Physics Commons^™

Single‐Molecule 3d Orientation Imaging Reveals Nanoscale Compositional Heterogeneity In Lipid Membranes, Jin Lu, Hesam Mazidi, Tianben Ding, Oumeng Zhang, Matthew D. Lew

Electrical & Systems Engineering Publications and Presentations

In soft matter, thermal energy causes molecules to continuously translate and rotate, even in crowded environments, thereby impacting the spatial organization and function of most molecular assemblies, such as lipid membranes. Directly measuring the orientation and spatial organization of large collections (>3000 molecules μm⁻²) of single molecules with nanoscale resolution remains elusive. In this paper, we utilize SMOLM, single‐molecule orientation localization microscopy, to directly measure the orientation spectra (3D orientation plus “wobble”) of lipophilic probes transiently bound to lipid membranes, revealing that Nile red's (NR) orientation spectra are extremely sensitive to membrane chemical composition. SMOLM images resolve …

X-Rays From Warped Black Hole Accretion Disks, Quincy Abarr

Arts & Sciences Electronic Theses and Dissertations

In this thesis, I present the results from my research to better understand accretion onto black holes and neutron stars based on spectropolarimetric X-ray observations.

I have developed a general relativistic ray-tracing code which simulates X-rays from warped accretion disks around black holes.

I used this to predict the polarization of the thermal X-ray emission and the energy spectrum the reflected power law emission.

Both of these can be used to measure properties of black hole systems, such as the spin parameter and the inclination of the observer to its spin axis.

My results enable the measurement of these parameters …

Production Of Medical Radioisotopes Using Titanium Accelerator Targets, Christopher Shaun Loveless

Arts & Sciences Electronic Theses and Dissertations

Theranostic radiopharmaceuticals enable diagnostic imaging and radionuclide therapy in patients using a single molecular agent labeled with a diagnostic-therapeutic pair (e.g., 68Ga/177Lu) or a theranostic radionuclide (e.g., 131I). This theranostic approach can help inform patient-specific treatment plans and improve clinical outcomes. Radionuclide pairs used in theranostic agents fall into two categories: pseudo matched-pairs (e.g., 68Ga/177Lu) and matched-pairs (e.g., 124I/131I). Pseudo matched-pair radionuclides have similar chemistries and pharmacokinetics when bound to the same bioconjugate molecule. In contrast, identical chemistries and pharmacokinetics can be obtained by using the matched-pair radionuclides.

The isotopes of Sc include two diagnostic radioisotopes, 43Sc & 44Sc, and …

New Physics With Ultra-High Energy Neutrinos, Yicong Sui

Arts & Sciences Electronic Theses and Dissertations

Ultra-high energy (UHE) astrophysical neutrinos are unique in the sense that they are the

only known particles that could travel through incredibly long distance unattenuated, with

TeV to EeV energy, much higher than the most powerful man-made collider could provide.

The detection of these UHE neutrinos has ushered a new era in neutrino astrophysics, as they

carry important information directly from the inside of energetic astrophysical objects. On the

other hand, from the particle physics point of view, the UHE neutrinos also offer a new window

of opportunity for studying beyond the Standard Model (BSM) phenomena. This is the main …

Biomedical Applications Of Polarimetry, Nathaniel Owen King

McKelvey School of Engineering Theses & Dissertations

Non- or minimally-invasive data collection is highly desirable for gathering the broad base of information that facilitates moving technology to the point of care. Polarimetry has been making this transition for years. Early forms of polarization-sensitive optics involved custom multiplexing a series of images to generate a single image, but today’s snapshot polarimeters are readily commercially available.

