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.
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 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.
2014-01-01
X-ray free-electron laser (XFEL) sources enable the use of crystallography to solve three-dimensional macromolecular structures under native conditions and free from 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 statistically significant high-resolution signals from fewer diffraction measurements. PMID:24633409
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.
A new class of atomic basis functions for accurate electronic structure calculations of molecules
NASA Astrophysics Data System (ADS)
Laikov, Dimitri N.
2005-11-01
A new general approach is developed for obtaining systematic sequences of atomic single-particle basis sets for use in correlated electronic structure calculations of molecules. All the constituent functions are defined as the solutions of variational problems and are of three types: a minimal Hartree-Fock set, additional functions to represent low-lying excited configurations, and general functions for describing electron correlation. The latter are determined to minimize a functional derived from the closed-shell second-order correlation energy expression. Generally-contracted Gaussian expansions are developed to approximate these general functions in the non-relativistic case and within a scalar-relativistic approximation.
NASA Astrophysics Data System (ADS)
Skone, Jonathan; Govoni, Marco; Galli, Giulia
2015-03-01
Building upon a recently proposed self-consistent hybrid (sc-hybrid) functional, where the optimal dielectric screening is included self-consistently, we propose an improved form by incorporating range-separation of the exchange part. We discuss the choice of the non-empirical parameters defining range separation, and we present results for condensed media including semiconductors, amorphous insulators, and molecular crystals. We find that the range-separated sc-hybrid functional further improves upon the electronic gaps obtained with full-range sc-hybrids, thus providing an accurate functional for high throughput band gap engineering. This work was supported by NSF-CCI Grant Number NSF-CHE-0802907 and ARL Grant Number W911NF-12-2-0023.
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)
Chen, Xiaolin; Ning, Chuangang
2016-05-01
The high-resolution photoelectron spectra of C o- were obtained via the slow-electron velocity-map imaging method. The electron affinity of cobalt element was determined to be 5341.45 (37 ) c m-1 or 662.256(46) meV. The fine structure of C o- was well resolved. The fine-structure intervals C o-(F34) -C o-(F33) and C o-(F34) -C o-(F32) were found to be 920.9 (6 ) c m-1 and 1550.3 (9 ) c m-1 , respectively. The accuracy was improved by a factor of more than ten with respect to the previous laser photodetachment threshold measurement.
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.
NASA Astrophysics Data System (ADS)
B. Araujo, Rafael; S. de Almeida, J.; Ferreira da Silva, A.; Ahuja, Rajeev
2015-09-01
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 LiFePO4 and FePO4 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 LiFePO4 and FePO4. However, it does not appear to have the same efficiency for evaluating the redox reaction energies for the investigated system.
NASA Astrophysics Data System (ADS)
Son, Sang-Kil; Chu, Shih-I.
2008-05-01
We introduce a new computational method on unstructured grids in the three-dimensional (3D) spaces to investigate the electronic structure of polyatomic molecules. The Voronoi-cell finite difference (VFD) method realizes a simple discrete Laplacian operator on unstructured grids based on Voronoi cells and their natural neighbors. The feature of unstructured grids enables us to choose intuitive pictures for an optimal molecular grid system. The new VFD method achieves highly adaptability by the Voronoi-cell diagram and yet simplicity by the finite difference scheme. It has no limitation in local refinement of grids in the vicinity of nuclear positions and provides an explicit expression at each grid without any integration. This method augmented by unstructured molecular grids is suitable for solving the Schr"odinger equation with the realistic 3D Coulomb potentials regardless of symmetry of molecules. For numerical examples, we test accuracies for electronic structures of one-electron polyatomic systems: linear H2^+ and triangular H3^++. We also extend VFD to the density functional theory (DFT) for many-electron polyatomic molecules.
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.
NASA Astrophysics Data System (ADS)
Malshe, M.; Pukrittayakamee, A.; Raff, L. M.; Hagan, M.; Bukkapatnam, S.; Komanduri, R.
2009-09-01
A novel method is presented that significantly reduces the computational bottleneck of executing high-level, electronic structure calculations of the energies and their gradients for a large database that adequately samples the configuration space of importance for systems containing more than four atoms that are undergoing multiple, simultaneous reactions in several energetically open channels. The basis of the method is the high-degree of correlation that generally exists between the Hartree-Fock (HF) and higher-level electronic structure energies. It is shown that if the input vector to a neural network (NN) includes both the configuration coordinates and the HF energies of a small subset of the database, MP4(SDQ) energies with the same basis set can be predicted for the entire database using only the HF and MP4(SDQ) energies for the small subset and the HF energies for the remainder of the database. The predictive error is shown to be less than or equal to the NN fitting error if a NN is fitted to the entire database of higher-level electronic structure energies. The general method is applied to the computation of MP4(SDQ) energies of 68 308 configurations that comprise the database for the simultaneous, unimolecular decomposition of vinyl bromide into six different reaction channels. The predictive accuracy of the method is investigated by employing successively smaller subsets of the database to train the NN to predict the MP4(SDQ) energies of the remaining configurations of the database. The results indicate that for this system, the subset can be as small as 8% of the total number of configurations in the database without loss of accuracy beyond that expected if a NN is employed to fit the higher-level energies for the entire database. The utilization of this procedure is shown to save about 78% of the total computational time required for the execution of the MP4(SDQ) calculations. The sampling error involved with selection of the subset is shown to be
Accurate equilibrium structures of fluoro- and chloroderivatives of methane
NASA Astrophysics Data System (ADS)
Vogt, Natalja; Demaison, Jean; Rudolph, Heinz Dieter
2014-11-01
This work is a systematic study of molecular structure of fluoro-, chloro-, and fluorochloromethanes. For the first time, the accurate ab initio structure is computed for 10 molecules (CF4, CClF3, CCl2F2, CCl3F, CHClF2, CHCl2F, CH2F2, CH2ClF, CH2Cl2, and CCl4) at the coupled cluster level of electronic structure theory including single and double excitations augmented by a perturbational estimate of the effects of connected triple excitations [CCSD(T)] with all electrons being correlated and Gaussian basis sets of at least quadruple-ζ quality. Furthermore, when possible, namely for the molecules CH2F2, CH2Cl2, CH2ClF, CHClF2, and CCl2F2, accurate semi-experimental equilibrium (rSEe) structure has also been determined. This is achieved through a least-squares structural refinement procedure based on the equilibrium rotational constants of all available isotopomers, determined by correcting the experimental ground-state rotational constants with computed ab initio vibration-rotation interaction constants and electronic g-factors. The computed and semi-experimental equilibrium structures are in excellent agreement with each other, but the rSEe structure is generally more accurate, in particular for the CF and CCl bond lengths. The carbon-halogen bond length is discussed within the framework of the ligand close-packing model as a function of the atomic charges. For this purpose, the accurate equilibrium structures of some other molecules with alternative ligands, such as CH3Li, CF3CCH, and CF3CN, are also computed.
Accurate Prediction of Docked Protein Structure Similarity.
Akbal-Delibas, Bahar; Pomplun, Marc; Haspel, Nurit
2015-09-01
One of the major challenges for protein-protein docking methods is to accurately discriminate nativelike structures. The protein docking community agrees on the existence of a relationship between various favorable intermolecular interactions (e.g. Van der Waals, electrostatic, desolvation forces, etc.) and the similarity of a conformation to its native structure. Different docking algorithms often formulate this relationship as a weighted sum of selected terms and calibrate their weights against specific training data to evaluate and rank candidate structures. However, the exact form of this relationship is unknown and the accuracy of such methods is impaired by the pervasiveness of false positives. Unlike the conventional scoring functions, we propose a novel machine learning approach that not only ranks the candidate structures relative to each other but also indicates how similar each candidate is to the native conformation. We trained the AccuRMSD neural network with an extensive dataset using the back-propagation learning algorithm. Our method achieved predicting RMSDs of unbound docked complexes with 0.4Å error margin. PMID:26335807
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. PMID:26529434
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. PMID:26169835
Accurate and efficient reconstruction of deep phylogenies from structured RNAs
Stocsits, Roman R.; Letsch, Harald; Hertel, Jana; Misof, Bernhard; Stadler, Peter F.
2009-01-01
Ribosomal RNA (rRNA) genes are probably the most frequently used data source in phylogenetic reconstruction. Individual columns of rRNA alignments are not independent as a consequence of their highly conserved secondary structures. Unless explicitly taken into account, these correlation can distort the phylogenetic signal and/or lead to gross overestimates of tree stability. Maximum likelihood and Bayesian approaches are of course amenable to using RNA-specific substitution models that treat conserved base pairs appropriately, but require accurate secondary structure models as input. So far, however, no accurate and easy-to-use tool has been available for computing structure-aware alignments and consensus structures that can deal with the large rRNAs. The RNAsalsa approach is designed to fill this gap. Capitalizing on the improved accuracy of pairwise consensus structures and informed by a priori knowledge of group-specific structural constraints, the tool provides both alignments and consensus structures that are of sufficient accuracy for routine phylogenetic analysis based on RNA-specific substitution models. The power of the approach is demonstrated using two rRNA data sets: a mitochondrial rRNA set of 26 Mammalia, and a collection of 28S nuclear rRNAs representative of the five major echinoderm groups. PMID:19723687
Accurate and efficient reconstruction of deep phylogenies from structured RNAs.
Stocsits, Roman R; Letsch, Harald; Hertel, Jana; Misof, Bernhard; Stadler, Peter F
2009-10-01
Ribosomal RNA (rRNA) genes are probably the most frequently used data source in phylogenetic reconstruction. Individual columns of rRNA alignments are not independent as a consequence of their highly conserved secondary structures. Unless explicitly taken into account, these correlation can distort the phylogenetic signal and/or lead to gross overestimates of tree stability. Maximum likelihood and Bayesian approaches are of course amenable to using RNA-specific substitution models that treat conserved base pairs appropriately, but require accurate secondary structure models as input. So far, however, no accurate and easy-to-use tool has been available for computing structure-aware alignments and consensus structures that can deal with the large rRNAs. The RNAsalsa approach is designed to fill this gap. Capitalizing on the improved accuracy of pairwise consensus structures and informed by a priori knowledge of group-specific structural constraints, the tool provides both alignments and consensus structures that are of sufficient accuracy for routine phylogenetic analysis based on RNA-specific substitution models. The power of the approach is demonstrated using two rRNA data sets: a mitochondrial rRNA set of 26 Mammalia, and a collection of 28S nuclear rRNAs representative of the five major echinoderm groups. PMID:19723687
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
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.
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 measurement of the electron beam polarization in JLab Hall A using Compton polarimetry
S. Escoffier; P.Y. Bertin; M. Brossard; E. Burtin; C. Cavata; N. Colombel; C.W. de Jager; A. Delbart; D. Lhuillier; F. Marie; J. Mitchell; D. Neyret; T. Pussieux
2005-05-01
A major advance in accurate electron beam polarization measurement has been achieved at Jlab Hall A with a Compton polarimeter based on a Fabry-Perot cavity photon beam amplifier. At an electron energy of 4.6 GeV and a beam current of 40 uA, a total relative uncertainty of 1.5% is typically achieved within 40 min of data taking. Under the same conditions monitoring of the polarization is accurate at a level of 1%. These unprecedented results make Compton polarimetry an essential tool for modern parity-violation experiments, which require very accurate electron beam polarization measurements.
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.
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
Accurate protein structure modeling using sparse NMR data and homologous structure information
Thompson, James M.; Sgourakis, Nikolaos G.; Liu, Gaohua; Rossi, Paolo; Tang, Yuefeng; Mills, Jeffrey L.; Szyperski, Thomas; Montelione, Gaetano T.; Baker, David
2012-01-01
While information from homologous structures plays a central role in X-ray structure determination by molecular replacement, such information is rarely used in NMR structure determination because it can be incorrect, both locally and globally, when evolutionary relationships are inferred incorrectly or there has been considerable evolutionary structural divergence. Here we describe a method that allows robust modeling of protein structures of up to 225 residues by combining , 13C, and 15N backbone and 13Cβ chemical shift data, distance restraints derived from homologous structures, and a physically realistic all-atom energy function. Accurate models are distinguished from inaccurate models generated using incorrect sequence alignments by requiring that (i) the all-atom energies of models generated using the restraints are lower than models generated in unrestrained calculations and (ii) the low-energy structures converge to within 2.0 Å backbone rmsd over 75% of the protein. Benchmark calculations on known structures and blind targets show that the method can accurately model protein structures, even with very remote homology information, to a backbone rmsd of 1.2–1.9 Å relative to the conventional determined NMR ensembles and of 0.9–1.6 Å relative to X-ray structures for well-defined regions of the protein structures. This approach facilitates the accurate modeling of protein structures using backbone chemical shift data without need for side-chain resonance assignments and extensive analysis of NOESY cross-peak assignments. PMID:22665781
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.
Dolgounitcheva, O; Díaz-Tinoco, Manuel; Zakrzewski, V G; Richard, Ryan M; Marom, Noa; Sherrill, C David; Ortiz, J V
2016-02-01
Comparison of ab initio electron-propagator predictions of vertical ionization potentials and electron affinities of organic, acceptor molecules with benchmark calculations based on the basis set-extrapolated, coupled cluster single, double, and perturbative triple substitution method has enabled identification of self-energy approximations with mean, unsigned errors between 0.1 and 0.2 eV. Among the self-energy approximations that neglect off-diagonal elements in the canonical, Hartree-Fock orbital basis, the P3 method for electron affinities, and the P3+ method for ionization potentials provide the best combination of accuracy and computational efficiency. For approximations that consider the full self-energy matrix, the NR2 methods offer the best performance. The P3+ and NR2 methods successfully identify the correct symmetry label of the lowest cationic state in two cases, naphthalenedione and benzoquinone, where some other methods fail. PMID:26730459
Accurate exchange-correlation energies for the warm dense electron gas
NASA Astrophysics Data System (ADS)
Malone, Fionn; Blunt, Nicholas; Shepherd, James; Lee, Derek; Spencer, James; Foulkes, Matthew
The accurate treatment of matter at high temperatures and densities is of increasing importance to many fields in physics and chemistry, with applications ranging from planetary physics to inertial confinement fusion and plasmonic catalysis. Faithfully including the effects of temperature in density functional theory simulations of warm dense matter requires accurate results for the uniform electron gas (UEG) across the whole temperature-density plane. While accurate ground state quantum Monte Carlo data have existed for over 30 years, there remains significant disagreement between results obtained using different path integral Monte Carlo methods at finite temperature. To resolve this disagreement, we use the systematically improvable density matrix quantum Monte Carlo method to calculate the exchange-correlation energy of the UEG. We also demonstrate how the evaluation of free energies emerges naturally from our method.
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.
Accurate calculation of phase shifts for electron collisions with positive ions
NASA Astrophysics Data System (ADS)
Gien, T. T.
2003-06-01
The Harris-Nesbet variational method was considered for the calculation of phase shifts of electron collisions with hydrogen-like ions (Li2+, Be3+, and B4+). Calculations were carried out for both singlet and triplet scattering. Very accurate results of phase shift of electron collisions with these ionic targets were obtained for the first time for partial waves of L up to six. The phase shifts that we obtained for low partial wave (S, P, and D) scattering were compared with those available in the literature by a few other research groups employing different numerical methods.
Accurate lifetime measurements for the noble gases by the electron beam alignment technique
NASA Astrophysics Data System (ADS)
Gorny, M. B.; Kazantsev, S. A.; Matisov, B. G.; Polezhaevs, N. T.
1985-03-01
Accurate lifetime measurement for the 41 P 1, 41 D 2, 51 D 2 helium and the atomic 2 p and 3 p states of other noble gases was performed by the low energy electron beam alignment technique. An account of the influence of magnetic field on the electron path was made to obtain the real Hanle signal shape. The influence of the radiation trapping in the collision chamber was analysed with regard to the metastables diffusion. The experimental data were compared with the results of other methods of the lifetime determination.
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
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
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.
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.
Can structured data fields accurately measure quality of care? The example of falls.
Ganz, David A; Almeida, Shone; Roth, Carol P; Reuben, David B; Wenger, Neil S
2012-01-01
By automating collection of data elements, electronic health records may simplify the process of measuring the quality of medical care. Using data from a quality improvement initiative in primary care medical groups, we sought to determine whether the quality of care for falls and fear of falling in outpatients aged 75 and older could be accurately measured solely from codable (non-free-text) data in a structured visit note. A traditional medical record review by trained abstractors served as the criterion standard. Among 215 patient records reviewed, we found a structured visit note in 54% of charts within 3 mo of the date patients had been identified as having falls or fear of falling. The reliability of an algorithm based on codable data was at least good (kappa of at least 0.61) compared with full medical record review for three care processes recommended for patients with two falls or one fall with injury in the past year: orthostatic vital signs, vision test/eye examination, and home safety evaluation. However, the automated algorithm routinely underestimated quality of care. Performance standards based on automated measurement of quality of care from electronic health records need to account for documentation occurring in nonstructured form. PMID:23408222
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.
Loco, Daniele; Jurinovich, Sandro; Di Bari, Lorenzo; Mennucci, Benedetta
2016-01-14
We present and discuss a simple and fast computational approach to the calculation of electronic circular dichroism spectra of nucleic acids. It is based on a exciton model in which the couplings are obtained in terms of the full transition-charge distributions, as resulting from TDDFT methods applied on the individual nucleobases. We validated the method on two systems, a DNA G-quadruplex and a RNA β-hairpin whose solution structures have been accurately determined by means of NMR. We have shown that the different characteristics of composition and structure of the two systems can lead to quite important differences in the dependence of the accuracy of the simulation on the excitonic parameters. The accurate reproduction of the CD spectra together with their interpretation in terms of the excitonic composition suggest that this method may lend itself as a general computational tool to both predict the spectra of hypothetic structures and define clear relationships between structural and ECD properties. PMID:26646952
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
Electronic structure of the multivacancies in Si
NASA Astrophysics Data System (ADS)
Ren, Shang Yuan; Mao, Deqiang; Li, Mingfu
A complete set of equations for determining the energy levels and the wavefunctions with different symmetries of electronic states of several well-known multivacancies in Si is given using the Koster-Slater Green's function method. By using an empirical tight binding Hamiltonian for the band structure of the host and the central-cell perturbation approximation for the defect, only the on-site and the off-site Green's functions of the host and their derivatives with respect to energy E appear in these equations. The electronic structure of the ideal multivacancies, especially the divacancy, are investigated and compared with known experimental results and previous qualitative analyses. Some misunderstandings of the experimental results are analyzed. The wavefunctions of some multivacancy states are accurately evaluated and compared with the EPR and ENDOR data for the first time.
Lattice Boltzmann Model for Electronic Structure Simulations
NASA Astrophysics Data System (ADS)
Mendoza, M.; Herrmann, H. J.; Succi, S.
2015-09-01
Recently, a new connection between density functional theory and kinetic theory has been proposed. In particular, it was shown that the Kohn-Sham (KS) equations can be reformulated as a macroscopic limit of the steady-state solution of a suitable single-particle kinetic equation. By using a discrete version of this new formalism, the exchange and correlation energies of simple atoms and the geometrical configuration of the methane molecule were calculated accurately. Here, we discuss the main ideas behind the lattice kinetic approach to electronic structure computations, offer some considerations for prospective extensions, and also show additional numerical results, namely the geometrical configuration of the water molecule.
Theoretical electronic structure of structurally modified graphene
NASA Astrophysics Data System (ADS)
Dvorak, Marc David
Graphene has emerged as a promising replacement for silicon in next-generation electronics and optoelectronic devices. If graphene is to be used in semiconductor devices, however, it must acquire an electronic band gap. Numerous approaches have been proposed to control the band gap of graphene, including the periodic patterning of defects. However, the mechanism for band gap opening and the associated physics in graphene patterned with defects remain unclear. Using both analytic theory and first-principles calculations, we show that periodic patterning of defects on graphene can open a large and tunable band gap, induce strong absorption peaks at optical wavelengths, and host a giant band gap quantum spin Hall phase. First, a geometric rule is analytically derived for the arrangements of defects that open a band gap in graphene, with one ninth of all possible patterns opening a band gap. Next, we perform ab-initio density functional calculations to compare the effects of structural vacancies, hexagonal BN dopants, and passivants on the electronic structure of graphene. Qualitatively, these three types of structural defects behave the same, with only slight differences in their resulting band structures. By adjusting the shape of structural defects, we show how to move the Dirac cones in reciprocal space in accordance with the tight-binding model for the anisotropic honeycomb lattice, while the fundamental mechanism for band gap opening remains the same. To quantitatively predict the band gap and optical properties of these materials, we employ many-body perturbation theory with Green's functions (GW/Bethe-Salpeter equation) to directly include electron-electron and electron-hole interactions. Structurally modified graphene shows a strong renormalization of the fundamental band gap over single particle descriptions, and a strong electron-hole interaction as indicated by strong exciton binding energies (> 0.5 eV). Finally, we show that structurally modified graphene
Accurate prediction of the ammonia probes of a variable proton-to-electron mass ratio
NASA Astrophysics Data System (ADS)
Owens, A.; Yurchenko, S. N.; Thiel, W.; Špirko, V.
2015-07-01
A comprehensive study of the mass sensitivity of the vibration-rotation-inversion transitions of 14NH3, 15NH3, 14ND3 and 15ND3 is carried out variationally using the TROVE approach. Variational calculations are robust and accurate, offering a new way to compute sensitivity coefficients. Particular attention is paid to the Δk = ±3 transitions between the accidentally coinciding rotation-inversion energy levels of the ν2 = 0+, 0-, 1+ and 1- states, and the inversion transitions in the ν4 = 1 state affected by the `giant' l-type doubling effect. These transitions exhibit highly anomalous sensitivities, thus appearing as promising probes of a possible cosmological variation of the proton-to-electron mass ratio μ. Moreover, a simultaneous comparison of the calculated sensitivities reveals a sizeable isotopic dependence which could aid an exclusive ammonia detection.
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
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.
2015-01-01
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
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.
2015-08-28
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.
Electronic structure and correlation effects in actinides
Albers, R.C.
1998-12-01
This report consists of the vugraphs given at a conference on electronic structure. Topics discussed are electronic structure, f-bonding, crystal structure, and crystal structure stability of the actinides and how they are inter-related.
Electron Scattering and Nuclear Structure
ERIC Educational Resources Information Center
Trower, W. P.; Ficenec, J. R.
1971-01-01
Presents information about the nucleus gained by studies of electron scattering. Discusses what can be implied about the shape of the charge distribution, the nucleus positions, the vibrational modes of the nucleus, the momentum of the nucleus, and the granularity and core structures of the nucleus. (DS)
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.
Comparisons of Accurate Electronic, Transport, and Bulk Properties of XP (X = B, Al, Ga, In)
NASA Astrophysics Data System (ADS)
Malozovsky, Yuriy; Ejembi, John; Saliev, Azizjon; Franklin, Lashounda; Bagayoko, Diola
We present comparisons of results from ab-initio,self-consistent local density approximation (LDA) calculations of accurate, electronic and related properties of zinc blende XP (X =B, Al, Ga, In) phosphides. We implemented the linear combination of atomic orbitals following the Bagayoko, Zhao, and Williams (BZW) method as enhanced by Ekuma and Franklin (BZW-EF). Consequently, our results have the full physical content of DFT and agree very well with corresponding experimental ones [AIP Advances, 4, 127104 (2014)]. Our calculated, indirect band gap of 2.02 eV for BP, 2.56 eV for AlP, and of 2.29 eV for GaP, from Γ to X-point, are in excellent agreement with experimental values. Our calculated direct band gap of 1.43 eV, at Γ, for InP is also in an excellent agreement with experimental value. We discuss calculated electron and hole effective masses, total (DOS) and partial (pDOS) densities of states, and the bulk modulus of these phosphides. Acknowledgments: NSF and the Louisiana Board of Regents, LASiGMA [Award Nos. EPS- 1003897, NSF (2010-15)-RII-SUBR] and NSF HRD-1002541, DOE - National, Nuclear Security Administration (NNSA) (Award Nos. DE-NA0001861 and DE- NA0002630), LaSPACE, and LONI-SUBR.
Benzi, Caterina; Cossi, Maurizio; Barone, Vincenzo
2005-11-15
High-level ab initio g and A tensor components have been calculated for PD-tempone and tempo-palmitate (TP) radical spin probes dissolved in n-pentyl and n-hexyl cyanobiphenyl liquid crystals. Solvent effects have been included in the proposed approach by means of the polarizable continuum model, allowing for solvent anisotropy. An in-depth analysis of the electronic structure of probes was performed to choose a suitable model for TP and make the calculations more accessible. Computed magnetic tensor components have been compared with corresponding values measured in the rigid limit. The quality of the results suggests the use of quantum-mechanical data to determine the order parameter of the nematic from experimental electron-spin resonance measurements. PMID:16321115
Electronic structure of black sodalite
NASA Astrophysics Data System (ADS)
Sankey, Otto F.; Demkov, Alexander A.; Lenosky, Thomas
1998-06-01
The electronic structure of black sodalite, Na8(AlSiO4)6, is determined in the local-spin-density approximation (LSDA). This structure has six Na atoms to compensate the six Al atoms, leaving two excess Na atoms. A band-gap electronic state is induced in the wide oxide gap by the excess sodium, and has ``particle in a box'' behavior. Magnetic orderings of these gap states are studied. Analytic models show that an antiferromagnetic ordering is lowest in energy in the LSDA. A self-consistent LSDA calculation shows the system to change from a metal to an antiferromagnetic insulator when spin orderings are allowed. Hopping and Hubbard-U parameters are estimated, and the many-body correlated Hubbard model is solved using a constrained path Monte Carlo technique, which again predicts the system to be antiferromagnetic with a Tc of order 50 K.
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.
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
Knight, Joseph W; Wang, Xiaopeng; Gallandi, Lukas; Dolgounitcheva, Olga; Ren, Xinguo; Ortiz, J Vincent; Rinke, Patrick; Körzdörfer, Thomas; Marom, Noa
2016-02-01
The performance of different GW methods is assessed for a set of 24 organic acceptors. Errors are evaluated with respect to coupled cluster singles, doubles, and perturbative triples [CCSD(T)] reference data for the vertical ionization potentials (IPs) and electron affinities (EAs), extrapolated to the complete basis set limit. Additional comparisons are made to experimental data, where available. We consider fully self-consistent GW (scGW), partial self-consistency in the Green's function (scGW0), non-self-consistent G0W0 based on several mean-field starting points, and a "beyond GW" second-order screened exchange (SOSEX) correction to G0W0. We also describe the implementation of the self-consistent Coulomb hole with screened exchange method (COHSEX), which serves as one of the mean-field starting points. The best performers overall are G0W0+SOSEX and G0W0 based on an IP-tuned long-range corrected hybrid functional with the former being more accurate for EAs and the latter for IPs. Both provide a balanced treatment of localized vs delocalized states and valence spectra in good agreement with photoemission spectroscopy (PES) experiments. PMID:26731609
Meek, Garrett A; Levine, Benjamin G
2014-07-01
Spikes in the time-derivative coupling (TDC) near surface crossings make the accurate integration of the time-dependent Schrödinger equation in nonadiabatic molecular dynamics simulations a challenge. To address this issue, we present an approximation to the TDC based on a norm-preserving interpolation (NPI) of the adiabatic electronic wave functions within each time step. We apply NPI and two other schemes for computing the TDC in numerical simulations of the Landau-Zener model, comparing the simulated transfer probabilities to the exact solution. Though NPI does not require the analytical calculation of nonadiabatic coupling matrix elements, it consistently yields unsigned population transfer probability errors of ∼0.001, whereas analytical calculation of the TDC yields errors of 0.0-1.0 depending on the time step, the offset of the maximum in the TDC from the beginning of the time step, and the coupling strength. The approximation of Hammes-Schiffer and Tully yields errors intermediate between NPI and the analytical scheme. PMID:26279558
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 structure of graphite oxide
NASA Astrophysics Data System (ADS)
Jeong, Hae Kyung; Yang, Cheolsoo; Kim, Bong Soo; Kim, Ki-Jeong
2011-03-01
We have investigated the electronic structure of graphite oxide by photoelectron spectroscopy at the Pohang Accelerator Laboratory, Korea. The typical sp 2 hybridization states found in graphite were also seen in graphite oxide. However, the π state disappeared near the Fermi level because of bonding between the π and oxygen-related states originating from graphite oxide, indicating electron transfer from graphite to oxygen and resulting in a downward shift of the highest occupied molecular orbital (HOMO) state to higher binding energies. The band gap opening increased to about 1.8 eV, and additional oxygen-related peaks were observed at 8.5 and 27 eV. This research was supported by the Basic Science Program through the National Research Foundation of Korea (NRF), funded by the Ministry of Education, Science and Technology (2010-0004592), and partly by the MEST (2009-0087138). Experiments at the PLS were supported in part by POSTECH and MEST.
