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Sample records for accurate electronic structure

  1. Accurate Electron Affinity of Iron and Fine Structures of Negative Iron ions

    PubMed Central

    Chen, Xiaolin; Luo, Zhihong; Li, Jiaming; Ning, Chuangang

    2016-01-01

    Ionization potential (IP) is defined as the amount of energy required to remove the most loosely bound electron of an atom, while electron affinity (EA) is defined as the amount of energy released when an electron is attached to a neutral atom. Both IP and EA are critical for understanding chemical properties of an element. In contrast to accurate IPs and structures of neutral atoms, EAs and structures of negative ions are relatively unexplored, especially for the transition metal anions. Here, we report the accurate EA value of Fe and fine structures of Fe− using the slow electron velocity imaging method. These measurements yield a very accurate EA value of Fe, 1235.93(28) cm−1 or 153.236(34) meV. The fine structures of Fe− were also successfully resolved. The present work provides a reliable benchmark for theoretical calculations, and also paves the way for improving the EA measurements of other transition metal atoms to the sub cm−1 accuracy. PMID:27138292

  2. Accurate Electron Affinity of Iron and Fine Structures of Negative Iron ions.

    PubMed

    Chen, Xiaolin; Luo, Zhihong; Li, Jiaming; Ning, Chuangang

    2016-05-03

    Ionization potential (IP) is defined as the amount of energy required to remove the most loosely bound electron of an atom, while electron affinity (EA) is defined as the amount of energy released when an electron is attached to a neutral atom. Both IP and EA are critical for understanding chemical properties of an element. In contrast to accurate IPs and structures of neutral atoms, EAs and structures of negative ions are relatively unexplored, especially for the transition metal anions. Here, we report the accurate EA value of Fe and fine structures of Fe(-) using the slow electron velocity imaging method. These measurements yield a very accurate EA value of Fe, 1235.93(28) cm(-1) or 153.236(34) meV. The fine structures of Fe(-) were also successfully resolved. The present work provides a reliable benchmark for theoretical calculations, and also paves the way for improving the EA measurements of other transition metal atoms to the sub cm(-1) accuracy.

  3. Accurate macromolecular structures using minimal measurements from X-ray free-electron lasers.

    PubMed

    Hattne, Johan; Echols, Nathaniel; Tran, Rosalie; Kern, Jan; Gildea, Richard J; Brewster, Aaron S; Alonso-Mori, Roberto; Glöckner, Carina; Hellmich, Julia; Laksmono, Hartawan; Sierra, Raymond G; Lassalle-Kaiser, Benedikt; Lampe, Alyssa; Han, Guangye; Gul, Sheraz; DiFiore, Dörte; Milathianaki, Despina; Fry, Alan R; Miahnahri, Alan; White, William E; Schafer, Donald W; Seibert, M Marvin; Koglin, Jason E; Sokaras, Dimosthenis; Weng, Tsu-Chien; Sellberg, Jonas; Latimer, Matthew J; Glatzel, Pieter; Zwart, Petrus H; Grosse-Kunstleve, Ralf W; Bogan, Michael J; Messerschmidt, Marc; Williams, Garth J; Boutet, Sébastien; Messinger, Johannes; Zouni, Athina; Yano, Junko; Bergmann, Uwe; Yachandra, Vittal K; Adams, Paul D; Sauter, Nicholas K

    2014-05-01

    X-ray free-electron laser (XFEL) sources enable the use of crystallography to solve three-dimensional macromolecular structures under native conditions and without radiation damage. Results to date, however, have been limited by the challenge of deriving accurate Bragg intensities from a heterogeneous population of microcrystals, while at the same time modeling the X-ray spectrum and detector geometry. Here we present a computational approach designed to extract meaningful high-resolution signals from fewer diffraction measurements.

  4. Accurate electronic-structure description of Mn complexes: a GGA+U approach

    NASA Astrophysics Data System (ADS)

    Li, Elise Y.; Kulik, Heather; Marzari, Nicola

    2008-03-01

    Conventional density-functional approach often fail in offering an accurate description of the spin-resolved energetics in transition metals complexes. We will focus here on Mn complexes, where many aspects of the molecular structure and the reaction mechanisms are still unresolved - most notably in the oxygen-evolving complex (OEC) of photosystem II and the manganese catalase (MC). We apply a self-consistent GGA + U approach [1], originally designed within the DFT framework for the treatment of strongly correlated materials, to describe the geometry, the electronic and the magnetic properties of various manganese oxide complexes, finding very good agreement with higher-order ab-initio calculations. In particular, the different oxidation states of dinuclear systems containing the [Mn2O2]^n+ (n= 2, 3, 4) core are investigated, in order to mimic the basic face unit of the OEC complex. [1]. H. J. Kulik, M. Cococcioni, D. A. Scherlis, N. Marzari, Phys. Rev. Lett., 2006, 97, 103001

  5. Accurate description of the electronic structure of organic semiconductors by GW methods

    NASA Astrophysics Data System (ADS)

    Marom, Noa

    2017-03-01

    Electronic properties associated with charged excitations, such as the ionization potential (IP), the electron affinity (EA), and the energy level alignment at interfaces, are critical parameters for the performance of organic electronic devices. To computationally design organic semiconductors and functional interfaces with tailored properties for target applications it is necessary to accurately predict these properties from first principles. Many-body perturbation theory is often used for this purpose within the GW approximation, where G is the one particle Green’s function and W is the dynamically screened Coulomb interaction. Here, the formalism of GW methods at different levels of self-consistency is briefly introduced and some recent applications to organic semiconductors and interfaces are reviewed.

  6. Coarse-graining away electronic structure: a rigorous route to accurate condensed phase interaction potentials

    NASA Astrophysics Data System (ADS)

    Knight, Chris; Voth, Gregory A.

    2012-05-01

    The molecular simulation of condensed phase systems with electronic structure methods can be prohibitively expensive if the length and time scales necessary to observe the desired chemical phenomena are too large. One solution is to map the results of a representative electronic structure simulation onto a computationally more efficient model that reproduces the original calculation, while allowing for statistical sampling relevant to the required length and time scales. The statistical mechanical multiscale coarse-graining procedure is one methodology in which a model can be developed by integrating over the subset of fast degrees of freedom to construct a reduced representation of the original system that reproduces thermodynamic, and in some instances dynamic, properties. The coarse-graining away of electronic structure is one application of this general method, wherein the electronic degrees of freedom are integrated out and the full dimensionality of the system is mapped to that of only the nuclei. The forces on the nuclei in this reduced representation are obtained from a variational force-matching procedure applied to the Hellman-Feynman forces of the original full electron + nuclear system. This work discusses the coarse-graining procedure and its application to ab initio molecular dynamics simulations of the aqueous hydroxide ion.

  7. The Dirac equation in electronic structure calculations: Accurate evaluation of DFT predictions for actinides

    SciTech Connect

    Wills, John M; Mattsson, Ann E

    2012-06-06

    Brooks, Johansson, and Skriver, using the LMTO-ASA method and considerable insight, were able to explain many of the ground state properties of the actinides. In the many years since this work was done, electronic structure calculations of increasing sophistication have been applied to actinide elements and compounds, attempting to quantify the applicability of DFT to actinides and actinide compounds and to try to incorporate other methodologies (i.e. DMFT) into DFT calculations. Through these calculations, the limits of both available density functionals and ad hoc methodologies are starting to become clear. However, it has also become clear that approximations used to incorporate relativity are not adequate to provide rigorous tests of the underlying equations of DFT, not to mention ad hoc additions. In this talk, we describe the result of full-potential LMTO calculations for the elemental actinides, comparing results obtained with a full Dirac basis with those obtained from scalar-relativistic bases, with and without variational spin-orbit. This comparison shows that the scalar relativistic treatment of actinides does not have sufficient accuracy to provide a rigorous test of theory and that variational spin-orbit introduces uncontrolled errors in the results of electronic structure calculations on actinide elements.

  8. Accurate electron affinity of V and fine-structure splittings of V- via slow-electron velocity-map imaging

    NASA Astrophysics Data System (ADS)

    Fu, Xiaoxi; Luo, Zhihong; Chen, Xiaolin; Li, Jiaming; Ning, Chuangang

    2016-10-01

    We report the high-resolution photoelectron spectra of negative vanadium ions obtained via the slow-electron velocity-map imaging method. The electron affinity of V was determined to be 4255.9(18) cm-1 or 0.527 66(20) eV. The accuracy was improved by a factor of 60 with regard to the previous measurement. The fine structure of V- was well resolved: 35.9(11) (5D1), 103.8(12) (5D2), 204.17(74) (5D3), and 330.58(40) cm-1 (5D4) above the ground state 5D0, respectively.

  9. Accurate electron affinity of V and fine-structure splittings of V(-) via slow-electron velocity-map imaging.

    PubMed

    Fu, Xiaoxi; Luo, Zhihong; Chen, Xiaolin; Li, Jiaming; Ning, Chuangang

    2016-10-28

    We report the high-resolution photoelectron spectra of negative vanadium ions obtained via the slow-electron velocity-map imaging method. The electron affinity of V was determined to be 4255.9(18) cm(-1) or 0.527 66(20) eV. The accuracy was improved by a factor of 60 with regard to the previous measurement. The fine structure of V(-) was well resolved: 35.9(11) ((5)D1), 103.8(12) ((5)D2), 204.17(74) ((5)D3), and 330.58(40) cm(-1) ((5)D4) above the ground state (5)D0, respectively.

  10. Towards Efficient and Accurate Description of Many-Electron Problems: Developments of Static and Time-Dependent Electronic Structure Methods

    NASA Astrophysics Data System (ADS)

    Ding, Feizhi

    Understanding electronic behavior in molecular and nano-scale systems is fundamental to the development and design of novel technologies and materials for application in a variety of scientific contexts from fundamental research to energy conversion. This dissertation aims to provide insights into this goal by developing novel methods and applications of first-principle electronic structure theory. Specifically, we will present new methods and applications of excited state multi-electron dynamics based on the real-time (RT) time-dependent Hartree-Fock (TDHF) and time-dependent density functional theory (TDDFT) formalism, and new development of the multi-configuration self-consist field theory (MCSCF) for modeling ground-state electronic structure. The RT-TDHF/TDDFT based developments and applications can be categorized into three broad and coherently integrated research areas: (1) modeling of the interaction between moleculars and external electromagnetic perturbations. In this part we will first prove both analytically and numerically the gauge invariance of the TDHF/TDDFT formalisms, then we will present a novel, efficient method for calculating molecular nonlinear optical properties, and last we will study quantum coherent plasmon in metal namowires using RT-TDDFT; (2) modeling of excited-state charge transfer in molecules. In this part, we will investigate the mechanisms of bridge-mediated electron transfer, and then we will introduce a newly developed non-equilibrium quantum/continuum embedding method for studying charge transfer dynamics in solution; (3) developments of first-principles spin-dependent many-electron dynamics. In this part, we will present an ab initio non-relativistic spin dynamics method based on the two-component generalized Hartree-Fock approach, and then we will generalized it to the two-component TDDFT framework and combine it with the Ehrenfest molecular dynamics approach for modeling the interaction between electron spins and nuclear

  11. Spectral Quadrature method for accurate O(N) electronic structure calculations of metals and insulators

    DOE PAGES

    Pratapa, Phanisri P.; Suryanarayana, Phanish; Pask, John E.

    2015-12-02

    We present the Clenshaw–Curtis Spectral Quadrature (SQ) method for real-space O(N) Density Functional Theory (DFT) calculations. In this approach, all quantities of interest are expressed as bilinear forms or sums over bilinear forms, which are then approximated by spatially localized Clenshaw–Curtis quadrature rules. This technique is identically applicable to both insulating and metallic systems, and in conjunction with local reformulation of the electrostatics, enables the O(N) evaluation of the electronic density, energy, and atomic forces. The SQ approach also permits infinite-cell calculations without recourse to Brillouin zone integration or large supercells. We employ a finite difference representation in order tomore » exploit the locality of electronic interactions in real space, enable systematic convergence, and facilitate large-scale parallel implementation. In particular, we derive expressions for the electronic density, total energy, and atomic forces that can be evaluated in O(N) operations. We demonstrate the systematic convergence of energies and forces with respect to quadrature order as well as truncation radius to the exact diagonalization result. In addition, we show convergence with respect to mesh size to established O(N3) planewave results. In conclusion, we establish the efficiency of the proposed approach for high temperature calculations and discuss its particular suitability for large-scale parallel computation.« less

  12. Spectral Quadrature method for accurate O(N) electronic structure calculations of metals and insulators

    NASA Astrophysics Data System (ADS)

    Pratapa, Phanisri P.; Suryanarayana, Phanish; Pask, John E.

    2016-03-01

    We present the Clenshaw-Curtis Spectral Quadrature (SQ) method for real-space O(N) Density Functional Theory (DFT) calculations. In this approach, all quantities of interest are expressed as bilinear forms or sums over bilinear forms, which are then approximated by spatially localized Clenshaw-Curtis quadrature rules. This technique is identically applicable to both insulating and metallic systems, and in conjunction with local reformulation of the electrostatics, enables the O(N) evaluation of the electronic density, energy, and atomic forces. The SQ approach also permits infinite-cell calculations without recourse to Brillouin zone integration or large supercells. We employ a finite difference representation in order to exploit the locality of electronic interactions in real space, enable systematic convergence, and facilitate large-scale parallel implementation. In particular, we derive expressions for the electronic density, total energy, and atomic forces that can be evaluated in O(N) operations. We demonstrate the systematic convergence of energies and forces with respect to quadrature order as well as truncation radius to the exact diagonalization result. In addition, we show convergence with respect to mesh size to established O(N3) planewave results. Finally, we establish the efficiency of the proposed approach for high temperature calculations and discuss its particular suitability for large-scale parallel computation.

  13. Accurate Electronic Structures of Eu-Doped SiAlON Green Phosphor with a Semilocal Exchange-Correlation Potential

    NASA Astrophysics Data System (ADS)

    Yoo, Dong Su; Ryu, Jeong Ho; Lee, Sung-Ho; Cho, Hyun; Chung, Yong-Chae

    2011-06-01

    The crystal structure, electronic structure, and photoluminescence properties of EuxSi6-zAlzOzN8-z (x = 0.01754, z = 0.25) green phosphor were calculated by modified version of the exchange potential proposed by Becke and Johnson [J. Chem. Phys. 124 (2006) 221101]. An interstitially doped Eu atom was found in the atomic channel parallel to the [0001] axis. The additional states originated from the hybridization of Eu 4f and Eu 5d with Si 3p and N 2p. The luminescence properties were analyzed using a quantitative calculation of the energy gap and the wavelength. The calculated emission peak wavelength of Eu from the energy gap between Eu 5d and Eu 4f was 552 nm. Conventional local or semi local density functionals always underestimate the band gap for wide gap semiconductor. In contrast, the calculated results using the semi local potential well agreed with experiment.

  14. Accurate Equilibrium Structures for trans-HEXATRIENE by the Mixed Estimation Method and for the Three Isomers of Octatetraene from Theory; Structural Consequences of Electron Delocalization

    NASA Astrophysics Data System (ADS)

    Craig, Norman C.; Demaison, Jean; Groner, Peter; Rudolph, Heinz Dieter; Vogt, Natalja

    2015-06-01

    An accurate equilibrium structure of trans-hexatriene has been determined by the mixed estimation method with rotational constants from 8 deuterium and carbon isotopologues and high-level quantum chemical calculations. In the mixed estimation method bond parameters are fit concurrently to moments of inertia of various isotopologues and to theoretical bond parameters, each data set carrying appropriate uncertainties. The accuracy of this structure is 0.001 Å and 0.1°. Structures of similar accuracy have been computed for the cis,cis, trans,trans, and cis,trans isomers of octatetraene at the CCSD(T) level with a basis set of wCVQZ(ae) quality adjusted in accord with the experience gained with trans-hexatriene. The structures are compared with butadiene and with cis-hexatriene to show how increasing the length of the chain in polyenes leads to increased blurring of the difference between single and double bonds in the carbon chain. In trans-hexatriene r(“C_1=C_2") = 1.339 Å and r(“C_3=C_4") = 1.346 Å compared to 1.338 Å for the “double" bond in butadiene; r(“C_2-C_3") = 1.449 Å compared to 1.454 Å for the “single" bond in butadiene. “Double" bonds increase in length; “single" bonds decrease in length.

  15. Accurate equilibrium structures for piperidine and cyclohexane.

    PubMed

    Demaison, Jean; Craig, Norman C; Groner, Peter; Écija, Patricia; Cocinero, Emilio J; Lesarri, Alberto; Rudolph, Heinz Dieter

    2015-03-05

    Extended and improved microwave (MW) measurements are reported for the isotopologues of piperidine. New ground state (GS) rotational constants are fitted to MW transitions with quartic centrifugal distortion constants taken from ab initio calculations. Predicate values for the geometric parameters of piperidine and cyclohexane are found from a high level of ab initio theory including adjustments for basis set dependence and for correlation of the core electrons. Equilibrium rotational constants are obtained from GS rotational constants corrected for vibration-rotation interactions and electronic contributions. Equilibrium structures for piperidine and cyclohexane are fitted by the mixed estimation method. In this method, structural parameters are fitted concurrently to predicate parameters (with appropriate uncertainties) and moments of inertia (with uncertainties). The new structures are regarded as being accurate to 0.001 Å and 0.2°. Comparisons are made between bond parameters in equatorial piperidine and cyclohexane. Another interesting result of this study is that a structure determination is an effective way to check the accuracy of the ground state experimental rotational constants.

  16. Accurate prediction of higher-level electronic structure energies for large databases using neural networks, Hartree-Fock energies, and small subsets of the database.

    PubMed

    Malshe, M; Pukrittayakamee, A; Raff, L M; Hagan, M; Bukkapatnam, S; Komanduri, R

    2009-09-28

    A novel method is presented that significantly reduces the computational bottleneck of executing high-level, electronic structure calculations of the energies and their gradients for a large database that adequately samples the configuration space of importance for systems containing more than four atoms that are undergoing multiple, simultaneous reactions in several energetically open channels. The basis of the method is the high-degree of correlation that generally exists between the Hartree-Fock (HF) and higher-level electronic structure energies. It is shown that if the input vector to a neural network (NN) includes both the configuration coordinates and the HF energies of a small subset of the database, MP4(SDQ) energies with the same basis set can be predicted for the entire database using only the HF and MP4(SDQ) energies for the small subset and the HF energies for the remainder of the database. The predictive error is shown to be less than or equal to the NN fitting error if a NN is fitted to the entire database of higher-level electronic structure energies. The general method is applied to the computation of MP4(SDQ) energies of 68,308 configurations that comprise the database for the simultaneous, unimolecular decomposition of vinyl bromide into six different reaction channels. The predictive accuracy of the method is investigated by employing successively smaller subsets of the database to train the NN to predict the MP4(SDQ) energies of the remaining configurations of the database. The results indicate that for this system, the subset can be as small as 8% of the total number of configurations in the database without loss of accuracy beyond that expected if a NN is employed to fit the higher-level energies for the entire database. The utilization of this procedure is shown to save about 78% of the total computational time required for the execution of the MP4(SDQ) calculations. The sampling error involved with selection of the subset is shown to be

  17. Accurate prediction of higher-level electronic structure energies for large databases using neural networks, Hartree-Fock energies, and small subsets of the database

    NASA Astrophysics Data System (ADS)

    Malshe, M.; Pukrittayakamee, A.; Raff, L. M.; Hagan, M.; Bukkapatnam, S.; Komanduri, R.

    2009-09-01

    A novel method is presented that significantly reduces the computational bottleneck of executing high-level, electronic structure calculations of the energies and their gradients for a large database that adequately samples the configuration space of importance for systems containing more than four atoms that are undergoing multiple, simultaneous reactions in several energetically open channels. The basis of the method is the high-degree of correlation that generally exists between the Hartree-Fock (HF) and higher-level electronic structure energies. It is shown that if the input vector to a neural network (NN) includes both the configuration coordinates and the HF energies of a small subset of the database, MP4(SDQ) energies with the same basis set can be predicted for the entire database using only the HF and MP4(SDQ) energies for the small subset and the HF energies for the remainder of the database. The predictive error is shown to be less than or equal to the NN fitting error if a NN is fitted to the entire database of higher-level electronic structure energies. The general method is applied to the computation of MP4(SDQ) energies of 68 308 configurations that comprise the database for the simultaneous, unimolecular decomposition of vinyl bromide into six different reaction channels. The predictive accuracy of the method is investigated by employing successively smaller subsets of the database to train the NN to predict the MP4(SDQ) energies of the remaining configurations of the database. The results indicate that for this system, the subset can be as small as 8% of the total number of configurations in the database without loss of accuracy beyond that expected if a NN is employed to fit the higher-level energies for the entire database. The utilization of this procedure is shown to save about 78% of the total computational time required for the execution of the MP4(SDQ) calculations. The sampling error involved with selection of the subset is shown to be

  18. Electron Microprobe Analysis Techniques for Accurate Measurements of Apatite

    NASA Astrophysics Data System (ADS)

    Goldoff, B. A.; Webster, J. D.; Harlov, D. E.

    2010-12-01

    Apatite [Ca5(PO4)3(F, Cl, OH)] is a ubiquitous accessory mineral in igneous, metamorphic, and sedimentary rocks. The mineral contains halogens and hydroxyl ions, which can provide important constraints on fugacities of volatile components in fluids and other phases in igneous and metamorphic environments in which apatite has equilibrated. Accurate measurements of these components in apatite are therefore necessary. Analyzing apatite by electron microprobe (EMPA), which is a commonly used geochemical analytical technique, has often been found to be problematic and previous studies have identified sources of error. For example, Stormer et al. (1993) demonstrated that the orientation of an apatite grain relative to the incident electron beam could significantly affect the concentration results. In this study, a variety of alternative EMPA operating conditions for apatite analysis were investigated: a range of electron beam settings, count times, crystal grain orientations, and calibration standards were tested. Twenty synthetic anhydrous apatite samples that span the fluorapatite-chlorapatite solid solution series, and whose halogen concentrations were determined by wet chemistry, were analyzed. Accurate measurements of these samples were obtained with many EMPA techniques. One effective method includes setting a static electron beam to 10-15nA, 15kV, and 10 microns in diameter. Additionally, the apatite sample is oriented with the crystal’s c-axis parallel to the slide surface and the count times are moderate. Importantly, the F and Cl EMPA concentrations are in extremely good agreement with the wet-chemical data. We also present EMPA operating conditions and techniques that are problematic and should be avoided. J.C. Stormer, Jr. et al., Am. Mineral. 78 (1993) 641-648.

  19. An Inexpensive and Accurate Tensiometer Using an Electronic Balance

    NASA Astrophysics Data System (ADS)

    Dolz, Manuel; Delegido, Jesús; Hernández, María-Jesús; Pellicer, Julio

    2001-09-01

    A method for measuring surface tension of liquid-air interfaces that consists of a modification of the du Noüy tensiometer is proposed. An electronic balance is used to determine the detachment force with high resolution and the relative displacement ring/plate-liquid surface is carried out by the descent of the liquid-free surface. The procedure familiarizes undergraduate students in applied science and technology with the experimental study of surface tension by means of a simple and accurate method that offers the advantages of sophisticated devices at considerably less cost. The operational aspects that must be taken into account are analyzed: the measuring system and determination of its effective length, measurement of the detachment force, and the relative system-liquid interface displacement rate. To check the accuracy of the proposed tensiometer, measurements of the surface tension of different known liquids have been performed, and good agreement with results reported in the literature was obtained.

  20. Accurate protein crystallography at ultra-high resolution: Valence electron distribution in crambin

    PubMed Central

    Jelsch, Christian; Teeter, Martha M.; Lamzin, Victor; Pichon-Pesme, Virginie; Blessing, Robert H.; Lecomte, Claude

    2000-01-01

    The charge density distribution of a protein has been refined experimentally. Diffraction data for a crambin crystal were measured to ultra-high resolution (0.54 Å) at low temperature by using short-wavelength synchrotron radiation. The crystal structure was refined with a model for charged, nonspherical, multipolar atoms to accurately describe the molecular electron density distribution. The refined parameters agree within 25% with our transferable electron density library derived from accurate single crystal diffraction analyses of several amino acids and small peptides. The resulting electron density maps of redistributed valence electrons (deformation maps) compare quantitatively well with a high-level quantum mechanical calculation performed on a monopeptide. This study provides validation for experimentally derived parameters and a window into charge density analysis of biological macromolecules. PMID:10737790

  1. Accurate protein crystallography at ultra-high resolution: valence electron distribution in crambin.

    PubMed

    Jelsch, C; Teeter, M M; Lamzin, V; Pichon-Pesme, V; Blessing, R H; Lecomte, C

    2000-03-28

    The charge density distribution of a protein has been refined experimentally. Diffraction data for a crambin crystal were measured to ultra-high resolution (0.54 A) at low temperature by using short-wavelength synchrotron radiation. The crystal structure was refined with a model for charged, nonspherical, multipolar atoms to accurately describe the molecular electron density distribution. The refined parameters agree within 25% with our transferable electron density library derived from accurate single crystal diffraction analyses of several amino acids and small peptides. The resulting electron density maps of redistributed valence electrons (deformation maps) compare quantitatively well with a high-level quantum mechanical calculation performed on a monopeptide. This study provides validation for experimentally derived parameters and a window into charge density analysis of biological macromolecules.

  2. Accurate Nanoscale Crystallography in Real-Space Using Scanning Transmission Electron Microscopy.

    PubMed

    Dycus, J Houston; Harris, Joshua S; Sang, Xiahan; Fancher, Chris M; Findlay, Scott D; Oni, Adedapo A; Chan, Tsung-Ta E; Koch, Carl C; Jones, Jacob L; Allen, Leslie J; Irving, Douglas L; LeBeau, James M

    2015-08-01

    Here, we report reproducible and accurate measurement of crystallographic parameters using scanning transmission electron microscopy. This is made possible by removing drift and residual scan distortion. We demonstrate real-space lattice parameter measurements with <0.1% error for complex-layered chalcogenides Bi2Te3, Bi2Se3, and a Bi2Te2.7Se0.3 nanostructured alloy. Pairing the technique with atomic resolution spectroscopy, we connect local structure with chemistry and bonding. Combining these results with density functional theory, we show that the incorporation of Se into Bi2Te3 causes charge redistribution that anomalously increases the van der Waals gap between building blocks of the layered structure. The results show that atomic resolution imaging with electrons can accurately and robustly quantify crystallography at the nanoscale.

  3. Mapping methods for computationally efficient and accurate structural reliability

    NASA Technical Reports Server (NTRS)

    Shiao, Michael C.; Chamis, Christos C.

    1992-01-01

    Mapping methods are developed to improve the accuracy and efficiency of probabilistic structural analyses with coarse finite element meshes. The mapping methods consist of: (1) deterministic structural analyses with fine (convergent) finite element meshes, (2) probabilistic structural analyses with coarse finite element meshes, (3) the relationship between the probabilistic structural responses from the coarse and fine finite element meshes, and (4) a probabilistic mapping. The results show that the scatter of the probabilistic structural responses and structural reliability can be accurately predicted using a coarse finite element model with proper mapping methods. Therefore, large structures can be analyzed probabilistically using finite element methods.

  4. Toward the Accurate Simulation of Two-Dimensional Electronic Spectra

    NASA Astrophysics Data System (ADS)

    Giussani, Angelo; Nenov, Artur; Segarra-Martí, Javier; Jaiswal, Vishal K.; Rivalta, Ivan; Dumont, Elise; Mukamel, Shaul; Garavelli, Marco

    2015-06-01

    Two-dimensional pump-probe electronic spectroscopy is a powerful technique able to provide both high spectral and temporal resolution, allowing the analysis of ultrafast complex reactions occurring via complementary pathways by the identification of decay-specific fingerprints. [1-2] The understanding of the origin of the experimentally recorded signals in a two-dimensional electronic spectrum requires the characterization of the electronic states involved in the electronic transitions photoinduced by the pump/probe pulses in the experiment. Such a goal constitutes a considerable computational challenge, since up to 100 states need to be described, for which state-of-the-art methods as RASSCF and RASPT2 have to be wisely employed. [3] With the present contribution, the main features and potentialities of two-dimensional electronic spectroscopy are presented, together with the machinery in continuous development in our groups in order to compute two-dimensional electronic spectra. The results obtained using different level of theory and simulations are shown, bringing as examples the computed two-dimensional electronic spectra for some specific cases studied. [2-4] [1] Rivalta I, Nenov A, Cerullo G, Mukamel S, Garavelli M, Int. J. Quantum Chem., 2014, 114, 85 [2] Nenov A, Segarra-Martí J, Giussani A, Conti I, Rivalta I, Dumont E, Jaiswal V K, Altavilla S, Mukamel S, Garavelli M, Faraday Discuss. 2015, DOI: 10.1039/C4FD00175C [3] Nenov A, Giussani A, Segarra-Martí J, Jaiswal V K, Rivalta I, Cerullo G, Mukamel S, Garavelli M, J. Chem. Phys. submitted [4] Nenov A, Giussani A, Fingerhut B P, Rivalta I, Dumont E, Mukamel S, Garavelli M, Phys. Chem. Chem. Phys. Submitted [5] Krebs N, Pugliesi I, Hauer J, Riedle E, New J. Phys., 2013,15, 08501

  5. Accurate Cross-section Calculations for Low-Energy Electron-Atom Collisions

    SciTech Connect

    Zatsarinny, Oleg; Bartschat, Klaus

    2011-05-11

    We describe a recently developed fully relativistic B-spline R-matrix method for atomic structure as well as calculations for electron and photon collision with atoms and ions. The method is based on the solution of the many-electron Fock-Dirac equation and allows to employ non-orthogonal sets of atomic orbitals. A B-spline basis is used to generate both the target description and the R-matrix basis functions in the inner region. Employing B-splines of different orders for the large and small components prevents the appearance of spurious states in the spectrum of the Dirac equation. Using term-dependent and thus nonorthogonal sets of one-electron functions enables us to generate accurate and flexible representations of the target states and the scattering function. Our method is based upon the Dirac-Coulomb Hamiltonian and thus may be employed for any complex atom or ion, without the use of phenomenological core potentials. Example results from recent applications of the method for accurate calculations of low-energy electron scattering from noble gases are presented. In most cases we obtained a substantial improvement over results obtained in previous Breit-Pauli R-matrix calculations.

  6. Electron Structure of Francium

    NASA Astrophysics Data System (ADS)

    Koufos, Alexander

    2012-02-01

    This talk presents the first calculations of the electronic structure of francium for the bcc, fcc and hcp structures, using the Augmented Plane Wave (APW) method in its muffin-tin and linearized general potential forms. Both the Local Density Approximation (LDA) and Generalized Gradient Approximation (GGA), were used to calculate the electronic structure and total energy of francium (Fr). The GGA and LDA both found the total energy of the hcp structure slightly below that of the fcc and bcc structure, respectively. This is in agreement with similar results for the other alkali metals using the same methodology. The equilibrium lattice constant, bulk modulus and superconductivity parameters were calculated. We found that under pressures, in the range of 1-5 GPa, Fr could be a superconductor at a critical temperature of about 4K.

  7. Modeling for accurate dimensional scanning electron microscope metrology: then and now.

    PubMed

    Postek, Michael T; Vladár, András E

    2011-01-01

    A review of the evolution of modeling for accurate dimensional scanning electron microscopy is presented with an emphasis on developments in the Monte Carlo technique for modeling the generation of the electrons used for imaging and measurement. The progress of modeling for accurate metrology is discussed through a schematic technology timeline. In addition, a discussion of a future vision for accurate SEM dimensional metrology and the requirements to achieve it are presented.

  8. FragBag, an accurate representation of protein structure, retrieves structural neighbors from the entire PDB quickly and accurately.

    PubMed

    Budowski-Tal, Inbal; Nov, Yuval; Kolodny, Rachel

    2010-02-23

    Fast identification of protein structures that are similar to a specified query structure in the entire Protein Data Bank (PDB) is fundamental in structure and function prediction. We present FragBag: An ultrafast and accurate method for comparing protein structures. We describe a protein structure by the collection of its overlapping short contiguous backbone segments, and discretize this set using a library of fragments. Then, we succinctly represent the protein as a "bags-of-fragments"-a vector that counts the number of occurrences of each fragment-and measure the similarity between two structures by the similarity between their vectors. Our representation has two additional benefits: (i) it can be used to construct an inverted index, for implementing a fast structural search engine of the entire PDB, and (ii) one can specify a structure as a collection of substructures, without combining them into a single structure; this is valuable for structure prediction, when there are reliable predictions only of parts of the protein. We use receiver operating characteristic curve analysis to quantify the success of FragBag in identifying neighbor candidate sets in a dataset of over 2,900 structures. The gold standard is the set of neighbors found by six state of the art structural aligners. Our best FragBag library finds more accurate candidate sets than the three other filter methods: The SGM, PRIDE, and a method by Zotenko et al. More interestingly, FragBag performs on a par with the computationally expensive, yet highly trusted structural aligners STRUCTAL and CE.

  9. A program for accurate solutions of two-electron atoms

    NASA Astrophysics Data System (ADS)

    Edvardsson, Sverker; Åberg, Daniel; Uddholm, Per

    2005-02-01

    We present a comprehensible computer program capable of treating non-relativistic ground and excited states for a two-electron atom having infinite nuclear mass. An iterative approach based on the implicitly restarted Arnoldi method (IRAM) is employed. The Hamiltonian matrix is never explicitly computed. Instead the action of the Hamiltonian operator on discrete pair functions is implemented. The finite difference method is applied and subsequent extrapolations gives the continuous grid result. The program is written in C and is highly optimized. All computations are made in double precision. Despite this relatively low degree of floating point precision (48 digits are not uncommon), the accuracy in the results can reach about 10 significant figures. Both serial and parallel versions are provided. The parallel program is particularly suitable for shared memory machines such as the Sun Starcat series. The serial version is simple to compile and should run on any platform. Program summaryTitle of program: corr2el Catalogue identifier: ADUX Program summary URL:http://cpc.cs.qub.ac.uk/summaries/ADUX Program obtainable from:CPC Program Library, Queen's University of Belfast, N. Ireland Distribution format: tar.gz Computer for which the program is designed and others on which it has been tested: Computers: Sun Fire 15K StarCat, Sun Ultra SPARC III, PC Operating systems or monitors under which the program has been tested: Sun Solaris 9, Linux Programming language used: ANSI C Memory required to execute with typical data: 3 Mwords or more No. bits in a word: 32 No. processors used: arbitrary Has the code been vectorized or parallelized: parallelized Number of lines in distributed program, including test data, etc.:5885 Number of bytes in distributed program, including test data, etc.: 26 199 Nature of physical problem: The Schrödinger equation for two-electron atoms is solved using finite differences. Method of solution: An iterative eigenvalue-solver that requires only

  10. Efficient and accurate calculations on the electronic structure of B-type poly(dG)•poly(dC) DNA by elongation method: First step toward the understanding of the biological properties of aperiodic DNA

    NASA Astrophysics Data System (ADS)

    Orimoto, Yuuichi; Gu, Feng Long; Imamura, Akira; Aoki, Yuriko

    2007-06-01

    Elongation method was applied to determine the electronic structures of B-type poly(dG)•poly(dC) DNA at the ab initio molecular orbital level as a first step toward the calculation of aperiodic DNA. The discrepancy in total energy between the elongation method and a conventional calculation was negligibly small in the order of 10-8hartree/at. for 14 G-C base pair model. The local density of states for 10 G-C base pair model estimated by the elongation method well reproduced the results by the conventional calculation. It was found that the band gap of the whole system is mainly due to the energy difference between the valence band of guanine and the conduction band of cytosine. Moreover, the electron transfer path through stacking G-C base pairs rather than sugar-phosphate backbones has been confirmed by the authors' calculations.

  11. Accurate SHAPE-directed RNA secondary structure modeling, including pseudoknots

    PubMed Central

    Hajdin, Christine E.; Bellaousov, Stanislav; Huggins, Wayne; Leonard, Christopher W.; Mathews, David H.; Weeks, Kevin M.

    2013-01-01

    A pseudoknot forms in an RNA when nucleotides in a loop pair with a region outside the helices that close the loop. Pseudoknots occur relatively rarely in RNA but are highly overrepresented in functionally critical motifs in large catalytic RNAs, in riboswitches, and in regulatory elements of viruses. Pseudoknots are usually excluded from RNA structure prediction algorithms. When included, these pairings are difficult to model accurately, especially in large RNAs, because allowing this structure dramatically increases the number of possible incorrect folds and because it is difficult to search the fold space for an optimal structure. We have developed a concise secondary structure modeling approach that combines SHAPE (selective 2′-hydroxyl acylation analyzed by primer extension) experimental chemical probing information and a simple, but robust, energy model for the entropic cost of single pseudoknot formation. Structures are predicted with iterative refinement, using a dynamic programming algorithm. This melded experimental and thermodynamic energy function predicted the secondary structures and the pseudoknots for a set of 21 challenging RNAs of known structure ranging in size from 34 to 530 nt. On average, 93% of known base pairs were predicted, and all pseudoknots in well-folded RNAs were identified. PMID:23503844

  12. Accurate Classification of RNA Structures Using Topological Fingerprints

    PubMed Central

    Li, Kejie; Gribskov, Michael

    2016-01-01

    While RNAs are well known to possess complex structures, functionally similar RNAs often have little sequence similarity. While the exact size and spacing of base-paired regions vary, functionally similar RNAs have pronounced similarity in the arrangement, or topology, of base-paired stems. Furthermore, predicted RNA structures often lack pseudoknots (a crucial aspect of biological activity), and are only partially correct, or incomplete. A topological approach addresses all of these difficulties. In this work we describe each RNA structure as a graph that can be converted to a topological spectrum (RNA fingerprint). The set of subgraphs in an RNA structure, its RNA fingerprint, can be compared with the fingerprints of other RNA structures to identify and correctly classify functionally related RNAs. Topologically similar RNAs can be identified even when a large fraction, up to 30%, of the stems are omitted, indicating that highly accurate structures are not necessary. We investigate the performance of the RNA fingerprint approach on a set of eight highly curated RNA families, with diverse sizes and functions, containing pseudoknots, and with little sequence similarity–an especially difficult test set. In spite of the difficult test set, the RNA fingerprint approach is very successful (ROC AUC > 0.95). Due to the inclusion of pseudoknots, the RNA fingerprint approach both covers a wider range of possible structures than methods based only on secondary structure, and its tolerance for incomplete structures suggests that it can be applied even to predicted structures. Source code is freely available at https://github.rcac.purdue.edu/mgribsko/XIOS_RNA_fingerprint. PMID:27755571

  13. Using an Educational Electronic Documentation System to Help Nursing Students Accurately Identify Nursing Diagnoses

    ERIC Educational Resources Information Center

    Pobocik, Tamara J.

    2013-01-01

    The use of technology and electronic medical records in healthcare has exponentially increased. This quantitative research project used a pretest/posttest design, and reviewed how an educational electronic documentation system helped nursing students to identify the accurate related to statement of the nursing diagnosis for the patient in the case…

  14. Final Report for "Accurate Numerical Models of the Secondary Electron Yield from Grazing-incidence Collisions".

    SciTech Connect

    Seth A Veitzer

    2008-10-21

    Effects of stray electrons are a main factor limiting performance of many accelerators. Because heavy-ion fusion (HIF) accelerators will operate in regimes of higher current and with walls much closer to the beam than accelerators operating today, stray electrons might have a large, detrimental effect on the performance of an HIF accelerator. A primary source of stray electrons is electrons generated when halo ions strike the beam pipe walls. There is some research on these types of secondary electrons for the HIF community to draw upon, but this work is missing one crucial ingredient: the effect of grazing incidence. The overall goal of this project was to develop the numerical tools necessary to accurately model the effect of grazing incidence on the behavior of halo ions in a HIF accelerator, and further, to provide accurate models of heavy ion stopping powers with applications to ICF, WDM, and HEDP experiments.

  15. A fast but accurate excitonic simulation of the electronic circular dichroism of nucleic acids: how can it be achieved?

    PubMed

    Loco, Daniele; Jurinovich, Sandro; Di Bari, Lorenzo; Mennucci, Benedetta

    2016-01-14

    We present and discuss a simple and fast computational approach to the calculation of electronic circular dichroism spectra of nucleic acids. It is based on a exciton model in which the couplings are obtained in terms of the full transition-charge distributions, as resulting from TDDFT methods applied on the individual nucleobases. We validated the method on two systems, a DNA G-quadruplex and a RNA β-hairpin whose solution structures have been accurately determined by means of NMR. We have shown that the different characteristics of composition and structure of the two systems can lead to quite important differences in the dependence of the accuracy of the simulation on the excitonic parameters. The accurate reproduction of the CD spectra together with their interpretation in terms of the excitonic composition suggest that this method may lend itself as a general computational tool to both predict the spectra of hypothetic structures and define clear relationships between structural and ECD properties.

  16. Accurate model of electron beam profiles with emittance effects for pierce guns

    NASA Astrophysics Data System (ADS)

    Zeng, Peng; Wang, Guangqiang; Wang, Jianguo; Wang, Dongyang; Li, Shuang

    2016-09-01

    Accurate prediction of electron beam profile is one of the key objectives of electron optics, and the basis for design of the practical electron gun. In this paper, an improved model describing electron beam in Pierce gun with both space charge effects and emittance effects is proposed. The theory developed by Cutler and Hines is still applied for the accelerating region of the Pierce gun, while the motion equations of the electron beams in the anode aperture and drift tunnel are improved by modifying electron optics theory with emittance. As a result, a more universal and accurate formula of the focal length of the lens for the electron beam with both effects is derived for the anode aperture with finite dimension, and a modified universal spread curve considering beam emittance is introduced in drift tunnel region. Based on these improved motion equations of the electron beam, beam profiles with space charge effects and emittance effects can be theoretically predicted, which are subsequently approved to agree well with the experimentally measured ones. The developed model here is helpful to design more applicable Pierce guns at high frequencies.

  17. Accurate protein structure modeling using sparse NMR data and homologous structure information.

    PubMed

    Thompson, James M; Sgourakis, Nikolaos G; Liu, Gaohua; Rossi, Paolo; Tang, Yuefeng; Mills, Jeffrey L; Szyperski, Thomas; Montelione, Gaetano T; Baker, David

    2012-06-19

    While information from homologous structures plays a central role in X-ray structure determination by molecular replacement, such information is rarely used in NMR structure determination because it can be incorrect, both locally and globally, when evolutionary relationships are inferred incorrectly or there has been considerable evolutionary structural divergence. Here we describe a method that allows robust modeling of protein structures of up to 225 residues by combining (1)H(N), (13)C, and (15)N backbone and (13)Cβ chemical shift data, distance restraints derived from homologous structures, and a physically realistic all-atom energy function. Accurate models are distinguished from inaccurate models generated using incorrect sequence alignments by requiring that (i) the all-atom energies of models generated using the restraints are lower than models generated in unrestrained calculations and (ii) the low-energy structures converge to within 2.0 Å backbone rmsd over 75% of the protein. Benchmark calculations on known structures and blind targets show that the method can accurately model protein structures, even with very remote homology information, to a backbone rmsd of 1.2-1.9 Å relative to the conventional determined NMR ensembles and of 0.9-1.6 Å relative to X-ray structures for well-defined regions of the protein structures. This approach facilitates the accurate modeling of protein structures using backbone chemical shift data without need for side-chain resonance assignments and extensive analysis of NOESY cross-peak assignments.

  18. Accurate molecular structure and spectroscopic properties for nucleobases: A combined computational - microwave investigation of 2-thiouracil as a case study

    PubMed Central

    Puzzarini, Cristina; Biczysko, Malgorzata; Barone, Vincenzo; Peña, Isabel; Cabezas, Carlos; Alonso, José L.

    2015-01-01

    The computational composite scheme purposely set up for accurately describing the electronic structure and spectroscopic properties of small biomolecules has been applied to the first study of the rotational spectrum of 2-thiouracil. The experimental investigation was made possible thanks to the combination of the laser ablation technique with Fourier Transform Microwave spectrometers. The joint experimental – computational study allowed us to determine accurate molecular structure and spectroscopic properties for the title molecule, but more important, it demonstrates a reliable approach for the accurate investigation of isolated small biomolecules. PMID:24002739

  19. Fast Monte Carlo Electron-Photon Transport Method and Application in Accurate Radiotherapy

    NASA Astrophysics Data System (ADS)

    Hao, Lijuan; Sun, Guangyao; Zheng, Huaqing; Song, Jing; Chen, Zhenping; Li, Gui

    2014-06-01

    Monte Carlo (MC) method is the most accurate computational method for dose calculation, but its wide application on clinical accurate radiotherapy is hindered due to its poor speed of converging and long computation time. In the MC dose calculation research, the main task is to speed up computation while high precision is maintained. The purpose of this paper is to enhance the calculation speed of MC method for electron-photon transport with high precision and ultimately to reduce the accurate radiotherapy dose calculation time based on normal computer to the level of several hours, which meets the requirement of clinical dose verification. Based on the existing Super Monte Carlo Simulation Program (SuperMC), developed by FDS Team, a fast MC method for electron-photon coupled transport was presented with focus on two aspects: firstly, through simplifying and optimizing the physical model of the electron-photon transport, the calculation speed was increased with slightly reduction of calculation accuracy; secondly, using a variety of MC calculation acceleration methods, for example, taking use of obtained information in previous calculations to avoid repeat simulation of particles with identical history; applying proper variance reduction techniques to accelerate MC method convergence rate, etc. The fast MC method was tested by a lot of simple physical models and clinical cases included nasopharyngeal carcinoma, peripheral lung tumor, cervical carcinoma, etc. The result shows that the fast MC method for electron-photon transport was fast enough to meet the requirement of clinical accurate radiotherapy dose verification. Later, the method will be applied to the Accurate/Advanced Radiation Therapy System ARTS as a MC dose verification module.

  20. Conformational energy range of ligands in protein crystal structures: The difficult quest for accurate understanding.

    PubMed

    Peach, Megan L; Cachau, Raul E; Nicklaus, Marc C

    2017-02-24

    In this review, we address a fundamental question: What is the range of conformational energies seen in ligands in protein-ligand crystal structures? This value is important biophysically, for better understanding the protein-ligand binding process; and practically, for providing a parameter to be used in many computational drug design methods such as docking and pharmacophore searches. We synthesize a selection of previously reported conflicting results from computational studies of this issue and conclude that high ligand conformational energies really are present in some crystal structures. The main source of disagreement between different analyses appears to be due to divergent treatments of electrostatics and solvation. At the same time, however, for many ligands, a high conformational energy is in error, due to either crystal structure inaccuracies or incorrect determination of the reference state. Aside from simple chemistry mistakes, we argue that crystal structure error may mainly be because of the heuristic weighting of ligand stereochemical restraints relative to the fit of the structure to the electron density. This problem cannot be fixed with improvements to electron density fitting or with simple ligand geometry checks, though better metrics are needed for evaluating ligand and binding site chemistry in addition to geometry during structure refinement. The ultimate solution for accurately determining ligand conformational energies lies in ultrahigh-resolution crystal structures that can be refined without restraints.

  1. Mapping methods for computationally efficient and accurate structural reliability

    NASA Technical Reports Server (NTRS)

    Shiao, Michael C.; Chamis, Christos C.

    1992-01-01

    Mapping methods are developed to improve the accuracy and efficiency of probabilistic structural analyses with coarse finite element meshes. The mapping methods consist of the following: (1) deterministic structural analyses with fine (convergent) finite element meshes; (2) probabilistic structural analyses with coarse finite element meshes; (3) the relationship between the probabilistic structural responses from the coarse and fine finite element meshes; and (4) a probabilistic mapping. The results show that the scatter in the probabilistic structural responses and structural reliability can be efficiently predicted using a coarse finite element model and proper mapping methods with good accuracy. Therefore, large structures can be efficiently analyzed probabilistically using finite element methods.

  2. Linear Scaling Electronic Structure Methods with Periodic Boundary Conditions

    SciTech Connect

    Gustavo E. Scuseria

    2008-02-08

    The methodological development and computational implementation of linear scaling quantum chemistry methods for the accurate calculation of electronic structure and properties of periodic systems (solids, surfaces, and polymers) and their application to chemical problems of DOE relevance.

  3. Screened exchange hybrid density functional for accurate and efficient structures and interaction energies.

    PubMed

    Brandenburg, Jan Gerit; Caldeweyher, Eike; Grimme, Stefan

    2016-06-21

    We extend the recently introduced PBEh-3c global hybrid density functional [S. Grimme et al., J. Chem. Phys., 2015, 143, 054107] by a screened Fock exchange variant based on the Henderson-Janesko-Scuseria exchange hole model. While the excellent performance of the global hybrid is maintained for small covalently bound molecules, its performance for computed condensed phase mass densities is further improved. Most importantly, a speed up of 30 to 50% can be achieved and especially for small orbital energy gap cases, the method is numerically much more robust. The latter point is important for many applications, e.g., for metal-organic frameworks, organic semiconductors, or protein structures. This enables an accurate density functional based electronic structure calculation of a full DNA helix structure on a single core desktop computer which is presented as an example in addition to comprehensive benchmark results.

  4. Mapping methods for computationally efficient and accurate structural reliability

    NASA Technical Reports Server (NTRS)

    Shiao, Michael C.; Chamis, Christos C.

    1991-01-01

    The influence of mesh coarseness in the structural reliability is evaluated. The objectives are to describe the alternatives and to demonstrate their effectiveness. The results show that special mapping methods can be developed by using: (1) deterministic structural responses from a fine (convergent) finite element mesh; (2) probabilistic distributions of structural responses from a coarse finite element mesh; (3) the relationship between the probabilistic structural responses from the coarse and fine finite element meshes; and (4) probabilistic mapping. The structural responses from different finite element meshes are highly correlated.

  5. New Accurate Oscillator Strengths and Electron Excitation Collision Strengths for N1

    NASA Technical Reports Server (NTRS)

    Tayal, S. S.

    2006-01-01

    The nonorthogonal orbitals technique in a multiconfiguration Hartree-Fock approach is used to calculate oscillator strengths and transition probabilities of N(I) lines. The relativistic effects are allowed by means of Breit-Pauli operators. The length and velocity forms of oscillator strengths show good agreement for most transitions. The B-spline R-matrix with pseudostates approach has been used to calculate electron excitation collision strengths and rates. The nonorthogonal orbitals are used for an accurate description of both target wave functions and the R-matrix basis functions. The 24 spectroscopic bound and autoionizing states together with 15 pseudostates are included in the close-coupling expansion. The collision strengths for transitions between fine-structure levels are calculated by transforming the LS-coupled K-matrices to K-matrices in an intermediate coupling scheme. Thermally averaged collision strengths have been determined by integrating collision strength over a Maxwellian distribution of electron energies over a temperature range suitable for the modeling of astrophysical plasmas. The oscillator strengths and thermally averaged collision strengths are presented for transitions between the fine-structure levels of the 2s(sup 2)p(sup 3) (sup 4)S(sup 0), (sup 2)D(sup 0), (sup 2)P(sup 0), 2s2p(sup 4) (sup 4)P, 2s(sup 2)2p(sup 2)3s (sup 4)P, and (sup 2)P terms and from these levels to the levels of the 2s(sup 2)2p(sup 2)3p (sup 2)S(sup 0), (sup 4)D(sup 0), (sup 4)P(sup 0), (sup 4)S(sup 0), (sup 2)D(sup 0), (sup 2)P(sup 0),2s(sup 2)2p(sup 2)3s(sup 2)D, 2s(sup 2)2p(sup 2)4s(sup 4)P, (sup 2)P, 2s(sup 2)2p(sup 2)3d(sup 2)P, (sup 4)F,(sup 2)F,(sup 4)P, (sup 4)D, and (sup 2)D terms. Thermally averaged collision strengths are tabulated over a temperature range from 500 to 50,000 K.

  6. Accurate NMR structures through minimization of an extended hybrid energy.

    PubMed

    Nilges, Michael; Bernard, Aymeric; Bardiaux, Benjamin; Malliavin, Thérèse; Habeck, Michael; Rieping, Wolfgang

    2008-09-10

    The use of generous distance bounds has been the hallmark of NMR structure determination. However, bounds necessitate the estimation of data quality before the calculation, reduce the information content, introduce human bias, and allow for major errors in the structures. Here, we propose a new rapid structure calculation scheme based on Bayesian analysis. The minimization of an extended energy function, including a new type of distance restraint and a term depending on the data quality, results in an estimation of the data quality in addition to coordinates. This allows for the determination of the optimal weight on the experimental information. The resulting structures are of better quality and closer to the X-ray crystal structure of the same molecule. With the new calculation approach, the analysis of discrepancies from the target distances becomes meaningful. The strategy may be useful in other applications-for example, in homology modeling.

  7. Accurate Structure Parameters for Tunneling Ionization Rates of Gas-Phase Linear Molecules

    NASA Astrophysics Data System (ADS)

    Zhao, Song-Feng; Li, Jian-Ke; Wang, Guo-Li; Li, Peng-Cheng; Zhou, Xiao-Xin

    2017-03-01

    In the molecular Ammosov–Delone–Krainov (MO-ADK) model of Tong et al. [Phys. Rev. A 66 (2002) 033402], the ionization rate depends on the structure parameters of the molecular orbital from which the electron is removed. We determine systematically and tabulate accurate structure parameters of the highest occupied molecular orbital (HOMO) for 123 gas-phase linear molecules by solving time-independent Schrödinger equation with B-spline functions and molecular potentials which are constructed numerically using the modified Leeuwen–Baerends (LBα) model. Supported by National Natural Science Foundation of China under Grant Nos. 11664035, 11674268, 11465016, 11364038, 11364039, the Specialized Research Fund for the Doctoral Program of Higher Education of China under Grant No. 20116203120001 and the Basic Scientific Research Foundation for Institution of Higher Learning of Gansu Province

  8. Fast and accurate automatic structure prediction with HHpred.

    PubMed

    Hildebrand, Andrea; Remmert, Michael; Biegert, Andreas; Söding, Johannes

    2009-01-01

    Automated protein structure prediction is becoming a mainstream tool for biological research. This has been fueled by steady improvements of publicly available automated servers over the last decade, in particular their ability to build good homology models for an increasing number of targets by reliably detecting and aligning more and more remotely homologous templates. Here, we describe the three fully automated versions of the HHpred server that participated in the community-wide blind protein structure prediction competition CASP8. What makes HHpred unique is the combination of usability, short response times (typically under 15 min) and a model accuracy that is competitive with those of the best servers in CASP8.

  9. Fitmunk: improving protein structures by accurate, automatic modeling of side-chain conformations.

    PubMed

    Porebski, Przemyslaw Jerzy; Cymborowski, Marcin; Pasenkiewicz-Gierula, Marta; Minor, Wladek

    2016-02-01

    Improvements in crystallographic hardware and software have allowed automated structure-solution pipelines to approach a near-`one-click' experience for the initial determination of macromolecular structures. However, in many cases the resulting initial model requires a laborious, iterative process of refinement and validation. A new method has been developed for the automatic modeling of side-chain conformations that takes advantage of rotamer-prediction methods in a crystallographic context. The algorithm, which is based on deterministic dead-end elimination (DEE) theory, uses new dense conformer libraries and a hybrid energy function derived from experimental data and prior information about rotamer frequencies to find the optimal conformation of each side chain. In contrast to existing methods, which incorporate the electron-density term into protein-modeling frameworks, the proposed algorithm is designed to take advantage of the highly discriminatory nature of electron-density maps. This method has been implemented in the program Fitmunk, which uses extensive conformational sampling. This improves the accuracy of the modeling and makes it a versatile tool for crystallographic model building, refinement and validation. Fitmunk was extensively tested on over 115 new structures, as well as a subset of 1100 structures from the PDB. It is demonstrated that the ability of Fitmunk to model more than 95% of side chains accurately is beneficial for improving the quality of crystallographic protein models, especially at medium and low resolutions. Fitmunk can be used for model validation of existing structures and as a tool to assess whether side chains are modeled optimally or could be better fitted into electron density. Fitmunk is available as a web service at http://kniahini.med.virginia.edu/fitmunk/server/ or at http://fitmunk.bitbucket.org/.

  10. Fitmunk: improving protein structures by accurate, automatic modeling of side-chain conformations

    PubMed Central

    Porebski, Przemyslaw Jerzy; Cymborowski, Marcin; Pasenkiewicz-Gierula, Marta; Minor, Wladek

    2016-01-01

    Improvements in crystallographic hardware and software have allowed automated structure-solution pipelines to approach a near-‘one-click’ experience for the initial determination of macromolecular structures. However, in many cases the resulting initial model requires a laborious, iterative process of refinement and validation. A new method has been developed for the automatic modeling of side-chain conformations that takes advantage of rotamer-prediction methods in a crystallographic context. The algorithm, which is based on deterministic dead-end elimination (DEE) theory, uses new dense conformer libraries and a hybrid energy function derived from experimental data and prior information about rotamer frequencies to find the optimal conformation of each side chain. In contrast to existing methods, which incorporate the electron-density term into protein-modeling frameworks, the proposed algorithm is designed to take advantage of the highly discriminatory nature of electron-density maps. This method has been implemented in the program Fitmunk, which uses extensive conformational sampling. This improves the accuracy of the modeling and makes it a versatile tool for crystallographic model building, refinement and validation. Fitmunk was extensively tested on over 115 new structures, as well as a subset of 1100 structures from the PDB. It is demonstrated that the ability of Fitmunk to model more than 95% of side chains accurately is beneficial for improving the quality of crystallographic protein models, especially at medium and low resolutions. Fitmunk can be used for model validation of existing structures and as a tool to assess whether side chains are modeled optimally or could be better fitted into electron density. Fitmunk is available as a web service at http://kniahini.med.virginia.edu/fitmunk/server/ or at http://fitmunk.bitbucket.org/. PMID:26894674

  11. Accurate electron densities from the Hiller-Sucher-Feinberg identity applied to constrained wavefunctions

    NASA Astrophysics Data System (ADS)

    Challacombe, Matt; Cioslowski, Jerzy

    When applied to electronic wavefunctions calculated with Gaussian-type basis functions, the Hiller-Sucher-Feinberg (HSF) identity improves the accuracy of the electron density at non-hydrogen nuclei by more than an order of magnitude, yielding approximate electron-nuclear cusps. However, the HSF electron densities at hydrogen nuclei bound to heavy atoms are greatly overestimated. This phenomenon is associated with the asymptotic behaviour of the HSF density, which incorrectly decreases to a constant when the sum of Hellmann-Feynman forces acting on nuclei is finite. A method for constraining variational wavefunctions to yield vanishing Hellmann-Feynman forces is described. Hartree-Fock calculations of the constrained HSF (CHSF) electron densities with the 6-31G, 6-31G**, and 6-311++G** basis sets are reported at the nuclei of various diatomic molecules, and are compared with their corresponding conventional, HSF, and Hartree-Fock limit values. These calculations show that differences between HSF and CHSF densities are minor at nonhydrogen nuclei. Importantly, the calculated HF/6-311++G** CHSF densities are on average three times more accurate than the conventional densities at hydrogen nuclei.

  12. Accurate Electron Densities at Nuclei Using Small Ramp-Gaussian Basis Sets.

    PubMed

    McKemmish, Laura K; Gilbert, Andrew T B

    2015-08-11

    Electron densities at nuclei are difficult to calculate accurately with all-Gaussian basis sets because they lack an electron-nuclear cusp. The newly developed mixed ramp-Gaussian basis sets, such as R-31G, possess electron-nuclear cusps due to the presence of ramp functions in the basis. The R-31G basis set is a general-purpose mixed ramp-Gaussian basis set modeled on the 6-31G basis set. The prediction of electron densities at nuclei using R-31G basis sets for Li-F outperforms Dunning, Pople, and Jensen general purpose all-Gaussian basis sets of triple-ζ quality or lower and the cc-pVQZ basis set. It is of similar quality to the specialized pcJ-0 basis set which was developed with partial decontraction of core functions and extra high exponent s-Gaussians to predict electron density at the nucleus. These results show significant advantages in the properties of mixed ramp-Gaussian basis sets compared to all-Gaussian basis sets.

  13. Is automated electronic surveillance for healthcare-associated infections accurate in the burn unit?

    PubMed

    Venable, Amanda; Dissanaike, Sharmila

    2013-01-01

    As monitoring requirements for healthcare-acquired infection increase, an efficient and accurate method for surveillance has been sought. The authors evaluated the accuracy of electronic surveillance in multiple intensive care unit settings. Data from 500 intensive care unit patients were reviewed to determine the presence of central line-associated blood stream infection (CLABSI) and catheter-associated urinary tract infection (CAUTI). An electronic surveillance report was obtained to determine whether patients had a blood-line nosocomial infection marker or a urine nosocomial infection marker. Manual review was based on Centers for Disease Control and Prevention criteria. An infection preventionist then reviewed all discrepant cases and made a final determination, which was used as the gold standard. Sensitivity, specificity, false-positive rate, and false-negative rate were then calculated for electronic surveillance. In the burn population the sensitivity of electronic surveillance for CAUTI was 66.66%, specificity 96.5%, false-positive rate 3.44%, false-negative rate 33%; and for CLABSI the sensitivity was 100%, specificity 95%, false-positive rate 4.96%, false-negative rate 0%. In the nonburn population the sensitivity for CAUTI was 50%, specificity 97.9%, false-positive rate 2%, and false-negative rate 30%; and for CLABSI sensitivity was 60%, specificity 98.8%, false-positive rate 1%, and false-negative rate 60%. Burn centers may experience a higher false-positive rate for electronic surveillance of CLABSI and CAUTI than other critical care units.

  14. Development and application of accurate analytical models for single active electron potentials

    NASA Astrophysics Data System (ADS)

    Miller, Michelle; Jaron-Becker, Agnieszka; Becker, Andreas

    2015-05-01

    The single active electron (SAE) approximation is a theoretical model frequently employed to study scenarios in which inner-shell electrons may productively be treated as frozen spectators to a physical process of interest, and accurate analytical approximations for these potentials are sought as a useful simulation tool. Density function theory is often used to construct a SAE potential, requiring that a further approximation for the exchange correlation functional be enacted. In this study, we employ the Krieger, Li, and Iafrate (KLI) modification to the optimized-effective-potential (OEP) method to reduce the complexity of the problem to the straightforward solution of a system of linear equations through simple arguments regarding the behavior of the exchange-correlation potential in regions where a single orbital dominates. We employ this method for the solution of atomic and molecular potentials, and use the resultant curve to devise a systematic construction for highly accurate and useful analytical approximations for several systems. Supported by the U.S. Department of Energy (Grant No. DE-FG02-09ER16103), and the U.S. National Science Foundation (Graduate Research Fellowship, Grants No. PHY-1125844 and No. PHY-1068706).

  15. Novel method for accurate g measurements in electron-spin resonance

    NASA Astrophysics Data System (ADS)

    Stesmans, A.; Van Gorp, G.

    1989-09-01

    In high-accuracy work, electron-spin-resonance (ESR) g values are generally determined by calibrating against the accurately known proton nuclear magnetic resonance (NMR). For that method—based on leakage of microwave energy out of the ESR cavity—a convenient technique is presented to obtain accurate g values without needing conscientious precalibration procedures or cumbersome constructions. As main advantages, the method allows the easy monitoring of the positioning of the ESR and NMR samples while they are mounted as close as physically realizable at all time during their simultaneous resonances. Relative accuracies on g of ≊2×10-6 are easily achieved for ESR signals of peak-to-peak width ΔBpp≲0.3 G. The method has been applied to calibrate the g value of conduction electrons of small Li particles embedded in LiF—a frequently used g marker—resulting in gLiF: Li=2.002 293±0.000 002.

  16. Theoretical electronic structure of structurally modified graphene

    NASA Astrophysics Data System (ADS)

    Dvorak, Marc David

    Graphene has emerged as a promising replacement for silicon in next-generation electronics and optoelectronic devices. If graphene is to be used in semiconductor devices, however, it must acquire an electronic band gap. Numerous approaches have been proposed to control the band gap of graphene, including the periodic patterning of defects. However, the mechanism for band gap opening and the associated physics in graphene patterned with defects remain unclear. Using both analytic theory and first-principles calculations, we show that periodic patterning of defects on graphene can open a large and tunable band gap, induce strong absorption peaks at optical wavelengths, and host a giant band gap quantum spin Hall phase. First, a geometric rule is analytically derived for the arrangements of defects that open a band gap in graphene, with one ninth of all possible patterns opening a band gap. Next, we perform ab-initio density functional calculations to compare the effects of structural vacancies, hexagonal BN dopants, and passivants on the electronic structure of graphene. Qualitatively, these three types of structural defects behave the same, with only slight differences in their resulting band structures. By adjusting the shape of structural defects, we show how to move the Dirac cones in reciprocal space in accordance with the tight-binding model for the anisotropic honeycomb lattice, while the fundamental mechanism for band gap opening remains the same. To quantitatively predict the band gap and optical properties of these materials, we employ many-body perturbation theory with Green's functions (GW/Bethe-Salpeter equation) to directly include electron-electron and electron-hole interactions. Structurally modified graphene shows a strong renormalization of the fundamental band gap over single particle descriptions, and a strong electron-hole interaction as indicated by strong exciton binding energies (> 0.5 eV). Finally, we show that structurally modified graphene

  17. Electronic Structure Principles and Aromaticity

    ERIC Educational Resources Information Center

    Chattaraj, P. K.; Sarkar, U.; Roy, D. R.

    2007-01-01

    The relationship between aromaticity and stability in molecules on the basis of quantities such as hardness and electrophilicity is explored. The findings reveal that aromatic molecules are less energetic, harder, less polarizable, and less electrophilic as compared to antiaromatic molecules, as expected from the electronic structure principles.

  18. Electron Scattering and Nuclear Structure

    ERIC Educational Resources Information Center

    Trower, W. P.; Ficenec, J. R.

    1971-01-01

    Presents information about the nucleus gained by studies of electron scattering. Discusses what can be implied about the shape of the charge distribution, the nucleus positions, the vibrational modes of the nucleus, the momentum of the nucleus, and the granularity and core structures of the nucleus. (DS)

  19. Fuzzy Reasoning to More Accurately Determine Void Areas on Optical Micrographs of Composite Structures

    NASA Technical Reports Server (NTRS)

    Dominquez, Jesus A.; Tate, Lanetra C.; Wright, M. Clara; Caraccio, Anne

    2013-01-01

    Accomplishing the best-performing composite matrix (resin) requires that not only the processing method but also the cure cycle generate low-void-content structures. If voids are present, the performance of the composite matrix will be significantly reduced. This is usually noticed by significant reductions in matrix-dominated properties, such as compression and shear strength. Voids in composite materials are areas that are absent of the composite components: matrix and fibers. The characteristics of the voids and their accurate estimation are critical to determine for high performance composite structures. One widely used method of performing void analysis on a composite structure sample is acquiring optical micrographs or Scanning Electron Microscope (SEM) images of lateral sides of the sample and retrieving the void areas within the micrographs/images using an image analysis technique. Segmentation for the retrieval and subsequent computation of void areas within the micrographs/images is challenging as the gray-scaled values of the void areas are close to the gray-scaled values of the matrix leading to the need of manually performing the segmentation based on the histogram of the micrographs/images to retrieve the void areas. The use of an algorithm developed by NASA and based on Fuzzy Reasoning (FR) proved to overcome the difficulty of suitably differentiate void and matrix image areas with similar gray-scaled values leading not only to a more accurate estimation of void areas on composite matrix micrographs but also to a faster void analysis process as the algorithm is fully autonomous.

  20. Electronic structure interpolation via atomic orbitals.

    PubMed

    Chen, Mohan; Guo, G-C; He, Lixin

    2011-08-17

    We present an efficient scheme for accurate electronic structure interpolation based on systematically improvable optimized atomic orbitals. The atomic orbitals are generated by minimizing the spillage value between the atomic basis calculations and the converged plane wave basis calculations on some coarse k-point grid. They are then used to calculate the band structure of the full Brillouin zone using the linear combination of atomic orbitals algorithms. We find that usually 16-25 orbitals per atom can give an accuracy of about 10 meV compared to the full ab initio calculations, and the accuracy can be systematically improved by using more atomic orbitals. The scheme is easy to implement and robust, and works equally well for metallic systems and systems with complicated band structures. Furthermore, the atomic orbitals have much better transferability than Shirley's basis and Wannier functions, which is very useful for perturbation calculations.

  1. Accurate MRCI calculations of the low-lying electronic states of the NCl molecule

    NASA Astrophysics Data System (ADS)

    Song, Ziyue; Shi, Deheng; Sun, Jinfeng; Zhu, Zunlue

    2017-03-01

    Characterization of 22 electronic states of NCl correlating to the two lowest dissociation channels are carried out using high level CASSCF/MRCI calculations with a sextuple-ζ basis set including Davidson modification, core-valence correlation correction and scalar relativistic effects. As far as we know, this radical has never been the preference of theoretical researchers and experimental investigations only concern the ground state and the two low-lying metastable states. Accurate potential energy curves, dissociation energies as well as the equilibrium constants are determined and avoided crossings between the Π symmetry are studied. Moreover, spin-orbit splitting of several states and transition probabilities and radiative lifetimes for some allowed or forbidden transitions are presented.

  2. Efficient and accurate treatment of electron correlations with Correlation Matrix Renormalization theory

    PubMed Central

    Yao, Y. X.; Liu, J.; Liu, C.; Lu, W. C.; Wang, C. Z.; Ho, K. M.

