Physics Theses and Dissertations
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Item Continuous Imaginary Time Histories Representing Black Hold Nucleation in Desitter Spacetime(2000) Branoff, Paul M.; Brill, Dieter R.; Physics; Digital Repository at the University of Maryland; University of Maryland (College Park, Md)We address the issues involved in finding and constructing continuous imaginary time histories (CITHs) representing black hold nucleation in a background de Sitter spacetime. Such rates are often calculated by adopting the instanton methods used to calculate ordinary particle-antiparticle production rates in background fields. Unlike the particle production case, there are certain instances of black hole nucleation described by two separate and distinct solution to the Euclidean Einstein's equations, i.e., the instanton is disconnected. Hence, one must justify including such histories in a path integral. We first discuss the existence of continuous imaginary time histories for black hole nucleation in theories consisting of modifications to Einstein's equations. First, we consider adding powers of the Ricci scalar to Einstein-Hilbert gravity with a cosmological constant. When the higher curvature coupling constants are negative, we find continuous instantons describing a background de Sitter to de Sitter transition characterized by a periodic, non-singular scale factor α (τ). Negative coupling constants imply an equivalent theory of Einstein gravity coupled to a negative energy density scalar field. This motivates our exploration of Einstein gravity coupled to Narlikar's negative energy density C-field. We again find a continuous background instanton, but such a solution exists only when small violations of the Hamiltonian constraint are allowed. Because of the unattractive features of the above solutions, we explore how one can construct CITHs by surgically altering the disconnected instanton. In the spirit of the path integral, we claim that one should sum over all possible geometries which can connect the instanton. We limit attention to connections with topology S^3 and S^1 x S^2. We find that the S^3 connection is preferred in the context of "no-boundary" quantum cosmology. However, we believe that the S^1 x S^2 connection may be more preferred for two reasons. First, the S^1 x S^2 connection allows two of its dimensions to-be large, implying via holography, that information from the initial state can "survive" the near-annihilation, recreation process. Second, Planck sized perturbations on the S^2 portion of the connection give rise to more histories over which to sum in the path integral.Item SCANNING TUNNELING MICROSCOPY / SPECTROSCOPY STUDIES OF BINARY ORGANIC FILMS(2009) Jin, Wei; Reutt-Robey, Janice E; Chemical Physics; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)Multi-component organic molecular films have seen increasing applications in photovoltaic technologies and other organic electronic applications. These applications have been based upon assumptions regarding film structure and electronic properties. This thesis provides an increased understanding of factors that control structure in binary molecular films and begins to establish structure-electronic property relations. In this thesis, three technologically relevant "donor-acceptor" systems are studied with variable temperature STM/STS: pentacene (Pn):C60, zinc phthalocyanine (ZnPc): C60 and ZnPc: perfluorinated zinc phthalocyanine (F16ZnPc). These three model systems provide a systematic exploration of the impact of molecular shape and molecular band offset on morphology-electronic relations in thin film heterostructures. For Pn:C60, I show how domain size and architecture are controlled by composition and film processing conditions. Sequential deposition of pentacene, followed by C60, yields films that range from nanophase-separated, to co-crystalline phases, to a templated structure. These distinct structures are selectively produced from distinct pentacene phases which are controlled via pentacene coverage. For the ZnPc:C60 system, the shape of ZnPc and the lattice mismatch between ZnPc and C60 are quite different from the Pn:C60 films. Nonetheless, ZnPc:C60 films also yield chemical morphologies that can be similarly controlled from phase separated, to co-crystalline phases, to templated structures. In both of these binary films, I exploit relative differences in the component cohesive energies to control phase selection. In bilayer films of both systems, a common structural element of stress-induced defects is also observed. In ZnPc:F16ZnPc, I explore two components with similar shapes and cohesive energies while retaining molecular band offsets comparable to Pn:C60. In this shape-matched system, a checkerboard