VictorJuiz/thesis huggingface dataset:
Soft X-ray spectroscopy and X-ray scattering of ice and water in aqueous solutions [electronic resource]

Water has many anomalous thermodynamic and physical properties as a result of the intermolecular hydrogen-bonding (H-bonding). In this dissertation, several synchrotron x-ray techniques were used to investigate the structure of ice and liquid water, both neat, pure water, and in aqueous solutions. First, the effect of protons and hydroxide ions was explored using x-ray Raman Scattering (XRS) and small angle x-ray scattering (SAXS). Both excess protons and hydroxide ions induce strong H-bonds in water molecules in their vicinity. However, proton appears to have only a local effect while hydroxide induces more density fluctuations on the long length scale. Then the effect of ionic charge was explored using SAXS. It was observed that multivalent cations such as magnesium and aluminum ions form "quasi-lattice" in the solution due to the repulsive interactions between the hydrated cations. Higher-charged molecular anions such as sulfate and phosphate do not have such a pronounced effect due to the fundamental difference in cation and anion hydration mechanisms in water. Following the study of molecular anions, the perchlorate anion, a most structure-breaking anion, was studied in more depth using x-ray absorption spectroscopy (XAS) and SAXS. It was observed that perchlorate not only breaks H-bonds in water, but also interacts with water in the hydration shells of multivalent cations such that the "quasi-lattice" structure is significantly disrupted. Finally, temperature-dependent XAS of supercooled water was studied and the absorption cross section was compared with ice data to further understand the interpretation of XAS in this dissertation.

Keywords: Chemistry.
Advisor: Nilsson Anders primary advisor. Thesis advisor
Cegelski Lynette advisor. Thesis advisor
Pecora Robert
A solid-state doping technology for carbon nanotubes [electronic resource]

Single wall carbon nanotubes (SWCNTs) have great potential of becoming the channel material for future high-speed transistor technology. Despite tremendous progress in the recent years, certain challenges still remain to be addressed to realize a scaled CNT based transistor technology. In this thesis I address three fundamental challenges that are essential to realizing a SWCNT-based transistor technology. One of the fundamental issues in carbon nanotube transistor technology originates from material synthesis which provides us a mixture of metallic and semiconducting CNTs. To use the semiconducting CNT as the transistor channel material, we developed a solution-based carbon nanotube sorting process where semiconducting CNTs can be sorted from metallic CNTs to a > 99% of purity. The main application of CNTs following this sorting process is for thin film transistors (TFTs) that can be utilized on flexible transparent substrates. In order to achieve carbon nanotube field effect transistors (CNTFETs) with excellent gate control, it is essential to understand the interactions between CNTs and gate insulation materials - ALD high-k dielectrics. In the second section I will investigate the effects of atomic layer deposited (ALD) high-k dielectrics (Al2O3 & HfO2) on SWCNTs. We study the ALD nucleation and growth on SWCNTs and we confirm our findings and gain insightful information using Raman Spectroscopy. In the third part of the thesis I present a novel, VLSI-compatible solid-state doping technique to fabricate n-type carbon nanotube transistors using low work-function metal oxides as gate dielectrics. Using this technique we demonstrate wafer-scale, aligned CNT transistors with yttrium oxide (Y2Ox) gate dielectrics that exhibit excellent n-type behavior. We confirm this mechanism by carrying out a variety of characterization techniques and provide a general guideline for CNT doping that could also be applicable for MoS2 and graphene. This thesis paves the way to exploiting a wide range of materials for an effective n-type carbon nanotube transistor for a complementary (p- and n-type) transistor technology.

