Physics Commons^™

Biomolecular Function From Structural Snapshots, Roshanak Etemadpour

Theses and Dissertations

Biological molecules can assume a continuous range of conformations during function. Near equilibrium, the Boltzmann relation connects a particular conformation's free energy to the conformation's occupation probability, thus giving rise to one or more energy landscapes. Biomolecular function proceeds along minimum-energy pathways on such landscapes. Consequently, a comprehensive understanding of biomolecular function often involves the determination of the free-energy landscapes and the identification of functionally relevant minimum-energy conformational paths on these landscapes. Specific techniques are necessary to determine continuous conformational spectra and identify functionally relevant conformational trajectories from a collection of raw single-particle snapshots from, e.g. cryogenic electron microscopy (cryo-EM) …

Synthesis, Characterization, And Simulation Of Two-Dimensional Materials, Lawrence Hudy

Theses and Dissertations

ABSTRACT

SYNTHESIS, CHARACTERIZATION, AND SIMULATION OF TWO-DIMENSIONAL MATERIALS

by

Lawrence Hudy

The University of Wisconsin-Milwaukee, 2023Under the Supervision of Professor Michael Weinert

This dissertation focuses on my journey through many aspects of surface science leading to the first principles investigation of transition metal dichalcogenides studying the impact of defects, twist, and decreasing interlayer separation to probe their effect on the electronic properties of these materials. My journey started out learning many aspects of material science such as methods for material synthesis and characterization but later ended on simulation of material properties using density functional theory. In the first experiments, we …

Two-Dimensional Crystal Phases Of Graphene Monoxide & Interaction Of Lithium With Graphene Monoxide, Danylo Radevych

Theses and Dissertations

This work explores the possible existence, properties, and potential applications of different polytypes of graphene monoxide (GmO) - two-dimensional crystalline monolayers composed of equal numbers of O and C atoms. In addition to previously experimentally discovered and theoretically modeled α phase, prediction and discovery of the second phase - β-GmO - is reported along with evaluation of six other possible phases. Structural parameters, electronic and mechanical properties of all the phases, including α-GmO, are determined using density functional calculations and compared. It is suggested that multiple phases of GmO can co-exist in the same composite, and developing a synthesis process …

Construction Of Zinc Oxide And Magnesium Oxide Heterostructures By Atomic Layer Deposition, Netra Sharma

Theses and Dissertations

Zinc oxide (ZnO) has gained wide technological interest due to its direct bandgap of ~3.37 eV and high exciton binding energy of ~60 meV and has exhibited promise for numerous electronics and opto-electronics applications. ZnO can also be alloyed with materials like magnesium oxide (MgO) to tailor the bandgap. Such heterostructures (Zn, Mg)O can be used in optoelectronic devices like quantum well lasers, photodetectors, etc.In this work, we studied the physical properties of zinc oxide (ZnO), magnesium oxide (MgO) and the heterostructures of zinc and magnesium oxide (Zn,Mg)O grown by atomic layer deposition (ALD) using a homemade viscous flow type …

Topological Superconductors And Dark Matter Searches In Gravitational Wave Interferometers, Han Gyeol Suh

Theses and Dissertations

This work is comprised of research in two areas: superconductors and gravitational waves.

Superconductors have led to novel fundamental discoveries, including new topological states. These states are robust, in that they are not altered by common changes to their environment. Here, I will introduce three studies focused on topological properties of various superconductors. First, newly proposed even-parity superconducting state in Sr$_2$RuO$_4$ introduces the emergence of topologically protected Bogoliubov Fermi surfaces. Next, I will discuss topological bands and odd-parity superconductivity in UTe$_2$, which suggest Weyl nodes and their potential topological properties. Lastly, anomalous pseudospin in non-symmorphic materials shows different symmetry properties …

Chasing Transients: Constructing Local Galaxy Catalogs For Electromagnetic Follow-Up Of Gravitational Wave Events, Chaoran Zhang

Theses and Dissertations

Gravitational waves (GWs) provide a new window for observing the universe which is not possible using traditional electromagnetic (EM) wave astronomy. The coalescence of compact object binaries, such as black holes (BHs) and neutron stars (NSs) generates “loud" GW signals that are detectable by the LIGO-Virgo-KAGRA (LVK) GW Observa- tory. If the binary contains at least one NS, there is a possibility that an observable EM counterpart will be launched during and/or after the merger. The first joint detection of GW radiation (GW170817) and its EM counterpart (AT 2017gfo) greatly extended our understanding of the universe in many fields, such …

