Digital Commons Network^™

Systems Level Analysis Of Organelle Biogenesis In Saccharomyces Cerevisiae, Kiandokht Panjtan Amiri

Arts & Sciences Graduate Student Theses and Dissertations

Eukaryotic cells contain hundreds of subcellular structures that serve different functions to maintain cellular homeostasis. A hallmark of Eukaryotic cells is its compartmentalization into membrane-bound organelles. One of the grand challenges in quantitative cell biology is understanding the precision with which cells assemble and maintain subcellular organelles. Despite identification of numerous molecular factors that regulate organelle sizes we lack insight into the quantitative principles underlying organelle size control. We examine organelle sizes from Saccharomyces cerevisiae and human iPS cells with mathematical theory to show that cells can robustly control average fluctuations in organelle size. By demonstrating that organelle sizes obey …

Quasiparticle And Excitonic Effects In Two-Dimensional Van Der Waals Materials, Linghan Zhu

Arts & Sciences Graduate Student Theses and Dissertations

Since their discovery, low dimensional van der Waals materials have attracted increasing research interests. They serve as ideal platforms to study novel physics in reduced-dimensional systems, and are critical in nowadays’ nanotechnology applications. Due to the reduced dielectric screening in low dimensions, strong excited state properties dictate their electronic, transport and optical properties, the study of which calls for a description of the many-particle interactions beyond the traditional density functional theory. This is where the many-body perturbation theory comes into play. In this thesis, I will present a comprehensive study of the quasiparticle and excitonic properties of a variety of …

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. …

Does Science Need Intersubjectivity? The Problem Of Confirmation In Orthodox Interpretations Of Quantum Mechanics, Emily Adlam

Mathematics, Physics, and Computer Science Faculty Articles and Research

Any successful interpretation of quantum mechanics must explain how our empirical evidence allows us to come to know about quantum mechanics. In this article, we argue that this vital criterion is not met by the class of ‘orthodox interpretations,’ which includes QBism, neo-Copenhagen interpretations, and some versions of relational quantum mechanics. We demonstrate that intersubjectivity fails in radical ways in these approaches, and we explain why intersubjectivity matters for empirical confirmation. We take a detailed look at the way in which belief-updating might work in the kind of universe postulated by an orthodox interpretation, and argue that observers in such …

Powerful Yet Lonely: Is 3c 297 A High-Redshift Fossil Group?, Valentina Missaglia, Juan P. Madrid, Mischa Schirmer, Francesco Massaro, Alberto Rodríguez-Ardila, Carlos J. Donzelli, Martell Valencia, Alessandro Paggi, Ralph P. Kraft, Chiara Stuardi, Belinda J. Wilkes

Physics & Astronomy Faculty Publications

The environment of the high-redshift (z = 1.408), powerful radio-loud galaxy 3C 297 has several distinctive features of a galaxy cluster. Among them, a characteristic halo of hot gas revealed by Chandra X-ray observations. In addition, a radio map obtained with the Very Large Array shows a bright hotspot in the northwestern direction, created by the interaction of the active galactic nucleus (AGN) jet arising from 3C 297 with its environment. In the X-ray images, emission cospatial with the northwestern radio lobe is detected, and peaks at the position of the radio hotspot. The extended, complex X-ray emission observed …

Proposal For A Definitive Search For Gut-Scale Qcd Axions, L. Brouwer, S. Chaudhuri, H. M. Cho, J. Corbin, C. S. Dawson, A. Droster, J. W. Foster, J. T. Fry, P. W. Graham, R. Henning, K. D. Irwin, F. Kadribasic, Y. Kahn, A. Keller, R. Kolevatov, S. Kuenstner, A. F. Leder, D. Li, J. L. Ouellet, K. M. W. Pappas, A. Phipps, N. M. Rapidis, B. R. Safdi, C. P. Salemi, M. Simanovskaia, J. Singh, E. C. Van Assendelft, K. Van Bibber, K. Wells, L. Winslow, W. J. Wisniewski, Betty A. Young

Physics

The QCD axion is a leading dark matter candidate that emerges as part of the solution to the strong 𝐶⁢𝑃 problem in the Standard Model. The coupling of the axion to photons is the most common experimental probe, but much parameter space remains unexplored. The coupling of the QCD axion to the Standard Model scales linearly with the axion mass; therefore, the highly motivated region 0.4–120 neV, corresponding to a GUT-scale axion, is particularly difficult to reach. This paper presents the design requirements for a definitive search for GUT-scale axions and reviews the technological advances needed to enable this program.

