Liu Zejian; Zhang Qi; Qin Luchang
2005-05-09
We report a method that allows direct, systematic, and accurate determination of the atomic structure of multiwalled carbon nanotubes by analyzing the scattering intensities on the nonequatorial layer lines in the electron diffraction pattern. Complete structure determination of a quadruple-walled carbon nanotube is described as an example, and it was found that the intertubular distance varied from 0.36 nm to 0.5 nm with a mean value of 0.42 nm.
Accurate Electron Affinity of Iron and Fine Structures of Negative Iron ions
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
Accurate Electron Affinity of Iron and Fine Structures of Negative Iron ions
NASA Astrophysics Data System (ADS)
Chen, Xiaolin; Luo, Zhihong; Li, Jiaming; Ning, Chuangang
2016-05-01
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.
Accurate Electron Affinity of Iron and Fine Structures of Negative Iron ions.
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
Accurate macromolecular structures using minimal measurements from X-ray free-electron lasers.
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.
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
NASA Astrophysics Data System (ADS)
Skone, Jonathan; Govoni, Marco; Galli, Giulia
Dielectric-dependent hybrid [DDH] functionals have recently been shown to yield highly accurate energy gaps and dielectric constants for a wide variety of solids, at a computational cost considerably less than standard GW calculations. The fraction of exact exchange included in the definition of DDH functionals depends (self-consistently) on the dielectric constant of the material. In the present talk we introduce a range-separated (RS) version of DDH functionals where short and long-range components are matched using material dependent, non-empirical parameters. Comparing with state of the art GW calculations and experiment, we show that such RS hybrids yield accurate electronic properties of both molecules and solids, including energy gaps, photoelectron spectra and absolute ionization potentials. This work was supported by NSF-CCI Grant Number NSF-CHE-0802907 and DOE-BES.
Son, Sang-Kil
2011-03-01
We introduce a new numerical grid-based method on unstructured grids in the three-dimensional real-space to investigate the electronic structure of polyatomic molecules. The Voronoi-cell finite difference (VFD) method realizes a discrete Laplacian operator based on Voronoi cells and their natural neighbors, featuring high adaptivity and simplicity. To resolve multicenter Coulomb singularity in all-electron calculations of polyatomic molecules, this method utilizes highly adaptive molecular grids which consist of spherical atomic grids. It provides accurate and efficient solutions for the Schroedinger equation and the Poisson equation with the all-electron Coulomb potentials regardless of the coordinate system and the molecular symmetry. For numerical examples, we assess accuracy of the VFD method for electronic structures of one-electron polyatomic systems, and apply the method to the density-functional theory for many-electron polyatomic molecules.
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.
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
NASA Astrophysics Data System (ADS)
Teng, H.; Fujiwara, T.; Hoshi, T.; Sogabe, T.; Zhang, S.-L.; Yamamoto, S.
2011-04-01
The need for large-scale electronic structure calculations arises recently in the field of material physics, and efficient and accurate algebraic methods for large simultaneous linear equations become greatly important. We investigate the generalized shifted conjugate orthogonal conjugate gradient method, the generalized Lanczos method, and the generalized Arnoldi method. They are the solver methods of large simultaneous linear equations of the one-electron Schrödinger equation and map the whole Hilbert space to a small subspace called the Krylov subspace. These methods are applied to systems of fcc Au with the NRL tight-binding Hamiltonian [F. Kirchhoff , Phys. Rev. BJCOMEL1098-012110.1103/PhysRevB.63.195101 63, 195101 (2001)]. We compare results by these methods and the exact calculation and show them to be equally accurate. The system size dependence of the CPU time is also discussed. The generalized Lanczos method and the generalized Arnoldi method are the most suitable for the large-scale molecular dynamics simulations from the viewpoint of CPU time and memory size.
Araujo, Rafael B.; Almeida, J. de S; Ferreira da Silva, A.; Ahuja, Rajeev
2015-09-28
The main goals of this paper are to investigate the accuracy of the Tran-Blaha modified Becke Johnson (TB-mBJ) potential to predict the electronic structure of lithium iron phosphate and the related redox reaction energy with the lithium deintercalation process. The computed electronic structures show that the TB-mBJ method is able to partially localize Fe-3d electrons in LiFePO{sub 4} and FePO{sub 4} which usually is a problem for the generalized gradient approximation (GGA) due to the self interaction error. The energy band gap is also improved by the TB-mBJ calculations in comparison with the GGA results. It turned out, however, that the redox reaction energy evaluated by the TB-mBJ technique is not in good agreement with the measured one. It is speculated that this disagreement in the computed redox energy and the experimental value is due to the lack of a formal expression to evaluate the exchange and correlation energy. Therefore, the TB-mBJ is an efficient method to improve the prediction of the electronic structures coming form the standard GGA functional in LiFePO{sub 4} and FePO{sub 4}. However, it does not appear to have the same efficiency for evaluating the redox reaction energies for the investigated system.
An accurate dynamical electron diffraction algorithm for reflection high-energy electron diffraction
NASA Astrophysics Data System (ADS)
Huang, J.; Cai, C. Y.; Lv, C. L.; Zhou, G. W.; Wang, Y. G.
2015-12-01
The conventional multislice method (CMS) method, one of the most popular dynamical electron diffraction calculation procedures in transmission electron microscopy, was introduced to calculate reflection high-energy electron diffraction (RHEED) as it is well adapted to deal with the deviations from the periodicity in the direction parallel to the surface. However, in the present work, we show that the CMS method is no longer sufficiently accurate for simulating RHEED with the accelerating voltage 3-100 kV because of the high-energy approximation. An accurate multislice (AMS) method can be an alternative for more accurate RHEED calculations with reasonable computing time. A detailed comparison of the numerical calculation of the AMS method and the CMS method is carried out with respect to different accelerating voltages, surface structure models, Debye-Waller factors and glancing angles.
Accurate SHAPE-directed RNA structure determination
Deigan, Katherine E.; Li, Tian W.; Mathews, David H.; Weeks, Kevin M.
2009-01-01
Almost all RNAs can fold to form extensive base-paired secondary structures. Many of these structures then modulate numerous fundamental elements of gene expression. Deducing these structure–function relationships requires that it be possible to predict RNA secondary structures accurately. However, RNA secondary structure prediction for large RNAs, such that a single predicted structure for a single sequence reliably represents the correct structure, has remained an unsolved problem. Here, we demonstrate that quantitative, nucleotide-resolution information from a SHAPE experiment can be interpreted as a pseudo-free energy change term and used to determine RNA secondary structure with high accuracy. Free energy minimization, by using SHAPE pseudo-free energies, in conjunction with nearest neighbor parameters, predicts the secondary structure of deproteinized Escherichia coli 16S rRNA (>1,300 nt) and a set of smaller RNAs (75–155 nt) with accuracies of up to 96–100%, which are comparable to the best accuracies achievable by comparative sequence analysis. PMID:19109441
Isomerism of Cyanomethanimine: Accurate Structural, Energetic, and Spectroscopic Characterization.
Puzzarini, Cristina
2015-11-25
The structures, relative stabilities, and rotational and vibrational parameters of the Z-C-, E-C-, and N-cyanomethanimine isomers have been evaluated using state-of-the-art quantum-chemical approaches. Equilibrium geometries have been calculated by means of a composite scheme based on coupled-cluster calculations that accounts for the extrapolation to the complete basis set limit and core-correlation effects. The latter approach is proved to provide molecular structures with an accuracy of 0.001-0.002 Å and 0.05-0.1° for bond lengths and angles, respectively. Systematically extrapolated ab initio energies, accounting for electron correlation through coupled-cluster theory, including up to single, double, triple, and quadruple excitations, and corrected for core-electron correlation and anharmonic zero-point vibrational energy, have been used to accurately determine relative energies and the Z-E isomerization barrier with an accuracy of about 1 kJ/mol. Vibrational and rotational spectroscopic parameters have been investigated by means of hybrid schemes that allow us to obtain rotational constants accurate to about a few megahertz and vibrational frequencies with a mean absolute error of ∼1%. Where available, for all properties considered, a very good agreement with experimental data has been observed.
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.
Accurate Nanoscale Crystallography in Real-Space Using Scanning Transmission Electron Microscopy.
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.
Lambrechts, P; Vanherle, G; Davidson, C
1981-09-01
One of the main concerns of dental research is the observation of the oral tissues and the materials applied to the dentition. The changes in composition and structure of the outer surfaces and the materials deposited on these surfaces are of special interest. In the literature, a variety of replica techniques for these purposes is described (Grundy in 1971 [12]; Saxton in 1973 [25]). The use of these techniques is limited because of artifacts in the samples, and a restricted resolution power resulting from useful magnifications in the order of 800x. An accurate and universal replica technique for the examination of specimens to be viewed under the SEM has been developed. The first impression is made by a light body silicone elastomer (President Coltene). The positive replica is made by electrodeposition of copper in an electro plating bath (Acru plat 5 electronic, Dr. Th. Wieland, D-7530 Pforzheim). The reliability and accuracy of this replica technique was verified by a scanning electron microscopic comparison of the replicas and the actual structures of etched enamel. To illustrate the applicability of the replica technique to structures with much lower hardness, also high resolution images of dental plaque were produced. The copper surface offers a perfect, original and proper electroconductive medium that withstands the bombardment of electrons and the relatively severe conditions in the scanning electron microscope. Reproducibility was accurate as judged by the duplication in position, size, and shape of the fine detail at magnifications of 7500x offering a resolution of 25 nm.
Surface electron density models for accurate ab initio molecular dynamics with electronic friction
NASA Astrophysics Data System (ADS)
Novko, D.; Blanco-Rey, M.; Alducin, M.; Juaristi, J. I.
2016-06-01
Ab initio molecular dynamics with electronic friction (AIMDEF) is a valuable methodology to study the interaction of atomic particles with metal surfaces. This method, in which the effect of low-energy electron-hole (e-h) pair excitations is treated within the local density friction approximation (LDFA) [Juaristi et al., Phys. Rev. Lett. 100, 116102 (2008), 10.1103/PhysRevLett.100.116102], can provide an accurate description of both e-h pair and phonon excitations. In practice, its applicability becomes a complicated task in those situations of substantial surface atoms displacements because the LDFA requires the knowledge at each integration step of the bare surface electron density. In this work, we propose three different methods of calculating on-the-fly the electron density of the distorted surface and we discuss their suitability under typical surface distortions. The investigated methods are used in AIMDEF simulations for three illustrative adsorption cases, namely, dissociated H2 on Pd(100), N on Ag(111), and N2 on Fe(110). Our AIMDEF calculations performed with the three approaches highlight the importance of going beyond the frozen surface density to accurately describe the energy released into e-h pair excitations in case of large surface atom displacements.
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
NASA Astrophysics Data System (ADS)
Frolov, Alexei M.; Wardlaw, David M.
2016-09-01
We discuss an approach to accurate numerical computations of slowly convergent properties in two-electron atoms/ions which include the negatively charged Ps- ( e - e + e -) and H- ions, He atom and positively charged, helium-like ions from Li+ to Ni26+. All these ions are considered in their ground 11S-state(s). The slowly convergent properties selected in this study include the electron-nulceus ( r 2k eN) and electron-electron ( r 2k ee) expectation values for k = 2, 3, 4 and 5.
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.
Accurate characterization of Monte Carlo calculated electron beams for radiotherapy.
Ma, C M; Faddegon, B A; Rogers, D W; Mackie, T R
1997-03-01
Monte Carlo studies of dose distributions in patients treated with radiotherapy electron beams would benefit from generalized models of clinical beams if such models introduce little error into the dose calculations. Methodology is presented for the design of beam models, including their evaluation in terms of how well they preserve the character of the clinical beam, and the effect of the beam models on the accuracy of dose distributions calculated with Monte Carlo. This methodology has been used to design beam models for electron beams from two linear accelerators, with either a scanned beam or a scattered beam. Monte Carlo simulations of the accelerator heads are done in which a record is kept of the particle phase-space, including the charge, energy, direction, and position of every particle that emerges from the treatment head, along with a tag regarding the details of the particle history. The character of the simulated beams are studied in detail and used to design various beam models from a simple point source to a sophisticated multiple-source model which treats particles from different parts of a linear accelerator as from different sub-sources. Dose distributions calculated using both the phase-space data and the multiple-source model agree within 2%, demonstrating that the model is adequate for the purpose of Monte Carlo treatment planning for the beams studied. Benefits of the beam models over phase-space data for dose calculation are shown to include shorter computation time in the treatment head simulation and a smaller disk space requirement, both of which impact on the clinical utility of Monte Carlo treatment planning.
Accurate Classification of RNA Structures Using Topological Fingerprints
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
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…
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.
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
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.
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. PMID:27240749
Linear Scaling Electronic Structure Methods with Periodic Boundary Conditions
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.
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.
Electronics for Piezoelectric Smart Structures
NASA Technical Reports Server (NTRS)
Warkentin, D. J.; Tani, J.
1997-01-01
This paper briefly presents work addressing some of the basic considerations for the electronic components used in smart structures incorporating piezoelectric elements. After general remarks on the application of piezoelectric elements to the problem of structural vibration control, three main topics are described. Work to date on the development of techniques for embedding electronic components within structural parts is presented, followed by a description of the power flow and dissipation requirements of those components. Finally current work on the development of electronic circuits for use in an 'active wall' for acoustic noise is introduced.
Lorber, Bernard
2002-09-23
The crystallization of proteins and other biological particles (including nucleic acids, nucleo-protein complexes and large assemblies such as nucleosomes, ribosomal subunits or viruses) in a microgravity environment can produce crystals having lesser defects than crystals prepared under normal gravity on earth. Such microgravity-grown crystals can diffract X-rays to a higher resolution and have a lower mosaic spread. The inferred electron density maps can be richer in details owing to which more accurate three-dimensional structure models can be built. Major results reported in this field of research are reviewed. Novel ones obtained with the Advanced Protein Crystallization Facility are presented. For structural biology, practical applications and implications associated with crystallization and crystallography onboard the International Space Station are discussed.
Accurate measurements of the collision stopping powers for 5 to 30 MeV electrons
NASA Astrophysics Data System (ADS)
MacPherson, Miller Shawn
Accurate knowledge of electron stopping powers is crucial for accurate radiation dosimetry and radiation transport calculations. Current values for stopping powers are based on a theoretical model, with estimated uncertainties of 0.5-1% (1σ) for electron energies greater than 100 keV. This work presents the first measurements of electron collision stopping powers capable of testing the theoretical values within these stated uncertainties. A large NaI spectrometer was used to measure the change in electron energy when an absorbing disk of known thickness was placed in an electron beam. Monte Carlo simulations of the experiment were performed to account for the effects of surrounding materials. Energy differences between the calculated and measured spectra were used to determine corrections to the soft collision component of the theoretical stopping powers employed by the Monte Carlo simulations. Four different elemental materials were studied: Be, Al, Cu, and Ta. This provided a wide range of atomic numbers and densities over which to test the theory. In addition, stopping powers were measured for graphite (both standard and pyrolytic), A-150 tissue equivalent plastic, C-552 air equivalent plastic, and water. The incident electron energies ranged from 5 to 30 MeV. Generally, the measured stopping powers agree with the theoretical values within the experimental uncertainties, which range from 0.4% to 0.7% (1σ). Aluminum, however, exhibits a 0.7% discrepancy at higher electron energies. Furthermore, these measurements have established that the grain density stopping power is appropriate for graphite, contrary to the recommendations of ICRU Report 37. This removes a 0.2% uncertainty in air kerma calibrations, and impacts on dosimetric quantities determined via graphite calorimetry, such as ɛG for Fricke dosimetry and (W/ e)air for ion chamber measurements.
Fitmunk: improving protein structures by accurate, automatic modeling of side-chain conformations.
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/.
Fitmunk: improving protein structures by accurate, automatic modeling of side-chain conformations
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
Fitmunk: improving protein structures by accurate, automatic modeling of side-chain conformations.
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/. PMID:26894674
Johnson, Erin R; Contreras-García, Julia
2011-08-28
We develop a new density-functional approach combining physical insight from chemical structure with treatment of multi-reference character by real-space modeling of the exchange-correlation hole. We are able to recover, for the first time, correct fractional-charge and fractional-spin behaviour for atoms of groups 1 and 2. Based on Becke's non-dynamical correlation functional [A. D. Becke, J. Chem. Phys. 119, 2972 (2003)] and explicitly accounting for core-valence separation and pairing effects, this method is able to accurately describe dissociation and strong correlation in s-shell many-electron systems.
An accurate single-electron pump based on a highly tunable silicon quantum dot.
Rossi, Alessandro; Tanttu, Tuomo; Tan, Kuan Yen; Iisakka, Ilkka; Zhao, Ruichen; Chan, Kok Wai; Tettamanzi, Giuseppe C; Rogge, Sven; Dzurak, Andrew S; Möttönen, Mikko
2014-06-11
Nanoscale single-electron pumps can be used to generate accurate currents, and can potentially serve to realize a new standard of electrical current based on elementary charge. Here, we use a silicon-based quantum dot with tunable tunnel barriers as an accurate source of quantized current. The charge transfer accuracy of our pump can be dramatically enhanced by controlling the electrostatic confinement of the dot using purposely engineered gate electrodes. Improvements in the operational robustness, as well as suppression of nonadiabatic transitions that reduce pumping accuracy, are achieved via small adjustments of the gate voltages. We can produce an output current in excess of 80 pA with experimentally determined relative uncertainty below 50 parts per million.
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).
French, Dustin D; Gill, Manjot; Mitchell, Christopher; Jackson, Kathryn; Kho, Abel; Bryar, Paul J
2016-01-01
Background Visual acuity is the primary measure used in ophthalmology to determine how well a patient can see. Visual acuity for a single eye may be recorded in multiple ways for a single patient visit (eg, Snellen vs. Jäger units vs. font print size), and be recorded for either distance or near vision. Capturing the best documented visual acuity (BDVA) of each eye in an individual patient visit is an important step for making electronic ophthalmology clinical notes useful in research. Objective Currently, there is limited methodology for capturing BDVA in an efficient and accurate manner from electronic health record (EHR) notes. We developed an algorithm to detect BDVA for right and left eyes from defined fields within electronic ophthalmology clinical notes. Methods We designed an algorithm to detect the BDVA from defined fields within 295,218 ophthalmology clinical notes with visual acuity data present. About 5668 unique responses were identified and an algorithm was developed to map all of the unique responses to a structured list of Snellen visual acuities. Results Visual acuity was captured from a total of 295,218 ophthalmology clinical notes during the study dates. The algorithm identified all visual acuities in the defined visual acuity section for each eye and returned a single BDVA for each eye. A clinician chart review of 100 random patient notes showed a 99% accuracy detecting BDVA from these records and 1% observed error. Conclusions Our algorithm successfully captures best documented Snellen distance visual acuity from ophthalmology clinical notes and transforms a variety of inputs into a structured Snellen equivalent list. Our work, to the best of our knowledge, represents the first attempt at capturing visual acuity accurately from large numbers of electronic ophthalmology notes. Use of this algorithm can benefit research groups interested in assessing visual acuity for patient centered outcome. All codes used for this study are currently
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.
NASA Astrophysics Data System (ADS)
Dominguez, Jesus A.; Tate, Lanetra C.; Wright, M. Clara; Caraccio, Anne
2013-12-01
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.
NASA Astrophysics Data System (ADS)
Feller, David; Peterson, Kirk A.; Dixon, David A.
2008-11-01
High level electronic structure predictions of thermochemical properties and molecular structure are capable of accuracy rivaling the very best experimental measurements as a result of rapid advances in hardware, software, and methodology. Despite the progress, real world limitations require practical approaches designed for handling general chemical systems that rely on composite strategies in which a single, intractable calculation is replaced by a series of smaller calculations. As typically implemented, these approaches produce a final, or "best," estimate that is constructed from one major component, fine-tuned by multiple corrections that are assumed to be additive. Though individually much smaller than the original, unmanageable computational problem, these corrections are nonetheless extremely costly. This study presents a survey of the widely varying magnitude of the most important components contributing to the atomization energies and structures of 106 small molecules. It combines large Gaussian basis sets and coupled cluster theory up to quadruple excitations for all systems. In selected cases, the effects of quintuple excitations and/or full configuration interaction were also considered. The availability of reliable experimental data for most of the molecules permits an expanded statistical analysis of the accuracy of the approach. In cases where reliable experimental information is currently unavailable, the present results are expected to provide some of the most accurate benchmark values available.
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.
Electronic structure interpolation via atomic orbitals.
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.
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 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
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.
NASA Astrophysics Data System (ADS)
Yao, Y. X.; Liu, J.; Liu, C.; Lu, W. C.; Wang, C. Z.; Ho, K. M.
2015-08-01
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.
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
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.
2012-01-01
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 15N 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 15N 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 15N. 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. PMID:22329704
Electronic structure of Calcium hexaborides
Lee, Byounghak; Wang, Lin-Wang
2005-06-15
We present a theoretical study of crystal and electronic structures of CaB6 within a screened-exchange local density approximation (sX-LDA). Our ab initio total energy calculations show that CaB6 is a semiconductor with a gap of >1.2 eV, in agreement with recent experimental observations. We show a very sensitive band gap dependence on the crystal internal parameter, which might partially explain the scatter of previous theoretical results. Our calculation demonstrates that it is essential to study this system simultaneously for both crystal structures and electronic properties, and that the sX-LDA provides an ideal method for this problem.
Electron Coherence in Mesoscopic Structures
Kamenev, Alex; Glazman, Leonid
2011-03-20
The recent rapid progress in nanofabrication and experimental techniques made it possible to investigate a variety of meso-- and nano--scale systems, which were unavailable only a few years ago. Examples include fabrication of high-quality quantum wires in semiconductor heterostructures, of nanoscale hybrid superconductor--normal metal structures, and of a variety of novel (and much smaller) quantum dot and q-bit designs. These technological advances have led to formulation of a number of condensed matter theory problems which are equally important for applications and for the fundamental science. The present proposal aims at filling the exposed gaps in knowledge and at facilitating further development of experimental and theoretical physics of nanoscale structures. Specifically, the two PIs address the following issues: (i) The theory of interacting electrons in a quantum wire which accounts adequately for the non-linear dispersion relation of the electrons. The existing approaches rely on models with {\\em linearized} electron spectrum, which fall short of addressing a growing list of experimentally relevant phenomena. (ii) Dynamics of hybrid normal--superconducting systems. A reliable treatment of dissipative phenomena in such structures is not developed as of yet, while rapid progress in fabrication makes finding the proper theoretical treatment methods highly desirable. (iii)~The fundamental limits on relaxation times of a superconducting charge q-bit. The latter is one of the most advanced scalable realizations of a quantum computing device. (iv)~The dynamics and relaxation times of a spin of an electron in a small semiconductor quantum dot. Besides the fundamental importance, these structures are also valuable candidates for quantum computing applications.
Electronic Structure of Few-Electron Quantum Dot Molecules
NASA Astrophysics Data System (ADS)
Popsueva, V.; Hansen, J. P.; Caillat, J.
2007-12-01
We present a study of strongly correlated few-electron quantum dots, exploring the spectra of various few-electron quantum dot molecules: a double (diatomic) structure a quadruple two-electron quantum dot, and a three-electron double dot. Electron energy spectra are computed for different values of dot separation. All spectra show clear band structures and can be understood from asymptotical properties of the system.
A quantum accurate waveform synthesizer as a voltage reference for an electronic primary thermometer
NASA Astrophysics Data System (ADS)
Pollarolo, Alessio; Benz, Samuel; Rogalla, Horst; Dresselhaus, Paul
2014-03-01
We are using a quantum voltage noise source (QVNS) for use as an intrinsically accurate voltage reference for a new type of electronic temperature standard. In Johnson Noise Thermometry (JNT) the noise of a resistor is used to measure temperature or Boltzmann's constant k, because the Nyquist equation
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.
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.
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.
Electronic Structure of B12 coenzymes
NASA Astrophysics Data System (ADS)
Ouyang, Lizhi; Ching, W. Y.; Randaccio, Lucio
2001-06-01
We have carried out an ab-initio local density functional calculations of the two most important B12 coenzymes, adoensyl-cobalamin (Ado-Cbl) and methyl-cobalamin (Me-Cbl). The crystal structures were determined by accurate X-ray synchrotron radiation measurements. Both crystals have space group P2121 with four molecules, or about 800 atoms, per unit cell. Our electronic structure calculation is based on one full molecule including the side chains. Results are analyzed in terms of atom and orbital resolved partial density of states (PDOS), Mulliken effective charges and bond orders. The PDOS analysis shows that the Co complexes of both B12 coenzymes had a HOMO/LUMO gap of about 1.5 eV. The Co-C bond order in Me-Cbl is smaller than that in Ado-Cbl. This appears to be in contradiction with the measured bond dissociated energies. However, this could also indicate the importance of the effects of solvents, which were not included in the calculation. We are investigating whether the effect of the solvents could dramatically modify the electronic structures of Ado-Cbl and Me-Cbl.
Communication: An accurate global potential energy surface for the ground electronic state of ozone
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.
Puzzarini, Cristina; Biczysko, Malgorzata; Barone, Vincenzo; Peña, Isabel; Cabezas, Carlos; Alonso, José L
2013-10-21
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 the accurate molecular structure and spectroscopic properties of the title molecule, but more importantly, it demonstrates a reliable approach for the accurate investigation of isolated small biomolecules.
Pentacene Derivatives: Electronic Structure and Spectra
NASA Astrophysics Data System (ADS)
Netusil, Ross; Ilie, Carolina; Kane, Thorin; Damkaci, Fehmi
2013-03-01
The variation in composition and structure of the substituent groups of pentacene compounds promises a broad range of electronic structures and behaviors and provides a vast and alluring field of inquiry with avenues of exploration. These include the development of synthetic schema, the process of design for novel derivatives and, in order to identify those hypothesized compounds which demonstrate the desired behavior, the identification and refinement of computational tools that make accurate predictions about the electronic behavior of theoretical compounds. Two computational techniques and six pentacene derivatives are here examined. One technique was used to predict the vibrational spectra of the compounds, in order to both acquire data about the optical conductivity of the compounds and to establish a pool of theoretical data against which experimental data will be compared. The molecular orbital energy level diagram of the same six compounds was derived using a second approach, with the same goals of discerning between valid and invalid predictive schema by comparison with pending experimental data and between hypothesized compounds which show promise and those which present little potential for use in organic semiconductor technology.
Electronic Structure of Ethynyl Substituted Cyclobutadienes
NASA Astrophysics Data System (ADS)
Emmert, Frank Lee Emmert, III; Thompson, Stephanie J.; Slipchenko, Lyudmila V.
2011-06-01
We investigated the effects of ethynyl substitution on the electronic structure of cyclobutadiene. These species are involved in Bergman Cyclization reactionsand are possible intermediates in the formation of fullerenes and graphite sheets. Prediction of the electronic energy of cyclobutadiene is challenging for single-reference ab initio methods such as HF, MP2 or DFT because of Jahn-Teller distortions and the diradical character of the singlet state. We determined the vertical and adiabatic singlet-triplet energy splittings, the natural charges and spin densities in substituted cyclobutadienes, using the equations of motion spin flip coupled cluster with single and double excitations (EOM-SF-CCSD) method that accurately describes diradical states. The adiabatic singlet-triplet gaps decrease upon substituent addition, but the singlet state is always lower in energy. However, we found that the results are affected by spin-contamination of the reference state and deteriorate when an unrestricted HF reference is employed. O. L. Chapman, C. L. McIntosh, J. Pacansky, "Cyclobutadiene" J. Am. Chem. Soc. 1973, 95, (2), 614-617. N. S. Goroff, "Mechanism of Fullerene Formation." Acc. Chem. Res. 1996, 29, (2), 77-83. L.V. Slipchenko and A.I. Krylov, "Singlet-triplet gaps in diradicals by the Spin-Flip approach: A benchmark study", J. Chem. Phys. 2002, 117, 4694-4708.
An accurate, efficient algorithm for calculation of quantum transport in extended structures
Godin, T.J.; Haydock, R.
1994-05-01
In device structures with dimensions comparable to carrier inelastic scattering lengths, the quantum nature of carriers will cause interference effects that cannot be modeled by conventional techniques. The basic equations that govern these ``quantum`` circuit elements present significant numerical challenges. The authors describe the block recursion method, an accurate, efficient method for solving the quantum circuit problem. They demonstrate this method by modeling dirty inversion layers.
Electronic Structure of Dense Plasmas by X-Ray Scattering
Gregori, G; Glenzer, S H; Rogers, F J; Pollaine, S M; Froula, D H; Blancard, C; Faussurier, G; Renaudin, P; Kuhlbrodt, S; Redmer, R; Landen, O L
2003-10-07
We present an improved analytical expression for the x-ray dynamic structure factor from a dense plasma which includes the effects of weakly bound electrons. This result can be applied to describe scattering from low to moderate Z plasmas, and it covers the entire range of plasma conditions that can be found in inertial confinement fusion experiments, from ideal to degenerate up to moderately coupled systems. We use our theory to interpret x-ray scattering experiments from solid density carbon plasma and to extract accurate measurements of electron temperature, electron density and charge state. We use our experimental results to validate various equation-of-state models for carbon plasmas.
Electronic structure of herbicides: Atrazine and bromoxynil
NASA Astrophysics Data System (ADS)
Novak, Igor; Kovač, Branka
2011-06-01
The electronic structures of herbicides atrazine and bromoxynil have been investigated by UV photoelectron spectroscopy (UPS), quantum chemical calculations and comparison with X-ray diffraction, molecular docking and molecular dynamics studies. Their electronic and molecular structures are discussed in the context of their biological activity. This is the first report which correlates the molecular mechanism of biological activity of these herbicides with their experimentally determined electronic and molecular structures.
CoMOGrad and PHOG: From Computer Vision to Fast and Accurate Protein Tertiary Structure Retrieval
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
NASA Astrophysics Data System (ADS)
Oudini, N.; Sirse, N.; Taccogna, F.; Ellingboe, A. R.; Bendib, A.
2016-09-01
Laser pulse induced photo-detachment combined with Langmuir probing has been introduced to diagnose plasma electronegativity. This technique uses a laser pulse to convert negative ions into electron-atom pairs and tracks the change of electron saturation current by a Langmuir probe. The existing model determines plasma electronegativity as the ratio of electron saturation current before and after detachment. However, this model depends on various assumptions and neglects the formation of a potential barrier between the laser channel and surrounding electronegative plasma. In this letter, we present a new analytical model to analyze photo-detachment signals in order to improve the accuracy of electronegativity measurements and extend this technique for measuring electron temperature and charged species density. This analytical model is supported by Particle-In-Cell simulation of electronegative plasma dynamics following laser photo-detachment. The analysis of the signal, detected on a simulated probe, shows that the present analytical model determines electronegativity, electron temperature, and plasma density with a relative error of ˜20%, ˜20%, and ˜50%, respectively, whereas the electronegativity obtained from a previous model is underestimated by an order of magnitude.
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.
Accurate electron affinity of Pb and isotope shifts of binding energies of Pb(.).
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. PMID:27586918
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.
Accurate simulation of the electron cloud in the Fermilab Main Injector with VORPAL
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.
NASA Technical Reports Server (NTRS)
Livne, Eli
1989-01-01
A method is presented for generating mode shapes for model order reduction in a way that leads to accurate calculation of eigenvalue derivatives and eigenvalues for a class of control augmented structures. The method is based on treating degrees of freedom where control forces act or masses are changed in a manner analogous to that used for boundary degrees of freedom in component mode synthesis. It is especially suited for structures controlled by a small number of actuators and/or tuned by a small number of concentrated masses whose positions are predetermined. A control augmented multispan beam with closely spaced natural frequencies is used for numerical experimentation. A comparison with reduced-order eigenvalue sensitivity calculations based on the normal modes of the structure shows that the method presented produces significant improvements in accuracy.