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.
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.
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.
Electronic structure of lithium amide
NASA Astrophysics Data System (ADS)
Kamakura, N.; Takeda, Y.; Saitoh, Y.; Yamagami, H.; Tsubota, M.; Paik, B.; Ichikawa, T.; Kojima, Y.; Muro, T.; Kato, Y.; Kinoshita, T.
2011-01-01
The electronic structure of the insulator lithium amide (LiNH2), which is a lightweight complex hydride being considered as a high-capacity hydrogen storage material, is investigated by N 1s soft x-ray emission spectroscopy (XES) and absorption spectroscopy (XAS). The XES and XAS spectra show a band gap between the valence and conduction bands. The valence band in the XES spectrum consists of three peaks, which extend up to ~-8 eV from the valence band top. The band calculation within the local-density approximation (LDA) for LiNH2shows energetically separated three peaks in the occupied N 2p partial density of states (pDOS) and the band gap. The energy distribution of three peaks in the XES spectrum agrees with that in the calculated pDOS except for the peak at the highest binding energy, which is attributed to the strongly hybridized state between N 2p and H 1s. The XES experiment has clarified that the strongly hybridized state with H 1s in LiNH2is located at binding energy higher than that of the LDA calculation, while the overall feature of the electronic structure of LiNH2experimentally obtained by XES and XAS is consistent with the calculated result.
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
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
Geng, Hao; Jiang, Fan; Wu, Yun-Dong
2016-05-19
Cyclic peptides (CPs) are promising candidates for drugs, chemical biology tools, and self-assembling nanomaterials. However, the development of reliable and accurate computational methods for their structure prediction has been challenging. Here, 20 all-trans CPs of 5-12 residues selected from Cambridge Structure Database have been simulated using replica-exchange molecular dynamics with four different force fields. Our recently developed residue-specific force fields RSFF1 and RSFF2 can correctly identify the crystal-like conformations of more than half CPs as the most populated conformation. The RSFF2 performs the best, which consistently predicts the crystal structures of 17 out of 20 CPs with rmsd < 1.1 Å. We also compared the backbone (ϕ, ψ) sampling of residues in CPs with those in short linear peptides and in globular proteins. In general, unlike linear peptides, CPs have local conformational free energies and entropies quite similar to globular proteins. PMID:27128113
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.
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.
Reeves, Patrick A.; Richards, Christopher M.
2009-01-01
Background Accurate inference of genetic discontinuities between populations is an essential component of intraspecific biodiversity and evolution studies, as well as associative genetics. The most widely-used methods to infer population structure are model-based, Bayesian MCMC procedures that minimize Hardy-Weinberg and linkage disequilibrium within subpopulations. These methods are useful, but suffer from large computational requirements and a dependence on modeling assumptions that may not be met in real data sets. Here we describe the development of a new approach, PCO-MC, which couples principal coordinate analysis to a clustering procedure for the inference of population structure from multilocus genotype data. Methodology/Principal Findings PCO-MC uses data from all principal coordinate axes simultaneously to calculate a multidimensional “density landscape”, from which the number of subpopulations, and the membership within subpopulations, is determined using a valley-seeking algorithm. Using extensive simulations, we show that this approach outperforms a Bayesian MCMC procedure when many loci (e.g. 100) are sampled, but that the Bayesian procedure is marginally superior with few loci (e.g. 10). When presented with sufficient data, PCO-MC accurately delineated subpopulations with population Fst values as low as 0.03 (G'st>0.2), whereas the limit of resolution of the Bayesian approach was Fst = 0.05 (G'st>0.35). Conclusions/Significance We draw a distinction between population structure inference for describing biodiversity as opposed to Type I error control in associative genetics. We suggest that discrete assignments, like those produced by PCO-MC, are appropriate for circumscribing units of biodiversity whereas expression of population structure as a continuous variable is more useful for case-control correction in structured association studies. PMID:19172174
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 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.
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
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. PMID:26931817
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.
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.
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.
Electronic structure of lithium tetraborate
NASA Astrophysics Data System (ADS)
Wooten, David J.
Due to many of its attributes, Li2B4O7 provides a possible material for incorporation as either a primary or companion material in future solid state neutron detectors. There is however a lack of fundamental characterization information regarding this useful material, particularly its electronic configuration. To address this, an investigation of Li2B4O7(110) and Li2B 4O7(100) was undertaken, utilizing photoemission and inverse photoemission spectroscopic techniques. The measured band gap depended on crystallographic direction with the band gaps ranging from 8.9+/-0.5 eV to 10.1+/-0.5 eV. The measurement yielded a density of states that qualitatively agreed with the theoretical results from model bulk band structure calculations for Li2B4O7; albeit with a larger band gap than predicted, but consistent with the known deficiencies of Local Density Approximation and Density Functional Theory calculations. The occupied states of both surfaces were extremely flat; to the degree that resolving periodic dispersion of the occupied states was inconclusive, within the resolution of the system. However, both surfaces demonstrated clear periodic dispersion within the empty states very close to theoretical Brillouin zone values. These attributes also translated to a lighter charge carrier effective mass in the unoccupied states. Of the two surfaces, Li2B4O 7(110) yielded the more consistent values in orthogonal directions for energy states. The presence of a bulk band gap surface state and image potential state in Li2B4O7(110) was indicative of a defect-free surface. The absence of both in the more polar, more dielectric Li2B4O7(100) was attributed to the presence of defects determined to be O vacancies. The results from Li2B 4O7(110) were indicative of a more stable surface than Li 2B4O7(100). In addition, Li 1s bulk and surface core level components were determined at the binding energies of -56.5+0.4 and -53.7+0.5 eV. Resonance features were observed along the [001
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.
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.
conSSert: Consensus SVM Model for Accurate Prediction of Ordered Secondary Structure.
Kieslich, Chris A; Smadbeck, James; Khoury, George A; Floudas, Christodoulos A
2016-03-28
Accurate prediction of protein secondary structure remains a crucial step in most approaches to the protein-folding problem, yet the prediction of ordered secondary structure, specifically beta-strands, remains a challenge. We developed a consensus secondary structure prediction method, conSSert, which is based on support vector machines (SVM) and provides exceptional accuracy for the prediction of beta-strands with QE accuracy of over 0.82 and a Q2-EH of 0.86. conSSert uses as input probabilities for the three types of secondary structure (helix, strand, and coil) that are predicted by four top performing methods: PSSpred, PSIPRED, SPINE-X, and RAPTOR. conSSert was trained/tested using 4261 protein chains from PDBSelect25, and 8632 chains from PISCES. Further validation was performed using targets from CASP9, CASP10, and CASP11. Our data suggest that poor performance in strand prediction is likely a result of training bias and not solely due to the nonlocal nature of beta-sheet contacts. conSSert is freely available for noncommercial use as a webservice: http://ares.tamu.edu/conSSert/ . PMID:26928531
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.
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.
Constantin, V; Carăp, A; Bobic, S; Pâun, I; Brâtilâ, E; Socea, B; Moroşanu, A-M; Mirancea, N
2015-01-01
Endometriosis is described as the presence of functioning endometrial tissue at sites outside the uterus. Up to 15% ofwomen in their reproductive period are affected by this condition. Endometriosis is mostly foundon the uterosacral ligaments, inside the rectovaginalseptum or vagina, in the rectosigmoid area, ovarianfossa, pelvic peritoneum, ureters, and bladder, causinga distortion of the pelvic anatomy. Colonic involvement is rare but is usually found at the level of the rectum or the sigmoid colon. Acute presentation with intestinal obstruction or perforation is rare. While malignant transformation of endometrial lesions is rare, findings of dysplasia on pathology sections can give rise to questions of management. Immunohistochemistry and electron microscopy can help decision making. We present the case of a 38 year old woman with intestinal obstruction caused by sigmoid colon endometriosis with moderate dysplasia in which transmission electron microscopy was used for postoperative diagnosis. Detailed analysis of these cases, while logistically difficult, can prove useful in understanding the etiology and pathophysiology of the disease. PMID:26531796
Ab-initio Calculations of Accurate Electronic Properties of ZnS
NASA Astrophysics Data System (ADS)
Khamala, Bethuel; Franklin, Loushanda; Malozovski, Yuriy; Stewart, Anthony; Bagayoko, Diola; Bagayoko Research Group Team
2014-03-01
We present the results from ab-initio, self consistent, local density approximation (LDA) calculations of the electronic and related properties of zinc-blende zinc sulphide (zb-ZnS). We employed the Ceperley and Alder LDA potential and the linear combination of atomic orbital (LCAO) formalism in our non-relativistic computations. The implementation of the LCAO formalism followed the Bagayoko, Zhao, and Williams method as enhanced by Ekuma and Franklin (BZW-EF). The BZW-EF method includes a methodical search for the optimal basis set that yields the minima of the occupied energies. This search entails increasing the size of the basis set and related modifications of angular symmetry and of radial orbitals. Our calculated, direct gap of 3.725 eV, at the Γ point, is in excellent agreement with experiment. We have also calculated the total (DOS) and partial (pDOS) densities of states, electron and hole effective masses and total energies that agree very well with available, corresponding experimental results. Acknowledgement: This research is funded in part by the National Science Foundation (NSF) and the Louisiana Board of Regents, through LASiGMA [Award Nos. EPS- 1003897, NSF (2010-15)-RII-SUBR] and NSF HRD-1002541, the US Department of Energy - National, Nuclear Security Administration (NNSA) (Award No. DE-NA0001861), LaSPACE, and LONI-SUBR.
Kieslich, Chris A.; Tamamis, Phanourios; Guzman, Yannis A.; Onel, Melis; Floudas, Christodoulos A.
2016-01-01
HIV-1 entry into host cells is mediated by interactions between the V3-loop of viral glycoprotein gp120 and chemokine receptor CCR5 or CXCR4, collectively known as HIV-1 coreceptors. Accurate genotypic prediction of coreceptor usage is of significant clinical interest and determination of the factors driving tropism has been the focus of extensive study. We have developed a method based on nonlinear support vector machines to elucidate the interacting residue pairs driving coreceptor usage and provide highly accurate coreceptor usage predictions. Our models utilize centroid-centroid interaction energies from computationally derived structures of the V3-loop:coreceptor complexes as primary features, while additional features based on established rules regarding V3-loop sequences are also investigated. We tested our method on 2455 V3-loop sequences of various lengths and subtypes, and produce a median area under the receiver operator curve of 0.977 based on 500 runs of 10-fold cross validation. Our study is the first to elucidate a small set of specific interacting residue pairs between the V3-loop and coreceptors capable of predicting coreceptor usage with high accuracy across major HIV-1 subtypes. The developed method has been implemented as a web tool named CRUSH, CoReceptor USage prediction for HIV-1, which is available at http://ares.tamu.edu/CRUSH/. PMID:26859389
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.
Robert, Stéphane; Battie, Yann; Jamon, Damien; Royer, Francois
2007-04-10
Optimal performances of integrated optical devices are obtained by the use of an accurate and reliable characterization method. The parameters of interest, i.e., optical indices and thickness of the waveguide structure, are calculated from effective indices by means of an inversion procedure. We demonstrate how an artificial neural network can achieve such a process. The artificial neural network used is a multilayer perceptron. The first result concerns a simulated anisotropic waveguide. The accuracy in the determination of optical indices and waveguide thickness is 5 x 10(-5) and 4 nm, respectively. Then an experimental application on a silica-titania thin film is performed. In addition, effective indices are measured by m-lines spectroscopy. Finally, a comparison with a classical optimization algorithm demonstrates the robustness of the neural method. PMID:17384718
Accurate Q-Value for the ^{74}Se Double Electron Capture Decay
Kolhinen, V. S.; Elomaa, V.-V.; Eronen, T.; Hakala, J.; Jokinen, A.; Kortelainen, M.; Suhonen, J.; Aysto, J.
2010-01-01
The Q value of the neutrinoless double electron capture (0{nu}ECEC) decay of ^{74}Se was measured by using the JYFLTRAP Penning trap. The determined value is 1209.169(49) keV, which practically excludes the possibility of a complete energy degeneracy with the second 2^{+} state (1204-205(7) keV) of ^{74}Ge in a resoant 0{nu}ECEC decay. We have also computed the associated nuclear matrix element by using a microscopic nuclear model with realistic two-nucleon interactions. The computed matrix element is found to be quite small. The failure of the resonant condition, combined with the small nuclear matrix element and needed p-wave capture, suppresses the decay rate strongly and thus excludes ^{74}Se as a possible candidate to search for resonant 0{nu}ECEC processes.
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.
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.
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.
Barone, Vincenzo; Biczysko, Malgorzata Bloino, Julien; Puzzarini, Cristina
2014-07-21
Oxirane derivatives are the most used benchmarks for chiroptical spectroscopies in view of their small size and relative rigidity. The molecular structure, vibrational harmonic and anharmonic frequencies, and infrared intensities of the ground electronic states are analyzed in this paper. Equilibrium structure and harmonic force fields have been evaluated by means of high-level quantum-chemical calculations at the coupled-cluster level including single and double excitations together with a perturbative treatment of triples (CCSD(T)). Extrapolation to the complete basis-set limit as well as core-correlation effects have also been taken into account. Anharmonic contributions have been computed at the CCSD(T)/cc-pVTZ level for trans-2,3-dideuterooxirane. These data can serve as references to evaluate the accuracy of less expensive computational approaches rooted in the density functional theory (DFT). The latter have been used within hybrid CC/DFT approaches, which have been applied to simulate fully anharmonic infrared (IR) spectra. Finally, the best theoretical estimates of the equilibrium structures and vibrational wavenumbers are compared to the most accurate experimental data and show in all cases very good agreement, i.e., within 0.001 Å, 0.1 deg, 10 cm{sup −1}, and 0.5 km mol{sup −1}, for bond lengths, angles, wavenumbers, and IR intensities, respectively.
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
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.
Accurate modeling of SiPM detectors coupled to FE electronics for timing performance analysis
NASA Astrophysics Data System (ADS)
Ciciriello, F.; Corsi, F.; Licciulli, F.; Marzocca, C.; Matarrese, G.; Del Guerra, A.; Bisogni, M. G.
2013-08-01
It has already been shown how the shape of the current pulse produced by a SiPM in response to an incident photon is sensibly affected by the characteristics of the front-end electronics (FEE) used to read out the detector. When the application requires to approach the best theoretical time performance of the detection system, the influence of all the parasitics associated to the coupling SiPM-FEE can play a relevant role and must be adequately modeled. In particular, it has been reported that the shape of the current pulse is affected by the parasitic inductance of the wiring connection between SiPM and FEE. In this contribution, we extend the validity of a previously presented SiPM model to account for the wiring inductance. Various combinations of the main performance parameters of the FEE (input resistance and bandwidth) have been simulated in order to evaluate their influence on the time accuracy of the detection system, when the time pick-off of each single event is extracted by means of a leading edge discriminator (LED) technique.
Ab-initio Calculations of Accurate Electronic Properties of Wurzite AlN
NASA Astrophysics Data System (ADS)
Nwigboji, Ifeanyi; Malozovsky, Yuriy; Bagayoko, Diola; Bagayoko Research Group Team
2014-03-01
We present results from ab-initio, self consistent local density approximation (LDA) calculations of electronic and related properties of wurtzite Aluminum Nitride (w-AlN). Our non-relativistic computations employed the Ceperley and Alder LDA potential and the linear combination of atomic orbital (LCAO) formalism. The implementation of the LCAO formalism followed the Bagayoko, Zhao, and Williams' method as enhanced by Ekuma and Franklin (BZW-EF). The BZW-EF method verifiably obtains the minima of the occupied energies; these minima provide the most variationally and physically valid density functional theory (DFT) description of the ground states of materials under study. Our preliminary results for w-AlN show that w-AlN has a direct band gap of 5.82 eV at the Γ point. The preliminary energy bands were obtained with a basis set comprising 48 functions. None of the several, larger basis sets tested to date led to occupied energies lower than those obtained with the above 48. While most previous LDA calculations are 2 eV smaller or more than the experimental value of 5.9 eV that is in excellent agreement with our finding, considering the typical experimental uncertainty of 0.2 eV for absorption measurements on AlN. We also discuss our calculated density of states (DOS) and partial densities of states (pDOS).
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.
About zitterbewegung and electron structure
NASA Astrophysics Data System (ADS)
Rodrigues, Waldyr A.; Vaz, Jayme; Recami, Erasmo; Salesi, Giovanni
1993-12-01
We start from the spinning electron model by Barut and Zanghi, which has been recently translated into the Clifford algebra language. We ``complete'' such a translation, first of all, by expressing in the Clifford formalism a particular Barut-Zanghi (BZ) solution, which refers (at the classical limit) to an ``internal'' helical motion with a time-like speed (and is here shown to originate from the superposition of positive and negative frequency solutions of the Dirac equation). Then, we show how to construct solutions of the Dirac equation describing helical motions with light-like speed, which meet very well the standard interpretation of the velocity operator in the Dirac equation theory (and agree with the solution proposed by Hestenes, on the basis - however - of ad-hoc assumptions that are unnecessary in the present approach). The above results appear to support the conjecture that the zitterbewegung motion (a helical motion, at the classical limit) is responsible for the electron spin.
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.
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
Discrete state model and accurate estimation of loop entropy of RNA secondary structures.
Zhang, Jian; Lin, Ming; Chen, Rong; Wang, Wei; Liang, Jie
2008-03-28
Conformational entropy makes important contribution to the stability and folding of RNA molecule, but it is challenging to either measure or compute conformational entropy associated with long loops. We develop optimized discrete k-state models of RNA backbone based on known RNA structures for computing entropy of loops, which are modeled as self-avoiding walks. To estimate entropy of hairpin, bulge, internal loop, and multibranch loop of long length (up to 50), we develop an efficient sampling method based on the sequential Monte Carlo principle. Our method considers excluded volume effect. It is general and can be applied to calculating entropy of loops with longer length and arbitrary complexity. For loops of short length, our results are in good agreement with a recent theoretical model and experimental measurement. For long loops, our estimated entropy of hairpin loops is in excellent agreement with the Jacobson-Stockmayer extrapolation model. However, for bulge loops and more complex secondary structures such as internal and multibranch loops, we find that the Jacobson-Stockmayer extrapolation model has large errors. Based on estimated entropy, we have developed empirical formulae for accurate calculation of entropy of long loops in different secondary structures. Our study on the effect of asymmetric size of loops suggest that loop entropy of internal loops is largely determined by the total loop length, and is only marginally affected by the asymmetric size of the two loops. Our finding suggests that the significant asymmetric effects of loop length in internal loops measured by experiments are likely to be partially enthalpic. Our method can be applied to develop improved energy parameters important for studying RNA stability and folding, and for predicting RNA secondary and tertiary structures. The discrete model and the program used to calculate loop entropy can be downloaded at http://gila.bioengr.uic.edu/resources/RNA.html. PMID:18376982
Electron-phonon renormalization of the electronic structure of diamond
NASA Astrophysics Data System (ADS)
Giustino, Feliciano; Louie, Steven G.; Cohen, Marvin L.
2011-03-01
The calculation of band structures from first-principles has reached a high level of accuracy. Calculations combining density-functional theory with many-body perturbation theory often are in good agreement with measurements by photoemission, tunneling, and other spectroscopic probes. While significant efforts have been devoted to improving the description of electron-electron interactions in these calculations, the effect of lattice vibrations has largely been overlooked so far. In this work we study from first principles the electron-phonon renormalization of the band gap of diamond. The calculated temperature dependence of the gap and the broadening of the absorption edge are in excellent agreement with spectroscopic ellipsometry data. Interestingly we find a gap renormalization due to zero-point vibrations as large as 0.6 eV. We discuss the implications of our findings for the electronic structure of other carbon-based bulk materials and nanostructures.
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
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)
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.
Electronic structure and photophysical properties of polyimides
LaFemina, J.P.; Kafafi, S.A.
1992-04-01
The quantum mechanical AM1 and CNDO/S3 models were used to examine the effect of isoelectronic substitutions on the conformation, electronic structure, and optical absorption spectra for a series of aromatic polyimides. An analysis of the geometric changes at the substitution site and its effect on the electronic structure allowed for the prediction of changes in the ICT band of the optical absorption spectra.
MCSNA: Experimental Benchmarking of Pu Electronic Structure
Tobin, J G
2007-01-29
The objective of this work is to develop and/or apply advanced diagnostics to the understanding of aging of Pu. Advanced characterization techniques such as photoelectron and x-ray absorption spectroscopy will provide fundamental data on the electronic structure of Pu phases. These data are crucial for the validation of the electronic structure methods. The fundamental goal of this project is to narrow the parameter space for the theoretical modeling of Pu aging. The short-term goal is to perform experiments to validate electronic structure calculations of Pu. The long-term goal is to determine the effects of aging upon the electronic structure of Pu. Many of the input parameters for aging models are not directly measurable. These parameters will need to be calculated or estimated. Thus a First Principles-Approach Theory is needed, but it is unclear what terms are important in the Hamiltonian. (H{Psi} = E{Psi}) Therefore, experimental data concerning the 5f electronic structure are needed, to determine which terms in the Hamiltonian are important. The data obtained in this task are crucial for reducing the uncertainty of Task LL-01-developed models and predictions. The data impact the validation of electronic structure methods, the calculation of defect properties, the evaluation of helium diffusion, and the validation of void nucleation models. The importance of these activities increases if difficulties develop with the accelerating aging alloy approach.
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
Structural stability augmentation system design using BODEDIRECT: A quick and accurate approach
NASA Technical Reports Server (NTRS)
Goslin, T. J.; Ho, J. K.
1989-01-01
A methodology is presented for a modal suppression control law design using flight test data instead of mathematical models to obtain the required gain and phase information about the flexible airplane. This approach is referred to as BODEDIRECT. The purpose of the BODEDIRECT program is to provide a method of analyzing the modal phase relationships measured directly from the airplane. These measurements can be achieved with a frequency sweep at the control surface input while measuring the outputs of interest. The measured Bode-models can be used directly for analysis in the frequency domain, and for control law design. Besides providing a more accurate representation for the system inputs and outputs of interest, this method is quick and relatively inexpensive. To date, the BODEDIRECT program has been tested and verified for computational integrity. Its capabilities include calculation of series, parallel and loop closure connections between Bode-model representations. System PSD, together with gain and phase margins of stability may be calculated for successive loop closures of multi-input/multi-output systems. Current plans include extensive flight testing to obtain a Bode-model representation of a commercial aircraft for design of a structural stability augmentation system.
Fang, Tao; Li, Wei; Gu, Fangwei; Li, Shuhua
2015-01-13
We extend the generalized energy-based fragmentation (GEBF) approach to molecular crystals under periodic boundary conditions (PBC), and we demonstrate the performance of the method for a variety of molecular crystals. With this approach, the lattice energy of a molecular crystal can be obtained from the energies of a series of embedded subsystems, which can be computed with existing advanced molecular quantum chemistry methods. The use of the field compensation method allows the method to take long-range electrostatic interaction of the infinite crystal environment into account and make the method almost translationally invariant. The computational cost of the present method scales linearly with the number of molecules in the unit cell. Illustrative applications demonstrate that the PBC-GEBF method with explicitly correlated quantum chemistry methods is capable of providing accurate descriptions on the lattice energies and structures for various types of molecular crystals. In addition, this approach can be employed to quantify the contributions of various intermolecular interactions to the theoretical lattice energy. Such qualitative understanding is very useful for rational design of molecular crystals. PMID:26574207
Sharma, Virag; Elghafari, Anas; Hiller, Michael
2016-01-01
Identifying coding genes is an essential step in genome annotation. Here, we utilize existing whole genome alignments to detect conserved coding exons and then map gene annotations from one genome to many aligned genomes. We show that genome alignments contain thousands of spurious frameshifts and splice site mutations in exons that are truly conserved. To overcome these limitations, we have developed CESAR (Coding Exon-Structure Aware Realigner) that realigns coding exons, while considering reading frame and splice sites of each exon. CESAR effectively avoids spurious frameshifts in conserved genes and detects 91% of shifted splice sites. This results in the identification of thousands of additional conserved exons and 99% of the exons that lack inactivating mutations match real exons. Finally, to demonstrate the potential of using CESAR for comparative gene annotation, we applied it to 188 788 exons of 19 865 human genes to annotate human genes in 99 other vertebrates. These comparative gene annotations are available as a resource (http://bds.mpi-cbg.de/hillerlab/CESAR/). CESAR (https://github.com/hillerlab/CESAR/) can readily be applied to other alignments to accurately annotate coding genes in many other vertebrate and invertebrate genomes. PMID:27016733
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. PMID:26833260
Foil support structure for large electron guns
Brucker, J.P.; Rose, E.A.
1993-08-01
This paper describes a novel support structure for a vacuum diode used to pump a gaseous laser with an electron beam. Conventional support structures are designed to hold a foil flat and rigid. This new structure takes advantage of the significantly greater strength of metals in pure tension, utilizing curved shapes for both foil and support structure. The shape of the foil is comparable to the skin of a balloon, and the shape of the support structures is comparable to the cables of a suspension bridge. This design allows a significant reduction in foil thickness and support structure mass, resulting in a lower electron-beam loss between diode and laser gas. In addition, the foil is pre-formed in the support structure at pressures higher than operating pressure. Therefore, the foil is operated far from the yield point. Increased reliability is anticipated.
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.
Fazio, Massimo A.; Bruno, Luigi; Reynaud, Juan F.; Poggialini, Andrea; Downs, J. Crawford
2012-01-01
We proposed and validated a compensation method that accounts for the optical distortion inherent in measuring displacements on specimens immersed in aqueous solution. A spherically-shaped rubber specimen was mounted and pressurized on a custom apparatus, with the resulting surface displacements recorded using electronic speckle pattern interferometry (ESPI). Point-to-point light direction computation is achieved by a ray-tracing strategy coupled with customized B-spline-based analytical representation of the specimen shape. The compensation method reduced the mean magnitude of the displacement error induced by the optical distortion from 35% to 3%, and ESPI displacement measurement repeatability showed a mean variance of 16 nm at the 95% confidence level for immersed specimens. The ESPI interferometer and numerical data analysis procedure presented herein provide reliable, accurate, and repeatable measurement of sub-micrometer deformations obtained from pressurization tests of spherically-shaped specimens immersed in aqueous salt solution. This method can be used to quantify small deformations in biological tissue samples under load, while maintaining the hydration necessary to ensure accurate material property assessment. PMID:22435090
Gaggiotti, Oscar E
2010-11-01
Ever since the introduction of allozymes in the 1960s, evolutionary biologists and ecologists have continued to search for more powerful molecular markers to estimate important parameters such as effective population size and migration rates and to make inferences about the demographic history of populations, the relationships between individuals and the genetic architecture of phenotypic variation (Bensch & Akesson 2005; Bonin et al. 2007). Choosing a marker requires a thorough consideration of the trade-offs associated with the different techniques and the type of data obtained from them. Some markers can be very informative but require substantial amounts of start-up time (e.g. microsatellites), while others require very little time but are much less polymorphic. Amplified fragment length polymorphism (AFLP) is a firmly established molecular marker technique that falls in this latter category. AFLPs are widely distributed throughout the genome and can be used on organisms for which there is no a priori sequence information (Meudt & Clarke 2007). These properties together with their moderate cost and short start-up time have made them the method of choice for many molecular ecology studies of wild species (Bensch & Akesson 2005). However, they have a major disadvantage, they are dominant. This represents a very important limitation because many statistical genetics methods appropriate for molecular ecology studies require the use of codominant markers. In this issue, Foll et al. (2010) present an innovative hierarchical Bayesian method that overcomes this limitation. The proposed approach represents a comprehensive statistical treatment of the fluorescence of AFLP bands and leads to accurate inferences about the genetic structure of natural populations. Besides allowing a quasi-codominant treatment of AFLPs, this new method also solves the difficult problems posed by subjectivity in the scoring of AFLP bands. PMID:20958811
Nicolotti, Orazio; Gillet, Valerie J; Fleming, Peter J; Green, Darren V S
2002-11-01
Deriving quantitative structure-activity relationship (QSAR) models that are accurate, reliable, and easily interpretable is a difficult task. In this study, two new methods have been developed that aim to find useful QSAR models that represent an appropriate balance between model accuracy and complexity. Both methods are based on genetic programming (GP). The first method, referred to as genetic QSAR (or GPQSAR), uses a penalty function to control model complexity. GPQSAR is designed to derive a single linear model that represents an appropriate balance between the variance and the number of descriptors selected for the model. The second method, referred to as multiobjective genetic QSAR (MoQSAR), is based on multiobjective GP and represents a new way of thinking of QSAR. Specifically, QSAR is considered as a multiobjective optimization problem that comprises a number of competitive objectives. Typical objectives include model fitting, the total number of terms, and the occurrence of nonlinear terms. MoQSAR results in a family of equivalent QSAR models where each QSAR represents a different tradeoff in the objectives. A practical consideration often overlooked in QSAR studies is the need for the model to promote an understanding of the biochemical response under investigation. To accomplish this, chemically intuitive descriptors are needed but do not always give rise to statistically robust models. This problem is addressed by the addition of a further objective, called chemical desirability, that aims to reward models that consist of descriptors that are easily interpretable by chemists. GPQSAR and MoQSAR have been tested on various data sets including the Selwood data set and two different solubility data sets. The study demonstrates that the MoQSAR method is able to find models that are at least as good as models derived using standard statistical approaches and also yields models that allow a medicinal chemist to trade statistical robustness for chemical
The Electronic Structure of Amorphous Carbon Nanodots.
