Browsing by Author "Heremans, Jean J."

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    Analysis of B Meson Decays to Three Charged Pions
    Li, Yao (Virginia Tech, 2015-12-23)
    Decays of B mesons to three-body charmless final states probe the properties of the weak interaction through their dependence on the complex quark couplings in the CKM matrix. They also test dynamical models for hadronic B decays. Based on a sample of 772 million BB pairs collected by the Belle experiment, we present a study of direct CP violation in the decay of charged B to three charged pions.
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    Application of Steepest-Entropy-Ascent Quantum Thermodynamics to Solid-State Phenomena
    Yamada, Ryo (Virginia Tech, 2018-11-16)
    Steepest-entropy-ascent quantum thermodynamics (SEAQT) is a mathematical and theoretical framework for intrinsic quantum thermodynamics (IQT), a unified theory of quantum mechanics and thermodynamics. In the theoretical framework, entropy is viewed as a measure of energy load sharing among available energy eigenlevels, and a unique relaxation path of a system from an initial non-equilibrium state to a stable equilibrium is determined from the greatest entropy generation viewpoint. The SEAQT modeling has seen a great development recently. However, the applications have mainly focused on gas phases, where a simple energy eigenstructure (a set of energy eigenlevels) can be constructed from appropriate quantum models by assuming that gas-particles behave independently. The focus of this research is to extend the applicability to solid phases, where interactions between constituent particles play a definitive role in their properties so that an energy eigenstructure becomes quite complicated and intractable from quantum models. To cope with the problem, a highly simplified energy eigenstructure (so-called ``pseudo-eigenstructure") of a condensed matter is constructed using a reduced-order method, where quantum models are replaced by typical solid-state models. The details of the approach are given and the method is applied to make kinetic predictions in various solid-state phenomena: the thermal expansion of silver, the magnetization of iron, and the continuous/discontinuous phase separation and ordering in binary alloys where a pseudo-eigenstructure is constructed using atomic/spin coupled oscillators or a mean-field approximation. In each application, the reliability of the approach is confirmed and the time-evolution processes are tracked from different initial states under varying conditions (including interactions with a heat reservoir and external magnetic field) using the SEAQT equation of motion derived for each specific application. Specifically, the SEAQT framework with a pseudo-eigenstructure successfully predicts: (i) lattice relaxations in any temperature range while accounting explicitly for anharmonic effects, (ii) low-temperature spin relaxations with fundamental descriptions of non-equilibrium temperature and magnetic field strength, and (iii) continuous and discontinuous mechanisms as well as concurrent ordering and phase separation mechanisms during the decomposition of solid-solutions.
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    The Application of Thin Film Ionic Self-assembled Multilayer (ISAM) Nanostructures in Electromechanical Bending Actuators and Micro-fabricated Gas Chromatography (uGC) Devices
    Wang, Dong (Virginia Tech, 2015-01-14)
    Ionic self-assembled multilayer (ISAM) thin film nanostructures, including highly porous and conductive gold nanoparticles (GNP), and highly porous and thermally stable silica nanoparticles (SNP), were fabricated via the layer-by-layer (LbL) self-assembly technique. Their application in ionic polymer-metal composite (IPMC) electromechanical bending actuators and microfabricated gas chromatography (microGC) devices were investigated and significant performance improvements of these devices were achieved. IPMC bending actuators, consisting of an ionic electroactive polymer (iEAP) membrane as backbone, ionic liquids (IL) as electrolyte, and ISAM GNP thin film as porous electrode, were fabricated and investigated. The influences of humidity, conductive network composite (CNC), and IL uptake on the bending performance were examined and discussed. An equivalent circuit model to simulate both the electrical and mechanical responses was also proposed and experimentally verified. Moreover, IPMC actuators made from other newly synthesized iEAP membranes were fabricated and tested. Some of them showed promising performance that was comparable or even better as compared to the ones made from Nafion. LbL fabricated ISAM SNPs thin film coatings were also applied in the microGC devices including micro fabricated thermal preconcentrators (microTPC) and separation columns (microSC) as adsorbent and stationary phase materials, respectively. New fabrication approaches were developed to selectively coat uniform conformal ISAM SNP coatings in these devices with different 3D microstructures. Thus, functionalized microTPCs and microSCs showed good performance, which can be further improved by using the ISAM SNPs coating as a nanotemplate for modifying additional polymer adsorbents or as the anchor sites for incorporating functional molecules for targeting detection.
