VictorJuiz/thesis huggingface dataset:
Regularizability and bosonization of relativistic massless fermion

In this dissertation, we discuss the non-regularizability and the bosonization of massless fermions with relativistic dispersion in 1,2,3 spatial dimensions. The non-regularizability is the root of various quantum anomalies and plays a central role in the physics of symmetry-protected topological phases. We generalized the Nielsen-Ninomiya theorem to all minimal nodal free fermion field theories protected by the time reversal, charge conservation, and charge conjugation symmetries. We prove that these massless field theories cannot be regularized on a lattice while respecting the protection symmetries. However, they can be realized on the boundaries of symmetry-protected topological phases in one higher dimension. We then generalize Witten's non-abelian bosonization of massless free fermion theories in one spatial dimension to two and three spatial dimensions. We shown the resulting boson theories share the same emergent symmetries and anomalies with the fermion theories. Moreover, we also show the boson theories possess fermion degrees of freedom, namely solitons. These bosonized models are non-linear sigma models with level-1 Wess-Zumino-Witten terms. As applications, we apply the bosonization results to the SU(2) gauge theory of the Mott insulating phase of nearest-neighbor hopping Hubbard model, ``bipartite-Mott insulators'' in 1,2,3 spatial dimensions and twisted bilayer graphene.

Advisor: Lee, Dung-Hai
Introducing the Individual-Quadruple Process Model - Investigating the Validity,Reliability, and Predictive Utility of this Multinomial Processing Model

Discussions about the measurement and conceptualization of implicit bias through the Implicit Association Test (IAT) have become increasingly prominent. Critiques center around the reliability of its measurement, such that individual level measurements tend to show a degree of instability that is not common for individual difference measures. The traditional scoring method of the IAT is the d-score, which uses reaction times to create a standardized difference score that serves as the measure of implicit bias. Sherman and colleagues’ (2005) quadruple process (QUAD) model argues that since the IAT is not a process-pure measure, both automatic and controlled processes should be estimated and analyzed. In the published literature the QUAD model has been validated at the condition (i.e. group) level. Reports of its use at the individual level (e.g., Wrzus et al. 2017; Calanchini et al. 2014; Gonsalkorale et al. 2014) suggests that the model can be fruitfully used at the individual level as well. We introduce such a methodology here, building upon the work of Sherman and Colleagues’ to validate the QUAD model parameters at the individual level. We offer an open-source, freely available R code for others to use. We were able to demonstrate that at the individual level, QUAD model parameters related to the IAT d-score in theoretically consistent ways while also providing novel information. We note that the d-score and iQUAD use very different scoring algorithms and suggest looking at both in unison to get the most information out of IAT data. Our findings provide a valuable tool to the field for disentangling, at the individual level, the d-score into its constituent components.

Advisor: Mendoza-Denton, Rodolfo
A probabilistic approach to studying alternative splicing in single cell data

Alternative splicing is a post-transcriptional gene regulatory process that increases transcriptomic diversity through the differential selection of exons. Over the past decade, single cell RNA sequencing (scRNA-seq) experiments have allowed the study of the complex heterogeneity of tissues, and the gene expression regulation mechanisms that determine the identity of individual cells. However the study of alternative splicing has largely lagged behind in single-cell approaches. This is in part due to a number of technical limitations that make this study particularly difficult. In this dissertation, I first demonstrate that the technical distortion of splicing observations in single cells produces the appearance of bimodality in single cell splicing. I discuss how this limitation has affected our understanding of single cell splicing, and what computational approaches can be used to extract meaningful biological information from this exceptionally noisy data. I then present Psix: a computational tool that implements an updated model for single cell splicing observations that takes into account this distortion. Using Psix, I identify alternative splicing that changes across a phenotypic landscape, as well as groups of potentially co-spliced exons. Finally, I explore potential regulatory roles for these poison exons in the production of Serine/Arginine-rich (SR) splicing factor proteins.

