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Flux-Tunable Superconducting Transmons For Quantum Information Processing, Matthew Ware

Dissertations - ALL

In this thesis, I describe a series of experiments using flux-tunable transmon qubits for quantum information processing. These qubits are designed with different levels of Josephson junction asymmetry. The first two chapters of this thesis will introduce the reader to superconducting qubits and circuit quantum electrodynamics. I will present experiments using the cQED architecture to implement fast photon swapping between an asymmetric qubit and a superconducting resonator using flux-driven sidebands. This is the first experimental observation of flux-driven sidebands in a superconducting system. This process also allows photon swaps between qubit and resonator to first order in the qubit-resonator coupling …

Benzo-Fused Lactams From A Diversity-Oriented Synthesis (Dos) Library As Inhibitors Of Scavenger Receptor Bi (Sr-Bi)-Mediated Lipid Uptake, Chris Dockendorff, Patrick W. Faloon, Jun Pu, Miao Yu, Stephen Johnston, Melissa Bennion, Marsha Penman, Thomas J.F. Nieland, Sivaraman Dandapani, José R. Perez, Benito Munoz, Michelle A. Palmer, Stuart L. Schreiber, Monty Krieger

Chemistry Faculty Research and Publications

We report a new series of 8-membered benzo-fused lactams that inhibit cellular lipid uptake from HDL particles mediated by Scavenger Receptor, Class B, Type I (SR-BI). The series was identified via a high-throughput screen of the National Institutes of Health Molecular Libraries Small Molecule Repository (NIH MLSMR), measuring the transfer of the fluorescent lipid DiI from HDL particles to CHO cells overexpressing SR-BI. The series is part of a previously reported diversity-oriented synthesis (DOS) library prepared via a build-couple-pair approach. Detailed structure–activity relationship (SAR) studies were performed with a selection of the original library, as well as additional analogs prepared …

Probing Mechanical Forces In Flagella By Manipulation Of Media Viscosity And Axonemal Structure, Kate Wilson

McKelvey School of Engineering Graduate Student Theses & Dissertations

Cilia and flagella are subcellular organelles used to generate fluid flow or propel the cell. These long cylindrical structures are composed of cytoskeletal elements activated by the unidirectional motor protein dynein. Cilia and flagella are crucial to a number of physiological functions, yet the specific mechanisms of dynein activation and coordination remain unclear. This work investigates the response of the flagellum of Chlamydomonas reinhardtii to increased mechanical loading achieved by variation of media viscosity, and to structural changes achieved by genetic manipulation. Effects of these perturbations are quantified using high spatiotemporal resolution recordings; the results demonstrate mutation-specific changes to the …

Development Of Nanofiber Scaffolds With Controllable Structure And Mineral Content For Tendon-To-Bone Repair, Justin Herrold Lipner

McKelvey School of Engineering Graduate Student Theses & Dissertations

Rotator cuff tears are common and lead to significant pain and disability. Effective repair of torn rotator cuff tendons requires healing of tendon to bone. Unfortunately, healing does not reproduce the structural and compositional features of the natural tendon-to-bone bone attachment that are necessary for effective load transfer, and surgical repairs often rupture.

Recent efforts for improving tendon-to-bone healing have focused on tissue engineering approaches. Scaffolds, cells, and/or growth factors are implanted at the repair site to guide the healing process and improve outcomes. To that end, a polymer-mineral tissue engineered scaffold was developed for this thesis which mimics two …

Xiap And Ciap1 Amplifications Induce Beclin 1-Dependent Autophagy Through Nfκb Activation., Fang Lin, Ghita Ghislat, Shouqing Luo, Maurizio Renna, Farah Siddiqi, David C. Rubinsztein

Peninsula Medical School

Perturbations in autophagy and apoptosis are associated with cancer development. XIAP and cIAP1 are two members of the inhibitors of apoptosis protein family whose expression is elevated in different cancers. Here we report that XIAP and cIAP1 induce autophagy by upregulating the transcription of Beclin 1, an essential autophagy gene. The E3 ubiquitin ligase activity of both proteins activates NFκB signalling, leading to the direct binding of p65 to the promoter of Beclin 1 and to its transcriptional activation. This mechanism may be relevant in cancer cells, since we found increased levels of autophagy in different B-cell lymphoma-derived cell lines …

An Exploratory Examination Of Spirituality And Black Student Academic Success At Historically Black Colleges And Universities, Sheika N. Square