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    Characterization of electrical conductivity in a zeolitelike material
    Soghomonian, Victoria G.; Heremans, Jean J. (AIP Publishing, 2009-10)
    We present the electrical characterization of a zeolitelike oxo-vanadium arsenate framework. The experimentally obtained electronic and ionic conductivities and their interactions are discussed. Further, we investigate the potential use of electrically conducting zeolitelike materials in electrical energy storage applications, in light of the material's structural and electronic characteristics. (C) 2009 American Institute of Physics. [doi:10.1063/1.3251070]
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    Computational Studies of Polyetherimides: Beyond All-Atom Molecular Dynamics Simulations
    Wen, Chengyuan (Virginia Tech, 2020-01-24)
    Polyetherimides are an important class of engineering thermoplastics used in a broad range of industries and applications because of their high heat resistance and stability, high strength and moduli, excellent electrical properties over a wide range of temperatures and frequencies, good processability, good adhesive properties, and chemical stability. All-atom molecular dynamics (MD) simulation is a useful tool to study polymers, but the accessible length and time scales are limited. In this thesis, we explore several computational methods that go beyond all-atom MD simulations to investigate polyetherimides. First, we have developed a transferable coarse-grained MD model of polyetherimides that captures their mechanical and thermal expansion properties. Our results show that in order to make the model transferable, it is critical to include an entropic correction term in the coarse-grained force field and require the coarse-grained model to capture the thermal expansion property of polyetherimides. Secondly, we have constructed a predictive model of the glass transition temperature (Tg) for polyimides by using machine-learning algorithms to analyze existing data on Tg reported in the literature. The predictive model is validated by comparing its predictions to experimental data not used in the training process of the model. We further demonstrate that the diffusion coefficients of small gas molecules can be quickly computed with all-atom MD simulations and used to determine Tg. Finally, we have developed a Monte Carlo (MC) program to model the polymerization process of branched polyetherimides and to compute their molecular weight distribution for a wide range of systems, including fully reacted, partially reacted, stoichiometric, and nonstoichiometric ones. The MC results are compared to the predictions of the Flory-Stockmayer theory of branched polymers and an excellent agreement is found below the gel point of the system under consideration. Above the gel point, the Flory- Stockmayer theory starts to fail but the MC method can still be used to quickly determine the molecular weight distribution of branched polyetherimides under very general conditions.
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    Design of optical characteristics of ceria nanoparticles for applications including gas sensing and up-conversion
    Shehata, Nader (Virginia Tech, 2012-12-13)
    This thesis investigates the impact of doping on the optical and structural characteristics of cerium oxide (ceria) nanoparticles synthesized using chemical precipitation. The dopants selected are samarium and neodymium, which have positive association energy with oxygen vacancies in the ceria host, and negative association lanthanides, holmium and erbium, as well as two metal dopants, aluminum and iron. Characteristics measured are absorption and fluorescence spectra and the diameter and lattice parameter of ceria. Analysis of the characteristics indicates qualitatively that the dopant controls the O-vacancy concentration and the ratio of the two cerium ionization states: Ce+3 and Ce+4. A novel conclusion is proposed that the negative association lanthanide dopants can act as O-vacancies scavengers in ceria while the O-vacancy concentration increases in ceria doped with positive association lanthanide elements. Doped ceria nanoparticles are evaluated in two applications: dissolved oxygen (DO) sensing and up-conversion. In the first application, ceria doped with either Sm or Nd and ceria doped with aluminum have a strong correlation between the fluorescence quenching with the DO concentration in the aqueous solution in which the ceria nanoparticles are suspended. Stern-Volmer constants (KSV) of doped ceria are found to strongly depend upon the O-vacancy concentration and are larger than some of the fluorescent molecular probes currently used to measure DO. The KSV measured between 25-50oC is found to be significantly less temperature dependent as compared to the constants of commercially-available DO molecular probes. In the second application, up-conversion, ceria nanoparticles doped with erbium and an additional lanthanide, either Sm or Nd, are exposed to IR radiation at 780 nm. Visible emission is only observed after the nanoparticles are calcinated at high temperature, greatly diminishing the concentration of O-vacancies. It is concluded that O-vacancies do not play a dominant role in up-conversion, unlike that drawn for down-conversion, where the fluorescence intensity is strongly correlated with the O-vacancy concentration. Correlations between annealing temperatures, dopant, and dopant concentrations with the power dependence of up-conversion on the pump and the origin of the intensities of the visible emission are presented. These studies show the promise of doped ceria nanoparticles.