Keywords: Electrical Engineering.
Advisor: Wong Hon-Sum Philip
Bao Zhenan advisor. Thesis advisor
Nishi Yoshio
Solution-processing of organic semiconductors for field-effect transistors [electronic resource]

Solution-processability is a key advantage of organic semiconductors, enabling us to easily deposit these materials at low-cost. Among organic semiconductors, small molecule semiconductors are typically highly crystalline and thus exhibit high carrier mobilities; however, small molecules are generally difficult to deposit into uniform films by solution-processing. In this thesis, we focus on developing solution-processing methods for semiconducting small molecules and understanding the mechanism behind film formation / charge transport in these systems for applications in organic field-effect transistors (OFETs). First, a modified capillary force lithography (MCFL) technique is introduced for fabricating highly textured micro-patterns of a crystalline semiconducting small molecule, C8-BTBT. As this technique is based on soft lithography, various geometries can be patterned onto substrates of interest and the size of the patterns is also easily controlled. Detailed characterizations reveal that the walls of the PDMS stamp used for patterning play an important role in controlling nucleation and growth of C8-BTBT crystals. Fabricated micro-line patterns for high-performance active layers in OFETs are shown to exhibit field-effect mobilities as high as 2.6 cm2/Vs. Secondly, blending semiconducting small molecules with polymer binders is investigated for simultaneously utilizing the exceptional electronic property of small molecules and the good film-forming property of polymers. Our results reveal that residual solvent in blend films following spin-coating plays a critical role in inducing vertical phase separation. In addition, we deduce specific characteristics of polymer binder that are required to generate vertical phase separation and show how annealing temperature affects the type of crystalline phase of rubrene formed in blend films. Lastly, solvent effects are also investigated on the properties of rubrene small molecule blended with a polymer binder. The properties of blend films are analyzed in terms of morphology, crystallinity, and charge transport with various characterization techniques. From our results, we found that there exists a strong correlation between the properties of blend films and solvent characteristics such as solubility, boiling temperature, and surface tension.

Keywords: Materials Science and Engineering.
Advisor: Salleo Alberto
Bao Zhenan advisor. Thesis advisor
McIntyre Paul Cameron advisor. Thesis advisor
Some problems in multiplicative number theory [electronic resource]

Let q be a power of a prime p. In the first part of this thesis, we establish the upper bound of the least prime primitive root mod q by p^3.1. We say a polynomial in F_q [T] is m-smooth if all of its irreducible factors are of degree less than or equal to m. Let N(n, m) be the number of solutions to the polynomial equation X+Y=2Z where all variables are m-smooth polynomials of degree n. In the second part of this thesis, we establish a lower bound on N(n, m) when (8+d) log_q n < = m < = n^1/2 for small d, and prove the analog of the xyz conjecture of Lagarias and Soundararajan in the polynomial rings over finite fields.

Keywords: Mathematics.
Advisor: Soundararajan Kannan
Conrad Brian
Venkatesh Akshay
Space, mind, and discursive knowledge [electronic resource]

Two major philosophical debates are explored - one concerning the reality of space, and one concerning the physicality of qualia. What binds these explorations together is a set of observations Kant made concerning incongruent counterparts. Chapter 1 presents a novel reformulation of Kant's attempt to refute the relational theory of space using these observations. I argue that standard relationist replies fail to engage his 'handless body' thought-experiment, by treating the body as enantiomorphic rather than homomorphic. I then present novel relational replies to Kant's argument as properly understood. In Chapter 2 presents a novel refutation of Frank Jackson's Knowledge Argument (KA). I consider the advances made by John Perry and Torin Alter in identifying the 'discursive learnability' assumption central to KA. I show that this 'discursive learnability' criterion for physical facts must be rejected because straightforwardly physical facts about 'parity-violating' phenomena are not discursively learnable, and I substantiate this claim using Kant's observations about incongruent counterparts. Chapter 3 presents a critique of some popular strategies for rejecting KA, including those of David Lewis, Brian Loar, and Daniel Stoljar. I also propose a distinction between two ways that words fail to communicate concepts and knowledge, and suggest that this clarifies the debate concerning KA.

