VictorJuiz/thesis huggingface dataset:
Spectroscopic and theoretical studies of mononuclear non-heme iron enzymes [electronic resource] : insight into the role of the facial triad and substrate effects on reactivity

Mononuclear non-heme iron enzymes are an important class with a wide range of medical, pharmaceutical and environmental applications. Within this class, the oxygen activating enzymes use Fe(II) to activate O2 for reaction with the substrate. The focus of this thesis is on understanding two major themes of the oxygen activating enzymes - the role of the (2His/1 carboxylate) facial triad and the initial O2 reaction steps of alpha-keto acid-dependent dioxygenases - using a combination of spectroscopic techniques and DFT calculations. For ferrous systems, abs/CD/MCD/VTVH MCD studies define the geometric and electronic structure of the ferrous site. In combination with DFT calculations, a structure/function picture of the ferrous sites is developed. To extend these studies to the initial steps of O2 binding, studies with NO as an O2 analogue ({FeNO}7/{FeO2}8) utilize EPR/abs/CD/MCD/VTVH MCD spectroscopy with DFT calculations to elucidate important effects of the substrate on the {FeNO}7 bond. These effects are used in the computational extension to the experimentally inaccessible O2 bound complexes giving insight into the initial steps of O2 binding and activation. Taken together, these studies shed light on the rational for facial triad ligation at the Fe(II) site in the oxygen activating enzymes and how the Fe(II) ligand set tunes the specific reactivity of these enzymes.

Keywords: Chemistry
Advisor: Solomon Edward I. primary advisor. Thesis advisor
Boxer Steven G. (Steven George)
Cegelski Lynette advisor. Thesis advisor
The state of the art of constitutive modeling of engineered cementitious composites [electronic resource]

A comprehensive review on the state of the art of constitutive modeling of Engineered Cementitious Composites (ECC) is conducted. Different constitutive modeling approaches are examined in details, and their advantages and disadvantages pertaining to ECC modeling are discussed. An analytical model based on total strain concept is implemented using finite element software DIANA. The model is verified against experimental results. The model is applied to a large-scale shear wall simulation. The simulation results are compared to actual concrete shear wall experiments, and the implications of ECC as a building material on structural performance are discussed.

Advisor: Lepech Michael advisor. Thesis advisor
Statistical and algorithm aspects of optimal portfolios [electronic resource]

We address three key aspects of optimal portfolio construction: expected return, variance-covariance modeling and optimization in presence of cardinality constraints. On expected return modeling, we extend the self-excited point process framework to model conditional arrival intensities of bid and ask side market orders of listed stocks. The cross-excitation of market orders is modeled explicitly such that the ask side market order size and bid side probability weighted order book cumulative volume can affect the ask side order intensity, and vice versa. Different variations of the framework are estimated by using method of maximum likelihood estimation, based on a recursive application of the log-likelihood functions derived in this thesis. Results indicate that the self-excited point process framework is able to capture a significant amount of the underlying trading dynamics of market orders, both in-sample and out-of-sample. A new framework is introduced, Realized GARCH, for the joint modeling of returns and realized measures of volatility. A key feature is a measurement equation that relates the realized measure to the conditional variance of returns. The measurement equation facilitates a simple modeling of the dependence between returns and future volatility. Realized GARCH models with a linear or log-linear specification have many attractive features. They are parsimonious, simple to estimate, and imply an ARMA structure for the conditional variance and the realized measure. An empirical application with DJIA stocks and an exchange traded index fund shows that a simple Realized GARCH structure leads to substantial improvements in the empirical fit over standard GARCH models. Finally we describe a novel algorithm to obtain the solution of the optimal portfolio problem with NP-hard cardinality constraints. The algorithm is based on a local relaxation that exploits the inherent structure of the objective function. It solves a sequence of small, local, quadratic-programs by first projecting asset returns onto a reduced metric space, followed by clustering in this space to identify sub-groups of assets that best accentuate a suitable measure of similarity amongst different assets. The algorithm can either be cold started using the centroids of initial clusters or be warm started based on the output of a previous result. Empirical result, using baskets of up to 3,000 stocks and with different cardinality constraints, indicates that the algorithm is able to achieve significant performance gain over a sophisticated branch-and-cut method. One key application of this local relaxation algorithm is in dealing with large scale cardinality constrained portfolio optimization under tight time constraint, such as for the purpose of index tracking or index arbitrage at high frequency.

