VictorJuiz/thesis huggingface dataset:
Strain engineering the band structure of graphene [electronic resource]

The purpose of this work is to explore whether strain can modify the band structure of graphene and produce a bandgap. This thinnest material possible, has generated interest in the semiconductor industry for many reasons, including its potential for ballistic conduction, very high carrier mobility and saturation velocity, large current density and natural ambipolar (both n- and p-type) carrier transport. However, its lack of a bandgap suggests a limited future as a silicon replacement material in highly scaled electronics. One route towards the use of graphene transistors for logic devices relies on creating a controllable bandgap. A solution to this problem is sought that uses strain as a way to modulate the band structure and potentially open a bandgap. We have characterized changes in the electronic properties of biaxially strained graphene in the elastic range with Synchrotron Radiation Photoelectron Spectroscopy (SRPES) and Near Edge X-ray Absorption Fine Structure (NEXAFS). Biaxial tensile strain was induced in polycrystalline graphene that was attached to a nanostructured substrate. Strain of approximately 1% was determined by shifts in the Raman spectra. Band structure characterization was performed using photoemission from valence bands, shifts in the secondary electron emission, and NEXAFS absorption from the C1s to the unoccupied graphene conduction bands. We also have used 3-terminal FET structures to study changes in the transconductance of transistors with strained graphene as channel material as compared to FETs with flat graphene channel. The results shows that biaxial strain increased the graphene work function, which is due to the shift of the Fermi energy with strain, and induced band broadening in the valence bands and conduction bands. Furthermore, the ambipolar behavior in strained graphene is suppressed at positive gate voltages. This suggests that there is potentially an increase in the effective bandgap in strained graphene. Strained graphene can thus create a possible route toward a broad class of future graphene electronics. In chapter I, an overview of the current state of the nanoelectronic industry is given, followed by an overview of the electronic properties of graphene relevant to the experimental results of this work. Chapter II is a survey of theoretical and experimental work done on strained graphene. In chapter III, fabrication process, SEM images and Raman characterization of graphene is detailed. In chapter IV, band structure characterization of strained graphene is presented. In chapter V, fabrication of field effect transistors is given, and the effect of strain on electrical properties of graphene is examined. Finally, in chapter VI, possible future work about this project is suggested.

Keywords: Electrical Engineering.
Advisor: Nishi Yoshio
Garner C. Michael
Pianetta Piero advisor. Thesis advisor
Strategic sourcing under supplier responsibility and relationship risks [electronic resource]

Traditional literature in supply disruption examines strategies such as multi-sourcing, backup production options, and quick response. As supply chains have entered and grown on the global stage, new challenges emerge in light of strategic sourcing. And supplier risks caused by certain characteristics are no longer restricted to supply uncertainty or immune to other market conditions. In this dissertation, we focus on supplier risks caused by two aspects: supplier responsibility (Chapters 2 and 3) and supplier relationship (Chapter 4). Our study in supplier risk caused by responsibility is motivated by the series of incidents at Foxconn and subsequent media scrutiny centering on Apple, one of Foxconn's primary customers. And our study in supplier risk caused by relationship is motivated by the joint research project with Intel Corp, who is concerned with the consequences of uncertainty in supplier relationship, specifically for smartphone and tablet industries; whereas it has no such concern for traditional PC industry thanks to its strong leading position.

Keywords: Management Science and Engineering.
Advisor: Lee Hau Leung primary advisor. Thesis advisor
Swinney Robert (Robert Phillip)
Hausman Warren H. advisor. Thesis advisor
The string topology of holomorphic curves in BU(n) [electronic resource]

In this thesis we compute the string topology algebra structure on the homology of a stabilized version of the space of holomorphic maps from 1-dimensional complex projective space to a complex Grassmannian. This generalizes a computation of Kallel and Salvatore.

Keywords: Mathematics.
Advisor: Cohen Ralph
Carlsson Gunnar
Galatius Søren
STRING-assisted module searching with applications [electronic resource]

