Physics Commons^™

Composite Network Of Actin And Microtubule Filaments, Self-Organization And Steady-State Dynamics, Leila Farhadi

Doctoral Dissertations

Actin and microtubule filaments, with their auxiliary proteins, enable the cytoskeleton to perform vital processes in the cell by tuning the organizational, mechanical properties and dynamics of the network. Despite their critical importance and interactions in cells, we are only beginning to uncover information about the composite network. Here, I use florescence microscopy to explore the role of filaments characteristics, interactions and activities in the self-organization and steady-state dynamics of the composite network of filaments. First, I discuss active self-organization of semiflexible actin and rigid microtubule filaments in the 2D composite network while myosin II and kinesin-1 motor proteins propel …

Distortion-Controlled Isotropic Swelling And Self-Assembly Of Triply-Periodic Minimal Surfaces, Carlos M. Duque

Doctoral Dissertations

In the first part of this thesis, I propose a method that allows us to construct optimal swelling patterns that are compatible with experimental constraints. This is done using a greedy algorithm that systematically increases the perimeter of the target surface with the help of minimum length cuts. This reduces the areal distortion that comes from the changing Gaussian curvature of the sheet. The results of our greedy cutting algorithm are tested on surfaces of constant and varying Gaussian curvature, and are additionally validated with finite thickness simulations using a modified Seung-Nelson model. In the second part of the thesis, …

Searching For New Physics At Colliders And From Precision Measurements, Yong Du

Doctoral Dissertations

Beyond the great triumph of the Standard Model of particle physics, several fundamental questions remain unknown with the framework of the Standard Model. Among them are the non-zero neutrino masses, the dark matter and the baryon asymmetry of the Universe. Answers to these questions require new physics beyond the Standard Model and searching for the new physics beyond the SM has been a major task for modern particle physicists. The signal of this new physics can be searched through colliders, low- and high-energy precision measurements, as well as precision cosmological observation. Here I present my work in searching for the …

Experimental Study Of Viscoelastic Fluid-Structure Interactions, Anita Anup Dey

Doctoral Dissertations

It is well known that when a flexible or flexibly-mounted structure is placed perpendicular to a Newtonian fluid flow, it can oscillate due to the shedding of vortices at high Reynolds numbers. Unlike Newtonian fluids, viscoelastic fluid flow can become unstable even at infinitesimal Reynolds numbers due to a purely elastic flow instability occurring at large Weissenberg numbers. This thesis focuses on exploring the mechanisms of viscoelastic fluid-structure interactions (VFSI) through experimental investigations on several different combinations of flexible and flexibly-mounted circular cylinders, micro and macro-scale cantilevered beams and viscoelastic fluids such as wormlike micelle solutions and polymer solutions. VFSI …

Theory And Improved Methods For Probing The Cavitation To Fracture Transition, Christopher Barney

Doctoral Dissertations

A material is considered soft when its bulk modulus is significantly greater than its shear modulus. Rubbery polymers are a class of soft materials where resistance to extension is mainly entropic in nature. Polymeric soft solids differ from liquids due to the presence of a percolated network of strong bonds that resist deformation and flow on a given time scale. The incompressible nature, entropically driven elasticity, and molecular scale network structure of soft polymeric solids combine to impart unique mechanical behavior that often results in complex material responses to simple loading situations. An important example of this is cavitation in …

Filaments, Fibers, And Foliations In Frustrated Soft Materials, Daria Atkinson

Doctoral Dissertations

Assemblies of one-dimensional filaments appear in a wide range of physical systems: from biopolymer bundles, columnar liquid crystals, and superconductor vortex arrays; to familiar macroscopic materials, like ropes, cables, and textiles. Interactions between the constituent filaments in such systems are most sensitive to the distance of closest approach between the central curves which approximate their configuration, subjecting these distinct assemblies to common geometric constraints. Dual to strong dependence of inter-filament interactions on changes in the distance of closest approach is their relative insensitivity to reptations, translations along the filament backbone. In this dissertation, after briefly reviewing the mechanics and …

Transitions Between Radial And Bipolar Liquid Crystal Drops In The Presence Of Novel Surfactants, Jake Shechter

