieved.</p
Time and Fate in Shakespeare's Othello and Cinthio's "The Moor of Venice"
No full text[Introduction]Giraldi Cinthio's short story "The Moor of Venice" forms the basis for William
Shakespeare's tragedy Othello. In addition to altering a number of minor aspects of the original
tale, Shakespeare also introduces several overarching changes to the narrative by shortening the
time frame of the story and excluding fate as a primary driving force of the plot. By diminishing
the consequences of time and fate, Shakespeare allows the characters and their inner motivations
to be at the forefront of the action
Structure, Chemistry, and Energetics of Organic and Inorganic Adsorbates on Ga-rich GaAs and GaP(00l) Surfaces
Get PDFThe work described in this dissertation includes fundamental investigations into three surface processes, namely inorganic film growth, water-induced oxidation, and organic functionalization/passivation, on the GaP and GaAs(001) surfaces. The techniques used to carry out this work include scanning tunneling microscopy (STM), X-ray photoelectron spectroscopy (XPS), and density functional theory (DFT) calculations. Atomic structure, electronic structure, reaction mechanisms, and energetics related to these surface processes are discussed at atomic or molecular levels.
First, we investigate epitaxial Zn3P2 films grown on the Ga-rich GaAs(001)(6×6) surface. The film growth mechanism, electronic properties, and atomic structure of the Zn3P2/GaAs(001) system are discussed based on experimental and theoretical observations. We discover that a P-rich amorphous layer covers the crystalline Zn3P2 film during and after growth. We also propose more accurate picture of the GaP interfacial layer between Zn3P2 and GaAs, based on the atomic structure, chemical bonding, band diagram, and P-replacement energetics, than was previously anticipated.
Second, DFT calculations are carried out in order to understand water-induced oxidation mechanisms on the Ga-rich GaP(001)(2×4) surface. Structural and energetic information of every step in the gaseous water-induced GaP oxidation reactions are elucidated at the atomic level in great detail. We explore all reasonable ground states involved in most of the possible adsorption and decomposition pathways. We also investigate structures and energies of the transition states in the first hydrogen dissociation of a water molecule on the (2×4) surface.
Finally, adsorption structures and thermal decomposition reactions of 1-propanethiol on the Ga-rich GaP(001)(2×4) surface are investigated using high resolution STM, XPS, and DFT simulations. We elucidate adsorption locations and their associated atomic structures of a single 1-propanethiol molecule on the (2×4) surface as a function of annealing temperature. DFT calculations are carried out to optimize ground state structures and search transition states. XPS is used to investigate variations of the chemical bonding nature and coverage of the adsorbate species.</p