    2015-01-01

    We present an efficient method for calculating the electronic structure and total energy of strongly correlated electron systems. The method extends the traditional Gutzwiller approximation for one-particle operators to the evaluation of the expectation values of two particle operators in the many-electron Hamiltonian. The method is free of adjustable Coulomb parameters, and has no double counting issues in the calculation of total energy, and has the correct atomic limit. We demonstrate that the method describes well the bonding and dissociation behaviors of the hydrogen and nitrogen clusters, as well as the ammonia composed of hydrogen and nitrogen atoms. We also show that the method can satisfactorily tackle great challenging problems faced by the density functional theory recently discussed in the literature. The computational workload of our method is similar to the Hartree-Fock approach while the results are comparable to high-level quantum chemistry calculations. PMID:26315767

  3. Efficient and accurate treatment of electron correlations with Correlation Matrix Renormalization theory.

    PubMed

    Yao, Y X; Liu, J; Liu, C; Lu, W C; Wang, C Z; Ho, K M

    2015-08-28

    We present an efficient method for calculating the electronic structure and total energy of strongly correlated electron systems. The method extends the traditional Gutzwiller approximation for one-particle operators to the evaluation of the expectation values of two particle operators in the many-electron Hamiltonian. The method is free of adjustable Coulomb parameters, and has no double counting issues in the calculation of total energy, and has the correct atomic limit. We demonstrate that the method describes well the bonding and dissociation behaviors of the hydrogen and nitrogen clusters, as well as the ammonia composed of hydrogen and nitrogen atoms. We also show that the method can satisfactorily tackle great challenging problems faced by the density functional theory recently discussed in the literature. The computational workload of our method is similar to the Hartree-Fock approach while the results are comparable to high-level quantum chemistry calculations.

  4. Efficient and accurate treatment of electron correlations with correlation matrix renormalization theory

    DOE PAGES

    Yao, Y. X.; Liu, J.; Liu, C.; ...

    2015-08-28

    We present an efficient method for calculating the electronic structure and total energy of strongly correlated electron systems. The method extends the traditional Gutzwiller approximation for one-particle operators to the evaluation of the expectation values of two particle operators in the many-electron Hamiltonian. The method is free of adjustable Coulomb parameters, and has no double counting issues in the calculation of total energy, and has the correct atomic limit. We demonstrate that the method describes well the bonding and dissociation behaviors of the hydrogen and nitrogen clusters, as well as the ammonia composed of hydrogen and nitrogen atoms. We alsomore » show that the method can satisfactorily tackle great challenging problems faced by the density functional theory recently discussed in the literature. The computational workload of our method is similar to the Hartree-Fock approach while the results are comparable to high-level quantum chemistry calculations.« less

  5. Efficient and accurate treatment of electron correlations with correlation matrix renormalization theory

    SciTech Connect

    Yao, Y. X.; Liu, J.; Liu, C.; Lu, W. C.; Wang, C. Z.; Ho, K. M.

    2015-08-28

    We present an efficient method for calculating the electronic structure and total energy of strongly correlated electron systems. The method extends the traditional Gutzwiller approximation for one-particle operators to the evaluation of the expectation values of two particle operators in the many-electron Hamiltonian. The method is free of adjustable Coulomb parameters, and has no double counting issues in the calculation of total energy, and has the correct atomic limit. We demonstrate that the method describes well the bonding and dissociation behaviors of the hydrogen and nitrogen clusters, as well as the ammonia composed of hydrogen and nitrogen atoms. We also show that the method can satisfactorily tackle great challenging problems faced by the density functional theory recently discussed in the literature. The computational workload of our method is similar to the Hartree-Fock approach while the results are comparable to high-level quantum chemistry calculations.

  6. Comparisons of Accurate Electronic, Transport, and Bulk Properties of XP (X = B, Al, Ga, In)

    NASA Astrophysics Data System (ADS)

    Malozovsky, Yuriy; Ejembi, John; Saliev, Azizjon; Franklin, Lashounda; Bagayoko, Diola

    We present comparisons of results from ab-initio,self-consistent local density approximation (LDA) calculations of accurate, electronic and related properties of zinc blende XP (X =B, Al, Ga, In) phosphides. We implemented the linear combination of atomic orbitals following the Bagayoko, Zhao, and Williams (BZW) method as enhanced by Ekuma and Franklin (BZW-EF). Consequently, our results have the full physical content of DFT and agree very well with corresponding experimental ones [AIP Advances, 4, 127104 (2014)]. Our calculated, indirect band gap of 2.02 eV for BP, 2.56 eV for AlP, and of 2.29 eV for GaP, from Γ to X-point, are in excellent agreement with experimental values. Our calculated direct band gap of 1.43 eV, at Γ, for InP is also in an excellent agreement with experimental value. We discuss calculated electron and hole effective masses, total (DOS) and partial (pDOS) densities of states, and the bulk modulus of these phosphides. Acknowledgments: NSF and the Louisiana Board of Regents, LASiGMA [Award Nos. EPS- 1003897, NSF (2010-15)-RII-SUBR] and NSF HRD-1002541, DOE - National, Nuclear Security Administration (NNSA) (Award Nos. DE-NA0001861 and DE- NA0002630), LaSPACE, and LONI-SUBR.

  7. Accurate inference of subtle population structure (and other genetic discontinuities) using principal coordinates

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Accurate inference of genetic discontinuities between populations is an essential component of intraspecific biodiversity and evolution studies, as well as associative genetics. The most widely used methods to infer population structure are model based, Bayesian MCMC procedures that minimize Hardy...

  8. Accurate structure and dynamics of the metal-site of paramagnetic metalloproteins from NMR parameters using natural bond orbitals.

    PubMed

    Hansen, D Flemming; Westler, William M; Kunze, Micha B A; Markley, John L; Weinhold, Frank; Led, Jens J

    2012-03-14

    A natural bond orbital (NBO) analysis of unpaired electron spin density in metalloproteins is presented, which allows a fast and robust calculation of paramagnetic NMR parameters. Approximately 90% of the unpaired electron spin density occupies metal-ligand NBOs, allowing the majority of the density to be modeled by only a few NBOs that reflect the chemical bonding environment. We show that the paramagnetic relaxation rate of protons can be calculated accurately using only the metal-ligand NBOs and that these rates are in good agreement with corresponding rates measured experimentally. This holds, in particular, for protons of ligand residues where the point-dipole approximation breaks down. To describe the paramagnetic relaxation of heavy nuclei, also the electron spin density in the local orbitals must be taken into account. Geometric distance restraints for (15)N can be derived from the paramagnetic relaxation enhancement and the Fermi contact shift when local NBOs are included in the analysis. Thus, the NBO approach allows us to include experimental paramagnetic NMR parameters of (15)N nuclei as restraints in a structure optimization protocol. We performed a molecular dynamics simulation and structure determination of oxidized rubredoxin using the experimentally obtained paramagnetic NMR parameters of (15)N. The corresponding structures obtained are in good agreement with the crystal structure of rubredoxin. Thus, the NBO approach allows an accurate description of the geometric structure and the dynamics of metalloproteins, when NMR parameters are available of nuclei in the immediate vicinity of the metal-site.

  9. Actinide electronic structure and atomic forces

    NASA Astrophysics Data System (ADS)

    Albers, R. C.; Rudin, Sven P.; Trinkle, Dallas R.; Jones, M. D.

    2000-07-01

    We have developed a new method[1] of fitting tight-binding parameterizations based on functional forms developed at the Naval Research Laboratory.[2] We have applied these methods to actinide metals and report our success using them (see below). The fitting procedure uses first-principles local-density-approximation (LDA) linear augmented plane-wave (LAPW) band structure techniques[3] to first calculate an electronic-structure band structure and total energy for fcc, bcc, and simple cubic crystal structures for the actinide of interest. The tight-binding parameterization is then chosen to fit the detailed energy eigenvalues of the bands along symmetry directions, and the symmetry of the parameterization is constrained to agree with the correct symmetry of the LDA band structure at each eigenvalue and k-vector that is fit to. By fitting to a range of different volumes and the three different crystal structures, we find that the resulting parameterization is robust and appears to accurately calculate other crystal structures and properties of interest.

  10. Efficient floating diffuse functions for accurate characterization of the surface-bound excess electrons in water cluster anions.

    PubMed

    Zhang, Changzhe; Bu, Yuxiang

    2017-01-25

    In this work, the effect of diffuse function types (atom-centered diffuse functions versus floating functions and s-type versus p-type diffuse functions) on the structures and properties of three representative water cluster anions featuring a surface-bound excess electron is studied and we find that an effective combination of such two kinds of diffuse functions can not only reduce the computational cost but also, most importantly, considerably improve the accuracy of results and even avoid incorrect predictions of spectra and the EE shape. Our results indicate that (a) simple augmentation of atom-centered diffuse functions is beneficial for the vertical detachment energy convergence, but it leads to very poor descriptions for the singly occupied molecular orbital (SOMO) and lowest unoccupied molecular orbital (LUMO) distributions of the water cluster anions featuring a surface-bound excess electron and thus a significant ultraviolet spectrum redshift; (b) the ghost-atom-based floating diffuse functions can not only contribute to accurate electronic calculations of the ground state but also avoid poor and even incorrect descriptions of the SOMO and the LUMO induced by excessive augmentation of atom-centered diffuse functions; (c) the floating functions can be realized by ghost atoms and their positions could be determined through an optimization routine along the dipole moment vector direction. In addition, both the s- and p-type floating functions are necessary to supplement in the basis set which are responsible for the ground (s-type character) and excited (p-type character) states of the surface-bound excess electron, respectively. The exponents of the diffuse functions should also be determined to make the diffuse functions cover the main region of the excess electron distribution. Note that excessive augmentation of such diffuse functions is redundant and even can lead to unreasonable LUMO characteristics.

  11. Structural Dynamics of Electronic Systems

    NASA Astrophysics Data System (ADS)

    Suhir, E.

    2013-03-01

    The published work on analytical ("mathematical") and computer-aided, primarily finite-element-analysis (FEA) based, predictive modeling of the dynamic response of electronic systems to shocks and vibrations is reviewed. While understanding the physics of and the ability to predict the response of an electronic structure to dynamic loading has been always of significant importance in military, avionic, aeronautic, automotive and maritime electronics, during the last decade this problem has become especially important also in commercial, and, particularly, in portable electronics in connection with accelerated testing of various surface mount technology (SMT) systems on the board level. The emphasis of the review is on the nonlinear shock-excited vibrations of flexible printed circuit boards (PCBs) experiencing shock loading applied to their support contours during drop tests. At the end of the review we provide, as a suitable and useful illustration, the exact solution to a highly nonlinear problem of the dynamic response of a "flexible-and-heavy" PCB to an impact load applied to its support contour during drop testing.

  12. Electronic structure investigations of quasicrystals

    NASA Astrophysics Data System (ADS)

    Rotenberg, E.; Theis, W.; Horn, K.

    2004-08-01

    We present a review of the determination of density of states (DOS) of quasicrystals using valence band photoemission spectroscopy. The absence of fine or spiky structure in the angle-integrated DOS of quasicrystals suggests the possibility of delocalized electronic states. These were confirmed with angle-resolved photoemission studies, which clearly establish the presence of dispersing features attributed to momentum-dependent bandstructure. Such dispersing states are observed not only for deeper-lying sp states, but also for d-derived bands near the Fermi level. Data from three different high symmetry surfaces of decagonal Al-Ni-Co, an ideal model system, are presented. We find that only a few dominant reciprocal lattice vectors are sufficient to describe the quasiperiodic potential, and the implications for electronic properties are discussed.

  13. Electronic instrumentation for smart structures

    NASA Astrophysics Data System (ADS)

    Blanar, George J.

    1995-04-01

    The requirements of electronic instrumentation for smart structures are similar to those of data acquisition systems at our national particle physics laboratories. Modern high energy and heavy ion physics experiments may have tens of thousands of channels of data sources producing data that must be converted to digital form, compacted, stored and interpreted. In parallel, multiple sensors distributed in and around smart structures generate either binary or analog signals that are voltage, charge, or time like in their information content. In all cases, they must be transmitted, converted and preserved into a unified digital format for real-time processing. This paper will review the current status of practical large scale electronic measurement systems with special attention to architectures and physical organization. Brief surveys of the current state of the art will include preamplifiers and amplifiers, comparators and discriminators, voltage or charge analog-to-digital converters, time internal meters or time-to-digital converters, and finally, counting or scalar systems. The paper will conclude by integrating all of these ideas in a concept for an all-digital readout of a smart structure using the latest techniques used in physics research today.

  14. Accurate Ionization Potentials and Electron Affinities of Acceptor Molecules: A Benchmark of GW Methods

    NASA Astrophysics Data System (ADS)

    Marom, Noa; Knight, Joseph; Wang, Xiaopeng; Gallandi, Lukas; Dolgounitcheva, Olga; Ren, Xinguo; Ortiz, Vincent; Rinke, Patrick; Korzdorfer, Thomas

    The performance of different GW methods is assessed for a set of 24 organic acceptors. Errors are evaluated with respect to coupled cluster singles, doubles, perturbative triples [CCSD(T)] reference data for the vertical ionization potentials (IPs) and electron affinities (EAs), extrapolated to the complete basis set limit. Additional comparisons are made to experimental data, where available. We consider fully self-consistent GW (scGW), partial self-consistency in the Green's function (scGW0) , non-self-consistent G0W0 based on several mean-field starting points, and a ``beyond GW'' second order screened exchange (SOSEX) correction to G0W0. The best performers overall are G0W0 + SOSEX and G0W0 based on an IP-tuned long range corrected hybrid functional with the former being more accurate for EAs and the latter for IPs. Both provide a balanced treatment of localized vs. delocalized states and valence spectra in good agreement with photoemission spectroscopy (PES) experiments.

  15. Electronic structure theory of the superheavy elements

    NASA Astrophysics Data System (ADS)

    Eliav, Ephraim; Fritzsche, Stephan; Kaldor, Uzi

    2015-12-01

    High-accuracy calculations of atomic properties of the superheavy elements (SHE) up to element 122 are reviewed. The properties discussed include ionization potentials, electron affinities and excitation energies, which are associated with the spectroscopic and chemical behavior of these elements, and are therefore of considerable interest. Accurate predictions of these quantities require high-order inclusion of relativity and electron correlation, as well as large, converged basis sets. The Dirac-Coulomb-Breit Hamiltonian, which includes all terms up to second order in the fine-structure constant α, serves as the framework for the treatment; higher-order Lamb shift terms are considered in some selected cases. Electron correlation is treated by either the multiconfiguration self-consistent-field approach or by Fock-space coupled cluster theory. The latter is enhanced by the intermediate Hamiltonian scheme, allowing the use of larger model (P) spaces. The quality of the calculations is assessed by applying the same methods to lighter homologs of the SHEs and comparing with available experimental information. Very good agreement is obtained, within a few hundredths of an eV, and similar accuracy is expected for the SHEs. Many of the properties predicted for the SHEs differ significantly from what may be expected by straightforward extrapolation of lighter homologs, demonstrating that the structure and chemistry of SHEs are strongly affected by relativity. The major scientific challenge of the calculations is to find the electronic structure and basic atomic properties of the SHE and assign its proper place in the periodic table. Significant recent developments include joint experimental-computational studies of the excitation spectrum of Fm and the ionization energy of Lr, with excellent agreement of experiment and theory, auguring well for the future of research in the field.

  16. The electronic structure of Lu

    NASA Astrophysics Data System (ADS)

    Tibbetts, T. A.; Harmon, B. N.

    1982-12-01

    The electronic structure of hcp Lu has been calculated using a linearized augmented plane wave (LAPW) method and the Hedin-Lundqvist local density approximation for exchange and correlation. Although complete self-consistency was hindered by the proximity of the 4f levels to the Fermi energy, the valence bands were converged and the calculation yielded a Fermi surface remarkably similar to that calculated by Keeton and Loucks. Comparison is made with recent de Haas-van Alphen and neutron magnetic form factor experiments.

  17. Electronic structure quantum Monte Carlo

    NASA Astrophysics Data System (ADS)

    Bajdich, Michal; Mitas, Lubos

    2009-04-01

    Quantum Monte Carlo (QMC) is an advanced simulation methodology for studies of manybody quantum systems. The QMC approaches combine analytical insights with stochastic computational techniques for efficient solution of several classes of important many-body problems such as the stationary Schrödinger equation. QMC methods of various flavors have been applied to a great variety of systems spanning continuous and lattice quantum models, molecular and condensed systems, BEC-BCS ultracold condensates, nuclei, etc. In this review, we focus on the electronic structure QMC, i.e., methods relevant for systems described by the electron-ion Hamiltonians. Some of the key QMC achievements include direct treatment of electron correlation, accuracy in predicting energy differences and favorable scaling in the system size. Calculations of atoms, molecules, clusters and solids have demonstrated QMC applicability to real systems with hundreds of electrons while providing 90-95% of the correlation energy and energy differences typically within a few percent of experiments. Advances in accuracy beyond these limits are hampered by the so-called fixed-node approximation which is used to circumvent the notorious fermion sign problem. Many-body nodes of fermion states and their properties have therefore become one of the important topics for further progress in predictive power and efficiency of QMC calculations. Some of our recent results on the wave function nodes and related nodal domain topologies will be briefly reviewed. This includes analysis of few-electron systems and descriptions of exact and approximate nodes using transformations and projections of the highly-dimensional nodal hypersurfaces into the 3D space. Studies of fermion nodes offer new insights into topological properties of eigenstates such as explicit demonstrations that generic fermionic ground states exhibit the minimal number of two nodal domains. Recently proposed trial wave functions based on Pfaffians with

  18. Communication: An accurate global potential energy surface for the ground electronic state of ozone

    SciTech Connect

    Dawes, Richard E-mail: hguo@unm.edu; Lolur, Phalgun; Li, Anyang; Jiang, Bin; Guo, Hua E-mail: hguo@unm.edu

    2013-11-28

    We report a new full-dimensional and global potential energy surface (PES) for the O + O{sub 2} → O{sub 3} ozone forming reaction based on explicitly correlated multireference configuration interaction (MRCI-F12) data. It extends our previous [R. Dawes, P. Lolur, J. Ma, and H. Guo, J. Chem. Phys. 135, 081102 (2011)] dynamically weighted multistate MRCI calculations of the asymptotic region which showed the widely found submerged reef along the minimum energy path to be the spurious result of an avoided crossing with an excited state. A spin-orbit correction was added and the PES tends asymptotically to the recently developed long-range electrostatic model of Lepers et al. [J. Chem. Phys. 137, 234305 (2012)]. This PES features: (1) excellent equilibrium structural parameters, (2) good agreement with experimental vibrational levels, (3) accurate dissociation energy, and (4) most-notably, a transition region without a spurious reef. The new PES is expected to allow insight into the still unresolved issues surrounding the kinetics, dynamics, and isotope signature of ozone.

  19. Accurate Prediction of One-Dimensional Protein Structure Features Using SPINE-X.

    PubMed

    Faraggi, Eshel; Kloczkowski, Andrzej

    2017-01-01

    Accurate prediction of protein secondary structure and other one-dimensional structure features is essential for accurate sequence alignment, three-dimensional structure modeling, and function prediction. SPINE-X is a software package to predict secondary structure as well as accessible surface area and dihedral angles ϕ and ψ. For secondary structure SPINE-X achieves an accuracy of between 81 and 84 % depending on the dataset and choice of tests. The Pearson correlation coefficient for accessible surface area prediction is 0.75 and the mean absolute error from the ϕ and ψ dihedral angles are 20(∘) and 33(∘), respectively. The source code and a Linux executables for SPINE-X are available from Research and Information Systems at http://mamiris.com .

  20. Electronic transport in nanoscale structures

    NASA Astrophysics Data System (ADS)

    Lagerqvist, Johan

    In this dissertation electronic transport in nanoscale structures is discussed. An expression for the shot noise, a fluctuation in current due to the discreteness of charge, is derived directly from the wave functions of a nanoscale system. Investigation of shot noise is of particular interest due to the rich fundamental physics involved. For example, the study of shot noise can provide fundamental insight on the nature of electron transport in a nanoscale junction. We report calculations of the shot noise properties of parallel wires in the regime in which the interwire distance is much smaller than the inelastic mean free path. The validity of quantized transverse momenta in a nanoscale structure and its effect on shot noise is also discussed. We theoretically propose and show the feasibility of a novel protocol for DNA sequencing based on the electronic signature of single-stranded DNA while it translocates through a nanopore. We find that the currents for the bases are sufficiently different to allow for efficient sequencing. Our estimates reveal that sequencing of an entire human genome could be done with very high accuracy in a matter of hours, e.g., orders of magnitude faster than present techniques. We also find that although the overall magnitude of the current may change dramatically with different detection conditions, the intrinsic distinguishability of the bases is not significantly affected by pore size and transverse field strength. Finally, we study the ability of water to screen charges in nanopores by using all-atom molecular dynamics simulations coupled to electrostatic calculations. Due to the short length scales of the nanopore geometry and the large local field gradient of a single ion, the energetics of transporting an ion through the pore is strongly dependent on the microscopic details of the electric field. We show that as long as the pore allows the first hydration shell to stay intact, e.g., ˜6 nearby water molecules, the electric field

  1. Development of an accurate EPID-based output measurement and dosimetric verification tool for electron beam therapy

    PubMed Central

    Ding, Aiping; Xing, Lei; Han, Bin

    2015-01-01

    Purpose: To develop an efficient and robust tool for output measurement and absolute dose verification of electron beam therapy by using a high spatial-resolution and high frame-rate amorphous silicon flat panel electronic portal imaging device (EPID). Methods: The dosimetric characteristics of the EPID, including saturation, linearity, and ghosting effect, were first investigated on a Varian Clinac 21EX accelerator. The response kernels of the individual pixels of the EPID to all available electron energies (6, 9, 12, 16, and 20 MeV) were calculated by using Monte Carlo (MC) simulations, which formed the basis to deconvolve an EPID raw images to the incident electron fluence map. The two-dimensional (2D) dose distribution at reference depths in water was obtained by using the constructed fluence map with a MC simulated pencil beam kernel with consideration of the geometric and structural information of the EPID. Output factor measurements were carried out with the EPID at a nominal source–surface distance of 100 cm for 2 × 2, 3 × 3, 6 × 6, 10 × 10, and 15 × 15 cm2 fields for all available electron energies, and the results were compared with that measured in a solid water phantom using film and a Farmer-type ion chamber. The dose distributions at a reference depth specific to each energy and the flatness and symmetry of the 10 × 10 cm2 electron beam were also measured using EPID, and the results were compared with ion chamber array and water scan measurements. Finally, three patient cases with various field sizes and irregular cutout shapes were also investigated. Results: EPID-measured dose changed linearly with the monitor units and showed little ghosting effect for dose rate up to 600 MU/min. The flatness and symmetry measured with the EPID were found to be consistent with ion chamber array and water scan measurements. The EPID-measured output factors for standard square fields of 2 × 2, 3 × 3, 6 × 6, 10 × 10, 15 × 15 cm2 agreed with film and ion

  2. Accurate marker-free alignment with simultaneous geometry determination and reconstruction of tilt series in electron tomography.

    PubMed

    Winkler, Hanspeter; Taylor, Kenneth A

    2006-02-01

    An image alignment method for electron tomography is presented which is based on cross-correlation techniques and which includes a simultaneous refinement of the tilt geometry. A coarsely aligned tilt series is iteratively refined with a procedure consisting of two steps for each cycle: area matching and subsequent geometry correction. The first step, area matching, brings into register equivalent specimen regions in all images of the tilt series. It determines four parameters of a linear two-dimensional transformation, not just translation and rotation as is done during the preceding coarse alignment with conventional methods. The refinement procedure also differs from earlier methods in that the alignment references are now computed from already aligned images by reprojection of a backprojected volume. The second step, geometry correction, refines the initially inaccurate estimates of the geometrical parameters, including the direction of the tilt axis, a tilt angle offset, and the inclination of the specimen with respect to the support film or specimen holder. The correction values serve as an indicator for the progress of the refinement. For each new iteration, the correction values are used to compute an updated set of geometry parameters by a least squares fit. Model calculations show that it is essential to refine the geometrical parameters as well as the accurate alignment of the images to obtain a faithful map of the original structure.

  3. Electronic processes in multilayer memory structures

    NASA Astrophysics Data System (ADS)

    Plotnikov, A. F.

    The papers presented in this volume contain results of recent theoretical and experimental research related to electron processes in optoelectronic memory media based on structures consisting of a metal, an amorphous insulating layer, and a semiconductor. Topics discussed include photostimulated electron processes in metal-insulator-semiconductor structures, electron transfer phenomena in amorphous dielectric layers, degradation phenomena in MNOS memory elements under prolonged charge injection into the dielectric layer, and characteristics of charge relaxation in MNOS structures following multiple reprogramming.

  4. Electronic correlation contributions to structural energies

    NASA Astrophysics Data System (ADS)

    Haydock, Roger

    2015-03-01

    The recursion method is used to calculate electronic excitation spectra including electron-electron interactions within the Hubbard model. The effects of correlation on structural energies are then obtained from these spectra and applied to stacking faults. http://arxiv.org/abs/1405.2288 Supported by the Richmond F. Snyder Fund and Gifts.

  5. An accurate and efficient method to predict the electronic excitation energies of BODIPY fluorescent dyes.

    PubMed

    Wang, Jia-Nan; Jin, Jun-Ling; Geng, Yun; Sun, Shi-Ling; Xu, Hong-Liang; Lu, Ying-Hua; Su, Zhong-Min

    2013-03-15

    Recently, the extreme learning machine neural network (ELMNN) as a valid computing method has been proposed to predict the nonlinear optical property successfully (Wang et al., J. Comput. Chem. 2012, 33, 231). In this work, first, we follow this line of work to predict the electronic excitation energies using the ELMNN method. Significantly, the root mean square deviation of the predicted electronic excitation energies of 90 4,4-difluoro-4-bora-3a,4a-diaza-s-indacene (BODIPY) derivatives between the predicted and experimental values has been reduced to 0.13 eV. Second, four groups of molecule descriptors are considered when building the computing models. The results show that the quantum chemical descriptions have the closest intrinsic relation with the electronic excitation energy values. Finally, a user-friendly web server (EEEBPre: Prediction of electronic excitation energies for BODIPY dyes), which is freely accessible to public at the web site: http://202.198.129.218, has been built for prediction. This web server can return the predicted electronic excitation energy values of BODIPY dyes that are high consistent with the experimental values. We hope that this web server would be helpful to theoretical and experimental chemists in related research.

  6. Electronic structure of lithium tetraborate

    NASA Astrophysics Data System (ADS)

    Wooten, David J.

    Due to many of its attributes, Li2B4O7 provides a possible material for incorporation as either a primary or companion material in future solid state neutron detectors. There is however a lack of fundamental characterization information regarding this useful material, particularly its electronic configuration. To address this, an investigation of Li2B4O7(110) and Li2B 4O7(100) was undertaken, utilizing photoemission and inverse photoemission spectroscopic techniques. The measured band gap depended on crystallographic direction with the band gaps ranging from 8.9+/-0.5 eV to 10.1+/-0.5 eV. The measurement yielded a density of states that qualitatively agreed with the theoretical results from model bulk band structure calculations for Li2B4O7; albeit with a larger band gap than predicted, but consistent with the known deficiencies of Local Density Approximation and Density Functional Theory calculations. The occupied states of both surfaces were extremely flat; to the degree that resolving periodic dispersion of the occupied states was inconclusive, within the resolution of the system. However, both surfaces demonstrated clear periodic dispersion within the empty states very close to theoretical Brillouin zone values. These attributes also translated to a lighter charge carrier effective mass in the unoccupied states. Of the two surfaces, Li2B4O 7(110) yielded the more consistent values in orthogonal directions for energy states. The presence of a bulk band gap surface state and image potential state in Li2B4O7(110) was indicative of a defect-free surface. The absence of both in the more polar, more dielectric Li2B4O7(100) was attributed to the presence of defects determined to be O vacancies. The results from Li2B 4O7(110) were indicative of a more stable surface than Li 2B4O7(100). In addition, Li 1s bulk and surface core level components were determined at the binding energies of -56.5+0.4 and -53.7+0.5 eV. Resonance features were observed along the [001

  7. Accurate electron affinity of Pb and isotope shifts of binding energies of Pb-

    NASA Astrophysics Data System (ADS)

    Chen, Xiaolin; Ning, Chuangang

    2016-08-01

    Lead (Pb) was the last element of the group IVA whose electron affinity had a low accuracy around 10 meV before the present work. This was due to the generic threshold photodetachment measurement that cannot extent well below 0.5 eV due to the light source limitation. In the present work, the electron affinity of Pb was determined to be 2877.33(13) cm-1 or 0.356 743(16) eV for the isotope m = 208. The accuracy was improved by a factor of 500 with respect to the previous laser photodetachment electron spectroscopy. Moreover, remarkable isotope shifts of the binding energy of Pb- 6p3 4S3/2 - Pb 6p2 3P2 were observed for m = 206, 207, and 208.

  8. Accurate electron affinity of Pb and isotope shifts of binding energies of Pb(.).

    PubMed

    Chen, Xiaolin; Ning, Chuangang

    2016-08-28

    Lead (Pb) was the last element of the group IVA whose electron affinity had a low accuracy around 10 meV before the present work. This was due to the generic threshold photodetachment measurement that cannot extent well below 0.5 eV due to the light source limitation. In the present work, the electron affinity of Pb was determined to be 2877.33(13) cm(-1) or 0.356 743(16) eV for the isotope m = 208. The accuracy was improved by a factor of 500 with respect to the previous laser photodetachment electron spectroscopy. Moreover, remarkable isotope shifts of the binding energy of Pb(-) 6p(3) (4)S3/2 - Pb 6p(2) (3)P2 were observed for m = 206, 207, and 208.

  9. Accurate simulation of the electron cloud in the Fermilab Main Injector with VORPAL

    SciTech Connect

    Lebrun, Paul L.G.; Spentzouris, Panagiotis; Cary, John R.; Stoltz, Peter; Veitzer, Seth A.; /Tech-X, Boulder

    2010-05-01

    Precision simulations of the electron cloud at the Fermilab Main Injector have been studied using the plasma simulation code VORPAL. Fully 3D and self consistent solutions that includes E.M. field maps generated by the cloud and the proton bunches have been obtained, as well detailed distributions of the electron's 6D phase space. We plan to include such maps in the ongoing simulation of the space charge effects in the Main Injector. Simulations of the response of beam position monitors, retarding field analyzers and microwave transmission experiments are ongoing.

  10. CoMOGrad and PHOG: From Computer Vision to Fast and Accurate Protein Tertiary Structure Retrieval

    PubMed Central

    Karim, Rezaul; Aziz, Mohd. Momin Al; Shatabda, Swakkhar; Rahman, M. Sohel; Mia, Md. Abul Kashem; Zaman, Farhana; Rakin, Salman

    2015-01-01

    The number of entries in a structural database of proteins is increasing day by day. Methods for retrieving protein tertiary structures from such a large database have turn out to be the key to comparative analysis of structures that plays an important role to understand proteins and their functions. In this paper, we present fast and accurate methods for the retrieval of proteins having tertiary structures similar to a query protein from a large database. Our proposed methods borrow ideas from the field of computer vision. The speed and accuracy of our methods come from the two newly introduced features- the co-occurrence matrix of the oriented gradient and pyramid histogram of oriented gradient- and the use of Euclidean distance as the distance measure. Experimental results clearly indicate the superiority of our approach in both running time and accuracy. Our method is readily available for use from this website: http://research.buet.ac.bd:8080/Comograd/. PMID:26293226

  11. Are In-Bed Electronic Weights Recorded in the Medical Record Accurate?

    PubMed

    Gerl, Heather; Miko, Alexandra; Nelson, Mandy; Godaire, Lori

    2016-01-01

    This study found large discrepancies between in-bed weights recorded in the medical record and carefully obtained standing weights with a calibrated, electronic bedside scale. This discrepancy appears to be related to inadequate bed calibration before patient admission and having excessive linen, clothing, and/or equipment on the bed during weighing by caregivers.

  12. Fast and Accurate Electronic Excitations in Cyanines with the Many-Body Bethe-Salpeter Approach.

    PubMed

    Boulanger, Paul; Jacquemin, Denis; Duchemin, Ivan; Blase, Xavier

    2014-03-11

    The accurate prediction of the optical signatures of cyanine derivatives remains an important challenge in theoretical chemistry. Indeed, up to now, only the most expensive quantum chemical methods (CAS-PT2, CC, DMC, etc.) yield consistent and accurate data, impeding the applications on real-life molecules. Here, we investigate the lowest lying singlet excitation energies of increasingly long cyanine dyes within the GW and Bethe-Salpeter Green's function many-body perturbation theory. Our results are in remarkable agreement with available coupled-cluster (exCC3) data, bringing these two single-reference perturbation techniques within a 0.05 eV maximum discrepancy. By comparison, available TD-DFT calculations with various semilocal, global, or range-separated hybrid functionals, overshoot the transition energies by a typical error of 0.3-0.6 eV. The obtained accuracy is achieved with a parameter-free formalism that offers similar accuracy for metallic or insulating, finite size or extended systems.

  13. RESCU: A real space electronic structure method

    NASA Astrophysics Data System (ADS)

    Michaud-Rioux, Vincent; Zhang, Lei; Guo, Hong

    2016-02-01

    In this work we present RESCU, a powerful MATLAB-based Kohn-Sham density functional theory (KS-DFT) solver. We demonstrate that RESCU can compute the electronic structure properties of systems comprising many thousands of atoms using modest computer resources, e.g. 16 to 256 cores. Its computational efficiency is achieved from exploiting four routes. First, we use numerical atomic orbital (NAO) techniques to efficiently generate a good quality initial subspace which is crucially required by Chebyshev filtering methods. Second, we exploit the fact that only a subspace spanning the occupied Kohn-Sham states is required, and solving accurately the KS equation using eigensolvers can generally be avoided. Third, by judiciously analyzing and optimizing various parts of the procedure in RESCU, we delay the O (N3) scaling to large N, and our tests show that RESCU scales consistently as O (N2.3) from a few hundred atoms to more than 5000 atoms when using a real space grid discretization. The scaling is better or comparable in a NAO basis up to the 14,000 atoms level. Fourth, we exploit various numerical algorithms and, in particular, we introduce a partial Rayleigh-Ritz algorithm to achieve efficiency gains for systems comprising more than 10,000 electrons. We demonstrate the power of RESCU in solving KS-DFT problems using many examples running on 16, 64 and/or 256 cores: a 5832 Si atoms supercell; a 8788 Al atoms supercell; a 5324 Cu atoms supercell and a small DNA molecule submerged in 1713 water molecules for a total 5399 atoms. The KS-DFT is entirely converged in a few hours in all cases. Our results suggest that the RESCU method has reached a milestone of solving thousands of atoms by KS-DFT on a modest computer cluster.

  14. Electronic Structure of Lithium Tetraborate

    DTIC Science & Technology

    2010-06-01

    binding energies of -56.5+0.4 and -53.7+0.5 eV. Resonance features were observed along the [001] direction and were attributed to a Coster- Kronig ...could be theoretically explained as an Auger electron [12] or Coster- Kronig process [13] of a Li 1s electron photoexcitation to an unoccupied 2p...Coster Kronig , which requires only one Li atom. Such a Coster Kronig mechanism is pictorially displayed below in Figure 7.9. 128 Figure 7.9

  15. Electron tomography of dislocation structures

    SciTech Connect

    Liu, G.S.; House, S.D.; Kacher, J.; Tanaka, M.; Higashida, K.; Robertson, I.M.

    2014-01-15

    Recent developments in the application of electron tomography for characterizing microstructures in crystalline solids are described. The underlying principles for electron tomography are presented in the context of typical challenges in adapting the technique to crystalline systems and in using diffraction contrast imaging conditions. Methods for overcoming the limitations associated with the angular range, the number of acquired images, and uniformity of image contrast are introduced. In addition, a method for incorporating the real space coordinate system into the tomogram is presented. As the approach emphasizes development of experimental solutions to the challenges, the solutions developed and implemented are presented in the form of examples.

  16. Exchange-Hole Dipole Dispersion Model for Accurate Energy Ranking in Molecular Crystal Structure Prediction.

    PubMed

    Whittleton, Sarah R; Otero-de-la-Roza, A; Johnson, Erin R

    2017-02-14

    Accurate energy ranking is a key facet to the problem of first-principles crystal-structure prediction (CSP) of molecular crystals. This work presents a systematic assessment of B86bPBE-XDM, a semilocal density functional combined with the exchange-hole dipole moment (XDM) dispersion model, for energy ranking using 14 compounds from the first five CSP blind tests. Specifically, the set of crystals studied comprises 11 rigid, planar compounds and 3 co-crystals. The experimental structure was correctly identified as the lowest in lattice energy for 12 of the 14 total crystals. One of the exceptions is 4-hydroxythiophene-2-carbonitrile, for which the experimental structure was correctly identified once a quasi-harmonic estimate of the vibrational free-energy contribution was included, evidencing the occasional importance of thermal corrections for accurate energy ranking. The other exception is an organic salt, where charge-transfer error (also called delocalization error) is expected to cause the base density functional to be unreliable. Provided the choice of base density functional is appropriate and an estimate of temperature effects is used, XDM-corrected density-functional theory is highly reliable for the energetic ranking of competing crystal structures.

  17. Accurate measurement of relative tilt and azimuth angles in electron tomography: A comparison of fiducial marker method with electron diffraction

    SciTech Connect

    Hayashida, Misa; Malac, Marek; Egerton, Ray F.; Bergen, Michael; Li, Peng

    2014-08-15

    Electron tomography is a method whereby a three-dimensional reconstruction of a nanoscale object is obtained from a series of projected images measured in a transmission electron microscope. We developed an electron-diffraction method to measure the tilt and azimuth angles, with Kikuchi lines used to align a series of diffraction patterns obtained with each image of the tilt series. Since it is based on electron diffraction, the method is not affected by sample drift and is not sensitive to sample thickness, whereas tilt angle measurement and alignment using fiducial-marker methods are affected by both sample drift and thickness. The accuracy of the diffraction method benefits reconstructions with a large number of voxels, where both high spatial resolution and a large field of view are desired. The diffraction method allows both the tilt and azimuth angle to be measured, while fiducial marker methods typically treat the tilt and azimuth angle as an unknown parameter. The diffraction method can be also used to estimate the accuracy of the fiducial marker method, and the sample-stage accuracy. A nano-dot fiducial marker measurement differs from a diffraction measurement by no more than ±1°.

  18. Accurate measurement of relative tilt and azimuth angles in electron tomography: a comparison of fiducial marker method with electron diffraction.

    PubMed

    Hayashida, Misa; Malac, Marek; Bergen, Michael; Egerton, Ray F; Li, Peng

    2014-08-01

    Electron tomography is a method whereby a three-dimensional reconstruction of a nanoscale object is obtained from a series of projected images measured in a transmission electron microscope. We developed an electron-diffraction method to measure the tilt and azimuth angles, with Kikuchi lines used to align a series of diffraction patterns obtained with each image of the tilt series. Since it is based on electron diffraction, the method is not affected by sample drift and is not sensitive to sample thickness, whereas tilt angle measurement and alignment using fiducial-marker methods are affected by both sample drift and thickness. The accuracy of the diffraction method benefits reconstructions with a large number of voxels, where both high spatial resolution and a large field of view are desired. The diffraction method allows both the tilt and azimuth angle to be measured, while fiducial marker methods typically treat the tilt and azimuth angle as an unknown parameter. The diffraction method can be also used to estimate the accuracy of the fiducial marker method, and the sample-stage accuracy. A nano-dot fiducial marker measurement differs from a diffraction measurement by no more than ±1°.

  19. Electron gun controlled smart structure

    DOEpatents

    Martin, Jeffrey W.; Main, John Alan; Redmond, James M.; Henson, Tammy D.; Watson, Robert D.

    2001-01-01

    Disclosed is a method and system for actively controlling the shape of a sheet of electroactive material; the system comprising: one or more electrodes attached to the frontside of the electroactive sheet; a charged particle generator, disposed so as to direct a beam of charged particles (e.g. electrons) onto the electrode; a conductive substrate attached to the backside of the sheet; and a power supply electrically connected to the conductive substrate; whereby the sheet changes its shape in response to an electric field created across the sheet by an accumulation of electric charge within the electrode(s), relative to a potential applied to the conductive substrate. Use of multiple electrodes distributed across on the frontside ensures a uniform distribution of the charge with a single point of e-beam incidence, thereby greatly simplifying the beam scanning algorithm and raster control electronics, and reducing the problems associated with "blooming". By placing a distribution of electrodes over the front surface of a piezoelectric film (or other electroactive material), this arrangement enables improved control over the distribution of surface electric charges (e.g. electrons) by creating uniform (and possibly different) charge distributions within each individual electrode. Removal or deposition of net electric charge can be affected by controlling the secondary electron yield through manipulation of the backside electric potential with the power supply. The system can be used for actively controlling the shape of space-based deployable optics, such as adaptive mirrors and inflatable antennae.

  20. Three dimensional accurate morphology measurements of polystyrene standard particles on silicon substrate by electron tomography.

    PubMed

    Hayashida, Misa; Kumagai, Kazuhiro; Malac, Marek

    2015-12-01

    Polystyrene latex (PSL) nanoparticle (NP) sample is one of the most widely used standard materials. It is used for calibration of particle counters and particle size measurement tools. It has been reported that the measured NP sizes by various methods, such as Differential Mobility Analysis, dynamic light scattering (DLS), optical microscopy (OM), scanning electron microscopy (SEM) and atomic force microscopy (AFM), differ from each other. Deformation of PSL NPs on mica substrate has been reported in AFM measurements: the lateral width of PSL NPs is smaller than their vertical height. To provide a reliable calibration standard, the deformation must be measured by a method that can reliably visualize the entire three dimensional (3D) shape of the PSL NPs. Here we present a method for detailed measurement of PSL NP 3D shape by means of electron tomography in a transmission electron microscope. The observed shape of the PSL NPs with 100 nm and 50 nm diameter were not spherical, but squished in direction perpendicular to the support substrate by about 7.4% and 12.1%, respectively. The high difference in surface energy of the PSL NPs and that of substrate together with their low Young modulus appear to explain the squishing of the NPs without presence of water film.

  1. Accurate simulation of the electron cloud in the Fermilab Main Injector with VORPAL

    SciTech Connect

    Lebrun, Paul L.G.; Spentzouris, Panagiotis; Cary, John R.; Stoltz, Peter; Veitzer, Seth A.; /Tech-X, Boulder

    2011-01-01

    We present results from a precision simulation of the electron cloud (EC) in the Fermilab Main Injector using the code VORPAL. This is a fully 3d and self consistent treatment of the EC. Both distributions of electrons in 6D phase-space and E.M. field maps have been generated. This has been done for various configurations of the magnetic fields found around the machine have been studied. Plasma waves associated to the fluctuation density of the cloud have been analyzed. Our results are compared with those obtained with the POSINST code. The response of a Retarding Field Analyzer (RFA) to the EC has been simulated, as well as the more challenging microwave absorption experiment. Definite predictions of their exact response are difficult to obtain,mostly because of the uncertainties in the secondary emission yield and, in the case of the RFA, because of the sensitivity of the electron collection efficiency to unknown stray magnetic fields. Nonetheless, our simulations do provide guidance to the experimental program.

  2. Avoiding fractional electrons in subsystem DFT based ab-initio molecular dynamics yields accurate models for liquid water and solvated OH radical

    NASA Astrophysics Data System (ADS)

    Genova, Alessandro; Ceresoli, Davide; Pavanello, Michele

    2016-06-01

    In this work we achieve three milestones: (1) we present a subsystem DFT method capable of running ab-initio molecular dynamics simulations accurately and efficiently. (2) In order to rid the simulations of inter-molecular self-interaction error, we exploit the ability of semilocal frozen density embedding formulation of subsystem DFT to represent the total electron density as a sum of localized subsystem electron densities that are constrained to integrate to a preset, constant number of electrons; the success of the method relies on the fact that employed semilocal nonadditive kinetic energy functionals effectively cancel out errors in semilocal exchange-correlation potentials that are linked to static correlation effects and self-interaction. (3) We demonstrate this concept by simulating liquid water and solvated OH• radical. While the bulk of our simulations have been performed on a periodic box containing 64 independent water molecules for 52 ps, we also simulated a box containing 256 water molecules for 22 ps. The results show that, provided one employs an accurate nonadditive kinetic energy functional, the dynamics of liquid water and OH• radical are in semiquantitative agreement with experimental results or higher-level electronic structure calculations. Our assessments are based upon comparisons of radial and angular distribution functions as well as the diffusion coefficient of the liquid.

  3. Complex structures of dense lithium: Electronic origin

    NASA Astrophysics Data System (ADS)

    Degtyareva, V. F.

    2016-11-01

    Lithium—the lightest alkali metal exhibits unexpected structures and electronic behavior at high pressures. Like the heavier alkali metals, Li is bcc at ambient pressure and transforms first to fcc (at 7.5 GPa). The post-fcc high-pressure form Li-cI 16 (at 40-60 GPa) is similar to Na-cI 16 and related to more complex structures of heavy alkalis Rb-oC52 and Cs- oC84. The other high pressure phases for Li (oC88, oC40, oC24) observed at pressures up to 130 GPa are found only in Li. The different route of Li high-pressure structures correlates with its special electronic configuration containing the only 3 electrons (at 1s and 2s levels). Crystal structures for Li are analyzed within the model of Fermi sphere-Brillouin zone interactions. Stability of post-fcc structures for Li are supported by the Hume-Rothery arguments when new diffraction plains appear close to the Fermi level producing pseudogaps near the Fermi level and decreasing the crystal energy. The filling of Brillouin-Jones zones by electron states for a given structure defines the physical properties as optical reflectivity, electrical resistivity and superconductivity. To understand the complexity of structural and physical properties of Li above 60 GPa it is necessary to assume the valence electron band overlap with the core electrons and increase the valence electron count under compression.

  4. Electronic Structure of Small Lanthanide Containing Molecules

    NASA Astrophysics Data System (ADS)

    Kafader, Jared O.; Ray, Manisha; Topolski, Josey E.; Chick Jarrold, Caroline

    2016-06-01

    Lanthanide-based materials have unusual electronic properties because of the high number of electronic degrees of freedom arising from partial occupation of 4f orbitals, which make these materials optimal for their utilization in many applications including electronics and catalysis. Electronic spectroscopy of small lanthanide molecules helps us understand the role of these 4f electrons, which are generally considered core-like because of orbital contraction, but are energetically similar to valence electrons. The spectroscopy of small lanthanide-containing molecules is relatively unexplored and to broaden this understanding we have completed the characterization of small cerium, praseodymium, and europium molecules using photoelectron spectroscopy coupled with DFT calculations. The characterization of PrO, EuH, EuO/EuOH, and CexOy molecules have allowed for the determination of their electron affinity, the assignment of numerous anion to neutral state transitions, modeling of anion/neutral structures and electron orbital occupation.

  5. Accurate Damage Location in Complex Composite Structures and Industrial Environments using Acoustic Emission

    NASA Astrophysics Data System (ADS)

    Eaton, M.; Pearson, M.; Lee, W.; Pullin, R.

    2015-07-01

    The ability to accurately locate damage in any given structure is a highly desirable attribute for an effective structural health monitoring system and could help to reduce operating costs and improve safety. This becomes a far greater challenge in complex geometries and materials, such as modern composite airframes. The poor translation of promising laboratory based SHM demonstrators to industrial environments forms a barrier to commercial up take of technology. The acoustic emission (AE) technique is a passive NDT method that detects elastic stress waves released by the growth of damage. It offers very sensitive damage detection, using a sparse array of sensors to detect and globally locate damage within a structure. However its application to complex structures commonly yields poor accuracy due to anisotropic wave propagation and the interruption of wave propagation by structural features such as holes and thickness changes. This work adopts an empirical mapping technique for AE location, known as Delta T Mapping, which uses experimental training data to account for such structural complexities. The technique is applied to a complex geometry composite aerospace structure undergoing certification testing. The component consists of a carbon fibre composite tube with varying wall thickness and multiple holes, that was loaded under bending. The damage location was validated using X-ray CT scanning and the Delta T Mapping technique was shown to improve location accuracy when compared with commercial algorithms. The onset and progression of damage were monitored throughout the test and used to inform future design iterations.

  6. 5D model for accurate representation and visualization of dynamic cardiac structures

    NASA Astrophysics Data System (ADS)

    Lin, Wei-te; Robb, Richard A.

    2000-05-01

    Accurate cardiac modeling is challenging due to the intricate structure and complex contraction patterns of myocardial tissues. Fast imaging techniques can provide 4D structural information acquired as a sequence of 3D images throughout the cardiac cycle. To mode. The beating heart, we created a physics-based surface model that deforms between successive time point in the cardiac cycle. 3D images of canine hearts were acquired during one complete cardiac cycle using the DSR and the EBCT. The left ventricle of the first time point is reconstructed as a triangular mesh. A mass-spring physics-based deformable mode,, which can expand and shrink with local contraction and stretching forces distributed in an anatomically accurate simulation of cardiac motion, is applied to the initial mesh and allows the initial mesh to deform to fit the left ventricle in successive time increments of the sequence. The resulting 4D model can be interactively transformed and displayed with associated regional electrical activity mapped onto anatomic surfaces, producing a 5D model, which faithfully exhibits regional cardiac contraction and relaxation patterns over the entire heart. The model faithfully represents structural changes throughout the cardiac cycle. Such models provide the framework for minimizing the number of time points required to usefully depict regional motion of myocardium and allow quantitative assessment of regional myocardial motion. The electrical activation mapping provides spatial and temporal correlation within the cardiac cycle. In procedures which as intra-cardiac catheter ablation, visualization of the dynamic model can be used to accurately localize the foci of myocardial arrhythmias and guide positioning of catheters for optimal ablation.

  7. Efficient and accurate modeling of electron photoemission in nanostructures with TDDFT

    NASA Astrophysics Data System (ADS)

    Wopperer, Philipp; De Giovannini, Umberto; Rubio, Angel

    2017-03-01

    We derive and extend the time-dependent surface-flux method introduced in [L. Tao, A. Scrinzi, New J. Phys. 14, 013021 (2012)] within a time-dependent density-functional theory (TDDFT) formalism and use it to calculate photoelectron spectra and angular distributions of atoms and molecules when excited by laser pulses. We present other, existing computational TDDFT methods that are suitable for the calculation of electron emission in compact spatial regions, and compare their results. We illustrate the performance of the new method by simulating strong-field ionization of C60 fullerene and discuss final state effects in the orbital reconstruction of planar organic molecules.

  8. Development of a PCR free, fieldable, rapid, accurate, and sensitive bio-electronic DNA biosensor

    NASA Astrophysics Data System (ADS)

    Hill, Doyle; Chafin, David; Greco, Roberta; Jafri, Samina; Murante, Richard; Noonan, John; Pham, An; Seabridge, Scott; Tannous, Vera; VanDerMeid, Karl; Wang, Daguang; Wescott, Nate; McFarlane, Kristin; Shah, Sanjiv

    2005-05-01

    The objective of this study was to demonstrate proof of concept for the Integrated Nano-Technologies BioDetect Bacillus anthracis electronic DNA sensor. B. anthracis Ames strain DNA was successfully detected by the formation of DNA bridges on the sensor. The bridges were coated with metal, resulting in a significant drop in electrical resistance. In this small test, at a relatively high DNA concentration, the overall accuracy of the sensor was 90.7%. The technology shows significant promise for future development as a bio-agent detection system.

  9. The Importance of Accurate Secondary Electron Yields in Modeling Spacecraft Charging

    DTIC Science & Technology

    1986-05-01

    were determined primarily by ... electrons in the energy range < 30 keV and ... that surface charging occun-ed when the spectrum hardened." Olsen ...flux. (Note that the spectra exhibited by Olsen (1983) also show significant counts at 30 keV and above, despite a sharp drop in the 10-20 keV range.) A...to the findings of Olsen (1983) and MuWlen et at. (198M) ir the following manner. A given environment will not charge a material if "he actual

  10. Petascale self-consistent electromagnetic computations using scalable and accurate algorithms for complex structures

    NASA Astrophysics Data System (ADS)

    Cary, John R.; Abell, D.; Amundson, J.; Bruhwiler, D. L.; Busby, R.; Carlsson, J. A.; Dimitrov, D. A.; Kashdan, E.; Messmer, P.; Nieter, C.; Smithe, D. N.; Spentzouris, P.; Stoltz, P.; Trines, R. M.; Wang, H.; Werner, G. R.

    2006-09-01

    As the size and cost of particle accelerators escalate, high-performance computing plays an increasingly important role; optimization through accurate, detailed computermodeling increases performance and reduces costs. But consequently, computer simulations face enormous challenges. Early approximation methods, such as expansions in distance from the design orbit, were unable to supply detailed accurate results, such as in the computation of wake fields in complex cavities. Since the advent of message-passing supercomputers with thousands of processors, earlier approximations are no longer necessary, and it is now possible to compute wake fields, the effects of dampers, and self-consistent dynamics in cavities accurately. In this environment, the focus has shifted towards the development and implementation of algorithms that scale to large numbers of processors. So-called charge-conserving algorithms evolve the electromagnetic fields without the need for any global solves (which are difficult to scale up to many processors). Using cut-cell (or embedded) boundaries, these algorithms can simulate the fields in complex accelerator cavities with curved walls. New implicit algorithms, which are stable for any time-step, conserve charge as well, allowing faster simulation of structures with details small compared to the characteristic wavelength. These algorithmic and computational advances have been implemented in the VORPAL7 Framework, a flexible, object-oriented, massively parallel computational application that allows run-time assembly of algorithms and objects, thus composing an application on the fly.

  11. Structural physiology based on electron crystallography

    PubMed Central

    Fujiyoshi, Yoshinori

    2011-01-01

    There are many questions in brain science, which are extremely interesting but very difficult to answer. For example, how do education and other experiences during human development influence the ability and personality of the adult? The molecular mechanisms underlying such phenomena are still totally unclear. However, technological and instrumental advancements of electron microscopy have facilitated comprehension of the structures of biological components, cells, and organelles. Electron crystallography is especially good for studying the structure and function of membrane proteins, which are key molecules of signal transduction in neural and other cells. Electron crystallography is now an established technique to analyze the structures of membrane proteins in lipid bilayers, which are close to their natural biological environment. By utilizing cryo-electron microscopes with helium cooled specimen stages, which were developed through a personal motivation to understand functions of neural systems from a structural point of view, structures of membrane proteins were analyzed at a resolution higher than 3 Å. This review has four objectives. First, it is intended to introduce the new research field of structural physiology. Second, it introduces some of the personal struggles, which were involved in developing the cryo-electron microscope. Third, it discusses some of the technology for the structural analysis of membrane proteins based on cryo-electron microscopy. Finally, it reviews structural and functional analyses of membrane proteins. PMID:21416541

  12. An accurate theoretical description for electronic transport properties of single molecular junctions

    NASA Astrophysics Data System (ADS)

    Luo, Yi

    2002-03-01

    We have developed a new theoretical approach to characterize the electron transport process in molecular devices based on the elastic-scattering Green's function theory in connection with the hybrid density functional theory without using any fitting parameters. Two molecular devices with benzene-1,4-dithiol and octanedithiol molecules embedded between two gold electrodes have been studied. The calculated current-voltage characteristics are in very good agreement with existing experimental results reported by Reed et. al for benzene-1,4-dithiol [Science, 278(1997) 252] and by Cui et al. for octanedithiol [Science, 294(2001) 571]. Our approach is very straightforward and can apply to quite large systems. Most importantly, it provides a reliable way to design and optimize molecular devices theoretically, thereby avoiding extremely difficult, time consuming laboratory tests.

  13. Accurate modeling of F-region electron densities. Annual progress report, 1993-1994

    SciTech Connect

    Not Available

    1994-01-01

    In the past year, the authors have made considerable progress in a number of areas including algorithm development, completion of two major case studies, and the development of a new EUV flux model. As a result, there has been a major improvement in the ability to model global emissions in support of NASA's imaging plans. Activity highlights include the following: developed a new algorithm to allow physical models to reproduce observed NmF2; investigated the relationship between NmF2 and F10.7 at Millstone Hill during 1990; developed a new solar EUV flux model; statistical survey of anomalously high nighttime electron T(sub e) at Millstone Hill; conducted a case study of the March 1990 magnetic storm; and conducted a comparison between theory and data of magnetically quiet behavior of the winter ionosphere at Millstone Hill.

  14. Communication: Vibrationally resolved photoelectron spectroscopy of the tetracyanoquinodimethane (TCNQ) anion and accurate determination of the electron affinity of TCNQ

    NASA Astrophysics Data System (ADS)

    Zhu, Guo-Zhu; Wang, Lai-Sheng

    2015-12-01

    Tetracyanoquinodimethane (TCNQ) is widely used as an electron acceptor to form highly conducting organic charge-transfer solids. Surprisingly, the electron affinity (EA) of TCNQ is not well known and has never been directly measured. Here, we report vibrationally resolved photoelectron spectroscopy (PES) of the TCNQ- anion produced using electrospray and cooled in a cryogenic ion trap. Photoelectron spectrum taken at 354.7 nm represents the detachment transition from the ground state of TCNQ- to that of neutral TCNQ with a short vibrational progression. The EA of TCNQ is measured accurately to be 3.383 ± 0.001 eV (27 289 ± 8 cm-1), compared to the 2.8 ± 0.1 eV value known in the literature and measured previously using collisional ionization technique. In addition, six vibrational peaks are observed in the photoelectron spectrum, yielding vibrational frequencies for three totally symmetric modes of TCNQ. Two-photon PES via a bound electronic excited state of TCNQ- at 3.100 eV yields a broad low kinetic energy peak due to fast internal conversion to vibrationally excited levels of the anion ground electronic state. The high EA measured for TCNQ underlies its ability as a good electron acceptor.

  15. Communication: Vibrationally resolved photoelectron spectroscopy of the tetracyanoquinodimethane (TCNQ) anion and accurate determination of the electron affinity of TCNQ

    SciTech Connect

    Zhu, Guo-Zhu; Wang, Lai-Sheng

    2015-12-14

    Tetracyanoquinodimethane (TCNQ) is widely used as an electron acceptor to form highly conducting organic charge-transfer solids. Surprisingly, the electron affinity (EA) of TCNQ is not well known and has never been directly measured. Here, we report vibrationally resolved photoelectron spectroscopy (PES) of the TCNQ{sup −} anion produced using electrospray and cooled in a cryogenic ion trap. Photoelectron spectrum taken at 354.7 nm represents the detachment transition from the ground state of TCNQ{sup −} to that of neutral TCNQ with a short vibrational progression. The EA of TCNQ is measured accurately to be 3.383 ± 0.001 eV (27 289 ± 8 cm{sup −1}), compared to the 2.8 ± 0.1 eV value known in the literature and measured previously using collisional ionization technique. In addition, six vibrational peaks are observed in the photoelectron spectrum, yielding vibrational frequencies for three totally symmetric modes of TCNQ. Two-photon PES via a bound electronic excited state of TCNQ{sup −} at 3.100 eV yields a broad low kinetic energy peak due to fast internal conversion to vibrationally excited levels of the anion ground electronic state. The high EA measured for TCNQ underlies its ability as a good electron acceptor.

  16. Communication: Vibrationally resolved photoelectron spectroscopy of the tetracyanoquinodimethane (TCNQ) anion and accurate determination of the electron affinity of TCNQ.

    PubMed

    Zhu, Guo-Zhu; Wang, Lai-Sheng

    2015-12-14

    Tetracyanoquinodimethane (TCNQ) is widely used as an electron acceptor to form highly conducting organic charge-transfer solids. Surprisingly, the electron affinity (EA) of TCNQ is not well known and has never been directly measured. Here, we report vibrationally resolved photoelectron spectroscopy (PES) of the TCNQ(-) anion produced using electrospray and cooled in a cryogenic ion trap. Photoelectron spectrum taken at 354.7 nm represents the detachment transition from the ground state of TCNQ(-) to that of neutral TCNQ with a short vibrational progression. The EA of TCNQ is measured accurately to be 3.383 ± 0.001 eV (27,289 ± 8 cm(-1)), compared to the 2.8 ± 0.1 eV value known in the literature and measured previously using collisional ionization technique. In addition, six vibrational peaks are observed in the photoelectron spectrum, yielding vibrational frequencies for three totally symmetric modes of TCNQ. Two-photon PES via a bound electronic excited state of TCNQ(-) at 3.100 eV yields a broad low kinetic energy peak due to fast internal conversion to vibrationally excited levels of the anion ground electronic state. The high EA measured for TCNQ underlies its ability as a good electron acceptor.

  17. Instructional Approach to Molecular Electronic Structure Theory

    ERIC Educational Resources Information Center

    Dykstra, Clifford E.; Schaefer, Henry F.

    1977-01-01

    Describes a graduate quantum mechanics projects in which students write a computer program that performs ab initio calculations on the electronic structure of a simple molecule. Theoretical potential energy curves are produced. (MLH)

  18. Computational Chemistry Using Modern Electronic Structure Methods

    ERIC Educational Resources Information Center

    Bell, Stephen; Dines, Trevor J.; Chowdhry, Babur Z.; Withnall, Robert

    2007-01-01

    Various modern electronic structure methods are now days used to teach computational chemistry to undergraduate students. Such quantum calculations can now be easily used even for large size molecules.

  19. Fast and accurate search for non-coding RNA pseudoknot structures in genomes

    PubMed Central

    Huang, Zhibin; Wu, Yong; Robertson, Joseph; Feng, Liang; Malmberg, Russell L.; Cai, Liming

    2008-01-01

    Motivation: Searching genomes for non-coding RNAs (ncRNAs) by their secondary structure has become an important goal for bioinformatics. For pseudoknot-free structures, ncRNA search can be effective based on the covariance model and CYK-type dynamic programming. However, the computational difficulty in aligning an RNA sequence to a pseudoknot has prohibited fast and accurate search of arbitrary RNA structures. Our previous work introduced a graph model for RNA pseudoknots and proposed to solve the structure–sequence alignment by graph optimization. Given k candidate regions in the target sequence for each of the n stems in the structure, we could compute a best alignment in time O(ktn) based upon a tree width t decomposition of the structure graph. However, to implement this method to programs that can routinely perform fast yet accurate RNA pseudoknot searches, we need novel heuristics to ensure that, without degrading the accuracy, only a small number of stem candidates need to be examined and a tree decomposition of a small tree width can always be found for the structure graph. Results: The current work builds on the previous one with newly developed preprocessing algorithms to reduce the values for parameters k and t and to implement the search method into a practical program, called RNATOPS, for RNA pseudoknot search. In particular, we introduce techniques, based on probabilistic profiling and distance penalty functions, which can identify for every stem just a small number k (e.g. k ≤ 10) of plausible regions in the target sequence to which the stem needs to align. We also devised a specialized tree decomposition algorithm that can yield tree decomposition of small tree width t (e.g. t ≤ 4) for almost all RNA structure graphs. Our experiments show that with RNATOPS it is possible to routinely search prokaryotic and eukaryotic genomes for specific RNA structures of medium to large sizes, including pseudoknots, with high sensitivity and high

  20. Controlling the Electronic Structure of Bilayer Graphene

    NASA Astrophysics Data System (ADS)

    Ohta, Taisuke; Bostwick, Aaron; Seyller, Thomas; Horn, Karsten; Rotenberg, Eli

    2006-08-01

    We describe the synthesis of bilayer graphene thin films deposited on insulating silicon carbide and report the characterization of their electronic band structure using angle-resolved photoemission. By selectively adjusting the carrier concentration in each layer, changes in the Coulomb potential led to control of the gap between valence and conduction bands. This control over the band structure suggests the potential application of bilayer graphene to switching functions in atomic-scale electronic devices.

  1. Accurate Electronic, Transport, and Bulk Properties of Wurtzite Beryllium Oxide (BeO)

    NASA Astrophysics Data System (ADS)

    Bamba, Cheick Oumar; Malozovsky, Yuriy; Franklin, Lashounda; Bagayoko, Diola

    We present ab-initio, self-consistent density functional theory (DFT) description of electronic, transport, and bulk properties of wurtzite Beryllium oxide (w-BeO). We used a local density approximation potential (LDA) and the linear combination of atomic orbitals (LCOA) formalism. Our implementation of the Bagayoko, Zhao, and Williams (BZW) method, as enhanced by Ekuma and Franklin (BZW-EF), ensures the full, physical content of our local density approximation (LDA) calculations - as per the derivation of DFT [AIP Advances, 4, 127104 (2014) We report the band gap, density of states, partial density of state, effective masses, and the bulk modulus. Our calculated band gap of 10.29 eV, using an experimental, room temperature lattice constant of 2.6979 A at room temperature is in agreement with the experimental value of 10.6 eV. Acknowledgments:This work was funded in part the US National Science Foundation [NSF, Award Nos. EPS-1003897, NSF (2010-2015)-RII-SUBR, and HRD-1002541], the US Department of Energy, National Nuclear Security Administration (NNSA, Award No. DE-NA0002630), LaSPACE, and LONI-SUBR.

  2. Accurate Zero Parameter Correlation Energy Functional Obtained from the Homogeneous Electron Gas with an Energy Gap

    NASA Astrophysics Data System (ADS)

    Krieger, J. B.; Chen, Jiqiang; Iafrate, G. J.; Savin, A.

    1998-03-01

    We have obtained an analytic approximation to E_c(r_g, ζ,G) where G is an energy gap separating the occupied and unoccupied states of a homogeneous electron gas for ζ=3D0 and ξ=3D1. When G=3D0, E_c(r_g, ζ) reduces to the usual LSD result. This functional is employed in calculating correlation energies for unpolarized atoms and ions for Z <= 18 by taking G[n]=3D1/8|nabla ln n|^2, which reduces to the ionization energy in the large r limit in an exact Kohn-Sham (KS) theory. The resulting functional is self-interaction-corrected employing a method which is invariant under a unitary transformation. We find that the application of this approach to the calculation of the Ec functional reduces the error in the LSD result by more than 95%. When the value of G is approximately corrected to include the effect of higher lying unoccupied localized states, the resulting values of Ec are within a few percent of the exact results.

  3. Accurate modeling of SiPM detectors coupled to FE electronics for timing performance analysis

    NASA Astrophysics Data System (ADS)

    Ciciriello, F.; Corsi, F.; Licciulli, F.; Marzocca, C.; Matarrese, G.; Del Guerra, A.; Bisogni, M. G.

    2013-08-01

    It has already been shown how the shape of the current pulse produced by a SiPM in response to an incident photon is sensibly affected by the characteristics of the front-end electronics (FEE) used to read out the detector. When the application requires to approach the best theoretical time performance of the detection system, the influence of all the parasitics associated to the coupling SiPM-FEE can play a relevant role and must be adequately modeled. In particular, it has been reported that the shape of the current pulse is affected by the parasitic inductance of the wiring connection between SiPM and FEE. In this contribution, we extend the validity of a previously presented SiPM model to account for the wiring inductance. Various combinations of the main performance parameters of the FEE (input resistance and bandwidth) have been simulated in order to evaluate their influence on the time accuracy of the detection system, when the time pick-off of each single event is extracted by means of a leading edge discriminator (LED) technique.

  4. The R-factor gap in macromolecular crystallography: an untapped potential for insights on accurate structures

    PubMed Central

    Holton, James M; Classen, Scott; Frankel, Kenneth A; Tainer, John A

    2014-01-01

    In macromolecular crystallography, the agreement between observed and predicted structure factors (Rcryst and Rfree) is seldom better than 20%. This is much larger than the estimate of experimental error (Rmerge). The difference between Rcryst and Rmerge is the R-factor gap. There is no such gap in small-molecule crystallography, for which calculated structure factors are generally considered more accurate than the experimental measurements. Perhaps the true noise level of macromolecular data is higher than expected? Or is the gap caused by inaccurate phases that trap refined models in local minima? By generating simulated diffraction patterns using the program MLFSOM, and including every conceivable source of experimental error, we show that neither is the case. Processing our simulated data yielded values that were indistinguishable from those of real data for all crystallographic statistics except the final Rcryst and Rfree. These values decreased to 3.8% and 5.5% for simulated data, suggesting that the reason for high R-factors in macromolecular crystallography is neither experimental error nor phase bias, but rather an underlying inadequacy in the models used to explain our observations. The present inability to accurately represent the entire macromolecule with both its flexibility and its protein-solvent interface may be improved by synergies between small-angle X-ray scattering, computational chemistry and crystallography. The exciting implication of our finding is that macromolecular data contain substantial hidden and untapped potential to resolve ambiguities in the true nature of the nanoscale, a task that the second century of crystallography promises to fulfill. Database Coordinates and structure factors for the real data have been submitted to the Protein Data Bank under accession 4tws. PMID:25040949

  5. Efficient implementation of the Hiller-Sucher-Feinberg identity for the accurate determination of the electron density

    NASA Astrophysics Data System (ADS)

    Challacombe, Matt; Cioslowski, Jerzy

    1994-01-01

    A new, highly optimized implementation of the Hiller-Sucher-Feinberg (HSF) identity is presented. The HSF identity, when applied to molecular wave functions calculated with Gaussian-type basis functions, not only improves the overall accuracy of the electron density by more than an order of magnitude, but also yields approximate cusps at nuclei. The three classes of molecular integrals, L, U, and V, which are encountered in the calculation of the HSF density, are derived in compact form. Efficient algorithms for the accurate evaluation of these integrals are detailed, including a novel approach to the necessary numerical quadratures and the thresholding of two-electron V integrals. Hartree-Fock (HF) electron densities calculated with both the conventional definition and from the HSF identity are compared to their respective HF limits for a variety of diatomic molecules and basis sets. The average error in the calculated HSF electron densities at non-hydrogen nuclei equals 0.17%, which constitutes a marked improvement over an error of 5.77% in the conventional densities.