Margraf, Johannes T; Strauss, Volker; Guldi, Dirk M; Clark, Timothy
2015-06-18
We have studied hydrogen-passivated amorphous carbon nanostructures with semiempirical molecular orbital theory in order to provide an understanding of the factors that affect their electronic properties. Amorphous structures were first constructed using periodic calculations in a melt/quench protocol. Pure periodic amorphous carbon structures and their counterparts doped with nitrogen and/or oxygen feature large electronic band gaps. Surprisingly, descriptors such as the elemental composition and the number of sp(3)-atoms only influence the electronic structure weakly. Instead, the exact topology of the sp(2)-network in terms of effective conjugation defines the band gap. Amorphous carbon nanodots of different structures and sizes were cut out of the periodic structures. Our calculations predict the occurrence of localized electronic surface states, which give rise to interesting effects such as amphoteric reactivity and predicted optical band gaps in the near-UV/visible range. Optical and electronic gaps display a dependence on particle size similar to that of inorganic colloidal quantum dots. PMID:25731776
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.
Structure and Dynamics with Ultrafast Electron Microscopes
NASA Astrophysics Data System (ADS)
Siwick, Bradley
In this talk I will describe how combining ultrafast lasers and electron microscopes in novel ways makes it possible to directly `watch' the time-evolving structure of condensed matter, both at the level of atomic-scale structural rearrangements in the unit cell and at the level of a material's nano- microstructure. First, I will briefly describe my group's efforts to develop ultrafast electron diffraction using radio- frequency compressed electron pulses in the 100keV range, a system that rivals the capabilities of xray free electron lasers for diffraction experiments. I will give several examples of the new kinds of information that can be gleaned from such experiments. In vanadium dioxide we have mapped the detailed reorganization of the unit cell during the much debated insulator-metal transition. In particular, we have been able to identify and separate lattice structural changes from valence charge density redistribution in the material on the ultrafast timescale. In doing so we uncovered a previously unreported optically accessible phase/state of vanadium dioxide that has monoclinic crystallography like the insulator, but electronic structure and properties that are more like the rutile metal. We have also combined these dynamic structural measurements with broadband ultrafast spectroscopy to make detailed connections between structure and properties for the photoinduced insulator to metal transition. Second, I will show how dynamic transmission electron microscopy (DTEM) can be used to make direct, real space images of nano-microstructural evolution during laser-induced crystallization of amorphous semiconductors at unprecedented spatio-temporal resolution. This is a remarkably complex process that involves several distinct modes of crystal growth and the development of intricate microstructural patterns on the nanosecond to ten microsecond timescales all of which can be imaged directly with DTEM.
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.
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
Membrane protein structure determination by electron crystallography
Ubarretxena-Belandia, Iban; Stokes, David L.
2012-01-01
During the past year, electron crystallography of membrane proteins has provided structural insights into the mechanism of several different transporters and into their interactions with lipid molecules within the bilayer. From a technical perspective there have been important advances in high-throughput screening of crystallization trials and in automated imaging of membrane crystals with the electron microscope. There have also been key developments in software, and in molecular replacement and phase extension methods designed to facilitate the process of structure determination. PMID:22572457
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.
Supersampling method for efficient grid-based electronic structure calculations.
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. PMID:26957151
NASA Astrophysics Data System (ADS)
Shen, C.; Wu, C.; Gallet, S.; Cheng, H.; Edwards, R.; Hsieh, Y.; Lin, K.
2008-12-01
Contemporary multicollector-inductively coupled plasma mass spectrometry (MC-ICP-MS) with discrete dynode secondary electron multipliers (SEMs) can offer U-Th isotopic determinations with subpermil-permil- level precision in femtogram quantities. However, accurate isotopic measurement requires fully understanding SEM mass and intensity biases. In additional to dead-time effect, Richter et al (2001, Int. J. Mass Spectrom., 206, 105-127) reported a nonlinearity on SEMs produced by ETP and MasCom for count rates > 20 thousand counts per second (cps). We evaluated the possible biases for ion beams of 500- 1,600,000 cps on a latest MasCom SEM, SEV TE-Z/17, with more effective ion optical acceptance area (>50%) and better peak shape than previous models, used in a MC-ICP-MS, Thermo Fisher NEPTUNE. With the retarding potential quadruple lens (RPQ) turned off, ion beam intensity can be biased by only dead- time effect, which can be precisely corrected online or offline. With the RPQ on, two additional biases, an exponential-like increase of ion beam intensity from 100-100,000 s cps and an apparent dead-time effect (-2 to 2 ns) at high count rates, are observed. They are likely caused by the slightly defocused ions with a wide kinetic energy spread of ~5 eV, 10 times worse than that with thermal source, passing through the RPQ lens to the SEM, which is installed behind the focal plane. Fortunately, the two biases, which are stable during the daily measurements with the same settings of inlet system, source lenses, zoom optics, and RPQ, can be corrected effectively offline to earn accurate U-Th isotopic measurement.
NASA Astrophysics Data System (ADS)
Hiraiwa, Atsushi; Nishida, Akio
2012-03-01
The control of line-edge or line-width roughness (LER/LWR) is a challenge especially for future devices that are fabricated using extreme-ultraviolet lithography. Accurate analysis of the LER/LWR plays an essential role in this challenge and requires the noise involved in scanning-electron-microscope (SEM) images to be reduced by appropriate image processing prior to analyses. In order to achieve this, the authors simulated SEM images using the Monte-Carlo method and detected line edges in experimental and these theoretical images after noise filtering using new imageanalysis software. The validity of these simulation and software was confirmed by a good agreement between the experimental and theoretical results. In the case when the image pixels aligned perpendicular (crosswise) to line edges were averaged, the variance var(φ) that was additionally induced by the image noise decreased with the number NPIX,X of averaged pixels but turned to increase for relatively large NPIX,X's. Real LER/LWR, however, remained unaffected. On the other hand, averaging image pixels aligned parallel (longitudinal) to line edges not only reduced var(φ) but smoothed the real LER/LWR. As a result, the nominal variance of the real LWR, obtained using simple arithmetic, monotonically decreased with the number NPIX,L of averaged pixels. Artifactual oscillations were additionally observed in power spectral densities. var(φ) in this case decreased in an inverse proportion to the square root of NPIX,L according to the statistical mechanism clarified here. In this way, image processing has a marked effect on the LER/LWR analysis and needs to be much more cared and appropriately applied. All the aforementioned results not only constitute a solid basis of but improve previous empirical instructions for accurate analyses. The most important instruction is to avoid the longitudinal averaging and to crosswise average an optimized number of image pixels consulting the equation derived in this
Interdependence of spin structure, anion height and electronic structure of BaFe2As2
NASA Astrophysics Data System (ADS)
Sen, Smritijit; Ghosh, Haranath
2016-05-01
Superconducting as well as other electronic properties of Fe-based superconductors are quite sensitive to the structural parameters specially, on anion height which is intimately related to zAs, the fractional z co-ordinate of As atom. Due to presence of strong magnetic fluctuation in these Fe-based superconductors, optimized structural parameters (lattice parameters a, b, c) including zAs using density functional theory (DFT) under generalized gradient approximation (GGA) does not match experimental values accurately. In this work, we show that the optimized value of zAs is strongly influenced by the spin structures in the orthorhombic phase of BaFe2As2 system. We take all possible spin structures for the orthorhombic BaFe2As2 system and then optimize zAs. Using these optimized structures we calculate electronic structures like density of states, band structures etc., for each spin configurations. From these studies we show that the electronic structure, orbital order which is responsible for structural as well as related to nematic transition, are significantly influenced by the spin structures.
Electronic structure in the crossover regimes in lower dimensional structures
NASA Astrophysics Data System (ADS)
Batabyal, R.; Dev, B. N.
2014-11-01
Modern growth and fabrication techniques can produce lower dimensional structures in the crossover regimes. Such structures in the crossover regimes can provide tunability of various properties of materials. For example, a zero-dimensional (0-D) structure (quantum dot) evolving towards a 3-D structure (bulk) shows electronic structure, which is neither 0-D-like, nor 3-D-like in the dimensional crossover regime. Within the crossover regime the electronic density of states (DOS) at Fermi level (Ef) keeps on changing as the size of the system changes. DOS at Ef determines many properties of materials, such as electronic specific heat, spin susceptibility, etc. Such properties can be tuned by controlling the size of the system in the crossover regimes. Keeping the importance of DOS at Ef in mind, we determine their values and other details of electronic structure of lower dimensional structures, in the 0-D to 1-D, 1-D to 2-D, 2-D to 3-D, 0-D to 2-D, 0-D to 3-D and 1-D to 3-D crossover regimes, in a simple free electron model. We compare our results with analytical theory and experimental results, wherever available. We also present some results obtained by scanning tunneling spectroscopy measurements on Ag islands on Si(1 1 1) substrates evolving from a 0-D to a 2-D structure. This simple model is quite useful in understanding lower dimensional structures in the crossover regimes and, in general, in nanoscale science. Fabrication of such structures would provide control on materials properties.
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
Structure refinement from precession electron diffraction data.
Palatinus, Lukáš; Jacob, Damien; Cuvillier, Priscille; Klementová, Mariana; Sinkler, Wharton; Marks, Laurence D
2013-03-01
Electron diffraction is a unique tool for analysing the crystal structures of very small crystals. In particular, precession electron diffraction has been shown to be a useful method for ab initio structure solution. In this work it is demonstrated that precession electron diffraction data can also be successfully used for structure refinement, if the dynamical theory of diffraction is used for the calculation of diffracted intensities. The method is demonstrated on data from three materials - silicon, orthopyroxene (Mg,Fe)(2)Si(2)O(6) and gallium-indium tin oxide (Ga,In)(4)Sn(2)O(10). In particular, it is shown that atomic occupancies of mixed crystallographic sites can be refined to an accuracy approaching X-ray or neutron diffraction methods. In comparison with conventional electron diffraction data, the refinement against precession diffraction data yields significantly lower figures of merit, higher accuracy of refined parameters, much broader radii of convergence, especially for the thickness and orientation of the sample, and significantly reduced correlations between the structure parameters. The full dynamical refinement is compared with refinement using kinematical and two-beam approximations, and is shown to be superior to the latter two. PMID:23403968
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. PMID:27334095
Electronic structure and electron momentum density in TiSi
NASA Astrophysics Data System (ADS)
Ghaleb, A. M.; Mohammad, F. M.; Sahariya, Jagrati; Sharma, Mukesh; Ahuja, B. L.
2013-03-01
We report the electron momentum density in titanium monosilicide using 241Am Compton spectrometer. Experimental Compton profile has been compared with the theoretical profiles computed using linear combination of atomic orbitals (LCAO). The energy bands, density of states and Fermi surface structures of TiSi are reported using the LCAO and the full potential linearized augmented plane wave methods. Theoretical anisotropies in directional Compton profiles are interpreted in terms of energy bands. To confirm the conducting behavior, we also report the real space analysis of experimental Compton profile of TiSi.
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.
Structural and electronic properties of GaAsBi
NASA Astrophysics Data System (ADS)
Achour, H.; Louhibi, S.; Amrani, B.; Tebboune, A.; Sekkal, N.
2008-08-01
The structural and electronic properties of the GaAs 1- xBi x ternary alloy are investigated by means of two first principles and full potential methods, the linear augmented plane waves (FPLAPW) method and a recent version of the full potential linear muffin-tin orbitals method (FPLMTO) which enables an accurate treatment of the interstitial regions. In particular, we have found that the maximal GaBi mole fraction x for which GaBi xAs 1- x remains a semiconductor is probably around x=0.5. The electronic properties of (GaAs) m/(GaBi) n quantum well superlattices (SLs) have also been calculated and it is found that such SLs are semiconductors when m is larger or equal to n.
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.
NASA Astrophysics Data System (ADS)
Hiraiwa, Atsushi; Nishida, Akio
2012-10-01
The control of line-edge or line-width roughness (LER/LWR) is a challenge, especially for future devices that are fabricated using extreme-ultraviolet (EUV) lithography. Accurate analysis of the LER/LWR plays an essential role in this challenge and requires the noise involved in scanning-electron-microscope (SEM) images to be reduced by appropriate noise filtering prior to analysis. To achieve this, we simulated the SEM images using a Monte Carlo method, and detected line edges in both experimental and theoretical images after noise filtering using new image-analysis software. The validity of this software and these simulations was confirmed by a good agreement between the experimental and theoretical results. In the case when the image pixels aligned perpendicular (crosswise) to line edges were averaged, the variance var(φ) that was additionally induced by the image noise decreased with a number N of averaged pixels, with exceptions when N was relatively large, whereupon the variance increased. The optimal N to minimize var(φ) was formulated based on a statistical mechanism of this change. LER/LWR statistics estimated using the crosswise filtering remained unaffected when N was smaller than the aforementioned optimal value, but monotonically changed when N was larger contrary to expectations. This change was possibly caused by an asymmetric scan-signal profile at edges. On the other hand, averaging image pixels aligned parallel (longitudinal) to line edges not only reduced var(φ) but smoothed real LER/LWR. As a result, the nominal variance of real LWR, obtained using simple arithmetic, monotonically decreased with a number N of averaged pixels. Artifactual oscillations were additionally observed in power spectral densities. Var(φ) in this case decreased in inverse proportion to the square root of N according to the statistical mechanism clarified here. In this way, the noise filtering has a marked effect on the LER/LWR analysis and needs to be appropriately
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
Electronic structures of carbon nanotube peopods
NASA Astrophysics Data System (ADS)
Kuk, Young
2003-03-01
Carbon nanotubes have been successfully used for nanometer-sized devices such as diodes and transistors. These discrete devices utilize the spatially varying electronic structures of processed nanotubes by creating defect junctions or introducing substitutional or interstitial dopants. It was recently found that adsorption or insertion of molecules inside or outside of a nanotube modifies the electronic structure as observed with a low-temperature scanning tunneling microscope (LTSTM). We report a method to form spatial variation of the electronic structure by inserting various molecules such as fullerenes, metallo-fullerenes, metals or insulators. The results suggest that one can synthesize this band gap-engineered 1-dimensional wire by self-assembly instead of epitaxial growth. We propose a new type of device structure made by this processing technology. 1. J. Lee, H.J. Kim, G. Kim, Y.-W. Son, J. Ihm, S.J. Kahng, H. Kato, Z.W. Wang, T. Okazaki, H. Shinohara, and Y. Kuk, Nature, 415, 1005 (2002)
Electronic structure theory: Applications and geometrical aspects
NASA Astrophysics Data System (ADS)
Coh, Sinisa
This thesis contains several applications of the first-principles electronic-structure theory with special emphasis in parts of the thesis on the geometrical aspects of the theory. We start by reviewing the basics of the first-principles electronic-structure methods which are then used throughout the thesis. The first application of these methods is on the analysis of the stability and lattice dynamics of alpha- and beta-cristobalite phases of SiO2. We also map the complete low-energy landscape connecting these two structures and give implications on the phase transition in this compound. Next we study a family of Pbnm perovskites that are promising candidates for silicon-compatible high-K dielectrics. We calculate their structure and dielectric response, and compare with experimental results where available. The third application of these methods is to the large isosymmetric reorientation of oxygen octahedra rotation axes in epitaxially strained perovskites. We explain the origin of the peculiar energy landscape topology as a function of epitaxial strain. In the part of the thesis devoted to the geometrical aspects of electronic structure theory, we begin by extending the concept of electronic polarization to a Chern insulators. These insulators are characterized by a non-zero off-diagonal sigma_xy conductivity tensor component, quantized in units of e 2/h. Finally we discuss another geometrical quantity, the Chern-Simons orbital magnetoelectric coupling. We present a first-principles based calculation of this quantity in several compounds, and motivated by recent developments in the theory of topological insulators, we speculate about the existence of "large-theta materials," in which this kind of coupling could be unusually large.
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
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.
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.
Lagrange-Function Approach to Real-Space Order-N Electronic-Structure Calculations
Varga, Kalman; Pantelides, Sokrates T
2006-01-01
The Lagrange functions are a family of analytical, complete, and orthonormal basis sets that are suitable for efficient, accurate, real-space, order-N electronic-structure calculations. Convergence is controlled by a single monotonic parameter, the dimension of the basis set, and computational complexity is lower than that of conventional approaches. In this paper we review their construction and applications in linearscaling electronic-structure calculations.
Electronic structure of oxygen functionalized graphene nanoribbons
NASA Astrophysics Data System (ADS)
Simbeck, Adam; Gu, Deyang; Kharche, Neerav; Nayak, Saroj
2013-03-01
We investigate the electronic and magnetic properties of armchair graphene nanoribbons whose edges are passivated by oxygen. Using a first-principles density functional approach and the many-body GW method we find that oxygen-passivation results in a rich geometrical environment which in turn determines the electronic and magnetic properties of the ribbon. For planar systems we report magnetic ground states whose electronic structure depends upon the magnetic coupling between edges. For non-planar ribbons we report a nonmagnetic ground state with a band gap that decreases as a function of increasing ribbon width. Our results will be discussed in light of previous experimental and computational studies. Interconnect Focus Center (MARCO program), State of New York, NSF IGERT program, Grant no. 0333314, and computing resources of the Computationial Center for Nanotechnology Innovation (CCNI), RPI
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
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 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.
Electronic structure tuning of diamondoids through functionalization
NASA Astrophysics Data System (ADS)
Rander, Torbjörn; Staiger, Matthias; Richter, Robert; Zimmermann, Tobias; Landt, Lasse; Wolter, David; Dahl, Jeremy E.; Carlson, Robert M. K.; Tkachenko, Boryslav A.; Fokina, Natalie A.; Schreiner, Peter R.; Möller, Thomas; Bostedt, Christoph
2013-01-01
We investigated the changes in electronic structures induced by chemical functionalization of the five smallest diamondoids using valence photoelectron spectroscopy. Through the variation of three parameters, namely functional group (thiol, hydroxy, and amino), host cluster size (adamantane, diamantane, triamantane, [121]tetramantane, and [1(2,3)4]pentamantane), and functionalization site (apical and medial) we are able to determine to what degree these affect the electronic structures of the overall systems. We show that unlike, for example, in the case of halobenzenes, the ionization potential does not show a linear dependence on the electronegativity of the functional group. Instead, a linear correlation exists between the HOMO-1 ionization potential and the functional group electronegativity. This is due to localization of the HOMO on the functional group and the HOMO-1 on the diamondoid cage. Density functional theory supports our interpretations.
Structural and electronic properties of sodium nanoclusters
NASA Astrophysics Data System (ADS)
Perez, Luis A.; Reyes-Nava, Juan A.; Garzon, Ignacio L.
2006-03-01
Recent advances on mass selection of sodium nanoclusters and their characterization by photoemission electron spectroscopy [1] have given useful data for a variety of clusters sizes. These data may lead to assignments of the relevant structures by comparing the measured photoelectron spectra (PES) with the electronic density of states (DOS) obtained from DFT calculations. In this work, the lowest energy structures modeled by the many-body Gupta potential, are obtained by using molecular dynamics simulations for Nan (n= 178, 204, 271, 298-300, 309). DFT calculations were then performed for neutral, positively- and negatively-charged Nan clusters. A comparison between the DOS of clusters of the same size but different charge will be presented, as well as between the available experimental PES and the theoretical obtained DOS.[1] H. Haberland, T. Hippler, J. Donges, O. Kostko, M. Schmidt, B. von Issendorff, Phys. Rev. Lett. 94, 035701 (2005).
Peterson, Kirk A
2000-09-15
A global, analytical potential energy surface for the ground electronic state of HOBr has been determined using highly correlated multireference configuration interaction wave functions and explicit basis set extrapolations of large correlation consistent basis sets. The ab initio data have been fit to an analytical functional form that accurately includes both the HOBr and HBrO minima, as well as all dissociation asymptotes. Small adjustments to this surface are made based on the limited experimental data available and by indirectly taking into account the effects of spin-orbit coupling on the OH+Br dissociation channel. Vibrational energy levels are calculated variationally for both HOBr and HBrO up to the OH+Br dissociation limit using a truncation/recoupling method. The HOBr isomer is calculated to contain 708 bound vibrational energy levels, while the HBrO minimum lies above the OH+Br dissociation limit but is calculated to have 74 ''quasibound,'' localized eigenstates. Infrared intensities for all of these vibrational transitions are also calculated using MRCI dipole moment functions. The assignment of the HOBr states is complicated by strong stretch-bend resonances even at relatively low energies. In contrast to the HOCl case, these state mixings made it particularly difficult to assign the relatively intense OH overtone bands above v{sub 1}=2. The vibrational density of states of HOBr at the OH+Br dissociation limit is determined to be 0.16 states/cm-1. Comparisons to recent work on HOCl using similar methods are made throughout. (c) 2000 American Institute of Physics.
An Accurate Global Ab Initio Potential Energy Surface for the X(1)A' Electronic State of HOBr
Peterson, Kirk A.
1999-12-01
A global, analytical potential energy surface for the ground electronic state of HOBr has been determined using highly correlated multireference configuration interaction wave functions and explicit basis set extrapolations of large correlation consistent basis sets. The ab initio data have been fit to an analytical functional form that accurately includes both the HOBr and HBrO minima, as well as all dissociation asymptotes. Small adjustments to this surface are made based on the limited experimental data available and by indirectly taking into account the effects of spin-orbit coupling on the OH+Br dissociation channel. Vibrational energy levels are calculated variationally for both HOBr and HBrO up to the OH+Br dissociation limit using a truncation-recoupling method. The HOBr isomer is calculated to contain 708 bound vibrational energy levels, while the HBrO minimum lies above the OH+Br dissociation limit but is calculated to have 74 quasibound, localized eigenstates. Infrared intensities for all of these vibrational transitions are also calculated using MRCI dipole moment functions. The assignment of the HOBr states is complicated by strong stretch-bend resonances even at relatively low energies. In contrast to the HOCl case, these state mixings made it particularly difficult to assign the relatively intense OH overtone bands above v1=2. The vibrational density of states of HOBr at the OH+Br dissociation limit is determined to be 0.16 states/cm-1. Comparisons to recent work on HOCl using similar methods are made throughout.
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
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.
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.
Polycrystalline graphene with single crystalline electronic structure.
Brown, Lola; Lochocki, Edward B; Avila, José; Kim, Cheol-Joo; Ogawa, Yui; Havener, Robin W; Kim, Dong-Ki; Monkman, Eric J; Shai, Daniel E; Wei, Haofei I; Levendorf, Mark P; Asensio, María; Shen, Kyle M; Park, Jiwoong
2014-10-01
We report the scalable growth of aligned graphene and hexagonal boron nitride on commercial copper foils, where each film originates from multiple nucleations yet exhibits a single orientation. Thorough characterization of our graphene reveals uniform crystallographic and electronic structures on length scales ranging from nanometers to tens of centimeters. As we demonstrate with artificial twisted graphene bilayers, these inexpensive and versatile films are ideal building blocks for large-scale layered heterostructures with angle-tunable optoelectronic properties. PMID:25207847
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.
NASA Astrophysics Data System (ADS)
Baiardi, Alberto; Barone, Vincenzo; Biczysko, Malgorzata; Bloino, Julien
2014-06-01
Two parallel theories including Franck-Condon, Herzberg-Teller and Duschinsky (i.e., mode mixing) effects, allowing different approximations for the description of excited state PES have been developed in order to simulate realistic, asymmetric, electronic spectra line-shapes taking into account the vibrational structure: the so-called sum-over-states or time-independent (TI) method and the alternative time-dependent (TD) approach, which exploits the properties of the Fourier transform. The integrated TI-TD procedure included within a general purpose QM code [1,2], allows to compute one photon absorption, fluorescence, phosphorescence, electronic circular dichroism, circularly polarized luminescence and resonance Raman spectra. Combining both approaches, which use a single set of starting data, permits to profit from their respective advantages and minimize their respective limits: the time-dependent route automatically includes all vibrational states and, possibly, temperature effects, while the time-independent route allows to identify and assign single vibronic transitions. Interpretation, analysis and assignment of experimental spectra based on integrated TI-TD vibronic computations will be illustrated for challenging cases of medium-sized open-shell systems in the gas and condensed phases with inclusion of leading anharmonic effects. 1. V. Barone, A. Baiardi, M. Biczysko, J. Bloino, C. Cappelli, F. Lipparini Phys. Chem. Chem. Phys, 14, 12404, (2012) 2. A. Baiardi, V. Barone, J. Bloino J. Chem. Theory Comput., 9, 4097-4115 (2013)
Zimmermann, Olav; Hansmann, Ulrich H E
2008-09-01
Constraint generation for 3d structure prediction and structure-based database searches benefit from fine-grained prediction of local structure. In this work, we present LOCUSTRA, a novel scheme for the multiclass prediction of local structure that uses two layers of support vector machines (SVM). Using a 16-letter structural alphabet from de Brevern et al. (Proteins: Struct., Funct., Bioinf. 2000, 41, 271-287), we assess its prediction ability for an independent test set of 222 proteins and compare our method to three-class secondary structure prediction and direct prediction of dihedral angles. The prediction accuracy is Q16=61.0% for the 16 classes of the structural alphabet and Q3=79.2% for a simple mapping to the three secondary classes helix, sheet, and coil. We achieve a mean phi(psi) error of 24.74 degrees (38.35 degrees) and a median RMSDA (root-mean-square deviation of the (dihedral) angles) per protein chain of 52.1 degrees. These results compare favorably with related approaches. The LOCUSTRA web server is freely available to researchers at http://www.fz-juelich.de/nic/cbb/service/service.php. PMID:18763837
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.
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
Resolving presynaptic structure by electron tomography.