Advisor: Lareau, Liana F
Yosef, Nir
Development of Fluorescent and Bioluminescent Hybrid Voltage Imaging Strategies for Voltage Sensitive Dyes

Understanding the broader implications and functions of membrane potential in the brain,heart, and body requires accurate and simultaneous membrane-associate voltage measurements on a large array of single cells. Achieving high spatial resolution and millisecond time resolution with minimal perturbation to live cells is a long-standing challenge, especially within the field of neurobiology. Direct imaging of membrane potential changes with fluorescence-based voltage indicators has become a powerful and most popular approach to mapping electrical changes yet several challenges addressing indicator speed, brightness, sensitivity, and localization remain. The Miller lab focuses on addressing these issues using a relatively new class of small molecule voltage indicators, VoltageFlours, that depend on a photo-induced electron transfer (PeT) mechanism. The intramolecular electron transfer modulates fluorescence intensity based on the surrounding electric field and results in sub-microsecond response kinetics with high voltage sensitivity. As with all organic indicators, the cellular spatial resolution in dense tissue samples is limited since VoltageFluors indiscriminately stain all membrane types. Our group has worked on addressing this limitation by combining VoltageFluors with genetically encoded self-labeling enzymes like the well-known Halo- and SNAP-tag proteins. Portions of this dissertation will focus specifically on the SNAP-tag covalent tethering approach with fluorescein and rhodamine-based VoltageFluors. The remainder of this thesis is primarily focused on a new branch of voltage imaging using bioluminescence which has never been explored within our group. Fluorescent indicators are dependent on externally applied illumination leading to unavoidable light-induced damage, especially at shorter wavelengths, which alters cell physiology and confounds data. There are relatively few examples of bioluminescent indicators relative to fluorescent indicators, and even fewer that are voltage sensitive. This dissertation will explore the development of the first ever quenching bioluminescent voltage indicator, limitations to single cell bioluminescent voltage imaging, and other potential approaches to functionalize bioluminescence at the membrane.

Advisor: Miller, Evan W
The Techno-Political Assemblages of Urban Restitution

Land restitution in South Africa is a state-led program developed to return lost lands to those dispossessed by colonial and apartheid policies and practices. However, the program is widely lamented for its failure to deliver upon its post-apartheid promise for land during its first-wave (1994-8) and second-wave (2014-9) efforts. Though an important body of scholarship has emerged to investigate the legal, legislative and constitutional shortcomings that substantively limit its decolonizing potential, little research has been conducted to examine the program itself as a project of spatial governance. This dissertation examines the land restitution program as increasingly estranged from its central mandate, captured instead by a range of alternate politics, institutional imperatives and technological interventions. Drawing upon Actor-Network Theory (ANT) and assemblage thinking, the chapters therein explore an array of spatial assemblages corresponding with distinct phases or elements of the land claims process, each articulated by the circulation of policies, protocols, objects and technologies deployed to bring a disparate constellation of sites into communication and coherence. These spatial assemblages are shown to have agential capacities, producing several program outcomes and effects that unsettle the post-apartheid aspirations of land restitution. This dissertation calls for further research attending to the ways in which land restitution and reform efforts are increasingly repurposed as technocratic projects of socio-spatial governance in post-colonial contexts.

Advisor: Collier, Stephen J
Investigation of Novel Correlated Effects in Materials with Flat Band

Novel electronic phases induced by unusual electronic structures have attracted central attention in condensed matter physics communities. One of such exotic electronic structures is a dispersionless flat band. The fundamental physics and possibility of the induced phases, including high-temperature superconductivity, magnetism, and fractional quantum Hall effects, have been discussed for past decades, and such a flat band has been considered as the driver of new exotic phenomena. Hence, the system with a flat band could be fertile to many novel states of the matter. However, due to the limited number of the systems hosting the flat bands, the detail mechanisms of the flat band-induced unconventional states remain still elusive. In this dissertation, we provide the new platforms to explore what phases can be driven in the proximity of a flat band when it is coupled to a strong correlation or topological physics. We show the experimental electronic structures on two different systems, measured using angle-resolved photoemission spectroscopy (ARPES)./nChapter 1 briefly introduces the basic concept of flat band systems with examples of the unconventional states with flat bands, establishing the flat band as the tool to achieve various quantum states of matter. We also provide the motivation of each study in this dissertation. Chapter 2 introduces an overview of the primary experimental technique used in this dissertation, ARPES, a direct probe of the electronic structure. Additionally, we briefly introduce the principle of density functional theory calculation.Chapters 3, 4, and 5 describe three different studies. In Chapter 3, we build the correlation by coupling different oxides and creating the states at the interface. Unlike conventional semiconductors, oxide interface systems host strong correlations. If some unconventional phases are driven by the combination of flat band and correlation effects, this system can be the analog of cuprate high-$T_\text{c}$ superconductors. Chapters 4 and 5 are the case of topological materials. We establish a new playground where the topological physics can couple to the flat band. We investigate the bulk electronic properties of a new topological semimetal in Chapter 4. On the other hand, we focus on the surface localized states of the same material in Chapter 5. Finally, in Chapter 6, we briefly summarize the main findings and offer some concluding remarks.

