Electron cyclotron thruster new modeling results preparation for initial experiments

NASA Technical Reports Server (NTRS)

Hooper, E. Bickford

1993-01-01

The following topics are discussed: a whistler-based electron cyclotron resonance heating (ECRH) thruster; cross-field coupling in the helicon approximation; wave propagation; wave structure; plasma density; wave absorption; the electron distribution function; isothermal and adiabatic plasma flow; ECRH thruster modeling; a PIC code model; electron temperature; electron energy; and initial experimental tests. The discussion is presented in vugraph form.

Third-order polynomial model for analyzing stickup state laminated structure in flexible electronics

NASA Astrophysics Data System (ADS)

Meng, Xianhong; Wang, Zihao; Liu, Boya; Wang, Shuodao

2018-02-01

Laminated hard-soft integrated structures play a significant role in the fabrication and development of flexible electronics devices. Flexible electronics have advantageous characteristics such as soft and light-weight, can be folded, twisted, flipped inside-out, or be pasted onto other surfaces of arbitrary shapes. In this paper, an analytical model is presented to study the mechanics of laminated hard-soft structures in flexible electronics under a stickup state. Third-order polynomials are used to describe the displacement field, and the principle of virtual work is adopted to derive the governing equations and boundary conditions. The normal strain and the shear stress along the thickness direction in the bi-material region are obtained analytically, which agree well with the results from finite element analysis. The analytical model can be used to analyze stickup state laminated structures, and can serve as a valuable reference for the failure prediction and optimal design of flexible electronics in the future.

Structured electronic physiotherapy records.

PubMed

Buyl, Ronald; Nyssen, Marc

2009-07-01

With the introduction of the electronic health record, physiotherapists too are encouraged to store their patient records in a structured digital format. The typical nature of a physiotherapy treatment requires a specific record structure to be implemented, with special attention to user-friendliness and communication with other healthcare providers. The objective of this study was to establish a framework for the electronic physiotherapy record and to define a model for the interoperability with the other healthcare providers involved in the patients' care. Although we started from the Belgian context, we used a generic approach so that the results can easily be extrapolated to other countries. The framework we establish here defines not only the different building blocks of the electronic physiotherapy record, but also describes the structure and the content of the exchanged data elements. Through a combined effort by all involved parties, we elaborated an eight-level structure for the electronic physiotherapy record. Furthermore we designed a server-based model for the exchange of data between electronic record systems held by physicians and those held by physiotherapists. Two newly defined XML messages enable data interchange: the physiotherapy prescription and the physiotherapy report. We succeeded in defining a solid, structural model for electronic physiotherapist record systems. Recent wide scale implementation of operational elements such as the electronic registry has proven to make the administrative work easier for the physiotherapist. Moreover, within the proposed framework all the necessary building blocks are present for further data exchange and communication with other healthcare parties in the future. Although we completed the design of the structure and already implemented some new aspects of the electronic physiotherapy record, the real challenge lies in persuading the end-users to start using these electronic record systems. Via a quality label certification procedure, based on adequate criteria, the Ministry of Health tries to promote the use of electronic physiotherapy records. We must keep in mind that physiotherapists will show an interest in electronic record keeping, only if this will lead to a positive return for them.

Bias effects on the electronic spectrum of a molecular bridge

DOE Office of Scientific and Technical Information (OSTI.GOV)

Phillips, Heidi; Prociuk, Alexander; Dunietz, Barry D

2011-01-01

In this paper the effect of bias and geometric symmetry breaking on the electronic spectrum of a model molecular system is studied. Geometric symmetry breaking can either enhance the dissipative effect of the bias, where spectral peaks are disabled, or enable new excitations that are absent under zero bias conditions. The spectralanalysis is performed on a simple model system by solving for the electronic response to an instantaneously impulsive perturbation in the dipole approximation. The dynamical response is extracted from the electronic equations of motion as expressed by the Keldysh formalism. This expression provides for the accurate treatment of themore » electronic structure of a bulk-coupled system at the chosen model Hamiltonian electronic structure level.« less

Observations and Modeling of the Nighttime Electron Density Enhancement in the Mid-latitude Ionosphere

NASA Astrophysics Data System (ADS)

Chen, C.; Saito, A.; Lin, C.; Huba, J. D.; Liu, J. G.

2010-12-01

In this study, we compare the observational data from FORMOSAT-3/COSMIC and theoretical model results performed by SAMI2 (Sami2 is Another Model of the Ionosphere) for studying the longitudinal structure of the Mid-latitude Summer Nighttime Anomaly (MSNA). In order to study the occurrence of the nighttime electron density enhancement, we defined MSNA index by the ratio of the difference of the nighttime and daytime electron densities. The observational results by the FORMOSAT-3/COSMIC satellites show that there are three obvious nighttime electron density enhancement areas around South American, European, and Northeast Asian regions during local summer. The SAMI2 model can also successfully reproduce the ionospheric MSNA structure during local summer on both hemispheres, except for Northeast Asian region. This difference between observation and model simulation may be caused by the difference between the neutral wind model and the real winds. The physical mechanisms for the longitudinal structure of the MSNA are investigated in the different model conditions. Results show that the equatorward meridional neutral winds can drive the electron density up to a higher altitude along the magnetic field lines and the longer plasma production rate by solar EUV at higher latitudes in the summer time can provide the electron density source in the nighttime ionosphere. We concluded that the combination effect by the neutral wind and the plasma production rate play the important role of the MSNA longitudinal structure.

Quantum Impurity Models as Reference Systems for Strongly Correlated Materials: The Road from the Kondo Impurity Model to First Principles Electronic Structure Calculations with Dynamical Mean-Field Theory

NASA Astrophysics Data System (ADS)

Kotliar, Gabriel

2005-01-01

Dynamical mean field theory (DMFT) relates extended systems (bulk solids, surfaces and interfaces) to quantum impurity models (QIM) satisfying a self-consistency condition. This mapping provides an economic description of correlated electron materials. It is currently used in practical computations of physical properties of real materials. It has also great conceptual value, providing a simple picture of correlated electron phenomena on the lattice, using concepts derived from quantum impurity models such as the Kondo effect. DMFT can also be formulated as a first principles electronic structure method and is applicable to correlated materials.

Teaching Chemistry with Electron Density Models

NASA Astrophysics Data System (ADS)

Shusterman, Gwendolyn P.; Shusterman, Alan J.

1997-07-01

Linus Pauling once said that a topic must satisfy two criteria before it can be taught to students. First, students must be able to assimilate the topic within a reasonable amount of time. Second, the topic must be relevant to the educational needs and interests of the students. Unfortunately, the standard general chemistry textbook presentation of "electronic structure theory", set as it is in the language of molecular orbitals, has a difficult time satisfying either criterion. Many of the quantum mechanical aspects of molecular orbitals are too difficult for most beginning students to appreciate, much less master, and the few applications that are presented in the typical textbook are too limited in scope to excite much student interest. This article describes a powerful new method for teaching students about electronic structure and its relevance to chemical phenomena. This method, which we have developed and used for several years in general chemistry (G.P.S.) and organic chemistry (A.J.S.) courses, relies on computer-generated three-dimensional models of electron density distributions, and largely satisfies Pauling's two criteria. Students find electron density models easy to understand and use, and because these models are easily applied to a broad range of topics, they successfully convey to students the importance of electronic structure. In addition, when students finally learn about orbital concepts they are better prepared because they already have a well-developed three-dimensional picture of electronic structure to fall back on. We note in this regard that the types of models we use have found widespread, rigorous application in chemical research (1, 2), so students who understand and use electron density models do not need to "unlearn" anything before progressing to more advanced theories.

Atomic structures and electronic properties of 2H-NbSe2: The impact of Ti doping

NASA Astrophysics Data System (ADS)

Li, Hongping; Chen, Lin; Zhang, Kun; Liang, Jiaqing; Tang, Hua; Li, Changsheng; Liu, Xiaojuan; Meng, Jian; Wang, Zhongchang

2014-09-01

Layered transition metal dichalcogenides have aroused renewed interest as electronic materials, yet their electronic performances could be modified by chemical doping. Here, we perform a systematic first-principles calculation to investigate the effect of Ti doping on atomic structure and electronic properties of the 2H-NbSe2. We consider a total of three possible Ti-doping models and find that both the substitution and intercalated models are chemically preferred with the intercalation model being more favorable than the substitution one. Structural analyses reveal a slight lattice distortion triggered by Ti doping, but the original structure of 2H-NbSe2 is maintained. We also observe an expansion of c axis in the substituted model, which is attributed to the reduced van der Waals interaction arising from the increased Se-Se bond length. Our calculations also predict that the electron transport properties can be enhanced by the Ti doping, especially for the Ti-intercalated 2H-NbSe2, which should be beneficial for the realization of superconductivity. Furthermore, the covalence element is found in the Ti-Se bonds, which is ascribed to the hybridization of Ti 3d and Se 4p orbitals. The findings indicate that doping of transition metals can be regarded as a useful way to tailor electronic states so as to improve electron transport properties of 2H-NbSe2.

You are lost without a map: Navigating the sea of protein structures.

PubMed

Lamb, Audrey L; Kappock, T Joseph; Silvaggi, Nicholas R

2015-04-01

X-ray crystal structures propel biochemistry research like no other experimental method, since they answer many questions directly and inspire new hypotheses. Unfortunately, many users of crystallographic models mistake them for actual experimental data. Crystallographic models are interpretations, several steps removed from the experimental measurements, making it difficult for nonspecialists to assess the quality of the underlying data. Crystallographers mainly rely on "global" measures of data and model quality to build models. Robust validation procedures based on global measures now largely ensure that structures in the Protein Data Bank (PDB) are largely correct. However, global measures do not allow users of crystallographic models to judge the reliability of "local" features in a region of interest. Refinement of a model to fit into an electron density map requires interpretation of the data to produce a single "best" overall model. This process requires inclusion of most probable conformations in areas of poor density. Users who misunderstand this can be misled, especially in regions of the structure that are mobile, including active sites, surface residues, and especially ligands. This article aims to equip users of macromolecular models with tools to critically assess local model quality. Structure users should always check the agreement of the electron density map and the derived model in all areas of interest, even if the global statistics are good. We provide illustrated examples of interpreted electron density as a guide for those unaccustomed to viewing electron density. Copyright © 2014 Elsevier B.V. All rights reserved.

Correlation between morphology, electron band structure, and resistivity of Pb atomic chains on the Si(5 5 3)-Au surface

NASA Astrophysics Data System (ADS)

Jałochowski, M.; Kwapiński, T.; Łukasik, P.; Nita, P.; Kopciuszyński, M.

2016-07-01

Structural and electron transport properties of multiple Pb atomic chains fabricated on the Si(5 5 3)-Au surface are investigated using scanning tunneling spectroscopy, reflection high electron energy diffraction, angular resolved photoemission electron spectroscopy and in situ electrical resistance. The study shows that Pb atomic chains growth modulates the electron band structure of pristine Si(5 5 3)-Au surface and hence changes its sheet resistivity. Strong correlation between chains morphology, electron band structure and electron transport properties is found. To explain experimental findings a theoretical tight-binding model of multiple atomic chains interacting on effective substrate is proposed.

Structure analysis of Si(111)-7 × 7 reconstructed surface by transmission electron diffraction

NASA Astrophysics Data System (ADS)

Takayanagi, Kunio; Tanishiro, Yasumasa; Takahashi, Shigeki; Takahashi, Masaetsu

1985-12-01

The atomic structure of the 7 × 7 reconstructed Si(111) surface has been analysed by ultra-high vacuum (UHV) transmission electron diffraction (TED). A possible projected structure of the surface is deduced from the intensity distribution in TED patterns of normal electron incidence and from Patterson and Fourier syntheses of the intensities. A new three-dimensional structure model, the DAS model, is proposed: The model consists of 12 adatoms arranged locally in the 2 × 2 structure, a stacking fault layer and a layer with a vacancy at the corner and 9 dimers on the sides of each of the two triangular subcells of the 7 × 7 unit cell. The silicon layers in one subcell are stacked with the normal sequence, CcAaB + adatoms, while those in the other subcell are stacked with a faulted sequence, CcAa/C + adatoms. The model has only 19 dangling bonds, the smallest number among models so far proposed. Previously proposed models are tested quantitatively by the TED intensity. Advantages and limits of the TED analysis are discussed.

A graphical vector autoregressive modelling approach to the analysis of electronic diary data

PubMed Central

2010-01-01

Background In recent years, electronic diaries are increasingly used in medical research and practice to investigate patients' processes and fluctuations in symptoms over time. To model dynamic dependence structures and feedback mechanisms between symptom-relevant variables, a multivariate time series method has to be applied. Methods We propose to analyse the temporal interrelationships among the variables by a structural modelling approach based on graphical vector autoregressive (VAR) models. We give a comprehensive description of the underlying concepts and explain how the dependence structure can be recovered from electronic diary data by a search over suitable constrained (graphical) VAR models. Results The graphical VAR approach is applied to the electronic diary data of 35 obese patients with and without binge eating disorder (BED). The dynamic relationships for the two subgroups between eating behaviour, depression, anxiety and eating control are visualized in two path diagrams. Results show that the two subgroups of obese patients with and without BED are distinguishable by the temporal patterns which influence their respective eating behaviours. Conclusion The use of the graphical VAR approach for the analysis of electronic diary data leads to a deeper insight into patient's dynamics and dependence structures. An increasing use of this modelling approach could lead to a better understanding of complex psychological and physiological mechanisms in different areas of medical care and research. PMID:20359333

Electronic structures of Al-Si clusters and the magic number structure Al8Si4

NASA Astrophysics Data System (ADS)

Du, Ning; Su, Mingzhi; Chen, Hongshan

2018-02-01

The low-energy structures of Al8Sim (m = 1-6) have been determined by using the genetic algorithm combined with density functional theory and the Second-order Moller-Plesset perturbation theory (MP2) models. The results show that the close-packed structures are preferable in energy for Al-Si clusters and in most cases there exist a few isomers with close energies. The valence molecular orbitals, the orbital level structures and the electron localisation function (ELF) consistently demonstrate that the electronic structures of Al-Si clusters can be described by the jellium model. Al8Si4 corresponds to a magic number structure with pronounced stability and large energy gap; the 40 valence electrons form closed 1S21P61D102S21F142P6 shells. The ELF attractors also suggest weak covalent Si-Si, Si-Al and Al-Al bonding, and doping Si in aluminium clusters promotes the covalent interaction between Al atoms.

The structure of Escherichia coli signal recognition particle revealed by scanning transmission electron microscopy.

PubMed

Mainprize, Iain L; Beniac, Daniel R; Falkovskaia, Elena; Cleverley, Robert M; Gierasch, Lila M; Ottensmeyer, F Peter; Andrews, David W

2006-12-01

Structural studies on various domains of the ribonucleoprotein signal recognition particle (SRP) have not converged on a single complete structure of bacterial SRP consistent with the biochemistry of the particle. We obtained a three-dimensional structure for Escherichia coli SRP by cryoscanning transmission electron microscopy and mapped the internal RNA by electron spectroscopic imaging. Crystallographic data were fit into the SRP reconstruction, and although the resulting model differed from previous models, they could be rationalized by movement through an interdomain linker of Ffh, the protein component of SRP. Fluorescence resonance energy transfer experiments determined interdomain distances that were consistent with our model of SRP. Docking our model onto the bacterial ribosome suggests a mechanism for signal recognition involving interdomain movement of Ffh into and out of the nascent chain exit site and suggests how SRP could interact and/or compete with the ribosome-bound chaperone, trigger factor, for a nascent chain during translation.

The angular electronic band structure and free particle model of aromatic molecules: High-frequency photon-induced ring current

NASA Astrophysics Data System (ADS)

Öncan, Mehmet; Koç, Fatih; Şahin, Mehmet; Köksal, Koray

2017-05-01

This work introduces an analysis of the relationship of first-principles calculations based on DFT method with the results of free particle model for ring-shaped aromatic molecules. However, the main aim of the study is to reveal the angular electronic band structure of the ring-shaped molecules. As in the case of spherical molecules such as fullerene, it is possible to observe a parabolic dispersion of electronic states with the variation of angular quantum number in the planar ring-shaped molecules. This work also discusses the transition probabilities between the occupied and virtual states by analyzing the angular electronic band structure and the possibility of ring currents in the case of spin angular momentum (SAM) or orbital angular momentum (OAM) carrying light. Current study focuses on the benzene molecule to obtain its angular electronic band structure. The obtained electronic band structure can be considered as a useful tool to see the transition probabilities between the electronic states and possible contribution of the states to the ring currents. The photoinduced current due to the transfer of SAM into the benzene molecule has been investigated by using analytical calculations within the frame of time-dependent perturbation theory.

A guide to the design of electronic properties of graphene nanoribbons.

PubMed

Yazyev, Oleg V

2013-10-15

Graphene nanoribbons (GNRs) are one-dimensional nanostructures predicted to display a rich variety of electronic behaviors. Depending on their structure, GNRs realize metallic and semiconducting electronic structures with band gaps that can be tuned across broad ranges. Certain GNRs also exhibit a peculiar gapped magnetic phase for which the half-metallic state can be induced as well as the topologically nontrivial quantum spin Hall electronic phase. Because their electronic properties are highly tunable, GNRs have quickly become a popular subject of research toward the design of graphene-based nanostructures for technological applications. This Account presents a pedagogical overview of the various degrees of freedom in the atomic structure and interactions that researchers can use to tailor the electronic structure of these materials. The Account provides a broad picture of relevant physical concepts that would facilitate the rational design of GNRs with desired electronic properties through synthetic techniques. We start by discussing a generic model of zigzag GNR within the tight-binding model framework. We then explain how different modifications and extensions of the basic model affect the electronic band structures of GNRs. We classify the modifications based on the following categories: (1) electron-electron and spin-orbit interactions, (2) GNR configuration, which includes width and the crystallographic orientation of the nanoribbon (chirality), and (3) the local structure of the edge. We subdivide this last category into two groups: the effects of the termination of the π-electron system and the variations of electrostatic potential at the edge. This overview of the structure-property relationships provides a view of the many different electronic properties that GNRs can realize. The second part of this Account reviews three recent experimental methods for the synthesis of structurally well-defined GNRs. We describe a family of techniques that use patterning and etching of graphene and graphite to produce GNRs. Chemical unzipping of carbon nanotubes also provides a route toward producing chiral GNRs with atomically smooth edges. Scanning tunneling microscopy/spectroscopy investigations of these unzipped GNRs have revealed edge states and strongly suggest that these GNRs are magnetic. The third approach exploits the surface-assisted self-assembly of GNRs from molecular precursors. This powerful method can provide full control over the atomic structure of narrow nanoribbons and could eventually produce more complex graphene nanostructures.

Atomic structure solution of the complex quasicrystal approximant Al77Rh15Ru8 from electron diffraction data.

PubMed

Samuha, Shmuel; Mugnaioli, Enrico; Grushko, Benjamin; Kolb, Ute; Meshi, Louisa

2014-12-01

The crystal structure of the novel Al77Rh15Ru8 phase (which is an approximant of decagonal quasicrystals) was determined using modern direct methods (MDM) applied to automated electron diffraction tomography (ADT) data. The Al77Rh15Ru8 E-phase is orthorhombic [Pbma, a = 23.40 (5), b = 16.20 (4) and c = 20.00 (5) Å] and has one of the most complicated intermetallic structures solved solely by electron diffraction methods. Its structural model consists of 78 unique atomic positions in the unit cell (19 Rh/Ru and 59 Al). Precession electron diffraction (PED) patterns and high-resolution electron microscopy (HRTEM) images were used for the validation of the proposed atomic model. The structure of the E-phase is described using hierarchical packing of polyhedra and a single type of tiling in the form of a parallelogram. Based on this description, the structure of the E-phase is compared with that of the ε6-phase formed in Al-Rh-Ru at close compositions.

Full-potential theoretical investigations of electron inelastic mean free paths and extended x-ray absorption fine structure in molybdenum.

PubMed

Chantler, C T; Bourke, J D

2014-04-09

X-ray absorption fine structure (XAFS) spectroscopy is one of the most robust, adaptable, and widely used structural analysis tools available for a range of material classes from bulk solids to aqueous solutions and active catalytic structures. Recent developments in XAFS theory have enabled high-accuracy calculations of spectra over an extended energy range using full-potential cluster modelling, and have demonstrated particular sensitivity in XAFS to a fundamental electron transport property-the electron inelastic mean free path (IMFP). We develop electron IMFP theory using a unique hybrid model that simultaneously incorporates second-order excitation losses, while precisely accounting for optical transitions dictated by the complex band structure of the solid. These advances are coupled with improved XAFS modelling to determine wide energy-range absorption spectra for molybdenum. This represents a critical test case of the theory, as measurements of molybdenum K-edge XAFS represent the most accurate determinations of XAFS spectra for any material. We find that we are able to reproduce an extended range of oscillatory structure in the absorption spectrum, and demonstrate a first-time theoretical determination of the absorption coefficient of molybdenum over the entire extended XAFS range utilizing a full-potential cluster model.

Chemical Bonding in Sulfide Minerals

DOE Office of Scientific and Technical Information (OSTI.GOV)

Vaughan, David J.; Rosso, Kevin M.

An understanding of chemical bonding and electronic structure in sulfide minerals is central to any attempt at understanding their crystal structures, stabilities and physical properties. It is also an essential precursor to understanding reactivity through modeling surface structure at the molecular scale. In recent decades, there have been remarkable advances in first principles (ab initio) methods for the quantitative calculation of electronic structure. These advances have been made possible by the very rapid development of high performance computers. Several review volumes that chart the applications of these developments in mineralogy and geochemistry are available (Tossell and Vaughan, 1992; Cygan andmore » Kubicki, 2001). An important feature of the sulfide minerals is the diversity of their electronic structures, as evidenced by their electrical and magnetic properties (see Pearce et al. 2006, this volume). Thus, sulfide minerals range from insulators through semiconductors to metals, and exhibit every type of magnetic behavior. This has presented problems for those attempting to develop bonding models for sulfides, and also led to certain misconceptions regarding the kinds of models that may be appropriate. In this chapter, chemical bonding and electronic structure models for sulfides are reviewed with emphasis on more recent developments. Although the fully ab initio quantitative methods are now capable of a remarkable degree of sophistication in terms of agreement with experiment and potential to interpret and predict behavior with varying conditions, both qualitative and more simplistic quantitative approaches will also be briefly discussed. This is because we believe that the insights which they provide are still helpful to those studying sulfide minerals. In addition to the application of electronic structure models and calculations to solid sulfides, work on sulfide mineral surfaces (Rosso and Vaughan 2006a,b) and solution complexes and clusters (Rickard and Luther, 2006) are discussed in detail later in this volume.« less

Visualizing ligand molecules in twilight electron density

PubMed Central

Weichenberger, Christian X.; Pozharski, Edwin; Rupp, Bernhard

2013-01-01

Three-dimensional models of protein structures determined by X-ray crystallo­graphy are based on the interpretation of experimentally derived electron-density maps. The real-space correlation coefficient (RSCC) provides an easily comprehensible, objective measure of the residue-based fit of atom coordinates to electron density. Among protein structure models, protein–ligand complexes are of special interest, given their contribution to understanding the molecular underpinnings of biological activity and to drug design. For consumers of such models, it is not trivial to determine the degree to which ligand-structure modelling is biased by subjective electron-density interpretation. A standalone script, Twilight, is presented for the analysis, visualization and annotation of a pre-filtered set of 2815 protein–ligand complexes deposited with the PDB as of 15 January 2012 with ligand RSCC values that are below a threshold of 0.6. It also provides simplified access to the visualization of any protein–ligand complex available from the PDB and annotated by the Uppsala Electron Density Server. The script runs on various platforms and is available for download at http://www.ruppweb.org/twilight/. PMID:23385767

Visualizing ligand molecules in Twilight electron density.

PubMed

Weichenberger, Christian X; Pozharski, Edwin; Rupp, Bernhard

2013-02-01

Three-dimensional models of protein structures determined by X-ray crystallography are based on the interpretation of experimentally derived electron-density maps. The real-space correlation coefficient (RSCC) provides an easily comprehensible, objective measure of the residue-based fit of atom coordinates to electron density. Among protein structure models, protein-ligand complexes are of special interest, given their contribution to understanding the molecular underpinnings of biological activity and to drug design. For consumers of such models, it is not trivial to determine the degree to which ligand-structure modelling is biased by subjective electron-density interpretation. A standalone script, Twilight, is presented for the analysis, visualization and annotation of a pre-filtered set of 2815 protein-ligand complexes deposited with the PDB as of 15 January 2012 with ligand RSCC values that are below a threshold of 0.6. It also provides simplified access to the visualization of any protein-ligand complex available from the PDB and annotated by the Uppsala Electron Density Server. The script runs on various platforms and is available for download at http://www.ruppweb.org/twilight/.

The Lewis Electron-Pair Model, Spectroscopy, and the Role of the Orbital Picture in Describing the Electronic Sructure of Molecules.

ERIC Educational Resources Information Center

Gallup, G. A.

1988-01-01

Describes why specific forms of orbitals used to interpret spectroscopy involving electronic transitions may not say much about the electronic structure of molecules. Discusses several theoretical approaches to explain the anomoly. Determines that the Lewis electron-pair model for molecules is a good predictor of spectroscopic results. (ML)

The stabilities and electron structures of Al-Mg clusters with 18 and 20 valence electrons

NASA Astrophysics Data System (ADS)

Yang, Huihui; Chen, Hongshan

2017-07-01

The spherical jellium model predicts that metal clusters having 18 and 20 valence electrons correspond to the magic numbers and will show specific stabilities. We explore in detail the geometric structures, stabilities and electronic structures of Al-Mg clusters containing 18 and 20 valence electrons by using genetic algorithm combined with density functional theories. The stabilities of the clusters are governed by the electronic configurations and Mg/Al ratios. The clusters with lower Mg/Al ratios are more stable. The molecular orbitals accord with the shell structures predicted by the jellium model but the 2S level interweaves with the 1D levels and the 2S and 1D orbitals form a subgroup. The clusters having 20 valence electrons form closed 1S21P61D102S2 shells and show enhanced stability. The Al-Mg clusters with a valence electron count of 18 do not form closed shells because one 1D orbital is unoccupied. The ionization potential and electron affinity are closely related to the electronic configurations; their values are determined by the subgroups the HOMO or LUMO belong to. Supplementary material in the form of one pdf file available from the Journal web page at http://https://doi.org/10.1140/epjd/e2017-80042-9

Microscopic model for intersubband gain from electrically pumped quantum-dot structures

DOE PAGES

Michael, Stephan; Chow, Weng Wah; Schneider, Han Christian

2014-10-03

We study theoretically the performance of electrically pumped self-organized quantum dots as a gain material in the mid-infrared range at room temperature. We analyze an AlGaAs/InGaAs based structure composed of dots-in-a-well sandwiched between two quantum wells. We numerically analyze a comprehensive model by combining a many-particle approach for electronic dynamics with a realistic modeling of the electronic states in the whole structure. We investigate the gain both for quasi-equilibrium conditions and current injection. We find, comparing different structures, that steady-state gain can only be realized by an efficient extraction process, which prevents an accumulation of electrons in continuum states, thatmore » make the available scattering pathways through the quantum-dot active region too fast to sustain inversion.« less

Electron tomography and computer visualisation of a three-dimensional 'photonic' crystal in a butterfly wing-scale.

PubMed

Argyros, A; Manos, S; Large, M C J; McKenzie, D R; Cox, G C; Dwarte, D M

2002-01-01

A combination of transmission electron tomography and computer modelling has been used to determine the three-dimensional structure of the photonic crystals found in the wing-scales of the Kaiser-I-Hind butterfly (Teinopalpus imperialis). These scales presented challenges for electron microscopy because the periodicity of the structure was comparable to the thickness of a section and because of the complex connectivity of the object. The structure obtained has been confirmed by taking slices of the three-dimensional computer model constructed from the tomography and comparing these with transmission electron microscope (TEM) images of microtomed sections of the actual scale. The crystal was found to have chiral tetrahedral repeating units packed in a triclinic lattice.

Theoretical study of the noble metals on semiconductor surfaces and Ti-base shape memory alloys

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ding, Yungui

1994-07-27

The electronic and structural properties of the (√3 x√3) R30° Ag/Si(111) and (√3 x √3) R30° Au/Si(111) surfaces are investigated using first principles total energy calculations. We have tested almost all experimentally proposed structural models for both surfaces and found the energetically most favorable model for each of them. The lowest energy model structure of the (√3 x √3) R30° Ag/Si(111) surface consists of a top layer of Ag atoms arranged as ``honeycomb-chained-trimers`` lying above a distorted ``missing top layer`` Si(111) substrate. The coverage of Ag is 1 monolayer (ML). We find that the honeycomb structure observed in STM imagesmore » arise from the electronic charge densities of an empty surface band near the Fermi level. The electronic density of states of this model gives a ``pseudo-gap`` around the Fermi level, which is consistent with experimental results. The lowest energy model for the (√3 x √3) R30° Au/Si(111) surface is a conjugate honeycomb-chained-trimer (CHCT-1) configuration which consists of a top layer of trimers formed by 1 ML Au atoms lying above a ``missing top layer`` Si(111) substrate with a honeycomb-chained-trimer structure for its first layer. The structures of Au and Ag are in fact quite similar and belong to the same class of structural models. However, small variation in the structural details gives rise to quite different observed STM images, as revealed in the theoretical calculations. The electronic charge density from bands around the Fermi level for the (√3 x √3) R30°, Au/Si(111) surface also gives a good description of the images observed in STM experiments. First principles calculations are performed to study the electronic and structural properties of a series of Ti-base binary alloys TiFe, TiNi, TiPd, TiMo, and TiAu in the B2 structure.« less

Chemical Defects, Electronic Structure, and Transport in N-type and P-type Organic Semiconductors: First Principles Theory

DTIC Science & Technology

2012-11-29

of localized states extending into the gap. We also introduced a simple model allowing estimates of the upper limit of the intra-grain mobility in...well as to pentacene , and DATT. This research will be described below. In addition to our work on the electronic structure and charge mobility, we have...stacking distance gives rise to a tail of localized states which act as traps for electrons and holes. We introduced a simple effective Hamiltonian model

76 FR 68366 - Airworthiness Directives; The Boeing Company Model 777-200 and -300 Series Airplanes

Federal Register 2010, 2011, 2012, 2013, 2014

2011-11-04

...-induced currents and subsequent damage to composite structures, hydraulic tubes, and actuator control... and could subsequently damage composite structures, hydraulic tubes, and actuator control electronics... subsequent damage to composite structures, hydraulic tubes, and actuator control electronics. In the event of...

Three-Dimensional Electron Optics Model Developed for Traveling-Wave Tubes

NASA Technical Reports Server (NTRS)

Kory, Carol L.

2000-01-01

A three-dimensional traveling-wave tube (TWT) electron beam optics model including periodic permanent magnet (PPM) focusing has been developed at the NASA Glenn Research Center at Lewis Field. This accurate model allows a TWT designer to develop a focusing structure while reducing the expensive and time-consuming task of building the TWT and hot-testing it (with the electron beam). In addition, the model allows, for the first time, an investigation of the effect on TWT operation of the important azimuthally asymmetric features of the focusing stack. The TWT is a vacuum device that amplifies signals by transferring energy from an electron beam to a radiofrequency (RF) signal. A critically important component is the focusing structure, which keeps the electron beam from diverging and intercepting the RF slow wave circuit. Such an interception can result in excessive circuit heating and decreased efficiency, whereas excessive growth in the beam diameter can lead to backward wave oscillations and premature saturation, indicating a serious reduction in tube performance. The most commonly used focusing structure is the PPM stack, which consists of a sequence of cylindrical iron pole pieces and opposite-polarity magnets. Typically, two-dimensional electron optics codes are used in the design of magnetic focusing devices. In general, these codes track the beam from the gun downstream by solving equations of motion for the electron beam in static-electric and magnetic fields in an azimuthally symmetric structure. Because these two-dimensional codes cannot adequately simulate a number of important effects, the simulation code MAFIA (solution of Maxwell's equations by the Finite-Integration-Algorithm) was used at Glenn to develop a three-dimensional electron optics model. First, a PPM stack was modeled in three dimensions. Then, the fields obtained using the magnetostatic solver were loaded into a particle-in-cell solver where the fully three-dimensional behavior of the beam was simulated in the magnetic focusing field. For the first time, the effects of azimuthally asymmetric designs and critical azimuthally asymmetric characteristics of the focusing stack (such as shunts, C-magnets, or magnet misalignment) on electron beam behavior have been investigated. A cutaway portion of a simulated electron beam focused by a PPM stack is illustrated.

Modeling time-coincident ultrafast electron transfer and solvation processes at molecule-semiconductor interfaces

NASA Astrophysics Data System (ADS)

Li, Lesheng; Giokas, Paul G.; Kanai, Yosuke; Moran, Andrew M.

2014-06-01

Kinetic models based on Fermi's Golden Rule are commonly employed to understand photoinduced electron transfer dynamics at molecule-semiconductor interfaces. Implicit in such second-order perturbative descriptions is the assumption that nuclear relaxation of the photoexcited electron donor is fast compared to electron injection into the semiconductor. This approximation breaks down in systems where electron transfer transitions occur on 100-fs time scale. Here, we present a fourth-order perturbative model that captures the interplay between time-coincident electron transfer and nuclear relaxation processes initiated by light absorption. The model consists of a fairly small number of parameters, which can be derived from standard spectroscopic measurements (e.g., linear absorbance, fluorescence) and/or first-principles electronic structure calculations. Insights provided by the model are illustrated for a two-level donor molecule coupled to both (i) a single acceptor level and (ii) a density of states (DOS) calculated for TiO2 using a first-principles electronic structure theory. These numerical calculations show that second-order kinetic theories fail to capture basic physical effects when the DOS exhibits narrow maxima near the energy of the molecular excited state. Overall, we conclude that the present fourth-order rate formula constitutes a rigorous and intuitive framework for understanding photoinduced electron transfer dynamics that occur on the 100-fs time scale.

QUANTUM ESPRESSO: a modular and open-source software project for quantum simulations of materials.

PubMed

Giannozzi, Paolo; Baroni, Stefano; Bonini, Nicola; Calandra, Matteo; Car, Roberto; Cavazzoni, Carlo; Ceresoli, Davide; Chiarotti, Guido L; Cococcioni, Matteo; Dabo, Ismaila; Dal Corso, Andrea; de Gironcoli, Stefano; Fabris, Stefano; Fratesi, Guido; Gebauer, Ralph; Gerstmann, Uwe; Gougoussis, Christos; Kokalj, Anton; Lazzeri, Michele; Martin-Samos, Layla; Marzari, Nicola; Mauri, Francesco; Mazzarello, Riccardo; Paolini, Stefano; Pasquarello, Alfredo; Paulatto, Lorenzo; Sbraccia, Carlo; Scandolo, Sandro; Sclauzero, Gabriele; Seitsonen, Ari P; Smogunov, Alexander; Umari, Paolo; Wentzcovitch, Renata M

2009-09-30

QUANTUM ESPRESSO is an integrated suite of computer codes for electronic-structure calculations and materials modeling, based on density-functional theory, plane waves, and pseudopotentials (norm-conserving, ultrasoft, and projector-augmented wave). The acronym ESPRESSO stands for opEn Source Package for Research in Electronic Structure, Simulation, and Optimization. It is freely available to researchers around the world under the terms of the GNU General Public License. QUANTUM ESPRESSO builds upon newly-restructured electronic-structure codes that have been developed and tested by some of the original authors of novel electronic-structure algorithms and applied in the last twenty years by some of the leading materials modeling groups worldwide. Innovation and efficiency are still its main focus, with special attention paid to massively parallel architectures, and a great effort being devoted to user friendliness. QUANTUM ESPRESSO is evolving towards a distribution of independent and interoperable codes in the spirit of an open-source project, where researchers active in the field of electronic-structure calculations are encouraged to participate in the project by contributing their own codes or by implementing their own ideas into existing codes.

Electronic band structure effects in the stopping of protons in copper [Electronic band structure non-linear effects in the stopping of protons in copper

DOE PAGES

Quashie, Edwin E.; Saha, Bidhan C.; Correa, Alfredo A.

2016-10-05

Here, we present an ab initio study of the electronic stopping power of protons in copper over a wide range of proton velocities v = 0.02–10a.u. where we take into account nonlinear effects. Time-dependent density functional theory coupled with molecular dynamics is used to study electronic excitations produced by energetic protons. A plane-wave pseudopotential scheme is employed to solve the time-dependent Kohn-Sham equations for a moving ion in a periodic crystal. The electronic excitations and the band structure determine the stopping power of the material and alter the interatomic forces for both channeling and off-channeling trajectories. Our off-channeling results aremore » in quantitative agreement with experiments, and at low velocity they unveil a crossover region of superlinear velocity dependence (with a power of ~1.5) in the velocity range v = 0.07–0.3a.u., which we associate to the copper crystalline electronic band structure. The results are rationalized by simple band models connecting two separate regimes. We find that the limit of electronic stopping v → 0 is not as simple as phenomenological models suggest and it is plagued by band-structure effects.« less

Structure-function insights of membrane and soluble proteins revealed by electron crystallography.

PubMed

Dreaden, Tina M; Devarajan, Bharanidharan; Barry, Bridgette A; Schmidt-Krey, Ingeborg

2013-01-01

Electron crystallography is emerging as an important method in solving protein structures. While it has found extensive applications in the understanding of membrane protein structure and function at a wide range of resolutions, from revealing oligomeric arrangements to atomic models, electron crystallography has also provided invaluable information on the soluble α/β-tubulin which could not be obtained by any other method to date. Examples of critical insights from selected structures of membrane proteins as well as α/β-tubulin are described here, demonstrating the vast potential of electron crystallography that is first beginning to unfold.

Method for removing atomic-model bias in macromolecular crystallography

DOEpatents

Terwilliger, Thomas C [Santa Fe, NM

2006-08-01

Structure factor bias in an electron density map for an unknown crystallographic structure is minimized by using information in a first electron density map to elicit expected structure factor information. Observed structure factor amplitudes are combined with a starting set of crystallographic phases to form a first set of structure factors. A first electron density map is then derived and features of the first electron density map are identified to obtain expected distributions of electron density. Crystallographic phase probability distributions are established for possible crystallographic phases of reflection k, and the process is repeated as k is indexed through all of the plurality of reflections. An updated electron density map is derived from the crystallographic phase probability distributions for each one of the reflections. The entire process is then iterated to obtain a final set of crystallographic phases with minimum bias from known electron density maps.

Time-efficient simulations of tight-binding electronic structures with Intel Xeon PhiTM many-core processors

NASA Astrophysics Data System (ADS)

Ryu, Hoon; Jeong, Yosang; Kang, Ji-Hoon; Cho, Kyu Nam

2016-12-01

Modelling of multi-million atomic semiconductor structures is important as it not only predicts properties of physically realizable novel materials, but can accelerate advanced device designs. This work elaborates a new Technology-Computer-Aided-Design (TCAD) tool for nanoelectronics modelling, which uses a sp3d5s∗ tight-binding approach to describe multi-million atomic structures, and simulate electronic structures with high performance computing (HPC), including atomic effects such as alloy and dopant disorders. Being named as Quantum simulation tool for Advanced Nanoscale Devices (Q-AND), the tool shows nice scalability on traditional multi-core HPC clusters implying the strong capability of large-scale electronic structure simulations, particularly with remarkable performance enhancement on latest clusters of Intel Xeon PhiTM coprocessors. A review of the recent modelling study conducted to understand an experimental work of highly phosphorus-doped silicon nanowires, is presented to demonstrate the utility of Q-AND. Having been developed via Intel Parallel Computing Center project, Q-AND will be open to public to establish a sound framework of nanoelectronics modelling with advanced HPC clusters of a many-core base. With details of the development methodology and exemplary study of dopant electronics, this work will present a practical guideline for TCAD development to researchers in the field of computational nanoelectronics.