Advisor: Lai T. L. primary advisor. Thesis advisor
Murray Walter primary advisor. Thesis advisor
Hansen Peter advisor. Thesis advisor
Strictly proper mechanisms with cooperating players [electronic resource]

In order to obtain accurate information about the uncertainty in a decision situation, a decision maker may rely on the judgment of experts to obtain useful probabilistic forecasts. Strictly proper scoring rules have been shown to incentivize forecasters to provide truthful probabilistic forecasts and can be interpreted as a contract between a decision maker and a risk neutral forecaster rewarding greater expertise as well as truthful revelation. In recent years, prediction markets have been created to provide an efficient means to assess uncertain quantities from forecasters, and strictly proper scoring rules have been proposed for prediction markets, where the payment depends on the forecaster's score relative to others. However, we show that when those players can cooperate, these mechanisms can instead discourage them from reporting what they really believe. When players with different beliefs are able to cooperate and form a coalition, these mechanisms admit arbitrage and there is a report that will always pay coalition members more than their truthful forecasts. If the coalition were created by an intermediary, such as a web portal, the intermediary would be guaranteed a profit from this risk free surplus. Specifically, for the three most commonly used strictly proper scoring rules, we provide a cooperative report for coalition members and show the magnitude of the surplus from cooperation with numerical examples. We analyze the optimal behavior of coalition members within a coalition. Given a choice whether to participate in any coalition, players should participate. We show conditions under which coalition members should invite new members. We evaluate the optimal strategy of each coalition member under a set of simple assumptions including a quadratic scoring rule, and show that honest revelation within the coalition is a Bayesian Nash equilibrium. We show the consequence of players' cooperation to the decision maker receiving aggregated probabilities, and conclude with open challenges in the design and understanding of strictly proper mechanisms.

Keywords: Management Science and Engineering
Advisor: Shachter Ross D. primary advisor. Thesis advisor
Howard Ronald A. (Ronald Arthur)
Ye Yinyu advisor. Thesis advisor
Studies on time-reversal invariant topological insulators [electronic resource]

This dissertation brings together a number of topics in the theory of time-reversal invariant topological insulators. The first four chapters are devoted to the transport properties of the two-dimensional (2D) quantum spin Hall state. We explain nonlocal transport measurements in mercury telluride (HgTe) quantum wells in terms of a Landauer-Büttiker theory of helical edge transport and confirm the discovery of the quantum spin Hall state in this material. We find that decoherence can lead to backscattering without breaking microscopic time-reversal symmetry. As an example of incoherent scattering, we study a Kondo impurity in an interacting helical edge liquid. A renormalization group analysis shows the existence of an impurity quantum phase transition governed by the Luttinger parameter of the edge liquid between a local helical Fermi liquid with T^6 scaling of the low-temperature conductance, and an insulating strongly correlated phase with fractionally charged emergent excitations. In the presence of a time-reversal symmetry breaking magnetic field, it is known that even coherent scattering can lead to backscattering. Through exact numerical diagonalization we find that nonmagnetic quenched disorder has a strong localizing effect on the edge transport if the disorder strength is comparable to the bulk gap. The predicted magnetoconductance agrees qualitatively with experiment. The last two chapters are devoted to 3D topological insulators. We propose a combined magnetooptical Kerr and Faraday rotation experiment as a universal measure of the Z_2 invariant. Finally, we propose a fractional generalization of 3D topological insulators in strongly correlated systems, characterized by ground state degeneracy on topologically nontrivial spatial 3-manifolds, a quantized fractional bulk magnetoelectric polarizability without time-reversal symmetry breaking, and a halved fractional quantum Hall effect on the surface.

Keywords: Physics
Advisor: Zhang Shoucheng primary advisor. Thesis advisor
Goldhaber-Gordon David
Qi Xiaoliang advisor. Thesis advisor
Study of the decay of the bottom meson to an omega meson, charged lepton, and neutrino [electronic resource]

Using a sample of 467 million BB pairs recorded by the BABAR detector at the SLAC PEP-II e+e− collider, we measure the partial branching fraction of B^+ \to \omega\ell\nu decays in five ranges of q2, the momentum-transfer squared of the virtual W boson. We observe 1034 ± 131 signal decays, corresponding to a branching fraction of B(B^+ \to \omega\ell\nu) = (1.17 ± 0.15 ± 0.11) x 10^−4 , where the first error is statistical and the second is systematic. The q2 distribution is compared to theoretical predictions based on quark model and light cone sum rule form factor calculations.