  6. Accurate airway segmentation based on intensity structure analysis and graph-cut

    NASA Astrophysics Data System (ADS)

    Meng, Qier; Kitsaka, Takayuki; Nimura, Yukitaka; Oda, Masahiro; Mori, Kensaku

    2016-03-01

    This paper presents a novel airway segmentation method based on intensity structure analysis and graph-cut. Airway segmentation is an important step in analyzing chest CT volumes for computerized lung cancer detection, emphysema diagnosis, asthma diagnosis, and pre- and intra-operative bronchoscope navigation. However, obtaining a complete 3-D airway tree structure from a CT volume is quite challenging. Several researchers have proposed automated algorithms basically based on region growing and machine learning techniques. However these methods failed to detect the peripheral bronchi branches. They caused a large amount of leakage. This paper presents a novel approach that permits more accurate extraction of complex bronchial airway region. Our method are composed of three steps. First, the Hessian analysis is utilized for enhancing the line-like structure in CT volumes, then a multiscale cavity-enhancement filter is employed to detect the cavity-like structure from the previous enhanced result. In the second step, we utilize the support vector machine (SVM) to construct a classifier for removing the FP regions generated. Finally, the graph-cut algorithm is utilized to connect all of the candidate voxels to form an integrated airway tree. We applied this method to sixteen cases of 3D chest CT volumes. The results showed that the branch detection rate of this method can reach about 77.7% without leaking into the lung parenchyma areas.

  7. Beyond Ellipse(s): Accurately Modelling the Isophotal Structure of Galaxies with ISOFIT and CMODEL

    NASA Astrophysics Data System (ADS)

    Ciambur, B. C.

    2015-09-01

    This work introduces a new fitting formalism for isophotes that enables more accurate modeling of galaxies with non-elliptical shapes, such as disk galaxies viewed edge-on or galaxies with X-shaped/peanut bulges. Within this scheme, the angular parameter that defines quasi-elliptical isophotes is transformed from the commonly used, but inappropriate, polar coordinate to the “eccentric anomaly.” This provides a superior description of deviations from ellipticity, better capturing the true isophotal shape. Furthermore, this makes it possible to accurately recover both the surface brightness profile, using the correct azimuthally averaged isophote, and the two-dimensional model of any galaxy: the hitherto ubiquitous, but artificial, cross-like features in residual images are completely removed. The formalism has been implemented into the Image Reduction and Analysis Facility tasks Ellipse and Bmodel to create the new tasks “Isofit,” and “Cmodel.” The new tools are demonstrated here with application to five galaxies, chosen to be representative case-studies for several areas where this technique makes it possible to gain new scientific insight. Specifically: properly quantifying boxy/disky isophotes via the fourth harmonic order in edge-on galaxies, quantifying X-shaped/peanut bulges, higher-order Fourier moments for modeling bars in disks, and complex isophote shapes. Higher order (n > 4) harmonics now become meaningful and may correlate with structural properties, as boxyness/diskyness is known to do. This work also illustrates how the accurate construction, and subtraction, of a model from a galaxy image facilitates the identification and recovery of over-lapping sources such as globular clusters and the optical counterparts of X-ray sources.

  8. BEYOND ELLIPSE(S): ACCURATELY MODELING THE ISOPHOTAL STRUCTURE OF GALAXIES WITH ISOFIT AND CMODEL

    SciTech Connect

    Ciambur, B. C.

    2015-09-10

    This work introduces a new fitting formalism for isophotes that enables more accurate modeling of galaxies with non-elliptical shapes, such as disk galaxies viewed edge-on or galaxies with X-shaped/peanut bulges. Within this scheme, the angular parameter that defines quasi-elliptical isophotes is transformed from the commonly used, but inappropriate, polar coordinate to the “eccentric anomaly.” This provides a superior description of deviations from ellipticity, better capturing the true isophotal shape. Furthermore, this makes it possible to accurately recover both the surface brightness profile, using the correct azimuthally averaged isophote, and the two-dimensional model of any galaxy: the hitherto ubiquitous, but artificial, cross-like features in residual images are completely removed. The formalism has been implemented into the Image Reduction and Analysis Facility tasks Ellipse and Bmodel to create the new tasks “Isofit,” and “Cmodel.” The new tools are demonstrated here with application to five galaxies, chosen to be representative case-studies for several areas where this technique makes it possible to gain new scientific insight. Specifically: properly quantifying boxy/disky isophotes via the fourth harmonic order in edge-on galaxies, quantifying X-shaped/peanut bulges, higher-order Fourier moments for modeling bars in disks, and complex isophote shapes. Higher order (n > 4) harmonics now become meaningful and may correlate with structural properties, as boxyness/diskyness is known to do. This work also illustrates how the accurate construction, and subtraction, of a model from a galaxy image facilitates the identification and recovery of over-lapping sources such as globular clusters and the optical counterparts of X-ray sources.

  9. Foil support structure for large electron guns

    SciTech Connect

    Brucker, J.P.; Rose, E.A.

    1993-08-01

    This paper describes a novel support structure for a vacuum diode used to pump a gaseous laser with an electron beam. Conventional support structures are designed to hold a foil flat and rigid. This new structure takes advantage of the significantly greater strength of metals in pure tension, utilizing curved shapes for both foil and support structure. The shape of the foil is comparable to the skin of a balloon, and the shape of the support structures is comparable to the cables of a suspension bridge. This design allows a significant reduction in foil thickness and support structure mass, resulting in a lower electron-beam loss between diode and laser gas. In addition, the foil is pre-formed in the support structure at pressures higher than operating pressure. Therefore, the foil is operated far from the yield point. Increased reliability is anticipated.

  10. Perspective: Explicitly correlated electronic structure theory for complex systems

    NASA Astrophysics Data System (ADS)

    Grüneis, Andreas; Hirata, So; Ohnishi, Yu-ya; Ten-no, Seiichiro

    2017-02-01

    The explicitly correlated approach is one of the most important breakthroughs in ab initio electronic structure theory, providing arguably the most compact, accurate, and efficient ansatz for describing the correlated motion of electrons. Since Hylleraas first used an explicitly correlated wave function for the He atom in 1929, numerous attempts have been made to tackle the significant challenges involved in constructing practical explicitly correlated methods that are applicable to larger systems. These include identifying suitable mathematical forms of a correlated wave function and an efficient evaluation of many-electron integrals. R12 theory, which employs the resolution of the identity approximation, emerged in 1985, followed by the introduction of novel correlation factors and wave function ansätze, leading to the establishment of F12 theory in the 2000s. Rapid progress in recent years has significantly extended the application range of explicitly correlated theory, offering the potential of an accurate wave-function treatment of complex systems such as photosystems and semiconductors. This perspective surveys explicitly correlated electronic structure theory, with an emphasis on recent stochastic and deterministic approaches that hold significant promise for applications to large and complex systems including solids.

  11. Highly Accurate Structure-Based Prediction of HIV-1 Coreceptor Usage Suggests Intermolecular Interactions Driving Tropism.

    PubMed

    Kieslich, Chris A; Tamamis, Phanourios; Guzman, Yannis A; Onel, Melis; Floudas, Christodoulos A

    2016-01-01

    HIV-1 entry into host cells is mediated by interactions between the V3-loop of viral glycoprotein gp120 and chemokine receptor CCR5 or CXCR4, collectively known as HIV-1 coreceptors. Accurate genotypic prediction of coreceptor usage is of significant clinical interest and determination of the factors driving tropism has been the focus of extensive study. We have developed a method based on nonlinear support vector machines to elucidate the interacting residue pairs driving coreceptor usage and provide highly accurate coreceptor usage predictions. Our models utilize centroid-centroid interaction energies from computationally derived structures of the V3-loop:coreceptor complexes as primary features, while additional features based on established rules regarding V3-loop sequences are also investigated. We tested our method on 2455 V3-loop sequences of various lengths and subtypes, and produce a median area under the receiver operator curve of 0.977 based on 500 runs of 10-fold cross validation. Our study is the first to elucidate a small set of specific interacting residue pairs between the V3-loop and coreceptors capable of predicting coreceptor usage with high accuracy across major HIV-1 subtypes. The developed method has been implemented as a web tool named CRUSH, CoReceptor USage prediction for HIV-1, which is available at http://ares.tamu.edu/CRUSH/.

  12. Accurate ab initio tight-binding Hamiltonians: Effective tools for electronic transport and optical spectroscopy from first principles

    NASA Astrophysics Data System (ADS)

    D'Amico, Pino; Agapito, Luis; Catellani, Alessandra; Ruini, Alice; Curtarolo, Stefano; Fornari, Marco; Nardelli, Marco Buongiorno; Calzolari, Arrigo

    2016-10-01

    The calculations of electronic transport coefficients and optical properties require a very dense interpolation of the electronic band structure in reciprocal space that is computationally expensive and may have issues with band crossing and degeneracies. Capitalizing on a recently developed pseudoatomic orbital projection technique, we exploit the exact tight-binding representation of the first-principles electronic structure for the purposes of (i) providing an efficient strategy to explore the full band structure En(k ) , (ii) computing the momentum operator differentiating directly the Hamiltonian, and (iii) calculating the imaginary part of the dielectric function. This enables us to determine the Boltzmann transport coefficients and the optical properties within the independent particle approximation. In addition, the local nature of the tight-binding representation facilitates the calculation of the ballistic transport within the Landauer theory for systems with hundreds of atoms. In order to validate our approach we study the multivalley band structure of CoSb3 and a large core-shell nanowire using the ACBN0 functional. In CoSb3 we point the many band minima contributing to the electronic transport that enhance the thermoelectric properties; for the core-shell nanowire we identify possible mechanisms for photo-current generation and justify the presence of protected transport channels in the wire.

  13. Accurate, precise, and efficient theoretical methods to calculate anion-π interaction energies in model structures.

    PubMed

    Mezei, Pál D; Csonka, Gábor I; Ruzsinszky, Adrienn; Sun, Jianwei

    2015-01-13

    A correct description of the anion-π interaction is essential for the design of selective anion receptors and channels and important for advances in the field of supramolecular chemistry. However, it is challenging to do accurate, precise, and efficient calculations of this interaction, which are lacking in the literature. In this article, by testing sets of 20 binary anion-π complexes of fluoride, chloride, bromide, nitrate, or carbonate ions with hexafluorobenzene, 1,3,5-trifluorobenzene, 2,4,6-trifluoro-1,3,5-triazine, or 1,3,5-triazine and 30 ternary π-anion-π' sandwich complexes composed from the same monomers, we suggest domain-based local-pair natural orbital coupled cluster energies extrapolated to the complete basis-set limit as reference values. We give a detailed explanation of the origin of anion-π interactions, using the permanent quadrupole moments, static dipole polarizabilities, and electrostatic potential maps. We use symmetry-adapted perturbation theory (SAPT) to calculate the components of the anion-π interaction energies. We examine the performance of the direct random phase approximation (dRPA), the second-order screened exchange (SOSEX), local-pair natural-orbital (LPNO) coupled electron pair approximation (CEPA), and several dispersion-corrected density functionals (including generalized gradient approximation (GGA), meta-GGA, and double hybrid density functional). The LPNO-CEPA/1 results show the best agreement with the reference results. The dRPA method is only slightly less accurate and precise than the LPNO-CEPA/1, but it is considerably more efficient (6-17 times faster) for the binary complexes studied in this paper. For 30 ternary π-anion-π' sandwich complexes, we give dRPA interaction energies as reference values. The double hybrid functionals are much more efficient but less accurate and precise than dRPA. The dispersion-corrected double hybrid PWPB95-D3(BJ) and B2PLYP-D3(BJ) functionals perform better than the GGA and meta

  14. Efficient and Accurate Multiple-Phenotype Regression Method for High Dimensional Data Considering Population Structure.

    PubMed

    Joo, Jong Wha J; Kang, Eun Yong; Org, Elin; Furlotte, Nick; Parks, Brian; Hormozdiari, Farhad; Lusis, Aldons J; Eskin, Eleazar

    2016-12-01

    A typical genome-wide association study tests correlation between a single phenotype and each genotype one at a time. However, single-phenotype analysis might miss unmeasured aspects of complex biological networks. Analyzing many phenotypes simultaneously may increase the power to capture these unmeasured aspects and detect more variants. Several multivariate approaches aim to detect variants related to more than one phenotype, but these current approaches do not consider the effects of population structure. As a result, these approaches may result in a significant amount of false positive identifications. Here, we introduce a new methodology, referred to as GAMMA for generalized analysis of molecular variance for mixed-model analysis, which is capable of simultaneously analyzing many phenotypes and correcting for population structure. In a simulated study using data implanted with true genetic effects, GAMMA accurately identifies these true effects without producing false positives induced by population structure. In simulations with this data, GAMMA is an improvement over other methods which either fail to detect true effects or produce many false positive identifications. We further apply our method to genetic studies of yeast and gut microbiome from mice and show that GAMMA identifies several variants that are likely to have true biological mechanisms.

  15. Low-energy structures of benzene clusters with a novel accurate potential surface.

    PubMed

    Bartolomei, M; Pirani, F; Marques, J M C

    2015-12-05

    The benzene-benzene (Bz-Bz) interaction is present in several chemical systems and it is known to be crucial in understanding the specificity of important biological phenomena. In this work, we propose a novel Bz-Bz analytical potential energy surface which is fine-tuned on accurate ab initio calculations in order to improve its reliability. Once the Bz-Bz interaction is modeled, an analytical function for the energy of the Bzn clusters may be obtained by summing up over all pair potentials. We apply an evolutionary algorithm (EA) to discover the lowest-energy structures of Bzn clusters (for n=2-25), and the results are compared with previous global optimization studies where different potential functions were employed. Besides the global minimum, the EA also gives the structures of other low-lying isomers ranked by the corresponding energy. Additional ab initio calculations are carried out for the low-lying isomers of Bz3 and Bz4 clusters, and the global minimum is confirmed as the most stable structure for both sizes. Finally, a detailed analysis of the low-energy isomers of the n = 13 and 19 magic-number clusters is performed. The two lowest-energy Bz13 isomers show S6 and C3 symmetry, respectively, which is compatible with the experimental results available in the literature. The Bz19 structures reported here are all non-symmetric, showing two central Bz molecules surrounded by 12 nearest-neighbor monomers in the case of the five lowest-energy structures.

  16. Accurate response surface approximations for weight equations based on structural optimization

    NASA Astrophysics Data System (ADS)

    Papila, Melih

    Accurate weight prediction methods are vitally important for aircraft design optimization. Therefore, designers seek weight prediction techniques with low computational cost and high accuracy, and usually require a compromise between the two. The compromise can be achieved by combining stress analysis and response surface (RS) methodology. While stress analysis provides accurate weight information, RS techniques help to transmit effectively this information to the optimization procedure. The focus of this dissertation is structural weight equations in the form of RS approximations and their accuracy when fitted to results of structural optimizations that are based on finite element analyses. Use of RS methodology filters out the numerical noise in structural optimization results and provides a smooth weight function that can easily be used in gradient-based configuration optimization. In engineering applications RS approximations of low order polynomials are widely used, but the weight may not be modeled well by low-order polynomials, leading to bias errors. In addition, some structural optimization results may have high-amplitude errors (outliers) that may severely affect the accuracy of the weight equation. Statistical techniques associated with RS methodology are sought in order to deal with these two difficulties: (1) high-amplitude numerical noise (outliers) and (2) approximation model inadequacy. The investigation starts with reducing approximation error by identifying and repairing outliers. A potential reason for outliers in optimization results is premature convergence, and outliers of such nature may be corrected by employing different convergence settings. It is demonstrated that outlier repair can lead to accuracy improvements over the more standard approach of removing outliers. The adequacy of approximation is then studied by a modified lack-of-fit approach, and RS errors due to the approximation model are reduced by using higher order polynomials. In

  17. One-photon mass-analyzed threshold ionization (MATI) spectroscopy of pyridine: Determination of accurate ionization energy and cationic structure

    NASA Astrophysics Data System (ADS)

    Lee, Yu Ran; Kang, Do Won; Kim, Hong Lae; Kwon, Chan Ho

    2014-11-01

    Ionization energies and cationic structures of pyridine were intensively investigated utilizing one-photon mass-analyzed threshold ionization (MATI) spectroscopy with vacuum ultraviolet radiation generated by four-wave difference frequency mixing in Kr. The present one-photon high-resolution MATI spectrum of pyridine demonstrated a much finer and richer vibrational structure than that of the previously reported two-photon MATI spectrum. From the MATI spectrum and photoionization efficiency curve, the accurate ionization energy of the ionic ground state of pyridine was confidently determined to be 73 570 ± 6 cm-1 (9.1215 ± 0.0007 eV). The observed spectrum was almost completely assigned by utilizing Franck-Condon factors and vibrational frequencies calculated through adjustments of the geometrical parameters of cationic pyridine at the B3LYP/cc-pVTZ level. A unique feature unveiled through rigorous analysis was the prominent progression of the 10 vibrational mode, which corresponds to in-plane ring bending, and the combination of other totally symmetric fundamentals with the ring bending overtones, which contribute to the geometrical change upon ionization. Notably, the remaining peaks originate from the upper electronic state (2A2), as predicted by high-resolution photoelectron spectroscopy studies and symmetry-adapted cluster configuration interaction calculations. Based on the quantitatively good agreement between the experimental and calculated results, it was concluded that upon ionization the pyridine cation in the ground electronic state should have a planar structure of C2v symmetry through the C-N axis.

  18. One-photon mass-analyzed threshold ionization (MATI) spectroscopy of pyridine: Determination of accurate ionization energy and cationic structure

    SciTech Connect

    Lee, Yu Ran; Kang, Do Won; Kim, Hong Lae E-mail: hlkim@kangwon.ac.kr; Kwon, Chan Ho E-mail: hlkim@kangwon.ac.kr

    2014-11-07

    Ionization energies and cationic structures of pyridine were intensively investigated utilizing one-photon mass-analyzed threshold ionization (MATI) spectroscopy with vacuum ultraviolet radiation generated by four-wave difference frequency mixing in Kr. The present one-photon high-resolution MATI spectrum of pyridine demonstrated a much finer and richer vibrational structure than that of the previously reported two-photon MATI spectrum. From the MATI spectrum and photoionization efficiency curve, the accurate ionization energy of the ionic ground state of pyridine was confidently determined to be 73 570 ± 6 cm{sup −1} (9.1215 ± 0.0007 eV). The observed spectrum was almost completely assigned by utilizing Franck-Condon factors and vibrational frequencies calculated through adjustments of the geometrical parameters of cationic pyridine at the B3LYP/cc-pVTZ level. A unique feature unveiled through rigorous analysis was the prominent progression of the 10 vibrational mode, which corresponds to in-plane ring bending, and the combination of other totally symmetric fundamentals with the ring bending overtones, which contribute to the geometrical change upon ionization. Notably, the remaining peaks originate from the upper electronic state ({sup 2}A{sub 2}), as predicted by high-resolution photoelectron spectroscopy studies and symmetry-adapted cluster configuration interaction calculations. Based on the quantitatively good agreement between the experimental and calculated results, it was concluded that upon ionization the pyridine cation in the ground electronic state should have a planar structure of C{sub 2v} symmetry through the C-N axis.

  19. SCAN: An Efficient Density Functional Yielding Accurate Structures and Energies of Diversely-Bonded Materials

    NASA Astrophysics Data System (ADS)

    Sun, Jianwei

    The accuracy and computational efficiency of the widely used Kohn-Sham density functional theory (DFT) are limited by the approximation to its exchange-correlation energy Exc. The earliest local density approximation (LDA) overestimates the strengths of all bonds near equilibrium (even the vdW bonds). By adding the electron density gradient to model Exc, generalized gradient approximations (GGAs) generally soften the bonds to give robust and overall more accurate descriptions, except for the vdW interaction which is largely lost. Further improvement for covalent, ionic, and hydrogen bonds can be obtained by the computationally more expensive hybrid GGAs, which mix GGAs with the nonlocal exact exchange. Meta-GGAs are still semilocal in computation and thus efficient. Compared to GGAs, they add the kinetic energy density that enables them to recognize and accordingly treat different bonds, which no LDA or GGA can. We show here that the recently developed non-empirical strongly constrained and appropriately normed (SCAN) meta-GGA improves significantly over LDA and the standard Perdew-Burke-Ernzerhof GGA for geometries and energies of diversely-bonded materials (including covalent, metallic, ionic, hydrogen, and vdW bonds) at comparable efficiency. Often SCAN matches or improves upon the accuracy of a hybrid functional, at almost-GGA cost. This work has been supported by NSF under DMR-1305135 and CNS-09-58854, and by DOE BES EFRC CCDM under DE-SC0012575.

  20. Electronic structure and polarizability of metallic nanoshells

    NASA Astrophysics Data System (ADS)

    Prodan, E.; Nordlander, P.

    2002-01-01

    An efficient method for the calculation of the electronic structure of metallic nanoshells is developed. The method is applied to a large nanoshell (of 10 nm in diameter) containing more than 2.5×10 4 conduction electrons. The calculations show that the density of states of the nanoshell is relatively bulk-like. The frequency dependent polarizability is calculated and shown to display strong confinement effects and features similar to what is predicted by semi-classical electrodynamic theory.

  1. Discrete state model and accurate estimation of loop entropy of RNA secondary structures.

    PubMed

    Zhang, Jian; Lin, Ming; Chen, Rong; Wang, Wei; Liang, Jie

    2008-03-28

    Conformational entropy makes important contribution to the stability and folding of RNA molecule, but it is challenging to either measure or compute conformational entropy associated with long loops. We develop optimized discrete k-state models of RNA backbone based on known RNA structures for computing entropy of loops, which are modeled as self-avoiding walks. To estimate entropy of hairpin, bulge, internal loop, and multibranch loop of long length (up to 50), we develop an efficient sampling method based on the sequential Monte Carlo principle. Our method considers excluded volume effect. It is general and can be applied to calculating entropy of loops with longer length and arbitrary complexity. For loops of short length, our results are in good agreement with a recent theoretical model and experimental measurement. For long loops, our estimated entropy of hairpin loops is in excellent agreement with the Jacobson-Stockmayer extrapolation model. However, for bulge loops and more complex secondary structures such as internal and multibranch loops, we find that the Jacobson-Stockmayer extrapolation model has large errors. Based on estimated entropy, we have developed empirical formulae for accurate calculation of entropy of long loops in different secondary structures. Our study on the effect of asymmetric size of loops suggest that loop entropy of internal loops is largely determined by the total loop length, and is only marginally affected by the asymmetric size of the two loops. Our finding suggests that the significant asymmetric effects of loop length in internal loops measured by experiments are likely to be partially enthalpic. Our method can be applied to develop improved energy parameters important for studying RNA stability and folding, and for predicting RNA secondary and tertiary structures. The discrete model and the program used to calculate loop entropy can be downloaded at http://gila.bioengr.uic.edu/resources/RNA.html.

  2. Structural and electronic properties for atomic clusters

    NASA Astrophysics Data System (ADS)

    Sun, Yan

    We have studied the structural and electronic properties for different groups of atomic clusters by doing a global search on the potential energy surface using the Taboo Search in Descriptors Space (TSDS) method and calculating the energies with Kohn-Sham Density Functional Theory (KS-DFT). Our goal was to find the structural and electronic principles for predicting the structure and stability of clusters. For Ben (n = 3--20), we have found that the evolution of geometric and electronic properties with size reflects a change in the nature of the bonding from van der Waals to metallic and then bulk-like. The cluster sizes with extra stability agree well with the predictions of the jellium model. In the 4d series of transition metal (TM) clusters, as the d-type bonding becomes more important, the preferred geometric structure changes from icosahedral (Y, Zr), to distorted compact structures (Nb, Mo), and FCC or simple cubic crystal fragments (Tc, Ru, Rh) due to the localized nature of the d-type orbital. Analysis of relative isomer energies and their electronic density of states suggest that these clusters tend to follow a maximum hardness principle (MHP). For A4B12 clusters (A is divalent, B is monovalent), we found unusually large (on average 1.95 eV) HOMO-LUMO gap values. This shows the extra stability at an electronic closed shell (20 electrons) predicted by the jellium model. The importance of symmetry, closed electronic and ionic shells in stability is shown by the relative stability of homotops of Mg4Ag12 which also provides support for the hypothesis that clusters that satisfy more than one stability criterion ("double magic") should be particularly stable.

  3. Toward Hamiltonian Adaptive QM/MM: Accurate Solvent Structures Using Many-Body Potentials.

    PubMed

    Boereboom, Jelle M; Potestio, Raffaello; Donadio, Davide; Bulo, Rosa E

    2016-08-09

    Adaptive quantum mechanical (QM)/molecular mechanical (MM) methods enable efficient molecular simulations of chemistry in solution. Reactive subregions are modeled with an accurate QM potential energy expression while the rest of the system is described in a more approximate manner (MM). As solvent molecules diffuse in and out of the reactive region, they are gradually included into (and excluded from) the QM expression. It would be desirable to model such a system with a single adaptive Hamiltonian, but thus far this has resulted in distorted structures at the boundary between the two regions. Solving this long outstanding problem will allow microcanonical adaptive QM/MM simulations that can be used to obtain vibrational spectra and dynamical properties. The difficulty lies in the complex QM potential energy expression, with a many-body expansion that contains higher order terms. Here, we outline a Hamiltonian adaptive multiscale scheme within the framework of many-body potentials. The adaptive expressions are entirely general, and complementary to all standard (nonadaptive) QM/MM embedding schemes available. We demonstrate the merit of our approach on a molecular system defined by two different MM potentials (MM/MM'). For the long-range interactions a numerical scheme is used (particle mesh Ewald), which yields energy expressions that are many-body in nature. Our Hamiltonian approach is the first to provide both energy conservation and the correct solvent structure everywhere in this system.

  4. Defect Induced Electronic Structure of Uranofullerene

    PubMed Central

    Dai, Xing; Cheng, Cheng; Zhang, Wei; Xin, Minsi; Huai, Ping; Zhang, Ruiqin; Wang, Zhigang

    2013-01-01

    The interaction between the inner atoms/cluster and the outer fullerene cage is the source of various novel properties of endohedral metallofullerenes. Herein, we introduce an adatom-type spin polarization defect on the surface of a typical endohedral stable U2@C60 to predict the associated structure and electronic properties of U2@C61 based on the density functional theory method. We found that defect induces obvious changes in the electronic structure of this metallofullerene. More interestingly, the ground state of U2@C61 is nonet spin in contrast to the septet of U2@C60. Electronic structure analysis shows that the inner U atoms and the C ad-atom on the surface of the cage contribute together to this spin state, which is brought about by a ferromagnetic coupling between the spin of the unpaired electrons of the U atoms and the C ad-atom. This discovery may provide a possible approach to adapt the electronic structure properties of endohedral metallofullerenes. PMID:23439318

  5. Observation of Electronic Structure Minima in High-Harmonic Generation

    SciTech Connect

    Woerner, Hans Jakob; Villeneuve, D. M.; Niikura, Hiromichi; Bertrand, Julien B.; Corkum, P. B.

    2009-03-13

    We report detailed measurements of the high-harmonic spectra generated from argon atoms. The spectra exhibit a deep minimum that is shown to be independent of the laser intensity, and is thus a clear measure of the electronic structure of the atom. We show that exact field-free continuum wave functions reproduce the minimum, but plane wave and Coulomb wave functions do not. This remarkable observation suggests that electronic structure can be accurately determined in high-harmonic experiments despite the presence of the strong laser field. Our results clarify the relation between high-harmonic generation and photoelectron spectroscopy. The use of exact continuum functions also resolves the ambiguity associated with the choice of the dispersion relation.

  6. Compensation method for obtaining accurate, sub-micrometer displacement measurements of immersed specimens using electronic speckle interferometry.

    PubMed

    Fazio, Massimo A; Bruno, Luigi; Reynaud, Juan F; Poggialini, Andrea; Downs, J Crawford

    2012-03-01

    We proposed and validated a compensation method that accounts for the optical distortion inherent in measuring displacements on specimens immersed in aqueous solution. A spherically-shaped rubber specimen was mounted and pressurized on a custom apparatus, with the resulting surface displacements recorded using electronic speckle pattern interferometry (ESPI). Point-to-point light direction computation is achieved by a ray-tracing strategy coupled with customized B-spline-based analytical representation of the specimen shape. The compensation method reduced the mean magnitude of the displacement error induced by the optical distortion from 35% to 3%, and ESPI displacement measurement repeatability showed a mean variance of 16 nm at the 95% confidence level for immersed specimens. The ESPI interferometer and numerical data analysis procedure presented herein provide reliable, accurate, and repeatable measurement of sub-micrometer deformations obtained from pressurization tests of spherically-shaped specimens immersed in aqueous salt solution. This method can be used to quantify small deformations in biological tissue samples under load, while maintaining the hydration necessary to ensure accurate material property assessment.

  7. Boron Fullerenes: An Electronic Structure Study

    NASA Astrophysics Data System (ADS)

    Sadrzadeh, Arta; Pupysheva, Olga; Boustani, Ihsan; Yakobson, Boris

    2008-03-01

    Using ab initio calculations, we study electronic structure and frequency modes of B80, a member of boron fullerene family made from boron isomorphs of carbon fullerenes with additional atoms in the centers of hexagons. We also investigate geometrical and electronic structural properties of double-rings with various diameters, which are important as building blocks of boron nanotubes, and as the most stable clusters among the studied isomers with no more than 36 atoms. Double-rings also appear as building blocks of B80. Furthermore, we investigate the possibility of further stabilizing some of fullerenes by depleting them.

  8. The Electronic Structure of Heavy Element Complexes

    SciTech Connect

    Bursten, Bruce E.

    2000-07-25

    The area of study is the bonding in heavy element complexes, and the application of more sophisticated electronic structure theories. Progress is recounted in several areas: (a) technological advances and current methodologies - Relativistic effects are extremely important in gaining an understanding of the electronic structure of compounds of the actinides, transactinides, and other heavy elements. Therefore, a major part of the continual benchmarking was the proper inclusion of the appropriate relativistic effects for the properties under study. (b) specific applications - These include organoactinide sandwich complexes, CO activation by actinide atoms, and theoretical studies of molecules of the transactinide elements. Finally, specific directions in proposed research are described.

  9. Comparison of optimization methods for electronic-structure calculations

    NASA Astrophysics Data System (ADS)

    Garner, J.; Das, S. G.; Min, B. I.; Woodward, C.; Benedek, R.

    1989-06-01

    The performance of several local-optimization methods for calculating electronic structure is compared. The fictitious first-order equation of motion proposed by Williams and Soler is integrated numerically by three procedures: simple finite-difference integration, approximate analytical integration (the Williams-Soler algorithm), and the Born perturbation series. These techniques are applied to a model problem for which exact solutions are known, the Mathieu equation. The Williams-Soler algorithm and the second Born approximation converge equally rapidly, but the former involves considerably less computational effort and gives a more accurate converged solution. Application of the method of conjugate gradients to the Mathieu equation is discussed.

  10. Supersampling method for efficient grid-based electronic structure calculations.

    PubMed

    Ryu, Seongok; Choi, Sunghwan; Hong, Kwangwoo; Kim, Woo Youn

    2016-03-07

    The egg-box effect, the spurious variation of energy and force due to the discretization of continuous space, is an inherent vexing problem in grid-based electronic structure calculations. Its effective suppression allowing for large grid spacing is thus crucial for accurate and efficient computations. We here report that the supersampling method drastically alleviates it by eliminating the rapidly varying part of a target function along both radial and angular directions. In particular, the use of the sinc filtering function performs best because as an ideal low pass filter it clearly cuts out the high frequency region beyond allowed by a given grid spacing.

  11. Electronic and structural properties of functional nanostructures

    NASA Astrophysics Data System (ADS)

    Yang, Teng

    In this Thesis, I present a study of electronic and structural properties of functional nanostructures such as MoSxIy nanowires, self-assembled monolayer on top of metallic surfaces and structural changes induced in graphite by photo excitations. MoSxI y nanowires, which can be easily synthesized in one step, show many advantages over conventional carbon nanotubes in molecular electronics and many other applications. But how to self-assemble them into desired pattern for practical electronic network? Self-assembled monolayers of polymers on metallic surfaces may help to guide pattern formation of some nanomaterials such as MoSxIy nanowires. I have investigated the physical properties of these nanoscale wires and microscopic self-assembly mechanisms of patterns by total energy calculations combined with molecular dynamics simulations and structure optimization. First, I studied the stability of novel Molybdenum chaicohalide nanowires, a candidate for molecular electronics applications. Next, I investigated the self-assembly of nanoparticles into ordered arrays with the aid of a template. Such templates, I showed, can be formed by polymer adsorption on surfaces such as highly ordered pyrolytic graphite and Ag(111). Finally, I studied the physical origin of of structural changes induced in graphite by light in form of a femtosecond laser pulse.

  12. Structure refinement from precession electron diffraction data.

    PubMed

    Palatinus, Lukáš; Jacob, Damien; Cuvillier, Priscille; Klementová, Mariana; Sinkler, Wharton; Marks, Laurence D

    2013-03-01

    Electron diffraction is a unique tool for analysing the crystal structures of very small crystals. In particular, precession electron diffraction has been shown to be a useful method for ab initio structure solution. In this work it is demonstrated that precession electron diffraction data can also be successfully used for structure refinement, if the dynamical theory of diffraction is used for the calculation of diffracted intensities. The method is demonstrated on data from three materials - silicon, orthopyroxene (Mg,Fe)(2)Si(2)O(6) and gallium-indium tin oxide (Ga,In)(4)Sn(2)O(10). In particular, it is shown that atomic occupancies of mixed crystallographic sites can be refined to an accuracy approaching X-ray or neutron diffraction methods. In comparison with conventional electron diffraction data, the refinement against precession diffraction data yields significantly lower figures of merit, higher accuracy of refined parameters, much broader radii of convergence, especially for the thickness and orientation of the sample, and significantly reduced correlations between the structure parameters. The full dynamical refinement is compared with refinement using kinematical and two-beam approximations, and is shown to be superior to the latter two.

  13. Straightforward and accurate technique for post-coupler stabilization in drift tube linac structures

    NASA Astrophysics Data System (ADS)

    Khalvati, Mohammad Reza; Ramberger, Suitbert

    2016-04-01

    The axial electric field of Alvarez drift tube linacs (DTLs) is known to be susceptible to variations due to static and dynamic effects like manufacturing tolerances and beam loading. Post-couplers are used to stabilize the accelerating fields of DTLs against tuning errors. Tilt sensitivity and its slope have been introduced as measures for the stability right from the invention of post-couplers but since then the actual stabilization has mostly been done by tedious iteration. In the present article, the local tilt-sensitivity slope TSn' is established as the principal measure for stabilization instead of tilt sensitivity or some visual slope, and its significance is developed on the basis of an equivalent-circuit diagram of the DTL. Experimental and 3D simulation results are used to analyze its behavior and to define a technique for stabilization that allows finding the best post-coupler settings with just four tilt-sensitivity measurements. CERN's Linac4 DTL Tank 2 and Tank 3 have been stabilized successfully using this technique. The final tilt-sensitivity error has been reduced from ±100 %/MHz down to ±3 %/MHz for Tank 2 and down to ±1 %/MHz for Tank 3. Finally, an accurate procedure for tuning the structure using slug tuners is discussed.

  14. Structural stability augmentation system design using BODEDIRECT: A quick and accurate approach

    NASA Technical Reports Server (NTRS)

    Goslin, T. J.; Ho, J. K.

    1989-01-01

    A methodology is presented for a modal suppression control law design using flight test data instead of mathematical models to obtain the required gain and phase information about the flexible airplane. This approach is referred to as BODEDIRECT. The purpose of the BODEDIRECT program is to provide a method of analyzing the modal phase relationships measured directly from the airplane. These measurements can be achieved with a frequency sweep at the control surface input while measuring the outputs of interest. The measured Bode-models can be used directly for analysis in the frequency domain, and for control law design. Besides providing a more accurate representation for the system inputs and outputs of interest, this method is quick and relatively inexpensive. To date, the BODEDIRECT program has been tested and verified for computational integrity. Its capabilities include calculation of series, parallel and loop closure connections between Bode-model representations. System PSD, together with gain and phase margins of stability may be calculated for successive loop closures of multi-input/multi-output systems. Current plans include extensive flight testing to obtain a Bode-model representation of a commercial aircraft for design of a structural stability augmentation system.

  15. COSMOS: accurate detection of somatic structural variations through asymmetric comparison between tumor and normal samples.

    PubMed

    Yamagata, Koichi; Yamanishi, Ayako; Kokubu, Chikara; Takeda, Junji; Sese, Jun

    2016-05-05

    An important challenge in cancer genomics is precise detection of structural variations (SVs) by high-throughput short-read sequencing, which is hampered by the high false discovery rates of existing analysis tools. Here, we propose an accurate SV detection method named COSMOS, which compares the statistics of the mapped read pairs in tumor samples with isogenic normal control samples in a distinct asymmetric manner. COSMOS also prioritizes the candidate SVs using strand-specific read-depth information. Performance tests on modeled tumor genomes revealed that COSMOS outperformed existing methods in terms of F-measure. We also applied COSMOS to an experimental mouse cell-based model, in which SVs were induced by genome engineering and gamma-ray irradiation, followed by polymerase chain reaction-based confirmation. The precision of COSMOS was 84.5%, while the next best existing method was 70.4%. Moreover, the sensitivity of COSMOS was the highest, indicating that COSMOS has great potential for cancer genome analysis.

  16. Coding exon-structure aware realigner (CESAR) utilizes genome alignments for accurate comparative gene annotation

    PubMed Central

    Sharma, Virag; Elghafari, Anas; Hiller, Michael

    2016-01-01

    Identifying coding genes is an essential step in genome annotation. Here, we utilize existing whole genome alignments to detect conserved coding exons and then map gene annotations from one genome to many aligned genomes. We show that genome alignments contain thousands of spurious frameshifts and splice site mutations in exons that are truly conserved. To overcome these limitations, we have developed CESAR (Coding Exon-Structure Aware Realigner) that realigns coding exons, while considering reading frame and splice sites of each exon. CESAR effectively avoids spurious frameshifts in conserved genes and detects 91% of shifted splice sites. This results in the identification of thousands of additional conserved exons and 99% of the exons that lack inactivating mutations match real exons. Finally, to demonstrate the potential of using CESAR for comparative gene annotation, we applied it to 188 788 exons of 19 865 human genes to annotate human genes in 99 other vertebrates. These comparative gene annotations are available as a resource (http://bds.mpi-cbg.de/hillerlab/CESAR/). CESAR (https://github.com/hillerlab/CESAR/) can readily be applied to other alignments to accurately annotate coding genes in many other vertebrate and invertebrate genomes. PMID:27016733

  17. COSMOS: accurate detection of somatic structural variations through asymmetric comparison between tumor and normal samples

    PubMed Central

    Yamagata, Koichi; Yamanishi, Ayako; Kokubu, Chikara; Takeda, Junji; Sese, Jun

    2016-01-01

    An important challenge in cancer genomics is precise detection of structural variations (SVs) by high-throughput short-read sequencing, which is hampered by the high false discovery rates of existing analysis tools. Here, we propose an accurate SV detection method named COSMOS, which compares the statistics of the mapped read pairs in tumor samples with isogenic normal control samples in a distinct asymmetric manner. COSMOS also prioritizes the candidate SVs using strand-specific read-depth information. Performance tests on modeled tumor genomes revealed that COSMOS outperformed existing methods in terms of F-measure. We also applied COSMOS to an experimental mouse cell-based model, in which SVs were induced by genome engineering and gamma-ray irradiation, followed by polymerase chain reaction-based confirmation. The precision of COSMOS was 84.5%, while the next best existing method was 70.4%. Moreover, the sensitivity of COSMOS was the highest, indicating that COSMOS has great potential for cancer genome analysis. PMID:26833260

  18. C-A5-04: A Simple, Accurate SAS Algorithm for Electronic Abstraction of Race from Digitized Progress Notes

    PubMed Central

    Roblin, Douglas; Joski, Peter; Ren, Junling; Farmer, Robert; Baldwin, David; Carrell, David; Hart, Gene; Pardee, Roy; Bachman, Donald

    2010-01-01

    .006 (N=518 matches with Medicare surveys). McNemar’s tests were marginally significant for several datasets; and, misclassification was not systematically biased toward white or African American race. Conclusions: The SAS algorithm was highly accurate in electronically abstracting white and African American race from digitized progress notes of provider visits at KPG and GHC. We are expanding the evaluation to include additional sites and additional race/ ethnic categories (e.g. Asian, Hispanic).

  19. Accurate structures and binding energies for small water clusters: The water trimer

    SciTech Connect

    Nielsen, I.M.; Seidl, E.T.; Janssen, C.L.

    1999-05-01

    The global minimum on the water trimer potential energy surface has been investigated by means of second-order Mo/ller-Plesset (MP2) perturbation theory employing the series of correlation-consistent basis sets aug-cc-pVXZ (X = D, T, Q, 5, 6), the largest of which contains 1329 basis functions. Definitive predictions are made for the binding energy and equilibrium structure, and improved values are presented for the harmonic vibrational frequencies. A value of 15.82{plus_minus}0.05 kcal mol{sup {minus}1} is advanced for the infinite basis set frozen core MP2 binding energy, obtained by extrapolation of MP2 correlation energies computed at the aug-cc-pVQZ MP2 geometry. Inclusion of core correlation, using the aug-cc-pCV5Z basis set, has been found to increase the binding energy by 0.08 kcal mol{sup {minus}1}, and after consideration of core correlation and higher-order correlation effects, the classical binding energy for the water trimer is estimated to be 15.9{plus_minus}0.2 kcal mol{sup {minus}1}. A zero-point vibrational correction of {minus}5.43 kcal mol{sup {minus}1} has been computed from aug-cc-pVTZ MP2 harmonic vibrational frequencies. The accuracy of different computational schemes for obtaining the binding energies of the water dimer and trimer has been investigated, and computationally feasible methods are suggested for obtaining accurate structures and binding energies for larger water clusters.{copyright} {ital 1999 American Institute of Physics.}

  20. Structure-based constitutive model can accurately predict planar biaxial properties of aortic wall tissue.

    PubMed

    Polzer, S; Gasser, T C; Novak, K; Man, V; Tichy, M; Skacel, P; Bursa, J

    2015-03-01

    Structure-based constitutive models might help in exploring mechanisms by which arterial wall histology is linked to wall mechanics. This study aims to validate a recently proposed structure-based constitutive model. Specifically, the model's ability to predict mechanical biaxial response of porcine aortic tissue with predefined collagen structure was tested. Histological slices from porcine thoracic aorta wall (n=9) were automatically processed to quantify the collagen fiber organization, and mechanical testing identified the non-linear properties of the wall samples (n=18) over a wide range of biaxial stretches. Histological and mechanical experimental data were used to identify the model parameters of a recently proposed multi-scale constitutive description for arterial layers. The model predictive capability was tested with respect to interpolation and extrapolation. Collagen in the media was predominantly aligned in circumferential direction (planar von Mises distribution with concentration parameter bM=1.03 ± 0.23), and its coherence decreased gradually from the luminal to the abluminal tissue layers (inner media, b=1.54 ± 0.40; outer media, b=0.72 ± 0.20). In contrast, the collagen in the adventitia was aligned almost isotropically (bA=0.27 ± 0.11), and no features, such as families of coherent fibers, were identified. The applied constitutive model captured the aorta biaxial properties accurately (coefficient of determination R(2)=0.95 ± 0.03) over the entire range of biaxial deformations and with physically meaningful model parameters. Good predictive properties, well outside the parameter identification space, were observed (R(2)=0.92 ± 0.04). Multi-scale constitutive models equipped with realistic micro-histological data can predict macroscopic non-linear aorta wall properties. Collagen largely defines already low strain properties of media, which explains the origin of wall anisotropy seen at this strain level. The structure and mechanical

  1. Interdependence of spin structure, anion height and electronic structure of BaFe2As2

    NASA Astrophysics Data System (ADS)

    Sen, Smritijit; Ghosh, Haranath

    2016-05-01

    Superconducting as well as other electronic properties of Fe-based superconductors are quite sensitive to the structural parameters specially, on anion height which is intimately related to zAs, the fractional z co-ordinate of As atom. Due to presence of strong magnetic fluctuation in these Fe-based superconductors, optimized structural parameters (lattice parameters a, b, c) including zAs using density functional theory (DFT) under generalized gradient approximation (GGA) does not match experimental values accurately. In this work, we show that the optimized value of zAs is strongly influenced by the spin structures in the orthorhombic phase of BaFe2As2 system. We take all possible spin structures for the orthorhombic BaFe2As2 system and then optimize zAs. Using these optimized structures we calculate electronic structures like density of states, band structures etc., for each spin configurations. From these studies we show that the electronic structure, orbital order which is responsible for structural as well as related to nematic transition, are significantly influenced by the spin structures.

  2. Electronic structure of Mn and Fe oxides

    NASA Astrophysics Data System (ADS)

    Harrison, Walter

    2008-03-01

    We present a clear, simple tight-binding representation of the electronic structure and cohesive energy (energy of atomization) of MnO, Mn2O3, and MnO2, in which the formal charge states Mn^2+, Mn^3+, and Mn^4+, respectively, occur. It is based upon localized cluster orbitals for each Mn and its six oxygen neighbors. This approach is fundamentally different from local-density theory (or LDA+U), and perhaps diametrically opposite to Dynamical Mean Field Theory. Electronic states were calculated self-consistently using existing parameters [1], but it is found that the charge density is quite insensitive to charge state, so that the starting parameters are adequate. The cohesive energy per Mn is dominated by the transfer of two s electrons to oxygen p states, the same for all three compounds. The differing transfer of majority d electrons to oxygen p states, and the coupling between them, accounts for the observed variation in cohesion in the series. The same description applies to the perovskites, such as LaxSr1-xMnO3, and can be used for FeO, Fe2O3 (and FeO2), Because the formulation is local, it is equally applicable to impurities, defects and surfaces. [1] Walter A. Harrison, Elementary Electronic Structure, World Scientific (Singapore, 1999), revised edition (2004).

  3. Electronic structure engineering of various structural phases of phosphorene.

    PubMed

    Kaur, Sumandeep; Kumar, Ashok; Srivastava, Sunita; Tankeshwar, K

    2016-07-21

    We report the tailoring of the electronic structures of various structural phases of phosphorene (α-P, β-P, γ-P and δ-P) based homo- and hetero-bilayers through in-plane mechanical strains, vertical pressure and transverse electric field by employing density functional theory. In-plane biaxial strains have considerably modified the electronic bandgap of both homo- and hetero-bilayers while vertical pressure induces metallization in the considered structures. The γ-P homo-bilayer structure showed the highest ultimate tensile strength (UTS ∼ 6.21 GPa) upon in-plane stretching. Upon application of a transverse electric field, the variation in the bandgap of hetero-bilayers was found to be strongly dependent on the polarity of the applied field which is attributed to the counterbalance between the external electric field and the internal field induced by different structural phases and heterogeneity in the arrangements of atoms of each surface of the hetero-bilayer system. Our results demonstrate that the electronic structures of the considered hetero- and homo-bilayers of phosphorene could be modified by biaxial strain, pressure and electric field to achieve the desired properties for future nano-electronic devices.

  4. [Structured electronic consultation letter for shoulder disorders].

    PubMed

    Paloneva, Juha; Oikari, Marjo; Ylinen, Jari; Ingalsuo, Minna; Ilkka, Kunnamo; Ilkka, Kiviranta

    2012-01-01

    Referral to a specialist has a significant influence on management of the patient and costs associated with the treatments. However, development and research of the process by which patients are referred has been almost neglected. Expectations considering the purpose, contents, and timing of the referral of the consulting physician and the consultant do not always meet. A structured, electronic consultation letter was developed to respond this need. Functionality and interactivity are the key elements of the referral, including (1) an electronic referral letter to a specialist, (2) interactive education in clinical examination and management of shoulder disorders, and (3) an instrument of clinical examination and documentation of shoulder disorders.

  5. The electronic structure of nonpolyhex carbon nanotubes.

    PubMed

    László, István

    2004-01-01

    Generalizing the folding method to any periodic two-dimensional planar carbon structures we have calculated the corresponding electronic structures in the framework of the one orbital one site tight-binding (Bloch-Hückel) method by solving the eigenvalue problems in a numerical way. We discussed the metallic or the nonmetallic behavior of the nanotubes by applying the folding vectors of parameters (m, n). We extended the topological coordinate method to two-dimensional periodic planar structures as well. Nearly regular hexagonal, pentagonal, and heptagonal polygons were obtained. The curvatures of the final relaxed structures can be read from the sizes of the polygons. Thus relying only on the topological information we could describe the shape of the tubular structures and their conductivity behaviors.

  6. Probing Structural and Electronic Dynamics with Ultrafast Electron Microscopy

    SciTech Connect

    Plemmons, DA; Suri, PK; Flannigan, DJ

    2015-05-12

    In this Perspective, we provide an overview,of the field of ultrafast electron microscopy (UEM). We begin by briefly discussing the emergence of methods for probing ultrafast structural dynamics and the information that can be obtained. Distinctions are drawn between the two main types a probes for femtosecond (fs) dynamics fast electrons and X-ray photons and emphasis is placed on hour the nature of charged particles is exploited in ultrafast electron-based' experiments:. Following this, we describe the versatility enabled by the ease with which electron trajectories and velocities can be manipulated with transmission electron microscopy (TEM): hardware configurations, and we emphasize how this is translated to the ability to measure scattering intensities in real, reciprocal, and energy space from presurveyed and selected rianoscale volumes. Owing to decades of ongoing research and development into TEM instrumentation combined with advances in specimen holder technology, comprehensive experiments can be conducted on a wide range of materials in various phases via in situ methods. Next, we describe the basic operating concepts, of UEM, and we emphasize that its development has led to extension of several of the formidable capabilities of TEM into the fs domain, dins increasing the accessible temporal parameter spade by several orders of magnitude. We then divide UEM studies into those conducted in real (imaging), reciprocal (diffraction), and energy (spectroscopy) spate. We begin each of these sections by providing a brief description of the basic operating principles and the types of information that can be gathered followed by descriptions of how these approaches are applied in UM, the type of specimen parameter space that can be probed, and an example of the types of dynamics that can be resolved. We conclude with an Outlook section, wherein we share our perspective on some future directions of the field pertaining to continued instrument development and

  7. Accurate prediction of the electronic properties of low-dimensional graphene derivatives using a screened hybrid density functional.

    PubMed

    Barone, Veronica; Hod, Oded; Peralta, Juan E; Scuseria, Gustavo E

    2011-04-19

    Over the last several years, low-dimensional graphene derivatives, such as carbon nanotubes and graphene nanoribbons, have played a central role in the pursuit of a plausible carbon-based nanotechnology. Their electronic properties can be either metallic or semiconducting depending purely on morphology, but predicting their electronic behavior has proven challenging. The combination of experimental efforts with modeling of these nanometer-scale structures has been instrumental in gaining insight into their physical and chemical properties and the processes involved at these scales. Particularly, approximations based on density functional theory have emerged as a successful computational tool for predicting the electronic structure of these materials. In this Account, we review our efforts in modeling graphitic nanostructures from first principles with hybrid density functionals, namely the Heyd-Scuseria-Ernzerhof (HSE) screened exchange hybrid and the hybrid meta-generalized functional of Tao, Perdew, Staroverov, and Scuseria (TPSSh). These functionals provide a powerful tool for quantitatively studying structure-property relations and the effects of external perturbations such as chemical substitutions, electric and magnetic fields, and mechanical deformations on the electronic and magnetic properties of these low-dimensional carbon materials. We show how HSE and TPSSh successfully predict the electronic properties of these materials, providing a good description of their band structure and density of states, their work function, and their magnetic ordering in the cases in which magnetism arises. Moreover, these approximations are capable of successfully predicting optical transitions (first and higher order) in both metallic and semiconducting single-walled carbon nanotubes of various chiralities and diameters with impressive accuracy. This versatility includes the correct prediction of the trigonal warping splitting in metallic nanotubes. The results predicted

  8. Phosphorene Nanoribbons: Electronic Structure and Electric Field Modulation

    NASA Astrophysics Data System (ADS)

    Soleimanikahnoj, Sina; Knezevic, Irena

    Phosphorene, a newcomer among the 2D van der Waals materials, has attracted the attention of many scientists due to its promising electronic properties. Monolayer phosphorene has a direct band gap of 2 eV located at the Gamma point of the Brillouin zone. Increasing the number of layers reduces the bandgap due to the van der Waals interaction. The direct nature of the bandgap makes phosphorene particularly favorable for electronic transport and optoelectronic applications. While multilayer phosphorene sheets have been studied, the electronic properties of their 1D counterparts are still unexplored. An accurate tight-binding model was recently proposed for multilayer phosphorene nanoribbons. Employing this model along with the non-equilibrium Green's function method, we calculate the band structure and electronic properties of phosphorene nanoribbons. We show that, depending on the edge termination, phosphorene nanoribbons can be metallic or semiconducting. Our analysis also shows that the electronic properties of phosphorene nanoribbons are highly tunable by in-plane and out-of-plane electric fields. In metallic ribbons, the conductance can be switched off by a threshold electric field, similar to field effect devices. Support by the NSF through the University of Wisconsin MRSEC Seed (NSF Award DMR-1121288).

  9. Advancing Efficient All-Electron Electronic Structure Methods Based on Numeric Atom-Centered Orbitals for Energy Related Materials

    NASA Astrophysics Data System (ADS)

    Blum, Volker

    This talk describes recent advances of a general, efficient, accurate all-electron electronic theory approach based on numeric atom-centered orbitals; emphasis is placed on developments related to materials for energy conversion and their discovery. For total energies and electron band structures, we show that the overall accuracy is on par with the best benchmark quality codes for materials, but scalable to large system sizes (1,000s of atoms) and amenable to both periodic and non-periodic simulations. A recent localized resolution-of-identity approach for the Coulomb operator enables O (N) hybrid functional based descriptions of the electronic structure of non-periodic and periodic systems, shown for supercell sizes up to 1,000 atoms; the same approach yields accurate results for many-body perturbation theory as well. For molecular systems, we also show how many-body perturbation theory for charged and neutral quasiparticle excitation energies can be efficiently yet accurately applied using basis sets of computationally manageable size. Finally, the talk highlights applications to the electronic structure of hybrid organic-inorganic perovskite materials, as well as to graphene-based substrates for possible future transition metal compound based electrocatalyst materials. All methods described here are part of the FHI-aims code. VB gratefully acknowledges contributions by numerous collaborators at Duke University, Fritz Haber Institute Berlin, TU Munich, USTC Hefei, Aalto University, and many others around the globe.

  10. Accurate calculation of absolute one-electron redox potentials of some para-quinone derivatives in acetonitrile.

    PubMed

    Namazian, Mansoor; Coote, Michelle L

    2007-08-02

    Standard ab initio molecular orbital theory and density functional theory calculations have been used to calculate absolute one-electron reduction potentials of several para-quinones in acetonitrile. The high-level composite method of G3(MP2)-RAD is used for the gas-phase calculations and a continuum model of solvation, CPCM, has been employed to calculate solvation energies. To compare the theoretical reduction potentials with experiment, the reduction potentials relative to a standard calomel electrode (SCE) have also been calculated and compared to experimental values. The average error of the calculated reduction potentials using the proposed method is 0.07 V without any additional approximation. An ONIOM method in which the core is studied at G3(MP2)-RAD and the substituent effect of the rest of the molecule is studied at R(O)MP2/6-311+G(3df,2p) provides an accurate low-cost alternative to G3(MP2)-RAD for larger molecules.

  11. Electronic structure of worm-eaten graphene

    NASA Astrophysics Data System (ADS)

    Negishi, Hayato; Takeda, Kyozaburo

    2017-02-01

    We theoretically study the electronic structure of graphenes having several kinds of imperfections such as atomic vacancies and heteroatom replacements. We consider 12 different configurations of vacancies and 39 different geometries of heteroatom replacements in order to approximately take into account the random conformations of imperfections. To systematically provide a perspective understanding of the defect π and σ states caused by atomistic voids and/or vacancies and heteroatom replacements, we have carried out a tight-binding (TB) calculation. We study the orbital hybridization to clarify the origin and formation of π and σ defect states arising from such imperfections. We also discuss the electronic structure around the Fermi level through the TB band calculation.

  12. Electronic structure investigation of biphenylene films

    NASA Astrophysics Data System (ADS)

    Totani, R.; Grazioli, C.; Zhang, T.; Bidermane, I.; Lüder, J.; de Simone, M.; Coreno, M.; Brena, B.; Lozzi, L.; Puglia, C.

    2017-02-01

    Photoelectron Spectroscopy (PS) and Near-Edge X-ray Absorption Fine Structure (NEXAFS) spectroscopy have been used to investigate the occupied and empty density of states of biphenylene films of different thicknesses, deposited onto a Cu(111) crystal. The obtained results have been compared to previous gas phase spectra and single molecule Density Functional Theory (DFT) calculations to get insights into the possible modification of the molecular electronic structure in the film induced by the adsorption on a surface. Furthermore, NEXAFS measurements allowed characterizing the variation of the molecular arrangement with the film thickness and helped to clarify the substrate-molecule interaction.

  13. Atomic and Electronic Structure of Solids

    NASA Astrophysics Data System (ADS)

    Kaxiras, Efthimios

    2003-01-01

    Preface; Acknowledgements; Part I. Crystalline Solids: 1. Atomic structure of crystals; 2. The single-particle approximation; 3. Electrons in crystal potential; 4. Band structure of crystals; 5. Applications of band theory; 6. Lattice vibrations; 7. Magnetic behaviour of solids; 8. Superconductivity; Part II. Defects, Non-Crystalline Solids and Finite Structures: 9. Defects I: point defects; 10. Defects II: line defects; 11. Defects III: surfaces and interfaces; 12. Non-crystalline solids; 13. Finite structures; Part III. Appendices: A. Elements of classical electrodynamics; B. Elements of quantum mechanics; C. Elements of thermodynamics; D. Elements of statistical mechanics; E. Elements of elasticity theory; F. The Madelung energy; G. Mathematical tools; H. Nobel Prize citations; I. Units and symbols; References; Index.

  14. Controlling the Electronic Structure of Bilayer Graphene

    NASA Astrophysics Data System (ADS)

    Ohta, Taisuke; Bostwick, Aaron; McChesney, Jessica; Seyller, Thomas; Horn, Karsten; Rotenberg, Eli

    2007-03-01

    Carbon-based materials such as carbon nanotubes, graphite intercalation compounds, fullerenes, and ultrathin graphite films exhibit many exotic phenomena such as superconductivity and an anomalous quantum Hall effect. These findings have caused renewed interest in the electronic structure of ultrathin layers of graphene: a single honeycomb carbon layer that is the building block for these materials. There is a strong motivation to incorporate graphene multilayers into atomic-scale devices, spurred on by rapid progress in their fabrication and manipulation. We have synthesized bilayer graphene thin films deposited on insulating silicon carbide and characterized their electronic band structure using angle-resolved photoemission. By selectively adjusting the carrier concentration in each layer, changes in the Coulomb potential led to control of the gap between valence and conduction bands [1]. This control over the band structure suggests the potential application of bilayer graphene to switching functions in atomic scale electronic devices. [1] T. Ohta, A. Bostwick, T. Seyller, K. Horn, E. Rotenberg, Science, 313, 951 (2006).

  15. An efficient and accurate model of the coax cable feeding structure for FEM simulations

    NASA Technical Reports Server (NTRS)

    Gong, Jian; Volakis, John L.

    1995-01-01

    An efficient and accurate coax cable feed model is proposed for microstrip or cavity-backed patch antennas in the context of a hybrid finite element method (FEM). A TEM mode at the cavity-cable junction is assumed for the FEM truncation and system excitation. Of importance in this implementation is that the cavity unknowns are related to the model fields by enforcing an equipotential condition rather than field continuity. This scheme proved quite accurate and may be applied to other decomposed systems as a connectivity constraint. Comparisons of our predictions with input impedance measurements are presented and demonstrate the substantially improved accuracy of the proposed model.

  16. Modeling and simulation of electronic structure, material interface and random doping in nano electronic devices

    PubMed Central

    Chen, Duan; Wei, Guo-Wei

    2010-01-01

    The miniaturization of nano-scale electronic devices, such as metal oxide semiconductor field effect transistors (MOSFETs), has given rise to a pressing demand in the new theoretical understanding and practical tactic for dealing with quantum mechanical effects in integrated circuits. Modeling and simulation of this class of problems have emerged as an important topic in applied and computational mathematics. This work presents mathematical models and computational algorithms for the simulation of nano-scale MOSFETs. We introduce a unified two-scale energy functional to describe the electrons and the continuum electrostatic potential of the nano-electronic device. This framework enables us to put microscopic and macroscopic descriptions in an equal footing at nano scale. By optimization of the energy functional, we derive consistently-coupled Poisson-Kohn-Sham equations. Additionally, layered structures are crucial to the electrostatic and transport properties of nano transistors. A material interface model is proposed for more accurate description of the electrostatics governed by the Poisson equation. Finally, a new individual dopant model that utilizes the Dirac delta function is proposed to understand the random doping effect in nano electronic devices. Two mathematical algorithms, the matched interface and boundary (MIB) method and the Dirichlet-to-Neumann mapping (DNM) technique, are introduced to improve the computational efficiency of nano-device simulations. Electronic structures are computed via subband decomposition and the transport properties, such as the I-V curves and electron density, are evaluated via the non-equilibrium Green's functions (NEGF) formalism. Two distinct device configurations, a double-gate MOSFET and a four-gate MOSFET, are considered in our three-dimensional numerical simulations. For these devices, the current fluctuation and voltage threshold lowering effect induced by the discrete dopant model are explored. Numerical convergence

  17. Modeling and simulation of electronic structure, material interface and random doping in nano electronic devices.

    PubMed

    Chen, Duan; Wei, Guo-Wei

    2010-06-20

    The miniaturization of nano-scale electronic devices, such as metal oxide semiconductor field effect transistors (MOSFETs), has given rise to a pressing demand in the new theoretical understanding and practical tactic for dealing with quantum mechanical effects in integrated circuits. Modeling and simulation of this class of problems have emerged as an important topic in applied and computational mathematics. This work presents mathematical models and computational algorithms for the simulation of nano-scale MOSFETs. We introduce a unified two-scale energy functional to describe the electrons and the continuum electrostatic potential of the nano-electronic device. This framework enables us to put microscopic and macroscopic descriptions in an equal footing at nano scale. By optimization of the energy functional, we derive consistently-coupled Poisson-Kohn-Sham equations. Additionally, layered structures are crucial to the electrostatic and transport properties of nano transistors. A material interface model is proposed for more accurate description of the electrostatics governed by the Poisson equation. Finally, a new individual dopant model that utilizes the Dirac delta function is proposed to understand the random doping effect in nano electronic devices. Two mathematical algorithms, the matched interface and boundary (MIB) method and the Dirichlet-to-Neumann mapping (DNM) technique, are introduced to improve the computational efficiency of nano-device simulations. Electronic structures are computed via subband decomposition and the transport properties, such as the I-V curves and electron density, are evaluated via the non-equilibrium Green's functions (NEGF) formalism. Two distinct device configurations, a double-gate MOSFET and a four-gate MOSFET, are considered in our three-dimensional numerical simulations. For these devices, the current fluctuation and voltage threshold lowering effect induced by the discrete dopant model are explored. Numerical convergence

  18. Modeling and simulation of electronic structure, material interface and random doping in nano-electronic devices

    NASA Astrophysics Data System (ADS)

    Chen, Duan; Wei, Guo-Wei

    2010-06-01

    The miniaturization of nano-scale electronic devices, such as metal oxide semiconductor field effect transistors (MOSFETs), has given rise to a pressing demand in the new theoretical understanding and practical tactic for dealing with quantum mechanical effects in integrated circuits. Modeling and simulation of this class of problems have emerged as an important topic in applied and computational mathematics. This work presents mathematical models and computational algorithms for the simulation of nano-scale MOSFETs. We introduce a unified two-scale energy functional to describe the electrons and the continuum electrostatic potential of the nano-electronic device. This framework enables us to put microscopic and macroscopic descriptions in an equal footing at nano-scale. By optimization of the energy functional, we derive consistently coupled Poisson-Kohn-Sham equations. Additionally, layered structures are crucial to the electrostatic and transport properties of nano-transistors. A material interface model is proposed for more accurate description of the electrostatics governed by the Poisson equation. Finally, a new individual dopant model that utilizes the Dirac delta function is proposed to understand the random doping effect in nano-electronic devices. Two mathematical algorithms, the matched interface and boundary (MIB) method and the Dirichlet-to-Neumann mapping (DNM) technique, are introduced to improve the computational efficiency of nano-device simulations. Electronic structures are computed via subband decomposition and the transport properties, such as the I- V curves and electron density, are evaluated via the non-equilibrium Green's functions (NEGF) formalism. Two distinct device configurations, a double-gate MOSFET and a four-gate MOSFET, are considered in our three-dimensional numerical simulations. For these devices, the current fluctuation and voltage threshold lowering effect induced by the discrete dopant model are explored. Numerical

  19. Electronic bandstructure of semiconductor dilute bismide structures

    NASA Astrophysics Data System (ADS)

    Erucar, T.; Nutku, F.; Donmez, O.; Erol, A.

    2017-02-01

    In this work electronic band structure of dilute bismide GaAs/GaAs1-xBix quantum well structures with 1.8% and 3.75% bismuth compositions have been investigated both experimentally and theoretically. Photoluminescence (PL) measurements reveal that effective bandgap of the samples decreases approximately 65 meV per bismuth concentration. Temperature dependence of the effective bandgap is obtained to be higher for the sample with higher bismuth concentration. Moreover, both asymmetric characteristic at the low energy tail of the PL and full width at half maximum (FWHM) of PL peak increase with increasing bismuth composition as a result of increased Bi related defects located above valence band (VB). In order to explain composition dependence of the effective bandgap quantitatively, valence band anti-crossing (VBAC) model is used. Bismuth composition and temperature dependence of effective bandgap in a quantum well structure is modeled by solving Schrödinger equation and compared with experimental PL data.

  20. Thermal transfer structures coupling electronics card(s) to coolant-cooled structure(s)

    DOEpatents

    David, Milnes P; Graybill, David P; Iyengar, Madhusudan K; Kamath, Vinod; Kochuparambil, Bejoy J; Parida, Pritish R; Schmidt, Roger R

    2014-12-16

    Cooling apparatuses and coolant-cooled electronic systems are provided which include thermal transfer structures configured to engage with a spring force one or more electronics cards with docking of the electronics card(s) within a respective socket(s) of the electronic system. A thermal transfer structure of the cooling apparatus includes a thermal spreader having a first thermal conduction surface, and a thermally conductive spring assembly coupled to the conduction surface of the thermal spreader and positioned and configured to reside between and physically couple a first surface of an electronics card to the first surface of the thermal spreader with docking of the electronics card within a socket of the electronic system. The thermal transfer structure is, in one embodiment, metallurgically bonded to a coolant-cooled structure and facilitates transfer of heat from the electronics card to coolant flowing through the coolant-cooled structure.

  1. Determination of accurate electron chiral asymmetries in fenchone and camphor in the VUV range: sensitivity to isomerism and enantiomeric purity.

    PubMed

    Nahon, Laurent; Nag, Lipsa; Garcia, Gustavo A; Myrgorodska, Iuliia; Meierhenrich, Uwe; Beaulieu, Samuel; Wanie, Vincent; Blanchet, Valérie; Géneaux, Romain; Powis, Ivan

    2016-05-14

    Photoelectron circular dichroism (PECD) manifests itself as an intense forward/backward asymmetry in the angular distribution of photoelectrons produced from randomly-oriented enantiomers by photoionization with circularly-polarized light (CPL). As a sensitive probe of both photoionization dynamics and of the chiral molecular potential, PECD attracts much interest especially with the recent performance of related experiments with visible and VUV laser sources. Here we report, by use of quasi-perfect CPL VUV synchrotron radiation and using a double imaging photoelectron/photoion coincidence (i(2)PEPICO) spectrometer, new and very accurate values of the corresponding asymmetries on showcase chiral isomers: camphor and fenchone. These data have additionally been normalized to the absolute enantiopurity of the sample as measured by a chromatographic technique. They can therefore be used as benchmarking data for new PECD experiments, as well as for theoretical models. In particular we found, especially for the outermost orbital of both molecules, a good agreement with CMS-Xα PECD modeling over the whole VUV range. We also report a spectacular sensitivity of PECD to isomerism for slow electrons, showing large and opposite asymmetries when comparing R-camphor to R-fenchone (respectively -10% and +16% around 10 eV). In the course of this study, we could also assess the analytical potential of PECD. Indeed, the accuracy of the data we provide are such that limited departure from perfect enantiopurity in the sample we purchased could be detected and estimated in excellent agreement with the analysis performed in parallel via a chromatographic technique, establishing a new standard of accuracy, in the ±1% range, for enantiomeric excess measurement via PECD. The i(2)PEPICO technique allows correlating PECD measurements to specific parent ion masses, which would allow its application to analysis of complex mixtures.

  2. Low energy electrons and swift ion track structure in PADC

    SciTech Connect

    Fromm, Michel; Quinto, Michele A.; Weck, Philippe F.; Champion, Christophe

    2015-05-27

    The current work aims at providing an accurate description of the ion track-structure in poly-allyl dyglycol carbonate (PADC) by using an up-to-date Monte-Carlo code-called TILDA-V (a French acronym for Transport d’Ions Lourds Dans l’Aqua & Vivo). In this simulation the ion track-structure in PADC is mainly described in terms of ejected electrons with a particular attention done to the Low Energy Electrons (LEEs). After a brief reminder of the most important channels through which LEEs are prone to break a chemical bond, we will report on the simulated energetic distributions of LEEs along an ion track in PADC for particular incident energies located on both sides of the Bragg-peak position. Lastly, based on the rare data dealing with LEEs interaction with polymers or organic molecules, we will emphasise the role played by the LEEs in the formation of a latent track in PADC, and more particularly the one played by the sub-ionization electrons.