Structure resolution by electron diffraction tomography of the complex layered iron-rich Fe-2234-type Sr{sub 5}Fe{sub 6}O{sub 15.4}

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lepoittevin, Christophe, E-mail: christophe.lepoittevin@neel.cnrs.fr

2016-10-15

The crystal structure of the strontium ferrite Sr{sub 5}Fe{sub 6}O{sub 15.4}, was solved by direct methods on electron diffraction tomography data acquired on a transmission electron microscope. The refined cell parameters are a=27.4047(3) Å, b=5.48590(7) Å and c=42.7442(4) Å in Fm2m symmetry. Its structure is built up from the intergrowth sequence between a quadruple perovskite-type layer with a complex rock-salt (RS)-type block. In the latter iron atoms are found in two different environments : tetragonal pyramid and tetrahedron. The structural model was refined by Rietveld method based on the powder X-ray diffraction pattern. - Highlights: • Complex structure of Sr{submore » 5}Fe{sub 6}O{sub 15.4} solved by electron diffraction tomography. • Observed Fourier maps allow determining missing oxygen atoms in the structure. • Structural model refined from powder X-ray diffraction data. • Intergrowth between quadruple perovskite layer with double rock-salt-type layer.« less

Supercomputer modelling of an electronic structure for KCl nanocrystal with edge dislocation with the use of semiempirical and nonempirical models

NASA Astrophysics Data System (ADS)

Timoshenko, Yu K.; Shunina, V. A.; Shashkin, A. I.

2018-03-01

In the present work we used semiempirical and non-empirical models for electronic states of KCl nanocrystal containing edge dislocation for comparison of the obtained results. Electronic levels and local densities of states were calculated. As a result we found a reasonable qualitative correlation of semiempirical and non-empirical results. Using the results of computer modelling we discuss the problem of localization of electronic states near the line of edge dislocation.

The impact of chemical structure and molecular packing on the electronic polarisation of fullerene arrays.

PubMed

Few, Sheridan; Chia, Cleaven; Teo, Daniel; Kirkpatrick, James; Nelson, Jenny

2017-07-19

Electronic polarisation contributes to the electronic landscape as seen by separating charges in organic materials. The nature of electronic polarisation depends on the polarisability, density, and arrangement of polarisable molecules. In this paper, we introduce a microscopic, coarse-grained model in which we treat each molecule as a polarisable site, and use an array of such polarisable dipoles to calculate the electric field and associated energy of any arrangement of charges in the medium. The model incorporates chemical structure via the molecular polarisability and molecular packing patterns via the structure of the array. We use this model to calculate energies of charge pairs undergoing separation in finite fullerene lattices of different chemical and crystal structures. The effective dielectric constants that we estimate from this approach are in good quantitative agreement with those measured experimentally in C 60 and phenyl-C 61 -butyric acid methyl ester (PCBM) films, but we find significant differences in dielectric constant depending on packing and on direction of separation, which we rationalise in terms of density of polarisable fullerene cages in regions of high field. In general, we find lattices containing molecules of more isotropic polarisability tensors exhibit higher dielectric constants. By exploring several model systems we conclude that differences in molecular polarisability (and therefore, chemical structure) appear to be less important than differences in molecular packing and separation direction in determining the energetic landscape for charge separation. We note that the results are relevant for finite lattices, but not necessarily for infinite systems. We propose that the model could be used to design molecular systems for effective electronic screening.

Architecture of dermatophyte cell Walls: Electron microscopic and biochemical analysis

NASA Technical Reports Server (NTRS)

Nozawa, Y.; Kitajima, Y.

1984-01-01

A review with 83 references on the cell wall structure of dermatophytes is presented. Topics discussed include separation and preparation of cell walls; microstructure of cell walls by electron microscopy; chemical composition of cell walls; structural model of cell walls; and morphological structure of cell walls.

Simulation of charge transfer and orbital rehybridization in molecular and condensed matter systems

NASA Astrophysics Data System (ADS)

Nistor, Razvan A.

The mixing and shifting of electronic orbitals in molecules, or between atoms in bulk systems, is crucially important to the overall structure and physical properties of materials. Understanding and accurately modeling these orbital interactions is of both scientific and industrial relevance. Electronic orbitals can be perturbed in several ways. Doping, adding or removing electrons from systems, can change the bond-order and the physical properties of certain materials. Orbital rehybridization, driven by either thermal or pressure excitation, alters the short-range structure of materials and changes their long-range transport properties. Macroscopically, during bond formation, the shifting of electronic orbitals can be interpreted as a charge transfer phenomenon, as electron density may pile up around, and hence, alter the effective charge of, a given atom in the changing chemical environment. Several levels of theory exist to elucidate the mechanisms behind these orbital interactions. Electronic structure calculations solve the time-independent Schrodinger equation to high chemical accuracy, but are computationally expensive and limited to small system sizes and simulation times. Less fundamental atomistic calculations use simpler parameterized functional expressions called force-fields to model atomic interactions. Atomistic simulations can describe systems and time-scales larger and longer than electronic-structure methods, but at the cost of chemical accuracy. In this thesis, both first-principles and phenomenological methods are addressed in the study of several encompassing problems dealing with charge transfer and orbital rehybridization. Firstly, a new charge-equilibration method is developed that improves upon existing models to allow next-generation force-fields to describe the electrostatics of changing chemical environments. Secondly, electronic structure calculations are used to investigate the doping dependent energy landscapes of several high-temperature superconducting materials in order to parameterize the apparently large nonlinear electron-phonon coupling. Thirdly, ab initio simulations are used to investigate the role of pressure-driven structural re-organization in the crystalline-to-amorphous (or, metallic-to-insulating) transition of a common binary phase-change material composed of Ge and Sb. Practical applications of each topic will be discussed. Keywords. Charge-equilibration methods, molecular dynamics, electronic structure calculations, ab initio simulations, high-temperature superconductors, phase-change materials.

Splitting of the neutral mechanical plane depends on the length of the multi-layer structure of flexible electronics.

PubMed

Li, Shuang; Su, Yewang; Li, Rui

2016-06-01

Multi-layer structures with soft (compliant) interlayers have been widely used in flexible electronics and photonics as an effective design for reducing interactions among the hard (stiff) layers and thus avoiding the premature failure of an entire device. The analytic model for bending of such a structure has not been well established due to its complex mechanical behaviour. Here, we present a rational analytic model, without any parameter fitting, to study the bending of a multi-layer structure on a cylinder, which is often regarded as an important approach to mechanical reliability testing of flexible electronics and photonics. For the first time, our model quantitatively reveals that, as the key for accurate strain control, the splitting of the neutral mechanical plane depends not only on the relative thickness of the middle layer, but also on the length-to-thickness ratio of the multi-layer structure. The model accurately captures the key quantities, including the axial strains in the top and bottom layers, the shear strain in the middle layer and the locations of the neutral mechanical planes of the top and bottom layers. The effects of the length of the multi-layer and the thickness of the middle layer are elaborated. This work is very useful for the design of multi-layer structure-based flexible electronics and photonics.

Splitting of the neutral mechanical plane depends on the length of the multi-layer structure of flexible electronics

PubMed Central

Li, Shuang; Li, Rui

2016-01-01

Multi-layer structures with soft (compliant) interlayers have been widely used in flexible electronics and photonics as an effective design for reducing interactions among the hard (stiff) layers and thus avoiding the premature failure of an entire device. The analytic model for bending of such a structure has not been well established due to its complex mechanical behaviour. Here, we present a rational analytic model, without any parameter fitting, to study the bending of a multi-layer structure on a cylinder, which is often regarded as an important approach to mechanical reliability testing of flexible electronics and photonics. For the first time, our model quantitatively reveals that, as the key for accurate strain control, the splitting of the neutral mechanical plane depends not only on the relative thickness of the middle layer, but also on the length-to-thickness ratio of the multi-layer structure. The model accurately captures the key quantities, including the axial strains in the top and bottom layers, the shear strain in the middle layer and the locations of the neutral mechanical planes of the top and bottom layers. The effects of the length of the multi-layer and the thickness of the middle layer are elaborated. This work is very useful for the design of multi-layer structure-based flexible electronics and photonics. PMID:27436977

Enhanced electron-phonon coupling near the lattice instability of superconducting NbC1-xNx from density-functional calculations

NASA Astrophysics Data System (ADS)

Blackburn, Simon; Côté, Michel; Louie, Steven G.; Cohen, Marvin L.

2011-09-01

Using density-functional theory within the local-density approximation, we study the electron-phonon coupling in NbC1-xNx and NbN crystals in the rocksalt structure. The Fermi surface of these systems exhibits important nesting. The associated Kohn anomaly greatly increases the electron-phonon coupling and induces a structural instability when the electronic density of states reaches a critical value. Our results reproduce the observed rise in Tc from 11.2 to 17.3 K as the nitrogen doping is increased in NbC1-xNx. To further understand the contribution of the structural instability to the rise of the superconducting temperature, we develop a model for the Eliashberg spectral function in which the effect of the unstable phonons is set apart. We show that this model together with the McMillan formula can reproduce the increase of Tc near the structural phase transition.

Atomic and electronic structure of doped Si (111 ) (2 √{3 }×2 √{3 }) R 30∘ -Sn interfaces

NASA Astrophysics Data System (ADS)

Yi, Seho; Ming, Fangfei; Huang, Ying-Tzu; Smith, Tyler S.; Peng, Xiyou; Tu, Weisong; Mulugeta, Daniel; Diehl, Renee D.; Snijders, Paul C.; Cho, Jun-Hyung; Weitering, Hanno H.

2018-05-01

The hole-doped Si (111 ) (2 √ 3 ×2 √ 3 ) R 30∘ -Sn interface exhibits a symmetry-breaking insulator-insulator transition below 100 K that appears to be triggered by electron tunneling into the empty surface-state bands. No such transition is seen in electron-doped systems. To elucidate the nature and driving force of this phenomenon, the structure of the interface must be resolved. Here we report on an extensive experimental and theoretical study, including scanning tunneling microscopy and spectroscopy (STM/STS), dynamical low-energy electron diffraction (LEED) analysis, and density functional theory (DFT) calculations, to elucidate the structure of this interface. We consider six different structure models, three of which have been proposed before, and conclude that only two of them can account for the majority of experimental data. One of them is the model according to Törnevik et al. [C. Törnevik et al., Phys. Rev. B 44, 13144 (1991), 10.1103/PhysRevB.44.13144] with a total Sn coverage of 14/12 monolayers (ML). The other is the "revised trimer model" with a total Sn coverage of 13/12 ML, introduced in this work. These two models are very difficult to discriminate on the basis of DFT or LEED alone, but STS data clearly point toward the Törnevik model as the most viable candidate among the models considered here. The STS data also provide additional insights regarding the electron-injection-driven phase transformation. Similar processes may occur at other metal/semiconductor interfaces, provided they are nonmetallic and can be doped. This could open up a new pathway toward the creation of novel surface phases with potentially very interesting and desirable electronic properties.

Electronic Structures of Anti-Ferromagnetic Tetraradicals: Ab Initio and Semi-Empirical Studies.

PubMed

Zhang, Dawei; Liu, Chungen

2016-04-12

The energy relationships and electronic structures of the lowest-lying spin states in several anti-ferromagnetic tetraradical model systems are studied with high-level ab initio and semi-empirical methods. The Full-CI method (FCI), the complete active space second-order perturbation theory (CASPT2), and the n-electron valence state perturbation theory (NEVPT2) are employed to obtain reference results. By comparing the energy relationships predicted from the Heisenberg and Hubbard models with ab initio benchmarks, the accuracy of the widely used Heisenberg model for anti-ferromagnetic spin-coupling in low-spin polyradicals is cautiously tested in this work. It is found that the strength of electron correlation (|U/t|) concerning anti-ferromagnetically coupled radical centers could range widely from strong to moderate correlation regimes and could become another degree of freedom besides the spin multiplicity. Accordingly, the Heisenberg-type model works well in the regime of strong correlation, which reproduces well the energy relationships along with the wave functions of all the spin states. In moderately spin-correlated tetraradicals, the results of the prototype Heisenberg model deviate severely from those of multi-reference electron correlation ab initio methods, while the extended Heisenberg model, containing four-body terms, can introduce reasonable corrections and maintains its accuracy in this condition. In the weak correlation regime, both the prototype Heisenberg model and its extended forms containing higher-order correction terms will encounter difficulties. Meanwhile, the Hubbard model shows balanced accuracy from strong to weak correlation cases and can reproduce qualitatively correct electronic structures, which makes it more suitable for the study of anti-ferromagnetic coupling in polyradical systems.

Temperature dependence of the hydrated electron's excited-state relaxation. I. Simulation predictions of resonance Raman and pump-probe transient absorption spectra of cavity and non-cavity models

NASA Astrophysics Data System (ADS)

Zho, Chen-Chen; Farr, Erik P.; Glover, William J.; Schwartz, Benjamin J.

2017-08-01

We use one-electron non-adiabatic mixed quantum/classical simulations to explore the temperature dependence of both the ground-state structure and the excited-state relaxation dynamics of the hydrated electron. We compare the results for both the traditional cavity picture and a more recent non-cavity model of the hydrated electron and make definite predictions for distinguishing between the different possible structural models in future experiments. We find that the traditional cavity model shows no temperature-dependent change in structure at constant density, leading to a predicted resonance Raman spectrum that is essentially temperature-independent. In contrast, the non-cavity model predicts a blue-shift in the hydrated electron's resonance Raman O-H stretch with increasing temperature. The lack of a temperature-dependent ground-state structural change of the cavity model also leads to a prediction of little change with temperature of both the excited-state lifetime and hot ground-state cooling time of the hydrated electron following photoexcitation. This is in sharp contrast to the predictions of the non-cavity model, where both the excited-state lifetime and hot ground-state cooling time are expected to decrease significantly with increasing temperature. These simulation-based predictions should be directly testable by the results of future time-resolved photoelectron spectroscopy experiments. Finally, the temperature-dependent differences in predicted excited-state lifetime and hot ground-state cooling time of the two models also lead to different predicted pump-probe transient absorption spectroscopy of the hydrated electron as a function of temperature. We perform such experiments and describe them in Paper II [E. P. Farr et al., J. Chem. Phys. 147, 074504 (2017)], and find changes in the excited-state lifetime and hot ground-state cooling time with temperature that match well with the predictions of the non-cavity model. In particular, the experiments reveal stimulated emission from the excited state with an amplitude and lifetime that decreases with increasing temperature, a result in contrast to the lack of stimulated emission predicted by the cavity model but in good agreement with the non-cavity model. Overall, until ab initio calculations describing the non-adiabatic excited-state dynamics of an excess electron with hundreds of water molecules at a variety of temperatures become computationally feasible, the simulations presented here provide a definitive route for connecting the predictions of cavity and non-cavity models of the hydrated electron with future experiments.

Design and analysis of multifunctional structures for embedded electronics in unmanned aerial vehicles

NASA Astrophysics Data System (ADS)

Kothari, Rushabh M.

Multifunctional structures are a new trend in the aerospace industry for the next generation structural design. Many future structures are expected to be something in addition to a load bearing structure. The design and analysis of multifunctional structures combining structural, electrical and thermal functionalities are presented here. The sandwich beam is considered as a starting point for the load bearing structure and then it is modified with a cavity to embed avionics and thermal controls. The embedded avionics inside the load bearing structure would allow weight reduction of the aerospace vehicle due to elimination of separate electronics housing, interconnects, cables etc. The cavity reduces strength of the structure so various reinforcements methods are evaluated. The result of various reinforcements and their effectiveness are presented. The current generation of electronics produce massive amount of heat. In the case of embedded electronics, the excessive heat presents a major challenge to the structural and heat transfer engineers. The embedded nature of electronics prevents the use of the classical heat dissipative methods such as fans and high velocity air flows, etc. The integrated thermal control of the electronics has been designed using passive heat transfer device and highly optimized particulate composite thermal interface material (TIM). The TIMs are used to fill the air gaps and reduce contact resistance between two surfaces, such as electronics and heat dissipators. The efficiency of TIM directly affects the overall heat transfer ability of the integrated thermal control system. The effect of the particles at micron and nano scales are studied for the particulate composite TIM. The thermal boundary resistance study for the particulate composite TIM with nano silica particles is presented in this thesis. The FEA analysis is used to model thermal boundary resistance and compared with the theoretical micromechanics model. The heat pipes are chosen as a part of passive heat transfer device due to their durability and excellent thermal conductivities. The multifunctional system consisting of all above components is modeled for unmanned aerial vehicle (UAV) at subsonic air speeds to demonstrate the validity of the design.

Electron microscopy study of gold nanoparticles deposited on transition metal oxides.

PubMed

Akita, Tomoki; Kohyama, Masanori; Haruta, Masatake

2013-08-20

Many researchers have investigated the catalytic performance of gold nanoparticles (GNPs) supported on metal oxides for various catalytic reactions of industrial importance. These studies have consistently shown that the catalytic activity and selectivity depend on the size of GNPs, the kind of metal oxide supports, and the gold/metal oxide interface structure. Although researchers have proposed several structural models for the catalytically active sites and have identified the specific electronic structures of GNPs induced by the quantum effect, recent experimental and theoretical studies indicate that the perimeter around GNPs in contact with the metal oxide supports acts as an active site in many reactions. Thus, it is of immense importance to investigate the detailed structures of the perimeters and the contact interfaces of gold/metal oxide systems by using electron microscopy at an atomic scale. This Account describes our investigation, at the atomic scale using electron microscopy, of GNPs deposited on metal oxides. In particular, high-resolution transmission electron microscopy (HRTEM) and high-angle annular dark-field scanning transmission electron microscopy (HAADF-STEM) are valuable tools to observe local atomic structures, as has been successfully demonstrated for various nanoparticles, surfaces, and material interfaces. TEM can be applied to real powder catalysts as received without making special specimens, in contrast to what is typically necessary to observe bulk materials. For precise structure analyses at an atomic scale, model catalysts prepared by using well-defined single-crystalline substrates are also adopted for TEM observations. Moreover, aberration-corrected TEM, which has high spatial resolution under 0.1 nm, is a promising tool to observe the interface structure between GNPs and metal oxide supports including oxygen atoms at the interfaces. The oxygen atoms in particular play an important role in the behavior of gold/metal oxide interfaces, because they may participate in catalytic reaction steps. Detailed information about the interfacial structures between GNPs and metal oxides provides valuable structure models for theoretical calculations which can elucidate the local electronic structure effective for activating a reactant molecule. Based on our observations with HRTEM and HAADF-STEM, we report the detailed structure of gold/metal oxide interfaces.

Nanoscale Insight and Control of Structural and Electronic Properties of Organic Semiconductor / Metal Interfaces

NASA Astrophysics Data System (ADS)

Maughan, Bret

Organic semiconductor interfaces are promising materials for use in next-generation electronic and optoelectronic devices. Current models for metal-organic interfacial electronic structure and dynamics are inadequate for strongly hybridized systems. This work aims to address this issue by identifying the factors most important for understanding chemisorbed interfaces with an eye towards tuning the interfacial properties. Here, I present the results of my research on chemisorbed interfaces formed between thin-films of phthalocyanine molecules grown on monocrystalline Cu(110). Using atomically-resolved nanoscale imaging in combination with surface-sensitive photoemission techniques, I show that single-molecule level interactions control the structural and electronic properties of the interface. I then demonstrate that surface modifications aimed at controlling interfacial interactions are an effective way to tailor the physical and electronic structure of the interface. This dissertation details a systematic investigation of the effect of molecular and surface functionalization on interfacial interactions. To understand the role of molecular structure, two types of phthalocyanine (Pc) molecules are studied: non-planar, dipolar molecules (TiOPc), and planar, non-polar molecules (H2Pc and CuPc). Multiple adsorption configurations for TiOPc lead to configuration-dependent self-assembly, Kondo screening, and electronic energy-level alignment. To understand the role of surface structure, the Cu(110) surface is textured and passivated by oxygen chemisorption prior to molecular deposition, which gives control over thin-film growth and interfacial electronic structure in H2Pc and CuPc films. Overall, the work presented here demonstrates a method for understanding interfacial electronic structure of strongly hybridized interfaces, an important first step towards developing more robust models for metal-organic interfaces, and reliable, predictive tuning of interfacial properties.

Analogies in electronic properties of graphene wormhole and perturbed nanocylinder

NASA Astrophysics Data System (ADS)

Pincak, R.; Smotlacha, J.

2013-11-01

The electronic properties of the wormhole and the perturbed nanocylinder were investigated using two different methods: the continuum gauge field-theory model that deals with the continuum approximation of the surface and the Haydock recursion method that transforms the surface into a simplier structure and deals with the nearest-neighbor interactions. Furthermore, the changes of the electronic properties were investigated for the case of enclosing the appropriate structure, and possible substitutes for the encloser were derived. Finally, the character of the electron flux through the perturbed wormhole was predicted from the model based on the multiwalled nanotubes. The effect of the "graphene blackhole" is introduced.

Tight-binding modeling and low-energy behavior of the semi-Dirac point.

PubMed

Banerjee, S; Singh, R R P; Pardo, V; Pickett, W E

2009-07-03

We develop a tight-binding model description of semi-Dirac electronic spectra, with highly anisotropic dispersion around point Fermi surfaces, recently discovered in electronic structure calculations of VO2-TiO2 nanoheterostructures. We contrast their spectral properties with the well-known Dirac points on the honeycomb lattice relevant to graphene layers and the spectra of bands touching each other in zero-gap semiconductors. We also consider the lowest order dispersion around one of the semi-Dirac points and calculate the resulting electronic energy levels in an external magnetic field. In spite of apparently similar electronic structures, Dirac and semi-Dirac systems support diverse low-energy physics.

How the Electronic Structure in URu2Si2 Changes with Temperature: A High-Resolution Compton Scattering Study

NASA Astrophysics Data System (ADS)

Koizumi, Akihisa; Kubo, Yasunori; Motoyama, Gaku; Yamamura, Tomoo; Sakurai, Yoshiharu

2018-06-01

We have measured directional Compton profiles on the (001) plane in URu2Si2 single crystal at several temperatures. Two-dimensional electron occupation number densities (2D-EONDs) were obtained from the profiles through electron momentum reconstruction and Lock-Crisp-West folding analyses. We have also performed band calculations based on 5f-electron itinerant and localized models and derived theoretical 2D-EONDs for comparison. The experimental 2D-EOND at 300 K is well described by the localized model, and the 2D-EOND at 10 K is consistent with the theoretical one based on the itinerant model. The difference between 2D-EONDs at 30 and 100 K reflects a gradual change in the electronic structure, which reveals some of the crossover phenomena from localized to itinerant states. The change from localized to itinerant states is also reflected in a B(r) function, which is obtained in the reconstruction analysis and is an autocorrelation function of the wave function in the position space. The process by which the electronic structure in URu2Si2 changes is demonstrated through a series of experimental results.

Electronic structure and microscopic model of V(2)GeO(4)F(2)-a quantum spin system with S = 1.

PubMed

Rahaman, Badiur; Saha-Dasgupta, T

2007-07-25

We present first-principles density functional calculations and downfolding studies of the electronic and magnetic properties of the oxide-fluoride quantum spin system V(2)GeO(4)F(2). We discuss explicitly the nature of the exchange paths and provide quantitative estimates of magnetic exchange couplings. A microscopic modelling based on analysis of the electronic structure of this systems puts it in the interesting class of weakly coupled alternating chain S = 1 systems. Based on the microscopic model, we make inferrences about its spin excitation spectra, which needs to be tested by rigorous experimental study.

Elucidating nitric oxide synthase domain interactions by molecular dynamics.

PubMed

Hollingsworth, Scott A; Holden, Jeffrey K; Li, Huiying; Poulos, Thomas L

2016-02-01

Nitric oxide synthase (NOS) is a multidomain enzyme that catalyzes the production of nitric oxide (NO) by oxidizing L-Arg to NO and L-citrulline. NO production requires multiple interdomain electron transfer steps between the flavin mononucleotide (FMN) and heme domain. Specifically, NADPH-derived electrons are transferred to the heme-containing oxygenase domain via the flavin adenine dinucleotide (FAD) and FMN containing reductase domains. While crystal structures are available for both the reductase and oxygenase domains of NOS, to date there is no atomic level structural information on domain interactions required for the final FMN-to-heme electron transfer step. Here, we evaluate a model of this final electron transfer step for the heme-FMN-calmodulin NOS complex based on the recent biophysical studies using a 105-ns molecular dynamics trajectory. The resulting equilibrated complex structure is very stable and provides a detailed prediction of interdomain contacts required for stabilizing the NOS output state. The resulting equilibrated complex model agrees well with previous experimental work and provides a detailed working model of the final NOS electron transfer step required for NO biosynthesis. © 2015 The Protein Society.

Who Needs Lewis Structures to Get VSEPR Geometries?

ERIC Educational Resources Information Center

Lindmark, Alan F.

2010-01-01

Teaching the VSEPR (valence shell electron-pair repulsion) model can be a tedious process. Traditionally, Lewis structures are drawn and the number of "electron clouds" (groups) around the central atom are counted and related to the standard VSEPR table of possible geometries. A simpler method to deduce the VSEPR structure without first drawing…

Multiscale Processes in Magnetic Reconnection

NASA Astrophysics Data System (ADS)

Surjalal Sharma, A.; Jain, Neeraj

The characteristic scales of the plasma processes in magnetic reconnection range from the elec-tron skin-depth to the magnetohydrodynamic (MHD) scale, and cross-scale coupling among them play a key role. Modeling these processes requires different physical models, viz. kinetic, electron-magnetohydrodynamics (EMHD), Hall-MHD, and MHD. The shortest scale processes are at the electron scale and these are modeled using an EMHD code, which provides many features of the multiscale behavior. In simulations using initial conditions consisting of pertur-bations with many scale sizes the reconnection takes place at many sites and the plasma flows from these interact with each other. This leads to thin current sheets with length less than 10 electron skin depths. The plasma flows also generate current sheets with multiple peaks, as observed by Cluster. The quadrupole structure of the magnetic field during reconnection starts on the electron scale and the interaction of inflow to the secondary sites and outflow from the dominant site generates a nested structure. In the outflow regions, the interaction of the electron outflows generated at the neighboring sites lead to the development of electron vortices. A signature of the nested structure of the Hall field is seen in Cluster observations, and more details of these features are expected from MMS.

Modelling of nanoscale quantum tunnelling structures using algebraic topology method

NASA Astrophysics Data System (ADS)

Sankaran, Krishnaswamy; Sairam, B.

2018-05-01

We have modelled nanoscale quantum tunnelling structures using Algebraic Topology Method (ATM). The accuracy of ATM is compared to the analytical solution derived based on the wave nature of tunnelling electrons. ATM provides a versatile, fast, and simple model to simulate complex structures. We are currently expanding the method for modelling electrodynamic systems.

Adhesion and the Lamination/Failure of Stretchable Organic and Composite Organic/Inorganic Electronic Structures

NASA Astrophysics Data System (ADS)

Yu, Deying

Stretchable organic electronics have emerged as interesting technologies for several applications where stretchability is considered important. The easy and low-cost deposition procedures for the fabrication of stretchable organic solar cells and organic light emitting devices reduce the overall cost for the fabrication of these devices. However, the interfacial cracks and defects at the interfaces of the devices, during fabrication, are detrimental to the performance of stretchable organic electronic devices. Also, as the devices are deformed under service conditions, it is possible for cracks to grow. Furthermore, the multilayered structures of the devices can fail due to the delamination and buckling of the layered structures. There is, therefore, a need to study the failure mechanism in the layered structures that are relevant to stretchable organic electronic devices. Hence, in this study, a combined experimental, analytical and computational approach is used to study the effects of adhesion and deformation on the failure mechanisms in structures that are relevant to stretchable electronic devices. First, the failure mechanisms are studied in stretchable inorganic electronic structures. The wrinkles and buckles are formed by the unloading of pre-stretched PDMS/Au structure, after the evaporation of nano-scale Au layers. They are then characterized using atomic force microscopy and scanning electron microscopy. Analytical models are used to determine the critical stresses for wrinkling and buckling. The interfacial cracking and film buckling that can occur are also studied using finite element simulations. The implications of the results are then discussed for the potential applications of micro-wrinkles and micro-buckles in the stretchable electronic structures and biomedical devices. Subsequently, the adhesion between bi-material pairs that are relevant to organic light emitting devices, composite organic/inorganic light emitting devices, organic bulk heterojunction solar cells, and composite organic/inorganic solar cells on flexible substrates, is measured using force microscopy (AFM) techniques. The AFM measurements are incorporated into the Derjaguin-Muller-Toporov model to calculate the adhesion energies. The implications of the results are then discussed for the design of robust organic and composite organic/inorganic electronic devices. Finally, the lamination of organic solar cells and organic light emitting devices is studied using a combination of experimental, computational, and analytical approaches. First, the effects of applied lamination force (on contact between the laminated layers) are studied using experiments and models. The crack driving forces associated with the interfacial cracks that form at the interfaces between layers (at the bi-material interfaces) are estimated along with the critical interfacial crack driving forces associated with the separation of thin films, after layer transfer. The conditions for successful lamination are predicted using a combination of experiments and models. Guidelines are developed for the lamination of low-cost organic electronic structures.

Density functional study of the electronic structure of dye-functionalized fullerenes and their model donor-acceptor complexes containing P3HT

DOE Office of Scientific and Technical Information (OSTI.GOV)

Baruah, Tunna; Garnica, Amanda; Paggen, Marina

2016-04-14

We study the electronic structure of C{sub 60} fullerenes functionalized with a thiophene-diketo-pyrrolopyrrole-thiophene based chromophore using density functional theory combined with large polarized basis sets. As the attached chromophore has electron donor character, the functionalization of the fullerene leads to a donor-acceptor (DA) system. We examine in detail the effect of the linker and the addition site on the electronic structure of the functionalized fullerenes. We further study the electronic structure of these DA complexes with a focus on the charge transfer excitations. Finally, we examine the interface of the functionalized fullerenes with the widely used poly(3-hexylthiophene-2,5-diyl) (P3HT) donor. Ourmore » results show that all functionalized fullerenes with an exception of the C{sub 60}-pyrrolidine [6,6], where the pyrrolidine is attached at a [6,6] site, have larger electron affinities relative to the pristine C{sub 60} fullerene. We also estimate the quasi-particle gap, lowest charge transfer excitation energy, and the exciton binding energies of the functionalized fullerene-P3MT model systems. Results show that the exciton binding energies in these model complexes are slightly smaller compared to a similarly prepared phenyl-C{sub 61}-butyric acid methyl ester (PCBM)-P3MT complex.« less

On the applicability of one- and many-electron quantum chemistry models for hydrated electron clusters

DOE Office of Scientific and Technical Information (OSTI.GOV)

Turi, László, E-mail: turi@chem.elte.hu

2016-04-21

We evaluate the applicability of a hierarchy of quantum models in characterizing the binding energy of excess electrons to water clusters. In particular, we calculate the vertical detachment energy of an excess electron from water cluster anions with methods that include one-electron pseudopotential calculations, density functional theory (DFT) based calculations, and ab initio quantum chemistry using MP2 and eom-EA-CCSD levels of theory. The examined clusters range from the smallest cluster size (n = 2) up to nearly nanosize clusters with n = 1000 molecules. The examined cluster configurations are extracted from mixed quantum-classical molecular dynamics trajectories of cluster anions withmore » n = 1000 water molecules using two different one-electron pseudopotenial models. We find that while MP2 calculations with large diffuse basis set provide a reasonable description for the hydrated electron system, DFT methods should be used with precaution and only after careful benchmarking. Strictly tested one-electron psudopotentials can still be considered as reasonable alternatives to DFT methods, especially in large systems. The results of quantum chemistry calculations performed on configurations, that represent possible excess electron binding motifs in the clusters, appear to be consistent with the results using a cavity structure preferring one-electron pseudopotential for the hydrated electron, while they are in sharp disagreement with the structural predictions of a non-cavity model.« less

On the applicability of one- and many-electron quantum chemistry models for hydrated electron clusters

NASA Astrophysics Data System (ADS)

Turi, László

2016-04-01

We evaluate the applicability of a hierarchy of quantum models in characterizing the binding energy of excess electrons to water clusters. In particular, we calculate the vertical detachment energy of an excess electron from water cluster anions with methods that include one-electron pseudopotential calculations, density functional theory (DFT) based calculations, and ab initio quantum chemistry using MP2 and eom-EA-CCSD levels of theory. The examined clusters range from the smallest cluster size (n = 2) up to nearly nanosize clusters with n = 1000 molecules. The examined cluster configurations are extracted from mixed quantum-classical molecular dynamics trajectories of cluster anions with n = 1000 water molecules using two different one-electron pseudopotenial models. We find that while MP2 calculations with large diffuse basis set provide a reasonable description for the hydrated electron system, DFT methods should be used with precaution and only after careful benchmarking. Strictly tested one-electron psudopotentials can still be considered as reasonable alternatives to DFT methods, especially in large systems. The results of quantum chemistry calculations performed on configurations, that represent possible excess electron binding motifs in the clusters, appear to be consistent with the results using a cavity structure preferring one-electron pseudopotential for the hydrated electron, while they are in sharp disagreement with the structural predictions of a non-cavity model.

Composition Formulas of Inorganic Compounds in Terms of Cluster Plus Glue Atom Model.

PubMed

Ma, Yanping; Dong, Dandan; Wu, Aimin; Dong, Chuang

2018-01-16

The present paper attempts to identify the molecule-like structural units in inorganic compounds, by applying the so-called "cluster plus glue atom model". This model, originating from metallic glasses and quasi-crystals, describes any structure in terms of a nearest-neighbor cluster and a few outer-shell glue atoms, expressed in the cluster formula [cluster](glue atoms). Similar to the case for normal molecules where the charge transfer occurs within the molecule to meet the commonly known octet electron rule, the octet state is reached after matching the nearest-neighbor cluster with certain outer-shell glue atoms. These kinds of structural units contain information on local atomic configuration, chemical composition, and electron numbers, just as for normal molecules. It is shown that the formulas of typical inorganic compounds, such as fluorides, oxides, and nitrides, satisfy a similar octet electron rule, with the total number of valence electrons per unit formula being multiples of eight.

Possibility of transforming the electronic structure of one species of graphene adatoms into that of another by application of gate voltage: First-principles calculations

NASA Astrophysics Data System (ADS)

Chan, Kevin T.; Lee, Hoonkyung; Cohen, Marvin L.

2011-10-01

Graphene provides many advantages for controlling the electronic structure of adatoms and other adsorbates via gating. Using the projected density of states and charge density obtained from first-principles density-functional periodic supercell calculations, we investigate the possibility of performing “alchemy” of adatoms on graphene, i.e., transforming the electronic structure of one species of adatom into that of another species by application of a gate voltage. Gating is modeled as a change in the number of electrons in the unit cell, with the inclusion of a compensating uniform background charge. Within this model and the generalized gradient approximation to the exchange-correlation functional, we find that such transformations are possible for K, Ca, and several transition-metal adatoms. Gate control of the occupation of the p states of In on graphene is also investigated. The validity of the supercell approximation with uniform compensating charge and the model for exchange and correlation is also discussed.

Joint refinement model for the spin resolved one-electron reduced density matrix of YTiO3 using magnetic structure factors and magnetic Compton profiles data.

PubMed

Gueddida, Saber; Yan, Zeyin; Kibalin, Iurii; Voufack, Ariste Bolivard; Claiser, Nicolas; Souhassou, Mohamed; Lecomte, Claude; Gillon, Béatrice; Gillet, Jean-Michel

2018-04-28

In this paper, we propose a simple cluster model with limited basis sets to reproduce the unpaired electron distributions in a YTiO 3 ferromagnetic crystal. The spin-resolved one-electron-reduced density matrix is reconstructed simultaneously from theoretical magnetic structure factors and directional magnetic Compton profiles using our joint refinement algorithm. This algorithm is guided by the rescaling of basis functions and the adjustment of the spin population matrix. The resulting spin electron density in both position and momentum spaces from the joint refinement model is in agreement with theoretical and experimental results. Benefits brought from magnetic Compton profiles to the entire spin density matrix are illustrated. We studied the magnetic properties of the YTiO 3 crystal along the Ti-O 1 -Ti bonding. We found that the basis functions are mostly rescaled by means of magnetic Compton profiles, while the molecular occupation numbers are mainly modified by the magnetic structure factors.

Computational modeling of the effect of external electron injection into a direct-current microdischarge

DOE Office of Scientific and Technical Information (OSTI.GOV)

Panneer Chelvam, Prem Kumar; Raja, Laxminarayan L.

2015-12-28

Electron emission from the electrode surface plays an important role in determining the structure of a direct-current microdischarge. Here we have developed a computational model of a direct-current microdischarge to study the effect of external electron injection from the cathode surface into the discharge to manipulate its properties. The model provides a self-consistent, multi-species, multi-temperature fluid representation of the plasma. A microdischarge with a metal-insulator-metal configuration is chosen for this study. The effect of external electron injection on the structure and properties of the microdischarge is described. The transient behavior of the microdischarge during the electron injection is examined. Themore » nonlinearities in the dynamics of the plasma result in a large increase of conduction current after active electron injection. For the conditions simulated a switching time of ∼100 ns from a low-current to high-current discharge state is realized.« less

Electronic structure and microscopic model of CoNb2O6

NASA Astrophysics Data System (ADS)

Molla, Kaimujjaman; Rahaman, Badiur

2018-05-01

We present the first principle density functional calculations to figure out the underlying spin model of CoNb2O6. The first principles calculations define the main paths of superexchange interaction between Co spins in this compound. We discuss the nature of the exchange paths and provide quantitative estimates of magnetic exchange couplings. A microscopic modeling based on analysis of the electronic structure of this system puts it in the interesting class of weakly couple geometrically frustrated isosceles triangular Ising antiferromagnet.

The structure and properties of boron carbide ceramics modified by high-current pulsed electron-beam

NASA Astrophysics Data System (ADS)

Ivanov, Yuri; Tolkachev, Oleg; Petyukevich, Maria; Teresov, Anton; Ivanova, Olga; Ikonnikova, Irina; Polisadova, Valentina

2016-01-01

The present work is devoted to numerical simulation of temperature fields and the analysis of structural and strength properties of the samples surface layer of boron carbide ceramics treated by the high-current pulsed electron-beam of the submillisecond duration. The samples made of sintered boron carbide ceramics are used in these investigations. The problem of calculating the temperature field is reduced to solving the thermal conductivity equation. The electron beam density ranges between 8…30 J/cm2, while the pulse durations are 100…200 μs in numerical modelling. The results of modelling the temperature field allowed ascertaining the threshold parameters of the electron beam, such as energy density and pulse duration. The electron beam irradiation is accompanied by the structural modification of the surface layer of boron carbide ceramics either in the single-phase (liquid or solid) or two-phase (solid-liquid) states. The sample surface of boron carbide ceramics is treated under the two-phase state (solid-liquid) conditions of the structural modification. The surface layer is modified by the high-current pulsed electron-beam produced by SOLO installation at the Institute of High Current Electronics of the Siberian Branch of the Russian Academy of Sciences, Tomsk, Russia. The elemental composition and the defect structure of the modified surface layer are analyzed by the optical instrument, scanning electron and transmission electron microscopes. Mechanical properties of the modified layer are determined measuring its hardness and crack resistance. Research results show that the melting and subsequent rapid solidification of the surface layer lead to such phenomena as fragmentation due to a crack network, grain size reduction, formation of the sub-grained structure due to mechanical twinning, and increase of hardness and crack resistance.

