VictorJuiz/thesis huggingface dataset:
Efficient storage of and in DNA

The last decade has witnessed staggering improvements in DNA sequencing technologies, leading to the emergence of new frontiers in genomics and medical research. Low-cost DNA sequencing has led to multiple large scale sequencing initiatives such as the Thousand Genomes Project and the Million Veterans Project leading to a huge surge in the amount of genomic data being generated. This deluge of information has motivated the development of compression techniques for genomic data. The advances in genomic sequencing and synthesis technologies have also opened avenues for research into the potential for using DNA for storage of digital data. This thesis studies two related problems: compression techniques for efficient storage of genomic sequencing data, and error-correction for storing digital data in DNA. Both of these problems utilize special properties of the DNA sequencing process in the algorithmic design. We start with a brief introduction to the genomic sequencing pipeline. We then look at the problems of genomic data compression and storage of digital data in DNA in detail, analyzing both the theoretical aspects and practical algorithmic designs

Keywords: Electrical Engineering.
Advisor: Weissman Tsachy
Özgür Ayfer 
Wootters Mary
Elastomers for stretchable electronics : from molecular structure to mechanical properties

Elastomers that can sustain large reversible strain are essential components for stretchable electronics. In order to improve the stretchability and mechanical robustness of the elastomers without interfering with their electronic performance, one approach is to apply a multi-network structure that drives covalent cross-links easy to break, and another approach is to use dynamic (supramolecular) cross-links that can easily break and re-form. Using these approaches, the elastomers exhibit stress-strain hysteresis indicating strain-induced damage by bond breaking. On the other hand, the bond re-forming events can repair the damage and enable the self-healing of elastomers. Although modern chemical tools are available for controlling the bond property of cross-links, fundamental understanding of the underlying mechanisms is lacking due to the gap in knowledge about how the bond-dynamics governing microstructure relates to the emerging mechanical and self-healing properties. Using coarse-grained molecular dynamics (CGMD), network analysis and analytic modeling, the author of this thesis establishes an explicit microstructure-property relationship for multi-network elastomers and supramolecular elastomers in the form of shortest paths connecting distant cross-links. The average length and straightness of these shortest paths serve as key damage parameters that feature hysteresis, directionality, self-healing and control of the stress-strain responses. These findings serve as a basis for understanding the existing elastomers and a guide for the design of new ones

Keywords: Materials Science and Engineering.
Advisor: Cai Wei
Dauskardt R. H. (Reinhold H.)
Bao Zhenan
Elastoresistance of iron-based superconductors

Strong electronic nematic fluctuations have been discovered near optimal doping for several families of Fe-based superconductors, raising the question of what role, if any, these fluctuations might play in the superconducting pairing interaction. Underdoped Fe-based superconductors undergo a second order tetragonal-to-orthorhombic structural transition driven by electronic nematic order that accompanies or precedes an antiferromagnetic transition and borders the superconducting dome. In the tetragonal phase Fe-based superconductors are highly sensitive to perturbations of the same symmetry as the nematic order, such as antisymmetric (in this case B2g) strain. Elastoresistivity is described by a high rank tensor (fourth-rank +) as it relates changes in resistivity (second-rank) to strain (second-rank) experienced by a material and is a sensitive probe of broken symmetries. Previously, elastoresistivity measurements of the linear resistivity response to antisymmetric strain have revealed a divergent electronic nematic susceptibility in underdoped materials and has been used to characterize the nematic fluctuations in the tetragonal phase above the zero-field superconducting dome. In this work, I develop two new extensions to elastoresistivity measurements in order to probe the effects of electronic nematic fluctuations in greater detail in a representative family of these materials, the prototypical electron-doped pnictide Ba(Fe(1-x)Cox)2As2. First, I go beyond the first order response via a measurement of the nonlinear elastoresistivity. I find that the strong nematic fluctuations play a large role in the isotropic electronic response of these materials—as evidenced by a diverging nonlinear symmetric elastoresistivity response to antisymmetric strain. Second, I performed elastoresistivity measurements in magnetic fields large enough to suppress superconductivity to investigate the potential that the nematic fluctuations are related to a quantum critical point. I do not observe a magnetic field dependence of the nematic fluctuations and find that they continue to grow with decreasing temperature beneath the zero-field superconducting dome. I performed high magnetic field measurements on samples with a fine distribution of dopings and find that close to the putative quantum critical point, the nematic susceptibility appears to obey power law behavior over almost a decade of variation in composition. This is consistent with basic notions of nematic quantum criticality which, for clean systems, is associated with power law scaling in both doping and temperature. Paradoxically, however, I also find that the temperature dependence of the nematic susceptibility for compositions close to the critical value cannot be described by a single power law