Perkins, Guy A; Jackson, Dakota R; Spirou, George A
2015-05-01
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 15 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
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
Ergül, Özgür; Gürel, Levent
2013-03-01
Accurate electromagnetic modeling of complicated optical structures poses several challenges. Optical metamaterial and plasmonic structures are composed of multiple coexisting dielectric and/or conducting parts. Such composite structures may possess diverse values of conductivities and dielectric constants, including negative permittivity and permeability. Further challenges are the large sizes of the structures with respect to wavelength and the complexities of the geometries. In order to overcome these challenges and to achieve rigorous and efficient electromagnetic modeling of three-dimensional optical composite structures, we have developed a parallel implementation of the multilevel fast multipole algorithm (MLFMA). Precise formulation of composite structures is achieved with the so-called "electric and magnetic current combined-field integral equation." Surface integral equations are carefully discretized with piecewise linear basis functions, and the ensuing dense matrix equations are solved iteratively with parallel MLFMA. The hierarchical strategy is used for the efficient parallelization of MLFMA on distributed-memory architectures. In this paper, fast and accurate solutions of large-scale canonical and complicated real-life problems, such as optical metamaterials, discretized with tens of millions of unknowns are presented in order to demonstrate the capabilities of the proposed electromagnetic solver. PMID:23456127
Bellili, A; Linguerri, R; Hochlaf, M; Puzzarini, C
2015-11-14
In an effort to provide an accurate structural and spectroscopic characterization of acetyl cyanide, its two enolic isomers and the corresponding cationic species, state-of-the-art computational methods, and approaches have been employed. The coupled-cluster theory including single and double excitations together with a perturbative treatment of triples has been used as starting point in composite schemes accounting for extrapolation to the complete basis-set limit as well as core-valence correlation effects to determine highly accurate molecular structures, fundamental vibrational frequencies, and rotational parameters. The available experimental data for acetyl cyanide allowed us to assess the reliability of our computations: structural, energetic, and spectroscopic properties have been obtained with an overall accuracy of about, or better than, 0.001 Å, 2 kcal/mol, 1-10 MHz, and 11 cm(-1) for bond distances, adiabatic ionization potentials, rotational constants, and fundamental vibrational frequencies, respectively. We are therefore confident that the highly accurate spectroscopic data provided herein can be useful for guiding future experimental investigations and/or astronomical observations. PMID:26567669
Low energy electrons and swift ion track structure in PADC
NASA Astrophysics Data System (ADS)
Fromm, Michel; Quinto, Michele A.; Weck, Philippe F.; Champion, Christophe
2015-10-01
The current work aims at providing an accurate description of the ion track-structure in poly-allyl dyglycol carbonate (PADC) by using an up-to-date Monte-Carlo code-called TILDA-V (a French acronym for Transport d'Ions Lourds Dans l'Aqua & Vivo). In this simulation the ion track-structure in PADC is mainly described in terms of ejected electrons with a particular attention done to the Low Energy Electrons (LEEs). After a brief reminder of the most important channels through which LEEs are prone to break a chemical bond, we will report on the simulated energetic distributions of LEEs along an ion track in PADC for particular incident energies located on both sides of the Bragg-peak position. Finally, based on the rare data dealing with LEEs interaction with polymers or organic molecules, we will emphasise the role played by the LEEs in the formation of a latent track in PADC, and more particularly the one played by the sub-ionization electrons.
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.
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
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
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
Electronic tagging and population structure of Atlantic bluefin tuna.
Block, Barbara A; Teo, Steven L H; Walli, Andreas; Boustany, Andre; Stokesbury, Michael J W; Farwell, Charles J; Weng, Kevin C; Dewar, Heidi; Williams, Thomas D
2005-04-28
Electronic tags that archive or transmit stored data to satellites have advanced the mapping of habitats used by highly migratory fish in pelagic ecosystems. Here we report on the electronic tagging of 772 Atlantic bluefin tuna in the western Atlantic Ocean in an effort to identify population structure. Reporting electronic tags provided accurate location data that show the extensive migrations of individual fish (n = 330). Geoposition data delineate two populations, one using spawning grounds in the Gulf of Mexico and another from the Mediterranean Sea. Transatlantic movements of western-tagged bluefin tuna reveal site fidelity to known spawning areas in the Mediterranean Sea. Bluefin tuna that occupy western spawning grounds move to central and eastern Atlantic foraging grounds. Our results are consistent with two populations of bluefin tuna with distinct spawning areas that overlap on North Atlantic foraging grounds. Electronic tagging locations, when combined with US pelagic longline observer and logbook catch data, identify hot spots for spawning bluefin tuna in the northern slope waters of the Gulf of Mexico. Restrictions on the time and area where longlining occurs would reduce incidental catch mortalities on western spawning grounds. PMID:15858572
Electronic structure theory of weakly interacting bilayers
NASA Astrophysics Data System (ADS)
Fang, Shiang; Kaxiras, Efthimios
2016-06-01
We derive electronic structure models for weakly interacting bilayers such as graphene-graphene and graphene-hexagonal boron nitride, based on density functional theory calculations followed by Wannier transformation of electronic states. These transferable interlayer coupling models can be applied to investigate the physics of bilayers with arbitrary translations and twists. The functional form, in addition to the dependence on the distance, includes the angular dependence that results from higher angular momentum components in the Wannier pz orbitals. We demonstrate the capabilities of the method by applying it to a rotated graphene bilayer, which produces the analytically predicted renormalization of the Fermi velocity, Van Hove singularities in the density of states, and moiré pattern of the electronic localization at small twist angles. We further extend the theory to obtain the effective couplings by integrating out neighboring layers. This approach is instrumental for the design of van der Walls heterostructures with desirable electronic features and transport properties and for the derivation of low-energy theories for graphene stacks, including proximity effects from other layers.
Spin Structure Functions from Electron Scattering
Seonho Choi
2012-09-01
The spin structure of the nucleon can play a key testing ground for Quantum Chromo-Dynamics (QCD) at wide kinematic ranges from smaller to large four momentum transfer Q{sup 2}. The pioneering experiments have confirmed several QCD sum rules at high Q{sup 2} where a perturbative picture holds. For a full understanding of QCD at various scales, various measurements were made at intermediate and small Q{sup 2} region and their interpretation would be a challenging task due to the non-perturbative nature. Jefferson Lab has been one of the major experimental facilities for the spin structure with its polarized electron beams and various polarized targets. A few QCD sum rules have been compared with the measured spin structure functions g{sub 1}(x, Q{sup 2}) and g{sub 2}(x, Q{sup 2}) at low Q{sup 2} and surprising results have been obtained for the spin polarizabilities, {gamma}{sub 0} and {delta}{sub LT} . As for the proton spin structure functions, the lack of data for g{sub 2}(x,Q{sup 2}) structure functions has been complemented with a new experiment at Jefferson Lab, SANE. The results from SANE will provide a better picture of the proton spin structure at a wide kinematic range in x and Q{sup 2}.
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.
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
Discretely disordered photonic bandgap structures: a more accurate invariant measure calculation
NASA Astrophysics Data System (ADS)
Kissel, Glen J.
2009-02-01
In the one-dimensional optical analog to Anderson localization, a periodically layered medium has one or more parameters randomly disordered. Such a randomized system can be modeled by an infinite product of 2x2 random transfer matrices with the upper Lyapunov exponent of the matrix product identified as the localization factor (inverse localization length) for the model. The theorem of Furstenberg allows us, at least theoretically, to calculate this upper Lyapunov exponent. In Furstenberg's formula we not only integrate with respect to the probability measure of the random matrices, but also with respect to the invariant probability measure of the direction of the vector propagated by the random matrices. This invariant measure is difficult to find analytically, and, as a result, the most successful approach is to determine the invariant measure numerically. A Monte Carlo simulation which uses accumulated bin counts to track the direction of the propagated vector through a long chain of random matrices does a good job of estimating the invariant probability measure, but with a level of uncertainty. A potentially more accurate numerical technique by Froyland and Aihara obtains the invariant measure as a left eigenvector of a large sparse matrix containing probability values determined by the action of the random matrices on input vectors. We first apply these two techniques to a random Fibonacci sequence whose Lyapunov exponent was determined by Viswanath. We then demonstrate these techniques on a quarter-wave stack model with binary discrete disorder in layer thickness, and compare results to the continuously disordered counterpart.
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.
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.
NASA Astrophysics Data System (ADS)
Neese, Frank; Wennmohs, Frank; Hansen, Andreas
2009-03-01
Coupled-electron pair approximations (CEPAs) and coupled-pair functionals (CPFs) have been popular in the 1970s and 1980s and have yielded excellent results for small molecules. Recently, interest in CEPA and CPF methods has been renewed. It has been shown that these methods lead to competitive thermochemical, kinetic, and structural predictions. They greatly surpass second order Møller-Plesset and popular density functional theory based approaches in accuracy and are intermediate in quality between CCSD and CCSD(T) in extended benchmark studies. In this work an efficient production level implementation of the closed shell CEPA and CPF methods is reported that can be applied to medium sized molecules in the range of 50-100 atoms and up to about 2000 basis functions. The internal space is spanned by localized internal orbitals. The external space is greatly compressed through the method of pair natural orbitals (PNOs) that was also introduced by the pioneers of the CEPA approaches. Our implementation also makes extended use of density fitting (or resolution of the identity) techniques in order to speed up the laborious integral transformations. The method is called local pair natural orbital CEPA (LPNO-CEPA) (LPNO-CPF). The implementation is centered around the concepts of electron pairs and matrix operations. Altogether three cutoff parameters are introduced that control the size of the significant pair list, the average number of PNOs per electron pair, and the number of contributing basis functions per PNO. With the conservatively chosen default values of these thresholds, the method recovers about 99.8% of the canonical correlation energy. This translates to absolute deviations from the canonical result of only a few kcal mol-1. Extended numerical test calculations demonstrate that LPNO-CEPA (LPNO-CPF) has essentially the same accuracy as parent CEPA (CPF) methods for thermochemistry, kinetics, weak interactions, and potential energy surfaces but is up to 500
Braun, Tatjana; Koehler Leman, Julia; Lange, Oliver F.
2015-01-01
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. PMID:26713437
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
Abdelnour, Farras; Voss, Henning U.; Raj, Ashish
2014-01-01
The relationship between anatomic connectivity of large-scale brain networks and their functional connectivity is of immense importance and an area of active research. Previous attempts have required complex simulations which model the dynamics of each cortical region, and explore the coupling between regions as derived by anatomic connections. While much insight is gained from these non-linear simulations, they can be computationally taxing tools for predicting functional from anatomic connectivities. Little attention has been paid to linear models. Here we show that a properly designed linear model appears to be superior to previous non-linear approaches in capturing the brain’s long-range second order correlation structure that governs the relationship between anatomic and functional connectivities. We derive a linear network of brain dynamics based on graph diffusion, whereby the diffusing quantity undergoes a random walk on a graph. We test our model using subjects who underwent diffusion MRI and resting state fMRI. The network diffusion model applied to the structural networks largely predicts the correlation structures derived from their fMRI data, to a greater extent than other approaches. The utility of the proposed approach is that it can routinely be used to infer functional correlation from anatomic connectivity. And since it is linear, anatomic connectivity can also be inferred from functional data. The success of our model confirms the linearity of ensemble average signals in the brain, and implies that their long-range correlation structure may percolate within the brain via purely mechanistic processes enacted on its structural connectivity pathways. PMID:24384152
Electronic and magnetic structures of chain structured iron selenide compounds
NASA Astrophysics Data System (ADS)
Li, Wei; Setty, Chandan; Chen, X. H.; Hu, Jiangping
2014-08-01
Electronic and magnetic structures of iron selenide compounds Ce2O2FeSe2 (2212*) and BaFe2Se3 (123*) are studied by the first-principles calculations. We find that while all these compounds are composed of one-dimensional (1D) Fe chain (or ladder) structures, their electronic structures are not close to be quasi-1D. The magnetic exchange couplings between two nearest-neighbor (NN) chains in 2212* and between two NN two-leg-ladders in 123* are both antiferromagnetic (AFM), which is consistent with the presence of significant third NN AFM coupling, a common feature shared in other iron-chalcogenides, FeTe (11*) and K y Fe2- x Se2 (122*). In magnetic ground states, each Fe chain of 2212* is ferromagnetic and each two-leg ladder of 123* form a block-AFM structure. We suggest that all magnetic structures in iron-selenide compounds can be unified into an extended J 1- J 2- J 3 model. Spin-wave excitations of the model are calculated and can be tested by future experiments on these two systems.
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.
Surface structure and electronic properties of materials
NASA Technical Reports Server (NTRS)
Siekhaus, W. J.; Somorjai, G. A.
1975-01-01
A surface potential model is developed to explain dopant effects on chemical vapor deposition. Auger analysis of the interaction between allotropic forms of carbon and silicon films has shown Si-C formation for all forms by glassy carbon. LEED intensity measurements have been used to determine the mean square displacement of surface atoms of silicon single crystals, and electron loss spectroscopy has shown the effect of structure and impurities on surface states located within the band gap. A thin film of Al has been used to enhance film crystallinity at low temperature.
Electronic structure of cobalt nanocrystals suspended inliquid
Liu, Hongjian; Guo, Jinghua; Yin, Yadong; Augustsson, Andreas; Dong, Chungli; Nordgren, Joseph; Chang, Chinglin; Alivisatos, Paul; Thornton, Geoff; Ogletree, D. Frank; Requejo, Felix G.; de Groot, Frank; Salmeron, Miquel
2007-07-16
The electronic structure of cobalt nanocrystals suspended in liquid as a function of size has been investigated using in-situ x-ray absorption and emission spectroscopy. A sharp absorption peak associated with the ligand molecules is found that increases in intensity upon reducing the nanocrystal size. X-ray Raman features due to d-d and to charge-transfer excitations of ligand molecules are identified. The study reveals the local symmetry of the surface of {var_epsilon}-Co phase nanocrystals, which originates from a dynamic interaction between Co nanocrystals and surfactant + solvent molecules.
Song, Kwang Hyun; Snyder, Karen Chin; Kim, Jinkoo; Li, Haisen; Ning, Wen; Rusnac, Robert; Jackson, Paul; Gordon, James; Siddiqui, Salim M; Chetty, Indrin J
2016-01-01
2.5 MV electronic portal imaging, available on Varian TrueBeam machines, was characterized using various phantoms in this study. Its low-contrast detectability, spatial resolution, and contrast-to-noise ratio (CNR) were compared with those of conventional 6 MV and kV planar imaging. Scatter effect in large patient body was simulated by adding solid water slabs along the beam path. The 2.5 MV imaging mode was also evaluated using clinically acquired images from 24 patients for the sites of brain, head and neck, lung, and abdomen. With respect to 6 MV, the 2.5 MV achieved higher contrast and preserved sharpness on bony structures with only half of the imaging dose. The quality of 2.5 MV imaging was comparable to that of kV imaging when the lateral separation of patient was greater than 38 cm, while the kV image quality degraded rapidly as patient separation increased. Based on the results of patient images, 2.5 MV imaging was better for cranial and extracranial SRS than the 6 MV imaging. PMID:27455505
Pollastri, Gianluca; Martin, Alberto JM; Mooney, Catherine; Vullo, Alessandro
2007-01-01
Background Structural properties of proteins such as secondary structure and solvent accessibility contribute to three-dimensional structure prediction, not only in the ab initio case but also when homology information to known structures is available. Structural properties are also routinely used in protein analysis even when homology is available, largely because homology modelling is lower throughput than, say, secondary structure prediction. Nonetheless, predictors of secondary structure and solvent accessibility are virtually always ab initio. Results Here we develop high-throughput machine learning systems for the prediction of protein secondary structure and solvent accessibility that exploit homology to proteins of known structure, where available, in the form of simple structural frequency profiles extracted from sets of PDB templates. We compare these systems to their state-of-the-art ab initio counterparts, and with a number of baselines in which secondary structures and solvent accessibilities are extracted directly from the templates. We show that structural information from templates greatly improves secondary structure and solvent accessibility prediction quality, and that, on average, the systems significantly enrich the information contained in the templates. For sequence similarity exceeding 30%, secondary structure prediction quality is approximately 90%, close to its theoretical maximum, and 2-class solvent accessibility roughly 85%. Gains are robust with respect to template selection noise, and significant for marginal sequence similarity and for short alignments, supporting the claim that these improved predictions may prove beneficial beyond the case in which clear homology is available. Conclusion The predictive system are publicly available at the address . PMID:17570843
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
Variational quantum Monte Carlo calculation of electronic and structural properties of crystals
Louie, S.G.
1989-09-01
Calculation of the electronic and structural properties of solids using a variational quantum Monte Carlo nonlocal pseudopotential approach is described. Ionization potentials and electron affinities for atoms, and binding energies and structural properties for crystals are found to be in very good agreement with experiment. The approach employs a correlated many-electron wavefunction of the Jastrow-Slater form and the exact Coulomb interaction between valence electrons. One- and two-body terms in the Jastrow factor are used and found necessary for an accurate description of the electron-electron energy for the systems considered. The method has further been applied to compute various single-particle properties for solids including the single-particle orbital occupancy, electron pair correlation functions, and quasiparticle excitation energies. 23 refs., 3 figs., 3 tabs.
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.
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.
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.
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
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.
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…
Electronic structure of rare-earth hexaborides
NASA Astrophysics Data System (ADS)
Kimura, S.; Nanba, T.; Tomikawa, M.; Kunii, S.; Kasuya, T.
1992-11-01
Reflectivity spectra of all rare-earth hexaboride RB6 (R=La, Ce, Pr, Nd, Sm, Eu, Gd, Tb, Dy, Ho, Yb, and Y) single crystals have been measured systematically in the energy region from 1 meV to 40 eV at 300 K in order to investigate the electronic state and the contribution of the 4f electron to the band structure. The analysis of the optical conductivity and the loss-function spectra, which were derived from the Kramers-Kronig transformation of the reflectivity spectra, allowed us to make clear the origin of the peak structure in the spectrum due to the various interband transitions. The origins of the main peaks in the spectrum were assigned to the interband transitions from the bonding to the antibonding bands of the boron 2s and 2p states and to the rare-earth 5d state. The intra-atomic transition from the 4f and the 5p to the 5d(t2g) states in the rare-earth ion was also observed.
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.
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.
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.
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)
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.
Accurate structural study of langasite-family Ca3TaGa3Si2O14 crystal
NASA Astrophysics Data System (ADS)
Dudka, A. P.
2016-03-01
An accurate X-ray diffraction study of Ca3TaGa3Si2O14 single crystal has been performed using two datasets obtained on a diffractometer equipped with a CCD area detector ( a = 8.1056(2) Å, c = 4.9800(1) Å, sp. gr. P321, Z = 1, R/ wR = 0.486/0.488%). A model structure is determined which is characterized by a high degree of reproducibility of structural parameters. Each site in Ca3TaGa3Si2O14 is occupied by atoms of only one type. Nevertheless, its structural feature is asymmetric disordering of sites of Ca, Ta, Ga, and two out of three oxygen atoms occupying special and general sites. A transition of some part of Ca atoms (~3%) from 3 e sites on the twofold symmetry axis to general 6 g sites is revealed.
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
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
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
O(N) methods in electronic structure calculations
NASA Astrophysics Data System (ADS)
Bowler, D. R.; Miyazaki, T.
2012-03-01
Linear-scaling methods, or O(N) methods, have computational and memory requirements which scale linearly with the number of atoms in the system, N, in contrast to standard approaches which scale with the cube of the number of atoms. These methods, which rely on the short-ranged nature of electronic structure, will allow accurate, ab initio simulations of systems of unprecedented size. The theory behind the locality of electronic structure is described and related to physical properties of systems to be modelled, along with a survey of recent developments in real-space methods which are important for efficient use of high-performance computers. The linear-scaling methods proposed to date can be divided into seven different areas, and the applicability, efficiency and advantages of the methods proposed in these areas are then discussed. The applications of linear-scaling methods, as well as the implementations available as computer programs, are considered. Finally, the prospects for and the challenges facing linear-scaling methods are discussed.
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.
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 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.
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.
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.
Statistical learning for alloy design from electronic structure calculations
NASA Astrophysics Data System (ADS)
Broderick, Scott R.
The objective of this thesis is to explore how statistical learning methods can contribute to the interpretation and efficacy of electronic structure calculations. This study develops new applications of statistical learning and data mining methods to both semi-empirical and density functional theory (DFT) calculations. Each of these classes of electronic structure calculations serves as templates for different data driven discovery strategies for materials science applications. In our study of semi-empirical methods, we take advantage of the ability of data mining methods to quantitatively assess high dimensional parameterization schemes. The impact of this work includes the development of accelerated computational schemes for developing reduced order models. Another application is the use of these informatics based techniques to serve as a means for estimating parameters when data for such calculations are not available. Using density of states (DOS) spectra derived from DFT calculations we have demonstrated the classification power of singular value decomposition methods to accurately develop structural and stoichiometric classifications of compounds. Building on this work we have extended this analytical strategy to apply the predictive capacity of informatics methods to develop a new and far more robust modeling approach for DOS spectra, addressing an issue that has gone relatively unchallenged over two decades. By exploring a diverse array of materials systems (metals, ceramics, different crystal structures) this work has laid the foundations for expanding the linkages between statistical learning and statistical thermodynamics. The results of this work provide exciting new opportunities in computational based design of materials that have not been explored before.
NASA Astrophysics Data System (ADS)
Javad Fahimi, Mohammad; Fathi, Davood; Ansari-Rad, Mehdi
2015-09-01
Electron transfer rate from quantum dot (QD) to metal oxide (MO) in quantum dot sensitized solar cells (QDSSCs) has an important role in the efficiency. In this work, we analyse the electron transfer rate from CdSe, CdS and CdTe QDs to TiO2, ZnO and SnO2 MOs by extending the related equations with considering various effects, based on the Marcus theory. In this regard, the effects of QD diameter, QD-MO spacing, the crystalline defects, temperature, and the reorganizational energy, on the electron transfer rate are investigated. The results show that, the maximum electron transfer rate is achieved for CdTe QD with the mentioned three MOs. Moreover, in order to direct the designer to reach the appropriate QDs-MOs combinations for obtaining the maximum electron transfer rate, the average electron transfer rate for various combinations is calculated. For the verification of simulation method, a part of work has been compared with the previous experimental and theoretical results, which indicates the correctness of our simulation algorithm.
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.
Quasiparticle electronic structure of bismuth telluride in the GW approximation
Kioupakis, Emmanouil; Tiago, Murilo L; Louie, Steven G.
2010-01-01
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 interpo- lation 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.
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.
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.
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.
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}.
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
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
NASA Astrophysics Data System (ADS)
Maeda, Yuta; Yamaoka, Koshun; Miyamachi, Hiroki; Watanabe, Toshiki; Kunitomo, Takahiro; Ikuta, Ryoya; Yakiwara, Hiroshi; Iguchi, Masato
2015-07-01
Temporal variations of Green functions associated with the eruptive activity at Sakurajima Volcano, Japan, were estimated using an accurately controlled routinely operated signal system (ACROSS). We deconvolved 400 s waveforms of the ACROSS signal at nearby stations by a known source time function and stacked the results based on the time relative to individual eruptions and the eruption intervals; the quantities obtained by this procedure are Green functions corresponding to various stages of the eruptive activity. We found an energy decrease in the later phase of the Green functions in active eruptive periods. This energy decrease, localized in the 2-6 s window of the Green functions, is difficult to explain by contamination from volcanic earthquakes and tremors. The decrease could be more reasonably attributed to a subsurface structure change caused by the volcanic activity.
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
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.
NASA Astrophysics Data System (ADS)
Zhang, Lili
This work aims to improve the capability of accurate information extraction from high-dimensional data, with a specific neural learning paradigm, the Self-Organizing Map (SOM). The SOM is an unsupervised learning algorithm that can faithfully sense the manifold structure and support supervised learning of relevant information from the data. Yet open problems regarding SOM learning exist. We focus on the following two issues. (1) Evaluation of topology preservation. Topology preservation is essential for SOMs in faithful representation of manifold structure. However, in reality, topology violations are not unusual, especially when the data have complicated structure. Measures capable of accurately quantifying and informatively expressing topology violations are lacking. One contribution of this work is a new measure, the Weighted Differential Topographic Function (WDTF), which differentiates an existing measure, the Topographic Function (TF), and incorporates detailed data distribution as an importance weighting of violations to distinguish severe violations from insignificant ones. Another contribution is an interactive visual tool, TopoView, which facilitates the visual inspection of violations on the SOM lattice. We show the effectiveness of the combined use of the WDTF and TopoView through a simple two-dimensional data set and two hyperspectral images. (2) Learning multiple latent variables from high-dimensional data. We use an existing two-layer SOM-hybrid supervised architecture, which captures the manifold structure in its SOM hidden layer, and then, uses its output layer to perform the supervised learning of latent variables. In the customary way, the output layer only uses the strongest output of the SOM neurons. This severely limits the learning capability. We allow multiple, k, strongest responses of the SOM neurons for the supervised learning. Moreover, the fact that different latent variables can be best learned with different values of k motivates a
Electronic structure of III-V zinc-blende semiconductors from first principles
NASA Astrophysics Data System (ADS)
Wang, Yin; Yin, Haitao; Cao, Ronggen; Zahid, Ferdows; Zhu, Yu; Liu, Lei; Wang, Jian; Guo, Hong
2013-06-01
For analyzing quantum transport in semiconductor devices, accurate electronic structures are critical for quantitative predictions. Here we report theoretical analysis of electronic structures of all III-V zinc-blende semiconductor compounds. Our calculations are from density functional theory with the semilocal exchange proposed recently [Tran and Blaha, Phys. Rev. Lett.PRLTAO0031-900710.1103/PhysRevLett.102.226401 102, 226401 (2009)], within the linear muffin tin orbital scheme. The calculated band gaps and effective masses are compared to experimental data and good quantitative agreement is obtained. Using the theoretical scheme presented here, quantum transport in nanostructures of III-V compounds can be confidently predicted.
NASA Astrophysics Data System (ADS)
Wang, Qian; Li, Bincheng
2015-12-01
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.
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.
Graph-based linear scaling electronic structure theory
NASA Astrophysics Data System (ADS)
Niklasson, Anders M. N.; Mniszewski, Susan M.; Negre, Christian F. A.; Cawkwell, Marc J.; Swart, Pieter J.; Mohd-Yusof, Jamal; Germann, Timothy C.; Wall, Michael E.; Bock, Nicolas; Rubensson, Emanuel H.; Djidjev, Hristo
2016-06-01
We show how graph theory can be combined with quantum theory to calculate the electronic structure of large complex systems. The graph formalism is general and applicable to a broad range of electronic structure methods and materials, including challenging systems such as biomolecules. The methodology combines well-controlled accuracy, low computational cost, and natural low-communication parallelism. This combination addresses substantial shortcomings of linear scaling electronic structure theory, in particular with respect to quantum-based molecular dynamics simulations.
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
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.
Gallandi, Lukas; Marom, Noa; Rinke, Patrick; Körzdörfer, Thomas
2016-02-01
The performance of non-empirically tuned long-range corrected hybrid functionals for the prediction of vertical ionization potentials (IPs) and electron affinities (EAs) is assessed for a set of 24 organic acceptor molecules. Basis set-extrapolated coupled cluster singles, doubles, and perturbative triples [CCSD(T)] calculations serve as a reference for this study. Compared to standard exchange-correlation functionals, tuned long-range corrected hybrid functionals produce highly reliable results for vertical IPs and EAs, yielding mean absolute errors on par with computationally more demanding GW calculations. In particular, it is demonstrated that long-range corrected hybrid functionals serve as ideal starting points for non-self-consistent GW calculations. PMID:26731340
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.
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
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.
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
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.
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
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.
Roine, Antti; Saviauk, Taavi; Kumpulainen, Pekka; Karjalainen, Markus; Tuokko, Antti; Aittoniemi, Janne; Vuento, Risto; Lekkala, Jukka; Lehtimäki, Terho; Tammela, Teuvo L.; Oksala, Niku K. J.
2014-01-01
Urinary tract infection (UTI) is a common disease with significant morbidity and economic burden, accounting for a significant part of the workload in clinical microbiology laboratories. Current clinical chemisty point-of-care diagnostics rely on imperfect dipstick analysis which only provides indirect and insensitive evidence of urinary bacterial pathogens. An electronic nose (eNose) is a handheld device mimicking mammalian olfaction that potentially offers affordable and rapid analysis of samples without preparation at athmospheric pressure. In this study we demonstrate the applicability of ion mobility spectrometry (IMS) –based eNose to discriminate the most common UTI pathogens from gaseous headspace of culture plates rapidly and without sample preparation. We gathered a total of 101 culture samples containing four most common UTI bacteries: E. coli, S. saprophyticus, E. faecalis, Klebsiella spp and sterile culture plates. The samples were analyzed using ChemPro 100i device, consisting of IMS cell and six semiconductor sensors. Data analysis was conducted by linear discriminant analysis (LDA) and logistic regression (LR). The results were validated by leave-one-out and 5-fold cross validation analysis. In discrimination of sterile and bacterial samples sensitivity of 95% and specificity of 97% were achieved. The bacterial species were identified with sensitivity of 95% and specificity of 96% using eNose as compared to urine bacterial cultures. In conclusion: These findings strongly demonstrate the ability of our eNose to discriminate bacterial cultures and provides a proof of principle to use this method in urinanalysis of UTI. PMID:25526592
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
"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.
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].
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.