Black Holes, Disk Structures, And Cosmological Implications In E-Dimensional Space, Subhash Kak, Menas C. Kafatos

Mathematics, Physics, and Computer Science Faculty Articles and Research

We examine a modern view of the universe that builds on achieved successes of quantum mechanics, general relativity, and information theory, bringing them together in integrated approach that is founded on the realization that space itself is e-dimensional. The global and local implications of noninteger dimensionality are examined, and how it may have increased from the value of zero to its current value is investigated. We find surprising aspects that tie to structures in the universe, black holes, and the role of observations.

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 …

What Is Nonclassical About Uncertainty Relations?, Lorenzo Catani, Matthew S. Leifer, Giovanni Scala, David Schmid, Robert W. Spekkens

Mathematics, Physics, and Computer Science Faculty Articles and Research

Uncertainty relations express limits on the extent to which the outcomes of distinct measurements on a single state can be made jointly predictable. The existence of nontrivial uncertainty relations in quantum theory is generally considered to be a way in which it entails a departure from the classical worldview. However, this perspective is undermined by the fact that there exist operational theories which exhibit nontrivial uncertainty relations but which are consistent with the classical worldview insofar as they admit of a generalized-noncontextual ontological model. This prompts the question of what aspects of uncertainty relations, if any, cannot be realized in …

Nuclear Power Plant In Las Vegas, Ryan W. Murray

Undergraduate Research Symposium Posters

This research focuses on the impact of a “Nuclear Power Plant in Las Vegas” or ‘NPP in LV’ for short. Nuclear power is clean, has no greenhouse gas emissions, and has a moderate cost of kilowatt hours. Las Vegas, or more specifically Clark County uses Gas power plants to produce a majority of their electricity. My project will show what a nuclear plant could do if built in the city of Las Vegas. What is a Nuclear power plant? The EIA’s definition is “A nuclear power plant uses the heat that a nuclear reactor produces to turn water into steam, …

Trapping And Cooling Of Ca+ For Cold Ion-Radical Collisions, Bernardo Gutierrez

Undergraduate Research Symposium Posters

Free radicals are molecules that contain an unpaired valence electron which induces high reactivity. Ion radical reactions are typically exothermic and have low (or zero) activation energy. It is for these reasons that ion-radical reactions are believed to dominate in interstellar clouds where temperatures hover around 3-10K. State-to-state measurements require precision control of both reactants.

Precise Measurement Of The Nuclear Dependence Of The Emc Effect In Light Nuclei, Abishek Karki, Abishek Karki

Theses and Dissertations

Measurements of inclusive electron scattering cross-section ratios from light nuclei over a wide range of the Björken �� (0.3 < �� < 1) up to �� 2 = 8.3 GeV² were made as part of experiment E10-10-008, which was conducted in Hall C at the Thomas Jefferson National Accelerator Facility. The measurements were performed using a beam energy of 10.602 GeV and an average beam current of 45 ��A. This dissertation provides a thorough description of the experiment as well as the extracted ratios of inclusive nuclear cross-sections with respect to the deuterium cross-sections (the EMC effect) for the targets ⁹ Be, ¹² C, ¹⁰ B, and ¹¹ B. The …

Molecular Insights Into The Redox Of Atmospheric Mercury Through Laser Spectroscopy, Rongrong Wu Cohen

Theses and Dissertations

The widespread pollution of mercury motivates research into its atmospheric chemistry and transport. Gaseous elemental mercury (Hg(0)) dominates mercury emission to the atmosphere, but the rate of its oxidation to mercury compound (Hg(II)) plays a significant role in controlling where and when mercury deposits to ecosystems. Atomic bromine is regarded as the main oxidant for Hg(0) oxidation, known to initiate the oxidation via a two-step process in the atmosphere – formation of BrHg (R1) and subsequent reactions of BrHg with abundant free radicals Y, i.e., NO2, HOO, etc. (R2), where the reaction of BrHg +Y could also lead to the …

Evaluation Of Yttrium Stabilized Zirconium Thin Films With Secondary Ion Mass Spectrometry, Jeff Serfass

Seton Hall University Dissertations and Theses (ETDs)