Keywords: Applied Physics.
Advisor: Fisher Ian R. (Ian Randal) 
Kivelson Steven 
Moler Kathryn A.
Electrical, thermal, and strain-dependent characterization of transition metal dichalcogenide-based devices

For over half a century, the performance of integrated electronics has significantly improved by reducing the dimensions of silicon-based logic and memory devices. However, as silicon scaling approaches its limits, researchers are investigating new materials for transistors, memory, and their three-dimensional (3D) integration on the same chip to enable higher density and better energy efficiency. Two-dimensional (2D) materials, in particular semiconducting transition metal dichalcogenides (TMDs), have demonstrated excellent electrical properties even in atomically thin films. In addition, these materials are promising for 3D architectures due to their ability to be integrated with various device structures at low temperatures. In this thesis, I will describe various experimental techniques to study TMD-based memory and transistors. First, I study switching behavior in resistive memory devices based on molybdenum ditelluride (MoTe2). I use scanning thermal microscopy (SThM) combined with electro-thermal simulations to investigate heating in the devices during operation. The SThM measurements, together with electrical measurements and transmission electron microscopy imaging, help uncover the switching mechanism in these devices and provide the first thermal insights into the operation of such TMD-based resistive memory. Next, I demonstrate a simple pulsed voltage measurement technique to reduce hysteresis due to charge trapping in current-voltage measurements of MoS2 transistors. I compare devices fabricated from exfoliated and synthetic MoS2, with SiO2 and HfO2 gate insulators, using both DC and pulsed voltage measurements. The hysteresis is reduced by ~80% in all devices at modest voltage pulses of ~1 ms applied to the gate of the transistors, enabling accurate extractions of threshold voltage and field-effect mobility. Finally, I explore the effects of strain on the optical and electrical properties of monolayer TMDs. First, photoluminescence measurements of MoTe2 with tensile strain reveal narrowing of the optical band gap and indicate reduced exciton-phonon intervalley scattering. Next, I apply tensile strain to MoS2 transistors and demonstrate an improvement in current and mobility by up to a factor of two. These results suggest that strain might play an important role for integrated 2D electronics, as it has for silicon. This work improves our understanding of TMD-based devices, which are promising for both logic and memory in next-generation electronics

Keywords: Electrical Engineering.
Advisor: Pop Eric 
Reed Evan J. 
Saraswat Krishna
Electrochemical two-electron water oxidation toward hydrogen peroxide evolution

