Physics Commons^™

Vimentin Takes A Hike – Emerging Roles Of Extracellular Vimentin In Cancer And Wound Healing, Sepideh Parvanian, Leila S. Coelho-Rato, Alison E. Patteson, John E. Eriksson

Physics - All Scholarship

Vimentin is a cytoskeletal protein important for many cellular processes, including proliferation, migration, invasion, stress resistance, signaling, and many more. The vimentin-deficient mouse has revealed many of these functions as it has numerous severe phenotypes, many of which are found only following a suitable challenge or stress. While these functions are usually related to vimentin as a major intracellular protein, vimentin is also emerging as an extracellular protein, exposed at the cell surface in an oligomeric form or secreted to the extracellular environment in soluble and vesicle-bound forms. Thus, this review explores the roles of the extracellular pool of vimentin …

The Molecular Biophysics Of Extracellular Vimentin And Its Role In Pathogen–Host Interactions, Sepideh Parvanian, Leila S. Coelho-Rato, John E. Eriksson, Alison E. Patteson

Physics - All Scholarship

Vimentin, an intermediate filament protein typically located in the cytoplasm of mesenchymal cells, can also be secreted as an extracellular protein. The organization of extracellular vimentin strongly determines its functions in physiological and pathological conditions, making it a promising target for future therapeutic interventions. The extracellular form of vimentin has been found to play a role in the interaction between host cells and pathogens. In this review, we first discuss the molecular biophysics of extracellular vimentin, including its structure, secretion, and adhesion properties. We then provide a general overview of the role of extracellular vimentin in mediating pathogen-host interactions, with …

Antibacterial And Cytocompatible Ph-Responsive Peptide Hydrogel, Dona I. Edirisinghe, Areetha D'Souza, Maryam Ramezani, Robert J. Carroll, Quenten Chicón, Cheyene L. Muenzel, Jonathan Soule, Mary B. Monroe, Alison E. Patteson, Olga V. Makhlynets

Physics - All Scholarship

A short peptide, FHHF-11, was designed to change stiffness as a function of pH due to changing degree of protonation of histidines. As pH changes in the physiologically relevant range, G′ was measured at 0 Pa (pH 6) and 50,000 Pa (pH 8). This peptide-based hydrogel is antimicrobial and cytocompatible with skin cells (fibroblasts). It was demonstrated that the incorporation of unnatural AzAla tryptophan analog residue improves the antimicrobial properties of the hydrogel. The material developed can have a practical application and be a paradigm shift in the approach to wound treatment, and it will improve healing outcomes for millions …

Mechanobiology As A Tool For Addressing The Genotype-To- Phenotype Problem In Microbiology, Merrill E. Asp, Minh-Tri Ho Thanh, Subarna Dutta, Jessica A. Comstock, Roy D. Welch, Alison E. Patteson

Physics - All Scholarship

The central hypothesis of the genotype–phenotype relationship is that the phenotype of a developing organism (i.e., its set of observable attributes) depends on its genome and the environment. However, as we learn more about the genetics and biochemistry of living systems, our understanding does not fully extend to the complex multiscale nature of how cells move, interact, and organize; this gap in understanding is referred to as the genotype-to-phenotype problem. The physics of soft matter sets the background on which living organisms evolved, and the cell environment is a strong determinant of cell phenotype. This inevitably leads to challenges as …

Observation Of The Ξ_B^-→Λ_B^0 Π^- Decay And Measurement Of B(Ξ_B^-→Λ_B^0 Π^-), Zhuoming Li

Dissertations - ALL

We present the first observation of the weak decay Ξ−b → Λ0b π−, which is mediated by an s → u ̄ud transitionwithin the Ξ_b^- baryon. The analysis uses a pp collision data sample at a center-of-mass energy of 13 TeV corresponding to 5.5 fb^(−1) of integrated luminosity. The sample of Λb0 baryons used in this analysis are reconstructed through their decays to Λ+c π− and Λ+c π−π+π−. From a fit to the Ξ−b → Λ0b π− mass spectrum, the Ξ−b → Λ0b π− decay is observed with a significance of 11.3 standard deviations, thus establishing observation of this decay. …

