Engineering Commons^™

Development Of An Integrated Workflow For Nucleosome Modeling And Simulations, Ran Sun

Doctoral Dissertations

Nucleosomes are the building blocks of eukaryotic genomes and thus fundamental to to all genetic processes. Any protein or drug that binds DNA must either cooperate or compete with nucleosomes. Given that a nucleosome contains 147 base pairs of DNA, there are approximately 4^147 or 10^88 possible sequences for a single nucleosome. Exhaustive studies are not possible. However, genome wide association studies can identify individual nucleosomes of interest to a specific mechanism, and today's supercomputers enable comparative simulation studies of 10s to 100s of nucleosomes. The goal of this thesis is to develop and present and end-to-end workflow that serves …

Atomic-Level Mechanisms Of Fast Relaxation In Metallic Glasses, Leo W. Zella

Doctoral Dissertations

Glasses are ubiquitous in daily life and have unique properties which are a consequence of the underlying disordered structure. By understanding the fundamental processes that govern these properties, we can modify glasses for desired applications. Key to understanding the structure-dynamics relationship in glasses is the variety of relaxation processes that exist below the glass transition temperature. Though these relaxations are well characterized with macroscopic experimental techniques, the microscopic nature of these relaxations is difficult to elucidate with experimental tools due to the requirements of timescale and spatial resolution. There remain many questions regarding the microscopic nature of relaxation in glass …

Fabrication, Measurements, And Modeling Of Semiconductor Radiation Detectors For Imaging And Detector Response Functions, Corey David Ahl

Doctoral Dissertations

In the first part of this dissertation, we cover the development of a diamond semiconductor alpha-tagging sensor for associated particle imaging to solve challenges with currently employed scintillators. The alpha-tagging sensor is a double-sided strip detector made from polycrystalline CVD diamond. The performance goals of the alpha-tagging sensor are 700-picosecond timing resolution and 0.5 mm spatial resolution. A literature review summarizes the methodology, goals, and challenges in associated particle imaging. The history and current state of alpha-tagging sensors, followed by the properties of diamond semiconductors are discussed to close the literature review. The materials and methods used to calibrate the …

Total Absorption Spectroscopy Of Mo-106 And Tc-106, Michael Cooper

Doctoral Dissertations

Total absorption spectroscopy is a method of gamma-ray spectroscopy that has gained prominence in the past several decades, as nuclear data revisions are performed on older nuclear data, which is often incomplete. A strong understanding of underlying nuclear data, particularly fission and beta decay data, is essential for nuclear reactors and nuclear fuel decay heat. This PhD work involves the analysis of fission fragments 106Mo [Mo-106] and 106Tc [Tc-106]. These neutron rich isotopes contribute upwards of 6% of the cumulative fission yield of 241Pu [Pu-241] fission, and 4% of 239Pu [Pu-239] fission. Prior data for these two fission fragments only …

Synthesis And Assembly Of Polymer Materials At Interfaces, Xiaoshuang Wei

Doctoral Dissertations

The overarching goal of the thesis is to understand growth and assembly of polymer materials at interfaces. Chapter 2 and Chapter 3 study simultaneous polymer growth and assembly at fluid interfaces, where in-situ photopolymerization and vapor phase deposition were utilized to grow polymers, respectively. Chapter 4 leverages capillary condensation to pattern polymer growth at solid substrates. Chapter 1 provides background information on polymer materials at interfaces, and vapor phase deposition method (initiated chemical vapor deposition, iCVD) to grow polymers. This chapter also reviews polymer thin film wetting, and colloidal assemblies at interfaces. In Chapter 2, we demonstrate the preparation …