Searching For Gravitational Wave Associations With High-Energy Astrophysical Transients, Brandon Joseph Piotrzkowski

Theses and Dissertations

Gravitational waves (GW) have become an invaluable tool in modern astronomy, especiallyin conjunction with other astronomical observations. GWs are created in highly dynamical systems such as compact binary coalescences (CBC) which are comprised of black holes and/or neutron stars. The Laser Interferometer Gravitational Wave Observatory (LIGO), Virgo Observatory, and KAGRA have now collectively identified almost a hundred of these events. GWs have also been predicted to come from core collapse supernovae. Both of these types of systems have been shown to produce other detectable transients, such as gamma- ray bursts (GRB) and neutrino bursts. Observations of the same astrophysical system …

Data-Driven Population Inference From Gravitational-Wave Sources And Electromagnetic Counterparts, Siddharth Mohite

Theses and Dissertations

Gravitational-wave (GW) astronomy has presented an unprecedented way to view the universe and study populations of astrophysical objects such as merging compact binaries containing black holes (BHs) and neutron stars (NSs). With the latest catalog of observations detected by the Advanced LIGO-Virgo detector network, recent analyses are placing interesting constraints on the population of BHs and NSs in these binaries. In particular, we are learning a great deal about how these binaries are distributed as a function of their masses. Another aspect of GW astronomy that has the potential to provide insights into fundamental physics is the multi-messenger follow up …

Developing Effective Theories: A Case Study In Monolayer Iron Selenide, Joseph O'Halloran

Theses and Dissertations

In this work, we outline the development of a series of models which have allowed us to investigate the low-temperature phases of monolayer FeSe. These models are built using group theoretic arguments to ensure the constraints provided by the crystal symmetry are satisfied. We investigate the interplay between stripe antiferromagnetism and spin-vortex crystal order in the framework of the Landau theory of phase transitions. By considering inversion symmetry breaking terms in the Landau free-energy, we show that the spin-vortex crystal is preferred when the non-symmorphic parent symmetry group $P4/nmm$ is reduced to a symmorphic subgroup.

We also consider symmetry constraints …

Transport, Photoluminescence & Photoconduction Characteristics Of Free Standing Two-Dimensional Γ-Alumina & Titanium Superlattice Doped Two-Dimensional Γ-Alumina Grown By Graphene-Assisted Atomic Layer Deposition, Elaheh Kheirandish

Theses and Dissertations

This study presents a facile high-yield bottom-up fabrication, morphology, crystallographic and optoelectronic characterization of free-standing quasi-2D γ-alumina, a non van der Waals 2D material. The synthesis comprises a multi-cycle atomic layer deposition (ALD) of amorphous alumina on a porous interconnected graphene foam as a growth scaffold and removed next by annealing and sintering the alumina/graphene/alumina sandwich at ~ 800 °C in air . The crystallographic and structural characteristics of the formed non-van der Waals quasi 2D γ-alumina were studied by X-ray diffraction (XRD), selected area electron diffraction (SAED), and high-resolution transmission electron microscopy (HRTEM). This analysis revealed the synthesized 2D …

Gravitational Wave Timing Residual Models For Pulsar Timing Experiments, Casey Mcgrath

Theses and Dissertations

The ability to detect gravitational waves now gives scientists and astronomers a new way in which they can study the universe. So far, the scientific collaboration LIGO has been successful in detecting binary black hole and binary neutron star mergers. These types of sources produce gravitational waves with frequencies of the order hertz to millihertz. But there do exist other theoretical sources which would produce gravitational waves in different parts of the frequency spectrum. Of these are the theoretical mergers of supermassive black hole binaries (SMBHBs), which could occur upon the merging of two galaxies with supermassive black holes at …

Extracting Information From Compact Binary Coalescences With Gravitational Waves, Xiaoshu Liu