Analyzing genome wide association data in the context of biological pathways increases statistical power and helps us understand how genetic variation influences phenotype. However, the utility of pathway-based analysis tools is hampered by undercuration and reliance on a distribution of signal across all of the genes in a pathway. Methods that combine genome wide association results with genetic networks to infer the key phenotype- modulating subnetworks combat these issues, but have primarily been limited to network definitions with binary (yes/no) labels for gene-gene interactions. A recent method (EW dmGWAS) incorporates a biological network with weighted edge probability by requiring a secondary phenotype-specific expression dataset. In this dissertation, I combine an algorithm for weighted-edge module searching and a probabilistic interaction network in order to develop a method, STAMS, for recovering modules of genes with strong associations to the phenotype and probable biologic coherence. My method builds on EW dmGWAS but does not require a secondary expression dataset and performs better in six test cases. I show that my algorithm improves over EW dmGWAS and standard gene-based analysis by measuring precision and recall of each method on associations found in other datasets of the same phenotype. In the Wellcome Trust rheumatoid arthritis study, STAMS- identified modules were more enriched for associations replicated in other datasets than EW dmGWAS (STAMS p-value 3.0x10-4; EW dmGWAS- p-value=0.8). I demonstrate that the area under the precision-recall curve is 5.9 times higher with STAMS than with EW dmGWAS run on the Wellcome Trust type 1 diabetes data. I applied STAMS to two real world discovery Genome Wide Association Studies (GWAS). One of the top modules found in the AGRE autism GWAS contains CTTNBP2. Rare loss-of-function mutations in CTTNBP2 have been associated with autism, but have not been reported in common-variant autism GWAS. The application of STAMS to a large Alzheimer's disease GWAS also identified a module of genes in Complex I of the mitochondrial electron transport chain, which is a new association with Alzheimer's disease. I present compelling evidence for a mechanistic role for the module.

Advisor: Altman Russ primary advisor. Thesis advisor
Owen Art B. advisor. Thesis advisor
Sherlock Gavin advisor. Thesis advisor
Structural dynamics of G protein-coupled receptor activation [electronic resource]

G protein-coupled receptors (GPCRs) are transmembrane proteins that mediate complex cellular responses to hormones and neurotransmitters. GPCRs can activate many signaling pathways, either through interactions with heterotrimeric G proteins or through G protein-independent pathways. The function of GPCRs can be modulated by a variety of ligands with a broad range of efficacies, often in a signaling pathway specific manner. Understanding this complex signaling behavior requires insight into the molecular mechanisms of GPCR function. Recent advances in GPCR crystallography have elucidated the structure of a few prototypical receptors, rhodopsin and the β2 adrenergic receptor (β2AR), in both inactive and active conformations. Here, I describe my efforts to understand the structure and dynamics of GPCR activation. To extend the available model systems beyond rhodopsin and the β2AR, I describe the inactive-state structures of the μ and δ opioid receptors as well as a recently determined structure of an activated, agonist-bound μ opioid receptor. I also describe active state structures of the M2 muscarinic receptor and higher resolution structures of the activated β2AR bound its endogenous hormone adrenaline. Finally, I describe a set of studies utilizing 19F-fluorine nuclear magnetic resonance (NMR) and double electron-electron resonance spectroscopy to assess the conformational dynamics of β2AR activation. Together, these studies establish the conformational complexity associated with GPCR activation and how this structural plasticity is likely responsible for the broad versatility of GPCR signaling.

Advisor: Kobilka Brian K. primary advisor. Thesis advisor
Feng Liang
Pande Vijay advisor. Thesis advisor
Weis William I. advisor. Thesis advisor
Structural phase changes and strain engineering in two-dimensional materials [electronic resource]

Two-dimensional (2D) materials are a family of crystals that are only a few atomic layers thick. The discovery of 2D materials has triggered increasing research efforts, motivated by their unique properties, such as ultra-low thickness, high mechanical strength and high flexibility. In the first part of this dissertation, I show that electrostatic gating can induce structural semiconductor-to-semimetal phase changes in 2D materials. Dynamic control of conductivity and optical properties via atomic structure changes is of technological importance in information storage. Energy consumption considerations provide a driving force towards employing thin materials in devices. Monolayer transition metal dichalcogenides (TMDs) are nearly atomically thin materials that can exist in multiple crystal structures, each with distinct electrical properties. By developing new density functional-based methods, I discover that electrostatic gating device configurations have the potential to drive structural semiconductor-to-semimetal phase transitions in some monolayer TMDs. I show that semiconductor-to-semimetal phase transition in monolayer MoTe2 can be driven by a gate voltage of several volts with an appropriate choice of dielectric. I find that the transition gate voltage can be reduced arbitrarily by alloying, for example, for MoxW(1-x)Te2 monolayers. My findings identify a new physical mechanism nonexistent in bulk materials to dynamically control structural phase transitions in 2D materials, enabling potential applications in phase-change electronic devices. Next, I discuss low energy consumption phase change memory that utilizes electrostatically induced structural phase changes in 2D materials. I compare electrostatically driven phase transition with thermally induced phase transition from an energy perspective. I discover that electrostatically driven phase transition is much more energy efficient and does not necessarily generate heat dissipation into its surroundings, which is unavoidable and the most significant part of energy consumption in thermally driven phase transition. In the last part of this work, I describe strain engineering in 2D materials using lithographically or otherwise patterned adatom adsorption. I discover that the monolayer strain results from a competition between the in-plane elasticity and out-of-plane relaxation deformations. I find that some adsorption patterns have the potential to produce strains of as large as 5\%, larger than the strains applied using a substrate approach.

