7,681 Works

Data from: Catechol 2,3-dioxygenase and other meta-cleavage catabolic pathway genes in the ‘anaerobic’ termite gut spirochete Treponema primitia

Kaitlyn S. Lucey & Jared R. Leadbetter
Microorganisms have evolved a spectacular diversity of metabolisms, some of which allow them to overcome environmental constraints, utilize abundant but inaccessible resources and drive nutrient cycling in various ecosystems. The termite hindgut microbial community is optimized to metabolize wood, and in recent years, the in situ physiological and ecological functions of community members have been researched. Spirochetes are abundant in the termite gut, and herein, putative aromatic meta-cleavage pathway genes typical of aerobic pseudomonads were...

Data Driven Computing

Trenton Thomas Kirchdoerfer
Data Driven Computing is a new field of computational analysis which uses provided data to directly produce predictive outcomes. This thesis first establishes definitions of Data-Driven solvers and working examples of static mechanics problems to demonstrate efficacy. Significant extensions are then explored to both accommodate noisy data sets and apply the deveoloped methods to dynamic problems within mechanics. Possible method improvements discuss incorporation of data quality metrics and adaptive data sampling, while new applications focus...

Integrated Ultra-High-Q Nonlinear Photonic Platform for On-Chip Optoelectronic Systems

Kiyoul Yang
Silicon technology provided a concrete basis of the integrated microelectronics revolution, and it might usher disruptive advances in photonics again. An integrated photonic system can potentially revolutionize instrumentation, time standards, spectroscopy, and navigation. Driven by these applications, various high-Q platforms have emerged over the last decade. However, applications require to satisfy challenging combinations of ultra-high-Q (UHQ) cavity performance, monolithic integration, and nonlinear cavity designs: the monolithic integration of UHQ devices still remains elusive. In this...

Tensor Network Representation of Many-Body Quantum States and Unitary Operators

Sujeet Kumar Shukla
Understanding many-body quantum systems is one of the most challenging problems in contemporary condensed-matter physics. Tensor network representation of quantum states and operators are taking central stage in this pursuit and beyond. They prove to be a powerful numerical and conceptual tool, and indeed a new language altogether. This thesis investigates various aspects of these representations by focusing on two specific problems: the first half of the thesis is devoted to examining how 'stable' a...

Controlling Deformability in Metallic Glass Nanopillars and Nanolattices

Rachel Liontas
Metallic glasses offer desirable mechanical properties, including high strength, hardness, and elasticity. In bulk, they suffer from catastrophic failure upon mechanical loads. However, ductility may emerge upon (1) reducing the characteristic dimension of the metallic glass to the nanoscale or (2) irradiating the metallic glass. These two methods of controlling metallic glass deformability are investigated through a host of mechanical experiments on metallic glass nanopillars and nanolattices before and after irradiation. The mechanical experiments are...

Earthquake Source Characterization Through Seismic Observations and Numerical Modeling

Semechah Ka Yan Lui
In this thesis, I present a series of works on the characterization of source properties and physical mechanisms of various small to moderate earthquakes through both observational and numerical approaches. From the results, we find implications on a broader scheme of topics relating to larger earthquakes, shear zone structure, frictional properties of faults, and seismic hazard assessment. Part I consists of two studies using waveform modeling. In Chapter 2, we present an in-depth study of...

Toward Realizable Quantum Computers

Michael Edward Beverland
The work in this thesis splits naturally into two parts: (1) experimentally oriented work consisting of experimental proposals for systems that could be used to implement quantum information tasks with current technology, and (2) theoretical work focusing on universal fault-tolerant quantum computers which we hope can be scaled as experimental capabilities continue to move forward.

Single Particle Mass Spectrometry and Inertial Imaging with Nanomechanical Systems

Scott Ian Kelber
This thesis work describes the development of a new technology for mass spectrometry using nanoelectromechanical systems (NEMS-MS). Mass spectrometry is a technique used to identify molecules through mass measurement. Nanoelectromechanical systems (NEMS) feature low cost, scalable on-chip compatibility, and are highly sensitivity to the mass of accreted species. Using NEMS devices, we perform NEMS-MS where the inertial mass of individual molecules is directly measured. This contrasts with traditional MS techniques utilizing electromagnetic fields to measure...

Quasiparabolic Subgroups of Coxeter Groups and Their Hecke Algebra Module Structures

Daodi Lu
It is well known that the R-polynomial can be defined for the Hecke algebra of Coxeter groups, and the Kazhdan-Lusztig theory can be developed to understand the representations of Hecke algebra. There is also a generalization for the existence of R-polynomial and Kazhdan-Lusztig theory for the Hecke algebra module of standard parabolic subgroups of Coxeter groups. In recent work of Rains and Vazirani, a generalization of standard parabolic subgroups, called quasiparabolic subgroups, are introduced, and...