Fuel Cells using solid oxides for the electrolyte material, or Solid Oxide Fuel Cells (SOFCs), can operate at high temperatures and have many benefits when compared to other electrolyte material-based fuel cells. SOFCs can, however still have problems when operating at these high temperatures. (~1,000 degrees Celsius) At high temperatures, the SOFC electrolyte resistivity goes up making the ionic conductivity decrease and therefore a loss of performance. The inclusion of low level Yttria to Zirconium Oxide (the electrolyte material) has been known to help reduce the resistivity at high operating temperatures. In this study, a series of Yttria stabilized Zirconium …

Ultrafast Electron Diffraction: Visualizing Dynamic States Of Matter, D. Filippetto, P. Musumeci, R. K. Li, B. J. Siwick, M. R. Otto, Martin Centurion, J. P. F. Nunes

Department of Physics and Astronomy: Faculty Publications

Since the discovery of electron-wave duality, electron scattering instrumentation has developed into a powerful array of techniques for revealing the atomic structure of matter. Beyond detecting local lattice variations in equilibrium structures with the highest possible spatial resolution, recent research efforts have been directed toward the long-sought-after dream of visualizing the dynamic evolution of matter in real time. The atomic behavior at ultrafast timescales carries critical information on phase transition and chemical reaction dynamics, the coupling of electronic and nuclear degrees of freedom in materials and molecules, and the correlation among structure, function, and previously hidden metastable or nonequilibrium states …

Possibilities For Inertial Electrostatic Confinement Fusion, Jeffrey Edward Black

Dissertations and Theses

While most of the fusion energy research is focused on magnetic confinement, there have been several alternative confinement methods aimed at the development of smaller and less expensive reactors. A number of these devices utilize a spherically convergent beam of recirculating ions, a technique known as inertial electrostatic confinement (IEC). This study looks at several aspects of IEC devices, including measurements of the fusion rate of an IEC device with a wire mesh electrode cathode, and a solid titanium cathode. In addition, several computational studies were performed to explore the possibilities for IEC fusion. These include development of a 1D-1P …

Behaviors For Which Deinonychosaurs Used Their Feet, Alexander King

Honors Projects

This paper seeks to show for what purpose deinonychosaurs used their feet. Fowler et al., (2011) showed that D. antirrhopus’s feet were closest in function to accipitrids, as they found it was more built for grasping prey than running.

I answered this question by using 2D images of the feet of three modern birds (Buteo jamaicensis, Phasianus colchicus, and Gallus gallus domesticus), one eudromaeosaur (Deinonychus antirrhopus), and one troodontid (Borogovia gracilicrus). I used ImageJ to apply 73 landmarks to each foot, capturing the variation between species in the metatarsals and pedal phalanges. These data were then uploaded to the software …

Six-Dimensional Single-Molecule Imaging With Isotropic Resolution Using A Multi-View Reflector Microscope, Oumeng Zhang, Zijian Guo, Yuanyuan He, Tingting Wu, Michael D. Vahey, Matthew D. Lew

Electrical & Systems Engineering Publications and Presentations

Imaging of both the positions and orientations of single fluorophores, termed single-molecule orientation-localization microscopy, is a powerful tool for the study of biochemical processes. However, the limited photon budget associated with single-molecule fluorescence makes high-dimensional imaging with isotropic, nanoscale spatial resolution a formidable challenge. Here we realize a radially and azimuthally polarized multi-view reflector (raMVR) microscope for the imaging of the three-dimensional (3D) positions and 3D orientations of single molecules, with precisions of 10.9 nm and 2.0° over a 1.5-μm depth range. The raMVR microscope achieves 6D super-resolution imaging of Nile red molecules transiently bound to lipid-coated spheres, accurately resolving …

Ds2 As Excitation Of Ads2, Florian Ecker, Daniel Grumiller, Robert Mcnees

Physics: Faculty Publications and Other Works

Title- dS₂ as excitation of AdS₂

We introduce a family of 2D dilaton gravity models with state-dependent constant curvature so that dS₂ emerges as an excitation of AdS₂. Curiously, the strong coupling region corresponds to the asymptotic region geometrically. Apart from these key differences, many features resemble the Almheiri–Polchinski model. We discuss perturbative and non-perturbative thermodynamical stability, bubble nucleation through matter shockwaves, and semiclassical backreaction effects. In some of these models, we find that low temperatures are dominated by AdS₂ but high temperatures are dominated by dS₂, concurrent with a recent proposal …

Stabilization Of Zero-Energy Skin Modes In Finite Non-Hermitian Lattices, Cem Yuce, Hamidreza Ramezani