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    Development and calibration of NuLat, A new type of neutrino detector
    Ding, Xinjian (Virginia Tech, 2018-04-27)
    Over the past 20 years, the detection of neutrino oscillation has reported a lot of important results. The oscillation phenomenon itself has been well proved by various experiments. Some oscillation parameters has been measured and now in the area of precise determination. On the other hand, some new questions like the possibility of the existence of light sterile neutrinos and unexpected 5 MeV bump were raised during the measurement. The Neutrino Lattice Experiment (NuLat) is a detector based on the Raghavan Optical Lattice (ROL). It should be able to offer a compact design of an effective detector with good mobility. It can be extremely useful in the short baseline reactor neutrino oscillation detection community to resolve several confusing issues. In this thesis, we present the calibration results we got from the first active NuLat detector and show what kind of improvements we need for the next version of the NuLat detector based on these results.
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    Development of an Optical Fiber Biosensor with Nanoscale Self-Assembled Affinity Layer
    Zuo, Ziwei (Virginia Tech, 2014-01-29)
    Optical sensor systems that integrate Long-Period-Gratings (LPG) as the detection arm have been proven to be highly sensitive and reliable in many applications. With increasing public recognition of threats from bacteria-induced diseases and their potential outbreak among densely populated communities, an intrinsic, low-cost biosensor device that can perform quick and precise identification of the infection type is in high demand to respond to such challenging situations and control the damage those diseases could possibly cause. This dissertation describes the development of a biosensor platform that utilizes polymer thin films, known as ionic self-assembled multilayer (ISAM) films, to be the sensitivity- enhancing medium between an LPG fiber and specific, recognition layer. With the aid of cross- linking reactions, monoclonal antibodies (IgG) or DNA probes are immobilized onto the surface of the ISAM-coated fiber, which form the core component of the biosensor. By immersing such biosensor fiber into a sample suspension, the immobilized antibody molecules will bind the specific antigen and capture the target cells or cell fragments onto the surface of the fiber sensor, resulting in increasing the average thickness of the fiber cladding and changing the refractive index of the cladding. This change occurring at the surface of the fiber results in a decrease of optical power emerging from the LPG section of the fiber. By comparing the transmitted optical power before and after applying the sample suspension, we are able to determine whether or not certain bacterial species have attached to the surface of the fiber, and as a consequence, we are able to determine whether or not the solution contains the targeted bacteria. This platform has the potential for detection of a wide range of bacteria types. In our study, we have primarily investigated the sensitivity and specificity of the biosensor to methicillin- resistant Staphlococcus aureus (MRSA). The data we obtained have shown a sensitive threshold at as low as 102 cfu/ml with pure culture samples. A typical MRSA antibody-based biosensor assay with MRSA sample at this concentration has shown optical power reduction of 21.78%. In a detailed study involving twenty-six bacterial strains possessing the PBP2a protein that enables antibiotic resistance and sixteen strains that do not, the biosensor system was able to correctly identify every sample in pure culture samples at concentration of 104 cfu/ml. Further studies have also been conducted on infected mouse tissues and clinical swab samples from human ears, noses, and skin, and in each case, the system was in full agreement with the results of standard culture tests. However, the system is not yet able to correctly distinguish MRSA and non-MRSA infections in clinical swab samples taken from infected patient wounds. It is proposed that nonspecific binding due to insufficient blocking methods is the key issue. Other bacterial strains, such as Brucella and Francisella tularensis have also been studied using a similar biosensor platform with DNA probes and antibodies, respectively, and the outcomes are also promising. The Brucella DNA biosensor is able to reflect the existence of 3 Brucella strains at 100 cfu/ml with an average of 12.2% signal reduction, while negative control samples at 106cfu/ml generate an average signal reduction of -2.1%. Similarly, the F. tularensis antibodies biosensor has shown a 25.6% signal reduction to LVS strain samples at 100 cfu/ml, while for negative control samples at the same concentration, it only produces a signal reduction of 0.05%. In general, this biosensor platform has demonstrated the potential of detecting a wide range of bacteria in a rapid and relatively inexpensive manner.