Doctoral Dissertations

Liquid crystals (LCs) are a class of molecules that form a variety of configurations easily influenced by external interactions. Of particular interest are rod-like LC molecules confined to a spherical geometry, which have a competition between interfacial tension and elastic deformations. The configuration of the liquid crystal inside a droplet can be controlled using surfactants, influencing the boundary conditions, in an oil-in-water emulsion. I tested the effects of novel surfactants on the configuration of the LC droplets. These novel surfactant molecules, synthesized by collaborators, are oligomers with either a variable length hydrophobic domain or protein sensitive hydrophilic domain. I tested …

Controlled Membrane Remodeling By Nanospheres And Nanorods: Experiments Targeting The Design Principles For Membrane-Based Materials, Sarah Zuraw-Weston

Doctoral Dissertations

In this thesis we explore two experimental systems probing the interactions of nanoparticles with lipid bilayer membranes. Inspired by the ability of cell membranes to alter their shape in response to bound particles, we report two experimental studies: one of nanospheres the other of long, slender nano-rods binding to lipid bilayer vesicles and altering the membrane shape. Our work illuminates the role of particle geometry, particle concentration, adhesion strength and membrane tension in how membrane morphology is determined. We combine giant unilamellar vesicles with oppositely charged nanoparticles, carefully tuning adhesion strength, membrane tension and particle concentration. In the case of …

Laser-Induced Breakdown Spectroscopy And Plasmas Containing Cyanide, Christopher Matthew Helstern

Doctoral Dissertations

This dissertation focuses on laser-induced plasma of diatomic molecular cyanide. Optical breakdown plasma generation is produced by high-peak-power 1064 nm Q-switched nanosecond pulsed radiation. Laser-induced breakdown is performed on a 1:1 molar gas mixture of carbon dioxide and nitrogen held at a fixed pressure of 760 Torr, a 1:1 molar gas mixture of carbon dioxide and nitrogen held at a fixed pressure of 2069 Torr, and a flowing 1:1 molar gas mixture of carbon dioxide and nitrogen flowing at a rate of 100 mL per minute. Plasma shockwave measurements in laboratory air are shown to determine the shock front geometry …

Probing Structure, Function And Dynamics In Bacterial Primary And Secondary Transporter-Associated Binding Proteins, Shantanu Shukla

Doctoral Dissertations

Substrate binding proteins (SBPs) are ubiquitous in all life forms and have evolved to perform diverse physiological functions, such as in membrane transport, gene regulation, neurotransmission, and quorum sensing. It is quite astounding to observe such functional diversity among the SBPs even when they are restricted by their fold space. Therefore, the SBPs are an excellent set of proteins that can reveal how proteins evolution novel function in a structurally conserved/constrained fold. This study attempts to understand the phenomenon of affinity and specificity evolution in SBPs by combining a set of biochemical, biophysical, and structural studies on the SBPs involved …

Understanding The Fundamentals Of Ionic Conductivity In Polymer Electrolytes, Eric Wayne Stacy

Doctoral Dissertations

The rate of advancement for mobilized electronic technologies is outpacing the development of small efficient batteries. Lithium-ion batteries are currently the most widely used energy storage device for consumer electronics. Traditional lithium-ion batteries use a liquid electrolyte to separate the cathodes and anodes; however, conventional liquid electrolytes have inherent problems, such as consisting of flammable carbonate components, hazardous material, and have a significant cost/weight in the battery. In addition, the liquid electrolyte cannot prevent the growth of lithium dendrites during the charge/discharge cycle of the lithium-ion battery. These dendrites can connect the anode to the cathode of the battery cell …

Local Structure And Dynamic Studies Of Mixed Ch4-Co2 Gas Hydrates Via Computational Simulation And Neutron Scattering, Bernadette Rita Cladek

Doctoral Dissertations

Permeated throughout the ocean floor and arctic permafrost, natural gas hydrates contain an estimated 3000 trillion cubic meters, over three times that of traditional shale deposits, of CH₄ that is accessible for extraction. Gas hydrates are a crystal structure in which water molecules form a cage network, the host, through hydrogen bonds while trapping a guest molecule such as CH₄ in the cavities. These compounds form naturally where the appropriate low temperature and high pressure conditions occur. A promising and tested method of methane recovery is through exchange with CO₂, which energetically takes place of the …