LSU New Orleans Theses and Dissertations

Previous research has identified spirituality (Riggins, McNeal, & Herndon, 2008) as an important component of academic success for Black college students. Other factors researched include first year/ freshmen experiences, mentorships, faculty–student engagement (Caboni and Adisu, 2004), rigorous high-school curriculums, and summer bridge programs (Palmer, Moore, Davis, Hilton, 2010). Much of the research on college student success provides a comparison between Blacks, Whites, Asians, Latinos, and Native Americans (Caboni and Adisu, 2004; Carey, 2005; Palmer, Moore, Davis, Hilton, 2010; Townsend, 2007). However, few studies deal with Black students solely, and the influence of spirituality on the academic success within that one …

Gold Nanostructures For Sensing And Functional Bioimaging, Maximilian Y. Fei

McKelvey School of Engineering Graduate Student Theses & Dissertations

Gold nanostructures offer an extremely promising path forward in the fields of imaging and sensing because of their unique optical and chemical properties. Here, we demonstrate that plasmonic nanostructures can be employed as nanoscale transducers to monitor the growth and phase transitions in ultrathin polymer films. In particular, gold nanorods with high refractive index sensitivity (~150 nm / refractive index unit (RIU)) were employed to probe the growth and swelling of polyelectrolyte multilayers (PEM). By comparing the wavelength shift and extinction intensity of the localized surface plasmon resonance (LSPR) of the gold nanorods coated with PEM in air and water, …

Talking To Boxes, Hugging Robots, Vita Eruhimovitz

Graduate School of Art Theses

Relationships between humans and technology are at the core of my artistic research. Human-machine communication is defined by the technological level of the machines, but even more so by the way they are perceived by humans. Concepts of artificial life and artificial intelligence gradually have become part of the everyday life of growing numbers of people, and while there is an ongoing effort to design an increasingly anthropocentric technology, our minds also adapt to the new technological reality. Through immersive installations and sculptural objects my practice explores this reality. My artwork is designed to communicate with and stimulate the viewers, …

Japanese Women's Science Fiction: Posthuman Bodies And The Representation Of Gender, Kazue Harada

Arts & Sciences Graduate Student Theses and Dissertations

My dissertation explores the way Japanese women science fiction writers and manga (illustrated stories, often translated as comics) artists have used posthumans, cyborgs, and other hybrid creatures to question contemporary gender roles and identities. Traditionally, science fiction has been seen as a male domain. But by incorporating science fiction themes into manga and fiction intended for a female readership, these writers have carved out space for women in the genre and have stretched the boundaries of science fiction in the process. I focus primarily on the representation of posthuman bodies in the literary works of Ohara Mariko (b.1959) and Ueda …

Integration Of Alignment And Phylogeny In The Whole-Genome Era, Hongtao Sun

McKelvey School of Engineering Graduate Student Theses & Dissertations

With the development of new sequencing techniques, whole genomes of many species have become available. This huge amount of data gives rise to new opportunities and challenges. These new sequences provide valuable information on relationships among species, e.g. genome recombination and conservation. One of the principal ways to investigate such information is multiple sequence alignment (MSA). Currently, there is large amount of MSA data on the internet, such as the UCSC genome database, but how to effectively use this information to solve classical and new problems is still an area lacking of exploration. In this thesis, we explored how to …

Polarization Sensor Design For Biomedical Applications, Timothy York

McKelvey School of Engineering Graduate Student Theses & Dissertations

Advances in fabrication technology have enabled the development of compact, rigid polarization image sensors by integrating pixelated polarization filters with standard image sensing arrays. These compact sensors have the capability for allowing new applications across a variety of disciplines, however their design and use may be influenced by many factors. The underlying image sensor, the pixelated polarization filters, and the incident lighting conditions all directly impact how the sensor performs.

In this research endeavor, I illustrate how a complete understanding of these factors can lead to both new technologies and applications in polarization sensing. To investigate the performance of the …

Numerical Simulation And Optimization Of Carbon Dioxide Utilization For Enhanced Oil Recovery From Depleted Reservoirs, Razi Safi

McKelvey School of Engineering Graduate Student Theses & Dissertations

Due to concerns about rising CO₂ emissions from fossil fuel power plants, there has been a strong emphasis on the development of a safe and economical method for Carbon Capture Utilization and Storage (CCUS). One area of current interest in CO₂ utilization is the Enhanced Oil Recovery (EOR) from depleted reservoirs. In an Enhanced Oil Recovery system, a depleted or depleting oil reservoir is re-energized by injecting high-pressure CO₂ to increase the recovery factor of the oil from the reservoir. An additional benefit beyond oil recovery is that the reservoir could also serve as a long-term storage …

The Role Of Myc And Ap-1 Transcription Factors In The Development And Function Of The Dendritic Cell Lineage, Wumesh K.C.