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    Dual Spin-Cast Thermally Interdiffused Polymeric Photovoltaic Devices
    Kaur, Manpreet (Virginia Tech, 2011-08-04)
    An in depth study of the performance of thermally interdiffused concentration gradient polymer photovoltaic devices is carried out with particular attention to the effect of the thickness and the thermal treatments on the power conversion efficiency, short circuit current, open circuit voltage and other key electrical properties. Bilayer films of sequentially spin-cast donor and acceptor materials are exposed to various heat treatments in order to induce the interdiffusion. The depth profiles show concentration gradients in the donor and acceptor as a result of interdiffusion and these devices show an order of magnitude increase in the device performance compared to the bilayer devices. Dual spin-cast poly (3-octylthiophene-2,5-diyl) (P3OT)- [6,6] phenyl C61 butyric acid methyl ester (PCBM) and poly (3-hexylthiophene-2,5-diyl) (P3HT)-PCBM interdiffused devices are studied in detail by varying the thickness of the donor and acceptor layers as well as the annealing conditions for initial polymer layer and the time and temperature of the interdiffusion process. Auger spectroscopy and X-ray photoelectron spectroscopy along with ion beam milling are used to investigate the concentration gradient formed as a result of the interdiffusion. The sulfur signal present in the P3OT and P3HT backbone is detected to identify the concentration profiles in the P3OT-PCBM and P3HT-PCBM devices. The interdiffusion conditions and thickness of the active layers have been optimized to obtain the highest power conversion efficiency. The best device performance of the P3OT-PCBM interdiffused devices is achieved when the interdiffusion is carried out at 150°C for 20 minutes and the P3OT thickness is maintained at 70 nm and the PCBM thickness at 40-50 nm. The highest efficiency achieved for P3OT-PCBM interdiffused devices is 1.0% under AM1.5G solar simulated spectrum. In order to further increase the efficiency, P3OT is replaced by (P3HT) which has higher hole mobility. P3HT- PCBM based concentration gradient devices show improved device performance over P3OT-PCBM devices. Power conversion efficiency of the order of ~3.0% is obtained for P3HT-PCBM interdiffused devices when the interdiffusion is carried out at 150°C for 20 minutes. For both P3OT:PCBM and P3HT:PCBM devices, the optimum performance occurs when the concentration gradient extends across the entire film and is correlated with an increase in the short circuit current density and fill factor as well as a decrease in the series resistance. The results demonstrate that an interdiffused bilayer fabrication approach is a novel and efficient approach for fabrication of polymer solar cell devices. In addition, porphyrin derivative 5, 10, 15, 20-Tetraphenyl-21H, 23H-porphine zinc (ZnTPP) is studied as a new donor material for organic solar cells. ZnTPP: PCBM blend devices are investigated in detail by varying the weight ratio of the donor and acceptor materials in blend devices. The devices with ZnTPP: PCBM in 1:9 ratios showed the best device performance and the efficiency of the order of 0.2% is achieved under AM1.5G solar simulated conditions. Trimetallic Nitride Tempelated (TNT) endohedral fullerenes are also examined in this thesis as the novel acceptor materials. Bulk heterojunction or blend devices are fabricated with P3HT as the donor material and several TNT endohedral fullerenes as the acceptor material. Y3N@C₈₀PCBH based devices which are annealed both before and after the electrode deposition show improvement in the device performance compared to devices that are only annealed before the electrode deposition. The highest power conversion efficiency achieved for TNT endohedral fullerene devices is only 0.06%, suggesting that substantial additional work must be done to optimize the compatibility of the donor and acceptor as well as the device fabrication parameters.
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    Dynamically Corrected Quantum Control: A Geometrical Framework
    Zeng, Junkai (Virginia Tech, 2019-10-22)
    Implementing high-fidelity quantum control and suppressing the unwanted environmental noise has been one of the essential challenges in developing quantum information technologies. In the past, driving pulse sequences based on Dirac delta functions or square wave functions, such as Hahn spin echo or CPMG, have been developed to dynamically correcting the noise effects. However, implementing these ideal pulses with high fidelity is a challenging task in real experiments. In this thesis, we provide a new and simple method to explore the entire solution space of driving pulse shapes that suppress environmental noise in the evolution of the system. In this method, any single-qubit phase gate that is first-order robust against quasi-static transversal noise corresponds to a closed curve on a two-dimensional plane, and more general first-order robust single-qubit gates correspond to closed three-dimensional space curves. Second-order robust gates correspond to closed curves having the property that their projection onto any two-dimensional planes shall enclose a zero net area. The driving pulse shapes that implement the gates can be determined by the curvature, torsion, and the length of the curve. By utilizing the framework it is possible to obtain globally optimal solutions in pulse shaping in respect of experimental constraints by mapping them into geometrical optimization problems. One such problem we solved is to prove that the fastest possible single-qubit phase gates that are second-order noise-resistant shall be implemented using sign-flipping square functions. Since square waves are not experimentally feasible, we provide a method to smooth these pulses with minimal loss in gate speed while maintaining the robustness, based on the geometrical framework. This framework can also be useful in diagnosing the noise-cancellation properties of pulse shapes generated from numerical methods such as GRAPE. We show that this method for pulse shaping can significantly improve the fidelity of single-qubit gates through numerical simulation.