Benchmarks And Controls For Optimization With Quantum Annealing, Erica Kelley Grant

Doctoral Dissertations

Quantum annealing (QA) is a metaheuristic specialized for solving optimization problems which uses principles of adiabatic quantum computing, namely the adiabatic theorem. Some devices implement QA using quantum mechanical phenomena. These QA devices do not perfectly adhere to the adiabatic theorem because they are subject to thermal and magnetic noise. Thus, QA devices return statistical solutions with some probability of success where this probability is affected by the level of noise of the system. As these devices improve, it is believed that they will become less noisy and more accurate. However, some tuning strategies may further improve that probability of …

Approaches To Studying Bacterial Biofilms In The Bioeconomy With Nanofabrication Techniques And Engineered Platforms., Michelle Caroline Halsted

Doctoral Dissertations

Studies that estimate more than 90% of bacteria subsist in a biofilm state to survive environmental stressors. These biofilms persist on man-made and natural surfaces, and examples of the rich biofilm diversity extends from the roots of bioenergy crops to electroactive biofilms in bioelectrochemical reactors. Efforts to optimize microbial systems in the bioeconomy will benefit from an improved fundamental understanding of bacterial biofilms. An understanding of these microbial systems shows promise to increase crop yields with precision agriculture (e.g. biosynthetic fertilizer, microbial pesticides, and soil remediation) and increase commodity production yields in bioreactors. Yet conventional laboratory methods investigate these micron-scale …

Dynamic Neuromechanical Sets For Locomotion, Aravind Sundararajan

Doctoral Dissertations

Most biological systems employ multiple redundant actuators, which is a complicated problem of controls and analysis. Unless assumptions about how the brain and body work together, and assumptions about how the body prioritizes tasks are applied, it is not possible to find the actuator controls. The purpose of this research is to develop computational tools for the analysis of arbitrary musculoskeletal models that employ redundant actuators. Instead of relying primarily on optimization frameworks and numerical methods or task prioritization schemes used typically in biomechanics to find a singular solution for actuator controls, tools for feasible sets analysis are instead developed …

Using Second Harmonic Generation To Study Gram-Positive Bacterial Membranes, Lindsey N. Miller

Doctoral Dissertations

Understanding how small-molecules, such as drugs, interact with bacterial membranes can quickly unravel into much more perplexing questions. No two bacterial species are alike, especially when comparing their membrane compositions which can even be altered by incorporating fatty acids from their surrounding environment into their lipid-membrane composition. To further complicate the comparison, discrete alterations in small-molecule structures can result in vastly different membrane-interaction outcomes, giving rise to the need for more "label-free" studies when analyzing drug mechanisms. The work presented in this dissertation highlights the benefits to using nonlinear spectroscopy and microscopy techniques for probing small-molecule interactions in living bacteria. …

Characterization Of A Digital Holography Diagnostic For In Situ Erosion Measurement Of Plasma-Facing Components In Fusion Devices, Cary Dean Smith

Doctoral Dissertations

Fusion energy devices, particularly tokamaks, face the challenge of interior surface damage occurring over time from the heat flux of the high-energy plasma they generate. The ability to monitor the rate of surface modification is therefore imperative, but to date no proven technique exists for real-time erosion measurement of planar regions of interest on plasma-facing components in fusion devices. In order to fill this diagnostic gap, a digital holography system has been established at ORNL [Oak Ridge National Laboratory] for the purpose of measuring the erosion effects of plasma-material interaction in situ.

The diagnostic has been designed with the …

Exploring Structural And Electronic Properties Of Triangular Adatom Layers On The Silicon Surface Through Adsorbate Doping, Tyler S. Smith

Doctoral Dissertations

The analysis of the electronic structure and morphology of 1/3 monolayers (ML) of Sn or Pb on Si(111) and Ge(111) has played an important role in understanding the role of electronic correlations in two dimensions. Specifically, the two-dimensional lattice of partially filled dangling bonds of these so-called α-phases has been an important testbed for studying structural phase transitions and correlated electronic phenomena ever since the discovery of a surface charge density wave in the Pb/Ge(111) system more than two decades ago. With the exception of the novel Sn/Si(111) system, all $\alpha$-phases undergo a charge ordering transition at low temperature. The …