Atomistic simulation of defect formation and structure transitions in U-Mo alloys in swift heavy ion irradiation

NASA Astrophysics Data System (ADS)

Kolotova, L. N.; Starikov, S. V.

2017-11-01

In irradiation of swift heavy ions, the defects formation frequently takes place in crystals. High energy transfer into the electronic subsystem and relaxations processes lead to the formation of structural defects and cause specific effects, such as the track formation. There is a large interest to understanding of the mechanisms of defects/tracks formation due to the heating of the electron subsystem. In this work, the atomistic simulation of defects formation and structure transitions in U-Mo alloys in irradiation of swift heavy ions has been carried out. We use the two-temperature atomistic model with explicit account of electron pressure and electron thermal conductivity. This two-temperature model describes ionic subsystem by means of molecular dynamics while the electron subsystem is considered in the continuum approach. The various mechanisms of structure changes in irradiation are examined. In particular, the simulation results indicate that the defects formation may be produced without melting and subsequent crystallization. Threshold stopping power of swift ions for the defects formation in irradiation in the various conditions are calculated.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Huang, Yang; Liu, Zhiqiang, E-mail: lzq@semi.ac.cn, E-mail: spring@semi.ac.cn; Yi, Xiaoyan, E-mail: lzq@semi.ac.cn, E-mail: spring@semi.ac.cn

To evaluate electron leakage in InGaN/GaN multiple quantum well (MQW) light emitting diodes (LEDs), analytic models of ballistic and quasi-ballistic transport are developed. With this model, the impact of critical variables effecting electron leakage, including the electron blocking layer (EBL), structure of multiple quantum wells (MQWs), polarization field, and temperature are explored. The simulated results based on this model shed light on previously reported experimental observations and provide basic criteria for suppressing electron leakage, advancing the design of InGaN/GaN LEDs.

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

PubMed Central

Chen, Duan; Wei, Guo-Wei

2010-01-01

The miniaturization of nano-scale electronic devices, such as metal oxide semiconductor field effect transistors (MOSFETs), has given rise to a pressing demand in the new theoretical understanding and practical tactic for dealing with quantum mechanical effects in integrated circuits. Modeling and simulation of this class of problems have emerged as an important topic in applied and computational mathematics. This work presents mathematical models and computational algorithms for the simulation of nano-scale MOSFETs. We introduce a unified two-scale energy functional to describe the electrons and the continuum electrostatic potential of the nano-electronic device. This framework enables us to put microscopic and macroscopic descriptions in an equal footing at nano scale. By optimization of the energy functional, we derive consistently-coupled Poisson-Kohn-Sham equations. Additionally, layered structures are crucial to the electrostatic and transport properties of nano transistors. A material interface model is proposed for more accurate description of the electrostatics governed by the Poisson equation. Finally, a new individual dopant model that utilizes the Dirac delta function is proposed to understand the random doping effect in nano electronic devices. Two mathematical algorithms, the matched interface and boundary (MIB) method and the Dirichlet-to-Neumann mapping (DNM) technique, are introduced to improve the computational efficiency of nano-device simulations. Electronic structures are computed via subband decomposition and the transport properties, such as the I-V curves and electron density, are evaluated via the non-equilibrium Green's functions (NEGF) formalism. Two distinct device configurations, a double-gate MOSFET and a four-gate MOSFET, are considered in our three-dimensional numerical simulations. For these devices, the current fluctuation and voltage threshold lowering effect induced by the discrete dopant model are explored. Numerical convergence and model well-posedness are also investigated in the present work. PMID:20396650

Conformational Switching in PolyGln Amyloid Fibrils Resulting from a Single Amino Acid Insertion

PubMed Central

Huang, Rick K.; Baxa, Ulrich; Aldrian, Gudrun; Ahmed, Abdullah B.; Wall, Joseph S.; Mizuno, Naoko; Antzutkin, Oleg; Steven, Alasdair C.; Kajava, Andrey V.

2014-01-01

The established correlation between neurodegenerative disorders and intracerebral deposition of polyglutamine aggregates motivates attempts to better understand their fibrillar structure. We designed polyglutamines with a few lysines inserted to overcome the hindrance of extreme insolubility and two D-lysines to limit the lengths of β-strands. One is 33 amino acids long (PolyQKd-33) and the other has one fewer glutamine (PolyQKd-32). Both form well-dispersed fibrils suitable for analysis by electron microscopy. Electron diffraction confirmed cross-β structures in both fibrils. Remarkably, the deletion of just one glutamine residue from the middle of the peptide leads to substantially different amyloid structures. PolyQKd-32 fibrils are consistently 10–20% wider than PolyQKd-33, as measured by negative staining, cryo-electron microscopy, and scanning transmission electron microscopy. Scanning transmission electron microscopy analysis revealed that the PolyQKd-32 fibrils have 50% higher mass-per-length than PolyQKd-33. This distinction can be explained by a superpleated β-structure model for PolyQKd-33 and a model with two β-solenoid protofibrils for PolyQKd-32. These data provide evidence for β-arch-containing structures in polyglutamine fibrils and open future possibilities for structure-based drug design. PMID:24853742

Where Is the Electronic Oscillator Strength? Mapping Oscillator Strength across Molecular Absorption Spectra.

PubMed

Zheng, Lianjun; Polizzi, Nicholas F; Dave, Adarsh R; Migliore, Agostino; Beratan, David N

2016-03-24

The effectiveness of solar energy capture and conversion materials derives from their ability to absorb light and to transform the excitation energy into energy stored in free carriers or chemical bonds. The Thomas-Reiche-Kuhn (TRK) sum rule mandates that the integrated (electronic) oscillator strength of an absorber equals the total number of electrons in the structure. Typical molecular chromophores place only about 1% of their oscillator strength in the UV-vis window, so individual chromophores operate at about 1% of their theoretical limit. We explore the distribution of oscillator strength as a function of excitation energy to understand this circumstance. To this aim, we use familiar independent-electron model Hamiltonians as well as first-principles electronic structure methods. While model Hamiltonians capture the qualitative electronic spectra associated with π electron chromophores, these Hamiltonians mistakenly focus the oscillator strength in the fewest low-energy transitions. Advanced electronic structure methods, in contrast, spread the oscillator strength over a very wide excitation energy range, including transitions to Rydberg and continuum states, consistent with experiment. Our analysis rationalizes the low oscillator strength in the UV-vis spectral region in molecules, a step toward the goal of oscillator strength manipulation and focusing.

Bright-field electron tomography of individual inorganic fullerene-like structures

NASA Astrophysics Data System (ADS)

Bar Sadan, Maya; Wolf, Sharon G.; Houben, Lothar

2010-03-01

Nanotubes and fullerene-like nanoparticles of various inorganic layered compounds have been studied extensively in recent years. Their characterisation on the atomic scale has proven essential for progress in synthesis as well as for the theoretical modelling of their physical properties. We show that with electron tomography it is possible to achieve a reliable reconstruction of the 3D structure of nested WS2 or MoS2 fullerene-like and nanotube structures with sub-nanometre resolution using electron microscopes that are not aberration-corrected. Model-based simulations were used to identify imaging parameters, under which structural features such as the shell structure can be retained in the tomogram reconstructed from bright-field micrographs. The isolation of a particle out of an agglomerate for the analysis of a single structure and its interconnection with other particles is facilitated through the tomograms. The internal structure of the layers within the particle alongside the shape and content of its internal void are reconstructed. The tomographic reconstruction yields insights regarding the growth process as well as structural defects, such as non-continuous layers, which relate to the lubrication properties.Nanotubes and fullerene-like nanoparticles of various inorganic layered compounds have been studied extensively in recent years. Their characterisation on the atomic scale has proven essential for progress in synthesis as well as for the theoretical modelling of their physical properties. We show that with electron tomography it is possible to achieve a reliable reconstruction of the 3D structure of nested WS2 or MoS2 fullerene-like and nanotube structures with sub-nanometre resolution using electron microscopes that are not aberration-corrected. Model-based simulations were used to identify imaging parameters, under which structural features such as the shell structure can be retained in the tomogram reconstructed from bright-field micrographs. The isolation of a particle out of an agglomerate for the analysis of a single structure and its interconnection with other particles is facilitated through the tomograms. The internal structure of the layers within the particle alongside the shape and content of its internal void are reconstructed. The tomographic reconstruction yields insights regarding the growth process as well as structural defects, such as non-continuous layers, which relate to the lubrication properties. Electronic supplementary information (ESI) available: Figs. S1 and S2 and movies S1-S6. See DOI: 10.1039/b9nr00251k

Measurement of Strain and Stress Distributions in Structural Materials by Electron Moiré Method

NASA Astrophysics Data System (ADS)

Kishimoto, Satoshi; Xing, Yougming; Tanaka, Yoshihisa; Kagawa, Yutaka

A method for measuring the strain and stress distributions in structural materials has been introduced. Fine model grids were fabricated by electron beam lithography, and an electron beam scan by a scanning electron microscope (SEM) was used as the master grid. Exposure of the electron beam scan onto the model grid in an SEM produced the electron beam moiré fringes of bright and dark parts caused by the different amounts of the secondary electrons per a primary electron. For demonstration, the micro-creep deformation of pure copper was observed. The creep strain distribution and the grain boundary sliding were analyzed. The residual strain and stress at the interface between a fiber and a matrix of a fiber reinforced plastic (FRP) were measured using the pushing-out test and this electron moiré method. Also, a non-uniform deformation around the boundary of 3-point bended laminated steel was observed and the strain distribution analyzed.

RAPID COMMUNICATION: Study of superstructure II in multiferroic BiMnO3

NASA Astrophysics Data System (ADS)

Ge, Bing-Hui; Li, Fang-Hua; Li, Xue-Ming; Wang, Yu-Mei; Chi, Zhen-Hua; Jin, Chang-Qing

2008-09-01

The crystal structure of the minor phase, named superstructure II, existing in multiferroic compound BiMnO3 has been studied by electron diffraction and high-resolution transmission electron microscopy. Domains of major and minor phases coexisting in BiMnO3 were observed in high-resolution electron microscope images. The unit cell of minor phase was determined to be triclinic with the size 4×4×4 times as large as the distorted perovskite subcell. The [111] and [10bar 1] projected structure maps of the minor phase have been derived from the corresponding images by means of the image processing. A possible rough three-dimensional (3D) structure model was proposed based on the 3D structural information extracted from the two projected structure maps. Since there is no inversion centre in the proposed model, the minor phase may contribute to the ferroelectric property of BiMnO3.

Giant amplification in degenerate band edge slow-wave structures interacting with an electron beam

DOE Office of Scientific and Technical Information (OSTI.GOV)

Othman, Mohamed A. K.; Veysi, Mehdi; Capolino, Filippo

2016-03-15

We propose a new amplification regime based on a synchronous operation of four degenerate electromagnetic (EM) modes in a slow-wave structure and the electron beam, referred to as super synchronization. These four EM modes arise in a Fabry-Pérot cavity when degenerate band edge (DBE) condition is satisfied. The modes interact constructively with the electron beam resulting in superior amplification. In particular, much larger gains are achieved for smaller beam currents compared to conventional structures based on synchronization with only a single EM mode. We demonstrate giant gain scaling with respect to the length of the slow-wave structure compared to conventionalmore » Pierce type single mode traveling wave tube amplifiers. We construct a coupled transmission line model for a loaded waveguide slow-wave structure exhibiting a DBE, and investigate the phenomenon of giant gain via super synchronization using the Pierce model generalized to multimode interaction.« less

Atomicrex—a general purpose tool for the construction of atomic interaction models

NASA Astrophysics Data System (ADS)

Stukowski, Alexander; Fransson, Erik; Mock, Markus; Erhart, Paul

2017-07-01

We introduce atomicrex, an open-source code for constructing interatomic potentials as well as more general types of atomic-scale models. Such effective models are required to simulate extended materials structures comprising many thousands of atoms or more, because electronic structure methods become computationally too expensive at this scale. atomicrex covers a wide range of interatomic potential types and fulfills many needs in atomistic model development. As inputs, it supports experimental property values as well as ab initio energies and forces, to which models can be fitted using various optimization algorithms. The open architecture of atomicrex allows it to be used in custom model development scenarios beyond classical interatomic potentials while thanks to its Python interface it can be readily integrated e.g., with electronic structure calculations or machine learning algorithms.

Electronic structures of GaAs/AlxGa1-xAs quantum double rings

PubMed Central

Xia, Jian-Bai

2006-01-01

In the framework of effective mass envelope function theory, the electronic structures of GaAs/AlxGa1-xAs quantum double rings (QDRs) are studied. Our model can be used to calculate the electronic structures of quantum wells, wires, dots, and the single ring. In calculations, the effects due to the different effective masses of electrons and holes in GaAs and AlxGa1-xAs and the valence band mixing are considered. The energy levels of electrons and holes are calculated for different shapes of QDRs. The calculated results are useful in designing and fabricating the interrelated photoelectric devices. The single electron states presented here are useful for the study of the electron correlations and the effects of magnetic fields in QDRs.

Influence of molecular designs on polaronic and vibrational transitions in a conjugated push-pull copolymer

NASA Astrophysics Data System (ADS)

Cobet, Christoph; Gasiorowski, Jacek; Menon, Reghu; Hingerl, Kurt; Schlager, Stefanie; White, Matthew S.; Neugebauer, Helmut; Sariciftci, N. Serdar; Stadler, Philipp

2016-10-01

Electron-phonon interactions of free charge-carriers in doped pi-conjugated polymers are conceptually described by 1-dimensional (1D) delocalization. Thereby, polaronic transitions fit the 1D-Froehlich model in quasi-confined chains. However, recent developments in conjugated polymers have diversified the backbones to become elaborate heterocylcic macromolecules. Their complexity makes it difficult to investigate the electron-phonon coupling. In this work we resolve the electron-phonon interactions in the ground and doped state in a complex push-pull polymer. We focus on the polaronic transitions using in-situ spectroscopy to work out the differences between single-unit and push-pull systems to obtain the desired structural- electronic correlations in the doped state. We apply the classic 1D-Froehlich model to generate optical model fits. Interestingly, we find the 1D-approach in push-pull polarons in agreement to the model, pointing at the strong 1D-character and plain electronic structure of the push-pull structure. In contrast, polarons in the single-unit polymer emerge to a multi- dimensional problem difficult to resolve due to their anisotropy. Thus, we report an enhancement of the 1D-character by the push-pull concept in the doped state - an important view in light of the main purpose of push-pull polymers for photovoltaic devices.

A theoretical-electron-density databank using a model of real and virtual spherical atoms.

PubMed

Nassour, Ayoub; Domagala, Slawomir; Guillot, Benoit; Leduc, Theo; Lecomte, Claude; Jelsch, Christian

2017-08-01

A database describing the electron density of common chemical groups using combinations of real and virtual spherical atoms is proposed, as an alternative to the multipolar atom modelling of the molecular charge density. Theoretical structure factors were computed from periodic density functional theory calculations on 38 crystal structures of small molecules and the charge density was subsequently refined using a density model based on real spherical atoms and additional dummy charges on the covalent bonds and on electron lone-pair sites. The electron-density parameters of real and dummy atoms present in a similar chemical environment were averaged on all the molecules studied to build a database of transferable spherical atoms. Compared with the now-popular databases of transferable multipolar parameters, the spherical charge modelling needs fewer parameters to describe the molecular electron density and can be more easily incorporated in molecular modelling software for the computation of electrostatic properties. The construction method of the database is described. In order to analyse to what extent this modelling method can be used to derive meaningful molecular properties, it has been applied to the urea molecule and to biotin/streptavidin, a protein/ligand complex.

Atomic and electronic structure of Lomer dislocations at CdTe bicrystal interface

PubMed Central

Sun, Ce; Paulauskas, Tadas; Sen, Fatih G.; Lian, Guoda; Wang, Jinguo; Buurma, Christopher; Chan, Maria K. Y.; Klie, Robert F.; Kim, Moon J.

2016-01-01

Extended defects are of considerable importance in determining the electronic properties of semiconductors, especially in photovoltaics (PVs), due to their effects on electron-hole recombination. We employ model systems to study the effects of dislocations in CdTe by constructing grain boundaries using wafer bonding. Atomic-resolution scanning transmission electron microscopy (STEM) of a [1–10]/(110) 4.8° tilt grain boundary reveals that the interface is composed of three distinct types of Lomer dislocations. Geometrical phase analysis is used to map strain fields, while STEM and density functional theory (DFT) modeling determine the atomic structure at the interface. The electronic structure of the dislocation cores calculated using DFT shows significant mid-gap states and different charge-channeling tendencies. Cl-doping is shown to reduce the midgap states, while maintaining the charge separation effects. This report offers novel avenues for exploring grain boundary effects in CdTe-based solar cells by fabricating controlled bicrystal interfaces and systematic atomic-scale analysis. PMID:27255415

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

DOE PAGES

Larsen, Ross E.

2016-04-12

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

Atomic and electronic structure of Lomer dislocations at CdTe bicrystal interface

DOE PAGES

Sun, Ce; Paulauskas, Tadas; Sen, Fatih G.; ...

2016-06-03

Extended defects are of considerable importance in determining the electronic properties of semiconductors, especially in photovoltaics (PVs), due to their effects on electron-hole recombination. We employ model systems to study the effects of dislocations in CdTe by constructing grain boundaries using wafer bonding. Atomic-resolution scanning transmission electron microscopy (STEM) of a [1–10]/ (110) 4.8° tilt grain boundary reveals that the interface is composed of three distinct types of Lomer dislocations. Geometrical phase analysis is used to map strain fields, while STEM and density functional theory (DFT) modeling determine the atomic structure at the interface. The electronic structure of the dislocationmore » cores calculated using DFT shows significant mid-gap states and different charge-channeling tendencies. Cl-doping is shown to reduce the midgap states, while maintaining the charge separation effects. In conclusion, this report offers novel avenues for exploring grain boundary effects in CdTe-based solar cells by fabricating controlled bicrystal interfaces and systematic atomic-scale analysis.« less

Phase-space dynamics of runaway electrons in magnetic fields

DOE PAGES

Guo, Zehua; McDevitt, Christopher Joseph; Tang, Xian-Zhu

2017-02-16

Dynamics of runaway electrons in magnetic fields are governed by the competition of three dominant physics: parallel electric field acceleration, Coulomb collision, and synchrotron radiation. Examination of the energy and pitch-angle flows reveals that the presence of local vortex structure and global circulation is crucial to the saturation of primary runaway electrons. Models for the vortex structure, which has an O-point to X-point connection, and the bump of runaway electron distribution in energy space have been developed and compared against the simulation data. Lastly, identification of these velocity-space structures opens a new venue to re-examine the conventional understanding of runawaymore » electron dynamics in magnetic fields.« less

Simulation of Electronic Circular Dichroism of Nucleic Acids: From the Structure to the Spectrum.

PubMed

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

2016-11-14

We present a quantum mechanical (QM) simulation of the electronic circular dichroism (ECD) of nucleic acids (NAs). The simulation combines classical molecular dynamics, to obtain the structure and its temperature-dependent fluctuations, with a QM excitonic model to determine the ECD. The excitonic model takes into account environmental effects through a polarizable embedding and uses a refined approach to calculate the electronic couplings in terms of full transition densities. Three NAs with either similar conformations but different base sequences or similar base sequences but different conformations have been investigated and the results were compared with experimental observations; a good agreement was seen in all cases. A detailed analysis of the nature of the ECD bands in terms of their excitonic composition was also carried out. Finally, a comparison between the QM and the DeVoe models clearly revealed the importance of including fluctuations of the excitonic parameters and of accurately determining the electronic couplings. This study demonstrates the feasibility of the ab initio simulation of the ECD spectra of NAs, that is, without the need of experimental structural or electronic data. © 2016 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Electronic structure studies of La2CuO4

NASA Astrophysics Data System (ADS)

Wachs, A. L.; Turchi, P. E. A.; Jean, Y. C.; Wetzler, K. H.; Howell, R. H.; Fluss, M. J.; Harshman, D. R.; Remeika, J. P.; Cooper, A. S.; Fleming, R. M.

1988-07-01

We report results of positron-electron momentum-distribution measurements of single-crystal La2CuO4 using two-dimensional angular correlation of positron-annihilation-radiation techniques. The data contain two components: a large (~85%), isotropic corelike electron contribution and a remaining, anisotropic valence-electron contribution modeled using a linear combination of atomic orbitals-molecular orbital method and a localized ion scheme, within the independent-particle model approximation. This work suggests a ligand-field Hamiltonian to be justified for describing the electronic properties of perovskite materials.

Structural and electronic properties for atomic clusters

NASA Astrophysics Data System (ADS)

Sun, Yan

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

Electronic structure description of the cis-MoOS unit in models for molybdenum hydroxylases.

PubMed

Doonan, Christian J; Rubie, Nick D; Peariso, Katrina; Harris, Hugh H; Knottenbelt, Sushilla Z; George, Graham N; Young, Charles G; Kirk, Martin L

2008-01-09

The molybdenum hydroxylases catalyze the oxidation of numerous aromatic heterocycles and simple organics and, unlike other hydroxylases, utilize water as the source of oxygen incorporated into the product. The electronic structures of the cis-MoOS units in CoCp2[TpiPrMoVOS(OPh)] and TpiPrMoVIOS(OPh) (TpiPr = hydrotris(3-isopropylpyrazol-1-yl)borate), new models for molybdenum hydroxylases, have been studied in detail using S K-edge X-ray absorption spectroscopy, vibrational spectroscopy, and detailed bonding calculations. The results show a highly delocalized Mo=S pi* LUMO redox orbital that is formally Mo(dxy) with approximately 35% sulfido ligand character. Vibrational spectroscopy has been used to quantitate Mo-Ssulfido bond order changes in the cis-MoOS units as a function of redox state. Results support a redox active molecular orbital that has a profound influence on MoOS bonding through changes to the relative electro/nucleophilicity of the terminal sulfido ligand accompanying oxidation state changes. The bonding description for these model cis-MoOS systems supports enzyme mechanisms that are under orbital control and dominantly influenced by the unique electronic structure of the cis-MoOS site. The electronic structure of the oxidized enzyme site is postulated to play a role in polarizing a substrate carbon center for nucleophilic attack by metal activated water and acting as an electron sink in the two-electron oxidation of substrates.

Revisiting the Bohr Atom 100 Years Later

NASA Astrophysics Data System (ADS)

Wall, Ernst

2013-03-01

We use a novel electron model wherein the electron is modeled as a point charge behaving as a trapped photon revolving in a Compton wavelength orbit at light speed. The revolving point charge gives rise to spiraling Compton wavelets around the electron, which give rise to de Broglie waves. When applied to the Bohr model, the orbital radius of the electron scales to the first Bohr orbit's radius via the fine structure constant. The orbiting electron's orbital velocity, Vb, scales to that of the electron's charge's internal velocity (the velocity of light, c) via the fine structure constant. The Compton wavelets, if they reflect off the nucleus, have a round trip time just long enough to allow the electron to move one of its diameters in distance in the first Bohr orbit. The ratio of the electron's rotational frequency, fe, to its rotational frequency in the Bohr orbit fb, is fe/fb = 1/α2, which is also the number of electron rotations in single orbit. If we scale the electron's rotational energy (h*fe) to that of the orbit using this, the orbital energy value (h*fb) would be 27.2114 eV. However, the virial theorem reduces it to 13.6057, the ground state energy of the first Bohr orbit. Ref: www.tachyonmodel.com.

Ab initio investigation of the structural and electronic properties of amorphous HgTe.

PubMed

Zhao, Huxian; Chen, Xiaoshuang; Lu, Jianping; Shu, Haibo; Lu, Wei

2014-01-29

We present the structure and electronic properties of amorphous mercury telluride obtained from first-principle calculations. The initial configuration of amorphous mercury telluride is created by computation alchemy. According to different exchange–correlation functions in our calculations, we establish two 256-atom models. The topology of both models is analyzed in terms of radial and bond angle distributions. It is found that both the Te and the Hg atoms tend to be fourfold, but with a wrong bond rate of about 10%. The fraction of threefold and fivefold atoms also shows that there are a significant number of dangling and floating bonds in our models. The electronic properties are also obtained. It is indicated that there is a bandgap in amorphous HgTe, in contrast to the zero bandgap for crystalline HgTe. The structures of the band tail and defect states are also discussed.

The impact of new Geant4-DNA cross section models on electron track structure simulations in liquid water

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kyriakou, I., E-mail: ikyriak@cc.uoi.gr; Šefl, M.; Department of Dosimetry and Application of Ionizing Radiation, Faculty of Nuclear Sciences and Physical Engineering, Czech Technical University in Prague, 115 19 Prague

The most recent release of the open source and general purpose Geant4 Monte Carlo simulation toolkit (Geant4 10.2 release) contains a new set of physics models in the Geant4-DNA extension for improving the modelling of low-energy electron transport in liquid water (<10 keV). This includes updated electron cross sections for excitation, ionization, and elastic scattering. In the present work, the impact of these developments to track-structure calculations is examined for providing the first comprehensive comparison against the default physics models of Geant4-DNA. Significant differences with the default models are found for the average path length and penetration distance, as well asmore » for dose-point-kernels for electron energies below a few hundred eV. On the other hand, self-irradiation absorbed fractions for tissue-like volumes and low-energy electron sources (including some Auger emitters) reveal rather small differences (up to 15%) between these new and default Geant4-DNA models. The above findings indicate that the impact of the new developments will mainly affect those applications where the spatial pattern of interactions and energy deposition of very-low energy electrons play an important role such as, for example, the modelling of the chemical and biophysical stage of radiation damage to cells.« less

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

PubMed

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

2016-02-01

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

Interacting quasi-band model for electronic states in compound semiconductor alloys: Zincblende structure

NASA Astrophysics Data System (ADS)

Shinozuka, Yuzo; Oda, Masato

2015-09-01

The interacting quasi-band model proposed for electronic states in simple alloys is extended for compound semiconductor alloys with general lattice structures containing several atoms per unit cell. Using a tight-binding model, a variational electronic wave function for quasi-Bloch states yields a non-Hermitian Hamiltonian matrix characterized by matrix elements of constituent crystals and concentration of constituents. Solving secular equations for each k-state yields the alloy’s energy spectrum for any type of randomness and arbitrary concentration. The theory is used to address III-V (II-VI) alloys with a zincblende lattice with crystal band structures well represented by the sp3s* model. Using the resulting 15 × 15 matrix, the concentration dependence of valence and conduction bands is calculated in a unified scheme for typical alloys: Al1-xGaxAs, GaAs1-xPx, and GaSb1-xPx. Results agree well with experiments and are discussed with respect to the concentration dependence, direct-indirect gap transition, and band-gap-bowing origin.

Resonant tunneling assisted propagation and amplification of plasmons in high electron mobility transistors

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bhardwaj, Shubhendu; Sensale-Rodriguez, Berardi; Xing, Huili Grace

A rigorous theoretical and computational model is developed for the plasma-wave propagation in high electron mobility transistor structures with electron injection from a resonant tunneling diode at the gate. We discuss the conditions in which low-loss and sustainable plasmon modes can be supported in such structures. The developed analytical model is used to derive the dispersion relation for these plasmon-modes. A non-linear full-wave-hydrodynamic numerical solver is also developed using a finite difference time domain algorithm. The developed analytical solutions are validated via the numerical solution. We also verify previous observations that were based on a simplified transmission line model. Itmore » is shown that at high levels of negative differential conductance, plasmon amplification is indeed possible. The proposed rigorous models can enable accurate design and optimization of practical resonant tunnel diode-based plasma-wave devices for terahertz sources, mixers, and detectors, by allowing a precise representation of their coupling when integrated with other electromagnetic structures.« less

Quantum-chemical investigation of the structures and electronic spectra of the nucleic acid bases at the coupled cluster CC2 level.

PubMed

Fleig, Timo; Knecht, Stefan; Hättig, Christof

2007-06-28

We study the ground-state structures and singlet- and triplet-excited states of the nucleic acid bases by applying the coupled cluster model CC2 in combination with a resolution-of-the-identity approximation for electron interaction integrals. Both basis set effects and the influence of dynamic electron correlation on the molecular structures are elucidated; the latter by comparing CC2 with Hartree-Fock and Møller-Plesset perturbation theory to second order. Furthermore, we investigate basis set and electron correlation effects on the vertical excitation energies and compare our highest-level results with experiment and other theoretical approaches. It is shown that small basis sets are insufficient for obtaining accurate results for excited states of these molecules and that the CC2 approach to dynamic electron correlation is a reliable and efficient tool for electronic structure calculations on medium-sized molecules.

Electronic shell structure in Ga12 icosahedra and the relation to the bulk forms of gallium.

PubMed

Schebarchov, D; Gaston, N

2012-07-28

The electronic structure of known cluster compounds with a cage-like icosahedral Ga(12) centre is studied by first-principles theoretical methods, based on density functional theory. We consider these hollow metalloid nanostructures in the context of the polymorphism of the bulk, and identify a close relation to the α phase of gallium. This previously unrecognised connection is established using the electron localisation function, which reveals the ubiquitous presence of radially-pointing covalent bonds around the Ga(12) centre--analogous to the covalent bonds between buckled deltahedral planes in α-Ga. Furthermore, we find prominent superatom shell structure in these clusters, despite their hollow icosahedral motif and the presence of covalent bonds. The exact nature of the electronic shell structure is contrasted with simple electron shell models based on jellium, and we demonstrate how the interplay between gallium dimerisation, ligand- and crystal-field effects can alter the splitting of the partially filled 1F shell. Finally, in the unique compound where the Ga(12) centre is bridged by six phosphorus ligands, the electronic structure most closely resembles that of δ-Ga and there are no well-defined superatom orbitals. The results of this comprehensive study bring new insights into the nature of chemical bonding in metalloid gallium compounds and the relation to bulk gallium metal, and they may also guide the development of more general models for ligand-protected clusters.

Tests of Si(111)-7 × 7 structural models by comparison with transmission electron diffraction patterns

NASA Astrophysics Data System (ADS)

McRae, E. G.; Petroff, P. M.

1984-11-01

Several structural models of the Si(111)-7 × 7 surface are tested by comparing calculated and observed transmission electron diffraction (TED) patterns. The models comprise "adatom" models where the unit mesh contains 12 adatoms or atom clusters in a locally (2 × 2) arrangement, and "triangle-dimer" models where the unit mesh contains 9 dimers or pairs of dimers bordering a triangular subunit of the unit mesh. The distribution of diffraction intensity among fractional-order spots is calculated kinematically and compared with TED patterns observed by Petroff and Wilson and others. No agreement is found for adatom models. Good but not perfect agreement is found for one triangle-dimer model.

Bright-field electron tomography of individual inorganic fullerene-like structures.

PubMed

Bar Sadan, Maya; Wolf, Sharon G; Houben, Lothar

2010-03-01

Nanotubes and fullerene-like nanoparticles of various inorganic layered compounds have been studied extensively in recent years. Their characterisation on the atomic scale has proven essential for progress in synthesis as well as for the theoretical modelling of their physical properties. We show that with electron tomography it is possible to achieve a reliable reconstruction of the 3D structure of nested WS(2) or MoS(2) fullerene-like and nanotube structures with sub-nanometre resolution using electron microscopes that are not aberration-corrected. Model-based simulations were used to identify imaging parameters, under which structural features such as the shell structure can be retained in the tomogram reconstructed from bright-field micrographs. The isolation of a particle out of an agglomerate for the analysis of a single structure and its interconnection with other particles is facilitated through the tomograms. The internal structure of the layers within the particle alongside the shape and content of its internal void are reconstructed. The tomographic reconstruction yields insights regarding the growth process as well as structural defects, such as non-continuous layers, which relate to the lubrication properties.

Variational nonadiabatic dynamics in the moving crude adiabatic representation: Further merging of nuclear dynamics and electronic structure

NASA Astrophysics Data System (ADS)

Joubert-Doriol, Loïc; Izmaylov, Artur F.

2018-03-01

A new methodology of simulating nonadiabatic dynamics using frozen-width Gaussian wavepackets within the moving crude adiabatic representation with the on-the-fly evaluation of electronic structure is presented. The main feature of the new approach is the elimination of any global or local model representation of electronic potential energy surfaces; instead, the electron-nuclear interaction is treated explicitly using the Gaussian integration. As a result, the new scheme does not introduce any uncontrolled approximations. The employed variational principle ensures the energy conservation and leaves the number of electronic and nuclear basis functions as the only parameter determining the accuracy. To assess performance of the approach, a model with two electronic and two nuclear spacial degrees of freedom containing conical intersections between potential energy surfaces has been considered. Dynamical features associated with nonadiabatic transitions and nontrivial geometric (or Berry) phases were successfully reproduced within a limited basis expansion.

SU-E-T-489: Quantum versus Classical Trajectory Monte Carlo Simulations of Low Energy Electron Transport.

PubMed

Thomson, R; Kawrakow, I

2012-06-01

Widely-used classical trajectory Monte Carlo simulations of low energy electron transport neglect the quantum nature of electrons; however, at sub-1 keV energies quantum effects have the potential to become significant. This work compares quantum and classical simulations within a simplified model of electron transport in water. Electron transport is modeled in water droplets using quantum mechanical (QM) and classical trajectory Monte Carlo (MC) methods. Water droplets are modeled as collections of point scatterers representing water molecules from which electrons may be isotropically scattered. The role of inelastic scattering is investigated by introducing absorption. QM calculations involve numerically solving a system of coupled equations for the electron wavefield incident on each scatterer. A minimum distance between scatterers is introduced to approximate structured water. The average QM water droplet incoherent cross section is compared with the MC cross section; a relative error (RE) on the MC results is computed. RE varies with electron energy, average and minimum distances between scatterers, and scattering amplitude. The mean free path is generally the relevant length scale for estimating RE. The introduction of a minimum distance between scatterers increases RE substantially (factors of 5 to 10), suggesting that the structure of water must be modeled for accurate simulations. Inelastic scattering does not improve agreement between QM and MC simulations: for the same magnitude of elastic scattering, the introduction of inelastic scattering increases RE. Droplet cross sections are sensitive to droplet size and shape; considerable variations in RE are observed with changing droplet size and shape. At sub-1 keV energies, quantum effects may become non-negligible for electron transport in condensed media. Electron transport is strongly affected by the structure of the medium. Inelastic scatter does not improve agreement between QM and MC simulations of low energy electron transport in condensed media. © 2012 American Association of Physicists in Medicine.

Electronic structure of vitamin B12 within the framework of the Haldane-Anderson impurity model

NASA Astrophysics Data System (ADS)

Kandemir, Zafer; Mayda, Selma; Bulut, Nejat

2015-03-01

We study the electronic structure of vitamin B12 (cyanocobalamine C63H88CoN14O14P) by using the framework of the multi-orbital single-impurity Haldane-Anderson model of a transition-metal impurity in a semiconductor host. Here, our purpose is to understand the many-body effects originating from the transition-metal impurity. In this approach, the cobalt 3 d orbitals are treated as the impurity states placed in a semiconductor host which consists of the rest of the molecule. The parameters of the resulting effective Haldane-Anderson model are obtained within the Hartree-Fock approximation for the electronic structure of the molecule. The quantum Monte Carlo technique is then used to calculate the one-electron and magnetic correlation functions of this effective Haldane-Anderson model for vitamin B12. We find that new states form inside the semiconductor gap due to the on-site Coulomb interaction at the impurity 3 d orbitals and that these states become the highest occupied molecular orbitals. In addition, we present results on the charge distribution and spin correlations around the Co atom. We compare the results of this approach with those obtained by the density-functional theory calculations.

Structural simplicity as a restraint on the structure of amorphous silicon

NASA Astrophysics Data System (ADS)

Cliffe, Matthew J.; Bartók, Albert P.; Kerber, Rachel N.; Grey, Clare P.; Csányi, Gábor; Goodwin, Andrew L.

2017-06-01

Understanding the structural origins of the properties of amorphous materials remains one of the most important challenges in structural science. In this study, we demonstrate that local "structural simplicity", embodied by the degree to which atomic environments within a material are similar to each other, is a powerful concept for rationalizing the structure of amorphous silicon (a -Si) a canonical amorphous material. We show, by restraining a reverse Monte Carlo refinement against pair distribution function (PDF) data to be simpler, that the simplest model consistent with the PDF is a continuous random network (CRN). A further effect of producing a simple model of a -Si is the generation of a (pseudo)gap in the electronic density of states, suggesting that structural homogeneity drives electronic homogeneity. That this method produces models of a -Si that approach the state-of-the-art without the need for chemically specific restraints (beyond the assumption of homogeneity) suggests that simplicity-based refinement approaches may allow experiment-driven structural modeling techniques to be developed for the wide variety of amorphous semiconductors with strong local order.

Theoretical study of the electron affinities of MF6 and MF - 6 (M=Cr, Mo, and W) using a model potential method

NASA Astrophysics Data System (ADS)

Sakai, Yoshiko; Miyoshi, Eisaku

1987-09-01

Electronic structures of MF6, MF-6, and MF2-6 (M=Cr, Mo, and W) were calculated using a model potential method in the Hartree-Fock-Roothaan scheme. Major relativistic effects were taken into account for the calculations on MoFq6 and WFq6 (q=0, -1, and -2). It is shown that the calculated electron affinities (EAs) are extremely high for all the MF6 molecules, and that the CrF-6 and MoF-6 anions also have positive EAs, whereas the WF-6 anion has a slightly negative EA. The behaviors of the EAs are interpreted with reference to the electronic structures of the MFq6 systems.

Models of protein–ligand crystal structures: trust, but verify

PubMed Central

Deller, Marc C.

2015-01-01

X-ray crystallography provides the most accurate models of protein–ligand structures. These models serve as the foundation of many computational methods including structure prediction, molecular modelling, and structure-based drug design. The success of these computational methods ultimately depends on the quality of the underlying protein–ligand models. X-ray crystallography offers the unparalleled advantage of a clear mathematical formalism relating the experimental data to the protein–ligand model. In the case of X-ray crystallography, the primary experimental evidence is the electron density of the molecules forming the crystal. The first step in the generation of an accurate and precise crystallographic model is the interpretation of the electron density of the crystal, typically carried out by construction of an atomic model. The atomic model must then be validated for fit to the experimental electron density and also for agreement with prior expectations of stereochemistry. Stringent validation of protein–ligand models has become possible as a result of the mandatory deposition of primary diffraction data, and many computational tools are now available to aid in the validation process. Validation of protein–ligand complexes has revealed some instances of overenthusiastic interpretation of ligand density. Fundamental concepts and metrics of protein–ligand quality validation are discussed and we highlight software tools to assist in this process. It is essential that end users select high quality protein–ligand models for their computational and biological studies, and we provide an overview of how this can be achieved. PMID:25665575

Models of protein-ligand crystal structures: trust, but verify.

PubMed

Deller, Marc C; Rupp, Bernhard

2015-09-01

X-ray crystallography provides the most accurate models of protein-ligand structures. These models serve as the foundation of many computational methods including structure prediction, molecular modelling, and structure-based drug design. The success of these computational methods ultimately depends on the quality of the underlying protein-ligand models. X-ray crystallography offers the unparalleled advantage of a clear mathematical formalism relating the experimental data to the protein-ligand model. In the case of X-ray crystallography, the primary experimental evidence is the electron density of the molecules forming the crystal. The first step in the generation of an accurate and precise crystallographic model is the interpretation of the electron density of the crystal, typically carried out by construction of an atomic model. The atomic model must then be validated for fit to the experimental electron density and also for agreement with prior expectations of stereochemistry. Stringent validation of protein-ligand models has become possible as a result of the mandatory deposition of primary diffraction data, and many computational tools are now available to aid in the validation process. Validation of protein-ligand complexes has revealed some instances of overenthusiastic interpretation of ligand density. Fundamental concepts and metrics of protein-ligand quality validation are discussed and we highlight software tools to assist in this process. It is essential that end users select high quality protein-ligand models for their computational and biological studies, and we provide an overview of how this can be achieved.