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    Electrical injection and detection of spin polarization in InSb/ferromagnet nanostructures
    Kim, Yong-Jae (Virginia Tech, 2012-07-30)
    We present studies of the electical detection of spin injection and transport in InSb/CoFe heterostructures. As a narrow gap semiconductor, InSb has a high mobility and strong spin-orbit interaction. Using ferromagnetic CoFe, lateral InSb/CoFe devices are fabricated by semiconductor processing techniques. The saturation magnetizations of various CoFe electrodes with different widths are calculated from Hall measurements in which the fringing fields of the CoFe electrodes are detected. A magnetic model provides reasonable estimation of the saturation magnetization for micrometer scale geometries. The interface magnetoresistance measurements of InSb/CoFe thin film layered structures present a unique peak at low field, having a symmetric behavior in magnetic field with a critical field Hc and a strong temperature dependence. We attribute our signal to a ferromagnetic phase in the InSb induced by spin injection. In a non-local lateral spin valve measurement, we observed the following. Firstly, Hc of the lateral spin valve signals is identical to Hc of interface magnetoresistance signals. Secondly, the non-local lateral spin valve signals are strongly dependent on temperature, which is also a unique characteristic magnetoresistance. Thirdly, the signals are tunable in response to an applied injector bias. Lastly, the signals are dependent on the exact interfaces. Based on these observations, the detected signals may be considered as spin current signals. The Hall and magnetoresistance signals are measured locally and non-locally in InSb/CoFe Hall devices. The non-local magnetoresistance signals exhibit asymmetric behavior in applied magnetic field which are considered as signatures of spin phenomena. The non-local Hall signals present switching behavior with the CoFe magnetization switching at the coercive field. The non-local Hall signals in a perpendicular field show Hc, similarly seen in non-local lateral spin valves. Inverse spin Hall effect measurements with tilted magnetic fields show an in-plane magnetic field dependence in non-local type Hall signal and a perpendicular magnetic field dependence in the local Hall measurement. We have found that the signal can have its origin in a spin current from our observation of Hc and hysteresis in the magnetization traces. As yet, the spin current transport mechanism is unknown.
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    Electrically conducting microporous frameworks
    (United States Patent and Trademark Office, 2014-10-07)
    Electrically conducting vanadium arsenate or vanadium phosphate materials are described. The materials include a vanadium arsenate or vanadium phosphate framework structure about organic template and water molecules which may be removed to leave a microporous structure. The three-dimensional vanadium framework may provide electronic conductivity, while the extra-framework constituents may provide ionic conductivity.
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    Electronic and quantum phase coherence properties of bismuth thin films
    Rudolph, M.; Heremans, Jean J. (AIP Publishing, 2012-06)
    We present a method to deposit bulk-like Bi films by thermal evaporation and study the electrical, quantum coherence, and physical properties. A two stage growth procedure was found to optimize the film properties, with an initial wetting layer deposited at lower temperature followed by an active layer at higher temperature. Transport measurements indicate carrier properties comparable to molecular beam epitaxial films and display weak-antilocalization, from which the quantum phase coherence lengths are deduced. A 76 nm film is found to optimally exhibit both bulk-like Bi characteristics and the 2-dimensional quantum coherence properties desired for Bi-based quantum devices. (C) 2012 American Institute of Physics. [http://dx.doi.org/10.1063/1.4729035]
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    Electronic Transport in Highly Mismatched InAs Films on GaAs
    Zhang, Yao (Virginia Tech, 2013-12-09)
    Electrical properties of Si- and Mg-doped InAs epitaxial layers grown by MOCVD were studied by performing magneto-transport measurements at different temperatures, from 300 K down to 1.2 K. The longitudinal magnetoresistance and Hall effect indicate a three-band system existing in n-type (p-type) InAs, which consists of the surface accumulation (inversion) layer, the bulk electron (hole) layer, and the nucleation layer. Therefore, a classical parabolic background in magnetoresistance due to multi-carrier occurs at low fields. With the magnetic field being further applied, a linear magnetoresistance caused by inhomogeneities is revealed. At liquid helium temperature, the Shubnikov-de Haas magneto-oscillations are also observed. These transport characterizations provide a means of analyzing the band structure at the InAs surface. In a set of n-type InAs epilayers with Si doped at different levels, the bulk electron density increases as the doping level increases. The increased ionized impurities lead to lower electron mobilities due to more Coulomb