Physics Commons^™

X-Ray Characterization Of Mesophases And Phase Transitions Of Dna Analogues In Solutions, Mustafa Selcuk Yasar

Doctoral Dissertations

We think of DNA as double-stranded helices (duplex), but the polymer exists in many conformations. Several triplex and quadruplex DNA structures can be formed in laboratory settings and exist in nature. This thesis first provides a brief description of the nature of the order in arrays of duplex DNA under biologically relevant molecular crowding conditions. Then we compare the duplex DNA mesophases with the corresponding liquid crystalline phase behavior of the triplex and quadruplex DNA analogues. In particular, we focus on G-quadruplexes. Observed in the folds of guanine-rich oligonucleotides, G-quadruplex structures are based on G-quartets formed by hydrogen bonding and …

The Effect Of Attractive Polymer-Nanoparticle Interactions On The Local Segmental Dynamics Of Polymer Nanocomposites, Adam Prillaman Holt

Doctoral Dissertations

Considerable progress has been made in understanding the miscibility and morphology of polymer nanocomposites (PNCs). However, to date, there is little understood concerning the modification of segmental mobility at the polymer-nanoparticle interface, which due to prevalence of interfaces in PNCs, will predominately control the viscoelastic and mechanical properties of these materials.

In this dissertation, static and dynamic experimental techniques are combined to identify the specific parameters controlling the modification of segmental dynamics at the polymer-nanoparticle interface in the model system of poly(2-vinyl pyridine)/silica nanocomposites. In general, the experimental results clearly demonstrate that the segmental dynamics at the polymer-nanoparticle interface are …

Morphological And Material Effects In Van Der Waals Interactions, Jaime C. Hopkins

Doctoral Dissertations

Van der Waals (vdW) interactions influence a variety of mesoscale phenomena, such as surface adhesion, friction, and colloid stability, and play increasingly important roles as science seeks to design systems on increasingly smaller length scales. Using the full Lifshitz continuum formulation, this thesis investigates the effects of system materials, shapes, and configurations and presents open-source software to accurately calculate vdW interactions. In the Lifshitz formulation, the microscopic composition of a material is represented by its bulk dielectric response. Small changes in a dielectric response can result in substantial variations in the strength of vdW interactions. However, the relationship between these …

Designing Active Granular Squares, Christopher C. Olson

Masters Theses

The goal of this thesis has been to find a means of i) designing an active square particle, and ii) continuously varying its degree of activity with the objective of understanding the effects of activity on the various phases of granular matter. The motivations, results and limitations of our methods of creating active particles are discussed in this thesis. The applicability of a stochastic model based on the Langevin equation in 2D as well as implications for future experiments are also discussed.

Classical Transport In Disordered Systems, Antonios Papaioannou

Dissertations, Theses, and Capstone Projects

This thesis reports on the manifestation of structural disorder on molecular transport and it consists of two parts. Part I discusses the relations between classical transport and the underlying structural complexity of the system. Both types of molecular diffusion, namely Gaussian and non-Gaussian are presented and the relevant time regimes are discussed. In addition the concept of structural universality is introduced and connected with the diffusion metrics. One of the most robust techniques for measuring molecular mean square displacements is magnetic resonance. This method requires encoding and subsequently reading out after an experimentally controlled time, a phase ϕ to the …

Model For The Electrolysis Of Water And Its Use For Optimization, Roger Lascorz, Javier E. Hasbun Dr

Georgia Journal of Science

The goal of this research was to study the optimization of the electrolysis of water both theoretically and experimentally. For accuracy, 3 hr experiments were made with measurements recorded every 15 min. The results show that a better model than the classical one is needed for water electrolysis. A new model that fits experimental data better is proposed. The results of this new model not only predict hydrogen production in electrolysis of water better, but show a way to predict gas production of any liquid as well as what voltage to use to optimize it.

Dynamics Of Discs In A Nematic Liquid Crystal, Alena Antipova

Electronic Thesis and Dissertation Repository

In this thesis, a new way of simulating a two-way coupling between a liquid crystal and an immersed object is proposed. It can be used for objects of various geometries and can be expanded to be used for an object of any geometry. Additionally, a simple yet effective model was suggested for calculations of transmitted light through a nematic liquid crystal sample. This model allowed us to clarify the behavior of a ferromagnetic disc in a nematic liquid crystal observed in experiments and incorrectly interpreted at that time.

Our simulations have demonstrated the following: in the absence of external forces …

Spontaneous Parametric Down Conversion Of Photons Through Β-Barium Borate, Luke Horowitz

Physics

An apparatus for detecting pairs of entangled 405nm photons that have undergone Spontaneous Parametric Down Conversion through β-Barium Borate is described. By using avalanche photo-diodes to detect the low-intensity converted beam and a coincidence module to register coincident photons, it is possible to create an apparatus than can be used to perform quantum information experiments under a budget appropriate for an undergraduate physics lab.