Explicitly-correlated Gaussian geminals in electronic structure calculations
NASA Astrophysics Data System (ADS)
Szalewicz, Krzysztof; Jeziorski, Bogumił
2010-11-01
Explicitly correlated functions have been used since 1929, but initially only for two-electron systems. In 1960, Boys and Singer showed that if the correlating factor is of Gaussian form, many-electron integrals can be computed for general molecules. The capability of explicitly correlated Gaussian (ECG) functions to accurately describe many-electron atoms and molecules was demonstrated only in the early 1980s when Monkhorst, Zabolitzky and the present authors cast the many-body perturbation theory (MBPT) and coupled cluster (CC) equations as a system of integro-differential equations and developed techniques of solving these equations with two-electron ECG functions (Gaussian-type geminals, GTG). This work brought a new accuracy standard to MBPT/CC calculations. In 1985, Kutzelnigg suggested that the linear r 12 correlating factor can also be employed if n-electron integrals, n > 2, are factorised with the resolution of identity. Later, this factor was replaced by more general functions f (r 12), most often by ? , usually represented as linear combinations of Gaussian functions which makes the resulting approach (called F12) a special case of the original GTG expansion. The current state-of-art is that, for few-electron molecules, ECGs provide more accurate results than any other basis available, but for larger systems the F12 approach is the method of choice, giving significant improvements over orbital calculations.
Syntheses and electronic structures of decamethylmetallocenes
Robbins, J.L.
1981-04-01
The synthesis of decamethylmanganocene ((eta-C/sub 5/(CH/sub 3/)/sub 5/)/sub 2/Mn or (Me/sub 5/Cp)/sub 2/Mn)) is described. Magnetic susceptibility and electron paramagnetic resonance (EPR) studies show that (Me/sub 5/Cp)/sub 2/Mn is a low-spin, 17-electron compound with an orbitally degenerate, /sup 2/E/sub 2g/ (e/sub 2g//sup 3/ a/sub 1g//sup 2/) ground state. An x-ray crystallographic study of (Me/sub 5/Cp)/sub 2/Mn shows that it is a monomeric, D/sub 5d/ decamethylmetallocene with metal to ring carbon distances that are about 0.3 A shorter than those determined for high-spin manganocenes. The syntheses of new (Me/sub 5/Cp)/sub 2/M (M = Mg,V,Cr,Co, and Ni) and ((Me/sub 5/Cp)/sub 2/M)PF/sub 6/ (M = Cr,Co, and Ni) compounds are described. In addition, a preparative route to a novel, dicationic decamethylmetallocene, ((Me/sub 5/Cp)/sub 2/Ni)(PF/sub 6/)/sub 2/ is reported. Infrared, nuclear magnetic resonance, magnetic susceptibility, and/or x-ray crystallographic studies indicate that all the above compounds are D/sub 5d/ or D/sub 5h/ decamethylmetallocenes with low-spin electronic configurations. Cyclic voltammetry studies verify the reversibility and the one-electron nature of the (Me/sub 5/Cp)/sub 2/M ..-->.. ((Me/sub 5/Cp)/sub 2/M)/sup +/ (M = Cr,Mn,Fe,Co,Ni), ((Me/sub 5/Cp)/sub 2/Mn)/sup -/ ..-->.. (Me/sub 5/Cp)/sub 2/Mn and ((Me/sub 5/Cp)/sub 2/Ni)/sup +/ ..-->.. (Me/sub 5/Cp)/sub 2/Ni)/sup 2 +/ redox reactions. These studies reveal that the neutral decamethylmetallocenes are much more easily oxidized than their metallocene counterparts. This result attests to the electron-donating properties of the ten substituent methyl groups. Proton and carbon-13 NMR data are reported for the diamagnetic Mg(II), Mn(I), Fe(II), Co(III), and Ni(IV) decamethylmetallocenes and for ((Me/sub 5/Cp)/sub 2/V(CO)/sub 2/)/sup +/. The uv-visible absorption spectra of the 15-, 18- and 20- electron decamethylmetallocenes are also reported.
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 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.
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.
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.
Electronic Structure Contributions to Reactivity in Xanthine Oxidase Family Enzymes
Stein, Benjamin W.; Kirk, Martin L.
2016-01-01
We review the xanthine oxidase (XO) family of pyranopterin molybdenum enzymes with a specific emphasis on electronic structure contributions to reactivity. In addition to xanthine and aldehyde oxidoreductases, which catalyze the 2-electron oxidation of aromatic heterocycles and aldehyde substrates, this mini-review highlights recent work on the closely related carbon monoxide dehydrogenase (CODH) that catalyzes the oxidation of CO using a unique Mo-Cu heterobimetallic active site. A primary focus of this mini-review relates to how spectroscopy and computational methods have been used to develop an understanding of critical relationships between geometric structure, electronic structure, and catalytic function. PMID:25425163
Spectral differences in real-space electronic structure calculations
NASA Astrophysics Data System (ADS)
Jordan, D. K.; Mazziotti, D. A.
2004-01-01
Real-space grids for electronic structure calculations are efficient because the potential is diagonal while the second derivative in the kinetic energy may be sparsely evaluated with finite differences or finite elements. In applications to vibrational problems in chemical physics a family of methods known as spectral differences has improved finite differences by several orders of magnitude. In this paper the use of spectral differences for electronic structure is studied. Spectral differences are implemented in two electronic structure programs PARSEC and HARES which currently employ finite differences. Applications to silicon clusters and lattices indicate that spectral differences achieve the same accuracy as finite differences with less computational work.
NASA Astrophysics Data System (ADS)
Prendergast, David; Louie, Steven G.
2009-12-01
We present an efficient generalization of the k -space interpolation scheme for electronic structure presented by Shirley [Phys. Rev. B 54, 16464 (1996)]. The method permits the construction of a compact k -dependent Hamiltonian using a numerically optimal basis derived from a coarse-grained set of effective single-particle electronic-structure calculations (based on density-functional theory in this work). We provide some generalizations of the initial approach which reduce the number of required initial electronic-structure calculations, enabling accurate interpolation over the entire Brillouin zone based on calculations at the zone center only for large systems. We also generalize the representation of nonlocal Hamiltonians, leading to a more efficient implementation which permits the use of both norm-conserving and ultrasoft pseudopotentials in the input calculations. Numerically interpolated electronic eigenvalues with accuracy that is within 0.01 eV can be produced at very little computational cost. Furthermore, accurate eigenfunctions—expressed in the optimal basis—provide easy access to useful matrix elements for simulating spectroscopy and we provide details for computing optical transition amplitudes. The approach is also applicable to other theoretical frameworks such as the Dyson equation for quasiparticle excitations or the Bethe-Salpeter equation for optical responses.
Coto, Pedro B; Sharifzadeh, Sahar; Neaton, Jeffrey B; Thoss, Michael
2015-01-13
The lowest-lying electronic excited states of pentacene and its oligomers are investigated using accurate multireference wave function methods (CASPT2/CASSCF) and the many-body Greens's function approach (GW/BSE). The results obtained for dimers and trimers of different geometry reveal a complex electronic structure, which includes locally excited, charge transfer, and multiexciton states. For singlets of single-excitation character, both approaches yield excitation energies that are in good overall quantitative agreement. While the multiexciton states are located relatively high in energy in all systems investigated, charge transfer states exist in close proximity to the lowest-lying absorbing states. The implications of the results for the mechanisms of singlet fission in pentacene are discussed. PMID:26574213
Kinetic effects on robustness of electron magnetohydrodynamic structures
Hata, M.; Sakagami, H.; Das, A.
2013-04-15
Following recent remarkable progress in the development of high-power short-pulse lasers, exploration is ongoing into hitherto unknown phenomena at fast time scales of electrons, the understanding of which is becoming crucial. For a simplified description of such phenomena, the Electron Magnetohydrodynamics (EMHDs) fluid description is often adopted. For the possibility of electron transport in high-density plasma, exact solutions of the EMHD model in the form of electron vortex currents, together with their associated magnetic fields, have been considered. However, the fluid EMHD model does not incorporate kinetic effects. Here, the finite Larmor radius effects owing to a finite electron temperature on the robustness of the exact EMHD structures are investigated using two-dimensional particle-in-cell simulations. It is found that larger EMHD vortex structures can sustain themselves for long periods, even in high temperature plasma; however, sustaining structures at higher temperatures tends to be difficult. With increasing temperature, electrons with finite Larmor radii become disengaged from the localized region. It is also shown that structures localized in smaller regions are more difficult to sustain. A quantitative criterion in terms of the structure size and Larmor radius has been established by simulations over a wide range of parameters. Finally, we conclude that a structure, larger than about eight times the typical Larmor radius at r=R, could form and exist even under the effects of finite electron temperature.
Recent advances in electronic structure theory
NASA Astrophysics Data System (ADS)
Piecuch, Piotr; Kowalski, Karol; Pimienta, Ian S. O.; McGuire, Michael J.
The recently developed new approach to the many-electron correlation problem in atoms and molecules, termed the method of moments of coupled-cluster (CC) equations (MMCC), is reviewed. The ground-state MMCC formalism and its extension to excited electronic states via the equation-of-motion coupled-cluster (EOMCC) approach are discussed. The main principle of all MMCC methods is that of the non-iterative energy corrections which, when added to the ground- and excited-state energies obtained in the standard CC calculations, such as CCSD or EOMCCSD, recover the exact, full configuration interaction (CI) energies. Three types of the MMCC approximations are reviewed in detail: (i) the CI-corrected MMCC methods, which can be applied to ground and excited states; (ii) the renormalized and completely renormalized CC methods for ground states; and (iii) the quasi-variational MMCC approaches for the ground-state problem, including the quadratic MMCC models. It is demonstrated that the MMCC formalism provides a new theoretical framework for designing 'black-box' CC approaches that lead to an excellent description of entire potential energy surfaces of ground- and excited-state molecular systems with an ease of use of the standard single-reference methods. The completely renormalized (CR) CCSD(T) and CCSD(TQ) methods and their quadratic and excited-state MMCC analogues remove the failing of the standard CCSD, CCSD(T), EOMCCSD and similar methods at larger internuclear separations and for states that normally require a genuine multireference description. All theoretical ideas are illustrated by numerical examples involving bond breaking, excited vibrational states, reactive potential energy surfaces and difficult cases of excited electronic states. The description of the existing and well-established variants of the MMCC theory, such as CR-CCSD(T), is augmented by the discussion of future prospects and potentially useful recent developments, including the extension of the black
NASA Astrophysics Data System (ADS)
Xu, Zhongnan; Joshi, Yogesh V.; Raman, Sumathy; Kitchin, John R.
2015-04-01
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.
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.
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
Electronic-structure calculation for metals by local optimization
Woodward, C.; Min, B.I.; Benedek, R.; Garner, J.
1989-03-15
Recent work by Car and Parrinello has generated considerable interest in the calculation of electronic structure by nonlinear optimization. The technique introduced by these authors, dynamical simulated annealing, is designed for problems that involve energy barriers. When local optimization suffices to determine the energy minimum, more direct methods are available. In this paper we apply the algorithm suggested by Williams and Soler to calculate the electronic structure of metals, using a plane-wave expansion for the electronic orbitals and an electron-ion pseudopotential of the Kleinman-Bylander form. Radial pseudopotentials were taken from the compilation of Bachelet, Hamann, and Schlueter. Calculations are performed to optimize the electronic structure (i) with fixed atomic configuration, or (ii) with the atomic volume being optimized simultaneously. It is found that the dual optimization (ii) converges in essentially the same number of steps as the static lattice optimization (i). Numerical results are presented for Li, K, Al, and simple-cubic P.
Modeling Polymorphic Molecular Crystals with Electronic Structure Theory.
Beran, Gregory J O
2016-05-11
Interest in molecular crystals has grown thanks to their relevance to pharmaceuticals, organic semiconductor materials, foods, and many other applications. Electronic structure methods have become an increasingly important tool for modeling molecular crystals and polymorphism. This article reviews electronic structure techniques used to model molecular crystals, including periodic density functional theory, periodic second-order Møller-Plesset perturbation theory, fragment-based electronic structure methods, and diffusion Monte Carlo. It also discusses the use of these models for predicting a variety of crystal properties that are relevant to the study of polymorphism, including lattice energies, structures, crystal structure prediction, polymorphism, phase diagrams, vibrational spectroscopies, and nuclear magnetic resonance spectroscopy. Finally, tools for analyzing crystal structures and intermolecular interactions are briefly discussed. PMID:27008426
Electron structure: Shape, size, and generalized parton distributions in QED
NASA Astrophysics Data System (ADS)
Miller, Gerald A.
2014-12-01
The shape of the electron is studied using lowest-order perturbation theory. Quantities used to probe the structure of the proton—form factors, generalized parton distributions, transverse densities, Wigner distributions and the angular momentum content—are computed for the electron-photon component of the electron wave function. The influence of longitudinally polarized photons, demanded by the need for infrared regularization via a nonzero photon mass, is included. The appropriate value of the photon mass depends on experimental conditions, and consequently the size of the electron (as defined by the slope of its Dirac form factor) bound in a hydrogen atom is found to be about four times larger than when the electron is in a continuum scattering state. The shape of the electron, as determined from the transverse density and generalized parton distributions, is shown not to be round, and the continuum electron is shown to be far less round than the bound electron. An electron distribution function (analogous to the quark distribution function) is defined, and that of the bound electron is shown to be suppressed compared to that of the continuum electron. If the relative transverse momentum of the virtual electron and photon is large compared with the electron mass, the virtual electron and photon each carry nearly the total angular momentum of the physical electron (1 /2 ), with the orbital angular momentum being nearly (-1 /2 ). Including the nonzero photon mass leads to the suppression of end-point contributions to form factors. Implications for proton structure and color transparency are discussed.
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.
Atomic and electronic structure of Mo6S9-xIx nanowires
NASA Astrophysics Data System (ADS)
Meden, A.; Kodre, A.; Padeznik Gomilsek, J.; Arcon, I.; Vilfan, I.; Vrbanic, D.; Mrzel, A.; Mihailovic, D.
2005-09-01
Moybdenum-based subnanometre diameter nanowires are easy to synthesize and disperse, and they exhibit a variety of functional properties in which they are superior to other one-dimensional materials. However, further progress in the understanding of physical properties and the development of new and specific applications have so far been impeded by the fact that their structure was not accurately known. Here we report on a combination of systematic x-ray diffraction and extended x-ray absorption fine structure experiments, and first-principles theoretical structure calculations, which are used to determine the atomic skeletal structure of individual Mo6S9-xIx (MoSIx) nanowires, their packing arrangement within bundles and their electronic band structure. From this work we conclude that the variations in functional properties appear to arise from different stoichiometry, not skeletal structure. A supplementary data file is available from http://stacks.iop.org/0957-4484/16/1578
Basis functions for electronic structure calculations on spheres.
Gill, Peter M W; Loos, Pierre-François; Agboola, Davids
2014-12-28
We introduce a new basis function (the spherical Gaussian) for electronic structure calculations on spheres of any dimension D. We find general expressions for the one- and two-electron integrals and propose an efficient computational algorithm incorporating the Cauchy-Schwarz bound. Using numerical calculations for the D = 2 case, we show that spherical Gaussians are more efficient than spherical harmonics when the electrons are strongly localized. PMID:25554128
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.
Revealing the hidden correlated electronic structure of strained graphene
NASA Astrophysics Data System (ADS)
Craco, L.; Selli, D.; Seifert, G.; Leoni, S.
2015-05-01
We explore the effect of isotropic strain on the electronic structure of graphene. It is shown that the interplay between one-particle band narrowing and sizable multiorbital Coulomb interactions induces a transition from a Dirac-liquid semimetal to an orbital selective metal characterized by narrow π -orbital Kondo clouds and abrupt downshift of σ* states. The correlated electronic structure we derive is promising in the sense that it leads to results that might explain the reshaped electronic structure of graphene nanobubbles probed in scanning tunneling microscopy. Our proposal is a key step in understanding the intricate and interdependent changes in orbital and electronic degrees of freedom of strained materials with hexagonal lattice structure.
Secondary electron emission from surfaces with small structure
NASA Astrophysics Data System (ADS)
Dzhanoev, A. R.; Spahn, F.; Yaroshenko, V.; Lühr, H.; Schmidt, J.
2015-09-01
It is found that for objects possessing small surface structures with differing radii of curvature the secondary electron emission (SEE) yield may be significantly higher than for objects with smooth surfaces of the same material. The effect is highly pronounced for surface structures of nanometer scale, often providing a more than 100 % increase of the SEE yield. The results also show that the SEE yield from surfaces with structure does not show a universal dependence on the energy of the primary, incident electrons as it is found for flat surfaces in experiments. We derive conditions for the applicability of the conventional formulation of SEE using the simplifying assumption of universal dependence. Our analysis provides a basis for studying low-energy electron emission from nanometer structured surfaces under a penetrating electron beam important in many technological applications.
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.
Electronic structure of carbon-boron nitride nanotubes
NASA Astrophysics Data System (ADS)
Sanginés-Mendoza, Raúl; Martinez, Edgar
2013-03-01
Structures of carbon and boron nitride nanotubes (CNTs, BNNTs) are quite similar, conversely, electronic properties are radically different from each other. Carbon nanotubes, whose electronic properties can be either metallic or semiconducting depending on their chiral structure, boron nitride nanotubes are always semiconductors with bandgaps over 4 eV. We have looked to hybrid systems, to predict a new kind of nanostructures with novel electronic properties. In this way, we explore the electronic properties of C-BN nanotubes. In particular, we studied the electronic structure of armchair C-BN nanotubes. The calculations were performed using the pseudopotential LCAO method with a Generalized Gradient Approximation for the exchange-correlation energy functional. The band structure of most of these systems have semiconductor character with an indirect gap smaller than its analogous BNNTs. In addition, the most prominent feature of these systems is the existence of flat bands both at the valence band top and at the conduction band minimum. Such flat bands results in sharp and narrow peaks on the total density of states. The behavior of these flat bands mainly indicates that electrons are largely localized. Thus, a detailed analysis on the electronic band structure shows that hybridization between those orbitals on the interfaces is responsible to exhibit localization effects on the hybrid systems.This research was supported by Conacyt under Grant No. 133022.
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 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.
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.
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.
New Insight into Carbon Nanotube Electronic Structure Selectivity
Sumpter, Bobby G; Meunier, Vincent; Jiang, Deen
2009-01-01
The fundamental role of aryl diazonium salts for post synthesis selectivity of carbon nanotubes is investigated using extensive electronic structure calculations. The resulting understanding for diazonium salt based selective separation of conducting and semiconducting carbon nanotubes shows how the primary contributions come from the interplay between the intrinsic electronic structure of the carbon nanotubes and that of the anion of the salt. We demonstrate how the electronic transport properties change upon the formation of charge transfer complexes and upon their conversion into covalently attached functional groups. Our results are found to correlate well with experiments and provide for the first time an atomistic description for diazonium salt based chemical separation of carbon nanotubes
Improving Boundary Conditions for Electronic Structure Calculations
NASA Astrophysics Data System (ADS)
Benesh, G. A.; Haydock, Roger
Boundary conditions imposed on a local system joined to a much larger substrate system routinely introduce unphysical reflections that affect the calculation of electronic properties such as energies, charge densities, and densities of states. These problems persist in atomic cluster, slab, and supercell calculations alike. However, wave functions in real, physical systems do not reflect at artificial boundaries. Instead, they carry current smoothly across the surface separating the local system from the underlying medium. Haydock and Nex have derived a non-reflecting boundary condition that works well for discrete systems [Phys. Rev. B 75, 205121 (2006)]. Solutions satisfying their maximal breaking of time-reversal symmetry (MBTS) boundary condition carry current away from the boundary at a maximal rate--in much the same way as exact wave functions in physical systems. The MBTS approach has now been extended to studies employing continuous basis functions. In model systems, MBTS boundary conditions work well for calculating wave functions, eigenenergies, and densities of states. Results are reported for an Al(001) surface. Comparisons are made with slab calculations, embedding calculations, and experiment.
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.
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.
Graphene Oxide: Synthesis, Characterization, Electronic Structure, and Applications
NASA Astrophysics Data System (ADS)
Stewart, Derek A.; Mkhoyan, K. Andre
While graphite oxide was first identified in 1855 [1, 2], the recent discovery of stable graphene sheets has led to renewed interest in the chemical structure and potential applications of graphene oxide sheets. These structures have several physical properties that could aid in the large scale development of a graphene electronics industry. Depending on the degree of oxidization, graphene oxide layers can be either semiconducting or insulating and provide an important complement to metallic graphene layers. In addition, the electronic and optical properties of these films can be controlled by the selective removal or addition of oxygen. For example, selective oxidationof graphene sheets could lead to electronic circuit fabrication on the scale of a single atomic layer. Graphene oxide is also dispersible in water and other solvents and this provides a facile route for graphene deposition on a wide range of substrates for macroelectronics applications. Although graphite oxide has been known for roughly 150 years, key questions remain in regards to its chemical structure, electronic properties, and fabrication. Answering these issues has taken on special urgency with the development of graphene electronics. In this chapter, we will provide an overview of the field with special focus on synthesis, characterization, and first principles analysis of bonding and electronic structures. Finally, we will also address some of the most promising applications for graphene oxide in electronics and other industries.
Nano-structured electron transporting materials for perovskite solar cells
NASA Astrophysics Data System (ADS)
Liu, Hefei; Huang, Ziru; Wei, Shiyuan; Zheng, Lingling; Xiao, Lixin; Gong, Qihuang
2016-03-01
Organic-inorganic hybrid perovskite solar cells have been developing rapidly in the past several years, and their power conversion efficiency has reached over 20%, nearing that of polycrystalline silicon solar cells. Because the diffusion length of the hole in perovskites is longer than that of the electron, the performance of the device can be improved by using an electron transporting layer, e.g., TiO2, ZnO and TiO2/Al2O3. Nano-structured electron transporting materials facilitate not only electron collection but also morphology control of the perovskites. The properties, morphology and preparation methods of perovskites are reviewed in the present article. A comprehensive understanding of the relationship between the structure and property will benefit the precise control of the electron transporting process and thus further improve the performance of perovskite solar cells.
Nano-structured electron transporting materials for perovskite solar cells.
Liu, Hefei; Huang, Ziru; Wei, Shiyuan; Zheng, Lingling; Xiao, Lixin; Gong, Qihuang
2016-03-17
Organic-inorganic hybrid perovskite solar cells have been developing rapidly in the past several years, and their power conversion efficiency has reached over 20%, nearing that of polycrystalline silicon solar cells. Because the diffusion length of the hole in perovskites is longer than that of the electron, the performance of the device can be improved by using an electron transporting layer, e.g., TiO2, ZnO and TiO2/Al2O3. Nano-structured electron transporting materials facilitate not only electron collection but also morphology control of the perovskites. The properties, morphology and preparation methods of perovskites are reviewed in the present article. A comprehensive understanding of the relationship between the structure and property will benefit the precise control of the electron transporting process and thus further improve the performance of perovskite solar cells. PMID:26457406
Electronic spectra of structurally deformed lutein.
Macernis, Mindaugas; Sulskus, Juozas; Duffy, Christopher D P; Ruban, Alexander V; Valkunas, Leonas
2012-10-11
Quantum chemical calculations have been employed for the investigation of the lowest excited electronic states of lutein, with particular reference to its function within light harvesting antenna complexes of higher plants. Through comparative analysis obtained by using different methods based on gas-phase calculations of the spectra, it was determined that variations in the lengths of the long C-C valence bonds and the dihedral angles of the polyene chain are the dominant factors in determining the spectral properties of Lut 1 and Lut 2 corresponding to the deformed lutein molecules taken from crystallographic data of the major pigment-protein complex of photosystem II. By MNDO-CAS-CI method, it was determined that the two singlet B(u) states of lutein (nominally 1B(u)(-)* and 1B(u)(+)) arise as a result of mixing of the canonical 1B(u)(-) and 1B(u)(+) states of the all-trans polyene due to the presence of the ending rings in lutein. The 1B(u)(-)* state of lutein is optically allowed, while the 1B(u)(-) of a pure all-trans polyene chain is optically forbidden. As demonstrated, the B(u) states are much more sensitive to minor distortions of the conjugated chain due to mixing of the canonical states, resulting in states of poorly defined particle-hole symmetry. Conversely, the A(g) states are relatively robust with respect to geometric distortion, and their respective inversion and particle-hole symmetries remain relatively well-defined. PMID:22974387
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, Thermal and Structural Properties of Graphene Oxide Frameworks
Zhu, Pan; Sumpter, Bobby G; Meunier, V.
2013-01-01
We report a theoretical study of the electronic, thermal, and structural properties of a series of graphene oxide frameworks (GOFs) using first-principles calculations based on density functional theory. The molecular structure of GOFs is systematically studied by varying the nature and concentration of linear boronic acid pillars and the thermal stability is assessed using ab initio molecular dynamics. The results demonstrate that GOFs are thermally stable up to 550 K and that electronic properties, such as their band gap, can be modified controllably by an appropriate choice of pillaring unit and pillar concentration. The tunability of the electronic structure using non-chemical means, e.g., mechanical strain, is also quantified. Overall, this class of materials is predicted to offer highly tunable materials electronic properties ranging from metallic to semiconducting.
Electronic, Thermal, and Structural Properties of Graphene Oxide Frameworks
Zhu, Pan; Sumpter, Bobby G; Meunier, V.
2013-01-01
We report a theoretical study of the electronic, thermal, and structural properties of a series of graphene oxide frameworks (GOFs) using first-principles calculations based on density functional theory. The molecular structure of GOFs is systematically studied by varying the nature and concentration of linear boronic acid pillars, and the thermal stability is assessed using ab initio molecular dynamics. The results demonstrate that GOFs are thermally stable up to 550 K and that electronic properties, such as their band gap, can be modified controllably by an appropriate choice of pillaring unit and pillar concentration. The tunability of the electronic structure using nonchemical means, e.g., mechanical strain, is also quantified. Overall, this class of materials is predicted to offer highly tunable materials electronic properties ranging from metallic to semiconducting.
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.
ESTIMATION OF ELECTRON AFFINITY BASED ON STRUCTURE ACTIVITY RELATIONSHIPS
Electron affinity for a wide range of organic molecules was calculated from molecular structure using the chemical reactivity models developed in SPARC. hese models are based on fundamental chemical structure theory applied to the prediction of chemical reactivities for organic m...
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
Electronic properties in a quantum well structure of Weyl semimetal
NASA Astrophysics Data System (ADS)
You, Wen-Long; Wang, Xue-Feng; Oleś, Andrzej M.; Zhou, Jiao-Jiao
2016-04-01
We investigate the confined states and transport of three-dimensional Weyl electrons around a one-dimensional external rectangular electrostatic potential. The confined states with finite transverse wave vector exist at energies higher than the half well depth or lower than the half barrier height. The rectangular potential appears completely transparent to the normal incident electrons but not otherwise. The tunneling transmission coefficient is sensitive to their incident angle and shows resonant peaks when their energy coincides with the confined spectra. In addition, for the electrons in the conduction (valence) band through a potential barrier (well), the transmission spectrum has a gap of width increasing with the incident angle. Interestingly, the electron linear zero-temperature conductance over the potential can approach zero when the Fermi energy is aligned to the top and bottom energies of the potential, when only electron beams normal to the potential interfaces can pass through. The considered structure can be used to collimate the Weyl electron beams.
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.
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.
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.
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
Role of interface band structure on hot electron transport
NASA Astrophysics Data System (ADS)
Garramone, John J.
Knowledge of electron transport through materials and interfaces is fundamentally and technologically important. For example, metal interconnects within integrated circuits suffer increasingly from electromigration and signal delay due to an increase in resistance from grain boundary and sidewall scattering since their dimensions are becoming shorter than the electron mean free path. Additionally, all semiconductor based devices require the transport of electrons through materials and interfaces where scattering and parallel momentum conservation are important. In this thesis, the inelastic and elastic scattering of hot electrons are studied in nanometer thick copper, silver and gold films deposited on silicon substrates. Hot electrons are electron with energy greater than kBT above the Fermi level (EF). This work was performed utilizing ballistic electron emission microscopy (BEEM) which is a three terminal scanning tunneling microscopy (STM) technique that measures the percentage of hot electrons transmitted across a Schottky barrier interface. Hot electron attenuation lengths of the metals were extracted by measuring the BEEM current as a function of metal overlayer thickness for both hot electron and hot hole injection at 80 K and under ultra high vacuum. The inelastic and elastic scattering lengths were extracted by fitting the energetic dependence of the measured attenuation lengths to a Fermi liquid based model. A sharp increase in the attenuation length is observed at low injection energies, just above the Schottky barrier height, only for metals on Si(001) substrates. In contrast, the attenuation length measured on Si(111) substrates shows a sharp decrease. These results indicate that interface band structure and parallel momentum conservation have significant impact upon the transport of hot electrons across non epitaxial metal-semiconductor interfaces. In addition, they help to separate effects upon hot electron transport that are inherent to the metal
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.