Extracellular Vimentin Is Sufficient To Promote Cell Attachment, Spreading, And Motility By A Mechanism Involving N-Acetyl Glucosamine-Containing Structures, Robert Bucki, Daniel V. Iwamoto, Xuechen Shi, Katherine E. Kerr, Fitzroy J. Byfield, Lukasz Suprewicz, Karol Sklodowski, Julian Sutaria, Pawel Misiak, Agnieszka Z. Wilczewska, Sekar Ramachandran, Aaron Wolfe, Minh H. Thanh, Eli Whalen, Alison E. Patteson, Paul A. Janmey

Physics - All Scholarship

Vimentin intermediate !laments form part of the cytoskeleton

of mesenchymal cells, but under pathological conditions often

associatedwith in"ammation, vimentin !laments depolymerize as

the result of phosphorylation or citrullination, and vimentin

oligomers are secreted or released into the extracellular environment.

In the extracellular space, vimentin can bind surfaces of cells

and the extracellular matrix, and the interaction between extracellular

vimentin and cells can trigger changes in cellular functions,

such as activation of !broblasts to a !brotic phenotype. The

mechanism by which extracellular vimentin binds external cell

membranes and whether vimentin alone can act as an adhesive

anchor for cells is largely …

High Fidelity Universal Gates Performed On A Continuously-Decoupled Coherence Enhanced Transmon Qubit, Michael Senatore

Dissertations - ALL

Decoherence is the primary limiting factor for the utility of modern qubits and qubit networks; most chiefly, pure dephasing which limits the operational time any gate-sequence can produce a high-fidelity result. In this dissertation, I present the results of my experiment, performing fast, high fidelity, universal single-qubit gates, on a qubit which has been decoupled from pure dephasing resulting from environmental noise. This technique can expand operational ranges of qubits–such as allowing the high-coherence operation of a flux-tunable qubit far away from its flux-insensitive sweet-spot; broadening our selection of viable qubits by making otherwise low-coherence qubits operable with high coherence, …

A Torsion-Based Rheometer For Measuring Viscoelastic Material Properties, Merrill E. Asp, Elise Jutzeler, Jakub Kochanowski, Katherine Kerr, Dawei Song, Sarthak Gupta, Robert Carroll, Alison E. Patteson

Physics - All Scholarship

Rheology and the study of viscoelastic materials are an integral

part of engineering and the study of biophysical systems. Tissue rheology is even

used in the study of cancer and other diseases. However, the cost of a rheometer is

feasible only for colleges, universities, and research laboratories. Even if a rheometer

can be purchased, it is bulky and delicately calibrated, limiting its usefulness to the

laboratory itself. The design presented here is less than a tenth of the cost of a

professional rheometer. The design is also portable, making it the ideal solution to

introduce viscoelasticity to high school students …

Design And Modeling Of Superconducting Hardware For Implementing Quantum Stabilizers, Yebin Liu

Dissertations - ALL

Superconducting qubits are one of the leading systems for implementing quantum processors. Realizing fault-tolerant quantum computation requires some form of quantum error correction, which typically involves performing repeated stabilizer operations on groups of physical qubits in an array to form a logical qubit with enhanced protection against errors. Realizing a logical qubit that is suitable for running quantum algorithms requires an array with a significant number of physical qubits, which is extremely challenging. However, the physical qubit overhead can be reduced by lowering the error rate on the physical qubits. Current state-of-the-art superconducting qubit designs do not have robust protection …

Dynamic Remodeling Of Fiber Networks With Stiff Inclusions Under Compressive Loading, Robert J. Carroll, Minh H. Thanh, Alison E. Patteson