The research presented in this dissertation advances three areas of polarimetric imaging: First, this research develops a reflectance-based measurement for tracking changes in the alignment of dynamically loaded soft tissue, specifically tendon. This work highlights a range of mounting angles across which signal …

Peer-Led Team Learning In Calculus-Based Introductory Physics: Implementation And Evaluation, Siera Maia Stoen

Arts & Sciences Electronic Theses and Dissertations

Robust evidence shows that Peer-led Team Learning (PLTL) improves the academic success of college students in introductory Science, Technology, Engineering, and Mathematics (STEM) courses. However, further research is needed to gain a fuller understanding of the benefits of PLTL and the aim of this dissertation is to explore two key and understudied questions surrounding the effects of PLTL. First, does deviating from the optimal implementation of PLTL change its effectiveness? Second, what specific outcomes, in addition to academic success (e.g., exam scores), does PLTL improve? This dissertation will provide a fuller picture of the impact of PLTL by examining its …

Structural Organization And Chemical Activity Revealed By New Developments In Single-Molecule Fluorescence And Orientation Imaging, Tianben Ding

McKelvey School of Engineering Theses & Dissertations

Single-molecule (SM) fluorescence and its localization are important and versatile tools for understanding and quantifying dynamical nanoscale behavior of nanoparticles and biological systems. By actively controlling the concentration of fluorescent molecules and precisely localizing individual single molecules, it is possible to overcome the classical diffraction limit and achieve 'super-resolution' with image resolution on the order of 10 nanometers.

Single molecules also can be considered as nanoscale sensors since their fluorescence changes in response to their local nanoenvironment. This dissertation discusses extending this SM approach to resolve heterogeneity and dynamics of nanoscale materials and biophysical structures by using positions and orientations …

Growth Of Small Particles In Nonequilibrium Plasmas, Necip Berker Üner

McKelvey School of Engineering Theses & Dissertations

Nonequilibrium plasma (NEP) is an extraordinary environment for material synthesis. NEP is comprised of hot electrons with temperatures greater than 10000 K and of cold ions and neutrals that are usually at few hundred kelvins above room temperature. Due to this large difference in species’ temperatures, the assumption of local thermal equilibrium does not hold in NEP. Therefore, NEP can act as a unique processor of mass, and it can transform materials along pathways that are not accessible by methods wherein local thermal equilibrium is valid. For decades, NEPs have been employed in the semiconductor industry to manufacture many thin …

Separating Signal From Noise In High-Density Diffuse Optical Tomography, Arefeh Sherafati

Arts & Sciences Electronic Theses and Dissertations

High-density diffuse optical tomography (HD-DOT) is a relatively new neuroimaging technique that detects the changes in hemoglobin concentrations following neuronal activity through the measurement of near-infrared light intensities. Thus, it has the potential to be a surrogate for functional MRI (fMRI) as a more naturalistic, portable, and cost-effective neuroimaging system. As in other neuroimaging modalities, head motion is the most common source of noise in HD-DOT data that results in spurious effects in the functional brain images. Unlike other neuroimaging modalities, data quality assessment methods are still underdeveloped for HD-DOT. Therefore, developing robust motion detection and motion removal methods in …

Specificity Of Ssb Binding To Its Interacting Proteins And Multiple Allosteric Effects Of Ssb C-Terminal Tail On Assembly And Dna Binding Of E. Coli Recor Proteins, Min Kyung Shinn

Arts & Sciences Electronic Theses and Dissertations

The homo-tetrameric E. coli single strand (ss) DNA binding (SSB) protein is an essential component in DNA maintenance for its role in binding and protecting single stranded DNA intermediates via its N-terminal DNA binding domain (DBD). SSB also acts as a hub to recruit at least 17 SSB interacting proteins (SIPs) involved in DNA replication, recombination, and repair via its 9 amino acid C-terminal acidic tip region. A 56 amino acid intrinsically disordered linker connects the DBD and the acidic tip and plays a role in cooperative binding to ssDNA. Using isothermal titration calorimetry, I determined that the SSB-Ct peptides …

Measurement, Dissipation, And Quantum Control With Superconducting Circuits, Patrick Harrington

Arts & Sciences Electronic Theses and Dissertations

The interaction between a superconducting circuit and its environment can cause decoherence. However, interactions with an environment are necessary for quantum state preparation and measurement. Through the dynamics of open quantum systems, the environment is a resource to control and readout superconducting circuit states. I present an experimental result demonstrating qubit state stabilization from engineered dissipation with a microwave photonic crystal. In addition, I discuss the statistical arrow of time in the dynamics of continuous quantum measurement. These results demonstrate an interplay between open quantum system dynamics and statistics, which highlights the role of both dissipation and measurement for quantum …