  3. Low energy electrons and swift ion track structure in PADC

    NASA Astrophysics Data System (ADS)

    Fromm, Michel; Quinto, Michele A.; Weck, Philippe F.; Champion, Christophe

    2015-10-01

    The current work aims at providing an accurate description of the ion track-structure in poly-allyl dyglycol carbonate (PADC) by using an up-to-date Monte-Carlo code-called TILDA-V (a French acronym for Transport d'Ions Lourds Dans l'Aqua & Vivo). In this simulation the ion track-structure in PADC is mainly described in terms of ejected electrons with a particular attention done to the Low Energy Electrons (LEEs). After a brief reminder of the most important channels through which LEEs are prone to break a chemical bond, we will report on the simulated energetic distributions of LEEs along an ion track in PADC for particular incident energies located on both sides of the Bragg-peak position. Finally, based on the rare data dealing with LEEs interaction with polymers or organic molecules, we will emphasise the role played by the LEEs in the formation of a latent track in PADC, and more particularly the one played by the sub-ionization electrons.

  4. Low energy electrons and swift ion track structure in PADC

    DOE PAGES

    Fromm, Michel; Quinto, Michele A.; Weck, Philippe F.; ...

    2015-05-27

    The current work aims at providing an accurate description of the ion track-structure in poly-allyl dyglycol carbonate (PADC) by using an up-to-date Monte-Carlo code-called TILDA-V (a French acronym for Transport d’Ions Lourds Dans l’Aqua & Vivo). In this simulation the ion track-structure in PADC is mainly described in terms of ejected electrons with a particular attention done to the Low Energy Electrons (LEEs). After a brief reminder of the most important channels through which LEEs are prone to break a chemical bond, we will report on the simulated energetic distributions of LEEs along an ion track in PADC for particularmore » incident energies located on both sides of the Bragg-peak position. Lastly, based on the rare data dealing with LEEs interaction with polymers or organic molecules, we will emphasise the role played by the LEEs in the formation of a latent track in PADC, and more particularly the one played by the sub-ionization electrons.« less

  5. A Discontinuous Galerkin Framework for Electronic Structure Calculations

    NASA Astrophysics Data System (ADS)

    Baczewski, Andrew; Shanker, Balasubramaniam; Mahanti, Subhendra; Levine, Benjamin

    2012-02-01

    It is generally accepted that a good basis set for any calculation should possess a number of salient features, including systematic improvability, adaptive resolution of multiscale features, and fidelity in capturing the pertinent physics. Considering the progenitors of most modern electronic structure basis sets to be Gaussian-type orbitals or planewaves, descendants of these methods have inherited features that address either systematic improvability (planewaves) or adaptive resolution (Gaussians) separately, and use a variety of tricks to differentiate the core and valence physics. Discontinuous Galerkin methods provide a framework for defining adaptive local basis sets, that may be based on these canonical basis sets, that can be mixed and matched to simultaneously achieve all of these goals. Our group is presently developing a new electronic structure code to enable Density Functional and Hartree-Fock calculations within this framework, particularly in the context of all-electron formulations wherein the accurate resolution of both core and valence states is necessary. Numerous implementation details will be addressed, including the incorporation of hardware- and software-based acceleration, such as GPU-based parallelism, and fast electrostatics solvers.

  6. Dark matter scattering on electrons: Accurate calculations of atomic excitations and implications for the DAMA and XENON experiments

    NASA Astrophysics Data System (ADS)

    Roberts, Benjamin; Dzuba, Vladimir; Flambaum, Victor; Gribakin, Gleb; Pospelov, Maxim; Stadnik, Yevgeny

    2017-01-01

    Atoms can become ionised during the scattering of a slow, heavy particle off a bound electron. Such an interaction involving leptophilic WIMP dark matter is a potential explanation for the anomalous 9 sigma annual modulation in the DAMA direct detection experiment. We show that due to non-analytic, cusp-like behavior of Coulomb functions close to the nucleus leads to an effective atomic structure enhancement. Crucially, we also show that electron relativistic effects are important. With this in mind, we perform high-accuracy relativistic calculations of atomic ionisation. We scan the parameter space: the DM mass, the mediator mass, and the effective coupling strength, to determine if there is any region that could potentially explain the DAMA signal. While we find that the modulation fraction of all events with energy deposition above 2 keV in NaI can be quite significant, reaching 50%, the relevant parts of the parameter space are excluded by the XENON10 and XENON100 experiments.

  7. Simulation of Accurate Vibrationally Resolved Electronic Spectra: the Integrated Time-Dependent and Time-Independent Framework

    NASA Astrophysics Data System (ADS)

    Baiardi, Alberto; Barone, Vincenzo; Biczysko, Malgorzata; Bloino, Julien

    2014-06-01

    Two parallel theories including Franck-Condon, Herzberg-Teller and Duschinsky (i.e., mode mixing) effects, allowing different approximations for the description of excited state PES have been developed in order to simulate realistic, asymmetric, electronic spectra line-shapes taking into account the vibrational structure: the so-called sum-over-states or time-independent (TI) method and the alternative time-dependent (TD) approach, which exploits the properties of the Fourier transform. The integrated TI-TD procedure included within a general purpose QM code [1,2], allows to compute one photon absorption, fluorescence, phosphorescence, electronic circular dichroism, circularly polarized luminescence and resonance Raman spectra. Combining both approaches, which use a single set of starting data, permits to profit from their respective advantages and minimize their respective limits: the time-dependent route automatically includes all vibrational states and, possibly, temperature effects, while the time-independent route allows to identify and assign single vibronic transitions. Interpretation, analysis and assignment of experimental spectra based on integrated TI-TD vibronic computations will be illustrated for challenging cases of medium-sized open-shell systems in the gas and condensed phases with inclusion of leading anharmonic effects. 1. V. Barone, A. Baiardi, M. Biczysko, J. Bloino, C. Cappelli, F. Lipparini Phys. Chem. Chem. Phys, 14, 12404, (2012) 2. A. Baiardi, V. Barone, J. Bloino J. Chem. Theory Comput., 9, 4097-4115 (2013)

  8. Extraordinary electronic properties in uncommon structure types

    NASA Astrophysics Data System (ADS)

    Ali, Mazhar Nawaz

    In this thesis I present the results of explorations into several uncommon structure types. In Chapter 1 I go through the underlying idea of how we search for new compounds with exotic properties in solid state chemistry. The ideas of exploring uncommon structure types, building up from the simple to the complex, using chemical intuition and thinking by analogy are discussed. Also, the history and basic concepts of superconductivity, Dirac semimetals, and magnetoresistance are briefly reviewed. In chapter 2, the 1s-InTaS2 structural family is introduced along with the discovery of a new member of the family, Ag0:79VS2; the synthesis, structure, and physical properties of two different polymorphs of the material are detailed. Also in this chapter, we report the observation of superconductivity in another 1s structure, PbTaSe2. This material is especially interesting due to it being very heavy (resulting in very strong spin orbit coulping (SOC)), layered, and noncentrosymmetric. Electronic structure calculations reveal the presence of a bulk 3D Dirac cone (very similar to graphene) that is gapped by SOC originating from the hexagonal Pb layer. In Chapter 3 we show the re-investigation of the crystal structure of the 3D Dirac semimetal, Cd3As2. It is found to be centrosymmetric, rather than noncentrosymmetric, and as such all bands are spin degenerate and there is a 4-fold degenerate bulk Dirac point at the Fermi level, making Cd3As2 a 3D electronic analog to graphene. Also, for the first time, scanning tunneling microscopy experiments identify a 2x2 surface reconstruction in what we identify as the (112) cleavage plane of single crystals; needle crystals grow with a [110] long axis direction. Lastly, in chapter 4 we report the discovery of "titanic" (sadly dubbed ⪉rge, nonsaturating" by Nature editors and given the acronym XMR) magnetoresistance (MR) in the non-magnetic, noncentrosymmetric, layered transition metal dichalcogenide WTe2; over 13 million% at 0.53 K in

  9. Pu electronic structure and photoelectron spectroscopy

    SciTech Connect

    Joyce, John J; Durakiewicz, Tomasz; Graham, Kevin S; Bauer, Eric D; Moore, David P; Mitchell, Jeremy N; Kennison, John A; Martin, Richard L; Roy, Lindsay E; Scuseria, G. E.

    2010-01-01

    The electronic structure of PuCoGa{sub 5}, Pu metal, and PuO{sub 2} is explored using photoelectron spectroscopy. Ground state electronic properties are inferred from temperature dependent photoemission near the Fermi energy for Pu metal. Angle-resolved photoemission details the energy vs. crystaJ momentum landscape near the Fermi energy for PuCoGa{sub 5} which shows significant dispersion in the quasiparticle peak near the Fermi energy. For the Mott insulators AnO{sub 2}(An = U, Pu) the photoemission results are compared against hybrid functional calculations and the model prediction of a cross over from ionic to covalent bonding is found to be reasonable.

  10. Structural and electronic properties of fluorographene.

    PubMed

    Samarakoon, Duminda K; Chen, Zhifan; Nicolas, Chantel; Wang, Xiao-Qian

    2011-04-04

    The structural and electronic characteristics of fluorinated graphene are investigated based on first-principles density-functional calculations. A detailed analysis of the energy order for stoichiometric fluorographene membranes indicates that there exists prominent chair and stirrup conformations, which correlate with the experimentally observed in-plane lattice expansion contrary to a contraction in graphane. The optical response of fluorographene is investigated using the GW-Bethe-Salpeter equation approach. The results are in good conformity with the experimentally observed optical gap and reveal predominant charge-transfer excitations arising from strong electron-hole interactions. The appearance of bounded excitons in the ultraviolet region can result in an excitonic Bose-Einstein condensate in fluorographene.

  11. Electronic Structure of Buried Interfaces - Oral Presentation

    SciTech Connect

    Porter, Zachary

    2015-08-25

    In the electronics behind computer memory storage, the speed and size are dictated by the performance of permanent magnets inside devices called read heads. Complicated magnets made of stacked layers of thin films can be engineered to have properties that yield more energy storage and faster switching times compared to conventional iron or cobalt magnets. The reason is that magnetism is a result of subtle interactions amongst electrons; just how neurons come together on large scales to make cat brains and dog brains, ensembles of electrons interact and become ferromagnets and paramagnets. These interactions make magnets too difficult to study in their entirety, so I focus on the interfaces between layers, which are responsible for the coupling materials physicists hope to exploit to produce next-generation magnets. This project, I study a transition metal oxide material called LSCO, Lanthanum Cobaltite, which can be a paramagnet or a ferromagnet depending on how you tweak the electronic structure. It exhibits an exciting behavior: its sum is greater than the sum of its parts. When another similar material called a LSMO, Lanthanum Manganite, is grown on top of it, their interface has a different type of magnetism from the LSCO or the LSMO! I hope to explain this by demonstrating differently charged ions in the interface. The typical method for quantifying this is x-ray absorption, but all conventional techniques look at every layer simultaneously, averaging the interfaces and the LSCO layers that we want to characterize separately. Instead, I must use a new reflectivity technique, which tracks the intensity of reflected x-rays at different angles, at energies near the absorption peaks of certain elements, to track changes in the electronic structure of the material. The samples were grown by collaborators at the Takamura group at U.C. Davis and probed with this “resonant reflectivity” technique on Beamline 2-1 at the Stanford Synchrotron Radiation Lightsource

  12. Studying the electronic and phononic structure of penta-graphane

    PubMed Central

    Einollahzadeh, Hamideh; Fazeli, Seyed Mahdi; Dariani, Reza Sabet

    2016-01-01

    Abstract In this paper, we theoretically consider a two dimensional nanomaterial which is a form of hydrogenated penta-graphene; we call it penta-graphane. This structure is obtained by adding hydrogen atoms to the sp2 bonded carbon atoms of penta-graphene. We investigate the thermodynamic and mechanical stability of penta-graphane. We also study the electronic and phononic structure of penta-graphane. Firstly, we use density functional theory with the revised Perdew–Burke–Ernzerhof approximation to compute the band structure. Then one–shot GW (G0W0) approach for estimating accurate band gap is applied. The indirect band gap of penta-graphane is 5.78 eV, which is close to the band gap of diamond. Therefore, this new structure is a good electrical insulator. We also investigate the structural stability of penta-graphane by computing the phonon structure. Finally, we calculate its specific heat capacity from the phonon density of states. Penta-graphane has a high specific heat capacity, and can potentially be used for storing and transferring energy. PMID:27877907

  13. Removal of Vesicle Structures From Transmission Electron Microscope Images

    PubMed Central

    Jensen, Katrine Hommelhoff; Sigworth, Fred J.; Brandt, Sami Sebastian

    2016-01-01

    In this paper, we address the problem of imaging membrane proteins for single-particle cryo-electron microscopy reconstruction of the isolated protein structure. More precisely, we propose a method for learning and removing the interfering vesicle signals from the micrograph, prior to reconstruction. In our approach, we estimate the subspace of the vesicle structures and project the micrographs onto the orthogonal complement of this subspace. We construct a 2d statistical model of the vesicle structure, based on higher order singular value decomposition (HOSVD), by considering the structural symmetries of the vesicles in the polar coordinate plane. We then propose to lift the HOSVD model to a novel hierarchical model by summarizing the multidimensional HOSVD coefficients by their principal components. Along with the model, a solid vesicle normalization scheme and model selection criterion are proposed to make a compact and general model. The results show that the vesicle structures are accurately separated from the background by the HOSVD model that is also able to adapt to the asymmetries of the vesicles. This is a promising result and suggests even wider applicability of the proposed approach in learning and removal of statistical structures. PMID:26642456

  14. Accurate quantum chemical calculations

    NASA Technical Reports Server (NTRS)

    Bauschlicher, Charles W., Jr.; Langhoff, Stephen R.; Taylor, Peter R.

    1989-01-01

    An important goal of quantum chemical calculations is to provide an understanding of chemical bonding and molecular electronic structure. A second goal, the prediction of energy differences to chemical accuracy, has been much harder to attain. First, the computational resources required to achieve such accuracy are very large, and second, it is not straightforward to demonstrate that an apparently accurate result, in terms of agreement with experiment, does not result from a cancellation of errors. Recent advances in electronic structure methodology, coupled with the power of vector supercomputers, have made it possible to solve a number of electronic structure problems exactly using the full configuration interaction (FCI) method within a subspace of the complete Hilbert space. These exact results can be used to benchmark approximate techniques that are applicable to a wider range of chemical and physical problems. The methodology of many-electron quantum chemistry is reviewed. Methods are considered in detail for performing FCI calculations. The application of FCI methods to several three-electron problems in molecular physics are discussed. A number of benchmark applications of FCI wave functions are described. Atomic basis sets and the development of improved methods for handling very large basis sets are discussed: these are then applied to a number of chemical and spectroscopic problems; to transition metals; and to problems involving potential energy surfaces. Although the experiences described give considerable grounds for optimism about the general ability to perform accurate calculations, there are several problems that have proved less tractable, at least with current computer resources, and these and possible solutions are discussed.

  15. The structure of the hydrated electron in bulk and at interfaces: Does the hydrated electron occupy a cavity?

    NASA Astrophysics Data System (ADS)

    Casey, Jennifer Ryan

    Since its discovery over fifty years ago, the hydrated electron has been the subject of much interest. Hydrated electrons, which are free electrons in water, are found in fields ranging from biochemistry to radiation chemistry, so it is important that we understand the structure and dynamics of this species. Because of its high reactivity, the hydrated electron's structure has proven difficult to pin down, especially its molecular details. One-electron mixed quantum/classical molecular dynamics simulations have proven useful in helping elucidate the structure of the hydrated electron. The picture most commonly presented from these studies is one of the electron residing in a cavity, disrupting the local water structure much like an anion the size of bromide. Our group has recently proposed a completely different structure for the hydrated electron, which arose from rigorous calculations of a new electron-water potential. The picture that emerged was of an electron that does not occupy a cavity but instead draws water within itself; this non-cavity electron resides in a region of enhanced water density. The one-electron cavity and non-cavity models all predict similar experimental observables that probe the electronic structure of the hydrated electron, such as the optical absorption spectrum, which makes it difficult to determine which model most accurately describes the true structure of the hydrated electron. In this thesis, we work to calculate experimental observables for various simulated cavity and non-cavity models that are particularly sensitive to the local water structure near the electron, in an effort to distinguish the various models from each other. Two particular observables we are interested in are the resonance Raman spectrum and the temperature dependent optical absorption spectrum of the hydrated electron. We find that for both of these experiments, only the non-cavity model has qualitative agreement with experiment; the cavity models miss the

  16. Surface structure and electronic properties of materials

    NASA Technical Reports Server (NTRS)

    Siekhaus, W. J.; Somorjai, G. A.

    1975-01-01

    A surface potential model is developed to explain dopant effects on chemical vapor deposition. Auger analysis of the interaction between allotropic forms of carbon and silicon films has shown Si-C formation for all forms by glassy carbon. LEED intensity measurements have been used to determine the mean square displacement of surface atoms of silicon single crystals, and electron loss spectroscopy has shown the effect of structure and impurities on surface states located within the band gap. A thin film of Al has been used to enhance film crystallinity at low temperature.

  17. Structural, electronic and optical properties of carbonnitride

    SciTech Connect

    Cohen, Marvin L.

    1996-01-31

    Carbon nitride was proposed as a superhard material and a structural prototype, Beta-C3N4, was examined using several theoretical models. Some reports claiming experimental verifications have been made recently. The current status of the theory and experiment is reviewed, and a detailed discussion is presented of calculations of the electronic and optical properties of this material. These calculations predict that Beta-C3N4 will have a minimum gap which is indirect at 6.4 plus or minus 0.5 eV. A discussion of the possibility of carbon nitride nanotubes is also presented.

  18. The CECAM Electronic Structure Library: community-driven development of software libraries for electronic structure simulations

    NASA Astrophysics Data System (ADS)

    Oliveira, Micael

    The CECAM Electronic Structure Library (ESL) is a community-driven effort to segregate shared pieces of software as libraries that could be contributed and used by the community. Besides allowing to share the burden of developing and maintaining complex pieces of software, these can also become a target for re-coding by software engineers as hardware evolves, ensuring that electronic structure codes remain at the forefront of HPC trends. In a series of workshops hosted at the CECAM HQ in Lausanne, the tools and infrastructure for the project were prepared, and the first contributions were included and made available online (http://esl.cecam.org). In this talk I will present the different aspects and aims of the ESL and how these can be useful for the electronic structure community.

  19. Electronic-structural dynamics in graphene.

    PubMed

    Gierz, Isabella; Cavalleri, Andrea

    2016-09-01

    We review our recent time- and angle-resolved photoemission spectroscopy experiments, which measure the transient electronic structure of optically driven graphene. For pump photon energies in the near infrared ([Formula: see text]), we have discovered the formation of a population-inverted state near the Dirac point, which may be of interest for the design of THz lasing devices and optical amplifiers. At lower pump photon energies ([Formula: see text]), for which interband absorption is not possible in doped samples, we find evidence for free carrier absorption. In addition, when mid-infrared pulses are made resonant with an infrared-active in-plane phonon of bilayer graphene ([Formula: see text]), a transient enhancement of the electron-phonon coupling constant is observed, providing interesting perspective for experiments that report light-enhanced superconductivity in doped fullerites in which a similar lattice mode was excited. All the studies reviewed here have important implications for applications of graphene in optoelectronic devices and for the dynamical engineering of electronic properties with light.

  20. Electronic-structural dynamics in graphene

    PubMed Central

    Gierz, Isabella; Cavalleri, Andrea

    2016-01-01

    We review our recent time- and angle-resolved photoemission spectroscopy experiments, which measure the transient electronic structure of optically driven graphene. For pump photon energies in the near infrared (ℏωpump=950 meV), we have discovered the formation of a population-inverted state near the Dirac point, which may be of interest for the design of THz lasing devices and optical amplifiers. At lower pump photon energies (ℏωpump<400 meV), for which interband absorption is not possible in doped samples, we find evidence for free carrier absorption. In addition, when mid-infrared pulses are made resonant with an infrared-active in-plane phonon of bilayer graphene (ℏωpump=200 meV), a transient enhancement of the electron-phonon coupling constant is observed, providing interesting perspective for experiments that report light-enhanced superconductivity in doped fullerites in which a similar lattice mode was excited. All the studies reviewed here have important implications for applications of graphene in optoelectronic devices and for the dynamical engineering of electronic properties with light. PMID:27822486

  1. Electron beam coupling to a metamaterial structure

    SciTech Connect

    French, David M.; Shiffler, Don; Cartwright, Keith

    2013-08-15

    Microwave metamaterials have shown promise in numerous applications, ranging from strip lines and antennas to metamaterial-based electron beam driven devices. In general, metamaterials allow microwave designers to obtain electromagnetic characteristics not typically available in nature. High Power Microwave (HPM) sources have in the past drawn inspiration from work done in the conventional microwave source community. In this article, the use of metamaterials in an HPM application is considered by using an effective medium model to determine the coupling of an electron beam to a metamaterial structure in a geometry similar to that of a dielectric Cerenkov maser. Use of the effective medium model allows for the analysis of a wide range of parameter space, including the “mu-negative,”“epsilon-negative,” and “double negative” regimes of the metamaterial. The physics of such a system are modeled analytically and by utilizing the particle-in-cell code ICEPIC. For this geometry and effective medium representation, optimum coupling of the electron beam to the metamaterial, and thus the optimum microwave or RF production, occurs in the epsilon negative regime of the metamaterial. Given that HPM tubes have been proposed that utilize a metamaterial, this model provides a rapid method of characterizing a source geometry that can be used to quickly understand the basic physics of such an HPM device.

  2. Analysis of boron carbides' electronic structure

    NASA Technical Reports Server (NTRS)

    Howard, Iris A.; Beckel, Charles L.

    1986-01-01

    The electronic properties of boron-rich icosahedral clusters were studied as a means of understanding the electronic structure of the icosahedral borides such as boron carbide. A lower bound was estimated on bipolaron formation energies in B12 and B11C icosahedra, and the associated distortions. While the magnitude of the distortion associated with bipolaron formation is similar in both cases, the calculated formation energies differ greatly, formation being much more favorable on B11C icosahedra. The stable positions of a divalent atom relative to an icosahedral borane was also investigated, with the result that a stable energy minimum was found when the atom is at the center of the borane, internal to the B12 cage. If incorporation of dopant atoms into B12 cages in icosahedral boride solids is feasible, novel materials might result. In addition, the normal modes of a B12H12 cluster, of the C2B10 cage in para-carborane, and of a B12 icosahedron of reduced (D sub 3d) symmetry, such as is found in the icosahedral borides, were calculated. The nature of these vibrational modes will be important in determining, for instance, the character of the electron-lattice coupling in the borides, and in analyzing the lattice contribution to the thermal conductivity.

  3. Experimental Benchmarking of Pu Electronic Structure

    SciTech Connect

    Tobin, J.G.; Moore, K.T.; Chung, B.W.; Wall, M.A.; Schwartz, A.J.; Ebbinghaus, B.B.; Butterfield, M.T.; Teslich, Jr., N.E.; Bliss, R.A.; Morton, S.A.; Yu, S.W.; Komesu, T.; Waddill, G.D.; van der Laan, G.; Kutepov, A.L.

    2008-10-30

    The standard method to determine the band structure of a condensed phase material is to (1) obtain a single crystal with a well defined surface and (2) map the bands with angle resolved photoelectron spectroscopy (occupied or valence bands) and inverse photoelectron spectroscopy (unoccupied or conduction bands). Unfortunately, in the case of Pu, the single crystals of Pu are either nonexistent, very small and/or having poorly defined surfaces. Furthermore, effects such as electron correlation and a large spin-orbit splitting in the 5f states have further complicated the situation. Thus, we have embarked upon the utilization of unorthodox electron spectroscopies, to circumvent the problems caused by the absence of large single crystals of Pu with well-defined surfaces. Our approach includes the techniques of resonant photoelectron spectroscopy, x-ray absorption spectroscopy, electron energy loss spectroscopy, Fano Effect measurements, and Bremstrahlung Isochromat Spectroscopy, including the utilization of micro-focused beams to probe single-crystallite regions of polycrystalline Pu samples.

  4. Experimental Benchmarking of Pu Electronic Structure

    SciTech Connect

    Tobin, J G; Moore, K T; Chung, B W; Wall, M A; Schwartz, A J; Ebbinghaus, B B; Butterfield, M T; Teslich, Jr., N E; Bliss, R A; Morton, S A; Yu, S W; Komesu, T; Waddill, G D; der Laan, G v; Kutepov, A L

    2005-10-13

    The standard method to determine the band structure of a condensed phase material is to (1) obtain a single crystal with a well defined surface and (2) map the bands with angle resolved photoelectron spectroscopy (occupied or valence bands) and inverse photoelectron spectroscopy (unoccupied or conduction bands). Unfortunately, in the case of Pu, the single crystals of Pu are either nonexistent, very small and/or having poorly defined surfaces. Furthermore, effects such as electron correlation and a large spin-orbit splitting in the 5f states have further complicated the situation. Thus, we have embarked upon the utilization of unorthodox electron spectroscopies, to circumvent the problems caused by the absence of large single crystals of Pu with well-defined surfaces. Our approach includes the techniques of resonant photoelectron spectroscopy [1], x-ray absorption spectroscopy [1,2,3,4], electron energy loss spectroscopy [2,3,4], Fano Effect measurements [5], and Bremstrahlung Isochromat Spectroscopy [6], including the utilization of micro-focused beams to probe single-crystallite regions of polycrystalline Pu samples. [2,3,6

  5. Revisiting the blind tests in crystal structure prediction: accurate energy ranking of molecular crystals.

    PubMed

    Asmadi, Aldi; Neumann, Marcus A; Kendrick, John; Girard, Pascale; Perrin, Marc-Antoine; Leusen, Frank J J

    2009-12-24

    In the 2007 blind test of crystal structure prediction hosted by the Cambridge Crystallographic Data Centre (CCDC), a hybrid DFT/MM method correctly ranked each of the four experimental structures as having the lowest lattice energy of all the crystal structures predicted for each molecule. The work presented here further validates this hybrid method by optimizing the crystal structures (experimental and submitted) of the first three CCDC blind tests held in 1999, 2001, and 2004. Except for the crystal structures of compound IX, all structures were reminimized and ranked according to their lattice energies. The hybrid method computes the lattice energy of a crystal structure as the sum of the DFT total energy and a van der Waals (dispersion) energy correction. Considering all four blind tests, the crystal structure with the lowest lattice energy corresponds to the experimentally observed structure for 12 out of 14 molecules. Moreover, good geometrical agreement is observed between the structures determined by the hybrid method and those measured experimentally. In comparison with the correct submissions made by the blind test participants, all hybrid optimized crystal structures (apart from compound II) have the smallest calculated root mean squared deviations from the experimentally observed structures. It is predicted that a new polymorph of compound V exists under pressure.

  6. Structure and navigation for electronic publishing

    NASA Astrophysics Data System (ADS)

    Tillinghast, John; Beretta, Giordano B.

    1998-01-01

    The sudden explosion of the World Wide Web as a new publication medium has given a dramatic boost to the electronic publishing industry, which previously was a limited market centered around CD-ROMs and on-line databases. While the phenomenon has parallels to the advent of the tabloid press in the middle of last century, the electronic nature of the medium brings with it the typical characteristic of 4th wave media, namely the acceleration in its propagation speed and the volume of information. Consequently, e-publications are even flatter than print media; Shakespeare's Romeo and Juliet share the same computer screen with a home-made plagiarized copy of Deep Throat. The most touted tool for locating useful information on the World Wide Web is the search engine. However, due to the medium's flatness, sought information is drowned in a sea of useless information. A better solution is to build tools that allow authors to structure information so that it can easily be navigated. We experimented with the use of ontologies as a tool to formulate structures for information about a specific topic, so that related concepts are placed in adjacent locations and can easily be navigated using simple and ergonomic user models. We describe our effort in building a World Wide Web based photo album that is shared among a small network of people.

  7. Efficient and accurate local approximations to coupled-electron pair approaches: An attempt to revive the pair natural orbital method

    NASA Astrophysics Data System (ADS)

    Neese, Frank; Wennmohs, Frank; Hansen, Andreas

    2009-03-01

    Coupled-electron pair approximations (CEPAs) and coupled-pair functionals (CPFs) have been popular in the 1970s and 1980s and have yielded excellent results for small molecules. Recently, interest in CEPA and CPF methods has been renewed. It has been shown that these methods lead to competitive thermochemical, kinetic, and structural predictions. They greatly surpass second order Møller-Plesset and popular density functional theory based approaches in accuracy and are intermediate in quality between CCSD and CCSD(T) in extended benchmark studies. In this work an efficient production level implementation of the closed shell CEPA and CPF methods is reported that can be applied to medium sized molecules in the range of 50-100 atoms and up to about 2000 basis functions. The internal space is spanned by localized internal orbitals. The external space is greatly compressed through the method of pair natural orbitals (PNOs) that was also introduced by the pioneers of the CEPA approaches. Our implementation also makes extended use of density fitting (or resolution of the identity) techniques in order to speed up the laborious integral transformations. The method is called local pair natural orbital CEPA (LPNO-CEPA) (LPNO-CPF). The implementation is centered around the concepts of electron pairs and matrix operations. Altogether three cutoff parameters are introduced that control the size of the significant pair list, the average number of PNOs per electron pair, and the number of contributing basis functions per PNO. With the conservatively chosen default values of these thresholds, the method recovers about 99.8% of the canonical correlation energy. This translates to absolute deviations from the canonical result of only a few kcal mol-1. Extended numerical test calculations demonstrate that LPNO-CEPA (LPNO-CPF) has essentially the same accuracy as parent CEPA (CPF) methods for thermochemistry, kinetics, weak interactions, and potential energy surfaces but is up to 500

  8. Multigrid Methods in Electronic Structure Calculations

    NASA Astrophysics Data System (ADS)

    Briggs, Emil

    1996-03-01

    Multigrid techniques have become the method of choice for a broad range of computational problems. Their use in electronic structure calculations introduces a new set of issues when compared to traditional plane wave approaches. We have developed a set of techniques that address these issues and permit multigrid algorithms to be applied to the electronic structure problem in an efficient manner. In our approach the Kohn-Sham equations are discretized on a real-space mesh using a compact representation of the Hamiltonian. The resulting equations are solved directly on the mesh using multigrid iterations. This produces rapid convergence rates even for ill-conditioned systems with large length and/or energy scales. The method has been applied to both periodic and non-periodic systems containing over 400 atoms and the results are in very good agreement with both theory and experiment. Example applications include a vacancy in diamond, an isolated C60 molecule, and a 64-atom cell of GaN with the Ga d-electrons in valence which required a 250 Ry cutoff. A particular strength of a real-space multigrid approach is its ready adaptability to massively parallel computer architectures. The compact representation of the Hamiltonian is especially well suited to such machines. Tests on the Cray-T3D have shown nearly linear scaling of the execution time up to the maximum number of processors (512). The MPP implementation has been used for studies of a large Amyloid Beta Peptide (C_146O_45N_42H_210) found in the brains of Alzheimers disease patients. Further applications of the multigrid method will also be described. (in collaboration D. J. Sullivan and J. Bernholc)

  9. Electronic Structure and Bonding in Complex Biomolecule

    NASA Astrophysics Data System (ADS)

    Ouyang, Lizhi

    2005-03-01

    For over a century vitamin B12 and its enzyme cofactor derivates have persistently attracted research efforts for their vital biological role, unique Co-C bonding, rich red-ox chemistry, and recently their candidacies as drug delivery vehicles etc. However, our understanding of this complex metalorganic molecule's efficient enzyme activated catalytic power is still controversial. We have for the first time calculated the electronic structure, Mulliken effective charge and bonding of a whole Vitamin B12 molecule without any structural simplification by first- principles approaches based on density functional theory using structures determined by high resolution X-ray diffraction. A partial density of states analysis shows excellent agreement with X-ray absorption data and has been used successfully to interpret measured optical absorption spectra. Mulliken bonding analysis of B12 and its derivatives reveal noticeable correlations between the two axial ligands which could be exploited by the enzyme to control the catalytic process. Our calculated X-ray near edge structure of B12 and its derivates using Slater's transition state theory are also in good agreement with experiments. The same approach has been applied to other B12 derivatives, ferrocene peptides, and recently DNA molecules.

  10. Seeking: Accurate Measurement Techniques for Deep-Bone Density and Structure

    NASA Technical Reports Server (NTRS)

    Sibonga, Jean

    2009-01-01

    We are seeking a clinically-useful technology with enough sensitivity to assess the microstructure of "spongy" bone that is found in the marrow cavities of whole bones. However, this technology must be for skeletal sites surrounded by layers of soft tissues, such as the spine and the hip. Soft tissue interferes with conventional imaging and using a more accessible area -- for example, the wrist or the ankle of limbs-- as a proxy for the less accessible skeletal regions, will not be accurate. A non-radioactive technology is strongly preferred.

  11. Accurate Determination of the Frequency Response Function of Submerged and Confined Structures by Using PZT-Patches†.

    PubMed

    Presas, Alexandre; Valentin, David; Egusquiza, Eduard; Valero, Carme; Egusquiza, Mònica; Bossio, Matias

    2017-03-22

    To accurately determine the dynamic response of a structure is of relevant interest in many engineering applications. Particularly, it is of paramount importance to determine the Frequency Response Function (FRF) for structures subjected to dynamic loads in order to avoid resonance and fatigue problems that can drastically reduce their useful life. One challenging case is the experimental determination of the FRF of submerged and confined structures, such as hydraulic turbines, which are greatly affected by dynamic problems as reported in many cases in the past. The utilization of classical and calibrated exciters such as instrumented hammers or shakers to determine the FRF in such structures can be very complex due to the confinement of the structure and because their use can disturb the boundary conditions affecting the experimental results. For such cases, Piezoelectric Patches (PZTs), which are very light, thin and small, could be a very good option. Nevertheless, the main drawback of these exciters is that the calibration as dynamic force transducers (relationship voltage/force) has not been successfully obtained in the past. Therefore, in this paper, a method to accurately determine the FRF of submerged and confined structures by using PZTs is developed and validated. The method consists of experimentally determining some characteristic parameters that define the FRF, with an uncalibrated PZT exciting the structure. These parameters, which have been experimentally determined, are then introduced in a validated numerical model of the tested structure. In this way, the FRF of the structure can be estimated with good accuracy. With respect to previous studies, where only the natural frequencies and mode shapes were considered, this paper discuss and experimentally proves the best excitation characteristic to obtain also the damping ratios and proposes a procedure to fully determine the FRF. The method proposed here has been validated for the structure vibrating

  12. Accurate Determination of the Frequency Response Function of Submerged and Confined Structures by Using PZT-Patches †

    PubMed Central

    Presas, Alexandre; Valentin, David; Egusquiza, Eduard; Valero, Carme; Egusquiza, Mònica; Bossio, Matias

    2017-01-01

    To accurately determine the dynamic response of a structure is of relevant interest in many engineering applications. Particularly, it is of paramount importance to determine the Frequency Response Function (FRF) for structures subjected to dynamic loads in order to avoid resonance and fatigue problems that can drastically reduce their useful life. One challenging case is the experimental determination of the FRF of submerged and confined structures, such as hydraulic turbines, which are greatly affected by dynamic problems as reported in many cases in the past. The utilization of classical and calibrated exciters such as instrumented hammers or shakers to determine the FRF in such structures can be very complex due to the confinement of the structure and because their use can disturb the boundary conditions affecting the experimental results. For such cases, Piezoelectric Patches (PZTs), which are very light, thin and small, could be a very good option. Nevertheless, the main drawback of these exciters is that the calibration as dynamic force transducers (relationship voltage/force) has not been successfully obtained in the past. Therefore, in this paper, a method to accurately determine the FRF of submerged and confined structures by using PZTs is developed and validated. The method consists of experimentally determining some characteristic parameters that define the FRF, with an uncalibrated PZT exciting the structure. These parameters, which have been experimentally determined, are then introduced in a validated numerical model of the tested structure. In this way, the FRF of the structure can be estimated with good accuracy. With respect to previous studies, where only the natural frequencies and mode shapes were considered, this paper discuss and experimentally proves the best excitation characteristic to obtain also the damping ratios and proposes a procedure to fully determine the FRF. The method proposed here has been validated for the structure vibrating

  13. Electronic structure of Ca, Sr, and Ba under pressure.

    NASA Technical Reports Server (NTRS)

    Animalu, A. O. E.; Heine, V.; Vasvari, B.

    1967-01-01

    Electronic band structure calculations phase of Ca, Sr and Ba over wide range of atomic volumes under pressure electronic band structure calculations for fcc phase of Ca, Sr and Ba over wide range of atomic volumes under pressure electronic band structure calculations for fcc phase of Ca, Sr and Ba over wide range of atomic volumes under pressure

  14. Accurate first-principles structures and energies of diversely bonded systems from an efficient density functional

    NASA Astrophysics Data System (ADS)

    Sun, Jianwei; Remsing, Richard C.; Zhang, Yubo; Sun, Zhaoru; Ruzsinszky, Adrienn; Peng, Haowei; Yang, Zenghui; Paul, Arpita; Waghmare, Umesh; Wu, Xifan; Klein, Michael L.; Perdew, John P.

    2016-09-01

    One atom or molecule binds to another through various types of bond, the strengths of which range from several meV to several eV. Although some computational methods can provide accurate descriptions of all bond types, those methods are not efficient enough for many studies (for example, large systems, ab initio molecular dynamics and high-throughput searches for functional materials). Here, we show that the recently developed non-empirical strongly constrained and appropriately normed (SCAN) meta-generalized gradient approximation (meta-GGA) within the density functional theory framework predicts accurate geometries and energies of diversely bonded molecules and materials (including covalent, metallic, ionic, hydrogen and van der Waals bonds). This represents a significant improvement at comparable efficiency over its predecessors, the GGAs that currently dominate materials computation. Often, SCAN matches or improves on the accuracy of a computationally expensive hybrid functional, at almost-GGA cost. SCAN is therefore expected to have a broad impact on chemistry and materials science.

  15. Electronic Structure of Pi Systems: Part III--Applications in Spectroscopy and Chemical Reactivity.

    ERIC Educational Resources Information Center

    Fox, Marye Anne; Matsen, F. A.

    1985-01-01

    Shows that electronic structure diagrams make more accurate predictions of spectral properties and chemical reactivity for simple pi systems than do either Huckel molecular orbital or valence bond theory alone. Topics addressed include absorption and photoelectron spectra, spin density distribution in radicals, and several problems regarding…

  16. Accurate heat of formation for fully hydrided LaNi5 via the all-electron FLAPW approach

    NASA Astrophysics Data System (ADS)

    Zhao, Yu-Jun; Freeman, A. J.

    2003-03-01

    It is known that the theoretical/computational determination of the heat of formation for La_2Ni_10H_14, Δ H_f, is overestimated theoretically by 50% or more when a pseudopotential approach is employed.(Tatsumi et al), PRB 64, 184105(2001) Does this signify a failure of first-principles total energy calculations? Here, we employ the full-potential linearized augmented plane wave (FLAPW) method(Wimmer, Krakauer, Weinert, and Freeman, PRB 24), 864 (1981). within both the generalized gradient approximation (GGA) and the localized density approximation (LDA), with a highly precise treatment of the total energy of H2 molecule due to its critical role in the calculation of Δ H_f. The calculated Δ Hf (-31.1 KJ/mol-H_2) and geometry structure within GGA are in excellent agreement with experiment ( ˜ -32 KJ/mol-H_2). While LDA calculations underestimate the volume of LaNi5 by 10.4%, the final value of Δ Hf (-31.2 KJ/mol-H_2) is also in excellent agreement with experiment. These results show the success rather than failure of first-principles calculations. The electronic properties indicate that charge transfer from the interstitial region to the H atoms stabilizes the fully hydrided LaNi_5.

  17. Reversible Hydrogen Storage Materials – Structure, Chemistry, and Electronic Structure

    SciTech Connect

    Robertson, Ian M.; Johnson, Duane D.

    2014-06-21

    To understand the processes involved in the uptake and release of hydrogen from candidate light-weight metal hydride storage systems, a combination of materials characterization techniques and first principle calculation methods have been employed. In addition to conventional microstructural characterization in the transmission electron microscope, which provides projected information about the through thickness microstructure, electron tomography methods were employed to determine the three-dimensional spatial distribution of catalyst species for select systems both before and after dehydrogenation. Catalyst species identification as well as compositional analysis of the storage material before and after hydrogen charging and discharging was performed using a combination of energy dispersive spectroscopy, EDS, and electron energy loss spectroscopy, EELS. The characterization effort was coupled with first-principles, electronic-structure and thermodynamic techniques to predict and assess meta-stable and stable phases, reaction pathways, and thermodynamic and kinetic barriers. Systems studied included:NaAlH4, CaH2/CaB6 and Ca(BH4)2, MgH2/MgB2, Ni-Catalyzed Magnesium Hydride, TiH2-Catalyzed Magnesium Hydride, LiBH4, Aluminum-based systems and Aluminum

  18. Electronic band structure of defect chalcopyrites

    NASA Astrophysics Data System (ADS)

    Jiang, Xiaoshu; Lambrecht, Walter R. L.

    2001-03-01

    The defect chalcopyrites of chemical composition II-III-VI4 in which II, III and VI mean group-II elements such as Cd or Hg, group-III elements such as Al and Ga and group-VI elements such as S, Se, Te, form an interesting family of semiconductor compounds with potential nonlinear optical applications. They can be thought of as derived from the regular I-III-VI2 chalcopyrites by doubling the formula unit and replacing the group I element, for example, Ag by the group-II element and a vacancy in an ordered manner. The chalcopyrites themselves are derived from II-VI compounds by replacing the group-II by a group I and a group-III element. In this contribution we present electronic band structure calculations of some of these compounds, calculated using the linear muffin-tin orbital method combined with the local density functional approximation. We discuss the relation of the band structures of the corresponding zincblende, chalcopyrite and defect chalcopyrite compounds. In particular, the role of the group I or group II d-band energy will be shown to be important. The trends with chemical substutions and the effects of structural distortions c/a and internal parameters accompanying the chemical distortion will be discussed.

  19. Accurate alkynyl radical structures from density functional calculations without Hartree-Fock exchange

    NASA Astrophysics Data System (ADS)

    Janesko, Benjamin G.; Proynov, Emil

    2017-02-01

    Density functional approximations (DFAs) often suffer from self-repulsion and delocalization errors which are reduced by exact (Hartree-Fock-like) exchange admixture. Oyeyemi and co-workers recently showed that several DFAs with little exact exchange incorrectly predict bent alkynyl radical geometries, giving errors in ab initio composite methods using density functional theory geometries [V. B. Oyeyemi et al., J. Phys. Chem. Lett. 3, 289 (2012)]. We show that the simple Hartree-Fock-Slater and Xα DFAs, which have substantial delocalization error, predict linear alkynyl radical geometries without incorporating exact exchange. Our Rung 3.5 DFAs, and rescaled generalized gradient approximations, can give either linear σ, bent σ -π , or nearly linear π radicals, all without incorporating exact exchange. This highlights the complexity of delocalization error, the utility of accurate empirical DFA geometries for ab initio composite methods, and the insights to be gained from Rung 3.5 DFAs.

  20. Electronic structures of ytterbocene-imine complexes

    SciTech Connect

    Da Re, R. E.; Kuehl, C. J.; John, K. D.; Morris, D. E.

    2004-01-01

    The electronic structures of complexes of the form [(C{sub 5}Me{sub 5}){sub 2}Yb(L)]{sup +/0} (L = bipyridine, phenanthroline, terpyridine) have been probed using cyclic voltammetry and electronic spectroscopy. Remarkably, the voltammetric data reveal that the imine-based LUMO is stabilized and the redox-active metal f orbital is destabilized by ca. 1 V each upon formation of the ytterbocene-imine adduct, which is presumably responsible for the [(f){sup 13}({pi}*(L)){sup 1}] charge-transfer ground state characteristic of these complexes. The ca. 0.8 V separation between ligand-based oxidation and metal-based reduction waves for each ytterbocene adduct correlates with the energy of its optically promoted {pi}*(L)-f(Yb) charge transfer (LMCT) transition (ca. 5000 cm{sup -1}). The coupling between this LMCT excited state and the {sup 2}F{sub 7/2} ground and {sup 2}F{sub 5/2} excited states of Yb(III) leads to unusually large intensities ({var_epsilon} {approx} 1000) for the metal-localized f-f bands, which will be discussed in the context of an intensity borrowing mechanism that invokes exchange between the ligand-based {sup 2}S and metal-based {sup 2}F spin states.

  1. Electron Liquids in Semiconductor Quantum Structures

    SciTech Connect

    Aron Pinczuk

    2009-05-25

    The groups led by Stormer and Pinczuk have focused this project on goals that seek the elucidation of novel many-particle effects that emerge in two-dimensional electron systems (2DES) as the result from fundamental quantum interactions. This experimental research is conducted under extreme conditions of temperature and magnetic field. From the materials point of view, the ultra-high mobility systems in GaAs/AlGaAs quantum structures continue to be at the forefront of this research. The newcomer materials are based on graphene, a single atomic layer of graphite. The graphene research is attracting enormous attention from many communities involved in condensed matter research. The investigated many-particle phenomena include the integer and fractional quantum Hall effect, composite fermions, and Dirac fermions, and a diverse group of electron solid and liquid crystal phases. The Stormer group performed magneto-transport experiments and far-infrared spectroscopy, while the Pinczuk group explores manifestations of such phases in optical spectra.

  2. Polyallelic structural variants can provide accurate, highly informative genetic markers focused on diagnosis and therapeutic targets: Accuracy vs. Precision.

    PubMed

    Roses, A D

    2016-02-01

    Structural variants (SVs) include all insertions, deletions, and rearrangements in the genome, with several common types of nucleotide repeats including single sequence repeats, short tandem repeats, and insertion-deletion length variants. Polyallelic SVs provide highly informative markers for association studies with well-phenotyped cohorts. SVs can influence gene regulation by affecting epigenetics, transcription, splicing, and/or translation. Accurate assays of polyallelic SV loci are required to define the range and allele frequency of variable length alleles.

  3. Electronic structures of reconstructed zigzag silicene nanoribbons

    SciTech Connect

    Ding, Yi E-mail: wangyanli-04@tsinghua.org.cn; Wang, Yanli E-mail: wangyanli-04@tsinghua.org.cn

    2014-02-24

    Edge states and magnetism are crucial for spintronic applications of nanoribbons. Here, using first-principles calculations, we explore structural stabilities and electronic properties of zigzag silicene nanoribbons (ZSiNRs) with Klein and pentagon-heptagon reconstructions. Comparing to unreconstructed zigzag edges, deformed bare pentagon-heptagon ones are favored under H-poor conditions, while H-rich surroundings stabilize di-hydrogenated Klein edges. These Klein edges have analogous magnetism to zigzag ones, which also possess the electric-field-induced half-metallicity of nanoribbons. Moreover, diverse magnetic states can be achieved by asymmetric Klein and zigzag edges into ZSiNRs, which could be transformed from antiferromagnetic-semiconductors to bipolar spin-gapless-semiconductors and ferromagnetic-metals depending on edge hydrogenations.

  4. Multilevel domain decomposition for electronic structure calculations

    SciTech Connect

    Barrault, M. . E-mail: maxime.barrault@edf.fr; Cances, E. . E-mail: cances@cermics.enpc.fr; Hager, W.W. . E-mail: hager@math.ufl.edu; Le Bris, C. . E-mail: lebris@cermics.enpc.fr

    2007-03-01

    We introduce a new multilevel domain decomposition method (MDD) for electronic structure calculations within semi-empirical and density functional theory (DFT) frameworks. This method iterates between local fine solvers and global coarse solvers, in the spirit of domain decomposition methods. Using this approach, calculations have been successfully performed on several linear polymer chains containing up to 40,000 atoms and 200,000 atomic orbitals. Both the computational cost and the memory requirement scale linearly with the number of atoms. Additional speed-up can easily be obtained by parallelization. We show that this domain decomposition method outperforms the density matrix minimization (DMM) method for poor initial guesses. Our method provides an efficient preconditioner for DMM and other linear scaling methods, variational in nature, such as the orbital minimization (OM) procedure.

  5. Structure, Stability and Electronic Properties of Nanodiamonds

    NASA Astrophysics Data System (ADS)

    Galli, Giulia

    Diamond nanoparticles, or nanodiamonds, have the most disparate origins. They are found in crude oil at concentrations up to thousands of parts per million, in meteorites, interstellar dust, and protoplanetary nebulae, as well as in certain sediment layers on Earth. They can also be produced in the laboratory by chemical vapor deposition or by detonating high explosive materials. Here we summarize what is known about nanodiamond sources; we then describe the atomic and electronic structure, and stability of diamond nanoparticles, highlighting the role of theory and computations in understanding and predicting their properties. Possible technological applications of thin films composed of nanodiamonds, ranging from micro-resonators to substrates for drug delivery, are briefly discussed.

  6. Computational methods toward accurate RNA structure prediction using coarse-grained and all-atom models.

    PubMed

    Krokhotin, Andrey; Dokholyan, Nikolay V

    2015-01-01

    Computational methods can provide significant insights into RNA structure and dynamics, bridging the gap in our understanding of the relationship between structure and biological function. Simulations enrich and enhance our understanding of data derived on the bench, as well as provide feasible alternatives to costly or technically challenging experiments. Coarse-grained computational models of RNA are especially important in this regard, as they allow analysis of events occurring in timescales relevant to RNA biological function, which are inaccessible through experimental methods alone. We have developed a three-bead coarse-grained model of RNA for discrete molecular dynamics simulations. This model is efficient in de novo prediction of short RNA tertiary structure, starting from RNA primary sequences of less than 50 nucleotides. To complement this model, we have incorporated additional base-pairing constraints and have developed a bias potential reliant on data obtained from hydroxyl probing experiments that guide RNA folding to its correct state. By introducing experimentally derived constraints to our computer simulations, we are able to make reliable predictions of RNA tertiary structures up to a few hundred nucleotides. Our refined model exemplifies a valuable benefit achieved through integration of computation and experimental methods.

  7. Electronic Structure Theory and Multi-Structural Statistical Thermodynamics for Computational Chemical Kinetics

    NASA Astrophysics Data System (ADS)

    Papajak, Ewa

    This thesis involves the development and application of methods for accurate computational thermochemistry. It consists of two parts. The first part focuses on the accuracy of the electronic structure methods. In particular, various augmentation schemes for one-electron basis sets are presented and tested for density functional theory (DFT) calculations and for wave function theory (WFT) calculations. The relationship between diffuse basis functions and basis set superposition error is discussed. For WFT, we also compare the efficiency of conventional one-electron basis-sets to that of newly developed explicitly correlated methods. Various ways of approaching the complete basis set limit of WFT calculations are explained, and recommendations are made for the best ways of achieving balance between the basis set size, higher-order correlation, and relativistic corrections. Applications of this work include computation of barrier heights, reaction and bond energies, electron affinities, ionization potentials, and noncovalent interactions. The second part of this thesis focuses on the problem of incorporating multi-structural effects and anharmonicity effects in the torsional modes into partition function calculations, especially by using a new multi-structural torsion (MS-T) method. Applications of the MS-T method include partition functions of molecules and radicals important for combustion research. These partition functions are used to obtain thermodynamic functions that are the most reliable results available to date for these molecules. The multi-structural approach is also applied to two kinetics problems: The hydrogen abstraction from carbon-3 of 1-butanol by hydroperoxyl radical; The 1,5-hydrogen shift isomerization of the 1-butoxyl radical. In both cases multi-structural effects play an important role in the final results.

  8. Experimental and theoretical electronic structure of quinacridone

    NASA Astrophysics Data System (ADS)

    Lüftner, Daniel; Refaely-Abramson, Sivan; Pachler, Michael; Resel, Roland; Ramsey, Michael G.; Kronik, Leeor; Puschnig, Peter

    2014-08-01

    The energy positions of frontier orbitals in organic electronic materials are often studied experimentally by (inverse) photoemission spectroscopy and theoretically within density functional theory. However, standard exchange-correlation functionals often result in too small fundamental gaps, may lead to wrong orbital energy ordering, and do not capture polarization-induced gap renormalization. Here we examine these issues and a strategy for overcoming them by studying the gas phase and bulk electronic structure of the organic molecule quinacridone (5Q), a promising material with many interesting properties for organic devices. Experimentally we perform angle-resolved photoemission spectroscopy (ARUPS) on thin films of the crystalline β phase of 5Q. Theoretically we employ an optimally tuned range-separated hybrid functional (OT-RSH) within density functional theory. For the gas phase molecule, our OT-RSH result for the ionization potential (IP) represents a substantial improvement over the semilocal PBE and the PBE0 hybrid functional results, producing an IP in quantitative agreement with experiment. For the bulk crystal we take into account the correct screening in the bulk, using the recently developed optimally tuned screened range-separated hybrid (OT-SRSH) approach, while retaining the optimally tuned parameters for the range separation and the short-range Fock exchange. This leads to a band gap narrowing due to polarization effects and results in a valence band spectrum in excellent agreement with experimental ARUPS data, with respect to both peak positions and heights. Finally, full-frequency G0W0 results based on a hybrid functional starting point are shown to agree with the OT-SRSH approach, improving substantially on the PBE-starting point.

  9. Nonlinearity in structural and electronic materials

    SciTech Connect

    Bishop, A.R.; Beardmore, K.M.; Ben-Naim, E.

    1997-11-01

    This is the final report of a three-year, Laboratory Directed Research and Development (LDRD) project at the Los Alamos National Laboratory (LANL). The project strengthens a nonlinear technology base relevant to a variety of problems arising in condensed matter and materials science, and applies this technology to those problems. In this way the controlled synthesis of, and experiments on, novel electronic and structural materials provide an important focus for nonlinear science, while nonlinear techniques help advance the understanding of the scientific principles underlying the control of microstructure and dynamics in complex materials. This research is primarily focused on four topics: (1) materials microstructure: growth and evolution, and porous media; (2) textures in elastic/martensitic materials; (3) electro- and photo-active polymers; and (4) ultrafast photophysics in complex electronic materials. Accomplishments included the following: organization of a ``Nonlinear Materials`` seminar series and international conferences including ``Fracture, Friction and Deformation,`` ``Nonequilibrium Phase Transitions,`` and ``Landscape Paradigms in Physics and Biology``; invited talks at international conference on ``Synthetic Metals,`` ``Quantum Phase Transitions,`` ``1996 CECAM Euroconference,`` and the 1995 Fall Meeting of the Materials Research Society; large-scale simulations and microscopic modeling of nonlinear coherent energy storage at crack tips and sliding interfaces; large-scale simulation and microscopic elasticity theory for precursor microstructure and dynamics at solid-solid diffusionless phase transformations; large-scale simulation of self-assembling organic thin films on inorganic substrates; analysis and simulation of smoothing of rough atomic surfaces; and modeling and analysis of flux pattern formation in equilibrium and nonequilibrium Josephson junction arrays and layered superconductors.

  10. Accurate analysis of electron transfer from quantum dots to metal oxides in quantum dot sensitized solar cells

    NASA Astrophysics Data System (ADS)

    Javad Fahimi, Mohammad; Fathi, Davood; Ansari-Rad, Mehdi

    2015-09-01

    Electron transfer rate from quantum dot (QD) to metal oxide (MO) in quantum dot sensitized solar cells (QDSSCs) has an important role in the efficiency. In this work, we analyse the electron transfer rate from CdSe, CdS and CdTe QDs to TiO2, ZnO and SnO2 MOs by extending the related equations with considering various effects, based on the Marcus theory. In this regard, the effects of QD diameter, QD-MO spacing, the crystalline defects, temperature, and the reorganizational energy, on the electron transfer rate are investigated. The results show that, the maximum electron transfer rate is achieved for CdTe QD with the mentioned three MOs. Moreover, in order to direct the designer to reach the appropriate QDs-MOs combinations for obtaining the maximum electron transfer rate, the average electron transfer rate for various combinations is calculated. For the verification of simulation method, a part of work has been compared with the previous experimental and theoretical results, which indicates the correctness of our simulation algorithm.

  11. Electronic structure and phase equilibria in ternary substitutional alloys

    SciTech Connect

    Traiber, A.J.S.; Allen, S.M.; Turchi, P.E.A.; Waterstrat, R.M.

    1996-04-26

    A reliable, consistent scheme to study phase equilibria in ternary substitutional alloys based on the tight-binding approximation is presented. With electronic parameters from linear muffin-tin orbital calculations, the computed density of states and band structures compare well with those from more accurate {ital ab}{ital initio} calculations. Disordered alloys are studied within the tight-binding coherent-potential approximation extended to alloys; energetics of ordered systems are obtained through effective pair interactions computed with the general perturbation method; and partially ordered alloys are studied with a novel simplification of the molecular coherent-potential approximation combined with the general perturbation method. The formalism is applied to bcc-based Zr-Ru-Pd alloys which are promising candidates for medical implant devices. Using energetics obtained from the above scheme, we apply the cluster- variation method to study phase equilibria for particular pseudo- binary alloys and show that results are consistent with observed behavior of electronic specific heat coefficient with composition for Zr{sub 0.5}(Ru, Pd){sub 0.5}.

  12. Precession technique and electron diffractometry as new tools for crystal structure analysis and chemical bonding determination.

    PubMed

    Avilov, A; Kuligin, K; Nicolopoulos, S; Nickolskiy, M; Boulahya, K; Portillo, J; Lepeshov, G; Sobolev, B; Collette, J P; Martin, N; Robins, A C; Fischione, P

    2007-01-01

    We have developed a new fast electron diffractometer working with high dynamic range and linearity for crystal structure determinations. Electron diffraction (ED) patterns can be scanned serially in front of a Faraday cage detector; the total measurement time for several hundred ED reflections can be tens of seconds having high statistical accuracy for all measured intensities (1-2%). This new tool can be installed to any type of TEM without any column modification and is linked to a specially developed electron beam precession "Spinning Star" system. Precession of the electron beam (Vincent-Midgley technique) reduces dynamical effects allowing also use of accurate intensities for crystal structure analysis. We describe the technical characteristics of this new tool together with the first experimental results. Accurate measurement of electron diffraction intensities by electron diffractometer opens new possibilities not only for revealing unknown structures, but also for electrostatic potential determination and chemical bonding investigation. As an example, we present detailed atomic bonding information of CaF(2) as revealed for the first time by precise electron diffractometry.

  13. Accurate structure prediction of peptide–MHC complexes for identifying highly immunogenic antigens

    SciTech Connect

    Park, Min-Sun; Park, Sung Yong; Miller, Keith R.; Collins, Edward J.; Lee, Ha Youn

    2013-11-01

    Designing an optimal HIV-1 vaccine faces the challenge of identifying antigens that induce a broad immune capacity. One factor to control the breadth of T cell responses is the surface morphology of a peptide–MHC complex. Here, we present an in silico protocol for predicting peptide–MHC structure. A robust signature of a conformational transition was identified during all-atom molecular dynamics, which results in a model with high accuracy. A large test set was used in constructing our protocol and we went another step further using a blind test with a wild-type peptide and two highly immunogenic mutants, which predicted substantial conformational changes in both mutants. The center residues at position five of the analogs were configured to be accessible to solvent, forming a prominent surface, while the residue of the wild-type peptide was to point laterally toward the side of the binding cleft. We then experimentally determined the structures of the blind test set, using high resolution of X-ray crystallography, which verified predicted conformational changes. Our observation strongly supports a positive association of the surface morphology of a peptide–MHC complex to its immunogenicity. Our study offers the prospect of enhancing immunogenicity of vaccines by identifying MHC binding immunogens.

  14. Vibrational structure of defect luminescence bands in GaN from electronic structure calculations

    NASA Astrophysics Data System (ADS)

    Alkauskas, Audrius; van de Walle, Chris G.

    2012-02-01

    Optical methods are among the most powerful to characterize defects in materials. The study of optical signatures based on state-of-the-art electronic structure methods is therefore very important. In this work we investigate the vibrational structure of luminescence bands pertaining to deep defect levels in GaN. Since luminescence lineshapes depend sensitively on defect geometries and vibrational frequencies, these should be described accurately. The latter is achieved through the use of hybrid density functionals. Both quasi-localized and bulk phonons are included in our description. In the case of transitions accompanied by very large lattice relaxations, anharmonic effects become sizeable, and these are also accounted for. For the defects studied a very good agreement with available experimental data is achieved. For instance, in the case of wide luminescence bands the resulting line widths are within 0.05 eV of the experimental values. This work was supported by the Swiss NSF and by NSF.

  15. Electronic structure of cyclohexane on Ni(111)

    NASA Astrophysics Data System (ADS)

    Huber, W.; Zebisch, P.; Bornemann, T.; Steinrück, H.-P.

    1990-12-01

    Mono- and multilayers of cyclohexane adsorbed on a Ni(111) surface have been studied by angle resolved UV photoelectron spectroscopy (ARUPS) using linearly polarized synchrotron radiation, temperature programmed desorption (TPD) and low energy electron diffraction (LEED). Cyclohexane is molecularly adsorbed on Ni(111) at temperatures below 200 K and desorbs without dehydrogenation. Desorption from the first layer exhibits zeroth-order desorption behavior indicative of desorption from two-dimensional islands. The first layer exhibits a well ordered ( 7 × 7)R19.1° LEED structure starting at coverages of 0.04 ML up to the saturation coverage of 0.143 ML, also indicative of island formation. For cyclohexane in the first layer the binding energies of the various molecular levels are, apart from an overall shift to smaller values by 0.7 eV, within ± 0.1 eV identical to those of condensed cyclohexane. This absence of chemical shifts indicates that there is only very weak (if any) chemical interaction between cyclohexane and the Ni(111) surface. From the normal emission ARUPS spectra and symmetry selection rules we conclude that the symmetry of cyclohexane adsorbed on Ni(111) is lower than C 3v. This is attributed to a slightly inclined adsorption geometry with intramolecular C 3v symmetry of the adsorbed molecules.

  16. An Accurate Method for Free Vibration Analysis of Structures with Application to Plates

    NASA Astrophysics Data System (ADS)

    KEVORKIAN, S.; PASCAL, M.

    2001-10-01

    In this work, the continuous element method which has been used as an alternative to the finite element method of vibration analysis of frames is applied to more general structures like 3-D continuum and rectangular plates. The method is based on the concept of the so-called impedance matrix giving in the frequency domain, the linear relation between the generalized displacements of the boundaries and the generalized forces exerted on these boundaries. For a 3-D continuum, the concept of impedance matrix is introduced assuming a particular kind of boundary conditions. For rectangular plates, this new development leads to the solution of vibration problems for boundary conditions other than the simply supported ones.

  17. An accurate density functional theory calculation for electronic excitation energies: the least-squares support vector machine.

    PubMed

    Gao, Ting; Sun, Shi-Ling; Shi, Li-Li; Li, Hui; Li, Hong-Zhi; Su, Zhong-Min; Lu, Ying-Hua

    2009-05-14

    Support vector machines (SVMs), as a novel type of learning machine, has been very successful in pattern recognition and function estimation problems. In this paper we introduce least-squares (LS) SVMs to improve the calculation accuracy of density functional theory. As a demonstration, this combined quantum mechanical calculation with LS-SVM correction approach has been applied to evaluate the electronic excitation energies of 160 organic molecules. The newly introduced LS-SVM approach reduces the root-mean-square deviation of the calculated electronic excitation energies of 160 organic molecules from 0.32 to 0.11 eV for the B3LYP/6-31G(d) calculation. Thus, the LS-SVM correction on top of B3LYP/6-31G(d) is a better method to correct electronic excitation energies and can be used as the approximation of experimental results which are impossible to obtain experimentally.

  18. Toward Accurate Modelling of Enzymatic Reactions: All Electron Quantum Chemical Analysis combined with QM/MM Calculation of Chorismate Mutase

    NASA Astrophysics Data System (ADS)

    Ishida, Toyokazu

    2008-09-01

    To further understand the catalytic role of the protein environment in the enzymatic process, the author has analyzed the reaction mechanism of the Claisen rearrangement of Bacillus subtilis chorismate mutase (BsCM). By introducing a new computational strategy that combines all-electron QM calculations with ab initio QM/MM modelings, it was possible to simulate the molecular interactions between the substrate and the protein environment. The electrostatic nature of the transition state stabilization was characterized by performing all-electron QM calculations based on the fragment molecular orbital technique for the entire enzyme.

  19. Toward Accurate Modelling of Enzymatic Reactions: All Electron Quantum Chemical Analysis combined with QM/MM Calculation of Chorismate Mutase

    SciTech Connect

    Ishida, Toyokazu

    2008-09-17

    To further understand the catalytic role of the protein environment in the enzymatic process, the author has analyzed the reaction mechanism of the Claisen rearrangement of Bacillus subtilis chorismate mutase (BsCM). By introducing a new computational strategy that combines all-electron QM calculations with ab initio QM/MM modelings, it was possible to simulate the molecular interactions between the substrate and the protein environment. The electrostatic nature of the transition state stabilization was characterized by performing all-electron QM calculations based on the fragment molecular orbital technique for the entire enzyme.

  20. Electronic Structure and Dynamics of Nitrosyl Porphyrins

    PubMed Central

    Scheidt, W. Robert; Barabanschikov, Alexander; Pavlik, Jeffrey W.; Silvernail, Nathan J.; Sage, J. Timothy

    2010-01-01

    fully successful at capturing the interaction between the axial NO and imidazole ligands. This supports previous conclusions that hemeNO complexes exhibit an unusual degree of variability with respect to computational method, and we speculate that this variability hints at a genuine electronic instability that a protein can exploit to tune reactivity. We anticipate that ongoing characterization of heme-NO complexes will deepen our understanding of their structure, dynamics, and reactivity. PMID:20666384

  1. Control circuitry using electronic emulation of a synchro signal for accurate control of position and rate of rotation for shafts

    NASA Technical Reports Server (NTRS)

    Howard, David E. (Inventor); Smith, Dennis A. (Inventor)

    1991-01-01

    The invention disclosed is a digital circuit which emulates a synchro signal in a synchro-resolver follower system for precise control of shaft position and rotation at very low rotational rates. The invention replaces the synchro and drive motor in a synchro-resolver follower system with a digital and analog synchro emulation circuit for generating the resolver control signal. The synchro emulation circuit includes amplitude modulation means to provide relatively high frequency resolver excitation signals for accurate resolver response even with very low shaft rotation rates.

  2. Control Circuitry Using Electronic Emulation of a Synchro Signal for Accurate Control of Position and Rate of Rotation for Shafts

    NASA Technical Reports Server (NTRS)

    Howard, David E. (Inventor); Smith, Dennis A. (Inventor)

    1992-01-01

    The invention herein disclosed is a digital circuit which emulates a synchro signal in a synchro-resolver follower system for precise control of shaft position and rotation at very low rotational rates. The subject invention replaces the synchro and drive motor in a synchroresolver follower system with a digital and analog synchro emulation circuit for generating the resolver control signal. The synchro emulation circuit includes amplitude modulation means to provide relatively high frequency resolver excitation signals for accurate resolver response even with very low shaft rotation rates.

  3. Accurate quantification of width and density of bone structures by computed tomography

    SciTech Connect

    Hangartner, Thomas N.; Short, David F.

    2007-10-15

    In computed tomography (CT), the representation of edges between objects of different densities is influenced by the limited spatial resolution of the scanner. This results in the misrepresentation of density of narrow objects, leading to errors of up to 70% and more. Our interest is in the imaging and measurement of narrow bone structures, and the issues are the same for imaging with clinical CT scanners, peripheral quantitative CT scanners or micro CT scanners. Mathematical models, phantoms and tests with patient data led to the following procedures: (i) extract density profiles at one-degree increments from the CT images at right angles to the bone boundary; (ii) consider the outer and inner edge of each profile separately due to different adjacent soft tissues; (iii) measure the width of each profile based on a threshold at fixed percentage of the difference between the soft-tissue value and a first approximated bone value; (iv) correct the underlying material density of bone for each profile based on the measured width with the help of the density-versus-width curve obtained from computer simulations and phantom measurements. This latter curve is specific to a certain scanner and is not dependent on the densities of the tissues within the range seen in patients. This procedure allows the calculation of the material density of bone. Based on phantom measurements, we estimate the density error to be below 2% relative to the density of normal bone and the bone-width error about one tenth of a pixel size.

  4. Structural adjustment for accurate conditioning in large-scale subsurface systems

    NASA Astrophysics Data System (ADS)

    Tahmasebi, Pejman

    2017-03-01

    Most of the current subsurface simulation approaches consider a priority list for honoring the well and any other auxiliary data, and eventually adopt a middle ground between the quality of the model and conditioning it to hard data. However, as the number of datasets increases, such methods often produce undesirable features in the subsurface model. Due to their high flexibility, subsurface modeling based on training images (TIs) is becoming popular. Providing comprehensive TIs remains, however, an outstanding problem. In addition, identifying a pattern similar to those in the TI that honors the well and other conditioning data is often difficult. Moreover, the current subsurface modeling approaches do not account for small perturbations that may occur in a subsurface system. Such perturbations are active in most of the depositional systems. In this paper, a new methodology is presented that is based on an irregular gridding scheme that accounts for incomplete TIs and minor offsets. Use of the methodology enables one to use a small or incomplete TI and adaptively change the patterns in the simulation grid in order to simultaneously honor the well data and take into account the effect of the local offsets. Furthermore, the proposed method was used on various complex process-based models and their structures are deformed for matching with the conditioning point data. The accuracy and robustness of the proposed algorithm are successfully demonstrated by applying it to models of several complex examples.

  5. Probing Actinide Electronic Structure through Pu Cluster Calculations

    DOE PAGES

    Ryzhkov, Mickhail V.; Mirmelstein, Alexei; Yu, Sung-Woo; ...

    2013-02-26

    The calculations for the electronic structure of clusters of plutonium have been performed, within the framework of the relativistic discrete-variational method. Moreover, these theoretical results and those calculated earlier for related systems have been compared to spectroscopic data produced in the experimental investigations of bulk systems, including photoelectron spectroscopy. Observation of the changes in the Pu electronic structure as a function of size provides powerful insight for aspects of bulk Pu electronic structure.