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.
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
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.
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.
Electronic Structure and Phase Stability of PdPt Nanoparticles.
Ishimoto, Takayoshi; Koyama, Michihisa
2016-03-01
To understand the origin of the physicochemical nature of bimetallic PdPt nanoparticles, we theoretically investigated the phase stability and electronic structure employing the PdPt nanoparticles models consisting of 711 atoms (ca. 3 nm). For the Pd-Pt core-shell nanoparticle, the PdPt solid-solution phase was found to be a thermodynamically stable phase in the nanoparticle as the result of difference in surface energy of Pd and Pt nanoparticles and configurational entropy effect, while it is well known that the Pd and Pt are the immiscible combination in the bulk phase. The electronic structure of nanoparticles is conducted to find that the electron transfer occurs locally within surface and subsurface layers. In addition, the electron transfer from Pd to Pt at the interfacial layers in core-shell nanoparticles is observed, which leads to unique geometrical and electronic structure changes. Our results show a clue for the tunability of the electronic structure of nanoparticles by controlling the arrangement in the nanoparticles. PMID:26862885
Electronic and atomic structure computation of disordered low index surfaces of γ-alumina
NASA Astrophysics Data System (ADS)
Dyan, Anthony; Azevedo, Christophe; Cenedese, Pierre; Dubot, Pierre
2008-04-01
Electronic and atomic structure of low index polar (0 0 1, 0 1 1, 1 1 1) spinel γ-alumina surfaces have been investigated using a modified large-scale quantum semi-empirical simulations. Atomic structure optimization and electronic structure calculation were done in the direct space on periodic large unit cells in which random distribution of cationic vacancies close to the surface were included. Predicted electronic structures match more accurate ab initio Density Functional Theory (DFT) results on aluminum oxides. We found that the restructured surfaces behave as amorphous-like shapeless planes provided unit cell dimensions are much greater than primitive translations as periodicity constraints are weakened. Aluminum ions vacancies in the surface region are shown to induce a surface atomic disordering even at 0 K, correlated with the appearance of low coordinated ions, as proven experimentally and theoretically with classical Molecular Dynamics (MD) calculation on some aluminum oxide systems. The lowering of the surface charge density is obtained from two distinct mechanisms involving large ion movements. On the oxygen rich plane termination, this results from the formation of O 2δ- entities. On the aluminum rich plane termination, the same effect is related to a loss of co-ordination number together with a reduction of cationic charge. Furthermore, large-scale simulations allow to statistically quantify specific relaxed surface ion densities for which the Local Density of States (LDOS) is evaluated. Their inferred electronic properties are then compared to available probe molecule adsorption experiments investigated by infrared spectroscopy. We show that surface electronic states are not a simple function of ion coordination. Our large-scale quantum semi-empirical calculation fills the gap between atomic structures predicted by classical MD approach with electronic structure results obtained by DFT on small systems.
Subotnik, Joseph E; Alguire, Ethan C; Ou, Qi; Landry, Brian R; Fatehi, Shervin
2015-05-19
Electronically photoexcited dynamics are complicated because there are so many different relaxation pathways: fluorescence, phosphorescence, radiationless decay, electon transfer, etc. In practice, to model photoexcited systems is a very difficult enterprise, requiring accurate and very efficient tools in both electronic structure theory and nonadiabatic chemical dynamics. Moreover, these theoretical tools are not traditional tools. On the one hand, the electronic structure tools involve couplings between electonic states (rather than typical single state energies and gradients). On the other hand, the dynamics tools involve propagating nuclei on multiple potential energy surfaces (rather than the usual ground state dynamics). In this Account, we review recent developments in electronic structure theory as directly applicable for modeling photoexcited systems. In particular, we focus on how one may evaluate the couplings between two different electronic states. These couplings come in two flavors. If we order states energetically, the resulting adiabatic states are coupled via derivative couplings. Derivative couplings capture how electronic wave functions change as a function of nuclear geometry and can usually be calculated with straightforward tools from analytic gradient theory. One nuance arises, however, in the context of time-dependent density functional theory (TD-DFT): how do we evaluate derivative couplings between TD-DFT excited states (which are tricky, because no wave function is available)? This conundrum was recently solved, and we review the solution below. We also discuss the solution to a second, pesky problem of origin dependence, whereby the derivative couplings do not (strictly) satisfy translation variance, which can lead to a lack of momentum conservation. Apart from adiabatic states, if we order states according to their electronic character, the resulting diabatic states are coupled via electronic or diabatic couplings. The couplings
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.
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.
Structure and electronic properties of (+)-catechin: aqueous solvent effects.
Bentz, Erika N; Pomilio, Alicia B; Lobayan, Rosana M
2014-02-01
We report a study of the structure of (+)-catechin, which belongs to the family of the flavan-3-ols-one of the five most widely distributed phenolic groups. The biological activities and pharmaceutical utility of these compounds are related to antioxidant activity due to their ability to scavenge free radicals. A breakthrough in the study of the conformational space of this compound, so far absent in the literature, is presented herein. A detailed analysis of the electronic distribution, charge delocalization effects, and stereoelectronic effects is presented following application of the theory of atoms in molecules (AIM) and natural bond orbital analysis. The stability order, and the effects of electron delocalization in the structures were analyzed in depth. The molecular electrostatic potential (MEP) was also obtained, assessing changes in the electronic distribution in aqueous solution, the effects of the solvent on the intrinsic electronic properties, and molecular geometry. The effect of the aqueous solvent on MEP was also quantified, and rationalized by charge delocalization mechanisms, relating them to structural changes and topological properties of the electronic charge density. To further analyze the effects of the aqueous solvent, as well as investigating the molecular and structural properties of these compounds in a biological environment, the polarizabilities for all conformers characterized were also calculated. All results were interpreted on the basis of our accumulated knowledge on (4α→6", 2α→O→1")-phenylflavans in previous reports, thus enriching and deepening the analysis of both types of structure. PMID:24526380
Electronic structure of Fe-based amorphous alloys studied using electron-energy-loss spectroscopy
NASA Astrophysics Data System (ADS)
Wang, H. J.; Gu, X. J.; Poon, S. J.; Shiflet, G. J.
2008-01-01
The local atomic electronic structures of Fe-Mo-C-B metallic glasses are investigated using electron energy-loss spectroscopy (EELS). The fracture behavior of this Fe-based amorphous alloy system undergoes the transition from being ductile to exhibiting brittleness when alloyed with Cr or Er atoms. In addition, the glass-forming ability is also enhanced. This plastic-to-brittle transition is suggested to correlate with the change of local atomic short-range order or bonding configurations. Therefore, the bonding configuration of Fe-Mo-C-B-Er(Cr) amorphous alloys is investigated by studying the electronic structure of Fe and C atoms using electron energy-loss spectroscopy. It is shown that the normalized EELS white line intensities of Fe-L2,3 edges decrease slightly with an increasing amount of Er additions, while no noticeable difference is obtained with Cr additions. As for the C K edge, a prominent change of edge shape is observed for both alloy systems, where the first peak corresponding to a 1s→1π* transition increases with increasing Er and Cr additions. Accordingly, it is concluded that changes in the local atomic and electronic structure occur around Fe and C atoms when Er and Cr are introduced into the alloys. Furthermore, it is pointed out that the formation of Er-C and Cr-C carbide like local order inferred from the observed C K edge spectra can provide a plausible explanation for the plastic-to-brittle transition observed in these Fe-based amorphous alloys. In spite of the complexity of electronic and atomic structure in this multicomponent Fe-based metallic glass system, this study could serve as a starting point for providing a qualitative interpretation between electronic structure and plasticity in the Fe-Mo-C-B amorphous alloy system. Complimentary techniques, such as x-ray diffraction and high-resolution transmission electron microscope are also employed, providing a more complete structural characterization.
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
Enhancement of electron mobility in asymmetric coupled quantum well structures
Das, S.; Nayak, R. K.; Sahu, T. Panda, A. K.
2014-02-21
We study the low temperature multisubband electron mobility in a structurally asymmetric GaAs/Al{sub x}Ga{sub 1-x}As delta doped double quantum well. We calculate the subband energy levels and wave functions through selfconsistent solution of the coupled Schrodinger equation and Poisson's equation. We consider ionized impurity scattering, interface roughness scattering, and alloy disorder scattering to calculate the electron mobility. The screening of the scattering potentials is obtained by using static dielectric response function formalism within the random phase approximation. We analyze, for the first time, the effect of asymmetric structure parameters on the enhancement of multisubband electron mobility through intersubband interactions. We show that the asymmetric variation of well width, doping concentration, and spacer width considerably influences the interplay of scattering mechanisms on mobility. Our results of asymmetry induced enhancement of electron mobility can be utilized for low temperature device applications.
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
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
Structural and electronic features of a Broensted acid site in H-ZSM-5
Cook, S.J.; Chakraborty, A.K.; Bell, A.T.; Theodorou, D.N. Univ. of California, Berkeley )
1993-06-24
The authors report the results of local density functional theory calculations on a Broensted acid site of the zeolite H-ZSM-5. They have investigated the structural and electronic properties of the site. Comparison is made between their results and existing experimental data. It is shown that structural relaxation around an acid site must be performed to obtain accurate energetics for substitution of aluminum into the zeolite framework. The effects of cluster termination are studied by comparing results obtained for both isolated clusters and clusters embedded in a Madelung field generated by the zeolite framework. The properties of the electron density distribution in the region around an acidic proton indicate that the acidic moiety may be characterized as a rather soft acid. 47 refs., 5 figs., 4 tabs.
Electron Energy Loss Spectroscopy of a Chiral Plasmonic Structure
NASA Astrophysics Data System (ADS)
Paterson, G. W.; Karimullah, A.; Williamson, SDR; Kadodwala, M.; MacLaren, D. A.
2015-10-01
A detailed analysis of the plasmonic excitations within a nanopatterned gold chiral biosensor element, measured by scanning transmission electron microscopy electron energy loss spectroscopy, is presented. We discuss aspects of data acquisition, processing, analysis and simulation. The localised surface plasmonic resonance modes in the structure are extracted using non-negative matrix factorisation and we use simulations to correlate notable deviations from the idealised spectrum to nanometric fabrication imperfections. The methodology presented has wide applicability to a variety of metamaterials.
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.
Electron Crystallography – The Waking Beauty of Structural Biology
Pope, Christopher R; Unger, Vinzenz M
2012-01-01
Since its debut in the mid 70ties, electron crystallography has been a valuable alternative in the structure determination of biological macromolecules. Its reliance on single- 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. PMID:22525160
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.
The electronic structure of diodes probed under bias
NASA Astrophysics Data System (ADS)
Glans, Per-Anders; Guo, Jinghua; Park, Jeong; Gabor, Somorjai
2009-03-01
Chemists have known for decades that when metal nano-particles are affixed to a catalytically inactive oxide surface, the catalytic turnover rate of the array is more than 10 times that of a metal surface alone. However, the mechanism behind the effect is not clear. To understand the catalytic activity of the interface between the metal nano-structures and the oxide substrate, we have investigated the electronic structure of Pt and Pd doped diodes on a TiO2 substrate. The devices were put under bias during the measurements in an attempt to reproduce the potential differences found over the diode when used as a catalyst. This is challenging for electron based measuring techniques, but using photon-in, photon-out techniques we have successfully probed the electronic structure of Pt and Pd doped diodes under bias. The results from soft x-ray absorption and emission will be presented.
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.
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
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.
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. PMID:24871071
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 of spatially aligned graphene nanoribbons on Au(788).
Linden, S; Zhong, D; Timmer, A; Aghdassi, N; Franke, J H; Zhang, H; Feng, X; Müllen, K; Fuchs, H; Chi, L; Zacharias, H
2012-05-25
We report on a bottom-up approach of the selective and precise growth of subnanometer wide straight and chevron-type armchair nanoribbons (GNRs) on a stepped Au(788) surface using different specific molecular precursors. This process creates spatially well-aligned GNRs, as characterized by STM. High-resolution direct and inverse photoemission spectroscopy of occupied and unoccupied states allows the determination of the energetic position and momentum dispersion of electronic states revealing the existence of band gaps of several electron volts for straight 7-armchair, 13-armchair, and chevron-type GNRs in the electronic structure. PMID:23003288
Super instruction architecture of petascale electronic structure software: the story
NASA Astrophysics Data System (ADS)
Lotrich, V. F.; Ponton, J. M.; Perera, A. S.; Deumens, E.; Bartlett, R. J.; Sanders, B. A.
2010-11-01
Theoretical methods in chemistry lead to algorithms for the computation of electronic energies and other properties of electronic wave functions that require large numbers of floating point operations and involve large data sets. Thus, computational chemists are very interested in using massively parallel computer systems and in particular the new petascale systems. In this paper we discuss a new programming paradigm that was developed at the Quantum Theory Project to construct electronic structure software that can scale to large numbers of cores of the order of 100,000 and beyond to solve problems in materials engineering relevant to the problems facing society today.
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
Banded Electron Structure Formation in the Inner Magnetosphere
NASA Technical Reports Server (NTRS)
Liemohn, M. W.; Khazanov, G. V.
1997-01-01
Banded electron structures in energy-time spectrograms have been observed in the inner magnetosphere concurrent with a sudden relaxation of geomagnetic activity. In this study, the formation of these banded structures is considered with a global, bounce-averaged model of electron transport, and it is concluded that this structure is a natural occurrence when plasma sheet electrons are captured on closed drift paths near the Earth. These bands do not appear unless there is capture of plasma sheet electrons; convection along open drift paths making open pass around the Earth do not have time to develop this feature. The separation of high-energy bands from the injection population due to the preferential advection of the gradient-curvature drift creates spikes in the energy distribution, which overlap to form a series of bands in the energy spectrograms. The lowest band is the bulk of the injected population in the sub-key energy range. Using the Kp history for an observed banded structure event, a cloud of plasma sheet electrons is captured and the development of their distribution function is examined and discussed.
Sharapov, Vladimir A; Mandelshtam, Vladimir A
2007-10-18
We consider systems undergoing very-low-temperature solid-solid transitions associated with minima of similar energy but different symmetry, and separated by a high potential barrier. In such cases the well-known "broken-ergodicity" problem is often difficult to overcome, even using the most advanced Monte Carlo (MC) techniques, including the replica exchange method (REM). The methodology that we develop in this paper is suitable for the above specified cases and is numerically accurate and efficient. It is based on a new MC move implemented within the REM framework, in which trial points are generated analytically using an auxiliary harmonic superposition system that mimics well the true system at low temperatures. Due to the new move, the low-temperature random walks are able to frequently switch the relevant potential energy funnels leading to an efficient sampling. Numerically accurate results are obtained for a number of Lennard-Jones clusters, including those that have so far been treated only by the harmonic superposition approximation (HSA). The latter is believed to provide good estimates for low-temperature equilibrium properties but is manifestly uncontrollable and is difficult to validate. The present results provide a good test for the HSA and demonstrate its reliability, particularly for estimation of the solid-solid transition temperatures in most cases considered. PMID:17685597
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.
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.
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.
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.
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.
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.
High charge short electron bunches for wakefield accelerator structures development.
Conde, M. E.
1998-09-25
The Argonne Wakefield Accelerator group develops accelerating structures based on dielectric loaded waveguides. We use high charge short electron bunches to excite wakefields in dielectric loaded structures, and a second (low charge) beam to probe the wakefields left behind by the drive beam. We report measurements of beam parameters and also initial results of the dielectric loaded accelerating structures. We have studied acceleration of the probe beam in these structures and we have also made measurements on the RF pulses that are generated by the drive beam. Single drive bunches, as well as multiple bunches separated by an integer number of RF periods have been used to generate the accelerating wakefields.
New quinternary selenides: Syntheses, characterizations, and electronic structure calculations
Chung, Ming-Yan; Lee, Chi-Shen
2013-06-01
Five quinternary selenides, Sr₂.₆₃Y₀.₃₇Ge₀.₆₃Sb₂.₃₇Se₈ (I), Sr₂.₆₃La₀.₃₇Ge₀.₆₃Sb₂.₃₇Se₈ (II), Sr₂.₇₁La₀.₂₉Sn₀.₇₇Bi₂.₂₃Se₈ (III), Ba₂.₆₇ La₀.₃₃ Sn₀.₆₇Sb₂.₃₃Se₈ (IV), and Ba₂.₆₇ La₀.₃₃Sn₀.₆₇Bi₂.₃₃Se₈ (V), were synthesized by solid-state reaction in fused silica tubes. These compounds are isostructural and crystallize in the Sr₃GeSb₂Se₈ structural-type, which belongs to the orthorhombic space group Pnma (no. 62). Three structural units, ^{1}_{∞}[MSe₃], ^{1}_{∞}[M₄Se₁₀] (M=Tt, Pn) and M´ (M´=groups II and III element), comprise the entire one-dimensional structure, separated by M´. Measurements of electronic resistivity and diffused reflectance suggest that IV and V have semiconducting properties. Electronic structure calculations confirm the site preferences of Sr/La element discovered by crystal structure refinement. - Graphical abstract: Quinternary selenides Ae₂.₆₇M₀.₃₃Tt₀.₆₇Pn₂.₃₃Se₈ (Ae, M, Tt, Pn=Sr/Ba, Y/La, Ge/Sn, Sb/Bi) were synthesized and their site preferences were characterized by single-crystal X-ray diffraction and electronic structure calculation. Highlights: • Five new quinternary selenides were synthesized and characterized. • Structural units, ^{1}_{∞}[MSe₃] and ^{1}_{∞}[M₄Se₁₀] (M=Tt, Pn), construct the one-dimensional structure. • Calculations of electronic structure confirm site preference of Sr/La sites.
Li, Liqi; Cui, Xiang; Yu, Sanjiu; Zhang, Yuan; Luo, Zhong; Yang, Hua; Zhou, Yue; Zheng, Xiaoqi
2014-01-01
Protein structure prediction is critical to functional annotation of the massively accumulated biological sequences, which prompts an imperative need for the development of high-throughput technologies. As a first and key step in protein structure prediction, protein structural class prediction becomes an increasingly challenging task. Amongst most homological-based approaches, the accuracies of protein structural class prediction are sufficiently high for high similarity datasets, but still far from being satisfactory for low similarity datasets, i.e., below 40% in pairwise sequence similarity. Therefore, we present a novel method for accurate and reliable protein structural class prediction for both high and low similarity datasets. This method is based on Support Vector Machine (SVM) in conjunction with integrated features from position-specific score matrix (PSSM), PROFEAT and Gene Ontology (GO). A feature selection approach, SVM-RFE, is also used to rank the integrated feature vectors through recursively removing the feature with the lowest ranking score. The definitive top features selected by SVM-RFE are input into the SVM engines to predict the structural class of a query protein. To validate our method, jackknife tests were applied to seven widely used benchmark datasets, reaching overall accuracies between 84.61% and 99.79%, which are significantly higher than those achieved by state-of-the-art tools. These results suggest that our method could serve as an accurate and cost-effective alternative to existing methods in protein structural classification, especially for low similarity datasets. PMID:24675610
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.
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
Nägele, Edgar; Moritz, Ralf
2005-10-01
Today, it is necessary to identify relevant compounds appearing in discovery and development of new drug substances in the pharmaceutical industry. For that purpose, the measurement of accurate molecular mass and empirical formula calculation is very important for structure elucidation in addition to other available analytical methods. In this work, the identification and confirmation of degradation products in a finished dosage form of the antibiotic drug amoxicillin obtained under stress conditions will be demonstrated. Structure elucidation is performed utilizing liquid chromatography (LC) ion trap MS/MS and MS3 together with accurate mass measurement of the molecular ions and of the collision induced dissociation (CID) fragments by liquid chromatography electro spray ionization time-of-flight mass spectrometry (LC/ESI-TOF). PMID:16099170
NASA Astrophysics Data System (ADS)
Vogt, Natalja; Khaikin, Leonid S.; Grikina, Olga E.; Rykov, Anatolii N.
2013-10-01
The equilibrium structure of uracil, one of the nucleobases, which build nucleic acids, has been determined for the first time by the gas-phase electron diffraction (GED) method. The necessary rovibrational corrections to the experimental internuclear distances have been calculated with quadratic and cubic force constants in the MP2(all)/cc-pVTZ approximation. For the first time, the equilibrium structure has been optimized by the very time-consuming coupled-cluster method with single and double excitations and perturbative treatment of connected triples using the correlation-consistent polarized weighted core-valence triple-zeta basis set with all electrons being correlated (CCSD(T)(all)/cc-pwCVTZ). The optimized structural parameters have been corrected for the diffuse-function effects and extrapolated to the higher basis set (cc-pwCVQZ) using results of MP2 computations (named as best ab initio structure). The GED equilibrium structure remarkably agrees with the best ab initio one as well as with that one derived from microwave (MW) rotational constants by Puzzarini and Barone. Thus, it has been revealed that the precise experiment and coupled-cluster calculations yield the same results when accurate vibrational corrections (including anharmonic ones) are considered in the experimental structural analysis. Moreover, it has been shown that the equilibrium structure derived from the GED data, being in general of one order less accurate than that determined from the MW rotational constants, is still reliable and accurate.
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.
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
Hartree-Fock electronic structure calculations for free atoms and immersed atoms in an electron gas
NASA Astrophysics Data System (ADS)
Walsh, Kenneth Charles
Electronic structure calculations for free and immersed atoms are performed in the context of unrestricted Hartree-Fock Theory. Spherical symmetry is broken, lifting degeneracies in electronic configurations involving the magnetic quantum number mℓ. Basis sets, produced from density functional theory, are then explored for completeness. Comparison to spectroscopic data is done by a configurational interaction of the appropriate L and S symmetry. Finally, a perturbation technique by Lowdin is used to couple the bound atomic states to a neutral, uniform background electronic gas (jellium).
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
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.
Orenstein, Yaron; Wang, Yuhao; Berger, Bonnie
2016-01-01
Motivation: Protein–RNA interactions, which play vital roles in many processes, are mediated through both RNA sequence and structure. CLIP-based methods, which measure protein–RNA binding in vivo, suffer from experimental noise and systematic biases, whereas in vitro experiments capture a clearer signal of protein RNA-binding. Among them, RNAcompete provides binding affinities of a specific protein to more than 240 000 unstructured RNA probes in one experiment. The computational challenge is to infer RNA structure- and sequence-based binding models from these data. The state-of-the-art in sequence models, Deepbind, does not model structural preferences. RNAcontext models both sequence and structure preferences, but is outperformed by GraphProt. Unfortunately, GraphProt cannot detect structural preferences from RNAcompete data due to the unstructured nature of the data, as noted by its developers, nor can it be tractably run on the full RNACompete dataset. Results: We develop RCK, an efficient, scalable algorithm that infers both sequence and structure preferences based on a new k-mer based model. Remarkably, even though RNAcompete data is designed to be unstructured, RCK can still learn structural preferences from it. RCK significantly outperforms both RNAcontext and Deepbind in in vitro binding prediction for 244 RNAcompete experiments. Moreover, RCK is also faster and uses less memory, which enables scalability. While currently on par with existing methods in in vivo binding prediction on a small scale test, we demonstrate that RCK will increasingly benefit from experimentally measured RNA structure profiles as compared to computationally predicted ones. By running RCK on the entire RNAcompete dataset, we generate and provide as a resource a set of protein–RNA structure-based models on an unprecedented scale. Availability and Implementation: Software and models are freely available at http://rck.csail.mit.edu/ Contact: bab@mit.edu Supplementary information
Bitsie, Fernando; Jensen, Brian D.; de Boer, Maarten
1999-07-15
We have designed, fabricated, tested and modeled a first generation small area test structure for MEMS fracture studies by electrostatic rather than mechanical probing. Because of its small area, this device has potential applications as a lot monitor of strength or fatigue of the MEMS structural material. By matching deflection versus applied voltage data to a 3-D model of the test structure, we develop high confidence that the local stresses achieved in the gage section are greater than 1 GPa. Brittle failure of the polycrystalline silicon was observed.
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).
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.
NASA Astrophysics Data System (ADS)
Wu, Shunguang; Hong, Lang
2008-04-01
A framework of simultaneously estimating the motion and structure parameters of a 3D object by using high range resolution (HRR) and ground moving target indicator (GMTI) measurements with template information is given. By decoupling the motion and structure information and employing rigid-body constraints, we have developed the kinematic and measurement equations of the problem. Since the kinematic system is unobservable by using only one scan HRR and GMTI measurements, we designed an architecture to run the motion and structure filters in parallel by using multi-scan measurements. Moreover, to improve the estimation accuracy in large noise and/or false alarm environments, an interacting multi-template joint tracking (IMTJT) algorithm is proposed. Simulation results have shown that the averaged root mean square errors for both motion and structure state vectors have been significantly reduced by using the template information.
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
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
Surface crystallography and electronic structure of potassium yttrium tungstate
Atuchin, V. V.; Pokrovsky, L. D.; Khyzhun, O. Yu.; Sinelnichenko, A. K.; Ramana, C. V.
2008-08-01
Structural and electronic characteristics of KY(WO{sub 4}){sub 2} (KYW) (010) crystal surfaces have been studied using reflection high-energy electron diffraction (RHEED) and x-ray photoelectron spectroscopy (XPS). The results indicate that the crystal structure and chemical composition of the mechanically polished pristine surface is stoichiometrically well maintained as expected for KYW crystals. Combined measurements of RHEED and XPS as a function of 1.5 keV Ar{sup +} ion irradiation of the KYW (010) surfaces indicate amorphization, partial loss of potassium atoms, and partial transformation of chemical valence state of tungsten from W{sup 6+} to a lower valence state, W{sup 0} state predominantly, which induces electronic states at the top of valence band.
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}
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. PMID:26866276
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.
The electronic structure of grain boundaries in Nb
Sowa, E.C.; Gonis, A. ); Zhang, X.G. )
1990-11-01
We present first-principles calculations of the electronic structure of Nb grain boundaries. These are the first such calculations for a bcc metal using the real-space multiple-scattering theory (RSMST). Local densities of states near a {Sigma}5 twist grain boundary are compared to those for bulk Nb. 5 refs., 1 fig.
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.
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.
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.
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
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.
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)
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.
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. PMID:23000705
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.
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
Writing Electron Dot Structures: Abstract of Issue 9905M
NASA Astrophysics Data System (ADS)
Magnell, Kenneth R.
1999-10-01
Writing Electron Dot Structures is a computer program for Mac OS that provides drill with feedback for students learning to write electron dot structures. While designed for students in the first year of college general chemistry it may also be used by high school chemistry students. A systematic method similar to that found in many general chemistry texts is employed:
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
Electronics speckle interferometry applications for NDE of spacecraft structural components
NASA Astrophysics Data System (ADS)
Rao, M. V.; Samuel, R.; Ananthan, A.; Dasgupta, S.; Nair, P. S.
2008-09-01
The spacecraft components viz., central cylinder, deck plates, solar panel substrates, antenna reflectors are made of aluminium/composite honeycomb sandwich construction. Detection of these defects spacecraft structural components is important to assess the integrity of the spacecraft structure. Electronic Speckle Interferometry (ESI) techniques identify the defects as anomalous regions in the interferometric fringe patterns of the specklegram while the component is suitably stressed to give rise to differential displacement/strain around the defective region. Calibration studies, different phase shifting methods associated with ESI and the development of a prototype Twin Head ESSI System (THESSIS) and its use for the NDE of a typical satellite structural component are presented.
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. PMID:27114055
NASA Astrophysics Data System (ADS)
Raman, Ramani K.