Advanced spectroscopic analysis of 0.8-1.0-MA Mo x pinches and the influence of plasma electron beams on L-shell spectra of Mo ions.

PubMed

Shlyaptseva, A S; Hansen, S B; Kantsyrev, V L; Fedin, D A; Ouart, N; Fournier, K B; Safronova, U I

2003-02-01

This paper presents a detailed investigation of the temporal, spatial, and spectroscopic properties of L-shell radiation from 0.8 to 1.0 MA Mo x pinches. Time-resolved measurements of x-ray radiation and both time-gated and time-integrated spectra and pinhole images are presented and analyzed. High-current x pinches are found to have complex spatial and temporal structures. A collisional-radiative kinetic model has been developed and used to interpret L-shell Mo spectra. The model includes the ground state of every ionization stage of Mo and detailed structure for the O-, F-, Ne-, Na-, and Mg-like ionization stages. Hot electron beams generated by current-carrying electrons in the x pinch are modeled by a non-Maxwellian electron distribution function and have significant influence on L-shell spectra. The results of 20 Mo x-pinch shots with wire diameters from 24 to 62 microm have been modeled. Overall, the modeled spectra fit the experimental spectra well and indicate for time-integrated spectra electron densities between 2 x 10(21) and 2 x 10(22) cm(-3), electron temperatures between 700 and 850 eV, and hot electron fractions between 3% and 7%. Time-gated spectra exhibit wide variations in temperature and density of plasma hot spots during the same discharge.

L-Edge X-ray Absorption Spectroscopic Investigation of {FeNO} 6: Delocalization vs Antiferromagnetic Coupling

DOE PAGES

Yan, James J.; Gonzales, Margarita A.; Mascharak, Pradip K.; ...

2016-12-22

NO is a classic non-innocent ligand, and iron nitrosyls can have different electronic structure descriptions depending on their spin state and coordination environment. These highly covalent ligands are found in metalloproteins and are also used as models for Fe–O 2 systems. Here, this study utilizes iron L-edge X-ray absorption spectroscopy (XAS), interpreted using a valence bond configuration interaction multiplet model, to directly experimentally probe the electronic structure of the S = 0 {FeNO} 6 compound [Fe(PaPy 3)NO] 2+ (PaPy 3 = N,N-bis(2-pyridylmethyl)amine-N-ethyl-2-pyridine-2-carboxamide) and the S = 0 [Fe(PaPy 3)CO] + reference compound. This method allows separation of the σ-donation andmore » π-acceptor interactions of the ligand through ligand-to-metal and metal-to-ligand charge-transfer mixing pathways. The analysis shows that the {FeNO} 6 electronic structure is best described as Fe III–NO(neutral), with no localized electron in an NO π* orbital or electron hole in an Fe dπ orbital. This delocalization comes from the large energy gap between the Fe–NO π-bonding and antibonding molecular orbitals relative to the exchange interactions between electrons in these orbitals. This study demonstrates the utility of L-edge XAS in experimentally defining highly delocalized electronic structures.« less

Vlasov Simulation of Electrostatic Solitary Structures in Multi-Component Plasmas

NASA Technical Reports Server (NTRS)

Umeda, Takayuki; Ashour-Abdalla, Maha; Pickett, Jolene S.; Goldstein, Melvyn L.

2012-01-01

Electrostatic solitary structures have been observed in the Earth's magnetosheath by the Cluster spacecraft. Recent theoretical work has suggested that these solitary structures are modeled by electron acoustic solitary waves existing in a four-component plasma system consisting of core electrons, two counter-streaming electron beams, and one species of background ions. In this paper, the excitation of electron acoustic waves and the formation of solitary structures are studied by means of a one-dimensional electrostatic Vlasov simulation. The present result first shows that either electron acoustic solitary waves with negative potential or electron phase-space holes with positive potential are excited in four-component plasma systems. However, these electrostatic solitary structures have longer duration times and higher wave amplitudes than the solitary structures observed in the magnetosheath. The result indicates that a high-speed and small free energy source may be needed as a fifth component. An additional simulation of a five-component plasma consisting of a stable four-component plasma and a weak electron beam shows the generation of small and fast electron phase-space holes by the bump-on-tail instability. The physical properties of the small and fast electron phase-space holes are very similar to those obtained by the previous theoretical analysis. The amplitude and duration time of solitary structures in the simulation are also in agreement with the Cluster observation.

Molecular architecture of the yeast Mediator complex

PubMed Central

Robinson, Philip J; Trnka, Michael J; Pellarin, Riccardo; Greenberg, Charles H; Bushnell, David A; Davis, Ralph; Burlingame, Alma L; Sali, Andrej; Kornberg, Roger D

2015-01-01

The 21-subunit Mediator complex transduces regulatory information from enhancers to promoters, and performs an essential role in the initiation of transcription in all eukaryotes. Structural information on two-thirds of the complex has been limited to coarse subunit mapping onto 2-D images from electron micrographs. We have performed chemical cross-linking and mass spectrometry, and combined the results with information from X-ray crystallography, homology modeling, and cryo-electron microscopy by an integrative modeling approach to determine a 3-D model of the entire Mediator complex. The approach is validated by the use of X-ray crystal structures as internal controls and by consistency with previous results from electron microscopy and yeast two-hybrid screens. The model shows the locations and orientations of all Mediator subunits, as well as subunit interfaces and some secondary structural elements. Segments of 20–40 amino acid residues are placed with an average precision of 20 Å. The model reveals roles of individual subunits in the organization of the complex. DOI: http://dx.doi.org/10.7554/eLife.08719.001 PMID:26402457

Revisiting the Electronic Structure of FeS Monomers Using ab Initio Ligand Field Theory and the Angular Overlap Model.

PubMed

Chilkuri, Vijay Gopal; DeBeer, Serena; Neese, Frank

2017-09-05

Iron-sulfur (FeS) proteins are universally found in nature with actives sites ranging in complexity from simple monomers to multinuclear sites from two up to eight iron atoms. These sites include mononuclear (rubredoxins), dinuclear (ferredoxins and Rieske proteins), trinuclear (e.g., hydrogenases), and tetranuclear (various ferredoxins and high-potential iron-sulfur proteins). The electronic structure of the higher-nuclearity clusters is inherently extremely complex. Hence, it is reasonable to take a bottom-up approach in which clusters of increasing nuclearity are analyzed in terms of the properties of their lower nuclearity constituents. In the present study, the first step is taken by an in-depth analysis of mononuclear FeS systems. Two different FeS molecules with phenylthiolate and methylthiolate as ligands are studied in their oxidized and reduced forms using modern wave function-based ab initio methods. The ab initio electronic spectra and wave function are presented and analyzed in detail. The very intricate electronic structure-geometry relationship in these systems is analyzed using ab initio ligand field theory (AILFT) in conjunction with the angular overlap model (AOM) parametrization scheme. The simple AOM model is used to explain the effect of geometric variations on the electronic structure. Through a comparison of the ab initio computed UV-vis absorption spectra and the available experimental spectra, the low-energy part of the many-particle spectrum is carefully analyzed. We show ab initio calculated magnetic circular dichroism spectra and present a comparison with the experimental spectrum. Finally, AILFT parameters and the ab initio spectra are compared with those obtained experimentally to understand the effect of the increased covalency of the thiolate ligands on the electronic structure of FeS monomers.

Protein structure determination by electron diffraction using a single three-dimensional nanocrystal.

PubMed

Clabbers, M T B; van Genderen, E; Wan, W; Wiegers, E L; Gruene, T; Abrahams, J P

2017-09-01

Three-dimensional nanometre-sized crystals of macromolecules currently resist structure elucidation by single-crystal X-ray crystallography. Here, a single nanocrystal with a diffracting volume of only 0.14 µm 3 , i.e. no more than 6 × 10 5 unit cells, provided sufficient information to determine the structure of a rare dimeric polymorph of hen egg-white lysozyme by electron crystallography. This is at least an order of magnitude smaller than was previously possible. The molecular-replacement solution, based on a monomeric polyalanine model, provided sufficient phasing power to show side-chain density, and automated model building was used to reconstruct the side chains. Diffraction data were acquired using the rotation method with parallel beam diffraction on a Titan Krios transmission electron microscope equipped with a novel in-house-designed 1024 × 1024 pixel Timepix hybrid pixel detector for low-dose diffraction data collection. Favourable detector characteristics include the ability to accurately discriminate single high-energy electrons from X-rays and count them, fast readout to finely sample reciprocal space and a high dynamic range. This work, together with other recent milestones, suggests that electron crystallography can provide an attractive alternative in determining biological structures.

Protein structure determination by electron diffraction using a single three-dimensional nanocrystal

PubMed Central

Clabbers, M. T. B.; van Genderen, E.; Wiegers, E. L.; Gruene, T.; Abrahams, J. P.

2017-01-01

Three-dimensional nanometre-sized crystals of macromolecules currently resist structure elucidation by single-crystal X-ray crystallography. Here, a single nanocrystal with a diffracting volume of only 0.14 µm3, i.e. no more than 6 × 105 unit cells, provided sufficient information to determine the structure of a rare dimeric polymorph of hen egg-white lysozyme by electron crystallography. This is at least an order of magnitude smaller than was previously possible. The molecular-replacement solution, based on a monomeric polyalanine model, provided sufficient phasing power to show side-chain density, and automated model building was used to reconstruct the side chains. Diffraction data were acquired using the rotation method with parallel beam diffraction on a Titan Krios transmission electron microscope equipped with a novel in-house-designed 1024 × 1024 pixel Timepix hybrid pixel detector for low-dose diffraction data collection. Favourable detector characteristics include the ability to accurately discriminate single high-energy electrons from X-rays and count them, fast readout to finely sample reciprocal space and a high dynamic range. This work, together with other recent milestones, suggests that electron crystallography can provide an attractive alternative in determining biological structures. PMID:28876237

Average-atom model for two-temperature states and ionic transport properties of aluminum in the warm dense matter regime

NASA Astrophysics Data System (ADS)

Hou, Yong; Fu, Yongsheng; Bredow, Richard; Kang, Dongdong; Redmer, Ronald; Yuan, Jianmin

2017-03-01

The average-atom model combined with the hyper-netted chain approximation is an efficient tool for electronic and ionic structure calculations for warm dense matter. Here we generalize this method in order to describe non-equilibrium states with different electron and ion temperature as produced in laser-matter interactions on ultra-short time scales. In particular, the electron-ion and ion-ion correlation effects are considered when calculating the electron structure. We derive an effective ion-ion pair-potential using the electron densities in the framework of temperature-depended density functional theory. Using this ion-ion potential we perform molecular dynamics simulations in order to determine the ionic transport properties such as the ionic diffusion coefficient and the shear viscosity through the ionic velocity autocorrelation functions.

Constructing superconductors by graphene Chern-Simons wormholes

NASA Astrophysics Data System (ADS)

Capozziello, Salvatore; Pincak, Richard; Saridakis, Emmanuel N.

2018-03-01

We propose a new model which simulates the motion of free electrons in graphene by the evolution of strings on manifolds. In this model, molecules which constitute sheets of graphene are polygonal point-like structures which build (N + 1) -dimensional manifolds. By breaking the gravitational-analogue symmetry of graphene sheets, we show that two separated child sheets and a Chern-Simons bridge are produced giving rise to a wormhole. In this structure, free electrons are transmitted from one child sheet to the other producing superconductivity. An analogue between "effective gravitons" and "Cooper pairs" is found. In principle, this phenomenology provides the possibility to construct superconductor structures by using the analogue of cosmological models.

First-principle simulations of electronic structure in semicrystalline polyethylene

NASA Astrophysics Data System (ADS)

Moyassari, A.; Unge, M.; Hedenqvist, M. S.; Gedde, U. W.; Nilsson, F.

2017-05-01

In order to increase our fundamental knowledge about high-voltage cable insulation materials, realistic polyethylene (PE) structures, generated with a novel molecular modeling strategy, have been analyzed using first principle electronic structure simulations. The PE structures were constructed by first generating atomistic PE configurations with an off-lattice Monte Carlo method and then equilibrating the structures at the desired temperature and pressure using molecular dynamics simulations. Semicrystalline, fully crystalline and fully amorphous PE, in some cases including crosslinks and short-chain branches, were analyzed. The modeled PE had a structure in agreement with established experimental data. Linear-scaling density functional theory (LS-DFT) was used to examine the electronic structure (e.g., spatial distribution of molecular orbitals, bandgaps and mobility edges) on all the materials, whereas conventional DFT was used to validate the LS-DFT results on small systems. When hybrid functionals were used, the simulated bandgaps were close to the experimental values. The localization of valence and conduction band states was demonstrated. The localized states in the conduction band were primarily found in the free volume (result of gauche conformations) present in the amorphous regions. For branched and crosslinked structures, the localized electronic states closest to the valence band edge were positioned at branches and crosslinks, respectively. At 0 K, the activation energy for transport was lower for holes than for electrons. However, at room temperature, the effective activation energy was very low (˜0.1 eV) for both holes and electrons, which indicates that the mobility will be relatively high even below the mobility edges and suggests that charge carriers can be hot carriers above the mobility edges in the presence of a high electrical field.

Photosynthesis. Electronic structure of the oxygen-evolving complex in photosystem II prior to O-O bond formation.

PubMed

Cox, Nicholas; Retegan, Marius; Neese, Frank; Pantazis, Dimitrios A; Boussac, Alain; Lubitz, Wolfgang

2014-08-15

The photosynthetic protein complex photosystem II oxidizes water to molecular oxygen at an embedded tetramanganese-calcium cluster. Resolving the geometric and electronic structure of this cluster in its highest metastable catalytic state (designated S3) is a prerequisite for understanding the mechanism of O-O bond formation. Here, multifrequency, multidimensional magnetic resonance spectroscopy reveals that all four manganese ions of the catalyst are structurally and electronically similar immediately before the final oxygen evolution step; they all exhibit a 4+ formal oxidation state and octahedral local geometry. Only one structural model derived from quantum chemical modeling is consistent with all magnetic resonance data; its formation requires the binding of an additional water molecule. O-O bond formation would then proceed by the coupling of two proximal manganese-bound oxygens in the transition state of the cofactor. Copyright © 2014, American Association for the Advancement of Science.

Sn nanothreads in GaAs: experiment and simulation

NASA Astrophysics Data System (ADS)

Semenikhin, I.; Vyurkov, V.; Bugaev, A.; Khabibullin, R.; Ponomarev, D.; Yachmenev, A.; Maltsev, P.; Ryzhii, M.; Otsuji, T.; Ryzhii, V.

2016-12-01

The gated GaAs structures like the field-effect transistor with the array of the Sn nanothreads was fabricated via delta-doping of vicinal GaAs surface by Sn atoms with a subsequent regrowth. That results in the formation of the chains of Sn atoms at the terrace edges. Two device models were developed. The quantum model accounts for the quantization of the electron energy spectrum in the self-consistent two-dimensional electric potential, herewith the electron density distribution in nanothread arrays for different gate voltages is calculated. The classical model ignores the quantization and electrons are distributed in space according to 3D density of states and Fermi-Dirac statistics. It turned out that qualitatively both models demonstrate similar behavior, nevertheless, the classical one is in better quantitative agreement with experimental data. Plausibly, the quantization could be ignored because Sn atoms are randomly placed along the thread axis. The terahertz hot-electron bolometers (HEBs) could be based on the structure under consideration.

High quantum efficiency photocathode simulation for the investigation of novel structured designs

DOE PAGES

MacPhee, A. G.; Nagel, S. R.; Bell, P. M.; ...

2014-09-02

A computer model in CST Studio Suite has been developed to evaluate several novel geometrically enhanced photocathode designs. This work was aimed at identifying a structure that would increase the total electron yield by a factor of two or greater in the 1–30 keV range. The modeling software was used to simulate the electric field and generate particle tracking for several potential structures. The final photocathode structure has been tailored to meet a set of detector performance requirements, namely, a spatial resolution of <40 μm and a temporal spread of 1–10 ps. As a result, we present the details ofmore » the geometrically enhanced photocathode model and resulting static field and electron emission characteristics.« less

Bend-imitating models of abruptly bent electron waveguides

NASA Astrophysics Data System (ADS)

Vakhnenko, Oleksiy O.

2011-07-01

The fundamentals of bend-imitating approach regarding the one-electron quantum mechanics in abruptly bent ideal electron waveguides are given. In general, the theory allows to model each particular circularlike bend of a continuous quantum wire as some effective multichannel scatterer being pointlike in longitudinal direction. Its scattering ability is determined by the bending angle, mean bending radius, lateral coordinate (or coordinates) in wire cross section, time (or electronic energy), and possibly by the applied magnetic field. In an equivalent formulation, the theory gives rise to rather simple matching rules for the electron wave function and its longitudinal derivative affecting only the straight parts of a wire and thereby permitting to bypass a detailed quantum mechanical consideration of elbow domains. The proposed technique is applicable for the analytical investigation of spectral and transport electronic properties related to the ideal abruptly bent 3D wirelike structures of fixed cross section and is adaptable to the 2D wirelike structures as well as to the wirelike structures subjected to the magnetic field perpendicular to the plane of wire bending. In the framework of bend-imitating approach, the investigation of electron scattering in a singly bent 2D quantum wire and a doubly bent 2D quantum wire with S-like bend has been made and the explicit dependences of transmission and reflection coefficients on geometrical parameters of respective structure as well as on electron energy have been obtained. The total suppression of mixing between the scattering channels of S-like bent quantum wire is predicted.

Density-functional theory applied to d- and f-electron systems

NASA Astrophysics Data System (ADS)

Wu, Xueyuan

Density functional theory (DFT) has been applied to study the electronic and geometric structures of prototype d- and f-electron systems. For the d-electron system, all electron DFT with gradient corrections to the exchange and correlation functionals has been used to investigate the properties of small neutral and cationic vanadium clusters. Results are in good agreement with available experimental and other theoretical data. For the f-electron system, a hybrid DFT, namely, B3LYP (Becke's 3-parameter hybrid functional using the correlation functional of Lee, Yang and Parr) with relativistic effective core potentials and cluster models has been applied to investigate the nature of chemical bonding of both the bulk and the surfaces of plutonium monoxide and dioxide. Using periodic models, the electronic and geometric structures of PuO2 and its (110) surface, as well as water adsorption on this surface have also been investigated using DFT in both local density approximation (LDA) and generalized gradient approximation (GGA) formalisms.

Double differential cross sections for proton induced electron emission from molecular analogues of DNA constituents for energies in the Bragg peak region

NASA Astrophysics Data System (ADS)

Rudek, Benedikt; Bennett, Daniel; Bug, Marion U.; Wang, Mingjie; Baek, Woon Yong; Buhr, Ticia; Hilgers, Gerhard; Champion, Christophe; Rabus, Hans

2016-09-01

For track structure simulations in the Bragg peak region, measured electron emission cross sections of DNA constituents are required as input for developing parameterized model functions representing the scattering probabilities. In the present work, double differential cross sections were measured for the electron emission from vapor-phase pyrimidine, tetrahydrofuran, and trimethyl phosphate that are structural analogues to the base, the sugar, and the phosphate residue of the DNA, respectively. The range of proton energies was from 75 keV to 135 keV, the angles ranged from 15° to 135°, and the electron energies were measured from 10 eV to 200 eV. Single differential and total electron emission cross sections are derived by integration over angle and electron energy and compared to the semi-empirical Hansen-Kocbach-Stolterfoht (HKS) model and a quantum mechanical calculation employing the first Born approximation with corrected boundary conditions (CB1). The CB1 provides the best prediction of double and single differential cross section, while total cross sections can be fitted with semi-empirical models. The cross sections of the three samples are proportional to their total number of valence electrons.

Band structure of an electron in a kind of periodic potentials with singularities

NASA Astrophysics Data System (ADS)

Hai, Kuo; Yu, Ning; Jia, Jiangping

2018-06-01

Noninteracting electrons in some crystals may experience periodic potentials with singularities and the governing Schrödinger equation cannot be defined at the singular points. The band structure of a single electron in such a one-dimensional crystal has been calculated by using an equivalent integral form of the Schrödinger equation. Both the perturbed and exact solutions are constructed respectively for the cases of a general singular weak-periodic system and its an exactly solvable version, Kronig-Penney model. Any one of them leads to a special band structure of the energy-dependent parameter, which results in an effective correction to the previous energy-band structure and gives a new explanation for forming the band structure. The used method and obtained results could be a valuable aid in the study of energy bands in solid-state physics, and the new explanation may trigger investigation to different physical mechanism of electron band structures.

RCrane: semi-automated RNA model building.

PubMed

Keating, Kevin S; Pyle, Anna Marie

2012-08-01

RNA crystals typically diffract to much lower resolutions than protein crystals. This low-resolution diffraction results in unclear density maps, which cause considerable difficulties during the model-building process. These difficulties are exacerbated by the lack of computational tools for RNA modeling. Here, RCrane, a tool for the partially automated building of RNA into electron-density maps of low or intermediate resolution, is presented. This tool works within Coot, a common program for macromolecular model building. RCrane helps crystallographers to place phosphates and bases into electron density and then automatically predicts and builds the detailed all-atom structure of the traced nucleotides. RCrane then allows the crystallographer to review the newly built structure and select alternative backbone conformations where desired. This tool can also be used to automatically correct the backbone structure of previously built nucleotides. These automated corrections can fix incorrect sugar puckers, steric clashes and other structural problems.

Quantitative studies on structure-DPPH• scavenging activity relationships of food phenolic acids.

PubMed

Jing, Pu; Zhao, Shu-Juan; Jian, Wen-Jie; Qian, Bing-Jun; Dong, Ying; Pang, Jie

2012-11-01

Phenolic acids are potent antioxidants, yet the quantitative structure-activity relationships of phenolic acids remain unclear. The purpose of this study was to establish 3D-QSAR models able to predict phenolic acids with high DPPH• scavenging activity and understand their structure-activity relationships. The model has been established by using a training set of compounds with cross-validated q2 = 0.638/0.855, non-cross-validated r2 = 0.984/0.986, standard error of estimate = 0.236/0.216, and F = 139.126/208.320 for the best CoMFA/CoMSIA models. The predictive ability of the models was validated with the correlation coefficient r2(pred) = 0.971/0.996 (>0.6) for each model. Additionally, the contour map results suggested that structural characteristics of phenolics acids favorable for the high DPPH• scavenging activity might include: (1) bulky and/or electron-donating substituent groups on the phenol ring; (2) electron-donating groups at the meta-position and/or hydrophobic groups at the meta-/ortho-position; (3) hydrogen-bond donor/electron-donating groups at the ortho-position. The results have been confirmed based on structural analyses of phenolic acids and their DPPH• scavenging data from eight recent publications. The findings may provide deeper insight into the antioxidant mechanisms and provide useful information for selecting phenolic acids for free radical scavenging properties.

Computational Study on Atomic Structures, Electronic Properties, and Chemical Reactions at Surfaces and Interfaces and in Biomaterials

NASA Astrophysics Data System (ADS)

Takano, Yu; Kobayashi, Nobuhiko; Morikawa, Yoshitada

2018-06-01

Through computer simulations using atomistic models, it is becoming possible to calculate the atomic structures of localized defects or dopants in semiconductors, chemically active sites in heterogeneous catalysts, nanoscale structures, and active sites in biological systems precisely. Furthermore, it is also possible to clarify physical and chemical properties possessed by these nanoscale structures such as electronic states, electronic and atomic transport properties, optical properties, and chemical reactivity. It is sometimes quite difficult to clarify these nanoscale structure-function relations experimentally and, therefore, accurate computational studies are indispensable in materials science. In this paper, we review recent studies on the relation between local structures and functions for inorganic, organic, and biological systems by using atomistic computer simulations.

Measurement of the electron structure function F2e at LEP energies

NASA Astrophysics Data System (ADS)

Abdallah, J.; Abreu, P.; Adam, W.; Adzic, P.; Albrecht, T.; Alemany-Fernandez, R.; Allmendinger, T.; Allport, P. P.; Amaldi, U.; Amapane, N.; Amato, S.; Anashkin, E.; Andreazza, A.; Andringa, S.; Anjos, N.; Antilogus, P.; Apel, W.-D.; Arnoud, Y.; Ask, S.; Asman, B.; Augustin, J. E.; Augustinus, A.; Baillon, P.; Ballestrero, A.; Bambade, P.; Barbier, R.; Bardin, D.; Barker, G. J.; Baroncelli, A.; Battaglia, M.; Baubillier, M.; Becks, K.-H.; Begalli, M.; Behrmann, A.; Belous, K.; Ben-Haim, E.; Benekos, N.; Benvenuti, A.; Berat, C.; Berggren, M.; Bertrand, D.; Besancon, M.; Besson, N.; Bloch, D.; Blom, M.; Bluj, M.; Bonesini, M.; Boonekamp, M.; Booth, P. S. L.; Borisov, G.; Botner, O.; Bouquet, B.; Bowcock, T. J. V.; Boyko, I.; Bracko, M.; Brenner, R.; Brodet, E.; Bruckman, P.; Brunet, J. M.; Buschbeck, B.; Buschmann, P.; Calvi, M.; Camporesi, T.; Canale, V.; Carena, F.; Castro, N.; Cavallo, F.; Chapkin, M.; Charpentier, Ph.; Checchia, P.; Chierici, R.; Chliapnikov, P.; Chudoba, J.; Chung, S. U.; Cieslik, K.; Collins, P.; Contri, R.; Cosme, G.; Cossutti, F.; Costa, M. J.; Crennell, D.; Cuevas, J.; D'Hondt, J.; da Silva, T.; da Silva, W.; Della Ricca, G.; de Angelis, A.; de Boer, W.; de Clercq, C.; de Lotto, B.; de Maria, N.; de Min, A.; de Paula, L.; di Ciaccio, L.; di Simone, A.; Doroba, K.; Drees, J.; Eigen, G.; Ekelof, T.; Ellert, M.; Elsing, M.; Espirito Santo, M. C.; Fanourakis, G.; Fassouliotis, D.; Feindt, M.; Fernandez, J.; Ferrer, A.; Ferro, F.; Flagmeyer, U.; Foeth, H.; Fokitis, E.; Fulda-Quenzer, F.; Fuster, J.; Gandelman, M.; Garcia, C.; Gavillet, Ph.; Gazis, E.; Gokieli, R.; Golob, B.; Gomez-Ceballos, G.; Gonçalves, P.; Graziani, E.; Grosdidier, G.; Grzelak, K.; Guy, J.; Haag, C.; Hallgren, A.; Hamacher, K.; Hamilton, K.; Haug, S.; Hauler, F.; Hedberg, V.; Hennecke, M.; Hoffman, J.; Holmgren, S.-O.; Holt, P. J.; Houlden, M. A.; Jackson, J. N.; Jarlskog, G.; Jarry, P.; Jeans, D.; Johansson, E. K.; Jonsson, P.; Joram, C.; Jungermann, L.; Kapusta, F.; Katsanevas, S.; Katsoufis, E.; Kernel, G.; Kersevan, B. P.; Kerzel, U.; King, B. T.; Kjaer, N. J.; Kluit, P.; Kokkinias, P.; Kourkoumelis, C.; Kouznetsov, O.; Krumstein, Z.; Kucharczyk, M.; Lamsa, J.; Leder, G.; Ledroit, F.; Leinonen, L.; Leitner, R.; Lemonne, J.; Lepeltier, V.; Lesiak, T.; Liebig, W.; Liko, D.; Lipniacka, A.; Lopes, J. H.; Lopez, J. M.; Loukas, D.; Lutz, P.; Lyons, L.; MacNaughton, J.; Malek, A.; Maltezos, S.; Mandl, F.; Marco, J.; Marco, R.; Marechal, B.; Margoni, M.; Marin, J.-C.; Mariotti, C.; Markou, A.; Martinez-Rivero, C.; Masik, J.; Mastroyiannopoulos, N.; Matorras, F.; Matteuzzi, C.; Mazzucato, F.; Mazzucato, M.; Mc Nulty, R.; Meroni, C.; Migliore, E.; Mitaroff, W.; Mjoernmark, U.; Moa, T.; Moch, M.; Moenig, K.; Monge, R.; Montenegro, J.; Moraes, D.; Moreno, S.; Morettini, P.; Mueller, U.; Muenich, K.; Mulders, M.; Mundim, L.; Murray, W.; Muryn, B.; Myatt, G.; Myklebust, T.; Nassiakou, M.; Navarria, F.; Nawrocki, K.; Nemecek, S.; Nicolaidou, R.; Nikolenko, M.; Oblakowska-Mucha, A.; Obraztsov, V.; Olshevski, A.; Onofre, A.; Orava, R.; Osterberg, K.; Ouraou, A.; Oyanguren, A.; Paganoni, M.; Paiano, S.; Palacios, J. P.; Palka, H.; Papadopoulou, Th. D.; Pape, L.; Parkes, C.; Parodi, F.; Parzefall, U.; Passeri, A.; Passon, O.; Peralta, L.; Perepelitsa, V.; Perrotta, A.; Petrolini, A.; Piedra, J.; Pieri, L.; Pierre, F.; Pimenta, M.; Piotto, E.; Podobnik, T.; Poireau, V.; Pol, M. E.; Polok, G.; Pozdniakov, V.; Pukhaeva, N.; Pullia, A.; Radojicic, D.; Rebecchi, P.; Rehn, J.; Reid, D.; Reinhardt, R.; Renton, P.; Richard, F.; Ridky, J.; Rivero, M.; Rodriguez, D.; Romero, A.; Ronchese, P.; Roudeau, P.; Rovelli, T.; Ruhlmann-Kleider, V.; Ryabtchikov, D.; Sadovsky, A.; Salmi, L.; Salt, J.; Sander, C.; Savoy-Navarro, A.; Schwickerath, U.; Sekulin, R.; Siebel, M.; Sisakian, A.; Slominski, W.; Smadja, G.; Smirnova, O.; Sokolov, A.; Sopczak, A.; Sosnowski, R.; Spassov, T.; Stanitzki, M.; Stocchi, A.; Strauss, J.; Stugu, B.; Szczekowski, M.; Szeptycka, M.; Szumlak, T.; Szwed, J.; Tabarelli, T.; Tegenfeldt, F.; Timmermans, J.; Tkatchev, L.; Tobin, M.; Todorovova, S.; Tomé, B.; Tonazzo, A.; Tortosa, P.; Travnicek, P.; Treille, D.; Tristram, G.; Trochimczuk, M.; Troncon, C.; Turluer, M.-L.; Tyapkin, I. A.; Tyapkin, P.; Tzamarias, S.; Uvarov, V.; Valenti, G.; van Dam, P.; van Eldik, J.; van Remortel, N.; van Vulpen, I.; Vegni, G.; Veloso, F.; Venus, W.; Verdier, P.; Verzi, V.; Vilanova, D.; Vitale, L.; Vrba, V.; Wahlen, H.; Washbrook, A. J.; Weiser, C.; Wicke, D.; Wickens, J.; Wilkinson, G.; Winter, M.; Witek, M.; Yushchenko, O.; Zalewska, A.; Zalewski, P.; Zavrtanik, D.; Zhuravlov, V.; Zimin, N. I.; Zintchenko, A.; Zupan, M.; Delphi Collaboration

2014-10-01

The hadronic part of the electron structure function F2e has been measured for the first time, using e+e- data collected by the DELPHI experiment at LEP, at centre-of-mass energies of √{ s} = 91.2- 209.5 GeV. The data analysis is simpler than that of the measurement of the photon structure function. The electron structure function F2e data are compared to predictions of phenomenological models based on the photon structure function. It is shown that the contribution of large target photon virtualities is significant. The data presented can serve as a cross-check of the photon structure function F2γ analyses and help in refining existing parameterisations.

Determining crystal structures through crowdsourcing and coursework

NASA Astrophysics Data System (ADS)

Horowitz, Scott; Koepnick, Brian; Martin, Raoul; Tymieniecki, Agnes; Winburn, Amanda A.; Cooper, Seth; Flatten, Jeff; Rogawski, David S.; Koropatkin, Nicole M.; Hailu, Tsinatkeab T.; Jain, Neha; Koldewey, Philipp; Ahlstrom, Logan S.; Chapman, Matthew R.; Sikkema, Andrew P.; Skiba, Meredith A.; Maloney, Finn P.; Beinlich, Felix R. M.; Caglar, Ahmet; Coral, Alan; Jensen, Alice Elizabeth; Lubow, Allen; Boitano, Amanda; Lisle, Amy Elizabeth; Maxwell, Andrew T.; Failer, Barb; Kaszubowski, Bartosz; Hrytsiv, Bohdan; Vincenzo, Brancaccio; de Melo Cruz, Breno Renan; McManus, Brian Joseph; Kestemont, Bruno; Vardeman, Carl; Comisky, Casey; Neilson, Catherine; Landers, Catherine R.; Ince, Christopher; Buske, Daniel Jon; Totonjian, Daniel; Copeland, David Marshall; Murray, David; Jagieła, Dawid; Janz, Dietmar; Wheeler, Douglas C.; Cali, Elie; Croze, Emmanuel; Rezae, Farah; Martin, Floyd Orville; Beecher, Gil; de Jong, Guido Alexander; Ykman, Guy; Feldmann, Harald; Chan, Hugo Paul Perez; Kovanecz, Istvan; Vasilchenko, Ivan; Connellan, James C.; Borman, Jami Lynne; Norrgard, Jane; Kanfer, Jebbie; Canfield, Jeffrey M.; Slone, Jesse David; Oh, Jimmy; Mitchell, Joanne; Bishop, John; Kroeger, John Douglas; Schinkler, Jonas; McLaughlin, Joseph; Brownlee, June M.; Bell, Justin; Fellbaum, Karl Willem; Harper, Kathleen; Abbey, Kirk J.; Isaksson, Lennart E.; Wei, Linda; Cummins, Lisa N.; Miller, Lori Anne; Bain, Lyn; Carpenter, Lynn; Desnouck, Maarten; Sharma, Manasa G.; Belcastro, Marcus; Szew, Martin; Szew, Martin; Britton, Matthew; Gaebel, Matthias; Power, Max; Cassidy, Michael; Pfützenreuter, Michael; Minett, Michele; Wesselingh, Michiel; Yi, Minjune; Cameron, Neil Haydn Tormey; Bolibruch, Nicholas I.; Benevides, Noah; Kathleen Kerr, Norah; Barlow, Nova; Crevits, Nykole Krystyne; Dunn, Paul; Silveira Belo Nascimento Roque, Paulo Sergio; Riber, Peter; Pikkanen, Petri; Shehzad, Raafay; Viosca, Randy; James Fraser, Robert; Leduc, Robert; Madala, Roman; Shnider, Scott; de Boisblanc, Sharon; Butkovich, Slava; Bliven, Spencer; Hettler, Stephen; Telehany, Stephen; Schwegmann, Steven A.; Parkes, Steven; Kleinfelter, Susan C.; Michael Holst, Sven; van der Laan, T. J. A.; Bausewein, Thomas; Simon, Vera; Pulley, Warwick; Hull, William; Kim, Annes Yukyung; Lawton, Alexis; Ruesch, Amanda; Sundar, Anjali; Lawrence, Anna-Lisa; Afrin, Antara; Maheshwer, Bhargavi; Turfe, Bilal; Huebner, Christian; Killeen, Courtney Elizabeth; Antebi-Lerrman, Dalia; Luan, Danny; Wolfe, Derek; Pham, Duc; Michewicz, Elaina; Hull, Elizabeth; Pardington, Emily; Galal, Galal Osama; Sun, Grace; Chen, Grace; Anderson, Halie E.; Chang, Jane; Hewlett, Jeffrey Thomas; Sterbenz, Jennifer; Lim, Jiho; Morof, Joshua; Lee, Junho; Inn, Juyoung Samuel; Hahm, Kaitlin; Roth, Kaitlin; Nair, Karun; Markin, Katherine; Schramm, Katie; Toni Eid, Kevin; Gam, Kristina; Murphy, Lisha; Yuan, Lucy; Kana, Lulia; Daboul, Lynn; Shammas, Mario Karam; Chason, Max; Sinan, Moaz; Andrew Tooley, Nicholas; Korakavi, Nisha; Comer, Patrick; Magur, Pragya; Savliwala, Quresh; Davison, Reid Michael; Sankaran, Roshun Rajiv; Lewe, Sam; Tamkus, Saule; Chen, Shirley; Harvey, Sho; Hwang, Sin Ye; Vatsia, Sohrab; Withrow, Stefan; Luther, Tahra K.; Manett, Taylor; Johnson, Thomas James; Ryan Brash, Timothy; Kuhlman, Wyatt; Park, Yeonjung; Popović, Zoran; Baker, David; Khatib, Firas; Bardwell, James C. A.

2016-09-01

We show here that computer game players can build high-quality crystal structures. Introduction of a new feature into the computer game Foldit allows players to build and real-space refine structures into electron density maps. To assess the usefulness of this feature, we held a crystallographic model-building competition between trained crystallographers, undergraduate students, Foldit players and automatic model-building algorithms. After removal of disordered residues, a team of Foldit players achieved the most accurate structure. Analysing the target protein of the competition, YPL067C, uncovered a new family of histidine triad proteins apparently involved in the prevention of amyloid toxicity. From this study, we conclude that crystallographers can utilize crowdsourcing to interpret electron density information and to produce structure solutions of the highest quality.

Determining crystal structures through crowdsourcing and coursework.

PubMed

Horowitz, Scott; Koepnick, Brian; Martin, Raoul; Tymieniecki, Agnes; Winburn, Amanda A; Cooper, Seth; Flatten, Jeff; Rogawski, David S; Koropatkin, Nicole M; Hailu, Tsinatkeab T; Jain, Neha; Koldewey, Philipp; Ahlstrom, Logan S; Chapman, Matthew R; Sikkema, Andrew P; Skiba, Meredith A; Maloney, Finn P; Beinlich, Felix R M; Popović, Zoran; Baker, David; Khatib, Firas; Bardwell, James C A

2016-09-16

We show here that computer game players can build high-quality crystal structures. Introduction of a new feature into the computer game Foldit allows players to build and real-space refine structures into electron density maps. To assess the usefulness of this feature, we held a crystallographic model-building competition between trained crystallographers, undergraduate students, Foldit players and automatic model-building algorithms. After removal of disordered residues, a team of Foldit players achieved the most accurate structure. Analysing the target protein of the competition, YPL067C, uncovered a new family of histidine triad proteins apparently involved in the prevention of amyloid toxicity. From this study, we conclude that crystallographers can utilize crowdsourcing to interpret electron density information and to produce structure solutions of the highest quality.

Structure factor and radial distribution function of some liquid lanthanides using charged hard sphere

NASA Astrophysics Data System (ADS)

Patel, H. P.; Sonvane, Y. A.; Thakor, P. B.

2017-05-01

The structure factor S(q) and radial distribution function g(r) play vital role to study the various structural properties like electronic, dynamic, magnetic etc. The present paper deals with the structural studies of foresaid properties using our newly constructed parameter free model potential with the Charged Hard Sphere (CHS) approximation. The local field correction due to Sarkar et al. is used to incorporate exchange and correlation among the conduction electrons in dielectric screening. Here we report the S(q) and g(r) for some liquid lanthanides viz: La, Ce, Pr, Nd and Eu. Present computed results are compared with the available experimental data. Lastly we found that our parameter free model potential successfully explains the structural propertiesof4fliquidlanthanides.