  6. Graph-based linear scaling electronic structure theory

    NASA Astrophysics Data System (ADS)

    Niklasson, Anders M. N.; Mniszewski, Susan M.; Negre, Christian F. A.; Cawkwell, Marc J.; Swart, Pieter J.; Mohd-Yusof, Jamal; Germann, Timothy C.; Wall, Michael E.; Bock, Nicolas; Rubensson, Emanuel H.; Djidjev, Hristo

    2016-06-01

    We show how graph theory can be combined with quantum theory to calculate the electronic structure of large complex systems. The graph formalism is general and applicable to a broad range of electronic structure methods and materials, including challenging systems such as biomolecules. The methodology combines well-controlled accuracy, low computational cost, and natural low-communication parallelism. This combination addresses substantial shortcomings of linear scaling electronic structure theory, in particular with respect to quantum-based molecular dynamics simulations.

  7. Graph-based linear scaling electronic structure theory.

    PubMed

    Niklasson, Anders M N; Mniszewski, Susan M; Negre, Christian F A; Cawkwell, Marc J; Swart, Pieter J; Mohd-Yusof, Jamal; Germann, Timothy C; Wall, Michael E; Bock, Nicolas; Rubensson, Emanuel H; Djidjev, Hristo

    2016-06-21

    We show how graph theory can be combined with quantum theory to calculate the electronic structure of large complex systems. The graph formalism is general and applicable to a broad range of electronic structure methods and materials, including challenging systems such as biomolecules. The methodology combines well-controlled accuracy, low computational cost, and natural low-communication parallelism. This combination addresses substantial shortcomings of linear scaling electronic structure theory, in particular with respect to quantum-based molecular dynamics simulations.

  8. Dramatic changes in electronic structure revealed by fractionally charged nuclei

    NASA Astrophysics Data System (ADS)

    Cohen, Aron J.; Mori-Sánchez, Paula

    2014-01-01

    Discontinuous changes in the electronic structure upon infinitesimal changes to the Hamiltonian are demonstrated. These are revealed in one and two electron molecular systems by full configuration interaction (FCI) calculations when the realm of the nuclear charge is extended to be fractional. FCI electron densities in these systems show dramatic changes in real space and illustrate the transfer, hopping, and removal of electrons. This is due to the particle nature of electrons seen in stretched systems and is a manifestation of an energy derivative discontinuity at constant number of electrons. Dramatic errors of density functional theory densities are seen in real space as this physics is missing from currently used approximations. The movements of electrons in these simple systems encapsulate those in real physical processes, from chemical reactions to electron transport and pose a great challenge for the development of new electronic structure methods.

  9. Accurate determination of lattice parameters based on Niggli reduced cell theory by using digitized electron diffraction micrograph.

    PubMed

    Yang, Yi; Cai, Canying; Lin, Jianguo; Gong, Lunjun; Yang, Qibin

    2017-05-01

    In this paper, we used Niggli reduced cell theory to determine lattice constants of a micro/nano crystal by using electron diffraction patterns. The Niggli reduced cell method enhanced the accuracy of lattice constant measurement obviously, because the lengths and the angles of lattice vectors of a primitive cell can be measured directly on the electron micrographs instead of a double tilt holder. With the aid of digitized algorithm and least square optimization by using three digitized micrographs, a valid reciprocal Niggli reduced cell number can be obtained. Thus a reciprocal and real Bravais lattices are acquired. The results of three examples, i.e., Mg4Zn7, an unknown phase (Precipitate phase in nickel-base superalloy) and Ba4Ti13O30 showed that the maximum errors are 1.6% for lengths and are 0.3% for angles.

  10. Bottom-up coarse-grained models that accurately describe the structure, pressure, and compressibility of molecular liquids

    SciTech Connect

    Dunn, Nicholas J. H.; Noid, W. G.

    2015-12-28

    The present work investigates the capability of bottom-up coarse-graining (CG) methods for accurately modeling both structural and thermodynamic properties of all-atom (AA) models for molecular liquids. In particular, we consider 1, 2, and 3-site CG models for heptane, as well as 1 and 3-site CG models for toluene. For each model, we employ the multiscale coarse-graining method to determine interaction potentials that optimally approximate the configuration dependence of the many-body potential of mean force (PMF). We employ a previously developed “pressure-matching” variational principle to determine a volume-dependent contribution to the potential, U{sub V}(V), that approximates the volume-dependence of the PMF. We demonstrate that the resulting CG models describe AA density fluctuations with qualitative, but not quantitative, accuracy. Accordingly, we develop a self-consistent approach for further optimizing U{sub V}, such that the CG models accurately reproduce the equilibrium density, compressibility, and average pressure of the AA models, although the CG models still significantly underestimate the atomic pressure fluctuations. Additionally, by comparing this array of models that accurately describe the structure and thermodynamic pressure of heptane and toluene at a range of different resolutions, we investigate the impact of bottom-up coarse-graining upon thermodynamic properties. In particular, we demonstrate that U{sub V} accounts for the reduced cohesion in the CG models. Finally, we observe that bottom-up coarse-graining introduces subtle correlations between the resolution, the cohesive energy density, and the “simplicity” of the model.

  11. Fast and accurate approximate quasiparticle band structure calculations of ZnO, CdO, and MgO polymorphs

    NASA Astrophysics Data System (ADS)

    Ataide, C. A.; Pelá, R. R.; Marques, M.; Teles, L. K.; Furthmüller, J.; Bechstedt, F.

    2017-01-01

    We investigate ZnO, CdO, and MgO oxides crystallizing in rocksalt, wurtzite, and zincblende structures. Whereas in MgO calculations, the conventional LDA-1/2 method is employed through a self-energy potential (VS), the shallow d bands in ZnO and CdO are treated through an increased amplitude (A ) of VS to modulate the self-energy of the d states to place them in the quasiparticle position. The LDA+A -1/2 scheme is applied to calculate band structures and electronic density of states of ZnO and CdO. We compare the results with those of more sophisticated quasiparticle calculations and experiments. We demonstrate that this new LDA+A -1/2 method reaches accuracy comparable to state-of-the-art methods, opening a door to study more complex systems containing shallow core electrons to the prize of LDA studies.

  12. An accurate online calibration system based on combined clamp-shape coil for high voltage electronic current transformers

    SciTech Connect

    Li, Zhen-hua; Li, Hong-bin; Zhang, Zhi

    2013-07-15

    Electronic transformers are widely used in power systems because of their wide bandwidth and good transient performance. However, as an emerging technology, the failure rate of electronic transformers is higher than that of traditional transformers. As a result, the calibration period needs to be shortened. Traditional calibration methods require the power of transmission line be cut off, which results in complicated operation and power off loss. This paper proposes an online calibration system which can calibrate electronic current transformers without power off. In this work, the high accuracy standard current transformer and online operation method are the key techniques. Based on the clamp-shape iron-core coil and clamp-shape air-core coil, a combined clamp-shape coil is designed as the standard current transformer. By analyzing the output characteristics of the two coils, the combined clamp-shape coil can achieve verification of the accuracy. So the accuracy of the online calibration system can be guaranteed. Moreover, by employing the earth potential working method and using two insulating rods to connect the combined clamp-shape coil to the high voltage bus, the operation becomes simple and safe. Tests in China National Center for High Voltage Measurement and field experiments show that the proposed system has a high accuracy of up to 0.05 class.

  13. An approach to an accurate determination of the energy spectrum of high-energy electron beams using magnetic spectrometry

    NASA Astrophysics Data System (ADS)

    Renner, F.; Schwab, A.; Kapsch, R.-P.; Makowski, Ch; Jannek, D.

    2014-03-01

    At the national metrology institute of Germany, the Physikalisch-Technische Bundesanstalt, a research accelerator for dosimetry in radiation therapy has been installed. Magnetic spectrometry is used to determine the spectrum of high-energy electrons generated by this accelerator. Regarding the intended experiments at the accelerator, a high accuracy for the energy determination of the electron beam is required. For this purpose, an experimental setup is used that has a number of additional devices assembled around the spectrometer to determine geometric characteristics of the electron beam, which influence the energy analysis. For the analysis of the acquired data, a software was developed which meets specific needs. One important aspect is that the software is based on an algorithm for energy determination which considers the measured magnetic flux density of the spectrometer and geometric details of the beam and the spectrometer. The software also meets the demand that it can be used to estimate the uncertainty assigned to the energy. This paper covers the experimental and analytical background of magnetic spectrometry at the high-energy beamline of PTB's research accelerator. A comparison of results calculated with the specific algorithm for energy determination which was developed for this experimental setup and with well-known algorithms is given to show the advantage of the specific method. Results of measurements and their analysis with the algorithm are presented as well.

  14. An accurate online calibration system based on combined clamp-shape coil for high voltage electronic current transformers.

    PubMed

    Li, Zhen-hua; Li, Hong-bin; Zhang, Zhi

    2013-07-01

    Electronic transformers are widely used in power systems because of their wide bandwidth and good transient performance. However, as an emerging technology, the failure rate of electronic transformers is higher than that of traditional transformers. As a result, the calibration period needs to be shortened. Traditional calibration methods require the power of transmission line be cut off, which results in complicated operation and power off loss. This paper proposes an online calibration system which can calibrate electronic current transformers without power off. In this work, the high accuracy standard current transformer and online operation method are the key techniques. Based on the clamp-shape iron-core coil and clamp-shape air-core coil, a combined clamp-shape coil is designed as the standard current transformer. By analyzing the output characteristics of the two coils, the combined clamp-shape coil can achieve verification of the accuracy. So the accuracy of the online calibration system can be guaranteed. Moreover, by employing the earth potential working method and using two insulating rods to connect the combined clamp-shape coil to the high voltage bus, the operation becomes simple and safe. Tests in China National Center for High Voltage Measurement and field experiments show that the proposed system has a high accuracy of up to 0.05 class.

  15. An accurate online calibration system based on combined clamp-shape coil for high voltage electronic current transformers

    NASA Astrophysics Data System (ADS)

    Li, Zhen-hua; Li, Hong-bin; Zhang, Zhi

    2013-07-01

    Electronic transformers are widely used in power systems because of their wide bandwidth and good transient performance. However, as an emerging technology, the failure rate of electronic transformers is higher than that of traditional transformers. As a result, the calibration period needs to be shortened. Traditional calibration methods require the power of transmission line be cut off, which results in complicated operation and power off loss. This paper proposes an online calibration system which can calibrate electronic current transformers without power off. In this work, the high accuracy standard current transformer and online operation method are the key techniques. Based on the clamp-shape iron-core coil and clamp-shape air-core coil, a combined clamp-shape coil is designed as the standard current transformer. By analyzing the output characteristics of the two coils, the combined clamp-shape coil can achieve verification of the accuracy. So the accuracy of the online calibration system can be guaranteed. Moreover, by employing the earth potential working method and using two insulating rods to connect the combined clamp-shape coil to the high voltage bus, the operation becomes simple and safe. Tests in China National Center for High Voltage Measurement and field experiments show that the proposed system has a high accuracy of up to 0.05 class.

  16. Electronic Structure of Germanium Nanocrystal Films Probed with Synchrotron Radiation

    SciTech Connect

    Bostedt, C

    2002-05-01

    The fundamental structure--property relationship of semiconductor quantum dots has been investigated. For deposited germanium nanocrystals strong quantum confinement effects have been determined with synchrotron radiation based x-ray absorption and photoemission techniques. The nanocrystals are condensed out of the gas phase with a narrow size distribution and subsequently deposited in situ onto various substrates. The particles are crystalline in the cubic phase with a structurally disordered surface shell and the resulting film morphology depends strongly on the substrate material and condition. The disordered surface region has an impact on the overall electronic structure of the particles. In a size-dependent study, the conduction and valence band edge of germanium nanocrystals have been measured for the first time and compared to the bulk crystal. The band edges move to higher energies as the particle size is decreased, consistent with quantum confinement theory. To obtain a more accurate analysis of confinement effects in the empty states, a novel analysis method utilizing an effective particle size for the x-ray absorption experiment, which allows a deconvolution of absorption edge broadening effects, has been introduced. Comparison of the present study to earlier studies on silicon reveals that germanium exhibits stronger quantum confinement effects than silicon. Below a critical particle size of 2.3 {+-} 0.7 nm, the band gap of germanium becomes larger than that of silicon--even if it is the opposite for bulk materials. This result agrees phenomenologically with effective mass and tight binding theories but contradicts the findings of recent pseudopotential calculations. The discrepancy between theory and experiments is attributed to the differences in the theoretical models and experimental systems. The experimentally observed structural disorder of the particle surface has to be included in the theoretical models.

  17. Combining Structural Modeling with Ensemble Machine Learning to Accurately Predict Protein Fold Stability and Binding Affinity Effects upon Mutation

    PubMed Central

    Garcia Lopez, Sebastian; Kim, Philip M.

    2014-01-01

    Advances in sequencing have led to a rapid accumulation of mutations, some of which are associated with diseases. However, to draw mechanistic conclusions, a biochemical understanding of these mutations is necessary. For coding mutations, accurate prediction of significant changes in either the stability of proteins or their affinity to their binding partners is required. Traditional methods have used semi-empirical force fields, while newer methods employ machine learning of sequence and structural features. Here, we show how combining both of these approaches leads to a marked boost in accuracy. We introduce ELASPIC, a novel ensemble machine learning approach that is able to predict stability effects upon mutation in both, domain cores and domain-domain interfaces. We combine semi-empirical energy terms, sequence conservation, and a wide variety of molecular details with a Stochastic Gradient Boosting of Decision Trees (SGB-DT) algorithm. The accuracy of our predictions surpasses existing methods by a considerable margin, achieving correlation coefficients of 0.77 for stability, and 0.75 for affinity predictions. Notably, we integrated homology modeling to enable proteome-wide prediction and show that accurate prediction on modeled structures is possible. Lastly, ELASPIC showed significant differences between various types of disease-associated mutations, as well as between disease and common neutral mutations. Unlike pure sequence-based prediction methods that try to predict phenotypic effects of mutations, our predictions unravel the molecular details governing the protein instability, and help us better understand the molecular causes of diseases. PMID:25243403

  18. Affordable, Lightweight, Highly Conductive Polymer Composite Electronic Packaging Structures

    DTIC Science & Technology

    1996-06-01

    matrix composite materials and how various material designs can be utilized in various structural/thermal configurations to produce electronic housings and...conductive polymer composite electronic packaging (i.e., electronic housings and heat sinks). The research will center on predominately polymer

  19. Accurate determination of electronic transport properties of silicon wafers by nonlinear photocarrier radiometry with multiple pump beam sizes

    SciTech Connect

    Wang, Qian; Li, Bincheng

    2015-12-07

    In this paper, photocarrier radiometry (PCR) technique with multiple pump beam sizes is employed to determine simultaneously the electronic transport parameters (the carrier lifetime, the carrier diffusion coefficient, and the front surface recombination velocity) of silicon wafers. By employing the multiple pump beam sizes, the influence of instrumental frequency response on the multi-parameter estimation is totally eliminated. A nonlinear PCR model is developed to interpret the PCR signal. Theoretical simulations are performed to investigate the uncertainties of the estimated parameter values by investigating the dependence of a mean square variance on the corresponding transport parameters and compared to that obtained by the conventional frequency-scan method, in which only the frequency dependences of the PCR amplitude and phase are recorded at single pump beam size. Simulation results show that the proposed multiple-pump-beam-size method can improve significantly the accuracy of the determination of the electronic transport parameters. Comparative experiments with a p-type silicon wafer with resistivity 0.1–0.2 Ω·cm are performed, and the electronic transport properties are determined simultaneously. The estimated uncertainties of the carrier lifetime, diffusion coefficient, and front surface recombination velocity are approximately ±10.7%, ±8.6%, and ±35.4% by the proposed multiple-pump-beam-size method, which is much improved than ±15.9%, ±29.1%, and >±50% by the conventional frequency-scan method. The transport parameters determined by the proposed multiple-pump-beam-size PCR method are in good agreement with that obtained by a steady-state PCR imaging technique.

  20. First principles based multiparadigm modeling of electronic structures and dynamics

    NASA Astrophysics Data System (ADS)

    Xiao, Hai

    Electronic structures and dynamics are the key to linking the material composition and structure to functionality and performance. An essential issue in developing semiconductor devices for photovoltaics is to design materials with optimal band gaps and relative positioning of band levels. Approximate DFT methods have been justified to predict band gaps from KS/GKS eigenvalues, but the accuracy is decisively dependent on the choice of XC functionals. We show here for CuInSe2 and CuGaSe2, the parent compounds of the promising CIGS solar cells, conventional LDA and GGA obtain gaps of 0.0-0.01 and 0.02-0.24 eV (versus experimental values of 1.04 and 1.67 eV), while the historically first global hybrid functional, B3PW91, is surprisingly the best, with band gaps of 1.07 and 1.58 eV. Furthermore, we show that for 27 related binary and ternary semiconductors, B3PW91 predicts gaps with a MAD of only 0.09 eV, which is substantially better than all modern hybrid functionals, including B3LYP (MAD of 0.19 eV) and screened hybrid functional HSE06 (MAD of 0.18 eV). The laboratory performance of CIGS solar cells (> 20% efficiency) makes them promising candidate photovoltaic devices. However, there remains little understanding of how defects at the CIGS/CdS interface affect the band offsets and interfacial energies, and hence the performance of manufactured devices. To determine these relationships, we use the B3PW91 hybrid functional of DFT with the AEP method that we validate to provide very accurate descriptions of both band gaps and band offsets. This confirms the weak dependence of band offsets on surface orientation observed experimentally. We predict that the CBO of perfect CuInSe2/CdS interface is large, 0.79 eV, which would dramatically degrade performance. Moreover we show that band gap widening induced by Ga adjusts only the VBO, and we find that Cd impurities do not significantly affect the CBO. Thus we show that Cu vacancies at the interface play the key role in

  1. Simple extrapolation method to predict the electronic structure of conjugated polymers from calculations on oligomers

    SciTech Connect

    Larsen, Ross E.

    2016-04-12

    In this study, we introduce two simple tight-binding models, which we call fragment frontier orbital extrapolations (FFOE), to extrapolate important electronic properties to the polymer limit using electronic structure calculations on only a few small oligomers. In particular, we demonstrate by comparison to explicit density functional theory calculations that for long oligomers the energies of the highest occupied molecular orbital (HOMO), the lowest unoccupied molecular orbital (LUMO), and of the first electronic excited state are accurately described as a function of number of repeat units by a simple effective Hamiltonian parameterized from electronic structure calculations on monomers, dimers and, optionally, tetramers. For the alternating copolymer materials that currently comprise some of the most efficient polymer organic photovoltaic devices one can use these simple but rigorous models to extrapolate computed properties to the polymer limit based on calculations on a small number of low-molecular-weight oligomers.

  2. Simple extrapolation method to predict the electronic structure of conjugated polymers from calculations on oligomers

    DOE PAGES

    Larsen, Ross E.

    2016-04-12

    In this study, we introduce two simple tight-binding models, which we call fragment frontier orbital extrapolations (FFOE), to extrapolate important electronic properties to the polymer limit using electronic structure calculations on only a few small oligomers. In particular, we demonstrate by comparison to explicit density functional theory calculations that for long oligomers the energies of the highest occupied molecular orbital (HOMO), the lowest unoccupied molecular orbital (LUMO), and of the first electronic excited state are accurately described as a function of number of repeat units by a simple effective Hamiltonian parameterized from electronic structure calculations on monomers, dimers and, optionally,more » tetramers. For the alternating copolymer materials that currently comprise some of the most efficient polymer organic photovoltaic devices one can use these simple but rigorous models to extrapolate computed properties to the polymer limit based on calculations on a small number of low-molecular-weight oligomers.« less

  3. Highly accurate nuclear and electronic stopping cross sections derived using Monte Carlo simulations to reproduce measured range data

    NASA Astrophysics Data System (ADS)

    Wittmaack, Klaus; Mutzke, Andreas

    2017-03-01

    We have examined and confirmed the previously unexplored concept of using Monte Carlo calculations in combination with measured projected ranges of ions implanted in solids to derive a quantitative description of nuclear interaction and electronic stopping. The study involved 98 ranges of 11B in Si between 1 keV and 8 MeV, contained in 12 sets of 10 different groups. Systematic errors by up to ±8% were removed to establish a refined data base with 93 ranges featuring only statistical uncertainties (±1.8%). The Monte Carlo calculations could be set up to reproduce the refined ranges with a mean ratio 1.002 ± 1.7%. The input parameters required for this very high level of agreement are as follows. Nuclear interaction is best described by the Kr-C potential, but in obligatory combination with the Lindhard-Scharff (LS) screening length. Up to 300 keV, the electronic stopping cross section is proportional to the projectile velocity, Se = kSe,LS, with k = 1.46 ± 0.01. At higher energies, Se falls progressively short of kSe,LS. Around the Bragg peak, i.e., between 0.8 and 10 MeV, Se is modeled by an adjustable function serving to tailor the peak shape properly. Calculated and measured isotope effects for ranges of 10B and 11B in Si agree within the experimental uncertainty (±0.25%). The range-based Se,R(E) reported here predicts the scarce experimental data derived from the energy loss in projectile transmission through thin Si foils to within 2% or better. By contrast, Se(E) data of available stopping power tables exhibit deviations from Se,R(E) between -40% and +14%.

  4. Paper to Electronic Questionnaires: Effects on Structured Questionnaire Forms

    NASA Technical Reports Server (NTRS)

    Trujillo, Anna C.

    2009-01-01

    With the use of computers, paper questionnaires are being replaced by electronic questionnaires. The formats of traditional paper questionnaires have been found to effect a subject's rating. Consequently, the transition from paper to electronic format can subtly change results. The research presented begins to determine how electronic questionnaire formats change subjective ratings. For formats where subjects used a flow chart to arrive at their rating, starting at the worst and middle ratings of the flow charts were the most accurate but subjects took slightly more time to arrive at their answers. Except for the electronic paper format, starting at the worst rating was the most preferred. The paper and electronic paper versions had the worst accuracy. Therefore, for flowchart type of questionnaires, flowcharts should start at the worst rating and work their way up to better ratings.

  5. Velocity-space structure of runaway electrons

    SciTech Connect

    Fuchs, V.; Cairns, R.A.; Lashmore-Davies, C.N.; Shoucri, M.M.

    1986-09-01

    The region of velocity space is determined in which electron runaway occurs because of a dc electric field. Phase-space analysis of the relaxation equations describing test electrons, corroborated by two-dimensional (2-D) numerical integration of the Fokker--Planck equation, reveals that the Dreicer condition for runaway v-italic/sup 2//sub parallel/> or =(2+Z-italic/sub i-italic/)E-italic/sub c-italic//E-italic is only sufficient. A weaker condition v-italic/sup 2//sub parallel/> or =(2+Z-italic/sub i-italic/)/sup 1//sup ///sup 2/E-italic/sub c-italic//E-italic is established, and it is shown, in general, that runaway in velocity space only occurs for those electrons that are outside one of the separatrices of the relaxation equations. The scaling with v-italic/sub parallel/ of the parallel distribution function and of the perpendicular temperature is also derived.

  6. Electronic structure and properties of superheavy elements

    NASA Astrophysics Data System (ADS)

    Pershina, V.

    2015-12-01

    Spectacular developments in the relativistic quantum theory and computational algorithms in the last few decades allowed for accurate calculations of properties of the superheavy elements (SHE) and their compounds. Often conducted in a close link to the experimental research, these investigations helped predict and interpret an outcome of sophisticated and expensive experiments with single atoms. Most of the works, particularly those related to the experimental studies, are overviewed in this publication. The role of relativistic effects being of paramount importance for the heaviest elements is elucidated.

  7. A multi-channel opto-electronic sensor to accurately monitor heart rate against motion artefact during exercise.

    PubMed

    Alzahrani, Abdullah; Hu, Sijung; Azorin-Peris, Vicente; Barrett, Laura; Esliger, Dale; Hayes, Matthew; Akbare, Shafique; Achart, Jérôme; Kuoch, Sylvain

    2015-10-12

    This study presents the use of a multi-channel opto-electronic sensor (OEPS) to effectively monitor critical physiological parameters whilst preventing motion artefact as increasingly demanded by personal healthcare. The aim of this work was to study how to capture the heart rate (HR) efficiently through a well-constructed OEPS and a 3-axis accelerometer with wireless communication. A protocol was designed to incorporate sitting, standing, walking, running and cycling. The datasets collected from these activities were processed to elaborate sport physiological effects. t-test, Bland-Altman Agreement (BAA), and correlation to evaluate the performance of the OEPS were used against Polar and Mio-Alpha HR monitors. No differences in the HR were found between OEPS, and either Polar or Mio-Alpha (both p > 0.05); a strong correlation was found between Polar and OEPS (r: 0.96, p < 0.001); the bias of BAA 0.85 bpm, the standard deviation (SD) 9.20 bpm, and the limits of agreement (LOA) from -17.18 bpm to +18.88 bpm. For the Mio-Alpha and OEPS, a strong correlation was found (r: 0.96, p < 0.001); the bias of BAA 1.63 bpm, SD 8.62 bpm, LOA from -15.27 bpm to +18.58 bpm. These results demonstrate the OEPS to be capable of carrying out real time and remote monitoring of heart rate.

  8. A Multi-Channel Opto-Electronic Sensor to Accurately Monitor Heart Rate against Motion Artefact during Exercise

    PubMed Central

    Alzahrani, Abdullah; Hu, Sijung; Azorin-Peris, Vicente; Barrett, Laura; Esliger, Dale; Hayes, Matthew; Akbare, Shafique; Achart, Jérôme; Kuoch, Sylvain

    2015-01-01

    This study presents the use of a multi-channel opto-electronic sensor (OEPS) to effectively monitor critical physiological parameters whilst preventing motion artefact as increasingly demanded by personal healthcare. The aim of this work was to study how to capture the heart rate (HR) efficiently through a well-constructed OEPS and a 3-axis accelerometer with wireless communication. A protocol was designed to incorporate sitting, standing, walking, running and cycling. The datasets collected from these activities were processed to elaborate sport physiological effects. t-test, Bland-Altman Agreement (BAA), and correlation to evaluate the performance of the OEPS were used against Polar and Mio-Alpha HR monitors. No differences in the HR were found between OEPS, and either Polar or Mio-Alpha (both p > 0.05); a strong correlation was found between Polar and OEPS (r: 0.96, p < 0.001); the bias of BAA 0.85 bpm, the standard deviation (SD) 9.20 bpm, and the limits of agreement (LOA) from −17.18 bpm to +18.88 bpm. For the Mio-Alpha and OEPS, a strong correlation was found (r: 0.96, p < 0.001); the bias of BAA 1.63 bpm, SD 8.62 bpm, LOA from −15.27 bpm to +18.58 bpm. These results demonstrate the OEPS to be capable of carrying out real time and remote monitoring of heart rate. PMID:26473860

  9. StatSTEM: An efficient approach for accurate and precise model-based quantification of atomic resolution electron microscopy images.

    PubMed

    De Backer, A; van den Bos, K H W; Van den Broek, W; Sijbers, J; Van Aert, S

    2016-12-01

    An efficient model-based estimation algorithm is introduced to quantify the atomic column positions and intensities from atomic resolution (scanning) transmission electron microscopy ((S)TEM) images. This algorithm uses the least squares estimator on image segments containing individual columns fully accounting for overlap between neighbouring columns, enabling the analysis of a large field of view. For this algorithm, the accuracy and precision with which measurements for the atomic column positions and scattering cross-sections from annular dark field (ADF) STEM images can be estimated, has been investigated. The highest attainable precision is reached even for low dose images. Furthermore, the advantages of the model-based approach taking into account overlap between neighbouring columns are highlighted. This is done for the estimation of the distance between two neighbouring columns as a function of their distance and for the estimation of the scattering cross-section which is compared to the integrated intensity from a Voronoi cell. To provide end-users this well-established quantification method, a user friendly program, StatSTEM, is developed which is freely available under a GNU public license.

  10. Accurate all-electron correlation energies for the closed-shell atoms from Ar to Rn and their relationship to the corresponding MP2 correlation energies.

    PubMed

    McCarthy, Shane P; Thakkar, Ajit J

    2011-01-28

    All-electron correlation energies E(c) are not very well-known for atoms with more than 18 electrons. Hence, coupled-cluster calculations in carefully designed basis sets are combined with fully converged second-order Møller-Plesset perturbation theory (MP2) computations to obtain fairly accurate, nonrelativistic E(c) values for the 12 closed-shell atoms from Ar to Rn. These energies will be useful for the evaluation and parameterization of density functionals. The results show that MP2 overestimates ∣E(c)∣ for heavy atoms. Spin-component scaling of the MP2 correlation energy is used to provide a simple explanation for this overestimation.

  11. Rapid and Accurate Detection of Urinary Pathogens by Mobile IMS-Based Electronic Nose: A Proof-of-Principle Study

    PubMed Central

    Roine, Antti; Saviauk, Taavi; Kumpulainen, Pekka; Karjalainen, Markus; Tuokko, Antti; Aittoniemi, Janne; Vuento, Risto; Lekkala, Jukka; Lehtimäki, Terho; Tammela, Teuvo L.; Oksala, Niku K. J.

    2014-01-01

    Urinary tract infection (UTI) is a common disease with significant morbidity and economic burden, accounting for a significant part of the workload in clinical microbiology laboratories. Current clinical chemisty point-of-care diagnostics rely on imperfect dipstick analysis which only provides indirect and insensitive evidence of urinary bacterial pathogens. An electronic nose (eNose) is a handheld device mimicking mammalian olfaction that potentially offers affordable and rapid analysis of samples without preparation at athmospheric pressure. In this study we demonstrate the applicability of ion mobility spectrometry (IMS) –based eNose to discriminate the most common UTI pathogens from gaseous headspace of culture plates rapidly and without sample preparation. We gathered a total of 101 culture samples containing four most common UTI bacteries: E. coli, S. saprophyticus, E. faecalis, Klebsiella spp and sterile culture plates. The samples were analyzed using ChemPro 100i device, consisting of IMS cell and six semiconductor sensors. Data analysis was conducted by linear discriminant analysis (LDA) and logistic regression (LR). The results were validated by leave-one-out and 5-fold cross validation analysis. In discrimination of sterile and bacterial samples sensitivity of 95% and specificity of 97% were achieved. The bacterial species were identified with sensitivity of 95% and specificity of 96% using eNose as compared to urine bacterial cultures. In conclusion: These findings strongly demonstrate the ability of our eNose to discriminate bacterial cultures and provides a proof of principle to use this method in urinanalysis of UTI. PMID:25526592

  12. Syntheses and electronic structures of decamethylmetallocenes

    SciTech Connect

    Robbins, J.L.

    1981-04-01

    The synthesis of decamethylmanganocene ((eta-C/sub 5/(CH/sub 3/)/sub 5/)/sub 2/Mn or (Me/sub 5/Cp)/sub 2/Mn)) is described. Magnetic susceptibility and electron paramagnetic resonance (EPR) studies show that (Me/sub 5/Cp)/sub 2/Mn is a low-spin, 17-electron compound with an orbitally degenerate, /sup 2/E/sub 2g/ (e/sub 2g//sup 3/ a/sub 1g//sup 2/) ground state. An x-ray crystallographic study of (Me/sub 5/Cp)/sub 2/Mn shows that it is a monomeric, D/sub 5d/ decamethylmetallocene with metal to ring carbon distances that are about 0.3 A shorter than those determined for high-spin manganocenes. The syntheses of new (Me/sub 5/Cp)/sub 2/M (M = Mg,V,Cr,Co, and Ni) and ((Me/sub 5/Cp)/sub 2/M)PF/sub 6/ (M = Cr,Co, and Ni) compounds are described. In addition, a preparative route to a novel, dicationic decamethylmetallocene, ((Me/sub 5/Cp)/sub 2/Ni)(PF/sub 6/)/sub 2/ is reported. Infrared, nuclear magnetic resonance, magnetic susceptibility, and/or x-ray crystallographic studies indicate that all the above compounds are D/sub 5d/ or D/sub 5h/ decamethylmetallocenes with low-spin electronic configurations. Cyclic voltammetry studies verify the reversibility and the one-electron nature of the (Me/sub 5/Cp)/sub 2/M ..-->.. ((Me/sub 5/Cp)/sub 2/M)/sup +/ (M = Cr,Mn,Fe,Co,Ni), ((Me/sub 5/Cp)/sub 2/Mn)/sup -/ ..-->.. (Me/sub 5/Cp)/sub 2/Mn and ((Me/sub 5/Cp)/sub 2/Ni)/sup +/ ..-->.. (Me/sub 5/Cp)/sub 2/Ni)/sup 2 +/ redox reactions. These studies reveal that the neutral decamethylmetallocenes are much more easily oxidized than their metallocene counterparts. This result attests to the electron-donating properties of the ten substituent methyl groups. Proton and carbon-13 NMR data are reported for the diamagnetic Mg(II), Mn(I), Fe(II), Co(III), and Ni(IV) decamethylmetallocenes and for ((Me/sub 5/Cp)/sub 2/V(CO)/sub 2/)/sup +/. The uv-visible absorption spectra of the 15-, 18- and 20- electron decamethylmetallocenes are also reported.

  13. Electronic structure and optical properties of solid C 60

    NASA Astrophysics Data System (ADS)

    Mattesini, M.; Ahuja, R.; Sa, L.; Hugosson, H. W.; Johansson, B.; Eriksson, O.

    2009-06-01

    The electronic structure and the optical properties of face-centered-cubic C 60 have been investigated by using an all-electron full-potential method. Our ab initio results show that the imaginary dielectric function for high-energy values looks very similar to that of graphite, revealing close electronic structure similarities between the two systems. We have also identified the origin of different peaks in the dielectric function of fullerene by means of the calculated electronic density of states. The computed optical spectrum compares fairly well with the available experimental data for the Vis-UV absorption spectrum of solid C 60.

  14. Energy-filtered Electron Transport Structures for Low-power Low-noise 2-D Electronics

    PubMed Central

    Pan, Xuan; Qiu, Wanzhi; Skafidas, Efstratios

    2016-01-01

    In addition to cryogenic techniques, energy filtering has the potential to achieve high-performance low-noise 2-D electronic systems. Assemblies based on graphene quantum dots (GQDs) have been demonstrated to exhibit interesting transport properties, including resonant tunnelling. In this paper, we investigate GQDs based structures with the goal of producing energy filters for next generation lower-power lower-noise 2-D electronic systems. We evaluate the electron transport properties of the proposed GQD device structures to demonstrate electron energy filtering and the ability to control the position and magnitude of the energy passband by appropriate device dimensioning. We also show that the signal-to-thermal noise ratio performance of the proposed nanoscale device can be modified according to device geometry. The tunability of two-dimensional GQD structures indicates a promising route for the design of electron energy filters to produce low-power and low-noise electronics. PMID:27796343

  15. Energy-filtered Electron Transport Structures for Low-power Low-noise 2-D Electronics.

    PubMed

    Pan, Xuan; Qiu, Wanzhi; Skafidas, Efstratios

    2016-10-31

    In addition to cryogenic techniques, energy filtering has the potential to achieve high-performance low-noise 2-D electronic systems. Assemblies based on graphene quantum dots (GQDs) have been demonstrated to exhibit interesting transport properties, including resonant tunnelling. In this paper, we investigate GQDs based structures with the goal of producing energy filters for next generation lower-power lower-noise 2-D electronic systems. We evaluate the electron transport properties of the proposed GQD device structures to demonstrate electron energy filtering and the ability to control the position and magnitude of the energy passband by appropriate device dimensioning. We also show that the signal-to-thermal noise ratio performance of the proposed nanoscale device can be modified according to device geometry. The tunability of two-dimensional GQD structures indicates a promising route for the design of electron energy filters to produce low-power and low-noise electronics.

  16. Energy-filtered Electron Transport Structures for Low-power Low-noise 2-D Electronics

    NASA Astrophysics Data System (ADS)

    Pan, Xuan; Qiu, Wanzhi; Skafidas, Efstratios

    2016-10-01

    In addition to cryogenic techniques, energy filtering has the potential to achieve high-performance low-noise 2-D electronic systems. Assemblies based on graphene quantum dots (GQDs) have been demonstrated to exhibit interesting transport properties, including resonant tunnelling. In this paper, we investigate GQDs based structures with the goal of producing energy filters for next generation lower-power lower-noise 2-D electronic systems. We evaluate the electron transport properties of the proposed GQD device structures to demonstrate electron energy filtering and the ability to control the position and magnitude of the energy passband by appropriate device dimensioning. We also show that the signal-to-thermal noise ratio performance of the proposed nanoscale device can be modified according to device geometry. The tunability of two-dimensional GQD structures indicates a promising route for the design of electron energy filters to produce low-power and low-noise electronics.

  17. Electron Precipitation Associated with Small-Scale Auroral Structures

    NASA Astrophysics Data System (ADS)

    Michell, R.; Samara, M.; Grubbs, G. A., II; Hampton, D. L.; Bonnell, J. W.; Ogasawara, K.

    2014-12-01

    We present results from the Ground-to-Rocket Electrons Electrodynamics Correlative Experiment (GREECE) sounding rocket mission, where we combined high-resolution ground-based auroral imaging with high time-resolution precipitating electron measurements. The GREECE payload successfully launched from Poker Flat, Alaska on 03 March 2014 and reached an apogee of approximately 335 km. The narrow field-of-view auroral imaging was taken from Venetie, AK, which is directly under apogee. This enabled the small-scale auroral features at the magnetic footpoint of the rocket payload to be imaged in detail. The electron precipitation was measured with the Acute Precipitating Electron Spectrometer (APES) onboard the payload. Features in the electron data are matched up with their corresponding auroral structures and boundaries, enabling measurement of the exact electron distributions responsible for the specific small-scale auroral features. These electron distributions will then be used to infer what the potential electron acceleration processes were.

  18. Structural phase transition and electronic properties of NdBi

    SciTech Connect

    Sahu, Ashvini K.; Patiya, Jagdish; Sanyal, Sankar P.

    2015-06-24

    The structural and electronic properties of NdBi from an electronic structure calculation have been presented. The calculation is performed using self-consistent tight binding linear muffin tin orbital (TB-LMTO) method within the local density approximation (LDA). The calculated equilibrium structural parameters are in good agreement with the available experimental results. It is found that this compound shows metallic behavior under ambient condition and undergoes a structural phase transition from the NaCl structure to the CsCl structure at the pressure 20.1 GPa. The electronic structures of NdBi under pressure are investigated. It is found that NdBi have metallization and the hybridizations of atoms in NdBi under pressure become stronger.

  19. Writing silica structures in liquid with scanning transmission electron microscopy.

    PubMed

    van de Put, Marcel W P; Carcouët, Camille C M C; Bomans, Paul H H; Friedrich, Heiner; de Jonge, Niels; Sommerdijk, Nico A J M

    2015-02-04

    Silica nanoparticles are imaged in solution with scanning transmission electron microscopy (STEM) using a liquid cell with silicon nitride (SiN) membrane windows. The STEM images reveal that silica structures are deposited in well-defined patches on the upper SiN membranes upon electron beam irradiation. The thickness of the deposits is linear with the applied electron dose. Scanning electron microscopy (SEM) and atomic force microscopy (AFM) demonstrate that the deposited patches are a result of the merging of the original 20 nm-diameter nanoparticles, and that the related surface roughness depends on the electron dose rate used. Using this approach, sub-micrometer scale structures are written on the SiN in liquid by controlling the electron exposure as function of the lateral position.

  20. Electronic Structure of PbSe Nanowires

    NASA Astrophysics Data System (ADS)

    Avdeev, I. D.; Nestoklon, M. O.

    2016-11-01

    We present the tight binding calculations of the lead selenide nanowires: energy spectra of quantum confined states as a function of nanowire radius, dispersion in the full Brillouin zone, and the radial part of local electronic state density, which helps us to recognise valley splitting in the spectra. Also, we compare our results to KP perturbation theory predictions. We show that the value of the valley splitting is comparable with the distance between two levels of size quantization and that it strongly depends on the arrangement of the atoms in the wire.

  1. Electronic-structure calculation for metals by local optimization

    NASA Astrophysics Data System (ADS)

    Woodward, C.; Min, B. I.; Benedek, R.; Garner, J.

    1989-03-01

    Recent work by Car and Parrinello has generated considerable interest in the calculation of electronic structure by nonlinear optimization. The technique introduced by these authors, dynamical simulated annealing, is designed for problems that involve energy barriers. When local optimization suffices to determine the energy minimum, more direct methods are available. In this paper we apply the algorithm suggested by Williams and Soler to calculate the electronic structure of metals, using a plane-wave expansion for the electronic orbitals and an electron-ion pseudopotential of the Kleinman-Bylander form. Radial pseudopotentials were taken from the compilation of Bachelet, Hamann, and Schlüter. Calculations are performed to optimize the electronic structure (i) with fixed atomic configuration, or (ii) with the atomic volume being optimized simultaneously. It is found that the dual optimization (ii) converges in essentially the same number of steps as the static lattice optimization (i). Numerical results are presented for Li, K, Al, and simple-cubic P.

  2. Basis functions for electronic structure calculations on spheres

    SciTech Connect

    Gill, Peter M. W. Loos, Pierre-François Agboola, Davids

    2014-12-28

    We introduce a new basis function (the spherical Gaussian) for electronic structure calculations on spheres of any dimension D. We find general expressions for the one- and two-electron integrals and propose an efficient computational algorithm incorporating the Cauchy-Schwarz bound. Using numerical calculations for the D = 2 case, we show that spherical Gaussians are more efficient than spherical harmonics when the electrons are strongly localized.

  3. Secondary electron emission from surfaces with small structure

    NASA Astrophysics Data System (ADS)

    Dzhanoev, A. R.; Spahn, F.; Yaroshenko, V.; Lühr, H.; Schmidt, J.

    2015-09-01

    It is found that for objects possessing small surface structures with differing radii of curvature the secondary electron emission (SEE) yield may be significantly higher than for objects with smooth surfaces of the same material. The effect is highly pronounced for surface structures of nanometer scale, often providing a more than 100 % increase of the SEE yield. The results also show that the SEE yield from surfaces with structure does not show a universal dependence on the energy of the primary, incident electrons as it is found for flat surfaces in experiments. We derive conditions for the applicability of the conventional formulation of SEE using the simplifying assumption of universal dependence. Our analysis provides a basis for studying low-energy electron emission from nanometer structured surfaces under a penetrating electron beam important in many technological applications.

  4. Stacking dependent electronic structures of transition metal dichalcogenides heterobilayer

    NASA Astrophysics Data System (ADS)

    Lee, Yea-Lee; Park, Cheol-Hwan; Ihm, Jisoon

    The systematic study of the electronic structures and optical properties of the transition metal dichalcogenides (TMD) heterobilayers can significantly improve the designing of new electronic and optoelectronic devices. Here, we theoretically study the electronic structures and optical properties of TMD heterobilayers using the first-principles methods. The band structures of TMD heterobilayer are shown to be determined by the band alignments of the each layer, the weak interlayer interactions, and angle dependent stacking patterns. The photoluminescence spectra are investigated using the calculated band structures, and the optical absorption spectra are examined by the GW approximations including the electron-hole interaction through the solution of the Bethe-Salpeter equation. It is expected that the weak interlayer interaction gives rise to the substantial interlayer optical transition which will be corresponding to the interlayer exciton.

  5. Electron Diffraction Determination of Nanoscale Structures

    SciTech Connect

    Parks, Joel H

    2013-03-01

    Dominant research results on adsorption on gold clusters are reviewed, including adsorption of H{sub 2}O and O{sub 2} on gold cluster cations and anions, kinetics of CO adsorption to middle sized gold cluster cations, adsorption of CO on Au{sub n}{sup +} with induced changes in structure, and H{sub 2}O enhancement of CO adsorption.

  6. Enhanced Constraints for Accurate Lower Bounds on Many-Electron Quantum Energies from Variational Two-Electron Reduced Density Matrix Theory.

    PubMed

    Mazziotti, David A

    2016-10-07

    A central challenge of physics is the computation of strongly correlated quantum systems. The past ten years have witnessed the development and application of the variational calculation of the two-electron reduced density matrix (2-RDM) without the wave function. In this Letter we present an orders-of-magnitude improvement in the accuracy of 2-RDM calculations without an increase in their computational cost. The advance is based on a low-rank, dual formulation of an important constraint on the 2-RDM, the T2 condition. Calculations are presented for metallic chains and a cadmium-selenide dimer. The low-scaling T2 condition will have significant applications in atomic and molecular, condensed-matter, and nuclear physics.

  7. Enhanced Constraints for Accurate Lower Bounds on Many-Electron Quantum Energies from Variational Two-Electron Reduced Density Matrix Theory

    NASA Astrophysics Data System (ADS)

    Mazziotti, David A.

    2016-10-01

    A central challenge of physics is the computation of strongly correlated quantum systems. The past ten years have witnessed the development and application of the variational calculation of the two-electron reduced density matrix (2-RDM) without the wave function. In this Letter we present an orders-of-magnitude improvement in the accuracy of 2-RDM calculations without an increase in their computational cost. The advance is based on a low-rank, dual formulation of an important constraint on the 2-RDM, the T 2 condition. Calculations are presented for metallic chains and a cadmium-selenide dimer. The low-scaling T 2 condition will have significant applications in atomic and molecular, condensed-matter, and nuclear physics.

  8. Direct investigation of subsurface interface electronic structure by ballistic-electron-emission microscopy

    NASA Technical Reports Server (NTRS)

    Kaiser, W. J.; Bell, L. D.

    1988-01-01

    A new technique for spectroscopic investigation of subsurface interface electronic structure has been developed. The method, ballistic-electron-emission microscopy (BEEM), is based on scanning tunneling microscopy. BEEM makes possible, for the first time, direct imaging of subsurface interface properties with nanometer spatial resolution. The first application of BEEM to subsurface Schottky-barrier interfaces is reported.

  9. Atomic and electronic structure of Mo6S9-xIx nanowires

    NASA Astrophysics Data System (ADS)

    Meden, A.; Kodre, A.; Padeznik Gomilsek, J.; Arcon, I.; Vilfan, I.; Vrbanic, D.; Mrzel, A.; Mihailovic, D.

    2005-09-01

    Moybdenum-based subnanometre diameter nanowires are easy to synthesize and disperse, and they exhibit a variety of functional properties in which they are superior to other one-dimensional materials. However, further progress in the understanding of physical properties and the development of new and specific applications have so far been impeded by the fact that their structure was not accurately known. Here we report on a combination of systematic x-ray diffraction and extended x-ray absorption fine structure experiments, and first-principles theoretical structure calculations, which are used to determine the atomic skeletal structure of individual Mo6S9-xIx (MoSIx) nanowires, their packing arrangement within bundles and their electronic band structure. From this work we conclude that the variations in functional properties appear to arise from different stoichiometry, not skeletal structure. A supplementary data file is available from http://stacks.iop.org/0957-4484/16/1578

  10. Structure and properties of electronic and hole centers in CsBr from theoretical calculations

    SciTech Connect

    Halliday, Matthew T.; Hess, Wayne P.; Shluger, Alexander L.

    2015-06-24

    The electronic structure, geometry, diffusion barriers and optical properties of fundamental defects of CsBr are calculated using hybrid functional DFT and TD- DFT methods. The B3LYP functional with a modified exchange contribution has been used in an embedded cluster scheme to model the structure and spectroscopic properties of self-trapped triplet exciton, interstitial Br atoms and ions, self-trapped holes and Br vacancies. The calculated migration barriers and positions of maxima of optical absorption bands are in good agreement with experiment, justifying the obtained defect geometries. The o*-center triplet exciton luminescence energy is also accurately calculated.

  11. Electronic structure calculations of ESR parameters of melanin units.

    PubMed

    Batagin-Neto, Augusto; Bronze-Uhle, Erika Soares; Graeff, Carlos Frederico de Oliveira

    2015-03-21

    Melanins represent an important class of natural pigments present in plants and animals that are currently considered to be promising materials for applications in optic and electronic devices. Despite their interesting properties, some of the basic features of melanins are not satisfactorily understood, including the origin of their intrinsic paramagnetism. A number of experiments have been performed to investigate the electron spin resonance (ESR) response of melanin derivatives, but until now, there has been no consensus regarding the real structure of the paramagnetic centers involved. In this work, we have employed electronic structure calculations to evaluate the ESR parameters of distinct melanin monomers and dimers in order to identify the possible structures associated with unpaired spins in this biopolymer. The g-factors and hyperfine constants of the cationic, anionic and radicalar structures were investigated. The results confirm the existence of at least two distinct paramagnetic centers in melanin structure, identifying the chemical species associated with them and their roles in electrical conductivity.

  12. Structural properties of amorphous silicon produced by electron irradiation

    SciTech Connect

    Yamasaki, J.; Takeda, S.

    1999-07-01

    The structural properties of the amorphous Si (a-Si), which was created from crystalline silicon by 2 MeV electron irradiation at low temperatures about 25 K, are examined in detail by means of transmission electron microscopy and transmission electron diffraction. The peak positions in the radial distribution function (RDF) of the a-Si correspond well to those of a-Si fabricated by other techniques. The electron-irradiation-induced a-Si returns to crystalline Si after annealing at 550 C.

  13. Distinct electronic structure for the extreme magnetoresistance in YSb

    SciTech Connect

    He, Junfeng; Zhang, Chaofan; Ghimire, Nirmal J.; Liang, Tian; Jia, Chunjing; Jiang, Juan; Tang, Shujie; Chen, Sudi; He, Yu; Mo, S. -K.; Hwang, C. C.; Hashimoto, M.; Lu, D. H.; Moritz, B.; Devereaux, T. P.; Chen, Y. L.; Mitchell, J. F.; Shen, Z. -X.

    2016-12-23

    An extreme magnetoresistance (XMR) has recently been observed in several nonmagnetic semimetals. Increasing experimental and theoretical evidence indicates that the XMR can be driven by either topological protection or electron-hole compensation. Moreover, by investigating the electronic structure of a XMR material, YSb, we present spectroscopic evidence for a special case which lacks topological protection and perfect electron-hole compensation. Further investigations reveal that a cooperative action of a substantial difference between electron and hole mobility and a moderate carrier compensation might contribute to the XMR in YSb.

  14. Electronic structure modulation of graphene edges by chemical functionalization

    NASA Astrophysics Data System (ADS)

    Taira, Remi; Yamanaka, Ayaka; Okada, Susumu

    2016-11-01

    Using the density functional theory with the effective screening medium method, we study the electronic properties of graphene nanoribbons with zigzag edges that are terminated by hydrogen and ketone, hydroxyl, carbonyl, and carboxyl functional groups. Our calculations showed that the work function and electronic structures of the edges of the nanoribbons are sensitive to the functional groups attached to the edges. The nearly free electron state emerges in the vacuum region outside the hydroxylated edges and crosses the Fermi level, indicating the possibility of negative electron affinity at the edges.

  15. Electron beam enhanced surface modification for making highly resolved structures

    DOEpatents

    Pitts, John R.

    1986-01-01

    A method for forming high resolution submicron structures on a substrate is provided by direct writing with a submicron electron beam in a partial pressure of a selected gas phase characterized by the ability to dissociate under the beam into a stable gaseous leaving group and a reactant fragment that combines with the substrate material under beam energy to form at least a surface compound. Variations of the method provide semiconductor device regions on doped silicon substrates, interconnect lines between active sites, three dimensional electronic chip structures, electron beam and optical read mass storage devices that may include color differentiated data areas, and resist areas for use with selective etching techniques.

  16. Electron beam enhanced surface modification for making highly resolved structures

    DOEpatents

    Pitts, J.R.

    1984-10-10

    A method for forming high resolution submicron structures on a substrate is provided by direct writing with a submicron electron beam in a partial pressure of a selected gas phase characterized by the ability to dissociate under the beam into a stable gaseous leaving group and a reactant fragment that combines with the substrate material under beam energy to form at least a surface compound. Variations of the method provide semiconductor device regions on doped silicon substrates, interconnect lines between active sites, three dimensional electronic chip structures, electron beam and optical read mass storage devices that may include color differentiated data areas, and resist areas for use with selective etching techniques.

  17. Solitary structures with ion and electron thermal anisotropy

    NASA Astrophysics Data System (ADS)

    Khusroo, Murchana; Bora, Madhurjya P.

    2015-11-01

    The formation of electrostatic solitary structures is analysed for a magnetised plasma with ion and electron thermal anisotropies. The ion thermal anisotropy is modelled with the help of the Chew-Goldberger-Low (CGL) double adiabatic equations of state while the electrons are treated as inertia-less species with an anisotropic bi-Maxwellian velocity distribution function. A negative electron thermal anisotropy ≤ft({{T}e\\bot}/{{T}e\\parallel}>1\\right) is found to help form large amplitude solitary structures which are in agreement with observational data.

  18. Electron-interface phonon interaction in multiple quantum well structures

    NASA Astrophysics Data System (ADS)

    Sun, J. P.; Teng, H. B.; Haddad, G. I.; Stroscio, M. A.

    1998-08-01

    Intersubband relaxation rates due to electron interactions with the interface phonons are evaluated for multiple quantum well structures designed for step quantum well lasers operating at mid-infrared to submillimetre wavelengths. The interface phonon modes and electron-phonon interaction Hamiltonians for the structures are derived using the transfer matrix method, based on the macroscopic dielectric continuum model, whereas the electron wavefunctions are obtained by solving the Schrödinger equation. Fermi's golden rule is employed to calculate the electron relaxation rates between the subbands in these structures. The relaxation rates for two different structures are examined and compared with those calculated using the bulk phonon modes and the Fröhlich interaction Hamiltonian. The sum rule for the relationship between the form factors of the various localized phonon modes and the bulk phonon modes is verified. The results obtained in this work illustrate that the transfer matrix method provides a convenient way for deriving the properties of the interface phonon modes in different structures of current interest and that, for preferential electron relaxation in intersubband laser structures, the effects of the interface phonon modes are significant and should be considered for optimal design of these laser structures.

  19. 4-Component correlated all-electron study on Eka-actinium Fluoride (E121F) including Gaunt interaction: Accurate analytical form, bonding and influence on rovibrational spectra

    NASA Astrophysics Data System (ADS)

    Amador, Davi H. T.; de Oliveira, Heibbe C. B.; Sambrano, Julio R.; Gargano, Ricardo; de Macedo, Luiz Guilherme M.

    2016-10-01

    A prolapse-free basis set for Eka-Actinium (E121, Z = 121), numerical atomic calculations on E121, spectroscopic constants and accurate analytical form for the potential energy curve of diatomic E121F obtained at 4-component all-electron CCSD(T) level including Gaunt interaction are presented. The results show a strong and polarized bond (≈181 kcal/mol in strength) between E121 and F, the outermost frontier molecular orbitals from E121F should be fairly similar to the ones from AcF and there is no evidence of break of periodic trends. Moreover, the Gaunt interaction, although small, is expected to influence considerably the overall rovibrational spectra.

  20. Nano-structured electron transporting materials for perovskite solar cells

    NASA Astrophysics Data System (ADS)

    Liu, Hefei; Huang, Ziru; Wei, Shiyuan; Zheng, Lingling; Xiao, Lixin; Gong, Qihuang

    2016-03-01

    Organic-inorganic hybrid perovskite solar cells have been developing rapidly in the past several years, and their power conversion efficiency has reached over 20%, nearing that of polycrystalline silicon solar cells. Because the diffusion length of the hole in perovskites is longer than that of the electron, the performance of the device can be improved by using an electron transporting layer, e.g., TiO2, ZnO and TiO2/Al2O3. Nano-structured electron transporting materials facilitate not only electron collection but also morphology control of the perovskites. The properties, morphology and preparation methods of perovskites are reviewed in the present article. A comprehensive understanding of the relationship between the structure and property will benefit the precise control of the electron transporting process and thus further improve the performance of perovskite solar cells.

  1. Nano-structured electron transporting materials for perovskite solar cells.

    PubMed

    Liu, Hefei; Huang, Ziru; Wei, Shiyuan; Zheng, Lingling; Xiao, Lixin; Gong, Qihuang

    2016-03-28

    Organic-inorganic hybrid perovskite solar cells have been developing rapidly in the past several years, and their power conversion efficiency has reached over 20%, nearing that of polycrystalline silicon solar cells. Because the diffusion length of the hole in perovskites is longer than that of the electron, the performance of the device can be improved by using an electron transporting layer, e.g., TiO2, ZnO and TiO2/Al2O3. Nano-structured electron transporting materials facilitate not only electron collection but also morphology control of the perovskites. The properties, morphology and preparation methods of perovskites are reviewed in the present article. A comprehensive understanding of the relationship between the structure and property will benefit the precise control of the electron transporting process and thus further improve the performance of perovskite solar cells.

  2. Structural complexities in the active layers of organic electronics.

    PubMed

    Lee, Stephanie S; Loo, Yueh-Lin

    2010-01-01

    The field of organic electronics has progressed rapidly in recent years. However, understanding the direct structure-function relationships between the morphology in electrically active layers and the performance of devices composed of these materials has proven difficult. The morphology of active layers in organic electronics is inherently complex, with heterogeneities existing across multiple length scales, from subnanometer to micron and millimeter range. A major challenge still facing the organic electronics community is understanding how the morphology across all of the length scales in active layers collectively determines the device performance of organic electronics. In this review we highlight experiments that have contributed to the elucidation of structure-function relationships in organic electronics and also point to areas in which knowledge of such relationships is still lacking. Such knowledge will lead to the ability to select active materials on the basis of their inherent properties for the fabrication of devices with prespecified characteristics.

  3. Accurate electronic and chemical properties of 3d transition metal oxides using a calculated linear response U and a DFT + U(V) method.

    PubMed

    Xu, Zhongnan; Joshi, Yogesh V; Raman, Sumathy; Kitchin, John R

    2015-04-14

    We validate the usage of the calculated, linear response Hubbard U for evaluating accurate electronic and chemical properties of bulk 3d transition metal oxides. We find calculated values of U lead to improved band gaps. For the evaluation of accurate reaction energies, we first identify and eliminate contributions to the reaction energies of bulk systems due only to changes in U and construct a thermodynamic cycle that references the total energies of unique U systems to a common point using a DFT + U(V) method, which we recast from a recently introduced DFT + U(R) method for molecular systems. We then introduce a semi-empirical method based on weighted DFT/DFT + U cohesive energies to calculate bulk oxidation energies of transition metal oxides using density functional theory and linear response calculated U values. We validate this method by calculating 14 reactions energies involving V, Cr, Mn, Fe, and Co oxides. We find up to an 85% reduction of the mean average error (MAE) compared to energies calculated with the Perdew-Burke-Ernzerhof functional. When our method is compared with DFT + U with empirically derived U values and the HSE06 hybrid functional, we find up to 65% and 39% reductions in the MAE, respectively.

  4. Accurate electronic and chemical properties of 3d transition metal oxides using a calculated linear response U and a DFT + U(V) method

    SciTech Connect

    Xu, Zhongnan; Kitchin, John R.; Joshi, Yogesh V.; Raman, Sumathy

    2015-04-14

    We validate the usage of the calculated, linear response Hubbard U for evaluating accurate electronic and chemical properties of bulk 3d transition metal oxides. We find calculated values of U lead to improved band gaps. For the evaluation of accurate reaction energies, we first identify and eliminate contributions to the reaction energies of bulk systems due only to changes in U and construct a thermodynamic cycle that references the total energies of unique U systems to a common point using a DFT + U(V ) method, which we recast from a recently introduced DFT + U(R) method for molecular systems. We then introduce a semi-empirical method based on weighted DFT/DFT + U cohesive energies to calculate bulk oxidation energies of transition metal oxides using density functional theory and linear response calculated U values. We validate this method by calculating 14 reactions energies involving V, Cr, Mn, Fe, and Co oxides. We find up to an 85% reduction of the mean average error (MAE) compared to energies calculated with the Perdew-Burke-Ernzerhof functional. When our method is compared with DFT + U with empirically derived U values and the HSE06 hybrid functional, we find up to 65% and 39% reductions in the MAE, respectively.

  5. Electronic band structure of surface-doped black phosphorus

    NASA Astrophysics Data System (ADS)

    Kim, Jimin; Ryu, Sae Hee; Sohn, Yeongsup; Kim, Keun Su

    2015-03-01

    There are rapidly growing interests in the study of few-layer black phosphorus owing to its promising device characteristics that may impact our future electronics technology. The low-energy band structure of black phosphorus has been widely predicted to be controllable by external perturbations, such as strain and doping. In this work, we attempt to control the electronic band structure of black phosphorous by in-situ surface deposition of alkali-metal atoms. We found that surface doping induces steep band bending towards the bulk, leading to the emergence of new 2D electronic states that are confined within only few phosphorene layers of black phosphorus. Using angle-resolved photoemission spectroscopy, we directly measured the electronic band structure and its evolution as a function of dopant density. Supported by IBS.

  6. Electronic structure of a graphene superlattice with massive Dirac fermions

    SciTech Connect

    Lima, Jonas R. F.

    2015-02-28

    We study the electronic and transport properties of a graphene-based superlattice theoretically by using an effective Dirac equation. The superlattice consists of a periodic potential applied on a single-layer graphene deposited on a substrate that opens an energy gap of 2Δ in its electronic structure. We find that extra Dirac points appear in the electronic band structure under certain conditions, so it is possible to close the gap between the conduction and valence minibands. We show that the energy gap E{sub g} can be tuned in the range 0 ≤ E{sub g} ≤ 2Δ by changing the periodic potential. We analyze the low energy electronic structure around the contact points and find that the effective Fermi velocity in very anisotropic and depends on the energy gap. We show that the extra Dirac points obtained here behave differently compared to previously studied systems.

  7. Spatial distribution of electrons near the Fermi level in the metallic LaB6 through accurate X-ray charge density study

    PubMed Central

    Kasai, Hidetaka; Nishibori, Eiji

    2017-01-01

    Charge densities of iso-structural metal hexaborides, a transparent metal LaB6 and a semiconductor BaB6, have been determined using the d > 0.22 Å ultra-high resolution synchrotron radiation X-ray diffraction data by a multipole refinement and a maximum entropy method (MEM). The quality of the experimental charge densities was evaluated by comparison with theoretical charge densities. The strong inter-octahedral and relatively weak intra-octahedral boron-boron bonds were observed in the charge densities. A difference of valence charge densities between LaB6 and BaB6 was calculated to reveal a small difference between isostructural metal and semiconductor. The weak electron lobes distributed around the inter B6 octahedral bond were observed in the difference density. We found the electron lobes are the conductive π-electrons in LaB6 from the comparison with the theoretical valence charge density. We successfully observed a spatial distribution of electrons near the Fermi level from the X-ray charge density study of the series of iso-structural solids. PMID:28120900

  8. Spatial distribution of electrons near the Fermi level in the metallic LaB6 through accurate X-ray charge density study

    NASA Astrophysics Data System (ADS)

    Kasai, Hidetaka; Nishibori, Eiji

    2017-01-01

    Charge densities of iso-structural metal hexaborides, a transparent metal LaB6 and a semiconductor BaB6, have been determined using the d > 0.22 Å ultra-high resolution synchrotron radiation X-ray diffraction data by a multipole refinement and a maximum entropy method (MEM). The quality of the experimental charge densities was evaluated by comparison with theoretical charge densities. The strong inter-octahedral and relatively weak intra-octahedral boron-boron bonds were observed in the charge densities. A difference of valence charge densities between LaB6 and BaB6 was calculated to reveal a small difference between isostructural metal and semiconductor. The weak electron lobes distributed around the inter B6 octahedral bond were observed in the difference density. We found the electron lobes are the conductive π-electrons in LaB6 from the comparison with the theoretical valence charge density. We successfully observed a spatial distribution of electrons near the Fermi level from the X-ray charge density study of the series of iso-structural solids.

  9. Spatial distribution of electrons near the Fermi level in the metallic LaB6 through accurate X-ray charge density study.

    PubMed

    Kasai, Hidetaka; Nishibori, Eiji

    2017-01-25

    Charge densities of iso-structural metal hexaborides, a transparent metal LaB6 and a semiconductor BaB6, have been determined using the d > 0.22 Å ultra-high resolution synchrotron radiation X-ray diffraction data by a multipole refinement and a maximum entropy method (MEM). The quality of the experimental charge densities was evaluated by comparison with theoretical charge densities. The strong inter-octahedral and relatively weak intra-octahedral boron-boron bonds were observed in the charge densities. A difference of valence charge densities between LaB6 and BaB6 was calculated to reveal a small difference between isostructural metal and semiconductor. The weak electron lobes distributed around the inter B6 octahedral bond were observed in the difference density. We found the electron lobes are the conductive π-electrons in LaB6 from the comparison with the theoretical valence charge density. We successfully observed a spatial distribution of electrons near the Fermi level from the X-ray charge density study of the series of iso-structural solids.

  10. CONDENSED MATTER: ELECTRONIC STRUCTURE, ELECTRICAL, MAGNETIC, AND OPTICAL PROPERTIES: Fifth-Nearest-Neighbor Tight-Binding Description of Electronic Structure of Graphene

    NASA Astrophysics Data System (ADS)

    You, Jing-Han; Ju, Wei-Wei; Li, Er-Qiang; Pu, Tian-Song; Zhao, Yuan-Yuan; Wang, Hui

    2010-06-01

    An analytic expression for π and π* electronic structure of graphene is derived within the tight-binding approximation. Including up to fifth-nearest neighbors, the tight-binding description of electronic dispersion quite accurately reproduces the first-principle calculation result over the entire Brillouin zone. The maximal deviation of the fifth-nearest tight-binding result from the first-principle result is only 6 meV for π band, and 25 meV for π* band. This 25 meV deviation is only one-tenth of the maximal deviation of the third-nearest tight-binding result. It is more important that the fitted parameters exponentially approach to zero as the distance between interacting atoms increases.

  11. Topological Insulators: Electronic Band Structure and Spectroscopy

    NASA Astrophysics Data System (ADS)

    Palaz, S.; Koc, H.; Mamedov, A. M.; Ozbay, E.

    2017-02-01

    In this study, we present the results of our ab initio calculation of the elastic constants, density of states, charge density, and Born effective charge tensors for ferroelectric (rhombohedral) and paraelectric phases (cubic) of the narrow band ferroelectrics (GeTe, SnTe) pseudopotentials. The related quantities such as bulk modulus and shear modulus using obtained elastic constants have also been estimated in the present work. The total and partial densities of states corresponding to the band structure of Sn(Ge)Te(S,Se) were calculated. We also calculated the Born effective charge tensor of an atom (for instance, Ge, Sn, Te, etc.), which is defined as the induced polarization of the solid along the main direction by a unit displacement in the perpendicular direction of the sublattice of an atom at the vanishing electric field.

  12. Electronic Structure and Transport in Magnetic Multilayers

    SciTech Connect

    2008-02-18

    ORNL assisted Seagate Recording Heads Operations in the development of CIPS pin Valves for application as read sensors in hard disk drives. Personnel at ORNL were W. H. Butler and Xiaoguang Zhang. Dr. Olle Heinonen from Seagate RHO also participated. ORNL provided codes and materials parameters that were used by Seagate to model CIP GMR in their heads. The objectives were to: (1) develop a linearized Boltzmann transport code for describing CIP GMR based on realistic models of the band structure and interfaces in materials in CIP spin valves in disk drive heads; (2) calculate the materials parameters needed as inputs to the Boltzmann code; and (3) transfer the technology to Seagate Recording Heads.

  13. Electronic correlation in magnetic contributions to structural energies

    NASA Astrophysics Data System (ADS)

    Haydock, Roger

    For interacting electrons the density of transitions [see http://arxiv.org/abs/1405.2288] replaces the density of states in calculations of structural energies. Extending previous work on paramagnetic metals, this approach is applied to correlation effects on the structural stability of magnetic transition metals. Supported by the H. V. Snyder Gift to the University of Oregon.

  14. Electron vortex magnetic holes: A nonlinear coherent plasma structure

    SciTech Connect

    Haynes, Christopher T. Burgess, David; Sundberg, Torbjorn; Camporeale, Enrico

    2015-01-15

    We report the properties of a novel type of sub-proton scale magnetic hole found in two dimensional particle-in-cell simulations of decaying turbulence with a guide field. The simulations were performed with a realistic value for ion to electron mass ratio. These structures, electron vortex magnetic holes (EVMHs), have circular cross-section. The magnetic field depression is associated with a diamagnetic azimuthal current provided by a population of trapped electrons in petal-like orbits. The trapped electron population provides a mean azimuthal velocity and since trapping preferentially selects high pitch angles, a perpendicular temperature anisotropy. The structures arise out of initial perturbations in the course of the turbulent evolution of the plasma, and are stable over at least 100 electron gyroperiods. We have verified the model for the EVMH by carrying out test particle and PIC simulations of isolated structures in a uniform plasma. It is found that (quasi-)stable structures can be formed provided that there is some initial perpendicular temperature anisotropy at the structure location. The properties of these structures (scale size, trapped population, etc.) are able to explain the observed properties of magnetic holes in the terrestrial plasma sheet. EVMHs may also contribute to turbulence properties, such as intermittency, at short scale lengths in other astrophysical plasmas.

  15. Electron vortex magnetic holes: A nonlinear coherent plasma structure

    NASA Astrophysics Data System (ADS)

    Haynes, Christopher T.; Burgess, David; Camporeale, Enrico; Sundberg, Torbjorn

    2015-01-01

    We report the properties of a novel type of sub-proton scale magnetic hole found in two dimensional particle-in-cell simulations of decaying turbulence with a guide field. The simulations were performed with a realistic value for ion to electron mass ratio. These structures, electron vortex magnetic holes (EVMHs), have circular cross-section. The magnetic field depression is associated with a diamagnetic azimuthal current provided by a population of trapped electrons in petal-like orbits. The trapped electron population provides a mean azimuthal velocity and since trapping preferentially selects high pitch angles, a perpendicular temperature anisotropy. The structures arise out of initial perturbations in the course of the turbulent evolution of the plasma, and are stable over at least 100 electron gyroperiods. We have verified the model for the EVMH by carrying out test particle and PIC simulations of isolated structures in a uniform plasma. It is found that (quasi-)stable structures can be formed provided that there is some initial perpendicular temperature anisotropy at the structure location. The properties of these structures (scale size, trapped population, etc.) are able to explain the observed properties of magnetic holes in the terrestrial plasma sheet. EVMHs may also contribute to turbulence properties, such as intermittency, at short scale lengths in other astrophysical plasmas.