scatterings. For all the n-type InAs films, except the two active layers (surface and the bulk), the nucleation layer contributes to the film conductivity as well with an electron density of ~ 5 x 10¹⁷ cm⁻³ and a mobility of ~ 2000 cm²}/Vs. In a cooldown process, the electron density of each layer slightly and monotonically decreases whereas the mobility experiences a maximum from the competition between phonon scatterings and Coulomb scatterings. The phonon scattering overwhelms the Coulomb scatting at high temperatures, but declines as temperature decreases, thus the mobility increases. Around 100 K, the temperature-independent ionized impurity scattering becomes comparable with and starts exceeding the phonon scattering, as temperature further lowered, the screening effect of the Coulomb scattering is weakened because of the decreased carrier densities. As a result, the mobility starts dropping. The maximum mobility corresponds to a minimum resistance, which explains the non-trivial temperature dependence of the resistance in the cooldown history. For the p-type InAs film, the doping with Mg in the course of MOCVD growth allows us to obtain a large hole density and a low mobility at 300 K. At low temperatures, holes are frozen out, and a strong negative magnetoresistance with a dip at 0 field are observed, which is the antilocalization signal from accumulation electrons. This is a strong technique to probe the surface quantum states and derive the phase coherence length and the spin flip length of surface electrons.
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    Enzymatic Characterization of N-Acetyl-1-D-myo-inosityl-2-amino-2-deoxy-alpha-D-glucopyranoside Deacetylase (MshB)
    Huang, Xinyi (Virginia Tech, 2013-06-06)
    Mycobacterium species, which contain the causative agent for human tuberculosis (TB), produce inositol derivatives including mycothiol (MSH).  MSH is a unique and dominant cytosolic thiol that protects mycobacterial pathogens against the damaging effects of reactive oxygen species and is involved in antibiotic detoxification.  Therefore, MSH is considered a potential drug target.  The deacetylase MshB catalyzes the committed step in MSH biosynthesis by converting N-acetyl-1-D-myo-inosityl-2-amino-2-deoxy-alpha-D-glucopyranoside (GlcNAc-Ins) to 1-D-myo-inosityl-2-amino-2-deoxy-alpha-D-glucopyranoside (GlcN-Ins).  In this dissertation, we present detailed functional analysis of MshB.  Our work has shown that MshB is activated by divalent metal ions that can switch between Zn2+ and Fe2+ depending on environmental conditions, including  metal ion availability and oxidative conditions.  MshB employs a general acid-base catalyst mechanism wherein the Asp15 functions as a general base to activate the metal-bound water nucleophile for attack of the carbonyl carbon on substrate.  Proton-transfer from a general acid catalyst facilitates breakdown of the tetrahedral intermediate and release of products.  A dynamic tyrosine was identified that regulates access to the active site and participates in catalysis by stabilizing the oxyanion intermediate.  Molecular docking simulations suggest that the GlcNAc moiety on GlcNAc-Ins is stabilized by hydrogen bonding interactions with active site residues, while a hydrophobic stacking interaction between the inositol ring and Met98 also appears to contribute to substrate affinity for MshB.  Additional binding interactions with side chains in a hydrophobic cavity adjacent to the active site were suggested when the docking experiments were carried out with large amidase substrates.  Together the results from this study provide groundwork for the rational design of specific inhibitors against MshB, which may circumvent current challenges with TB treatment.
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    Epitaxial thin films of pyrochlore iridate Bi₂₊ₓIr₂₋ᵧO₇₋δ: structure, defects and transport properties
    Yang, W. C.; Xie, Y. T.; Zhu, W. K.; Park, K.; Chen, A. P.; Losovyj, Y.; Li, Z.; Liu, H. M.; Starr, M.; Acosta, J. A.; Tao, C. G.; Li, N.; Jia, Q. X.; Heremans, Jean J.; Zhang, S. X. (Nature, 2017-08-10)
    While pyrochlore iridate thin films are theoretically predicted to possess a variety of emergent topological properties, experimental verification of these predictions can be obstructed by the challenge in thin film growth. Here we report on the pulsed laser deposition and characterization of thin films of a representative pyrochlore compound Bi₂Ir₂O₇. The films were epitaxially grown on yttriastabilized zirconia substrates and have lattice constants that are a few percent larger than that of the bulk single crystals. The film composition shows a strong dependence on the oxygen partial pressure. Density-functional-theory calculations indicate the existence of BiIr antisite defects, qualitatively consistent with the high Bi: Ir ratio found in the films. Both Ir and Bi have oxidation states that are lower than their nominal values, suggesting the existence of oxygen deficiency. The iridate thin films show a variety of intriguing transport characteristics, including multiple charge carriers, logarithmic dependence of resistance on temperature, antilocalization corrections to conductance due to spin-orbit interactions, and linear positive magnetoresistance.