Effect of solute atoms on dislocation motion in Mg: An electronic structure perspective

PubMed Central

Tsuru, T.; Chrzan, D. C.

2015-01-01

Solution strengthening is a well-known approach to tailoring the mechanical properties of structural alloys. Ultimately, the properties of the dislocation/solute interaction are rooted in the electronic structure of the alloy. Accordingly, we compute the electronic structure associated with, and the energy barriers to dislocation cross-slip. The energy barriers so obtained can be used in the development of multiscale models for dislocation mediated plasticity. The computed electronic structure can be used to identify substitutional solutes likely to interact strongly with the dislocation. Using the example of a-type screw dislocations in Mg, we compute accurately the Peierls barrier to prismatic plane slip and argue that Y, Ca, Ti, and Zr should interact strongly with the studied dislocation, and thereby decrease the dislocation slip anisotropy in the alloy. PMID:25740411

Highly mismatched GaN1-x Sb x alloys: synthesis, structure and electronic properties

NASA Astrophysics Data System (ADS)

Yu, K. M.; Sarney, W. L.; Novikov, S. V.; Segercrantz, N.; Ting, M.; Shaw, M.; Svensson, S. P.; Martin, R. W.; Walukiewicz, W.; Foxon, C. T.

2016-08-01

Highly mismatched alloys (HMAs) is a class of semiconductor alloys whose constituents are distinctly different in terms of size, ionicity and/or electronegativity. Electronic properties of the alloys deviate significantly from an interpolation scheme based on small deviations from the virtual crystal approximation. Most of the HMAs were only studied in a dilute composition limit. Recent advances in understanding of the semiconductor synthesis processes allowed growth of thin films of HMAs under non-equilibrium conditions. Thus reducing the growth temperature allowed synthesis of group III-N-V HMAs over almost the entire composition range. This paper focuses on the GaN x Sb1-x HMA which has been suggested as a potential material for solar water dissociation devices. Here we review our recent work on the synthesis, structural and optical characterization of GaN1-x Sb x HMA. Theoretical modeling studies on its electronic structure based on the band anticrossing (BAC) model are also reviewed. In particular we discuss the effects of growth temperature, Ga flux and Sb flux on the incorporation of Sb, film microstructure and optical properties of the alloys. Results obtained from two separate MBE growths are directly compared. Our work demonstrates that a large range of direct bandgap energies from 3.4 eV to below 1.0 eV can be achieved for this alloy grown at low temperature. We show that the electronic band structure of GaN1-x Sb x HMA over the entire composition range is well described by a modified BAC model which includes the dependence of the host matrix band edges as well as the BAC model coupling parameters on composition. We emphasize that the modified BAC model of the electronic band structure developed for the full composition of GaN x Sb1-x is general and is applicable to any HMA.

Identification, display, and use of symmetry elements in atomic and electronic structure models.

PubMed

Khosrovani, N; Kung, P W; Freeman, C M; Gorman, A M; Kölmel, C M; Levine, S M; Newsam, J M

1999-01-01

Crystallographic symmetry plays an important role in structure determination from diffraction or scattering data, in spectroscopy and in simulations. It is convenient and insightful to integrate the display and use of such symmetry data with data analysis and modeling methods. We outline the integration of a suite of crystallographic algorithms, closely coupled with interactive graphical displays. These include techniques for identifying the unit cell of a solid, for automatically determining space and point group symmetries, for generalized displays of symmetry elements overlaid on structural models, and for construction, editing, and transformation of models subject to symmetry constraints. In addition, electron densities derived from periodic density functional calculations can be symmetrized and displayed with the corresponding symmetry elements. Applications of these various capabilities in crystallographic research are illustrated by topical examples.

Monte Carlo Simulations of Electron Energy-Loss Spectra with the Addition of Fine Structure from Density Functional Theory Calculations.

PubMed

Attarian Shandiz, Mohammad; Guinel, Maxime J-F; Ahmadi, Majid; Gauvin, Raynald

2016-02-01

A new approach is presented to introduce the fine structure of core-loss excitations into the electron energy-loss spectra of ionization edges by Monte Carlo simulations based on an optical oscillator model. The optical oscillator strength is refined using the calculated electron energy-loss near-edge structure by density functional theory calculations. This approach can predict the effects of multiple scattering and thickness on the fine structure of ionization edges. In addition, effects of the fitting range for background removal and the integration range under the ionization edge on signal-to-noise ratio are investigated.

Structural and electron charge density studies of a nonlinear optical compound 4,4 di-methyl amino cyano biphenyl

NASA Astrophysics Data System (ADS)

Naima, Boubegra; Abdelkader, Chouaih; Mokhtaria, Drissi; Fodil, Hamzaoui

2014-01-01

The 4,4 dimethyl amino cyano biphenyl crystal (DMACB) is characterized by its nonlinear activity. The intra molecular charge transfer of this molecule results mainly from the electronic transmission of the electro-acceptor (cyano) and electro-donor (di-methyl-amino) groups. An accurate electron density distribution around the molecule has been calculated based on a high-resolution X-ray diffraction study. The data were collected at 123 K using graphite-monochromated Mo K α radiation to sin(β)/λ = 1.24 Å-1. The integrated intensities of 13796 reflections were measured and reduced to 6501 independent reflections with I >= 3σ(I). The crystal structure was refined using the experimental model of Hansen and Coppens (1978). The crystal structure has been validated and deposited at the Cambridge Crystallographic Data Centre with the deposition number CCDC 876507. In this article, we present the thermal motion and the structural analysis obtained from the least-square refinement based on F2 and the electron density distribution obtained from the multipolar model.

POSSIBLE EVIDENCE FOR A FISK-TYPE HELIOSPHERIC MAGNETIC FIELD. I. ANALYZING ULYSSES/KET ELECTRON OBSERVATIONS

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sternal, O.; Heber, B.; Kopp, A.

The propagation of energetic charged particles in the heliospheric magnetic field is one of the fundamental problems in heliophysics. In particular, the structure of the heliospheric magnetic field remains an unsolved problem and is discussed as a controversial topic. The first successful analytic approach to the structure of the heliospheric magnetic field was the Parker field. However, the measurements of the Ulysses spacecraft at high latitudes revealed the possible need for refinements of the existing magnetic field model during solar minimum. Among other reasons, this led to the development of the Fisk field. This approach is highly debated and couldmore » not be ruled out with magnetic field measurements so far. A promising method to trace this magnetic field structure is to model the propagation of electrons in the energy range of a few MeV. Employing three-dimensional and time-dependent simulations of the propagation of energetic electrons, this work shows that the influence of a Fisk-type field on the particle transport in the heliosphere leads to characteristic variations of the electron intensities on the timescale of a solar rotation. For the first time it is shown that the Ulysses count rates of 2.5-7 MeV electrons contain the imprint of a Fisk-type heliospheric magnetic field structure. From a comparison of simulation results and the Ulysses count rates, realistic parameters for the Fisk theory are derived. Furthermore, these parameters are used to investigate the modeled relative amplitudes of protons and electrons, including the effects of drifts.« less

Anomalous High-Energy Waterfall-Like Electronic Structure in 5 d Transition Metal Oxide Sr2IrO4 with a Strong Spin-Orbit Coupling

NASA Astrophysics Data System (ADS)

Liu, Yan; Yu, Li; Jia, Xiaowen; Zhao, Jianzhou; Weng, Hongming; Peng, Yingying; Chen, Chaoyu; Xie, Zhuojin; Mou, Daixiang; He, Junfeng; Liu, Xu; Feng, Ya; Yi, Hemian; Zhao, Lin; Liu, Guodong; He, Shaolong; Dong, Xiaoli; Zhang, Jun; Xu, Zuyan; Chen, Chuangtian; Cao, Gang; Dai, Xi; Fang, Zhong; Zhou, X. J.

2015-08-01

The low energy electronic structure of Sr2IrO4 has been well studied and understood in terms of an effective Jeff = 1/2 Mott insulator model. However, little work has been done in studying its high energy electronic behaviors. Here we report a new observation of the anomalous high energy electronic structure in Sr2IrO4. By taking high-resolution angle-resolved photoemission measurements on Sr2IrO4 over a wide energy range, we have revealed for the first time that the high energy electronic structures show unusual nearly-vertical bands that extend over a large energy range. Such anomalous high energy behaviors resemble the high energy waterfall features observed in the cuprate superconductors. While strong electron correlation plays an important role in producing high energy waterfall features in the cuprate superconductors, the revelation of the high energy anomalies in Sr2IrO4, which exhibits strong spin-orbit coupling and a moderate electron correlation, points to an unknown and novel route in generating exotic electronic excitations.

Anomalous High-Energy Waterfall-Like Electronic Structure in 5 d Transition Metal Oxide Sr2IrO4 with a Strong Spin-Orbit Coupling.

PubMed

Liu, Yan; Yu, Li; Jia, Xiaowen; Zhao, Jianzhou; Weng, Hongming; Peng, Yingying; Chen, Chaoyu; Xie, Zhuojin; Mou, Daixiang; He, Junfeng; Liu, Xu; Feng, Ya; Yi, Hemian; Zhao, Lin; Liu, Guodong; He, Shaolong; Dong, Xiaoli; Zhang, Jun; Xu, Zuyan; Chen, Chuangtian; Cao, Gang; Dai, Xi; Fang, Zhong; Zhou, X J

2015-08-12

The low energy electronic structure of Sr2IrO4 has been well studied and understood in terms of an effective Jeff = 1/2 Mott insulator model. However, little work has been done in studying its high energy electronic behaviors. Here we report a new observation of the anomalous high energy electronic structure in Sr2IrO4. By taking high-resolution angle-resolved photoemission measurements on Sr2IrO4 over a wide energy range, we have revealed for the first time that the high energy electronic structures show unusual nearly-vertical bands that extend over a large energy range. Such anomalous high energy behaviors resemble the high energy waterfall features observed in the cuprate superconductors. While strong electron correlation plays an important role in producing high energy waterfall features in the cuprate superconductors, the revelation of the high energy anomalies in Sr2IrO4, which exhibits strong spin-orbit coupling and a moderate electron correlation, points to an unknown and novel route in generating exotic electronic excitations.

PRISM-EM: template interface-based modelling of multi-protein complexes guided by cryo-electron microscopy density maps.

PubMed

Kuzu, Guray; Keskin, Ozlem; Nussinov, Ruth; Gursoy, Attila

2016-10-01

The structures of protein assemblies are important for elucidating cellular processes at the molecular level. Three-dimensional electron microscopy (3DEM) is a powerful method to identify the structures of assemblies, especially those that are challenging to study by crystallography. Here, a new approach, PRISM-EM, is reported to computationally generate plausible structural models using a procedure that combines crystallographic structures and density maps obtained from 3DEM. The predictions are validated against seven available structurally different crystallographic complexes. The models display mean deviations in the backbone of <5 Å. PRISM-EM was further tested on different benchmark sets; the accuracy was evaluated with respect to the structure of the complex, and the correlation with EM density maps and interface predictions were evaluated and compared with those obtained using other methods. PRISM-EM was then used to predict the structure of the ternary complex of the HIV-1 envelope glycoprotein trimer, the ligand CD4 and the neutralizing protein m36.

Nanoscale inhomogeneity and photoacid generation dynamics in extreme ultraviolet resist materials

NASA Astrophysics Data System (ADS)

Wu, Ping-Jui; Wang, Yu-Fu; Chen, Wei-Chi; Wang, Chien-Wei; Cheng, Joy; Chang, Vencent; Chang, Ching-Yu; Lin, John; Cheng, Yuan-Chung

2018-03-01

The development of extreme ultraviolet (EUV) lithography towards the 22 nm node and beyond depends critically on the availability of resist materials that meet stringent control requirements in resolution, line edge roughness, and sensitivity. However, the molecular mechanisms that govern the structure-function relationships in current EUV resist systems are not well understood. In particular, the nanoscale structures of the polymer base and the distributions of photoacid generators (PAGs) should play a critical roles in the performance of a resist system, yet currently available models for photochemical reactions in EUV resist systems are exclusively based on homogeneous bulk models that ignore molecular-level details of solid resist films. In this work, we investigate how microscopic molecular organizations in EUV resist affect photoacid generations in a bottom-up approach that describes structure-dependent electron-transfer dynamics in a solid film model. To this end, molecular dynamics simulations and stimulated annealing are used to obtain structures of a large simulation box containing poly(4-hydroxystyrene) (PHS) base polymers and triphenylsulfonium based PAGs. Our calculations reveal that ion-pair interactions govern the microscopic distributions of the polymer base and PAG molecules, resulting in a highly inhomogeneous system with nonuniform nanoscale chemical domains. Furthermore, the theoretical structures were used in combination of quantum chemical calculations and the Marcus theory to evaluate electron transfer rates between molecular sites, and then kinetic Monte Carlo simulations were carried out to model electron transfer dynamics with molecular structure details taken into consideration. As a result, the portion of thermalized electrons that are absorbed by the PAGs and the nanoscale spatial distribution of generated acids can be estimated. Our data reveal that the nanoscale inhomogeneous distributions of base polymers and PAGs strongly affect the electron transfer and the performance of the resist system. The implications to the performances of EUV resists and key engineering requirements for improved resist systems will also be discussed in this work. Our results shed light on the fundamental structure dependence of photoacid generation and the control of the nanoscale structures as well as base polymer-PAG interactions in EVU resist systems, and we expect these knowledge will be useful for the future development of improved EUV resist systems.

Vertical electron transport in van der Waals heterostructures with graphene layers

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ryzhii, V., E-mail: v-ryzhii@riec.tohoku.ac.jp; Center for Photonics and Infrared Engineering, Bauman Moscow State Technical University and Institute of Ultra High Frequency Semiconductor Electronics of RAS, Moscow 111005; Otsuji, T.

We propose and analyze an analytical model for the self-consistent description of the vertical electron transport in van der Waals graphene-layer (GL) heterostructures with the GLs separated by the barriers layers. The top and bottom GLs serve as the structure emitter and collector. The vertical electron transport in such structures is associated with the propagation of the electrons thermionically emitted from GLs above the inter-GL barriers. The model under consideration describes the processes of the electron thermionic emission from and the electron capture to GLs. It accounts for the nonuniformity of the self-consistent electric field governed by the Poisson equationmore » which accounts for the variation of the electron population in GLs. The model takes also under consideration the cooling of electrons in the emitter layer due to the Peltier effect. We find the spatial distributions of the electric field and potential with the high-electric-field domain near the emitter GL in the GL heterostructures with different numbers of GLs. Using the obtained spatial distributions of the electric field, we calculate the current-voltage characteristics. We demonstrate that the Peltier cooling of the two-dimensional electron gas in the emitter GL can strongly affect the current-voltage characteristics resulting in their saturation. The obtained results can be important for the optimization of the hot-electron bolometric terahertz detectors and different devices based on GL heterostructures.« less

X-ray spectroscopic study of amorphous and polycrystalline PbO films, α-PbO, and β-PbO for direct conversion imaging.

PubMed

Qamar, A; LeBlanc, K; Semeniuk, O; Reznik, A; Lin, J; Pan, Y; Moewes, A

2017-10-13

We investigated the electronic structure of Lead Oxide (PbO) - one of the most promising photoconductor materials for direct conversion x-ray imaging detectors, using soft x-ray emission and absorption spectroscopy. Two structural configurations of thin PbO layers, namely the polycrystalline and the amorphous phase, were studied, and compared to the properties of powdered α-PbO and β-PbO samples. In addition, we performed calculations within the framework of density functional theory and found an excellent agreement between the calculated and the measured absorption and emission spectra, which indicates high accuracy of our structural models. Our work provides strong evidence that the electronic structure of PbO layers, specifically the width of the band gap and the presence of additional interband and intraband states in both conduction and valence band, depend on the deposition conditions. We tested several model structures using DFT simulations to understand what the origin of these states is. The presence of O vacancies is the most plausible explanation for these additional electronic states. Several other plausible models were ruled out including interstitial O, dislocated O and the presence of significant lattice stress in PbO.

Phase-field model of insulator-to-metal transition in VO2 under an electric field

NASA Astrophysics Data System (ADS)

Shi, Yin; Chen, Long-Qing

2018-05-01

The roles of an electric field and electronic doping in insulator-to-metal transitions are still not well understood. Here we formulated a phase-field model of insulator-to-metal transitions by taking into account both structural and electronic instabilities as well as free electrons and holes in VO2, a strongly correlated transition-metal oxide. Our phase-field simulations demonstrate that in a VO2 slab under a uniform electric field, an abrupt universal resistive transition occurs inside the supercooling region, in sharp contrast to the conventional Landau-Zener smooth electric breakdown. We also show that hole doping may decouple the structural and electronic phase transitions in VO2, leading to a metastable metallic monoclinic phase which could be stabilized through a geometrical confinement and the size effect. This work provides a general mesoscale thermodynamic framework for understanding the influences of electric field, electronic doping, and stress and strain on insulator-to-metal transitions and the corresponding mesoscale domain structure evolution in VO2 and related strongly correlated systems.

System design and verification of the precession electron diffraction technique

NASA Astrophysics Data System (ADS)

Own, Christopher Su-Yan

2005-07-01

Bulk structural crystallography is generally a two-part process wherein a rough starting structure model is first derived, then later refined to give an accurate model of the structure. The critical step is the determination of the initial model. As materials problems decrease in length scale, the electron microscope has proven to be a versatile and effective tool for studying many problems. However, study of complex bulk structures by electron diffraction has been hindered by the problem of dynamical diffraction. This phenomenon makes bulk electron diffraction very sensitive to specimen thickness, and expensive equipment such as aberration-corrected scanning transmission microscopes or elaborate methodology such as high resolution imaging combined with diffraction and simulation are often required to generate good starting structures. The precession electron diffraction technique (PED), which has the ability to significantly reduce dynamical effects in diffraction patterns, has shown promise as being a "philosopher's stone" for bulk electron diffraction. However, a comprehensive understanding of its abilities and limitations is necessary before it can be put into widespread use as a standalone technique. This thesis aims to bridge the gaps in understanding and utilizing precession so that practical application might be realized. Two new PED systems have been built, and optimal operating parameters have been elucidated. The role of lens aberrations is described in detail, and an alignment procedure is given that shows how to circumvent aberration in order to obtain high-quality patterns. Multislice simulation is used for investigating the errors inherent in precession, and is also used as a reference for comparison to simple models and to experimental PED data. General trends over a large sampling of parameter space are determined. In particular, we show that the primary reflection intensity errors occur near the transmitted beam and decay with increasing angle and decreasing specimen thickness. These errors, occurring at the lowest spatial frequencies, fortuitously coincide with reflections for which phases are easiest to determine via imaging methods. A general two-beam dynamical model based upon an existing approximate model is found to be fairly accurate across most experimental conditions, particularly where it is needed for providing a correction to distorted data. Finally, the practical structure solution procedure using PED is demonstrated for several model material systems. Of the experiment parameters investigated, the cone semi-angle is found to be the most important (it should be as large as possible), followed closely by specimen thickness (thinner is better). Assuming good structure projection characteristics in the specimen, the thickness tractable by PED is extended to 40-50 nm without correction, demonstrated for complex oxides. With a forward calculation based upon the two-beam dynamical model (using known structure factors), usable specimen thickness can be extended past 150 nm. For a priori correction, using the squared amplitudes approximates the two-beam model for most thicknesses if the scattering from the structure adheres to psuedo-kinematical behavior. Practically, crystals up to 60 nm in thickness can now be processed by the precession methods developed in this thesis.

Electron Transport Modeling of Molecular Nanoscale Bridges Used in Energy Conversion Schemes

DOE Office of Scientific and Technical Information (OSTI.GOV)

Dunietz, Barry D

2016-08-09

The goal of the research program is to reliably describe electron transport and transfer processes at the molecular level. Such insight is essential for improving molecular applications of solar and thermal energy conversion. We develop electronic structure models to study (1) photoinduced electron transfer and transport processes in organic semiconducting materials, and (2) charge and heat transport through molecular bridges. We seek fundamental understanding of key processes, which lead to design new experiments and ultimately to achieve systems with improved properties.

Study of photoirradiation for YBa 2Cu 3O 6+ x compounds and the electron structure by positron experiment

NASA Astrophysics Data System (ADS)

Guosheng, Cheng; Jiaxiang, Shang; Xigui, Li; xianqi, Dai; Xizhong, Wang; Jincang, Zhang

1997-08-01

We present positron lifetime data of YBa 2Cu 3O 6+ x (x=0.92, 0.43) compounds for different photo-irradiation time. It is given that change of the local electron density and vacancy concentration with photoirradiation time. It is found that there is transform at the electronic structure of CuO chains. We also have discussed the effect of photoirradiations time on the electronic structure of YBa 2Cu 3O 6+ x systems and their charge reservoir layer and CuO 2 plane conduction.layer. The positron experimental results support the model of photoinduced oxygen-diffusion mechanism.

ATOMIC RESOLUTION CRYO ELECTRON MICROSCOPY OF MACROMOLECULAR COMPLEXES

PubMed Central

ZHOU, Z. HONG

2013-01-01

Single-particle cryo electron microscopy (cryoEM) is a technique for determining three-dimensional (3D) structures from projection images of molecular complexes preserved in their “native,” noncrystalline state. Recently, atomic or near-atomic resolution structures of several viruses and protein assemblies have been determined by single-particle cryoEM, allowing ab initio atomic model building by following the amino acid side chains or nucleic acid bases identifiable in their cryoEM density maps. In particular, these cryoEM structures have revealed extended arms contributing to molecular interactions that are otherwise not resolved by the conventional structural method of X-ray crystallography at similar resolutions. High-resolution cryoEM requires careful consideration of a number of factors, including proper sample preparation to ensure structural homogeneity, optimal configuration of electron imaging conditions to record high-resolution cryoEM images, accurate determination of image parameters to correct image distortions, efficient refinement and computation to reconstruct a 3D density map, and finally appropriate choice of modeling tools to construct atomic models for functional interpretation. This progress illustrates the power of cryoEM and ushers it into the arsenal of structural biology, alongside conventional techniques of X-ray crystallography and NMR, as a major tool (and sometimes the preferred one) for the studies of molecular interactions in supramolecular assemblies or machines. PMID:21501817

Electron core ionization in compressed alkali metal cesium

NASA Astrophysics Data System (ADS)

Degtyareva, V. F.

2018-01-01

Elements of groups I and II in the periodic table have valence electrons of s-type and are usually considered as simple metals. Crystal structures of these elements at ambient pressure are close-packed and high-symmetry of bcc and fcc-types, defined by electrostatic (Madelung) energy. Diverse structures were found under high pressure with decrease of the coordination number, packing fraction and symmetry. Formation of complex structures can be understood within the model of Fermi sphere-Brillouin zone interactions and supported by Hume-Rothery arguments. With the volume decrease there is a gain of band structure energy accompanied by a formation of many-faced Brillouin zone polyhedra. Under compression to less than a half of the initial volume the interatomic distances become close to or smaller than the ionic radius which should lead to the electron core ionization. At strong compression it is necessary to assume that for alkali metals the valence electron band overlaps with the upper core electrons, which increases the valence electron count under compression.

The structural and electronic properties of amorphous HgCdTe from first-principles calculations

NASA Astrophysics Data System (ADS)

Zhao, Huxian; Chen, Xiaoshuang; Lu, Jianping; Shu, Haibo; Lu, Wei

2014-01-01

Amorphous mercury cadmium telluride (a-MCT) model structures, with x being 0.125 and 0.25, are obtained from first-principles calculations. We generate initial structures by computation alchemy method. It is found that most atoms in the network of amorphous structures tend to be fourfold and form tetrahedral structures, implying that the chemical ordered continuous random network with some coordination defects is the ideal structure for a-MCT. The electronic structure is also concerned. The gap is found to be 0.30 and 0.26 eV for a-Hg0.875Cd0.125Te and a-Hg0.75Cd0.25Te model structures, independent of the composition. By comparing with the properties of crystalline MCT with the same composition, we observe a blue-shift of energy band gap. The localization of tail states and its atomic origin are also discussed.

Computational methods for constructing protein structure models from 3D electron microscopy maps.

PubMed

Esquivel-Rodríguez, Juan; Kihara, Daisuke

2013-10-01

Protein structure determination by cryo-electron microscopy (EM) has made significant progress in the past decades. Resolutions of EM maps have been improving as evidenced by recently reported structures that are solved at high resolutions close to 3Å. Computational methods play a key role in interpreting EM data. Among many computational procedures applied to an EM map to obtain protein structure information, in this article we focus on reviewing computational methods that model protein three-dimensional (3D) structures from a 3D EM density map that is constructed from two-dimensional (2D) maps. The computational methods we discuss range from de novo methods, which identify structural elements in an EM map, to structure fitting methods, where known high resolution structures are fit into a low-resolution EM map. A list of available computational tools is also provided. Copyright © 2013 Elsevier Inc. All rights reserved.

Intrinsic charge trapping in amorphous oxide films: status and challenges

NASA Astrophysics Data System (ADS)

Strand, Jack; Kaviani, Moloud; Gao, David; El-Sayed, Al-Moatasem; Afanas’ev, Valeri V.; Shluger, Alexander L.

2018-06-01

We review the current understanding of intrinsic electron and hole trapping in insulating amorphous oxide films on semiconductor and metal substrates. The experimental and theoretical evidences are provided for the existence of intrinsic deep electron and hole trap states stemming from the disorder of amorphous metal oxide networks. We start from presenting the results for amorphous (a) HfO2, chosen due to the availability of highest purity amorphous films, which is vital for studying their intrinsic electronic properties. Exhaustive photo-depopulation spectroscopy measurements and theoretical calculations using density functional theory shed light on the atomic nature of electronic gap states responsible for deep electron trapping observed in a-HfO2. We review theoretical methods used for creating models of amorphous structures and electronic structure calculations of amorphous oxides and outline some of the challenges in modeling defects in amorphous materials. We then discuss theoretical models of electron polarons and bi-polarons in a-HfO2 and demonstrate that these intrinsic states originate from low-coordinated ions and elongated metal-oxygen bonds in the amorphous oxide network. Similarly, holes can be captured at under-coordinated O sites. We then discuss electron and hole trapping in other amorphous oxides, such as a-SiO2, a-Al2O3, a-TiO2. We propose that the presence of low-coordinated ions in amorphous oxides with electron states of significant p and d character near the conduction band minimum can lead to electron trapping and that deep hole trapping should be common to all amorphous oxides. Finally, we demonstrate that bi-electron trapping in a-HfO2 and a-SiO2 weakens Hf(Si)–O bonds and significantly reduces barriers for forming Frenkel defects, neutral O vacancies and O2‑ ions in these materials. These results should be useful for better understanding of electronic properties and structural evolution of thin amorphous films under carrier injection conditions.

Fluid theory and simulations of instabilities, turbulent transport and coherent structures in partially-magnetized plasmas of \\mathbf{E}\\times \\mathbf{B} discharges

NASA Astrophysics Data System (ADS)

Smolyakov, A. I.; Chapurin, O.; Frias, W.; Koshkarov, O.; Romadanov, I.; Tang, T.; Umansky, M.; Raitses, Y.; Kaganovich, I. D.; Lakhin, V. P.

2017-01-01

Partially-magnetized plasmas with magnetized electrons and non-magnetized ions are common in Hall thrusters for electric propulsion and magnetron material processing devices. These plasmas are usually in strongly non-equilibrium state due to presence of crossed electric and magnetic fields, inhomogeneities of plasma density, temperature, magnetic field and beams of accelerated ions. Free energy from these sources make such plasmas prone to various instabilities resulting in turbulence, anomalous transport, and appearance of coherent structures as found in experiments. This paper provides an overview of instabilities that exist in such plasmas. A nonlinear fluid model has been developed for description of the Simon-Hoh, lower-hybrid and ion-sound instabilities. The model also incorporates electron gyroviscosity describing the effects of finite electron temperature. The nonlinear fluid model has been implemented in the BOUT++ framework. The results of nonlinear simulations are presented demonstrating turbulence, anomalous current and tendency toward the formation of coherent structures.

Nonlinear structure formation in ion-temperature-gradient driven drift waves in pair-ion plasma with nonthermal electron distribution

NASA Astrophysics Data System (ADS)

Razzaq, Javaria; Haque, Q.; Khan, Majid; Bhatti, Adnan Mehmood; Kamran, M.; Mirza, Arshad M.

2018-02-01

Nonlinear structure formation in ion-temperature-gradient (ITG) driven waves is investigated in pair-ion plasma comprising ions and nonthermal electrons (kappa, Cairns). By using the transport equations of the Braginskii model, a new set of nonlinear equations are derived. A linear dispersion relation is obtained and discussed analytically as well as numerically. It is shown that the nonthermal population of electrons affects both the linear and nonlinear characteristics of the ITG mode in pair-ion plasma. This work will be useful in tokamaks and stellarators where non-Maxwellian population of electrons may exist due to resonant frequency heating, electron cyclotron heating, runaway electrons, etc.

Electronic structure and magnetic anisotropy of L1{sub 0}-FePt thin film studied by hard x-ray photoemission spectroscopy and first-principles calculations

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ueda, S.; Synchrotron X-ray Station at SPring-8, National Institute for Materials Science, Sayo, Hyogo 679-5148; Mizuguchi, M.

2016-07-25

We have studied the electronic structure of the L1{sub 0} ordered FePt thin film by hard x-ray photoemission spectroscopy (HAXPES), cluster model, and first-principles calculations to investigate the relationship between the electronic structure and perpendicular magneto-crystalline anisotropy (MCA). The Fe 2p core-level HAXPES spectrum of the ordered film revealed the strong electron correlation in the Fe 3d states and the hybridization between the Fe 3d and Pt 5d states. By comparing the experimental valence band structure with the theoretical density of states, the strong electron correlation in the Fe 3d states modifies the valence band electronic structure of the L1{submore » 0} ordered FePt thin film through the Fe 3d-Pt 5d hybridization. These results strongly suggest that the strong electron correlation effect in the Fe 3d states and the Fe 3d-Pt 5d hybridization as well as the spin-orbit interaction in the Pt 5d states play important roles in the perpendicular MCA for L1{sub 0}-FePt.« less

New Approach to Synthesis of Powder and Composite Materials by Electron Beam. Part 1. Technological Features of the Process

NASA Astrophysics Data System (ADS)

Rudskoy, A. I.; Kondrat'ev, S. Yu.; Sokolov, Yu. A.

2016-05-01

Possibilities of electron beam synthesis of structural and tool composite materials are considered. It is shown that a novel process involving mathematical modeling of each individual operation makes it possible to create materials with programmable structure and predictable properties from granules of various specified chemical compositions and sizes.

Atomic scale structure and chemistry of interfaces by Z-contrast imaging and electron energy loss spectroscopy in the stem

DOE Office of Scientific and Technical Information (OSTI.GOV)

McGibbon, M.M.; Browning, N.D.; Chisholm, M.F.

The macroscopic properties of many materials are controlled by the structure and chemistry at grain boundaries. A basic understanding of the structure-property relationship requires a technique which probes both composition and chemical bonding on an atomic scale. High-resolution Z-contrast imaging in the scanning transmission electron microscope (STEM) forms an incoherent image in which changes in atomic structure and composition across an interface can be interpreted directly without the need for preconceived atomic structure models. Since the Z-contrast image is formed by electrons scattered through high angles, parallel detection electron energy loss spectroscopy (PEELS) can be used simultaneously to provide complementarymore » chemical information on an atomic scale. The fine structure in the PEEL spectra can be used to investigate the local electronic structure and the nature of the bonding across the interface. In this paper we use the complimentary techniques of high resolution Z-contrast imaging and PEELS to investigate the atomic structure and chemistry of a 25{degree} symmetric tilt boundary in a bicrystal of the electroceramic SrTiO{sub 3}.« less

Experimental evidence and structural modeling of nonstoichiometric (010) surfaces coexisting in hydroxyapatite nano-crystals.

PubMed

Ospina, C A; Terra, J; Ramirez, A J; Farina, M; Ellis, D E; Rossi, A M

2012-01-01

High-resolution transmission electron microscopy (HRTEM) and ab initio quantum-mechanical calculations of electronic structure were combined to investigate the structure of the hydroxyapatite (HA) (010) surface, which plays an important role in HA interactions with biological media. HA was synthesized by in vitro precipitation at 37°C. HRTEM images revealed thin elongated rod nanoparticles with preferential growth along the [001] direction and terminations parallel to the (010) plane. The focal series reconstruction (FSR) technique was applied to develop an atomic-scale structural model of the high-resolution images. The HRTEM simulations identified the coexistence of two structurally distinct terminations for (010) surfaces: a rather flat Ca(II)-terminated surface and a zig-zag structure with open OH channels. Density functional theory (DFT) was applied in a periodic slab plane-wave pseudopotential approach to refine details of atomic coordination and bond lengths of Ca(I) and Ca(II) sites in hydrated HA (010) surfaces, starting from the HRTEM model. Copyright © 2011 Elsevier B.V. All rights reserved.

Hybrid simulations of magnetic reconnection with kinetic ions and fluid electron pressure anisotropy

DOE PAGES

Le, A.; Daughton, W.; Karimabadi, H.; ...

2016-03-16

We present the first hybrid simulations with kinetic ions and recently developed equations of state for the electron fluid appropriate for reconnection with a guide field. The equations of state account for the main anisotropy of the electron pressure tensor.Magnetic reconnection is studied in two systems, an initially force-free current sheet and a Harris sheet. The hybrid model with the equations of state is compared to two other models, hybrid simulations with isothermal electrons and fully kinetic simulations. Including the anisotropicequations of state in the hybrid model provides a better match to the fully kinetic model. In agreement with fullymore » kinetic results, the main feature captured is the formation of an electron current sheet that extends several ion inertial lengths. This electron current sheet modifies the Hall magnetic field structure near the X-line, and it is not observed in the standard hybrid model with isotropic electrons. The saturated reconnection rate in this regime nevertheless remains similar in all three models. Here, implications for global modeling are discussed.« less

Determining crystal structures through crowdsourcing and coursework

PubMed Central

Horowitz, Scott; Koepnick, Brian; Martin, Raoul; Tymieniecki, Agnes; Winburn, Amanda A.; Cooper, Seth; Flatten, Jeff; Rogawski, David S.; Koropatkin, Nicole M.; Hailu, Tsinatkeab T.; Jain, Neha; Koldewey, Philipp; Ahlstrom, Logan S.; Chapman, Matthew R.; Sikkema, Andrew P.; Skiba, Meredith A.; Maloney, Finn P.; Beinlich, Felix R. M.; Caglar, Ahmet; Coral, Alan; Jensen, Alice Elizabeth; Lubow, Allen; Boitano, Amanda; Lisle, Amy Elizabeth; Maxwell, Andrew T.; Failer, Barb; Kaszubowski, Bartosz; Hrytsiv, Bohdan; Vincenzo, Brancaccio; de Melo Cruz, Breno Renan; McManus, Brian Joseph; Kestemont, Bruno; Vardeman, Carl; Comisky, Casey; Neilson, Catherine; Landers, Catherine R.; Ince, Christopher; Buske, Daniel Jon; Totonjian, Daniel; Copeland, David Marshall; Murray, David; Jagieła, Dawid; Janz, Dietmar; Wheeler, Douglas C.; Cali, Elie; Croze, Emmanuel; Rezae, Farah; Martin, Floyd Orville; Beecher, Gil; de Jong, Guido Alexander; Ykman, Guy; Feldmann, Harald; Chan, Hugo Paul Perez; Kovanecz, Istvan; Vasilchenko, Ivan; Connellan, James C.; Borman, Jami Lynne; Norrgard, Jane; Kanfer, Jebbie; Canfield, Jeffrey M.; Slone, Jesse David; Oh, Jimmy; Mitchell, Joanne; Bishop, John; Kroeger, John Douglas; Schinkler, Jonas; McLaughlin, Joseph; Brownlee, June M.; Bell, Justin; Fellbaum, Karl Willem; Harper, Kathleen; Abbey, Kirk J.; Isaksson, Lennart E.; Wei, Linda; Cummins, Lisa N.; Miller, Lori Anne; Bain, Lyn; Carpenter, Lynn; Desnouck, Maarten; Sharma, Manasa G.; Belcastro, Marcus; Szew, Martin; Szew, Martin; Britton, Matthew; Gaebel, Matthias; Power, Max; Cassidy, Michael; Pfützenreuter, Michael; Minett, Michele; Wesselingh, Michiel; Yi, Minjune; Cameron, Neil Haydn Tormey; Bolibruch, Nicholas I.; Benevides, Noah; Kathleen Kerr, Norah; Barlow, Nova; Crevits, Nykole Krystyne; Dunn, Paul; Roque, Paulo Sergio Silveira Belo Nascimento; Riber, Peter; Pikkanen, Petri; Shehzad, Raafay; Viosca, Randy; James Fraser, Robert; Leduc, Robert; Madala, Roman; Shnider, Scott; de Boisblanc, Sharon; Butkovich, Slava; Bliven, Spencer; Hettler, Stephen; Telehany, Stephen; Schwegmann, Steven A.; Parkes, Steven; Kleinfelter, Susan C.; Michael Holst, Sven; van der Laan, T. J. A.; Bausewein, Thomas; Simon, Vera; Pulley, Warwick; Hull, William; Kim, Annes Yukyung; Lawton, Alexis; Ruesch, Amanda; Sundar, Anjali; Lawrence, Anna-Lisa; Afrin, Antara; Maheshwer, Bhargavi; Turfe, Bilal; Huebner, Christian; Killeen, Courtney Elizabeth; Antebi-Lerrman, Dalia; Luan, Danny; Wolfe, Derek; Pham, Duc; Michewicz, Elaina; Hull, Elizabeth; Pardington, Emily; Galal, Galal Osama; Sun, Grace; Chen, Grace; Anderson, Halie E.; Chang, Jane; Hewlett, Jeffrey Thomas; Sterbenz, Jennifer; Lim, Jiho; Morof, Joshua; Lee, Junho; Inn, Juyoung Samuel; Hahm, Kaitlin; Roth, Kaitlin; Nair, Karun; Markin, Katherine; Schramm, Katie; Toni Eid, Kevin; Gam, Kristina; Murphy, Lisha; Yuan, Lucy; Kana, Lulia; Daboul, Lynn; Shammas, Mario Karam; Chason, Max; Sinan, Moaz; Andrew Tooley, Nicholas; Korakavi, Nisha; Comer, Patrick; Magur, Pragya; Savliwala, Quresh; Davison, Reid Michael; Sankaran, Roshun Rajiv; Lewe, Sam; Tamkus, Saule; Chen, Shirley; Harvey, Sho; Hwang, Sin Ye; Vatsia, Sohrab; Withrow, Stefan; Luther, Tahra K; Manett, Taylor; Johnson, Thomas James; Ryan Brash, Timothy; Kuhlman, Wyatt; Park, Yeonjung; Popović, Zoran; Baker, David; Khatib, Firas; Bardwell, James C. A.

2016-01-01

We show here that computer game players can build high-quality crystal structures. Introduction of a new feature into the computer game Foldit allows players to build and real-space refine structures into electron density maps. To assess the usefulness of this feature, we held a crystallographic model-building competition between trained crystallographers, undergraduate students, Foldit players and automatic model-building algorithms. After removal of disordered residues, a team of Foldit players achieved the most accurate structure. Analysing the target protein of the competition, YPL067C, uncovered a new family of histidine triad proteins apparently involved in the prevention of amyloid toxicity. From this study, we conclude that crystallographers can utilize crowdsourcing to interpret electron density information and to produce structure solutions of the highest quality. PMID:27633552

Pressure tuning the lattice and optical response of silver sulfide

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zhao, Zhao, E-mail: zhaozhao@stanford.edu; Wei, Hua; Mao, Wendy L.