Theses and Dissertations

Gravitational waves (GWs) radiated by compact binary coalescences (CBCs) carry useful information about their sources. These source properties obtained via the parameter estimation technique can help us to answer a wide range of physics problems. In this dissertation, I will present three major research projects. Firstly, binary neutron stars (BNSs) detected by Advanced LIGO and Advanced Virgo are ideal to study the equation of state (EoS). The EoS enters GW waveforms through tidal deformability, which can be measured by Advanced LIGO and Advanced Virgo. By performing Bayesian model selection, we can test plausible models from a large set of proposed …

Investigation Of G Protein-Coupled Receptor Quaternary Structure Through Fluorescence Micro-Spectroscopy And Theoretical Modeling: Interdependence Between Receptor-Receptor And Receptor-Ligand Interactions, Joel David Paprocki

Theses and Dissertations

Proteins are of high interest in biophysics research due to the important roles they play within cells, such as sensing of chemical (ions and small molecules) and physical (e.g., light) stimuli, providing structure, transporting ions/molecules, signaling, and intercellular communication. The studies described in this dissertation focus on a particular type of membrane proteins known as G protein-coupled receptors (GPCR), which play a key role in cellular response to external stimuli. We used the sterile 2 α-factor mating pheromone receptor (Ste2), a prototypical class D GPCR present within Saccharomyces cerevisiae (baker’s yeast). Ste2 is responsible for initiating the second messenger signal …

Effects Of Intercalation And Deintercalation In Layered Materials: From Topological Insulators To Battery Cathodes, Uma Garg

Theses and Dissertations

Topological insulators are quantum materials which have insulating bulk and conducting surface. The surface states in these materials is protected by time reversal symmetry and spin-orbit coupling. The fascinating quantum properties of these materials could lead to high speed electronics and quantum computing. To explore the transport properties of these systems, I synthesized single crystals of SnTe and Sb2Se3 which are potential topological insulators. SnTe is a topological crystalline insulator in which topological surface states are protected by time reversal symmetry and crystal symmetry, in particular mirror symmetry. My Shubnikov-de Haas (SdH) oscillation study on the (001) surface of SnTe …

Lattice And Charge Order In Layered Bi-Based Topological Insulators, Yanan Li

Theses and Dissertations

Bi2X3 (X=Se/Te) is a topological insulator, as well as a layered dichalcogenide. The topological properties of Bi2Se3 have gained a lot of interest over the past decade. However, as a layered chalcogenide, much of its uniqueness has not been fully discovered, e.g. hosting Charge Density Wave as reported in most other chalcogenides. With intercalation of Nb, Cu and Sr, Bi2Se3 becomes an unconventional superconductor. Together with its topological properties, A-Bi2X3 (A=Nb, Cu and Sr) have been proposed to be potential Topological superconductors. However, the mechanism of the unconventional SC in these compounds is still under discussion.

For my PhD research, …

Characterization Of Fiber Bragg Grating Based, Geometry-Dependent, Magnetostrictive Composite Sensors, Edward Lynch

Theses and Dissertations

Optical sensors based on geometry dependent magnetostrictive composite, having potential applications in current sensing and magnetic field sensing are modeled and evaluated experimentally with an emphasis on their thermal immunity from thermal disturbances. Two sensor geometries composed of a fiber Bragg grating (FBG) embedded in a shaped Terfenol-D/epoxy composite material, which were previously prototyped and tested for magnetic field response, were investigated. When sensing magnetic fields or currents, the primary function of the magnetostrictive composite geometry is to modulate the magnetic flux such that a magnetostrictive strain gradient is induced on the embedded FBG. Simulations and thermal experiments reveal the …

Macromolecular Structure Determination At X-Ray Free Electron Lasers From Single-Particle Imaging To Time-Resolved X-Ray Crystallography, Ishwor Poudyal

Theses and Dissertations

X-ray free-electron lasers (XFELs) open the possibility of obtaining diffraction information from a single biological macromolecule. This is because XFELs can generate extremely intense X-ray pulses which are so short that diffraction data can be collected before the sample is destroyed. By collecting a sufficient number of single-particle diffraction patterns from many tilts of a molecule relative to the X-ray beam, the three-dimensional electron density can be reconstructed ab-initio. The resolution and therefore the information content of the data will ultimately depend largely on the number of patterns collected at the experiment. We estimate the number of diffraction patterns required …