Arts & Sciences Graduate Student Theses and Dissertations

Dendritic cells (DCs) orchestrate immune responses to foreign and self proteins by capturing, processing and presenting antigens to naïve CD4+ and CD8+ T cells in specialized regions of lymphoid organs. Consequently, DCs function in many disparate infectious settings, during which their activation can result in both pathogenic and protective responses. The diverse properties of DCs manifest through the actions of a limited set of lineage-specifying DNA-binding proteins called transcription factors (TFs). The precise molecular program controlled by these developmentally important TFs (such as Irf8 and Batf3) is largely unknown because most studies to date have been largely descriptive. We have …

Strategies For Increasing The Applicability Of Biological Network Inference, Ezekiel John Maier

McKelvey School of Engineering Graduate Student Theses & Dissertations

The manipulation of cellular state has many promising applications, including stem cell biology and regenerative medicine, biofuel production, and stress resistant crop development. The construction of interaction maps promises to enhance our ability to engineer cellular behavior. Within the last 15 years, many methods have been developed to infer the structure of the gene regulatory interaction map from gene abundance snapshots provided by high-throughput experimental data. However, relatively little research has focused on using gene regulatory network models for the prediction and manipulation of cellular behavior. This dissertation examines and applies strategies to utilize the predictive power of gene network …

Repurposing Vacant Lots For Stormwater Runoff Mitigation In Rochester, New York, Sandra Golberg

Theses

The area of the US known as the Rust Belt had an economic boom in the early 1900’s, and cities expanded rapidly to accommodate bustling manufacturing industries. This area then experienced a significant loss of population due to the migration of manufacturing industries to other areas beginning in the 1970’s. Many lots have become vacant and many homes have been abandoned because of this significant population loss. Industrialization introduces large areas of impervious surfaces and disturbs natural soils and landcovers, resulting in extensive stormwater runoff. While economies have declined, the problem of stormwater runoff remains. To mitigate the cascading problems …

Water Hyacinth - The Green Potential, Ratchanon Keawmanee

Theses

Aggressive invasion of floating water hyacinth has always been a big problem in Tropical countries, including Thailand. The ever growing amount of water hyacinth has polluted and block the flow of water in many rivers. A current solution for this problem is removal of water hyacinth from the rivers which basically harvest the plants from the rivers and dispose them someplace else. As stated, they are just plain and temporarily solutions, so such a problem still persists as time passes. My idea is to make use of what is so called "natural waste" and turn them into marketable goods which …

The Final Frontier: Navigating From Material To Virtual, Alexandra Neuman

Undergraduate Theses—Unrestricted

Humankind’s continual creation of and progression into virtual space is a hugely significant event on our evolutionary timeline, one that signifies a sort of imminent and already in-process departure. While the more popular notion of our species’ eventual exodus is linked to outer space and planetary exploration, our existing conceptualization of cyberspace connotes an identical unknowable vastness and sense of discovery, with its depiction relying on nearly identical imagery. The projection of a virtually based human future is thereby left with an already carved out spot in the collective imagination. The lone floating astronaut locked into a suit unable to …

Syncing Umbanda And Science (Sus): Using Umbanda’S Holistic Healing Methods To Increase Access To Healthcare, Alex E. Rosenthal

Undergraduate Theses—Unrestricted

In 1988, after the 1985 termination of the military dictatorship in Brazil, the constitution was rewritten to guarantee individual rights to all citizens of Brazil. Among the various other rights that the new constitution protected, anyone in Brazil was granted the right to government-funded healthcare under the regulation of the Unified Healthcare System, SUS. Because of structural inequalities in Brazil as well as the rise of privatized healthcare, equal access to healthcare is not a reality in modern-day Brazil. Many citizens who live in the periphery are limited to understaffed and underfunded primary health centers.