  16. Decoupling of structural and electronic phase transitions in VO2.

    PubMed

    Tao, Zhensheng; Han, Tzong-Ru T; Mahanti, Subhendra D; Duxbury, Phillip M; Yuan, Fei; Ruan, Chong-Yu; Wang, Kevin; Wu, Junqiao

    2012-10-19

    Using optical, TEM, and ultrafast electron diffraction experiments we find that single crystal VO(2) microbeams gently placed on insulating substrates or metal grids exhibit different behaviors, with structural and metal-insulator transitions occurring at the same temperature for insulating substrates, while for metal substrates a new monoclinic metal phase lies between the insulating monoclinic phase and the metallic rutile phase. The structural and electronic phase transitions in these experiments are strongly first order and we discuss their origins in the context of current understanding of multiorbital splitting, strong correlation effects, and structural distortions that act cooperatively in this system.

  17. Electronic states in hybrid boron nitride and graphene structures

    NASA Astrophysics Data System (ADS)

    Zhao, M.; Huang, Y. H.; Ma, F.; Hu, T. W.; Xu, K. W.; Chu, Paul K.

    2013-08-01

    The energy bands and electronic states of hybrid boron nitride (BN) and graphene structures are studied by first principle calculations. The electronic states change from semi-metallic to insulating depending on the number of B and N atoms as well as domain symmetry. When there are unequal numbers of B and N atoms, mid-gap states usually appear around the Fermi level and the corresponding hybrid structure possesses magnetic and semi-metallic properties. However, when the numbers of B and N atoms are equal, a band gap exists indicative of a semiconducting or insulating nature which depends on the structural symmetry.

  18. Engineering the Electronic Band Structure for Multiband Solar Cells

    SciTech Connect

    Lopez, N.; Reichertz, L.A.; Yu, K.M.; Campman, K.; Walukiewicz, W.

    2010-07-12

    Using the unique features of the electronic band structure of GaNxAs1-x alloys, we have designed, fabricated and tested a multiband photovoltaic device. The device demonstrates an optical activity of three energy bands that absorb, and convert into electrical current, the crucial part of the solar spectrum. The performance of the device and measurements of electroluminescence, quantum efficiency and photomodulated reflectivity are analyzed in terms of the Band Anticrossing model of the electronic structure of highly mismatched alloys. The results demonstrate the feasibility of using highly mismatched alloys to engineer the semiconductor energy band structure for specific device applications.

  19. Engineering the electronic band structure for multiband solar cells.

    PubMed

    López, N; Reichertz, L A; Yu, K M; Campman, K; Walukiewicz, W

    2011-01-14

    Using the unique features of the electronic band structure of GaN(x)As(1-x) alloys, we have designed, fabricated and tested a multiband photovoltaic device. The device demonstrates an optical activity of three energy bands that absorb, and convert into electrical current, the crucial part of the solar spectrum. The performance of the device and measurements of electroluminescence, quantum efficiency and photomodulated reflectivity are analyzed in terms of the band anticrossing model of the electronic structure of highly mismatched alloys. The results demonstrate the feasibility of using highly mismatched alloys to engineer the semiconductor energy band structure for specific device applications.

  20. Electronic structure and bonding in skutterudite-type phosphides

    NASA Astrophysics Data System (ADS)

    Llunell, Miquel; Alemany, Pere; Alvarez, Santiago; Zhukov, Vladlen P.; Vernes, Andreas

    1996-04-01

    The electronic structures of the skutterudite-type phosphides CoP3 and NiP3 have been investigated by means of first-principles linear muffin-tin orbital-atomic sphere approximation band-structure calculations. The presence of P4 rings in the skutterudite structure is of great importance in determining the nature of the electronic bands around the Fermi level, composed mainly of π-type molecular orbitals of these units. The metallic character found for NiP3 should be ascribed to the phosphorus framework rather than to the metal atoms.

  1. Goeppert-Mayer Award Recipient: Electron Scattering and Nucleon Structure

    NASA Astrophysics Data System (ADS)

    Beise, Elizabeth

    1998-04-01

    Electron scattering from hydrogen and light nuclear targets has long been recognized as one of the best tools for understanding the electromagnetic structure of protons, neutrons and few-nucleon systems. In the last decade, considerable progress has been made in the field through advances in polarized beams and polarized targets. Improvements in polarized electron sources has made it feasible to also study the structure of the nucleon through parity-violating electron scattering, where the nucleon's neutral weak structure is probed. In this talk, a summary of the present experimental status of the nucleon's electroweak structure will be presented, with an emphasis on recent results from the MIT-Bates and Jefferson Laboratories.

  2. Advanced accelerating structures and their interaction with electron beams.

    SciTech Connect

    Gai, W.; High Energy Physics

    2008-01-01

    In this paper, we give a brief description of several advanced accelerating structures, such as dielectric loaded waveguides, photonic band gap, metamaterials and improved iris-loaded cavities. We describe wakefields generated by passing high current electron beams through these structures, and applications of wakefields to advanced accelerator schemes. One of the keys to success for high gradient wakefield acceleration is to develop high current drive beam sources. As an example, the high current RF photo injector at the Argonne Wakefield Accelerator, passed a {approx}80 nC electron beam through a high gradient dielectric loaded structure to achieve a 100 MV/m gradient. We will summarize recent related experiments on beam-structure interactions and also discuss high current electron beam generation and propagation and their applications to wakefield acceleration.

  3. Advanced Accelerating Structures and Their Interaction with Electron Beams

    SciTech Connect

    Gai Wei

    2009-01-22

    In this paper, we give a brief description of several advanced accelerating structures, such as dielectric loaded waveguides, photonic band gap, metamaterials and improved iris-loaded cavities. We describe wakefields generated by passing high current electron beams through these structures, and applications of wakefields to advanced accelerator schemes. One of the keys to success for high gradient wakefield acceleration is to develop high current drive beam sources. As an example, the high current RF photo injector at the Argonne Wakefield Accelerator, passed a {approx}80 nC electron beam through a high gradient dielectric loaded structure to achieve a 100 MV/m gradient. We will summarize recent related experiments on beam-structure interactions and also discuss high current electron beam generation and propagation and their applications to wakefield acceleration.

  4. High-resolution photoelectron imaging of cold C{sub 60}{sup −} anions and accurate determination of the electron affinity of C{sub 60}

    SciTech Connect

    Huang, Dao-Ling; Dau, Phuong Diem; Liu, Hong-Tao; Wang, Lai-Sheng

    2014-06-14

    High-resolution photoelectron imaging and spectroscopy of cold C{sub 60}{sup −} anions are reported using a newly built photoelectron imaging apparatus coupled with an electrospray ionization source and a temperature-controlled cryogenic ion trap. Vibrationally resolved photoelectron spectra are obtained for the detachment transition from the ground state of C{sub 60}{sup −} to that of C{sub 60} at various detachment wavelengths from 354.84 nm to 461.35 nm. The electron affinity of C{sub 60} is accurately measured to be 2.6835 ± 0.0006 eV. Numerous unexpected vibrational excitations are observed in the photoelectron spectra due to the Jahn-Teller effect in C{sub 60}{sup −} and Hertzberg-Teller vibronic coupling in both C{sub 60}{sup −} and C{sub 60}. Both the relative intensities of vibrational peaks and their photoelectron angular distributions provide evidence for the vibronic couplings. The observed p-wave-like behavior in the angular distribution of the 0{sub 0}{sup 0} transition suggests that the electron is detached from an s-type orbital.

  5. The requisite electronic structure theory to describe photoexcited nonadiabatic dynamics: nonadiabatic derivative couplings and diabatic electronic couplings.

    PubMed

    Subotnik, Joseph E; Alguire, Ethan C; Ou, Qi; Landry, Brian R; Fatehi, Shervin

    2015-05-19

    Electronically photoexcited dynamics are complicated because there are so many different relaxation pathways: fluorescence, phosphorescence, radiationless decay, electon transfer, etc. In practice, to model photoexcited systems is a very difficult enterprise, requiring accurate and very efficient tools in both electronic structure theory and nonadiabatic chemical dynamics. Moreover, these theoretical tools are not traditional tools. On the one hand, the electronic structure tools involve couplings between electonic states (rather than typical single state energies and gradients). On the other hand, the dynamics tools involve propagating nuclei on multiple potential energy surfaces (rather than the usual ground state dynamics). In this Account, we review recent developments in electronic structure theory as directly applicable for modeling photoexcited systems. In particular, we focus on how one may evaluate the couplings between two different electronic states. These couplings come in two flavors. If we order states energetically, the resulting adiabatic states are coupled via derivative couplings. Derivative couplings capture how electronic wave functions change as a function of nuclear geometry and can usually be calculated with straightforward tools from analytic gradient theory. One nuance arises, however, in the context of time-dependent density functional theory (TD-DFT): how do we evaluate derivative couplings between TD-DFT excited states (which are tricky, because no wave function is available)? This conundrum was recently solved, and we review the solution below. We also discuss the solution to a second, pesky problem of origin dependence, whereby the derivative couplings do not (strictly) satisfy translation variance, which can lead to a lack of momentum conservation. Apart from adiabatic states, if we order states according to their electronic character, the resulting diabatic states are coupled via electronic or diabatic couplings. The couplings

  6. Structure refinement using precession electron diffraction tomography and dynamical diffraction: tests on experimental data.

    PubMed

    Palatinus, Lukáš; Corrêa, Cinthia Antunes; Steciuk, Gwladys; Jacob, Damien; Roussel, Pascal; Boullay, Philippe; Klementová, Mariana; Gemmi, Mauro; Kopeček, Jaromír; Domeneghetti, M Chiara; Cámara, Fernando; Petříček, Václav

    2015-12-01

    The recently published method for the structure refinement from three-dimensional precession electron diffraction data using dynamical diffraction theory [Palatinus et al. (2015). Acta Cryst. A71, 235-244] has been applied to a set of experimental data sets from five different samples - Ni2Si, PrVO3, kaolinite, orthopyroxene and mayenite. The data were measured on different instruments and with variable precession angles. For each sample a reliable reference structure was available. A large series of tests revealed that the method provides structure models with an average error in atomic positions typically between 0.01 and 0.02 Å. The obtained structure models are significantly more accurate than models obtained by refinement using kinematical approximation for the calculation of model intensities. The method also allows a reliable determination of site occupancies and determination of absolute structure. Based on the extensive tests, an optimal set of the parameters for the method is proposed.

  7. Structure of a Bacterial Cell Surface Decaheme Electron Conduit

    SciTech Connect

    Clarke, Thomas A.; Edwards, Marcus; Gates, Andrew J.; Hall, Andrea; White, Gaye; Bradley, Justin; Reardon, Catherine L.; Shi, Liang; Beliaev, Alex S.; Marshall, Matthew J.; Wang, Zheming; Watmough, Nicholas; Fredrickson, Jim K.; Zachara, John M.; Butt, Julea N.; Richardson, David J.

    2011-05-23

    Some bacterial species are able to utilize extracellular mineral forms of iron and manganese as respiratory electron acceptors. In Shewanella oneidensis this involves deca-heme cytochromes that are located on the bacterial cell surface at the termini of trans-outermembrane (OM) electron transfer conduits. The cell surface cytochromes can potentially play multiple roles in mediating electron transfer directly to insoluble electron sinks, catalyzing electron exchange with flavin electron shuttles or participating in extracellular inter-cytochrome electron exchange along ‘nanowire’ appendages. We present a 3.2 Å crystal structure of one of these deca-heme cytochromes, MtrF, that allows the spatial organization of the ten hemes to be visualized for the first time. The hemes are organized across four domains in a unique crossed conformation, in which a staggered 65 Å octa-heme chain transects the length of the protein and is bisected by a planar 45 Å tetra-heme chain that connects two extended Greek key split β-barrel domains. The structure provides molecular insight into how reduction of insoluble substrate (e.g. minerals), soluble substrates (e.g. flavins) and cytochrome redox partners might be possible in tandem at different termini of a trifurcated electron transport chain on the cell surface.

  8. Structure of a bacterial cell surface decaheme electron conduit.

    PubMed

    Clarke, Thomas A; Edwards, Marcus J; Gates, Andrew J; Hall, Andrea; White, Gaye F; Bradley, Justin; Reardon, Catherine L; Shi, Liang; Beliaev, Alexander S; Marshall, Matthew J; Wang, Zheming; Watmough, Nicholas J; Fredrickson, James K; Zachara, John M; Butt, Julea N; Richardson, David J

    2011-06-07

    Some bacterial species are able to utilize extracellular mineral forms of iron and manganese as respiratory electron acceptors. In Shewanella oneidensis this involves decaheme cytochromes that are located on the bacterial cell surface at the termini of trans-outer-membrane electron transfer conduits. The cell surface cytochromes can potentially play multiple roles in mediating electron transfer directly to insoluble electron sinks, catalyzing electron exchange with flavin electron shuttles or participating in extracellular intercytochrome electron exchange along "nanowire" appendages. We present a 3.2-Å crystal structure of one of these decaheme cytochromes, MtrF, that allows the spatial organization of the 10 hemes to be visualized for the first time. The hemes are organized across four domains in a unique crossed conformation, in which a staggered 65-Å octaheme chain transects the length of the protein and is bisected by a planar 45-Å tetraheme chain that connects two extended Greek key split β-barrel domains. The structure provides molecular insight into how reduction of insoluble substrate (e.g., minerals), soluble substrates (e.g., flavins), and cytochrome redox partners might be possible in tandem at different termini of a trifurcated electron transport chain on the cell surface.

  9. Electronic Structure and Phase Stability of PdPt Nanoparticles.

    PubMed

    Ishimoto, Takayoshi; Koyama, Michihisa

    2016-03-03

    To understand the origin of the physicochemical nature of bimetallic PdPt nanoparticles, we theoretically investigated the phase stability and electronic structure employing the PdPt nanoparticles models consisting of 711 atoms (ca. 3 nm). For the Pd-Pt core-shell nanoparticle, the PdPt solid-solution phase was found to be a thermodynamically stable phase in the nanoparticle as the result of difference in surface energy of Pd and Pt nanoparticles and configurational entropy effect, while it is well known that the Pd and Pt are the immiscible combination in the bulk phase. The electronic structure of nanoparticles is conducted to find that the electron transfer occurs locally within surface and subsurface layers. In addition, the electron transfer from Pd to Pt at the interfacial layers in core-shell nanoparticles is observed, which leads to unique geometrical and electronic structure changes. Our results show a clue for the tunability of the electronic structure of nanoparticles by controlling the arrangement in the nanoparticles.

  10. Structure and electronic properties of lead-selenide nanocrystal solids

    NASA Astrophysics Data System (ADS)

    Whitham, Kevin

    Recent advances in the controlled formation of nanocrystal superlattices have potential for creating materials with properties by design. The ability to tune nanocrystal size, shape and composition as well as symmetry of the superlattice opens routes to new materials. Calculations of such materials predict interesting electronic phenomena including topological states and Dirac cones, however experimental support is lacking. We have investigated electron localization in nanocrystal superlattices using a combination of advanced structural characterization techniques and charge transport measurements. Recent experimental efforts to improve the electronic properties of nanocrystal solids have focused on increasing inter-dot coupling. However, this approach only leads to electronic bands if the coupling energy can overcome energetic and translational disorder. We have investigated oriented-attachment as a method to create nanocrystal superlattices with increased coupling and translational order. We show that epitaxially connected superlattices form by a coherent phase transformation that is sensitive to structural defects and ligand length. In order to measure intrinsic electronic properties we demonstrate control over electronic defects by tailoring surface chemistry and device architecture. To probe charge transport in these structures we performed variable temperature field-effect measurements. By integrating structure analysis, surface chemistry, and transport measurements we find that carriers are localized to a few superlattice constants due to disorder. Importantly, our analysis shows that greater delocalization is possible by optimizing dot-to-dot bonding, thus providing a path forward to create quantum dot solids in which theoretically predicted properties can be realized.

  11. Parallel adaptive mesh refinement for electronic structure calculations

    SciTech Connect

    Kohn, S.; Weare, J.; Ong, E.; Baden, S.

    1996-12-01

    We have applied structured adaptive mesh refinement techniques to the solution of the LDA equations for electronic structure calculations. Local spatial refinement concentrates memory resources and numerical effort where it is most needed, near the atomic centers and in regions of rapidly varying charge density. The structured grid representation enables us to employ efficient iterative solver techniques such as conjugate gradients with multigrid preconditioning. We have parallelized our solver using an object-oriented adaptive mesh refinement framework.

  12. Variability of Protein Structure Models from Electron Microscopy.

    PubMed

    Monroe, Lyman; Terashi, Genki; Kihara, Daisuke

    2017-03-02

    An increasing number of biomolecular structures are solved by electron microscopy (EM). However, the quality of structure models determined from EM maps vary substantially. To understand to what extent structure models are supported by information embedded in EM maps, we used two computational structure refinement methods to examine how much structures can be refined using a dataset of 49 maps with accompanying structure models. The extent of structure modification as well as the disagreement between refinement models produced by the two computational methods scaled inversely with the global and the local map resolutions. A general quantitative estimation of deviations of structures for particular map resolutions are provided. Our results indicate that the observed discrepancy between the deposited map and the refined models is due to the lack of structural information present in EM maps and thus these annotations must be used with caution for further applications.

  13. Julius Edgar Lilienfeld Prize Talk: Measuring the Electron Magnetic Moment and the Fine Structure Constant

    NASA Astrophysics Data System (ADS)

    Gabrielse, Gerald

    2011-05-01

    The electron magnetic moment in Bohr magnetons has been measured to a precision of 3 parts in 1013. This measurement, with quantum electrodynamics (AED) theory, provides the most precise value of the fine structure constant. This measurement, with a value of the fine structure from other measurements, also tests QED and sets a limit on the internal structure of the electron. A one-electron quantum cyclotron is at the heart of the measurement -- an electron suspended in a magnetic field and cooled enough that its lowest cyclotron and spin quantum states can be deduced with quantum nondemolition (QND) measurements. A cylindrical Penning trap cavity inhibits spontaneous emission and feedback methods make the electron excite and sustain its own motion for detection. A new apparatus is being commissioned in pursuit of more precise measurements. Adapted methods are promising for observing a proton spin flip, which should make it possible to compare the antiproton and proton magnetic moments a million times more accurately than is currently possible.

  14. Electronic structure of tetraphenylporphyrin layers on Ag(100)

    NASA Astrophysics Data System (ADS)

    Classen, Andrej; Pöschel, Rebecca; Di Filippo, Gianluca; Fauster, Thomas; Malcıoǧlu, Osman Barış; Bockstedte, Michel

    2017-03-01

    The electronic structure of Mg and free-base tetraphenylporphyrin films on Ag(100) is investigated by one- and two-photon photoemission in combination with electronic structure calculations using density functional theory and the self-consistent G W0 method. We determine the two highest occupied and the nearly degenerate lowest unoccupied molecular orbitals. Higher unoccupied states are seen in an enhanced emission as a final-state effect. For photon energies close to the prominent absorption of the Soret band we observe a strong electron emission attributed to the break up of the bound electron-hole pairs in the S2 excited state. The experimental results on the occupied and unoccupied energy levels for the molecular films on Ag(100) nicely agree with calculated quasiparticle energies and experiments of the molecules in the gas phase.

  15. Enhancement of electron mobility in asymmetric coupled quantum well structures

    SciTech Connect

    Das, S.; Nayak, R. K.; Sahu, T. Panda, A. K.

    2014-02-21

    We study the low temperature multisubband electron mobility in a structurally asymmetric GaAs/Al{sub x}Ga{sub 1-x}As delta doped double quantum well. We calculate the subband energy levels and wave functions through selfconsistent solution of the coupled Schrodinger equation and Poisson's equation. We consider ionized impurity scattering, interface roughness scattering, and alloy disorder scattering to calculate the electron mobility. The screening of the scattering potentials is obtained by using static dielectric response function formalism within the random phase approximation. We analyze, for the first time, the effect of asymmetric structure parameters on the enhancement of multisubband electron mobility through intersubband interactions. We show that the asymmetric variation of well width, doping concentration, and spacer width considerably influences the interplay of scattering mechanisms on mobility. Our results of asymmetry induced enhancement of electron mobility can be utilized for low temperature device applications.

  16. Vibrational stability and electronic structure of a B80 fullerene

    NASA Astrophysics Data System (ADS)

    Baruah, Tunna; Pederson, Mark R.; Zope, Rajendra R.

    2008-07-01

    We investigate the vibrational stability and the electronic structure of the proposed icosahedral fullerenelike cage structure of B80 [N. G. Szwacki, A. Sadrzadeh, and B. I. Yakobson, Phys. Rev. Lett. 98, 166804 (2007)], by an all electron density-functional theory using polarized Gaussian basis functions containing 41 basis functions per atom. The vibrational analysis of B80 indicates that the icosahedral structure is vibrationally unstable with seven imaginary frequencies. The equilibrium structure has Th symmetry and a smaller gap of 0.96 eV between the highest occupied and the lowest unoccupied molecular orbital energy levels compared to the icosahedral structure. The static dipole polarizability of a B80 cage is 149Å3 , and the first ionization energy is 6.4 eV. The B80 cage has rather large electron affinity of 3 eV making it a useful candidate as electron acceptor if it is synthesized. The infrared and Raman spectra of the highly symmetric structure are characterized by a few absorption peaks.

  17. Human enamel structure studied by high resolution electron microscopy

    SciTech Connect

    Wen, S.L. )

    1989-01-01

    Human enamel structural features are characterized by high resolution electron microscopy. The human enamel consists of polycrystals with a structure similar to Ca10(PO4)6(OH)2. This article describes the structural features of human enamel crystal at atomic and nanometer level. Besides the structural description, a great number of high resolution images are included. Research into the carious process in human enamel is very important for human beings. This article firstly describes the initiation of caries in enamel crystal at atomic and unit-cell level and secondly describes the further steps of caries with structural and chemical demineralization. The demineralization in fact, is the origin of caries in human enamel. The remineralization of carious areas in human enamel has drawn more and more attention as its potential application is realized. This process has been revealed by high resolution electron microscopy in detail in this article. On the other hand, the radiation effects on the structure of human enamel are also characterized by high resolution electron microscopy. In order to reveal this phenomenon clearly, a great number of electron micrographs have been shown, and a physical mechanism is proposed. 26 references.

  18. Electronic and optical properties of novel carbon structures

    NASA Astrophysics Data System (ADS)

    Matthews, Manyalibo Joseph

    Novel carbon structures in the form of fullerenes and disordered carbon clusters offer a wide variety of physical systems, possessing both long or short range order, which can generally be tuned through non- combustive heat-treatment at various elevated temperatures, THT. Due to the sheer complexity and diversity of the possible nanoscale arrangements, the optical and electronic properties of carbon structures with finite dimensions and crystallinity are still not fully understood. In this study, we focus mainly on the structures produced from carbonization of the hydrocarbon polymer polyparaphenylene (PPP), but we also present experimental results from carbons based on other precursors (e.g. mesophase pitch) which yield quite different structures with both comparable and contrasting physical properties. In terms of electronic properties, we show that in the low-THT PPP-based structures, which exemplify extreme disorder, the electronic states are strongly localized, giving rise to a Mott T1/4 hopping conductivity and self-trapped spin defects AS evidenced by low-temperature transport and electron spin resonance experiments. Electronic transitions which give rise to ~2-3 eV photoluminescent emissions in PPP-based structures are found to be influenced most strongly by residual semi-localized polymeric states which weakly couple to low-frequency PPP phonon modes. However, at intermediate heat-treatment temperatures (THT~ 1500[-]2500oC), all sp2-bonded carbon compounds in this study exhibit a characteristic phonon spectrum (as evidenced by Raman spectroscopy) in which disorder may be characterized by non-zone-center phonon scattering arising from finite crystallite sizes. Because of its intimate connection to carrier confinement and structural disorder, the anomalous 'disorder-induced' graphite D-band is thoroughly investigated by use of Raman spectroscopy, showing that strong dispersion effects are due to a photon-phonon coupling mediated by electronic transitions

  19. Atomic and electronic structure of exfoliated black phosphorus

    SciTech Connect

    Wu, Ryan J.; Topsakal, Mehmet; Jeong, Jong Seok; Wentzcovitch, Renata M.; Mkhoyan, K. Andre; Low, Tony; Robbins, Matthew C.; Haratipour, Nazila; Koester, Steven J.

    2015-11-15

    Black phosphorus, a layered two-dimensional crystal with tunable electronic properties and high hole mobility, is quickly emerging as a promising candidate for future electronic and photonic devices. Although theoretical studies using ab initio calculations have tried to predict its atomic and electronic structure, uncertainty in its fundamental properties due to a lack of clear experimental evidence continues to stymie our full understanding and application of this novel material. In this work, aberration-corrected scanning transmission electron microscopy and ab initio calculations are used to study the crystal structure of few-layer black phosphorus. Directly interpretable annular dark-field images provide a three-dimensional atomic-resolution view of this layered material in which its stacking order and all three lattice parameters can be unambiguously identified. In addition, electron energy-loss spectroscopy (EELS) is used to measure the conduction band density of states of black phosphorus, which agrees well with the results of density functional theory calculations performed for the experimentally determined crystal. Furthermore, experimental EELS measurements of interband transitions and surface plasmon excitations are also consistent with simulated results. Finally, the effects of oxidation on both the atomic and electronic structure of black phosphorus are analyzed to explain observed device degradation. The transformation of black phosphorus into amorphous PO{sub 3} or H{sub 3}PO{sub 3} during oxidation may ultimately be responsible for the degradation of devices exposed to atmosphere over time.

  20. Momentum space analysis of the electronic structure of biphenyl

    NASA Astrophysics Data System (ADS)

    Morini, F.; Shojaei, S. H. Reza; Deleuze, M. S.

    2014-11-01

    The results of a yet to come experimental study of the electronic structure of biphenyl employing electron momentum spectroscopy (EMS) have been theoretically predicted, taking into account complications such as structural mobility in the electronic ground state, electronic correlation and relaxation, and a dispersion of the inner-valence ionization intensity to electronically excited (shake-up) configurations in the cation. The main purpose of this work is to explore the current limits of EMS in unraveling details of the molecular structure, namely the torsional characteristics of large and floppy aromatic molecules. At the benchmark ADC(3)/cc-pVDZ level of theory, the influence of the twist angle between the two phenyl rings is found to be extremely limited, except for individual orbital momentum profiles corresponding to ionization lines at electron binding energies ranging from 15 to 18 eV. When taking band overlap effects into account, this influence is deceptively far too limited to allow for any experimental determination of the torsional characteristics of biphenyl by means of EMS.

  1. Theoretical studies of the electronic structure of small metal clusters

    NASA Technical Reports Server (NTRS)

    Jordan, K. D.

    1982-01-01

    Theoretical studies of the electronic structure of metal clusters, in particular clusters of Group IIA and IIB atoms were conducted. Early in the project it became clear that electron correlation involving d orbitals plays a more important role in the binding of these clusters than had been previously anticipated. This necessitated that computer codes for calculating two electron integrals and for constructing the resulting CI Hamiltonions be replaced with newer, more efficient procedures. Program modification, interfacing and testing were performed. Results of both plans are reported.

  2. Electronic Structure Methods Based on Density Functional Theory

    DTIC Science & Technology

    2010-01-01

    L. Nordström, L. Tongming, and B. Johansson, “Relativistic Effects on the Thermal Expansion of the Actinide Elements ”, Phys. Rev. B 42, 1990, p 4544...In-house 5b. GRANT NUMBER 5c. PROGRAM ELEMENT NUMBER 62102F 6. AUTHOR(S) Christopher F. Woodward (AFRL/RXLMD) 5d. PROJECT NUMBER 4347 5e...in valence electrons change the structure of the core electrons. For example in the actinides , where the f-electrons are coupled to the core states

  3. Structural and electronic properties of dense liquid and amorphous nitrogen

    SciTech Connect

    Boates, B; Bonev, S A

    2011-02-11

    We present first-principles calculations of the structural and electronic properties of liquid nitrogen in the pressure-temperature range of 0-200 GPa and 2000-6000 K. The molecular-polymerization and molecular-atomic liquid phase boundaries have been mapped over this region. We find the polymeric liquid to be metallic, similar to what has been reported for the higher-temperature atomic fluid. An explanation of the electronic properties is given based on the structure and bonding character of the transformed liquids. We discuss the structural and bonding differences between the polymeric liquid and insulating solid cubic-gauche nitrogen to explain the differences in their electronic properties. Furthermore, we discuss the mechanism responsible for charge transport in polymeric nitrogen systems to explain the conductivity of the polymeric fluid and the semi-conducting nature of low-temperature amorphous nitrogen.

  4. Near-complete structural characterization of phosphatidylcholines using electron impact excitation of ions from organics.

    PubMed

    Campbell, J Larry; Baba, Takashi

    2015-06-02

    Although lipids are critical components of many cellular assemblies and biological pathways, accurate descriptions of their molecular structures remain difficult to obtain. Many benchtop characterization methods require arduous and time-consuming procedures, and multiple assays are required whenever a new structural feature is probed. Here, we describe a new mass-spectrometry-based workflow for enhanced structural lipidomics that, in a single experiment, can yield almost complete structural information for a given glycerophospholipid (GPL) species. This includes the lipid's sum (Brutto) composition from the accurate mass measured for the intact lipid ion and the characteristic headgroup fragment, the regioisomer composition from fragment ions unique to the sn-1 and sn-2 positions, and the positions of carbon-carbon double bonds in the lipid acyl chains. Here, lipid ions are fragmented using electron impact excitation of ions from organics (EIEIO)--a technique where the singly charged lipid ions are irradiated by an electron beam, producing diagnostic product ions. We have evaluated this methodology on various lipid standards, as well as on a biological extract, to demonstrate this new method's utility.

  5. Electronic structure and enthalpy of hydrogen and helium mixtures

    NASA Astrophysics Data System (ADS)

    Ross, M.; Klepeis, J. E.; Schafer, K. J.; Barbee, T. W., III

    1992-11-01

    The first local density approximation (LDA) calculations of the electronic structure, equation of state, and enthalpy of mixing were carried out for a number of different compositions of hydrogen and helium in bcc and fcc lattices. These are fully quantum mechanical, self-consistent calculations utilizing state-of-the-art methods of electron band theory, which make no assumptions regarding pressure ionization. The major approximation in the LDA method is that the exchange and correlation energy is given by a free electron functional in terms of the local electron density. The majority of previous mixture calculations start with the assumption that both hydrogen and helium are pressure-ionized so that the electronic structure is approximately that of free or weakly screened electrons in the presence of positive ions. Stevenson used a hard-sphere mixture model for the ions with an ion-ion pseudopotential to account for electron screening and predicted that a mixture containing 7% helium by number, the composition believed to be present in Jupiter and Saturn, would phase separate at a temperature of about 7000 K at 8 Mbar. Subsequent calculations carried out for the fully ionized mixture and for a mixture of screened ions (linear response theory) have all arrived at predictions similar to those of Stevenson. MacFarlane and Hubbard performed Thomas-Fermi-Dirac calculations for mixing enthalpies of hydrogen and helium in bcc and fcc lattices and predicted that phase separation would not occur at any temperature.

  6. Electronic Structure Analysis for Proteins on the FMO Method

    NASA Astrophysics Data System (ADS)

    Kobori, Tomoki; Tsuneyuki, Shinji; Sodeyama, Keitaro; Akagi, Kazuto; Terakura, Kiyoyuki; Fukuyama, Hidetoshi

    2009-03-01

    The enormity and complexity of proteins have rendered their electronic structure calculation very costly. Although recently established Fragment Molecular Orbital (FMO) method enables us to calculate total energy of a huge protein precisely based on quantum mechanics, the method does not refer to one-electron orbitals and one-electron energy spectrum. In this paper we propose a method of analyzing electronic structure of a protein based on first principles calculation with reasonable accuracy and CPU cost. We construct one- electron Hamiltonian of proteins by assembling the output of the FMO method: fragment orbitals are determined by fragment monomer calculation, while interaction and overlap between fragment orbitals in different fragments are obtained from dimer calculation. After one-electron Hamiltonian matrix of the whole system is fabricated with the fragment orbital basis, one- electron energy spectrum is obtained by its diagonalization. If the matrix dimension is too large, unimportant orbitals are eliminated from the matrix so that the diagonalization of the Hamiltonian becomes feasible. The method is applicable to both the Hartree-Fock method and the density functional theory. In this paper, validity of the method is verified by some test calculations of small peptides.

  7. Electronic Structure and Effectively Unpaired Electron Density Topology in closo-Boranes: Nonclassical Three-Center Two-Electron Bonding.

    PubMed

    Lobayan, Rosana M; Bochicchio, Roberto C; Torre, Alicia; Lain, Luis

    2011-04-12

    This article provides a detailed study of the structure and bonding in closo-borane cluster compounds X2B3H3 (X = BH(-), P, SiH, CH, N), with particular emphasis on the description of the electron distribution using the topology of the quantum many-body effectively unpaired density. The close relationship observed between the critical points of this quantity and the localization of the electron cloud allows us to characterize the nonclassical bonding patterns of these systems. The obtained results confirm the suitability of the local rule to detect three-center two-electron bonds, which was conjectured in our previous study on boron hydrides.

  8. NR2 and P3+: Accurate, Efficient Electron-Propagator Methods for Calculating Valence, Vertical Ionization Energies of Closed-Shell Molecules.

    PubMed

    Corzo, H H; Galano, Annia; Dolgounitcheva, O; Zakrzewski, V G; Ortiz, J V

    2015-08-20

    Two accurate and computationally efficient electron-propagator (EP) methods for calculating the valence, vertical ionization energies (VIEs) of closed-shell molecules have been identified through comparisons with related approximations. VIEs of a representative set of closed-shell molecules were calculated with EP methods using 10 basis sets. The most easily executed method, the diagonal, second-order (D2) EP approximation, produces results that steadily rise as basis sets are improved toward values based on extrapolated coupled-cluster singles and doubles plus perturbative triples calculations, but its mean errors remain unacceptably large. The outer valence Green function, partial third-order and renormalized partial third-order methods (P3+), which employ the diagonal self-energy approximation, produce markedly better results but have a greater tendency to overestimate VIEs with larger basis sets. The best combination of accuracy and efficiency with a diagonal self-energy matrix is the P3+ approximation, which exhibits the best trends with respect to basis-set saturation. Several renormalized methods with more flexible nondiagonal self-energies also have been examined: the two-particle, one-hole Tamm-Dancoff approximation (2ph-TDA), the third-order algebraic diagrammatic construction or ADC(3), the renormalized third-order (3+) method, and the nondiagonal second-order renormalized (NR2) approximation. Like D2, 2ph-TDA produces steady improvements with basis set augmentation, but its average errors are too large. Errors obtained with 3+ and ADC(3) are smaller on average than those of 2ph-TDA. These methods also have a greater tendency to overestimate VIEs with larger basis sets. The smallest average errors occur for the NR2 approximation; these errors decrease steadily with basis augmentations. As basis sets approach saturation, NR2 becomes the most accurate and efficient method with a nondiagonal self-energy.

  9. Banded Electron Structure Formation in the Inner Magnetosphere

    NASA Technical Reports Server (NTRS)

    Liemohn, M. W.; Khazanov, G. V.

    1997-01-01

    Banded electron structures in energy-time spectrograms have been observed in the inner magnetosphere concurrent with a sudden relaxation of geomagnetic activity. In this study, the formation of these banded structures is considered with a global, bounce-averaged model of electron transport, and it is concluded that this structure is a natural occurrence when plasma sheet electrons are captured on closed drift paths near the Earth. These bands do not appear unless there is capture of plasma sheet electrons; convection along open drift paths making open pass around the Earth do not have time to develop this feature. The separation of high-energy bands from the injection population due to the preferential advection of the gradient-curvature drift creates spikes in the energy distribution, which overlap to form a series of bands in the energy spectrograms. The lowest band is the bulk of the injected population in the sub-key energy range. Using the Kp history for an observed banded structure event, a cloud of plasma sheet electrons is captured and the development of their distribution function is examined and discussed.

  10. Impact of the Electronic Band Structure in High-Harmonic Generation Spectra of Solids.

    PubMed

    Tancogne-Dejean, Nicolas; Mücke, Oliver D; Kärtner, Franz X; Rubio, Angel

    2017-02-24

    An accurate analytic model describing the microscopic mechanism of high-harmonic generation (HHG) in solids is derived. Extensive first-principles simulations within a time-dependent density-functional framework corroborate the conclusions of the model. Our results reveal that (i) the emitted HHG spectra are highly anisotropic and laser-polarization dependent even for cubic crystals; (ii) the harmonic emission is enhanced by the inhomogeneity of the electron-nuclei potential; the yield is increased for heavier atoms; and (iii) the cutoff photon energy is driver-wavelength independent. Moreover, we show that it is possible to predict the laser polarization for optimal HHG in bulk crystals solely from the knowledge of their electronic band structure. Our results pave the way to better control and optimize HHG in solids by engineering their band structure.

  11. Impact of the Electronic Band Structure in High-Harmonic Generation Spectra of Solids

    NASA Astrophysics Data System (ADS)

    Tancogne-Dejean, Nicolas; Mücke, Oliver D.; Kärtner, Franz X.; Rubio, Angel

    2017-02-01

    An accurate analytic model describing the microscopic mechanism of high-harmonic generation (HHG) in solids is derived. Extensive first-principles simulations within a time-dependent density-functional framework corroborate the conclusions of the model. Our results reveal that (i) the emitted HHG spectra are highly anisotropic and laser-polarization dependent even for cubic crystals; (ii) the harmonic emission is enhanced by the inhomogeneity of the electron-nuclei potential; the yield is increased for heavier atoms; and (iii) the cutoff photon energy is driver-wavelength independent. Moreover, we show that it is possible to predict the laser polarization for optimal HHG in bulk crystals solely from the knowledge of their electronic band structure. Our results pave the way to better control and optimize HHG in solids by engineering their band structure.

  12. Realistic tight-binding model for the electronic structure of II-VI semiconductors

    NASA Astrophysics Data System (ADS)

    Sapra, Sameer; Shanthi, N.; Sarma, D. D.

    2002-11-01

    We analyze the electronic structure of group II-VI semiconductors obtained within linearized muffin-tin-orbital approach in order to arrive at a realistic and minimal tight-binding model, parametrized to provide an accurate description of both valence and conduction bands. It is shown that a nearest-neighbor sp3 d5 model is fairly sufficient to describe the electronic structure of these systems over a wide energy range, obviating the use of any fictitious s* orbital. The obtained hopping parameters obey the universal scaling law proposed by Harrison, ensuring transferability to other systems. Furthermore, we show that certain subtle features in the bonding of these compounds require the inclusion of anion-anion interactions in addition to the nearest-neighbor cation-anion interactions.

  13. Short-Range Correlation Models in Electronic Structure Theory

    NASA Astrophysics Data System (ADS)

    Goldey, Matthew Bryant

    Correlation methods within electronic structure theory focus on recovering the exact electron-electron interaction from the mean-field reference. For most chemical systems, including dynamic correlation, the correlation of the movement of electrons proves to be sufficient, yet exact methods for capturing dynamic correlation inherently scale polynomially with system size despite the locality of the electron cusp. This work explores a new family of methods for enhancing the locality of dynamic correlation methodologies with an aim toward improving accuracy and scalability. The introduction of range-separation into ab initio wavefunction methods produces short-range correlation methodologies, which can be supplemented with much faster approximate methods for long-range interactions. First, I examine attenuation of second-order Moller-Plesset perturbation theory (MP2) in the aug-cc-pVDZ basis. MP2 treats electron correlation at low computational cost, but suffers from basis set superposition error (BSSE) and fundamental inaccuracies in long-range contributions. The cost differential between complete basis set (CBS) and small basis MP2 restricts system sizes where BSSE can be removed. Range-separation of MP2 could yield more tractable and/or accurate forms for short- and long-range correlation. Retaining only short-range contributions proves to be effective for MP2 in the small aug-cc-pVDZ (aDZ) basis. Using one range-separation parameter within either the complementary error function (erfc) or a sum of two error functions (terfc), superior behavior is obtained versus both MP2/aDZ and MP2/CBS for inter- and intra-molecular test sets. Attenuation of the long-range helps to cancel both BSSE and intrinsic MP2 errors. Direct scaling of the MP2 correlation energy (SMP2) proves useful as well. The resulting SMP2/aDZ, MP2(erfc, aDZ), and MP2(terfc, aDZ) methods perform far better than MP2/aDZ across systems with hydrogen-bonding, dispersion, and mixed interactions at a

  14. The electronic structure and chemical bonding of vitamin B12

    NASA Astrophysics Data System (ADS)

    Kurmaev, E. Z.; Moewes, A.; Ouyang, L.; Randaccio, L.; Rulis, P.; Ching, W. Y.; Bach, M.; Neumann, M.

    2003-05-01

    The electronic structure and chemical bonding of vitamin B12 (cyanocobalamin) and B12-derivative (methylcobalamin) are studied by means of X-ray emission (XES) and photoelectron (XPS) spectroscopy. The obtained results are compared with ab initio electronic structure calculations using the orthogonalized linear combination of the atomic orbital method (OLCAO). We show that the chemical bonding in vitamin B12 is characterized by the strong Co-C bond and relatively weak axial Co-N bond. It is further confirmed that the Co-C bond in cyanocobalamin is stronger than that of methylcobalamin resulting in their different biological activity.

  15. Structural and luminescent properties of electron-irradiated silicon

    SciTech Connect

    Sobolev, N. A.; Loshachenko, A. S.; Aruev, P. N.; Kalyadin, A. E.; Shek, E. I.; Zabrodskiy, V. V.; Shtel'makh, K. F.; Vdovin, V. I.; Xiang, Luelue; Yang, Deren

    2014-02-21

    Structural defects induced by electron irradiation of p-Cz-Si wafers were identified. The influence of the annealing conditions in a chlorine-containing atmosphere on the structural and luminescent properties of the samples was examined. Light-emitting diodes based on electron-irradiated and high-temperature-annealed wafers were fabricated by a vapour-phase epitaxy technique and their luminescence properties were studied. A high-intensity dislocation-related D1 line was observed at 1.6 μm in the room-temperature electroluminescence spectrum.

  16. Electronic structure of Sn/Cu(100)-[Formula: see text].

    PubMed

    Martínez-Blanco, J; Joco, V; Fujii, J; Segovia, P; Michel, E G

    2009-02-04

    We present measurements of the Fermi surface and underlying band structure of Sn/Cu(100)-[Formula: see text]. This phase is observed for a coverage of 0.60-0.65 monolayers. Its electronic structure is characterized by a free-electron-like surface band folded with the reconstruction periodicity. At variance with other surface phases of Sn on Cu(100), no temperature-induced phase transition is observed for this phase from 100 K up to the desorption of Sn.

  17. Electronic Structure of Lanthanum Hydrides with Switchable Optical Properties

    SciTech Connect

    Ng, K.; Zhang, F.; Ng, K.; Zhang, F.; Anisimov, V.; Rice, T.; Anisimov, V.

    1997-02-01

    Recent dramatic changes in the optical properties of LaH{sub 2+x} and YH{sub 2+x} films discovered by Huiberts {ital et al.}[Nature (London) {bold 380}, 231 (1996)] suggest their electronic structure is described best by a local model. Electron correlation is important in H{sup -} centers and in explaining the transparent insulating behavior of LaH{sub 3}. The metal-insulator transition at x{approximately}0.8 takes place in a band of highly localized states centered on the H vacancies in the LaH{sub 3} structure. {copyright} {ital 1997} {ital The American Physical Society}

  18. Comparison of electronic structure between monolayer silicenes on Ag (111)

    NASA Astrophysics Data System (ADS)

    Chun-Liang, Lin; Ryuichi, Arafune; Maki, Kawai; Noriaki, Takagi

    2015-08-01

    The electronic structures of monolayer silicenes (4 × 4 and ) grown on Ag (111) surface are studied by scanning tunneling spectroscopy (STS) and density functional theory (DFT) calculations. While both phases have similar electronic structures around the Fermi level, significant differences are observed in the higher energy unoccupied states. The DFT calculations show that the contributions of Si 3pz orbitals to the unoccupied states are different because of their different buckled configurations. Project supported by the Ministry of Education, Culture, Sports, Science and Technology (MEXT) through Grants-in-Aid for Scientific Research (Grant Nos. 24241040 and 25110008) and the World Premier International Research Center Initiative (WPI), MEXT, Japan.

  19. Improving electronic structure methods to predict nano-optoelectronics and nano-catalyst functions.

    SciTech Connect

    Nielsen, Ida Marie B.; Marzari, Nicola; Shelnutt, John Allen; Kulik, Heather J.; Medforth, Craig John; Leung, Kevin

    2009-10-01

    This report focuses on quantum chemistry and ab initio molecular dynamics (AIMD) calculations applied to elucidate the mechanism of the multi-step, 2-electron, electrochemical reduction of the green house gas molecule carbon dioxide (CO{sub 2}) to carbon monoxide (CO) in aqueous media. When combined with H{sub 2} gas to form synthesis ('syn') gas, CO becomes a key precursor to methane, methanol, and other useful hydrocarbon products. To elucidate the mechanism of this reaction, we apply computational electrochemistry which is a fledgling, important area of basic science critical to energy storage. This report highlights several approaches, including the calculation of redox potentials, the explicit depiction of liquid water environments using AIMD, and free energy methods. While costly, these pioneering calculations reveal the key role of hydration- and protonation-stabilization of reaction intermediates, and may inform the design of CO{sub 2}-capture materials as well as its electrochemical reduction. In the course of this work, we have also dealt with the challenges of identifying and applying electronic structure methods which are sufficiently accurate to deal with transition metal ion complex-based catalyst. Such electronic structure methods are also pertinent to the accurate modeling of actinide materials and therefore to nuclear energy research. Our multi-pronged effort towards achieving this titular goal of the LDRD is discussed.

  20. Free electron laser-driven ultrafast rearrangement of the electronic structure in Ti

    PubMed Central

    Principi, E.; Giangrisostomi, E.; Cucini, R.; Bencivenga, F.; Battistoni, A.; Gessini, A.; Mincigrucci, R.; Saito, M.; Di Fonzo, S.; D'Amico, F.; Di Cicco, A.; Gunnella, R.; Filipponi, A.; Giglia, A.; Nannarone, S.; Masciovecchio, C.

    2015-01-01

    High-energy density extreme ultraviolet radiation delivered by the FERMI seeded free-electron laser has been used to create an exotic nonequilibrium state of matter in a titanium sample characterized by a highly excited electron subsystem at temperatures in excess of 10 eV and a cold solid-density ion lattice. The obtained transient state has been investigated through ultrafast absorption spectroscopy across the Ti M2,3-edge revealing a drastic rearrangement of the sample electronic structure around the Fermi level occurring on a time scale of about 100 fs. PMID:26798835

  1. Structural and electronic properties of monolayer group III monochalcogenides

    NASA Astrophysics Data System (ADS)

    Demirci, S.; Avazlı, N.; Durgun, E.; Cahangirov, S.

    2017-03-01

    We investigate the structural, mechanical, and electronic properties of the two-dimensional hexagonal structure of group III-VI binary monolayers, M X (M =B , Al, Ga, In and X =O , S, Se, Te) using first-principles calculations based on the density functional theory. The structural optimization calculations and phonon spectrum analysis indicate that all of the 16 possible binary compounds are thermally stable. In-plane stiffness values cover a range depending on the element types and can be as high as that of graphene, while the calculated bending rigidity is found to be an order of magnitude higher than that of graphene. The obtained electronic band structures show that M X monolayers are indirect band-gap semiconductors. The calculated band gaps span a wide optical spectrum from deep ultraviolet to near infrared. The electronic structure of oxides (M O ) is different from the rest because of the high electronegativity of oxygen atoms. The dispersions of the electronic band edges and the nature of bonding between atoms can also be correlated with electronegativities of constituent elements. The unique characteristics of group III-VI binary monolayers can be suitable for high-performance device applications in nanoelectronics and optics.

  2. Electron-Phonon Renormalization of Electronic Band Structures of C Allotropes and BN Polymorphs

    NASA Astrophysics Data System (ADS)

    Tutchton, Roxanne M.; Marchbanks, Christopher; Wu, Zhigang

    The effect of lattice vibration on electronic band structures has been mostly neglected in first-principles calculations because the electron-phonon (e-ph) renormalization of quasi-particle energies is often small (< 100 meV). However, in certain materials, such as diamond, the electron-phonon coupling reduces the band gap by nearly 0.5 eV, which is comparable to the many-body corrections of the electronic band structures calculated using the density functional theory (DFT). In this work, we compared two implementations of the Allen-Heine-Cardona theory in the EPW code and the ABINIT package respectively. Our computations of Si and diamond demonstrate that the ABINIT implementation converges much faster. Using this method, the e-ph renormalizations of electronic structures of three C allotropes (diamond, graphite, graphene) and four BN polymorphs (zincblend, wurtzite, mono-layer, and layered-hexagonal) were calculated. Our results suggest that (1) all of the zero-point renormalizations of band gaps in these materials, except for graphene, are larger than 100 meV, and (2) there are large variations in e-ph renormalization of band gaps due to differences in crystal structure. This work was supported by a U.S. DOE Early Career Award (Grant No. DE-SC0006433). Computations were carried out at the Golden Energy Computing Organization at CSM and the National Energy Research Scientific Computing Center (NERSC).

  3. Diurnal patterns of salivary cortisol and DHEA using a novel collection device: Electronic monitoring confirms accurate recording of collection time using this device

    PubMed Central

    Laudenslager, Mark L.; Calderone, Jacqueline; Philips, Sam; Natvig, Crystal; Carlson, Nichole E.

    2013-01-01

    The accurate indication of saliva collection time is important for defining the diurnal decline in salivary cortisol as well as characterizing the cortisol awakening response.. We tested a convenient and novel collection device for collecting saliva on strips of filter paper in a specially constructed booklet for determination of both cortisol and DHEA. In the present study, 31 healthy adults (mean age 43.5 yrs.) collected saliva samples four times a day on three consecutive days using filter paper collection devices (Saliva Procurement and Integrated Testing (SPIT) booklet) which were maintained during the collection period in a large plastic bottle with an electronic monitoring cap. Subjects were asked to collect saliva samples at awakening, 30 min. after awakening, before lunch and 600 min. after awakening. The time of awakening and the time of collection before lunch were allowed to vary by each subjects’ schedule. A reliable relationship was observed between the time recorded by the subject directly on the booklet and the time recorded by electronic collection device (n = 286 observations; r2 = 0.98). However, subjects did not consistently collect the saliva samples at the two specific times requested, 30 and 600 min. after awakening. Both cortisol and DHEA revealed diurnal declines.. In spite of variance in collection times at 30 min. and 600 min. after awakening, the slope of the diurnal decline in both salivary cortisol and DHEA were similar when we compared collection tolerances of ± 7.5 and ± 15 min. for each steroid.. These unique collection booklets proved to be a reliable method for recording collection times by subjects as well as for estimating diurnal salivary cortisol and DHEA patterns. PMID:23490073

  4. Structure refinement using precession electron diffraction tomography and dynamical diffraction: theory and implementation.

    PubMed

    Palatinus, Lukáš; Petříček, Václav; Corrêa, Cinthia Antunes

    2015-03-01

    Accurate structure refinement from electron-diffraction data is not possible without taking the dynamical-diffraction effects into account. A complete three-dimensional model of the structure can be obtained only from a sufficiently complete three-dimensional data set. In this work a method is presented for crystal structure refinement from the data obtained by electron diffraction tomography, possibly combined with precession electron diffraction. The principle of the method is identical to that used in X-ray crystallography: data are collected in a series of small tilt steps around a rotation axis, then intensities are integrated and the structure is optimized by least-squares refinement against the integrated intensities. In the dynamical theory of diffraction, the reflection intensities exhibit a complicated relationship to the orientation and thickness of the crystal as well as to structure factors of other reflections. This complication requires the introduction of several special parameters in the procedure. The method was implemented in the freely available crystallographic computing system Jana2006.

  5. Effects of inverse degree on electronic structure and electron energy-loss spectrum in zinc ferrites

    NASA Astrophysics Data System (ADS)

    Sun, D.; Wang, M. X.; Zhang, Z. H.; Tao, H. L.; He, M.; Song, B.; Li, Q.

    2015-12-01

    First-principles calculations were performed to study the effects of inverse degree in zinc ferrite on electronic structure and properties. The electron energy-loss near-edge fine structure (ELNES) were simulated, and the splitting of peak and intensities of the oxygen K-edges can be used to identify the inversion of zinc ferrite. More Fe3+ transferring from the octahedral sites to the tetrahedral sites lead to the changing of the ligand shells surrounding the absorbing atom, accounting for the observed changing in ELNES. The standard criterion for determining the reversal extent of the cations in zinc ferrite by ELNES was given.

  6. Electronic structure of nitrides PuN and UN

    NASA Astrophysics Data System (ADS)

    Lukoyanov, A. V.; Anisimov, V. I.

    2016-11-01

    The electronic structure of uranium and plutonium nitrides in ambient conditions and under pressure is investigated using the LDA + U + SO band method taking into account the spin-orbit coupling and the strong correlations of 5 f electrons of actinoid ions. The parameters of these interactions for the equilibrium cubic structure are calculated additionally. The application of pressure reduces the magnetic moment in PuN due to predominance of the f 6 configuration and the jj-type coupling. An increase in the occupancy of the 5 f state in UN leads to a decrease in the magnetic moment, which is also detected in the trigonal structure of the UN x β phase (La2O3-type structure). The theoretical results are in good agreement with the available experimental data.

  7. Chiral phosphorus nanotubes: structure, bonding, and electronic properties.

    PubMed

    Fernández-Escamilla, H N; Quijano-Briones, J J; Tlahuice-Flores, A

    2016-05-14

    The study of black phosphorus nanotubes (PNTs) had been devoted to zigzag and armchair structures, with no consideration of chiral structures to date. In this communication, we studied the structural and electronic (band structure) properties of chiral nanotubes using a periodic plane wave-pseudopotential approach. We found that some chiral nanotubes display similar bandgaps and binding energies per atom (BEA) as armchair PNTs and Born-Oppenheimer molecular dynamics (BOMD) calculations attest their thermal stability. Interestingly, we determined that the bandgap is tuned by varying the PNTs chirality and it is not related to their diameters. This feature can be exploited in optical and electronic applications wherein a direct and sizable bandgap is required.

  8. Structural and electronic properties of small silicon clusters

    NASA Astrophysics Data System (ADS)

    Baturin, V. S.; Lepeshkin, S. V.; Magnitskaya, M. V.; Matsko, N. L.; Uspenskii, Yu A.

    2014-05-01

    The atomic structure and electronic spectrum of silicon nanoclusters (Si-ncs) Si7, Si10,Si10H16 and Si10H20 are calculated using the evolutionary algorithm with total energy computed within density functional theory and generalized gradient approximation (DFT-GGA). When analysing the low-energy structures, we pay significant attention to their symmetry and interatomic bond geometry. The candidate structures arising in the process of evolutionary algorithm convergence are also considered and classified by their topology and grouping near local energy minima. Possible ways to improve the convergence of evolutionary computation are discussed. Addressing qualitative criteria for the ground-state atomic structure of Si-ncs, we consider correlations between the density of electronic states and the total energetics of clusters in the ground state and low-energy-isomer configurations.

  9. Layer-stacking effect on electronic structures of bilayer arsenene

    NASA Astrophysics Data System (ADS)

    Mi, Kui; Xie, Jiafeng; Si, M. S.; Gao, C. X.

    2017-01-01

    A monolayer of orthorhombic arsenic (arsenene) is a promising candidate for nano-electronic devices due to the uniquely electronic properties. To further extend its practical applications, an additional layer is introduced to tune the electronic structures. Four layer-stacking manners, namely AA-, AB-, AB‧-, and AC-stacking, are constructed and studied through using first-principles calculations. Compared with monolayer, an indirect-direct gap transition is realized in AB-stacking. More importantly, a semimetal feature appears in the AC- and AB‧-stacked bilayers, leaving the electronic structure of AA-stacking trivial. In addition, the energy dispersion around Γ is largely tuned from the layer-stacking effect. To understand the underlying physics, the \\textbf{k}\\cdot\\textbf{p} approximation is taken to address this issue. Our results show that the level repulsion from the additional layer domaintes the anisotropy of energy dispersion around Γ. The works like ours would shed new light on the tunability of the electronic structure in layered arsenene.

  10. Molecular and electronic structure of electroactive self-assembled monolayers

    NASA Astrophysics Data System (ADS)

    Méndez De Leo, Lucila P.; de la Llave, Ezequiel; Scherlis, Damián; Williams, Federico J.

    2013-03-01

    Self-assembled monolayers (SAMs) containing electroactive functional groups are excellent model systems for the formation of electronic devices by self-assembly. In particular ferrocene-terminated alkanethiol SAMs have been extensively studied in the past. However, there are still open questions related with their electronic structure including the influence of the ferrocene group in the SAM-induced work function changes of the underlying metal. We have thus carried out a thorough experimental and theoretical investigation in order to determine the molecular and electronic structure of ferrocene-terminated alkanethiol SAMs on Au surfaces. In agreement with previous studies we found that the Fc-containing alkanethiol molecules adsorb forming a thiolate bond with the Au surface with a molecular geometry 30° tilted with respect to the surface normal. Measured surface coverages indicate the formation of a compact monolayer. We found for the first time that the ferrocene group has little influence on the observed work function decrease which is largely determined by the alkanethiol. Furthermore, the ferrocene moiety lies 14 Å above the metal surface covalently bonded to the alkanethiol SAM and its HOMO is located at -1.6 eV below the Fermi level. Our results provide new valuable insight into the molecular and electronic structure of electroactive SAMs which are of fundamental importance in the field of molecular electronics.

  11. Molecular and electronic structure of electroactive self-assembled monolayers.

    PubMed

    Méndez De Leo, Lucila P; de la Llave, Ezequiel; Scherlis, Damián; Williams, Federico J

    2013-03-21

    Self-assembled monolayers (SAMs) containing electroactive functional groups are excellent model systems for the formation of electronic devices by self-assembly. In particular ferrocene-terminated alkanethiol SAMs have been extensively studied in the past. However, there are still open questions related with their electronic structure including the influence of the ferrocene group in the SAM-induced work function changes of the underlying metal. We have thus carried out a thorough experimental and theoretical investigation in order to determine the molecular and electronic structure of ferrocene-terminated alkanethiol SAMs on Au surfaces. In agreement with previous studies we found that the Fc-containing alkanethiol molecules adsorb forming a thiolate bond with the Au surface with a molecular geometry 30° tilted with respect to the surface normal. Measured surface coverages indicate the formation of a compact monolayer. We found for the first time that the ferrocene group has little influence on the observed work function decrease which is largely determined by the alkanethiol. Furthermore, the ferrocene moiety lies 14 Å above the metal surface covalently bonded to the alkanethiol SAM and its HOMO is located at -1.6 eV below the Fermi level. Our results provide new valuable insight into the molecular and electronic structure of electroactive SAMs which are of fundamental importance in the field of molecular electronics.

  12. A simple and inclusive method to determine the habit plane in transmission electron microscope based on accurate measurement of foil thickness

    SciTech Connect

    Qiu, Dong Zhang, Mingxing

    2014-08-15

    A simple and inclusive method is proposed for accurate determination of the habit plane between bicrystals in transmission electron microscope. Whilst this method can be regarded as a variant of surface trace analysis, the major innovation lies in the improved accuracy and efficiency of foil thickness measurement, which involves a simple tilt of the thin foil about a permanent tilting axis of the specimen holder, rather than cumbersome tilt about the surface trace of the habit plane. Experimental study has been done to validate this proposed method in determining the habit plane between lamellar α{sub 2} plates and γ matrix in a Ti–Al–Nb alloy. Both high accuracy (± 1°) and high precision (± 1°) have been achieved by using the new method. The source of the experimental errors as well as the applicability of this method is discussed. Some tips to minimise the experimental errors are also suggested. - Highlights: • An improved algorithm is formulated to measure the foil thickness. • Habit plane can be determined with a single tilt holder based on the new algorithm. • Better accuracy and precision within ± 1° are achievable using the proposed method. • The data for multi-facet determination can be collected simultaneously.

  13. On the feasibility of ab initio electronic structure calculations for Cu using a single s orbital basis

    SciTech Connect

    Hegde, Ganesh Bowen, R. Chris

    2015-10-15

    The accuracy of a single s-orbital representation of Cu towards enabling multi-thousand atom ab initio calculations of electronic structure is evaluated in this work. If an electrostatic compensation charge of 0.3 electron per atom is used in this basis representation, the electronic transmission in bulk and nanocrystalline Cu can be made to compare accurately to that obtained with a Double Zeta Polarized basis set. The use of this representation is analogous to the use of single band effective mass representation for semiconductor electronic structure. With a basis of just one s-orbital per Cu atom, the representation is extremely computationally efficient and can be used to provide much needed ab initio insight into electronic transport in nanocrystalline Cu interconnects at realistic dimensions of several thousand atoms.

  14. Electronic structure and formation of simple ferryloxo complexes: mechanism of the Fenton reaction.

    PubMed

    Petit, Alban S; Pennifold, Robert C R; Harvey, Jeremy N

    2014-07-07

    The Fenton reaction is a famous reaction in inorganic chemistry, with relevance to topics such as bioinorganic oxidation and fundamental redox chemistry of water and oxygen. It is also a reaction concerning which there has been very extensive mechanistic debate, with experimental and computational work leading to extensive evidence concerning its mechanism-not all of which is consistent. Here, we use this reaction as a challenge to modern electronic structure theory methods and show that density functional theory, when validated by accurate ab initio methods, can yield a picture of this reaction that is consistent with experiment. The article also highlights some of the challenges in accurate studies of reaction mechanisms of ionic species in water solution.

  15. A novel Gaussian-Sinc mixed basis set for electronic structure calculations

    SciTech Connect

    Jerke, Jonathan L.; Lee, Young; Tymczak, C. J.

    2015-08-14

    A Gaussian-Sinc basis set methodology is presented for the calculation of the electronic structure of atoms and molecules at the Hartree–Fock level of theory. This methodology has several advantages over previous methods. The all-electron electronic structure in a Gaussian-Sinc mixed basis spans both the “localized” and “delocalized” regions. A basis set for each region is combined to make a new basis methodology—a lattice of orthonormal sinc functions is used to represent the “delocalized” regions and the atom-centered Gaussian functions are used to represent the “localized” regions to any desired accuracy. For this mixed basis, all the Coulomb integrals are definable and can be computed in a dimensional separated methodology. Additionally, the Sinc basis is translationally invariant, which allows for the Coulomb singularity to be placed anywhere including on lattice sites. Finally, boundary conditions are always satisfied with this basis. To demonstrate the utility of this method, we calculated the ground state Hartree–Fock energies for atoms up to neon, the diatomic systems H{sub 2}, O{sub 2}, and N{sub 2}, and the multi-atom system benzene. Together, it is shown that the Gaussian-Sinc mixed basis set is a flexible and accurate method for solving the electronic structure of atomic and molecular species.

  16. Electron Diffraction and High-Resolution Electron Microscopy of Mineral Structures

    NASA Astrophysics Data System (ADS)

    Nord, Gordon L., Jr.

    This book is a well-written English translation of the original 1981 Russian edition, Strukturnoye issledovaniye mineralov metodami mikrodifraktsii i elechtronnoi mikroskopii vysokogo razresheniya. The 1987 English version has been extensively updated and includes references up to 1986. The book is essentially a text on the theoretical and experimental aspects of transmission electron microscopy and has chapters on the reciprocal lattice, electron diffraction (both kinematic and dynamic), and high-resolution electron microscopy.Electron diffraction is emphasized, especially its use for structure analysis of poorly crystalline and fine-grained phases not readily determined by the more exact X ray diffraction method. Two methods of electron diffraction are discussed: selected area electron diffraction (SAED) and oblique-texture electron diffraction (OTED); the latter technique is rarely used in the west and is never discussed in western electron microscopy texts. A SAED pattern is formed by isolating a small micrometer-size area with an aperture and obtaining single-crystal patterns from the diffracted beams. By tilting the sample and obtaining many patterns, a complete picture of the reciprocal lattice can be taken. An OTED pattern is formed when the incident electron beam passes through an inclined preparation consisting of a great number of thin platy crystals lying normal to the texture axis (axis normal to the support grid). To form an OTED pattern, the plates must all lie on a common face, such as a basal plane in phyllosilicates. Upon tilting the plates, an elliptical powder diffraction pattern is formed. Intensities measured from these patterns are used for a structural analysis of the platy minerals.

  17. Electronic Structure of Crystalline 4He at High Pressures

    SciTech Connect

    Mao, Ho Kwang; Shirley, Eric L.; Ding, Yang; Eng, Peter; Cai, Yong Q.; Chow, Paul; Xiao, Yuming; Jinfu Shu, A=Kao, Chi-Chang; Hemley, Russell J.; Kao, Chichang; Mao, Wendy L.; /Stanford U., Geo. Environ. Sci. /SLAC

    2011-01-10

    Using inelastic X-ray scattering techniques, we have succeeded in probing the high-pressure electronic structure of helium crystal at 300 K which has the widest known electronic energy bandgap of all materials, that was previously inaccessible to measurements due to the extreme energy and pressure range. We observed rich electron excitation spectrum, including a cut-off edge above 23 eV, a sharp exciton peak showing linear volume dependence, and a series of excitations and continuum at 26 to 45 eV. We determined electronic dispersion along the {Gamma}-M direction over two Brillouin zones, and provided a quantitative picture of the helium exciton beyond the simplified Wannier-Frenkel description.

  18. Modulated structures in calcian dolomite: A study by electron microscopy

    NASA Astrophysics Data System (ADS)

    van Tendeloo, G.; Wenk, H. R.; Gronsky, R.

    1985-11-01

    Calcian dolomite from the Devonian Lost Burro formation has been investigated with electron microscopy techniques. Electron diffraction shows evidence for “c” and “d” type reflections which may occur independently and are indicative of ordered superstructures. High resolution electron microscopy combined with selected area optical diffraction is the basis for models to explain the superstructures in calcian dolomite. It is proposed that “c” reflections are due to ordered substitution of Mg by Ca in basal cation layers. “d” reflections result when the rhombohedral stacking of basal layers is interrupted by intercalation of additional Ca layers. During electron irradiation at 1 MeV the Mg-Ca distribution becomes disordered and the crystal structure attains calcite symmetry. The arrangement of CO3 groups remains ordered.

  19. Electronic structure and isomer shifts of neptunium compounds

    NASA Astrophysics Data System (ADS)

    Svane, A.; Petit, L.; Temmerman, W. M.; Szotek, Z.

    2002-08-01

    The electronic structures of αNp metal and 28 Np compounds are calculated with the generalized gradient approximation to density-functional theory, implemented with the full-potential linear-muffin-tin-orbital method. The calculations are compared to experimental isomer shifts providing a calibration of the 237Np isomeric transition with a value of Δ=(-40.1+/-1.3)×10- 3 fm2 for the difference in nuclear radius between the excited isomeric level and the ground state. The isomer shift is primarily determined by the chemical environment. Decreasing the volume, either by external or chemical pressure, causes an f-->s+d charge transfer on Np, which leads to a higher electron contact density. The possible f-electron localization in Np compounds is discussed using self-interaction corrections, and it is concluded that f-electron localization has only a minor influence on the isomer shift.

  20. Superconducting properties and electronic structure of NaBi.

    PubMed

    Kushwaha, S K; Krizan, J W; Xiong, J; Klimczuk, T; Gibson, Q D; Liang, T; Ong, N P; Cava, R J

    2014-05-28

    Resistivity, dc magnetization, and heat capacity measurements are reported for superconducting NaBi. T(c), the electronic contribution to the specific heat γ, the ΔC(p)/γT(c) ratio, and the Debye temperature are found to be 2.15 K, 3.4 mJ mol(-1) K(-2), 0.78, and 140 K respectively. The calculated electron-phonon coupling constant (λ(ep) = 0.62) implies that NaBi is a moderately coupled superconductor. The upper critical field and coherence length are found to be 250 Oe and 115 nm, respectively. Electronic structure calculations show NaBi to be a good metal, in agreement with the experiments; the p(x) and p(y) orbitals of Bi dominate the electronic states at the Fermi Energy.

  1. Correlative Light Electron Microscopy: Connecting Synaptic Structure and Function

    PubMed Central

    Begemann, Isabell; Galic, Milos

    2016-01-01

    Many core paradigms of contemporary neuroscience are based on information obtained by electron or light microscopy. Intriguingly, these two imaging techniques are often viewed as complementary, yet separate entities. Recent technological advancements in microscopy techniques, labeling tools, and fixation or preparation procedures have fueled the development of a series of hybrid approaches that allow correlating functional fluorescence microscopy data and ultrastructural information from electron micrographs from a singular biological event. As correlative light electron microscopy (CLEM) approaches become increasingly accessible, long-standing neurobiological questions regarding structure-function relation are being revisited. In this review, we will survey what developments in electron and light microscopy have spurred the advent of correlative approaches, highlight the most relevant CLEM techniques that are currently available, and discuss its potential and limitations with respect to neuronal and synapse-specific applications. PMID:27601992

  2. Surface crystallography and electronic structure of potassium yttrium tungstate

    SciTech Connect

    Atuchin, V. V.; Pokrovsky, L. D.; Khyzhun, O. Yu.; Sinelnichenko, A. K.; Ramana, C. V.