Are In-Bed Electronic Weights Recorded in the Medical Record Accurate?
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. PMID:27522846
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.
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.
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.
NASA Astrophysics Data System (ADS)
Chachiyo, Teepanis
2016-07-01
A simple correlation energy functional for the uniform electron gas is derived based on the second-order Moller-Plesset perturbation theory. It can reproduce the known correlation functional in the high-density limit, while in the mid-density range maintaining a good agreement with the near-exact correlation energy of the uniform electron gas to within 2 × 10-3 hartree. The correlation energy is a function of a density parameter rs and is of the form a * ln ( 1 + /b r s + /b rs 2 ) . The constants "a" and "b" are derived from the known correlation functional in the high-density limit. Comparisons to the Ceperley-Alder's near-exact Quantum Monte Carlo results and the Vosko-Wilk-Nusair correlation functional are also reported.
Electron tomography of dislocation structures
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.
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.
Accurate simulation of the electron cloud in the Fermilab Main Injector with VORPAL
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.
NASA Astrophysics Data System (ADS)
Roberts, B. M.; Dzuba, V. A.; Flambaum, V. V.; Pospelov, M.; Stadnik, Y. V.
2016-06-01
We revisit the WIMP-type dark matter scattering on electrons that results in atomic ionization and can manifest itself in a variety of existing direct-detection experiments. Unlike the WIMP-nucleon scattering, where current experiments probe typical interaction strengths much smaller than the Fermi constant, the scattering on electrons requires a much stronger interaction to be detectable, which in turn requires new light force carriers. We account for such new forces explicitly, by introducing a mediator particle with scalar or vector couplings to dark matter and to electrons. We then perform state-of-the-art numerical calculations of atomic ionization relevant to the existing experiments. Our goals are to consistently take into account the atomic physics aspect of the problem (e.g., the relativistic effects, which can be quite significant) and to scan the parameter space—the dark matter mass, the mediator mass, and the effective coupling strength—to see if there is any part of the parameter space that could potentially explain the DAMA modulation 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.
NASA Astrophysics Data System (ADS)
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°.
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°.
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.
Electronic structures of endohedral fullerenes
Jin, Changming; Hettich, R.L.; Puretzky, A.A.; Ying, Z.C.; Haufler, R.E.; Compton, R.N.
1994-12-31
Fullerenes with different elements trapped inside the cage have been the subject of active research both experimentally and theoretically ever since the initial discovery of C{sub 60}. La@C{sub n}, were the first endohedral fullerenes produced both in gas phase and in macroscopic quantities. Early electron spin resonance investigation of La@C{sub 82} by R.D. Johnson, et.al indicated that La transfer nearly all of the three valence electrons to the fullerene cage, forming a La{sup 3+}@C{sub 82}{sup 3-} complex. Theoretical calculations also have shown that La transfers its valence electrons to the fullerene cage in molecules of La@C{sub n}. Investigations with ultraviolet photoelectron spectroscopy by L. Wang, et.al. indicated that attaching a potassium atom outside the C{sub 60} cage lowers the electron affinity (EA) while trapping Ca atom inside the C{sub 60} sphere increases the EA compared with parent C{sub 60} molecule. These results indicate that metallofullerenes appear to have substantially lower ionization potentials (IP) and higher EA than empty fullerenes.
Electron gun controlled smart structure
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.
An electronic structure perspective of graphene interfaces
NASA Astrophysics Data System (ADS)
Schultz, Brian J.; Dennis, Robert V.; Lee, Vincent; Banerjee, Sarbajit
2014-03-01
The unusual electronic structure of graphene characterized by linear energy dispersion of bands adjacent to the Fermi level underpins its remarkable transport properties. However, for practical device integration, graphene will need to be interfaced with other materials: 2D layered structures, metals (as ad-atoms, nanoparticles, extended surfaces, and patterned metamaterial geometries), dielectrics, organics, or hybrid structures that in turn are constituted from various inorganic or organic components. The structural complexity at these nanoscale interfaces holds much promise for manifestation of novel emergent phenomena and provides a means to modulate the electronic structure of graphene. In this feature article, we review the modifications to the electronic structure of graphene induced upon interfacing with disparate types of materials with an emphasis on iterative learnings from theoretical calculations and electronic spectroscopy (X-ray absorption fine structure (XAFS) spectroscopy, scanning transmission X-ray microscopy (STXM), angle-resolved photoemission spectroscopy (ARPES), and X-ray magnetic circular dichroism (XMCD)). We discuss approaches for engineering and modulating a bandgap in graphene through interfacial hybridization, outline experimental methods for examining electronic structure at interfaces, and overview device implications of engineered interfaces. A unified view of how geometric and electronic structure are correlated at interfaces will provide a rational means for designing heterostructures exhibiting emergent physical phenomena with implications for plasmonics, photonics, spintronics, and engineered polymer and metal matrix composites.
An electronic structure perspective of graphene interfaces.
Schultz, Brian J; Dennis, Robert V; Lee, Vincent; Banerjee, Sarbajit
2014-04-01
The unusual electronic structure of graphene characterized by linear energy dispersion of bands adjacent to the Fermi level underpins its remarkable transport properties. However, for practical device integration, graphene will need to be interfaced with other materials: 2D layered structures, metals (as ad-atoms, nanoparticles, extended surfaces, and patterned metamaterial geometries), dielectrics, organics, or hybrid structures that in turn are constituted from various inorganic or organic components. The structural complexity at these nanoscale interfaces holds much promise for manifestation of novel emergent phenomena and provides a means to modulate the electronic structure of graphene. In this feature article, we review the modifications to the electronic structure of graphene induced upon interfacing with disparate types of materials with an emphasis on iterative learnings from theoretical calculations and electronic spectroscopy (X-ray absorption fine structure (XAFS) spectroscopy, scanning transmission X-ray microscopy (STXM), angle-resolved photoemission spectroscopy (ARPES), and X-ray magnetic circular dichroism (XMCD)). We discuss approaches for engineering and modulating a bandgap in graphene through interfacial hybridization, outline experimental methods for examining electronic structure at interfaces, and overview device implications of engineered interfaces. A unified view of how geometric and electronic structure are correlated at interfaces will provide a rational means for designing heterostructures exhibiting emergent physical phenomena with implications for plasmonics, photonics, spintronics, and engineered polymer and metal matrix composites.
DR-TAMAS: Diffeomorphic Registration for Tensor Accurate Alignment of Anatomical Structures.
Irfanoglu, M Okan; Nayak, Amritha; Jenkins, Jeffrey; Hutchinson, Elizabeth B; Sadeghi, Neda; Thomas, Cibu P; Pierpaoli, Carlo
2016-05-15
In this work, we propose DR-TAMAS (Diffeomorphic Registration for Tensor Accurate alignMent of Anatomical Structures), a novel framework for intersubject registration of Diffusion Tensor Imaging (DTI) data sets. This framework is optimized for brain data and its main goal is to achieve an accurate alignment of all brain structures, including white matter (WM), gray matter (GM), and spaces containing cerebrospinal fluid (CSF). Currently most DTI-based spatial normalization algorithms emphasize alignment of anisotropic structures. While some diffusion-derived metrics, such as diffusion anisotropy and tensor eigenvector orientation, are highly informative for proper alignment of WM, other tensor metrics such as the trace or mean diffusivity (MD) are fundamental for a proper alignment of GM and CSF boundaries. Moreover, it is desirable to include information from structural MRI data, e.g., T1-weighted or T2-weighted images, which are usually available together with the diffusion data. The fundamental property of DR-TAMAS is to achieve global anatomical accuracy by incorporating in its cost function the most informative metrics locally. Another important feature of DR-TAMAS is a symmetric time-varying velocity-based transformation model, which enables it to account for potentially large anatomical variability in healthy subjects and patients. The performance of DR-TAMAS is evaluated with several data sets and compared with other widely-used diffeomorphic image registration techniques employing both full tensor information and/or DTI-derived scalar maps. Our results show that the proposed method has excellent overall performance in the entire brain, while being equivalent to the best existing methods in WM.
Structural change of graphite during electron irradiation
Koike, J. . Dept. of Mechanical Engineering); Pedraza, D.F. )
1992-01-01
Highly oriented pyrolytic graphite was irradiated at room temperature with 300-keV electrons. High resolution transmission electron microscopy and electron energy loss spectroscopy were employed to study the structure of electron-irradiated graphite. Results consistently indicated absence of long-range order periodicity in the basal plane, and loose retention of the c-axis periodicity. Structure was modeled based on a mixture of sixfold and non-sixfold atom rings. Formation of non-sixfold atom rings was related to the observed buckling and discontinuity of the original graphite basal plane.
Structural change of graphite during electron irradiation
Koike, J.; Pedraza, D.F.
1992-12-31
Highly oriented pyrolytic graphite was irradiated at room temperature with 300-keV electrons. High resolution transmission electron microscopy and electron energy loss spectroscopy were employed to study the structure of electron-irradiated graphite. Results consistently indicated absence of long-range order periodicity in the basal plane, and loose retention of the c-axis periodicity. Structure was modeled based on a mixture of sixfold and non-sixfold atom rings. Formation of non-sixfold atom rings was related to the observed buckling and discontinuity of the original graphite basal plane.
Fast and accurate search for non-coding RNA pseudoknot structures in genomes
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
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.
Structural physiology based on electron crystallography
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
Electronic structure of metallic glasses
Oelhafen, P.; Lapka, R.; Gubler, U.; Krieg, J.; DasGupta, A.; Guentherodt, H.J.; Mizoguchi, T.; Hague, C.; Kuebler, J.; Nagel, S.R.
1981-01-01
This paper is organized in six sections and deals with (1) the glassy transition metal alloys, their d-band structure, the d-band shifts on alloying and their relation to the alloy heat of formation (..delta..H) and the glass forming ability, (2) the glass to crystal phase transition viewed by valence band spectroscopy, (3) band structure calculations, (4) metallic glasses prepared by laser glazing, (5) glassy normal metal alloys, and (6) glassy hydrides.
Hoyer, Chad E; Ghosh, Soumen; Truhlar, Donald G; Gagliardi, Laura
2016-02-01
A correct description of electronically excited states is critical to the interpretation of visible-ultraviolet spectra, photochemical reactions, and excited-state charge-transfer processes in chemical systems. We have recently proposed a theory called multiconfiguration pair-density functional theory (MC-PDFT), which is based on a combination of multiconfiguration wave function theory and a new kind of density functional called an on-top density functional. Here, we show that MC-PDFT with a first-generation on-top density functional performs as well as CASPT2 for an organic chemistry database including valence, Rydberg, and charge-transfer excitations. The results are very encouraging for practical applications. PMID:26794241
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.
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.
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
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.
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.
Accurate Exchange-Correlation Energies for the Warm Dense Electron Gas.
Malone, Fionn D; Blunt, N S; Brown, Ethan W; Lee, D K K; Spencer, J S; Foulkes, W M C; Shepherd, James J
2016-09-01
The density matrix quantum Monte Carlo (DMQMC) method is used to sample exact-on-average N-body density matrices for uniform electron gas systems of up to 10^{124} matrix elements via a stochastic solution of the Bloch equation. The results of these calculations resolve a current debate over the accuracy of the data used to parametrize finite-temperature density functionals. Exchange-correlation energies calculated using the real-space restricted path-integral formalism and the k-space configuration path-integral formalism disagree by up to ∼10% at certain reduced temperatures T/T_{F}≤0.5 and densities r_{s}≤1. Our calculations confirm the accuracy of the configuration path-integral Monte Carlo results available at high density and bridge the gap to lower densities, providing trustworthy data in the regime typical of planetary interiors and solids subject to laser irradiation. We demonstrate that the DMQMC method can calculate free energies directly and present exact free energies for T/T_{F}≥1 and r_{s}≤2.
Accurate Exchange-Correlation Energies for the Warm Dense Electron Gas
NASA Astrophysics Data System (ADS)
Malone, Fionn D.; Blunt, N. S.; Brown, Ethan W.; Lee, D. K. K.; Spencer, J. S.; Foulkes, W. M. C.; Shepherd, James J.
2016-09-01
The density matrix quantum Monte Carlo (DMQMC) method is used to sample exact-on-average N -body density matrices for uniform electron gas systems of up to 10124 matrix elements via a stochastic solution of the Bloch equation. The results of these calculations resolve a current debate over the accuracy of the data used to parametrize finite-temperature density functionals. Exchange-correlation energies calculated using the real-space restricted path-integral formalism and the k -space configuration path-integral formalism disagree by up to ˜10 % at certain reduced temperatures T /TF≤0.5 and densities rs≤1 . Our calculations confirm the accuracy of the configuration path-integral Monte Carlo results available at high density and bridge the gap to lower densities, providing trustworthy data in the regime typical of planetary interiors and solids subject to laser irradiation. We demonstrate that the DMQMC method can calculate free energies directly and present exact free energies for T /TF≥1 and rs≤2 .
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.
Accurate Exchange-Correlation Energies for the Warm Dense Electron Gas.
Malone, Fionn D; Blunt, N S; Brown, Ethan W; Lee, D K K; Spencer, J S; Foulkes, W M C; Shepherd, James J
2016-09-01
The density matrix quantum Monte Carlo (DMQMC) method is used to sample exact-on-average N-body density matrices for uniform electron gas systems of up to 10^{124} matrix elements via a stochastic solution of the Bloch equation. The results of these calculations resolve a current debate over the accuracy of the data used to parametrize finite-temperature density functionals. Exchange-correlation energies calculated using the real-space restricted path-integral formalism and the k-space configuration path-integral formalism disagree by up to ∼10% at certain reduced temperatures T/T_{F}≤0.5 and densities r_{s}≤1. Our calculations confirm the accuracy of the configuration path-integral Monte Carlo results available at high density and bridge the gap to lower densities, providing trustworthy data in the regime typical of planetary interiors and solids subject to laser irradiation. We demonstrate that the DMQMC method can calculate free energies directly and present exact free energies for T/T_{F}≥1 and r_{s}≤2. PMID:27661699
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.
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.
Structure of Wet Specimens in Electron Microscopy
ERIC Educational Resources Information Center
Parsons, D. F.
1974-01-01
Discussed are past work and recent advances in the use of electron microscopes for viewing structures immersed in gas and liquid. Improved environmental chambers make it possible to examine wet specimens easily. (Author/RH)
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)
Low-energy structures of benzene clusters with a novel accurate potential surface.
Bartolomei, M; Pirani, F; Marques, J M C
2015-12-01
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.
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
Electronic structure calculations in arbitrary electrostatic environments
NASA Astrophysics Data System (ADS)
Watson, Mark A.; Rappoport, Dmitrij; Lee, Elizabeth M. Y.; Olivares-Amaya, Roberto; Aspuru-Guzik, Alán
2012-01-01
Modeling of electronic structure of molecules in electrostatic environments is of considerable relevance for surface-enhanced spectroscopy and molecular electronics. We have developed and implemented a novel approach to the molecular electronic structure in arbitrary electrostatic environments that is compatible with standard quantum chemical methods and can be applied to medium-sized and large molecules. The scheme denoted CheESE (chemistry in electrostatic environments) is based on the description of molecular electronic structure subject to a boundary condition on the system/environment interface. Thus, it is particularly suited to study molecules on metallic surfaces. The proposed model is capable of describing both electrostatic effects near nanostructured metallic surfaces and image-charge effects. We present an implementation of the CheESE model as a library module and show example applications to neutral and negatively charged molecules.
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.
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 ((2)A2), 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(2v) symmetry through the C-N axis.
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.
Toward Hamiltonian Adaptive QM/MM: Accurate Solvent Structures Using Many-Body Potentials.
Boereboom, Jelle M; Potestio, Raffaello; Donadio, Davide; Bulo, Rosa E
2016-08-01
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. PMID:27332140
Accurate Potential Energy Curves for the Ground Electronic States of NeH^{+} and ArH^{+}
NASA Astrophysics Data System (ADS)
Coxon, John A.; Hajigeorgiou, Photos G.
2013-06-01
All available microwave and infrared spectroscopic line positions for the ground electronic states of the molecular cations NeH^{+} and ArH^{+} were employed in a direct potential fitting procedure to determine compact analytical potential curves and radial functions describing breakdown of the Born-Oppenheimer approximation. For NeH^{+}, 17 adjustable parameters were required to represent a total of 183 line positions for 4 isotopologues, whereas for ArH^{+}, 23 adjustable parameters were required to represent 440 line positions for 6 isotopologues. The MLR3 potential energy functional form was employed, taking full account of the proper 1/r{^4} limiting long-range dependence of the ion-atom dispersion energy interactions. Accurate vibrational energies, rotational constants and centrifugal distortion constants have been calculated for both diatomic cations.
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.
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.
Sharma, Virag; Elghafari, Anas; Hiller, Michael
2016-06-20
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
Yamagata, Koichi; Yamanishi, Ayako; Kokubu, Chikara; Takeda, Junji; Sese, Jun
2016-05-01
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.
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
Observation of Electronic Structure Minima in High-Harmonic Generation
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.
Defect Induced Electronic Structure of Uranofullerene
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
Electronic structure of disordered conjugated polymers: Polythiophenes
Vukmirovic, Nenad; Wang, Lin-Wang
2008-11-26
Electronic structure of disordered semiconducting conjugated polymers was studied. Atomic structure was found from a classical molecular dynamics simulation and the charge patching method was used to calculate the electronic structure with the accuracy similar to the one of density functional theory in local density approximation. The total density of states, the local density of states at different points in the system and the wavefunctions of several states around the gap were calculated in the case of poly(3-hexylthiophene) (P3HT) and polythiophene (PT) systems to gain insight into the origin of disorder in the system, the degree of carrier localization and the role of chain interactions. The results indicated that disorder in the electronic structure of alkyl substituted polythiophenes comes from disorder in the conformation of individualchains, while in the case of polythiophene there is an additional contribution due to disorder in the electronic coupling between the chains. Each of the first several wavefunctions in the conduction and valence band of P3HT is localized over several rings of a single chain. It was shown that the localization can be caused in principle both by ring torsions and chain bending, however the effect of ring torsions is much stronger. PT wavefunctions are more complicated due to larger interchain electronic coupling and are not necessarily localized on a single chain.
The Electronic Structure of Heavy Element Complexes
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.
Supersampling method for efficient grid-based electronic structure calculations
NASA Astrophysics Data System (ADS)
Ryu, Seongok; Choi, Sunghwan; Hong, Kwangwoo; Kim, Woo Youn
2016-03-01
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.
Electronic structure of Si/disilicide interfaces
NASA Astrophysics Data System (ADS)
Fujitani, Hideaki; Asano, Setsuro
1990-01-01
Using supercells, the electronic structures of Si(111)/CoSi2 and Si(111)/NiSi2 interfaces are studied by the linear muffin-tin orbital atomic sphere approximation method (LMTO-ASA). Schottky barrier heights (SBH's) are strongly correlated with the interface atomic structures and are determined mainly by interface bonding states and the screening effect of the semiconductor. Metal-induced gap states (MIGS) are metal wave function tails caused by the Schottky barriers.
Electronic structure of Si/disilicide interfaces
NASA Astrophysics Data System (ADS)
Fujitani, Hideaki; Asano, Setsuro
1989-11-01
Using supercells, the electronic structures of Si(111)/CoSi 2 and Si(111)/NiSi 2 interfaces are studied by the linear muffin-tin orbital atomic sphere approximation method (LMTO-ASA). Schottky barrier heights (SBH's) are strongly correlated with the interface atomic structures and are determined mainly by interface bonding states and the screening effect of the semiconductor. Metal-induced gap states (MIGS) are metal wave function tails caused by the Schottky barriers.
Crystal structure refinement from electron diffraction data
Dudka, A. P. Avilov, A. S.; Lepeshov, G. G.
2008-05-15
A procedure of crystal structure refinement from electron diffraction data is described. The electron diffraction data on polycrystalline films are processed taking into account possible overlap of reflections and two-beam interaction. The diffraction from individual single crystals in an electron microscope equipped with a precession attachment is described using the Bloch-wave method, which takes into account multibeam scattering, and a special approach taking into consideration the specific features of the diffraction geometry in the precession technique. Investigations were performed on LiF, NaF, CaF{sub 2}, and Si crystals. A method for reducing experimental data, which allows joint electron and X-ray diffraction study, is proposed.
Beuc, R.; Movre, M.; Horvatic, V.; Vadla, C.; Dulieu, O.; Aymar, M.
2007-03-15
Experimental studies of the absorption spectrum of the Rb{sub 2} dimer are performed in the 600-1100 nm wavelength range for temperatures between 615 and 745 K. The reduced absorption coefficient is measured by spatially resolved white light absorption in overheated rubidium vapor with a radial temperature gradient, which enables simultaneous measurements at different temperatures. Semiclassical and quantum spectral simulations are obtained by taking into account all possible transitions involving the potential curves stemming from the 5 {sup 2}S+5 {sup 2}S and 5 {sup 2}S+5 {sup 2}P asymptotes. The most accurate experimental potential curves are used where available, and newly calculated potential curves and transition dipole moments otherwise. The overall consistency of the theoretical model with the experimental interpretation is obtained only if the radial dependence of both the calculated transition dipole moments and the spin-orbit coupling is taken into account. This highlights the low-resolution absorption spectroscopy as a valuable tool for checking the accuracy of molecular electronic structure calculations.
Electronic and crystallographic structure of apatites
NASA Astrophysics Data System (ADS)
Calderín, L.; Stott, M. J.; Rubio, A.
2003-04-01
An ab initio study of four different stoichiometric apatites (oxyapatite, hydroxyapatite, fluorapatite, and chlorapatite) is presented. The calculations were performed using density-functional theory with the local-density approximation for exchange and correlation, and a full relaxation of the electronic structure, the atomic arrangement, and the unit cell. Hexagonal unit cells were obtained for all four apatites, and the calculated atomic arrangements are in close agreement with observation in those cases for which the structure is firmly established. A zero-temperature structure is predicted for oxyapatite, and two possible configurations were found for the Cl- ions in chlorapatite. The possibility of the monoclinic structure in hydroxyapatite and chlorapatite was also studied but no indication of greater stability with respect to the hexagonal structure was found. A relationship between the structure of the apatites and that of pure calcium is discussed.
Kim, Kwan Sung; Ryu, Min Woo; Lee, Jeong Seop; Kim, Kyung Rok
2016-05-01
We report the nonresonant plasmonic terahertz (THz) wave detector based on the silicon (Si) field effect transistor (FET) with a technology computer-aided design (TCAD) platform. The plasma wave behavior has been modeled by a quasi-plasma electron box as a two-dimensional electron gas (2DEG) in the channel of the FET. The incoming alternating current (AC) signal as the THz wave radiation can induce the direct-current (DC) voltage difference between the source and drain, which is called the photoresponse. For accurate analysis of the modulation and propagation of the channel electron density as the plasma wave, we have characterized the quasi-plasma 2DEG model with two key parameters, such as quasi-plasma 2DEG length (I(QP)) and density (N(QP)). By using our normalization method, I(QP) and N(QP) is defined exactly as extracting the average point of the electron density. We also investigate the performance enhancement of the plasmonic terahertz wave detector based on Si FET by scaling down the gate oxide thickness (t(ox)), which is a significant parameter of FET-based plasmonic terahertz detector for the channel electron density modulation. According to scaling down t(ox), the responsivity (R(v)) and noise equivalent power (NEP), which are the important performance metrics of the THz wave detector, have been enhanced. The proposed methodologies will provide the advanced physical analysis and structural design platform for developing the plasmonic terahertz detectors operating in nonresonant regime. PMID:27483817
Electronic structure engineering of various structural phases of phosphorene.
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.
Advanced applications of reduced density matrices in electronic structure theory
NASA Astrophysics Data System (ADS)
Rothman, Adam Eric
This dissertation describes several applications of reduced density matrices (RDMs) in electronic structure theory. RDM methods are a valuable addition to the library of electronic structure theories because they reduce a many-electron problem to the space of just two electrons without approximation. New theoretical and computational avenues enabled by the two-electron RDM (2-RDM) have already shown substantial progress in calculating atomic and molecular energies and properties with an eye toward predictive chemistry. More than simply accurate calculations, RDM methods entail a paradigm shift in quantum chemistry. While one-electron approaches are conceptually easy to understand, the importance of the 2-RDM quantifies the centrality of a two-body framework. The 2-RDM facilitates a two-electron interpretation of quantum mechanics that will undoubtedly lead to a greater understanding of electron correlation. Two applications presented in the dissertation center around near-exact evaluation of the 2-RDM in chemical systems without the many-electron wave function, but approach the problem from different angles. The first applies variational 2-RDM theory to a model quantum dot; the second attempts non-variational determination of the 2-RDM in open-shell atomic and molecular systems using an extension of the anti-Hermitian contracted Schrodinger equation (ACSE). An example reaction is presented to demonstrate how energies computed with the 2-RDM can facilitate an understanding of chemical reactivity. A third application uses the one-electron RDM (1-RDM) as a tool for understanding molecular conductivity. In this case, the 1-RDM is valuable because it integrates out many extraneous degrees of freedom from metal baths, simplifying the electron transport problem but retaining enough information to predict the dependence of current on applied voltage. The results are competitive with other conductivity theories, including a dominant scattering-based understanding, but
Electronic structure of bacterial surface protein layers
Maslyuk, Volodymyr V.; Mertig, Ingrid; Bredow, Thomas; Mertig, Michael; Vyalikh, Denis V.; Molodtsov, Serguei L.
2008-01-15
We report an approach for the calculation of the electronic density of states of the dried two-dimensional crystalline surface protein layer (S layer) of the bacterium Bacillus sphaericus NCTC 9602. The proposed model is based on the consideration of individual amino acids in the corresponding conformation of the peptide chain which additively contribute to the electronic structure of the entire protein complex. The derived results agree well with the experimental data obtained by means of photoemission (PE), resonant PE, and near-edge x-ray absorption spectroscopy.
Probing Structural and Electronic Dynamics with Ultrafast Electron Microscopy
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
Electronic structure calculations on helical conducting polymers.
Ripoll, Juan D; Serna, Andrei; Guerra, Doris; Restrepo, Albeiro
2010-10-21
We present a study of the electronic structure and derived properties of polyfurane (PFu), polypyrrol (PPy), and polythiophene (PTh). Two spatial arrangements are considered: trans chain (tc-PFu, tc-PPy, tc-PTh) and cis α-helical (α-PFu, α-PPy, α-PTh). Even at the small sizes considered here, helical conformations appear to be stable. Band gaps of pure, undoped oligomers fall into the semiconductor range. Density of states (DOS) analysis suggest dense valence and conduction bands. Bond length alternation analysis predicts almost complete delocalization of the π clouds in all spatial arrangements. Doping with electron donors or electron-withdrawing impurities reduces all band gaps close to the metallic regime in addition to increasing the DOS for the valence and conduction bands.
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).
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.
NASA Astrophysics Data System (ADS)
Nabok, Dmitrii; Gulans, Andris; Draxl, Claudia
2016-07-01
The G W approach of many-body perturbation theory has become a common tool for calculating the electronic structure of materials. However, with increasing number of published results, discrepancies between the values obtained by different methods and codes become more and more apparent. For a test set of small- and wide-gap semiconductors, we demonstrate how to reach the numerically best electronic structure within the framework of the full-potential linearized augmented plane-wave (FLAPW) method. We first evaluate the impact of local orbitals in the Kohn-Sham eigenvalue spectrum of the underlying starting point. The role of the basis-set quality is then further analyzed when calculating the G0W0 quasiparticle energies. Our results, computed with the exciting code, are compared to those obtained using the projector-augmented plane-wave formalism, finding overall good agreement between both methods. We also provide data produced with a typical FLAPW basis set as a benchmark for other G0W0 implementations.
Electronic Structure of Iridium Clusters on Graphene
NASA Astrophysics Data System (ADS)
Barker, Bradford A.; Bradley, Aaron J.; Ugeda, Miguel M.; Coh, Sinisa; Zettl, Alex; Crommie, Michael F.; Cohen, Marvin L.; Louie, Steven G.
2015-03-01
Graphene was predicted to exhibit non-trivial Z2 topology, but its exceedingly weak spin-orbit coupling prevented this from being observed. Previous theoretical work has proposed enhancing the spin-orbit coupling strength by depositing individual adatoms adsorbed onto the surface of graphene. We show experimental evidence that the iridium adatoms cluster, with a cluster size of at least two atoms. We investigate through theoretical calculations the orientation of the iridium dimers on graphene, contrast the electronic structure of iridium dimers with iridium monomers, and compare the theoretical iridium dimer electronic structure calculations with the experimental results determined via scanning tunneling spectroscopy. This work was supported by NSF Grant No. DMR10-1006184 and U.S. DOE under Contract No. DE-AC02-05CH11231. Computational resources have been provided by DOE at LBNL's NERSC facility.
Mackie, G C; Schlicht, S M
2004-09-01
Reoperation for refractory or recurrent hyperparathyroidism following parathyroidectomy carries the potential for increased morbidity and the possibility of failure to localize and remove the lesion intraoperatively. Reported herein are three cases demonstrating the combined use of sestamibi scintigraphy, CT and MR for accurate localization of mediastinal parathyroid adenomas.
Electronic structure studies of topological materials
NASA Astrophysics Data System (ADS)
Zhou, Shuyun
Three-dimensional (3D) Dirac fermions are a new class of topological quantum materials. In 3D Dirac semimetals, the conduction and valence bands touch each other at discrete points in the momentum space and show linear dispersions along all momentum directions, forming 3D Dirac cones which are protected by the crystal symmetry. Here I will present our recent studies of the electronic structures of novel materials which host 3D Dirac fermions by using angle-resolved photoemission spectroscopy.
Structure and Electronic Properties of Polycrystalline Dielectrics
Mckenna, Keith P.; Shluger, AL
2013-07-07
We present an overview of the theoretical approaches that can be employed to model polycrystalline oxides along with a discussion of their limitations and associated challenges. We then present results for two metal oxide materials, MgO and HfO2, where theory and experiment have come together to provide insight into the structure and electronic properties of grain boundaries. Finally, we conclude with a discussion and outlook.
Structural and electronic properties of thallium compounds
NASA Astrophysics Data System (ADS)
Paliwal, Neetu; Srivastava, Vipul
2016-05-01
The tight binding linear muffin-tin-orbital (TB-LMTO) method within the local density approximation (LDA has been used to calculate structural and electronic properties of thallium pnictides TlX (X=Sb, Bi) at high pressure. As a function of volume, the total energy is evaluated. Apart from this, the lattice parameter (a0), bulk modulus (B0), band structure (BS) and density of states (DOS) are calculated. From energy band diagram we observed metallic behaviour in TlSb and TlBi compounds. The values of equilibrium lattice constants and bulk modulus are agreed well with the available data.
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).
Smart electronics and MEMS for aerospace structures
NASA Astrophysics Data System (ADS)
Varadan, Vijay K.; Varadan, Vasundara V.
1995-09-01
In this paper, smart electronics and MEMS are employed to sense and control the drag in aircraft structures. The sensors are fabricated with interdigital transducers printed on a piezoelectric polymer. They in turn are mounted onto an ultra thin Penn State's novel RF antenna (Patent field). The sensor are designed to measure both pressure and shear of the fluid flow on aerospace structures. The wave form measurements may be monitored at a remote location either at the cockpit or elsewhere via the antennas in the sensors and an outside antenna. The integrated MEMS actuators which comprise of cantilever-, diaphram- and microbridge-based MEMS with suitable smart electronics etched onto the structure are controlled by the built-in antennas through feedback and feedforward control architecture. The integration of such materials and smart electronics into the skin of airfoil is ideal for sensing and controlling drag. The basic idea of this concept involves detection of the point of transition from laminar to turbulent flow and transmitting acoustical energy into the boundary layer so that the low energy fluid particles accelerate in the transverse direction and mix with the high energy flow outside of the boundary layer. 3D microriblets can be fabricated using stereo lithography and UV curable conducting polymers. The control of drag using these active microriblets are outlined.