Numerical Studies Of Multi-Orbital Hubbard Models, Nitin Kaushal

Doctoral Dissertations

This thesis examines the emergence of exotic phases in multi-orbital Hubbard models due to competition between Coulomb interaction, spin-orbit coupling and kinetic energy. Exact diagonalization and numerically accurate density matrix renormalization group methods are used to study small clusters and one dimensional chains. Two dimensional lattices are solved using unrestricted real-space Hartree-Fock approximation. Novel excitonic insulators, due to condensation of spin-orbit excitons, are found in the spin-orbit coupling vs Coulomb interation phase diagrams of (t_2g)ⁿ systems for n = 4 and 3.5. Moreover, the presence of a BCS-BEC crossover in the (t_2g)4 excitonic insulator is …

Probability Distribution Of Equations Of State For Astrophysical Simulations, Xingfu Du

Doctoral Dissertations

The detection of gravitational wave during the neutron star merger event GW170817 greatly enhanced our ability to probe the interiors of neutron stars. Future measurements of similar events will put further constraints to the equation of state (EOS) of nuclear matter. Also, uncertainties in the EOS create variations in the results of astrophysical simulations of core-collapse supernovae and neutron star mergers. In order to quantify the uncertainties, we construct a probability distribution of equations of state (EOSs). We create a new EOS which respects experimental, observational and theoretical constraints on the nature of matter in various density and temperature regimes. …

Theoretical Modeling Of Metallic Compounds With Versatile Properties By Combining First-Principles Calculations And Global Structure Prediction Algorithms, Jinseon Park

Doctoral Dissertations

Improving the target properties of existing materials or finding new materials with enhanced functionality for practical applications is at the heart of the materials research. In this respect, the first-principles approaches, which have been successfully integrated into modern high- performance computers, have become an indispensable part of the materials research, providing a better understanding of existing materials and guidance on the design of new materials. Using state-of-the-art computational/theoretical approaches that couple global structure prediction with ab initio density functional theory calculations, we investigate structural and electronic properties of Cs_xO [cesium oxides], Li_1+xMn₂O₄ [lithium …

Nano- And Micro-Structured Temperature-Sensitive Hydrogels For Rapidly Responsive Devices, Qi Lu

Doctoral Dissertations

This thesis aims to extend the understanding and explore the application of temperature-responsive hydrogel systems by integrating microelectromechanical systems (MEMS). Stimuli-responsive hydrogel systems are immensely investigated and applied in numerous fields, and interfacing with micro- and nano-fabrication techniques will open up more possibilities. In Chapter 2, the first biologically relevant, in vitro cell stretching device based on hydrogel surface instability was developed. This dynamic platform is constructed by embedding micro-heater devices under temperature-responsive surface-attached hydrogels. The fast and regional temperature change actuates the stretching and relaxation of the seeded human artery smooth muscle cell (HASMC) via controllable surface creasing instability. …

Kinetics Of The Crystal-Melt Phase Transformation In Semicrystalline Polymers, Kiran Subramaniam Iyer

Doctoral Dissertations

The assembly of long-chain polymers into an ordered state is a process that has puzzled polymer scientists for several decades. A process that is largely controlled by the strength of intermolecular attractions in small molecular systems, this crystallization in the case of polymers is controlled by a competition between the aforementioned force of attraction between monomers and the formidable conformational entropy of polymer chains. Any factor that affects this conformational entropy, whether that is an equilibrium thermodynamic factor or a kinetic factor, has the ability to control polymer crystallization. In this thesis, we focus on understanding the underlying kinetic processes …

The Parity-Violating Asymmetry In The N→Δ Transition At Low Q2, Thamraa A. Alshayeb

Doctoral Dissertations

Qweak has used the parity violating asymmetry to test the Standard Model (SM) by constantly flipping helicity states of a longitudinally polarized electron beam that scatters in the unpolarized LH2 target. The main focus of the Qweak experiment at Jefferson Lab was the recently published determination of the proton’s weak charge. In order to make corrections to the measured asymmetry at low 𝑄 2 due to inelastically scattered electrons, dedicated measurements were made of the parity violating asymmetry in the N→∆ transition at two different beam energies.