This monograph explores the healing …

Pharmacology Of Organic Cation Transporters: Focus On Structure-Function Relationships In Oct3 (Slc22a3), Dan C. Li

Undergraduate Theses—Unrestricted

Organic Cation Transporters (OCTs) are polyspecific, facilitative transporters that play major roles in metabolite and drug clearance. OCTs are promising drug targets and elucidating their mechanisms of substrate recognition is crucial for rational drug design. OCT-mediated transport of polyvalent cations remains unexplored. OCT-expressing Xenopus laevis oocytes were used to assess transport of polyamines, ubiquitous polyvalent cations of broad physiological import, but for which transport mechanisms are unknown. Dose-response analysis of radiolabelled substrate uptake revealed that polyamines are relatively low affinity, but high turnover substrates for OCTs compared to model substrate methyl-4-phenylpyridinium (MPP⁺). Polyamine analogs of varying hydrophobic character …

Investigating The Role Of Wolbachia Endosymbionts In The Expansion Of The F Element In Drosophila Ananassae, Elizabeth J. Chen

Undergraduate Theses—Unrestricted

At 4.2 Mb overall, the Drosophila melanogaster Muller F element (dot chromosome) is an unusual autosome; it is broadly heterochromatic, but the distal 1.3 Mb has a gene density and expression pattern similar to other autosomes. More intriguing is the large expansion of the D. ananassae F element (~20 Mb). Elucidating the factors that contribute to this expansion could improve our understanding of how heterochromatic domains are maintained and amplified.

Previous analyses show that the lateral gene transfer (LGT) of Wolbachia (the most widespread intracellular bacteria in the Rickettsiales order) into the D. ananassae genome is an important contributor to …

The C-Terminal Linker Of Ftsz Acts As An Intrinsically Disordered Peptide During Cell Division In Bacillus Subtilis, Steven Grigsby

Undergraduate Theses—Unrestricted

The bacterial tubulin homologue FtsZ polymerizes in vitro in a GTP-dependent manner to form long, single stranded filaments. In cells, these filaments assemble at the nascent division site, interacting laterally to form the contractile Z ring. The Z ring serves as a scaffold for the rest of the division machinery and constricts at the leading edge of the invaginating septum during cytokinesis. The FtsZ polypeptide consists of three primary domains: the N-terminal globular core consisting of 315 residues that contains the GTP binding site, a variable and flexible C-terminal linker (CTL) consisting of 50 residues, and a conserved region at …

K-Ras, But Not H-Ras Or N-Ras, Hyperactivation Regulates Brain Neural Stem Cell Proliferation In A Raf/Rb-Dependent Manner, R. Hugh F. Bender

Arts & Sciences Graduate Student Theses and Dissertations

Neural stem cells (NSCs) give rise to all the major cell types in the brain, including neurons, oligodendrocytes, and astrocytes. However, the intracellular signaling pathways that govern brain NSC proliferation and differentiation have been incompletely characterized to date. Since several neurodevelopmental brain disorders (i.e., Costello syndrome, Noonan syndrome) are caused by germline mutations in the RAS genes, Ras small GTPases are likely critical regulators of brain NSC function. In the mammalian brain, Ras exists as three distinct molecules (H-Ras, K-Ras, and N-Ras), each with different subcellular localizations, downstream signaling effectors, and biological effects. Leveraging a novel series of conditional Ras …

1. What Is The Relationship Of The Finite Subject To The Infinite Ground? 2. How Do We Use Where We Segregate The Subject From The Ground To Construct Reality? 3. In What Ways Can We Destabilize This Constructed Reality To Highlight Its Inherent Instability?, Calvin M. Miceli-Nelson

Undergraduate Theses—Unrestricted

This essay catalogs interests within my works and traces connections between these works and particular structuralist, post-modern, and post-structuralist themes. Artists influential to or congruent with the aims of my work are also discussed within this three-part essay around these discussions present in my work: 1. What is the relationship of the finite subject to the infinite ground? 2. How do we use where we segregate the subject from the ground to construct reality? 3. In what ways can we destabilize this constructed reality to highlight its inherent instability?