Physics - All Scholarship

The ability of tissues to sustain and withstand mechanical stress is critical to tissue development and healthy tissue maintenance. The mechanical properties of tissues are typically considered to be dominated by the fibrous extracellular matrix (ECM) component of tissues. Fiber network mechanics can capture certain mechanical features of tissues, such as shear strain stiffening, but is insufficient in describing the compressive response of certain tissues and blood clots that are rich in extracellular matrix. To understand the mechanical response of tissues, we employ a contemporary mechanical model, a fibrous network of fibrin embedded with inert bead inclusions that preserve the …

Characterization Of Superconducting Hardware For Implementing Quantum Stabilizers, Kenneth Richard Dodge

Dissertations - ALL

Superconducting qubits are one of the leading approaches being investigated for building a scalable quantum computer. In the presence of external noise and perturbations plus local microscopic fluctuations and dissipation in the qubit environment, arbitrary quantum states will decohere, leading to bit-flip and phase-flip errors of the qubit. In order to build a fault-tolerant quantum computer that can preserve and process quantum information in the presence of noise and dissipation, one must implement some form of quantum error correction. Stabilizer operations are at the heart of quantum error correction and are typically implemented in software-controlled entangling gates and measurements of …

Search For Numi Mudar Electron Neutrinos In Microboone, Ohana Benevides Rodrigues

Dissertations - ALL

Muon Decay-at-Rest (μDAR) produces electron-neutrinos (νe) in the 0 to 53 MeV energy range. The given range is especially interesting for its similarity to Supernovae-produced νe. The Deep Underground Neutrino Experiment (DUNE) has as one of its main goals to measure Supernovae neutrinos on the occasion of a Galactic Supernova burst. To optimize the chances of detection, a low-energy neutrino-LAr cross-section (XS) measurement is a piece of important information to have at hand. MicroBooNE presents a good opportunity to explore the low-energy ν-LAr detection and XS using the μDAR neutrinos and therefore develop the tools necessary for DUNE to interpret …

Measurements Of B → D(∗)−,0d(∗)+,0k+Π− Branching Fractions In The K∗0 Mass Window, Harris Bernstein

Dissertations - ALL

This thesis presents measurements of 11 branching fractions of the form B →D(∗)−,0D(∗)+,0K+π− within the K∗0 mass window using LHCb data taken in 2016, 2017 and 2018. All 11 branching fractions are measured simultaneously and are reported alongside the covariance and correlation matrices for the final measurement.

How Green Lakes State Park Got Its Name: The Optics And Appearance Of Fayetteville Green Lakes, Eric A. Schiff

Physics - All Scholarship

The extraordinary and variable appearance of the Fayetteville Green Lakes in the spring, summer, and fall has been the subject of journalistic and scientific attention for more than 150 years. This article addresses the subject in two sections for differing readerships. The first section is a description of the essential science for a general readership. The second section is an abstract of the science for technically knowledgeable readers. The layout of the article is designed for a folded paper flier suitable for distribution to visitors to the lakes.

The article describes the three key properties of the lakes’ waters that …

Mechanologic: Designing Mechanical Devices That Compute, Michelle Berry

Dissertations - ALL

Despite their initial success and impact on the development of the modern computer, mechanical computers were quickly replaced once electronic computers became viable. Recently, there has been increased interest in designing devices that compute using modern and unconventional materials. In this dissertation, we investigate multiple ways to realize a mechanical device that can compute, with a main focus on designing mechanical equivalents for wires and transistors. For our first approach at designing mechanical wires, we present results on the propagation of signals in a soft mechanical wire composed of bistable elements. When we send a signal along bistable wires that …

Investigation Of Holographic Lattice Theories, Muhammad Asaduzzaman

Dissertations - ALL

The Anti-de Sitter/Conformal Field theory (AdS/CFT) correspondence, also known as holography, has been the focus of a great deal of interest and research for the last two decades. It has improved our understanding of general relativity and quantum field theories simultaneously through the interplay between these two different kinds of theories. However, there are still many aspects of holography that we do not understand or demand further analysis. Perturbative quantum field theory and perturbative metric expansion techniques are not equipped to investigate holography in some of the most interesting regimes such as the strongly interacting gravitational theory in anti-de Sitter …