Keywords: Physics
Advisor: Burchat P. (Patricia) primary advisor. Thesis advisor
Lüth Vera primary advisor. Thesis advisor
Quinn Helen R.
Roodman Aaron J. (Aaron Jay)
Studying bonding and electronic structures of materials under extreme conditions [electronic resource]

Recent advances in high pressure diamond anvil cell techniques and synchrotron radiation characterization methods have enabled investigation of a wide range of materials properties in-situ under extreme conditions. High pressure studies have made significant contribution to our understanding in a number of scientific fields, e.g. condensed matter physics, chemistry, Earth and planetary sciences, and material sciences. Pressure, as a fundamental thermodynamic variable, can induce changes in the electronic and structural configuration of a material, which in turn can dramatically alter its properties. The novel phases and new compounds existing at high pressure have improved our basic understanding of bonding and interactions in condensed matter. This dissertation focuses on how pressure affects materials' bonding and electronic structures in two types of systems: hydrogen rich molecular compounds and strongly correlated transition metal oxides. The interaction of boranes and hydrogen was studied using optical microscopy and Raman spectroscopy and their hydrogen storage potential is discussed in the context of practical applications. The pressure-induced behavior of the SiH4 + H2 binary system and the formation of a newly formed compound SiH4(H2)2 were investigated using a combination of optical microscopy, Raman spectroscopy and x-ray diffraction. The experimental work along with DFT calculations on the electronic properties of the compound up to the possible metallization pressure, indicated that there are strong intermolecular interactions between SiH4 and H2 in the condensed phase. By using a newly developed synchrotron x-ray spectroscopy technique, we were able to follow the evolution of the 3d band of a 3d transition metal oxide, Fe2O3 under pressure, which experiences a series of structural, electronic and spin transitions at approximately 50 GPa. Together with theoretical calculations we revisited its electronic phase transition mechanism, and found that the electronic transitions are reflected in the pre-edge region.

Keywords: Applied Physics.
Advisor: Mao Wendy (Wendy Li-wen) primary advisor. Thesis advisor
Fisher Ian R. (Ian Randal) primary advisor. Thesis advisor
Nilsson Anders
Studying people, organizations, and the web with statistical text models [electronic resource]

From social networks to academic publications, information technologies have enabled companies, organizations, and governments to collect huge datasets about the world. Many of these datasets have major textual components organized by human-applied labels or tags, promising to improve our understanding of large scale topical and social phenomena through the words people write. Doing so requires tools that can discover and quantify word usage patterns that are interpretable, trustworthy, and flexible. In particular, the discovered patterns should exploit the implicit domain knowledge embodied in tags, labels, or other categories of interest, when they are available, and lend themselves to visual exploration and interpretation. This dissertation presents studies of topical structure of the tagged web, social language in microblogs, and innovation in academia through statistical analyses of text. Several new probabilistic topic models of metadata-enriched document collections are introduced, facilitating domain specific studies of words associated with tags, emoticons, library subject codes, and other human-provided labels. I find that tags improve high-level clustering of web pages; that language on Twitter can be quantified with respect to its role as substance, status, social, or style; and that interdisciplinary research consistently uses language that looks like academia's future. These results are evaluated both quantitatively, with gold standard and task driven metrics, and qualitatively with visualizations of the textual patterns discovered by the models.

Advisor: Manning Christopher D. primary advisor. Thesis advisor
Jurafsky Dan
McFarland Daniel (Daniel A.) advisor. Thesis advisor
Subsampling GPS receiver front-end [electronic resource]

Research in RFIC design has recently shifted towards direct conversion and subsampling architectures as an alternative to the conventional super-heterodyne architectures. Bandpass sampling architectures, also called subsampling architectures, exhibit several advantages over super-heterodyne architectures, notably, the complexity of subsampling architectures is significantly lower since no phase-locked loop is required. A direct consequence is that downconversion from RF to IF can be achieved with significant power savings as compared to the super-heterodyne architecture. Another significant benefit of such architectures is the capability for processing multiple signals in parallel. The ability to simultaneously handle multiple carriers makes subsampling architectures particularly well suited for GNSS applications, as downconversion of multiple frequency bands is required in GNSS environments. With the advent of the new civilian GPS signals, L2C and L5, and the onset of the new Galileo signal, a receiver that can process multiple signals without adding complexity, is highly desired. An integrated proof-of-concept subsampling GPS receiver front-end in 130 nm BiCMOS is presented in this dissertation. The receiver achieves a noise figure of less than 3.8 dB, the lowest ever recorded noise figure of a subsampling based receiver.