2016-06-27

Binary transition metal chalcogenides have attracted increasing attention for their unique structural and electronic properties. High pressure is a powerful tool for tuning the lattice and electronic structure of transition metal chalcogenides away from their pristine states. In this work, we systematically studied the in situ structural and optical behavior of silver sulfide (Ag{sub 2}S) under pressure by synchrotron X-ray diffraction and infrared spectroscopy measurements in a diamond anvil cell. Upon compression, Ag{sub 2}S undergoes structural symmetrization accompanied by a series of structural transitions while the crystallographic inequivalence of the two Ag sites is maintained. Electronically, pressure effectively tunes themore » ambient semiconducting Ag{sub 2}S into a metal at ∼22 GPa. Drude model analysis shows that the optical conductivity evolves significantly, reaching the highest value of 100 Ω{sup −1} cm{sup −1} at ∼40 GPa. Our results highlight the structural and electronic tunability of silver chalcogenides as a function of pressure and suggest the potential of Ag{sub 2}S as a platform for developing optical and opto-electronic applications.« less

Hole doping, hybridization gaps, and electronic correlation in graphene on a platinum substrate

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hwang, Jinwoong; Hwang, Hwihyeon; Kim, Min-Jeong

The interaction between graphene and substrates provides a viable route to enhance the functionality of both materials. Depending on the nature of electronic interaction at the interface, the electron band structure of graphene is strongly influenced, allowing us to make use of the intrinsic properties of graphene or to design additional functionalities in graphene. In this paper, we present an angle-resolved photoemission study on the interaction between graphene and a platinum substrate. The formation of an interface between graphene and platinum leads to a strong deviation in the electronic structure of graphene not only from its freestanding form but alsomore » from the behavior observed on typical metals. Finally, the combined study on the experimental and theoretical electron band structure unveils the unique electronic properties of graphene on a platinum substrate, which singles out graphene/platinum as a model system investigating graphene on a metallic substrate with strong interaction.« less

Hole doping, hybridization gaps, and electronic correlation in graphene on a platinum substrate

DOE PAGES

Hwang, Jinwoong; Hwang, Hwihyeon; Kim, Min-Jeong; ...

2017-08-02

The interaction between graphene and substrates provides a viable route to enhance the functionality of both materials. Depending on the nature of electronic interaction at the interface, the electron band structure of graphene is strongly influenced, allowing us to make use of the intrinsic properties of graphene or to design additional functionalities in graphene. In this paper, we present an angle-resolved photoemission study on the interaction between graphene and a platinum substrate. The formation of an interface between graphene and platinum leads to a strong deviation in the electronic structure of graphene not only from its freestanding form but alsomore » from the behavior observed on typical metals. Finally, the combined study on the experimental and theoretical electron band structure unveils the unique electronic properties of graphene on a platinum substrate, which singles out graphene/platinum as a model system investigating graphene on a metallic substrate with strong interaction.« less

Structural, electronic and thermal properties of super hard ternary boride, WAlB

NASA Astrophysics Data System (ADS)

Rajpoot, Priyanka; Rastogi, Anugya; Verma, U. P.

2018-04-01

A first principle study of the structural, electronic and thermal properties of Tungsten Aluminum Boride (WAlB) using full-potential linearized augmented plane wave (FP-LAPW) in the frame work of density function theory (DFT) have been calculated. The calculated equilibrium structural parameters are in excellent agreement with available experimental results. The calculated electronic band structure reveals that WAlB is metallic in nature. The quasi-harmonic Debye model is applied to study of the temperature and pressure effect on volume, Debye temperature, thermal expansion coefficient and specific heat at constant volume and constant pressure. To the best of our knowledge theoretical investigation of these properties of WAlB is reported for the first time.

Spin-dependent dwell times of electron tunneling through double- and triple-barrier structures

NASA Astrophysics Data System (ADS)

Erić, Marko; Radovanović, Jelena; Milanović, Vitomir; Ikonić, Zoran; Indjin, Dragan

2008-04-01

We have analyzed the influence of Dresselhaus and Rashba spin-orbit couplings (caused by the bulk inversion asymmetry and the structural asymmetry, respectively) on electron tunneling through a double- and triple-barrier structures, with and without an externally applied electric field. The results indicate that the degree of structural asymmetry and external electric field can greatly affect the dwell times of electrons with opposite spin orientation. This opens up the possibilities of obtaining efficient spin separation in the time domain. The material system of choice is AlxGa1-xSb, and the presented model takes into account the position dependence of material parameters, as well as the effects of band nonparabolicity.

Low energy electron diffraction and low energy electron microscopy microspot I/V analysis of the (4 x 4)O structure on Ag(111): surface oxide or reconstruction?

PubMed

Reichelt, R; Günther, S; Wintterlin, J; Moritz, W; Aballe, L; Mentes, T O

2007-10-07

A low energy electron diffraction (LEED) I/V analysis was performed of the (4 x 4) oxygen structure on Ag(111). Two data sets were used, one recorded with a conventional LEED system and a second with a low energy electron microscope (LEEM). The data sets agree well with each other, demonstrating that I/V structure analyses can be performed with the same quality with LEEM as with conventional LEED. The structure obtained confirms the recently proposed model that involves a reconstruction of the Ag(111) surface. Previous models based on a thin layer of Ag(2)O that had been accepted for more than 30 years are disproved. The reconstruction model contains two units of six triangularly arranged Ag atoms and a stacking fault in one half of the unit cell. The six O atoms per unit cell occupy sites in the trenches between the Ag(6) triangles. Small lateral displacements of the Ag atoms lift the mirror symmetry of the structure, leading to two nonequivalent groups of O atoms. The atoms of both groups are located approximately 0.5 Angstrom below the top Ag layer, on fourfold positions with respect to the top layer Ag atoms. Ag-O distances between 2.05 and 2.3 Angstrom are found. The oxygen atoms exhibit large static or dynamic displacements of up to 0.3 Angstrom at 300 K.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Morris, J.R.; Lu, Z.; Ring, D.M.

We have examined a variety of structures for the {l_brace}510{r_brace} symmetric tilt boundary in Si and Ge, using tight-binding and first-principles calculations. These calculations show that the observed structure in Si is the lowest-energy structure, despite the fact that it is more complicated than what is necessary to preserve fourfold coordination. Contrary to calculations using a Tersoff potential, first-principles calculations show that the energy depends strongly upon the structure. A recently developed tight-binding model for Si produces results in very good agreement with the first-principles calculations. Electronic density of states calculations based upon this model show no evidence of midgapmore » states and little evidence of electronic states localized to the grain boundary. {copyright} {ital 1998} {ital The American Physical Society}« less

Modeling the Structure of Helical Assemblies with Experimental Constraints in Rosetta.

PubMed

André, Ingemar

2018-01-01

Determining high-resolution structures of proteins with helical symmetry can be challenging due to limitations in experimental data. In such instances, structure-based protein simulations driven by experimental data can provide a valuable approach for building models of helical assemblies. This chapter describes how the Rosetta macromolecular package can be used to model homomeric protein assemblies with helical symmetry in a range of modeling scenarios including energy refinement, symmetrical docking, comparative modeling, and de novo structure prediction. Data-guided structure modeling of helical assemblies with experimental information from electron density, X-ray fiber diffraction, solid-state NMR, and chemical cross-linking mass spectrometry is also described.

3D image reconstruction algorithms for cryo-electron-microscopy images of virus particles

NASA Astrophysics Data System (ADS)

Doerschuk, Peter C.; Johnson, John E.

2000-11-01

A statistical model for the object and the complete image formation process in cryo electron microscopy of viruses is presented. Using this model, maximum likelihood reconstructions of the 3D structure of viruses are computed using the expectation maximization algorithm and an example based on Cowpea mosaic virus is provided.

Ground-state properties of rare-earth metals: an evaluation of density-functional theory.

PubMed

Söderlind, Per; Turchi, P E A; Landa, A; Lordi, V

2014-10-15

The rare-earth metals have important technological applications due to their magnetic properties, but are scarce and expensive. Development of high-performance magnetic materials with less rare-earth content is desired, but theoretical modeling is hampered by complexities of the rare earths electronic structure. The existence of correlated (atomic-like) 4f electrons in the vicinity of the valence band makes any first-principles theory challenging. Here, we apply and evaluate the efficacy of density-functional theory for the series of lanthanides (rare earths), investigating the influence of the electron exchange and correlation functional, spin-orbit interaction, and orbital polarization. As a reference, the results are compared with those of the so-called 'standard model' of the lanthanides in which electrons are constrained to occupy 4f core states with no hybridization with the valence electrons. Some comparisons are also made with models designed for strong electron correlations. Our results suggest that spin-orbit coupling and orbital polarization are important, particularly for the magnitude of the magnetic moments, and that calculated equilibrium volumes, bulk moduli, and magnetic moments show correct trends overall. However, the precision of the calculated properties is not at the level of that found for simpler metals in the Periodic Table of Elements, and the electronic structures do not accurately reproduce x-ray photoemission spectra.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ivanov, Yuri, E-mail: yufi55@mail.ru; National Research Tomsk State University, 36 Lenina Str., Tomsk, 634050; National Research Tomsk Polytechnic University, 30 Lenina Str., Tomsk, 634050

The present work is devoted to numerical simulation of temperature fields and the analysis of structural and strength properties of the samples surface layer of boron carbide ceramics treated by the high-current pulsed electron-beam of the submillisecond duration. The samples made of sintered boron carbide ceramics are used in these investigations. The problem of calculating the temperature field is reduced to solving the thermal conductivity equation. The electron beam density ranges between 8…30 J/cm{sup 2}, while the pulse durations are 100…200 μs in numerical modelling. The results of modelling the temperature field allowed ascertaining the threshold parameters of the electronmore » beam, such as energy density and pulse duration. The electron beam irradiation is accompanied by the structural modification of the surface layer of boron carbide ceramics either in the single-phase (liquid or solid) or two-phase (solid-liquid) states. The sample surface of boron carbide ceramics is treated under the two-phase state (solid-liquid) conditions of the structural modification. The surface layer is modified by the high-current pulsed electron-beam produced by SOLO installation at the Institute of High Current Electronics of the Siberian Branch of the Russian Academy of Sciences, Tomsk, Russia. The elemental composition and the defect structure of the modified surface layer are analyzed by the optical instrument, scanning electron and transmission electron microscopes. Mechanical properties of the modified layer are determined measuring its hardness and crack resistance. Research results show that the melting and subsequent rapid solidification of the surface layer lead to such phenomena as fragmentation due to a crack network, grain size reduction, formation of the sub-grained structure due to mechanical twinning, and increase of hardness and crack resistance.« less

Modeling of projection electron lithography

NASA Astrophysics Data System (ADS)

Mack, Chris A.

2000-07-01

Projection Electron Lithography (PEL) has recently become a leading candidate for the next generation of lithography systems after the successful demonstration of SCAPEL by Lucent Technologies and PREVAIL by IBM. These systems use a scattering membrane mask followed by a lens with limited angular acceptance range to form an image of the mask when illuminated by high energy electrons. This paper presents an initial modeling system for such types of projection electron lithography systems. Monte Carlo modeling of electron scattering within the mask structure creates an effective mask 'diffraction' pattern, to borrow the standard optical terminology. A cutoff of this scattered pattern by the imaging 'lens' provides an electron energy distribution striking the wafer. This distribution is then convolved with a 'point spread function,' the results of a Monte Carlo scattering calculation of a point beam of electrons striking the resist coated substrate and including the effects of beam blur. Resist exposure and development models from standard electron beam lithography simulation are used to simulate the final three-dimensional resist profile.

Exciton scattering approach for optical spectra calculations in branched conjugated macromolecules

NASA Astrophysics Data System (ADS)

Li, Hao; Wu, Chao; Malinin, Sergey V.; Tretiak, Sergei; Chernyak, Vladimir Y.

2016-12-01

The exciton scattering (ES) technique is a multiscale approach based on the concept of a particle in a box and developed for efficient calculations of excited-state electronic structure and optical spectra in low-dimensional conjugated macromolecules. Within the ES method, electronic excitations in molecular structure are attributed to standing waves representing quantum quasi-particles (excitons), which reside on the graph whose edges and nodes stand for the molecular linear segments and vertices, respectively. Exciton propagation on the linear segments is characterized by the exciton dispersion, whereas exciton scattering at the branching centers is determined by the energy-dependent scattering matrices. Using these ES energetic parameters, the excitation energies are then found by solving a set of generalized "particle in a box" problems on the graph that represents the molecule. Similarly, unique energy-dependent ES dipolar parameters permit calculations of the corresponding oscillator strengths, thus, completing optical spectra modeling. Both the energetic and dipolar parameters can be extracted from quantum-chemical computations in small molecular fragments and tabulated in the ES library for further applications. Subsequently, spectroscopic modeling for any macrostructure within a considered molecular family could be performed with negligible numerical effort. We demonstrate the ES method application to molecular families of branched conjugated phenylacetylenes and ladder poly-para-phenylenes, as well as structures with electron donor and acceptor chemical substituents. Time-dependent density functional theory (TD-DFT) is used as a reference model for electronic structure. The ES calculations accurately reproduce the optical spectra compared to the reference quantum chemistry results, and make possible to predict spectra of complex macromolecules, where conventional electronic structure calculations are unfeasible.

Cluster molecular orbital description of the electronic structures of mixed-valence iron oxides and silicates

USGS Publications Warehouse

Sherman, David M.

1986-01-01

A molecular orbital description, based on spin-unrestricted X??-scattered wave calculations, is given for the electronic structures of mixed valence iron oxides and silicates. The cluster calculations show that electron hopping and optical intervalence charge-transger result from weak FeFe bonding across shared edges of FeO6 coordination polyhedra. In agreement with Zener's double exchange model, FeFe bonding is found to stabilize ferromagnetic coupling between Fe2+ and Fe3+ cations. ?? 1986.

Structure of the alternative complex III in a supercomplex with cytochrome oxidase.

PubMed

Sun, Chang; Benlekbir, Samir; Venkatakrishnan, Padmaja; Wang, Yuhang; Hong, Sangjin; Hosler, Jonathan; Tajkhorshid, Emad; Rubinstein, John L; Gennis, Robert B

2018-05-01

Alternative complex III (ACIII) is a key component of the respiratory and/or photosynthetic electron transport chains of many bacteria 1-3 . Like complex III (also known as the bc 1 complex), ACIII catalyses the oxidation of membrane-bound quinol and the reduction of cytochrome c or an equivalent electron carrier. However, the two complexes have no structural similarity 4-7 . Although ACIII has eluded structural characterization, several of its subunits are known to be homologous to members of the complex iron-sulfur molybdoenzyme (CISM) superfamily 8 , including the proton pump polysulfide reductase 9,10 . We isolated the ACIII from Flavobacterium johnsoniae with native lipids using styrene maleic acid copolymer 11-14 , both as an independent enzyme and as a functional 1:1 supercomplex with an aa 3 -type cytochrome c oxidase (cyt aa 3 ). We determined the structure of ACIII to 3.4 Å resolution by cryo-electron microscopy and constructed an atomic model for its six subunits. The structure, which contains a [3Fe-4S] cluster, a [4Fe-4S] cluster and six haem c units, shows that ACIII uses known elements from other electron transport complexes arranged in a previously unknown manner. Modelling of the cyt aa 3 component of the supercomplex revealed that it is structurally modified to facilitate association with ACIII, illustrating the importance of the supercomplex in this electron transport chain. The structure also resolves two of the subunits of ACIII that are anchored to the lipid bilayer with N-terminal triacylated cysteine residues, an important post-translational modification found in numerous prokaryotic membrane proteins that has not previously been observed structurally in a lipid bilayer.

Twilight reloaded: the peptide experience

PubMed Central

Weichenberger, Christian X.; Pozharski, Edwin; Rupp, Bernhard

2017-01-01

The de facto commoditization of biomolecular crystallography as a result of almost disruptive instrumentation automation and continuing improvement of software allows any sensibly trained structural biologist to conduct crystallo­graphic studies of biomolecules with reasonably valid outcomes: that is, models based on properly interpreted electron density. Robust validation has led to major mistakes in the protein part of structure models becoming rare, but some depositions of protein–peptide complex structure models, which generally carry significant interest to the scientific community, still contain erroneous models of the bound peptide ligand. Here, the protein small-molecule ligand validation tool Twilight is updated to include peptide ligands. (i) The primary technical reasons and potential human factors leading to problems in ligand structure models are presented; (ii) a new method used to score peptide-ligand models is presented; (iii) a few instructive and specific examples, including an electron-density-based analysis of peptide-ligand structures that do not contain any ligands, are discussed in detail; (iv) means to avoid such mistakes and the implications for database integrity are discussed and (v) some suggestions as to how journal editors could help to expunge errors from the Protein Data Bank are provided. PMID:28291756

Twilight reloaded: the peptide experience.

PubMed

Weichenberger, Christian X; Pozharski, Edwin; Rupp, Bernhard

2017-03-01

The de facto commoditization of biomolecular crystallography as a result of almost disruptive instrumentation automation and continuing improvement of software allows any sensibly trained structural biologist to conduct crystallographic studies of biomolecules with reasonably valid outcomes: that is, models based on properly interpreted electron density. Robust validation has led to major mistakes in the protein part of structure models becoming rare, but some depositions of protein-peptide complex structure models, which generally carry significant interest to the scientific community, still contain erroneous models of the bound peptide ligand. Here, the protein small-molecule ligand validation tool Twilight is updated to include peptide ligands. (i) The primary technical reasons and potential human factors leading to problems in ligand structure models are presented; (ii) a new method used to score peptide-ligand models is presented; (iii) a few instructive and specific examples, including an electron-density-based analysis of peptide-ligand structures that do not contain any ligands, are discussed in detail; (iv) means to avoid such mistakes and the implications for database integrity are discussed and (v) some suggestions as to how journal editors could help to expunge errors from the Protein Data Bank are provided.

The effects of temperature and magnetic flux on electron transport through a four-channel DNA model

NASA Astrophysics Data System (ADS)

Lee, Sunhee; Hedin, Eric; Joe, Yong

2010-03-01

The temperature dependence of the conductivity of lambda phage DNA has been measured by Tran et al [1] experimentally, where the conductivity displayed strong (weak) temperature dependence above (below) a threshold temperature. In order to understand the temperature effects of electron transport theoretically, we study a two-dimensional and four-channel DNA model using a tight-binding (TB) Hamiltonian. The thermal effects within a TB model are incorporated into the hopping integral and the relative twist angle from its equilibrium value between base-pairs. Since these thermal structural fluctuations localize the electronic wave functions in DNA, we examine a temperature-dependent localization length, a temperature-driven transmission, and current-voltage characteristics in this system. In addition, we incorporate magnetic field effects into the analysis of the transmission through DNA in order to modulate the quantum interference between the electron paths that comprise the 4-channel structure. [1] P. Tran, B. Alavi, and G. Gruner, PRL 85, 1564 (2000).

Cancer biomarkers: the role of structured data reporting.

PubMed

Simpson, Ross W; Berman, Michael A; Foulis, Philip R; Divaris, Dimitrios X G; Birdsong, George G; Mirza, Jaleh; Moldwin, Richard; Spencer, Samantha; Srigley, John R; Fitzgibbons, Patrick L

2015-05-01

The College of American Pathologists has been producing cancer protocols since 1986 to aid pathologists in the diagnosis and reporting of cancer cases. Many pathologists use the included cancer case summaries as templates for dictation/data entry into the final pathology report. These summaries are now available in a computer-readable format with structured data elements for interoperability, packaged as "electronic cancer checklists." Most major vendors of anatomic pathology reporting software support this model. To outline the development and advantages of structured electronic cancer reporting using the electronic cancer checklist model, and to describe its extension to cancer biomarkers and other aspects of cancer reporting. Peer-reviewed literature and internal records of the College of American Pathologists. Accurate and usable cancer biomarker data reporting will increasingly depend on initial capture of this information as structured data. This process will support the standardization of data elements and biomarker terminology, enabling the meaningful use of these datasets by pathologists, clinicians, tumor registries, and patients.

Dynamical simulation of electron transfer processes in self-assembled monolayers at metal surfaces using a density matrix approach.

PubMed

Prucker, V; Bockstedte, M; Thoss, M; Coto, P B

2018-03-28

A single-particle density matrix approach is introduced to simulate the dynamics of heterogeneous electron transfer (ET) processes at interfaces. The characterization of the systems is based on a model Hamiltonian parametrized by electronic structure calculations and a partitioning method. The method is applied to investigate ET in a series of nitrile-substituted (poly)(p-phenylene)thiolate self-assembled monolayers adsorbed at the Au(111) surface. The results show a significant dependence of the ET on the orbital symmetry of the donor state and on the molecular and electronic structure of the spacer.

Sub-nanometer surface chemistry and orbital hybridization in lanthanum-doped ceria nano-catalysts revealed by 3D electron microscopy.

PubMed

Collins, Sean M; Fernandez-Garcia, Susana; Calvino, José J; Midgley, Paul A

2017-07-14

Surface chemical composition, electronic structure, and bonding characteristics determine catalytic activity but are not resolved for individual catalyst particles by conventional spectroscopy. In particular, the nano-scale three-dimensional distribution of aliovalent lanthanide dopants in ceria catalysts and their effect on the surface electronic structure remains unclear. Here, we reveal the surface segregation of dopant cations and oxygen vacancies and observe bonding changes in lanthanum-doped ceria catalyst particle aggregates with sub-nanometer precision using a new model-based spectroscopic tomography approach. These findings refine our understanding of the spatially varying electronic structure and bonding in ceria-based nanoparticle aggregates with aliovalent cation concentrations and identify new strategies for advancing high efficiency doped ceria nano-catalysts.

CoCrMo cellular structures made by Electron Beam Melting studied by local tomography and finite element modelling

DOE Office of Scientific and Technical Information (OSTI.GOV)

Petit, Clémence; Maire, Eric, E-mail: eric.maire@insa-lyon.fr; Meille, Sylvain

The work focuses on the structural and mechanical characterization of Co-Cr-Mo cellular samples with cubic pore structure made by Electron Beam Melting (EBM). X-ray tomography was used to characterize the architecture of the sample. High resolution images were also obtained thanks to local tomography in which the specimen is placed close to the X-ray source. These images enabled to observe some defects due to the fabrication process: small pores in the solid phase, partially melted particles attached to the surface. Then, in situ compression tests were performed in the tomograph. The images of the deformed sample show a progressive bucklingmore » of the vertical struts leading to final fracture. The deformation initiated where the defects were present in the strut i.e. in regions with reduced local thickness. The finite element modelling confirmed the high stress concentrations of these weak points leading to the fracture of the sample. - Highlights: • CoCrMo samples fabricated by Electron Beam Melting (EBM) process are considered. • X-ray Computed Tomography is used to observe the structure of the sample. • The mechanical properties are tested thanks to an in situ test in the tomograph. • A finite element model is developed to model the mechanical behaviour.« less

Influence of the plasma environment on atomic structure using an ion-sphere model

NASA Astrophysics Data System (ADS)

Belkhiri, Madeny; Fontes, Christopher J.; Poirier, Michel

2015-09-01

Plasma environment effects on atomic structure are analyzed using various atomic structure codes. To monitor the effect of high free-electron density or low temperatures, Fermi-Dirac and Maxwell-Boltzmann statistics are compared. After a discussion of the implementation of the Fermi-Dirac approach within the ion-sphere model, several applications are considered. In order to check the consistency of the modifications brought here to extant codes, calculations have been performed using the Los Alamos Cowan Atomic Structure (cats) code in its Hartree-Fock or Hartree-Fock-Slater form and the parametric potential Flexible Atomic Code (fac). The ground-state energy shifts due to the plasma effects for the six most ionized aluminum ions have been calculated using the fac and cats codes and fairly agree. For the intercombination resonance line in Fe22 +, the plasma effect within the uniform electron gas model results in a positive shift that agrees with the multiconfiguration Dirac-Fock value of B. Saha and S. Fritzsche [J. Phys. B 40, 259 (2007), 10.1088/0953-4075/40/2/002]. Last, the present model is compared to experimental data in titanium measured on the terawatt Astra facility and provides values for electron temperature and density in agreement with the maria code.

Anomalous High-Energy Waterfall-Like Electronic Structure in 5 d Transition Metal Oxide Sr2IrO4 with a Strong Spin-Orbit Coupling

PubMed Central

Liu, Yan; Yu, Li; Jia, Xiaowen; Zhao, Jianzhou; Weng, Hongming; Peng, Yingying; Chen, Chaoyu; Xie, Zhuojin; Mou, Daixiang; He, Junfeng; Liu, Xu; Feng, Ya; Yi, Hemian; Zhao, Lin; Liu, Guodong; He, Shaolong; Dong, Xiaoli; Zhang, Jun; Xu, Zuyan; Chen, Chuangtian; Cao, Gang; Dai, Xi; Fang, Zhong; Zhou, X. J.

2015-01-01

The low energy electronic structure of Sr2IrO4 has been well studied and understood in terms of an effective Jeff = 1/2 Mott insulator model. However, little work has been done in studying its high energy electronic behaviors. Here we report a new observation of the anomalous high energy electronic structure in Sr2IrO4. By taking high-resolution angle-resolved photoemission measurements on Sr2IrO4 over a wide energy range, we have revealed for the first time that the high energy electronic structures show unusual nearly-vertical bands that extend over a large energy range. Such anomalous high energy behaviors resemble the high energy waterfall features observed in the cuprate superconductors. While strong electron correlation plays an important role in producing high energy waterfall features in the cuprate superconductors, the revelation of the high energy anomalies in Sr2IrO4, which exhibits strong spin-orbit coupling and a moderate electron correlation, points to an unknown and novel route in generating exotic electronic excitations. PMID:26267653

1H NMR study of the effect of variable ligand on heme oxygenase electronic and molecular structure

PubMed Central

Ma, Li-Hua; Liu, Yangzhong; Zhang, Xuhong; Yoshida, Tadashi; La Mar, Gerd N.

2009-01-01

Heme oxygenase carries out stereospecific catabolism of protohemin to yield iron, CO and biliverdin. Instability of the physiological oxy complex has necessitated the use of model ligands, of which cyanide and azide are amenable to solution NMR characterization. Since cyanide and azide are contrasting models for bound oxygen, it is of interest to characterize differences in their molecular and/or electronic structures. We report on detailed 2D NMR comparison of the azide and cyanide substrate complexes of heme oxygenase from Neisseria meningitidis, which reveals significant and widespread differences in chemical shifts between the two complexes. To differentiate molecular from electronic structural changes between the two complexes, the anisotropy and orientation of the paramagnetic susceptibility tensor were determined for the azide complex for comparison with those for the cyanide complex. Comparison of the predicted and observed dipolar shifts reveals that shift differences are strongly dominated by differences in electronic structure and do not provide any evidence for detectable differences in molecular structure or hydrogen bonding except in the immediate vicinity of the distal ligand. The readily cleaved C-terminus interacts with the active site and saturation-transfer allows difficult heme assignments in the high-spin aquo complex. PMID:18976815

A deterministic model of electron transport for electron probe microanalysis

NASA Astrophysics Data System (ADS)

Bünger, J.; Richter, S.; Torrilhon, M.

2018-01-01

Within the last decades significant improvements in the spatial resolution of electron probe microanalysis (EPMA) were obtained by instrumental enhancements. In contrast, the quantification procedures essentially remained unchanged. As the classical procedures assume either homogeneity or a multi-layered structure of the material, they limit the spatial resolution of EPMA. The possibilities of improving the spatial resolution through more sophisticated quantification procedures are therefore almost untouched. We investigate a new analytical model (M 1-model) for the quantification procedure based on fast and accurate modelling of electron-X-ray-matter interactions in complex materials using a deterministic approach to solve the electron transport equations. We outline the derivation of the model from the Boltzmann equation for electron transport using the method of moments with a minimum entropy closure and present first numerical results for three different test cases (homogeneous, thin film and interface). Taking Monte Carlo as a reference, the results for the three test cases show that the M 1-model is able to reproduce the electron dynamics in EPMA applications very well. Compared to classical analytical models like XPP and PAP, the M 1-model is more accurate and far more flexible, which indicates the potential of deterministic models of electron transport to further increase the spatial resolution of EPMA.

Combined electron beam imaging and ab initio modeling of T1 precipitates in Al-Li-Cu alloys

NASA Astrophysics Data System (ADS)

Dwyer, C.; Weyland, M.; Chang, L. Y.; Muddle, B. C.

2011-05-01

Among the many considerable challenges faced in developing a rational basis for advanced alloy design, establishing accurate atomistic models is one of the most fundamental. Here we demonstrate how advanced imaging techniques in a double-aberration-corrected transmission electron microscope, combined with ab initio modeling, have been used to determine the atomic structure of embedded 1 nm thick T1 precipitates in precipitation-hardened Al-Li-Cu aerospace alloys. The results provide an accurate determination of the controversial T1 structure, and demonstrate how next-generation techniques permit the characterization of embedded nanostructures in alloys and other nanostructured materials.

Calculation of the Energy-Band Structure of the Kronig-Penney Model Using the Nearly-Free and Tightly-Bound-Electron Approximations

ERIC Educational Resources Information Center

Wetsel, Grover C., Jr.

1978-01-01

Calculates the energy-band structure of noninteracting electrons in a one-dimensional crystal using exact and approximate methods for a rectangular-well atomic potential. A comparison of the two solutions as a function of potential-well depth and ratio of lattice spacing to well width is presented. (Author/GA)

Electronic states of carbon alloy catalysts and nitrogen substituent effects on catalytic activity

NASA Astrophysics Data System (ADS)

Hata, Tomoyuki; Ushiyama, Hiroshi; Yamashita, Koichi

2013-03-01

In recent years, Carbon Alloy Catalysts (CACs) are attracting attention as a candidate for non-platinum-based cathode catalysts in fuel cells. Oxygen reduction reactions at the cathode are divided into two elementary processes, electron transfer and oxygen adsorption. The electron transfer reaction is the rate-determining, and by comparison of energy levels, catalytic activity can be evaluated quantitatively. On the other hand, to begin with, adsorption mechanism is obscure. The purpose of this study is to understand the effect of nitrogen substitution and oxygen adsorption mechanism, by first-principle electronic structure calculations for nitrogen substituted models. To reproduce the elementary processes of oxygen adsorption, we assumed that the initial structures are formed based on the Pauling model, a CACs model and nitrogen substituted CACs models in which various points are replaced with nitrogen. When we try to focus only on the DOS peaks of oxygen, in some substituted model that has high adsorption activity, a characteristic partial occupancy state was found. We conclude that this state will affect the adsorption activity, and discuss on why partially occupied states appear with simplification by using an orbital correlation diagram.

Rotational and fine structure of open-shell molecules in nearly degenerate electronic states

NASA Astrophysics Data System (ADS)

Liu, Jinjun

2018-03-01

An effective Hamiltonian without symmetry restriction has been developed to model the rotational and fine structure of two nearly degenerate electronic states of an open-shell molecule. In addition to the rotational Hamiltonian for an asymmetric top, this spectroscopic model includes the energy separation between the two states due to difference potential and zero-point energy difference, as well as the spin-orbit (SO), Coriolis, and electron spin-molecular rotation (SR) interactions. Hamiltonian matrices are computed using orbitally and fully symmetrized case (a) and case (b) basis sets. Intensity formulae and selection rules for rotational transitions between a pair of nearly degenerate states and a nondegenerate state have also been derived using all four basis sets. It is demonstrated using real examples of free radicals that the fine structure of a single electronic state can be simulated with either a SR tensor or a combination of SO and Coriolis constants. The related molecular constants can be determined precisely only when all interacting levels are simulated simultaneously. The present study suggests that analysis of rotational and fine structure can provide quantitative insights into vibronic interactions and related effects.

Covariance and correlation estimation in electron-density maps.

PubMed

Altomare, Angela; Cuocci, Corrado; Giacovazzo, Carmelo; Moliterni, Anna; Rizzi, Rosanna

2012-03-01

Quite recently two papers have been published [Giacovazzo & Mazzone (2011). Acta Cryst. A67, 210-218; Giacovazzo et al. (2011). Acta Cryst. A67, 368-382] which calculate the variance in any point of an electron-density map at any stage of the phasing process. The main aim of the papers was to associate a standard deviation to each pixel of the map, in order to obtain a better estimate of the map reliability. This paper deals with the covariance estimate between points of an electron-density map in any space group, centrosymmetric or non-centrosymmetric, no matter the correlation between the model and target structures. The aim is as follows: to verify if the electron density in one point of the map is amplified or depressed as an effect of the electron density in one or more other points of the map. High values of the covariances are usually connected with undesired features of the map. The phases are the primitive random variables of our probabilistic model; the covariance changes with the quality of the model and therefore with the quality of the phases. The conclusive formulas show that the covariance is also influenced by the Patterson map. Uncertainty on measurements may influence the covariance, particularly in the final stages of the structure refinement; a general formula is obtained taking into account both phase and measurement uncertainty, valid at any stage of the crystal structure solution.

Electronic Structure and Properties of Deformed Carbon Nanotubes

NASA Technical Reports Server (NTRS)

Yang, Liu; Arnold, Jim (Technical Monitor)

2001-01-01

A theoretical framework based on Huckel tight-binding model has been formulated to analyze the electronic structure of carbon nanotubes under uniform deformation. The model successfully quantifies the dispersion relation, density of states and bandgap change of nanotubes under uniform stretching, compression, torsion and bending. Our analysis shows that the shifting of the Fermi point away from the Brillouin zone vertices is the key reason for these changes. As a result of this shifting, the electronic structure of deformed carbon nanotubes varies dramatically depending on their chirality and deformation mode. Treating the Fermi point as a function of strain and tube chirality, the analytical solution preserves the concise form of undeformed carbon nanotubes. It predicts the shifting, merging and splitting of the Van Hove singularities in the density of states and the zigzag pattern of bandgap change under strains. Four orbital tight-binding simulations of carbon nanotubes under uniform stretching, compression, torsion and bending have been performed to verify the analytical solution. Extension to more complex systems are being performed to relate this analytical solution to the spectroscopic characterization, device performance and proposed quantum structures induced by the deformation. The limitations of this model will also be discussed.

Model of photoinduced structural change induced by THz pulse irradiation

NASA Astrophysics Data System (ADS)

Ishida, Kunio; Nasu, Keiichiro

Recently intense optical pulses with THz frequency have been obtained, and it is of interest to study the effect of irradiated THz pulses on electronic systems. We theoretically study the photoinduced cooperative dynamics triggered by irradiation of THz pulses. We employed a model of two-level localized electrons coupled with an optical phonon mode taking into account the nonadiabaticity of the electron dynamics, and solved the time-dependent Schrödinger equation numerically. We consider the cases in which the THz pulses create phonons near the surface of the system, and pursue the electronic transitions induced by the propagation of the phonons. We found that they are able to induce excited-state domain growth, and that the interference between them plays an important role in the growth dynamics. Hence, the domain growth is affected by the geometry of the surface of the system, which is different from the photoinduced structural change by visible/UV pulses. We also show that the nonadiabatic/adiabatic electronic transitions should be taken into account though the domain growth mainly proceeds on the ground-state potential energy surfaces(PESs). In other words, the energy level/structure of excited-state PESs are relevant to the domain-growth dynamics.

Spin-orbit coupling, electron transport and pairing instabilities in two-dimensional square structures

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kocharian, Armen N.; Fernando, Gayanath W.; Fang, Kun

Rashba spin-orbit effects and electron correlations in the two-dimensional cylindrical lattices of square geometries are assessed using mesoscopic two-, three- and four-leg ladder structures. Here the electron transport properties are systematically calculated by including the spin-orbit coupling in tight binding and Hubbard models threaded by a magnetic flux. These results highlight important aspects of possible symmetry breaking mechanisms in square ladder geometries driven by the combined effect of a magnetic gauge field spin-orbit interaction and temperature. The observed persistent current, spin and charge polarizations in the presence of spin-orbit coupling are driven by separation of electron and hole charges andmore » opposite spins in real-space. The modeled spin-flip processes on the pairing mechanism induced by the spin-orbit coupling in assembled nanostructures (as arrays of clusters) engineered in various two-dimensional multi-leg structures provide an ideal playground for understanding spatial charge and spin density inhomogeneities leading to electron pairing and spontaneous phase separation instabilities in unconventional superconductors. Such studies also fall under the scope of current challenging problems in superconductivity and magnetism, topological insulators and spin dependent transport associated with numerous interfaces and heterostructures.« less

DOE Office of Scientific and Technical Information (OSTI.GOV)

Quashie, Edwin E.; Saha, Bidhan C.; Correa, Alfredo A.

Here, we present an ab initio study of the electronic stopping power of protons in copper over a wide range of proton velocities v = 0.02–10a.u. where we take into account nonlinear effects. Time-dependent density functional theory coupled with molecular dynamics is used to study electronic excitations produced by energetic protons. A plane-wave pseudopotential scheme is employed to solve the time-dependent Kohn-Sham equations for a moving ion in a periodic crystal. The electronic excitations and the band structure determine the stopping power of the material and alter the interatomic forces for both channeling and off-channeling trajectories. Our off-channeling results aremore » in quantitative agreement with experiments, and at low velocity they unveil a crossover region of superlinear velocity dependence (with a power of ~1.5) in the velocity range v = 0.07–0.3a.u., which we associate to the copper crystalline electronic band structure. The results are rationalized by simple band models connecting two separate regimes. We find that the limit of electronic stopping v → 0 is not as simple as phenomenological models suggest and it is plagued by band-structure effects.« less

Evaluating Uncertainties in Coronal Electron Temperature and Radial Speed Measurements Using a Simulation of the Bastille Day Eruption

NASA Astrophysics Data System (ADS)

Reginald, Nelson; St. Cyr, Orville; Davila, Joseph; Rastaetter, Lutz; Török, Tibor

2018-05-01

Obtaining reliable measurements of plasma parameters in the Sun's corona remains an important challenge for solar physics. We previously presented a method for producing maps of electron temperature and speed of the solar corona using K-corona brightness measurements made through four color filters in visible light, which were tested for their accuracies using models of a structured, yet steady corona. In this article we test the same technique using a coronal model of the Bastille Day (14 July 2000) coronal mass ejection, which also contains quiet areas and streamers. We use the coronal electron density, temperature, and flow speed contained in the model to determine two K-coronal brightness ratios at (410.3, 390.0 nm) and (423.3, 398.7 nm) along more than 4000 lines of sight. Now assuming that for real observations, the only information we have for each line of sight are these two K-coronal brightness ratios, we use a spherically symmetric model of the corona that contains no structures to interpret these two ratios for electron temperature and speed. We then compare the interpreted (or measured) values for each line of sight with the true values from the model at the plane of the sky for that same line of sight to determine the magnitude of the errors. We show that the measured values closely match the true values in quiet areas. However, in locations of coronal structures, the measured values are predictably underestimated or overestimated compared to the true values, but can nevertheless be used to determine the positions of the structures with respect to the plane of the sky, in front or behind. Based on our results, we propose that future white-light coronagraphs be equipped to image the corona using four color filters in order to routinely create coronal maps of electron density, temperature, and flow speed.

The Development of a Framework for and a Model Teaching-Learning System in Electronics Technology for the Elementary School.

