Alumni Dissertations and Theses

 
 

Alumni Dissertations and Theses

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  • Averaged dynamics of the advection-diffusion equation and applications to ocean flows.

    Author:
    Yauheni Dzedzits
    Year of Dissertation:
    2012
    Program:
    Physics
    Advisor:
    Tobias Schafer
    Abstract:

    This dissertation presents some aspects of an advection-diffusion equation and its applications to physical oceanography. We propose a perturbative scheme of averaging the advection-diffusion equation in the limit of vanishing diffusivity. Under the restriction that the time-dependence of the advective field is completely separable we construct an exact solution of the purely advective part via action-angle coordinates and treat diffusion as a perturbation using Lie transform techniques. The developed method is applied to a regularized vortical flow field which is periodically modulated in time. Numerical simulations of the vortical flow advection in presence of small diffusion are discussed. We present numerical evidence that the spectrum of of the averaged time-independent advection-diffusion operator converges to the spectrum of the operator with fully enabled time dynamics. A formal generalization of the method for three-dimensional time-periodic flows is discussed. We also discuss the importance of advection and diffusion in problems of transport and mixing in complicated dynamical systems, such as hydrodynamical systems, in particular describing ocean currents. We propose a method to visualize and analyze the structure of complex flows using data from HYbrid Coordinate Ocean Model (HYCOM) as an example. We present results of simulations obtained with highly parallel Co-array Fortran code that can be run on modern computing systems that support partitioned global address space (PGAS) programming model.

  • OPTICAL SPECTROSCOPY OF XENON-RELATED DEFECTS IN DIAMOND

    Author:
    Yury Dziashko
    Year of Dissertation:
    2014
    Program:
    Physics
    Advisor:
    Anshel Gorokhovsky
    Abstract:

    The work presents the results of optical studies of Xe-related defect in diamond. This defect is one of a few having narrow zero-phonon line in the near-infrared part of the photo-luminescence spectra. It appears in diamond after Xe+ ion implantation followed by thermal annealing. Given unique physical properties of diamond (hardness, optical transparency in wide spectral range, chemical inertness, high thermal conductivity, low thermal expansion coefficient) and stability of Xe-related center it can be viewed as an potential candidate for the source of single-photons, or as optically manipulated qubit, not unlike nitrogen-vacancy center. However, compared to the latter Xe-related center is not as well understood and it is necessary to gain thorough understanding of its spatial structure, symmetry, electronic states and mechanisms of interaction with the host diamond lattice. This thesis addresses several questions, in regard to Xe-related center: 1) How efficiently this center is formed in the implantation/annealing process; 2) How does it interact with the host lattice to produce both homogeneous and inhomogeneous shape of the 811.7 nm zero-phonon line; and 3) What is the type and nature of transitions responsible for the 811.7 nm zero-phonon line. In answering the first question two methods for measuring the conversion efficiency of any kind of optically active defect have been developed and applied to Xe-related center in diamond. The study of line-broadening mechanisms showed how this center interacts with the strain produced by other neighboring Xe-centers, distributed in a plane-like geometry. Also, interaction with vibrational motions of the diamond lattice localized in the vicinity of the Xe-centers is analyzed and the parameters of this pseudo-local mode are found. Finally, using the effects of optical saturation in photo-luminescence under excitation with Gaussian laser beams it has been shown that 811.7 nm zero-phonon line is due to absorption and emission by circular magnetic dipole. Also, the site symmetry of Xe-related center has been confirmed as trigonal with the threefold axis oriented along <111> direction in the diamond crystal.