Electronically induced structure transformations are a unique class of phenomena in which material transformation can be effected by impulsive excitation of the electronic system, often resulting in exotic structural phases and transformation pathways inaccessible to thermodynamic channels. Using ultrafast electron crystallography (UEC), we have directly observed such photodinduced atomic dynamics in two systems - graphite and silver nanocrystals (Ag NC) that appear to be driven by the strong coupling between the laser excitation and lattice perturbations in the form of strongly coupled optical phonons and laser induced electron redistribution. In graphite, structural changes resulting from photoexcitation with p-polarized, near-IR, femtosecond laser pulses are observed to lead to the nonthermal creation of a transient state with sp3 like bonding characteristics. At laser fluences approaching, but below the damage threshold, the average inter-layer spacing contracts along with creation of new inter-layer distances at ≈ 2 A while the lattice is only moderately heated. The advantage of using electrons (which carry a charge) as a probe is demonstrated, as it reveals the transformation to be driven by a hitherto unobserved surface dipole field, observed here via a Coulomb refraction shift of the scattered electrons within the sub-surface region. Ab initio density functional theory calculations are employed to relate these structural changes to a nonthermal heating of the electrons, followed by a photoinduced charge separation causing a compressive Coulomb stress. To quantify the role and dynamics of electrons emitted from photoexcited surfaces, a novel 'point-projection method' is introduced, capable of directly imaging the spatiotemporal evolution of such photoemitted electron bunches. The method is shown to provide sufficient sensitivity to image electron bunches (as small as 1010 e/cm3) and permit quantitative investigation of the electron emission from
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
Electronic Structure Studies of Silicon Carbide Cationic Nanoclusters
NASA Astrophysics Data System (ADS)
Pradhan, Prachi
2005-03-01
As a continuation of our studies on the high stabilities and associated electronic structure properties of Si8C2 to Si14C2 and Si20Cn (n=3-6) clusters,^1 we report here detailed ab initio electronic and geometric structure studies of small SimCn^+ (1< m, n < 4) cationic clusters. The theoretical formalism used is the local density approximation (LDA) to density functional theory (DFT) and the Gaussian03 suite of programs^2 with an all electron 6-311++G** basis set has been used. Complete geometry optimizations of different possible structures have been carried out. The stability of the clusters varies with the ratio of the number of silicon to carbon atoms in the cluster. In contrast to the neutral clusters,^3 cationic clusters appear to prefer more open structures. Results will be presented for binding energies, relative energies, fragmentation energies, vibrational frequencies, and adiabatic ionization potentials^3 for the optimized clusters. Detailed comparisons with published data in the literature will also be presented. * Work supported, in part, by the Welch Foundation, Houston, Texas (Grant No. Y-1525) ^1M. N. Huda and A. K. Ray, Phys. Rev. A (R) 69, 011201 (2004); Eur. Phys. J. D 31, 63 (2004). ^2 Gaussian03, Revision A.1, M. J. Frisch et al., Gaussian Inc., Pittsburgh, PA , 2003. ^3 P. Pradhan and A. K. Ray, J. Mol. Structure (Theochem), in press.
Ultrafast Structural Dynamics of Tertiary Amines upon Electronic Excitation
NASA Astrophysics Data System (ADS)
Cheng, Xinxin; Minitti, Michael P.; Deb, Sanghamitra; Zhang, Yao; Budarz, James; Weber, Peter M.
2011-06-01
The structural response of several tertiary amines to electronic excitation has been investigated using Rydberg Fingerprint Spectroscopy. The 3p Rydberg states are reached by excitation with a 5.93 eV photon while 3s states are populated by electronic relaxation from 3p state. We observe binding energy shifts on ultrafast time scales in all peaks that reflect the structural change of the molecular ion cores. The shifts are in the range of 15 meV to 30 meV, within time scales of less than 500 fs, depending on the specific molecular systems and the nature of the electronic state. In cases where the p states are spectrally separate, the trends of the energy shifts are different for the p_z and p_x_y Rydberg states whereas the p_z and s states are similar. This suggests that the response of the Rydberg states to structural displacements depends on the symmetry. Very fast binding energy shifts, observed on sub-picosecond time scales, are attributed to the structural adjustment from a pyramidal to a planar structure upon Rydberg excitation. The quantitative values of the binding energy shifts can also be affected by laser chirp, which we model using simulations.
Defective graphene and nanoribbons: electronic, magnetic and structural properties
NASA Astrophysics Data System (ADS)
Guerra, Thiago; Azevedo, Sérgio; Machado, Marcelo
2016-03-01
We make use of first-principles calculations, based on the density functional theory (DFT), to investigate the alterations at the structural, energetic, electronic and magnetic properties of graphene and zigzag graphene nanoribbons (ZGNRs) due to the inclusion of different types of line and punctual defects. For the graphene it is found that the inclusion of defects breaks the translational symmetry of the crystal with drastic changes at its electronic structure, going from semimetallic to semiconductor and metallic. Regarding the magnetic properties, no magnetization is observed for the defective graphene. We also show that the inclusion of defects at ZGNRs is a good way to create and control pronounced peaks at the Fermi level. Furthermore, defective ZGNRs structures show magnetic moment by supercell up to 2.0 μ B . For the non defective ZGNRs is observed a switch of the magnetic coupling between opposite ribbon edges from the antiferromagnetic to the ferrimagnetic and ferromagnetic configurations.
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.
Correlation of Local Structure and Electronic Properties of Glass Materials
NASA Astrophysics Data System (ADS)
Lordi, Vincenzo; Adelstein, Nicole
2015-03-01
Wide band gap glasses such as silica and its derivatives are typically considered insulators. However, electronic transport in glasses can be important for certain applications, such as when used as the host material for a scintillator radiation detector. Here we explore the relationship between local structure in glass materials and the corresponding electronic properties of carrier transport and charge trapping. We present a novel analysis that decomposes the distribution of localized band tail states in terms of specific local structural features in the glass. Comparison of the structure-related transport properties of different glass compositions is given, using silica and sodium silicate as prototypes. Prepared by LLNL under Contract DE-AC52-07NA27344.
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.
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.
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.
Electronic structures of Ascaris trypsin inhibitor in solution
NASA Astrophysics Data System (ADS)
Zheng, Haoping
2003-11-01
The electronic structures of Ascaris trypsin inhibitor in solution are obtained by the first-principles, all-electron, ab initio calculation using the self-consistent cluster-embedding (SCCE) method. The inhibitor, made up of 62 amino acid residues with 912 atoms, has two three-dimensional solution structures: 1ata and 1atb. The calculated ground-state energy of structure 1atb is lower than that of structure 1ata by 6.12 eV. The active sites are determined and explained: only structure 1atb has a N terminal at residue ARG+31. This shows that the structure 1atb is the stable and active form of the inhibitor, which is in agreement with the experimental results. The calculation reveals that some parts of the inhibitor can be easily changed while the inhibitor’s biological activity may be kept. This kind of information may be helpful in fighting viruses such as AIDS, SARS, and flu, since these viruses have higher variability. The calculation offers an independent theoretical estimate of the precision of structure determination.
Woon, D.E.; Dunning, T.H. Jr.; Peterson, K.A.
1996-04-01
Augmented correlation consistent basis sets of double (aug-cc-pVDZ), triple (aug-cc-pVTZ), and modified quadruple zeta (aug-cc-pVQZ{prime}) quality have been employed to describe the N{sub 2}{endash}HF potential energy surface at the Hartree{endash}Fock level and with single reference correlated wave functions including Mo/ller{endash}Plesset perturbation theory (MP2, MP3, MP4) and coupled cluster methods [CCSD, CCSD(T)]. The most accurate computed equilibrium binding energies {ital D}{sub {ital e}} are (with counterpoise correction) 810 cm{sup {minus}1} (MP4/aug-cc-pVQZ{prime}) and 788 cm{sup {minus}1} [CCSD(T)/aug-cc-pVQZ{prime}]. Estimated complete basis set limits of 814 cm{sup {minus}1} (MP4) and 793 cm{sup {minus}1} [CCSD(T)] indicate that the large basis set results are essentially converged. Harmonic frequencies and zero-point energies were determined through the aug-cc-pVTZ level. Combining the zero point energies computed at the aug-cc-pVTZ level with the equilibrium binding energies computed at the aug-cc-pVQZ{prime} level, we predict {ital D}{sub 0} values of 322 and 296 cm{sup {minus}1}, respectively, at the MP4 and CCSD(T) levels of theory. Using experimental anharmonic frequencies, on the other hand, the CCSD(T) value of {ital D}{sub 0} is increased to 415 cm{sup {minus}1}, in good agreement with the experimental value recently reported by Miller and co-workers, 398{plus_minus}2 cm{sup {minus}1}. {copyright} {ital 1996 American Institute of Physics.}
Mapping the Electronic States of One Dimensional Peapod Structures
NASA Astrophysics Data System (ADS)
Hornbaker, D. J.
2003-03-01
A key issue of potential technological importance is how the electronic properties of single wall carbon nanotubes are altered by their interactions with other molecules. We address this question by examining the properties of carbon heterostructures formed by the encapsulation of C_60 molecules within the hollow interiors of single wall nanotubes.^1 We study the properties of these novel macromolecules (dubbed 'peapods') using a low temperature, ultra-high vacuum scanning tunneling microscope (STM). Our experiments reveal that while no discernable change in the atomic structure of the encapsulating nanotubes is evident, the presence of interior C_60 molecules can dramatically affect the electronic structure of the nanotube cage. Constant current STM images of peapods display pronounced spatial modulation of the electronic density at sample biases greater than 1V, with a periodicity consistent with the intermolecular spacing of close-packed C_60 molecules inside the nanotube. This effect has been observed on peapods displaying both semiconducting and metallic densities of states. Coincident with this modulation is the appearance of characteristic features in the electronic band structure measured via tunneling spectroscopy. Theoretical modeling^2,3 indicates these features arise from coupling between the valence states of the encapsulated fullerenes, leading to the formation of a hybrid electronic band. Our experiments demonstrate that encapsulation of molecules is a viable route for selectively altering the electronic properties of carbon nanotubes. ^1B.W. Smith and D.E. Luzzi, Chem. Phys. Lett. 321, 169 (2000). ^2D.J. Hornbaker et al. Science 295, 828 (2002). ^3C. Kane et al. Phys. Rev. B (submitted).
Shigella flexneri Spa15 Crystal Structure Verified in Solution by Double Electron Electron Resonance
Lillington, James E.D.; Lovett, Janet E.; Johnson, Steven; Roversi, Pietro; Timmel, Christiane R.; Lea, Susan M.
2011-01-01
Shigella flexneri Spa15 is a chaperone of the type 3 secretion system, which binds a number of effectors to ensure their stabilization prior to secretion. One of these effectors is IpgB1, a mimic of the human Ras-like Rho guanosine triphosphatase RhoG. In this study, Spa15 alone and in complex with IpgB1 has been studied by double electron electron resonance, an experiment that gives distance information showing the spacial separation of attached spin labels. This distance is explained by determining the crystal structure of the spin-labeled Spa15 where labels are seen to be buried in hydrophobic pockets. The double electron electron resonance experiment on the Spa15 complex with IpgB1 shows that IpgB1 does not bind Spa15 in the same way as is seen in the homologous Salmonella sp. chaperone:effector complex InvB:SipA. PMID:21075116
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
Antistiction technique using elastomer contact structure in woven electronic textiles
NASA Astrophysics Data System (ADS)
Yamashita, Takahiro; Takamatsu, Seiichi; Miyake, Koji; Itoh, Toshihiro
2014-01-01
In this paper, we present an antistiction technique using an elastomer contact structure in woven electronic textiles (e-textiles). A coating of poly(3,4-ethylenedioxythiophene):poly(4-styrene sulfonate) (PEDOT:PSS) in the form of a solid conductive film on a hemispherical silicone elastomer structure is employed in creating an electrical circuit embedded into the fabric of a woven e-textile, where the contact structure reduces the contact area and capillary force generated by the moisture in air between weft and warp ribbons. Stiction occurs between a weft and a warp without the contact structure under an RH of 80%, and the detachment of the stuck ribbon requires a delamination load of about 0.2 N. On the other hand, in the case of contact between the contact structure and the ribbon coated with plain PEDOT:PSS, stiction does not occur as the relative humidity increases from 20 to 80%.
Local atomic order, electronic structure and electron transport properties of Cu-Zr metallic glasses
Antonowicz, J. Pietnoczka, A.; Pękała, K.; Latuch, J.; Evangelakis, G. A.
2014-05-28
We studied atomic and electronic structures of binary Cu-Zr metallic glasses (MGs) using combined experimental and computational methods including X-ray absorption fine structure spectroscopy, electrical resistivity, thermoelectric power (TEP) measurements, molecular dynamics (MD) simulations, and ab-initio calculations. The results of MD simulations and extended X-ray absorption fine structure analysis indicate that atomic order of Cu-Zr MGs and can be described in terms of interpenetrating icosahedral-like clusters involving five-fold symmetry. MD configurations were used as an input for calculations of theoretical electronic density of states (DOS) functions which exhibits good agreement with the experimental X-ray absorption near-edge spectra. We found no indication of minimum of DOS at Fermi energy predicted by Mott's nearly free electron (NFE) model for glass-forming alloys. The theoretical DOS was subsequently used to test Mott's model describing the temperature variation of electrical resistivity and thermoelectric power of transition metal-based MGs. We demonstrate that the measured temperature variations of electrical resistivity and TEP remain in a contradiction with this model. On the other hand, the experimental temperature dependence of electrical resistivity can be explained by incipient localization of conduction electrons. It is shown that weak localization model works up to relatively high temperatures when localization is destroyed by phonons. Our results indicate that electron transport properties of Cu-Zr MGs are dominated by localization effects rather than by electronic structure. We suggest that NFE model fails to explain a relatively high glass-forming ability of binary Cu-Zr alloys.
Local atomic order, electronic structure and electron transport properties of Cu-Zr metallic glasses
NASA Astrophysics Data System (ADS)
Antonowicz, J.; Pietnoczka, A.; Pekała, K.; Latuch, J.; Evangelakis, G. A.
2014-05-01
We studied atomic and electronic structures of binary Cu-Zr metallic glasses (MGs) using combined experimental and computational methods including X-ray absorption fine structure spectroscopy, electrical resistivity, thermoelectric power (TEP) measurements, molecular dynamics (MD) simulations, and ab-initio calculations. The results of MD simulations and extended X-ray absorption fine structure analysis indicate that atomic order of Cu-Zr MGs and can be described in terms of interpenetrating icosahedral-like clusters involving five-fold symmetry. MD configurations were used as an input for calculations of theoretical electronic density of states (DOS) functions which exhibits good agreement with the experimental X-ray absorption near-edge spectra. We found no indication of minimum of DOS at Fermi energy predicted by Mott's nearly free electron (NFE) model for glass-forming alloys. The theoretical DOS was subsequently used to test Mott's model describing the temperature variation of electrical resistivity and thermoelectric power of transition metal-based MGs. We demonstrate that the measured temperature variations of electrical resistivity and TEP remain in a contradiction with this model. On the other hand, the experimental temperature dependence of electrical resistivity can be explained by incipient localization of conduction electrons. It is shown that weak localization model works up to relatively high temperatures when localization is destroyed by phonons. Our results indicate that electron transport properties of Cu-Zr MGs are dominated by localization effects rather than by electronic structure. We suggest that NFE model fails to explain a relatively high glass-forming ability of binary Cu-Zr alloys.
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
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.
Electronic and magnetic structures of CeTe2
NASA Astrophysics Data System (ADS)
Shim, J. H.; Youn, S. J.; Park, Min Sik; Min, B. I.
2005-05-01
We have investigated electronic structures of CeTe2 to explore the correlation between the magnetic, charge density wave, and superconducting phases by using the local spin density approximation (LSDA) and LSDA +U (U =on-site Coulomb interaction) methods. We have found that the contribution near EF from Ce 4f states is negligible, suggesting that Ce 4f electrons are not the superconducting carriers. The total energy calculation indicates that the ABBA-type antiferromagnetic configuration is the most stable, while the stability is weakened by pressure. We have discussed the possible superconducting mechanism in the magnetic phase of CeTe1.82.
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.
Electronic structure basis for the extraordinary magnetoresistance in WTe2.
Pletikosić, I; Ali, Mazhar N; Fedorov, A V; Cava, R J; Valla, T
2014-11-21
The electronic structure basis of the extremely large magnetoresistance in layered nonmagnetic tungsten ditelluride has been investigated by angle-resolved photoelectron spectroscopy. Hole and electron pockets of approximately the same size were found at low temperatures, suggesting that carrier compensation should be considered the primary source of the effect. The material exhibits a highly anisotropic Fermi surface from which the pronounced anisotropy of the magnetoresistance follows. 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 of the magnetoresistance in WTe2 was identified. PMID:25479512
Electronic Structure Basis for the Extraordinary Magnetoresistance in WTe2
NASA Astrophysics Data System (ADS)
Pletikosić, I.; Ali, Mazhar N.; Fedorov, A. V.; Cava, R. J.; Valla, T.
2014-11-01
The electronic structure basis of the extremely large magnetoresistance in layered nonmagnetic tungsten ditelluride has been investigated by angle-resolved photoelectron spectroscopy. Hole and electron pockets of approximately the same size were found at low temperatures, suggesting that carrier compensation should be considered the primary source of the effect. The material exhibits a highly anisotropic Fermi surface from which the pronounced anisotropy of the magnetoresistance follows. 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 of the magnetoresistance in WTe2 was identified.
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.
The surface electronic structure of silicon terminated (100) diamond.
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. PMID:27211214
Structure and dynamics in two-electron atoms
NASA Astrophysics Data System (ADS)
Shuman, Edward Somerville
In this dissertation, I present experimental studies of two-electron atoms. I have been primarily concerned with the effects of external perturbations on dielectronic recombination (DR). Specifically I have examined dielectronic recombination in the presence of electric, microwave, and combined electric and magnetic fields. These measurements illustrate that any external perturbation must have a coupling in excess of the autoionization rate to affect the DR rate. I have also studied the structure of two-electron atoms using microwave resonance techniques. In particular I present experiments which provide new insight into the core polarization model and which provide techniques for measuring both bound and autoionizing energy levels with microwaves.
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. PMID:26497974
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. PMID:26460680
van Deelen, Rutger; Hasekamp, Otto P; Landgraf, Jochen
2007-01-10
We present what we believe to be a novel approach to simulating the spectral fine structure (<1 nm) in measurements of spectrometers such as the Global Ozone Monitoring Experiment (GOME). GOME measures the Earth's radiance spectra and daily solar irradiance spectra from which a reflectivity spectrum is commonly extracted. The high-frequency structures contained in such a spectrum are, apart from atmospheric absorption, caused by Raman scattering and by a shift between the solar irradiance and the Earth's radiance spectrum. Normally, an a priori high-resolution solar spectrum is used to simulate these structures. We present an alternative method in which all the required information on the solar spectrum is retrieved from the GOME measurements. We investigate two approaches for the spectral range of 390-400 nm. First, a solar spectrum is reconstructed on a fine spectral grid from the GOME solar measurement. This approach leads to undersampling errors of up to 0.5% in the modeling of the Earth's radiance spectra. Second, a combination of the solar measurement and one of the Earth's radiance measurement is used to retrieve a solar spectrum. This approach effectively removes the undersampling error and results in residuals close to the GOME measurement noise of 0.1%. PMID:17268571
NASA Astrophysics Data System (ADS)
Chen, Hanghui; Millis, Andrew J.
2016-05-01
We systematically compare predictions of various exchange correlation functionals for the structural and magnetic properties of perovskite Sr1 -xBaxMnO3 (0 ≤x ≤1 )—a representative class of multiferroic oxides. The local spin density approximation (LSDA) and spin-dependent generalized gradient approximation with Perdew-Burke-Ernzerhof parametrization (sPBE) make substantial different predictions for ferroelectric atomic distortions, tetragonality, and ground state magnetic ordering. Neither approximation quantitatively reproduces all the measured structural and magnetic properties of perovskite Sr0.5Ba0.5MnO3 . The spin-dependent generalized gradient approximation with Perdew-Burke-Ernzerhof revised for solids parametrization (sPBEsol) and the charge-only Perdew-Burke-Ernzerhof parametrized generalized gradient approximation with Hubbard U and Hund's J extensions both provide overall better agreement with measured structural and magnetic properties of Sr0.5Ba0.5MnO3 , compared to LSDA and sPBE. Using these two methods, we find that different from previous predictions, perovskite BaMnO3 has large Mn off-center displacements and is close to a ferromagnetic-to-antiferromagnetic phase boundary, making it a promising candidate to induce effective giant magnetoelectric effects and to achieve cross-field control of polarization and magnetism.
Coulomb-interaction effects on the electronic structure of radially polarized excitons in nanorings
NASA Astrophysics Data System (ADS)
Barticevic, Z.; Pacheco, M.; Simonin, J.; Proetto, C. R.
2006-04-01
The electronic structure of radially polarized excitons in structured nanorings is analyzed, with emphasis in the ground-state properties and their dependence under applied magnetic fields perpendicular to the ring plane. The electron-hole Coulomb attraction has been treated rigorously, through numerical diagonalization of the full exciton Hamiltonian in the noninteracting electron-hole pairs basis. Depending on the relative weight of the kinetic energy and Coulomb contributions, the ground-state of polarized excitons has “extended” or “localized” features. In the first case, corresponding to small rings dominated by the kinetic energy, the ground-state shows Aharonov-Bohm (AB) oscillations due to the individual orbits of the building particles of the exciton. In the localized regime, corresponding to large rings dominated by the Coulomb interaction, the only remaining AB oscillations are due to the magnetic flux trapped between the electron and hole orbits. This dependence of the exciton, a neutral excitation, on the flux difference confirms this feature as a signature of Coulomb dominated polarized excitons. Analytical approximations are provided in both regimes, which accurately reproduce the numerical results.
Real-time feedback from iterative electronic structure calculations.
Vaucher, Alain C; Haag, Moritz P; Reiher, Markus
2016-04-01
Real-time feedback from iterative electronic structure calculations requires to mediate between the inherently unpredictable execution times of the iterative algorithm used and the necessity to provide data in fixed and short time intervals for real-time rendering. We introduce the concept of a mediator as a component able to deal with infrequent and unpredictable reference data to generate reliable feedback. In the context of real-time quantum chemistry, the mediator takes the form of a surrogate potential that has the same local shape as the first-principles potential and can be evaluated efficiently to deliver atomic forces as real-time feedback. The surrogate potential is updated continuously by electronic structure calculations and guarantees to provide a reliable response to the operator for any molecular structure. To demonstrate the application of iterative electronic structure methods in real-time reactivity exploration, we implement self-consistent semiempirical methods as the data source and apply the surrogate-potential mediator to deliver reliable real-time feedback. © 2015 Wiley Periodicals, Inc. PMID:26678030
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
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
Electronic structure and insulating gap in epitaxial VO2 polymorphs
Lee, Shinbuhm; Meyer, Tricia L.; Sohn, Changhee; Lee, Donghwa; Nichols, John A.; Lee, Dongkyu; Seo, Sung Seok Ambrose; Freeland, John W.; Noh, Tae Won; Lee, Ho Nyung
2015-12-24
Here, determining the origin of the insulating gap in the monoclinic VO2(M1) is a long-standing issue. The difficulty of this study arises from the simultaneous occurrence of structural and electronic transitions upon thermal cycling. Here, we compare the electronic structure of the M1 phase with that of single crystalline insulating VO2(A) and VO2(B) thin films to better understand the insulating phase of VO2. As these A and B phases do not undergo a structural transition upon thermal cycling, we comparatively study the origin of the gap opening in the insulating VO2 phases. By x-ray absorption and optical spectroscopy, we findmore » that the shift of unoccupied t2g orbitals away from the Fermi level is a common feature, which plays an important role for the insulating behavior in VO2 polymorphs. The distinct splitting of the half-filled t2g orbital is observed only in the M1 phase, widening the bandgap up to ~0.6 eV. Our approach of comparing all three insulating VO2 phases provides insight into a better understanding of the electronic structure and the origin of the insulating gap in VO2.« less
Oligothiophene wires: impact of torsional conformation on the electronic structure.
Kislitsyn, D A; Taber, B N; Gervasi, C F; Zhang, L; Mannsfeld, S C B; Prell, J S; Briseno, A L; Nazin, G V
2016-02-14
Charge transport in polymer- and oligomer-based semiconductor materials depends strongly on the structural ordering of the constituent molecules. Variations in molecular conformations influence the electronic structures of polymers and oligomers, and thus impact their charge-transport properties. In this study, we used Scanning Tunneling Microscopy and Spectroscopy (STM/STS) to investigate the electronic structures of different alkyl-substituted oligothiophenes displaying varied torsional conformations on the Au(111) surface. STM imaging showed that on Au(111), oligothiophenes self-assemble into chain-like structures, binding to each other via interdigitated alkyl ligands. The molecules adopted distinct planar conformations with alkyl ligands forming cis- or trans- mutual orientations. For each molecule, by using STS mapping, we identify a progression of particle-in-a-box-like states corresponding to the LUMO, LUMO+1 and LUMO+2 orbitals. Analysis of STS data revealed very similar unoccupied molecular orbital energies for different possible molecular conformations. By using density functional theory calculations, we show that the lack of variation in molecular orbital energies among the different oligothiophene conformers implies that the effect of the Au-oligothiophene interaction on molecular orbital energies is nearly identical for all studied torsional conformations. Our results suggest that cis-trans torsional disorder may not be a significant source of electronic disorder and charge carrier trapping in organic semiconductor devices based on oligothiophenes. PMID:26804474
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.
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.
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.
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.
Electronic structure of the unoccupied electron energy states in FeSe1-xTex
NASA Astrophysics Data System (ADS)
Mishra, Pramita; Lohani, Himanshu; Maniraj, M.; Nayak, Jayita; Zargar, R. A.; Awana, V. P. S.; Barman, Sudipta Roy; Sekhar, Biju Raja
2015-10-01
Inverse photoemission spectroscopic (IPES) measurements along with LDA based band structure calculations have been used to investigate the unoccupied electronic structure of FeSe1-xTex system. The observed doping and temperature dependent pseudogap in this system is found to be linked to the change in the chalcogen height in their geometric structure. The depletion in spectral weight from the near EF states at low temperature in IPES has been correlated with the enhancement of the 3z2-r2 orbitals in the photoemission spectroscopy (PES). The Coulomb correlation energy U, estimated from the combined PES and IPES spectra, signifies the enhancement in electron correlations in FeSe1-xTex, with doping. The formation of pseudogap in PES and IPES confirms the importance of correlations in the 11 family of Fe superconductors.
Chen, Kewei; Ríos, José Julián; Roca, María; Pérez-Gálvez, Antonio
2015-09-18
Dephytylated chlorophylls (chlorophyllides and pheophorbides) are the starting point of the chlorophyll catabolism in green tissues, components of the chlorophyll pattern in storage/processed food vegetables, as well as the favoured structural arrangement for chlorophyll absorption. In addition, dephytylated native chlorophylls are prone to several modifications of their structure yielding pyro-, 13(2)-hydroxy- and 15(1)-hydroxy-lactone derivatives. Despite of these outstanding remarks only few of them have been analysed by MS(n). Besides new protocols for obtaining standards, we have developed a new high throughput methodology able to determine the fragmentation pathway of 16 dephytylated chlorophyll derivatives, elucidating the structures of the new product ions and new mechanisms of fragmentation. The new methodology combines, by first time, high resolution time-of-flight mass spectrometry and powerful post-processing software. Native chlorophyllides and pheophorbides mainly exhibit product ions that involve the fragmentation of D ring, as well as additional exclusive product ions. The introduction of an oxygenated function at E ring enhances the progress of fragmentation reactions through the β-keto ester group, developing also exclusive product ions for 13(2)-hydroxy derivatives and for 15(1)-hydroxy-lactone ones. Consequently, while MS(2)-based reactions of phytylated chlorophyll derivatives point to fragmentations at the phytyl and propionic chains, dephytylated chlorophyll derivatives behave different as the absence of phytyl makes β-keto ester group and E ring more prone to fragmentation. Proposals of the key reaction mechanisms underlying the origin of new product ions have been made. PMID:26277027
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.
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.
DFT investigation on the electronic structure of Faujasite
Popeneciu, Horea; Calborean, Adrian; Tudoran, Cristian; Buimaga-Iarinca, Luiza
2013-11-13
We report here first-principle pseudopotential DFT calculations to investigate relevant aspects of the electronic structure of zeolites based FAU. Fundamental molecular issues of the band-gap and electronic population analysis were reviewed under GGA/RPBE level of theory, corroborated with a DZP basis set and Troullier-Martins norm conserving pseudo-potentials. The atom-projected density of states and the analysis of HOMO-LUMO frontier orbitals at Gamma point were performed. Their electronic transfers are discussed through the alignment and relative positions of orbitals in order to determine the way that the molecule interacts with adsorbed molecules and other practical applications. Mulliken population analysis was employed for describing atomic charge distribution in the chosen systems.