Hydrogen peroxide (H2O2) is a green chemical oxidant widely used for disinfection, water treatment, chemical synthesis, and paper bleaching. Industrially, H2O2 is produced through the energy-intensive anthraquinone process and distributed to the point-of-use. To mitigate the transportation cost and safety concern and to leverage the renewable electricity, a new approach has emerged to produce H2O2 onsite by electrochemically reducing O2 on the cathode and/or oxidizing water on the anode. Between these two reactions, the water oxidation reaction (WOR) is more desirable as it only needs water as the reactant and doesn't need continuous gas purging. Several pioneering works have demonstrated the feasibility of water oxidation to evolve H2O2 by using electrocatalysts, but it remains unclear what factors affect the activity and selectivity of the electrocatalysts. In my thesis work, I have investigated three aspects to facilitate the water oxidation reaction to evolve H2O2. First, our theoretical collaborators have suggested that the Gibbs adsorption energy of OH* on a catalyst surface is a descriptor to describe the activity and selectivity of WOR. I have experimentally verified the validity of overpotential and faradaic efficiency for H2O2 evolution by testing four metal oxide catalysts, i.e., WO3, BiVO4, SnO2, and TiO2. This study shows that BiVO4 has better activity and selectivity for WOR to evolve H2O2 than the other three catalysts. Second, our theoretical collaborators further use the descriptor ΔGOH* to screen and identify that ZnO with (101 ̅0) as the dominated facet will be a better catalyst than BiVO4. I have experimentally synthesized two types of ZnO, and demonstrated that one achieves the peak faradic efficiency of 80%, which is the highest among other reported catalysts. Finally, I built a photoelectrochemical device that uses BiVO4 as photoanode and electrocatalyst for water oxidation and CMK-3 carbon as electrocatalyst on the cathode for oxygen reduction. This device produces H2O2 on both electrodes under illumination and produces electricity simultaneously

Keywords: Mechanical Engineering.
Advisor: Zheng Xiaolin
Cappelli Mark A. (Mark Antony)
Prinz F. B.
Electron beam manipulations at the angstrom level and attosecond timescale for X-ray FELs

X-ray Free-Electron Lasers (FELs) like the Linac Coherent Light Source (LCLS) have now operated for a decade, delivering linearly polarized pulses as short as a few femtoseconds to users. I will discuss two experiments and associated theoretical developments on manipulating the FEL gain medium -- a relativistic electron beam -- in order to extend the capabilities of LCLS. The first is the production of isolated, circularly polarized x-ray pulses with a helical undulator and non-intuitive electron microbunch rotation. The microbunch rotation required for isolating circular pulses is also useful to multiplex LCLS and for outcoupling radiation from cavity-based FELs. The second project is on the production of sub-femtosecond x-ray pulses with a tailored electron beam phase space. We tailor the longitudinal phase space of the electron beam core with coherent radiation from the electron beam tail produced in a magnetic undulator. The resultant x-ray pulses contain six orders of magnitude more energy than otherwise comparable sub-femtosecond x-ray sources. These two projects involved relativistic electron beams interacting with radiation in previously unexplored parameter regimes. We therefore also discuss several theoretical contributions and associated simulation work. In particular, we present an improved understanding of coherent radiation from a kicked electron beam, undulator impedance, reverse tapered undulators, and rest-frame simulation of FELs

Keywords: Physics.
Advisor: Huang Zhirong
Bucksbaum Philip H. 
Hastings Jerome
Reis David A.
Electron, oxygen, and spin transport in complex oxide perovskites

The manipulation of the spin of charge carriers within solid-state materials has the potential to greatly reduce power consumption and increase computational speeds and information storage densities. The development of these spintronic devices requires development of new materials which can be used to efficiently generate, propagate, and detect spin currents. One promising class of materials to use are the complex oxide perovskites, which exhibit a rich variety of tunable electronic and magnetic properties and which can be interfaced and combined to create emergent interfacial phenomena. In this thesis, I will cover two efforts to develop materials for spintronics applications. The first part of this thesis focuses on the surprising discovery that the pulsed laser deposition process used to grow homoepitaxial thin films of oxygen-deficient SrTiO(3-x) can significantly change the properties of the underlying SrTiO3 substrate. In the search for a low-dimensional metal with high mobility and high spin-orbit coupling, I find that the plume dynamics and kinetics during thin film growth cause significant oxygen-reduction of and conductivity in the entire substrate, significantly faster than by other processes. This has significant implications for thin film growth of many different materials. In the second part of the thesis, I will focus on spin current generation via microwaves in a low-loss ferromagnetic metal, (La2/3Sr1/3)MnO3, and the transmission of spin angular momentum across an epitaxial interface with a non-magnetic, high spin-orbit coupled metal, CaRuO3. Using ferromagnetic resonance spectroscopy to both generate these spin currents as well as measure magnetic properties, I not only find evidence of efficient spin pumping across the interface, but also find that the orthorhombic CaRuO3 can affect the magnetic and electronic anisotropy in these heterostructures, likely due to structural effects. While complex oxides remain promising candidates for spintronics, the integration of different materials offers additional degrees of freedom which must be fully understood to engineer additional functionality