The measured inelastic asymmetries are used to extract the low energy constant dΔ, …

Search For Displaced Hadronic Vertices In The Atlas Inner Detector And Muon Spectrometer In P-P Collisions At √S = 13 Tev At The Lhc, Margaret S. Lutz

Doctoral Dissertations

A search is performed for long-lived neutral particles using 33 fb−1 of 13 TeV proton-proton collision data produced by the LHC and collected by the ATLAS detector during 2016. This search focuses on the topology in which pairs of displaced hadronic jets are produced, with one in the inner detector and the other in the muon spectrometer. Special techniques are used to reconstruct the displaced decays. One event is found passing the full signal selection, which is consistent with the back- ground estimation. Limits are set at a 95% upper confidence level on the BR × σ for a SM …

Acoustic Confinement And Characterization Of A Microwave Plasma, Seth Lee Pree '09

Doctoral Dissertations

High amplitude acoustic fields are used to confine, characterize, and manipulate collisional plasmas with temperatures of a few thousand Kelvin. This dissertation describes the theory, experimental techniques, and apparatus necessary both to generate high amplitude sound in a few thousand Kelvin plasma and to use that sound field to manipulate the plasma within a resonant acoustic cavity. The acoustic field in a spherically symmetric oscillating plasma has been measured to have a Mach number of .03, which is sufficient to cause acoustic radiation pressure effects to confine the plasma to the center of its container. This field also generates convection …

Modification Of The Optical Response Of Alpha Quartz Via The Deposition Of Gold Nanoparticles In Etched Ion Tracks, Maria C. Garcia Toro

Doctoral Dissertations

”This study addresses the experimental methods used to develop and characterize plasmonic devices capable of modifying the optical response of alpha quartz via the deposition of gold nanoparticles in etched ion tracks. In the first part of the research, the microstructural characterization of latent and etched ion tracks produced in alpha quartz (α-SiO₂) is presented. Single crystals of α-SiO₂ were irradiated with two highly energetic ions to different nominal fluences. As expected, the morphology of the resulting ion tracks depends on the energy of the incident ion and their stopping powers within the target material. Subsequent chemical …

A Framework Of Multi-Dimensional And Multi-Scale Modeling With Applications, Zilong Li

Doctoral Dissertations

In this dissertation, a framework for multi-dimensional and multi-scale modeling is proposed. The essential idea is based on oriented space curves, which can be represented as a 3D slender object or 1D step parameters. SMILES and Masks provide functionalities that extend slender objects into branched and other objects. We treat the conversion between 1D, 2D, 3D, and 4D representations as data unification. A mathematical analysis of different methods applied to helices (a special type of space curves) is also provided. Computational implementation utilizes Model-ViewController design principles to integrate data unification with graphical visualizations to create a dashboard. Applications of multi-dimensional …

Magnetic Control Of Transport Of Particles And Droplets In Low Reynolds Number Shear Flows, Jie Zhang

Doctoral Dissertations

“Magnetic particles and droplets have been used in a wide range applications including biomedicine, biological analysis and chemical reaction. The manipulation of magnetic microparticles or microdroplets in microscale fluid environments is one of the most critical processes in the systems and platforms based on microfluidic technology. The conventional methods are based on magnetic forces to manipulate magnetic particles or droplets in a viscous fluid.

In contrast to conventional magnetic separation method, several recent experimental and theoretical studies have demonstrated a different way to manipulate magnetic non-spherical particles by using a uniform magnetic field in the microchannel. However, the fundamental mechanism …

A Molecular Dynamics Study Of Temperature Dependent Wetting In Alkane-Water Systems, Pauf Neupane

Doctoral Dissertations

“The wetting behavior of aqueous organic systems is of great importance in several environmental and industrial processes such as the formation and growth of atmospheric aerosols, crude oil recovery from an oil field, onsite cleaning of natural gas, and clean-up of oil spills. In this work, we employed molecular dynamics (MD) simulations to explore the temperature dependent wetting behavior of octane and nonane on water in planar interfaces as well as in nanodroplets using PYS alkane and SPC/E and TIP4P/2005 water models.

For planar interfaces, we found unusual wetting behavior of octane and nonane on SPC/E water, but generally not …