Keywords: Applied Physics.
Advisor: Reed Evan J. primary advisor. Thesis advisor
Suzuki Yuri (Applied physicist) primary advisor. Thesis advisor
Lindenberg Aaron Michael advisor. Thesis advisor
Structure-based engineering of immunomodulatory agents for the treatment of cancer [electronic resource]

Immune-based therapies for cancer are powerful, lasting, and generally less toxic than most other cancer treatment paradigms. Consequently, the development of new immunotherapeutic agents and the study of the interplay between tumors and the immune system have emerged as central lines of research for this nascent field of medicine. Here, I describe my efforts to improve an existing cancer immunotherapy (Interleukin-2), to study an experimental immunotherapeutic agent (Interleukin-15), and to generate novel protein therapeutics against an emerging target of cancer immune evasion (CD47). These studies highlight a structure- and mechanism-based approach to protein engineering in the development of next-generation cancer immunotherapies.

Keywords: Structural Biology.
Advisor: Garcia K. Christopher
Kobilka Brian K. advisor. Thesis advisor
Majeti Ravindra
Weissman Irving L. advisor. Thesis advisor
Studies in covariance estimation and applications in finance [electronic resource]

This thesis examines estimation of covariance and correlation matrices. More specifically we will in the first part study dynamical properties of the top eigenvalue and eigenvector for sample estimators of covariance and correlation matrices. This is done under the assumption that the top eigenvalue is separated from the others, which is reasonable when the data comes from financial returns. We show exactly how these quantities behave when the true covariance or correlation is stationary and derive theoretical values of related quantities that can be useful when quantifying the amount of non-stationarity for real data. We also validate the results by using Monte-Carlo simulations. A major contribution from the analysis is that it shows how and under which regimes correlation matrices differ from covariance matrices from a dynamic viewpoint. This effect has been observed in financial data, but never explained. In the second part of the thesis we study modifications to covariance estimators that find the optimal estimator within a certain sub-class. This type of estimators is generally known as shrinkage estimators as they modify only eigenvalues of the original estimator. We will do this when the original estimator takes the form A1/2XBXT A1/2, where A and B are matrices and X is a matrix of i.i.d. variables. The analysis is done in the asymptotic limit where both the number of samples and variables approach infinity jointly so that random-matrix theory can be used. Our goal is to find the shrinkage estimator which minimizes expected value of the Frobenius norm between the estimator and the true covariance matrix. To do this we first derive a generalization to the Marchenko-Pastur equation for this class of estimators. This theorem allows us to calculate the asymptotic value of the projection of the sample eigenvectors onto the true covariance matrix. We then show how to use these to find the optimal covariance estimator. At last, we show with simulations that these estimators are close to the optimal bound when used on finite data sets.

Advisor: Papanicolaou George primary advisor. Thesis advisor
Johnstone Iain advisor. Thesis advisor
Ryzhik Leonid advisor. Thesis advisor
Studies of unconventional superconductivity [electronic resource]

The physics of unconventional superconductors has been studied for decades but is still not well understood. The present thesis consists of two parts, each intended to shed light on some aspects of this long-standing problem. In the first part, I discuss, based on the Hubbard model in the weak-coupling limit, how the repulsion between electrons gives rise to Cooper pairing. I present simple rules that connect the features of the band structure to those of the gap function, as well as detailed numerical results for various model systems. In the second part, I focus on symmetry constraints on light reflection; a precise understanding of this issue is essential for identifying broken symmetries in various unconventional superconductors from polar Kerr effect measurements. Using a Green's function approach, I prove that the Onsager symmetry of the nonlocal electromagnetic response function implies the absence of the polar Kerr effect in backscattering.

Keywords: Physics.
Advisor: Kivelson Steven primary advisor. Thesis advisor
Kapitulnik Aharon advisor. Thesis advisor
Raghu Srinivas
Studies towards the total synthesis of bryostatin 3 [electronic resource]

The bryostatins, first isolated by Petit et al. from the marine bryozoan Bugula neritina, are a family of 21 macrolides with potent antineoplastic, immunopotentiating, synaptogenesis-inducing and latent HIV-modulating activity. Beneficial effects as a post-stroke treatment and for restoring the blood brain barrier after traumatic blast injuries have also been reported. While the exact mechanism of action remains an ongoing area of research, it has become clear that bryostatins act as agonists of protein kinase C with low nanomolar affinities for their target. Within the bryostatins bryostatin 3 stands out as the most complex member of this family of natural products. While the majority of bryostatins share a common macrocyclic backbone with three tetrahydropyran rings bryostatin 3 features an additional butenolide ring fused to the C-ring. Our retrosynthetic plan for bryostatin 3 disconnects the target into three fragments of similar complexity and we were able to elaborate these fragments to a protected version of bryostatin 3. This direct precursor to the natural product was synthesized in 22 steps (longest linear, 31 total). The only previous total synthesis of bryostatin 3 was accomplished in 43 steps (longest linear, 89 total).