Keywords: Physics.
Advisor: Suzuki Yuri (Applied physicist) 
Goldhaber-Gordon David
Lee Young Sang
Electro-optic devices for quantum transduction

Quantum computers are a fundamentally new type of supercomputer which have the potential to make major impacts in drug discovery, material science, cryptography and machine learning. Connecting quantum computers together into a quantum network opens up even more applications, such as secure communication and enhanced sensing, and provides a path to scaling quantum computers to larger numbers of qubits. In order to connect quantum computers over long-distances, we require a new kind of transducer to bridge the gap between the microwave regime, in which the qubits operate, and the optical regime, in which we can use fiber optic communication. This dissertation describes my work towards building a microwave-to-optical transducer, pushing electro-optic modulators towards the quantum limit by combining low-loss optical waveguides with superconducting circuits. This effort led us to explore three different nanophotonic platforms. The first, silicon-on-lithium-niobate, combines the straightforward waveguide fabrication available in silicon with the large electro-optic coefficient of lithium niobate. The second, silicon-organic hybrid, leverages the exceptionally large electro-optic coefficients available in electro-optic polymers. The third, lithium-niobate-on-sapphire, employs waveguides fabricated directly in lithium niobate to further increase performance. Here I describe results from each of these platforms, as well as some of the interesting problems we've had to address along the way, including challenging nanofabrication, cryogenic optical packaging, light-induced quasiparticles, and unintentional piezoelectricity

Keywords: Applied Physics.
Advisor: Safavi-Naeini Amir H. 
Fejer Martin M. (Martin Michael)
Miller D. A. B.
Electrostatics in solvation, catalysis, and enzyme evolution

The study of catalysis, whether biological or chemical, enables life on both a micro- and macroscopic level, the former controlling metabolism, the latter enabling nearly many of the advances of modern civilization. However, the underlying physics that governs these catalytic processes still remains largely a mystery. Towards that goal, enzymes have served as both an inspiration and great source material for unravelling the chemical and physical mechanisms of catalysis, exhibiting uniquely arranged 3D structures and functions that make up the canonical structure-function relationship. However, fundamental limitations in our understanding still persist as many labs working on de novo design have demonstrated the ability to construct both new and old protein architectures, but instilling function remains a fundamental challenge. Towards that goal, this thesis describes my research on elucidating the electrostatic origins of non-covalent interactions in complex environments like enzyme active sites, to better understand their structural and functional importance. As such, the vibrational Stark effect (VSE) is the hallmark and basis of most of my research as a tool to better understand environments in terms of their electrostatic components as projected along small local molecular probes, such as carbonyls. In order to utilize the VSE to its fullest, the first half of my thesis focuses on exploring and testing the fundamental spectroscopic and physical limits underlying the VSE with diverse carbonyl probes for applications such as organocatalysis, electrochemical energy storage, solvation, and enzymatic catalysis. After developing and benchmarking the VSE, I've combined this approach with biophysical characterization and mechanistic enzymology approaches to better unravel these relationships in the model enzymatic system TEM β-lactamase over its evolutionary trajectory to extended-spectrum activity and antibiotic resistance in order to disentangle the role of electrostatics in guiding enzyme evolution. This thesis expands upon our understanding of the role of electrostatics in solvation, catalysis, and enzyme evolution

Keywords: Chemistry.
Advisor: Boxer Steven G. (Steven George)
Kool Eric T.
Solomon Edward I.
Emerging technology integration for improving water reuse treatment