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    Exact Diagonalization Studies of Strongly Correlated Systems
    Raum, Peter Thomas (Virginia Tech, 2020-01-14)
    In this dissertation, we use exact diagonalization to study a few strongly correlated systems, ranging from the Fermi-Hubbard model to the fractional quantum Hall effect (FQHE). The discussion starts with an overview of strongly correlated systems and what is meant by strongly correlated. Then, we extend cluster perturbation theory (CPT), an economic method for computing the momentum and energy resolved Green's function for Hubbard models to higher order correlation functions, specifically the spin susceptibility. We benchmark our results for the one-dimensional Fermi-Hubbard model at half-filling. In addition we study the FQHE at fillings $nu = 5/2$ for fermions and $nu = 1/2$ for bosons. For the $nu = 5/2$ system we investigate a two-body model that effectively captures the three-body model that generates the Moore-Read Pfaffian state. The Moore-Read Pfaffian wave function pairs composite fermions and is believed to cause the FQHE at $nu = 5/2$. For the $nu = 1/2$ system we estimate the entropy needed to observe Laughlin correlations with cold atoms via an ansatz partition function. We find entropies achieved with conventional cooling techniques are adequate.
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    Examining Topological Insulators and Topological Semimetals Using First Principles Calculations
    Villanova, John William (Virginia Tech, 2018-04-30)
    The importance and promise that topological materials hold has been recently underscored by the award of the Nobel Prize in Physics in 2016 ``for theoretical discoveries of topological phase transitions and topological phases of matter." This dissertation explores the novel qualities and useful topologically protected surface states of topological insulators and semimetals. Topological materials have protected qualities which are not removed by weak perturbations. The manifestations of these qualities in topological insulators are spin-momentum-locked surface states, and in Weyl and Dirac semimetals they are unconventional open surface states (Fermi arcs) with anomalous electrical transport properties. There is great promise in utilizing the topologically protected surface states in electronics of the future, including spintronics, quantum computers, and highly sensitive devices. Physicists and chemists are also interested in the fundamental physics and exotic fermions exhibited in topological materials and in heterostructures including them. Chapter 1 provides an introduction to the concepts and methods of topological band theory. Chapter 2 investigates the spin and spin-orbital texture and electronic structures of the surface states at side surfaces of a topological insulator, Bi2Se3, by using slab models within density functional theory. Two representative, experimentally achieved surfaces are examined, and it is shown that careful consideration of the crystal symmetry is necessary to understand the physics of the surface state Dirac cones at these surfaces. This advances the existing literature by properly taking into account surface relaxation and symmetry beyond what is contained in effective bulk model Hamiltonians. Chapter 3 examines the Fermi arcs of a topological Dirac semimetal (DSM) in the presence of asymmetric charge transfer, of the kind which would be present in heterostructures. Asymmetric charge transfer allows one to accurately identify the projections of Dirac nodes despite the existence of a band gap and to engineer the properties of the Fermi arcs, including spin texture. Chapter 4 investigates the effect of an external magnetic field applied to a DSM. The breaking of time reversal symmetry splits the Dirac nodes into topologically charged Weyl nodes which exhibit Fermi arcs as well as conventionally-closed surface states as one varies the chemical potential.