Keywords: Electrical Engineering
Advisor: Inan Umran S. primary advisor. Thesis advisor
Lee Thomas advisor. Thesis advisor
Linscott Ivan advisor. Thesis advisor
Sunny Side Up: Characterizing the US Military's Approach to Solar Energy Policy

Since 2007, the Department of Defense (DoD) has invested considerable resources and research into deploying solar panels to power its domestic military bases. This thesis seeks to apply theoretical models of policymaking to explain the enactment, implementation, and revision of the DoD‘s solar energy policy. In none of these stages can an idealized rational actor model account for the military‘s decision-making process; the panels purport to enhance energy security but do not do so, they are expensive, and they appear to strive for but fail to achieve federally mandated renewable electricity targets. Kingdon‘s multiple streams analysis best accounts for the timing of the DoD‘s decision to pursue solar, due to an open policy window in 2005. Furthermore, theories of ritualistic bureaucratic compliance in hierarchies explain the haphazard pattern of implementation. Finally, bounded rationality and incrementalism correctly predict the DoD‘s incomplete decision-making process when revising solar energy policy to include secure microgrid technology. These insights can and should inform DoD officials to critically analyze the motivations behind pursuing solar technology, consider nonrenewable microgrids to meet their stated goals of energy security, and lobby Congress to either allocate more funding for expensive renewable technology or relax its mandates in light of national security concerns.

Keywords: solar energy
solar panels
military
multiple streams analysis
microgrid
policy
Thesis
Advisor: May Michael
Crenshaw Martha
Super string theory and the calculation of metastable ground states [electronic resource]

Super string theory is a candidate theory for the unification of gravity and all the other forces. It is also the arena in which explicit examples of gravity duals of strongly coupled field theories are constructed. In this thesis, we explore various degrees of supersymmetry breaking for strings propagating on gravitational backgrounds which have field theory duals. We analyze a class of cascading quivers arising from near horizon limits of branes at singularities, starting with RG flows which preserve some degree of supersymmetry. We then apply this analysis to cases with supersymmetry breaking. We provide examples in which supersymmetry breaks spontaneously around a metastable groundstate and calculate some of its properties. We finally discuss string models in which supersymmetry is completely broken, including the potential phenomenological applications.

Keywords: Physics
Advisor: Kachru Shamit
Kallosh Renata advisor. Thesis advisor
Shenker Stephen Hart
Supply chain contracts for perishable goods with a fixed shelf life [electronic resource]

Managing a supply chain for a perishable good with extremely short shelf life and high value is a challenging task. In such a supply chain, the availability and the utilization of this perishable good become important performance measures. Especially when the supply chain is decentralized, these performance measures may generate conflicting incentives between supply chain partners, where utilization is critical for a supplier and availability for buyers. In this dissertation, we address channel coordination problems for various forms of decentralized supply chains that deal with perishable goods with a fixed shelf life to investigate how to reconcile such misaligned incentives between the supplier and the buyer(s). A platelet supply chain between blood centers and hospitals is a typical example of such a supply chain, where utilization is critical for blood centers and availability for hospitals. Due to such misaligned incentives, blood centers prefer to push older units to hospitals for better utilization of platelets, while hospitals prefer to receive younger units to achieve higher availability. Although there may be various approaches to address the issue of decentralized supply chains, this dissertation particularly focuses on the supply chain contracts.

Keywords: Management Science and Engineering
Advisor: Erhun Feryal primary advisor. Thesis advisor
Fontaine Magali advisor. Thesis advisor
Hausman Warren H. advisor. Thesis advisor
Suppression of tensor decoherence in QND measurements of atomic ensembles [electronic resource]

Atomic ensembles have assumed a central role in modern high precision sensing applications including atomic clocks, magnetometers, gravimeters, and accelerometers. In the past decade significant advances have been made pushing these sensors to, and in some cases beyond the standard quantum limit of sensitivity. Much recent interest has been in the use of Quantum Non-Demolition (QND) measurements to perform state-preparation and metrology simultaneously. QND measurements are typically accomplished through interaction with an off-resonant optical probe. I present techniques to recreate QND measurements in the case that the Probe-Atom interaction is non-QND due to the presence of a tensor light-shift Hamiltonian. The tensor interaction naturally arises in detuned systems with spin one or higher and leads to a series of effects, including Hamiltonian evolution, technical noise enhancement, inhomogeneous and homogeneous dephasing that reduce measurement accuracy in these systems. I demonstrate several techniques for active cancellation of the tensor Hamiltonian and show compatibility with QND measurement and sub-shotnoise metrology performance.

Keywords: Applied Physics
Advisor: Mabuchi Hideo primary advisor. Thesis advisor
Kasevich Mark A. advisor. Thesis advisor
Miller D. A. B. advisor. Thesis advisor
Yamamoto Yoshihisa advisor. Thesis advisor