Geometry Of Discrete And Continuous Bounded Surfaces, Kyung Eun Kim

Dissertations - ALL

We work on reconstructing discrete and continuous surfaces with boundaries using length constraints. First, for a bounded discrete surface, we discuss the rigidity and number of embeddings in three-dimensional space, modulo rigid transformations, for given real edge lengths. Our work mainly considers the maximal number of embeddings of rigid graphs in three-dimensional space for specific geometries (annulus, strip). We modify a commonly used semi-algebraic, geometrical formulation using Bézout's theorem, from Euclidean distances corresponding to edge lengths. We suggest a simple way to construct a rigid graph having a finite upper bound. We also implement a generalization of counting embeddings for …

Characterization Of Scintillation Light In Large Liquid Argon Detectors And The Implications For Proton Decay Searches, Kyle Spurgeon

Dissertations - ALL

The Deep Underground Neutrino Experiment (DUNE) is a planned long baseline neutrino experi- ment. The detector will be comprised of four modules with 10kt of active volume each, making it an ideal target to neutrino oscillation physics and searches for proton decay. ProtoDUNE-SP was a single-phase liquid argon time projection chamber - a prototype for the first far detector module of DUNE with an active volume of 700 tons operating until 2020. It was installed at the CERN Neutrino Platform and took particle beam and cosmic ray data over its two year lifespan. Liquid argon scin- tillation light is still …

Measurement Of |Vcb| Using The Semileptonic Decay Λb → Λcμνμ, Scott Edward Ely

Dissertations - ALL

A preliminary measurement of the quark-mixing parameter |Vcb| using the exclusive decay Λ0b→ Λ+c μ−νμ is presented. A sample of Λb semileptonic decays is provided by √s = 13TeV proton-proton collisions collected by the LHCb detector in 2017. Λ0b → Λ+c μ−νμX decays are identified from muon tracks, combined with a Λc baryon. The ground state Λ0b → Λ+c μ−νμ is isolated by a fit to the Λb corrected mass spectrum. The raw yield NRaw(Λ0b → Λ+c μ−νμ) is corrected, and the semileptonic width ΓMeas. (Λ0b → Λ+c μ−νμ) is obtained. Lattice QCD calculations predict ΓTh.(Λ0b → Λ+c μ−νμ)/|Vcb|2. A …

Constraining Beam Backgrounds And Analyzing The Detector Response In A Test Beam With The Nova Experiment, Abhilash Yallappa Dombara

Dissertations - ALL

NOvA is a long-baseline neutrino oscillation experiment with two functionallyidentical detectors with the Near Detector at Fermilab, Illinois, and the Far Detector at Ash River, Minnesota. NOvA measures the rate of muon neutrino disappearance and electron neutrino appearance using muon neutrinos generated by the NuMI beam from the Accelerator Division(AD), thus NOvA measures neutrino oscillation parameters in the Pontecorvo-Maki- Nakagawa-Sakata matrix. The main experimental goal of NOvA is to determine the mass hierarchy, probe Charge-Parity violation and measure sin2 θ23 precisely. In this dissertation, the experimental setup, the latest analysis methods used in NOvA, and its results from analyzing 6 …

Unique Role Of Vimentin Networks In Compression Stiffening Of Cells And Protection Of Nuclei From Compressive Stress, Katarzyna Pogoda, Fitzroy Byfield, Piotr Deptuła, Mateusz Cieśluk, Łukasz Suprewicz, Karol Skłodowski, Jordan L. Shivers, Anne Van Oosten, Katrina Cruz, Ekaterina Tarasovetc, Ekaterina L. Grishchuk, Fred C. Mackintosh, Robert Bucki, Alison E. Patteson, Paul A. Janmey