    2008-08-01

    Structural and electronic characteristics of KY(WO{sub 4}){sub 2} (KYW) (010) crystal surfaces have been studied using reflection high-energy electron diffraction (RHEED) and x-ray photoelectron spectroscopy (XPS). The results indicate that the crystal structure and chemical composition of the mechanically polished pristine surface is stoichiometrically well maintained as expected for KYW crystals. Combined measurements of RHEED and XPS as a function of 1.5 keV Ar{sup +} ion irradiation of the KYW (010) surfaces indicate amorphization, partial loss of potassium atoms, and partial transformation of chemical valence state of tungsten from W{sup 6+} to a lower valence state, W{sup 0} state predominantly, which induces electronic states at the top of valence band.

  3. Structural and electronic properties of a tetrahedral amorphous carbon surface

    NASA Astrophysics Data System (ADS)

    Dong, Jianjun; Drabold, D. A.

    1997-03-01

    We present ab initio studies of a model of tetrahedral amorphous carbon (ta-C) surface. Our methodology is LDA (with Harris functional and local basis) molecular dynamics simulations. The surface is modeled by a 216 atom slab supercell. Several candidate slabs are constructed by starting with the DTW model (B.R. Djordjevic, M.F. Thorpe and F. Wooten, Phys. Rev. B 52) 5685 (1995) and applying various simulated heating/quenching cycles. We analyze the structural and electronic properties of the surface , with special attention forcused on the electronic signatures of surface structural defects. Preliminary results indicate that the surface layer significantly graphitizes, and many surface gap states are present in the electronic density of states.

  4. Electronic, magnetic, and geometric structure of metallo-carbohedrenes

    SciTech Connect

    Reddy, B.V.; Khanna, S.N.; Jena, P. )

    1992-12-04

    The energetics and the electronic, magnetic, and geometric structure of the metallocarbohedrene Ti[sub 8]C[sub 12] have been calculated self-consistently in the density functional formulation. The structure of Ti[sub 8]C[sub 12] is a distorted dodecahedron with a binding energy of 6.1 electron volts per atom. The unusual stability is derived from covalent-like bonding between carbon atoms and between titanium and carbon atoms with no appreciable interaction between titanium atoms. The density of states at the Fermi energy is high and is derived from a strong hybridization between titanium 3d and carbon sp electrons. Titanium sites carry a small magnetic moment of 0.35 Bohr magneton per atom and the cluster is only weakly magnetic. 13 refs., 3 figs., 1 tab.

  5. Electronic origin of structural transition in 122 Fe based superconductors

    NASA Astrophysics Data System (ADS)

    Ghosh, Haranath; Sen, Smritijit; Ghosh, Abyay

    2017-03-01

    Direct quantitative correlations between the orbital order and orthorhombicity is achieved in a number of Fe-based superconductors of 122 family. The former (orbital order) is calculated from first principles simulations using experimentally determined doping and temperature dependent structural parameters while the latter (the orthorhombicity) is taken from already established experimental studies; when normalized, both the above quantities quantitatively corresponds to each other in terms of their doping as well as temperature variations. This proves that the structural transition in Fe-based materials is electronic in nature due to orbital ordering. An universal correlations among various structural parameters and electronic structure are also obtained. Most remarkable among them is the mapping of two Fe-Fe distances in the low temperature orthorhombic phase, with the band energies Edxz, Edyz of Fe at the high symmetry points of the Brillouin zone. The fractional co-ordinate zAs of As which essentially determines anion height is inversely (directly) proportional to Fe-As bond distances (with exceptions of K doped BaFe2As2) for hole (electron) doped materials as a function of doping. On the other hand, Fe-As bond-distance is found to be inversely (directly) proportional to the density of states at the Fermi level for hole (electron) doped systems. Implications of these results to current issues of Fe based superconductivity are discussed.

  6. Highlighting material structure with transmission electron diffraction correlation coefficient maps.

    PubMed

    Kiss, Ákos K; Rauch, Edgar F; Lábár, János L

    2016-04-01

    Correlation coefficient maps are constructed by computing the differences between neighboring diffraction patterns collected in a transmission electron microscope in scanning mode. The maps are shown to highlight material structural features like grain boundaries, second phase particles or dislocations. The inclination of the inner crystal interfaces are directly deduced from the resulting contrast.

  7. Electron Heat Flux in Pressure Balance Structures at Ulysses

    NASA Technical Reports Server (NTRS)

    Yamauchi, Yohei; Suess, Steven T.; Sakurai, Takashi; Whitaker, Ann F. (Technical Monitor)

    2001-01-01

    Pressure balance structures (PBSs) are a common feature in the high-latitude solar wind near solar minimum. Rom previous studies, PBSs are believed to be remnants of coronal plumes and be related to network activity such as magnetic reconnection in the photosphere. We investigated the magnetic structures of the PBSs, applying a minimum variance analysis to Ulysses/Magnetometer data. At 2001 AGU Spring meeting, we reported that PBSs have structures like current sheets or plasmoids, and suggested that they are associated with network activity at the base of polar plumes. In this paper, we have analyzed high-energy electron data at Ulysses/SWOOPS to see whether bi-directional electron flow exists and confirm the conclusions more precisely. As a result, although most events show a typical flux directed away from the Sun, we have obtained evidence that some PBSs show bi-directional electron flux and others show an isotropic distribution of electron pitch angles. The evidence shows that plasmoids are flowing away from the Sun, changing their flow direction dynamically in a way not caused by Alfven waves. From this, we have concluded that PBSs are generated due to network activity at the base of polar plumes and their magnetic structures axe current sheets or plasmoids.

  8. Structural and electronic properties of perylene from first principles calculations.

    PubMed

    Fedorov, I A; Zhuravlev, Y N; Berveno, V P

    2013-03-07

    The electronic structure of crystalline perylene has been investigated within the framework of density functional theory including van der Waals interactions. The computations of the lattice parameters and cohesive energy have good agreement with experimental values. We have also calculated the binding distance and energy of perylene dimers, using different schemes, which include van der Waals interactions.

  9. Synchrotron-Radiation-based Investigationsof the Electronic Structure of Pu

    SciTech Connect

    Tobin, J; Chung, B; Terry, J; Schulze, R; Farr, J; Heinzelman, K; Rotenberg, E; Shuh, D

    2004-09-27

    Synchrotron radiation from the Advanced Light Source has been used to investigate the electronic structure of {alpha}-Pu and {delta}-Pu. Measurements include core level and valence band photoelectron spectroscopy, Resonant Photoelectron Spectroscopy (REPES), and X-ray Absorption Spectroscopy (XAS).

  10. Geometric and electronic structures of potassium-adsorbed rubrene complexes

    SciTech Connect

    Li, Tsung-Lung; Lu, Wen-Cai

    2015-06-28

    The geometric and electronic structures of potassium-adsorbed rubrene complexes are studied in this article. It is found that the potassium-rubrene (K{sub 1}RUB) complexes inherit the main symmetry characteristics from their pristine counterparts and are thus classified into D{sub 2}- and C{sub 2h}-like complexes according to the relative orientations of the four phenyl side groups. The geometric structures of K{sub 1}RUB are governed by two general effects on the total energy: Deformation of the carbon frame of the pristine rubrene increases the total energy, while proximity of the potassium ion to the phenyl ligands decreases the energy. Under these general rules, the structures of D{sub 2}- and C{sub 2h}-like K{sub 1}RUB, however, exhibit their respective peculiarities. These peculiarities can be illustrated by their energy profiles of equilibrium structures. For the potassium adsorption-sites, the D{sub 2}-like complexes show minimum-energy basins, whereas the C{sub 2h}-like ones have single-point minimum-energies. If the potassium atom ever has the energy to diffuse from the minimum-energy site, the potassium diffusion path on the D{sub 2}-like complexes is most likely along the backbone in contrast to the C{sub 2h}-like ones. Although the electronic structures of the minimum-energy structures of D{sub 2}- and C{sub 2h}-like K{sub 1}RUB are very alike, decompositions of their total spectra reveal insights into the electronic structures. First, the spectral shapes are mainly determined by the facts that, in comparison with the backbone carbons, the phenyl carbons have more uniform chemical environments and far less contributions to the electronic structures around the valence-band edge. Second, the electron dissociated from the potassium atom mainly remains on the backbone and has little effects on the electronic structures of the phenyl groups. Third, the two phenyls on the same side of the backbone as the potassium atom have more similar chemical environments

  11. Electronic structure of NSO- and SNO- anions: Stability, electron affinity, and spectroscopic properties

    NASA Astrophysics Data System (ADS)

    Trabelsi, T.; Yazidi, O.; Francisco, J. S.; Linguerri, R.; Hochlaf, M.

    2015-10-01

    The low-energy electronic states of NSO anion and its SNO isomeric form for the singlet, triplet, and quintet spin multiplicities have been investigated by accurate ab initio approaches and large atomic basis sets. One-dimensional cuts of the three-dimensional potential energy surfaces (PESs) along selected interatomic distances and bending angles for these states have been calculated to assess the formation and stability of NSO- and SNO- in the gas phase. Results show that these anions have two low-energy states ( X ˜ 1 A ' and 13A″) that are bound and stable with respect to electron detachment. Owing to the energetic position of the dissociating asymptotes of the neutral and anionic species, several electronic excited states are suggested to be stable with respect to the electron autodetachment process in the long-range parts of the potentials before reaching the molecular region. The nature of the PESs in these regions and their implications and effects on the formation of SNO- from atomic and molecular fragments are discussed. This information is essential for a better understanding of the potential role of these species in diverse media.

  12. Electronic-structure calculations of praseodymium metal by means of modified density-functional theory

    SciTech Connect

    Svane, A.; Trygg, J.; Johansson, B.; Eriksson, O. |

    1997-09-01

    Electronic-structure calculations of elemental praseodymium are presented. Several approximations are used to describe the Pr f electrons. It is found that the low-pressure, trivalent phase is well described using either the self-interaction corrected (SIC) local-spin-density (LSD) approximation or the generalized-gradient approximation (GGA) with spin and orbital polarization (OP). In the SIC-LSD approach the Pr f electrons are treated explicitly as localized with a localization energy given by the self-interaction of the f orbital. In the GGA+OP scheme the f-electron localization is described by the onset of spin and orbital polarization, the energetics of which is described by spin-moment formation energy and a term proportional to the total orbital moment, L{sub z}{sup 2}. The high-pressure phase is well described with the f electrons treated as band electrons, in either the LSD or the GGA approximations, of which the latter describes more accurately the experimental equation of state. The calculated pressure of the transition from localized to delocalized behavior is 280 kbar in the SIC-LSD approximation and 156 kbar in the GGA+OP approach, both comparing favorably with the experimentally observed transition pressure of 210 kbar. {copyright} {ital 1997} {ital The American Physical Society}

  13. A combined photoelectron spectroscopy and relativistic ab initio studies of the electronic structures of UFO and UFO-

    NASA Astrophysics Data System (ADS)

    Roy, Soumendra K.; Jian, Tian; Lopez, Gary V.; Li, Wei-Li; Su, Jing; Bross, David H.; Peterson, Kirk A.; Wang, Lai-Sheng; Li, Jun

    2016-02-01

    The observation of the gaseous UFO- anion is reported, which is investigated using photoelectron spectroscopy and relativisitic ab initio calculations. Two strong photoelectron bands are observed at low binding energies due to electron detachment from the U-7sσ orbital. Numerous weak detachment bands are also observed due to the strongly correlated U-5f electrons. The electron affinity of UFO is measured to be 1.27(3) eV. High-level relativistic quantum chemical calculations have been carried out on the ground state and many low-lying excited states of UFO to help interpret the photoelectron spectra and understand the electronic structure of UFO. The ground state of UFO- is linear with an O-U-F structure and a 3H4 spectral term derived from a U 7sσ25fφ15fδ1 electron configuration, whereas the ground state of neutral UFO has a 4H7/2 spectral term with a U 7sσ15fφ15fδ1 electron configuration. Strong electron correlation effects are found in both the anionic and neutral electronic configurations. In the UFO neutral, a high density of electronic states with strong configuration mixing is observed in most of the scalar relativistic and spin-orbit coupled states. The strong electron correlation, state mixing, and spin-orbit coupling of the electronic states make the excited states of UFO very challenging for accurate quantum chemical calculations.

  14. Writing Electron Dot Structures: Abstract of Issue 9905M

    NASA Astrophysics Data System (ADS)

    Magnell, Kenneth R.

    1999-10-01

    Writing Electron Dot Structures is a computer program for Mac OS that provides drill with feedback for students learning to write electron dot structures. While designed for students in the first year of college general chemistry it may also be used by high school chemistry students. A systematic method similar to that found in many general chemistry texts is employed:

    1. determine the number of valence shell electrons,
    2. select the central atom,
    3. construct a skeleton,
    4. add electrons to complete octets,
    5. examine the structure for resonance forms.
    During the construction of a structure, the student has the option of quitting, selecting another formula, or returning to a previous step. If an incorrect number of electrons is entered the student may not proceed until the correct number is entered. The symbol entered for the central atom must follow accepted upper/lower case practice, and entry of the correct symbol must be accomplished before proceeding to the next step. A periodic table is accessible and feedback provides assistance for these steps. Construction of the skeleton begins with the placement of the central atom. Atoms can be added, moved, or removed. Prompts and feedback keep the student informed of progress and problems. A correct skeleton is required before proceeding to the next step. Completion of the structure begins with the addition of electron pairs to form the required bonds. Remaining electrons are added to complete the formation of multiple bonds, assure compliance with the octet rule, and form expanded octets. Resonance forms are made by moving or removing and replacing electron pairs in the existing skeleton. Prompts and feedback guide the student through this process. A running tally of bond pairs, unshared pairs, octets, electrons used, and electrons remaining is provided during this step. Structural and Electronic Investigations of Complex Intermetallic Compounds

    SciTech Connect

    Ko, Hyunjin

    2008-01-01

    In solid state chemistry, numerous investigations have been attempted to address the relationships between chemical structure and physical properties. Such questions include: (1) How can we understand the driving forces of the atomic arrangements in complex solids that exhibit interesting chemical and physical properties? (2) How do different elements distribute themselves in a solid-state structure? (3) Can we develop a chemical understanding to predict the effects of valence electron concentration on the structures and magnetic ordering of systems by both experimental and theoretical means? Although these issues are relevant to various compound classes, intermetallic compounds are especially interesting and well suited for a joint experimental and theoretical effort. For intermetallic compounds, the questions listed above are difficult to answer since many of the constituent atoms simply do not crystallize in the same manner as in their separate, elemental structures. Also, theoretical studies suggest that the energy differences between various structural alternatives are small. For example, Al and Ga both belong in the same group on the Periodic Table of Elements and share many similar chemical properties. Al crystallizes in the fcc lattice with 4 atoms per unit cell and Ga crystallizes in an orthorhombic unit cell lattice with 8 atoms per unit cell, which are both fairly simple structures (Figure 1). However, when combined with Mn, which itself has a very complex cubic crystal structure with 58 atoms per unit cell, the resulting intermetallic compounds crystallize in a completely different fashion. At the 1:1 stoichiometry, MnAl forms a very simple tetragonal lattice with two atoms per primitive unit cell, while MnGa crystallizes in a complicated rhombohedral unit cell with 26 atoms within the primitive unit cell. The mechanisms influencing the arrangements of atoms in numerous crystal structures have been studied theoretically by calculating electronic

  15. Shigella flexneri Spa15 Crystal Structure Verified in Solution by Double Electron Electron Resonance

    PubMed Central

    Lillington, James E.D.; Lovett, Janet E.; Johnson, Steven; Roversi, Pietro; Timmel, Christiane R.; Lea, Susan M.

    2011-01-01

    Shigella flexneri Spa15 is a chaperone of the type 3 secretion system, which binds a number of effectors to ensure their stabilization prior to secretion. One of these effectors is IpgB1, a mimic of the human Ras-like Rho guanosine triphosphatase RhoG. In this study, Spa15 alone and in complex with IpgB1 has been studied by double electron electron resonance, an experiment that gives distance information showing the spacial separation of attached spin labels. This distance is explained by determining the crystal structure of the spin-labeled Spa15 where labels are seen to be buried in hydrophobic pockets. The double electron electron resonance experiment on the Spa15 complex with IpgB1 shows that IpgB1 does not bind Spa15 in the same way as is seen in the homologous Salmonella sp. chaperone:effector complex InvB:SipA. PMID:21075116

  16. Effect of chemical fixatives on accurate preservation of Escherichia coli and Bacillus subtilis structure in cells prepared by freeze-substitution

    SciTech Connect

    Graham, L.L.; Beveridge, T.J. )

    1990-04-01

    Five chemical fixatives were evaluated for their ability to accurately preserve bacterial ultrastructure during freeze-substitution of select Escherichia coli and Bacillus subtilis strains. Radioisotopes were specifically incorporated into the peptidoglycan, lipopolysaccharide, and nucleic acids of E. coli SFK11 and W7 and into the peptidoglycan and RNA of B. subtilis 168 and W23. The ease of extraction of radiolabels, as assessed by liquid scintillation counting during all stages of processing for freeze-substitution, was used as an indicator of cell structural integrity and retention of cellular chemical composition. Subsequent visual examination by electron microscopy was used to confirm ultrastructural conformation. The fixatives used were: 2% (wt/vol) osmium tetroxide and 2% (wt/vol) uranyl acetate; 2% (vol/vol) glutaraldehyde and 2% (wt/vol) uranyl acetate; 2% (vol/vol) acrolein and 2% (wt/vol) uranyl acetate; 2% (wt/vol) gallic acid; and 2% (wt/vol) uranyl acetate. All fixatives were prepared in a substitution solvent of anhydrous acetone. Extraction of cellular constituents depended on the chemical fixative used. A combination of 2% osmium tetroxide-2% uranyl acetate or 2% gallic acid alone resulted in optimum fixation as ascertained by least extraction of radiolabels. In both gram-positive and gram-negative organisms, high levels of radiolabel were detected in the processing fluids in which 2% acrolein-2% uranyl acetate, 2% glutaraldehyde-2% uranyl acetate, or 2% uranyl acetate alone were used as fixatives. Ultrastructural variations were observed in cells freeze-substituted in the presence of different chemical fixatives. We recommend the use of osmium tetroxide and uranyl acetate in acetone for routine freeze-substitution of eubacteria, while gallic acid is recommended for use when microanalytical processing necessitates the omission of osmium.

  17. Electronic structure tuning via surface modification in semimetallic nanowires

    NASA Astrophysics Data System (ADS)

    Sanchez-Soares, Alfonso; O'Donnell, Conor; Greer, James C.

    2016-12-01

    Electronic structure properties of nanowires (NWs) with diameters of 1.5 and 3 nm based on semimetallic α -Sn are investigated by employing density functional theory and perturbative GW methods. We explore the dependence of electron affinity, band structure, and band-gap values with crystallographic orientation, NW cross-sectional size, and surface passivants of varying electronegativity. We consider four chemical terminations in our study: methyl (CH3), hydrogen (H ), hydroxyl (OH ), and fluorine (F ). Results suggest a high degree of elasticity of Sn-Sn bonds within the Sn NWs' cores with no significant structural variations for nanowires with different surface passivants. Direct band gaps at Brillouin-zone centers are found for most studied structures with quasiparticle corrected band-gap magnitudes ranging from 0.25 to 3.54 eV in 1.5-nm-diameter structures, indicating an exceptional range of properties for semimetal NWs below the semimetal-to-semiconductor transition. Band-gap variations induced by changes in surface passivants indicate the possibility of realizing semimetal-semiconductor interfaces in NWs with constant cross-section and crystallographic orientation, allowing the design of novel dopant-free NW-based electronic devices.

  18. Nuclear structure with accurate chiral perturbation theory nucleon-nucleon potential: Application to 6Li and 10B

    SciTech Connect

    Navratil, P; Caurier, E

    2003-10-14

    The authors calculate properties of A = 6 system using the accurate charge-dependent nucleon-nucleon (NN) potential at fourth order of chiral perturbation theory. By application of the ab initio no-core shell model (NCSM) and a variational calculation in the harmonic oscillator basis with basis size up to 16 {h_bar}{Omega} they obtain the {sup 6}Li binding energy of 28.5(5) MeV and a converged excitation spectrum. Also, they calculate properties of {sup 10}B using the same NN potential in a basis space of up to 8 {h_bar}{Omega}. The results are consistent with results obtained by standard accurate NN potentials and demonstrate a deficiency of Hamiltonians consisting of only two-body terms. At this order of chiral perturbation theory three-body terms appear. It is expected that inclusion of such terms in the Hamiltonian will improve agreement with experiment.

  19. Unraveling the structure of membrane proteins in situ by transfer function corrected cryo-electron tomography.

    PubMed

    Eibauer, Matthias; Hoffmann, Christian; Plitzko, Jürgen M; Baumeister, Wolfgang; Nickell, Stephan; Engelhardt, Harald

    2012-12-01

    Cryo-electron tomography in combination with subtomogram averaging allows to investigate the structure of protein assemblies in their natural environment in a close to live state. To make full use of the structural information contained in tomograms it is necessary to analyze the contrast transfer function (CTF) of projections and to restore the phases of higher spatial frequencies. CTF correction is however hampered by the difficulty of determining the actual defocus values from tilt series data, which is due to the low signal-to-noise ratio of electron micrographs. In this study, an extended acquisition scheme is introduced that enables an independent CTF determination. Two high-dose images are recorded along the tilt axis on both sides of each projection, which allow an accurate determination of the defocus values of these images. These values are used to calculate the CTF for each image of the tilt series. We applied this scheme to the mycobacterial outer membrane protein MspA reconstituted in lipid vesicles and tested several variants of CTF estimation in combination with subtomogram averaging and correction of the modulation transfer function (MTF). The 3D electron density map of MspA was compared with a structure previously determined by X-ray crystallography. We were able to demonstrate that structural information up to a resolution of 16.8Å can be recovered using our CTF correction approach, whereas the uncorrected 3D map had a resolution of only 26.2Å.

  1. Molecular and electronic structures of cerium and cerium suboxide clusters

    NASA Astrophysics Data System (ADS)

    Kafader, Jared O.; Topolski, Josey E.; Jarrold, Caroline Chick

    2016-10-01

    The anion photoelectron (PE) spectra of Ce2Oy- (y = 1, 2), Ce3Oy- (y = 0-4), Ce4Oy- (y = 0-2), and Ce5Oy- (y = 1, 2) are reported and analyzed with supporting results from density functional theory calculations. The PE spectra all exhibit an intense electronic transition to the neutral ground state, all falling in the range of 0.7 to 1.1 eV electron binding energy, with polarization dependence consistent with detachment from diffuse Ce 6s-based molecular orbitals. There is no monotonic increase in electron affinity with increasing oxidation. A qualitative picture of how electronic structure evolves with an oxidation state emerges from comparison between the spectra and the computational results. The electronic structure of the smallest metallic cluster observed in this study, Ce3, is similar to the bulk structure in terms of atomic orbital occupancy (4f 5d2 6s). Initial cerium cluster oxidation involves largely ionic bond formation via Ce 5d and O 2p orbital overlap (i.e., larger O 2p contribution), with Ce—O—Ce bridge bonding favored over Ce=O terminal bond formation. With subsequent oxidation, the Ce 5d-based molecular orbitals are depleted of electrons, with the highest occupied orbitals described as diffuse Ce 6s based molecular orbitals. In the y ≤ (x + 1) range of oxidation states, each Ce center has a singly occupied non-bonding 4f orbital. The PE spectrum of Ce3O4- is unique in that it exhibits a single nearly vertical transition. The highly symmetric structure predicted computationally is the same structure determined from Ce3O4+ IR predissociation spectra [A. M. Burow et al., Phys. Chem. Chem. Phys. 13, 19393 (2011)], indicating that this structure is stable in -1, 0, and +1 charge states. Spectra of clusters with x ≥ 3 exhibit considerable continuum signal above the ground state transition; the intensity of the continuum signal decreases with increasing oxidation. This feature is likely the result of numerous quasi-bound anion states or two-electron

  2. Defective graphene and nanoribbons: electronic, magnetic and structural properties

    NASA Astrophysics Data System (ADS)

    Guerra, Thiago; Azevedo, Sérgio; Machado, Marcelo

    2016-03-01

    We make use of first-principles calculations, based on the density functional theory (DFT), to investigate the alterations at the structural, energetic, electronic and magnetic properties of graphene and zigzag graphene nanoribbons (ZGNRs) due to the inclusion of different types of line and punctual defects. For the graphene it is found that the inclusion of defects breaks the translational symmetry of the crystal with drastic changes at its electronic structure, going from semimetallic to semiconductor and metallic. Regarding the magnetic properties, no magnetization is observed for the defective graphene. We also show that the inclusion of defects at ZGNRs is a good way to create and control pronounced peaks at the Fermi level. Furthermore, defective ZGNRs structures show magnetic moment by supercell up to 2.0 μ B . For the non defective ZGNRs is observed a switch of the magnetic coupling between opposite ribbon edges from the antiferromagnetic to the ferrimagnetic and ferromagnetic configurations.

  3. Biomechanics of DNA structures visualized by 4D electron microscopy

    PubMed Central

    Lorenz, Ulrich J.; Zewail, Ahmed H.

    2013-01-01

    We present a technique for in situ visualization of the biomechanics of DNA structural networks using 4D electron microscopy. Vibrational oscillations of the DNA structure are excited mechanically through a short burst of substrate vibrations triggered by a laser pulse. Subsequently, the motion is probed with electron pulses to observe the impulse response of the specimen in space and time. From the frequency and amplitude of the observed oscillations, we determine the normal modes and eigenfrequencies of the structures involved. Moreover, by selective “nano-cutting” at a given point in the network, it was possible to obtain Young’s modulus, and hence the stiffness, of the DNA filament at that position. This experimental approach enables nanoscale mechanics studies of macromolecules and should find applications in other domains of biological networks such as origamis. PMID:23382239

  4. Characterization of electronic structure of periodically strained graphene

    SciTech Connect

    Aslani, Marjan; Garner, C. Michael Nishi, Yoshio; Kumar, Suhas; Nordlund, Dennis; Pianetta, Piero

    2015-11-02

    We induced periodic biaxial tensile strain in polycrystalline graphene by wrapping it over a substrate with repeating pillar-like structures with a periodicity of 600 nm. Using Raman spectroscopy, we determined to have introduced biaxial strains in graphene in the range of 0.4% to 0.7%. Its band structure was characterized using photoemission from valance bands, shifts in the secondary electron emission, and x-ray absorption from the carbon 1s levels to the unoccupied graphene conduction bands. It was observed that relative to unstrained graphene, strained graphene had a higher work function and higher density of states in the valence and conduction bands. We measured the conductivity of the strained and unstrained graphene in response to a gate voltage and correlated the changes in their behavior to the changes in the electronic structure. From these sets of data, we propose a simple band diagram representing graphene with periodic biaxial strain.

  5. Characterization of electronic structure of periodically strained graphene

    SciTech Connect

    Aslani, Marjan; Garner, C. Michael; Kumar, Suhas; Nordlund, Dennis; Pianetta, Piero; Nishi, Yoshio

    2015-11-03

    We induced periodic biaxial tensile strain in polycrystalline graphene by wrapping it over a substrate with repeating pillar-like structures with a periodicity of 600 nm. Using Raman spectroscopy, we determined to have introduced biaxial strains in graphene in the range of 0.4% to 0.7%. Its band structure was characterized using photoemission from valance bands, shifts in the secondary electron emission, and x-ray absorption from the carbon 1s levels to the unoccupied graphene conduction bands. It was observed that relative to unstrained graphene, strained graphene had a higher work function and higher density of states in the valence and conduction bands. Furthermore, we measured the conductivity of the strained and unstrained graphene in response to a gate voltage and correlated the changes in their behavior to the changes in the electronic structure. From these sets of data, we propose a simple band diagram representing graphene with periodic biaxial strain.

  6. Local atomic order, electronic structure and electron transport properties of Cu-Zr metallic glasses

    NASA Astrophysics Data System (ADS)

    Antonowicz, J.; Pietnoczka, A.; Pekała, K.; Latuch, J.; Evangelakis, G. A.

    2014-05-01

    We studied atomic and electronic structures of binary Cu-Zr metallic glasses (MGs) using combined experimental and computational methods including X-ray absorption fine structure spectroscopy, electrical resistivity, thermoelectric power (TEP) measurements, molecular dynamics (MD) simulations, and ab-initio calculations. The results of MD simulations and extended X-ray absorption fine structure analysis indicate that atomic order of Cu-Zr MGs and can be described in terms of interpenetrating icosahedral-like clusters involving five-fold symmetry. MD configurations were used as an input for calculations of theoretical electronic density of states (DOS) functions which exhibits good agreement with the experimental X-ray absorption near-edge spectra. We found no indication of minimum of DOS at Fermi energy predicted by Mott's nearly free electron (NFE) model for glass-forming alloys. The theoretical DOS was subsequently used to test Mott's model describing the temperature variation of electrical resistivity and thermoelectric power of transition metal-based MGs. We demonstrate that the measured temperature variations of electrical resistivity and TEP remain in a contradiction with this model. On the other hand, the experimental temperature dependence of electrical resistivity can be explained by incipient localization of conduction electrons. It is shown that weak localization model works up to relatively high temperatures when localization is destroyed by phonons. Our results indicate that electron transport properties of Cu-Zr MGs are dominated by localization effects rather than by electronic structure. We suggest that NFE model fails to explain a relatively high glass-forming ability of binary Cu-Zr alloys.

  7. Local atomic order, electronic structure and electron transport properties of Cu-Zr metallic glasses

    SciTech Connect

    Antonowicz, J. Pietnoczka, A.; Pękała, K.; Latuch, J.; Evangelakis, G. A.

    2014-05-28

    We studied atomic and electronic structures of binary Cu-Zr metallic glasses (MGs) using combined experimental and computational methods including X-ray absorption fine structure spectroscopy, electrical resistivity, thermoelectric power (TEP) measurements, molecular dynamics (MD) simulations, and ab-initio calculations. The results of MD simulations and extended X-ray absorption fine structure analysis indicate that atomic order of Cu-Zr MGs and can be described in terms of interpenetrating icosahedral-like clusters involving five-fold symmetry. MD configurations were used as an input for calculations of theoretical electronic density of states (DOS) functions which exhibits good agreement with the experimental X-ray absorption near-edge spectra. We found no indication of minimum of DOS at Fermi energy predicted by Mott's nearly free electron (NFE) model for glass-forming alloys. The theoretical DOS was subsequently used to test Mott's model describing the temperature variation of electrical resistivity and thermoelectric power of transition metal-based MGs. We demonstrate that the measured temperature variations of electrical resistivity and TEP remain in a contradiction with this model. On the other hand, the experimental temperature dependence of electrical resistivity can be explained by incipient localization of conduction electrons. It is shown that weak localization model works up to relatively high temperatures when localization is destroyed by phonons. Our results indicate that electron transport properties of Cu-Zr MGs are dominated by localization effects rather than by electronic structure. We suggest that NFE model fails to explain a relatively high glass-forming ability of binary Cu-Zr alloys.

  8. Electronic structure of multi-walled carbon fullerenes

    NASA Astrophysics Data System (ADS)

    Doore, Keith; Cook, Matthew; Clausen, Eric; Lukashev, Pavel V.; Kidd, Tim E.; Stollenwerk, Andrew J.

    2017-02-01

    Despite an enormous amount of research on carbon based nanostructures, relatively little is known about the electronic structure of multi-walled carbon fullerenes, also known as carbon onions. In part, this is due to the very high computational expense involved in estimating electronic structure of large molecules. At the same time, experimentally, the exact crystal structure of the carbon onion is usually unknown, and therefore one relies on qualitative arguments only. In this work we present the results of a computational study on a series of multi-walled fullerenes and compare their electronic structures to experimental data. Experimentally, the carbon onions were fabricated using ultrasonic agitation of isopropanol alcohol and deposited onto the surface of highly ordered pyrolytic graphite using a drop cast method. Scanning tunneling microscopy images indicate that the carbon onions produced using this technique are ellipsoidal with dimensions on the order of 10 nm. The majority of differential tunneling spectra acquired on individual carbon onions are similar to that of graphite with the addition of molecular-like peaks, indicating that these particles span the transition between molecules and bulk crystals. A smaller, yet sizable number exhibited a semiconducting gap between the highest occupied molecular orbital (HOMO) and the lowest unoccupied molecular orbital (LUMO) levels. These results are compared with the electronic structure of different carbon onion configurations calculated using first-principles. Similar to the experimental results, the majority of these configurations are metallic with a minority behaving as semiconductors. Analysis of the configurations investigated here reveals that each carbon onion exhibiting an energy band gap consisted only of non-metallic fullerene layers, indicating that the interlayer interaction is not significant enough to affect the total density of states in these structures.

  9. Electronic structure and crystal phase stability of palladium hydrides

    SciTech Connect

    Houari, Abdesalem; Matar, Samir F.; Eyert, Volker

    2014-11-07

    The results of electronic structure calculations for a variety of palladium hydrides are presented. The calculations are based on density functional theory and used different local and semilocal approximations. The thermodynamic stability of all structures as well as the electronic and chemical bonding properties are addressed. For the monohydride, taking into account the zero-point energy is important to identify the octahedral Pd-H arrangement with its larger voids and, hence, softer hydrogen vibrational modes as favorable over the tetrahedral arrangement as found in the zincblende and wurtzite structures. Stabilization of the rocksalt structure is due to strong bonding of the 4d and 1s orbitals, which form a characteristic split-off band separated from the main d-band group. Increased filling of the formerly pure d states of the metal causes strong reduction of the density of states at the Fermi energy, which undermines possible long-range ferromagnetic order otherwise favored by strong magnetovolume effects. For the dihydride, octahedral Pd-H arrangement as realized, e.g., in the pyrite structure turns out to be unstable against tetrahedral arrangement as found in the fluorite structure. Yet, from both heat of formation and chemical bonding considerations, the dihydride turns out to be less favorable than the monohydride. Finally, the vacancy ordered defect phase Pd{sub 3}H{sub 4} follows the general trend of favoring the octahedral arrangement of the rocksalt structure for Pd:H ratios less or equal to one.

  10. Electronic structures of Ascaris trypsin inhibitor in solution

    NASA Astrophysics Data System (ADS)

    Zheng, Haoping

    2003-11-01

    The electronic structures of Ascaris trypsin inhibitor in solution are obtained by the first-principles, all-electron, ab initio calculation using the self-consistent cluster-embedding (SCCE) method. The inhibitor, made up of 62 amino acid residues with 912 atoms, has two three-dimensional solution structures: 1ata and 1atb. The calculated ground-state energy of structure 1atb is lower than that of structure 1ata by 6.12 eV. The active sites are determined and explained: only structure 1atb has a N terminal at residue ARG+31. This shows that the structure 1atb is the stable and active form of the inhibitor, which is in agreement with the experimental results. The calculation reveals that some parts of the inhibitor can be easily changed while the inhibitor’s biological activity may be kept. This kind of information may be helpful in fighting viruses such as AIDS, SARS, and flu, since these viruses have higher variability. The calculation offers an independent theoretical estimate of the precision of structure determination.

  11. Electronic structure and crystal phase stability of palladium hydrides

    NASA Astrophysics Data System (ADS)

    Houari, Abdesalem; Matar, Samir F.; Eyert, Volker

    2014-11-01

    The results of electronic structure calculations for a variety of palladium hydrides are presented. The calculations are based on density functional theory and used different local and semilocal approximations. The thermodynamic stability of all structures as well as the electronic and chemical bonding properties are addressed. For the monohydride, taking into account the zero-point energy is important to identify the octahedral Pd-H arrangement with its larger voids and, hence, softer hydrogen vibrational modes as favorable over the tetrahedral arrangement as found in the zincblende and wurtzite structures. Stabilization of the rocksalt structure is due to strong bonding of the 4d and 1s orbitals, which form a characteristic split-off band separated from the main d-band group. Increased filling of the formerly pure d states of the metal causes strong reduction of the density of states at the Fermi energy, which undermines possible long-range ferromagnetic order otherwise favored by strong magnetovolume effects. For the dihydride, octahedral Pd-H arrangement as realized, e.g., in the pyrite structure turns out to be unstable against tetrahedral arrangement as found in the fluorite structure. Yet, from both heat of formation and chemical bonding considerations, the dihydride turns out to be less favorable than the monohydride. Finally, the vacancy ordered defect phase Pd3H4 follows the general trend of favoring the octahedral arrangement of the rocksalt structure for Pd:H ratios less or equal to one.

  12. Electronic and structural reconstruction in titanate heterostructures from first principles

    NASA Astrophysics Data System (ADS)

    Mulder, Andrew T.; Fennie, Craig J.

    2014-03-01

    Recent advances in transition metal oxide heterostructures have opened new routes to create materials with novel functionalities and properties. One direction has been to combine a Mott insulating perovskite with an electronic d1 configuration, such as LaTiO3, with a band insulating d0 perovskite, such as SrTiO3. An exciting recent development is the demonstration of interfacial conductivity in GdTiO3/SrTiO3 heterostructures that display a complex structural motif of octahedral rotations and ferromagnetic properties similar to bulk GdTiO3. In this talk we present our first principles investigation of the interplay of structural, electronic, magnetic, and orbital degrees of freedom for a wide range of d1/d0 titanate heterostructures. We find evidence for both rotation driven ferroelectricity and a symmetry breaking electronic reconstruction with a concomitant structural distortion at the interface. We argue that these materials represent an ideal platform to realize novel functionalities such as the electric field control of electronic and magnetic properties.

  13. Toward the origin of exciton electronic structure in phycobiliproteins

    NASA Astrophysics Data System (ADS)

    Womick, Jordan M.; Miller, Stephen A.; Moran, Andrew M.

    2010-07-01

    Femtosecond laser spectroscopies are used to examine the electronic structures of two proteins found in the phycobilisome antenna of cyanobacteria, allophycocyanin (APC) and C-phycocyanin (CPC). The wave function composition involving the pairs of phycocyanobilin pigments (i.e., dimers) found in both proteins is the primary focus of this investigation. Despite their similar geometries, earlier experimental studies conducted in our laboratory and elsewhere observe clear signatures of exciton electronic structure in APC but not CPC. This issue is further investigated here using new experiments. Transient grating (TG) experiments employing broadband quasicontinuum probe pulses find a redshift in the signal spectrum of APC, which is almost twice that of CPC. Dynamics in the TG signal spectra suggest that the sub-100 fs dynamics in APC and CPC are respectively dominated by internal conversion and nuclear relaxation. A specialized technique, intraband electronic coherence spectroscopy (IECS), photoexcites electronic and nuclear coherences with nearly full suppression of signals corresponding to electronic populations. The main conclusion drawn by IECS is that dephasing of intraband electronic coherences in APC occurs in less than 25 fs. This result rules out correlated pigment fluctuations as the mechanism enabling exciton formation in APC and leads us to propose that the large Franck-Condon factors of APC promote wave function delocalization in the vibronic basis. For illustration, we compute the Hamiltonian matrix elements involving the electronic origin of the α84 pigment and the first excited vibronic level of the β84 pigment associated with a hydrogen out-of-plane wagging mode at 800 cm-1. For this pair of vibronic states, the -51 cm-1 coupling is larger than the 40 cm-1 energy gap, thereby making wave function delocalization a feasible prospect. By contrast, CPC possesses no pair of vibronic levels for which the intermolecular coupling is larger than the energy

  14. Grid-based electronic structure calculations: The tensor decomposition approach

    SciTech Connect

    Rakhuba, M.V.; Oseledets, I.V.

    2016-05-01

    We present a fully grid-based approach for solving Hartree–Fock and all-electron Kohn–Sham equations based on low-rank approximation of three-dimensional electron orbitals. Due to the low-rank structure the total complexity of the algorithm depends linearly with respect to the one-dimensional grid size. Linear complexity allows for the usage of fine grids, e.g. 8192{sup 3} and, thus, cheap extrapolation procedure. We test the proposed approach on closed-shell atoms up to the argon, several molecules and clusters of hydrogen atoms. All tests show systematical convergence with the required accuracy.

  15. Multi-million atom electronic structure calculations for quantum dots

    NASA Astrophysics Data System (ADS)

    Usman, Muhammad

    Quantum dots grown by self-assembly process are typically constructed by 50,000 to 5,000,000 structural atoms which confine a small, countable number of extra electrons or holes in a space that is comparable in size to the electron wavelength. Under such conditions quantum dots can be interpreted as artificial atoms with the potential to be custom tailored to new functionality. In the past decade or so, these nanostructures have attracted significant experimental and theoretical attention in the field of nanoscience. The new and tunable optical and electrical properties of these artificial atoms have been proposed in a variety of different fields, for example in communication and computing systems, medical and quantum computing applications. Predictive and quantitative modeling and simulation of these structures can help to narrow down the vast design space to a range that is experimentally affordable and move this part of nanoscience to nano-Technology. Modeling of such quantum dots pose a formidable challenge to theoretical physicists because: (1) Strain originating from the lattice mismatch of the materials penetrates deep inside the buffer surrounding the quantum dots and require large scale (multi-million atom) simulations to correctly capture its effect on the electronic structure, (2) The interface roughness, the alloy randomness, and the atomistic granularity require the calculation of electronic structure at the atomistic scale. Most of the current or past theoretical calculations are based on continuum approach such as effective mass approximation or k.p modeling capturing either no or one of the above mentioned effects, thus missing some of the essential physics. The Objectives of this thesis are: (1) to model and simulate the experimental quantum dot topologies at the atomistic scale; (2) to theoretically explore the essential physics i.e. long range strain, linear and quadratic piezoelectricity, interband optical transition strengths, quantum confined

  16. Excited state X-ray absorption spectroscopy: Probing both electronic and structural dynamics

    NASA Astrophysics Data System (ADS)

    Neville, Simon P.; Averbukh, Vitali; Ruberti, Marco; Yun, Renjie; Patchkovskii, Serguei; Chergui, Majed; Stolow, Albert; Schuurman, Michael S.

    2016-10-01

    We investigate the sensitivity of X-ray absorption spectra, simulated using a general method, to properties of molecular excited states. Recently, Averbukh and co-workers [M. Ruberti et al., J. Chem. Phys. 140, 184107 (2014)] introduced an efficient and accurate L 2 method for the calculation of excited state valence photoionization cross-sections based on the application of Stieltjes imaging to the Lanczos pseudo-spectrum of the algebraic diagrammatic construction (ADC) representation of the electronic Hamiltonian. In this paper, we report an extension of this method to the calculation of excited state core photoionization cross-sections. We demonstrate that, at the ADC(2)x level of theory, ground state X-ray absorption spectra may be accurately reproduced, validating the method. Significantly, the calculated X-ray absorption spectra of the excited states are found to be sensitive to both geometric distortions (structural dynamics) and the electronic character (electronic dynamics) of the initial state, suggesting that core excitation spectroscopies will be useful probes of excited state non-adiabatic dynamics. We anticipate that the method presented here can be combined with ab initio molecular dynamics calculations to simulate the time-resolved X-ray spectroscopy of excited state molecular wavepacket dynamics.

  17. Excited state X-ray absorption spectroscopy: Probing both electronic and structural dynamics.

    PubMed

    Neville, Simon P; Averbukh, Vitali; Ruberti, Marco; Yun, Renjie; Patchkovskii, Serguei; Chergui, Majed; Stolow, Albert; Schuurman, Michael S

    2016-10-14

    We investigate the sensitivity of X-ray absorption spectra, simulated using a general method, to properties of molecular excited states. Recently, Averbukh and co-workers [M. Ruberti et al., J. Chem. Phys. 140, 184107 (2014)] introduced an efficient and accurate L(2) method for the calculation of excited state valence photoionization cross-sections based on the application of Stieltjes imaging to the Lanczos pseudo-spectrum of the algebraic diagrammatic construction (ADC) representation of the electronic Hamiltonian. In this paper, we report an extension of this method to the calculation of excited state core photoionization cross-sections. We demonstrate that, at the ADC(2)x level of theory, ground state X-ray absorption spectra may be accurately reproduced, validating the method. Significantly, the calculated X-ray absorption spectra of the excited states are found to be sensitive to both geometric distortions (structural dynamics) and the electronic character (electronic dynamics) of the initial state, suggesting that core excitation spectroscopies will be useful probes of excited state non-adiabatic dynamics. We anticipate that the method presented here can be combined with ab initio molecular dynamics calculations to simulate the time-resolved X-ray spectroscopy of excited state molecular wavepacket dynamics.

  18. Comparison of optimization methods for electronic-structure calculations

    SciTech Connect

    Garner, J.; Das, S. G.; Min, B. I.; Woodward, C.; Benedek, R.

    1989-06-15

    The performance of several local-optimization methods for calculatingelectronic structure is compared. The fictitious first-order equation of motionproposed by Williams and Soler is integrated numerically by three procedures:simple finite-difference integration, approximate analytical integration (theWilliams-Soler algorithm), and the Born perturbation series. These techniquesare applied to a model problem for which exact solutions are known, the Mathieuequation. The Williams-Soler algorithm and the second Born approximationconverge equally rapidly, but the former involves considerably lesscomputational effort and gives a more accurate converged solution. Applicationof the method of conjugate gradients to the Mathieu equation is discussed.

  19. Electronic structures of solids made of C20 clusters

    NASA Astrophysics Data System (ADS)

    Hussain, M. B.; Xu, L. H.; Wu, S. Q.; Zhu, Z. Z.

    2017-02-01

    By performing first-principles calculations based on the density functional theory, we have investigated the optimized structures, cohesive energies and electronic properties of crystalline solids made of C20 clusters. A very interesting result is found from the optimized diamond structure made of C20's, where the dimered C20 clusters, i.e., (C20)2 dimmers, are formed. Such (C20)2 dimers are then condensed by weak van der Waals interaction between them, leading to the formation of a molecular solid. We also found that one-dimensional molecular solid could be formed when C20 clusters are head to head. Results on C20 clusters arranged in the two-dimensional graphene structure and in fcc structure both show that there are significant coalescences of neighboring C20 fullerenes, leading to metallic characters for both the graphene and fcc structures.

  20. Antistiction technique using elastomer contact structure in woven electronic textiles

    NASA Astrophysics Data System (ADS)

    Yamashita, Takahiro; Takamatsu, Seiichi; Miyake, Koji; Itoh, Toshihiro

    2014-01-01

    In this paper, we present an antistiction technique using an elastomer contact structure in woven electronic textiles (e-textiles). A coating of poly(3,4-ethylenedioxythiophene):poly(4-styrene sulfonate) (PEDOT:PSS) in the form of a solid conductive film on a hemispherical silicone elastomer structure is employed in creating an electrical circuit embedded into the fabric of a woven e-textile, where the contact structure reduces the contact area and capillary force generated by the moisture in air between weft and warp ribbons. Stiction occurs between a weft and a warp without the contact structure under an RH of 80%, and the detachment of the stuck ribbon requires a delamination load of about 0.2 N. On the other hand, in the case of contact between the contact structure and the ribbon coated with plain PEDOT:PSS, stiction does not occur as the relative humidity increases from 20 to 80%.

  1. Fluctuation electron microscopy studies of complex structured materials

    NASA Astrophysics Data System (ADS)

    Zhao, Gongpu; Rougée, Annick; Buseck, Peter; Treacy, Michael

    2008-03-01

    Fluctuation electron microscopy (FEM) is a hybrid imaging-diffraction technique. This technique is particularly sensitive to paracrystalline structures of dimension 0.5-2 nm, which are difficult to detect by either imaging or diffraction techniques alone. It has been successfully deployed to study paracrystalline structures in amorphous silicon, germanium thin film. This technique has also been used to study metallic glasses and oxide glasses. Until now, FEM has not been used to study disordered geological materials. In this talk we present our FEM studies of shungite, a naturally occurring disordered carbonaceous material, reveal that trace quantities of tightly curved graphene structures such as C60, or fragments of C60, is present in shungite. We also present results from our study of metamict zircon, whose crystal structure is destroyed by self-radiation during naturally occurring α decay events. Work is in progress to study the structural evolution during the metamictization process.

  2. Electronic and Thermal Properties of Graphene and Carbon Structures

    NASA Astrophysics Data System (ADS)

    Anthony, Gilmore; Khatun, Mahfuza

    2011-10-01

    We will present the general properties of carbon structures. The research involves the study of carbon structures: Graphene, Graphene nanoribbons (GNRs), and Carbon Nanotubes (CNTs). A review of electrical and thermal conduction phenomena of the structures will be discussed. Particularly carbon nanoribbons and CNTs have many interesting physical properties, and have the potential for device applications. Our research interests include the study of electronic structures, electrical and thermal transport properties of the carbon structures. Results are produced analytically as well as by simulation. The numerical simulations are conducted using various tools such as Visual Molecular Dynamics (VMD), Large Large-scale Atomic/Molecular Massively Parallel Simulator (LAMMPS), NanoHub at Purdue University and the Beowulf Cluster at Ball State University.

  3. Compressed Sensing Electron Tomography for Determining Biological Structure

    NASA Astrophysics Data System (ADS)

    Guay, Matthew D.; Czaja, Wojciech; Aronova, Maria A.; Leapman, Richard D.

    2016-06-01

    There has been growing interest in applying compressed sensing (CS) theory and practice to reconstruct 3D volumes at the nanoscale from electron tomography datasets of inorganic materials, based on known sparsity in the structure of interest. Here we explore the application of CS for visualizing the 3D structure of biological specimens from tomographic tilt series acquired in the scanning transmission electron microscope (STEM). CS-ET reconstructions match or outperform commonly used alternative methods in full and undersampled tomogram recovery, but with less significant performance gains than observed for the imaging of inorganic materials. We propose that this disparity stems from the increased structural complexity of biological systems, as supported by theoretical CS sampling considerations and numerical results in simulated phantom datasets. A detailed analysis of the efficacy of CS-ET for undersampled recovery is therefore complicated by the structure of the object being imaged. The numerical nonlinear decoding process of CS shares strong connections with popular regularized least-squares methods, and the use of such numerical recovery techniques for mitigating artifacts and denoising in reconstructions of fully sampled datasets remains advantageous. This article provides a link to the software that has been developed for CS-ET reconstruction of electron tomographic data sets.

  4. Oligothiophene wires: impact of torsional conformation on the electronic structure.

    PubMed

    Kislitsyn, D A; Taber, B N; Gervasi, C F; Zhang, L; Mannsfeld, S C B; Prell, J S; Briseno, A L; Nazin, G V

    2016-02-14

    Charge transport in polymer- and oligomer-based semiconductor materials depends strongly on the structural ordering of the constituent molecules. Variations in molecular conformations influence the electronic structures of polymers and oligomers, and thus impact their charge-transport properties. In this study, we used Scanning Tunneling Microscopy and Spectroscopy (STM/STS) to investigate the electronic structures of different alkyl-substituted oligothiophenes displaying varied torsional conformations on the Au(111) surface. STM imaging showed that on Au(111), oligothiophenes self-assemble into chain-like structures, binding to each other via interdigitated alkyl ligands. The molecules adopted distinct planar conformations with alkyl ligands forming cis- or trans- mutual orientations. For each molecule, by using STS mapping, we identify a progression of particle-in-a-box-like states corresponding to the LUMO, LUMO+1 and LUMO+2 orbitals. Analysis of STS data revealed very similar unoccupied molecular orbital energies for different possible molecular conformations. By using density functional theory calculations, we show that the lack of variation in molecular orbital energies among the different oligothiophene conformers implies that the effect of the Au-oligothiophene interaction on molecular orbital energies is nearly identical for all studied torsional conformations. Our results suggest that cis-trans torsional disorder may not be a significant source of electronic disorder and charge carrier trapping in organic semiconductor devices based on oligothiophenes.

  5. Electronic structural investigations of ruthenium compounds and anticancer prodrugs.

    PubMed

    Harris, Travis V; Szilagyi, Robert K; McFarlane Holman, Karen L

    2009-08-01

    Several Ru(III) compounds are propitious anticancer agents although the precise mechanisms of action remain unknown. With this paper we start to establish an experimental library of X-ray absorption spectroscopy (XAS) data for ten Ru compounds wherein the ligands [Cl(-), dimethyl sulfoxide, imidazole, and indazole] were varied systematically to provide electronic structural information for future use in correlating spectroscopic signatures with chemical properties. Despite the considerable difference in the coordination environments of the complexes studied, the overall differences in spectral features and electronic structures calculated using density functional theory are unexpectedly small. However, the differences in the electronic structure of the Ru(III) prodrugs KP1019 ([IndH][trans-RuCl(4)(Ind)(2)], Ind is indazole) and ICR ([ImH][trans-RuCl(4)(Im)(2)], Im is imidazole) observed in the XAS data show correlation with known chemical and biological activities in addition to the donor abilities of imidazole compared with indazole and reduction potentials of the complexes. These semiquantitative results lay the groundwork for future biochemical studies into the structure-function relationships of Ru-based anticancer drugs.

  6. Compressed Sensing Electron Tomography for Determining Biological Structure

    PubMed Central

    Guay, Matthew D.; Czaja, Wojciech; Aronova, Maria A.; Leapman, Richard D.

    2016-01-01

    There has been growing interest in applying compressed sensing (CS) theory and practice to reconstruct 3D volumes at the nanoscale from electron tomography datasets of inorganic materials, based on known sparsity in the structure of interest. Here we explore the application of CS for visualizing the 3D structure of biological specimens from tomographic tilt series acquired in the scanning transmission electron microscope (STEM). CS-ET reconstructions match or outperform commonly used alternative methods in full and undersampled tomogram recovery, but with less significant performance gains than observed for the imaging of inorganic materials. We propose that this disparity stems from the increased structural complexity of biological systems, as supported by theoretical CS sampling considerations and numerical results in simulated phantom datasets. A detailed analysis of the efficacy of CS-ET for undersampled recovery is therefore complicated by the structure of the object being imaged. The numerical nonlinear decoding process of CS shares strong connections with popular regularized least-squares methods, and the use of such numerical recovery techniques for mitigating artifacts and denoising in reconstructions of fully sampled datasets remains advantageous. This article provides a link to the software that has been developed for CS-ET reconstruction of electron tomographic data sets. PMID:27291259

  7. Real-time feedback from iterative electronic structure calculations.

    PubMed

    Vaucher, Alain C; Haag, Moritz P; Reiher, Markus

    2016-04-05

    Real-time feedback from iterative electronic structure calculations requires to mediate between the inherently unpredictable execution times of the iterative algorithm used and the necessity to provide data in fixed and short time intervals for real-time rendering. We introduce the concept of a mediator as a component able to deal with infrequent and unpredictable reference data to generate reliable feedback. In the context of real-time quantum chemistry, the mediator takes the form of a surrogate potential that has the same local shape as the first-principles potential and can be evaluated efficiently to deliver atomic forces as real-time feedback. The surrogate potential is updated continuously by electronic structure calculations and guarantees to provide a reliable response to the operator for any molecular structure. To demonstrate the application of iterative electronic structure methods in real-time reactivity exploration, we implement self-consistent semiempirical methods as the data source and apply the surrogate-potential mediator to deliver reliable real-time feedback.

  8. Molecular structural formulas as one-electron density and hamiltonian operators: the VIF method extended.

    PubMed

    Alia, Joseph D

    2007-03-29

    The valency interaction formula (VIF) method is given a broader and more general interpretation in which these simple molecular structural formulas implicitly include all overlaps between valence atomic orbitals even for interactions not drawn in the VIF picture. This applies for VIF pictures as one-electron Hamiltonian operators as well as VIF pictures as one-electron density operators that constitute a new implementation of the VIF method simpler in its application and more accurate in its results than previous approaches. A procedure for estimating elements of the effective charge density-bond order matrix, Pmunu, from electron configurations in atoms is presented, and it is shown how these lead to loop and line constants in the VIF picture. From these structural formulas, one finds the number of singly, doubly, and unoccupied molecular orbitals, as well as the number of molecular orbitals with energy lower, equal, and higher than -1/2Eh, the negative of the hydrogen atom's ionization energy. The VIF results for water are in qualitative agreement with MP2/6311++G3df3pd, MO energy levels where the simple VIF for water presented in the earlier literature does not agree with computed energy levels. The method presented here gives the simplest accurate VIF pictures for hydrocarbons. It is shown how VIF can be used to predict thermal barriers to chemical reactions. Insertion of singlet carbene into H2 is given as an example. VIF pictures as one-electron density operators describe the ground-state multiplicities of B2, N2, and O2 molecules and as one-electron Hamiltonian operators give the correct electronegativity trend across period two. Previous implementations of VIF do not indicate singly occupied molecular orbitals directly from the pictorial VIF rules for these examples. The direct comparison between structural formulas that represent electron density and those that represent energy is supported by comparison of a simple electronegativity scale, chiD=N/n2, with

  9. Self-Consistent Hybrid Functional Calculations: Implications for Structural, Electronic, and Optical Properties of Oxide Semiconductors

    NASA Astrophysics Data System (ADS)

    Fritsch, Daniel; Morgan, Benjamin J.; Walsh, Aron

    2017-01-01

    The development of new exchange-correlation functionals within density functional theory means that increasingly accurate information is accessible at moderate computational cost. Recently, a newly developed self-consistent hybrid functional has been proposed (Skone et al., Phys. Rev. B 89:195112, 2014), which allows for a reliable and accurate calculation of material properties using a fully ab initio procedure. Here, we apply this new functional to wurtzite ZnO, rutile SnO2, and rocksalt MgO. We present calculated structural, electronic, and optical properties, which we compare to results obtained with the PBE and PBE0 functionals. For all semiconductors considered here, the self-consistent hybrid approach gives improved agreement with experimental structural data relative to the PBE0 hybrid functional for a moderate increase in computational cost, while avoiding the empiricism common to conventional hybrid functionals. The electronic properties are improved for ZnO and MgO, whereas for SnO2 the PBE0 hybrid functional gives the best agreement with experimental data.

  10. CONDENSED MATTER: STRUCTURE, MECHANICAL AND THERMAL PROPERTIES: An Accurate Image Simulation Method for High-Order Laue Zone Effects

    NASA Astrophysics Data System (ADS)

    Cai, Can-Ying; Zeng, Song-Jun; Liu, Hong-Rong; Yang, Qi-Bin

    2008-05-01

    A completely different formulation for simulation of the high order Laue zone (HOLZ) diffractions is derived. It refers to the new method, i.e. the Taylor series (TS) method. To check the validity and accuracy of the TS method, we take polyvinglidene fluoride (PVDF) crystal as an example to calculate the exit wavefunction by the conventional multi-slice (CMS) method and the TS method. The calculated results show that the TS method is much more accurate than the CMS method and is independent of the slice thicknesses. Moreover, the pure first order Laue zone wavefunction by the TS method can reflect the major potential distribution of the first reciprocal plane.

  11. Structural, optical and electronic structure studies of Al doped ZnO thin films

    NASA Astrophysics Data System (ADS)

    Devi, Vanita; Kumar, Manish; Shukla, D. K.; Choudhary, R. J.; Phase, D. M.; Kumar, Ravindra; Joshi, B. C.

    2015-07-01

    Structural, optical and electronic structure of Al doped ZnO thin films grown using pulsed laser deposition on glass substrate are investigated. X-ray diffraction measurements reveal that all the films are textured along the c-axis and have wurtzite structure. Al doping in ZnO films leads to increase in grain size due to relaxation in compressive stress. Enhancement in band gap of ZnO films with the Al doping is also noticed which can be ascribed to the Brustein-Moss shift. The changes in the electronic structure caused by Al in the doped thin film samples are understood through X-ray absorption measurements.

  12. Electronic Structure of Crystalline 4He at High Pressure

    SciTech Connect

    Mao, H.K.; Cai, Y.; Shirley, E.L.; Ding, Y.; Eng, P.; Chow, P.; Xiao, Y.; Shu, J.; Hemley, R.J.; Kao, C.C.; Mao, W.L.

    2010-10-29

    Using inelastic x-ray scattering techniques, we have succeeded in probing the high-pressure electronic structure of helium at 300 K. Helium has the widest known valence-conduction band gap of all materials a property whose high-pressure response has been inaccessible to direct measurements. We observed a rich electron excitation spectrum, including a cutoff edge above 23 eV, a sharp exciton peak showing linear volume dependence, and a series of excitations and continuum at 26 to 45 eV. We determined the electronic dispersion along the {Gamma}-M direction over two Brillouin zones, and provided a quantitative picture of the helium exciton beyond the simplified Wannier-Frenkel description.

  13. Approximate ab initio calculations of electronic structure of amorphous silicon

    NASA Astrophysics Data System (ADS)

    Durandurdu, M.; Drabold, D. A.; Mousseau, N.

    2000-12-01

    We report on ab initio calculations of electronic states of two large and realistic models of amorphous silicon generated using a modified version of the Wooten-Winer-Weaire algorithm and relaxed, in both cases, with a Keating and a modified Stillinger-Weber potentials. The models have no coordination defects and a very narrow bond-angle distribution. We compute the electronic density-of-states and pay particular attention to the nature of the band-tail states around the electronic gap. All models show a large and perfectly clean optical gap and realistic Urbach tails. Based on these results and the extended quasi-one-dimensional stringlike structures observed for certain eigenvalues in the band tails, we postulate that the generation of model a-Si without localized states might be achievable under certain circumstances.

  14. DFT investigation on the electronic structure of Faujasite

    NASA Astrophysics Data System (ADS)

    Popeneciu, Horea; Calborean, Adrian; Tudoran, Cristian; Buimaga-Iarinca, Luiza

    2013-11-01

    We report here first-principle pseudopotential DFT calculations to investigate relevant aspects of the electronic structure of zeolites based FAU. Fundamental molecular issues of the band-gap and electronic population analysis were reviewed under GGA/RPBE level of theory, corroborated with a DZP basis set and Troullier-Martins norm conserving pseudo-potentials. The atom-projected density of states and the analysis of HOMO-LUMO frontier orbitals at Gamma point were performed. Their electronic transfers are discussed through the alignment and relative positions of orbitals in order to determine the way that the molecule interacts with adsorbed molecules and other practical applications. Mulliken population analysis was employed for describing atomic charge distribution in the chosen systems.

  15. Sorting carbon nanotubes by electronic structure using density differentiation.

    PubMed

    Arnold, Michael S; Green, Alexander A; Hulvat, James F; Stupp, Samuel I; Hersam, Mark C

    2006-10-01

    The heterogeneity of as-synthesized single-walled carbon nanotubes (SWNTs) precludes their widespread application in electronics, optics and sensing. We report on the sorting of carbon nanotubes by diameter, bandgap and electronic type using structure-discriminating surfactants to engineer subtle differences in their buoyant densities. Using the scalable technique of density-gradient ultracentrifugation, we have isolated narrow distributions of SWNTs in which >97% are within a 0.02-nm-diameter range. Furthermore, using competing mixtures of surfactants, we have produced bulk quantities of SWNTs of predominantly a single electronic type. These materials were used to fabricate thin-film electrical devices of networked SWNTs characterized by either metallic or semiconducting behaviour.

  16. Electronic structure and energetics of graphene antidot lattice

    NASA Astrophysics Data System (ADS)

    Sakurai, Masahiro; Saito, Susumu; Takada, Yasutami

    2012-02-01

    We have made a systematic study of the electronic structure and the energetics of graphene with periodic array of vacancy clusters (graphene antidot lattice) in the framework of the density-functional theory (DFT). We find that the electronic property of the system is well controlled by its lattice periodicity. More specifically, this system can be either metallic or semiconducting, depending on its lattice geometry. Interestingly, some of them are predicted to be direct-gap semiconductors. For example, graphene sheet with high-symmetry arrangements of periodic circle-shape vacancies always has a direct fundamental gap [1]. The DFT total-energy calculations indicate that the geometry of hole edges plays an important role in determining its stability. [1] ``Electronic properties of graphene and boron-nitride based nanostructured materials'' M. Sakurai, Y. Sakai, and S. Saito, J. Phys.: Conf. Ser. 302 (2011) 012018.

  17. Spatially Resolved Electronic Structures of Atomically Precise Armchair Graphene Nanoribbons

    PubMed Central

    Huang, Han; Wei, Dacheng; Sun, Jiatao; Wong, Swee Liang; Feng, Yuan Ping; Neto, A. H. Castro; Wee, Andrew Thye Shen

    2012-01-01

    Graphene has attracted much interest in both academia and industry. The challenge of making it semiconducting is crucial for applications in electronic devices. A promising approach is to reduce its physical size down to the nanometer scale. Here, we present the surface-assisted bottom-up fabrication of atomically precise armchair graphene nanoribbons (AGNRs) with predefined widths, namely 7-, 14- and 21-AGNRs, on Ag(111) as well as their spatially resolved width-dependent electronic structures. STM/STS measurements reveal their associated electron scattering patterns and the energy gaps over 1 eV. The mechanism to form such AGNRs is addressed based on the observed intermediate products. Our results provide new insights into the local properties of AGNRs, and have implications for the understanding of their electrical properties and potential applications. PMID:23248746

  18. Anomalous electronic structure and magnetoresistance in TaAs2

    PubMed Central

    Luo, Yongkang; McDonald, R. D.; Rosa, P. F. S.; Scott, B.; Wakeham, N.; Ghimire, N. J.; Bauer, E. D.; Thompson, J. D.; Ronning, F.

    2016-01-01

    The change in resistance of a material in a magnetic field reflects its electronic state. In metals with weakly- or non-interacting electrons, the resistance typically increases upon the application of a magnetic field. In contrast, negative magnetoresistance may appear under some circumstances, e.g., in metals with anisotropic Fermi surfaces or with spin-disorder scattering and semimetals with Dirac or Weyl electronic structures. Here we show that the non-magnetic semimetal TaAs2 possesses a very large negative magnetoresistance, with an unknown scattering mechanism. Density functional calculations find that TaAs2 is a new topological semimetal [ℤ2 invariant (0;111)] without Dirac dispersion, demonstrating that a negative magnetoresistance in non-magnetic semimetals cannot be attributed uniquely to the Adler-Bell-Jackiw chiral anomaly of bulk Dirac/Weyl fermions. PMID:27271852

  19. Anomalous electronic structure and magnetoresistance in TaAs2

    DOE PAGES

    Luo, Yongkang; McDonald, R. D.; Rosa, P. F. S.; ...

    2016-01-01

    We report that the change in resistance of a material in a magnetic field reflects its electronic state. In metals with weakly- or non-interacting electrons, the resistance typically increases upon the application of a magnetic field. In contrast, negative magnetoresistance may appear under some circumstances, e.g., in metals with anisotropic Fermi surfaces or with spin-disorder scattering and semimetals with Dirac or Weyl electronic structures. Here we show that the non-magnetic semimetal TaAs2 possesses a very large negative magnetoresistance, with an unknown scattering mechanism. In conclusion, density functional calculations find that TaAs2 is a new topological semimetal [Z2 invariant (0;111)] withoutmore » Dirac dispersion, demonstrating that a negative magnetoresistance in non-magnetic semimetals cannot be attributed uniquely to the Adler-Bell-Jackiw chiral anomaly of bulk Dirac/Weyl fermions.« less

  20. {ELECTRONIC Structure and Spectroscopy of O_2 and O_2^+}

    NASA Astrophysics Data System (ADS)

    Vazquez, Gabriel J.; Lefebvre-Brion, H.; Liebermann, Hans P.

    2014-06-01

    We carried out a comprehensive SCF MRD--CI ab initio study of the electronic structure of O_2 and O_2^+. Potential energy curves (PECs) of about 150 electronic states of O_2 and about 100 of O_2^+, as well as a number of states of O_2++ were computed. The cc--pVQZ basis set augmented with diffuse functions was employed. Spectroscopic parameters (T_e, T_v, ω_e, ω_ex_e, B_e, D_e, D_0, μ, IP, etc.) are reported. A preliminary sample of the results will be presented. The electronic absorption spectrum of O_2 has proved difficult to analyze/interpret due to the unusually large number of electronic states which arise from the peculiar open--shell structure of both the oxygen atomic fragments and the O_2 molecule. For instance, there are 62 valence molecular electronic states which correlate to the six lowest dissociation limits resulting from the three valence O atom fragment states (^3P, ^1D, ^1S). In addition, there are several nlλ Rydberg series converging to the X^2Π_g ground ionic state and to the lowest two excited states of the cation, a^4Π_u_i and A^2Π_u. Furthermore, a number of interactions of various types among several electronic states result in rovibronic perturbations which manifest themselves, e.g., as irregular vibronic structure, hence severely complicating the assignment of the absorption features and the analysis and interpretation of the spectrum. An overview of the electronic states and spectroscopy of O_2 will be presented. A chief motivation of this study of O_2 was to try to provide a theoretical insight on the nature, energetic position, shape, and dissociation asymptotes, of electronic states located in the 4 eV energy region encompassed between the O_2^+ ground state X^2Π_g (IP=12.07 eV) and the first excited state of the cation a^4Π_u_i (IP=16.10 eV). This in order to aid in the interpretation of experimental data related to the mechanism(s) of the neutral dissociation of the O_2** (Rydberg) superexcited states, which competes with

  1. Electronic Structure Calculations for Heavy Elements: Radon (Z=86) and Francium (Z=87)

    NASA Astrophysics Data System (ADS)

    Koufos, Alexander; Papaconstantopoulos, Dimitrios

    2010-03-01

    Electronic structure calculations allow scientists to predict the properties of solids without the use of physical material. Although the ability to manipulate matter has improved dramatically within the past couple decades, some matter is still hard to study. Modern computers not only let us study this matter, but allow us to do it more quickly and just as accurately. The electronic structure of two rare and mostly unstudied elements, Radon (Z=86) and Francium (Z=87), has been calculated. The augmented plane wave (APW) method with local density approximation (LDA) functional as well as the linearized augmented plane wave (LAPW) method with both LDA and generalized gradient approximation (GGA) functionals were used to perform the calculations. Francium total energy calculations gave the fcc structure slightly below the bcc structure with a minimal energy difference of δE=0.33mRy. The difference found is consistent with other alkali metal total energy calculations which do not verify the bcc structure to be the ground state. Radon was predicted to be an insulator with a gap of 0.931 Ry similar to the other noble gases.