Simulation Of Heterogeneous Colloidal Particles Immersed In Liquid Crystals, Setarehalsadat Changizrezaei

Electronic Thesis and Dissertation Repository

This thesis describes an investigation of interactions between colloidal particles immersed in a liquid crystal. The presence of colloidal particles in the liquid crystal distorts the director field distorted from its uniform orientation. These elastic distortions produce topological defects around the particles, which induce anisotropic interactions between them, and these anisotropic interactions can be used to manufacture non-closed packed colloidal crystals, such as diamond lattices, which are interesting in photonic applications. First, different types of liquid crystals, the mathematical tools to describe the anisotropic nature of liquid crystals, the Landau-de Gennes free-energy model to investigate the particle’s interaction, and different …

Structure Of Sheared And Rotating Turbulence: Multiscale Statistics Of Lagrangian And Eulerian Accelerations And Passive Scalar Dynamics, Frank G. Jacobitz, Kai Schneider, Wouter J. T. Bos, Marie Farge

School of Engineering: Faculty Scholarship

The acceleration statistics of sheared and rotating homogeneous turbulence are studied using direct numerical simulation results. The statistical properties of Lagrangian and Eulerian accelerations are considered together with the influence of the rotation to shear ratio, as well as the scale dependence of their statistics. The probability density functions (pdfs) of both Lagrangian and Eulerian accelerations show a strong and similar dependence on the rotation to shear ratio. The variance and flatness of both accelerations are analyzed and the extreme values of the Eulerian acceleration are observed to be above those of the Lagrangian acceleration. For strong rotation it is …

Event Generator Tunes Obtained From Underlying Event And Multiparton Scattering Measurements, Cms Collaboration, Ekaterina Cms Avdeeva, Kenneth A. Bloom, S. Bose, Daniel Claes, Aaron Dominguez, Caleb Fangmeier, Rebeca Gonzalez Suarez, Rami Kamalieddin, J. Keller, D. Knowlton, Ilya Kravchenko, F. Meier, Jose Monroy, F. Ratnikov, J. E. Siado, Gregory Snow

Kenneth Bloom Publications

New sets of parameters (“tunes”) for the underlying-event (UE) modelling of the PYTHIA8, PYTHIA6 and HERWIG++ MonteCarlo event generators are constructed using different parton distribution functions. Combined fits to CMS UE proton–proton (pp) data at √s = 7 TeV and to UE proton–antiproton (pp) data from the CDF experiment at lower √s, are used to study the UE models and constrain their parameters, providing thereby improved predictions for proton–proton collisions at 13 TeV. In addition, it is investigated whether the values of the parameters obtained from fits to UE observables are consistent with the values determined from fitting observables sensitive …

The Global Stability Of The Solution To The Morse Potential In A Catastrophic Regime, Weerapat Pittayakanchit

HMC Senior Theses

Swarms of animals exhibit aggregations whose behavior is a challenge for mathematicians to understand. We analyze this behavior numerically and analytically by using the pairwise interaction model known as the Morse potential. Our goal is to prove the global stability of the candidate local minimizer in 1D found in A Primer of Swarm Equilibria. Using the calculus of variations and eigenvalues analysis, we conclude that the candidate local minimizer is a global minimum with respect to all solution smaller than its support. In addition, we manage to extend the global stability condition to any solutions whose support has a single …

Postural Responses To Perturbations Of The Vestibular System During Walking In Healthy Young And Older Adults, Jung Hung Chien

Theses & Dissertations

It has been shown that approximate one-third of US adults aged 40 years and older (69 million US citizens) have some type of vestibular problems. These declining abilities of the vestibular system affect quality of life. Difficulties in performing daily activities (dressing, bathing, getting in and out of the bed and etc.) have been highly correlated to loss of balance due to vestibular disorders. The exact number of people affected by vestibular disorders is still difficult to quantify. This might be because symptoms are difficult to describe and differences exist in the qualifying criteria within and across studies. Thus, it …

The Effect Of Composition And Architecture On Polymer Behavior In Homopolymer Blends And Inter-Filament Bonding In 3d Printed Models, Edward Roy Duranty

Doctoral Dissertations

This dissertation presents work that increases our understanding of the effects of composition and architecture on copolymer structure and dynamics and how they affect material diffusion between filaments in a 3D printed model. Copolymers are polymer chains made up of at least two different monomers. The ordering and arrangement of the two monomer species within a copolymer can have drastic effects on the behavior and properties of the copolymer.