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    Exchange and superexchange interactions in quantum dot systems
    Deng, Kuangyin (Virginia Tech, 2021-02-10)
    Semiconductor quantum dot systems offer a promising platform for quantum computation. And these quantum computation candidates are normally based on spin or charge properties of electrons. In these systems, we focus on quantum computation based on electron spins since these systems has good scalability, long coherence times, and rapid gate operations. And this thesis focuses on building a theoretical description of quantum dot systems and the link between theory and experiments. In many quantum dot systems, exchange interactions are the primary mechanism used to control spins and generate entanglement. And exchange energies are normally positive, which limits control flexibility. However, recent experiments show that negative exchange interactions can arise in a linear three-dot system when a two-electron double quantum dot is exchange coupled to a larger quantum dot containing on the order of one hundred electrons. The origin of this negative exchange can be traced to the larger quantum dot exhibiting a spin triplet-like rather than singlet-like ground state. Here we show using a microscopic model based on the configuration interaction (CI) method that both triplet-like and singlet-like ground states are realized depending on the number of electrons. In the case of only four electrons, a full CI calculation reveals that triplet-like ground states occur for sufficiently large dots. These results hold for symmetric and asymmetric quantum dots in both Si and GaAs, showing that negative exchange interactions are robust in few-electron double quantum dots and do not require large numbers of electrons. Recent experiments also show the potential to utilize large quantum dots to mediate superexchange interaction and generate entanglement between distant spins. This opens up a possible mechanism for selectively coupling pairs of remote spins in a larger network of quantum dots. Taking advantage of this opportunity requires a deeper understanding of how to control superexchange interactions in these systems. Here, we consider a triple-dot system arranged in linear and triangular geometries. We use CI calculations to investigate the interplay of superexchange and nearest-neighbor exchange interactions as the location, detuning, and electron number of the mediating dot are varied. We show that superexchange processes strongly enhance and increase the range of the net spin-spin exchange as the dots approach a linear configuration. Furthermore, we show that the strength of the exchange interaction depends sensitively on the number of electrons in the mediator. Our results can be used as a guide to assist further experimental efforts towards scaling up to larger, two-dimensional quantum dot arrays.
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    Experimental Measurements by Antilocalization of the Interactions between Two-Dimensional Electron Systems and Magnetic Surface Species
    Zhang, Yao (Virginia Tech, 2014-06-18)
    Low-temperature weak-localization (WL) and antilocalization (AL) magnetotransport measurements are sensitive to electron interference, and thus can be used as a probe of quantum states. The spin-dependent interactions between controllable surface magnetism and itinerant electrons in a non-magnetic host provide insight for spin-based technologies, magnetic data storage and quantum information processing. This dissertation studies two different host systems, an In$_{0.53}$Ga$_{0.47}$As quantum well at a distance from the surface of a heterostructure, and an accumulation layer on an InAs surface. Both the systems are two-dimensional electron systems (2DESs), and possess prominent Rashba spin-orbit interaction caused by structural inversion asymmetry, which meets the prerequisites for AL. The surface local moments influence the surrounding electrons in two ways, increasing their spin-orbit scattering, and inducing magnetic spin-flip scattering, which carries information about magnetic interactions. The two effects modify the AL signals in opposing directions: the spin-flip scattering of electrons shrinks the signal, and requires a close proximity to the species, whereas the increase of spin-orbit scattering broadens and increases the signal. Accordingly, we only observe an increase in spin-orbit scattering in the study of the interactions between ferromagnetic Co$_{0.6}$Fe$_{0.4}$ nanopillars and the relatively distant InGaAs quantum well. With these CoFe nanopillars, a decrease in spin decoherence time is observed, attributed to the spatially varying magnetic field from the local moments. A good agreement between the data and a theoretical calculation suggests that the CoFe nanopillars also generate an appreciable average magnetic field normal to the surface, of value $\sim$ 35 G. We also performed a series of comparative AL measurements to experimentally investigate the interactions and spin-exchange between InAs surface accumulation electrons and local magnetic moments of rare earth ions Sm$^{3+}$, Gd$^{3+}$, Ho$^{3+}$, of transition metal ions Ni$^{2+}$, Co$^{2+}$, and Fe$^{3+}$, and of Ni$^{2+}$-, Co$^{2+}$-, and Fe$^{3+}$-phthalocyanines deposited on the surface. The deposited species generate magnetic scattering with magnitude dependent on their electron configurations and effective moments. Particularly for Fe$^{3+}$, the significant spin-flip scattering due to the outermost 3d shell and the fairly high magnetic moments modifies the AL signal into a WL signal. Experiments indicate a temperature-independent magnetic spin-flip scattering for most of the species except for Ho$^{3+}$ and Co$^{2+}$. Ho$^{3+}$ yields electron spin-flip rates proportional to the square root of temperature, resulting from transitions between closely spaced energy levels of spin-orbit multiplets. In the case of Co$^{2+}$, either a spin crossover or a spin-glass system forms, and hence spin-flip rates transit between two saturation regions as temperature varies. Concerning the spin-orbit scattering rate, we observe an increase for all the species, and the increase is correlated with the effective electric fields produced by the species. In both 2DESs, the inelastic time is inversely proportional to temperature, consistent with phase decoherence via the Nyquist mechanism. Our method provides a controlled way to probe the quantum spin interactions of 2DESs, either in a quantum well, or on the surface of InAs.