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
DFT investigation on the electronic structure of Faujasite
NASA Astrophysics Data System (ADS)
Popeneciu, Horea; Calborean, Adrian; Tudoran, Cristian; Buimaga-Iarinca, Luiza
2013-11-01
We report here first-principle pseudopotential DFT calculations to investigate relevant aspects of the electronic structure of zeolites based FAU. Fundamental molecular issues of the band-gap and electronic population analysis were reviewed under GGA/RPBE level of theory, corroborated with a DZP basis set and Troullier-Martins norm conserving pseudo-potentials. The atom-projected density of states and the analysis of HOMO-LUMO frontier orbitals at Gamma point were performed. Their electronic transfers are discussed through the alignment and relative positions of orbitals in order to determine the way that the molecule interacts with adsorbed molecules and other practical applications. Mulliken population analysis was employed for describing atomic charge distribution in the chosen systems.
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
Anomalous electronic structure and magnetoresistance in TaAs2
NASA Astrophysics Data System (ADS)
Luo, Yongkang; McDonald, R. D.; Rosa, P. F. S.; Scott, B.; Wakeham, N.; Ghimire, N. J.; Bauer, E. D.; Thompson, J. D.; Ronning, F.
2016-06-01
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.
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.
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
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
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 chemical bonding in PuO2
NASA Astrophysics Data System (ADS)
Teterin, Yu. A.; Maslakov, K. I.; Teterin, A. Yu.; Ivanov, K. E.; Ryzhkov, M. V.; Petrov, V. G.; Enina, D. A.; Kalmykov, St. N.
2013-06-01
Quantitative analysis of the x-ray photoelectron spectra structure in the binding energy (BE) range of 0 eV-˜35 eV for plutonium dioxide (PuO2) valence electrons was done. The BEs and structure of the core electronic shells (35 eV-1250 eV BE), as well as the relativistic discrete variation calculation results for the finite fragments of the PuO2 lattice and the data of other authors, were taken into account. The experimental data show that the many-body effects and the multiplet splitting contribute to the spectral structure much less than the outer (0 eV-˜15 eV) and the inner (˜15 eV-˜35 eV) valence molecular orbitals (OVMO and IVMO, respectively). The filled Pu 5f electronic states were shown to form in the PuO2 valence band. The Pu 6p electrons participate in the formation of both the IVMO and the OVMO (bands). The filled Pu 6p3/2 and the O 2s electronic shells were found to take maximum part in the IVMO formation. The MO composition and the sequence order in the BE range of 0 eV-˜35 eV in PuO2 were established. The experimental and theoretical data allowed a quantitative MO scheme for PuO2, which is fundamental for understanding both the chemical bond nature in plutonium dioxide and the interpretation of other x-ray spectra of PuO2.
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.
Molecular structures of porphyrin-quinone models for electron transfer
Fajer, J.; Barkigia, K.M.; Melamed, D.; Sweet, R.M.; Kurreck, H.; Gersdorff, J. von; Plato, M.; Rohland, H.C.; Elger, G.; Moebius, K.
1996-08-15
Synthetic porphyrin-quinone complexes are commonly used to mimic electron transport in photosynthetic reaction centers and to probe the effects of energetics, distances, and relative orientations on rates of electron transfer between donor-acceptor couples. The structures of two such models have been determined by X-ray diffraction. The redox pairs consist of a zinc porphyrin covalently linked to benzoquinone in cis and trans configurations via a cyclohexanediyl bridge. The crystallographic studies were undertaken to provide a structural foundation for the extensive body of experimental and theoretical results that exists for these compounds in both the ground and photoinduced charge-separated states. The results validate conclusions reached from theoretical calculations, EPR and two-dimensional NMR results for these states. 15 refs., 6 figs., 2 tabs.
Atomic and electronic structure of Ni-Nb metallic glasses
Yuan, C. C.; Yang, Y.-F. Xi, X. K.
2013-12-07
Solid state {sup 93}Nb nuclear magnetic resonance spectroscopy has been employed to investigate the atomic and electronic structures in Ni-Nb based metallic glass (MG) model system. {sup 93}Nb nuclear magnetic resonance (NMR) isotropic metallic shift of Ni{sub 60}Nb{sub 35}Sn{sub 5} has been found to be ∼100 ppm lower than that of Ni{sub 60}Nb{sub 35}Zr{sub 5} MG, which is correlated with their intrinsic fracture toughness. The evolution of {sup 93}Nb NMR isotropic metallic shifts upon alloying is clearly an electronic origin, as revealed by both local hyperfine fields analysis and first-principle computations. This preliminary result indicates that, in addition to geometrical considerations, atomic form factors should be taken into a description of atomic structures for better understanding the mechanical behaviors of MGs.
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.
A Synchrotron Investigation Of The Electronic Structure Of Lanthanide Zirconates
NASA Astrophysics Data System (ADS)
Clements, Richard; Kennedy, Brendan; Ling, Christopher; Stampfl, Anton P. J.
2010-03-01
abstract- The lanthanide zirconates are of interest for use in inert matrix fuels and nuclear wasteforms. For use in these applications, the material's structure must be resistant to radiation damage and its thermal, thermodynamic and mechanical properties must be known. The rare earth zirconates are interesting model systems to explore such problems. In such materials the f-electrons may play a localized valence decisive role in determining their thermo-mechanical properties. We have undertaken a synthesis of the full range of the lanthanide zirconate series using solid state techniques. We have performed X-ray photoemission spectroscopy (XPS) and X-ray absorption near edge spectroscopy (XANES) with synchrotron radiation on a selection of the series, in conjunction with a density functional theory (DFT) determination of the electronic structure. -
Strongly correlated electron materials. I. Theory of the quasiparticle structure
Lopez-Aguilar, F.; Costa-Quintana, J.; Puig-Puig, L. )
1993-07-01
In this paper we give a method for analyzing the renormalized electronic structure of the Hubbard systems. The first step is the determination of effective interactions from the random-phase approximation (RPA) and from an extended RPA (ERPA) that introduces vertex effects within the bubble polarization. The second step is the determination of the density of states deduced from the spectral functions. Its analysis leads us to conclude that these systems can exhibit three types of resonances in their electronic structures: the lower-, middle-, and upper-energy resonances. Furthermore, we analyze the conditions for which there is only one type of resonance and the causes that lead to the disappearance of the heavy-fermion state. We finally introduce the RPA and ERPA effective interactions within the strong-coupling theory and we give the conditions for obtaining coupling and superconductivity.
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.
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. PMID:26768147
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
Elongation method for electronic structure calculations of random DNA sequences.
Orimoto, Yuuichi; Liu, Kai; Aoki, Yuriko
2015-10-30
We applied ab initio order-N elongation (ELG) method to calculate electronic structures of various deoxyribonucleic acid (DNA) models. We aim to test potential application of the method for building a database of DNA electronic structures. The ELG method mimics polymerization reactions on a computer and meets the requirements for linear scaling computational efficiency and high accuracy, even for huge systems. As a benchmark test, we applied the method for calculations of various types of random sequenced A- and B-type DNA models with and without counterions. In each case, the ELG method maintained high accuracy with small errors in energy on the order of 10(-8) hartree/atom compared with conventional calculations. We demonstrate that the ELG method can provide valuable information such as stabilization energies and local densities of states for each DNA sequence. In addition, we discuss the "restarting" feature of the ELG method for constructing a database that exhaustively covers DNA species. PMID:26337429
Wang, Lin-Wang; Zhao, Zhengji; Meza, Juan; Wang, Lin-Wang
2008-07-11
We present a new linear scaling ab initio total energy electronic structure calculation method based on the divide-and-conquer strategy. This method is simple to implement, easily to parallelize, and produces very accurate results when compared with the direct ab initio method. The method has been tested using up to 8,000 processors, and has been used to calculate nanosystems up to 15,000 atoms.
Quantum mirages formed by coherent projection of electronic structure
Manoharan; Lutz; Eigler
2000-02-01
Image projection relies on classical wave mechanics and the use of natural or engineered structures such as lenses or resonant cavities. Well-known examples include the bending of light to create mirages in the atmosphere, and the focusing of sound by whispering galleries. However, the observation of analogous phenomena in condensed matter systems is a more recent development, facilitated by advances in nanofabrication. Here we report the projection of the electronic structure surrounding a magnetic Co atom to a remote location on the surface of a Cu crystal; electron partial waves scattered from the real Co atom are coherently refocused to form a spectral image or 'quantum mirage'. The focusing device is an elliptical quantum corral, assembled on the Cu surface. The corral acts as a quantum mechanical resonator, while the two-dimensional Cu surface-state electrons form the projection medium. When placed on the surface, Co atoms display a distinctive spectroscopic signature, known as the many-particle Kondo resonance, which arises from their magnetic moment. By positioning a Co atom at one focus of the ellipse, we detect a strong Kondo signature not only at the atom, but also at the empty focus. This behaviour contrasts with the usual spatially-decreasing response of an electron gas to a localized perturbation. PMID:10676952
NASA Astrophysics Data System (ADS)
Zhao, Jun; Zeng, Hui; Wei, Jianwei; Li, Biao; Xu, Dahai
2014-01-01
Using the first principles calculations associated with nonequilibrium Green's function, we have studied the electronic structures and quantum transport properties of defective armchair graphene nanoribbon (AGNR) in the presence of divacancy defects. The triple pentagon-triple heptagon (555-777) defect in the defective AGNR is energetically more favorable than the pentagon-octagon-pentagon (5-8-5) defect. Our calculated results reveal that both 5-8-5-like defect and 555-777-like defect in AGNR could improve the electron transport. It is anticipated that defective AGNRs can exhibit large range variations in transport behaviors, which are strongly dependent on the distributions of the divacancy defect.
Electronic Structure of NiPdP Amorphous Metals
NASA Astrophysics Data System (ADS)
Swihart, J. C.; Nicholson, D. M. C.; Shelton, W. A.; Wang, Y.
1996-03-01
The understanding of the structure, properties and required cooling rates for bulk amorphous alloys is hindered by the the large number of constituents in the typical alloy. One of the compositionally simplest systems that can be cast into bulk specimens is Ni_0.4Pd_0.4P_0.2. Furthermore, the thoroughly studied structure of amorphous Ni_0.8P_0.2 provides a useful starting point for its investigation. We use the locally selfconsistent multiple scattering (LSMS) method to determine the electronic structure, mass density, and energy as Pd is substituted at random for Ni in the Ni_0.8P_0.2 amorphous structure. Work supported by Laboratory Directors Research Development program at Oak Ridge National Laboratory, Division of Materials Science, and the Mathematical Information and Computational Science Division of the Office of Computational Technology Research, US DOE under subcontract DEAC05-84OR21400 with Lockheed-Martin Energy Systems, Inc.
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.
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.
Structure and electronic properties of nanodiamond and its fluorination effect
NASA Astrophysics Data System (ADS)
Takai, Kazuyuki; Kogane, Kenta; Touhara, Hidekazu; Hattori, Yoshiyuki
2015-03-01
Fluorination of nano-sized diamond (ND) is expected not only to stabilize the surface structure, but also to introduce functional groups on the surface, the conduction carriers, and so on. In this study, we evaluate the structure and magnetic properties of ND and fluorinated ND (FND) in order to consider the change in the electronic state and the surface structure by fluorination. Fluorination of ND was carried out by the direct reaction between gaseous fluorine (1 atm) and commercially available detonation diamond at 623 - 873 K. X-ray Diffraction study reveals the structural stability of core part of ND during fluorination. X-ray photoemission spectroscopy exhibits F1s peak at the lower binding energy region than that for physisorbed molecular fluorine, indicating the formation of the chemical bonding between C and F in the sample. The Electron Paramagnetic Resonance results suggest that fluorination induces not only changes in the surface structure but also relaxation of defects in the core part.
Electronic Structure Studies of Amorphous Hydrogenated Boron Carbide
NASA Astrophysics Data System (ADS)
Sky Driver, M.; Sandstrom, Joseph; Boyko, Teak; Moewes, Alexander; Caruso, Anthony
2010-03-01
Boron carbide is a technologically relevant material with importance in voltaic transduction. However, the local physical, chemical and electronic structure of low temperature deposited thin films of amorphous boron carbide is far from understood, hindering its progress in application. X-ray absorption and emission spectroscopies (XAS/XES) were applied to thin films of B4C and B5C:Hx to study the near Fermi edge structure; the films were prepared by RF magnetron sputtering and plasma enhanced chemical vapor deposition (PECVD) and were thermally treated after deposition from 400 to 800 C. XES spectra indicate a physical structure transition from amorphous to nanocrystalline at 700 C, a much lower temperature than expected from traditional physical vapor deposition or flash annealing temperatures reported. These structural differences are of significant interest to transport measurements and will be discussed as a correlation. Further, x-ray and ultraviolet photoemission were also collected as a compliment to XES/XAS and will be discussed in the context of understanding the local intra vs. intermolecular electronic structure of these boron-rich molecular based solids.
On the filamentary structure of energetic electrons during flares
NASA Astrophysics Data System (ADS)
Drake, J.; Swisdak, M.; Shay, M.
2007-12-01
Simulations and analytic arguments are presented that demonstrate that magnetic reconnection in the tenuous high temperature corona does not occur as a single large-scale x-line. Rather the narrow current layers that form at x-lines form secondary magnetic islands at small spatial scales. An electron acceleration model based on the interaction of particles with many contracting islands has been developed. A consequence of particle acceleration in any multi-island system is that energetic particles are released in narrow streams with characteristic widths of the order of the electron skin depth. This is because electrons are released from islands as they reconnect with the macro-scale field of the corona or magnetosphere. The characteristic width of the released energetic electron streams correspond to the width of the reconnection dissipation region. Thus, energetic electrons do not propagate away from the reconnection site in the corona as a single large-scale front but as a filamentary web. As a result, the return current problem is transformed: the narrow filaments of energetic particles propagate parallel to the magnetic field as kinetic Alfven waves with propagation speeds comparable to the thermal velocity of the energetic particles. Simple estimates suggest that the conversion of particle to kinetic Alfven wave energy is efficient so that the wave and particle energy propagates together as a radiation front from the corona toward the solar surface. The structure and dynamics of this radiation front are being explored.
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.
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.
Electronic Structure Studies of Silicon Carbide Anionic Nanoclusters
NASA Astrophysics Data System (ADS)
Pradhan, Prachi
2005-03-01
As a continuation of our studies on the high stabilities and electronic structure properties of Si8C2 to Si14C2 clusters and Si60Cn (n=3-6) clusters,^1 we report here ab initio studies of small SimCn^- (1< m, n < 4) anionic clusters. The theoretical formalism used is the local density approximation (LDA) to density functional theory (DFT) and the Gaussian03 suite of programs^2 with an all electron 6-311++G** basis set has been used. Complete geometry optimizations of different possible structures have been carried out. Carbon-rich and silicon rich species show distinctly different patterns with respect to the vertical detachment energies. For carbon-rich aggregates, the VDE's show an even odd alternation, similar to that of the carbon anions. We present results on binding energies, relative energies, fragmentation energies, vertical detachment energies, vibrational frequencies, and adiabatic electron affinities^3 for the optimized clusters. Detailed comparisons with published data in the literature will also be presented. * Work supported, in part, by the Welch Foundation, Houston, Texas (Grant No. Y-1525). ^1M. N. Huda and A. K. Ray, Phys. Rev. A (R) 69, 011201 (2004); Eur. Phys. J. D 31, 63 (2004). ^2 Gaussian03, Revision A.1, M. J. Frisch et al., Gaussian Inc., Pittsburgh, PA , 2003. ^3 P. Pradhan and A. K. Ray, J. Mol. Structure (Theochem), in press.
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
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
2015-01-01
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. PMID:26687009
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
Kim, Seungill; Kim, Myung-Shin; Kim, Yong-Min; Yeom, Seon-In; Cheong, Kyeongchae; Kim, Ki-Tae; Jeon, Jongbum; Kim, Sunggil; Kim, Do-Sun; Sohn, Seong-Han; Lee, Yong-Hwan; Choi, Doil
2015-01-01
The onion (Allium cepa L.) is one of the most widely cultivated and consumed vegetable crops in the world. Although a considerable amount of onion transcriptome data has been deposited into public databases, the sequences of the protein-coding genes are not accurate enough to be used, owing to non-coding sequences intermixed with the coding sequences. We generated a high-quality, annotated onion transcriptome from de novo sequence assembly and intensive structural annotation using the integrated structural gene annotation pipeline (ISGAP), which identified 54,165 protein-coding genes among 165,179 assembled transcripts totalling 203.0 Mb by eliminating the intron sequences. ISGAP performed reliable annotation, recognizing accurate gene structures based on reference proteins, and ab initio gene models of the assembled transcripts. Integrative functional annotation and gene-based SNP analysis revealed a whole biological repertoire of genes and transcriptomic variation in the onion. The method developed in this study provides a powerful tool for the construction of reference gene sets for organisms based solely on de novo transcriptome data. Furthermore, the reference genes and their variation described here for the onion represent essential tools for molecular breeding and gene cloning in Allium spp. PMID:25362073
Chen, Kewei; Ríos, José Julián; Pérez-Gálvez, Antonio; Roca, María
2015-08-01
Phytylated chlorophyll derivatives undergo specific oxidative reactions through the natural metabolism or during food processing or storage, and consequently pyro-, 13(2)-hydroxy-, 15(1)-hydroxy-lactone chlorophylls, and pheophytins (a and b) are originated. New analytical procedures have been developed here to reproduce controlled oxidation reactions that specifically, and in reasonable amounts, produce those natural target standards. At the same time and under the same conditions, 16 natural chlorophyll derivatives have been analyzed by APCI-HPLC-hrMS(2) and most of them by the first time. The combination of the high-resolution MS mode with powerful post-processing software has allowed the identification of new fragmentation patterns, characterizing specific product ions for some particular standards. In addition, new hypotheses and reaction mechanisms for the established MS(2)-based reactions have been proposed. As a general rule, the main product ions involve the phytyl and the propionic chains but the introduction of oxygenated functional groups at the isocyclic ring produces new and specific productions and at the same time inhibits some particular fragmentations. It is noteworthy that all b derivatives, except 15(1)-hydroxy-lactone compounds, undergo specific CO losses. We propose a new reaction mechanism based in the structural configuration of a and b chlorophyll derivatives that explain the exclusive CO fragmentation in all b series except for 15(1)-hydroxy-lactone b and all a series compounds. PMID:26091781
Imai, Shunsuke; Kumar, Parimal; Hellen, Christopher U T; D'Souza, Victoria M; Wagner, Gerhard
2016-09-01
Many viruses bypass canonical cap-dependent translation in host cells by using internal ribosomal entry sites (IRESs) in their transcripts; IRESs hijack initiation factors for the assembly of initiation complexes. However, it is currently unknown how IRES RNAs recognize initiation factors that have no endogenous RNA binding partners; in a prominent example, the IRES of encephalomyocarditis virus (EMCV) interacts with the HEAT-1 domain of eukaryotic initiation factor 4G (eIF4G). Here we report the solution structure of the J-K region of this IRES and show that its stems are precisely organized to position protein-recognition bulges. This multisite interaction mechanism operates on an all-or-nothing principle in which all domains are required. This preorganization is accomplished by an 'adjuster module': a pentaloop motif that acts as a dual-sided docking station for base-pair receptors. Because subtle changes in the orientation abrogate protein capture, our study highlights how a viral RNA acquires affinity for a target protein. PMID:27525590
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
Wang, H.-Q.; Henrich, Victor E.; Altman, Eric I.
2008-01-07
We explore the use of electron spectroscopy that samples the near-surface region of a crystal to study the electronic structure at the buried interfaces between two dissimilar transition-metal oxides. The interface is probed by comparing experimental ultraviolet photoelectron spectra to model spectra and by taking sequential differences between the experimental spectra as one oxide is grown on another. Using (100) Fe{sub 3}O{sub 4}-NiO and Fe{sub 3}O{sub 4}-CoO interfaces grown by molecular beam epitaxy, we show that there is a much higher density of electronic states at the Fe{sub 3}O{sub 4}-CoO interface than at the Fe{sub 3}O{sub 4}-NiO interface. The origin of this difference is discussed.
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
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.
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.
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
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
A new parametrizable model of molecular electronic structure
NASA Astrophysics Data System (ADS)
Laikov, Dimitri N.
2011-10-01
A new electronic structure model is developed in which the ground state energy of a molecular system is given by a Hartree-Fock-like expression with parametrized one- and two-electron integrals over an extended (minimal + polarization) set of orthogonalized atom-centered basis functions, the variational equations being solved formally within the minimal basis but the effect of polarization functions being included in the spirit of second-order perturbation theory. It is designed to yield good dipole polarizabilities and improved intermolecular potentials with dispersion terms. The molecular integrals include up to three-center one-electron and two-center two-electron terms, all in simple analytical forms. A method to extract the effective one-electron Hamiltonian of nonlocal-exchange Kohn-Sham theory from the coupled-cluster one-electron density matrix is designed and used to get its matrix representation in a molecule-intrinsic minimal basis as an input to the parametrization procedure - making a direct link to the correlated wavefunction theory. The model has been trained for 15 elements (H, Li-F, Na-Cl, 720 parameters) on a set of 5581 molecules (including ions, transition states, and weakly bound complexes) whose first- and second-order properties were computed by the coupled-cluster theory as a reference, and a good agreement is seen. The model looks promising for the study of large molecular systems, it is believed to be an important step forward from the traditional semiempirical models towards higher accuracy at nearly as low a computational cost.
A new parametrizable model of molecular electronic structure.
Laikov, Dimitri N
2011-10-01
A new electronic structure model is developed in which the ground state energy of a molecular system is given by a Hartree-Fock-like expression with parametrized one- and two-electron integrals over an extended (minimal + polarization) set of orthogonalized atom-centered basis functions, the variational equations being solved formally within the minimal basis but the effect of polarization functions being included in the spirit of second-order perturbation theory. It is designed to yield good dipole polarizabilities and improved intermolecular potentials with dispersion terms. The molecular integrals include up to three-center one-electron and two-center two-electron terms, all in simple analytical forms. A method to extract the effective one-electron Hamiltonian of nonlocal-exchange Kohn-Sham theory from the coupled-cluster one-electron density matrix is designed and used to get its matrix representation in a molecule-intrinsic minimal basis as an input to the parametrization procedure--making a direct link to the correlated wavefunction theory. The model has been trained for 15 elements (H, Li-F, Na-Cl, 720 parameters) on a set of 5581 molecules (including ions, transition states, and weakly bound complexes) whose first- and second-order properties were computed by the coupled-cluster theory as a reference, and a good agreement is seen. The model looks promising for the study of large molecular systems, it is believed to be an important step forward from the traditional semiempirical models towards higher accuracy at nearly as low a computational cost. PMID:21992295
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.
Electronic structure of SrRuO{sub 3}
Fujioka, K.; Okamoto, J.; Mizokawa, T.; Fujimori, A.; Hase, I.; Abbate, M.; Lin, H.J.; Chen, C.T.; Takeda, Y.; Takano, M.
1997-09-01
We have measured photoemission and oxygen 1s x-ray absorption spectra of the ferromagnetic metal SrRuO{sub 3} and compared them with a first-principles band-structure calculation. The overall distribution of Ru 4d and O 2p spectral weight is in good agreement with that predicted by the band-structure calculation. However, the observed spectral line shape of the Ru 4d band is spread over a wide energy range and the emission intensity at the Fermi level is weakened compared to the band-structure calculation. This implies the importance of electron correlation in the Ru oxide. {copyright} {ital 1997} {ital The American Physical Society}
Model for the hyperfine structure of electronically excited KCs molecules
NASA Astrophysics Data System (ADS)
Orbán, A.; Vexiau, R.; Krieglsteiner, O.; Nägerl, H.-C.; Dulieu, O.; Crubellier, A.; Bouloufa-Maafa, N.
2015-09-01
A model for determining the hyperfine structure of the excited electronic states of diatomic bialkali heteronuclear molecules is formulated from the atomic hyperfine interactions and is applied to the case of bosonic 39KCs and fermionic 40KCs molecules. The hyperfine structure of the potential-energy curves of the states correlated to the K (4 s 2S1 /2) +Cs (6 p 2P1 /2 ,3 /2) dissociation limits is described in terms of different coupling schemes depending on the internuclear distance R . These results provide a step in the calculation of the hyperfine structure of rovibrational levels of these excited molecular states in the perspective of the identification of efficient paths for creating ultracold ground-state KCs molecules.
NASA Astrophysics Data System (ADS)
Prendergast, David; Louie, Steven G.
2010-03-01
We present an efficient generalization of the k-space interpolation scheme for electronic structure presented by E. L. Shirley, Phys. Rev. B 54, 16464 (1996), which permits the construction of a compact k-dependent Hamiltonian using a numerically optimal basis derived from a coarse-grained set of density functional theory calculations. We provide some generalizations of the initial approach which reduce the number of required initial electronic structure calculations, enabling accurate interpolation over the entire Brillouin zone based on calculations at the zone-center only for large systems. We also generalize the representation of non-local Hamiltonians, leading to a more efficient implementation which permits the use of both norm-conserving and ultrasoft pseudopotentials in the input calculations. Numerically interpolated electronic eigenvalues with accuracy that is within 0.01 eV can be produced at very little computational cost. The approach is also applicable to other theoretical frameworks such as the Dyson equation for quasiparticle excitations or the Bethe-Salpeter equation for optical responses.
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
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
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.
Semiempirical electronic structure calculation on Ca and Pb apatites
NASA Astrophysics Data System (ADS)
Matos, Maria; Terra, Joice; Ellis, D. E.
A systematic study is made on the electronic structure of stoichiometric calcium and lead apatites, using the tight binding extended Hückel method (eHT). The aim is to investigate the applicability of the semiempirical theory to study this family of compounds. A10(BO4)6X2 (A = Ca, Pb) apatites, differing by substitutions in the BO4 tetrahedral unit (B = P, As, and V) and X-channel ion (X = OH, Cl), are considered. The calculations show that eHT is suitable to describe basic properties especially concerning trends with atomic substitution and geometry changes. Band structure, Mulliken charge distribution, and bond orders are in good agreement with results of ab initio density functional theory (DFT) found in the literature. Large variations in the optical gap due to vanadium and lead substitutions are newly found. Changes in the anion X-channel affect the optical gap, which is in close agreement with DFT results. Analysis involving subnets are performed to determine the role of halogenic orbitals in the electronic structure of chloroapatites, showing evidence of covalent Cl bonding. It was also found that Pb=OH bonding in hydroxy-vanadinite Pb10(VO4)6(OH)2, recently synthesized, is weaker than that of Ca=OH in vanadate Ca10(VO4)6(OH)2. Arsenium is found to be more weakely bound to the O-tetrahedron than phosphorous, although Ca=O bond is increased with the substitution. We investigate, in addition, the electronic structure of a model system Ca10(AsO4)6(OH)2, obtained from direct As substitution in the vanadate Ca10(VO4)6(OH)2.
Electronic structure of LaPt2Si2
NASA Astrophysics Data System (ADS)
Hase, I.; Yanagisawa, T.
2013-01-01
Iron-pnictide superconductor (Ba, K)Fe2As2 has the ThCr2Si2-type crystal structure. On the other hand, recently found arsenide superconductor SrPt2As2 has the CaBe2Ge2-type structure, which is a different polymorphic form of the ThCr2Si2-type structure. LaPt2Si2 shows superconductivity with Tc = 2.2 K and the above-shown two different crystal structures have been reported previously. In this paper we have calculated the electronic structure of LaPt2Si2 from first-principles. From the total energy calculation, we show that the CaBe2Ge2-type structure is more stable in this compound. The density of states at the Fermi level (D(EF)) mainly consists of Pt1-d orbitals, while the Pt2-d orbitals contribute to D(EF) only half of Pt1-d orbitals. In contrast to iron-pnictide system, the total density of states at the Fermi level does not depend so much on the distortion of the PtX4 tetrahedra and/or the height of the X atom from the two-dimensional Pt plane. The calculated electronic specific heat coefficient is 7.0 mJ/mol K2 for LaPt2Si2, which is comparable with that of SrPt2As2, but larger than the experimental value 4 mJ/mol K2.