Nuclear Magnetic Resonance Under Extreme Conditions, Anand Prashant Dwivedi

Theses and Dissertations

Nuclear Magnetic Resonance (NMR) is a prime characterization tool used to understand the structures and interactions in organic molecules, crystals, as well as non-crystalline materials. However, until now, the combination of NMR with high-pressure instrumentation such as Diamond Anvil Cells (DAC) was deemed unfeasible due to the high spatial and electrical costs of standard NMR electromagnets or the regular refill of cryogenic liquids for superconducting magnets. Standard NMR techniques also raises technical difficulties when combining high-pressure instrumentation with high-temperature techniques such as laser heating. In the first part of this thesis, we present the development of a low-cost and space-saving …

Light Scattering In Diffraction Limit Infrared Imaging, Ghazal Azarfar

Theses and Dissertations

Fourier Transform Infrared (FTIR) microspectroscopy is a noninvasive technique for chemical imaging of micrometer size samples. Employing an infrared microscope, an infrared source and FTIR spectrometer coupled to a microscope with an array of detectors (128 x 128 detectors), enables collecting combined spectral and spatial information simultaneously. Wavelength dependent images are collected, that reveal biochemical signatures of disease pathology and cell cycle. Single cell biochemistry can be evaluated with this technique, since the wavelength of light is comparable to the size of the objects of interest, which leads to additional spectral and spatial effects disturb biological signatures and can confound …

Scattering In Infrared Microspectroscopy, Alex James Schofield

Theses and Dissertations

Mid-infrared absorbance spectra obtained from spatially inhomogeneous and finite samples often contain scattering effects that undermine the Beer-Lambert law assumption. Such spectra contain generally non-linear contributions from the scattering material’s complex refractive index, which may result in derivative-like bands with shifted peak positions. It is first shown using Mie theory for spherical scatterers, that these band distortions may be interpreted and accurately modeled by Fano theory when the imaginary part of its complex dielectric function is small and Lorentzian in nature—as is the case for many biological media. By fitting Fano line shapes to isolated absorbance bands, recovery of the …

Optimizing Advanced Ligo's Scientific Output With Fast, Accurate, Clean Calibration, Aaron Daniel Viets

Theses and Dissertations

Since 2015, the direct observation of gravitational waves has opened a new window to observe the universe and made strong-field tests of Einstein's general theory of relativity possible for the first time. During the first two observing runs of the Advanced gravitational-wave detector network, the Laser Interferometer Gravitational-wave Observatory (LIGO) and the Virgo detector have made 10 detections of binary black hole mergers and one detection of a binary neutron star merger with a coincident gamma-ray burst. This dissertation discusses methods used in low and high latency to produce Advanced LIGO's calibrated strain data, highlighting improvements to accuracy, latency, and …

Nominalization And Interpretation: A Critique Of Global Nominalization Criteria, Jason Alen Dewitt

Theses and Dissertations

Nominalization is the process which removes abstract objects from our scientific theories. But what makes a proposed nominalization a good or successful one? In the paper “Is It Possible to Nominalize Quantum Mechanics,” Otávio Bueno develops criteria for any successful nominalization. In the present work, I discuss one of these criteria that I call the “interpretation criterion.” It claims that a nominalization of a scientific theory should be neutral with regards to the interpretations of that theory. I argue that the interpretation criterion is problematic, and that it should be replaced with an alternative criterion of nominalization. I first explicate …

Scanning Tunneling Microscopy Studies Of Superconducting Single Layer Iron Selenide On Strontium Titanate, Zhuozhi Ge

Theses and Dissertations

The search for high temperature superconductivity has been a prominent topic in the field of condensed matter physics ever since the discovery of this novel phenomenon more than 100 years ago. In addition to the search for new materials, interfacial superconductivity has shown great potential as demonstrated recently in monolayer FeSe grown on SrTiO3 (STO) (001) substrate, where superconducting transition temperature (Tc) has been enhanced by more than an order of magnitude compared to the bulk value. The uniqueness of this approach is the direct placement of the superconducting layer on a secondary substrate, which facilitates the independent control of …

Internal And External Harmonic Functions In Flat-Ring Coordinates, Lijuan Bi

Theses and Dissertations

The goal of this dissertation is to derive expansions for a fundamental solution of Laplace's equation in flat-ring coordinates in three-dimensional Euclidean space. These expansions are in terms of harmonic functions in the interior and the exterior of two different types of regions, "flat rings" and "peanuts" according to their shapes. We solve Laplace's equation in the interior and the exterior of these regions using the method of separation of variables. The internal and external "flat-ring" and "peanut" harmonic functions are expressed in terms of Lamé functions.