Water reuse is an increasingly popular approach to augmenting water supplies. In potable water reuse, sewage is treated to drinking water quality through a combination of wastewater treatment and Full Advanced Treatment (FAT). While effective at producing high quality water, the FAT-based potable reuse treatment train is energy-intensive, complex, and costly, which lowers its potential for widespread adoption. This dissertation explores how emerging technologies can be integrated into potable reuse trains to improve water treatment, and how reverse osmosis, the backbone of FAT, can be applied to treat impaired groundwater

Advisor: Mitch William A. 
Boehm Alexandria
Luthy Richard G.
Emotive Rhetoric as Strategic Intent: Sentiment Analysis of LVMH and Kering’s Environmental Reporting

Luxury conglomerates LVMH and Kering have recently gained public attention due to their aggressive sustainability campaigns – which include environmental reporting. This thesis suggests that these companies’ signaling power as industry leaders, their operational complexity, and their historic rivalry make their environmental reports worth studying. Using sentiment analysis to investigate LVMH and Kering’s annual environmental reports from 2013 to 2018, what emotions can we identify in these documents’ language and how has their use changed throughout the years? Guiding this project is the desire to determine why these companies are interested in communicating their environmental performance and in using reports. To that end, I perform lexicon-based sentiment analysis using the VADER tool and the NRC Sentiment and Emotion Lexicons. This novel approach to content analysis reveals that when LVMH and Kering engage in emotive rhetoric, they predominantly evoke ‘positive’ feelings, ‘trust,’ ‘anticipation,’ and ‘joy.’ By contrast, sentiments with negative connotations are the least evoked. This research also finds both companies’ language to be extremely similar throughout the six-year period. Based on a prior synthesis of literature on environmental reporting and an analysis of luxury strategy, this thesis proposes that LVMH and Kering evoke such sentiments to assert their proactivity working against environmental threats. In turn, this emotive rhetoric reassures shareholders, whose support is essential to their long-term survival. Further, such emotive rhetoric contributes to these companies’ reputations. This is important for luxury companies like LVMH and Kering, whose operational longevity and cultural significance rest upon long-term planning. As such, LVMH and Kering’s emotive rhetoric aligns with their strategic intent. This thesis concludes by encouraging future research on rhetoric and other subtle strategic actions taken by luxury fashion companies, especially in the context of environmental threats. In addition, it calls attention to sentiment analysis as an innovative research method in fashion.

Keywords: Science Technology and Society
fashion
sustainability
sentiment analysis
strategic intent
luxury
strategy
LVMH
Kering
Thesis
Advisor: Hoyos Héctor
Empirical analysis of complex wavefields

The principal focus of this thesis is exploring the passive seismic wavefield, including both ambient seismic noise and earthquake ground motion. On the one hand, ambient noise, though appearing to be a nuisance and treated as an unwanted component, has seen flourishing applications in the past decades. However, the discrepancy between the reality of noise properties and theoretical assumptions leads to considerable bias in those applications. A better understanding of the noise wavefield is therefore crucial. One the other hand, significant earthquakes pose continuous threats to human life and habitat. Mitigating seismic hazard demands detailed knowledge of these seismic waves that carry tremendous energy and cause damage. In this thesis, I first give a background introduction on seismic wavefields and the connection between seismic noise and earthquake ground shaking. Then I demon- strate that it's possible to convert the noise data into signals, which can be used to simulate long-period earthquake ground motion. I introduce an improved multi-component C3 method. It enhances the signal-to-noise ratio of the simulation and yields more reliable amplitude estimates. Starting from a puzzling observation, I carefully examine the C3 method and propose a new interpretation of it. Inspired by this insight, I develop a modified signal processing procedure that increases the resolving power of traditional seismic interferometry techniques on relatively sparse networks. I then switch the focus to the coda of repeating earthquakes, which are used to extract velocity perturbations. Studying earthquake coda provides insights into the coda of correlations. The chapter following focuses on the spatial variability of earthquake ground motions by exploring the similarity of earthquake recordings on dense seismic arrays. The spatial coherence revealed from waveform similarity is consistent with that from amplitude measurement

Keywords: Geophysics.
Advisor: Beroza Gregory C. (Gregory Christian) 
Baker Jack W. 
Ellsworth William L.