Resolving Presynaptic Structure by Electron Tomography
Perkins, Guy A.; Jackson, Dakota R.; Spirou, George A.
2016-01-01
A key goal in neurobiology is to generate a theoretical framework that merges structural, physiological and molecular explanations of brain function. These categories of explanation do not advance in synchrony; advances in one category define new experiments in other categories. For example, the synapse was defined physiologically and biochemically before it was visualized using electron microscopy. Indeed, the original descriptions of synapses in the 1950s were lent credence by the presence of spherical vesicles in presynaptic terminals that were considered to be the substrate for quantal neurotransmission. In the last few decades, our understanding of synaptic function has again been driven by physiological and molecular techniques. The key molecular players for synaptic vesicle structure, mobility and fusion were identified and applications of the patch clamp technique permitted physiological estimation of neurotransmitter release and receptor properties. These advances demand higher resolution structural images of synapses. During the 1990s a second renaissance in cell biology driven by EM was fueled by improved techniques for electron tomography (ET) with the ability to compute virtual images with nm resolution between image planes. Over the last fifteen years, ET has been applied to the presynaptic terminal with special attention to the active zone and organelles of the nerve terminal. In this review, we first summarize the technical improvements that have led to a resurgence in utilization of ET and then we summarize new insights gained by the application of ET to reveal the high-resolution structure of the nerve terminal. PMID:25683026
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. PMID:27095534
Thermal transfer structures coupling electronics card(s) to coolant-cooled structure(s)
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.
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.
Electronic structure and bonding in crystalline peroxides
NASA Astrophysics Data System (ADS)
Königstein, Markus; Sokol, Alexei A.; Catlow, C. Richard A.
1999-08-01
Hartree-Fock and density-functional PW91 theories as realized in the CRYSTAL95 code have been applied to investigate the structural and electronic properties of Ba, Sr, and Ca peroxide materials with the calcium carbide crystal structure, results for which are compared with those for the corresponding oxides. Special attention is paid to the stabilization of the peroxide molecular ion O2-2 in the ionic environment provided by the lattice, and to chemical bonding effects. In order to describe the covalent bonding within the O2-2 ion and the polarization of the O- ion in the crystal electrostatic field, it is essential to include an account of the effects of electron correlation. The PW91 density functional has allowed us to reproduce the crystallographic parameters within a 3% error. The chemical bonding within the peroxide molecular ion has a complex nature with a balance between the weak covalent bond of σz type and the strong electrostatic repulsion of the closed-shell electron groups occupying O 2s and O 2px and 2py states. Compression of the peroxide ion in the ionic crystals gives rise to an excessive overlap of the O 2s closed shells of the two O- ions of a peroxide molecular ion O2-2, which in turn determines the antibonding character of the interaction and chemical bonding in the O2-2 molecular ion.
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
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
PROMALS3D web server for accurate multiple protein sequence and structure alignments.
Pei, Jimin; Tang, Ming; Grishin, Nick V
2008-07-01
Multiple sequence alignments are essential in computational sequence and structural analysis, with applications in homology detection, structure modeling, function prediction and phylogenetic analysis. We report PROMALS3D web server for constructing alignments for multiple protein sequences and/or structures using information from available 3D structures, database homologs and predicted secondary structures. PROMALS3D shows higher alignment accuracy than a number of other advanced methods. Input of PROMALS3D web server can be FASTA format protein sequences, PDB format protein structures and/or user-defined alignment constraints. The output page provides alignments with several formats, including a colored alignment augmented with useful information about sequence grouping, predicted secondary structures and consensus sequences. Intermediate results of sequence and structural database searches are also available. The PROMALS3D web server is available at: http://prodata.swmed.edu/promals3d/. PMID:18503087
Low energy electrons and swift ion track structure in PADC
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 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
Low energy electrons and swift ion track structure in PADC
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.
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.
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. PMID:19950907
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
Ryde, Ulf
2007-02-14
The use of molecular mechanics calculations to supplement experimental data in standard X-ray crystallography and NMR refinements is discussed and it is shown that structures can be locally improved by the use of quantum chemical calculations. Such calculations can also be used to interpret the structures, e.g. to decide the protonation state of metal-bound ligands. They have shown that metal sites in crystal structures are frequently photoreduced or disordered, which makes the interpretation of the structures hard. Similar methods can be used for EXAFS refinements to obtain a full atomic structure, rather than a set of metal-ligand distances.
Pu electronic structure and photoelectron spectroscopy
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.
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.
Electronic Structure of Buried Interfaces - Oral Presentation
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
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.
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. PMID:27554409
Electronic structure and optical properties of resin
NASA Astrophysics Data System (ADS)
Rao, Zhi-Fan; Zhou, Rong-Feng
2013-03-01
We used the density of functional theory (DFT) to study the electronic structure and density of states of resin by ab initio calculation. The results show the band gap of resin is 1.7 eV. The covalent bond is combined C/O atoms with H atoms. The O 2p orbital is the biggest effect near the Fermi level. The results of optical properties show the reflectivity is low, and the refractive index is 1.7 in visible light range. The highest absorption coefficient peak is in 490 nm and the value is 75,000.
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
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.
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.
Experimental Benchmarking of Pu Electronic Structure
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
Experimental Benchmarking of Pu Electronic Structure
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.
Towards scalable electronic structure calculations for alloys
Stocks, G.M.; Nicholson, D.M.C.; Wang, Y.; Shelton, W.A.; Szotek, Z.; Temmermann, W.M.
1994-06-01
A new approach to calculating the properties of large systems within the local density approximation (LDA) that offers the promise of scalability on massively parallel supercomputers is outlined. The electronic structure problem is formulated in real space using multiple scattering theory. The standard LDA algorithm is divided into two parts. Firstly, finding the self-consistent field (SCF) electron density, Secondly, calculating the energy corresponding to the SCF density. We show, at least for metals and alloys, that the former problem is easily solved using real space methods. For the second we take advantage of the variational properties of a generalized Harris-Foulkes free energy functional, a new conduction band Fermi function, and a fictitious finite electron temperature that again allow us to use real-space methods. Using a compute-node {R_arrow} atom equivalence the new method is naturally highly parallel and leads to O(N) scaling where N is the number of atoms making up the system. We show scaling data gathered on the Intel XP/S 35 Paragon for systems up to 512-atoms/simulation cell. To demonstrate that we can achieve metallurgical-precision, we apply the new method to the calculation the energies of disordered CuO{sub 0.5}Zn{sub 0.5} alloys using a large random sample.
Electron beam coupling to a metamaterial structure
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.
Structure and electronic properties of azadirachtin.
de Castro, Elton A S; de Oliveira, Daniel A B; Farias, Sergio A S; Gargano, Ricardo; Martins, João B L
2014-02-01
We performed a combined DFT and Monte Carlo (13)C NMR chemical-shift study of azadirachtin A, a triterpenoid that acts as a natural insect antifeedant. A conformational search using a Monte Carlo technique based on the RM1 semiempirical method was carried out in order to establish its preferred structure. The B3LYP/6-311++G(d,p), wB97XD/6-311++G(d,p), M06/6-311++G(d,p), M06-2X/6-311++G(d,p), and CAM-B3LYP/6-311++G(d,p) levels of theory were used to predict NMR chemical shifts. A Monte Carlo population-weighted average spectrum was produced based on the predicted Boltzmann contributions. In general, good agreement between experimental and theoretical data was obtained using both methods, and the (13)C NMR chemical shifts were predicted highly accurately. The geometry was optimized at the semiempirical level and used to calculate the NMR chemical shifts at the DFT level, and these shifts showed only minor deviations from those obtained following structural optimization at the DFT level, and incurred a much lower computational cost. The theoretical ultraviolet spectrum showed a maximum absorption peak that was mainly contributed by the tiglate group. PMID:24509732
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.
Electronic and structural properties of metallic microclusters
Maiti, A.
1992-04-01
The first part of this thesis presents a first-order pseudopotential calculation at T=O of the total energy of small sodium clusters of size N<800. The calculation is based on a local-pseudopotential scheme and local-density correlation and exchange. A temperature-size (T-N) phase-diagram is then derived using the T=O results and Lindemann`s criterion for melting. The phase-diagram contains three regions of stability: (1) a liquid (jellium) phase at temperatures above the melting line T{sub M}(N) where cluster-stability occurs at electronic magic numbers: (2) a phase related to complete geometrical shells of body-centered-cubic structure at temperatures below the melting line; and (3) a close-packed structure at very low temperatures and sufficiently large N. The melting line drops to T{sub M}(N)=O for N<65, where electronic magic numbers are stable even at T=O. The phase diagram reduces asymptotically to the known phases of sodium as N{yields}{infinity}, including the known martensitic transformation at T{approximately}5 K. The second and the last part of this thesis consists of a study of small-cluster many-body systems by means of an on-site ``local`` chemical potential which allows the continuous variation of local electron-density. This method yields a criterion to distinguish particular features of a small cluster that are likely to survive in the large-N thermodynamic limit from those discontinuities that arise only from finite-size effects.
Electronic and structural properties of metallic microclusters
Maiti, A.
1992-04-01
The first part of this thesis presents a first-order pseudopotential calculation at T=O of the total energy of small sodium clusters of size N<800. The calculation is based on a local-pseudopotential scheme and local-density correlation and exchange. A temperature-size (T-N) phase-diagram is then derived using the T=O results and Lindemann's criterion for melting. The phase-diagram contains three regions of stability: (1) a liquid (jellium) phase at temperatures above the melting line T{sub M}(N) where cluster-stability occurs at electronic magic numbers: (2) a phase related to complete geometrical shells of body-centered-cubic structure at temperatures below the melting line; and (3) a close-packed structure at very low temperatures and sufficiently large N. The melting line drops to T{sub M}(N)=O for N<65, where electronic magic numbers are stable even at T=O. The phase diagram reduces asymptotically to the known phases of sodium as N{yields}{infinity}, including the known martensitic transformation at T{approximately}5 K. The second and the last part of this thesis consists of a study of small-cluster many-body systems by means of an on-site local'' chemical potential which allows the continuous variation of local electron-density. This method yields a criterion to distinguish particular features of a small cluster that are likely to survive in the large-N thermodynamic limit from those discontinuities that arise only from finite-size effects.
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)
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. PMID:26517180
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.
First-principles calculation of electronic structure and optical absorption of BN ZnO
NASA Astrophysics Data System (ADS)
Zhang, Xiao; Schleife, Andre
2015-03-01
The α-BN structure of ZnO, a nonequilibrium phase with a transition pressure of 25 GPa, has been found in nano structures of ZnO. The structural difference between the BN structure and the equilibrium wurtzite structure can play an important role for applications of nanostructured ZnO. In order to understand the difference, first principles calculations have been performed on both phases. The electronic structure is computed using the GW method based on Density Functional Theory and HSE hybrid functional calculations. The GW method includes the quasiparticle effects due to the screened electron-electron interaction which gives an accurate description of the electronic band structure and density of states. After that, by solving the Bethe-Salpeter Equation for the optical polarization function, which take excitonic effects into account, we have achieved an accurate description of optical absorption spectra for both structures. We find a good agreement with experimental and previous computational results for WZ structure, and predict the absorption for the BN structure. The BN structure shows a larger band gap and we found a very large optical anisotropy: The gap for extraordinary light polarization is almost 0.7eV larger than that for ordinary light polarization.
HAAD: A quick algorithm for accurate prediction of hydrogen atoms in protein structures.
Li, Yunqi; Roy, Ambrish; Zhang, Yang
2009-08-20
Hydrogen constitutes nearly half of all atoms in proteins and their positions are essential for analyzing hydrogen-bonding interactions and refining atomic-level structures. However, most protein structures determined by experiments or computer prediction lack hydrogen coordinates. We present a new algorithm, HAAD, to predict the positions of hydrogen atoms based on the positions of heavy atoms. The algorithm is built on the basic rules of orbital hybridization followed by the optimization of steric repulsion and electrostatic interactions. We tested the algorithm using three independent data sets: ultra-high-resolution X-ray structures, structures determined by neutron diffraction, and NOE proton-proton distances. Compared with the widely used programs CHARMM and REDUCE, HAAD has a significantly higher accuracy, with the average RMSD of the predicted hydrogen atoms to the X-ray and neutron diffraction structures decreased by 26% and 11%, respectively. Furthermore, hydrogen atoms placed by HAAD have more matches with the NOE restraints and fewer clashes with heavy atoms. The average CPU cost by HAAD is 18 and 8 times lower than that of CHARMM and REDUCE, respectively. The significant advantage of HAAD in both the accuracy and the speed of the hydrogen additions should make HAAD a useful tool for the detailed study of protein structure and function. Both an executable and the source code of HAAD are freely available at http://zhang.bioinformatics.ku.edu/HAAD.
Ogura, Toshihiko; Iwasaki, Kenji; Sato, Chikara
2003-09-01
In single-particle analysis, a three-dimensional (3-D) structure of a protein is constructed using electron microscopy (EM). As these images are very noisy in general, the primary process of this 3-D reconstruction is the classification of images according to their Euler angles, the images in each classified group then being averaged to reduce the noise level. In our newly developed strategy of classification, we introduce a topology representing network (TRN) method. It is a modified method of a growing neural gas network (GNG). In this system, a network structure is automatically determined in response to the images input through a growing process. After learning without a masking procedure, the GNG creates clear averages of the inputs as unit coordinates in multi-dimensional space, which are then utilized for classification. In the process, connections are automatically created between highly related units and their positions are shifted where the inputs are distributed in multi-dimensional space. Consequently, several separated groups of connected units are formed. Although the interrelationship of units in this space are not easily understood, we succeeded in solving this problem by converting the unit positions into two-dimensional (2-D) space, and by further optimizing the unit positions with the simulated annealing (SA) method. In the optimized 2-D map, visualization of the connections of units provided rich information about clustering. As demonstrated here, this method is clearly superior to both the multi-variate statistical analysis (MSA) and the self-organizing map (SOM) as a classification method and provides a first reliable classification method which can be used without masking for very noisy images. PMID:14572474
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
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…
Reversible Hydrogen Storage Materials – Structure, Chemistry, and Electronic Structure
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
Arumugam, P.; Ferreira, L. S.; Maglione, E.
2008-10-15
With a proper formalism for proton emission from triaxially deformed nuclei, we perform exact calculations of decay widths for the decays to ground and first excited 2{sup +} states in the daughter nucleus. Our results for rotational spectrum, decay width and fine structure in the case of the nucleus {sup 145}Tm lead for the first time to an accurate identification of triaxial deformation using proton emission. This work also puts in evidence the advantage of proton emission over the conventional probes to study nuclear structure at the proton drip-line.
NASA Astrophysics Data System (ADS)
Maeda, Chiaki; Tasaki, Satoko; Kirihara, Soshu
2011-05-01
Computer graphic models of bioscaffolds with four-coordinate lattice structures of solid rods in artificial bones were designed by using a computer aided design. The scaffold models composed of acryl resin with hydroxyapatite particles at 45vol. % were fabricated by using stereolithography of a computer aided manufacturing. After dewaxing and sintering heat treatment processes, the ceramics scaffold models with four-coordinate lattices and fine hydroxyapatite microstructures were obtained successfully. By using a computer aided analysis, it was found that bio-fluids could flow extensively inside the sintered scaffolds. This result shows that the lattice structures will realize appropriate bio-fluid circulations and promote regenerations of new bones.
Study of electronic structures of solids with strongly interacting electrons
NASA Astrophysics Data System (ADS)
Su, Yen-Sheng
This work contains studies of two classes of perovskite transition metal oxides. The first class is the layered perovskite cuprates and the related nickelate. The second class is the three dimensional perovskite manganites. Both model and ab initio calculations are carried out for the two classes of systems. The dissertation is therefore divided into the following four parts. The first part is about the 3-band Hubbard model. The model is commonly used for describing the electronic properties of the important CuO2 layers in the crystals of high-Tc superconducting cuprates, such as doped La2CuO4 and YBa2Cu3O 7. The straightforward perturbation expansion on the model taking tpd/ɛpd (~0.36 for the cuprates) as the small parameter does not converge. In this work, I show that there exist canonical transformations on the model Hamiltonian such that the perturbation expansion based on the transformed Hamiltonians converges. In the second part, crystal Hartree-Fock calculations are carried out for La2NiO4 and La2CuO4. The results predict correctly that these two materials are antiferromagnetic insulators, in contrast to the wrong predictions made by the density functional calculations using the local spin density approximation (LSDA). The spin form factors of the materials are also calculated. The results agree with previous theoretical works using an embedded cluster model. The calculated spin form factor of La2CuO4 is consistent with the few experimental data currently available, while the results for La2NiO4 show a large discrepancy between theory and experiment. We question the accuracy of the experimental results of La2NiO4 and call for more experiments to settle the issue. In the third part, crystal Hartree-Fock calculations are carried out for LaMnO3. Our main focus is on the magnetic and orbital orderings, the effect of the crystal distortion from the cubic perovskite structure, and the analysis of the projected density of states. In addition, we also find
Braun, Tatjana; Koehler Leman, Julia; Lange, Oliver F
2015-12-01
Recent work has shown that the accuracy of ab initio structure prediction can be significantly improved by integrating evolutionary information in form of intra-protein residue-residue contacts. Following this seminal result, much effort is put into the improvement of contact predictions. However, there is also a substantial need to develop structure prediction protocols tailored to the type of restraints gained by contact predictions. Here, we present a structure prediction protocol that combines evolutionary information with the resolution-adapted structural recombination approach of Rosetta, called RASREC. Compared to the classic Rosetta ab initio protocol, RASREC achieves improved sampling, better convergence and higher robustness against incorrect distance restraints, making it the ideal sampling strategy for the stated problem. To demonstrate the accuracy of our protocol, we tested the approach on a diverse set of 28 globular proteins. Our method is able to converge for 26 out of the 28 targets and improves the average TM-score of the entire benchmark set from 0.55 to 0.72 when compared to the top ranked models obtained by the EVFold web server using identical contact predictions. Using a smaller benchmark, we furthermore show that the prediction accuracy of our method is only slightly reduced when the contact prediction accuracy is comparatively low. This observation is of special interest for protein sequences that only have a limited number of homologs.
Electronic Structure Calculations of Highly Charged Ions
NASA Astrophysics Data System (ADS)
Bromley, Steve; Ziolkowski, Marcin; Marler, Joan
2016-05-01
Exotic systems like Highly Charged Ions (HCIs) are attracting more attention based on their properties and possible interactions. Abundance of HCIs in the solar wind and their interaction with the upper atmosphere puts them in the attention of astro- and atmospheric physicists. Also, their unique properties originating in the high charge make them an excellent candidate for precision measurements and the next generation of atomic clocks. For a better understanding of the dynamics of processes involving HCIs a combined theoretical and experimental effort is needed to study their basic properties and interactions. Both theory and experiment need to be combined due to the extreme nature of these systems. We present preliminary insight into electronic structure of light HCIs, their interactions with neutral atoms and dynamics of charge transfer processes.
Electronic structures of reconstructed zigzag silicene nanoribbons
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.
Electronic structures of reconstructed zigzag silicene nanoribbons
NASA Astrophysics Data System (ADS)
Ding, Yi; Wang, Yanli
2014-02-01
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.
Multilevel domain decomposition for electronic structure calculations
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.
Electron Liquids in Semiconductor Quantum Structures
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.
Silicene oxides: formation, structures and electronic properties.
Wang, Rong; Pi, Xiaodong; Ni, Zhenyi; Liu, Yong; Lin, Shisheng; Xu, Mingsheng; Yang, Deren
2013-12-16
Understanding the oxidation of silicon has been critical to the success of all types of silicon materials, which are the cornerstones of modern silicon technologies. For the recent experimentally obtained two-dimensional silicene, oxidation should also be addressed to enable the development of silicene-based devices. Here we focus on silicene oxides (SOs) that result from the partial or full oxidation of silicene in the framework of density functional theory. It is found that the formation of SOs greatly depends on oxidation conditions, which concern the oxidizing agents of oxygen and hydroxyl. The honeycomb lattice of silicene may be preserved, distorted or destroyed after oxidation. The charge state of Si in partially oxidized silicene ranges from +1 to +3, while that in fully oxidized silicene is +4. Metals, semimetals, semiconductors and insulators can all be found among the SOs, which show a wide spectrum of electronic structures. Our work indicates that the oxidation of silicene should be exquisitely controlled to obtain specific SOs with desired electronic properties.
Mizianty, Marcin J; Kurgan, Lukasz A
2012-01-01
Relatively low success rates of X-ray crystallography, which is the most popular method for solving proteins structures, motivate development of novel methods that support selection of tractable protein targets. This aspect is particularly important in the context of the current structural genomics efforts that allow for a certain degree of flexibility in the target selection. We propose CRYSpred, a novel in-silico crystallization propensity predictor that uses a set of 15 novel features which utilize a broad range of inputs including charge, hydrophobicity, and amino acid composition derived from the protein chain, and the solvent accessibility and disorder predicted from the protein sequence. Our method outperforms seven modern crystallization propensity predictors on three, independent from training dataset, benchmark test datasets. The strong predictive performance offered by the CRYSpred is attributed to the careful design of the features, utilization of the comprehensive set of inputs, and the usage of the Support Vector Machine classifier. The inputs utilized by CRYSpred are well-aligned with the existing rules-of-thumb that are used in the structural genomics studies. PMID:21919861
Mizianty, Marcin J; Kurgan, Lukasz A
2012-01-01
Relatively low success rates of X-ray crystallography, which is the most popular method for solving proteins structures, motivate development of novel methods that support selection of tractable protein targets. This aspect is particularly important in the context of the current structural genomics efforts that allow for a certain degree of flexibility in the target selection. We propose CRYSpred, a novel in-silico crystallization propensity predictor that uses a set of 15 novel features which utilize a broad range of inputs including charge, hydrophobicity, and amino acid composition derived from the protein chain, and the solvent accessibility and disorder predicted from the protein sequence. Our method outperforms seven modern crystallization propensity predictors on three, independent from training dataset, benchmark test datasets. The strong predictive performance offered by the CRYSpred is attributed to the careful design of the features, utilization of the comprehensive set of inputs, and the usage of the Support Vector Machine classifier. The inputs utilized by CRYSpred are well-aligned with the existing rules-of-thumb that are used in the structural genomics studies.
Accurate structure prediction of peptide–MHC complexes for identifying highly immunogenic antigens
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.
Friedrich, Joachim
2015-08-11
In this work we analyze the accuracy and the efficiency of different schemes to obtain the complete basis set limit for CCSD(T). It is found that composite schemes using an MP2 increment to reach the basis set limit provide high accuracy combined with high efficiency. In these composite schemes the MP2-F12/cc-pVTZ-F12 method is suitable to compute the MP2 contribution at the basis set limit. We propose to use the def2-TZVP or the TZVPP basis sets at the coupled cluster level in combination with the cc-pVTZ-F12 basis set at the MP2 level to compute reaction energies close to the basis set limit, if high accuracy methods like CCSD(T)(F12*) or 56-extrapolations are no longer feasible due to the computational effort. The standard deviation of CCSD(T)+ΔMP2/cc-pVTZ-F12/def2-TZVP and CCSD(T)+ΔMP2/cc-pVTZ-F12/TZVPP is found to be only 0.93 and 0.65 kJ/mol for a test set of 51 closed shell reactions. Furthermore, we provide a comprehensive list of different computational strategies to obtain CCSD(T) reaction energies with an efficiency and accuracy measure. Finally we analyze how different choices of the exponent in the correlation factor (γ) change the results when using explicitly correlated methods. The statistical results in this study are based on a set of 51 reaction energies in the range of 0.7 to 631.5 kJ/mol.
A FIB-nanotomography method for accurate 3D reconstruction of open nanoporous structures.
Mangipudi, K R; Radisch, V; Holzer, L; Volkert, C A
2016-04-01
We present an automated focused ion beam nanotomography method for nanoporous microstructures with open porosity, and apply it to reconstruct nanoporous gold (np-Au) structures with ligament sizes on the order of a few tens of nanometers. This method uses serial sectioning of a well-defined wedge-shaped geometry to determine the thickness of individual slices from the changes in the sample width in successive cross-sectional images. The pore space of a selected region of the np-Au is infiltrated with ion-beam-deposited Pt composite before serial sectioning. The cross-sectional images are binarized and stacked according to the individual slice thicknesses, and then processed using standard reconstruction methods. For the image conditions and sample geometry used here, we are able to determine the thickness of individual slices with an accuracy much smaller than a pixel. The accuracy of the new method based on actual slice thickness is assessed by comparing it with (i) a reconstruction using the same cross-sectional images but assuming a constant slice thickness, and (ii) a reconstruction using traditional FIB-tomography method employing constant slice thickness. The morphology and topology of the structures are characterized using ligament and pore size distributions, interface shape distribution functions, interface normal distributions, and genus. The results suggest that the morphology and topology of the final reconstructions are significantly influenced when a constant slice thickness is assumed. The study reveals grain-to-grain variations in the morphology and topology of np-Au. PMID:26906523
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.
Quasiparticle electronic structure of bismuth telluride in the GW approximation
NASA Astrophysics Data System (ADS)
Kioupakis, Emmanouil; Tiago, Murilo L.; Louie, Steven G.
2010-12-01
The quasiparticle band structure of bismuth telluride (Bi2Te3) , an important thermoelectric material that exhibits topologically insulating surface states, is calculated from first principles in the GW approximation. The quasiparticle energies are evaluated in fine detail in the first Brillouin zone using a Wannier-function interpolation method, allowing the accurate determination of the location of the band extrema (which is in the mirror plane) as well as the values of the quasiparticle band gap (0.17 eV) and effective-mass tensors. Spin-orbit interaction effects were included. The valence band exhibits two distinct maxima in the mirror plane that differ by just 1 meV, giving rise to one direct and one indirect band gap of very similar magnitude. The effective-mass tensors are in reasonable agreement with experiment. The Wannier interpolation coefficients can be used for the tight-binding parametrization of the band structure. Our work elucidates the electronic structure of Bi2Te3 and sheds light on its exceptional thermoelectric and topologically insulating properties.
Nonlinearity in structural and electronic materials
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.
The electronic structure of hard materials
NASA Astrophysics Data System (ADS)
Winarski, Robert Paul
This research dissertation involves an experimental as well as a theoretical examination of the electronic structure of hard materials. The materials that are presented in this dissertation cover a wide class of materials, consisting of transition metal borides, irradiated polymer films, theoretically predicted superhard semiconductors, doped intermetallic alloys, and transition metal carbides. The borides are traditionally used in high temperature, hard coating applications, such as rocket nozzle linings, extreme wear surfaces, and corrosion coatings. Measurements of the borides appear to show that the bonding in these hard materials is primarily between the boron atoms in these systems. Also of note are the remarkably short interatomic distances between the boron atoms and between the boron and metal atoms in these materials. Irradiated polymer films are being developed for electronic applications, in the hopes that circuits can be developed that can benefit from the high thermal stability, dielectric properties, and mechanical properties provided by these materials. C3N4 is a theoretically predicted superhard material, and some of the first soft x-ray emission measurements of well-characterized samples of this compound are discussed in this work. Intermetallic alloys, in particular Ni3Al, are rather hard, but brittle metallic alloys. It has been found that the addition of boron atoms, in rather low concentrations, can increase the ductility of these alloys, allowing them to be utilized in a wider variety of applications. Measurements of this system have examined a question regarding the positioning of the boron atoms in the structures of this alloy. Finally, the transition metal carbides are used extensively as coatings in industrial applications such as cutting and grinding tools, and polishing compounds. Measurements of these materials suggest that the high degree of covalency between the metal and carbon atoms is primarily responsible for the hardness of
Electronic structure and phase equilibria in ternary substitutional alloys
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}.
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.
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.
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.
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.
NASA Astrophysics Data System (ADS)
Dunn, Nicholas J. H.; Noid, W. G.
2015-12-01
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, UV(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 UV, 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 UV 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.
Electronic Structure and Dynamics of Nitrosyl Porphyrins
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
A Simple and Accurate Analysis of Conductivity Loss in Millimeter-Wave Helical Slow-Wave Structures
NASA Astrophysics Data System (ADS)
Datta, S. K.; Kumar, Lalit; Basu, B. N.
2009-04-01
Electromagnetic field analysis of a helix slow-wave structure was carried out and a closed form expression was derived for the inductance per unit length of the transmission-line equivalent circuit of the structure, taking into account the actual helix tape dimensions and surface current on the helix over the actual metallic area of the tape. The expression of the inductance per unit length, thus obtained, was used for estimating the increment in the inductance per unit length caused due to penetration of the magnetic flux into the conducting surfaces following Wheeler’s incremental inductance rule, which was subsequently interpreted for the attenuation constant of the propagating structure. The analysis was computationally simple and accurate, and accrues the accuracy of 3D electromagnetic analysis by allowing the use of dispersion characteristics obtainable from any standard electromagnetic modeling. The approach was benchmarked against measurement for two practical structures, and excellent agreement was observed. The analysis was subsequently applied to demonstrate the effects of conductivity on the attenuation constant of a typical broadband millimeter-wave helical slow-wave structure with respect to helix materials and copper plating on the helix, surface finish of the helix, dielectric loading effect and effect of high temperature operation - a comparative study of various such aspects are covered.
Electronic structure of Mg: From monolayers to bulk
Schiller, F.; Laubschat, C.; Heber, M.; Servedio, V.D.P.
2004-09-15
The structure of thin Mg films epitaxially grown onto a W(110) crystal was analyzed by low energy electron and Auger electron diffraction verifying a growth of bulk Mg. Normal-emission angle-resolved photoemission spectra of the growing films reveal quantum well states on both sides of a surface state. These states result from electron confinement in the Mg layer and are used to derive the electronic structure perpendicular to the surface. Off-normal, the electronic structure is dominated by the parabolic dispersion of surface states forming circles around the {gamma}-points and ellipses around the M-points in the Fermi surface cuts.
Probing Actinide Electronic Structure through Pu Cluster Calculations
Ryzhkov, Mickhail V.; Mirmelstein, Alexei; Yu, Sung-Woo; Chung, Brandon W.; Tobin, James G.
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.
Graph-based linear scaling electronic structure theory.
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. PMID:27334148
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.
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.
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. PMID:23902112
Dramatic changes in electronic structure revealed by fractionally charged nuclei
Cohen, Aron J.; Mori-Sánchez, Paula
2014-01-28
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.
Electronic Structure of Germanium Nanocrystal Films Probed with Synchrotron Radiation
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.
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.