Advisor: Lanzara, Alessandra
Millivolt Micro-Electro-Mechanical Relay Devices & Circuits

The emergence of the Internet of Things (IoT) has brought energy consumption to the forefront of challenges for future information processing devices. Digital logic integrated circuits (ICs) implemented with complementary metal-oxide-semiconductor (CMOS) transistors have a fundamental lower limit on energy consumption due to their non-zero OFF-state current (I_OFF) and finite sub-threshold slope. In contrast, micro-electro-mechanical (MEM) switches (relays) can achieve zero I_OFF and have abrupt switching characteristics; therefore, they have attracted growing interest for ultra-low-power computing applications./nThis dissertation first addresses challenges for realizing millivolt operation of relay ICs. The impact of electrode configuration on contact resistance and hysteresis voltage is investigated, and it is found that reducing the number of contact dimples from 4 to 2 improves the tradeoff between on-state resistance and minimum operating voltage. With an anti-stiction self-assembled monolayer (SAM) coating, a variety of pass-gate logic circuits using the new 2-contact-dimple relay design are demonstrated to operate with sub-50 mV voltage signals; these include AND, OR and XOR gates and a 2:1 multiplexer (MUX). Multi-functional MEM relay circuits are also demonstrated including a majority gate, 2-bit 2:1 MUX, and dual-polarity gates (XOR/XNOR)./nNext, this dissertation addresses remaining practical challenges and discusses opportunities for MEM relay technology. A new method using voltage pulses to reliably break down native oxide on contact-electrode surfaces is developed. SAM coating and operation in liquid dielectric media are explored for improving on-state resistance stability for tungsten contacts in ambient conditions. Finally, MEM relays are demonstrated to function well in extreme environments across a wide temperature range./nFinally, this dissertation proposes a novel relay design that incorporates a beam with negative stiffness to reduce the body bias voltage necessary for millivolt operation. This compensated relay design is investigated with the aid of computer simulations, and is found to provide for improved tradeoff between relay switching energy and turn-on delay under certain conditions. The effects of process-induced variations on relay switching voltage are studied and compared for the compensated relay design vs. a conventional relay design.

Advisor: King Liu, Tsu-Jae
The Role of Intermediaries in Shaping Fair Use

Fair use is a mechanism to balance public interest with a copyright holder’s rights. A missing element in fair use disputes is adequate consideration of the role intermediaries, such as for-profit companies, libraries, universities, and other institutions, play in shaping how the public makes fair uses. I contend that intermediaries have been central in shaping copyright law on the books and on the ground, and that the law of fair use should be even more attentive to the intermediary-user dynamic./nChapter One is a glimpse of the gap between law on paper and law on the ground when it comes to maintaining a balance in copyright law. This is illustrated by the enduring role that intermediaries have had a in shaping copyright law and practice in the developing world, and particularly in South Asia. I describe the role of publishers as key intermediaries in Colonial India, and the shortcomings in international instruments to fulfill the needs of developing countries. I discuss this gap as manifesting in the form of shadow libraries and the legal response to them. In Chapter Two, I draw inspiration from the insights in Chapter One to take a deeper look at the intermediary-user dynamic in fair use in the United States. Intermediaries are often found to be the facilitators of individual fair use, especially with the advent of digital technologies. The intermediary-user dynamic needs to be a central part of the fair use analysis involving intermediaries, and I propose a tiered framework that incorporates the relationship between users and intermediaries into the analysis. Fair use needs to incorporate both the end user’s benefit and the intermediary’s position in order to balance the use with the copyright holder’s interest. The proposed framework would lend stability and certainty to the various intermediary activities highlighted in the dissertation, and others like them around the world—leading to a better understanding of how fair use and other copyright exceptions may be customized for different contexts.