ZnPc:F16ZnPc arrangement stabilized by hydrogen bonds readily forms. This supramolecular structure introduces a new hybridization state close to the Fermi Level, yielding electronic properties distinct from the component phases. Through investigations of these three model systems, I have developed an understanding the control of chemical morphology along the donor-acceptor interface and the way this morphology influences electronic transport.Item Dispersion of ion gyrocenters in models of anisotropic plasma turbulence(2009) Gustafson, Kyle Bergin; Dorland, William D; Physics; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)Turbulent dispersion of ion gyrocenters in a magnetized plasma is studied in the context of a stochastic Hamiltonian transport model and nonlinear, self-consistent gyrokinetic simulations. The Hamiltonian model consists of a superposition of drift waves derived from the linearized Hasegawa-Mima equation and a zonal shear flow perpendicular to the density gradient. Finite Larmor radius (FLR) effects are included. Because there is no particle transport in the direction of the density gradient, the focus is on transport parallel to the shear flow. The prescribed flow produces strongly asymmetric non-Gaussian probability distribution functions (PDFs) of particle displacements, as was previously known. For kρ=0, where k is the characteristic wavelength of the flow and ρ is the thermal Larmor radius, a transition is observed in the scaling of the second moment of particle displacements. The transition separates nearly ballistic superdiffusive dispersion from weaker superdiffusion at later times. FLR effects eliminate this transition. Important features of the PDFs of displacements are reproduced accurately with a fractional diffusion model. The gyroaveraged ExB drift dispersion of a sample of tracer ions is also examined in a two-dimensional, nonlinear, self-consistent gyrokinetic particle-in-cell (PIC) simulation. Turbulence in the simulation is driven by a density gradient and magnetic curvature, resulting in the unstable ρ scale kinetic entropy mode. The dependence of dispersion in both the axial and radial directions is characterized by displacement and velocity increment distributions. The strength of the density gradient is varied, using the local approximation, in three separate trials. A filtering procedure is used to separate trajectories according to whether they were caught in an eddy during a set observation time. Axial displacements are compared to results from the Hasegawa-Mima model. Superdiffusion and ballistic transport are found, depending on filtering and strength of the gradient. The radial dispersion of particles, as measured by the variance of tracer displacements, is diffusive. The dependence of the running diffusion coefficient on ρ for each value of the density gradient is considered.Item Numerical studies on new techniques for gravitational wave extraction and binary black hole simulations(2009) Pazos, Enrique; Tiglio, Manuel; Physics; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)This dissertation presents numerical studies of gravitational waves produced by black holes in two scenarios: perturbations of a single black hole, and the collision of a binary pair. Their detection plays a crucial roll in further testing General Relativity and opens a whole new field of observational astronomy. First, a technique called Cauchy--perturbative matching is revisited in one dimension through the use of new numerical methods, such as high order finite difference operators, constraint-preserving boundary conditions and, most important, a multi-domain decomposition (also referred to as multi-patch, or multi-block approach). These methods are then used to numerically solve the fully non-linear three-dimensional Einstein vacuum equations representing a non-rotating distorted black hole. In combination with a generalization of the Regge-Wheeler-Zerilli formalism, we quantify the effect of the background choice in the wave extraction techniques. It is found that a systematic error is introduced at finite distances. Furthermore, such error is found to be larger than those due to numerical discretization. Subsequently, the first simulations ever of binary black holes with a finite-difference multi-domain approach are presented. The case is one in which the black holes orbit for about twelve cycles before merging. The salient features of this multi-domain approach are: i) the complexity of the problem scales linearly with the size of the computational domain, ii) excellent scaling, in both weak and strong senses, for several thousand processors. As a next step, binary black hole simulations from inspiral to merger and ringdown are performed using a new technique, turduckening, and a standard