  2. The dynamics of zinc sites in proteins: electronic basis for coordination sphere expansion at structural sites.

    PubMed

    Daniel, A Gerard; Farrell, Nicholas P

    2014-12-01

    The functional role assumed by zinc in proteins is closely tied to the variable dynamics around its coordination sphere arising by virtue of its flexibility in bonding. Modern experimental and computational methods allow the detection and study of previously unknown features of bonding between zinc and its ligands in protein environment. These discoveries are occurring just in time as novel biological functions of zinc, which involve rather unconventional coordination trends, are emerging. In this sense coordination sphere expansion of structural zinc sites, as observed in our previous experiments, is a novel phenomenon. Here we explore the electronic and structural requirements by simulating this phenomenon in structural zinc sites using DFT computations. For this purpose, we have chosen MPW1PW91 and a mixed basis set combination as the DFT method through benchmarking, because it accurately reproduces structural parameters of experimentally characterized zinc compounds. Using appropriate models, we show that the greater ionic character of zinc coordination would allow for coordination sphere expansion if the steric and electrostatic repulsions of the ligands are attenuated properly. Importantly, through the study of electronic and structural aspects of the models used, we arrive at a comprehensive bonding model, explaining the factors that influence coordination of zinc in proteins. The proposed model along with the existing knowledge would enhance our ability to predict zinc binding sites in proteins, which is today of growing importance given the predicted enormity of the zinc proteome.

  3. Electronic structures and optical properties of TiO2: Improved density-functional-theory investigation

    NASA Astrophysics Data System (ADS)

    Gong, Sai; Liu, Bang-Gui

    2012-05-01

    TiO2 has been recently used to realize high-temperature ferromagnetic semiconductors. In fact, it has been widely used for a long time as white pigment and sunscreen because of its whiteness, high refractive index, and excellent optical properties. However, its electronic structures and the related properties have not been satisfactorily understood. Here, we use Tran and Blaha's modified Becke-Johnson (TB-mBJ) exchange potential (plus a local density approximation correlation potential) within the density functional theory to investigate electronic structures and optical properties of rutile and anatase TiO2. Our comparative calculations show that the energy gaps obtained from mBJ method agree better with the experimental results than that obtained from local density approximation (LDA) and generalized gradient approximation (GGA), in contrast with substantially overestimated values from many-body perturbation (GW) calculations. As for optical dielectric functions (both real and imaginary parts), refractive index, and extinction coefficients as functions of photon energy, our mBJ calculated results are in excellent agreement with the experimental curves. Our further analysis reveals that these excellent improvements are achieved because mBJ potential describes accurately the energy levels of Ti 3d states. These results should be helpful to understand the high temperature ferromagnetism in doped TiO2. This approach can be used as a standard to understand electronic structures and the related properties of such materials as TiO2.

  4. Quantum mirages formed by coherent projection of electronic structure

    PubMed

    Manoharan; Lutz; Eigler

    2000-02-03

    Image projection relies on classical wave mechanics and the use of natural or engineered structures such as lenses or resonant cavities. Well-known examples include the bending of light to create mirages in the atmosphere, and the focusing of sound by whispering galleries. However, the observation of analogous phenomena in condensed matter systems is a more recent development, facilitated by advances in nanofabrication. Here we report the projection of the electronic structure surrounding a magnetic Co atom to a remote location on the surface of a Cu crystal; electron partial waves scattered from the real Co atom are coherently refocused to form a spectral image or 'quantum mirage'. The focusing device is an elliptical quantum corral, assembled on the Cu surface. The corral acts as a quantum mechanical resonator, while the two-dimensional Cu surface-state electrons form the projection medium. When placed on the surface, Co atoms display a distinctive spectroscopic signature, known as the many-particle Kondo resonance, which arises from their magnetic moment. By positioning a Co atom at one focus of the ellipse, we detect a strong Kondo signature not only at the atom, but also at the empty focus. This behaviour contrasts with the usual spatially-decreasing response of an electron gas to a localized perturbation.

  5. Electronic absorption and ground state structure of carotenoid molecules.

    PubMed

    Mendes-Pinto, Maria M; Sansiaume, Elodie; Hashimoto, Hideki; Pascal, Andrew A; Gall, Andrew; Robert, Bruno

    2013-09-26

    Predicting the complete electronic structure of carotenoid molecules remains an extremely complex problem, particularly in anisotropic media such as proteins. In this paper, we address the electronic properties of nine relatively simple carotenoids by the combined use of electronic absorption and resonance Raman spectroscopies. Linear carotenoids exhibit an excellent correlation between (i) the inverse of their conjugation chain length N, (ii) the energy of their S0 → S2 electronic transition, and (iii) the position of their ν1 Raman band (corresponding to the stretching mode of their conjugated C═C bonds). For cyclic carotenoids such as β-carotene, this correlation is also observed between the latter two parameters (S0 → S2 energy and ν1 frequency), whereas their "nominal" conjugation length N does not follow the same relationship. We conclude that β-carotene and cyclic carotenoids in general exhibit a shorter effective conjugation length than that expected from their chemical structure. In addition, the effect of solvent polarizability on these molecular parameters was investigated for four of the carotenoids used in this study. We demonstrate that resonance Raman spectroscopy can discriminate between the different effects underlying shifts in the S0 → S2 transition of carotenoid molecules.

  6. Electronic Structure of Silicon Nanowires Matrix from Ab Initio Calculations

    NASA Astrophysics Data System (ADS)

    Monastyrskii, Liubomyr S.; Boyko, Yaroslav V.; Sokolovskii, Bogdan S.; Potashnyk, Vasylyna Ya.

    2016-01-01

    An investigation of the model of porous silicon in the form of periodic set of silicon nanowires has been carried out. The electronic energy structure was studied using a first-principle band method—the method of pseudopotentials (ultrasoft potentials in the basis of plane waves) and linearized mode of the method of combined pseudopotentials. Due to the use of hybrid exchange-correlation potentials (B3LYP), the quantitative agreement of the calculated value of band gap in the bulk material with experimental data is achieved. The obtained results show that passivation of dangling bonds with hydrogen atoms leads to substantial transformation of electronic energy structure. At complete passivation of the dangling silicon bonds by hydrogen atoms, the band gap value takes the magnitude which substantially exceeds that for bulk silicon. The incomplete passivation gives rise to opposite effect when the band gap value decreases down the semimetallic range.

  7. Strongly correlated electron materials. I. Theory of the quasiparticle structure

    SciTech Connect

    Lopez-Aguilar, F.; Costa-Quintana, J.; Puig-Puig, L. )

    1993-07-01

    In this paper we give a method for analyzing the renormalized electronic structure of the Hubbard systems. The first step is the determination of effective interactions from the random-phase approximation (RPA) and from an extended RPA (ERPA) that introduces vertex effects within the bubble polarization. The second step is the determination of the density of states deduced from the spectral functions. Its analysis leads us to conclude that these systems can exhibit three types of resonances in their electronic structures: the lower-, middle-, and upper-energy resonances. Furthermore, we analyze the conditions for which there is only one type of resonance and the causes that lead to the disappearance of the heavy-fermion state. We finally introduce the RPA and ERPA effective interactions within the strong-coupling theory and we give the conditions for obtaining coupling and superconductivity.

  8. Electronic structure of Gd-doped MgO

    NASA Astrophysics Data System (ADS)

    Lukoyanov, A. V.; Anisimov, V. I.

    2016-02-01

    The electronic structure of Gd-doped MgO is investigated using the LSDA+U (local spin density approximation with U-correction) method and compared with the MgO structure. The total density of states obtained accounting for the correlation effects in the 4 f shell of gadolinium is found to be formed by the oxygen 2 p states at the valence band and the 4 f gadolinium occupied states, while the conduction band is represented by a mixture of empty electronic states. Magnetic properties of the calculated Gd-doped MgO are found to be formed solely by the Gd-4 f-magnetic moment of about 7μB, in good agreement with recent experimental results suggesting a ferromagnetic coupling of the local magnetic moments induced by Gd.

  9. Atomic and electronic structure of Ni-Nb metallic glasses

    SciTech Connect

    Yuan, C. C.; Yang, Y.-F. Xi, X. K.

    2013-12-07

    Solid state {sup 93}Nb nuclear magnetic resonance spectroscopy has been employed to investigate the atomic and electronic structures in Ni-Nb based metallic glass (MG) model system. {sup 93}Nb nuclear magnetic resonance (NMR) isotropic metallic shift of Ni{sub 60}Nb{sub 35}Sn{sub 5} has been found to be ∼100 ppm lower than that of Ni{sub 60}Nb{sub 35}Zr{sub 5} MG, which is correlated with their intrinsic fracture toughness. The evolution of {sup 93}Nb NMR isotropic metallic shifts upon alloying is clearly an electronic origin, as revealed by both local hyperfine fields analysis and first-principle computations. This preliminary result indicates that, in addition to geometrical considerations, atomic form factors should be taken into a description of atomic structures for better understanding the mechanical behaviors of MGs.

  10. Structural and electronic properties of arsenic nitrogen monolayer

    NASA Astrophysics Data System (ADS)

    Liu, Pei; Nie, Yao-zhuang; Xia, Qing-lin; Guo, Guang-hua

    2017-03-01

    We present our first-principles calculations of a new two-dimensional material, arsenic nitrogen monolayer. The structural, electronic, and mechanical properties are investigated in detail by means of density functional theory computations. The calculated binding energy and the phonon spectra demonstrate that the AsN can form stable monolayer in puckered honeycomb structure. It is a semiconductor with indirect band gap of 0.73 eV, and displays highly anisotropic mechanical properties. Strain has obvious influence on the electronic properties of AsN monolayer. It is found that in the armchair direction, a moderate compression strain (-12%) can trigger an indirect to direct band gap transition and a tensile strain of 18% can make the AsN becoming a stable metal. In the zigzag direction, a rather smaller strain than armchair direction (12% for compression and 8% for stretch) can induce the indirect band gap to metal transition.

  11. Electronic structure of polyimide and related monomers: Theory and experiment

    NASA Astrophysics Data System (ADS)

    Kowalczyk, Steven P.; Stafström, Sven; Brédas, J. L.; Salaneck, William R.; Jordan-Sweet, Jean L.

    1990-01-01

    The electronic structure of polymide and several related compounds was investigated theoretically and experimentally. The compounds include pyromellitic dianhydride, oxydianiline, and polyamic acid. Experimental electronic-structure determinations for poly(methyl phenylene oxide) and poly(vinyl methyl ketone) are also reported. The theoretical approach employed valence-effective-Hamiltonian calculations. Photoelectron spectroscopy (x-ray photoelectron spectroscopy, soft-x-ray photoelectron spectroscopy, and ultraviolet photoelectron spectroscopy) was used to experimentally measure the total valence-band density of states (VBDOS) from thin films of the above compounds. The theoretical VBDOS's were cross-section modulated to facilitate comparison with experiment. Very good agreement is found between the theoretical results and the experimental VBDOS's.

  12. Electronic structure of spontaneously strained graphene on hexagonal boron nitride

    NASA Astrophysics Data System (ADS)

    San-Jose, Pablo; Gutiérrez-Rubio, A.; Sturla, Mauricio; Guinea, Francisco

    2014-09-01

    Hexagonal boron nitride substrates have been shown to dramatically improve the electric properties of graphene. Recently, it has been observed that when the two honeycomb crystals are close to perfect alignment, strong lattice distortions develop in graphene due to the moiré adhesion landscape. Simultaneously, a gap opens at the Dirac point. Here, we derive a simple low-energy electronic model for graphene aligned with the substrate, taking into account spontaneous strains at equilibrium and pseudogauge fields. We carry out a detailed characterization of the modified band structure, gap, local and global density of states, and band topology in terms of physical parameters. We show that the overall electronic structure is strongly modified by the spontaneous strains.

  13. Electronic Structure Rearrangements in Hybrid Ribozyme/Protein Catalysis

    NASA Astrophysics Data System (ADS)

    Kang, Jiyoung; Kino, Hiori; Field, Martin J.; Tateno, Masaru

    2017-04-01

    We analyzed the electronic structural changes that occur in the reaction cycle of a biological catalyst composed of RNA and protein, and elucidated the dynamical rearrangements of the electronic structure that was obtained from our previous study in which ab initio quantum mechanics/molecular mechanics molecular dynamics simulations were performed. Notable results that we obtained include the generation of a reactive HOMO that is responsible for bond formation in the initial stages of the reaction, and the appearance of a reactive LUMO that is involved in the bond rupture that leads to products. We denote these changes as dynamical induction of the reactive HOMO (DIRH) and LUMO (DIRL), respectively. Interestingly, we also find that the induction of the reactive HOMO is enhanced by the formation of a low-barrier hydrogen bond (LBHB), which, to the best of our knowledge, represents a novel role for LBHBs in enzymatic systems.

  14. Electronic Structure of Silicon Nanowires Matrix from Ab Initio Calculations.

    PubMed

    Monastyrskii, Liubomyr S; Boyko, Yaroslav V; Sokolovskii, Bogdan S; Potashnyk, Vasylyna Ya

    2016-12-01

    An investigation of the model of porous silicon in the form of periodic set of silicon nanowires has been carried out. The electronic energy structure was studied using a first-principle band method-the method of pseudopotentials (ultrasoft potentials in the basis of plane waves) and linearized mode of the method of combined pseudopotentials. Due to the use of hybrid exchange-correlation potentials (B3LYP), the quantitative agreement of the calculated value of band gap in the bulk material with experimental data is achieved. The obtained results show that passivation of dangling bonds with hydrogen atoms leads to substantial transformation of electronic energy structure. At complete passivation of the dangling silicon bonds by hydrogen atoms, the band gap value takes the magnitude which substantially exceeds that for bulk silicon. The incomplete passivation gives rise to opposite effect when the band gap value decreases down the semimetallic range.

  15. On the Electronic Structure of Cocaine and its Metabolites

    NASA Astrophysics Data System (ADS)

    Rincón, David A.; Dias Soeiro Cordeiro, Maria Natália; Mosquera, Ricardo A.

    2009-11-01

    This work aims at describing the electronic features of cocaine and how they are modified by the different substituents present in its metabolites. The QTAIM analysis of B3LYP and MP2 electron densities obtained with the 6-311++G** 6d basis set for cocaine and its principal metabolites indicates: (i) its positive charge is shared among the amino hydrogen, those of the methylamino group, and all of the hydrogens attached to the bicycle structure; (ii) the zwitterionic structure of benzoylecgonine can be described as two partial charges of 0.63 au, the negative one shared by the oxygens of the carboxylate group, whereas the positive charge is distributed among all the hydrogens that bear the positive charge in cocaine; (iii) its hydrogen bond is strengthened in the derivatives without benzoyloxy group and is also slightly strengthened as the size of the alkyl ester group at position 2 increases.

  16. Electronic structure of polymeric KC 60 - a crystal orbital analysis

    NASA Astrophysics Data System (ADS)

    Schulte, Joachim; Böhm, Michael C.

    1996-04-01

    The band structure of orthorhombic KC 60 is investigated by a crystal approach based on an intermediate neglect of differential orbital Hamiltonian. The title compound crystallizes in the space group Pnnm with covalent intermolecular carboncarbon bonds. Polymeric KC 60 is a metal with a low electronic density of states (DOS) at the Fermi energy ɛF. This metallic behaviour differs from the electronic ground state calculated for isotropic fcc KC 60 with potassium occupying the octahedral intersitial site. The reduced width of the conduction band in the fcc structure favours an insulating Mott state relative to the metallic configuration. The dimensionality of the title compound is discussed on the basis of intercell energies, the DOS profile and dispersion curves. The theoretical results are compared with experimental observations. Wiberg bond-indices are employed to describe the chemical bonding within the distorted C 60 soccerball.

  17. Molecular structures of porphyrin-quinone models for electron transfer

    SciTech Connect

    Fajer, J.; Barkigia, K.M.; Melamed, D.; Sweet, R.M.; Kurreck, H.; Gersdorff, J. von; Plato, M.; Rohland, H.C.; Elger, G.; Moebius, K.

    1996-08-15

    Synthetic porphyrin-quinone complexes are commonly used to mimic electron transport in photosynthetic reaction centers and to probe the effects of energetics, distances, and relative orientations on rates of electron transfer between donor-acceptor couples. The structures of two such models have been determined by X-ray diffraction. The redox pairs consist of a zinc porphyrin covalently linked to benzoquinone in cis and trans configurations via a cyclohexanediyl bridge. The crystallographic studies were undertaken to provide a structural foundation for the extensive body of experimental and theoretical results that exists for these compounds in both the ground and photoinduced charge-separated states. The results validate conclusions reached from theoretical calculations, EPR and two-dimensional NMR results for these states. 15 refs., 6 figs., 2 tabs.

  18. Crystallization of germanium-carbon alloys -- Structure and electronic transport

    SciTech Connect

    John, T.M.; Blaesing, J.; Veit, P.; Druesedau, T.

    1997-07-01

    Amorphous Ge{sub 1{minus}x}C{sub x} alloys were deposited by rf-magnetron sputtering from a germanium target in methane-argon atmosphere. Structural investigations were performed by means of wide and small angle X-ray scattering, X-ray reflectometry and cross-sectional transmission electron microscopy. The electronic transport properties were characterized using Hall-measurements and temperature depended conductivity. The results of X-ray techniques together with the electron microscopy clearly prove the existence of a segregation of the electronic conductivity in the as-prepared films follows the Mott' T{sup {minus}1/4} law, indicating transport by a hopping process. After annealing at 870 K, samples with x {le} 0.4 show crystallization of the Ge-clusters with a crystallite size being a function of x. After Ge-crystallization, the conductivity increases by 4 to 5 orders of magnitude. Above room temperature, electronic transport is determined by a thermally activated process. For lower temperatures, the {sigma}(T) curves show a behavior which is determined by the crystallite size and the free carrier concentration, both depending on the carbon content.

  19. Electronic structure and shearing in nanolaminated ternary carbides

    NASA Astrophysics Data System (ADS)

    Music, Denis; Sun, Zhimei; Voevodin, Andrey A.; Schneider, Jochen M.

    2006-07-01

    We have studied shearing in M 2AlC phases (M=Sc,Y,La,Ti,Zr,Hf,V,Nb,Ta,Cr,Mo,W) using ab initio calculations. We propose that these phases can be classified into two groups based on the valence electron concentration induced changes in C 44. One group comprises M=V B and VIB, where the C 44 values are approximately 170 GPa and independent of the corresponding MC. The other group includes M=IIIB and IVB, where the C 44 shows a linear dependency with the corresponding MC. This may be understood based on the electronic structure: shear resistant bands are filled in M 2AlC phases with M=V B and VIB, while they are not completely filled when M=IIIB and IVB. This notion is also consistent with our stress-strain analysis. These valence electron concentration induced changes in shear behaviour were compared to previously published valence electron concentration induced changes in compression behaviour [Z. Sun, D. Music, R. Ahuja, S. Li, J.M. Schneider, Phys. Rev. B 70 (2004) 092102]. These classification proposals exhibit identical critical valence electron concentration values for the group boundary. However, the physical mechanisms are not identical: the classification proposal for the bulk modulus is based on MC-A coupling, while shearing is based on MC-MC coupling.

  20. Atomic structures and electronic properties of phosphorene grain boundaries

    NASA Astrophysics Data System (ADS)

    Guo, Yu; Zhou, Si; Zhang, Junfeng; Bai, Yizhen; Zhao, Jijun

    2016-06-01

    Grain boundary (GB) is one main type of defects in two-dimensional (2D) crystals, and has significant impact on the physical properties of 2D materials. Phosphorene, a recently synthesized 2D semiconductor, possesses a puckered honeycomb lattice and outstanding electronic properties. It is very interesting to know the possible GBs present in this novel material, and how their properties differ from those in the other 2D materials. Based on first-principles calculations, we explore the atomic structure, thermodynamic stability, and electronic properties of phosphorene GBs. A total of 19 GBs are predicted and found to be energetically stable with formation energies much lower than those in graphene. These GBs do not severely affect the electronic properties of phosphorene: the band gap of perfect phosphorene is preserved, and the electron mobilities are only moderately reduced in these defective systems. Our theoretical results provide vital guidance for experimental tailoring the electronic properties of phosphorene as well as the device applications using phosphorene materials.

  1. Electronic structure and superconductivity of FeSe-related superconductors.

    PubMed

    Liu, Xu; Zhao, Lin; He, Shaolong; He, Junfeng; Liu, Defa; Mou, Daixiang; Shen, Bing; Hu, Yong; Huang, Jianwei; Zhou, X J

    2015-05-13

    FeSe superconductors and their related systems have attracted much attention in the study of iron-based superconductors owing to their simple crystal structure and peculiar electronic and physical properties. The bulk FeSe superconductor has a superconducting transition temperature (Tc) of ~8 K and it can be dramatically enhanced to 37 K at high pressure. On the other hand, its cousin system, FeTe, possesses a unique antiferromagnetic ground state but is non-superconducting. Substitution of Se with Te in the FeSe superconductor results in an enhancement of Tc up to 14.5 K and superconductivity can persist over a large composition range in the Fe(Se,Te) system. Intercalation of the FeSe superconductor leads to the discovery of the AxFe2-ySe2 (A = K, Cs and Tl) system that exhibits a Tc higher than 30 K and a unique electronic structure of the superconducting phase. A recent report of possible high temperature superconductivity in single-layer FeSe/SrTiO3 films with a Tc above 65 K has generated much excitement in the community. This pioneering work opens a door for interface superconductivity to explore for high Tc superconductors. The distinct electronic structure and superconducting gap, layer-dependent behavior and insulator-superconductor transition of the FeSe/SrTiO3 films provide critical information in understanding the superconductivity mechanism of iron-based superconductors. In this paper, we present a brief review of the investigation of the electronic structure and superconductivity of the FeSe superconductor and related systems, with a particular focus on the FeSe films.

  2. The valence electronic structure and conformational flexibility of epichlorohydrin.

    PubMed

    Stranges, S; Alagia, M; Decleva, P; Stener, M; Fronzoni, G; Toffoli, D; Speranza, M; Catone, D; Turchini, S; Prosperi, T; Zema, N; Contini, G; Keheyan, Y

    2011-07-21

    The electronic structure of epichlorohydrin is investigated in the whole valence region by a combined experimental and theoretical study. The issue of controversial assignments of the molecular electronic structure is here addressed. Photoelectron spectra (PES) and Threshold Photoelectron spectra (TPES) of room temperature molecules in the gas phase are recorded. Geometries and energies of the stable conformers due to internal rotation of the C-C-C-Cl dihedral angle, gauche-II (g-II), gauche-I (g-I), and cis, are calculated, and the effect of the conformational flexibility on the photoionization energetics is studied by DFT and 2h-1p Configuration Interaction (CI) methods. Strong breakdown of the Koopmans Theorem (KT) is obtained for the four outermost ionizations, which are further investigated by higher level ab initio calculations. The full assignment of the spectrum is put on a firm basis by the combination of experimental and theoretical results. The orbital composition from correlated calculations is found closer to the DFT orbitals, which are then used to analyze the electronic structure of the molecule. The Highest Occupied Molecular Orbital (HOMO) and HOMO--2 are n(O)/n(Cl) mixed orbitals. The nature of each valence MO is generally preserved in all the conformers, although the magnitude of the n(O)/n(Cl) mixing in HOMO and HOMO--2 varies to some extent with the C-C-C-Cl dihedral angle. The low energy part of the HOMO PE band is predicted to be substantially affected by the conformational flexibility, as experimentally observed in the spectra. The rest of the spectrum is described in terms of the dominant conformer g-II, and a good agreement between experiment and theory is found. The inner-valence PE spectrum is characterized by satellite structures, due to electron correlation effects, which are interpreted by means of 2h-1p CI calculations.

  3. Final Technical Report: Electronic Structure Workshop (ES13)

    SciTech Connect

    Zhang, Shiwei

    2015-02-26

    The 25th Annual Workshop on Recent Developments in Electronic Structure Methods (ES2013) was successfully held at the College of William & Mary in Williamsburg VA on June 11-14, 2013. The workshop website is at http://es13.wm.edu/ , which contains updated information on the workshop and a permanent archive of the scientific contents. DOE's continued support has been instrumental to the success of the workshop.

  4. Electronic and chemical structure of metal-silicon interfaces

    NASA Technical Reports Server (NTRS)

    Grunthaner, P. J.; Grunthaner, F. J.

    1984-01-01

    This paper reviews our current understanding of the near-noble metal silicides and the interfaces formed with Si(100). Using X-ray photoemission spectroscopy, we compare the chemical composition and electronic structure of the room temperature metal-silicon and reacted silicide-silicon interfaces. The relationship between the interfacial chemistry and the Schottky barrier heights for this class of metals on silicon is explored.

  5. Structured electron beams from nano-engineered cathodes

    NASA Astrophysics Data System (ADS)

    Lueangaramwong, A.; Mihalcea, D.; Andonian, G.; Piot, P.

    2017-03-01

    The ability to engineer cathodes at the nano-scale have opened new possibilities such as enhancing quantum efficiency via surface-plasmon excitation, forming ultra-low-emittance beams, or producing structured electron beams. In this paper, we present numerical investigations of the beam dynamics associated with this class of cathode in the weak- and strong-field regimes. We finally discuss the possible applications of some of the achievable cathode patterns when coupled with other phase space manipulations.

  6. PSSP-RFE: accurate prediction of protein structural class by recursive feature extraction from PSI-BLAST profile, physical-chemical property and functional annotations.

    PubMed

    Li, Liqi; Cui, Xiang; Yu, Sanjiu; Zhang, Yuan; Luo, Zhong; Yang, Hua; Zhou, Yue; Zheng, Xiaoqi

    2014-01-01

    Protein structure prediction is critical to functional annotation of the massively accumulated biological sequences, which prompts an imperative need for the development of high-throughput technologies. As a first and key step in protein structure prediction, protein structural class prediction becomes an increasingly challenging task. Amongst most homological-based approaches, the accuracies of protein structural class prediction are sufficiently high for high similarity datasets, but still far from being satisfactory for low similarity datasets, i.e., below 40% in pairwise sequence similarity. Therefore, we present a novel method for accurate and reliable protein structural class prediction for both high and low similarity datasets. This method is based on Support Vector Machine (SVM) in conjunction with integrated features from position-specific score matrix (PSSM), PROFEAT and Gene Ontology (GO). A feature selection approach, SVM-RFE, is also used to rank the integrated feature vectors through recursively removing the feature with the lowest ranking score. The definitive top features selected by SVM-RFE are input into the SVM engines to predict the structural class of a query protein. To validate our method, jackknife tests were applied to seven widely used benchmark datasets, reaching overall accuracies between 84.61% and 99.79%, which are significantly higher than those achieved by state-of-the-art tools. These results suggest that our method could serve as an accurate and cost-effective alternative to existing methods in protein structural classification, especially for low similarity datasets.

  7. DFTB Parameters for the Periodic Table: Part 1, Electronic Structure.

    PubMed

    Wahiduzzaman, Mohammad; Oliveira, Augusto F; Philipsen, Pier; Zhechkov, Lyuben; van Lenthe, Erik; Witek, Henryk A; Heine, Thomas

    2013-09-10

    A parametrization scheme for the electronic part of the density-functional based tight-binding (DFTB) method that covers the periodic table is presented. A semiautomatic parametrization scheme has been developed that uses Kohn-Sham energies and band structure curvatures of real and fictitious homoatomic crystal structures as reference data. A confinement potential is used to tighten the Kohn-Sham orbitals, which includes two free parameters that are used to optimize the performance of the method. The method is tested on more than 100 systems and shows excellent overall performance.

  8. Mechanical Deformation and Electronic Structure of Carbon Nanotorus

    NASA Astrophysics Data System (ADS)

    Liu, Lei; Wu, Shi-Yu; Jayanthi, Chakram

    2000-03-01

    The mechanical deformation and the electronic structure of carbon nanotorus of various radii are studied using an order(N) non-orthogonal tight-binding molecular dynamics[1] at finite temperature. The onset of the development of kinks in the torus is investigated as a function of radius. The defect structures associated with the kinks are analyzed in terms of local bonding configurations and the bond charge between pairs of atoms. [1] C.S. Jayanthi, S.Y. Wu, J. Cocks, N.S. Luo, Z.L. Xie, M.Menon, and G. Yang, Phys. Rev. B57, 3799 (1998).

  9. Electronic structure of icosahedral cobalt-sulfur clusters

    SciTech Connect

    Hoffman, G.G.; Bashkin, J.K.; Karplus, M. )

    1990-11-21

    This paper uses the multiple scattering (MS)-X{alpha} method to calculate the electronic structure of several clusters that contain an octahedral Co{sub 8}S{sub 6} core. Two of the cluster are analogous to compounds that have been previously synthesized, and the results of these calculations are consistent with the experimentally observed spin states, absorption spectra, and structural similarity of these compounds. These clusters are of particular interest because they are related to the component structures of the mineral cobalt pentlandite. To obtain information that can be extended to cobalt pentlandite, the effects of oxidation state and added ligands to the core structure of the clusters are studied. An extended Hueckel theory (EHT) study of similar clusters has been performed by Burdett and Miller. The spectra from the two types of calculations correspond in general and the central conclusions of Burdett and Miller are supported by the MS-X{alpha} results.

  10. Potassium under pressure: Electronic origin of complex structures

    NASA Astrophysics Data System (ADS)

    Degtyareva, V. F.

    2014-10-01

    Recent high-pressure X-ray diffraction studies of alkali metals revealed unusual complex structures that follow the body-centred and face-centred cubic structures on compression. The structural sequence of potassium under compression to 1 Mbar is as follows: bcc-fcc-h-g (tI19*), hP4-oP8-tI4-oC16. We consider configurations of Brillouin-Jones zones and the Fermi surface within a nearly-free-electron model in order to analyze the importance of these configurations for the crystal structure stability. Formation of Brillouin zone planes close to the Fermi surface is related to opening an energy gap at these planes and reduction of crystal energy. Under pressure, this mechanism becomes more important leading to appearance of complex low-symmetry structures. The stability of the post-fcc phases in K is attributed to the changes in the valence electron configuration under strong compression.

  11. Electronic band structure of TiN/MgO nanostructures

    NASA Astrophysics Data System (ADS)

    Kobayashi, Kazuaki; Takaki, Hirokazu; Shimono, Masato; Kobayashi, Nobuhiko; Hirose, Kenji

    2017-04-01

    Various nanostructured TiN(001)/MgO(001) superlattices based on a repeated slab model with a vacuum region have been investigated by the total energy pseudopotential method. They are rectangular and rectangular parallelepiped TiN(001) dot structures on MgO(001)-2×2 and 3×3 substrates. A rectangular TiN(001) structure on a MgO(001)-2×1 substrate has also been calculated. Their detailed electronic and internal lattice properties were investigated systematically. The internal atomic coordinates in a unit cell were fully relaxed. The rectangular TiN(001) structure on the MgO(001)-2×1 superlattice, which is not a dot owing to its periodicity, corresponds to metallicity. The electronic states of relaxed rectangular TiN(001) dot/MgO(001)-2×2 and MgO(001)-3×3 superlattices are semiconducting. All relaxed rectangular parallelepiped TiN(001) dot/MgO(001)-2×2 and MgO(001)-3×3 superlattices correspond to metallicity. The electronic properties depend on the shape of the TiN dot and the size of the MgO substrate.

  12. Structural basis of interprotein electron transfer in bacterial sulfite oxidation

    PubMed Central

    McGrath, Aaron P; Laming, Elise L; Casas Garcia, G Patricia; Kvansakul, Marc; Guss, J Mitchell; Trewhella, Jill; Calmes, Benoit; Bernhardt, Paul V; Kappler, Ulrike; Maher, Megan J

    2015-01-01

    Interprotein electron transfer underpins the essential processes of life and relies on the formation of specific, yet transient protein-protein interactions. In biological systems, the detoxification of sulfite is catalyzed by the sulfite-oxidizing enzymes (SOEs), which interact with an electron acceptor for catalytic turnover. Here, we report the structural and functional analyses of the SOE SorT from Sinorhizobium meliloti and its cognate electron acceptor SorU. Kinetic and thermodynamic analyses of the SorT/SorU interaction show the complex is dynamic in solution, and that the proteins interact with Kd = 13.5 ± 0.8 μM. The crystal structures of the oxidized SorT and SorU, both in isolation and in complex, reveal the interface to be remarkably electrostatic, with an unusually large number of direct hydrogen bonding interactions. The assembly of the complex is accompanied by an adjustment in the structure of SorU, and conformational sampling provides a mechanism for dissociation of the SorT/SorU assembly. DOI: http://dx.doi.org/10.7554/eLife.09066.001 PMID:26687009

  13. Optoelectronic properties and electronic structure of YCuOSe

    NASA Astrophysics Data System (ADS)

    Ueda, Kazushige; Takafuji, Kouhei; Yanagi, Hiroshi; Kamiya, Toshio; Hosono, Hideo; Hiramatsu, Hidenori; Hirano, Masahiro; Hamada, Noriaki

    2007-12-01

    YCuOSe was prepared by solid-state reaction, and its wide gap semiconducting properties were examined. The single phase of YCuOSe was obtained in a limited temperature range around 750°C and decomposed into Y2O2Se and Cu2Se at higher temperatures. The obtained YCuOSe sample showed a p-type semiconducting behavior with the electrical conductivity of 1.4×10-1Scm-1 at room temperature. The band gap of YCuOSe was estimated to be 2.58eV, which is much smaller than that of LaCuOSe (2.82eV). The electronic structure of YCuOSe was investigated by ultraviolet photoemission spectroscopy and energy band calculations to understand the differences in the electronic structures between LnCuOSe (Ln=La,Y). It was found that the Cu-Cu distance rather than the Cu-Se distance influences the electronic structures, and the smaller band gap of YCuOSe is attributed to the downshift of the Cu 4s energy level due to the smaller Cu-Cu distance and the consequent larger Cu-Cu interaction in YCuOSe.

  14. Electronic structure of ternary rhodium hydrides with lithium and magnesium.

    PubMed

    Becker, Jonas Nils; Bauer, Jessica; Giehr, Andreas; Chu, Pui Ieng; Kunkel, Nathalie; Springborg, Michael; Kohlmann, Holger

    2014-01-21

    Chemical bonding in and electronic structure of lithium and magnesium rhodium hydrides are studied theoretically using DFT methods. For Li3RhH4 with planar complex RhH4 structural units, Crystal Orbital Hamilton Populations reveal significant Rh−Rh interactions within infinite one-dimensional ∞ 1 [RhH4] stacks in addition to strong rhodium−hydrogen bonding. These metal−metal interactions are considerably weaker in the hypothetical, heavier homologue Na3RhH4. Both compounds are small-band gap semiconductors. The electronic structures of Li3RhH6 and Na3RhH6 with rhodium surrounded octahedrally by hydrogen, on the other hand, are compatible with a classical complex hydride model according to the limiting ionic formula (M+)3[RhH6]3− without any metal−metal interaction between the 18-electron hydridorhodate complexes. In MgRhH, building blocks of the composition (RhH2)4 are formed with strong rhodium−hydrogen and significant rhodium−rhodium bonding (bond lengths of 298 pm within Rh4 squares). These units are linked together to infinite two-dimensional layers ∞ 2 [(RhH2/2)4] via common hydrogen atoms. Li3RhH4 and MgRhH are accordingly examples for border cases of chemical bonding where the classical picture of hydridometalate complexes in complex hydrides is not sufficient to properly describe the chemical bonding situation.

  15. Transmission electron microscopy in molecular structural biology: A historical survey.

    PubMed

    Harris, J Robin

    2015-09-01

    In this personal, historic account of macromolecular transmission electron microscopy (TEM), published data from the 1940s through to recent times is surveyed, within the context of the remarkable progress that has been achieved during this time period. The evolution of present day molecular structural biology is described in relation to the associated biological disciplines. The contribution of numerous electron microscope pioneers to the development of the subject is discussed. The principal techniques for TEM specimen preparation, thin sectioning, metal shadowing, negative staining and plunge-freezing (vitrification) of thin aqueous samples are described, with a selection of published images to emphasise the virtues of each method. The development of digital image analysis and 3D reconstruction is described in detail as applied to electron crystallography and reconstructions from helical structures, 2D membrane crystals as well as single particle 3D reconstruction of icosahedral viruses and macromolecules. The on-going development of new software, algorithms and approaches is highlighted before specific examples of the historical progress of the structural biology of proteins and viruses are presented.

  16. Electronic structure of the polar molecules XF (X: Be, Mg, Ca) with rovibrational and dipole moment calculations

    NASA Astrophysics Data System (ADS)

    El-Kork, Nayla; Abu el kher, Nariman; Korjieh, Farah; Chtay, John Anwar; Korek, Mahmoud

    2017-04-01

    A theoretical investigation for the feasibility of laser-cooling is performed through the calculation of accurate potential energy curves, static dipole moments, spectroscopic constants and rovibrational calculations for 24, 26 and 27 highly excited electronic states for BeF, CaF and MgF molecules respectively. In order to understand the electronic structure of their lowest lying electronic states and to learn the characteristic behavior of their chemical bonding, a high level of calculation is realized by using the complete active space self-consistent field (CASSCF) with multi-reference configuration interaction MRCI method including single and double excitations with Davidson correction (+ Q) for the three considered molecules. The comparison between the values of the present work and those available in the literature for several electronic states shows a good agreement. Fifty new excited electronic states have been investigated, in the present work, for the first time for the three studied molecules.

  17. Electronic structure of the polar molecules XF (X: Be, Mg, Ca) with rovibrational and dipole moment calculations.

    PubMed

    El-Kork, Nayla; Abu El Kher, Nariman; Korjieh, Farah; Chtay, John Anwar; Korek, Mahmoud

    2017-04-15

    A theoretical investigation for the feasibility of laser-cooling is performed through the calculation of accurate potential energy curves, static dipole moments, spectroscopic constants and rovibrational calculations for 24, 26 and 27 highly excited electronic states for BeF, CaF and MgF molecules respectively. In order to understand the electronic structure of their lowest lying electronic states and to learn the characteristic behavior of their chemical bonding, a high level of calculation is realized by using the complete active space self-consistent field (CASSCF) with multi-reference configuration interaction MRCI method including single and double excitations with Davidson correction (+Q) for the three considered molecules. The comparison between the values of the present work and those available in the literature for several electronic states shows a good agreement. Fifty new excited electronic states have been investigated, in the present work, for the first time for the three studied molecules.

  18. Pebbles and PebbleJuggler: software for accurate, unbiased, and fast measurement and analysis of nanoparticle morphology from transmission electron microscopy (TEM) micrographs

    NASA Astrophysics Data System (ADS)

    Mondini, S.; Ferretti, A. M.; Puglisi, A.; Ponti, A.

    2012-08-01

    Pebbles is a user-friendly software program which implements an accurate, unbiased, and fast method to measure the morphology of a population of nanoparticles (NPs) from TEM micrographs. The morphological parameters of the projected NP shape are obtained by fitting intensity models to the TEM micrograph. Pebbles can be used either in automatic mode, where both fitting and validation are reliably carried out with minimal human intervention, and in manual mode, where the user has full control on the fitting and validation steps. Accuracy in diameter measurement has been shown to be <~1%. When operated in automatic mode, Pebbles can be very fast. The effective speed of 1 NP s-1 has been achieved in favorable cases (packed monolayer of NPs). Since Pebbles is based on a local modeling procedure, it successfully treats cases such as low contrast NPs, NPs with significant diffraction scattering, and inhomogeneous background which often make conventional thresholding procedures fail. Pebbles is accompanied by PebbleJuggler, a software program for the statistical analysis of the sets of best-fit NP models created by Pebbles. Effort has been devoted to make Pebbles and PebbleJuggler the most user-friendly and the least user-tedious we could. Pebbles and PebbleJuggler are available at http://pebbles.istm.cnr.it.Pebbles is a user-friendly software program which implements an accurate, unbiased, and fast method to measure the morphology of a population of nanoparticles (NPs) from TEM micrographs. The morphological parameters of the projected NP shape are obtained by fitting intensity models to the TEM micrograph. Pebbles can be used either in automatic mode, where both fitting and validation are reliably carried out with minimal human intervention, and in manual mode, where the user has full control on the fitting and validation steps. Accuracy in diameter measurement has been shown to be <~1%. When operated in automatic mode, Pebbles can be very fast. The effective speed of 1

  19. Structure elucidation of degradation products of the antibiotic amoxicillin with ion trap MS(n) and accurate mass determination by ESI TOF.

    PubMed

    Nägele, Edgar; Moritz, Ralf

    2005-10-01

    Today, it is necessary to identify relevant compounds appearing in discovery and development of new drug substances in the pharmaceutical industry. For that purpose, the measurement of accurate molecular mass and empirical formula calculation is very important for structure elucidation in addition to other available analytical methods. In this work, the identification and confirmation of degradation products in a finished dosage form of the antibiotic drug amoxicillin obtained under stress conditions will be demonstrated. Structure elucidation is performed utilizing liquid chromatography (LC) ion trap MS/MS and MS3 together with accurate mass measurement of the molecular ions and of the collision induced dissociation (CID) fragments by liquid chromatography electro spray ionization time-of-flight mass spectrometry (LC/ESI-TOF).

  20. Glycine in an electronically excited state: ab initio electronic structure and dynamical calculations.

    PubMed

    Muchová, Eva; Slavícek, Petr; Sobolewski, Andrzej L; Hobza, Pavel

    2007-06-21

    The goal of this study is to explore the photochemical processes following optical excitation of the glycine molecule into its two low-lying excited states. We employed electronic structure methods at various levels to map the PES of the ground state and the two low-lying excited states of glycine. It follows from our calculations that the photochemistry of glycine can be regarded as a combination of photochemical behavior of amines and carboxylic acid. The first channel (connected to the presence of amino group) results in ultrafast decay, while the channels characteristic for the carboxylic group occur on a longer time scale. Dynamical calculations provided the branching ratio for these channels. We also addressed the question whether conformationally dependent photochemistry can be observed for glycine. While electronic structure calculations favor this possibility, the ab initio multiple spawning (AIMS) calculations showed only minor relevance of the reaction path resulting in conformationally dependent dynamics.

  1. RCK: accurate and efficient inference of sequence- and structure-based protein–RNA binding models from RNAcompete data

    PubMed Central

    Orenstein, Yaron; Wang, Yuhao; Berger, Bonnie

    2016-01-01

    Motivation: Protein–RNA interactions, which play vital roles in many processes, are mediated through both RNA sequence and structure. CLIP-based methods, which measure protein–RNA binding in vivo, suffer from experimental noise and systematic biases, whereas in vitro experiments capture a clearer signal of protein RNA-binding. Among them, RNAcompete provides binding affinities of a specific protein to more than 240 000 unstructured RNA probes in one experiment. The computational challenge is to infer RNA structure- and sequence-based binding models from these data. The state-of-the-art in sequence models, Deepbind, does not model structural preferences. RNAcontext models both sequence and structure preferences, but is outperformed by GraphProt. Unfortunately, GraphProt cannot detect structural preferences from RNAcompete data due to the unstructured nature of the data, as noted by its developers, nor can it be tractably run on the full RNACompete dataset. Results: We develop RCK, an efficient, scalable algorithm that infers both sequence and structure preferences based on a new k-mer based model. Remarkably, even though RNAcompete data is designed to be unstructured, RCK can still learn structural preferences from it. RCK significantly outperforms both RNAcontext and Deepbind in in vitro binding prediction for 244 RNAcompete experiments. Moreover, RCK is also faster and uses less memory, which enables scalability. While currently on par with existing methods in in vivo binding prediction on a small scale test, we demonstrate that RCK will increasingly benefit from experimentally measured RNA structure profiles as compared to computationally predicted ones. By running RCK on the entire RNAcompete dataset, we generate and provide as a resource a set of protein–RNA structure-based models on an unprecedented scale. Availability and Implementation: Software and models are freely available at http://rck.csail.mit.edu/ Contact: bab@mit.edu Supplementary information

  2. Tictoid expanded pyridiniums: assessing structural, electrochemical, electronic, and photophysical features.

    PubMed

    Fortage, Jérôme; Tuyèras, Fabien; Peltier, Cyril; Dupeyre, Grégory; Calboréan, Adrian; Bedioui, Fethi; Ochsenbein, Philippe; Puntoriero, Fausto; Campagna, Sebastiano; Ciofini, Ilaria; Lainé, Philippe P

    2012-08-02

    In regard to semirigid donor-spacer-acceptor (D-S-A) dyads devised for photoinduced charge separation and built from an unsaturated spacer, there exists a strategy of design referred to as "geometrical decoupling" that consists in introducing an inner-S twist angle approaching 90° to minimize adverse D/A mutual electronic influence. The present work aims at gaining further insights into the actual impact of the use of bulky substituents (R) of the alkyl type on the electronic structure of spacers (S) of the oligo-p-phenylene type, which can be critical in the functioning of derived dyads. To this end, a series of 12 novel expanded pyridiniums (EPs), regarded as model S-A assemblies, was synthesized and its structural, electronic, and photophysical properties were investigated at both experimental and theoretical levels. These EPs result from the combination of 4 types of pyridinium-based acceptor moieties with the three following types of S subunits connected at position 4 of the pyridinum core: xylyl (X), xylyl-phenyl (XP), and xylyl-tolyl (XT). From comparison of collected data with those already reported for eight other EPs based on the same A components but linked to S fragments of two other types (i.e., phenyl, P, and biphenyl, PP), the following quantitative order in regard to the pivotal S-centered HOMO energy perturbation was derived (sorted by increasing destabilization): P < X ≪ PP ≈< XP ≈< XT. This indicates that spacers (S) are primarily distinguished on the basis of their mono- or biaryl composition and secondarily by their number of methyl substituents (R). The electron-donating inductive contribution of methyl substituents (HOMO destabilization) more than counterbalances the effect of conjugation disruption (HOMO stabilization). This "compensation effect" suggests that mildly electron-withdrawing hindering groups are better suited for "geometrical decoupling", given that high-energy S-centered occupied MOs can assist charge recombination

  3. Angle-Resolved Photoemission Spectroscopy on Electronic Structure and Electron-Phonon Coupling in Cuprate Superconductors

    SciTech Connect

    Zhou, X.J.

    2010-04-30

    In addition to the record high superconducting transition temperature (T{sub c}), high temperature cuprate superconductors are characterized by their unusual superconducting properties below T{sub c}, and anomalous normal state properties above T{sub c}. In the superconducting state, although it has long been realized that superconductivity still involves Cooper pairs, as in the traditional BCS theory, the experimentally determined d-wave pairing is different from the usual s-wave pairing found in conventional superconductors. The identification of the pairing mechanism in cuprate superconductors remains an outstanding issue. The normal state properties, particularly in the underdoped region, have been found to be at odd with conventional metals which is usually described by Fermi liquid theory; instead, the normal state at optimal doping fits better with the marginal Fermi liquid phenomenology. Most notable is the observation of the pseudogap state in the underdoped region above T{sub c}. As in other strongly correlated electrons systems, these unusual properties stem from the interplay between electronic, magnetic, lattice and orbital degrees of freedom. Understanding the microscopic process involved in these materials and the interaction of electrons with other entities is essential to understand the mechanism of high temperature superconductivity. Since the discovery of high-T{sub c} superconductivity in cuprates, angle-resolved photoemission spectroscopy (ARPES) has provided key experimental insights in revealing the electronic structure of high temperature superconductors. These include, among others, the earliest identification of dispersion and a large Fermi surface, an anisotropic superconducting gap suggestive of a d-wave order parameter, and an observation of the pseudogap in underdoped samples. In the mean time, this technique itself has experienced a dramatic improvement in its energy and momentum resolutions, leading to a series of new discoveries not

  4. Probing the bonding and electronic structure of single atom dopants in graphene with electron energy loss spectroscopy.

    PubMed

    Ramasse, Quentin M; Seabourne, Che R; Kepaptsoglou, Despoina-Maria; Zan, Recep; Bangert, Ursel; Scott, Andrew J

    2013-10-09

    A combination of scanning transmission electron microscopy, electron energy loss spectroscopy, and ab initio calculations reveal striking electronic structure differences between two distinct single substitutional Si defect geometries in graphene. Optimised acquisition conditions allow for exceptional signal-to-noise levels in the spectroscopic data. The near-edge fine structure can be compared with great accuracy to simulations and reveal either an sp(3)-like configuration for a trivalent Si or a more complicated hybridized structure for a tetravalent Si impurity.

  5. Electronic structure and partial charge distribution of doxorubicin under different molecular environments

    NASA Astrophysics Data System (ADS)

    Poudel, Lokendra

    Doxorubicin (trade name Adriamycin, abbreviated DOX) is a well-known an- thracyclic chemotherapeutic used in treating a variety of cancers including acute leukemia, lymphoma, multiple myeloma, and a range of stomach, lung, bladder, bone, breast, and ovarian cancers. The purpose of the present work is to study electronic structure, partial charge distribution and interaction energy of DOX under different environments. It provides a framework for better understanding of bioactivity of DOX with DNA. While in this work, we focus on DOX -- DNA interactions; the obtained knowledge could be translated to other drug -- target interactions or biomolecular interactions. The electronic structure and partial charge distribution of DOX in three dierent molecular environments: isolated, solvated, and intercalated into a DNA complex,were studied by rst principles density functional methods. It is shown that the addition of solvating water molecules to DOX and the proximity and interaction with DNA has a signicant impact on the electronic structure as well as the partial charge distribution. The calculated total partial charges for DOX in the three models are 0.0, +0.123 and -0.06 electrons for the isolated, solvated, and intercalated state, respectively. Furthermore, by using the more accurate ab initio partial charge values on every atom in the models, signicant improvement in estimating the DOX-DNA interaction energy is obtained in conjunction with the NAnoscale Molecular Dynamics (NAMD) code. The electronic structure of the DOX-DNA is further elucidated by resolving the total density of states (TDOS) into dierent functional groups of DOX, DNA, water, co-crystallized Spermine molecule, and Na ions. The surface partial charge distribution in the DOX-DNA is calculated and displayed graphically. We conclude that the presence of the solvent as well as the details of the interaction geometry matter greatly in the determination of the stability of the DOX complexion. Ab initio

  6. Structural and electronic properties of chiral gold nanoclusters

    NASA Astrophysics Data System (ADS)

    Garzon, Ignacio; Santizo, Itzel; Perez, Luis

    2008-03-01

    Chiral structures had been found as the most stable isomers of bare and thiolate-passivated gold nanoparticles of several sizes, from density functional calculations (DFT). These results provided theoretical support for the existence of chirality in metal clusters, suggested by the intense optical activity measured from the metal-based electronic transitions of size-separated glutathione-passivated gold nanoclusters, and more recently, of penicillamine-passivated gold clusters with metal core mean diameters of 0.57, 1.1, and 1.75 nm. A further structural analysis using the Hausdorff chirality measure, as well as, a semiclassical calculation of the circular dichroism spectrum, has confirmed the existence of chirality in Au nanoparticles. In this work, the structural and electronic properties of chiral Au nanoclusters are studied by using global optimization methods combined with semiempirical many body potentials and first principles density functional calculations. In particular, we study the Au34 cluster. For this system there exists experimental evidence on the energetic stability of a chiral structure with C3 symmetry. Our calculations theoretically confirm these results, providing further evidence on the existence of chiral gold nanoclusters.

  7. Atomic and electronic structures of an extremely fragile liquid

    PubMed Central

    Kohara, Shinji; Akola, Jaakko; Patrikeev, Leonid; Ropo, Matti; Ohara, Koji; Itou, Masayoshi; Fujiwara, Akihiko; Yahiro, Jumpei; Okada, Junpei T.; Ishikawa, Takehiko; Mizuno, Akitoshi; Masuno, Atsunobu; Watanabe, Yasuhiro; Usuki, Takeshi

    2014-01-01

    The structure of high-temperature liquids is an important topic for understanding the fragility of liquids. Here we report the structure of a high-temperature non-glass-forming oxide liquid, ZrO2, at an atomistic and electronic level. The Bhatia–Thornton number–number structure factor of ZrO2 does not show a first sharp diffraction peak. The atomic structure comprises ZrO5, ZrO6 and ZrO7 polyhedra with a significant contribution of edge sharing of oxygen in addition to corner sharing. The variety of large oxygen coordination and polyhedral connections with short Zr–O bond lifetimes, induced by the relatively large ionic radius of zirconium, disturbs the evolution of intermediate-range ordering, which leads to a reduced electronic band gap and increased delocalization in the ionic Zr–O bonding. The details of the chemical bonding explain the extremely low viscosity of the liquid and the absence of a first sharp diffraction peak, and indicate that liquid ZrO2 is an extremely fragile liquid. PMID:25520236

  8. Towards accurate structural characterization of metal centres in protein crystals: the structures of Ni and Cu T{sub 6} bovine insulin derivatives

    SciTech Connect

    Frankaer, Christian Grundahl; Mossin, Susanne; Ståhl, Kenny; Harris, Pernille

    2014-01-01

    The level of structural detail around the metal sites in Ni{sup 2+} and Cu{sup 2+} T{sub 6} insulin derivatives was significantly improved by using a combination of single-crystal X-ray crystallography and X-ray absorption spectroscopy. Photoreduction and subsequent radiation damage of the Cu{sup 2+} sites in Cu insulin was followed by XANES spectroscopy. Using synchrotron radiation (SR), the crystal structures of T{sub 6} bovine insulin complexed with Ni{sup 2+} and Cu{sup 2+} were solved to 1.50 and 1.45 Å resolution, respectively. The level of detail around the metal centres in these structures was highly limited, and the coordination of water in Cu site II of the copper insulin derivative was deteriorated as a consequence of radiation damage. To provide more detail, X-ray absorption spectroscopy (XAS) was used to improve the information level about metal coordination in each derivative. The nickel derivative contains hexacoordinated Ni{sup 2+} with trigonal symmetry, whereas the copper derivative contains tetragonally distorted hexacoordinated Cu{sup 2+} as a result of the Jahn–Teller effect, with a significantly longer coordination distance for one of the three water molecules in the coordination sphere. That the copper centre is of type II was further confirmed by electron paramagnetic resonance (EPR). The coordination distances were refined from EXAFS with standard deviations within 0.01 Å. The insulin derivative containing Cu{sup 2+} is sensitive towards photoreduction when exposed to SR. During the reduction of Cu{sup 2+} to Cu{sup +}, the coordination geometry of copper changes towards lower coordination numbers. Primary damage, i.e. photoreduction, was followed directly by XANES as a function of radiation dose, while secondary damage in the form of structural changes around the Cu atoms after exposure to different radiation doses was studied by crystallography using a laboratory diffractometer. Protection against photoreduction and subsequent

  9. An Electronic Health Record Based on Structured Narrative

    PubMed Central

    Johnson, Stephen B.; Bakken, Suzanne; Dine, Daniel; Hyun, Sookyung; Mendonça, Eneida; Morrison, Frances; Bright, Tiffani; Van Vleck, Tielman; Wrenn, Jesse; Stetson, Peter

    2008-01-01

    Objective To develop an electronic health record that facilitates rapid capture of detailed narrative observations from clinicians, with partial structuring of narrative information for integration and reuse. Design We propose a design in which unstructured text and coded data are fused into a single model called structured narrative. Each major clinical event (e.g., encounter or procedure) is represented as a document that is marked up to identify gross structure (sections, fields, paragraphs, lists) as well as fine structure within sentences (concepts, modifiers, relationships). Marked up items are associated with standardized codes that enable linkage to other events, as well as efficient reuse of information, which can speed up data entry by clinicians. Natural language processing is used to identify fine structure, which can reduce the need for form-based entry. Validation The model is validated through an example of use by a clinician, with discussion of relevant aspects of the user interface, data structures and processing rules. Discussion The proposed model represents all patient information as documents with standardized gross structure (templates). Clinicians enter their data as free text, which is coded by natural language processing in real time making it immediately usable for other computation, such as alerts or critiques. In addition, the narrative data annotates and augments structured data with temporal relations, severity and degree modifiers, causal connections, clinical explanations and rationale. Conclusion Structured narrative has potential to facilitate capture of data directly from clinicians by allowing freedom of expression, giving immediate feedback, supporting reuse of clinical information and structuring data for subsequent processing, such as quality assurance and clinical research. PMID:17947628

  10. Accurate determination of the fine-structure intervals in the 3P ground states of C-13 and C-12 by far-infrared laser magnetic resonance

    NASA Technical Reports Server (NTRS)

    Cooksy, A. L.; Saykally, R. J.; Brown, J. M.; Evenson, K. M.

    1986-01-01

    Accurate values are presented for the fine-structure intervals in the 3P ground state of neutral atomic C-12 and C-13 as obtained from laser magnetic resonance spectroscopy. The rigorous analysis of C-13 hyperfine structure, the measurement of resonant fields for C-12 transitions at several additional far-infrared laser frequencies, and the increased precision of the C-12 measurements, permit significant improvement in the evaluation of these energies relative to earlier work. These results will expedite the direct and precise measurement of these transitions in interstellar sources and should assist in the determination of the interstellar C-12/C-13 abundance ratio.

  11. Theory of silicon superlattices - Electronic structure and enhanced mobility

    NASA Technical Reports Server (NTRS)

    Moriarty, J. A.; Krishnamurthy, S.

    1983-01-01

    A realistic tight-binding band-structure model of silicon superlattices is formulated and used to study systems of potential applied interest, including periodic layered Si-Si(1-x)Ge(x) heterostructures. The results suggest a possible new mechanism for achieving enhanced transverse carrier mobility in such structures: reduced transverse conductivity effective masses associated with the superlattice band structure. For electrons in 100-line-oriented superlattices, a reduced conductivity mass arises intrinsically from the lower symmetry of the superlattice and its unique effect on the indirect bulk silicon band gap. An order of magnitude estimate of the range of mobility enhancement expected from this mechanism appears to be consistent with preliminary experimental results on Si-Si(1-x)Ge(x) superlattices.

  12. Quantum Monte Carlo finite temperature electronic structure of quantum dots

    NASA Astrophysics Data System (ADS)

    Leino, Markku; Rantala, Tapio T.

    2002-08-01

    Quantum Monte Carlo methods allow a straightforward procedure for evaluation of electronic structures with a proper treatment of electronic correlations. This can be done even at finite temperatures [1]. We test the Path Integral Monte Carlo (PIMC) simulation method [2] for one and two electrons in one and three dimensional harmonic oscillator potentials and apply it in evaluation of finite temperature effects of single and coupled quantum dots. Our simulations show the correct finite temperature excited state populations including degeneracy in cases of one and three dimensional harmonic oscillators. The simulated one and two electron distributions of a single and coupled quantum dots are compared to those from experiments and other theoretical (0 K) methods [3]. Distributions are shown to agree and the finite temperature effects are discussed. Computational capacity is found to become the limiting factor in simulations with increasing accuracy. Other essential aspects of PIMC and its capability in this type of calculations are also discussed. [1] R.P. Feynman: Statistical Mechanics, Addison Wesley, 1972. [2] D.M. Ceperley, Rev.Mod.Phys. 67, 279 (1995). [3] M. Pi, A. Emperador and M. Barranco, Phys.Rev.B 63, 115316 (2001).

  13. Structural Electronic and Magnetic Properties of Semiconductor Interfaces

    NASA Astrophysics Data System (ADS)

    Continenza, Alessandra

    1990-01-01

    This work is focussed on the structural, electronic and magnetic properties of semiconductor interfaces. The issues and the interest involved in these particular systems are various and have engaged both the scientific and the technological community for more than three decades. The technological interest toward semiconductors is obviously related to device applications while the scientific interest is mainly focussed on the understanding of some characteristic properties, such as potential barriers, carrier properties and band gaps, and how these can be modified by changing different external factors, such as epitaxial growth, strain effects, junctions and doping. A complete knowledge and understanding of these complex issues is, in fact, the basic requirement necessary in order to achieve the ability to "tune" basic properties "at will" and designing the "ad hoc" material for each different device application. We have performed a study of the magnetic, structural and electronic properties of a few particular examples of semiconductor interfaces and heterojunctions namely, rm Fe_{n}/(ZnSe)_ {m}, rm(InAs)_{n }/(InP)_{n} and rm( alpha-Sn)_{n}/(CdTe)_{n }, using the all-electron full-potential linearized augmented plane wave (FLAPW) method. Together with a study of the interface properties, we present results of calculations performed on all the pure constituents, in order to provide comparisons and to better understand how the bulk properties are modified by the interface. In particular, we have analyzed how the properties of these structures can be tailored by changing quantities such as the superlattice periodicity, the epitaxial strain and the interface morphology. We found that the relevance of these factors changes depending on the particular material under study and that it is possible, indeed, to model the characteristics electronic and transport properties of each structure by properly tuning the growth conditions. Our results are in very good agreement with

  14. The Electronic Structure of Transition Metal Coated Fullerenes

    NASA Astrophysics Data System (ADS)

    Patton, David C.; Pederson, Mark R.; Kaxiras, Efthimios

    1998-03-01

    Clusters composed of fullerene molecules with an outer shell of transition metal atoms in the composition C_60M_62 (M being a transition metal) have been produced with laser vaporisation techniques(F. Tast, N. Malinowski, S. Frank, M. Heinebrodt, I.M.L. Billas, and T. P. Martin, Z. Phys D 40), 351 (1997).. We have studied several of these very large systems with a parallel version of the all-electron NRLMOL cluster code. Optimized geometries of the metal encased fullerenes C_60Ti_62 and C_60V_62 are presented along with their HOMO-LUMO gaps, electron affinities, ionization energies, and cohesive energies. We compare the stability of these clusters to relaxed met-car structures (e.g. Ti_8C_12) and to relaxed rocksalt metal-carbide fragments (TiC)n with n=8 and 32. In addition to metal-coated fullerenes we consider the possibility of a trilayered structure consisting of a small shell of metal atoms enclosed by a metal coated fullerene. The nature of bonding in these systems is analyzed by studying the electronic charge distributions.

  15. Novel electronic structures of superlattice composed of graphene and silicene

    SciTech Connect

    Yu, S.; Li, X.D.; Wu, S.Q.; Wen, Y.H.; Zhou, S.; Zhu, Z.Z.

    2014-02-01

    Highlights: • Graphene/silicene superlattices exhibit metallic electronic properties. • Dirac point of graphene is folded to the Γ-point in the superlattice system. • Significant changes in the transport properties of the graphene layers are expected. • Small amount of charge transfer from the graphene to the silicene layers is found. - Abstract: Superlattice is a major force in providing man-made materials with unique properties. Here we report a study of the structural and electronic properties of a superlattice made with alternate stacking of graphene and hexagonal silicene. Three possible stacking models, i.e., the top-, bridge- and hollow-stacking, are considered. The top-stacking is found to be the most stable pattern. Although both the free-standing graphene and silicene are semi-metals, our results suggest that the graphene and silicene layers in the superlattice both exhibit metallic electronic properties due to a small amount of charge transfer from the graphene to the silicene layers. More importantly, the Dirac point of graphene is folded to the Γ-point of the superlattice, instead of the K-point in the isolated graphene. Such a change in the Dirac point of graphene could lead to significant change in the transportation property of the graphene layer. Moreover, the band structure and the charge transfer indicate that the interaction between the stacking sheets in the graphene/silicene superlattice is more than just the van der Waals interaction.

  16. Structural Fingerprinting of Nanocrystals in the Transmission Electron Microscope

    NASA Astrophysics Data System (ADS)

    Rouvimov, Sergei; Plachinda, Pavel; Moeck, Peter

    2010-03-01

    Three novel strategies for the structurally identification of nanocrystals in a transmission electron microscope are presented. Either a single high-resolution transmission electron microscopy image [1] or a single precession electron diffractogram (PED) [2] may be employed. PEDs from fine-grained crystal powders may also be utilized. Automation of the former two strategies is in progress and shall lead to statistically significant results on ensembles of nanocrystals. Open-access databases such as the Crystallography Open Database which provides more than 81,500 crystal structure data sets [3] or its mainly inorganic and educational subsets [4] may be utilized. [1] http://www.scientificjournals.org/journals 2007/j/of/dissertation.htm [2] P. Moeck and S. Rouvimov, in: {Drugs and the Pharmaceutical Sciences}, Vol. 191, 2009, 270-313 [3] http://cod.ibt.lt, http://www.crystallography.net, http://cod.ensicaen.fr, http://nanocrystallography.org, http://nanocrystallography.net, http://journals.iucr.org/j/issues/2009/04/00/kk5039/kk5039.pdf [4] http://nanocrystallography.research.pdx.edu/CIF-searchable

  17. Electronic structure, aromaticity and spectra of hetero[8]circulenes

    NASA Astrophysics Data System (ADS)

    Baryshnikov, G. V.; Minaev, B. F.; Minaeva, V. A.

    2015-05-01

    The present review highlights recent advances in experimental and theoretical chemistry dealing with investigation of the electronic structures and physicochemical properties of hetero[8]circulenes. These compounds are the only representatives of planar heteroannulated cyclooctatetraenes. It is shown that high molecular symmetry of hetero[8]circulenes and the extended specific π-conjugated chain are the main factors responsible for high stability of the crystal packing modes and the optical and magnetic properties of these compounds. These effects also determine numerous selection rules for electronic and vibrational transitions in UV-Vis, IR and Raman spectra. Emphasis is given to the aromaticity of hetero[8]circulenes containing the inner antiaromatic cyclooctatetraene core. The planar structure of the latter is stabilized by a polyaromatic system composed of benzene rings and five-membered heterocycles. Due to high thermal and chemical stability of most hetero[8]circulenes combined with semiconducting properties, these compounds can be considered as promising materials for molecular electronics and nanophotonics, in particular for the production of organic light-emitting diodes and field-effect transistors. The bibliography includes 154 references.

  18. Electron microscopic examination of wastewater biofilm formation and structural components.

    PubMed Central

    Eighmy, T T; Maratea, D; Bishop, P L

    1983-01-01

    This research documents in situ wastewater biofilm formation, structure, and physiochemical properties as revealed by scanning and transmission electron microscopy. Cationized ferritin was used to label anionic sites of the biofilm glycocalyx for viewing in thin section. Wastewater biofilm formation paralleled the processes involved in marine biofilm formation. Scanning electron microscopy revealed a dramatic increase in cell colonization and growth over a 144-h period. Constituents included a variety of actively dividing morphological types. Many of the colonizing bacteria were flagellated. Filaments were seen after primary colonization of the surface. Transmission electron microscopy revealed a dominant gram-negative cell wall structure in the biofilm constituents. At least three types of glycocalyces were observed. The predominant glycocalyx possessed interstices and was densely labeled with cationized ferritin. Two of the glycocalyces appeared to mediate biofilm adhesion to the substratum. The results suggest that the predominant glycocalyx of this thin wastewater biofilm serves, in part, to: (i) enclose the bacteria in a matrix and anchor the biofilm to the substratum and (ii) provide an extensive surface area with polyanionic properties. Images PMID:6881965

  19. Multiscale approach to the electronic structure of doped semiconductor surfaces

    NASA Astrophysics Data System (ADS)

    Sinai, Ofer; Hofmann, Oliver T.; Rinke, Patrick; Scheffler, Matthias; Heimel, Georg; Kronik, Leeor

    2015-02-01

    The inclusion of the global effects of semiconductor doping poses a unique challenge for first-principles simulations, because the typically low concentration of dopants renders an explicit treatment intractable. Furthermore, the width of the space-charge region (SCR) at charged surfaces often exceeds realistic supercell dimensions. Here, we present a multiscale technique that fully addresses these difficulties. It is based on the introduction of a charged sheet, mimicking the SCR-related field, along with free charge which mimics the bulk charge reservoir, such that the system is neutral overall. These augment a slab comprising "pseudoatoms" possessing a fractional nuclear charge matching the bulk doping concentration. Self-consistency is reached by imposing charge conservation and Fermi level equilibration between the bulk, treated semiclassically, and the electronic states of the slab, which are treated quantum-mechanically. The method, called CREST—the charge-reservoir electrostatic sheet technique—can be used with standard electronic structure codes. We validate CREST using a simple tight-binding model, which allows for comparison of its results with calculations encompassing the full SCR explicitly. Specifically, we show that CREST successfully predicts scenarios spanning the range from no to full Fermi level pinning. We then employ it with density functional theory, obtaining insight into the doping dependence of the electronic structures of the metallic "clean-cleaved" Si(111) surface and its semiconducting (2 ×1 ) reconstructions.

  20. Functional connectivity and structural covariance between regions of interest can be measured more accurately using multivariate distance correlation.

    PubMed

    Geerligs, Linda; Cam-Can; Henson, Richard N

    2016-07-15

    Studies of brain-wide functional connectivity or structural covariance typically use measures like the Pearson correlation coefficient, applied to data that have been averaged across voxels within regions of interest (ROIs). However, averaging across voxels may result in biased connectivity estimates when there is inhomogeneity within those ROIs, e.g., sub-regions that exhibit different patterns of functional connectivity or structural covariance. Here, we propose a new measure based on "distance correlation"; a test of multivariate dependence of high dimensional vectors, which allows for both linear and non-linear dependencies. We used simulations to show how distance correlation out-performs Pearson correlation in the face of inhomogeneous ROIs. To evaluate this new measure on real data, we use resting-state fMRI scans and T1 structural scans from 2 sessions on each of 214 participants from the Cambridge Centre for Ageing & Neuroscience (Cam-CAN) project. Pearson correlation and distance correlation showed similar average connectivity patterns, for both functional connectivity and structural covariance. Nevertheless, distance correlation was shown to be 1) more reliable across sessions, 2) more similar across participants, and 3) more robust to different sets of ROIs. Moreover, we found that the similarity between functional connectivity and structural covariance estimates was higher for distance correlation compared to Pearson correlation. We also explored the relative effects of different preprocessing options and motion artefacts on functional connectivity. Because distance correlation is easy to implement and fast to compute, it is a promising alternative to Pearson correlations for investigating ROI-based brain-wide connectivity patterns, for functional as well as structural data.