Physics & Astronomy Faculty Publications

The zero energy of a one-dimensional semi-infinite non-Hermitian lattice with nontrivial spectral topology may disappear when we introduce boundaries to the system. While the corresponding zero-energy state can be considered as a quasi-edge state for the finite lattice with a long survival time, any small disruption (noise) in the initial form of the quasi-edge state can significantly shorten the survival time. Here, by tailoring the couplings at one edge we form an exceptional point allowing for a topological phase transition and the stabilization of the quasi-edge state in a finite-size lattice with open edges. Such a small modification in the …

(R1978) Heated Laminar Vertical Jet Of Psudoplastic Fluids-Against Gravity, Manisha Patel, M. G. Timol

Applications and Applied Mathematics: An International Journal (AAM)

A heated laminar jet of Pseudo-plastic fluid flowing vertically upwards from a long narrow slit into a region of the same fluid which is at a rest and at a uniform temperature is considered. The governing non-linear Partial differential equations (PDEs) for the defined flow problem are transformed into non-linear ordinary differential equations using the effective similarity technique-one parameter deductive group theory method. The obtained non-linear coupled Ordinary differential equations are solved and the results are presented by graphs. The effect of the Prandtl number and Grashof number on the velocity and temperature of the jet flow is discussed. Also, …

Supercontinuum Light Generation Via Non-Linear Effects In Hollow-Core Fiber, Skyler Gulati

Physics Student Works

The field of non-linear optics has gained traction in the last couple decades due to the variable generation of wavelengths which are less deterministic than within traditional optics. Using non-linear mediums, including hollow-core fibers (HCF), generation of wavelengths spanning into the vacuum ultraviolet (VUV) wavelength range is possible. These short wavelengths can be utilized within electron spectroscopy-based methods of material science like angle-resolved photoemission spectroscopy (ARPES). This technique most often uses specific photoemission lines of atoms in discharge lamps, however, with the frequency dispersion capabilities of HCF, broad band creation can allow for variable wavelength selection through filtering specific wavelengths …

Phase Transitions In Evolutionary Dynamics, Adam D. Scott, Dawn M. King, Stephen W. Ordway, Sonya Bahar

Physics Faculty Works

Sharp changes in state, such as transitions from survival to extinction, are hallmarks of evolutionary dynamics in biological systems. These transitions can be explored using the techniques of statistical physics and the physics of nonlinear and complex systems. For example, a survival-to-extinction transition can be characterized as a non-equilibrium phase transition to an absorbing state. Here, we review the literature on phase transitions in evolutionary dynamics. We discuss directed percolation transitions in cellular automata and evolutionary models, and models that diverge from the directed percolation universality class. We explore in detail an example of an absorbing phase transition in an …

A Study Of The Structural, Optical, And Ferroelectric Characteristics Of Pb-Ge-Te Nanocrystalline Alloys As Potential Candidates For Memory Devices And Near-Infrared (Nir) Applications, Asmaa Elkhodary, Salah M. Elsheikh, Hosny A. Omar, Manal A. Mahdy, Iman A. Mahdy

Basic Science Engineering

Pb_50-xGe_xTe₅₀ (x = 15, 20, 25, 30 at. %) nanocrystalline bulk alloys were prepared using solid-state direct reaction. X-ray diffraction and high-resolution transmission electron microscopy (HR-TEM) analysis of the reference structure (Ge = 15 at.%) revealed a slightly distorted cubic structure, with a lattice parameter of 6.43 Å and an inter-axis unit cell angle of 88.69◦. Atomic force images’ analysis and histograms displayed a homogenous particle size distribution in the nanoscale for all samples. Density measurements showed a gradual decrease from 7.89 to 6.98 g/cm3 with increasing Ge content in agreement with the calculated values. …

A Long Time Ago In A Galaxy Far, Far Away: A Candidate Z ~ 12 Galaxy In Early Jwst Ceers Imaging, Steven L. Finkelstein, Micaela B. Bagley, Pablo Arrabal Haro, Mark Dickinson, Henry C. Ferguson, Jeyhan S. Kartaltepe, Casey Papovich, Denis Burgarella, Dale D. Kocevski, Marc Huertas-Company, Kartheik G. Iyer, Anton M. Koekemoer, Rebecca L. Larson, Pablo G. Pérez-González, Caitlin Rose, Sandro Tacchella, Stephen M. Wilkins, Katherine Chworowsky, Aubrey Medrano, Alexa M. Morales, Rachel S. Somerville, L. Y. Aaron Yung, Guillermo Barro