Srajer, V; Crosson, S; Schmidt, M; Key, J; Schotte, F; Anderson, S; Perman, B; Ren, Z; Teng, T Y; Bourgeois, D; Wulff, M; Moffat, K
2000-07-01
Wavelength normalization is an essential part of processing of Laue X-ray diffraction data and is critically important for deriving accurate structure-factor amplitudes. The results of wavelength normalization for Laue data obtained in nanosecond time-resolved experiments at the ID09 beamline at the European Synchrotron Radiation Facility, Grenoble, France, are presented. Several wiggler and undulator insertion devices with complex spectra were used. The results show that even in the most challenging cases, such as wiggler/undulator tandems or single-line undulators, accurate wavelength normalization does not require unusually redundant Laue data and can be accomplished using typical Laue data sets. Single-line undulator spectra derived from Laue data compare well with the measured incident X-ray spectra. Successful wavelength normalization of the undulator data was also confirmed by the observed signal in nanosecond time-resolved experiments. Single-line undulators, which are attractive for time-resolved experiments due to their high peak intensity and low polychromatic background, are compared with wigglers, based on data obtained on the same crystal. PMID:16609201
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
NASA Astrophysics Data System (ADS)
Kim, Seoktae; Nguyen, Cam
2014-04-01
This paper discusses the RF interferometry at millimeter-wave frequencies for sensing applications and reports the development of a millimeter-wave interferometric sensor operating around 35 GHz. The sensor is completely realized using microwave integrated circuits (MICs) and microwave monolithic integrated circuits (MMICs). It has been used for various sensing including displacement and velocity measurement. The sensor achieves a resolution and maximum error of only 10 μm and 27 μm, respectively, for displacement sensing and can measure velocity as low as 27.7 mm/s with a resolution about 2.7mm/s. Quick response and accurate sensing, as demonstrated by the developed millimeter-wave interferometric sensor, make the millimeter-wave interferometry attractive for sensing of various civil and mechanical structures.
Electronic band structure and photoemission: A review and projection
Falicov, L.M.
1987-09-01
A brief review of electronic-structure calculations in solids, as a means of interpreting photoemission spectra, is presented. The calculations are, in general, of three types: ordinary one-electron-like band structures, which apply to bulk solids and are the basis of all other calculations; surface modified calculations, which take into account, self-consistently if at all possible, the presence of a vacuum-solid interface and of the electronic modifications caused thereby; and many-body calculations, which go beyond average-field approximations and consider dynamic rearrangement effects caused by electron-electron correlations during the photoemission process. 44 refs.
Spatial and electron structure of substituted gold clusters
NASA Astrophysics Data System (ADS)
Yarzhemsky, V. G.; Kazaryan, M. A.; Bulychev, N. A.; Dyakov, Y. A.; Kosheleva, O. K.; Chen, C. H.
2015-12-01
The structure of intermetallic clusters Au12M (M=Hf, Ta, W, Re, Os) and features of their interaction with electron donors and acceptor atoms, i.e. H and F, were investigated making use computer calculation based of density functional theory. In was found that metal clusters with effective electron number equal to 18 have more symmetrical shape then that with a number of electrons differing from 18. The interaction of gold nanoparticles with silica was modeled by attachment of SiO4H groups and the connection of the electronic structure with electronic transitions in spaser is discussed.
Subotnik, Joseph E.; Vura-Weis, Josh; Sodt, Alex J.; Ratner, Mark A.
2010-05-06
We model the triplet-triplet energy-transfer experiments from the Closs group [Closs, G. L.; et al. J. Am. Chem. Soc. 1988, 110, 2652.] using a combination of Marcus theory and either Boys or Edmiston-Ruedenberg localized diabatization, and we show that relative and absolute rates of electronic excitation transfer may be computed successfully. For the case where both the donor and acceptor occupy equatorial positions on a rigid cyclohexane bridge, we find β_{calc} = 2.8 per C-C bond, compared with the experimental value β_{exp} = 2.6. This work highlights the power of using localized diabatization methods as a tool for modeling nonequilibrium processes.
Electronic structure of atomically precise graphene nanoribbons.
Ruffieux, Pascal; Cai, Jinming; Plumb, Nicholas C; Patthey, Luc; Prezzi, Deborah; Ferretti, Andrea; Molinari, Elisa; Feng, Xinliang; Müllen, Klaus; Pignedoli, Carlo A; Fasel, Roman
2012-08-28
Some of the most intriguing properties of graphene are predicted for specifically designed nanostructures such as nanoribbons. Functionalities far beyond those known from extended graphene systems include electronic band gap variations related to quantum confinement and edge effects, as well as localized spin-polarized edge states for specific edge geometries. The inability to produce graphene nanostructures with the needed precision, however, has so far hampered the verification of the predicted electronic properties. Here, we report on the electronic band gap and dispersion of the occupied electronic bands of atomically precise graphene nanoribbons fabricated via on-surface synthesis. Angle-resolved photoelectron spectroscopy and scanning tunneling spectroscopy data from armchair graphene nanoribbons of width N = 7 supported on Au(111) reveal a band gap of 2.3 eV, an effective mass of 0.21 m(0) at the top of the valence band, and an energy-dependent charge carrier velocity reaching 8.2 × 10(5) m/s in the linear part of the valence band. These results are in quantitative agreement with theoretical predictions that include image charge corrections accounting for screening by the metal substrate and confirm the importance of electron-electron interactions in graphene nanoribbons.
QWalk: A quantum Monte Carlo program for electronic structure
Wagner, Lucas K. Bajdich, Michal Mitas, Lubos
2009-05-20
We describe QWalk, a new computational package capable of performing quantum Monte Carlo electronic structure calculations for molecules and solids with many electrons. We describe the structure of the program and its implementation of quantum Monte Carlo methods. It is open-source, licensed under the GPL, and available at the web site (http://www.qwalk.org)
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
Finite Elements in Ab Initio Electronic-Structure Calulations
NASA Astrophysics Data System (ADS)
Pask, J. E.; Sterne, P. A.
Over the course of the past two decades, the density functional theory (DFT) (see e.g., [1]) of Hohenberg, Kohn, and Sham has proven to be an accurate and reliable basis for the understanding and prediction of a wide range of materials properties from first principles (ab initio), with no experimental input or empirical parameters. However, the solution of the Kohn-Sham equations of DFT is a formidable task and this has limited the range of physical systems which can be investigated by such rigorous, quantum mechanical means. In order to extend the interpretive and predictive power of such quantum mechanical theories further into the domain of "real materials", involving nonstoichiometric deviations, defects, grain boundaries, surfaces, interfaces, and the like; robust and efficient methods for the solution of the associated quantum mechanical equations are critical. The finite-element (FE) method (see e.g., [2]) is a general method for the solution of partial differential and integral equations which has found wide application in diverse fields ranging from particle physics to civil engineering. Here, we discuss its application to large-scale ab initio electronic-structure calculations.
"Lagrange functions" for order(N) electronic structure calculations
NASA Astrophysics Data System (ADS)
Varga, Kalman; Zhang, Zhenyu; Pantelides, S. T.
2004-03-01
"Plane waves" have several highly desirable properties for electronic structure calculations, but effectively scale as N3, where N is the number of atoms, because they impose a uniform grid on which one must perform fast Fourier transforms (FFTs). To achieve near-order-N methods, it is imperative to adopt "real-space methods and non-uniform grids. The objective is usually pursued either by discretization or by adopting local basis sets, either numerical or analytical, with optimized short range. Here we report on a novel basis set, which we label "Lagrange functions" that are defined to satisfy the Lagrange interpolation condition and on a grid that corresponds to a Gaussian quadrature for integrations with optimized numerical accuracy. Lagrange functions combine the best attributes of plane waves and real-space methods. Just like plane waves, convergence is controlled by a single parameter in a systematic way, are orthonormal and defined analytically everywhere, but have the added flexibility of a weight function that controls the distribution of grid points and can be used to optimize the calculation for each system. They do not require FFTs and integrals are trivial and accurate since each Lagrange function is nonzero on a single grid point. The power of the method will be illustrated with several examples.
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
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.
NASA Astrophysics Data System (ADS)
Patchkovskii, Serguei; Muller, H. G.
2016-02-01
Modelling atomic processes in intense laser fields often relies on solving the time-dependent Schrödinger equation (TDSE). For processes involving ionisation, such as above-threshold ionisation (ATI) and high-harmonic generation (HHG), this is a formidable task even if only one electron is active. Several powerful ideas for efficient implementation of atomic TDSE were introduced by H.G. Muller some time ago (Muller, 1999), including: separation of Hamiltonian terms into tri-diagonal parts; implicit representation of the spatial derivatives; and use of a rotating reference frame. Here, we extend these techniques to allow for non-uniform radial grids, arbitrary laser field polarisation, and non-Hermitian terms in the Hamiltonian due to the implicit form of the derivatives (previously neglected). We implement the resulting propagator in a parallel Fortran program, adapted for multi-core execution. Cost of TDSE propagation scales linearly with the problem size, enabling full-dimensional calculations of strong-field ATI and HHG spectra for arbitrary field polarisations on a standard desktop PC.
Scanning transmission electron microscopy of biological structures.
Colliex, C; Mory, C
1994-01-01
The design of the scanning transmission electron microscope (STEM) has been conceived to optimize its detection efficiency of the different elastic and inelastic signals resulting from the interaction of the high energy primary electrons with the specimen. Its potential use to visualize and measure biological objects was recognized from the first studies by Crewe and coworkers in the seventies. Later the real applications have not followed the initial hopes. The purpose of the present paper is to describe how the instrument has practically evolved and recently begun to demonstrate all its potentialities for quantitative electron microscopy of a wide range of biological specimens, from freeze-dried isolated macromolecules to unstained cryosections. Emphasis will be put on the mass-mapping, multi-signal and elemental mapping modes which are unique features of the STEM instruments.
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.
NASA Astrophysics Data System (ADS)
Moeck, Peter; Rouvimov, Sergei; Nicolopoulos, Stavros
2009-09-01
Precession electron diffraction (PED) in a transmission electron microscope (TEM) is discussed in order to illustrate its utility for structural fingerprinting of nanocrystals. While individual nanocrystals may be fingerprinted structurally from PED spot patterns, ensembles of nanocrystals may be fingerprinted from powder PED ring patterns.
Guermant, C; Azarkan, M; Smolders, N; Baeyens-Volant, D; Nijs, M; Paul, C; Brygier, J; Vincentelli, J; Looze, Y
2000-01-01
Oxidation at 120 degrees C of inorganic and organic (including amino acids, di- and tripeptides) model compounds by K(2)Cr(2)O(7) in the presence of H(2)SO(4) (mass fraction: 0.572), Ag(2)SO(4) (catalyst), and HgSO(4) results in the quantitative conversion of their C-atoms into CO(2) within 24 h or less. Under these stressed, well-defined conditions, the S-atoms present in cysteine and cystine residues are oxidized into SO(3) while, interestingly, the oxidation states of all the other (including the N-) atoms normally present in a protein do remain quite unchanged. When the chemical structure of a given protein is available, the total number of electrons the protein is able to transfer to K(2)Cr(2)O(7) and thereof, the total number of moles of Cr(3+) ions which the protein is able to generate upon oxidation can be accurately calculated. In such cases, unknown protein molar concentrations can thus be determined through straightforward spectrophotometric measurements of Cr(3+) concentrations. The values of molar absorption coefficients for several well-characterized proteins have been redetermined on this basis and observed to be in excellent agreement with the most precise values reported in the literature, which fully assesses the validity of the method. When applied to highly purified proteins of known chemical structure (more generally of known atomic composition), this method is absolute and accurate (+/-1%). Furthermore, it is well adapted to series measurements since available commercial kits for chemical oxygen demand (COD) measurements can readily be adapted to work under the experimental conditions recommended here for the protein assay. PMID:10610688
Electron crystallography for structural and functional studies of membrane proteins.
Fujiyoshi, Yoshinori
2011-01-01
Membrane proteins are important research targets for basic biological sciences and drug design, but studies of their structure and function are considered difficult to perform. Studies of membrane structures have been greatly facilitated by technological and instrumental advancements in electron microscopy together with methodological advancements in biology. Electron crystallography is especially useful in studying the structure and function of membrane proteins. Electron crystallography is now an established method of analyzing the structures of membrane proteins in lipid bilayers, which resembles their natural biological environment. To better understand the neural system function from a structural point of view, we developed the cryo-electron microscope with a helium-cooled specimen stage, which allows for analysis of the structures of membrane proteins at a resolution higher than 3 Å. This review introduces recent instrumental advances in cryo-electron microscopy and presents some examples of structure analyses of membrane proteins, such as bacteriorhodopsin, water channels and gap junction channels. This review has two objectives: first, to provide a personal historical background to describe how we came to develop the cryo-electron microscope and second, to discuss some of the technology required for the structural analysis of membrane proteins based on cryo-electron microscopy.
The change of the electronic structure of alkali halide films on W(110) under electron bombardment
NASA Astrophysics Data System (ADS)
Dieckhoff, S.; Maus-Friedrichs, W.; Kempter, V.
1992-03-01
NaCl and Csl films of up to four layers were deposited onto W(110) surfaces and investigated by metastable impact electron spectroscopy (MIES), UPS and AES. The electronic structure of the films under electron bombardment was then studied by MIES/UPS. The results are compared with the corresponding ones obtained by thermal desorption spectroscopy (TDS). An interpretation of the results is attempted on the basis of existing theories for desorption induced by electronic transitions (DIET) of alkali halides.
Cellulose Acetate Membranes: Electron Microscopy of Structure.
Riley, R; Gardner, J O; Merten, U
1964-02-21
Electron photomicrographs of cellulose acetate membranes used in the reverse osmosis processof water desalination reveal a dense surface layer with a porous substructure. The high rate oftransmission for water can be correlated with the thickness of the dense layer on the air-driedsurface of the membrane.
NASA Astrophysics Data System (ADS)
Maroulis, George
1998-06-01
A large (18s 13p 8d 5f / 12s 7p 3d 2f) basis set consisting of 256 uncontracted gaussian-type functions is expected to yield values near the Hartree-Fock limit for the static hyperpolarizability of H 2O: βzxx=-9.40, βzyy=-1.35, βzzz=-7.71 and β¯=-11.07 for βαβγ ( e3a03Eh-2) and γxxxx=569, γyyyy=1422, γzzzz=907, γxxyy=338, γyyzz=389, γzzxx=287 and γ¯=985 for γαβγδ ( e4a04Eh-3) at the experimental equilibrium geometry (with z as the C 2 axis, molecule on the xz plane). The respective electron correlation corrections obtained with the single, double and perturbatively linked triple excitations coupled-cluster method and a [9s 6p 6d 3f / 6s 4p 2d 1f] basis set are βzxx=-0.45, βzyy=-4.19, βzzz=-6.09, β¯=-6.44 and γxxxx=267, γyyyy=1228, γzzzz=574, γxxyy=295, γyyzz=322, γzzxx=152, γ¯=721 . For the static limit we propose β¯=-17.5±0.3 e3a03Eh-2 and γ¯=(171±6)×10 1e4a04Eh-3, in near agreement with the experimental findings of β¯=-19.2±0.9 e3a03Eh-2 and γ¯=1800±150 e4a04Eh-3 deduced from EFISH measurements at 1064 nm by Kaatz et al. [P. Kaatz, E.A. Donley, D.P. Shelton, J. Chem. Phys. 108 (1998) 849].
Electronic transmission in quasiperiodic serial stub structures
NASA Astrophysics Data System (ADS)
Chattopadhyay, Samar; Chakrabarti, Arunava
2004-01-01
We present exact results on the electronic transmission through quantum stub waveguides arranged in a Fibonacci quasiperiodic pattern. Discretizing the Schrödinger equation, we map the problem into an equivalent tight binding form and study the transmission spectrum using the transfer matrix method. We emphasize the effect of local positional correlations in a Fibonacci quantum stub array that may lead to resonant eigenstates. Using the real space renormalization group ideas we unravel various local clusters of stubs responsible for resonance. Extended eigenstates have been shown to exist and we find that, under some special circumstances, the electronic charge density exhibits a totally periodic character in such a non-periodic sequence. Our method is completely general and can be applied to any arbitrary sequence of stubs: periodic, quasiperiodic or random. This may lead to a possible experimental verification of the role of positional correlations in the transport behaviour of a class of mesoscopic devices.
Electronic structure of trypsin inhibitor from squash seeds in aqueous solution
NASA Astrophysics Data System (ADS)
Zheng, Haoping
2000-10-01
The electronic structure of the trypsin inhibitor from seeds of the squash Cucurbita maxima (CMTI-I) in aqueous solution is obtained by ab initio, all-electron, full-potential calculations using the self-consistent cluster-embedding (SCCE) method. The reactive site of the inhibitor is explained theoretically, which is in agreement with the experimental results. It is shown that the coordinates of oxygen atoms in the inhibitor, determined by nuclear magnetic resonance and combination of distance geometry and dynamical simulated annealing, are systematically less accurate than that of other kinds of heavy atoms.
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.
Energy-filtered Electron Transport Structures for Low-power Low-noise 2-D Electronics
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
Structural phase transition and electronic properties of NdBi
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.
Electronic structure and stability of some silicon compounds
NASA Astrophysics Data System (ADS)
Novak, Igor; Abu-Izneid, Tareq; Kovač, Branka
2010-05-01
The electronic structures of N,1,3-tris(1,1-dimethylethyl)-cyclodisilazan-2-amine ( I) and 2,3,5,5-tetrakis(trimethylsilyl)cyclopentadiene ( II) have been investigated by HeI and HeII UV photoelectron spectroscopy (UPS) and quantum chemical calculations. We discuss the influence of substituent effects on their electronic structure and thermodynamic stability. Our study shows that trimethylsilyl substituents have strong influence on the electronic structure of cyclopentadiene via inductive effect. Their influence on thermodynamic stability is also pronounced. In substituted cyclodisilazanes hyperconjugative influence of alkylsilyl groups was shown to cause relative thermodynamic stabilization of the cyclodisilazane system.
New fine structure cooling rate. [electron impact transitions in the ionosphere
NASA Technical Reports Server (NTRS)
Hoegy, W. R.
1976-01-01
One of the dominant electron cooling processes in the ionosphere is caused by electron impact induced fine structure transitions among the ground state levels of atomic oxygen. This fine structure cooling rate is based on theoretical cross sections. Recent advances in the numerical cross section determinations to include polarization effects and more accurate representations of the atomic target result in new lower values. These cross sections are employed in this paper to derive a new fine structure cooling rate which is between 40% and 60% of the currently used rate. A new generalized formula is presented for the cooling rate (from which the fine structure cooling rate is derived), valid for arbitrary mass and temperature difference of the colliding particles and arbitrary inelastic energy difference.
Structural and electronic properties of endohedral metallofullerenes.
Akasaka, Takeshi; Lu, Xing
2012-04-01
This account presents an overview of our achievements in structural and chemical understanding of endohedral metallofullerenes (EMFs), a new class of metal-carbon hybrid materials formed by encapsulation of metals inside fullerene cavities. Structural determination of EMFs is of fundamental importance for understanding their intrinsic properties and the formation mechanism, and for broadening their applications. We have developed an effective method for determining the structures of paramagnetic EMFs, and also succeeded in observing the motion of cluster in a di-metal EMF for the first time. Recently, we unambiguously established the structures of some carbide EMFs which had been wrongly assumed as conventional EMFs previously. More importantly, we have obtained some insoluble EMF species which had never been explored or even expected before. Meanwhile, the chemical properties of various EMFs with different cage structures or different metallic cores have been systematically investigated by means of both covalent and supramolecular considerations, yielding many fascinating results relating to the dictating effect of internal metals. It is noteworthy that all these achievements are based on unambiguous X-ray results of pristine or functionalized EMFs.
Writing silica structures in liquid with scanning transmission electron microscopy.
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
2015-02-01
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.
Fuentes-Cabrera, Miguel; Zhao, Xiongce; Kent, P R C; Sumpter, Bobby G
2007-08-01
xDNA is an artificial duplex made of natural and benzo-homologated bases. The latter can be seen as a fusion between benzene and a natural base. We have used two different ab initio techniques, one based on B3LYP and a Gaussian expansion of the wave functions, and the other on GGA and plane-waves, to investigate the electronic properties of an xDNA duplex and a natural one with an analogous sequence. The calculations were performed in dry conditions, i.e., H atoms were used to neutralize the charge. It is found that the HOMO-LUMO gap of xDNA is about 0.5 eV smaller than that of B-DNA, independent of the technique used. The pi-pi* gap of xDNA is 1.3 or 1.0 eV smaller than that of B-DNA, depending on whether one uses B3LYP/6-31G or GGA/plane-waves, respectively. An analysis of how saturation changes the electronic properties of the nucleotide pairs that make up these duplexes suggests that different saturation schemes significantly affect the HOMO-LUMO gap value of xDNA and B-DNA. The same is not true for the pi-pi* gap. That xDNA has a smaller pi-pi* gap than B-DNA suggests that xDNA could be a plausible candidate for molecular-wire applications.
Electron microscopy of myelin: Structure preservation by high-pressure freezing.
Möbius, Wiebke; Nave, Klaus-Armin; Werner, Hauke B
2016-06-15
Electron microscopic visualization of nervous tissue morphology is crucial when aiming to understand the biogenesis and structure of myelin in healthy and pathological conditions. However, accurate interpretation of electron micrographs requires excellent tissue preservation. In this short review we discuss the recent utilization of tissue fixation by high-pressure freezing and freeze-substitution, which now supplements aldehyde fixation in the preparation of samples for electron microscopy of myelin. Cryofixation has proven well suited to yield both, improved contrast and excellent preservation of structural detail of the axon/myelin-unit in healthy and mutant mice and can also be applied to other model organisms, including aquatic species. This article is part of a Special Issue entitled SI: Myelin Evolution. PMID:26920467
Solid state effects on the electronic structure of H2OEP.
Marsili, M; Umari, P; Di Santo, G; Caputo, M; Panighel, M; Goldoni, A; Kumar, M; Pedio, M
2014-12-28
We present the results of a joint experimental and theoretical investigation concerning the effect of crystal packing on the electronic properties of the H2OEP molecule. Thin films, deposited in ultra high vacuum on metal surfaces, are investigated by combining valence band photoemission, inverse photoemission, and X-ray absorption spectroscopy. The spectra of the films are compared, when possible, with those measured in the gas phase. Once many-body effects are included in the calculations through the GW method, the electronic structure of H2OEP in the film and gas phase are accurately reproduced for both valence and conduction states. Upon going from an isolated molecule to the film phase, the electronic gap shrinks significantly and the lowest unoccupied molecular orbital (LUMO) and LUMO + 1 degeneracy is removed. The calculations show that the reduction of the transport gap in the film is entirely addressable to the enhancement of the electronic screening. PMID:25388091
Electron Diffraction Determination of Nanoscale Structures
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.
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.
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.
Structure and properties of electronic and hole centers in CsBr from theoretical calculations
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.
NASA Astrophysics Data System (ADS)
Maibam, Jameson; Indrajit Sharma, B.; Bhattacharjee, Ramendu; Thapa, R. K.; Brojen Singh, R. K.
2011-11-01
We have studied the electronic, structural, and elastic properties of scandium carbide and yttrium carbide by means of accurate first principles total energy calculations using the full-potential linearized plane wave method (FP-LAPW). We have used the generalized gradient approximation (GGA) for the exchange and correlation potential. Volume optimization, energy band structure, and density of states (DOS) of the systems are presented. The second order elastic constants have been calculated and other related quantities such as the Zener anisotropy factor, Poisson's ratio, Young's modulus, Kleinman parameter, Debye temperature, and sound velocities have been determined. The band gap calculation shows that YC is relatively more ionic than ScC.
Mezey, P.G.; Zimpel, Z.; Warburton, P.; Walker, P.D.; Irvine, D.G.; Huang, X.D.; Dixon, D.G.; Greenberg, B.M.
1998-07-01
The quantitative shape-activity relationship (QShAR) methodology, based on accurate three-dimensional electron densities and detailed shape analysis methods, has been applied to a Lemna gibba photoinduced toxicity data set of 16 polycyclic aromatic hydrocarbon (PAH) molecules. In the first phase of the studies, a shape fragment QShAR database of PAHs was developed. The results provide a very good match to toxicity based on a combination of the local shape features of single rings in comparison to the central ring of anthracene and a more global shape feature involving larger molecular fragments. The local shape feature appears as a descriptor of the susceptibility of PAHs to photomodification and the global shape feature is probably related to photosensitization activity.
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.
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.
Accurate γ and MeV-electron track reconstruction with an ultra-low diffusion Xenon/TMA TPC at 10 atm
NASA Astrophysics Data System (ADS)
González-Díaz, Diego; Álvarez, V.; Borges, F. I. G.; Camargo, M.; Cárcel, S.; Cebrián, S.; Cervera, A.; Conde, C. A. N.; Dafni, T.; Díaz, J.; Esteve, R.; Fernandes, L. M. P.; Ferrario, P.; Ferreira, A. L.; Freitas, E. D. C.; Gehman, V. M.; Goldschmidt, A.; Gómez-Cadenas, J. J.; Gutiérrez, R. M.; Hauptman, J.; Hernando Morata, J. A.; Herrera, D. C.; Irastorza, I. G.; Labarga, L.; Laing, A.; Liubarsky, I.; Lopez-March, N.; Lorca, D.; Losada, M.; Luzón, G.; Marí, A.; Martín-Albo, J.; Martínez-Lema, G.; Martínez, A.; Miller, T.; Monrabal, F.; Monserrate, M.; Monteiro, C. M. B.; Mora, F. J.; Moutinho, L. M.; Muñoz Vidal, J.; Nebot-Guinot, M.; Nygren, D.; Oliveira, C. A. B.; Pérez, J.; Pérez Aparicio, J. L.; Querol, M.; Renner, J.; Ripoll, L.; Rodríguez, J.; Santos, F. P.; dos Santos, J. M. F.; Serra, L.; Shuman, D.; Simón, A.; Sofka, C.; Sorel, M.; Toledo, J. F.; Torrent, J.; Tsamalaidze, Z.; Veloso, J. F. C. A.; Villar, J. A.; Webb, R.; White, J. T.; Yahlali, N.; Azevedo, C.; Aznar, F.; Calvet, D.; Castel, J.; Ferrer-Ribas, E.; García, J. A.; Giomataris, I.; Gómez, H.; Iguaz, F. J.; Lagraba, A.; Le Coguie, A.; Mols, J. P.; Şahin, Ö.; Rodríguez, A.; Ruiz-Choliz, E.; Segui, L.; Tomás, A.; Veenhof, R.
2015-12-01
We report the performance of a 10 atm Xenon/trimethylamine time projection chamber (TPC) for the detection of X-rays (30 keV) and γ-rays (0.511-1.275 MeV) in conjunction with the accurate tracking of the associated electrons. When operated at such a high pressure and in 1%-admixtures, trimethylamine (TMA) endows Xenon with an extremely low electron diffusion (1.3 ± 0.13 mm - σ (longitudinal), 0.95 ± 0.20 mm - σ (transverse) along 1 m drift) besides forming a convenient 'Penning-Fluorescent' mixture. The TPC, that houses 1.1 kg of gas in its fiducial volume, operated continuously for 100 live-days in charge amplification mode. The readout was performed through the recently introduced microbulk Micromegas technology and the AFTER chip, providing a 3D voxelization of 8 mm × 8 mm × 1.2 mm for approximately 10 cm/MeV-long electron tracks. Resolution in energy (ε) at full width half maximum (R) inside the fiducial volume ranged from R = 14.6 % (30 keV) to R = 4.6 %(1.275 MeV). This work was developed as part of the R&D program of the NEXT collaboration for future detector upgrades in the search of the neutrino-less double beta decay (ββ 0 ν) in 136Xe, specifically those based on novel gas mixtures. Therefore we ultimately focus on the calorimetric and topological properties of the reconstructed MeV-electron tracks. In particular, the obtained energy resolution has been decomposed in its various contributions and improvements towards achieving the R = 1.4 %√{ 1 MeV / ε } levels obtained in small sensors are discussed.
Electronic structure calculations of ESR parameters of melanin units.
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.
Electronic structure control of single-walled carbon nanotube functionalization.
Strano, Michael S; Dyke, Christopher A; Usrey, Monica L; Barone, Paul W; Allen, Mathew J; Shan, Hongwei; Kittrell, Carter; Hauge, Robert H; Tour, James M; Smalley, Richard E
2003-09-12
Diazonium reagents functionalize single-walled carbon nanotubes suspended in aqueous solution with high selectivity and enable manipulation according to electronic structure. For example, metallic species are shown to react to the near exclusion of semiconducting nanotubes under controlled conditions. Selectivity is dictated by the availability of electrons near the Fermi level to stabilize a charge-transfer transition state preceding bond formation. The chemistry can be reversed by using a thermal treatment that restores the pristine electronic structure of the nanotube. PMID:12970561
Electronic structure of EuFe2As2.
Adhikary, Ganesh; Sahadev, Nishaina; Biswas, Deepnarayan; Bindu, R; Kumar, Neeraj; Thamizhavel, A; Dhar, S K; Maiti, Kalobaran
2013-06-01
Employing high resolution photoemission spectroscopy, we studied the temperature evolution of the electronic structure of EuFe2As2, a unique pnictide, where antiferromagnetism of the Eu layer survives within the superconducting phase due to 'FeAs' layers, achieved via substitution and/or pressure. High energy and angle resolution helped to reveal the signature of peak-dip features, having significant p orbital character and spin density wave transition induced band folding in the electronic structure. A significant spectral weight redistribution is observed below 20 K manifesting the influence of antiferromagnetic order on the conduction electrons.
Electron beam enhanced surface modification for making highly resolved structures
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.
Electronic structure and magnetism of ThFeAsN
NASA Astrophysics Data System (ADS)
Wang, Guangtao; Shi, Xianbiao
2016-03-01
The electronic structure and magnetic properties of ThFeAsN, a newly discovered superconductor, are investigated by means of first-principles calculations. ThFeAsN shares electronic structure and magnetic properties similar to those of LaOFeAs. Its calculated ground state is the stripe antiferromagnetic state. The hole-like Fermi surfaces (FSs) along the Γ\\text-Z line largely overlap with the electron-like FS along the M\\text-A line with the vector q= (π, π, 0) . Such significant FS nesting induces a peak of the bare susceptibility χ0(q ) at the M-point.
Electron beam enhanced surface modification for making highly resolved structures
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.
Structural properties of amorphous silicon produced by electron irradiation
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.
Thermal-structural analysis of electron gun with control grid.
Yao, Lieming; Zhang, Kai; Yu, Hailong; Huang, Tao; Li, Bin
2012-02-01
Steady state thermal-structural analysis of electron guns is essential due to the requirement of high reliability in beam performance. Temperatures and displacements for all the components of an electron gun with a control grid are computed. Steady-state thermal analysis has been carried out for various cathode temperatures and various intercepted powers on the control grid to determine the temperature of the control grid. These results are verified experimentally based on measured results from an assembled electron gun. Structural analysis of the electron gun is used to evaluate the deformation of the inner electrodes under the hot condition. The results show that the thermal stress slightly changes the characteristics of the gun. The obtained thermal deformation data can be helpful to modify the design dimensions and assembly of an electron gun.
Structural complexities in the active layers of organic electronics.
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.
MATERIALS WITH COMPLEX ELECTRONIC/ATOMIC STRUCTURES
D. M. PARKIN; L. CHEN; ET AL
2000-09-01
We explored both experimentally and theoretically the behavior of materials at stresses close to their theoretical strength. This involves the preparation of ultra fine scale structures by a variety of fabrication methods. In the past year work has concentrated on wire drawing of in situ composites such as Cu-Ag and Cu-Nb. Materials were also fabricated by melting alloys in glass and drawing them into filaments at high temperatures by a method known as Taylor wire technique. Cu-Ag microwires have been drawn by this technique to produce wires 10 {micro}m in diameter that consist of nanoscale grains of supersaturated solid solution. Organogels formed from novel organic gelators containing cholesterol tethered to squaraine dyes or trans-stilbene derivatives have been studied from several different perspectives. The two types of molecules are active toward several organic liquids, gelling in some cases at w/w percentages as low as 0.1. While relatively robust, acroscopically dry gels are formed in several cases, studies with a variety of probes indicate that much of the solvent may exist in domains that are essentially liquid-like in terms of their microenvironment. The gels have been imaged by atomic force microscopy and conventional and fluorescence microscopy, monitoring both the gelator fluorescence in the case of the stilbene-cholesterol gels and, the fluorescence of solutes dissolved in the solvent. Remarkably, our findings show that several of the gels are composed of similarly appearing fibrous structures visible at the nano-, micro-, and macroscale.