ERIC Educational Resources Information Center

Inaba, Lawrence Akio

Developing a rationale and a structure of knowledge as the basis for an instructional system in electronics technology and designing and developing a packaged instructional system in electronics technology for the sixth grade is the two-fold purpose of this study. The study identifies electronics technology within the broad framework of industrial…

A reexamination of pitch angle diffusion of electrons at the boundary of the lunar wake

NASA Astrophysics Data System (ADS)

Nakagawa, T.; Iizima, M.

2006-05-01

Velocity distribution of the solar wind electrons injected into the lunar wake boundary is re-examined by using a simple model structure of inward electric field. The electrons that were flowing along the magnetic field lines undergo pitch angle scattering due to the electric field component perpendicular to the magnetic field. The electrons obtain perpendicular speeds twice as much as the drift speed. On the basis of the GEOTAIL observations of the whistler mode waves and strahl electrons, the intensity of the electric field and the thickness of the wake structure are estimated to be 28-40 mVm-1 and less than 20 km, respectively.

Introduction to electron crystallography.

PubMed

Kühlbrandt, Werner

2013-01-01

From the earliest work on regular arrays in negative stain, electron crystallography has contributed greatly to our understanding of the structure and function of biological macromolecules. The development of electron cryo-microscopy (cryo-EM) then lead to the first groundbreaking atomic models of the membrane proteins bacteriorhodopsin and light harvesting complex II within lipid bilayers. Key contributions towards cryo-EM and electron crystallography methods included specimen preparation and vitrification, liquid-helium cooling, data collection, and image processing. These methods are now applied almost routinely to both membrane and soluble proteins. Here we outline the advances and the breakthroughs that paved the way towards high-resolution structures by electron crystallography, both in terms of methods development and biological milestones.

Band structure and phonon properties of lithium fluoride at high pressure

DOE Office of Scientific and Technical Information (OSTI.GOV)

Panchal, J. M., E-mail: amitjignesh@yahoo.co.in; Department of Physics, University School of Sciences, Gujarat University, Ahmedabad 380009, Gujarat; Joshi, Mitesh

2016-05-23

High pressure structural and electronic properties of Lithium Fluoride (LiF) have been studied by employing an ab-initio pseudopotential method and a linear response scheme within the density functional theory (DFT) in conjunction with quasi harmonic Debye model. The band structure and electronic density of states conforms that the LiF is stable and is having insulator behavior at ambient as well as at high pressure up to 1 Mbar. Conclusions based on Band structure, phonon dispersion and phonon density of states are outlined.

Probing the structural and dynamical properties of liquid water with models including non-local electron correlation

NASA Astrophysics Data System (ADS)

Del Ben, Mauro; Hutter, Jürg; VandeVondele, Joost

2015-08-01

Water is a ubiquitous liquid that displays a wide range of anomalous properties and has a delicate structure that challenges experiment and simulation alike. The various intermolecular interactions that play an important role, such as repulsion, polarization, hydrogen bonding, and van der Waals interactions, are often difficult to reproduce faithfully in atomistic models. Here, electronic structure theories including all these interactions at equal footing, which requires the inclusion of non-local electron correlation, are used to describe structure and dynamics of bulk liquid water. Isobaric-isothermal (NpT) ensemble simulations based on the Random Phase Approximation (RPA) yield excellent density (0.994 g/ml) and fair radial distribution functions, while various other density functional approximations produce scattered results (0.8-1.2 g/ml). Molecular dynamics simulation in the microcanonical (NVE) ensemble based on Møller-Plesset perturbation theory (MP2) yields dynamical properties in the condensed phase, namely, the infrared spectrum and diffusion constant. At the MP2 and RPA levels of theory, ice is correctly predicted to float on water, resolving one of the anomalies as resulting from a delicate balance between van der Waals and hydrogen bonding interactions. For several properties, obtaining quantitative agreement with experiment requires correction for nuclear quantum effects (NQEs), highlighting their importance, for structure, dynamics, and electronic properties. A computed NQE shift of 0.6 eV for the band gap and absorption spectrum illustrates the latter. Giving access to both structure and dynamics of condensed phase systems, non-local electron correlation will increasingly be used to study systems where weak interactions are of paramount importance.

Charge-density analysis of a protein structure at subatomic resolution: the human aldose reductase case.

PubMed

Guillot, Benoît; Jelsch, Christian; Podjarny, Alberto; Lecomte, Claude

2008-05-01

The valence electron density of the protein human aldose reductase was analyzed at 0.66 angstroms resolution. The methodological developments in the software MoPro to adapt standard charge-density techniques from small molecules to macromolecular structures are described. The deformation electron density visible in initial residual Fourier difference maps was significantly enhanced after high-order refinement. The protein structure was refined after transfer of the experimental library multipolar atom model (ELMAM). The effects on the crystallographic statistics, on the atomic thermal displacement parameters and on the structure stereochemistry are analyzed. Constrained refinements of the transferred valence populations Pval and multipoles Plm were performed against the X-ray diffraction data on a selected substructure of the protein with low thermal motion. The resulting charge densities are of good quality, especially for chemical groups with many copies present in the polypeptide chain. To check the effect of the starting point on the result of the constrained multipolar refinement, the same charge-density refinement strategy was applied but using an initial neutral spherical atom model, i.e. without transfer from the ELMAM library. The best starting point for a protein multipolar refinement is the structure with the electron density transferred from the database. This can be assessed by the crystallographic statistical indices, including Rfree, and the quality of the static deformation electron-density maps, notably on the oxygen electron lone pairs. The analysis of the main-chain bond lengths suggests that stereochemical dictionaries would benefit from a revision based on recently determined unrestrained atomic resolution protein structures.

Thomson scattering from a three-component plasma.

PubMed

Johnson, W R; Nilsen, J

2014-02-01

A model for a three-component plasma consisting of two distinct ionic species and electrons is developed and applied to study x-ray Thomson scattering. Ions of a specific type are assumed to be identical and are treated in the average-atom approximation. Given the plasma temperature and density, the model predicts mass densities, effective ionic charges, and cell volumes for each ionic type, together with the plasma chemical potential and free-electron density. Additionally, the average-atom treatment of individual ions provides a quantum-mechanical description of bound and continuum electrons. The model is used to obtain parameters needed to determine the dynamic structure factors for x-ray Thomson scattering from a three-component plasma. The contribution from inelastic scattering by free electrons is evaluated in the random-phase approximation. The contribution from inelastic scattering by bound electrons is evaluated using the bound-state and scattering wave functions obtained from the average-atom calculations. Finally, the partial static structure factors for elastic scattering by ions are evaluated using a two-component version of the Ornstein-Zernike equations with hypernetted chain closure, in which electron-ion interactions are accounted for using screened ion-ion interaction potentials. The model is used to predict the x-ray Thomson scattering spectrum from a CH plasma and the resulting spectrum is compared with experimental results obtained by Feltcher et al. [Phys. Plasmas 20, 056316 (2013)].

Electron transfer and atom exchange between aqueous Fe(II) and structural Fe(III) in clays. Role in U and Hg(II) transformations

DOE Office of Scientific and Technical Information (OSTI.GOV)

Scherer, Michelle

2016-08-31

During this project, we investigated Fe electron transfer and atom exchange between aqueous Fe(II) and structural Fe(III) in clay minerals. We used selective chemical extractions, enriched Fe isotope tracer experiments, computational molecular modeling, and Mössbauer spectroscopy. Our findings indicate that structural Fe(III) in clay minerals is reduced by aqueous Fe(II) and that electron transfer occurs when Fe(II) is sorbed to either basal planes and edge OH-groups of clay mineral. Findings from highly enriched isotope experiments suggest that up to 30 % of the Fe atoms in the structure of some clay minerals exhanges with aqueous Fe(II). First principles calculations usingmore » a small polaron hopping approach suggest surprisingly fast electron mobility at room temperature in a nontronite clay mineral and are consistent with temperature dependent Mössbauer data Fast electron mobility suggests that electrons may be able to conduct through the mineral fast enough to enable exchange of Fe between the aqueous phase and clay mineral structure. over the time periods we observed. Our findings suggest that Fe in clay minerals is not as stable as previously thought.« less

Electronic and magnetic behaviors of B, N, and 3d transition metal substitutions in germanium carbide monolayer

NASA Astrophysics Data System (ADS)

Xu, Zhuo; Li, Yangping; Liu, Zhengtang; Liu, Shengzhong (Frank)

2018-04-01

The structural, electronic, and magnetic behaviors of two-dimensional GeC (2D-GeC) with single vacancy, substitutional B, N, and 3d transition metal atoms (Sc, Ti, V, Cr, Mn, Fe, Co, and Ni) are investigated based on the density functional theory. These impurities are tightly bonded to the surrounding atoms and found energetically more favorable at Ge sub-lattice site. In addition, the electronic band structures and magnetic properties of the doped systems indicate that (i) tunable electronic structures and magnetic moments of 2D-GeC can be obtained depending on different dopant species and sub-lattice sites, (ii) systems such as VC@Sc, VC@Fe, VC@Co, VGe@Fe, and VGe@Co are found to be half-metals, while the other systems all show semiconductor behavior. Simple models of the impurity-vacancy interaction is put forwards to illustrate the origin of the electronic structures and magnetic moments.

Molecular and electronic structure of terminal and alkali metal-capped uranium(V) nitride complexes

PubMed Central

King, David M.; Cleaves, Peter A.; Wooles, Ashley J.; Gardner, Benedict M.; Chilton, Nicholas F.; Tuna, Floriana; Lewis, William; McInnes, Eric J. L.; Liddle, Stephen T.

2016-01-01

Determining the electronic structure of actinide complexes is intrinsically challenging because inter-electronic repulsion, crystal field, and spin–orbit coupling effects can be of similar magnitude. Moreover, such efforts have been hampered by the lack of structurally analogous families of complexes to study. Here we report an improved method to U≡N triple bonds, and assemble a family of uranium(V) nitrides. Along with an isoelectronic oxo, we quantify the electronic structure of this 5f1 family by magnetometry, optical and electron paramagnetic resonance (EPR) spectroscopies and modelling. Thus, we define the relative importance of the spin–orbit and crystal field interactions, and explain the experimentally observed different ground states. We find optical absorption linewidths give a potential tool to identify spin–orbit coupled states, and show measurement of UV···UV super-exchange coupling in dimers by EPR. We show that observed slow magnetic relaxation occurs via two-phonon processes, with no obvious correlation to the crystal field. PMID:27996007

An Electron Density Model above the Sunspot from a Mapping of NOAA 7260 at 17 GHz

NASA Astrophysics Data System (ADS)

Yu, Xing-Feng; Yao, Jin-Xing Yao

2002-06-01

The brightness temperature distribution of microwave emission in a solar active region generally shows a ring structure, with a dip at the centre. However, no dip was found in the Nobeyama Radioheliograph left handed circular polarization (LCP) image on 1992 August 18; instead, there was a peak. This is a completely LCP source with zero right-handed circular polarization (RCP). We examine this structure in terms of the joint effect of gyroresonance and bremsstrahlung mechanism with a raised electron density above the central part of the sunspot, and the commonly assumed temperature and vertical dipole magnetic field models. The raised electron density is found to be 1.4 × 1011 cm-3 at the chromosphere base.

Modelling of electron beam induced nanowire attraction

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bitzer, Lucas A.; Benson, Niels, E-mail: niels.benson@uni-due.de; Schmechel, Roland

2016-04-14

Scanning electron microscope (SEM) induced nanowire (NW) attraction or bundling is a well known effect, which is mainly ascribed to structural or material dependent properties. However, there have also been recent reports of electron beam induced nanowire bending by SEM imaging, which is not fully explained by the current models, especially when considering the electro-dynamic interaction between NWs. In this article, we contribute to the understanding of this phenomenon, by introducing an electro-dynamic model based on capacitor and Lorentz force interaction, where the active NW bending is stimulated by an electromagnetic force between individual wires. The model includes geometrical, electrical,more » and mechanical NW parameters, as well as the influence of the electron beam source parameters and is validated using in-situ observations of electron beam induced GaAs nanowire (NW) bending by SEM imaging.« less

Bilayered graphene/h-BN with folded holes as new nanoelectronic materials: modeling of structures and electronic properties

PubMed Central

Chernozatonskii, Leonid A.; Demin, Viсtor A.; Bellucci, Stefano

2016-01-01

The latest achievements in 2-dimensional (2D) material research have shown the perspective use of sandwich structures in nanodevices. We demonstrate the following generation of bilayer materials for electronics and optoelectronics. The atomic structures, the stability and electronic properties of Moiré graphene (G)/h-BN bilayers with folded nanoholes have been investigated theoretically by ab-initio DFT method. These perforated bilayers with folded hole edges may present electronic properties different from the properties of both graphene and monolayer nanomesh structures. The closing of the edges is realized by C-B(N) bonds that form after folding the borders of the holes. Stable ≪round≫ and ≪triangle≫ holes organization are studied and compared with similar hole forms in single layer graphene. The electronic band structures of the considered G/BN nanomeshes reveal semiconducting or metallic characteristics depending on the sizes and edge terminations of the created holes. This investigation of the new types of G/BN nanostructures with folded edges might provide a directional guide for the future of this emerging area. PMID:27897237

Combined effects of metal complexation and size expansion in the electronic structure of DNA base pairs

NASA Astrophysics Data System (ADS)

Brancolini, Giorgia; Di Felice, Rosa

2011-05-01

Novel DNA derivatives have been recently investigated in the pursuit of modified DNA duplexes to tune the electronic structure of DNA-based assemblies for nanotechnology applications. Size-expanded DNAs (e.g., xDNA) and metalated DNAs (M-DNA) may enhance stacking interactions and induce metallic conductivity, respectively. Here we explore possible ways of tailoring the DNA electronic structure by combining the aromatic size expansion with the metal-doping. We select the salient structures from our recent study on natural DNA pairs complexed with transition metal ions and consider the equivalent model configurations for xDNA pairs. We present the results of density functional theory electronic structure calculations of the metalated expanded base-pairs with various localized basis sets and exchange-correlation functionals. Implicit solvent and coordination water molecules are also included. Our results indicate that the effect of base expansion is largest in Ag-xGC complexes, while Cu-xGC complexes are the most promising candidates for nanowires with enhanced electron transfer and also for on-purpose modification of the DNA double-helix for signal detection.

TED analysis of the Si(113) surface structure

NASA Astrophysics Data System (ADS)

Suzuki, T.; Minoda, H.; Tanishiro, Y.; Yagi, K.

1999-09-01

We carried out a TED (transmission electron diffraction) analysis of the Si(113) surface structure. The TED patterns taken at room temperature showed reflections due to the 3×2 reconstructed structure. The TED pattern indicated that a glide plane parallel to the <332> direction suggested in some models is excluded. We calculated the R-factors (reliability factors) for six surface structure models proposed previously. All structure models with energy-optimized atomic positions have large R-factors. After revision of the atomic positions, the R-factors of all the structure models decreased below 0.3, and the revised version of Dabrowski's 3×2 model has the smallest R-factor of 0.17.

Electronic Structure of Small Lanthanide Containing Molecules

NASA Astrophysics Data System (ADS)

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

2016-06-01

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

Structural optimization of structured carbon-based energy-storing composite materials used in space vehicles.

PubMed

Yu, Jia; Yu, Zhichao; Tang, Chenlong

2016-07-04

The hot work environment of electronic components in the instrument cabin of spacecraft was researched, and a new thermal protection structure, namely graphite carbon foam, which is an impregnated phase-transition material, was adopted to implement the thermal control on the electronic components. We used the optimized parameters obtained from ANSYS to conduct 2D optimization, 3-D modeling and simulation, as well as the strength check. Finally, the optimization results were verified by experiments. The results showed that after optimization, the structured carbon-based energy-storing composite material could reduce the mass and realize the thermal control over electronic components. This phase-transition composite material still possesses excellent temperature control performance after its repeated melting and solidifying.

Electronic structure of alloys

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ehrenreich, H.; Schwartz, L.M.

1976-01-01

The description of electronic properties of binary substitutional alloys within the single particle approximation is reviewed. Emphasis is placed on a didactic exposition of the equilibrium properties of the transport and magnetic properties of such alloys. Topics covered include: multiple scattering theory; the single band alloy; formal extensions of the theory; the alloy potential; realistic model state densities; the s-d model; and the muffin tin model. 43 figures, 3 tables, 151 references. (GHT)

Extracting the Density of States of Copper Phthalocyanine at the SiO2 Interface with Electronic Sum Frequency Generation.

PubMed

Pandey, Ravindra; Moon, Aaron P; Bender, Jon A; Roberts, Sean T

2016-03-17

Organic semiconductors (OSCs) constitute an attractive platform for optoelectronics design due to the ease of their processability and chemically tunable properties. Incorporating OSCs into electrical circuits requires forming junctions between them and other materials, yet the change in dielectric properties about these junctions can strongly perturb the electronic structure of the OSC. Here we adapt an interface-selective optical technique, electronic sum frequency generation (ESFG), to the study of a model OSC thin-film system, copper phthalocyanine (CuPc) deposited on SiO2. We find that by modeling the thickness dependence of our measured spectra, we can identify changes in CuPc's electronic density of states at both its buried interface with SiO2 and air-exposed surface. Our work demonstrates that ESFG can be used to noninvasively probe the interfacial electronic structure of optically thick OSC films, indicating that it can be used for the study of OSC-based optoelectronics in situ.

Multi-Dimensional Quantum Tunneling and Transport Using the Density-Gradient Model

NASA Technical Reports Server (NTRS)

Biegel, Bryan A.; Yu, Zhi-Ping; Ancona, Mario; Rafferty, Conor; Saini, Subhash (Technical Monitor)

1999-01-01

We show that quantum effects are likely to significantly degrade the performance of MOSFETs (metal oxide semiconductor field effect transistor) as these devices are scaled below 100 nm channel length and 2 nm oxide thickness over the next decade. A general and computationally efficient electronic device model including quantum effects would allow us to monitor and mitigate these effects. Full quantum models are too expensive in multi-dimensions. Using a general but efficient PDE solver called PROPHET, we implemented the density-gradient (DG) quantum correction to the industry-dominant classical drift-diffusion (DD) model. The DG model efficiently includes quantum carrier profile smoothing and tunneling in multi-dimensions and for any electronic device structure. We show that the DG model reduces DD model error from as much as 50% down to a few percent in comparison to thin oxide MOS capacitance measurements. We also show the first DG simulations of gate oxide tunneling and transverse current flow in ultra-scaled MOSFETs. The advantages of rapid model implementation using the PDE solver approach will be demonstrated, as well as the applicability of the DG model to any electronic device structure.

Integration of design, structural, thermal and optical analysis: And user's guide for structural-to-optical translator (PATCOD)

NASA Technical Reports Server (NTRS)

Amundsen, R. M.; Feldhaus, W. S.; Little, A. D.; Mitchum, M. V.

1995-01-01

Electronic integration of design and analysis processes was achieved and refined at Langley Research Center (LaRC) during the development of an optical bench for a laser-based aerospace experiment. Mechanical design has been integrated with thermal, structural and optical analyses. Electronic import of the model geometry eliminates the repetitive steps of geometry input to develop each analysis model, leading to faster and more accurate analyses. Guidelines for integrated model development are given. This integrated analysis process has been built around software that was already in use by designers and analysis at LaRC. The process as currently implemented used Pro/Engineer for design, Pro/Manufacturing for fabrication, PATRAN for solid modeling, NASTRAN for structural analysis, SINDA-85 and P/Thermal for thermal analysis, and Code V for optical analysis. Currently, the only analysis model to be built manually is the Code V model; all others can be imported for the Pro/E geometry. The translator from PATRAN results to Code V optical analysis (PATCOD) was developed and tested at LaRC. Directions for use of the translator or other models are given.

FEAST fundamental framework for electronic structure calculations: Reformulation and solution of the muffin-tin problem

NASA Astrophysics Data System (ADS)

Levin, Alan R.; Zhang, Deyin; Polizzi, Eric

2012-11-01

In a recent article Polizzi (2009) [15], the FEAST algorithm has been presented as a general purpose eigenvalue solver which is ideally suited for addressing the numerical challenges in electronic structure calculations. Here, FEAST is presented beyond the “black-box” solver as a fundamental modeling framework which can naturally address the original numerical complexity of the electronic structure problem as formulated by Slater in 1937 [3]. The non-linear eigenvalue problem arising from the muffin-tin decomposition of the real-space domain is first derived and then reformulated to be solved exactly within the FEAST framework. This new framework is presented as a fundamental and practical solution for performing both accurate and scalable electronic structure calculations, bypassing the various issues of using traditional approaches such as linearization and pseudopotential techniques. A finite element implementation of this FEAST framework along with simulation results for various molecular systems is also presented and discussed.

Relations for lipid bilayers. Connection of electron density profiles to other structural quantities.

PubMed Central

Nagle, J F; Wiener, M C

1989-01-01

Three relations are derived that connect low angle diffraction/scattering results obtained from lipid bilayers to other structural quantities of interest. The first relates the area along the surface of the bilayer, the measured specific volume, and the zeroth order structure factor, F(0). The second relates the size of the trough in the center of the electron density profile, the volume of the terminal methyl groups, and the volume of the methylene groups in the fatty acid chains. The third relates the size of the headgroup electron density peak, the volume of the headgroup, and the volumes of water and hydrocarbon in the headgroup region. These relations, which are easily modified for neutron diffraction, are useful for obtaining structural quantities from electron density profiles obtained by fitting model profiles to measured low angle x-ray intensities. PMID:2713444

Geometric modeling of subcellular structures, organelles, and multiprotein complexes

PubMed Central

Feng, Xin; Xia, Kelin; Tong, Yiying; Wei, Guo-Wei

2013-01-01

SUMMARY Recently, the structure, function, stability, and dynamics of subcellular structures, organelles, and multi-protein complexes have emerged as a leading interest in structural biology. Geometric modeling not only provides visualizations of shapes for large biomolecular complexes but also fills the gap between structural information and theoretical modeling, and enables the understanding of function, stability, and dynamics. This paper introduces a suite of computational tools for volumetric data processing, information extraction, surface mesh rendering, geometric measurement, and curvature estimation of biomolecular complexes. Particular emphasis is given to the modeling of cryo-electron microscopy data. Lagrangian-triangle meshes are employed for the surface presentation. On the basis of this representation, algorithms are developed for surface area and surface-enclosed volume calculation, and curvature estimation. Methods for volumetric meshing have also been presented. Because the technological development in computer science and mathematics has led to multiple choices at each stage of the geometric modeling, we discuss the rationales in the design and selection of various algorithms. Analytical models are designed to test the computational accuracy and convergence of proposed algorithms. Finally, we select a set of six cryo-electron microscopy data representing typical subcellular complexes to demonstrate the efficacy of the proposed algorithms in handling biomolecular surfaces and explore their capability of geometric characterization of binding targets. This paper offers a comprehensive protocol for the geometric modeling of subcellular structures, organelles, and multiprotein complexes. PMID:23212797

Electronic cooling design and test validation

NASA Astrophysics Data System (ADS)

Murtha, W. B.

1983-07-01

An analytical computer model has been used to design a counterflow air-cooled heat exchanger according to the cooling, structural and geometric requirements of a U.S. Navy shipboard electronics cabinet, emphasizing high reliability performance through the maintenance of electronic component junction temperatures lower than 110 C. Environmental testing of the design obtained has verified that the analytical predictions were conservative. Model correlation to the test data furnishes an upgraded capability for the evaluation of tactical effects, and has established a two-orders of magnitude growth potential for increased electronics capabilities through enhanced heat dissipation. Electronics cabinets of this type are destined for use with Vertical Launching System-type combatant vessel magazines.

A systematic study on the effect of electron beam irradiation on structural, electrical, thermo-electric power and magnetic property of LaCoO3

NASA Astrophysics Data System (ADS)

Benedict, Christopher J.; Rao, Ashok; Sanjeev, Ganesh; Okram, G. S.; Babu, P. D.

2016-01-01

In this communication, the effect of electron beam irradiation on the structural, electrical, thermo-electric power and magnetic properties of LaCoO3 cobaltites have been investigated. Rietveld refinement of XRD data reveals that all samples are single phased with rhombohedral structure. Increase in electrical resistivity data is observed with increase in dosage of electron beam irradiation. Analysis of the measured electrical resistivity data indicates that the small polaron hopping model is operative in the high temperature regime for all samples. The Seebeck coefficient (S) of the pristine and the irradiated samples exhibits a crossover from positive to negative values, and a colossal value of Seebeck coefficient (32.65 mV/K) is obtained for pristine sample, however, the value of S decreases with increase in dosage of irradiation. The analysis of Seebeck coefficient data confirms that the small polaron hopping model is operative in the high temperature region. The magnetization results give clear evidence of increase in effective magnetic moment due to increase in dosage of electron beam irradiation.

Model of Ni-63 battery with realistic PIN structure

DOE Office of Scientific and Technical Information (OSTI.GOV)

Munson, Charles E.; Voss, Paul L.; Ougazzaden, Abdallah, E-mail: aougazza@georgiatech-metz.fr

2015-09-14

GaN, with its wide bandgap of 3.4 eV, has emerged as an efficient material for designing high-efficiency betavoltaic batteries. An important part of designing efficient betavoltaic batteries involves a good understanding of the full process, from the behavior of the nuclear material and the creation of electron-hole pairs all the way through the collection of photo-generated carriers. This paper presents a detailed model based on Monte Carlo and Silvaco for a GaN-based betavoltaic battery device, modeled after Ni-63 as an energy source. The accuracy of the model is verified by comparing it with experimental values obtained for a GaN-based p-i-nmore » structure under scanning electron microscope illumination.« less

Model of Ni-63 battery with realistic PIN structure

NASA Astrophysics Data System (ADS)

Munson, Charles E.; Arif, Muhammad; Streque, Jeremy; Belahsene, Sofiane; Martinez, Anthony; Ramdane, Abderrahim; El Gmili, Youssef; Salvestrini, Jean-Paul; Voss, Paul L.; Ougazzaden, Abdallah

2015-09-01

GaN, with its wide bandgap of 3.4 eV, has emerged as an efficient material for designing high-efficiency betavoltaic batteries. An important part of designing efficient betavoltaic batteries involves a good understanding of the full process, from the behavior of the nuclear material and the creation of electron-hole pairs all the way through the collection of photo-generated carriers. This paper presents a detailed model based on Monte Carlo and Silvaco for a GaN-based betavoltaic battery device, modeled after Ni-63 as an energy source. The accuracy of the model is verified by comparing it with experimental values obtained for a GaN-based p-i-n structure under scanning electron microscope illumination.

Tools for Model Building and Optimization into Near-Atomic Resolution Electron Cryo-Microscopy Density Maps.

PubMed

DiMaio, F; Chiu, W

2016-01-01

Electron cryo-microscopy (cryoEM) has advanced dramatically to become a viable tool for high-resolution structural biology research. The ultimate outcome of a cryoEM study is an atomic model of a macromolecule or its complex with interacting partners. This chapter describes a variety of algorithms and software to build a de novo model based on the cryoEM 3D density map, to optimize the model with the best stereochemistry restraints and finally to validate the model with proper protocols. The full process of atomic structure determination from a cryoEM map is described. The tools outlined in this chapter should prove extremely valuable in revealing atomic interactions guided by cryoEM data. © 2016 Elsevier Inc. All rights reserved.

DiSCaMB: a software library for aspherical atom model X-ray scattering factor calculations with CPUs and GPUs.

PubMed

Chodkiewicz, Michał L; Migacz, Szymon; Rudnicki, Witold; Makal, Anna; Kalinowski, Jarosław A; Moriarty, Nigel W; Grosse-Kunstleve, Ralf W; Afonine, Pavel V; Adams, Paul D; Dominiak, Paulina Maria

2018-02-01

It has been recently established that the accuracy of structural parameters from X-ray refinement of crystal structures can be improved by using a bank of aspherical pseudoatoms instead of the classical spherical model of atomic form factors. This comes, however, at the cost of increased complexity of the underlying calculations. In order to facilitate the adoption of this more advanced electron density model by the broader community of crystallographers, a new software implementation called DiSCaMB , 'densities in structural chemistry and molecular biology', has been developed. It addresses the challenge of providing for high performance on modern computing architectures. With parallelization options for both multi-core processors and graphics processing units (using CUDA), the library features calculation of X-ray scattering factors and their derivatives with respect to structural parameters, gives access to intermediate steps of the scattering factor calculations (thus allowing for experimentation with modifications of the underlying electron density model), and provides tools for basic structural crystallographic operations. Permissively (MIT) licensed, DiSCaMB is an open-source C++ library that can be embedded in both academic and commercial tools for X-ray structure refinement.

Combinatorial and High Throughput Discovery of High Temperature Piezoelectric Ceramics

DTIC Science & Technology

2011-10-10

the known candidate piezoelectric ferroelectric perovskites. Unlike most computational studies on crystal chemistry, where the starting point is some...studies on crystal chemistry, where the starting point is some form of electronic structure calculation, we use a data driven approach to initiate our...experimental measurements reported in the literature. Given that our models are based solely on crystal and electronic structure data and did not

Screening of ligands for the Ullmann synthesis of electron-rich diaryl ethers.

PubMed

Otto, Nicola; Opatz, Till

2012-01-01

In the search for new ligands for the Ullmann diaryl ether synthesis, permitting the coupling of electron-rich aryl bromides at relatively low temperatures, 56 structurally diverse multidentate ligands were screened in a model system that uses copper iodide in acetonitrile with potassium phosphate as the base. The ligands differed largely in their performance, but no privileged structural class could be identified.

Quantum interference on electron scattering in graphene by carbon impurities in underlying h -BN

NASA Astrophysics Data System (ADS)

Kaneko, Tomoaki; Koshino, Mikito; Saito, Riichiro

2017-03-01

Electronic structures and transport properties of graphene on h -BN with carbon impurities are investigated by first-principles calculation and the tight-binding model. We show that the coupling between the impurity level and the graphene's Dirac cone sensitively depends on the impurity position, and in particular, it nearly vanishes when the impurity is located right below the center of the six membered ring of graphene. The Bloch phase factor at the Brillouin zone edge plays a decisive role in the cancellation of the hopping integrals. The impurity position dependence on the electronic structures of graphene on h -BN is investigated by the first-principles calculation, and its qualitative feature is well explained by a tight-binding model with graphene and a single impurity site. We also propose a simple one-dimensional chain-impurity model to analytically describe the role of the quantum interference in the position-dependent coupling.

Magnetically Controlled Upper Ionosphere of Mars

NASA Astrophysics Data System (ADS)

Majeed, T.; Al Aryani, O.; Al Mutawa, S.; Bougher, S. W.; Haider, S. A.

2017-12-01

The electron density (Ne) profiles measured by the Mars Express spacecraft over regions of strong crustal magnetic fields have shown anomalous characteristics of the topside plasma distribution with variable scale heights. One of such Ne profiles is located at 82oS and 180oE whose topside ionosphere is extended up to an altitude of 700 km. The crustal magnetic field at this southern site is nearly vertical and open to the access of solar wind plasma through magnetic reconnection with the interplanetary magnetic field. This can lead to the acceleration of electrons and ions during the daytime ionosphere. The downward accelerated electrons with energies >200 eV can penetrate deep into the Martian upper ionosphere along vertical magnetic field lines and cause heating, excitation and ionization of the background atmosphere. The upward acceleration of ions resulting from energy input by precipitating electrons can lead to enhance ion escape rate and modify scale heights of the topside ionosphere. We have developed a 1-D chemical diffusive model from 100 km to 400 km to interpret the Martian ionospheric structure at 82oS latitude. The primary source of ionization in the model is due to solar EUV radiation. An extra ionization source due to precipitating electrons of 0.25 keV, peaking near an altitude of 145 km is added in the model to reasonably reproduce the measured ionospheric structure below an altitude of 180 km. The behavior of the topside ionosphere can be interpreted by the vertical plasma transport caused by precipitating electrons. The vertical transport of plasma in our model is simulated by vertical ion velocities, whose values can be interpreted as drift velocities along magnetic field lines. We find that the variation of the topside Ne scale heights is sensitive to the magnitudes of upward and downward drifts with an imposed outward flux boundary condition at the top of the model. The model requires an upward flux of more than 107 ions cm-2 s-1 for both O2+ and O+, and drift speeds of 200 m/s to interpret the measured topside ionospheric structure for altitudes >180 km. The magnitudes of outward ion fluxes and drift velocities are compared with those simulated by existing models. The model results will be presented in comparison with the measured electron density profile. This work is supported by MBRSC, Dubai, UAE.

An automatic chip structure optical inspection system for electronic components

NASA Astrophysics Data System (ADS)

Song, Zhichao; Xue, Bindang; Liang, Jiyuan; Wang, Ke; Chen, Junzhang; Liu, Yunhe

2018-01-01

An automatic chip structure inspection system based on machine vision is presented to ensure the reliability of electronic components. It consists of four major modules, including a metallographic microscope, a Gigabit Ethernet high-resolution camera, a control system and a high performance computer. An auto-focusing technique is presented to solve the problem that the chip surface is not on the same focusing surface under the high magnification of the microscope. A panoramic high-resolution image stitching algorithm is adopted to deal with the contradiction between resolution and field of view, caused by different sizes of electronic components. In addition, we establish a database to storage and callback appropriate parameters to ensure the consistency of chip images of electronic components with the same model. We use image change detection technology to realize the detection of chip images of electronic components. The system can achieve high-resolution imaging for chips of electronic components with various sizes, and clearly imaging for the surface of chip with different horizontal and standardized imaging for ones with the same model, and can recognize chip defects.

Research Update: Spatially resolved mapping of electronic structure on atomic level by multivariate statistical analysis

NASA Astrophysics Data System (ADS)

Belianinov, Alex; Ganesh, Panchapakesan; Lin, Wenzhi; Sales, Brian C.; Sefat, Athena S.; Jesse, Stephen; Pan, Minghu; Kalinin, Sergei V.

2014-12-01

Atomic level spatial variability of electronic structure in Fe-based superconductor FeTe0.55Se0.45 (Tc = 15 K) is explored using current-imaging tunneling-spectroscopy. Multivariate statistical analysis of the data differentiates regions of dissimilar electronic behavior that can be identified with the segregation of chalcogen atoms, as well as boundaries between terminations and near neighbor interactions. Subsequent clustering analysis allows identification of the spatial localization of these dissimilar regions. Similar statistical analysis of modeled calculated density of states of chemically inhomogeneous FeTe1-xSex structures further confirms that the two types of chalcogens, i.e., Te and Se, can be identified by their electronic signature and differentiated by their local chemical environment. This approach allows detailed chemical discrimination of the scanning tunneling microscopy data including separation of atomic identities, proximity, and local configuration effects and can be universally applicable to chemically and electronically inhomogeneous surfaces.

Rapid model building of beta-sheets in electron-density maps.

PubMed

Terwilliger, Thomas C

2010-03-01

A method for rapidly building beta-sheets into electron-density maps is presented. beta-Strands are identified as tubes of high density adjacent to and nearly parallel to other tubes of density. The alignment and direction of each strand are identified from the pattern of high density corresponding to carbonyl and C(beta) atoms along the strand averaged over all repeats present in the strand. The beta-strands obtained are then assembled into a single atomic model of the beta-sheet regions. The method was tested on a set of 42 experimental electron-density maps at resolutions ranging from 1.5 to 3.8 A. The beta-sheet regions were nearly completely built in all but two cases, the exceptions being one structure at 2.5 A resolution in which a third of the residues in beta-sheets were built and a structure at 3.8 A in which under 10% were built. The overall average r.m.s.d. of main-chain atoms in the residues built using this method compared with refined models of the structures was 1.5 A.

Electron beam-plasma interaction and electron-acoustic solitary waves in a plasma with suprathermal electrons

NASA Astrophysics Data System (ADS)

Danehkar, A.

2018-06-01

Suprathermal electrons and inertial drifting electrons, so called electron beam, are crucial to the nonlinear dynamics of electrostatic solitary waves observed in several astrophysical plasmas. In this paper, the propagation of electron-acoustic solitary waves (EAWs) is investigated in a collisionless, unmagnetized plasma consisting of cool inertial background electrons, hot suprathermal electrons (modeled by a κ-type distribution), and stationary ions. The plasma is penetrated by a cool electron beam component. A linear dispersion relation is derived to describe small-amplitude wave structures that shows a weak dependence of the phase speed on the electron beam velocity and density. A (Sagdeev-type) pseudopotential approach is employed to obtain the existence domain of large-amplitude solitary waves, and investigate how their nonlinear structures depend on the kinematic and physical properties of the electron beam and the suprathermality (described by κ) of the hot electrons. The results indicate that the electron beam can largely alter the EAWs, but can only produce negative polarity solitary waves in this model. While the electron beam co-propagates with the solitary waves, the soliton existence domain (Mach number range) becomes narrower (nearly down to nil) with increasing the beam speed and the beam-to-hot electron temperature ratio, and decreasing the beam-to-cool electron density ratio in high suprathermality (low κ). It is found that the electric potential amplitude largely declines with increasing the beam speed and the beam-to-cool electron density ratio for co-propagating solitary waves, but is slightly decreased by raising the beam-to-hot electron temperature ratio.

Investigations of mechanical, electronic, and magnetic properties of non-magnetic MgTe and ferro-magnetic Mg0.75 TM 0.25Te (TM = Fe, Co, Ni): An ab-initio calculation

NASA Astrophysics Data System (ADS)

Q, Mahmood; S, M. Alay-e.-Abbas; I, Mahmood; Mahmood, Asif; N, A. Noor

2016-04-01

The mechanical, electronic and magnetic properties of non-magnetic MgTe and ferro-magnetic (FM) Mg0.75 TM 0.25Te (TM = Fe, Co, Ni) in the zinc-blende phase are studied by ab-initio calculations for the first time. We use the generalized gradient approximation functional for computing the structural stability, and mechanical properties, while the modified Becke and Johnson local (spin) density approximation (mBJLDA) is utilized for determining the electronic and magnetic properties. By comparing the energies of non-magnetic and FM calculations, we find that the compounds are stable in the FM phase, which is confirmed by their structural stabilities in terms of enthalpy of formation. Detailed descriptions of elastic properties of Mg0.75 TM 0.25Te alloys in the FM phase are also presented. For electronic properties, the spin-polarized electronic band structures and density of states are computed, showing that these compounds are direct bandgap materials with strong hybridizations of TM 3d states and Te p states. Further, the ferromagnetism is discussed in terms of the Zener free electron model, RKKY model and double exchange model. The charge density contours in the (110) plane are calculated to study bonding properties. The spin exchange splitting and crystal field splitting energies are also calculated. The distribution of electron spin density is employed in computing the magnetic moments appearing at the magnetic sites (Fe, Co, Ni), as well as at the non-magnetic sites (Mg, Te). It is found that the p-d hybridization causes not only magnetic moments on the magnetic sites but also induces negligibly small magnetic moments at the non-magnetic sites.

Ionization in liquids. Progress report, September 1, 1977-April 30, 1981

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bakale, G.