  • STRUCTURAL AND DYNAMICAL FEATURES OF PROTEIN P7 FROM BACTERIOPHAGE 12: INSIGHTS INTO A FUNCTIONAL ROLE IN THE CYSTOVIRAL POLYMERASE COMPLEX

    Author:
    Ertan Eryilmaz
    Year of Dissertation:
    2010
    Program:
    Physics
    Advisor:
    Ranajeet Ghose
    Abstract:

    Cystoviruses are a class of enveloped double-stranded RNA viruses that use a multi- protein polymerase complex (PX) to replicate and transcribe the viral genome. The cystoviral PX, that is amenable to in vitro and in vivo manipulation, comprises a unique model system for similar polymerase machinery. Containing three segmented double stranded RNA genome, the cystoviral PX is a simplified model for the polymerase machinery in more complex RNA viruses like reoviruses sharing structural and functional similarities at the level of the constituent proteins. Though the structures of the RNA dependent RNA polymerase (RdRp) and ATPase components of the cystoviral PX are known and their functional behaviors understood to a large extent, no atomic- resolution structural information is available for the major capsid protein P1 that defines the overall structure and symmetry of the viral capsid, and the essential protein P7. Towards obtaining a complete structural and functional understanding of the cystoviral PX, we have obtained the structure of P7 from the cystovirus 12 at a resolution of 1.8 Å. The N-terminal core region (1-129) of P7 forms a novel homodimeric αβ-fold with structural similarities with BRCT domains implicated in multiple protein-protein interactions in DNA repair proteins. Our results combined with the known role of P7 in stabilizing the nucleation complex during capsid assembly hints towards its participation in key protein-protein interactions within the cystoviral PX. Additionally, we have found through solution NMR studies that the C-terminal tail of P7 (130-169) that is essential for virus viability, though highly disordered, contains a nascent helix. We demonstrate through NMR-based titrations, that P7 is capable of interacting with RNA. We find that both the N-terminal core and the dynamic C-terminus tail of P7 play a role in RNA recognition leading to a significant reduction of the degree of disorder in the C-terminal tail. Given the additional role of P7 in maintaining transcriptional fidelity, our data suggest a central biological role for P7/RNA interactions.

  • DE NOVO DESIGN AND ENGINEERING OF FUNCTIONAL METAL AND PORPHYRIN-BINDING PROTEIN DOMAINS

    Author:
    Bernard Everson
    Year of Dissertation:
    2015
    Program:
    Physics
    Advisor:
    Ronald Koder
    Abstract:

    In this work, I describe an approach to the rational, iterative design and characterization of two functional cofactor-binding protein domains. First, a hybrid computational/experimental method was developed with the aim of algorithmically generating a suite of porphyrin-binding protein sequences with minimal mutual sequence information. This method was explored by generating libraries of sequences, which were then expressed and evaluated for function. One successful sequence is shown to bind a variety of porphyrin-like cofactors, and exhibits light- activated electron transfer in mixed hemin:chlorin e6 and hemin:Zn(II)-protoporphyrin IX complexes. These results imply that many sophisticated functions such as cofactor binding and electron transfer require only a very small number of residue positions in a protein sequence to be fixed. Net charge and hydrophobic content are important in determining protein solubility and stability. Accordingly, rational modifications were made to the aforementioned design procedure in order to improve its overall success rate. The effects of these modifications are explored using two `next-generation' sequence libraries, which were separately expressed and evaluated. Particular modifications to these design parameters are demonstrated to effectively double the purification success rate of the procedure. Finally, I describe the redesign of the artificial di-iron protein DF2 into CDM13, a single chain di-Manganese four-helix bundle. CDM13 acts as a functional model of natural manganese catalase, exhibiting a kcat of 0.08s-1 under steady-state conditions. The bound manganese cofactors have a reduction potential of +805 mV vs NHE, which is too high for efficient dismutation of hydrogen peroxide. These results indicate that as a high-potential manganese complex, CDM13 may represent a promising first step toward a polypeptide model of the Oxygen Evolving Complex of the photosynthetic enzyme Photosystem II.