Electronic structure of CoPt based systems: from bulk to nanoalloys
NASA Astrophysics Data System (ADS)
Zosiak, L.; Goyhenex, C.; Kozubski, R.; Tréglia, G.
2015-11-01
An accurate description of the local electronic structure is necessary for guiding the design of materials with targeted properties in a controlled way. For complex materials like nanoalloys, self-consistent tight-binding calculations should be a good alternative to ab initio methods, for handling the most complex and large systems (hundreds to thousands of atoms), provided that these parameterized method is well founded from ab initio ones that they intend to replace. Ab initio calculations (density functional theory) enabled us to derive rules for charge distribution as a function of structural change and alloying effects in Co and Pt based systems, from bulk to nanoalloys. A general local neutrality rule per site, orbital and species was found. Based on it, self-consistent tight-binding calculations could be implemented and applied to CoPt nanoalloys. A very good agreement is obtained between tight-binding and DFT calculations in terms of local electronic structure.
Electronic structure of a graphene superlattice with massive Dirac fermions
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.
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.
Richard, Ryan M; Marshall, Michael S; Dolgounitcheva, O; Ortiz, J V; Brédas, Jean-Luc; Marom, Noa; Sherrill, C David
2016-02-01
In designing organic materials for electronics applications, particularly for organic photovoltaics (OPV), the ionization potential (IP) of the donor and the electron affinity (EA) of the acceptor play key roles. This makes OPV design an appealing application for computational chemistry since IPs and EAs are readily calculable from most electronic structure methods. Unfortunately reliable, high-accuracy wave function methods, such as coupled cluster theory with single, double, and perturbative triples [CCSD(T)] in the complete basis set (CBS) limit are too expensive for routine applications to this problem for any but the smallest of systems. One solution is to calibrate approximate, less computationally expensive methods against a database of high-accuracy IP/EA values; however, to our knowledge, no such database exists for systems related to OPV design. The present work is the first of a multipart study whose overarching goal is to determine which computational methods can be used to reliably compute IPs and EAs of electron acceptors. This part introduces a database of 24 known organic electron acceptors and provides high-accuracy vertical IP and EA values expected to be within ±0.03 eV of the true non-relativistic, vertical CCSD(T)/CBS limit. Convergence of IP and EA values toward the CBS limit is studied systematically for the Hartree-Fock, MP2 correlation, and beyond-MP2 coupled cluster contributions to the focal point estimates. PMID:26731487
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.
YU,L.H.
2003-04-01
Synchronization between seed laser pulse and electron bunch to below 50 fs is a critically important issue in carrying out cascading HGHG stages to achieve intense temporally coherent x-ray FEL. The single stage HGHG experiment in the IR and recently in UV region has achieved significant success. Hence the next step, to demonstrate the cascading of 2 stages of HGHG becomes crucially important in confirming the viability of this scheme. Based on our experiences at DUVFEL during the HGHG experiment, we can measure the time jitter between the electron bunch and the RF phase before compression to a high precision of order of 50 fs. Without the compression, this is equal to the time jitter between the laser and the RF phase. An analysis of this measurement suggests that it is possible to use a fast feedback system to reduce the jitter significantly. However, during the successful HGHG experiment at 266 nm recently, we realized that there is a simpler way to achieve highly accurate synchronization. Here we describe the method.
Electron vortex magnetic holes: A nonlinear coherent plasma structure
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.
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.
Engineering the Electronic Band Structure for Multiband Solar Cells
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.
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.
Advanced Accelerating Structures and Their Interaction with Electron Beams
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.
Advanced accelerating structures and their interaction with electron beams.
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.
Vertical Electron Transport through PbS-EuS Structures
NASA Technical Reports Server (NTRS)
Wrotek, S.; Dybko, K.; Morawski, A.; Makosa, A.; Wosinski, T.; Figielski, T.; Tkaczyk, Z.; Lusakowska, E.; Story, T.; Sipatov, A. Yu
2003-01-01
Temperature dependence of current-voltage I-V characteristics and resistivity is studied in ferromagnetic PbS-EuS semiconductor tunnel structures grown on n-PbS (100) substrates. For the structures with a single (2-4 nm thick) ferromagnetic EuS electron barrier we observe strongly non-linear I-V characteristics with an effective tunneling barrier height of 0.3-0.7 eV. The experimentally observed non-monotonic temperature dependence of the (normal to the plane of the structure) electrical resistance of these structures is discussed in terms of the electron tunneling mechanism taking into account the temperature dependent shift of the band offsets at the EuS-PbS heterointerface as well as the exchange splitting of the electronic states at the bottom of the conduction band of EuS.
NASA Astrophysics Data System (ADS)
Zhu, Chun
Electron tomography was originally developed in 1968, and has been primarily applied to determine the three-dimensional (3D) structure of biological systems. In the last decade, the application of electron tomography in materials science and nanoscience has revived due to the utilization of scanning transmission electron microscopy (STEM) in the high-angle annular dark-field (HAADF) mode, and a highest resolution of ˜1 nm3 has been achieved. However, improving the resolution from ˜1 nm 3 to the atomic level remains a challenging task, which requires new tomographic reconstruction algorithms, better projection alignment methods, state-of-the-art STEM instruments, and more accurate data-acquisition procedures. In this thesis, important progress has been made in all these four areas. First, a novel tomographic method, termed equally sloped tomography (EST), was developed and allows the 3D image reconstruction of tilt series with a limited number projections and a "missing wedge" (i.e. specimens cannot usually be tilted beyond +/-70°). Second, an alignment method which can be used to align the projections of a tilt series at atomic-level resolution was developed based on center of mass. Finally, by using a Titan 80-300 STEM instrument at the California NanoSystems Institute, UCLA, more accurate data acquisition procedures were developed and a number of tomographic tilt series of atomic resolution projections from different nanoparticles have been obtained. With all these combinations, the 3D structure of a 10 nm gold nanoparticle was determined at 2.4 A resolution, the highest resolution ever achieved in any general tomography method. More recently, this novel electron tomography method has been applied to observe nearly all the atoms in a Pt nanoparticle, and imaged for the first time the 3D core structure of edge and screw dislocations at atomic resolution. Furthermore, through numerical simulations the feasibility of determining the 3D atomic structure of
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.
Spectroscopic investigations of the electronic structure of neptunyl ions.
Wilkerson, M. P.; Berg, J. M.; Dewey, H. J.
2003-01-01
Molecular electronic structures are innately sensitive to the geometric and chemical environments around the metal center of coordination compounds . However, the interrelationships between the electronic structures and molecular geometries of actinide species, which often contain more than one electron in the Sf valence shell, are quite complex due to the large numbers of possible electronic states and high densities of vibronically enabled transitions .1'2 Investigations of the optical signatures of simple, well-defined molecular systems should provide the most straightforward approach for unharnessing these fundamental relationships, and in particular, systems with a single electron in the valence Sf shell, such as the neptunyl ion (Np0 22+), should provide the most viable means for characte rizing actinide electronic structure. Furthermore, Sf orbital-occupied actinide systems exhibit not only visible and ultraviolet ligand-to-metal charge-transfer spectral bands, but also near-infrared Sf-Sf transitions resulting from promotion of a Sf electron to an orbital of primarily Sf character .
Membrane protein structures without crystals, by single particle electron cryomicroscopy
Vinothkumar, Kutti R
2015-01-01
It is an exciting period in membrane protein structural biology with a number of medically important protein structures determined at a rapid pace. However, two major hurdles still remain in the structural biology of membrane proteins. One is the inability to obtain large amounts of protein for crystallization and the other is the failure to get well-diffracting crystals. With single particle electron cryomicroscopy, both these problems can be overcome and high-resolution structures of membrane proteins and other labile protein complexes can be obtained with very little protein and without the need for crystals. In this review, I highlight recent advances in electron microscopy, detectors and software, which have allowed determination of medium to high-resolution structures of membrane proteins and complexes that have been difficult to study by other structural biological techniques. PMID:26435463
Structure of a Bacterial Cell Surface Decaheme Electron Conduit
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.
Parallel adaptive mesh refinement for electronic structure calculations
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.
The Electronic Structure of Single-Layer Graphene
NASA Astrophysics Data System (ADS)
Siegel, David Alan
Single-layer graphene has been widely researched in recent years due to its perceived technological applicability and its scientific importance as a unique model system with relativistic Dirac Fermions. Because of its unique geometric and electronic structure, the properties of graphene can be tuned or manipulated in several ways. This tunability is important for technological applications in its own right, and it also allows us to study the fundamental properties of Dirac Fermions, including unique many-body interactions and the nature of the quasiparticles at half-filling. This thesis is a detailed examination of the electronic and structural properties of graphene, studied with angle-resolved photoemission spectroscopy (ARPES) and other surface science techniques like low-energy electron microscopy and diffraction. This thesis is organized as follows. Chapter 1 gives an introduction to the electronic and structural properties of single-layer graphene. It provides a brief historical overview of major theoretical and experimental milestones and sets the stage for the important theoretical and experimental questions that this thesis addresses. Chapters 2 and 3 describe the experimental setup. Chapter 2 discusses the experimental techniques used in this thesis with particular focus on the mechanics of ARPES. Chapter 3 discusses the different graphene growth techniques that were used to create our sample with particular focus on our characterization of epitaxial graphene on SiC(0001). Chapters 4 and 5 form the meat of this thesis: they provide a thorough discussion of the electronic properties of graphene as studied by ARPES. Chapter 4 describes how various perturbations can result in the manipulation of the bare electronic band structure, including the deposition of atomic or molecular species on top of an epitaxial graphene sheet as well as the interactions between graphene and its substrate. Chapter 5 describes the many-body physics in single-layer graphene. It
Electronic structure of the silicon vacancy color center in diamond.
Hepp, Christian; Müller, Tina; Waselowski, Victor; Becker, Jonas N; Pingault, Benjamin; Sternschulte, Hadwig; Steinmüller-Nethl, Doris; Gali, Adam; Maze, Jeronimo R; Atatüre, Mete; Becher, Christoph
2014-01-24
The negatively charged silicon vacancy (SiV) color center in diamond has recently proven its suitability for bright and stable single photon emission. However, its electronic structure so far has remained elusive. We here explore the electronic structure by exposing single SiV defects to a magnetic field where the Zeeman effect lifts the degeneracy of magnetic sublevels. The similar responses of single centers and a SiV ensemble in a low strain reference sample prove our ability to fabricate almost perfect single SiVs, revealing the true nature of the defect's electronic properties. We model the electronic states using a group-theoretical approach yielding a good agreement with the experimental observations. Furthermore, the model correctly predicts polarization measurements on single SiV centers and explains recently discovered spin selective excitation of SiV defects. PMID:24484153
Electronic structure and photoelectron spectra of osmium and ruthenium tetraoxides
Topol', I.A.; Vovna, V.I.; Kazachek, M.V.
1988-01-01
The X/sub ..cap alpha../-SW method has been used in the nonrelativistic and quasirelativistic approximations to calculate the electronic structures of OsO/sub 4/, RuO/sub 4/, and FeO/sub 4/. When the 5d element is replaced by a 4d or 3d one, the electron-density redistribution is due mainly to the d electrons. All the d electrons in FeO/sub 4/ are localized on the iron atom, which markedly reduced the ionic and covalent bonding on the transition from RuO/sub 4/ to FeO/sub 4/, which explains the instability of FeO/sub 4/. The calculated spin-orbit splittings agree well with the structure of the PES bands, which enables one to establish the sequence of MO ionization energies unambiguously.
Aguirre, Néstor F; Villarreal, Pablo; Delgado-Barrio, Gerardo; Posada, Edwin; Reyes, Andrés; Biczysko, Malgorzata; Mitrushchenkov, Alexander O; de Lara-Castells, María Pilar
2013-05-14
An interface between the APMO code and the electronic structure package MOLPRO is presented. The any particle molecular orbital APMO code [González et al., Int. J. Quantum Chem. 108, 1742 (2008)] implements the model where electrons and light nuclei are treated simultaneously at Hartree-Fock or second-order Möller-Plesset levels of theory. The APMO-MOLPRO interface allows to include high-level electronic correlation as implemented in the MOLPRO package and to describe nuclear quantum effects at Hartree-Fock level of theory with the APMO code. Different model systems illustrate the implementation: (4)He2 dimer as a protype of a weakly bound van der Waals system; isotopomers of [He-H-He](+) molecule as an example of a hydrogen bonded system; and molecular hydrogen to compare with very accurate non-Born-Oppenheimer calculations. The possible improvements and future developments are outlined.
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. PMID:26226061
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.
Studying Atomic Structures by Aberration-Corrected Transmission Electron Microscopy
NASA Astrophysics Data System (ADS)
Urban, Knut W.
2008-07-01
Seventy-five years after its invention, transmission electron microscopy has taken a great step forward with the introduction of aberration-corrected electron optics. An entirely new generation of instruments enables studies in condensed-matter physics and materials science to be performed at atomic-scale resolution. These new possibilities are meeting the growing demand of nanosciences and nanotechnology for the atomic-scale characterization of materials, nanosynthesized products and devices, and the validation of expected functions. Equipped with electron-energy filters and electron-energy loss spectrometers, the new instruments allow studies not only of structure but also of elemental composition and chemical bonding. The energy resolution is about 100 milli electron volts, and the accuracy of spatial measurements has reached a few picometers. However, understanding the results is generally not straightforward and only possible with extensive quantum-mechanical computer calculations.
Studying atomic structures by aberration-corrected transmission electron microscopy.
Urban, Knut W
2008-07-25
Seventy-five years after its invention, transmission electron microscopy has taken a great step forward with the introduction of aberration-corrected electron optics. An entirely new generation of instruments enables studies in condensed-matter physics and materials science to be performed at atomic-scale resolution. These new possibilities are meeting the growing demand of nanosciences and nanotechnology for the atomic-scale characterization of materials, nanosynthesized products and devices, and the validation of expected functions. Equipped with electron-energy filters and electron-energy-loss spectrometers, the new instruments allow studies not only of structure but also of elemental composition and chemical bonding. The energy resolution is about 100 milli-electron volts, and the accuracy of spatial measurements has reached a few picometers. However, understanding the results is generally not straightforward and only possible with extensive quantum-mechanical computer calculations. PMID:18653874
Campbell, J Larry; Baba, Takashi
2015-06-01
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.
Human enamel structure studied by high resolution electron microscopy
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.
Chen, Shengli; Liu, Yuwen; Chen, Junxiang
2014-08-01
Heterogeneous electron-transfer (ET) processes at solid electrodes play key roles in molecular electronics and electrochemical energy conversion and sensing. Electrode nanosization and/or nanostructurization are among the major current strategies for performance promotion in these fields. Besides, nano-sized/structured electrodes offer great opportunities to characterize electrochemical structures and processes with high spatial and temporal resolution. This review presents recent insights into the nanoscopic size and structure effects of electrodes and electrode materials on heterogeneous ET kinetics, by emphasizing the importance of the electric double-layer (EDL) at the electrode/electrolyte interface and the electronic structure of electrode materials. It is shown, by general conceptual analysis and recent example demonstrations of representative electrode systems including electrodes of nanometer sizes and gaps and of nanomaterials such as sp(2) hybridized nanocarbons and semiconductor quantum dots, how the heterogeneous ET kinetics, the electronic structures of electrodes, the EDL structures at the electrode/electrolyte interface and the nanoscopic electrode sizes and structures may be related.
Multidomain decomposition approach to large scale electronic structure calculations
NASA Astrophysics Data System (ADS)
Varga, Kalman
2010-03-01
A first-principles electronic structure calculation is presented using a domain decomposition technique. The domain decomposition leads to block tridiagonal Hamiltonian and overlap matrices. With the help of an LDL decomposition the block tridiagonal structure can be exploited and the Kohn-Sham states and/or the electron density can be calculated in an computationally efficient way. The electron density can be calculated from the Green's function or from the eigensolution obtained using subspace iteration. In both cases, the calculation of the density is divided into a series of independent computations that can be done in parallel. This approach allows us to determine tens of thousands of eigenstates with any desired accuracy. If the Kohn-Sham states are not required, the density can be calculated from the Green's function in a linearly scaling fashion. The linear scaling is achieved by using the special structure resulting from the domain decomposition and not by truncation or cutoff.
Cellular structural biology as revealed by cryo-electron tomography.
Irobalieva, Rossitza N; Martins, Bruno; Medalia, Ohad
2016-02-01
Understanding the function of cellular machines requires a thorough analysis of the structural elements that underline their function. Electron microscopy (EM) has been pivotal in providing information about cellular ultrastructure, as well as macromolecular organization. Biological materials can be physically fixed by vitrification and imaged with cryo-electron tomography (cryo-ET) in a close-to-native condition. Using this technique, one can acquire three-dimensional (3D) information about the macromolecular architecture of cells, depict unique cellular states and reconstruct molecular networks. Technical advances over the last few years, such as improved sample preparation and electron detection methods, have been instrumental in obtaining data with unprecedented structural details. This presents an exciting opportunity to explore the molecular architecture of both individual cells and multicellular organisms at nanometer to subnanometer resolution. In this Commentary, we focus on the recent developments and in situ applications of cryo-ET to cell and structural biology.
Wiring of metallized microtubules by electron beam-induced structuring
NASA Astrophysics Data System (ADS)
Fritzsche, Wolfgang; Köhler, J. Michael; Böhm, Konrad J.; Unger, Eberhard; Wagner, Thomas; Kirsch, Remo; Mertig, Michael; Pompe, Wolfgang
1999-09-01
Molecular electronics emerge as a possibility to continue the miniaturization of electronic circuits down to the lower nanometre scale. One significant challenge is the electrical connection of molecular devices by nanowires. We present here the realization of a new approach for the wiring of nanostructures by linking metallized microtubules (MTs) to prestructured microelectrodes. MTs (tube-like protein structures) were metallized and deposited on microstructured substrates. Electron beam-induced deposition was used for structuring connecting gold lines as nanoelectrodes, which wire a single MT to microelectrodes created by photolithography. Initial electrical measurements confirmed the suitability of the set-up for linking nanometre-scale structures to a measurement device. A metallized MT yielded a resistance below 50 icons/Journals/Common/Omega" ALT="Omega" ALIGN="TOP"/> over the length of 1 µm.
Electron crystallography--the waking beauty of structural biology.
Pope, Christopher R; Unger, Vinzenz M
2012-08-01
Since its debut in the mid 1970s, electron crystallography has been a valuable alternative in the structure determination of biological macromolecules. Its reliance on single-layered or double-layered two-dimensionally ordered arrays and the ability to obtain structural information from small and disordered crystals make this approach particularly useful for the study of membrane proteins in a lipid bilayer environment. Despite its unique advantages, technological hurdles have kept electron crystallography from reaching its full potential. Addressing the issues, recent initiatives developed high-throughput pipelines for crystallization and screening. Adding progress in automating data collection, image analysis and phase extension methods, electron crystallography is poised to raise its profile and may lead the way in exploring the structural biology of macromolecular complexes.
Structural and electronic properties of dense liquid and amorphous nitrogen
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.
Atomic and electronic structure of exfoliated black phosphorus
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.
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.
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.
Sinha Ray, Suvonil; Ghosh, Anirban; Chattopadhyay, Sudip; Chaudhuri, Rajat K
2016-07-28
Recently a state-specific multireference perturbation theory (SSMRPT) with an improved virtual orbitals complete active space configuration interaction (IVO-CASCI) reference function has been proposed for treating electronic structures of radicals such as methylene, m-benzyne, pyridyne, and pyridynium cation. This new development in MRPT, termed as IVO-SSMRPT, ensures that it is able to describe the structure of radicaloids with reasonable accuracy even with small reference spaces. IVO-SSMRPT is also capable of predicting the correct ordering of the lowest singlet-triplet gaps. Investigation of the first three electronic states of the oxygen molecule has also been used for rating our method. The agreement of our estimates with the available far more expensive benchmark state-of-the-art ab initio calculations is creditable. The IVO-SSMRPT method provides an effective avenue with manageable cost/accuracy ratio for accurately dealing with radicaloid systems possessing varying degrees of quasidegeneracy. PMID:27355260
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
Chemistry and Electronic Structure of Iron-Based Superconductors
Safa-Sefat, Athena; Singh, David J
2011-01-01
The solid state provides a richly varied fabric for intertwining chemical bonding, electronic structure, and magnetism. The discovery of superconductivity in iron pnictides and chalcogenides has revealed new aspects of this interplay, especially involving magnetism and superconductivity. Moreover, it has challenged prior thinking about high-temperature superconductivity by providing a set of materials that differ in many crucial aspects from the previously known cuprate superconductors. Here we review some of what is known about the superconductivity and its interplay with magnetism, chemistry, and electronic structure in Fe-based superconductors.
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.
Orientation-dependent C-60 electronic structures revealed byphotoemission spectroscopy
Brouet, V.; Yang, W.L.; Zhou, X.J.; Choi, H.J.; Louie, S.G.; Cohen, M.L.; Goldoni, A.; Parmigiani, F.; Hussain, Z.; Shen, Z.X.
2008-01-17
We observe, with angle-resolved photoemission, a dramaticchange in the electronic structure of two C60 monolayers, deposited,respectively, on Ag (111) and (100) substrates, and similarly doped withpotassium to half filling of the C60 lowest unoccupied molecular orbital.The Fermi surface symmetry, the bandwidth, and the curvature of thedispersion at gamma point are different. Orient ations of the C60molecules on the two substrates are known to be the main structuraldifference between the two monolayers, and we present new band-structurecalculations for some of these orientations. We conclude thatorientations play a key role in the electronic structure offullerides.
Structural and luminescent properties of electron-irradiated silicon
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.
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.
Improving electronic structure methods to predict nano-optoelectronics and nano-catalyst functions.
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.
Electronic structure and electron correlation in weakly confining spherical quantum dot potentials
NASA Astrophysics Data System (ADS)
Kimani, Peter Borgia Ndungu
The electronic structure and electron correlations in weakly confining spherical quantum dots potentials are investigated. Following a common practice, the investigation starts with the restricted Hartree-Fock (HF) approximation. Then electron correlation is added in steps in a series of approximations based on the single particle Green's function approach: (i) Second-order Green function (GF) (ii) 2ph-Tamm-Dancoff approximation (TDA) and (iii) an extended version thereof (XTDA) which introduces ground-state correlation into the TDA. The study includes as well Hartree-Fock V (N-1) potential approximation in which framework the Hartree-Fock virtual orbitals are calculated in the field of the N-1 electrons as opposed to the regular but unphysical N-electron field Hartree-Fock calculation of virtual orbitals. For contrast and comparison, the same approximation techniques are applied to few-electron closed-shell atoms and few-electron negative ions for which pertinent data is readily available. The results for the weakly confining spherical quantum dot potentials and the standard atomic systems exhibit fundamental similarities as well as significant differences. For the most part the results of these calculations are in favor of application of HF, GF, and TDA techniques in the modeling of three-dimensional weakly confining quantum dot potentials. The observed differences emphasize the significance of confinement and electronic features unique to quantum dots such as the increased binding of electrons with higher angular momentum and the modified shell filling sequences.
Laudenslager, Mark L; Calderone, Jacqueline; Philips, Sam; Natvig, Crystal; Carlson, Nichole E
2013-09-01
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 years) 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; r(2)=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 was 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.
Laudenslager, Mark L; Calderone, Jacqueline; Philips, Sam; Natvig, Crystal; Carlson, Nichole E
2013-09-01
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 years) 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; r(2)=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 was 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
Structural surface investigations with low-energy backscattered electrons
NASA Astrophysics Data System (ADS)
De Crescenzi, Maurizio
The development of electron spectroscopies based on inelastic scattering fine structure is driven mainly by the need for structural methods which allow the investigation of the geometrical environment of different atomic species of the surface region of the sample. The EELFS (Extended Energy Loss Fine Structure) technique, using low-kinetic-energy electrons (1000-2000 eV) in reflection geometry, has been proven a useful tool for local structural investigation of clean surfaces, thin films and chemisorbed species. The main appeal of this technique, besides its experimental accessibility, is that the data analysis follows the procedure used for EXAFS (Extended X-ray Absorption Fine Structure) spectroscopy to obtain the atomic selectivity, the radial distribution function, the coordination number and the thermal and anisotropic effects. The near-edge energy-loss feature has been used to investigate the density of empty states close to EF and it appeeal particularly sensitive for following the structural changes and for discriminating among various phases and compound formations which occur in the surface region. In this work I review some recent developments, applications and theoretical considerations of the EELFS technique to give local structural parameters and to assess the basic mechanisms which dominate the low-energy electron-surface interaction.
Electronic structure of scandium-doped MgB2
NASA Astrophysics Data System (ADS)
de La Peña, Omar; Agrestini, Stefano
2005-03-01
Recently has been reported the synthesis of a new superconducting alloy based on MgB2, where Mg is partially substituted with Sc. In order to analyze the effect of Sc doping on the structural and superconducting properties of Mg1-xScxB2, we have performed a detailed study of the electronic structure for this new diboride. The calculations have been done using the first-principles LAPW method, within the supercell approach for modeling the doping. In this work we report results for the electronic band structure, Fermi surface, and density of states. The effect of the Sc-d orbitals on the structural and electronic properties of Mg1-xScxB2 is analyzed. Increasing the Sc concentration (x) the σ-band is gradually filled, because Sc have one valence electron more than Mg. Interestingly, the analysis of the band structure shows that even for ScB2 the top of the σ-band remain above the Fermi level, nevertheless the σ-band presents high dispersion and has an important contribution of d states. In this way, in addition to the band filling effect, Sc doping gradually reduces the two-dimensional character of the σ- band in Mg1-xScxB2 as a result of increasing the sp(B)-d(Sc) hybridization. This research was partially supported by Consejo Nacional de Ciencia y Tecnolog'ia (CONACYT, M'exico) under Grant. No. 43830-F
Free electron laser-driven ultrafast rearrangement of the electronic structure in Ti
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
Zhang, P; Wang, H Y; Li, Y G; Mao, S F; Ding, Z J
2012-01-01
Monte Carlo simulation methods for the study of electron beam interaction with solids have been mostly concerned with specimens of simple geometry. In this article, we propose a simulation algorithm for treating arbitrary complex structures in a real sample. The method is based on a finite element triangular mesh modeling of sample geometry and a space subdivision for accelerating simulation. Simulation of secondary electron image in scanning electron microscopy has been performed for gold particles on a carbon substrate. Comparison of the simulation result with an experiment image confirms that this method is effective to model complex morphology of a real sample.
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.
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.
Electronic band structure imaging of three layer twisted graphene on single crystal Cu(111)
Marquez Velasco, J.; Kelaidis, N.; Xenogiannopoulou, E.; Tsoutsou, D.; Tsipas, P.; Speliotis, Th.; Pilatos, G.; Likodimos, V.; Falaras, P.; Dimoulas, A.; Raptis, Y. S.
2013-11-18
Few layer graphene (FLG) is grown on single crystal Cu(111) by Chemical Vapor Deposition, and the electronic valence band structure is imaged by Angle-Resolved Photo-Emission Spectroscopy. It is found that graphene essentially grows polycrystalline. Three nearly ideal Dirac cones are observed along the Cu Γ{sup ¯}K{sup ¯} direction in k-space, attributed to the presence of ∼4° twisted three layer graphene with negligible interlayer coupling. The number of layers and the stacking order are compatible with Raman data analysis demonstrating the complementarity of the two techniques for a more accurate characterization of FLG.
Spin-orbit interactions in electronic structure quantum Monte Carlo methods
NASA Astrophysics Data System (ADS)
Melton, Cody A.; Zhu, Minyi; Guo, Shi; Ambrosetti, Alberto; Pederiva, Francesco; Mitas, Lubos
2016-04-01
We develop generalization of the fixed-phase diffusion Monte Carlo method for Hamiltonians which explicitly depends on particle spins such as for spin-orbit interactions. The method is formulated in a zero-variance manner and is similar to the treatment of nonlocal operators in commonly used static-spin calculations. Tests on atomic and molecular systems show that it is very accurate, on par with the fixed-node method. This opens electronic structure quantum Monte Carlo methods to a vast research area of quantum phenomena in which spin-related interactions play an important role.
Chiral phosphorus nanotubes: structure, bonding, and electronic properties.
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. PMID:27094567
Stacking-dependent electronic structure of bilayer silicene
Fu, Huixia; Zhang, Jin; Ding, Zijing; Li, Hui E-mail: smeng@iphy.ac.cn; Meng, Sheng E-mail: smeng@iphy.ac.cn
2014-03-31
Bilayer silicene (BLS) is a class of material that possibly holds both topological and superconducting properties; however, its structure is not fully understood. By scanning stacking modes and lattice constants using first principles calculations, several meta-stable configurations are identified, including a slightly faulted-AA packing structure, named slide-2AA. Different from the metallic properties of conventional AA and AB stacking forms, band structure of slide-2AA bilayer presents a sizeable indirect energy gap of ∼1.16 eV. A metal-semiconductor phase transition along the sliding pathway with a small energy barrier is also observed, indicating its electronic properties can be easily tuned by applying small shear force along the BLS surface plane. Such unique quantitative relationship of structure and electronic properties has profound implications in nanoelectronics and electromechanical devices.
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.
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).
Two-vortex structure of electron, nonlocality and Dirac equation
NASA Astrophysics Data System (ADS)
Tiwari, S. C.
2012-02-01
The dimensionless electromagnetic coupling constant α=e2/planckc may have three interpretations: as the well-known ratio between the electron charge radius e2/mc2 and the Compton wavelength of an electron λc=planck/mc, as the ratio of two angular momenta since the Planck constant has the dimension of angular momentum and as the ratio of two flux quanta e and hc/e . The anomalous part of the electron magnetic moment together with the unified picture of the three interpretations of α is suggested to have deep physical significance. The electric charge is proposed to be a new quantum of flux that leads to a new model of the electron envisaging a two-vortex structure. In analogy with quantum conditions, we postulate sub-quantum conditions applicable in a region of the order of λc replacing planck by a universal constant f=e2/2πc and we apply it to the Dirac equation in internal space that gives rise to the anomalous magnetic moment of an electron. The Dirac spinor and two-spinor representations for the vortex structure of an electron in the single-particle Dirac framework are discussed. The role of sub-quantum rules and internal variables in developing the present ideas is also discussed. A critical discussion of past attempts at giving fundamental importance to magnetism and flux quantum is presented in order to delineate the new ideas in the present work.
Strain fields and electronic structure of CrN
NASA Astrophysics Data System (ADS)
Rojas, Tomas; Ulloa, Sergio E.
Chromium nitride (CrN) has a promising future for its resistance to corrosion and hardness, and very interesting magnetic and electronic properties. CrN presents a phase transition in which the crystal structure, magnetic ordering and electronic properties change at a (Néel) temperature ~ 280 K . Thin films from different labs exhibit different conductance behavior at low temperature. We study the unusual electronic and magnetic properties of thin layers. For that purpose we develop a tight binding Hamiltonian based on the Slater-Koster approach, and estimate the interaction between the Cr-3d and N-2p orbitals, by analyzing the band structure and comparing it with ab initio calculations performed using the LSDA+U method. These calculations show the system to behave as a semiconductor below the Néel temperature. Based on our model we calculate the effective masses and analyze the effect of strain fields in the electronic structure in order to understand the electronic behavior near the phase transition. Supported by NSF DMR-1508325.