An Unprecedented Nadph Domain Conformation In Lysine Monooxygenase Nbtg Provides Insights Into Uncoupling Of Oxygen Consumption From Substrate Hydroxylation, Claudia Binda, Reeder M. Robinson, Julia S. Martin Del Campo, Nicholas D. Keul, Pedro J. Rodriguez, Howard H. Robinson, Andrea Mattevi, Pablo Sobrado

Chemistry Faculty Research & Creative Works

N-Hydroxylating monooxygenases are involved in the biosynthesis of iron-chelating hydroxamate-containing siderophores that play a role in microbial virulence. These flavoenzymes catalyze the NADPH-and oxygen-dependent hydroxylation of amines such as those found on the side chains of lysine and ornithine. In this work we report the biochemical and structural characterization of Nocardia farcinica Lys monooxygenase (NbtG), which has similar biochemical properties to mycobacterial homologs. NbtG is also active on D-Lys, although it binds L-Lys with a higher affinity. Differently from the ornithine monooxygenases PvdA, SidA, and KtzI, NbtG can use both NADH and NADPH and is highly uncoupled, producing more superoxide …

A Critical Review Of Postoperative Use Of Metacam In Cats, Naomi S. Leung

Undergraduate University Honors Capstones

Metacam®, or meloxicam, a nonsteroidal anti-inflammatory drug (NSAID) known for its suppression of pain and inflammation, was developed in 1993 and approved first for humans and dogs after clinical trials showed minor adverse effects on their kidney functions. NSAIDs in general work by blocking the actions of two enzymes called cyclo-oxygenase-1 (cox-1), responsible for the production of prostaglandins that produces protective gastrointestinal mucus, and cyclo-oxygenase-2 (cox-2), responsible for the production of prostaglandins (lipid compounds) that initiates inflammation and pain in the body. Metacam® blocks one of these enzymes, cox-2, causing the inflammation to decrease subsequently without disturbing gastrointestinal mucus. In …

Development And Application Of Mass Spectrometry-Based Biophysical Approaches, Ying Zhang

Arts & Sciences Graduate Student Theses and Dissertations

Mass spectrometry (MS)-based biophysical approaches are new "tools" for protein characterization owing to its capability to analyze proteins and protein complexes that range in molecular weight from kDa to MDa. Protein characterization requires more than identifying the primary structure. More importantly, protein high order structures (i.e., secondary, tertiary and quaternary structures) are needed for biological studies. MS has become the major tool in studies of protein primary structure and post translational modifications (PTMs) over the past two decades. Because MS has high sensitivity and fast turnaround, more and more biophysical approaches rely on MS to generate information for protein higher …

Effects Of An Interdisciplinary Gerontology Course On First-Year Undergraduate Students, Christine Caroline Merz

Arts & Sciences Graduate Student Theses and Dissertations

This study evaluated the impact of an interdisciplinary course on aging designed to improve attitudes toward older adults and aging, and generate interest in aging-related careers. Main outcomes included knowledge of older adults and aging, attitudes toward older adults and aging, and anxiety about personal aging. Participants included first-year undergraduate students enrolled in the course (curricular intervention group) and first-year undergraduate students not enrolled in the course (control group). Data were collected at the beginning and end of one semester. At the end of the semester curricular intervention students had increased in their knowledge about aging and showed more positive …

Stories In Mind – The Relationship Between The Narratological Categories Of Order And Time And The Reader’S Cognitive Structures As Exemplified In Büchner’S Play Woyzeck, Marc Breetzke

Arts & Sciences Graduate Student Theses and Dissertations

No abstract provided.

Application Of Machine Learning To Mapping And Simulating Gene Regulatory Networks, Hien-Haw Liow

Arts & Sciences Graduate Student Theses and Dissertations

This dissertation explores, proposes, and examines methods of applying modernmachine learning and Bayesian statistics in the quantitative and qualitative modeling of gene regulatory networks using high-throughput gene expression data. A semi-parametric Bayesian model based on random forest is developed to infer quantitative aspects of gene regulation relations; a parametric model is developed to predict geneexpression levels solely from genotype information. Simulation of network behavior is shown to complement regression analysis greatly in capturing the dynamics of gene regulatory networks. Finally, as an application and extension of novel approaches in gene expression analysis, new methods of discovering topological structure of gene …

Assessing Vascular Inflammation With Bioluminescence Imaging, Reece Joseph Goiffon

Arts & Sciences Graduate Student Theses and Dissertations

Cardiovascular disease (CVD) is the leading cause of morbidity, mortality, and health care costs in the developed world and is often undiagnosed until clinical presentation with a major adverse cardiovascular event (MACE). Plasma myeloperoxidase (MPO) content is an emerging biomarker for risk, progression, and prognosis at different stages of CVD. Enzyme-linked immunosorbent assays (ELISAs) are currently used to measure clinical plasma MPO concentration, but ELISAs are costly and time-intensive. Luminol is a chemiluminescent compound with specificity for MPO activity in vivo, but is not sensitive enough for use as a bioluminescence reporter of plasma MPO oxidation. The luminol derivative L-012 …