Keywords: Chemistry.
Advisor: Trost Barry M. primary advisor. Thesis advisor
Kool Eric T. advisor. Thesis advisor
Wender Paul A. advisor. Thesis advisor
A study of environmental contributions to the growth and function of the gentle touch receptor neurons in Caenorhabditis elegans [electronic resource]

Eukaryotic organisms use sensory systems to receive information about the world in which they live. They convert environmental stimuli into signals, usually electrical, which can then be processed and translated into pro survival behavior. A key capability for many of these organisms is the ability to sense direct mechanical stimulation, or mechanosensation. Mechanosensory systems consist of the core transduction machinery and the surrounding cellular environment that houses and supports that machinery. In this work, I discuss three studies in which I examined the contribution of the cellular environment to the development and function of the gentle touch mechanosensory system in the nematode Caenorhabditis elegans. In the first study, we show that alterations of the lipid environment in the touch receptor neurons impairs their function. In the second, we demonstrate that the roles of various tubulin isotypes in the touch receptor neurons is context dependent. Finally, in the third study I explore the contribution of the mechanical environment surrounding the TRNs to their length. Taken together, these three studies demonstrate that mechanosensation relies on the interplay between the core transduction machinery and the environmental context in which it acts.

Keywords: Molecular and Cellular Physiology.
Advisor: Goodman Miriam Beth primary advisor. Thesis advisor
Clandinin Thomas R. (Thomas Robert)
Dunn Alexander Robert advisor. Thesis advisor
Ricci Anthony advisor. Thesis advisor
Sub nano kelvin thermometry and temperature stabilization using resonant cavity thermometry [electronic resource]

This thesis describes a general purpose high resolution thermometer based on measuring the resonant frequency of an optical cavity with high coefficient of expansion. It is capable of operating at an arbitrary temperature near room temperature and we have demonstrated an exceptionally low noise figure of 6.6 nK/rtHz at 1Hz. The thermometer has a continuous dynamic range of 0.74 K and an estimated total dynamic range of > 400 K. We evaluate its performance by observing the beat note between the cavity resonance and a reference frequency derived from an ultra low expansion coefficient glass cavity operating near its expansion coefficient null. A hyperfine line feature at a10 transition in iodine near 532 nm is used to calibrate both optical cavities. The temperature sensitivity of the device estimated from its expansion coefficient was found to agree with thermistor measurements to within measurement uncertainty. The device shows a steady drift when compared with the thermistor over many hours. After removing this drift, the resulting calibrated signal is used as an error signal for thermal control, and 7.6 nK stability is achieved with 1 s integration time. When averaged over longer time spans the device shows improved noise performance reaching 200 pK temperature stability at 10,000 s integration time. We describe its construction and performance and mention some modifications to improve its utility.

Keywords: Mechanical Engineering.
Advisor: Byer R. L. (Robert L.)
Goodson Kenneth E.
DeBra D. B. (Daniel B.) advisor. Thesis advisor
Lipa John A. advisor. Thesis advisor
A sub-nyquist ultrasound imager with subarray beamforming [electronic resource]

Ultrasound is a popular imaging modality today. In the medical community, it is commonly used for a wide variety of applications, including early-stage cancer detection and gallstone detection. When compared to other imaging methods such as X-ray or MRI, ultrasound is safe, fast, noninvasive, and low-cost. Traditional ultrasound imagers suffer from high data rates between their sensors and their digital processing back end. This seemingly fundamental data rate is caused both by the use of many analog-to-digital converters (ADCs), each of which samples at a rate corresponding to a traditional interpretation of the Shannon-Nyquist sampling theorem. These data rates can often exceed 4 GB/s (128 sensor elements with 12 bit sampling at 20 MS/s). These data rates hold back the development of fully integrated imagers with high transducer element counts, such as 2D imaging arrays. In a departure from traditional imager design, I sample received ultrasound signals at rates below their physical bandwidth, leveraging compressive sensing (CS) techniques for digital reconstruction. These techniques allow us to reduce data rate on a per-ADC basis. I additionally introduce a mixer-based subarray beamforming technique which exploits the narrowband nature of the receiver to reduce the required number of data converters. Reducing the number of digitizers results in a multiplicative reduction in aggregate data rate. These techniques are demonstrated with a 32- channel ultrasound receiver in a PCB-based hardware implementation which reduces aggregate data rates by a factor of 50 times when compared to a conventional ultrasound topology. There exists a tradeoff between the accuracy of the reconstructed image and the fraction of the bandwidth sampled; we evaluate this tradeoff using experimental data.

Keywords: Electrical Engineering.
Advisor: Murmann Boris primary advisor. Thesis advisor
Arbabian Amin advisor. Thesis advisor
Lee Thomas H.