Frontiers In The Self-Assembly Of Charged Macromolecules, Khatcher O. Margossian

Doctoral Dissertations

The self-assembly of charged macromolecules forms the basis of all life on earth. From the synthesis and replication of nucleic acids, to the association of DNA to chromatin, to the targeting of RNA to various cellular compartments, to the astonishingly consistent folding of proteins, all life depends on the physics of the organization and dynamics of charged polymers. In this dissertation, I address several of the newest challenges in the assembly of these types of materials. First, I describe the exciting new physics of the complexation between polyzwitterions and polyelectrolytes. These materials open new questions and possibilities within the context …

How Dynamic Bond Results In The Unique Viscoelastic Behavior Of The Associating Polymers, Sirui Ge

Doctoral Dissertations

Associating polymer is a special kind of polymer possessing transient reversible bonds in addition to the conventional covalent bonds. The reversible bonds provide unique dynamics and fascinating viscoelastic properties, resulting in attractive applications for these polymers, such as self-healing and shape memory materials. Despite many years of studies, the understanding of dynamics of polymers with reversible bonds, especially on molecular level, is still in the rudimentary stage, preventing the rational design of the potential novel functional materials based on associating polymers. In this dissertation, we provide a detailed and quantitative understanding of the dynamics and viscoelastic properties of associating polymers. …

Direct Calculation Of Configurational Entropy: Pair Correlation Functions And Disorder, Clifton C. Sluss

Doctoral Dissertations

Techniques such as classical molecular dynamics [MD] simulation provide ready access to the thermodynamic data of model material systems. However, the calculation of the Helmholtz and Gibbs free energies remains a difficult task due to the tedious nature of extracting accurate values of the excess entropy from MD simulation data. Thermodynamic integration, a common technique for the calculation of entropy requires numerous simulations across a range of temperatures. Alternative approaches to the direct calculation of entropy based on functionals of pair correlation functions [PCF] have been developed over the years. This work builds upon the functional approach tradition by extending …

Tokamak 3d Heat Load Investigations Using An Integrated Simulation Framework, Thomas Looby

Doctoral Dissertations

Reactor class nuclear fusion tokamaks will be inherently complex. Thousands of interconnected systems that span orders of magnitude in physical scale must operate cohesively for the machine to function. Because these reactor class tokamaks are all in an early design stage, it is difficult to quantify exactly how each subsystem will act within the context of the greater systems. Therefore, to predict the engineering parameters necessary to design the machine, simulation frameworks that can model individual systems as well as the interfaced systems are necessary. This dissertation outlines a novel framework developed to couple otherwise disparate computational domains together into …

A High Rate Pixelated Neutron Detector For Neutron Reflectometry At The Spallation Neutron Source, Su-Ann Chong

Doctoral Dissertations

This work presents the development of a high-rate 6Li-based pixelated neutron detector for neutron reflectometry instruments at the Spallation Neutron Source (SNS), Oak Ridge National Laboratory. The current detector technology falls short on the instrument requirements, particularly on the counting rate capability. This detector was designed specifically to overcome the limitation in counting rate by having a fully pixelated design from neutron conversion layer to photodetector and readout system. For the neutron converting layer, a 6Li-based neutron scintillator was used. Each scintillator element was coupled to a photodetector, in this case, a silicon photomultiplier (SiPM). The output of each SiPM …

Modeling Chain Packing In Complex Phases Of Self-Assembled Block Copolymers, Anugu Abhiram Reddy

Doctoral Dissertations

Block copolymer (BCP) melts undergo microphase seperation and form ordered soft matter crystals with varying domain shapes and symmetries. We study the con- nection between diblock copolymer molecular designs and thermodynamic selection of ordered crystals by modeling features of variable sub-domain geometry filled with individual blocks within non-canonical sphere-like and network phases that together with layered, cylindrical and canonical spherical phases forms “natural forms” of self- assembled amphiphilic soft matter at large. First, we present a model to revise our understanding of optimal Frank-Kasper sphere-like morphologies by advancing the- ory to account for varying domain volumes. We then develop generic …