The first chapter of this dissertation examines how the copolymer composition affects the structure and dynamics of the chain in a homopolymer blend. This study used a modified Monte Carlo BFM …

Contact Angles And Contact Lines Around Particles At Isotropic And Anisotropic Liquid Interfaces, Nesrin Senbil

Doctoral Dissertations

Liquid interfaces, capillarity and self-assembly of particles at interfaces are important in nature and technology. When a particle is adsorbed to a liquid interface, the contact line of the particle with the liquid interface and the associated contact angle are the crucial parameters that drive assembly of the particles. We looked at how the shape of the liquid interface and the shape of the particle affect the contact angle and the shape of the contact line. We used millimeter-sized PDMS-coated glass spheres and measured the contact angles at isotropic (planar) and anisotropic interfaces (saddle and cylindrical in shape). Anisotropy of …

Emergent Structure Of Multi-Dislocation Ground States In Frustrated Assemblies, Amir Azadi

Doctoral Dissertations

In this dissertation we study the emergent patterns of multi-dislocation ground states in two geometrically related classes of frustrated assemblies, twisted filament bundles and crystalline spherical cap. We discuss the fundamental role played by characteristic patterns of dislocations in restructuring the ordered phase of theses geometrically frustrated systems in the presence of external stresses. Our analysis on the formation of grain boundary scars leads to universal predictions for the features of defect patterns and their underlying energetic principles.

Geometry And Thermodynamics Of Filament Bundles, Isaac Bruss

Doctoral Dissertations

In this dissertation I present a study of the geometry and energetics of bundles composed of flexible cohesive filaments. This is a general class of materials, both biological and artificial, existing across many length scales. The aim of this thesis is to investigate the interdependence between the 2D organization of filaments in a bundle’s cross section, and the 3D structure, with an emphasis on the twisting mode of deformation. First we present a model of filament contacts and interactions, which we employ in numerical simulations to study the connection between the ground state energies of constant-pitch bundles and their interior …

Distributions Of Long-Lived Radioactive Nuclei Provided By Star-Forming Environments, Marco Fatuzzo, Fred Adams

Faculty Scholarship

Radioactive nuclei play an important role in planetary evolution by providing an internal heat source, which affects planetary structure and helps facilitate plate tectonics. A minimum level of nuclear activity is thought to be necessary—but not sufficient—for planets to be habitable. Extending previous work that focused on short-lived nuclei, this paper considers the delivery of long-lived radioactive nuclei to circumstellar disks in star forming regions. Although the long-lived nuclear species are always present, their abundances can be enhanced through multiple mechanisms. Most stars form in embedded cluster environments, so that disks can be enriched directly by intercepting ejecta from supernovae …

Phase Transition And Surface Sublimation Of A Mobile Potts Model, A. Bailly Reyre, H. T. Diep, M. Kaufman

Miron Kaufman

We study in this paper the phase transition in a mobile Potts model by the use of Monte Carlo simulation. The mobile Potts model is related to a diluted Potts model, which is also studied here by a mean-field approximation. We consider a lattice where each site is either vacant or occupied by a q-state Potts spin. The Potts spin can move from one site to a nearby vacant site. In order to study the surface sublimation, we consider a system of Potts spins contained in a recipient with a concentration c defined as the ratio of the number of …

Student Understanding Of The Boltzmann Factor, Trevor I. Smith, Donald B. Mountcastle, John R. Thompson

Physics and Astronomy Faculty Scholarship

We present results of our investigation into student understanding of the physical significance and utility of the Boltzmann factor in several simple models. We identify various justifications, both correct and incorrect, that students use when answering written questions that require application of the Boltzmann factor. Results from written data as well as teaching interviews suggest that many students can neither recognize situations in which the Boltzmann factor is applicable nor articulate the physical significance of the Boltzmann factor as an expression for multiplicity, a fundamental quantity of statistical mechanics. The specific student difficulties seen in the written data led us …

Identifying Student Difficulties With Heat Engines, Entropy, And The Carnot Cycle, Trevor I. Smith, Warren M. Christensen, Donald B. Mountcastle, John R. Thompson

Physics and Astronomy Faculty Scholarship

We report on several specific student difficulties regarding the second law of thermodynamics in the context of heat engines within upper-division undergraduate thermal physics courses. Data come from ungraded written surveys, graded homework assignments, and videotaped classroom observations of tutorial activities. Written data show that students in these courses do not clearly articulate the connection between the Carnot cycle and the second law after lecture instruction. This result is consistent both within and across student populations. Observation data provide evidence for myriad difficulties related to entropy and heat engines, including students’ struggles in reasoning about situations that are physically impossible …

Thermodynamic Effects Of A Local Bell State Projection Interaction In A One-Dimensional Dynamic Spin System, Nickolas H. Pilgram

Physics

No abstract provided.