finite difference, adaptive mesh-refinement code. The computed gravitational waveforms are compared to those obtained through evolution of the same exact initial configuration but with a pseudo-spectral collocation code. Both the gravitational waves extracted at finite locations and their extrapolated values to null infinity are compared. Finally, a numerical study of generic second order perturbations of Schwarzschild black holes is presented using a new gauge invariant high order perturbative formalism. A study of the self-coupling of first order modes and the resulting radiated energy, in particular its dependence on the type of initial perturbation, is detailed.Item Photon Pair Production from a Hot Atomic Ensemble in the Diamond Configuration(2009) Willis, Richard Thomas; Rolston, Steven; Physics; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)This thesis discusses four-wave mixing (4WM) in a warm ensemble of rubidium using the diamond configuration level structure. Both classical 4WM and non- classical photon-pair production are investigated. Quantum information science has spawned a great amount of experimental work on the interaction of light with collective modes of excitation in atomic ensem- bles. Plans to build quantum networks and quantum repeaters with atom ensembles take advantage of nonlinear interactions to produce and store non-classical states of light. These technologies will require photon sources that not only generate non- classical light, but also resonant, narrow band light. Here we investigate a system which could be used as such a source. We take advantage of the 4WM interaction in a warm ensemble of Rubidium atoms. Our scheme utilizes the diamond energy level configuration which, in ru- bidium, allows for correlated pairs at telecommunications wavelengths. We start by examining the properties of classical 4WM in the system. We measure the reso- nance structure and see that it can be understood in terms of velocity class selective resonant enhancement and power splitting effects. The efficiency of the process is low and limited by linear absorption of the pumps. Our observations agree with a semi-classical Maxwell-Bloch theoretical treatment. Next we observe pair generation by spontaneous 4WM from the warm ensem- ble. The temporal profile of the cross-correlation function (CCF) for the photons depends on pump-laser power and detuning. This allows us to produce biphotons with controllable spectra. A simple quantum optical theoretical treatment based on linear filtering gives qualitative agreement with the data. We show that the photon pairs are polarization entangled, clearly violating Bell's Inequality. A perturbative quantum optical treatment predicts the polariza- tion state of the pairs and agrees with our measurements. We analyze the photon statistics of the source and find the largest violation of the two beam Cauchy-Schwarz inequality from a warm atomic source yet. We cast the system as a heralded sin- gle photon source at telecommunications wavelengths and see that it is competitive with other systems in terms of spectral brightness.Item Measurement of the Electric Form Factor of the Neutron at High Momentum Transfer(2009) Miller, Jonathan Andrew; Beise, Elizabeth J; Physics; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)The electric form factor of the neutron, $G_{E}^{n}$, provides key understanding of the structure of one of the basic building blocks of visible matter in the universe. Recent interest in this quantity is the result of the improved quality of data provided by double polarization experiments, which have substantially improved in the last decade. This thesis presents precision measurements of $G_{E}^{n}$ by the E02-013 collaboration at $Q^{2}$ of 1.7, 2.5, and 3.5 GeV$^{2}$. This measurement used a double polarization technique, a highly polarized $^{3}$He target, a polarized electron beam, a large acceptance spectrometer to detect the scattered electrons, and a large neutron detector to detect the recoiling hadrons in the reaction $^{3}\vec{\mathrm{He}}(\vec{e},e'n)$. These measurements will be compared to a variety of models of the nucleon's internal structure, as well as used to extract individual contributions of the up and down quarks to the nucleon form factors.Item DENSITY FUNCTIONAL CALCULATIONS OF BACKBONE 15N CHEMICAL SHIELDINGS IN PEPTIDES AND PROTEINS(2009) Cai, Ling; Fushman, David; Kosov, Daniel S; Chemical Physics; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)In this dissertation, we describe computational and theoretical study of backbone 15N chemical shieldings in peptides and proteins. Comprehensive density functional calculations have been performed on systems of different complexity, ranging from model dipeptides to real proteins and