Applications Of Nonlinear Dynamics, And Critical Phenomena To Measure Neural Populations Using Inputs To Single Neurons, James Kenneth Johnson

Arts & Sciences Electronic Theses and Dissertations

A compelling vision for the future of neuroscience is the ability to sense neural activity throughout the bulk of the brain with exquisite resolution. Popular visions usually include intricate electrode technology intruding into the neuropil, meandering along nerve tracts, and sensing the whole brain. These popular visions stem from the belief that we must always have an outsider’s perspective of neural activity. According to this belief the closest thing neuroscientists can achieve to an insider’s perspective is to shadow every neuron (or almost every neuron) with an electrical or optical recording device. Yet, the brain naturally has an expansive sensor …

Phantoms To Placentas: Mr Methods For Oxygen Quantification, Kelsey Meinerz

Arts & Sciences Electronic Theses and Dissertations

Molecular oxygen (O2) is vital for efficient energy production and improper oxygenation is a hallmark of disease or metabolic dysfunction. In many pathologies, knowledge of tissue oxygen levels (pO2) could aid in diagnosis and treatment planning. The gold standard for pO2 measures in tissue are implantable probes, which are invasive, require surgery for placement, and are inaccessible to certain regions of the body. Methods for determining pO2 both non-invasively and quantitatively are lacking. The slight paramagnetic nature of O2 provides opportunities to non-invasively characterize pO2 in tissue via magnetic resonance (MR) techniques. As such, O2 can be treated as a …

Supertiger Elemental Abundances For The Charge Range $41 \Leq Z \Leq 56$, Nathan Elliot Walsh

Arts & Sciences Electronic Theses and Dissertations

No abstract provided.

Molecular Insights Into Microbial Adhesion, Roger Davies Klein

Arts & Sciences Electronic Theses and Dissertations

Antibiotic-resistant bacterial infections are a serious and immediate threat to global public health. In the United States alone, over 2 million individuals develop antibiotic-resistant infections annually, resulting in 23,000 deaths and $20 billion in excess health care costs. Virulence factors that allow bacteria to invade and persist within the host are promising targets for novel antimicrobial agents that could be used to curb the spread of antibiotic resistance. Development of therapeutics that can selectively eliminate pathogenic bacteria while sparing the beneficial host microbiota requires a detailed molecular understanding of critical virulence factors that facilitate interactions between pathogens and their environments. …

Thermophysical Properties And Phase Transformations In Metallic Liquids And Silicate Glasses, Daniel Christian Van Hoesen

Arts & Sciences Electronic Theses and Dissertations

The first quantitative measurements of the electrical resistivity in binary metallic liquids, used to probe local order in the liquid, are reported in this dissertation. The electrical resistivity is very sensitive to short and medium range ordering because the electron mean free path is approximately the same length scale as the atomic spacing. Particular attention is given to the resistivity value at a crossover temperature that, based on molecular dynamics (MD) simulations, is the onset of cooperative motion in liquid alloys. Experimental evidence for the crossover is found in measurements of the shear viscosity, a dynamical property. An indication of …

First-Principles Studies Of Anion Engineering In Functional Ceramics, Steven Timothy Hartman

McKelvey School of Engineering Theses & Dissertations

Ceramic materials display a wide variety of valuable properties, such as ferroelectricity, superconductivity, and magnetic ordering, due to the partially covalent bonds which connect the cations and anions. While many breakthroughs have been made by mixing multiple cations on a sublattice, the equivalent mixed-anion ceramics have not received nearly as much attention, despite the key role the anion plays in the materials’ properties. There is great potential for functional ceramics design using anion engineering, which aims to tune the materials properties by adding and removing different types of anions in existing classes of ceramic materials. In this dissertation, I present …