Experiments on Gas Phase Chemistry with High Sensitivity Laser Spectroscopy

Laura Anna Mertens
Gas phase chemistry is important to many environments on Earth and beyond. The Earth’s atmosphere is dominated by free radical reactions that, when perturbed by pollution, can lead to serious environmental problems like stratospheric ozone depletion and urban smog. Outside Earth, many other planetary atmospheres are affected by gas phase, radical chemistry, including the atmosphere of Saturn’s Moon Titan. Gas phase chemistry in interstellar clouds can synthesize the molecular building blocks of our universe. Studying...

Spectroscopic, Electronic, and Mechanistic Studies of Silicon Surfaces Chemically Modified with Short Alkyl Chains

Noah Thomas Plymale
The chemical, structural, and electronic properties of semiconductor surfaces are known to strongly influence the energetics at semiconductor interfaces. Inexpensive and scalable wet chemical modification of semiconductor surfaces provides a means to impart a desired functionality at semiconductor interfaces for the development of new devices based on precise and cost-effective chemistry. This thesis is composed of three studies that focused on identifying the spectroscopic, electronic, and mechanistic properties of reactions at Si surfaces. First, ethynyl-...

Identifying Isoprene and Toluene Gas-Phase Oxidation Products to Better Constrain Ozone and Secondary Organic Aerosol Formation in the Atmosphere

Rebecca Helen Schwantes
Anthropogenic pollutants such as NOx interact with volatile organic compounds (VOCs) such as isoprene and toluene to produce ozone (O3) and oxidized low volatility compounds that are responsible for forming secondary organic aerosol (SOA). Understanding the processes that form O3 and SOA from VOCs is important for understanding climate interactions and air quality. Both O3 and SOA are harmful air pollutants. O3 directly contributes to warming while the influence of aerosols is far more complicated,...

Enantioselective Total Synthesis of Diketopiperazinecontaining Natural Products: (–)-Lansai B, (+)-Nocardioazines A and B, and (–)-Acetylapoaranotin

Haoxuan Wang
Diketopiperazine (DKP) motif is found in a wide range of biologically active natural products. This work details our efforts toward two classes of DKP-containing natural products. Class one features the pyrroloindoline structure, derived from tryptophans. Our group developed a highly enantioselective (3 + 2) formal cycloaddition between indoles and acrylates to provide pyrroloindoline products possessing three stereocenters. Utilizing this methodology, we accomplished asymmetric total synthesis of three natural products: (–)-lansai B, (+)-nocardioazines A and B....

Nonlinear and Ultrafast Optical Investigations of Correlated Materials

Hao Chu
This thesis comprises studies of 3d-5d transition metal oxides with various degrees of electronic correlation using nonlinear harmonic generation rotational anisotropy as well as time-resolved optical reflectivity methods. Specifically, we explored photo-induced phase transition in Ca2RuO4 and Sr2IrO4, discovered novel electronic phases in doped Sr2IrO4 and Sr3Ir2O7, and investigated different types of antiferromagnetic orders in transition metal trichalcogenides MPX3.

Experimental Investigation of Thrust Fault Rupture Mechanics

Vahe Gabuchian
Thrust fault earthquakes are investigated in the laboratory by generating dynamic shear ruptures along pre-existing frictional faults in rectangular plates. A considerable body of evidence suggests that dip-slip earthquakes exhibit enhanced ground motions in the acute hanging wall wedge as an outcome of broken symmetry between hanging and foot wall plates with respect to the earth surface. To understand the physical behavior of thrust fault earthquakes, particularly ground motions near the earth surface, ruptures are...

Data from: A submersible, off-axis holographic microscope for detection of microbial motility and morphology in aqueous and icy environments

Christian A. Lindensmith, Stephanie Rider, Manuel Bedrossian, J. Kent Wallace, Eugene Serabyn, Gordon M. Showalter, Jody W. Deming, Jay L. Nadeau & G. Max Showalter
Sea ice is an analog environment for several of astrobiology’s near-term targets: Mars, Europa, Enceladus, and perhaps other Jovian or Saturnian moons. Microorganisms, both eukaryotic and prokaryotic, remain active within brine channels inside the ice, making it unnecessary to penetrate through to liquid water below in order to detect life. We have developed a submersible digital holographic microscope (DHM) that is capable of resolving individual bacterial cells, and demonstrated its utility for immediately imaging samples...