Advisor: Van Houweling, Molly S
Synthesis, Electronic Properties, and Oxidative Reactivity of High-Valent Multimetallic-Oxo Cubane Complexes

Cobalt oxides have been recognized as one of the most efficient earth-abundant catalysts for challenging oxidation chemistry, with substrates ranging from water to organic compounds. In these oxidations, cobalt−oxo species with formal oxidation states greater than three are commonly invoked as reactive intermediates. However, there is a dearth of mechanistic information regarding how these high-valent cobalt catalysts operate. This Perspective describes how the study of molecular cobalt oxo clusters, with an emphasis on the [Co4O4] oxo cubane complexes, has helped to shed light on the operative mechanisms of cobalt-catalyzed oxidation reactions. Implications for high-valent CoIV– and CoV–oxo intermediates and remaining mechanistic questions concerning how these intermediates mediate O–O bond formation are also discussed. Furthermore, structural modifications of these oxo cubane clusters (i.e., incorporation of heteroatoms and modulation of ligands) have provided insight into multimetallic cooperativity, but the influence of such a metal-metal interaction on oxidation activity remains to be explored. A more detailed understanding of these structure-activity relationships may enable fine-tuning of reactivity and stability of synthetic multimetallic catalysts for energy storage and challenging organic transformations.

Advisor: Tilley, T. Don
Structural and mechanistic studies of membrane associated signaling proteins

Cellular signaling is controlled by many different processes which make up a signaling cascade. The timing and spatial organization of the steps within a signaling cascade are crucial to a cell’s development and proliferation. In this work I explore the structural and biochemical processes that mediate activity of two important signaling proteins: Bruton’s tyrosine kinase (Btk) and Ras. In the case of Btk I explore the mechanistic details of dimerization of its lipid binding domain and how this corresponds to signaling by Btk in the cell. In addition, I characterize the interaction of growth factor receptor-bound protein 2 (Grb2) with Btk and outline a novel role for Grb2 in Btk signaling. Finally, I explore the specificity constraints on Btk substrates as compared to an upstream kinase, Spleen tyrosine kinase (Syk). In the case of Ras, this work explores how stability of the protein, both local conformational stability and global stability, impact the activity and structure of the enzyme. This work is carried out using a variety of structural, biochemical, and biophysical methods, from molecular dynamics and nuclear magnetic resonance (NMR) to reconstitution of signaling proteins on supported lipid bilayers.

Advisor: Kuriyan, John
Single-Mode Waveguide Coupling of Optical Antenna-LED for Optical Interconnects

Optical interconnects have displaced electrical wires in data centers and high performance computers due to higher efficiency and bandwidth. The development of on-chip optical interconnects is the next frontier for development, with the promise of reducing on-chip energy consumption. Light emitting diodes have high efficiencies and can achieve low footprint; however, spontaneous emission is typically far too slow to be useful in an interconnect. This can be understood by modeling spontaneous emission as dipole emission with a dipole length on the order of the atomic spacing (~1.3nm) which is much smaller than the radiation wavelength at 1550nm. This becomes a familiar radio frequency (RF) engineering problem: to make the light-emitting diode faster we just need to make it a better antenna./nBy placing the radiating dipoles in the feed-gap of an optical antenna we can dramatically enhance the spontaneous emission rate, potentially allowing for >100GHz direction modulation. However, to create a useful on-chip interconnect, we need to couple the output light to a single mode waveguide so we can guide the light across the chip to a photodetector. Additionally, both the device and waveguide coupling scheme need to be compatible with top-down fabrication and electrical injection./nIn this dissertation we focus on the cavity backed slot antenna geometry, showing that this device can be efficiently coupled to a single mode waveguide. The first part of this dissertation reviews the theory behind spontaneous emission enhancement, the cavity backed slot antenna, and waveguide coupling./nThe waveguide coupled cavity backed slot antenna is then fabricated and measured. Clear evidence of waveguide coupling is demonstrated. The collected data is then compared to theory showing excellent agreement between experiment and finite difference time domain (FDTD) simulations. The estimated experimental waveguide coupling efficiency to a single mode waveguide is ~85.9%./nThe efficiency of the device is improved through a novel surface passivation process, leading to a record low surface recombination velocity. Detailed time decay models are presented, including a method to model an arbitrary rate equation. The internal quantum efficiency of a 60nm wide LED ridge is estimated to be 10-20% - with these devices showing >180x increase in photoluminescence./nFinally, the dissertation concludes with a full-link system model and a discussion of how to increase the power from the cavity backed slot antenna-LED and the importance of close integration with CMOS. The modeled end-to-end energy per bit can be <1fJ/bit, showing the great potential for on-chip optical interconnects.

Advisor: Wu, Ming C