Pacific Faculty Work

We report the discovery of a candidate galaxy with a photo-z of z ~ 12 in the first epoch of the James Webb Space Telescope (JWST) Cosmic Evolution Early Release Science Survey. Following conservative selection criteria, we identify a source with a robust zphot = 11.8-0.2+0.3 (1σ uncertainty) with mF200W = 27.3 and ≥7σ detections in five filters. The source is not detected at λ < 1.4 μm in deep imaging from both Hubble Space Telescope (HST) and JWST and has faint ~3σ detections in JWST F150W and HST F160W, which signal a Lyα break near the red edge of both filters, implying z ~ 12. This object (Maisie's Galaxy) exhibits F115W-F200W > 1.9 mag (2σ lower limit) with a blue continuum slope, resulting in 99.6% of the photo-z probability distribution function favoring z > 11. All data-quality images show no artifacts at the candidate's position, and independent analyses …

Spacecraft Charging Test Considerations For Composite Materials, Allen Andersen, Wousik Kim, J. R. Dennison, Brian Wood, Todd A. Schneider, Jason Vaughn, Kenneth H. Wright Jr., Nelson W. Green, Eric Suh, Joel Schwartz, Abdul-Majeed Azad

Journal Articles

Composite materials present a growing challenge for spacecraft charging assessments. We review some recent lessons learned for charging tests of composite materials using both parallel-plate and electron beam test geometries. We also discuss examples of materials that exhibit significant variations between samples, despite them all having the same trade name.

Probability Distributions Of The Scalar Potential, Candace Mathews

Legacy Theses & Dissertations (2009 - 2024)

In the study of cosmological inflation, string theory and supersymmetry have motivated a wide range of possible inflationary models. These models can be parameterized by a scalar potential V, which is a function of N scalar fields, and determines cosmological parameters such as the vacuum stability and energy density. In principle, we can determine V through high energy physics, such as string theory. In practice, though we may not know the details of V we might have clues about a distribution of plausible V’s, which we can build statistics on to further analyze. The purpose of this thesis defense is …

Turning Density Functional Theory Calculations Into Molecular Mechanics Simulations : Establishing The Fluctuating Density Model For Rna Nucleobases, Christopher A. Myers

Legacy Theses & Dissertations (2009 - 2024)

Molecular mechanics (MD) simulations and density functional theory (DFT) have been the backbone of computational chemistry for decades. Due to its accuracy and computational feasibility, DFT has become the go-to method for theoretically predicting interaction energies, polarizability, and other electronic properties of small molecules at the quantum mechanical level. Although less fundamental than DFT, molecular mechanics (MM) algorithms have been just as influential in the fields of biology and chemistry, owing their success to the ability to compute measurable, macroscopic quantities for systems with tens of thousands to hundreds of thousands of atoms at a time. Nevertheless, MD simulations would …

Atomic Force Microscopy Cantilever-Based Nanoindentation: Mechanical Property Measurements At The Nanoscale In Air And Fluid, Ashton E. Enrriques, Sean Howard, Raju Timsina, Nawal K. Khadka, Amber N. Hoover, Allison E. Ray, Ling Ding, Chioma Onwumelu, Stephan Nordeng, Laxman Mainali, Gunes Uzer, Paul H. Davis

Physics Faculty Publications and Presentations

An atomic force microscope (AFM) fundamentally measures the interaction between a nanoscale AFM probe tip and the sample surface. If the force applied by the probe tip and its contact area with the sample can be quantified, it is possible to determine the nanoscale mechanical properties (e.g., elastic or Young's modulus) of the surface being probed. A detailed procedure for performing quantitative AFM cantilever-based nanoindentation experiments is provided here, with representative examples of how the technique can be applied to determine the elastic moduli of a wide variety of sample types, ranging from kPa to GPa. These include live mesenchymal …

Building Structures From Mycelium, Noah M. Brown

Physics

The purpose of this project was to develop a method for creating bricks from mycelium and agricultural waste. The bulk of the research happened in two parts, the first part being a period in which different substrates, strains, and methods were used build the bricks. This research took place in San Luis Obispo and was aided by a group of students in PSC392 under Dr. Pete Schwartz in early 2022. After developing a method for constructing these bricks, the research was moved to St. Thomas, Jamaica, in collaboration with an ecovillage called The Source Farm from July to September. The …