  • Variable Pressure and Temperature NMR Studies of Fuel Cell Polymer Electrolyte Membranes

    Author:
    Jaime Farrington
    Year of Dissertation:
    2010
    Program:
    Physics
    Advisor:
    Steve Greenbaum
    Abstract:

    It was not until the latter half of the 20th century, with the technological developments associated with the space race, that the technical feasibility of the fuel cell was demonstrated. Various fuel cell technologies have emerged in this time period of which Proton Exchange Membrane Fuel Cells (PEMFCs) are of particular interest due to their lower operating temperatures, as compared with other types of fuel cells. Thus, they are ideal for applications such as small portable electronics and transportation. However, there are several challenges facing PEMFC`s such as the development of efficient and durable proton exchange membranes (PEMs). There are several techniques for the characterization of PEMs, One of these techniques is nuclear magnetic resonance (NMR), which has been an important tool in the characterization of ionic motion in liquids and solids. The ionic self-diffusion coefficient is of great importance in understanding the ionic conduction mechanism of electrolytic materials for fuel cells. In hydrated fuel cell membranes, the diffusion coefficient of water molecules also plays a vital role in ionic (protonic) transport. The measurements of the diffusion coefficients are performed by standard NMR methods. These measurements are usually performed as a function of temperature to obtain vital parameters such as activation energies. If an independent thermodynamic parameter such as pressure is employed, additional information about the ion transport process, such as activation volume, may be obtained. Studies of several types of fuel cell membranes based on sulfonated flouoropolymers are presented.

  • The Evolution of and Starburst-AGN Connection in Luminous and Ultraluminous Infrared Galaxies and their Link to Globular Cluster Formation

    Author:
    Stephanie Fiorenza
    Year of Dissertation:
    2014
    Program:
    Physics
    Advisor:
    Charles Liu
    Abstract:

    The evolutionary connection between nuclear starbursts and active galactic nuclei (AGN) in luminous infrared galaxies (LIRGs; 1011o125 Myr) agree with previous results, while those with younger starbursts show a large dispersion in Mstar. I conclude that this is supporting evidence that the star formation histories and timescales at which the IR power sources in U/LIRGs evolve are responsible for the scatter found for the SFR-Mstar relationship. U/LIRGs that form from merging gas-rich disk galaxies could also represent a stage of galaxy evolution involving heavy formation of globular clusters (GCs). It has been suggested that a large number of stellar clusters form during the merging of two gas-rich disk galaxies, leading to open and young massive clusters with the latter likely evolving into GCs. Furthering our understanding of GC formation can uncover the connection between GCs and their host galaxies, which could, at some point during their formation or evolution, be U/LIRGs. To understand GC formation in the context of hierarchical galaxy formation, it is necessary to understand the origin of their abundance patterns. To this effort, I use SDSS spectra from Data Release 8 and 9 to estimate carbon (C) abundances for five GCs by matching synthetic spectra, created with TURBOSPECTRUM using atmospheric parameters derived from the Segue Stellar Parameter Pipeline, with observed spectra at the CH G-band feature. I find large spreads in the C abundances throughout the color magnitude diagrams of the GCs, which serves as evidence for multiple stellar populations, in contrast to standard models of GC formation.

  • Discrimination and Identification of Quantum States

    Author:
    Ulrike Futschik
    Year of Dissertation:
    2010
    Program:
    Physics
    Advisor:
    Janos Bergou
    Abstract:

    Determining the state of a quantum system is an essential step in quantum information processing. While the case of N=2 arbitrary states is well known the extension to N>2 is highly non-trivial. Unambiguous discrimination among N>2 pure states is one of the longest standing unsolved problems in quantum information. We develop a complete geometric picture that encompasses all aspects of the problem: linear independence of the states, positivity of the detection operators, and a graphic method for finding and classifying the optimal solutions. We illustrate it on the example of three states and also show that the problem depends on an invariant combination of the phases of the complex inner products, the Berry phase. For arbitrary inner products and prior probabilities only numerical solutions are possible but the features of the solution are universal, they hold for any value of the Berry phase up to φ=π at which point it greatly simplifies. We, therefore, present the complete analytical solution for the case of vanishing Berry phase. The corresponding optimal failure probability exhibits full permutational symmetry for a large range of the parameters. However, when the parameters have very different values, a second-order symmetry-breaking phase transition takes place: at a particular value of the parameters the optimal failure probability becomes bi-valued: a second, less symmetric solution branches away in a continuous way from the symmetric one which is optimal in the new regime for some set of parameters. We also study some special cases where the inner products of two or all three states coincide but the phase is arbitrary as well as the case of weighted equal probability measurement. The optimum measurement is derived and it is a general measurement (POVM). The generalization of our results to the discrimination of more than three states will discussed in the conclusion. Finally, we address the problem of identifying one probe qudit with one out of N reference qudits. Two strategies, the unambiguous and the minimum error identification, are studied. The reference states are assumed to be pure states and no classical knowledge about them is available. The probe state is guaranteed to match one of the reference states with equal probability. The problem is shown to be equivalent to distinguishing between mixed quantum states. Through the example of three ququartz states the form of the optimal measurement operators is derived for the unambiguous strategy. Using the positivity constraint for the operator of the inconclusive result the optimum success probability is calculated. In the minimum error identification an upper and a lower bound are derived, the latter by using a square-root measurement. Numerical values of the success probability are calculated to which the lower bound compares favorable.

  • Mathematical and Physical Analysis of Pricing Models for Structured Financial Securities

    Author:
    Xin Gao
    Year of Dissertation:
    2012
    Program:
    Physics
    Advisor:
    Brian Schwartz
    Abstract:

    In this thesis, we present an extension of the one-factor Gaussian copula model for pricing collateralized debt obligations (CDOs): Instead of using flat default correlation and rate parameters across the whole portfolio, we use individual correlation coefficients between each reference entity and the market (S&P 500 index) based on 5-year daily stock prices, and we use specific rate parameter for each entity by curve-fitting the default probability term structure. Spreads from this improved model are compared to those obtained from the one-factor Gaussian copula model with flat correlation. Results show that uniform correlation and rate parameters fail to capture that a few or even one single asset can substantially impact the credit quality of the whole portfolio. Heterogeneity of correlations and rate parameters of different reference entities is indispensable for constructing reliable and realistic models for pricing synthetic CDOs. We also introduce analytical solutions to the pricing of both homogeneous and heterogeneous CDOs. We compare these analytical solutions with results obtained from simulation models. Results show very good consistency. At the end, we introduce the analysis of another financial derivative - Securitized Life Settlements (SLSs) and present an analytical solution to the pricing of homogeneous SLSs.

  • INVESTIGATION OF NANOSTRUCTURED ELECTROCATALYSTS AND MASS TRANSPORT PHENOMENA IN POLYMER ELECTROLYTE FUEL CELLS

    Author:
    Gabriel Goenaga
    Year of Dissertation:
    2010
    Program:
    Physics
    Advisor:
    Steven Greenbaum
    Abstract:

    Abstract NVESTIGATION OF NANOSTRUCTURED ELECTROCATALYSTS AND MASS TRANSPORT PHENOMENA IN POLYMER ELECTROLYTE FUEL CELLS by Gabriel A. Goenaga Adviser: Professor Steven Greenbaum Proton exchange membrane (PEM) fuel cells (FC) are promising devices in the search of clean and efficient technologies to reduce the use of fossil fuels. However, their poor performance in dynamic applications and high cost of platinum group metal (PGM) catalysts, have prevented them from becoming an affordable solution. This dissertation comprehend three research projects that study the mass transport phenomena in modified PEMs, the reduction of the amount of PGM catalyst used for oxygen reduction reaction (ORR) and the use of non-PGM catalysts as alternative catalyst to Pt for ORR. Nafion is the most used PEM for FC applications. Nafion proton conductivity is proportional to its degree of hydration, what imposes low temperature operation to maintain appropriate water content. In this research, Nafion composite membranes doped with hydrophilic metal inorganic particles have been studied using pulse field gradient (PFG) nuclear magnetic resonance (NMR). The Nafion composite membranes were found to have higher water uptake, higher water retention, higher water diffusion and, in some cases, lower methanol diffusion (crossover) than the filler free Nafion membrane. The amount of Pt and PGM catalysts supported on carbon used in the electrodes, has a great impact in the PEMFC cost. In particular, it is of high relevance to reduce the amount of Pt in the cathode electrode, in which the sluggish ORR demands four to five times more Pt catalyst than in the anode. In this thesis is shown that the use of aligned carbon nanotubes (ACNTs) as Pt support, allows a more uniform distribution of the Pt nanoparticles, what in addition to their high hydrophobicity and high corrosive resistance, lead to improved mass transport and stability of the membrane electrode assembly (MEA), when compared to a benchmark MEA that uses Pt catalyst supported on carbon black. The improvement was accomplished using less Pt than in the benchmark MEA. Replacing Pt with non-PGM catalyst can lead to an affordable PEMFC. However, finding a non-PGM catalyst with similar ORR performance than Pt has been a challenge for over two decades. In the present work, two novel Co-based non-PGM catalysts have been studied, showing promising preliminary results. Both are 3-D structured materials, a Co containing porous conjugated polymer and a Co imidazolate metal organic framework (MOF). Rotating disk and rotating ring disk electrode experiments show that both materials, present ORR catalytic activity compared to state of the art non-PGM catalyst. A major advantage of this approach is that the 3-D structure can be used as a template for different transition metals or metal alloys (Fe, Ni, Ta) that can potentially be used to improve the ORR catalytic activity.

  • Resonant Photonic Structures for Control of Light-Matter Interaction in Semiconductor Nanostructures

    Author:
    David Goldberg
    Year of Dissertation:
    2012
    Program:
    Physics
    Advisor:
    Vinod Menon
    Abstract:

    In this thesis, the control of light-matter interaction in semiconductor nanostructures was investigated using resonant photonic structures. This study is categorized in two parts: collective phenomena of quantum confined excitons, and quantum dots in microcavity structures. The collective behavior of excitons is studied in a resonant multiple-quantum-well structure. In this system, the quantum-wells are separated by barrier layers such that the distance between excitons of neighboring quantum-wells is half of their resonant wavelength, the so-called Bragg condition. The Bloch modes of the background photonic crystal introduced by the refractive index contrast between the well and barrier layers interact coherently with the ensemble of excitons forming Bloch-polaritons. These Bloch-polaritons are characterized by low-temperature angle resolved spectroscopic measurements. Large changes in reflectance are observed in response to an externally applied electric field due to the system transition between strong and weak coupling regimes. In addition, a system of colloidal quantum-dot clusters were investigated for evidence of superradiant emission by means of time-resolved and steady state photoluminescence spectroscopy. Microcavities incorporating quantum dots in the cavity layer were investigated under low, and high concentration regimes. With low concentrations of quantum dots, spectroscopic measurements reveal the quantum dots emit through the cavity resonance, and power dependent studies show the emission intensity has a linear dependence on pumping fluence, with no reduction in linewidth, resulting from the system being below the gain threshold. However, a similar investigation on a system with a high quantum dot concentration reveal gain occurring at the biexciton energy accompanied by highly directional emission. Systems of coupled-cavities were also studied where features similar to electromagnetically-induced-transparency were observed from spectroscopic measurements. Under specific coupling criteria, the photon field intensity distribution of the system exhibits a bright and a dark cavity. When incorporating quantum dots in the bright cavity, resonant emission is observed. However, when incorporating quantum dots in the dark cavity, only uncoupled emission is observed.