protein complexes. We begin with examining the effects of solvation, hydrogen bonding, backbone conformation, and the side chain identity on 15N chemical shielding in proteins by density functional calculations. N-methylacetamide (NMA) and N-formyl-alanyl-X (with X being one of the 19 naturally occurring amino acids excluding proline) were used as model systems for this purpose. The conducting polarizable continuum model was employed to include the effect of solvent in the calculations. We show that the augmentation of the polarizable continuum model with the explicit water molecules in the first solvation shell has a significant influence on isotropic 15N chemical shift but not as much on the chemical shift anisotropy. The difference in the isotropic chemical shift between the standard &beta-sheet and standard &alpha-helical conformations ranges from 0.8 ppm to 6.2 ppm depending on the residue type, with the mean of 2.7 ppm. This is in good agreement with the experimental chemical shifts averaged over a database of 36 proteins containing >6100 amino acid residues. The orientation of the 15N chemical shielding tensor as well as its anisotropy and asymmetry are also in the range of values experimentally observed for peptides and proteins. Having applied density functional calculation successfully to model peptides, we develop a computationally efficient methodology to include most of the important effects in the calculation of chemical shieldings of backbone 15N in a protein. We present the application to selected &alpha-helical and &beta-sheet residues of protein G. The role of long-range intra-protein electrostatic interactions by comparing models with different complexity in vacuum and in charge field is analyzed. We show that the dipole moment of the &alpha-helix can cause significant deshielding of 15N; therefore, it needs to be considered when calculating 15N chemical shielding. We emphasize the importance of including interactions with the side chains that are close in space when the charged form for ionizable side chains is adopted in the calculation. We also illustrate how the ionization state of these side chains can affect the chemical shielding tensor elements. For &alpha-helical residues, chemical shielding calculations using a 8-residue fragment model in vacuum and adopting the charged form of ionizable side chains yield a generally good agreement with experimental data. We also performed computational modeling of the chemical shift perturbations occurring upon protein-protein or protein-ligand binding. We show that the chemical shift perturbations in ubiquitin upon dimer formation can be explained qualitatively through computation. This dissertation hence demonstrates that quantum chemical calculations can be successfully used to obtain a fundamental understanding of the relationship between chemical shielding and the surrounding protein environment for the elusive case of 15N and therefore enhance the role of 15N chemical shift measurements in the analysis of protein structure and dynamics.Item EXPLORATION OF NOVEL METHODS FOR THE FABRICATION AND CHARACTERIZATION OF ORGANIC FIELD-EFFECT TRANSISTORS AND EXAMINATION OF FACTORS INFLUENCING OFET PERFORMANCE(2009) Southard, Adrian Edward; Fuhrer, Michael S.; Chemical Physics; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)This thesis explores novel methods for fabricating organic field effect transistors (OFETs) and characterizing OFET devices. Transfer printing is a promising process for fabricating organic thin-film devices. In this work, a transfer-printing process is developed for the polymer organic semiconductor P3HT. Pre-patterned P3HT is printed onto different dielectrics such as PMMA, polystyrene and polycarbonate. The P3HT layer is spun on a smooth silicon interface made hydrophobic by treatment with octyltrichlorosilane, which functions as a release layer. This method has distinct advantages over standard OFET fabrication methods in that 1) the active layer can be pre-patterned, 2) the solvent for the P3HT need not be compatible with the target substrate, and 3) the electrical contact formed mimics the properties of top contacts but with the spatial resolution of bottom contacts. Transparent, conducting films of carbon nanotubes (CNTs) are prepared by airbrushing, and characterized optically and electronically. OFETs with CNT films as source and drain electrodes are fabricated using various patterning techniques, and the organic/CNT contact resistance is characterized. CNT films make transparent, flexible electrodes with contact resistance comparable to that found for Au bottom-contacted P3HT transistors and comparable to CNT-film bottom-contacted pentacene transistors with CNTs deposited by other less flexible methods. A transparent OFET is