Neutron Star Tidal Deformability And Gravitational Self-Force, Eric Van Oeveren

Theses and Dissertations

The recent direct observations of gravitational waves by the LIGO-Virgo collaboration [1-6] have been important pieces of evidence in agreement with Einstein's theory of gravity, the General Theory of Relativity. In addition, they open an era of gravitational wave astronomy that promises to give us much more information on the systems that produce gravitational radiation. Perhaps most prominent among these are binary systems composed of either two black holes, two neutron stars, or one black hole and one neutron star. This dissertation details theoretical predictions regarding such systems.

It is hoped that gravitational radiation emanating from binary systems that include …

Crystal Growth And Manipulation Of Intercalated Chalcogenides As Superconductors And Topological Insulators, Nathaniel Smith

Theses and Dissertations

Superconductors are unusual quantum materials which offer no resistance to electric current. The fascinating physics of this phenomenon is complemented by wide-ranging technical applications from power transmission to magnetic levitation. Commercially successful superconductors are found in powerful magnets in medical imaging, particle accelerators, and next-generation quantum computing. In my effort to uncover the mysteries and fundamental mechanisms of superconductivity, I use an array of techniques to synthesize and study single crystals of unconventional superconductors including the iron telluride and bismuth selenide family of superconductors. My study of atomic valence and crystal structure in iron telluride has uncovered previously unknown chemical …

Time-Resolved Structural Enzymology At X-Ray Free Electron Lasers, Tyler Norwood

Theses and Dissertations

Within the last decade, X-ray Free Electron Lasers (XFELs) have emerged across the world. These XFELs produce X-ray pulses with a duration on the order of femtoseconds, each of which contains 1012 photons. Before the XFEL, the brightest X-ray sources were 3rd generation synchrotrons. While these facilities are still very important for many experiments, XFELs allow for time-resolved experiments with femtosecond time resolution and mixing experiments that are not possible at the synchrotron. Enzymatic processes have promising prospects for medicine which use proteins as drug targets and enhance our understanding of these important biomolecules.

A number of procedures are involved …

Studies In Gravitational-Wave Astronomy And Tests Of General Relativity, Hong Qi

Theses and Dissertations

Modern astronomical data sets provide the opportunity to test our physical theories of the Universe at unprecedented levels of accuracy. This dissertation examines approaches to testing gravitational theories using a) observations of stars orbiting the center of the Milky Way; b) observations of the pulsations of Cepheid variable stars in dwarf galaxies; and c) gravitational-wave observations of compact binary mergers.

Observations of stars orbiting the center of the Milky Way have been used to infer the mass of the putative black hole that exists there. I discuss how well present and future measurements of stellar orbits can constrain the black …

Search For Compact Object Coalescences And Understanding Their Significance Using Data From Advanced Ligo, Debnandini Mukherjee

Theses and Dissertations

Gravitational waves were observed for the first time on September 14, 2015. A 36 and a 29 solar mass black holes were seen to inspiral around each other and merge about 410 Mpc away. This gave momentum to the areas of gravitational wave astrophysics and astronomy. While the universe could be perceived in the electromagnetic spectrum so far, enabling us to "see" it with telescopes, it could now be "listened to" using gravitational waves. Also, black holes being optically dark, could be observed directly for the very first time after this discovery. The 100 year old theory of General Relativity …

Star Formation Density And Galactic Outflows At Z~2, Matthew Coon

Theses and Dissertations

Galactic-scale outflows of gas play a significant role in galaxy evolution. They push gas to larger radii, slowing the star formation rate near the center of the galaxy, and increasing it at larger radii. Eventually, these outflows can expel the gas from the galaxy, depositing metals into the intergalactic medium, and limiting star formation in the galaxy. Galaxies from the Keck Baryonic Structure Survey (KBSS) and 3D- Hubble Space Telescope (3D-HST) Survey were used in order to measure the velocities of galactic outflows from the KBSS spectra, and the grism spectra from the 3D- HST survey were used in order …