Keywords: Philosophy.
Advisor: Friedman Michael primary advisor. Thesis advisor
Lawlor Krista advisor. Thesis advisor
Perry John advisor. Thesis advisor
Ryckman Thomas advisor. Thesis advisor
Spectroscopic and computational studies of mononuclear nonheme iron enzymes [electronic resource] : insights into the priming of oxygen-activating Fe(II) enzymes and the mechanism of nitrile hydratase

Mononuclear nonheme iron enzymes (NH Fe enzymes) catalyze a variety of biological reactions. A large group of NH Fe enzymes use a ferrous active site to activate dioxygen towards reaction with substrate, and require an additional cofactor as a source of electrons necessary for catalysis. The main part of this thesis involves the application of a circular dichroism (CD), magnetic circular dichroism (MCD) and variable temperature, variable-field MCD (VTVH MCD) spectroscopic methodology to a series of alpha-ketoglurate-dependent (alpha-KG-dependent) enzymes for the purpose of understanding how this enzyme family and the NH Ferrous enzymes in general induce the dissociation the generation of a 5C site for dioxgyen reactivity, as well as how dioxygen binding is oriented for proper catalysis. In addition to catalyzing oxidation of organic substrates, NH Fe enzymes are also involved in the catalytic hydrolysis and hydration of substrates. A prominent example of this is nitrile hydratases (NHases), unusual low-spin (LS) Ferric or Cobaltic enzymes that catalyze the conversion of nitriles to amides in soil bacteria. Another part of this thesis involves the spectroscopic characterization of a ferric NHase for the determination of its active site geometric and electronic structure, which are used to calibrate a computational model which is extended to explore the NHase catalytic mechanism.

Keywords: Chemistry.
Advisor: Solomon Edward I. primary advisor. Thesis advisor
Hodgson Keith
Stack T. (T. Daniel P.)
State space reduction for dynamic symbolic execution [electronic resource]

Many recent tools use dynamic symbolic execution to perform tasks ranging from automatic test generation, finding security flaws, equivalence verification, and exploit generation. However, while symbolic execution is promising, it perennially struggles with the fact that the number of paths in a program increases roughly exponentially with both code and input size. This dissertation presents a technique that attacks this problem by eliminating paths that cannot reach new code before they are executed and evaluates it on 63 system intensive, complicated, and widely-used programs. Experiments demonstrate that the analysis speeds up dynamic symbolic execution by an average of 115.9 X, with a median of 10.5 X, and increases coverage by an average of 5.2 %.

Advisor: Engler Dawson R. primary advisor. Thesis advisor
Aiken Alexander advisor. Thesis advisor
Dill David L. advisor. Thesis advisor
Statistical analyses on high-thoughput sequencing of B cell and T cell receptors [electronic resource]

The immune system is typically described as having two major branches: the adaptive branch, and the innate branch. In the adaptive immune system, T cells and B cells learn to discern foreign pathogens from self. B cell repertoires mediate the host's ability to mount appropriately pathogen-specific humoral responses against immunological challenges. VDJ somatic recombination of the immunoglobulin chains, affinity maturation, and B cell clonal selection all contribute to the generation of a healthy B cell repertoire. Despite starting from only a limited number of genomic segments, these processes lead to diverse and optimized repertoires of clones, where each clone has its own distinct binding specificity for foreign antigens. High depth sequencing data on the repertoire of B cell receptors has enabled us to examine the diverse receptors in great detail. My thesis will showcase three aspects of the B cell repertoire in terms of how they relate to ageing and/or pathology: clonal convergence, clonal expansion, and phylogenetic hypermutation. In a separate but related work, we apply a novel combination of sequencing method and statistical techniques to examine T cell receptors. We raised the lower bounds on T cell receptor repertoires beta chain richness in healthy humans, and examined how T cell receptor diversity relates to age.

Keywords: Biomedical Informatics.
Advisor: Boyd Scott
Koller Daphne primary advisor. Thesis advisor
Fire Andrew Zachary advisor. Thesis advisor
Olshen Richard A.
Statistical Analysis of the Epistasis Between ApoE and its Genetic Neighbors on Hippocampal Atrophy