Electronic structure of hydrogenated diamond: Microscopical insight into surface conductivity
NASA Astrophysics Data System (ADS)
Iacobucci, S.; Alippi, Paola; Calvani, P.; Girolami, M.; Offi, F.; Petaccia, L.; Trucchi, D. M.
2016-07-01
We have correlated the surface conductivity of hydrogen-terminated diamond to the electronic structure in the Fermi region. Significant density of electronic states (DOS) in proximity of the Fermi edge has been measured by photoelectron spectroscopy (PES) on surfaces exposed to air, corresponding to a p -type electric conductive regime, while upon annealing a depletion of the DOS has been achieved, resembling the diamond insulating state. The surface and subsurface electronic structure has been determined, exploiting the different probing depths of PES applied in a photon energy range between 7 and 31 eV. Ab initio density functional calculations including surface charge depletion and band-bending effects favorably compare with electronic states measured by angular-resolved photoelectron spectroscopy. Such states are organized in the energy-momentum space in a twofold structure: one, bulk-derived, band disperses in the Γ -X direction with an average hole effective mass of (0.43 ±0.02 ) m0 , where m0 is the bare electron mass; a second flatter band, with an effective mass of (2.2 ±0.9 ) m0 , proves that a hole gas confined in the topmost layers is responsible for the conductivity of the (2 ×1 ) hydrogen-terminated diamond (100 ) surface.
Volkmann, Niels
2012-02-01
A complete understanding of complex dynamic cellular processes such as cell migration or cell adhesion requires the integration of atomic level structural information into the larger cellular context. While direct atomic-level information at the cellular level remains inaccessible, electron microscopy, electron tomography and their associated computational image processing approaches have now matured to a point where sub-cellular structures can be imaged in three dimensions at the nanometer scale. Atomic-resolution information obtained by other means can be combined with this data to obtain three-dimensional models of large macromolecular assemblies in their cellular context. This article summarizes some recent advances in this field.
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.
A novel Gaussian-Sinc mixed basis set for electronic structure calculations
NASA Astrophysics Data System (ADS)
Jerke, Jonathan L.; Lee, Young; Tymczak, C. J.
2015-08-01
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 H2, O2, and N2, 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.
A novel Gaussian-Sinc mixed basis set for electronic structure calculations
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.
A novel Gaussian-Sinc mixed basis set for electronic structure calculations.
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 H2, O2, and N2, 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. PMID:26277128
Electronic structure of solid uranium tetrafluoride UF4
NASA Astrophysics Data System (ADS)
Teterin, A. Yu.; Teterin, Yu. A.; Maslakov, K. I.; Panov, A. D.; Ryzhkov, M. V.; Vukcevic, L.
2006-07-01
X-ray photoelectron spectra (XPS) and conversion electron spectra of the outer (0-15eV) and inner (15-40eV) valence electrons for UF4 were measured. Relativistic Xα discrete variation ( RXα DV) calculation data for the UF84-(C4v) cluster reflecting uranium close environment in solid UF4 were used for the quantitative interpretation of the fine spectral structure. Quantitative agreement between the experimental and theoretical data was established. The U5f electrons ( ≈1 U5f electron) were shown to participate directly in the chemical bond formation. This U 5 f electron was shown to be delocalized within the outer valence molecular orbitals (OVMO) range (1-15eV) . The other U5f electrons were shown to be localized and to participate weakly in the chemical bond formation. The XPS line associated with these electrons was observed at 3.8eV . The vacant U5f states are generally delocalized in the range of the low positive energies (0-7 eV). The contribution of the U6p electronic density to the molecular orbitals of UF4 was experimentally and theoretically evaluated. The U6p electrons were experimentally shown to participate significantly ( 0.6U6p electrons) in the formation of the OVMO beside the formation of the inner valence molecular orbitals (IVMO). IVMO composition and sequence order in the binding energy range 15-40eV in UF4 were determined.
On the versatility of electronic structures in polymethine dyes
NASA Astrophysics Data System (ADS)
Pascal, Simon; Haefele, Alexandre; Monnereau, Cyrille; Charaf-Eddin, Azzam; Jacquemin, Denis; Le Guennic, Boris; Maury, Olivier; Andraud, Chantal
2014-10-01
This article provides an overview of the photophysical behavior diversity of polymethine chromophores which are ubiquitous in biological imaging and material sciences. One major challenge in this class of chromophore is to correlate the chemical structure to the observed optical properties, especially when symmetry-breaking phenomena occur. With the constant concern for rationalization of their spectroscopy, we propose an extended classification of polymethine dyes based on their ground state electronic configuration using three limit forms namely: cyanine, dipole and bis-dipole. The chemical modifications of the dye and the influence of exogenous parameters can promote dramatic spectroscopic changes that can be correlated to significant electronic reorganization between the three-abovementioned forms. The deep understanding of such phenomena should allow to identify, predict and take advantage of the versatile electronic structure of polymethines.
Electronic structure of the superconducting layered perovskite niobate
NASA Astrophysics Data System (ADS)
Hase, Izumi; Nishihara, Yoshikazu
1998-07-01
The electronic energy-band structure for RbLaNb2O7, which is closely related to the layered perovskite niobate superconducting KCa2Nb3O10 and metallic KLaNb2O7 with Li intercalation, has been calculated by using the scalar-relativistic full-potential linearized augmented-plane-wave method within the local-density approximation. The result of the calculation shows that this compound is a band insulator with a small gap, and its conduction band is a typical two-dimensional one and the valence band is rather three dimensional. We can conclude that the layered perovskite niobate KCa2Nb3O10 is a band insulator that can be superconducting with electron doping, and have the highly two-dimensional electronic structure.
Electronic Structure and Properties of Organic Bulk-Heterojunction Interfaces.
Street, Robert A
2016-05-01
The electronic structure and physical mechanisms of carrier generation and transport in the organic bulk heterojunction are reviewed. The electronic structure describes the bands and band-tail states, the band alignment at the bulk-heterojunction interface, and the overall density-of-states model. The different electronic character of excitons and mobile charge is discussed, the former being highly molecular and the latter more delocalized. Dissociation of the exciton via the charge-transfer (CT) states is attributed to weak binding of the CT state arising from charge delocalization. Carrier transport and charge collection is strongly influenced by the presence of localized band-tail states. Recombination is attributed primarily to transitions from mobile carriers to band-tail or deep trap states. PMID:26603977
Controlling electron-phonon scattering with metamaterial plasmonic structures
NASA Astrophysics Data System (ADS)
Kempa, Krzysztof; Wu, Xueyuan; Kong, Jiantao; Broido, David
Electron-plasmon scattering can be faster than electron-phonon scattering. While in metals plasmons occur in the UV range, phonons dominate behavior at much lower frequencies (far IR range), and this typically decouples these phenomena. In metamaterial plasmonic structures, however, plasma effects can be tuned down to the far IR range, allowing for their interference with phonons. It was recently shown, that such interference can protect hot electron energy induced in a solar cell, from dissipation into heat. In this work we explore the possibility of using such an effect to control the electron-phonon interaction and transport in semiconductors. We demonstrate, that this could lead to a novel path to enhancing the electrical and thermal conductivities and the thermoelectric figure of merit.
Electronic Structure of Crystalline 4He at High Pressures
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.
Correlative Light Electron Microscopy: Connecting Synaptic Structure and Function
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.
Correlative Light Electron Microscopy: Connecting Synaptic Structure and Function.
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
Correlative Light Electron Microscopy: Connecting Synaptic Structure and Function
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
Superconducting properties and electronic structure of NaBi.
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. PMID:24804822
Superconducting properties and electronic structure of NaBi.
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.
Correlative Light Electron Microscopy: Connecting Synaptic Structure and Function.
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.
Geometric and electronic structures of potassium-adsorbed rubrene complexes
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
Geometric and electronic structures of potassium-adsorbed rubrene complexes
NASA Astrophysics Data System (ADS)
Li, Tsung-Lung; Lu, Wen-Cai
2015-06-01
The geometric and electronic structures of potassium-adsorbed rubrene complexes are studied in this article. It is found that the potassium-rubrene (K1RUB) complexes inherit the main symmetry characteristics from their pristine counterparts and are thus classified into D2- and C2h-like complexes according to the relative orientations of the four phenyl side groups. The geometric structures of K1RUB 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 D2- and C2h-like K1RUB, however, exhibit their respective peculiarities. These peculiarities can be illustrated by their energy profiles of equilibrium structures. For the potassium adsorption-sites, the D2-like complexes show minimum-energy basins, whereas the C2h-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 D2-like complexes is most likely along the backbone in contrast to the C2h-like ones. Although the electronic structures of the minimum-energy structures of D2- and C2h-like K1RUB 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 than the other two on the opposite side, which leads to the largely enhanced
Geometric and electronic structures of potassium-adsorbed rubrene complexes.
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 (K1RUB) complexes inherit the main symmetry characteristics from their pristine counterparts and are thus classified into D2- and C2h-like complexes according to the relative orientations of the four phenyl side groups. The geometric structures of K1RUB 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 D2- and C2h-like K1RUB, however, exhibit their respective peculiarities. These peculiarities can be illustrated by their energy profiles of equilibrium structures. For the potassium adsorption-sites, the D2-like complexes show minimum-energy basins, whereas the C2h-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 D2-like complexes is most likely along the backbone in contrast to the C2h-like ones. Although the electronic structures of the minimum-energy structures of D2- and C2h-like K1RUB 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 than the other two on the opposite side, which leads to the largely enhanced
Electronic Structure of Endohedral Metallofullerenes: Evidences of the Ionic Model
NASA Astrophysics Data System (ADS)
Rodríguez-Fortea, Antonio; Valencia, Ramón; Poblet, Josep M.
2009-08-01
The electronic structure of the metal nitride M3N and metal carbide M2C2 endohedral fullerenes is rationalized by means of the simple ionic model that assumes a charge transfer from the internal metal cluster to the carbon framework. Experimental evidences of such an ionic model are also presented.
Highlighting material structure with transmission electron diffraction correlation coefficient maps.
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.
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.
The electronic structure of heavy fermions: Narrow temperature independent bands
Arko, A.J.; Joyce, J.J.; Smith, J.L.; Andrews, A.B.
1996-08-01
The electronic structure of both Ce and U heavy fermions appears to consist of extremely narrow temperature independent bands. There is no evidence from photoemission for a collective phenomenon normally referred to as the Kondo resonance. In uranium compounds a small dispersion of the bands is easily measurable.
Flat pack interconnection structure simplifies modular electronic assemblies
NASA Technical Reports Server (NTRS)
Katzin, L.
1967-01-01
Flat pack interconnection structure composed of stick modules simplifies modular electronic assemblies by allowing a single axis mother board. Two of the wiring planes are located in the stick module, which is the lower level of assembly, with the third wiring plane in the mother board.
Electronic Structure, Localization and 5f Occupancy in Pu Materials
Joyce, John J.; Beaux, Miles F.; Durakiewicz, Tomasz; Graham, Kevin S.; Bauer, Eric D.; Mitchell, Jeremy N.; Tobash, Paul H.; Richmond, Scott
2012-05-03
The electronic structure of delta plutonium ({delta}-Pu) and plutonium compounds is investigated using photoelectron spectroscopy (PES). Results for {delta}-Pu show a small component of the valence electronic structure which might reasonably be associated with a 5f{sup 6} configuration. PES results for PuTe are used as an indication for the 5f{sup 6} configuration due to the presence of atomic multiplet structure. Temperature dependent PES data on {delta}-Pu indicate a narrow peak centered 20 meV below the Fermi energy and 100 meV wide. The first PES data for PuCoIn5 indicate a 5f electronic structure more localized than the 5fs in the closely related PuCoGa{sub 5}. There is support from the PES data for a description of Pu materials with an electronic configuration of 5f{sup 5} with some admixture of 5f{sup 6} as well as a localized/delocalized 5f{sup 5} description.
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}
Small Scale Reconnection : Structure and Electron Jet Emission
NASA Astrophysics Data System (ADS)
Roth, I.
2012-04-01
The effects of small scale processes on the formation and evolution of macroscopic inhomogeneous magnetic configurations and the resulting super-Alfvenic jets have been investigated in space and lab over many years. Various satellite measurements at the magneto-sheath crossings observe features with small spatial scale of the order of electron skin depth, indicating the importance of processes dominated by electron dynamics. The data show structures which are (a) spatially non-symmetric with densities and magnetic field differing substantially on both sides of the region, while (b) the inhomogeneous magnetic and electric field structures consist of narrow, three-dimensional electron diffusion regions, with (c) bifurcated current over electron skin depth or below and (d) ejection of energetic, super-Alfvenic, non-Gaussian electrons perpendicularly to the magnetic field, away from the X-line. At small scales the main Alfven mode which describes the MHD regime is replaced by a helicon/whistler. The eMHD model, which includes the full dynamics of the electrons and stationary ions, with density gradients and asymptotically different values of the magnetic field is implemented for the experimentally observed configurations. Over the small scales the electron fluid follows the lines of the generalized vorticity (GV) as it decouples from the magnetic field. The regions of a significant deviation of the GV from the magnetic field become the potential sites for non-adiabatic electron acceleration. Effects of geometry, compressibility and thermal effects on this deviation will be discussed. The non-thermal jet distribution is conjectured to form when the standard diffusion is replaced by a non Markovian with large jumps random walk process, describing its evolution through the fractional diffusion equation and resulting in a non-Gaussian distribution.
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.
Effect of Structural Relaxation on the Electronic Structure of Graphene on Hexagonal Boron Nitride.
Slotman, G J; van Wijk, M M; Zhao, Pei-Liang; Fasolino, A; Katsnelson, M I; Yuan, Shengjun
2015-10-30
We performed calculations of electronic, optical, and transport properties of graphene on hexagonal boron nitride with realistic moiré patterns. The latter are produced by structural relaxation using a fully atomistic model. This relaxation turns out to be crucially important for electronic properties. We describe experimentally observed features such as additional Dirac points and the "Hofstadter butterfly" structure of energy levels in a magnetic field. We find that the electronic structure is sensitive to many-body renormalization of the local energy gap. PMID:26565485
Effect of Structural Relaxation on the Electronic Structure of Graphene on Hexagonal Boron Nitride
NASA Astrophysics Data System (ADS)
Slotman, G. J.; van Wijk, M. M.; Zhao, Pei-Liang; Fasolino, A.; Katsnelson, M. I.; Yuan, Shengjun
2015-10-01
We performed calculations of electronic, optical, and transport properties of graphene on hexagonal boron nitride with realistic moiré patterns. The latter are produced by structural relaxation using a fully atomistic model. This relaxation turns out to be crucially important for electronic properties. We describe experimentally observed features such as additional Dirac points and the "Hofstadter butterfly" structure of energy levels in a magnetic field. We find that the electronic structure is sensitive to many-body renormalization of the local energy gap.
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.
Structural and Electronic Investigations of Complex Intermetallic Compounds
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
Structural electronic and phonon properties of some transition metal aluminides
NASA Astrophysics Data System (ADS)
Fatima, Bushra; Pandit, Premlata; Sanyal, Sankar P.
2012-06-01
The structural and electronic properties of some Transition metal Aluminides (TMAl) namely ruthenium aluminide (RuAl), nickel aluminide (NiAl) and cobalt aluminide (CoAl) have been studied using plane wave pseudopotential method (PWSCF) within the local density approximation (LDA). The three TMAl's crystallizes in the CsCl-type structure (B2 phase). From the analysis of band structure and density of state, we found that these TMAl's are metallic in nature. The vibrational properties in terms of phonon dispersion curves and density of state have also been reported for RuAl using density functional perturbation theory (DFPT).
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.
Nanographene and graphene edges: electronic structure and nanofabrication.
Fujii, Shintaro; Enoki, Toshiaki
2013-10-15
Graphene can be referred to as an infinite polycyclic aromatic hydrocarbon (PAH) consisting of an infinite number of benzene rings fused together. However, at the nanoscale, nanographene's properties lie in between those of bulk graphene and large PAH molecules, and its electronic properties depend on the influence of the edges, which disrupt the infinite π-electron system. The resulting modulation of the electronic states depends on whether the nanographene edge is the armchair or zigzag type, corresponding to the two fundamental crystal axes. In this Account, we report the results of fabricating both types of edges in the nanographene system and characterizing their electronic properties using a scanning probe microscope. We first introduce the theoretical background to understand the two types of finite size effects on the electronic states of nanographene (i) the standing wave state and (ii) the edge state which correspond to the armchair and zigzag edges, respectively. Most importantly, characterizing the standing wave and edge states could play a crucial role in understanding the chemical reactivity, thermodynamic stability and magnetism of nanosized graphene--important knowledge in the design and realization of promising functionalized nanocarbon materials. In the second part, we present scanning probe microscopic characterization of both edge types to experimentally characterize the two electronic states. As predicted, we find the armchair-edged nanographene to have an energetically stable electronic pattern. The zigzag-edged nanographene shows a nonbonding (π radical) pattern, which is the source of the material's electronic and magnetic properties and its chemical activity. Precise control of the edge geometry is a practical requirement to control the electronic structure. We show that we can fabricate the energetically unstable zigzag edges using scanning probe manipulation techniques, and we discuss challenges in using these techniques for that
Biomechanics of DNA structures visualized by 4D electron microscopy
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
Characterization of electronic structure of periodically strained graphene
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.
Characterization of electronic structure of periodically strained graphene
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.
Theoretical bioinorganic chemistry: the electronic structure makes a difference.
Kirchner, Barbara; Wennmohs, Frank; Ye, Shengfa; Neese, Frank
2007-04-01
Theoretical bioinorganic and biomimetic chemistry involves the careful description of the electronic structure: for example, 'valence bond reading' of broken-symmetry density functional theory computations gives insight into the structure and bonding of metal-radical systems with complex electronic structures. Exploring the reactivities of such systems leads to the design of novel compounds with better reactivities. Combined quantum-mechanics/molecular-mechanics (QM/MM), where the QM part is a sophisticated ab initio method, aids in understanding nature's most complicated reaction mechanisms in atomic detail. First principles molecular dynamics simulations (Car-Parrinello simulations) open up exciting new avenues for studying transition metal centers and enable several questions to be addressed that cannot be resolved with either standard quantum chemical or traditional force-field methods. PMID:17349817
Fabrication of graphitic nanowire structure by electron beam lithography
NASA Astrophysics Data System (ADS)
Takai, Kazuyuki; Enoki, Toshiaki
2007-12-01
The graphitic nanowire structure was fabricated by local graphitization induced by direct electron-beam irradiation or the annealing treatment of wire-shaped nano-sized pattern, where glassy carbon film was used as the precursor materials. The direct irradiation of the 50 keV electron beam hardly causes the local graphitization of the sample, while the annealing of nanowire-patterned glassy carbon with 50 nm width successfully gives graphitic nanowire structure. The electrical conductivity of the fabricated nanowire structure shows metallic temperature dependence. However, the graphitic domain size of the wire was found to be very small (ca. 5 nm) by using Raman spectroscopy and the magnetoresistance. Higher temperature annealing is expected to improve the crystallinity of the graphitic nanowire.
Electronic structure of α-oligothiophenes with various substituents
NASA Astrophysics Data System (ADS)
Vikramaditya, Talapunur; Saisudhakar, Mukka; Sumithra, Kanakamma
2015-02-01
Density functional theory is employed to investigate the effect of various substituents on the electronic structure of α-oligothiophenes. The effect of electron donating and withdrawing groups of oligothiophenes in the regio regular HT-HT form is studied. Depending on the type of substituent and the substitution pattern, large differences in the delocalization pattern are observed between the substituted and unsubstituted oligomers. It is found that the band gaps critically depend on the chemical structure and regioselectivity of the building blocks. For the 3-substitued systems, electron donating and electron withdrawing substituents are shown to decrease and increase band gaps respectively compared to unsubstituted systems. There are charge separation effects introduced as a result of lack of symmetry in some of the substituted oligothiophenes. A new strategy is explained to achieve low band gap materials by making use of the regioselective form with lesser symmetry. Push-pull substitution with an electron donor at one end of the conjugation and an acceptor the other end is also investigated. Comparisons of band gaps of the substituted oligothiophenes with the corresponding polymeric systems are also done.
Electronic structure and crystal phase stability of palladium hydrides
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.
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
Toward the origin of exciton electronic structure in phycobiliproteins.
Womick, Jordan M; Miller, Stephen A; Moran, Andrew M
2010-07-14
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 alpha84 pigment and the first excited vibronic level of the beta84 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
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. PMID:24675610
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
The characteristic electronic structure needed for high-temperature superconductivity
NASA Astrophysics Data System (ADS)
Pyper, N. C.; Edwards, P. P.
1991-01-01
It is shown that the magnon mechanism proposed by Goddard and co-workers to explain high-temperature superconductivity in oxidized cuprates can also account for such superconductivity in both oxidized barium bismuthate and the electron superconductors based on neodynium cuprate. The specific and characteristic electronic structure required for the operation of the magnon mechanism naturally accounts for why only a small number of basic types of high-temperature superconductors are currently known. This mechanism can readily explain the effects of doping cuprate superconductors with both magnetic and non-magnetic ions.
The surface electronic structure of silicon terminated (100) diamond
NASA Astrophysics Data System (ADS)
Schenk, A. K.; Tadich, A.; Sear, M. J.; Qi, D.; Wee, A. T. S.; Stacey, A.; Pakes, C. I.
2016-07-01
A combination of synchrotron-based x-ray spectroscopy and contact potential difference measurements have been used to examine the electronic structure of the (3 × 1) silicon terminated (100) diamond surface under ultra high vacuum conditions. An occupied surface state which sits 1.75 eV below the valence band maximum has been identified, and indications of mid-gap unoccupied surface states have been found. Additionally, the pristine silicon terminated surface is shown to possess a negative electron affinity of ‑0.86 ± 0.1 eV.
Grid-based electronic structure calculations: The tensor decomposition approach
NASA Astrophysics Data System (ADS)
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. 81923 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.
Dual-phase steel structure visualized by extremely slow electrons.
Mikmeková, Šárka; Yamada, Katsumi; Noro, Hisato
2015-12-01
Mechanical properties of complex steels are affected by their multi-phase structure. Scanning electron microscopy (SEM) is routinely used for characterizing dual-phase (DP) steels, although the identification of steel constituents is not straightforward. In fact, there are several ways of enabling the ferrite-martensite segmentation by SEM, and a wide range of electron energies can be utilized. This study demonstrates the phase identification of DP steels at high, low and extremely low landing energies of the primary electrons from tens of keV to tens of eV. Visualization of the specimen surface at very low landing energies has been achieved by inserting an earthed detector between the pole piece and the negatively biased specimen. This 'cathode lens mode' enables the use of the full energy range up to the primary electron energies. It has been found that extremely slow electrons (<100 eV) are exceptionally suitable for separation of the martensite from the ferrite matrix due to high surface sensitivity, enabling visualization of very fine features. Moreover, the channelling contrast is significantly suppressed at the landing energy of tens of eV of the primary electrons, which enables separation of the phases clearly even in the images acquired at low magnification. The contrast between the phases at tens of eV can be explained by the different thickness of native oxide covering the martensite and the ferrite phase.
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.
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.
NASA Astrophysics Data System (ADS)
Mishra, P.; Lohani, H.; Kundu, A. K.; Patel, R.; Solanki, G. K.; Menon, Krishnakumar S. R.; Sekhar, B. R.
2015-07-01
The valence band electronic structure of GeSe single crystals has been investigated using angle resolved photoemission spectroscopy (ARPES) and x-ray photoelectron spectroscopy. The experimentally observed bands from ARPES, match qualitatively with our LDA-based band structure calculations along the Γ-Z, Γ-Y and Γ-T symmetry directions. The valence band maximum occurs nearly midway along the Γ-Z direction, at a binding energy of -0.5 eV, substantiating the indirect band gap of GeSe. Non-dispersive features associated with surface states and indirect transitions have been observed. The difference in hybridization of Se and Ge 4p orbitals leads to the variation of dispersion along the three symmetry directions. The predominance of the Se 4pz orbitals, evidenced from theoretical calculations, may be the cause for highly dispersive bands along the Γ-T direction. Detailed electronic structure analysis reveals the significance of the cation-anion 4p orbitals hybridization in the valence band dispersion of IV-VI semiconductors. This is the first comprehensive report of the electronic structure of a GeSe single crystal using ARPES in conjugation with theoretical band structure analysis.
Plane-wave DFT-LDA calculation of the electronic structure and absorption spectrum of copper
NASA Astrophysics Data System (ADS)
Marini, Andrea; Onida, Giovanni; del Sole, Rodolfo
2001-11-01
We present an accurate, first-principles study of the electronic structure and absorption spectrum of bulk copper within density functional theory in the local density approximation, including the study of intraband transitions. We construct norm-conserving pseudopotentials (PP's) including the 3d shell (and optionally the underlying 3s and 3p shells) in the valence and requiring a relatively small plane-wave basis (60 and 140 Ry cutoff, respectively). As a consequence, these PP's are strongly nonlocal, yielding macroscopically wrong results in the absorption spectrum when momentum matrix elements are computed naively. Our results are compared with experimental photoemission, absorption, and electron energy loss data, and suggest nontrivial self-energy effects in the quasiparticle spectrum of Cu.
Gdanitz, Robert J; Black, Gary D; Lansing, Carina S; Palmer, Bruce J; Schuchardt, Karen L
2005-02-01
We describe the integration and use of the Amica software package ("Atoms & Molecules In Chemical Accuracy") within the Extensible Computational Chemistry Environment (Ecce). Amica is capable of accurately solving the electronic Schrodinger equation of small atoms and molecules using terms that are linear in the interelectronic distances, r(12), on multireference level of theory, but it requires expert knowledge to configure and execute its algorithms. Ecce is a comprehensive suite of tools that support the computational chemistry research processes of computation setup, execution, and analysis through a convenient graphical user interface. Additionally, Ecce was architected with mechanisms to integrate alternative electronic structure codes. The successful integration of Amica within Ecce validates the architecture of the latter and brings the high-accuracy capabilities of Amica to a wider audience.
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.
The Electronic Structure of Nonpolar Surfaces in Insulating Metal Oxides
NASA Astrophysics Data System (ADS)
Zherebetskyy, Danylo; Wang, Lin-Wang
2013-03-01
Understanding the electronic and geometric structures of metal oxide surfaces has a key interest in many technological areas. A randomly chosen crystal surface has a high probability of being polar, unstable and containing in-gap states due to surface dangling bonds. As a result, the surface should be stabilized by passivation or reconstruction. However, do the nonpolar surfaces of ionic crystals of insulating metal oxides need the passivation or reconstruction similar to covalent crystals? We address this question by analyzing the nonpolar surfaces and their electronic structure for the common crystal structures of metal oxides. The study using periodic DFT calculations is performed for following representatives: Cu2O, ZnO, Al2O3, TiO2, V2O5, WO3, CaTiO3, Mg2SiO4. It has been shown that the nonpolar surface can be constructed out of dipole-free, charge-neutral and stoichiometric unit cells for each crystal. We demonstrate that all constructed and relaxed nonpolar surfaces of the metal oxides show a clear band gap. It should be emphasized that the constructed surfaces are neither reconstructed nor passivated. Additionally, we show a correlation between the electronic structure of the relaxed surfaces and Ewald energies calculated for the surface ions.
Electronic Structure of II-Vi Semiconductors and Their Alloys
NASA Astrophysics Data System (ADS)
Wei, Su-Huai
The II-VI semiconductors ZnXVI, CdXVI, and HgXVI are known to have a metal d band inside the main valence band. Using all-electron self-consistent electronic structure techniques, we study their effects on valence properties. For II-VI semiconductors, we find that p-d repulsion and hybridization (i) lower the band gaps, (ii) alter the sign of the crystal-field splitting, (iii) reduce the spin-orbit splitting, (iv) change the valence band offset between common-anion semiconductors, and (v) increase the equilibrium lattice parameters, p-d repulsion is also shown to be responsible for the anomalously small band gaps in chalcopyrites, and for the negative exchange splitting in MnTe. We also study the electronic structure of ordered and random II-VI substitutional alloys and identify the mechanism for their band gap narrowing. The random {A_{1-x}^{II}B_{x}^{II}C^{VI}} alloys are represented by the "special quasirandom structures." We show how chemical and structural perturbations lead to (i) distinct A-like and B-like features in the density of states and (ii) different C-like features associated with fluctuations in the local environments around the common sublattice.
Compressed Sensing Electron Tomography for Determining Biological Structure
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
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.
Accelerated electronic structure-based molecular dynamics simulations of shock-induced chemistry
NASA Astrophysics Data System (ADS)
Cawkwell, Marc
2015-06-01
The initiation and progression of shock-induced chemistry in organic materials at moderate temperatures and pressures are slow on the time scales available to regular molecular dynamics simulations. Accessing the requisite time scales is particularly challenging if the interatomic bonding is modeled using accurate yet expensive methods based explicitly on electronic structure. We have combined fast, energy conserving extended Lagrangian Born-Oppenheimer molecular dynamics with the parallel replica accelerated molecular dynamics formalism to study the relatively sluggish shock-induced chemistry of benzene around 13-20 GPa. We model interatomic bonding in hydrocarbons using self-consistent tight binding theory with an accurate and transferable parameterization. Shock compression and its associated transient, non-equilibrium effects are captured explicitly by combining the universal liquid Hugoniot with a simple shrinking-cell boundary condition. A number of novel methods for improving the performance of reactive electronic structure-based molecular dynamics by adapting the self-consistent field procedure on-the-fly will also be discussed. The use of accelerated molecular dynamics has enabled us to follow the initial stages of the nucleation and growth of carbon clusters in benzene under thermodynamic conditions pertinent to experiments.
Geometric, electronic, and magnetic structure of FexOy+ clusters
NASA Astrophysics Data System (ADS)
Logemann, R.; de Wijs, G. A.; Katsnelson, M. I.; Kirilyuk, A.
2015-10-01
Correlation between geometry, electronic structure, and magnetism of solids is both intriguing and elusive. This is particularly strongly manifested in small clusters, where a vast number of unusual structures appear. Here, we employ density functional theory in combination with a genetic search algorithm GGA +U and a hybrid functional to determine the structure of gas phase FexOy+/0 clusters. For FexOy+ cation clusters we also calculate the corresponding vibration spectra and compare them with experiments. We successfully identify Fe3O4+ , Fe4O5+ , Fe4O6+ , Fe5O7+ and propose structures for Fe6O8+ . Within the triangular geometric structure of Fe3O4+ , a noncollinear, ferrimagnetic, and ferromagnetic state are comparable in energy. Fe4O5+ and Fe4O6+ are ferrimagnetic with a residual magnetic moment of 1 μB due to ionization. Fe5O7+ is ferrimagnetic due to the odd number of Fe atoms. We compare the electronic structure with bulk magnetite and find Fe4O5+ , Fe4O6+ , Fe6O8+ to be mixed valence clusters. In contrast, in Fe3O4+ and Fe5O7+ , all Fe are found to be trivalent.