Mechanics Of Helical And Fabric-Like Mesostructures From Polymer-Nanoparticle Hybrids, Jonathan T. Pham

Doctoral Dissertations

Hierarchical structures developed from nanoscale building blocks offer an excellent opportunity to control properties on all length scales, from the molecular level up to the macroscale. Many beautiful examples in Nature have demonstrated the significance of controlling geometry and mechanics on small length scales to control function on an organism-level, shown by the strength of bones, the toughness of a mollusk's shell, or the gecko's ability to climb walls. Inspired by stunning examples in both Nature and common man-made materials and structures, we assemble polymers and inorganic nanoparticles (NPs) with well-defined surface chemistry into long ribbons and fabric-like networks with …

Global Optimized Isothermal And Nonlinear Models Of Earth’S Standard Atmosphere, Nihad E. Daidzic, Ph.D.,

International Journal of Aviation, Aeronautics, and Aerospace

Both, a global isothermal temperature model and a nonlinear quadratic temperature model of the ISA was developed and presented here. Constrained optimization techniques in conjunction with the least-square-root approximations were used to design best-fit isothermal models for ISA pressure and density changes up to 47 geopotential km for NLPAM, and 86 orthometric km for ISOAM respectively. The mass of the dry atmosphere and the relevant fractional-mass scale heights have been computed utilizing the very accurate eight-point Gauss-Legendre numerical quadrature for both ISOAM and NLPAM. Both, the ISOAM and the NLPAM represent viable alternatives to ISA in many practical applications and …

Gait Transition Dynamics Are Modulated By Experimental Protocol, Mohammad Abdolvahab, Jason Gordon

Mohammad Abdolvahab

No abstract provided.

Temperature Dependent Surface Reconstruction Of Freely Suspended Films Of 4-N-Heptyloxybenzylidene-4-N-Heptylaniline, Daniel E. Martinez Zambrano

Lawrence University Honors Projects

Surfaces of freely suspended thick films of 4-n-heptyloxybenzylidene-4-n-heptylaniline (7O.7) in the crystalline-B phase have been imaged using non-contact mode atomic force microscopy. Steps are observed on the surface of the film with a height of 3.0 +/- 0.1 nm corresponding to the upright molecular length of 7O.7. In addition, we find that the step width varies with temperature between 56 and 59 degrees C. The steps are many times wider than the molecular length, suggesting that the steps are not on the surface but instead originate from edge dislocations in the interior. Using a strain model for liquid crystalline layers …

Time-Frequency Analysis Reveals Pairwise Interactions In Insect Swarms, James G. Puckett, Rui Ni, Nicholas T. Ouellette

Physics and Astronomy Faculty Publications

The macroscopic emergent behavior of social animal groups is a classic example of dynamical self-organization, and is thought to arise from the local interactions between individuals. Determining these interactions from empirical data sets of real animal groups, however, is challenging. Using multicamera imaging and tracking, we studied the motion of individual flying midges in laboratory mating swarms. By performing a time-frequency analysis of the midge trajectories, we show that the midge behavior can be segmented into two distinct modes: one that is independent and composed of low-frequency maneuvers, and one that consists of higher-frequency nearly harmonic oscillations conducted in synchrony …

Application Of Transfer Matrix Method To Secondharmonic Generation In Nonlinear Photonic Bandgap Structures: Oblique Incidence, Han Li

Han Li

No abstract provided.

The Impact Of Imperfect Information On Network Attack, A. Melchionna, Jesus Caloca, S. Squires, T. Antonsen, E. Ott, M. Girvan

McNair Scholars Research Journal

This paper explores the effectiveness of network attack when the attacker has imperfect information about the network. For Erdös-Rényi networks, we observe that dynamical importance and betweenness centrality-based attacks are surprisingly robust to the presence of a moderate amount of imperfect information and are more effective compared with simpler degree-based attacks even at moderate levels of network information error. In contrast, for scale-free networks the effectiveness of attack is much less degraded by a moderate level of information error. Furthermore, in the Erdös-Rényi case the effectiveness of network attack is much more degraded by missing links as compared with the …

Sucralose Destabilization Of Protein Structure, Christina M. Othon

Christina M Othon

Sucralose is a commonly employed artificial sweetener that behaves very differently than its natural disaccharide counterpart, sucrose, in terms of its interaction with biomolecules. The presence of sucralose in solution is found to destabilize the native structure of two model protein systems: the globular protein bovine serum albumin and an enzyme staphylococcal nuclease. The melting temperature of these proteins decreases as a linear function of sucralose concentration. We correlate this destabilization to the increased polarity of the molecule. The strongly polar nature is manifested as a large dielectric friction exerted on the excited-state rotational diffusion of tryptophan using time-resolved fluorescence …