Transport In Neutron Star Mergers, Steven Patrick Harris

Arts & Sciences Electronic Theses and Dissertations

Neutron star mergers are the only situation in nature in which we find matter compressed to several times nuclear saturation density and temperatures of several tens of MeV. By observing and numerically simulating neutron star mergers, we can learn about the nature of matter at high temperatures and densities. Neutron star merger simulations evolve Einstein's equations of general relativity coupled to the equations of relativistic hydrodynamics along with a nuclear equation of state, which describes the neutron star matter. Many simulations also take into account neutrino transport and electrodynamics. The purpose of this thesis is to see whether other physical …

Studies Of Maximum Supercooling And Stirring In Levitated Liquid Metallic Alloys, Mark Edward Sellers

Arts & Sciences Electronic Theses and Dissertations

Nucleation—or the formation of some cluster in a medium undergoing a phase transition—is usually the initial step in a phase transition. However, this process is still not fully understood, as outstanding questions related to the role of structure, local order, and diffusion remain unanswered. Systematic supercooling studies on metallic liquids performed using electrostatic and electromagnetic (ESL and EML, respectively) will be presented and discussed within the context of several nucleation theories, such as the Classical Nucleation Theory, Diffuse Interface Theory, and Coupled-Flux theory. To study the role of diffusion on nucleation, studies on the International Space Station using the on-board …

Measuring Localization Confidence For Quantifying Accuracy And Heterogeneity In Single-Molecule Super-Resolution Microscopy, Hesam Mazidi, Tianben Ding, Arye Nehorai, Matthew D. Lew

Electrical & Systems Engineering Publications and Presentations

We present a computational method, termed Wasserstein-induced flux (WIF), to robustly quantify the accuracy of individual localizations within a single-molecule localization microscopy (SMLM) dataset without ground- truth knowledge of the sample. WIF relies on the observation that accurate localizations are stable with respect to an arbitrary computational perturbation. Inspired by optimal transport theory, we measure the stability of individual localizations and develop an efficient optimization algorithm to compute WIF. We demonstrate the advantage of WIF in accurately quantifying imaging artifacts in high-density reconstruction of a tubulin network. WIF represents an advance in quantifying systematic errors with unknown and complex distributions, …

A Computationally-Efficient Bound For The Variance Of Measuring The Orientation Of Single Molecules, Tingting Wu, Tianben Ding, Hesam Mazidi, Oumeng Zhang, Matthew D. Lew

Electrical & Systems Engineering Publications and Presentations

Modulating the polarization of excitation light, resolving the polarization of emitted fluorescence, and point spread function (PSF) engineering have been widely leveraged for measuring the orientation of single molecules. Typically, the performance of these techniques is optimized and quantified using the Cramér-Rao bound (CRB), which describes the best possible measurement variance of an unbiased estimator. However, CRB is a local measure and requires exhaustive sampling across the measurement space to fully characterize measurement precision. We develop a global variance upper bound (VUB) for fast quantification and comparison of orientation measurement techniques. Our VUB tightly bounds the diagonal elements of the …

Nanoscale Colocalization Of Fluorogenic Probes Reveals The Role Of Oxygen Vacancies In The Photocatalytic Activity Of Tungsten Oxide Nanowires, Meikun Shen, Tianben Ding, Steven T. Hartman, Fudong Wang, Christina Krucylak, Zheyu Wang, Che Tan, Bo Yin, Rohan Mishra, Matthew D. Lew, Bryce Sadtler

Electrical & Systems Engineering Publications and Presentations

Defect engineering is a strategy that has been widely used to design active semiconductor photocatalysts. However, understanding the role of defects, such as oxygen vacancies, in controlling photocatalytic activity remains a challenge. Here, we report the use of chemically triggered fluorogenic probes to study the spatial distribution of active regions in individual tungsten oxide nanowires using super-resolution fluorescence microscopy. The nanowires show significant heterogeneity along their lengths for the photocatalytic generation of hydroxyl radicals. Through quantitative, coordinate-based colocalization of multiple probe molecules activated by the same nanowires, we demonstrate that the nanoscale regions most active for the photocatalytic generation of …