Structural stability and electronic properties of small gold clusters induced by 3p electron atoms
NASA Astrophysics Data System (ADS)
Zhang, Meng; Yang, Su-Bin; Feng, Xiao-Juan; Zhao, Li-Xia; Zhang, Hong-Yu; Luo, You-Hua
2013-01-01
The geometries and electronic properties of gold clusters doped with atoms containing 3 p valence electrons (MAu n ; M = Al, Si, P, S, Cl; n = 2-8) have been systematically investigated using density functional theory (DFT) at the PBE/LANL2DZ level. A number of low-energy isomers are identified for neutral MAu n clusters. It is found that doping with different 3 p impurity atoms can drastically influence the geometrical structures, relative stabilities, electronic properties, and growth-pattern behaviors of gold clusters, which is very different from the case of 3 d transition-metal impurity doped Au n clusters. Partially filled 3 p electron impurities can stabilize Au clusters. In particular, SiAu4 cluster with T d symmetry have been found to have highly stable geometries and electronic structures with binding energies of 2.43 eV per atom (0.96 eV higher than pristine Au5 clusters), large HOMO-LUMO gaps (2.17 eV), and vertical ionization potentials of 8.68 eV. Using scalar relativistic molecular dynamics at T = 300 K, we show that the T d symmetry structure of SiAu4 is stable. The frontier molecular orbitals (HOMO and LUMO) and the partial densities of states (PDOS) show that strong hybridization occurs between the atomic orbitals of Si and Au atoms, resulting in strong Si-Au bonding. In addition, the vertical ionization potential, the vertical electron affinity, and charge transfers of MAu n clusters have also been analyzed. Our results are in good agreement with available experimental data.
Electronic structure and electron energy-loss spectroscopy of ZrO2 zirconia
NASA Astrophysics Data System (ADS)
Dash, L. K.; Vast, Nathalie; Baranek, Philippe; Cheynet, Marie-Claude; Reining, Lucia
2004-12-01
The atomic and electronic structures of zirconia are calculated within density functional theory, and their evolution is analyzed as the crystal-field symmetry changes from tetrahedral [cubic (c-ZrO2) and tetragonal (t-ZrO2) phases] to octahedral (hypothetical rutile ZrO2 ), to a mixing of these symmetries (monoclinic phase, m-ZrO2 ). We find that the theoretical bulk modulus in c-ZrO2 is 30% larger than the experimental value, showing that the introduction of yttria in zirconia has a significant effect. Electronic structure fingerprints which characterize each phase from their electronic spectra are identified. We have carried out electron energy-loss spectroscopy experiments at low momentum transfer and compared these results to the theoretical spectra calculated within the random phase approximation. We show a dependence of the valence and 4p ( N2,3 edge) plasmons on the crystal structure, the dependence of the latter being brought into the spectra by local-field effects. Last, we attribute low energy excitations observed in EELS of m-ZrO2 to defect states 2eV above the top of the intrinsic valence band, and the EELS fundamental band gap value is reconciled with the 5.2 or 5.8eV gaps determined by vacuum ultraviolet spectroscopy.
Anomalous electronic structure and magnetoresistance in TaAs2
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
Electronic Structure of Crystalline [superscript 4]He at High Pressures
Mao, Ho Kwang; Shirley, Eric L.; Ding, Yang; Eng, Peter; Cai, Yong Q.; Chow, Paul; Xiao, Yuming; Shu, Jinfu; Hemley, Russell J.; Kao, Chichang; Mao, Wendy L.
2010-11-12
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.
Spatially Resolved Electronic Structures of Atomically Precise Armchair Graphene Nanoribbons
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
Anomalous electronic structure and magnetoresistance in TaAs2.
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
Spatially Resolved Electronic Structures of Atomically Precise Armchair Graphene Nanoribbons
NASA Astrophysics Data System (ADS)
Huang, Han; Wei, Dacheng; Sun, Jiatao; Wong, Swee Liang; Feng, Yuan Ping; Neto, A. H. Castro; Wee, Andrew Thye Shen
2012-12-01
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.
Anomalous electronic structure and magnetoresistance in TaAs2
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
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
Electronic Structure of Crystalline 4He at High Pressure
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.
Linear Multigrid Techniques in Self-consistent Electronic Structure Calculations
Fattebert, J-L
2000-05-23
Ab initio DFT electronic structure calculations involve an iterative process to solve the Kohn-Sham equations for an Hamiltonian depending on the electronic density. We discretize these equations on a grid by finite differences. Trial eigenfunctions are improved at each step of the algorithm using multigrid techniques to efficiently reduce the error at all length scale, until self-consistency is achieved. In this paper we focus on an iterative eigensolver based on the idea of inexact inverse iteration, using multigrid as a preconditioner. We also discuss how this technique can be used for electrons described by general non-orthogonal wave functions, and how that leads to a linear scaling with the system size for the computational cost of the most expensive parts of the algorithm.
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.
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.
NASA Astrophysics Data System (ADS)
Collins, Daniel
Ubiquitous concerns in device fabrication are nanoscale positioning and the integration of complex combinations of diverse materials, many of which are extremely fragile. Frequently the completed device requires one or more of the constituent materials to be synthesized under suboptimal conditions, thus compromising the performance of the final structure. We have developed a platform to fabricate multi-component electrode crossbar structures, where each material can be synthesized under its own ideal conditions. Furthermore, surface treatments and procedures that may otherwise be incompatible can be performed without concern of damage to the other constituent materials. We demonstrate our approach by fabricating an all carbon cross-bar electrode structure comprised of a graphene-graphite heterojunction. Initially, a graphene field effect transistor is fabricated using electron beam and optical lithography. The top graphite electrode is sculpted from a bulk piece of highly oriented pyrolytic graphite with the aid of a focused ion beam (FIB) and integrated micromanipulator system. This requires realtime shaping, cutting, accurate positioning (circa 100 nm precision) and wiring of the graphite top electrode. Electron transport characteristics of each electrode component and the final heterostructure have been measured. We show that this process is effective for the production of micron and submicron-scale multi-layer device structures including other materials such as gold. This fabrication scheme could be extended to produce novel structures such as mechanical resonators, and provide a foundation for combining fragile materials that have otherwise been incompatible with traditional fabrication techniques.
Electronic structure study of strongly correlated Mott-insulators
NASA Astrophysics Data System (ADS)
Yin, Quan
Strongly correlated electronic systems have presented the most challenging problems to condensed matter theorists for many years and this continues to be the case. They are complicated materials with active d or f orbitals, whose valence electrons are in the intermediate region between itinerant (band-like) and highly localized (atomic-like) limits, which demand genuine many-body treatment. Although dealing with strongly correlated systems is a notorious problem, they have drawn broad interests of both theoretical and experimental condensed matter physicists, with intensive studies carried out in the past and present. This is due to the most exotic properties associated with strongly correlated materials, such as high-temperature superconductivity, metal-insulator transition, volume collapse, Kondo effect, colossal magnetoresistance, and many others. Although density functional theory (DFT) within local density approximation (LDA) is very successful in describing a wide range of materials, it encounters difficulty in predicting strongly correlated systems. Traditionally, they have been studied by model Hamiltonians with empirical parameters. The development of dynamical mean field theory (DMFT) and its marriage to DFT have brought new hope for first-principle study of strongly correlated systems. In this work, electronic structures of select strongly correlated systems are studied using LDA+DMFT. As theoretical backgrounds, reviews of DFT and DMFT are given in the first few chapters, where we also introduce the philosophy and workflow of LDA+DMFT. In the following chapters, applications to transition metal oxides, undoped high-temperature superconductors and actinide oxides are presented, where electronic structures of these materials and other properties derived from electronic structures are calculated and compared with experiments where available. Generally good agreements have been found between theory and experiments.
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.
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
Structure and Process of Infrared Hot Electron Transistor Arrays
Fu, Richard
2012-01-01
An infrared hot-electron transistor (IHET) 5 × 8 array with a common base configuration that allows two-terminal readout integration was investigated and fabricated for the first time. The IHET structure provides a maximum factor of six in improvement in the photocurrent to dark current ratio compared to the basic quantum well infrared photodetector (QWIP), and hence it improved the array S/N ratio by the same factor. The study also showed for the first time that there is no electrical cross-talk among individual detectors, even though they share the same emitter and base contacts. Thus, the IHET structure is compatible with existing electronic readout circuits for photoconductors in producing sensitive focal plane arrays. PMID:22778655
Electronic Structure and Geometries of Small Compound Metal Clusters
1999-04-14
During the tenure of the DOE grant DE-FG05-87EI145316 we have concentrated on equilibrium geometries, stability, and the electronic structure of transition metal-carbon clusters (met-cars), clusters designed to mimic the chemistry of atoms, and reactivity of homo-nuclear metal clusters and ions with various reactant molecules. It is difficult to describe all the research the authors have accomplished as they have published 38 papers. In this report, they outline briefly the salient features of their work on the following topics: (1) Designer Clusters: Building Blocks for a New Class of Solids; (2) Atomic Structure, Stability, and Electronic Properties of Metallo-Carbohedrenes; (3) Reactivity of Metal Clusters with H{sub 2} and NO; and (4) Anomalous Spectroscopy of Li{sub 4} Clusters.
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.
Electronic structure of a metal-insulator interface
NASA Astrophysics Data System (ADS)
Bordier, G.; Noguera, C.
1991-07-01
We present an analytical study of the electronic structure of a metal-insulator interface with special emphasis on the metal induced gap states (MIGS). It includes three steps: (i) a tight-binding approach of the dispersion relation and Green's function of insulators of NaCl or ZnS structure; (ii) a matching with free electron-like wavefunctions at the NaCl(100) or ZnS(110) surfaces, which yields the density and penetration depth of the MIGS as a function of the ionocovalent characteristics of the insulator and of the metal Fermi level; (iii) a self-consistent determination of the Fermi level position in a Thomas-Fermi approximation. The Schottky barrier height is derived under a simple analytic form and its dependence upon the metal work function is found in good agreement with experimental results.
Phase Diagram and Electronic Structure of Praseodymium and Plutonium
NASA Astrophysics Data System (ADS)
Lanatà, Nicola; Yao, Yongxin; Wang, Cai-Zhuang; Ho, Kai-Ming; Kotliar, Gabriel
2015-01-01
We develop a new implementation of the Gutzwiller approximation in combination with the local density approximation, which enables us to study complex 4 f and 5 f systems beyond the reach of previous approaches. We calculate from first principles the zero-temperature phase diagram and electronic structure of Pr and Pu, finding good agreement with the experiments. Our study of Pr indicates that its pressure-induced volume-collapse transition would not occur without change of lattice structure—contrarily to Ce. Our study of Pu shows that the most important effect originating the differentiation between the equilibrium densities of its allotropes is the competition between the Peierls effect and the Madelung interaction and not the dependence of the electron correlations on the lattice structure.
Electronic Structure of Silicon Nanowires Matrix from Ab Initio Calculations.
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.
Electronic structure and optic absorption of phosphorene under strain
NASA Astrophysics Data System (ADS)
Duan, Houjian; Yang, Mou; Wang, Ruiqiang
2016-07-01
We studied the electronic structure and optic absorption of phosphorene (monolayer of black phosphorus) under strain. Strain was found to be a powerful tool for the band structure engineering. The in-plane strain in armchair or zigzag direction changes the effective mass components along both directions, while the vertical strain only has significant effect on the effective mass in the armchair direction. The band gap is narrowed by compressive in-plane strain and tensile vertical strain. Under certain strain configurations, the gap is closed and the energy band evolves to the semi-Dirac type: the dispersion is linear in the armchair direction and is gapless quadratic in the zigzag direction. The band-edge optic absorption is completely polarized along the armchair direction, and the polarization rate is reduced when the photon energy increases. Strain not only changes the absorption edge (the smallest photon energy for electron transition), but also the absorption polarization.
Electronic structures of two-dimensional metallic oxides and bronzes
NASA Astrophysics Data System (ADS)
Guyot, H.; Motta, N.; Marcus, J.; Drouard, S.; Balaska, B.
2001-06-01
The electronic structures of some molybdenum and tungsten oxides or bronzes exhibiting Peierls transitions are investigated at room temperature. The detection of a weak conduction band, well separated from a large valence band, evidences the metallic character of each oxide. The distributions of the valences of the different transition metals are analyzed by XPS. In each oxide, the presence of atleast two contributive components to the main core levels reveals a mixed valence state of the transition metal. But the proportions of the different components do not reflect the distribution of the cationic valences, as expected from the crystallographic structures. To understand this disagreement, we suggest that two alternative ways, including or rejecting a screening effect generated by the conduction electrons contribute to the photoemission processes and alter the real distribution of the cationic charges.
Electronic structure of self-assembled amorphous polyfluorenes.
Kilina, Svetlana; Batista, Enrique R; Yang, Ping; Tretiak, Sergei; Saxena, Avadh; Martin, Richard L; Smith, Darryl L
2008-07-01
We investigate the role of conformational disorder and intermolecular interactions on the electronic structure of amorphous clusters of polyfluorenes. Classical molecular dynamics simulations are used to determine probable molecular geometries and chain packing, and first-principles density functional theory calculations are employed to determine electronic structure and orbital localization properties. Intramolecular and intermolecular effects are disentangled by contrasting results for densely packed oligomer clusters and for ensembles of isolated oligomers with the same intramolecular geometries. Our simulations show that intermolecular disorder allows for nearly planar configurations of interacting fluorenes compared to the isolated molecules. This rationalizes the experimentally detected formation of the planar crystalline morphologies that frequently accompany twisted glassy configurations in fluorene films. The energy gap (HOMO-LUMO gap) significantly decreases for planar configurations. The electron and hole orbital energies are strongly dependent on both torsional angles and intermolecular interactions. This leads to strong localization of electronic states in amorphous polymer aggregates, which is analyzed by examining the respective orbital participation ratios. Notably, the energies of unoccupied levels show stronger dependence on the conformational disorder, compared to that of occupied levels. This results in the more probable formation of trap states near the edge of the conduction band than near the valence band. PMID:19206305
Structure of Halothiobacillus neapolitanus carboxysomes by cryo-electron tomography.
Schmid, Michael F; Paredes, Angel M; Khant, Htet A; Soyer, Ferda; Aldrich, Henry C; Chiu, Wah; Shively, Jessup M
2006-12-01
Carboxysomes are polyhedral bodies consisting of a proteinaceous shell filled with ribulose 1,5-bisphosphate carboxylase/oxygenase (RuBisCO). They are found in the cytoplasm of all cyanobacteria and some chemoautotrophic bacteria. Previous studies of Halothiobacillus neapolitanus and Nitrobacter agilis carboxysomes suggest that the structures are either icosahedral or dodecahedral. To determine the protein shell structure more definitively, purified H. neapolitanus carboxysomes were re-examined by cryo-electron tomography and scanning transmission electron microscopy (STEM). Due to the limited tilt angles in the electron microscope, the tomographic reconstructions are distorted. Corrections were made in the 3D orientation searching and averaging of the computationally extracted carboxysomes to minimize the missing data effects. It was found that H. neapolitanus carboxysomes vary widely in size and mass as shown by cryo-electron tomography and STEM mass measurements, respectively. We have aligned and averaged carboxysomes in several size classes from the 3D tomographic reconstruction by methods that are not model-biased. The averages reveal icosahedral symmetry of the shell, but not of the density inside it, for all the size classes.
Fast electronic structure methods for strongly correlated molecular systems
NASA Astrophysics Data System (ADS)
Head-Gordon, Martin; Beran, Gregory J. O.; Sodt, Alex; Jung, Yousung
2005-01-01
A short review is given of newly developed fast electronic structure methods that are designed to treat molecular systems with strong electron correlations, such as diradicaloid molecules, for which standard electronic structure methods such as density functional theory are inadequate. These new local correlation methods are based on coupled cluster theory within a perfect pairing active space, containing either a linear or quadratic number of pair correlation amplitudes, to yield the perfect pairing (PP) and imperfect pairing (IP) models. This reduces the scaling of the coupled cluster iterations to no worse than cubic, relative to the sixth power dependence of the usual (untruncated) coupled cluster doubles model. A second order perturbation correction, PP(2), to treat the neglected (weaker) correlations is formulated for the PP model. To ensure minimal prefactors, in addition to favorable size-scaling, highly efficient implementations of PP, IP and PP(2) have been completed, using auxiliary basis expansions. This yields speedups of almost an order of magnitude over the best alternatives using 4-center 2-electron integrals. A short discussion of the scope of accessible chemical applications is given.
Electronic structure and superconductivity of FeSe-related superconductors.
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.
The valence electronic structure and conformational flexibility of epichlorohydrin.
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.
Electronic structure and superconductivity of FeSe-related superconductors.
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. PMID:25879999
Electron spectra and structure of atomic and molecular clusters
Dehmer, Patricia M.
1980-01-01
Changes in electronic structure that occur during the stepwise transition from gas phase monomers to large clusters which resemble the condensed phase were studied. This basic information on weakly bound clusters is critical to the understanding of such phenomena as nucleation, aerosol formation, catalysis, and gas-to-particle conversion, yet there exist almost no experimental data on neutral particle energy levels or binding energies as a function of cluster size. (GHT)
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.
Final Technical Report: Electronic Structure Workshop (ES13)
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.
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.
DFTB Parameters for the Periodic Table: Part 1, Electronic Structure.
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.
Electronic structure of substitutionally disordered alloys: Direct configurational averaging
Wolverton, C.; de Fontaine, D.; Dreysse, H.; Ceder, G.
1992-04-01
The method of direct configurational averaging (DCA) has been proposed to study the electronic structure of disordered alloys. Local density of states and band structure energies are obtained by averaging over a small number of configrations within a tight-binding Hamiltonian. Effective cluster interactions, the driving quantities for ordering in solids, are computed for various alloys using a tight-binding form of the linearized muffin-tin orbital method (TB-LMTO). The DCA calculations are used to determine various energetic and thermodynamic quantities for binary and ternasy alloys. (Pd, Rh, V).
Electronic structure and luminescence center of blue luminescent carbon nanocrystals
NASA Astrophysics Data System (ADS)
Zhou, Jigang; Zhou, Xingtai; Li, Ruying; Sun, Xueliang; Ding, Zhifeng; Cutler, Jeffrey; Sham, Tsun-Kong
2009-06-01
The electronic structure and the origin of luminescence from blue luminescent carbon nanocrystals (CNC) have been investigated with X-ray absorption near-edge structures (XANES) and X-ray excited optical luminescence (XEOL). XANES shows that nitrogen has been incorporated into the carbon nanocrystals matrix (dominated by sp 2 carbon). XEOL from CNC is compared with that from natural diamond and previously reported CVD nanodiamond containing N impurities. The results reveal that N doping is almost certainly responsible for the blue luminescence in carbon nanocrystals. The implication of the results is discussed.
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.
Ground-state Electronic Structure of Actinide Monocarbides and Mononitrides
Petit, Leon; Svane, Axel; Szotek, Zdzislawa; Temmerman, Walter M; Stocks, George Malcolm
2009-01-01
The self-interaction corrected local spin-density approximation is used to investigate the ground-state valency configuration of the actinide ions in the actinide monocarbides, AC (A=U,Np,Pu,Am,Cm), and the actinide mononitrides, AN. The electronic structure is characterized by a gradually increasing degree of f electron localization from U to Cm, with the tendency toward localization being slightly stronger in the (more ionic) nitrides compared to the (more covalent) carbides. The itinerant band picture is found to be adequate for UC and acceptable for UN, while a more complex manifold of competing localized and delocalized f-electron configurations underlies the ground states of NpC, PuC, AmC, NpN, and PuN. The fully localized 5f-electron configuration is realized in CmC (f{sup 7}), CmN (f{sup 7}), and AmN (f{sup 6}). The observed sudden increase in lattice parameter from PuN to AmN is found to be related to the localization transition. The calculated valence electron densities of states are in good agreement with photoemission data.
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.
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.
Structural basis of interprotein electron transfer in bacterial sulfite oxidation
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
Stability, electronic structure and reactivity of the polymerized fullerite forms
NASA Astrophysics Data System (ADS)
Belavin, V. V.; Bulusheva, L. G.; Okotrub, A. V.; Tomanek, D.
2000-12-01
A study of band structure, stability and electron density distribution from selected crystal orbitals of polymerized C60 forms was carried out. Linear chain, tetragonal and hexagonal layers, and three-dimensional (3D) polymer with a simple cubic lattice were calculated using an empirical tight-binding method. The hopping parameters were chosen to fit a theoretical X-ray emission spectrum of C60 to the experimental one. Our results indicate that all calculated polymers are semiconductors with the smallest energy gap for hexagonal structure. Though the molecules C60 are linked by strong covalent bonds, the crystal orbitals characterized by the electron density localization on an individual carbon cage are separated in the electronic structure of polymers. The suggestions about reactivity of the 1D and 2D tetragonal polymers were made from the analyses of crystal orbitals accompanied with the highest occupied (HO) and lowest unoccupied (LU) bands. The polymerized C60 forms were found to be less stable than an icosahedral fullerene molecule.
Transmission electron microscopy in molecular structural biology: A historical survey.
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.
Transmission electron microscopy in molecular structural biology: A historical survey.
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. PMID:25475529
Structural basis of interprotein electron transfer in bacterial sulfite oxidation.
McGrath, Aaron P; Laming, Elise L; Casas Garcia, G Patricia; Kvansakul, Marc; Guss, J Mitchell; Trewhella, Jill; Calmes, Benoit; Bernhardt, Paul V; Hanson, Graeme R; Kappler, Ulrike; Maher, Megan J
2015-12-19
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.
Barone, Vincenzo; Biczysko, Malgorzata; Bloino, Julien; Cimino, Paola; Penocchio, Emanuele; Puzzarini, Cristina
2015-09-01
The structures and relative stabilities as well as the rotational and vibrational spectra of the three low-energy conformers of pyruvic acid (PA) have been characterized using a state-of-the-art quantum-mechanical approach designed for flexible molecules. By making use of the available experimental rotational constants for several isotopologues of the most stable PA conformer, Tc-PA, the semiexperimental equilibrium structure has been derived. The latter provides a reference for the pure theoretical determination of the equilibrium geometries for all conformers, thus confirming for these structures an accuracy of 0.001 Å and 0.1 deg for bond lengths and angles, respectively. Highly accurate relative energies of all conformers (Tc-, Tt-, and Ct-PA) and of the transition states connecting them are provided along with the thermodynamic properties at low and high temperatures, thus leading to conformational enthalpies accurate to 1 kJ mol(-1). Concerning microwave spectroscopy, rotational constants accurate to about 20 MHz are provided for the Tt- and Ct-PA conformers, together with the computed centrifugal-distortion constants and dipole moments required to simulate their rotational spectra. For Ct-PA, vibrational frequencies in the mid-infrared region accurate to 10 cm(-1) are reported along with theoretical estimates for the transitions in the near-infrared range, and the corresponding infrared spectrum including fundamental transitions, overtones, and combination bands has been simulated. In addition to the new data described above, theoretical results for the Tc- and Tt-PA conformers are compared with all available experimental data to further confirm the accuracy of the hybrid coupled-cluster/density functional theory (CC/DFT) protocol applied in the present study. Finally, we discuss in detail the accuracy of computational models fully based on double-hybrid DFT functionals (mainly at the B2PLYP/aug-cc-pVTZ level) that avoid the use of very expensive CC
Barone, Vincenzo; Biczysko, Malgorzata; Bloino, Julien; Cimino, Paola; Penocchio, Emanuele; Puzzarini, Cristina
2015-09-01
The structures and relative stabilities as well as the rotational and vibrational spectra of the three low-energy conformers of pyruvic acid (PA) have been characterized using a state-of-the-art quantum-mechanical approach designed for flexible molecules. By making use of the available experimental rotational constants for several isotopologues of the most stable PA conformer, Tc-PA, the semiexperimental equilibrium structure has been derived. The latter provides a reference for the pure theoretical determination of the equilibrium geometries for all conformers, thus confirming for these structures an accuracy of 0.001 Å and 0.1 deg for bond lengths and angles, respectively. Highly accurate relative energies of all conformers (Tc-, Tt-, and Ct-PA) and of the transition states connecting them are provided along with the thermodynamic properties at low and high temperatures, thus leading to conformational enthalpies accurate to 1 kJ mol(-1). Concerning microwave spectroscopy, rotational constants accurate to about 20 MHz are provided for the Tt- and Ct-PA conformers, together with the computed centrifugal-distortion constants and dipole moments required to simulate their rotational spectra. For Ct-PA, vibrational frequencies in the mid-infrared region accurate to 10 cm(-1) are reported along with theoretical estimates for the transitions in the near-infrared range, and the corresponding infrared spectrum including fundamental transitions, overtones, and combination bands has been simulated. In addition to the new data described above, theoretical results for the Tc- and Tt-PA conformers are compared with all available experimental data to further confirm the accuracy of the hybrid coupled-cluster/density functional theory (CC/DFT) protocol applied in the present study. Finally, we discuss in detail the accuracy of computational models fully based on double-hybrid DFT functionals (mainly at the B2PLYP/aug-cc-pVTZ level) that avoid the use of very expensive CC
Puzzarini, Cristina; Barone, Vincenzo
2011-04-21
The equilibrium structure of uracil has been investigated using both theoretical and experimental data. With respect to the former, quantum-chemical calculations at the coupled-cluster level in conjunction with a triple-zeta basis set have been carried out. Extrapolation to the basis set limit, performed employing the second-order Møller-Plesset perturbation theory, and inclusion of core-correlation and diffuse-function corrections have also been considered. Based on the available rotational constants for various isotopic species together with corresponding computed vibrational corrections, the semi-experimental equilibrium structure of uracil has been determined for the first time. Theoretical and semi-experimental structures have been found in remarkably good agreement, thus pointing out the limitations of previous experimental determinations. Molecular and spectroscopic properties of uracil have then been studied by means of the composite computational approach introduced for the molecular structure evaluation. Among the results achieved, we mention the revision of the dipole moment. On the whole, it has been proved that the computational procedure presented is able to provide parameters with the proper accuracy to support experimental investigations of large molecules of biological interest.
NASA Astrophysics Data System (ADS)
Mita, Akira
2016-04-01
The importance of the structural health monitoring system for tall buildings is now widely recognized by at least structural engineers and managers at large real estate companies to ensure the structural safety immediately after a large earthquake and appeal the quantitative safety of buildings to potential tenants. Some leading real estate companies decided to install the system into all tall buildings. Considering this tendency, a pilot project for the west area of Shinjuku Station supported by the Japan Science and Technology Agency was started by the author team to explore a possibility of using the system to provide safe spaces for commuters and residents. The system was installed into six tall buildings. From our experience, it turned out that viewing only from technological aspects was not sufficient for the system to be accepted and to be really useful. Safe spaces require not only the structural safety but also the soundness of key functions of the building. We need help from social scientists, medical doctors, city planners etc. to further improve the integrity of the system.
Venner, Eric; Lisewski, Andreas Martin; Erdin, Serkan; Ward, R Matthew; Amin, Shivas R; Lichtarge, Olivier
2010-01-01
High-throughput Structural Genomics yields many new protein structures without known molecular function. This study aims to uncover these missing annotations by globally comparing select functional residues across the structural proteome. First, Evolutionary Trace Annotation, or ETA, identifies which proteins have local evolutionary and structural features in common; next, these proteins are linked together into a proteomic network of ETA similarities; then, starting from proteins with known functions, competing functional labels diffuse link-by-link over the entire network. Every node is thus assigned a likelihood z-score for every function, and the most significant one at each node wins and defines its annotation. In high-throughput controls, this competitive diffusion process recovered enzyme activity annotations with 99% and 97% accuracy at half-coverage for the third and fourth Enzyme Commission (EC) levels, respectively. This corresponds to false positive rates 4-fold lower than nearest-neighbor and 5-fold lower than sequence-based annotations. In practice, experimental validation of the predicted carboxylesterase activity in a protein from Staphylococcus aureus illustrated the effectiveness of this approach in the context of an increasingly drug-resistant microbe. This study further links molecular function to a small number of evolutionarily important residues recognizable by Evolutionary Tracing and it points to the specificity and sensitivity of functional annotation by competitive global network diffusion. A web server is at http://mammoth.bcm.tmc.edu/networks.
Electronic structure of the [MgO3]+ cation
NASA Astrophysics Data System (ADS)
Ben Houria, A.; Yazidi, O.; Jaidane, N.; Senent, M. L.; Hochlaf, M.
2012-01-01
Accurate ab initio calculations are performed to investigate the stable isomers of [MgO3]+ and its lowest electronic states at both molecular and asymptotic regions. The calculations are done using large basis sets and configuration interaction methods including the complete active space self-consistent field, the internally contracted multi-reference configuration interaction, the standard coupled cluster (RCCSD(T)) approaches and the newly implemented explicitly correlated coupled cluster method (RCCSD(T)-F12). The presence of three stable forms is predicted: a cyclic global minimum c-MgO3+, which is followed by a quasi-linear isomer, l2-MgO3+. A third isomer of Cs symmetry (l1-MgO3+) is also found. Moreover, we computed the one-dimensional cuts of the six-dimensional potential energy surfaces of the lowest doublet and quartet electronic states of [MgO3]+ along the RMgO and ROO stretching coordinates covering both the molecular and the asymptotic regions. These curves are used later for discussing the metastability of this cation and to propose plausible mechanisms for the Mg+ + O3 atmospherically important ion-molecule reaction and related reactive channels.
NASA Astrophysics Data System (ADS)
Koslowski, Thorsten
2000-12-01
In this work, we present a theoretical and numerical study of the microscopic and electronic structure of solutions of refractory metal halides in alkali halide melts, [NbCl5]x[KCl]1-x and [TaCl5]x[KCl]1-x with 0⩽x⩽0.5. The geometry of the melts is described by ensembles of charged hard spheres, the electronic structure is modeled by a tight-binding Hamiltonian, which is extended by a reaction field to describe the diabatic energy profile of the electronic self-exchange in many-orbital mixed-valence systems. Despite its simplicity, the model leads to the formation of distorted octahedral [NbCl6]- and [TaCl6]- clusters, as evident both from the inspection of the simulation geometries and from the analysis of the partial pair distribution functions. Even in the presence of the strong potential energy fluctuations characteristic of ionic liquids, the octahedral structure is manifest in the density of states in a t2g-eg splitting of the conduction band. The Hamiltonian that describes mixed-valence systems is solved self-consistently. Using an attractive Hubbard parameter of 1.5 eV, we show that the numerical results can be interpreted by Marcus' theory of outer-sphere electron transfer reactions with a reorganization energy of 2.2 eV, an electronic coupling parameter of 0.12 eV, and an activation energy of 0.42 eV. Both anion-d metal cation and intervalence charge transfer excitations contribute to the optical absorption spectrum, the latter leads to a pronounced polaron absorption peak. These findings are compared to recent experimental results.
Meyer, Jens; Zilberberg, K; Riedl, T.; Kahn, Antoine
2011-01-01
The electronic structure of Vanadium pentoxide (V₂O₅), a transition metal oxide with an exceedingly large work function of 7.0 eV, is studied via ultraviolet, inverse and x-ray photoemission spectroscopy. Very deep lying electronic states with electron affinity and ionization energy (IE) of 6.7 eV and 9.5 eV, respectively, are found. Contamination due to air exposure changes the electronic structure due to the partial reduction of vanadium to V⁺⁴ state. It is shown that V₂O₅ is a n-type material that can be used for efficient hole-injection into materials with an IE larger than 6 eV, such as 4,4'-Bis(N-carbazolyl)-1,1'-bipheny (CBP). The formation of an interface dipole and band bending is found to lead to a very small energy barrier between the transport levels at the V₂O₅/CBP interface.