Moving Polygon Methods For Incompressible Fluid Dynamics, Chris Chartrand

Doctoral Dissertations

Hybrid particle-mesh numerical approaches are proposed to solve incompressible fluid flows. The methods discussed in this work consist of a collection of particles each wrapped in their own polygon mesh cell, which then move through the domain as the flow evolves. Variables such as pressure, velocity, mass, and momentum are located either on the mesh or on the particles themselves, depending on the specific algorithm described, and each will be shown to have its own advantages and disadvantages. This work explores what is required to obtain local conservation of mass, momentum, and convergence for the velocity and pressure in a …

Synthesis, Fabrication, And Assembly Of Mesoscale Polymer Filaments, Dylan M. Barber

Doctoral Dissertations

Mesoscale materials, with feature sizes in the range of one hundred nanometers to tens of micrometers, are ubiquitous in Nature. In organisms, mesoscale building blocks connect the properties of underlying molecular and nanoscructures to those of macroscale, organism-scale materials through hierarchical assemblies of recurring structural motifs. The collective action of large numbers of mesoscale features can afford stunning features like the structural color of the morpho butterfly wing, calcium ion-mediated movement in muscle, and wood structures like xylem that can support enormous external compressive loads and negative internal pressure to transport nutrients throughout an organism. In synthetic systems, the design, …

Effects Of Vacancies And Electron Temperature On The Electron Phonon Coupling In Cubic Silicon Carbide And Their Connection To The Inelastic Thermal Spike, Salah Al-Smairat

Doctoral Dissertations

“The electron-phonon interaction is an important interaction in many solids as it influences transport phenomena and related quantities such as the electrical and thermal conductivities, especially in nuclear and space applications. The importance of the electron-phonon interaction in primary damage production in 3C-SiC is the subject of this research.

The electron-phonon coupling factor was calculated using a hybrid Density Functional Perturbation Theory - Classical Electron Gas model. The coupling factor was calculated as a function of electron temperature in pristine and defective 3C-SiC, and relaxed defective cells. The electron-phonon coupling is found to depend strongly on the electronic temperature and …

Impurity Production And Transport In The Prototype Material Plasma Exposure Experiment, Clyde J. Beers

Doctoral Dissertations

The Prototype Material Plasma Exposure eXperiment (Proto-MPEX) is a linear pulse plasma device at Oak Ridge National Laboratory with the purpose of doing the research and development for the heating concepts on the planned full MPEX device. The goal of MPEX is to perform material studies at fusion relevant conditions. To understand the conditions at the material target for performing plasma-material interaction studies the ion temperature and density, the electron temperature and density, and the particle flux and fluence must be known. Impurities within Proto-MPEX can alter the desired conditions at the material target and need to be understood for …

Production Of Protactinium-229 Via Deuteron Irradiation Of Thorium-232, Naser Burahmah

Doctoral Dissertations

²²⁵Ac [Actinium-225] is a promising radionuclide for targeted alpha therapy of cancer. ²²⁹Pa can lead to the production of ²²⁹Th [Thorium-229] and ²²⁵Ac [Actinium-225]. Deuteron bombardment on natural thorium targets has been investigated to measure cross sections of protactinium isotopes. In this work, ²²⁹Pa [Protactinium-229] excitation function was measured via deuteron energies up to 50 MeV [Mega electron volt] of thin thorium foils. The irradiation took place at Lawrence Berkeley National Laboratory’s (LBNL) 88-Inch Cyclotron. The target processing and analysis were performed at Oak Ridge National Laboratory (ORNL). The target consisted of 4 thin foils …

Fabrication Of Specialized Scintillators For Nuclear Security Applications, Cordell James Delzer

Doctoral Dissertations

Radiation detectors are important for a variety of fields including medical imaging, oil drilling, and nuclear security. Within nuclear security, they can serve a multitude of purposes whether that be imaging, localization, isotopic identification, or even just activity measurement. Even without directly seeing a nuclear material it is often able to notice their existence without a detector. Scintillators make up an important part of these detectors due to their large intrinsic efficiency, low cost, large volume, and relatively low upkeep. Due to the importance of the large number of purposes these scintillators may be used for, it can often be …