A Direct Approach to Robustness Optimization

Seungil You
This dissertation reformulates and streamlines the core tools of robustness analysis for linear time invariant systems using now-standard methods in convex optimization. In particular, robust performance analysis can be formulated as a primal convex optimization in the form of a semidefinite program using a semidefinite representation of a set of Gramians. The same approach with semidefinite programming duality is applied to develop a linear matrix inequality test for well-connectedness analysis, and many existing results such...

The Mechanical Genome in Regulation and Infection

Yi-Ju Chen
Biological information storage and retrieval is a dynamic process that requires the genome to undergo dramatic structural rearrangements. Recent advances in single-molecule techniques have allowed precise quantification of the nano-mechanical properties of DNA [1, 2], and direct in vivo observation of molecules in action [3]. In this work, we will examine elasticity in protein-mediated DNA looping, whose structural rearrangement is essential for transcriptional regulation in both prokaryotes and eukaryotes. We will look at hydrodynamics in...

On the Link Floer Homology of L-space Link

Nakul Dawra
We will prove that, for a 2 or 3 component L-space link, HFL- is completely determined by the multi-variable Alexander polynomial of all the sub-links of L, as well as the pairwise linking numbers of all the components of L. We will also give some restrictions on the multi-variable Alexander polynomial of an L-space link. Finally, we use the methods in this paper to prove a conjecture of Yajing Liu classifying all 2-bridge L-space links.

Noise Cancellation for Gravitational Wave Detectors

Jennifer Clair Driggers
The LIGO gravitational wave detectors are on the brink of making the first direct detections of gravi- tational waves. Noise cancellation techniques are described, in order to simplify the commissioning of these detectors as well as significantly improve their sensitivity to astrophysical sources. Future upgrades to the ground based detectors will require further cancellation of Newtonian gravitational noise in order to make the transition from detectors striving to make the first direct detection of gravitational...

Instrumentation for Kinetic-Inductance-Detector-Based Submillimeter Radio Astronomy

Ran Duan
A substantial amount of important scientific information is contained within astronomical data at the submillimeter and far-infrared (FIR) wavelengths, including information regarding dusty galaxies, galaxy clusters, and star-forming regions; however, these wavelengths are among the least-explored fields in astronomy because of the technological difficulties involved in such research. Over the past 20 years, considerable efforts have been devoted to developing submillimeter- and millimeter-wavelength astronomical instruments and telescopes. The number of detectors is an important property...

Rewriting Schemes for Flash Memory

Eyal En Gad
Flash memory is a leading storage media with excellent features such as random access and high storage density. However, it also faces significant reliability and endurance challenges. In flash memory, the charge level in the cells can be easily increased, but removing charge requires an expensive erasure operation. In this thesis we study rewriting schemes that enable the data stored in a set of cells to be rewritten by only increasing the charge level in...

Engineering and Characterization of Cytochrome P450 Enzymes for Nitrogen-Atom Transfer Reactions

Christopher C. Farwell
The creation of novel enzyme activity is a great challenge to protein engineers, but nature has done so repeatedly throughout the process of natural selection. I begin by outlining the multitude of distinct reactions catalyzed by a single enzyme class, cytochrome P450 monooxygenases. I discuss the ability of cytochrome P450 to generate reactive intermediates capable of diverse reactivity, suggesting this enzyme can also be used to generate novel reactive intermediates in the form of metal-carbenoid...

Value Estimation and Comparison in Multi-Attribute Choice

Geoffrey W. Fisher
The following work explores the processes individuals utilize when making multi-attribute choices. With the exception of extremely simple or familiar choices, most decisions we face can be classified as multi-attribute choices. In order to evaluate and make choices in such an environment, we must be able to estimate and weight the particular attributes of an option. Hence, better understanding the mechanisms involved in this process is an important step for economists and psychologists. For example,...

Metallaboratrane Facilitated E‒H Bond Activation and Hydrogenation Catalysis

Henry Fong
The E‒H bond activation chemistry of tris-phosophino-iron and -cobalt metallaboratranes is discussed. The ferraboratrane complex (TPB)Fe(N2) heterolytically activates H‒H and the C‒H bonds of formaldehyde and arylacetylenes across an Fe‒B bond. In particular, H‒H bond cleavage at (TPB)Fe(N2) is reversible and affords the iron-hydride-borohydride complex (TPB)(μ‒H)Fe(L)(H) (L = H2, N2). (TPB)(μ‒H)Fe(L)(H) and (TPB)Fe(N2) are competent olefin and arylacetylene hydrogenation catalysts. Stoichiometric studies indicate that the B‒H unit is capable of acting as a hydride shuttle...

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