Physics - All Scholarship

In this work, we investigate whether stiffening in compression is a feature of single cells and whether the intracellular polymer networks that comprise the cytoskeleton (all of which stiffen with increasing shear strain) stiffen or soften when subjected to compressive strains. We find that individual cells, such as fibroblasts, stiffen at physiologically relevant compressive strains, but genetic ablation of vimentin diminishes this effect. Further, we show that unlike networks of purified F-actin or microtubules, which soften in compression, vimentin intermediate filament networks stiffen in both compression and extension, and we present a theoretical model to explain this response based on …

Probing Lepton Flavour Universality With $\Bz \To \Kstarz \Taup \Taum$, Aravindhan Venkateswaran

Dissertations - ALL

Neutral current $\bquark \to \squark ll$ processes have long been known to be precise probes of physics beyond the Standard Model. A pattern of anomalies seen in $\bquark \to \squark \mup \mun$ and in $\bquark \to \cquark \tau \nu$ data has hinted at the violation of lepton flavour universality. Effective field theories which attempt to find an explanation for these anomalies predict sizeable enhancements to the rate of $\bquark \to \squark \taup \taum$ currents. We use $pp$ collision data collected by the LHCb detector to estimate a sensitivity of $\BF(\Bz \to \Kstarz \taup \taum) < 1.5 \times 10^{-3}$ at 95\% C.L.

Monitoring Bacteria Cultures Using Near Infrared (Nir) Binary Spectronephelometry (Bsn), Raman Spectra And Principal Component Analysis (Pca), Steven Ortiz

Dissertations - ALL

Current noninvasive methods cannot continuously and simultaneously monitor the concentrations of cells and media components that define the state of native bacterial cultures, because of changing turbidity. A new technique, binary spectronephelometry (BSN) has the same or better sensitivity and precision for population monitoring as optical density at 600nm (OD600), while simultaneously measuring metabolic processes. The BSN algorithm uses laser induced emission to probe mildly turbid media i.e., propagation of light occurs in the single scattering regime. A BSN "training set" associates a grid of elastic emission measurements, comprising Rayleigh and Mie scattering, and inelastic emission measurements, comprising fluorescence and …

Spreading Rates Of Bacterial Colonies Depend On Substrate Stiffness And Permeability, Alison Patteson, Merrill Asp, Minh H. Thanh, Danielle A. Germann, Robert J. Carroll, Alana Franceski, Roy D. Welch, Arvind Gopinath

Physics - All Scholarship

The ability of bacteria to colonize and grow on different surfaces is an essential process for biofilm development. Here, we report the use of synthetic hydrogels with tunable stiffness and porosity to assess physical effects of the substrate on biofilm development. Using time-lapse microscopy to track the growth of expanding Serratia marcescens colonies, we find that biofilm colony growth can increase with increasing substrate stiffness, unlike what is found on traditional agar substrates. Using traction force microscopy-based techniques, we find that biofilms exert transient stresses correlated over length scales much larger than a single bacterium, and that the magnitude of …

Materials Science And Mechanosensitivity Of Living Matter, Alison E. Patteson, Merrill E. Asp, Paul A. Janmey

Physics - All Scholarship

Living systems are composed of molecules that are synthesized by cells that use energy sources within their surroundings to create fascinating materials that have mechanical properties optimized for their biological function. Their functionality is a ubiquitous aspect of our lives. We use wood to construct furniture, bacterial colonies to modify the texture of dairy products and other foods, intestines as violin strings, bladders in bagpipes, and so on. The mechanical properties of these biological materials differ from those of other simpler synthetic elastomers, glasses, and crystals. Reproducing their mechanical properties synthetically or from first principles is still often unattainable. The …

Rab11 Endosomes And Pericentrin Coordinate Centrosome Movement During Pre-Abscission In Vivo, Nikhila Krishnan, Maxx Swoger, Lindsay I. Rathbun, Peter J. Fioramonti, Judy Freshour, Michael Bates, Alison E. Patteson, Heidi Hehnly