Late-onset Alzheimer’s disease (AD), in comparison to familial AD, accounts for 95% of all AD cases. Previous genomic association studies have shown the e4 allele of the apolipoprotein E gene (ApoE4) to significantly increase the risk of late-onset AD. Using single nucleotide polymorphism (SNP) and structural magnetic resonance imaging (MRI) data of 1018 subjects from the Alzheimer’s Disease Neuroimaging Initiative, this study investigated how SNPs in 50 genes functionally related to, or co-expressed with ApoE modulate the risk associated with ApoE4 and whether any genetic variant within these 50 genes shows sex-specific interaction. Three linear models were constructed to separately quantify the effect of 1) SNP only 2) SNP-by-ApoE4 interaction 3) SNP-by-Sex interaction on hippocampal gray matter density extracted from structural MRIs. After filtering for SNPs with a minor allele frequency over 0.05, a total of 7760 SNPs were tested. No SNP remained significant after adjusting for multiple comparisons (adjusted p-value threshold = 5.04 x 10-5). A SNP in the aminolevulinate dehydratase gene, rs818691, came close to the threshold in the SNP-by-Sex model with a p-value of 5.26 x 10-5. Our results suggest that no common polymorphisms in genes known to be functionally related to, or co-expressed with ApoE, contributes significantly to hippocampal atrophy and that ApoE modulates risk of AD through pathways that have yet to be clarified.

Keywords:  Department of Biology
Biology
Alzheimer's disease
ApoE
GWAS
Thesis
Advisor: Greicius Michael
Sapolsky Robert
Statistical methods on graphs [electronic resource]

In relational data the most basic statistical questions focus on modeling the structure of the network and on making inferences about the nodes. These questions are addressed separately with a simple but novel model for each. On the side of graph structure, a class of "monotone random graphs" are examined where n vertices are totally ordered such that independent edge probabilities satisfy the partial ordering p_{i, j} ≤ p_{k, l} for i ≤ k and j ≤ l. The MLE of the graph's edge parameters can be solved by isotonic regression (equivalent to projection onto a convex cone), and this MLE is a consistent estimator. On the nodal inference side, the focus is specifically on multi-relational networks. This approach constructs a design matrix by multiplying a vector of nodal features with each adjacency matrix in which the nodes are embedded. After constructing this design matrix through nodal diffusion, standard statistical learning techniques can be applied to the design matrix.

Keywords: Statistics.
Advisor: Holmes Susan
Chatterjee Sourav advisor. Thesis advisor
Diaconis Persi advisor. Thesis advisor
Stochastic effects in the grammar [electronic resource] : toward a usage-based model of copula contraction

The aim of this analysis of conversational English corpus data is to unearth living effects of phonological, syntactic, and frequency information in an area of the grammar prone to variation: copula contraction. "Living" effects arise during active language processing and may be contrasted with the products of diachronic coalescence of sev- eral forms into fused units. Researchers have found that English auxiliary contraction (have > 've, has > 's, be > 'm/'re/'s, will/shall > 'll ) is subject to phonological, processing, and grammatical constraints. These constraints are most evident in the study of the copula, as "to be" contracts with a wider range of hosts than other auxiliaries, or preceding words, i.e., with pronominal and lexical noun phrase hosts. The analysis reveals three novel e ndings about copula contraction. First, copula con- traction is sensitive to both the collocational frequency of the copula and its host and the following word, even when lexical noun phrase hosts (as opposed to pronominal hosts) are considered in light of known grammatical constraints. The more frequent the host or the following word, the more likely the copula is to contract. The results also suggest that the role of preceding phonology in predicting contraction may be more sensitive to voicing than the vowel/consonant distinction that has generally been observed. Persistence is also shown to play a role in predicting contraction . Finally, the results suggest that copula reduction and contraction are sensitive to many of the same factors and argue that this is evidence of the same constraints creating allomorphic variation at the morphological level.

Keywords: Linguistics.
Advisor: Rickford John R.
Anttila Arto advisor. Thesis advisor
Wasow Thomas advisor. Thesis advisor
String theory, geometry and (mock) modular forms [electronic resource]

Monstrous moonshine (Conway and Norton, c. 1980) is a relation between the "monster", the largest of the sporadic finite simple groups, and the j-function, the unique holomorphic weight zero modular function under SL(2, Z) with a simple pole at the infinite cusp. Recently, string theory has been the impetus for the discovery of a host of similar such relations, connecting many smaller finite groups to mock modular forms, the recalcitrant cousins of the j-function. Here I discuss some of these mysterious new connections, and progress we have made in understanding them by studying string theory on K3 manifolds. This thesis is based on the papers [157], [153], and [127] written with Miranda Cheng, Xi Dong, John Duncan, Shamit Kachru, Natalie Paquette, and Timm Wrase. It should not be cited without also referencing those papers.