demonstrated using transfer printing for the assembly of an organic semiconductor (pentacene), CNT film source, drain, and gate electrodes, and polymer gate dielectric and substrate. The dependence of the conductance and mobility in pentacene OFETs on temperature, gate voltage, and source-drain electric field is studied. The data are analyzed by extending a multiple trapping and release model to account for lowering of the energy required to excite carriers into the valence band (Poole-Frenkel effect). The temperature-dependent conductivity shows activated behavior, and the activation energy is lowered roughly linearly with the square-root of electric field, as expected for the Poole-Frenkel effect. The gate voltage dependence of the activation energy is used to extract the trap density of states, in good agreement with other measurements in the literature.Item STEPS ON VICINAL SURFACES: DENSITY-FUNCTIONAL THEORY CALCULATIONS AND TRANSCENDING MINIMAL STATISTICAL-MECHANICAL MODELS(2009) Sathiyanarayanan, Rajesh; Einstein, Theodore L; Physics; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)Using both density-functional theory calculations and Monte Carlo simulations, we compute various key parameters that are used to model steps on vicinal surfaces. In the first part, we discuss the importance of multi-site interactions (trios and quartos) in the lattice-gas characterization of adatom interactions. Using density-functional theory calculations, we show that multi-site interactions with substantial contributions from direct interactions are sensitive to adatom relaxations. Such sensitivity to adatom relaxations complicates the lattice-gas approach to modeling overlayer systems. Our results show that a careful consideration of relaxation effects is required to make connections with experiments. In the second part, we use both density-functional theory calculations and kinetic Monte Carlo simulations to identify the impurity atom responsible for growth instabilities on Cu vicinals. In addition to that, we also show that a small quantity of codeposited impurities significantly alters the growth behavior. Our results indicate that growth morphologies could be controlled through the codeposition of an appropriate impurity. Hence, impurities could play a crucial role in nanostructuring of surfaces. Step configurations have fruitfully been related to the worldlines of spinless fermions in one dimension. However, in addition to the realistic no-crossing condition, the fermion picture imposes a more restrictive non-touching condition. in the third part of this thesis, we use Metropolis Monte Carlo method to study the effects of loosening this non-touching condition on the resulting TWDs. Our results show that allowing step touching leads to an effective attraction in the step-step interaction strength measurements. We show that this effective attraction can be incorporated into the fermion picture as a finite-size effect.Item TYPE I COLLAGEN HOMOTRIMERS; THEIR ROLE IN COLLAGEN FIBRIL FORMATION AND TISSUE REMODELING(2009) Han, Sejin; Losert, Wolfgang; Physics; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)Formation and remodeling of type I collagen fibril networks are paradigms of biopolymer self-assembly, yet many of their aspects remain poorly understood. Type I collagen is the most abundant vertebrate protein which self assembles into fibrils and hierarchical fibril network structures, forming scaffolds of bone, skin, tendons and other tissues. The normal isoform of type I collagen is a heterotrimer of two &alpha1(I) and one &alpha2(I) chains, but homotrimers of three &alpha1(I) chains have been reported, e.g., in cancer and fibrosis. Despite their importance in various disorders, very little is known about potential effects of the type I collagen homotrimers on self-assembly, physical properties, and remodeling of collagen fibrils and fibril networks. Thus, we selected characterization of these effects and understanding the underlying physical mechanisms as the topic of the present thesis. Some of our most important findings were: (i) different nucleation mechanism and morphology in homotrimer fibrils compared to the normal heterotrimers fibrils; (ii) segregation of the homo- and heterotrimers within fibrils; (iii) increased bending rigidity of homotrimer fibrils; and (iv) homotrimer resistance to cleavage by enzymes responsible for fibril degradation and remodeling due to increased triple helix stability at the cleavage site. The corresponding in vitro experiments and theoretical analysis of the results suggested drastically different physics of the fibril networks composed of the homo/heterotrimer mixtures and pointed to a potential role of these physics in various disorders, e.g., in cancer and fibrosis pathology.