Physics - All Scholarship

The last stage of cell division involves two daughter cells remaining interconnected by a cytokinetic bridge that is cleaved during abscission. Conserved between the zebrafish embryo and human cells, we found that the oldest centrosome moves in a Rab11-dependent manner towards the cytokinetic bridge sometimes followed by the youngest. Rab11-endosomes are organized in a Rab11-GTP dependent manner at the mother centriole during pre-abscission, with Rab11 endosomes at the oldest centrosome being more mobile compared with the youngest. The GTPase activity of Rab11 is necessary for the centrosome protein, Pericentrin, to be enriched at the centrosome. Reduction in Pericentrin expression or …

Vimentin Intermediate Filaments Mediate Cell Morphology On Viscoelastic Substrates, Maxx Swoger, Sarthak Gupta, Elisabeth E. Charrier, Michael Bates, Heidi Hehnly, Alison E. Patteson

Physics - All Scholarship

The ability of cells to take and change shape is a fundamental feature underlying development, wound repair, and tissue maintenance. Central to this process is physical and signaling interactions between the three cytoskeletal polymeric networks: F-actin, microtubules, and intermediate filaments (IFs). Vimentin is an IF protein that is essential to the mechanical resilience of cells and regulates cross-talk among the cytoskeleton, but its role in how cells sense and respond to the surrounding extracellular matrix is largely unclear. To investigate vimentin’s role in substrate sensing, we designed polyacrylamide hydrogels that mimic the elastic and viscoelastic nature of in vivo tissues. …

A Solid-State Phase Camera For Advanced Gravitational Wave Detectors, Erik Muniz

Dissertations - ALL

I present a novel way of wavefront sensing using a commercially available, continuouswavetime-of- ight camera with QVGA-resolution. This CMOS phase camera is capable of sensing externally modulated light sources with frequencies up to 100 MHz. The high-spatial-resolution of the sensor, combined with our integrated control electronics, allows the camera to image power modulation index as low as -62 dBc/second/pixel. The phase camera is applicable to problems where alignment and mode-mismatch sensing is needed and suited for diagnostic and control applications in gravitationalwave detectors. Specically, I explore the use of the phase camera in sensing the beat signals due to thermal …

Observation Of Ω Contribution In The C1(3872) → Π+Π−J/Ψ Decays, Baasansuren Batsukh

Dissertations - ALL

Resonant structure in the dipion mass spectrum produced via \decay{\Bu}{\X\Kp}, \decay{\X}{\jpsi \pip \pim}, with \decay{\jpsi}{\mu^+\mu^-} is analyzed using Run 1 and Run 2 data samples from the LHCb experiment. The spectrum is dominated by $\rhoz\to\pi^+\pi^-$, but cannot be described by this contribution alone. A significant $\omega\to\pi^+\pi^-$ contribution, interfering with $\rhoz$, is observed for the first time. This is a more significant observation ($>7.1\sigma$) of $\X\to\omega\jpsi$ decays, than previously achieved with $\omega\to\pi^+\pi^-\pi^0$ decays. The relative contribution of $\omega$ to the total $\X\to\pi^+\pi^-\jpsi$ rate is at the level expected from the measured $\X\to(\omega\to\pi^+\pi^-\pi^0)\jpsi$ rate, if the interference between the $\rho^0$ and …

Buckling Patterns And Mechanics Of Thin Interfacial Polymer Films, Monica M. Ripp

Dissertations - ALL

Thin elastic solids are easily deformed and will readily collapse into complex buckling modes. They can also transition between distinct buckling modes when the confining forces evolve over time, forming a variety of robust and striking patterns. Here we explore how thin interfacial films and the buckling modes they present couple with evolving macroscopic forces and how multi-scale features of the systems give rise to patterns.

In the indentation of a circular film floating on a liquid bath three buckling modes arise: wrinkling, crumpling, and folding. This work shows that striking transitions between these states accompany four regimes in the …