Keywords: Physics.
Advisor: Kachru Shamit
Hartnoll Sean advisor. Thesis advisor
Silverstein Eva
Structural damage detection using ultrasonic guided waves under varying ambient temperature and loading environments [electronic resource]

Accurate interpretation of in-situ piezoelectric sensor signals for guided-wave based structural health monitoring is a challenging task owing to the influence of varying environments and operating conditions. This research presents the development of environmental compensation models based on physical insight to aid in structural damage detection using in-situ piezo-sensor signals. Analytical as well as numerical simulation studies are carried out to understand the influence of varying ambient temperature and loading environments on signals collected from thin, metallic, plate-like structures, instrumented with surface mounted piezoelectric transducers. A system identification model is proposed wherein changes in the signal parameters are related to the changes in the material properties of different physical components. Numerical compensation models are developed and validated to estimate piezo-sensor response under known strain field and temperature distribution in a structure. Numerically reconstructed first wave packets of the sensor signals are found to match quite well with the experimental measurements for both flat as well as stiffened plates made up of aluminum alloy. A very limited amount of in-situ sensor measurements is required to estimate unknown model parameters, underlying the practical efficacy and usefulness of the proposed compensation methodology. The outputs of the compensation models are also linked with an anomaly detection algorithm to detect structural damage under varying environments.

Keywords: Aeronautics and Astronautics.
Advisor: Chang Fu-Kuo primary advisor. Thesis advisor
Christensen R. M. (Richard M.) advisor. Thesis advisor
Goebel Kai
Structural modeling of short-run price dynamics in commodities markets [electronic resource]

This dissertation addresses the gap between commodity price models in economics and finance. The literature in finance often abstracts from market forces and calibrates a stochastic process of price dynamics in order to follow them closely and to price commodity derivatives, most importantly futures contracts. On the other hand models in economics literature often focus on supply, demand and inventories in the long-run. I have developed short-run structural models of commodity prices. These models provide a better description of price dynamics by considering the underlying structure of the economy. Since these models incorporate actions of market participants, they have the advantage of being able to process information signals about probabilities of future supply/demand shocks. The other advantage of short-run structural models is their power in prediction of unobservable states of the economy. Hence, these models provide a better description of forward curves in commodities markets. Recent advances in the theory of storage have been able to associate specific behaviors of commodity prices with inventory dynamics. These models assume producers and consumers who only consider current price, and storage units who consider the whole stochastic process of price in the future. This thesis improves upon these models in two aspects. First, I remove the assumption that the producers and consumers take into account only the current price. For depletable commodities specifically, and for many commodities in general, it is more plausible to assume that the producer has the option to sell the commodity now or postpone the extraction until a future time. The expected future dynamics of prices can change the current production decisions and as a result the current and future prices. My model characterizes the equilibrium of such a system and its comparative dynamics. Second, I introduce an advanced calibration algorithm for this model. Traditional models calibrate their parameters by minimizing their prediction error on aggregate measures such as the average volatility of forward prices. My approach considers the instances of forwards curves and tries to matches each of them. One advantage of this model is the ability to estimate the state of the system (e.g. remaining inventories) as well as the transient and permanent shocks in supply/demand. The theoretical framework of this dissertation shows that actions of rational market participants impose certain price dynamics to the market. Most examples in this work consider crude oil as it is the most traded commodity, with liquid future contracts for longer horizons. Calibration results demonstrate the improvements that short-run structural models could create in describing price dynamics.

Keywords: Management Science and Engineering.
Advisor: Sweeney James L. primary advisor. Thesis advisor
Luenberger David G.
Weyant John P. (John Peter) advisor. Thesis advisor