Collector Probe Measurements Of Sol Impurity Accumulation And The Implications Of Sol Flows On The Accumulation Amount, Shawn Zamperini

Doctoral Dissertations

A collector probe in its simplest form is a rod inserted into a plasma so that impurities are deposited onto it. These probes are then removed and analyzed to determine the deposition profile both along the length of probe and across the width of it. This dissertation covers a series of collector probes experiments and accompanying interpretive modelling all with the main goal of providing evidence for long-hypothesized near scrape-off layer (SOL) accumulation of impurities that can lead to efficient core contamination. The structure of this dissertation is as follows. A brief outline of fusion energy and why we need …

Local Dynamics And Atomic-Level Structures In Metallic Liquids And Glasses, Zengquan Wang

Doctoral Dissertations

Structure and dynamics at the atomic level in metallic glasses and liquids are poorly understood when compared to the crystalline solids. For instance, even though viscosity is the basic property of liquids, its atomistic origin is not well elucidated. Also, the physics of the fragility of liquids and the crossover phenomenon is far from full understanding. Earlier, through molecular dynamics (MD) simulations a direct connection was found between the timescale describing the macroscopic viscous behavior, the Maxwell relaxation time (t_M = h/G_∞, h is the shear viscosity and G_∞ is the high-frequency shear modulus) and …

Multi-Scale Computational Modeling Of Metal/Ceramic Interfaces, Abu Shama Mohammad Miraz

Doctoral Dissertations

Multi-scale atomistic calculations were carried out to understand the interfacial features that dictate the mechanical integrity of the metal/ceramic nanolaminates. As such, first principles density functional theory (DFT) calculations were performed to understand the electronic and atomistic factors governing adhesion and resistance to shear for simple metal/ceramic interfaces, whereas molecular dynamics (MD) simulations were performed to observe the impact of interfacial structures, such as misfit dislocation network geometries and orientation relationships, on interfacial mechanical properties.

For the DFT investigation, we choose metals with different crystal structures, namely - Cu (fcc), Cr (bcc) and Ti (hcp) along with a variety of …

Fiber Optic Sensors For Industry And Military Applications, Yiyang Zhuang

Doctoral Dissertations

"Fiber optic sensors (FOSs) have been widely used for measuring various physical and chemical measurands owing to their unique advantages over traditional sensors such as small size, high resolution, distributed sensing capabilities, and immunity to electromagnetic interference. This dissertation focuses on the development of robust FOSs with ultrahigh sensitivity and their applications in industry and military areas.

Firstly, novel fiber-optic extrinsic Fabry-Perot interferometer (EFPI) inclinometers for one- and two-dimensional tilt measurements with 20 nrad resolution were demonstrated. Compared to in-line fiber optic inclinometers, an extrinsic sensing motif was used in our prototype inclinometer. The variations in tilt angle of the …

Semi-Empirical Modeling Of Liquid Carbon's Containerless Solidification, Philip C. Chrostoski

Doctoral Dissertations

“Elemental carbon has important structural diversity, ranging from nanotubes through graphite to diamond. Previous studies of micron-size core/rim carbon spheres extracted from primitive meteorites suggest they formed around such stars via the solidification of condensed carbon-vapor droplets, followed by gas-to-solid carbon coating to form the graphite rims. Similar core/rim particles result from the slow cooling of carbon vapor in the lab. The long-range carbon bond-order potential was used to computationally study liquid-like carbon in (1.8 g/cm³) periodic boundary (tiled-cube supercell) and containerless (isolated cluster) settings. Relaxations via conjugate-gradient and simulated-annealing nucleation and growth simulations using molecular dynamics were …

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 …

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 …

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 …

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 …

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 …

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. …