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
Impact of lattice distortion and electron doping on α-MoO3 electronic structure
Huang, Peng-Ru; He, Yao; Cao, Chao; Lu, Zheng-Hong
2014-01-01
Band structure of transition metal oxides plays a critical role in many applications such as photo-catalysis, photovoltaics, and electroluminescent devices. In this work we report findings that the band structure of MoO3 can be significantly altered by a distortion in the octahedral coordination structure. We discovered that, in addition to epitaxial type of structural strain, chemical force such as hydrogen inclusion can also cause extended lattice distortion. The lattice distortion in hydrogenated MoO3 led to a significant reduction of the energy gap, overshadowing the Moss-Burstein effect of band filling. Charge doping simulations revealed that filling of conduction band drives the lattice distortion. This suggests that any charge transfer or n-type electron doping could lead to lattice distortion and consequentially a reduction in energy gap. PMID:25410814
Li, Xiaowei; Liu, Taigang; Tao, Peiying; Wang, Chunhua; Chen, Lanming
2015-12-01
Structural class characterizes the overall folding type of a protein or its domain. Many methods have been proposed to improve the prediction accuracy of protein structural class in recent years, but it is still a challenge for the low-similarity sequences. In this study, we introduce a feature extraction technique based on auto cross covariance (ACC) transformation of position-specific score matrix (PSSM) to represent a protein sequence. Then support vector machine-recursive feature elimination (SVM-RFE) is adopted to select top K features according to their importance and these features are input to a support vector machine (SVM) to conduct the prediction. Performance evaluation of the proposed method is performed using the jackknife test on three low-similarity datasets, i.e., D640, 1189 and 25PDB. By means of this method, the overall accuracies of 97.2%, 96.2%, and 93.3% are achieved on these three datasets, which are higher than those of most existing methods. This suggests that the proposed method could serve as a very cost-effective tool for predicting protein structural class especially for low-similarity datasets.
Electronic and structural transitions in dense liquid sodium
NASA Astrophysics Data System (ADS)
Raty, Jean-Yves; Schwegler, Eric; Bonev, Stanimir A.
2007-09-01
At ambient conditions, the light alkali metals are free-electron-like crystals with a highly symmetric structure. However, they were found recently to exhibit unexpected complexity under pressure. It was predicted from theory-and later confirmed by experiment-that lithium and sodium undergo a sequence of symmetry-breaking transitions, driven by a Peierls mechanism, at high pressures. Measurements of the sodium melting curve have subsequently revealed an unprecedented (and still unexplained) pressure-induced drop in melting temperature from 1,000K at 30GPa down to room temperature at 120GPa. Here we report results from ab initio calculations that explain the unusual melting behaviour in dense sodium. We show that molten sodium undergoes a series of pressure-induced structural and electronic transitions, analogous to those observed in solid sodium but commencing at much lower pressure in the presence of liquid disorder. As pressure is increased, liquid sodium initially evolves by assuming a more compact local structure. However, a transition to a lower-coordinated liquid takes place at a pressure of around 65GPa, accompanied by a threefold drop in electrical conductivity. This transition is driven by the opening of a pseudogap, at the Fermi level, in the electronic density of states-an effect that has not hitherto been observed in a liquid metal. The lower-coordinated liquid emerges at high temperatures and above the stability region of a close-packed free-electron-like metal. We predict that similar exotic behaviour is possible in other materials as well.
Atomic and electronic structures of an extremely fragile liquid
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
Atomic and electronic structures of an extremely fragile liquid.
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
2014-12-18
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.
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
Zheng, Wenjun; Tekpinar, Mustafa
2011-12-21
Small-angle x-ray scattering (SAXS) is a powerful technique widely used to explore conformational states and transitions of biomolecular assemblies in solution. For accurate model reconstruction from SAXS data, one promising approach is to flexibly fit a known high-resolution protein structure to low-resolution SAXS data by computer simulations. This is a highly challenging task due to low information content in SAXS data. To meet this challenge, we have developed what we believe to be a novel method based on a coarse-grained (one-bead-per-residue) protein representation and a modified form of the elastic network model that allows large-scale conformational changes while maintaining pseudobonds and secondary structures. Our method optimizes a pseudoenergy that combines the modified elastic-network model energy with a SAXS-fitting score and a collision energy that penalizes steric collisions. Our method uses what we consider a new implicit hydration shell model that accounts for the contribution of hydration shell to SAXS data accurately without explicitly adding waters to the system. We have rigorously validated our method using five test cases with simulated SAXS data and three test cases with experimental SAXS data. Our method has successfully generated high-quality structural models with root mean-squared deviation of 1 ∼ 3 Å from the target structures.
Kohn, S.; Weare, J.; Ong, E.; Baden, S.
1997-05-01
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 gradient with FAC multigrid preconditioning. We have parallelized our solver using an object- oriented adaptive mesh refinement framework.
The structure and electronic properties of hexagonal Fe2Si
NASA Astrophysics Data System (ADS)
Tang, Chi Pui; Tam, Kuan Vai; Xiong, Shi Jie; Cao, Jie; Zhang, Xiaoping
2016-06-01
On the basis of first principle calculations, we show that a hexagonal structure of Fe2Si is a ferromagnetic crystal. The result of the phonon spectra indicates that it is a stable structure. Such material exhibits a spin-polarized and half-metal-like band structure. From the calculations of generalized gradient approximation, metallic and semiconducting behaviors are observed with a direct and nearly 0 eV band gap in various spin channels. The densities of states in the vicinity of the Fermi level is mainly contributed from the d-electrons of Fe. We calculate the reflection spectrum of Fe2Si, which has minima at 275nm and 3300nm with reflectance of 0.27 and 0.49, respectively. Such results may provide a reference for the search of hexagonal Fe2Si in experiments. With this band characteristic, the material may be applied in the field of novel spintronics devices.
Electron microscopic examination of wastewater biofilm formation and structural components.
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
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.
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
Novel electronic structures of superlattice composed of graphene and silicene
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.
Silicane nanoribbons: electronic structure and electric field modulation
NASA Astrophysics Data System (ADS)
Fang, D. Q.; Zhang, Y.; Zhang, S. L.
2014-11-01
We present electronic band structure, Gibbs free energy of formation, and electric field modulation calculations for silicane nanoribbons (NRs), i.e., completely hydrogenated or fluorinated silicene NRs, using density functional theory. We find that although the completely hydrogenated silicene (H-silicane) sheet in the chair-like configuration is an indirect-band-gap semiconductor, a direct band gap can be achieved in the zigzag H-silicane NRs by using Brillouin-zone folding. Compared to H-silicane NRs, the band gaps of completely fluorinated silicene (F-silicane) NRs reduce at least by half. For all silicane NRs considered here, the Gibbs free energy of formation is negative but shows different trends by changing the ribbon width for H-silicane NRs and F-silicane NRs. Furthermore, by analyzing the effect of transverse electric fields on the electronic properties of silicane NRs, we show that an external electric field can make the electrons and holes states spatially separated and even render silicane NRs self-doped. The tunable electronic properties of silicane NRs make them suitable for nanotechnology application.
NASA Astrophysics Data System (ADS)
Jahanshahi, Mohammad R.; Masri, Sami F.
2013-03-01
In mechanical, aerospace and civil structures, cracks are important defects that can cause catastrophes if neglected. Visual inspection is currently the predominant method for crack assessment. This approach is tedious, labor-intensive, subjective and highly qualitative. An inexpensive alternative to current monitoring methods is to use a robotic system that could perform autonomous crack detection and quantification. To reach this goal, several image-based crack detection approaches have been developed; however, the crack thickness quantification, which is an essential element for a reliable structural condition assessment, has not been sufficiently investigated. In this paper, a new contact-less crack quantification methodology, based on computer vision and image processing concepts, is introduced and evaluated against a crack quantification approach which was previously developed by the authors. The proposed approach in this study utilizes depth perception to quantify crack thickness and, as opposed to most previous studies, needs no scale attachment to the region under inspection, which makes this approach ideal for incorporation with autonomous or semi-autonomous mobile inspection systems. Validation tests are performed to evaluate the performance of the proposed approach, and the results show that the new proposed approach outperforms the previously developed one.
Observation of laser-induced electronic structure in oriented polyatomic molecules
Kraus, P. M.; Tolstikhin, O. I.; Baykusheva, D.; Rupenyan, A.; Schneider, J.; Bisgaard, C. Z.; Morishita, T.; Jensen, F.; Madsen, L. B.; Wörner, H. J.
2015-01-01
All attosecond time-resolved measurements have so far relied on the use of intense near-infrared laser pulses. In particular, attosecond streaking, laser-induced electron diffraction and high-harmonic generation all make use of non-perturbative light–matter interactions. Remarkably, the effect of the strong laser field on the studied sample has often been neglected in previous studies. Here we use high-harmonic spectroscopy to measure laser-induced modifications of the electronic structure of molecules. We study high-harmonic spectra of spatially oriented CH3F and CH3Br as generic examples of polar polyatomic molecules. We accurately measure intensity ratios of even and odd-harmonic orders, and of the emission from aligned and unaligned molecules. We show that these robust observables reveal a substantial modification of the molecular electronic structure by the external laser field. Our insights offer new challenges and opportunities for a range of emerging strong-field attosecond spectroscopies. PMID:25940229
Structural phase transition and electronic properties in samarium chalcogenides
NASA Astrophysics Data System (ADS)
Panwar, Y. S.; Aynyas, Mahendra; Pataiya, J.; Sanyal, Sankar P.
2016-05-01
The electronic structure and high pressure properties of samarium monochalcogenides SmS, SmSe and SmTe have been reported by using tight binding linear muffin-tin-orbital (TB-LMTO) method within the local density approximation (LDA). The total energy as a function of volume is evaluated. It is found that these monochalcogenides are stable in NaCl-type structure under ambient pressure. We predict a structural phase transition from NaCl-type (B1-phase) structure to CsCl-type (B2-type) structure for these compounds. Phase transition pressures were found to be 1.7, 4.4 and 6.6 GPa, for SmS, SmSe and SmTe respectively. Apart from this, the lattice parameter (a0), bulk modulus (B0), band structure (BS) and density of states (DOS) are calculated. From energy band diagram we observed that these compounds exhibit metallic character. The calculated values of equilibrium lattice parameter and phase transition pressure are in general good agreement with available data.
Lin, Lin; Yang, Chao; Lu, Jiangfeng; Ying, Lexing; E, Weinan
2009-09-25
We present an efficient parallel algorithm and its implementation for computing the diagonal of $H^-1$ where $H$ is a 2D Kohn-Sham Hamiltonian discretized on a rectangular domain using a standard second order finite difference scheme. This type of calculation can be used to obtain an accurate approximation to the diagonal of a Fermi-Dirac function of $H$ through a recently developed pole-expansion technique \\cite{LinLuYingE2009}. The diagonal elements are needed in electronic structure calculations for quantum mechanical systems \\citeHohenbergKohn1964, KohnSham 1965,DreizlerGross1990. We show how elimination tree is used to organize the parallel computation and how synchronization overhead is reduced by passing data level by level along this tree using the technique of local buffers and relative indices. We analyze the performance of our implementation by examining its load balance and communication overhead. We show that our implementation exhibits an excellent weak scaling on a large-scale high performance distributed parallel machine. When compared with standard approach for evaluating the diagonal a Fermi-Dirac function of a Kohn-Sham Hamiltonian associated a 2D electron quantum dot, the new pole-expansion technique that uses our algorithm to compute the diagonal of $(H-z_i I)^-1$ for a small number of poles $z_i$ is much faster, especially when the quantum dot contains many electrons.
Electron and hole dynamics in the electronic and structural phase transitions of VO2
NASA Astrophysics Data System (ADS)
Haglund, Richard
2015-03-01
The ultrafast, optically induced insulator-to-metal transition (IMT) and the associated structural phase transition (SPT) in vanadium dioxide (VO2) have been studied for over a decade. However, only recently have effects due to the combined presence of electron-hole pairs and injected electrons been observed. Here we compare and contrast IMT dynamics when both hot electrons and optically excited electron-hole pairs are involved, in (1) thin films of VO2 overlaid by a thin gold foil, in which hot electrons are generated by 1.5 eV photons absorbed in the foil and accelerated through the VO2 by an applied electric field; (2) VO2 nanoparticles covered with a sparse mesh of gold nanoparticles averaging 20-30 nm in diameter in which hot electrons are generated by resonant excitation and decay of the localized surface plasmon; and (3) bare VO2 thin films excited by intense near-single-cycle THz pulses. In the first case, the IMT is driven by excitation of the bulk gold plasmon, and the SPT appears on a few-picosecond time scale. In the second case, density-functional calculations indicate that above a critical carrier density, the addition of a single electron to a 27-unit supercell drives the catastrophic collapse of the coherent phonon associated with, and leading to, the SPT. In the third case, sub-bandgap-energy photons (approximately 0.1 eV) initiate the IMT, but exhibit the same sub-100 femtosecond switching time and coherent phonon dynamics as observed when the IMT is initiated by 1.5 eV photons. This suggests that the underlying mechanism must be quite different, possibly THz-field induced interband tunneling of spatially separated electron-hole pairs. The implications of these findings for ultrafast switching in opto-electronic devices - such as hybrid VO2 silicon ring resonators - are briefly considered. Support from the National Science Foundation (DMR-1207407), the Office of Science, U.S. Department of Energy (DE-FG02-01ER45916) and the Defense Threat
The electronic structure of free aluminum clusters: Metallicity and plasmons
Andersson, Tomas; Zhang Chaofan; Svensson, Svante; Maartensson, Nils; Bjoerneholm, Olle; Tchaplyguine, Maxim
2012-05-28
The electronic structure of free aluminum clusters with {approx}3-4 nm radius has been investigated using synchrotron radiation-based photoelectron and Auger electron spectroscopy. A beam of free clusters has been produced using a gas-aggregation source. The 2p core level and the valence band have been probed. Photoelectron energy-loss features corresponding to both bulk and surface plasmon excitation following photoionization of the 2p level have been observed, and the excitation energies have been derived. In contrast to some expectations, the loss features have been detected at energies very close to those of the macroscopic solid. The results are discussed from the point of view of metallic properties in nanoparticles with a finite number of constituent atoms.
Electronic structure of Sc3N@C68
NASA Astrophysics Data System (ADS)
Hino, Shojun; Ogasawara, Naoko; Ohta, Tomona; Yagi, Hajime; Miyazaki, Takafumi; Nishi, Tatsuhiko; Shinohara, Hisanori
2013-06-01
Ultraviolet photoelectron spectra (UPS) and X-ray photoelectron spectra (XPS) of non-IPR endohedral fullerene Sc3N@C68 are measured. A simulated spectrum generated from a geometry optimized structure calculated by the density functional theory reproduces the UPS very well. XPS chemical shift of Sc2p3/2 level and electron population analysis of Sc3N@C68 suggest the electronic configuration of (Sc3N)6+@C686-. The Sc2p3/2 and N1s levels of Sc3N@C68, Sc3N@C78 and Sc3N@C80 move toward lower binding energy in accordance with cage size contraction.
Electronic Structures of Clusters of Hydrogen Vacancies on Graphene
Wu, Bi-Ru; Yang, Chih-Kai
2015-01-01
Hydrogen vacancies in graphane are products of incomplete hydrogenation of graphene. The missing H atoms can alter the electronic structure of graphane and therefore tune the electronic, magnetic, and optical properties of the composite. We systematically studied a variety of well-separated clusters of hydrogen vacancies in graphane, including the geometrical shapes of triangles, parallelograms, hexagons, and rectangles, by first-principles density functional calculation. The results indicate that energy levels caused by the missing H are generated in the broad band gap of pure graphane. All triangular clusters of H vacancies are magnetic, the larger the triangle the higher the magnetic moment. The defect levels introduced by the missing H in triangular and parallelogram clusters are spin-polarized and can find application in optical transition. Parallelograms and open-ended rectangles are antiferromagnetic and can be used for nanoscale registration of digital information. PMID:26468677
Topological Signatures in the Electronic Structure of Graphene Spirals
Avdoshenko, Stas M.; Koskinen, Pekka; Sevinçli, Haldun; Popov, Alexey A.; Rocha, Claudia G.
2013-01-01
Topology is familiar mostly from mathematics, but also natural sciences have found its concepts useful. Those concepts have been used to explain several natural phenomena in biology and physics, and they are particularly relevant for the electronic structure description of topological insulators and graphene systems. Here, we introduce topologically distinct graphene forms - graphene spirals - and employ density-functional theory to investigate their geometric and electronic properties. We found that the spiral topology gives rise to an intrinsic Rashba spin-orbit splitting. Through a Hamiltonian constrained by space curvature, graphene spirals have topologically protected states due to time-reversal symmetry. In addition, we argue that the synthesis of such graphene spirals is feasible and can be achieved through advanced bottom-up experimental routes that we indicate in this work. PMID:23568379
Electronic structure basis for the extraordinary magnetoresistance in WTe2
Pletikosić, I.; Ali, Mazhar N.; Fedorov, A. V.; Cava, R. J.; Valla, T.
2014-11-19
The electronic structure basis of the extremely large magnetoresistance in layered non-magnetic tungsten ditelluride has been investigated by angle-resolved photoelectron spectroscopy. Hole and electron pockets of approximately the same size were found at the Fermi level, suggesting that carrier compensation should be considered the primary source of the effect. The material exhibits a highly anisotropic, quasi one-dimensional Fermi surface from which the pronounced anisotropy of the magnetoresistance follows. As a result, a change in the Fermi surface with temperature was found and a high-density-of-states band that may take over conduction at higher temperatures and cause the observed turn-on behavior ofmore » the magnetoresistance in WTe₂ was identified.« less
Cryo electron microscopy to determine the structure of macromolecular complexes.
Carroni, Marta; Saibil, Helen R
2016-02-15
Cryo-electron microscopy (cryo-EM) is a structural molecular and cellular biology technique that has experienced major advances in recent years. Technological developments in image recording as well as in processing software make it possible to obtain three-dimensional reconstructions of macromolecular assemblies at near-atomic resolution that were formerly obtained only by X-ray crystallography or NMR spectroscopy. In parallel, cryo-electron tomography has also benefitted from these technological advances, so that visualization of irregular complexes, organelles or whole cells with their molecular machines in situ has reached subnanometre resolution. Cryo-EM can therefore address a broad range of biological questions. The aim of this review is to provide a brief overview of the principles and current state of the cryo-EM field.
Electronic structure of a linear C 60 polymer
NASA Astrophysics Data System (ADS)
Tanaka, Kazuyoshi; Matsuura, Yukihito; Oshima, Yoshiaki; Yamabe, Tokio; Asai, Yoshihiro; Tokumoto, Madoka
1995-01-01
The electronic structure of a C 60-polymer chain was studied based on the tight-binding calculation including both σ and π electrons. The C 60-polymer turns out semiconducting with a finite band gap ( ca 1.1 eV) and its lowest unoccupied (LU) band is no more degenerate. The LU bandwidth of this polymer is generally smaller than that of A 3C 60 by more than one order of magnitude around the Fermi level assuring that C 60-1-polymer ( o-RbC 60) is a strongly correlated system ( {U}/{t ≫ 1}) and can have the antiferromagnetic ground state. Such reduction of t comes from the cut of π-conjugation on the surface of C 60 molecule by the bridging.
Electronic structure of benzene adsorbed on Ni and Cu surfaces
Weinelt, M.; Nilsson, A.; Wassdahl, N.
1997-04-01
Benzene has for a long time served as a prototype adsorption system of large molecules. It adsorbs with the molecular plane parallel to the surface. The bonding of benzene to a transition metal is typically viewed to involve the {pi} system. Benzene adsorbs weakly on Cu and strongly on Ni. It is interesting to study how the adsorption strength is reflected in the electronic structure of the adsorbate-substrate complex. The authors have used X-ray Emission (XE) and X-ray Absorption (XA) spectroscopies to selectively study the electronic states localized on the adsorbed benzene molecule. Using XES the occupied states can be studies and with XAS the unoccupied states. The authors have used beamline 8.0 and the Swedish endstation equipped with a grazing incidence x-ray spectrometer and a partial yield absorption detector. The resolution in the XES and XAS were 0.5 eV and 0.05 eV, respectively.
Graphene gate electrode for MOS structure-based electronic devices.
Park, Jong Kyung; Song, Seung Min; Mun, Jeong Hun; Cho, Byung Jin
2011-12-14
We demonstrate that the use of a monolayer graphene as a gate electrode on top of a high-κ gate dielectric eliminates mechanical-stress-induced-gate dielectric degradation, resulting in a quantum leap of gate dielectric reliability. The high work function of hole-doped graphene also helps reduce the quantum mechanical tunneling current from the gate electrode. This concept is applied to nonvolatile Flash memory devices, whose performance is critically affected by the quality of the gate dielectric. Charge-trap flash (CTF) memory with a graphene gate electrode shows superior data retention and program/erase performance that current CTF devices cannot achieve. The findings of this study can lead to new applications of graphene, not only for Flash memory devices but also for other high-performance and mass-producible electronic devices based on MOS structure which is the mainstream of the electronic device industry.
The electronic structure of free aluminum clusters: metallicity and plasmons.
Andersson, Tomas; Zhang, Chaofan; Tchaplyguine, Maxim; Svensson, Svante; Mårtensson, Nils; Björneholm, Olle
2012-05-28
The electronic structure of free aluminum clusters with ∼3-4 nm radius has been investigated using synchrotron radiation-based photoelectron and Auger electron spectroscopy. A beam of free clusters has been produced using a gas-aggregation source. The 2p core level and the valence band have been probed. Photoelectron energy-loss features corresponding to both bulk and surface plasmon excitation following photoionization of the 2p level have been observed, and the excitation energies have been derived. In contrast to some expectations, the loss features have been detected at energies very close to those of the macroscopic solid. The results are discussed from the point of view of metallic properties in nanoparticles with a finite number of constituent atoms.
The electronic structure of free aluminum clusters: Metallicity and plasmons
NASA Astrophysics Data System (ADS)
Andersson, Tomas; Zhang, Chaofan; Tchaplyguine, Maxim; Svensson, Svante; Mârtensson, Nils; Björneholm, Olle
2012-05-01
The electronic structure of free aluminum clusters with ˜3-4 nm radius has been investigated using synchrotron radiation-based photoelectron and Auger electron spectroscopy. A beam of free clusters has been produced using a gas-aggregation source. The 2p core level and the valence band have been probed. Photoelectron energy-loss features corresponding to both bulk and surface plasmon excitation following photoionization of the 2p level have been observed, and the excitation energies have been derived. In contrast to some expectations, the loss features have been detected at energies very close to those of the macroscopic solid. The results are discussed from the point of view of metallic properties in nanoparticles with a finite number of constituent atoms.
Tang, Wenbo; Chan, Pak Wai; Haller, George
2010-03-01
Locating Lagrangian coherent structures (LCS) for dynamical systems defined on a spatially limited domain present a challenge because trajectory integration must be stopped at the boundary for lack of further velocity data. This effectively turns the domain boundary into an attractor, introduces edge effects resulting in spurious ridges in the associated finite-time Lyapunov exponent (FTLE) field, and causes some of the real ridges of the FTLE field to be suppressed by strong spurious ridges. To address these issues, we develop a finite-domain FTLE method that renders LCS with an accuracy and fidelity that is suitable for automated feature detection. We show the application of this technique to the analysis of velocity data from aircraft landing at the Hong Kong International Airport.
Physics of small metal clusters: Topology, magnetism, and electronic structure
NASA Astrophysics Data System (ADS)
Rao, B. K.; Jena, P.
1985-08-01
The electronic structure of small clusters of lithium atoms has been calculated using the self-consistent-field, molecular-orbital method. The exchange interaction is treated at the unrestricted Hartree-Fock level whereas the correlation is treated perturbatively up to second order by including pair excitations. This is done in two steps, one involving only the valence electrons and the other including all the electrons. A configuration-interaction calculation has also been done with all possible pair excitations. The equilibrium geometries of both the neutral and ionized clusters have been obtained by starting from random configurations and using the Hellmann-Feynman forces to follow the path of steepest descent to a minimum of the energy surface. The clusters of Li atoms each containing one to five atoms are found to be planar. The equilibrium geometry of a cluster is found to be intimately related to its electronic structure. The preferred spin configuration of a cluster has been found by minimizing the total energy of the cluster with respect to various spin assignments. The planar clusters are found to be less magnetic than expected by Hund's-rule coupling. For three-dimensional clusters, however, the magnetism is governed by Hund's rule. The effect of correlation has been found to have decisive influence on the equilibrium topology and magnetism of the clusters. The binding energy per atom, the energy of dissociation, and the ionization potential of the clusters are compared with experiment and with previous calculations. The physical origin of the magic numbers and the effect of the basis functions on the calculated properties have also been investigated.
Electronic structure and magnetic properties of zigzag blue phosphorene nanoribbons
Hu, Tao; Hong, Jisang
2015-08-07
We investigated the electronic structure and magnetism of zigzag blue phosphorene nanoribbons (ZBPNRs) using first principles density functional theory calculations by changing the widths of ZBPNRs from 1.5 to 5 nm. In addition, the effect of H and O passivation was explored as well. The ZBPNRs displayed intra-edge antiferromagnetic ground state with a semiconducting band gap of ∼0.35 eV; and this was insensitive to the edge structure relaxation effect. However, the edge magnetism of ZBPNRs disappeared with H-passivation. Moreover, the band gap of H-passivated ZBPNRs was greatly enhanced because the calculated band gap was ∼1.77 eV, and this was almost the same as that of two-dimensional blue phosphorene layer. For O-passivated ZBPNRs, we also found an intra-edge antiferromagnetic state. Besides, both unpassivated and O-passivated ZBPNRs preserved almost the same band gap. We predict that the electronic band structure and magnetic properties can be controlled by means of passivation. Moreover, the edge magnetism can be also modulated by the strain. Nonetheless, the intrinsic physical properties are size independent. This feature can be an advantage for device applications because it may not be necessary to precisely control the width of the nanoribbon.
Characterization of electronic structure of periodically strained graphene
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.more » 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.« less
Electronic Structure and Molecular Dynamics Calculations for KBH4
NASA Astrophysics Data System (ADS)
Papaconstantopoulos, Dimitrios; Shabaev, Andrew; Hoang, Khang; Mehl, Michael; Kioussis, Nicholas
2012-02-01
In the search for hydrogen storage materials, alkali borohydrides MBH4 (M=Li, Na, K) are especially interesting because of their light weight and the high number of hydrogen atoms per metal atom. Electronic structure calculations can give insights into the properties of these complex hydrides and provide understanding of the structural properties and of the bonding of hydrogen. We have performed first-principles density-functional theory (DFT) and tight-binding (TB) calculations for KBH4 in both the high temperature (HT) and low temperature (LT) phases to understand its electronic and structural properties. Our DFT calculations were carried out using the VASP code. The results were then used as a database to develop a tight-binding Hamiltonian using the NRL-TB method. This approach allowed for computationally efficient calculations of phonon frequencies and elastic constants using the static module of the NRL-TB, and also using the molecular dynamics module to calculate mean-square displacements and formation energies of hydrogen vacancies.
Electronic Structure and Properties of Deformed Carbon Nanotubes
NASA Technical Reports Server (NTRS)
Yang, Liu; Arnold, Jim (Technical Monitor)
2001-01-01
A theoretical framework based on Huckel tight-binding model has been formulated to analyze the electronic structure of carbon nanotubes under uniform deformation. The model successfully quantifies the dispersion relation, density of states and bandgap change of nanotubes under uniform stretching, compression, torsion and bending. Our analysis shows that the shifting of the Fermi point away from the Brillouin zone vertices is the key reason for these changes. As a result of this shifting, the electronic structure of deformed carbon nanotubes varies dramatically depending on their chirality and deformation mode. Treating the Fermi point as a function of strain and tube chirality, the analytical solution preserves the concise form of undeformed carbon nanotubes. It predicts the shifting, merging and splitting of the Van Hove singularities in the density of states and the zigzag pattern of bandgap change under strains. Four orbital tight-binding simulations of carbon nanotubes under uniform stretching, compression, torsion and bending have been performed to verify the analytical solution. Extension to more complex systems are being performed to relate this analytical solution to the spectroscopic characterization, device performance and proposed quantum structures induced by the deformation. The limitations of this model will also be discussed.
Phase Diagram and Electronic Structure of Praseodymium and Plutonium systems
NASA Astrophysics Data System (ADS)
Yao, Yong-Xin; Nicola, Lanata; Wang, Cai-Zhuang; Kotliar, Gabriel; Ho, Kai-Ming
2015-03-01
We apply a new implementation of LDA +Gutzwiller to calculate the zero-temperature phase diagram and electronic structure of Pr and Pu. Our study of Pr indicates that its pressure-induced volume-collapse transition would not occur without change of lattice structure -- contrarily to Ce. Our study of Pu shows that the most important effect originating the differentiation between the equilibrium densities of its allotropes is the competition between the Peierls effect and the Madelung interaction. However, the proper treatment of electron correlation effects is crucial to reach good agreement with experiment. A similar interplay between correlation effects and bands structure is also displayed in Pr, and might emerge in even greater generality. N.L. and G.K. supported by U.S. DOE BES under Grant No. DE-FG02- 99ER45761. Research at Ames Lab supported by the U.S. DOE, Office of BES, DMSE, Ames Laboratory is operated for the U.S. DOE by Iowa State University under Contract No. DE-AC02-07CH11358.
Amyloid structure and assembly: insights from scanning transmission electron microscopy.
Goldsbury, Claire; Baxa, Ulrich; Simon, Martha N; Steven, Alasdair C; Engel, Andreas; Wall, Joseph S; Aebi, Ueli; Müller, Shirley A
2011-01-01
Amyloid fibrils are filamentous protein aggregates implicated in several common diseases such as Alzheimer's disease and type II diabetes. Similar structures are also the molecular principle of the infectious spongiform encephalopathies such as Creutzfeldt-Jakob disease in humans, scrapie in sheep, and of the so-called yeast prions, inherited non-chromosomal elements found in yeast and fungi. Scanning transmission electron microscopy (STEM) is often used to delineate the assembly mechanism and structural properties of amyloid aggregates. In this review we consider specifically contributions and limitations of STEM for the investigation of amyloid assembly pathways, fibril polymorphisms and structural models of amyloid fibrils. This type of microscopy provides the only method to directly measure the mass-per-length (MPL) of individual filaments. Made on both in vitro assembled and ex vivo samples, STEM mass measurements have illuminated the hierarchical relationships between amyloid fibrils and revealed that polymorphic fibrils and various globular oligomers can assemble simultaneously from a single polypeptide. The MPLs also impose strong constraints on possible packing schemes, assisting in molecular model building when combined with high-resolution methods like solid-state nuclear magnetic resonance (NMR) and electron paramagnetic resonance (EPR).
Amyloid Structure and Assembly: Insights from Scanning Transmission Electron Microscopy
Goldsbury, C.; Wall, J.; Baxa, U.; Simon, M. N.; Steven, A. C.; Engel, A.; Aebi, U.; Muller, S. A.
2011-01-01
Amyloid fibrils are filamentous protein aggregates implicated in several common diseases such as Alzheimer's disease and type II diabetes. Similar structures are also the molecular principle of the infectious spongiform encephalopathies such as Creutzfeldt-Jakob disease in humans, scrapie in sheep, and of the so-called yeast prions, inherited non-chromosomal elements found in yeast and fungi. Scanning transmission electron microscopy (STEM) is often used to delineate the assembly mechanism and structural properties of amyloid aggregates. In this review we consider specifically contributions and limitations of STEM for the investigation of amyloid assembly pathways, fibril polymorphisms and structural models of amyloid fibrils. This type of microscopy provides the only method to directly measure the mass-per-length (MPL) of individual filaments. Made on both in vitro assembled and ex vivo samples, STEM mass measurements have illuminated the hierarchical relationships between amyloid fibrils and revealed that polymorphic fibrils and various globular oligomers can assemble simultaneously from a single polypeptide. The MPLs also impose strong constraints on possible packing schemes, assisting in molecular model building when combined with high-resolution methods like solid-state nuclear magnetic resonance (NMR) and electron paramagnetic resonance (EPR).