Alumni Dissertations and Theses

 
 

Alumni Dissertations and Theses

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  • 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.

  • 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.

  • TIME RESOLVED OPTICAL STUDIES OF SPIN AND QUASIPARTICLE DYNAMICS IN FERROMAGNETIC THIN FILMS AND SUPERCONDUCTORS

    Author:
    YU GONG
    Year of Dissertation:
    2013
    Program:
    Physics
    Advisor:
    Yuhang Ren
    Abstract:

    This thesis presents the studies of spin and quasiparticle dynamics in ferromagnetic thin films and iron based superconductors by ferromagnetic resonance (FMR) and time-resolved pump-probe optical techniques. First, the FMR spectroscopies were applied to study the spin dynamics both in frequency and time domains for the epitaxially grown Fe/GaAs thin films and FeCoB/Cr/FeCoB multilayer structures. In the single layer Fe/GaAs thin films, magnetization precessions were studied to characterize the magnetic dynamical parameters. Our results show that the magnetic crystalline anisotropy is dominative and the magnetic damping is strongly dependent on the in-plane magnetic field orientations. In FeCoB/Cr/FeCoB multilayer films, both the acoustic and the optical spin wave modes were identified in the FMR spectra. We reveal that the adjacent magnetic layers in the trilayer structures are antiferromagnetic coupled with an effective interlayer coupling constant Jeff. The magnetic dynamical parameters can be accurately optimized by the interlayer coupling constant Jeff. Second, we employed the time-resolved pump-probe magneto-optical Kerr effect (MOKE) spectroscopy to study the spin dynamics in the Fe/GaAs thin films at picosecond time scale. The time-resolved MOKE results were combined with static magnetic hysteresis loops at various time delays to understand the ultrafast demagnetization dynamics. The ultrafast demagnetization process is faster than the time required for the electron-phonon equilibration and therefore the spin-orbital coupling has to be included with the conventional electron thermalization model to understand our results. Moreover, we show that the ultrafast magnetization excitation and reorientation can be coherently controlled by varying the polarization of the pump beam. The magnetization excitation and reorientation are attributed to the laser induced effective magnetic field in the sample. Third, the quasiparticle relaxation dynamics were studied in electron-doped BaFe1.9Ni0.1As2 and BaFe1.85Co0.15As2 superconductors by time-resolved pump-probe optical spectroscopy. Two distinct relaxation components observed in the transient reflectivity spectra are attributed to the quasiparticle recombination in the superconducting state and quasiparticle relaxations from the higher excited band due to the multiband excitation. The results show the multi-gap characteristic in BaFe1.9Ni0.1As2 and BaFe1.85Co0.15As2 superconductors. Moreover, the estimated electron-phonon coupling constant and the Coulomb pseudopotential indicate that the electron-phonon interaction is not large enough to induce the SC transition. A spin mediated pairing mechanism is necessary to understand the SC phase transition in the iron based superconductors.

  • THEORY OF BCS-BEC CROSSOVER IN ULTRACOLD ATOMIC GASES

    Author:
    Yasemin Gurcan
    Year of Dissertation:
    2012
    Program:
    Physics
    Advisor:
    SULTAN CATTO
    Abstract:

    In ultracold atomic fermions, the sign and the magnitude of pairing interactions can be controlled by using the magnetically-tuned Feshbach resonances to achieve a continuos transition between Cooper pairs of dilute fermi gas to BEC of diatomic molecules, which is known as the "BCS-BEC crossover". At present, although several models have been proposed, there is still no exact analytical solution of the many-body problem of BCS-BEC crossover region. The standard BCS mean field theory of superconductivity was used [1-3] to describe the whole crossover resulting a useful approximation. In our studies, we investigated solvable models for the best variational analytical solution for BCS-BEC crossover at T= 0.

  • Planar Waveguide Structures for Post-EDFA Broadband Near Infrared Optical Amplifiers

    Author:
    Islam Hoxha
    Year of Dissertation:
    2014
    Program:
    Physics
    Advisor:
    Vladimir Petricevic
    Abstract:

    This thesis reports on optical gain of up to 5.7 dB from a planar waveguide with core made of tetravalent chromium-doped calcium germanate single crystal.