1980-12-19

Quasifree electrons simulate the behavior of unsolvated or dry electrons in aqueous media including the special case of biological systems. A model of direct radiosensitization was developed based on dry charge-carriers having an extended lifetime in the sheath of structured water that surrounds polar biomolecules. In this model, the pre-solvation lifetimes of dry electrons increased with an increase in the rotational times of solvent molecules. During the development of this model, an increasing number of radiosensitizers were found to be carcinogenic. Measurement of the k/sub e/'s of known carcinogens and noncarcinogens revealed that carcinogens attached quasifree electrons at diffusion-controlled rates,more » whereas the k/sub e/'s of noncarcinogens were significantly less. To explore the k/sub e/-carcinogenicity correlation further, a study of quasifree electron attachment to the water pools of reversed micelles was conducted. The degree of structuredness of the water pools which determines the k/sub e/ of the reversed micellar systems was also controlled. Another approach to controlling the microenvironment of quasifree electrons in biological systems was done in studies of radiation-induced damage to DNA in concentrated DNA solutions. The high concentration of DNA introduces more structure into the solutions than that occurring in typical in vitro experiments. The structural enhancement by DNA extends the lifetime of unsolvated charge-carriers. The DNA-damaging effects of radiolyticaly produced charge-carriers were also determined in studies of synergistic mutagenesis in bacteria simultaneously exposed to ionizing radiation and electrophilic chemical carcinogens. The attachment-detachment equilibrium of nicotine in hexane solutions was also studied. Both the kinetics and the thermodynamics of electron reactions were studied. (ERB)« less

Structural and electron diffraction scaling of twisted graphene bilayers

NASA Astrophysics Data System (ADS)

Zhang, Kuan; Tadmor, Ellad B.

2018-03-01

Multiscale simulations are used to study the structural relaxation in twisted graphene bilayers and the associated electron diffraction patterns. The initial twist forms an incommensurate moiré pattern that relaxes to a commensurate microstructure comprised of a repeating pattern of alternating low-energy AB and BA domains surrounding a high-energy AA domain. The simulations show that the relaxation mechanism involves a localized rotation and shrinking of the AA domains that scales in two regimes with the imposed twist. For small twisting angles, the localized rotation tends to a constant; for large twist, the rotation scales linearly with it. This behavior is tied to the inverse scaling of the moiré pattern size with twist angle and is explained theoretically using a linear elasticity model. The results are validated experimentally through a simulated electron diffraction analysis of the relaxed structures. A complex electron diffraction pattern involving the appearance of weak satellite peaks is predicted for the small twist regime. This new diffraction pattern is explained using an analytical model in which the relaxation kinematics are described as an exponentially-decaying (Gaussian) rotation field centered on the AA domains. Both the angle-dependent scaling and diffraction patterns are in quantitative agreement with experimental observations. A Matlab program for extracting the Gaussian model parameters accompanies this paper.

Chemical and quantum simulation of electron transfer through a polypeptide

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ungar, L.W.; Voth, G.A.; Newton, M.D.

1999-08-26

Quantum rate theory, molecular dynamics simulations, and semiempirical electronic structure calculations are used to fully investigate electron transfer mediated by a solvated polypeptide for the first time. Using a stationary-phase approximation, the nonadiabatic electron-transfer rate constant is calculated from the nuclear free energies and the electronic coupling between the initial and final states. The former are obtained from quantum path integral and classical molecular dynamics simulations; the latter are calculated using semiempirical electronic structure calculations and the generalized Mulliken-Hush method. Importantly, no parameters are fit to kinetic data. The simulated system consists of a solvated four-proline polypeptide with a tris(bipyridine)rutheniummore » donor group and an oxypentamminecobalt acceptor group. From the simulation data entropy and energy contributions to the free energies are distinguished. Quantum suppression of the barrier, including important solvent contributions, is demonstrated. Although free energy profiles along the reaction coordinate are nearly parabolic, pronounced departures from harmonic behavior are found for the separate energy and entropy functions. Harmonic models of the system are compared to simulation results in order to quantify anharmonic effects. Electronic structure calculations show that electronic coupling elements vary considerably with system conformation, even when the effective donor-acceptor separation remains roughly constant. The calculations indicate that electron transfer in a significant range of conformations linking the polypeptide to the acceptor may contribute to the overall rate constant. After correction for limitations of the solvent model, the simulations and calculations agree well with the experimental activation energy and Arrhenius prefactor.« less

Entire plasmas can be restructured when electrons are emitted from the boundaries

DOE PAGES

Campanell, M. D.

2015-04-14

It is well known that electron emission can restructure the thin sheaths at plasma-facing surfaces. But conventional models assume that the plasma's structure negligibly changes (the “presheath” is still thought to be governed by ion acceleration to the Bohm speed). Here, it is shown by theory and simulation that the presheath can take a fundamentally different structure where the emitted electrons entering the quasineutral region cause numerous changes. As a result, gradients of total plasma density, ion and electron pressures, and electric potential throughout the “inverted” presheath can carry different magnitudes, and opposite signs, from Bohm presheaths.

FOLD-EM: automated fold recognition in medium- and low-resolution (4-15 Å) electron density maps.

PubMed

Saha, Mitul; Morais, Marc C

2012-12-15

Owing to the size and complexity of large multi-component biological assemblies, the most tractable approach to determining their atomic structure is often to fit high-resolution radiographic or nuclear magnetic resonance structures of isolated components into lower resolution electron density maps of the larger assembly obtained using cryo-electron microscopy (cryo-EM). This hybrid approach to structure determination requires that an atomic resolution structure of each component, or a suitable homolog, is available. If neither is available, then the amount of structural information regarding that component is limited by the resolution of the cryo-EM map. However, even if a suitable homolog cannot be identified using sequence analysis, a search for structural homologs should still be performed because structural homology often persists throughout evolution even when sequence homology is undetectable, As macromolecules can often be described as a collection of independently folded domains, one way of searching for structural homologs would be to systematically fit representative domain structures from a protein domain database into the medium/low resolution cryo-EM map and return the best fits. Taken together, the best fitting non-overlapping structures would constitute a 'mosaic' backbone model of the assembly that could aid map interpretation and illuminate biological function. Using the computational principles of the Scale-Invariant Feature Transform (SIFT), we have developed FOLD-EM-a computational tool that can identify folded macromolecular domains in medium to low resolution (4-15 Å) electron density maps and return a model of the constituent polypeptides in a fully automated fashion. As a by-product, FOLD-EM can also do flexible multi-domain fitting that may provide insight into conformational changes that occur in macromolecular assemblies.

Boxes of Model Building and Visualization.

PubMed

Turk, Dušan

2017-01-01

Macromolecular crystallography and electron microscopy (single-particle and in situ tomography) are merging into a single approach used by the two coalescing scientific communities. The merger is a consequence of technical developments that enabled determination of atomic structures of macromolecules by electron microscopy. Technological progress in experimental methods of macromolecular structure determination, computer hardware, and software changed and continues to change the nature of model building and visualization of molecular structures. However, the increase in automation and availability of structure validation are reducing interactive manual model building to fiddling with details. On the other hand, interactive modeling tools increasingly rely on search and complex energy calculation procedures, which make manually driven changes in geometry increasingly powerful and at the same time less demanding. Thus, the need for accurate manual positioning of a model is decreasing. The user's push only needs to be sufficient to bring the model within the increasing convergence radius of the computing tools. It seems that we can now better than ever determine an average single structure. The tools work better, requirements for engagement of human brain are lowered, and the frontier of intellectual and scientific challenges has moved on. The quest for resolution of new challenges requires out-of-the-box thinking. A few issues such as model bias and correctness of structure, ongoing developments in parameters defining geometric restraints, limitations of the ideal average single structure, and limitations of Bragg spot data are discussed here, together with the challenges that lie ahead.

Investigation of charge injection and transport behavior in multilayer structure consisted of ferromagnetic metal and organic polymer under external fields

NASA Astrophysics Data System (ADS)

Zhao, Hua; Meng, Wei-Feng

2017-10-01

In this paper a five layer organic electronic device with alternately placed ferromagnetic metals and organic polymers: ferromagnetic metal/organic layer/ferromagnetic metal/organic layer/ferromagnetic metal, which is injected a spin-polarized electron from outsides, is studied theoretically using one-dimensional tight binding model Hamiltonian. We calculated equilibrium state behavior after an electron with spin is injected into the organic layer of this structure, charge density distribution and spin polarization density distribution of this injected spin-polarized electron, and mainly studied possible transport behavior of the injected spin polarized electron in this multilayer structure under different external electric fields. We analyze the physical process of the injected electron in this multilayer system. It is found by our calculation that the injected spin polarized electron exists as an electron-polaron state with spin polarization in the organic layer and it can pass through the middle ferromagnetic layer from the right-hand organic layer to the left-hand organic layer by the action of increasing external electric fields, which indicates that this structure may be used as a possible spin-polarized charge electronic device and also may provide a theoretical base for the organic electronic devices and it is also found that in the boundaries between the ferromagnetic layer and the organic layer there exist induced interface local dipoles due to the external electric fields.

Ab initio quantum mechanical calculation of the reaction probability for the Cl-+PH2Cl→ClPH2+Cl- reaction

NASA Astrophysics Data System (ADS)

Farahani, Pooria; Lundberg, Marcus; Karlsson, Hans O.

2013-11-01

The SN2 substitution reactions at phosphorus play a key role in organic and biological processes. Quantum molecular dynamics simulations have been performed to study the prototype reaction Cl-+PH2Cl→ClPH2+Cl-, using one and two-dimensional models. A potential energy surface, showing an energy well for a transition complex, was generated using ab initio electronic structure calculations. The one-dimensional model is essentially reflection free, whereas the more realistic two-dimensional model displays involved resonance structures in the reaction probability. The reaction rate is almost two orders of magnitude smaller for the two-dimensional compared to the one-dimensional model. Energetic errors in the potential energy surface is estimated to affect the rate by only a factor of two. This shows that for these types of reactions it is more important to increase the dimensionality of the modeling than to increase the accuracy of the electronic structure calculation.

Tailoring Dirac Fermions in Molecular Graphene

NASA Astrophysics Data System (ADS)

Gomes, Kenjiro K.; Mar, Warren; Ko, Wonhee; Camp, Charlie D.; Rastawicki, Dominik K.; Guinea, Francisco; Manoharan, Hari C.

2012-02-01

The dynamics of electrons in solids is tied to the band structure created by a periodic atomic potential. The design of artificial lattices, assembled through atomic manipulation, opens the door to engineer electronic band structure and to create novel quantum states. We present scanning tunneling spectroscopic measurements of a nanoassembled honeycomb lattice displaying a Dirac fermion band structure. The artificial lattice is created by atomic manipulation of single CO molecules with the scanning tunneling microscope on the surface of Cu(111). The periodic potential generated by the assembled CO molecules reshapes the band structure of the two-dimensional electron gas, present as a surface state of Cu(111), into a ``molecular graphene'' system. We create local defects in the lattice to observe the quasiparticle interference patterns that unveil the underlying band structure. We present direct comparison between the tunneling data, first-principles calculations of the band structure, and tight-binding models.

Ion-acoustic double-layers in a magnetized plasma with nonthermal electrons

DOE Office of Scientific and Technical Information (OSTI.GOV)

Rios, L. A.; Galvão, R. M. O.; Instituto de Física, Universidade de São Paulo, 05508-900 São Paulo

2013-11-15

In the present work we investigate the existence of obliquely propagating ion-acoustic double layers in magnetized two-electron plasmas. The fluid model is used to describe the ion dynamics, and the hot electron population is modeled via a κ distribution function, which has been proved to be appropriate for modeling non-Maxwellian plasmas. A quasineutral condition is assumed to investigate these nonlinear structures, which leads to the formation of double-layers propagating with slow ion-acoustic velocity. The problem is investigated numerically, and the influence of parameters such as nonthermality is discussed.

Estimation of the characteristic parameters of the multilayered film model using the patterson differential function

DOE Office of Scientific and Technical Information (OSTI.GOV)

Astaf'ev, S. B., E-mail: webmaster@ns.crys.ras.ru; Shchedrin, B. M.; Yanusova, L. G.

The possibility of estimating the layered film structural parameters by constructing the autocorrelation function P{sub F}(z) (referred to as the Patterson differential function) for the derivative d{rho}/dz of electron density along the normal to the sample surface has been considered. An analytical expression P{sub F}(z) is presented for a multilayered film within the box model of the electron density profile. The possibilities of selecting structural information about layered films by analyzing the features of this function are demonstrated by model and real examples, in particular, by applying the method of shifted systems of peaks for the function P{sub F}(z).

Electronic and geometric structure of thin CoO(100) films studied by angle-resolved photoemission spectroscopy and Auger electron diffraction

NASA Astrophysics Data System (ADS)

Heiler, M.; Chassé, A.; Schindler, K.-M.; Hollering, M.; Neddermeyer, H.

2000-05-01

We have prepared ordered thin films of CoO by evaporating cobalt in an O 2 atmosphere on to a heated (500 K) Ag(100) substrate. The geometric and electronic structure of the films was characterized by means of Auger electron diffraction (AED) and angle-resolved photoemission spectroscopy (ARUPS), respectively. The experimental AED results were compared with simulated data, which showed that the film grows in (100) orientation on the Ag(100) substrate. Synchrotron-radiation-induced photoemission investigations were performed in the photon energy range from 25 eV to 67 eV. The dispersion of the transitions was found to be similar to that of previous results on a single-crystal CoO(100) surface. The resonance behaviour of the photoemission lines in the valence-band region was investigated by constant-initial-state (CIS) spectroscopy. The implications of this behaviour for assignment of the photoemission lines to specific electronic transitions is discussed and compared with published theoretical models of the electronic structure.

Protonated o-semiquinone radical as a mimetic of the humic acids native radicals: A DFT approach to the molecular structure and EPR properties

NASA Astrophysics Data System (ADS)

Witwicki, Maciej; Jezierska, Julia

2012-06-01

Organic radicals are known to be an indispensable component of the humic acids (HA) structure. In HA two forms of radicals, stable (native) and short-lived (transient), are identified. Importantly, these radical forms can be easily differentiated by electron paramagnetic resonance (EPR) spectroscopy. This article provides a DFT-based insight into the electronic and molecular structure of the native radicals. The molecular models including an increase of the radical aromaticity and the hydrogen bonding between the radical and other functional groups of HA are taken under investigation. In consequence the interesting pieces of information on the structure of the native radical centers in HA are revealed and discussed, especially in terms of differences between the electronic structure of the native and transient forms.

Definition of molecular structure: by choice or by appeal to observation?

PubMed

Bader, Richard F W

2010-07-22

There are two schools of thought in chemistry: one derived from the valence bond and molecular orbital models of bonding, the other appealing directly to the measurable electron density and the quantum mechanical theorems that determine its behavior, an approach embodied in the quantum theory of atoms in molecules, QTAIM. No one questions the validity of the former approach, and indeed molecular orbital models and QTAIM play complementary roles, the models finding expression in the principles of physics. However, some orbital proponents step beyond the models to impose their personal stamp on their use in interpretive chemistry, by denying the possible existence of a physical basis for the concepts of chemistry. This places them at odds with QTAIM, whose very existence stems from the discovery in the observable topology of the electron density, the definitions of atoms, of the bonding between atoms and hence of molecular structure. Relating these concepts to the electron density provides the necessary link for their ultimate quantum definition. This paper explores in depth the possible causes of the difficulties some have in accepting the quantum basis of structure beginning with the arguments associated with the acceptance of a "bond path" as a criterion for bonding. This identification is based on the finding that all classical structures may be mapped onto molecular graphs consisting of bond paths linking neighboring atoms, a mapping that has no known exceptions and one that is further bolstered by the finding that there are no examples of "missing bond paths". Difficulties arise when the quantum concept is applied to systems that are not amenable to the classical models of bonding. Thus one is faced with the recurring dilemma of science, of having to escape the constraints of a model that requires a change in the existing paradigm, a process that has been in operation since the discovery of new and novel structures necessitated the extension of the Lewis model and the octet rule. The paper reviews all facets of bonding beginning with the work of Pauling and Slater in their accounting for crystal structures, taking note of Pauling's advocating possible bonding between large anions. Many examples of nonbonded or van der Waals interactions are considered from both points of view. The final section deals with the consequences of the realization that bonded quantum atoms that share an interatomic surface do not "overlap". The time has come for entering students of chemistry to be taught that the electron density can be seen, touched, and measured and that the chemical structures they learn are in fact the tracings of "bonds" onto lines of maximum density that link bonded nuclei. Matter, as we perceive it, is bound by the electrostatic force of attraction between the nuclei and the electron density.

Modeling of electron-specimen interaction in scanning electron microscope for e-beam metrology and inspection: challenges and perspectives

NASA Astrophysics Data System (ADS)

Suzuki, Makoto; Kameda, Toshimasa; Doi, Ayumi; Borisov, Sergey; Babin, Sergey

2018-03-01

The interpretation of scanning electron microscopy (SEM) images of the latest semiconductor devices is not intuitive and requires comparison with computed images based on theoretical modeling and simulations. For quantitative image prediction and geometrical reconstruction of the specimen structure, the accuracy of the physical model is essential. In this paper, we review the current models of electron-solid interaction and discuss their accuracy. We perform the comparison of the simulated results with our experiments of SEM overlay of under-layer, grain imaging of copper interconnect, and hole bottom visualization by angular selective detectors, and show that our model well reproduces the experimental results. Remaining issues for quantitative simulation are also discussed, including the accuracy of the charge dynamics, treatment of beam skirt, and explosive increase in computing time.

Recombination Rates of Electrons with Interstellar PAH Molecules

NASA Technical Reports Server (NTRS)

Ballester, Jorge (Cartographer)

1996-01-01

The goal of this project is to develop a general model for the recombination of electrons with PAH molecules in an interstellar environment. The model is being developed such that it can be applied to a small number of families of PAHs without reference to specific molecular structures. Special attention will be focused on modeling the approximately circular compact PAHs in a way that only depends on the number of carbon atoms.

Internal structure of copper(II)-phthalocyanine thin films on SiO2/Si substrates investigated by grazing incidence x-ray reflectometry

NASA Astrophysics Data System (ADS)

Brieva, A. C.; Jenkins, T. E.; Jones, D. G.; Strössner, F.; Evans, D. A.; Clark, G. F.

2006-04-01

The internal structure of copper(II)-phthalocyanine (CuPc) thin films grown on SiO2/Si by organic molecular beam deposition has been studied by grazing incidence x-ray reflectometry (GIXR) and atomic force microscopy. The electronic density profile is consistent with a structure formed by successive monolayers of molecules in the α form with the b axis lying in the substrate surface plane. The authors present an electronic density profile model of CuPc films grown on SiO2/Si. The excellent agreement between the model and experimental data allows postdeposition monitoring of the internal structure of the CuPc films with the nondestructive GIXR technique, providing a tool for accurate control of CuPc growth on silicon-based substrates. In addition, since the experiments have been carried out ex situ, they show that these structures can endure ambient conditions.

Local electronic structure and nanolevel hierarchical organization of bone tissue: theory and NEXAFS study

NASA Astrophysics Data System (ADS)

Pavlychev, A. A.; Avrunin, A. S.; Vinogradov, A. S.; Filatova, E. O.; Doctorov, A. A.; Krivosenko, Yu S.; Samoilenko, D. O.; Svirskiy, G. I.; Konashuk, A. S.; Rostov, D. A.

2016-12-01

Theoretical and experimental investigations of native bone are carried out to understand relationships between its hierarchical organization and local electronic and atomic structure of the mineralized phase. The 3D superlattice model of a coplanar assembly of the hydroxyapatite (HAP) nanocrystallites separated by the hydrated nanolayers is introduced to account the interplay of short-, long- and super-range order parameters in bone tissue. The model is applied to (i) predict and rationalize the HAP-to-bone spectral changes in the electronic structure and (ii) describe the mechanisms ensuring the link of the hierarchical organization with the electronic structure of the mineralized phase in bone. To check the predictions the near-edge x-ray absorption fine structure (NEXAFS) at the Ca 2p, P 2p and O 1s thresholds is measured for native bone and compared with NEXAFS for reference compounds. The NEXAFS analysis has demonstrated the essential hierarchy induced HAP-to-bone red shifts of the Ca and P 2p-to-valence transitions. The lowest O 1s excitation line at 532.2 eV in bone is assigned with superposition of core transitions in the hydroxide OH-(H2O) m anions, Ca2+(H2O) n cations, the carboxyl groups inside the collagen and [PO4]2- and [PO4]- anions with unsaturated P-O bonds.

Structure of the ripple phase in lecithin bilayers.

PubMed Central

Sun, W J; Tristram-Nagle, S; Suter, R M; Nagle, J F

1996-01-01

The phases of the x-ray form factors are derived for the ripple (Pbeta') thermodynamic phase in the lecithin bilayer system. By combining these phases with experimental intensity data, the electron density map of the ripple phase of dimyristoyl-phosphatidylcholine is constructed. The phases are derived by fitting the intensity data to two-dimensional electron density models, which are created by convolving an asymmetric triangular ripple profile with a transbilayer electron density profile. The robustness of the model method is indicated by the result that many different models of the transbilayer profile yield essentially the same phases, except for the weaker, purely ripple (0,k) peaks. Even with this residual ambiguity, the ripple profile is well determined, resulting in 19 angstroms for the ripple amplitude and 10 degrees and 26 degrees for the slopes of the major and the minor sides, respectively. Estimates for the bilayer head-head spacings show that the major side of the ripple is consistent with gel-like structure, and the minor side appears to be thinner with lower electron density. Images Fig. 1 Fig. 2 PMID:8692934

Exciton Scattering approach for conjugated macromolecules: from electronic spectra to electron-phonon coupling

NASA Astrophysics Data System (ADS)

Tretiak, Sergei

2014-03-01

The exciton scattering (ES) technique is a multiscale approach developed for efficient calculations of excited-state electronic structure and optical spectra in low-dimensional conjugated macromolecules. Within the ES method, the electronic excitations in the molecular structure are attributed to standing waves representing quantum quasi-particles (excitons), which reside on the graph. The exciton propagation on the linear segments is characterized by the exciton dispersion, whereas the exciton scattering on the branching centers is determined by the energy-dependent scattering matrices. Using these ES energetic parameters, the excitation energies are then found by solving a set of generalized ``particle in a box'' problems on the graph that represents the molecule. All parameters can be extracted from quantum-chemical computations of small molecular fragments and tabulated in the ES library for further applications. Subsequently, spectroscopic modeling for any macrostructure within considered molecular family could be performed with negligible numerical effort. The exciton scattering properties of molecular vertices can be further described by tight-binding or equivalently lattice models. The on-site energies and hopping constants are obtained from the exciton dispersion and scattering matrices. Such tight-binding model approach is particularly useful to describe the exciton-phonon coupling, energetic disorder and incoherent energy transfer in large branched conjugated molecules. Overall the ES applications accurately reproduce the optical spectra compared to the reference quantum chemistry results, and make possible to predict spectra of complex macromolecules, where conventional electronic structure calculations are unfeasible.

Magnetosonic solitons in semiconductor plasmas in the presence of quantum tunneling and exchange correlation effects

NASA Astrophysics Data System (ADS)

Hussain, S.; Mahmood, S.

2018-01-01

Low frequency magnetosonic wave excitations are investigated in semiconductor hole-electron plasmas. The quantum mechanical effects such as Fermi pressure, quantum tunneling, and exchange-correlation of holes and electrons in the presence of the magnetic field are considered. The two fluid quantum magnetohydrodynamic model is used to study magnetosonic wave dynamics, while electric and magnetic fields are coupled via Maxwell equations. The dispersion relation of the magnetosonic wave in electron-hole semiconductor plasma propagating in the perpendicular direction of the magnetic field is obtained, and its dispersion effects are discussed. The Korteweg-de Vries equation (KdV) for magnetosonic solitons is derived by employing the reductive perturbation method. For numerical analysis, the plasma parameters are taken from the semiconductors such as GaAs, GaSb, GaN, and InP already existing in the literature. It is found that the phase velocity of the magnetosonic wave is increased with the inclusion of exchange-correlation force in the model. The soliton dip structures of the magnetosonic wave in GaN semiconductor plasma are obtained, which satisfy the quantum plasma conditions for electron and hole fluids. The magnetosonic soliton dip structures move with speed less than the magnetosonic wave phase speed in the lab frame. The effects of exchange-correlation force in the model and variations of magnetic field intensity and electron/hole density on the magnetosonic wave dip structures are also investigated numerically for illustration.

Interaction between adatoms on surfaces: Application to the system H/Ni(111)

NASA Astrophysics Data System (ADS)

Muscat, J. P.; Newns, D. M.

1981-04-01

The interaction of adatoms on a metal surface is looked at from a novel viewpoint, using the techniques of the embedded cluster model of chemisorption. Application is made to the problem of two hydrogen atoms on a free electron surface with simple derivation of the well known R-5 asymptotic behaviour for the interaction, at large inter-adatom distances R, compared to the corresponding R-3 behaviour for two impurities in a bulk free electron gas. Application of the free electron model to the case of H/Ni(111) does not reproduce the experimental observation of formation of a graphitic structure on the surface. Inclusion of the l = 2 nickel muffin tins corrects for this anomaly, and is seen to favour the formation of the above mentioned structure.

Brickworx builds recurrent RNA and DNA structural motifs into medium- and low-resolution electron-density maps

DOE Office of Scientific and Technical Information (OSTI.GOV)

Chojnowski, Grzegorz, E-mail: gchojnowski@genesilico.pl; Waleń, Tomasz; University of Warsaw, Banacha 2, 02-097 Warsaw

2015-03-01

A computer program that builds crystal structure models of nucleic acid molecules is presented. Brickworx is a computer program that builds crystal structure models of nucleic acid molecules using recurrent motifs including double-stranded helices. In a first step, the program searches for electron-density peaks that may correspond to phosphate groups; it may also take into account phosphate-group positions provided by the user. Subsequently, comparing the three-dimensional patterns of the P atoms with a database of nucleic acid fragments, it finds the matching positions of the double-stranded helical motifs (A-RNA or B-DNA) in the unit cell. If the target structure ismore » RNA, the helical fragments are further extended with recurrent RNA motifs from a fragment library that contains single-stranded segments. Finally, the matched motifs are merged and refined in real space to find the most likely conformations, including a fit of the sequence to the electron-density map. The Brickworx program is available for download and as a web server at http://iimcb.genesilico.pl/brickworx.« less

Atomic and electronic structure of a copper/graphene interface as prepared and 1.5 years after

NASA Astrophysics Data System (ADS)

Boukhvalov, D. W.; Bazylewski, P. F.; Kukharenko, A. I.; Zhidkov, I. S.; Ponosov, Yu. S.; Kurmaev, E. Z.; Cholakh, S. O.; Lee, Y. H.; Chang, G. S.

2017-12-01

We report the results of X-ray spectroscopy and Raman measurements of as-prepared graphene on a high quality copper surface and the same materials after 1.5 years under different conditions (ambient and low humidity). The obtained results were compared with density functional theory calculations of the formation energies and electronic structures of various structural defects in graphene/Cu interfaces. For evaluation of the stability of the carbon cover, we propose a two-step model. The first step is oxidation of the graphene, and the second is perforation of graphene with the removal of carbon atoms as part of the carbon dioxide molecule. Results of the modeling and experimental measurements provide evidence that graphene grown on high-quality copper substrate becomes robust and stable in time (1.5 years). However, the stability of this interface depends on the quality of the graphene and the number of native defects in the graphene and substrate. The effect of the presence of a metallic substrate with defects on the stability and electronic structure of graphene is also discussed

Extensive domain motion and electron transfer in the human electron transferring flavoprotein.medium chain Acyl-CoA dehydrogenase complex.

PubMed

Toogood, Helen S; van Thiel, Adam; Basran, Jaswir; Sutcliffe, Mike J; Scrutton, Nigel S; Leys, David

2004-07-30

The crystal structure of the human electron transferring flavoprotein (ETF).medium chain acyl-CoA dehydrogenase (MCAD) complex reveals a dual mode of protein-protein interaction, imparting both specificity and promiscuity in the interaction of ETF with a range of structurally distinct primary dehydrogenases. ETF partitions the functions of partner binding and electron transfer between (i) the recognition loop, which acts as a static anchor at the ETF.MCAD interface, and (ii) the highly mobile redox active FAD domain. Together, these enable the FAD domain of ETF to sample a range of conformations, some compatible with fast interprotein electron transfer. Disorders in amino acid or fatty acid catabolism can be attributed to mutations at the protein-protein interface. Crucially, complex formation triggers mobility of the FAD domain, an induced disorder that contrasts with general models of protein-protein interaction by induced fit mechanisms. The subsequent interfacial motion in the MCAD.ETF complex is the basis for the interaction of ETF with structurally diverse protein partners. Solution studies using ETF and MCAD with mutations at the protein-protein interface support this dynamic model and indicate ionic interactions between MCAD Glu(212) and ETF Arg alpha(249) are likely to transiently stabilize productive conformations of the FAD domain leading to enhanced electron transfer rates between both partners.

The Chemical Modeling of Electronic Materials and Interconnections

NASA Astrophysics Data System (ADS)

Kivilahti, J. K.

2002-12-01

Thermodynamic and kinetic modeling, together with careful experimental work, is of great help for developing new electronic materials such as lead-free solders, their compatible metallizations and diffusion-barrier layers, as well as joining and bonding processes for advanced electronics manufacturing. When combined, these modeling techniques lead to a rationalization of the trial-and-error methods employed in the electronics industry, limiting experimentation and, thus, reducing significantly time-to-market of new products. This modeling provides useful information on the stabilities of phases (microstructures), driving forces for chemical reactions, and growth rates of reaction products occurring in interconnections or thin-film structures during processing, testing, and in longterm use of electronic devices. This is especially important when manufacturing advanced lead-free electronics where solder joint volumes are decreasing while the number of dissimilar reactive materials is increasing markedly. Therefore, a new concept of local nominal composition was introduced and applied together with the relevant ternary and multicomponent phase diagrams to some solder/conductor systems.

Electron-density critical points analysis and catastrophe theory to forecast structure instability in periodic solids.

PubMed

Merli, Marcello; Pavese, Alessandro

2018-03-01

The critical points analysis of electron density, i.e. ρ(x), from ab initio calculations is used in combination with the catastrophe theory to show a correlation between ρ(x) topology and the appearance of instability that may lead to transformations of crystal structures, as a function of pressure/temperature. In particular, this study focuses on the evolution of coalescing non-degenerate critical points, i.e. such that ∇ρ(x c ) = 0 and λ 1 , λ 2 , λ 3 ≠ 0 [λ being the eigenvalues of the Hessian of ρ(x) at x c ], towards degenerate critical points, i.e. ∇ρ(x c ) = 0 and at least one λ equal to zero. The catastrophe theory formalism provides a mathematical tool to model ρ(x) in the neighbourhood of x c and allows one to rationalize the occurrence of instability in terms of electron-density topology and Gibbs energy. The phase/state transitions that TiO 2 (rutile structure), MgO (periclase structure) and Al 2 O 3 (corundum structure) undergo because of pressure and/or temperature are here discussed. An agreement of 3-5% is observed between the theoretical model and experimental pressure/temperature of transformation.

Hyperfine field and electronic structure of magnetite below the Verwey transition

NASA Astrophysics Data System (ADS)

Řezníček, R.; Chlan, V.; Štěpánková, H.; Novák, P.

2015-03-01

Magnetite represents a prototype compound with a mixed valence of iron cations. Its structure and electron ordering below the Verwey transition have been studied for decades. A recently published precise crystallographic structure [Senn et al., Nature (London) 481, 173 (2012), 10.1038/nature10704] accompanied by a suggestion of a "trimeron" model has given a new impulse to magnetite research. Here we investigate hyperfine field anisotropy in the C c phase of magnetite by quantitative reanalysis of published measurements of the dependences of the 57Fe nuclear magnetic resonance frequencies on the external magnetic field direction. Further, ab initio density-functional-theory-based calculations of hyperfine field depending on the magnetization direction using the recently reported crystal structure are carried out, and analogous hyperfine anisotropy data linked to particular crystallographic sites are determined. These two sets of data are compared, and mutually matching groups of the iron B sites in the 8:5:3 ratio are found. Moreover, information on electronic structure is obtained from the ab initio calculations. Our results are compared with the trimeron model and with an alternative analysis [Patterson, Phys. Rev. B 90, 075134 (2014), 10.1103/PhysRevB.90.075134] as well.

ECE-imaging of the H-mode pedestal (invited).

PubMed

Tobias, B J; Austin, M E; Boom, J E; Burrell, K H; Classen, I G J; Domier, C W; Luhmann, N C; Nazikian, R; Snyder, P B

2012-10-01

A synthetic diagnostic has been developed that reproduces the highly structured electron cyclotron emission (ECE) spectrum radiated from the edge region of H-mode discharges. The modeled dependence on local perturbations of the equilibrium plasma pressure allows for interpretation of ECE data for diagnosis of local quantities. Forward modeling of the diagnostic response in this region allows for improved mapping of the observed fluctuations to flux surfaces within the plasma, allowing for the poloidal mode number of coherent structures to be resolved. In addition, other spectral features that are dependent on both T(e) and n(e) contain information about pedestal structure and the electron energy distribution of localized phenomena, such as edge filaments arising during edge-localized mode (ELM) activity.

Stabilization of non-productive conformations underpins rapid electron transfer to electron-transferring flavoprotein.

PubMed

Toogood, Helen S; van Thiel, Adam; Scrutton, Nigel S; Leys, David

2005-08-26

Crystal structures of protein complexes with electron-transferring flavoprotein (ETF) have revealed a dual protein-protein interface with one region serving as anchor while the ETF FAD domain samples available space within the complex. We show that mutation of the conserved Glu-165beta in human ETF leads to drastically modulated rates of interprotein electron transfer with both medium chain acyl-CoA dehydrogenase and dimethylglycine dehydrogenase. The crystal structure of free E165betaA ETF is essentially identical to that of wild-type ETF, but the crystal structure of the E165betaA ETF.medium chain acyl-CoA dehydrogenase complex reveals clear electron density for the FAD domain in a position optimal for fast interprotein electron transfer. Based on our observations, we present a dynamic multistate model for conformational sampling that for the wild-type ETF. medium chain acyl-CoA dehydrogenase complex involves random motion between three distinct positions for the ETF FAD domain. ETF Glu-165beta plays a key role in stabilizing positions incompatible with fast interprotein electron transfer, thus ensuring high rates of complex dissociation.

Structural Health Monitoring of Large Structures

NASA Technical Reports Server (NTRS)

Kim, Hyoung M.; Bartkowicz, Theodore J.; Smith, Suzanne Weaver; Zimmerman, David C.

1994-01-01

This paper describes a damage detection and health monitoring method that was developed for large space structures using on-orbit modal identification. After evaluating several existing model refinement and model reduction/expansion techniques, a new approach was developed to identify the location and extent of structural damage with a limited number of measurements. A general area of structural damage is first identified and, subsequently, a specific damaged structural component is located. This approach takes advantage of two different model refinement methods (optimal-update and design sensitivity) and two different model size matching methods (model reduction and eigenvector expansion). Performance of the proposed damage detection approach was demonstrated with test data from two different laboratory truss structures. This space technology can also be applied to structural inspection of aircraft, offshore platforms, oil tankers, ridges, and buildings. In addition, its applications to model refinement will improve the design of structural systems such as automobiles and electronic packaging.

Magneto-optical response of InAs lens-shaped self-assembled quantum dots

NASA Technical Reports Server (NTRS)

Klimeck, G.; Oyafuso, F.; Lee, S.; Allmen, P. von

2003-01-01

In this work, we demonstrate a realistic modeling of the electronic structure for InAs self-assembled quantum dots and investigate the magneto-optical response, i.e., Zeeman splitting and transition rates between electron and hole levels.

Structural and electronic features of binary Li₂S-P₂S₅ glasses.

PubMed

Ohara, Koji; Mitsui, Akio; Mori, Masahiro; Onodera, Yohei; Shiotani, Shinya; Koyama, Yukinori; Orikasa, Yuki; Murakami, Miwa; Shimoda, Keiji; Mori, Kazuhiro; Fukunaga, Toshiharu; Arai, Hajime; Uchimoto, Yoshiharu; Ogumi, Zempachi

2016-02-19

The atomic and electronic structures of binary Li2S-P2S5 glasses used as solid electrolytes are modeled by a combination of density functional theory (DFT) and reverse Monte Carlo (RMC) simulation using synchrotron X-ray diffraction, neutron diffraction, and Raman spectroscopy data. The ratio of PSx polyhedral anions based on the Raman spectroscopic results is reflected in the glassy structures of the 67Li2S-33P2S5, 70Li2S-30P2S5, and 75Li2S-25P2S5 glasses, and the plausible structures represent the lithium ion distributions around them. It is found that the edge sharing between PSx and LiSy polyhedra increases at a high Li2S content, and the free volume around PSx polyhedra decreases. It is conjectured that Li(+) ions around the face of PSx polyhedra are clearly affected by the polarization of anions. The electronic structure of the DFT/RMC model suggests that the electron transfer between the P ion and the bridging sulfur (BS) ion weakens the positive charge of the P ion in the P2S7 anions. The P2S7 anions of the weak electrostatic repulsion would causes it to more strongly attract Li(+) ions than the PS4 and P2S6 anions, and suppress the lithium ionic conduction. Thus, the control of the edge sharing between PSx and LiSy polyhedra without the electron transfer between the P ion and the BS ion is expected to facilitate lithium ionic conduction in the above solid electrolytes.

Modeling of reduced effective secondary electron emission yield from a velvet surface

DOE PAGES

Swanson, Charles; Kaganovich, Igor D.

2016-12-05

Complex structures on a material surface can significantly reduce total secondary electron emission from that surface. A velvet is a surface that consists of an array of vertically standing whiskers. The reduction occurs due to the capture of low-energy, true secondary electrons emitted at the bottom of the structure and on the sides of the velvet whiskers. We performed numerical simulations and developed an approximate analytical model that calculates the net secondary electron emission yield from a velvet surface as a function of the velvet whisker length and packing density, and the angle of incidence of primary electrons. We foundmore » that to suppress secondary electrons, the following condition on dimensionless parameters must be met: (π/2) DΑ tan θ >> 1, where theta is the angle of incidence of the primary electron from the normal, D is the fraction of surface area taken up by the velvet whisker bases, and A is the aspect ratio, A = h/r, the ratio of height to radius of the velvet whiskers. We find that velvets available today can reduce the secondary electron yield by 90% from the value of a flat surface. As a result, the values of optimal velvet whisker packing density that maximally suppresses the secondary electron emission yield are determined as a function of velvet aspect ratio and the electron angle of incidence.« less

The structure of denisovite, a fibrous nanocrystalline polytypic disordered ‘very complex’ silicate, studied by a synergistic multi-disciplinary approach employing methods of electron crystallography and X-ray powder diffraction

PubMed Central

Schowalter, Marco; Schmidt, Martin U.; Czank, Michael; Depmeier, Wulf; Rosenauer, Andreas

2017-01-01

Denisovite is a rare mineral occurring as aggregates of fibres typically 200–500 nm diameter. It was confirmed as a new mineral in 1984, but important facts about its chemical formula, lattice parameters, symmetry and structure have remained incompletely known since then. Recently obtained results from studies using microprobe analysis, X-ray powder diffraction (XRPD), electron crystallography, modelling and Rietveld refinement will be reported. The electron crystallography methods include transmission electron microscopy (TEM), selected-area electron diffraction (SAED), high-angle annular dark-field imaging (HAADF), high-resolution transmission electron microscopy (HRTEM), precession electron diffraction (PED) and electron diffraction tomography (EDT). A structural model of denisovite was developed from HAADF images and later completed on the basis of quasi-kinematic EDT data by ab initio structure solution using direct methods and least-squares refinement. The model was confirmed by Rietveld refinement. The lattice parameters are a = 31.024 (1), b = 19.554 (1) and c = 7.1441 (5) Å, β = 95.99 (3)°, V = 4310.1 (5) Å3 and space group P12/a1. The structure consists of three topologically distinct dreier silicate chains, viz. two xonotlite-like dreier double chains, [Si6O17]10−, and a tubular loop-branched dreier triple chain, [Si12O30]12−. The silicate chains occur between three walls of edge-sharing (Ca,Na) octahedra. The chains of silicate tetrahedra and the octahedra walls extend parallel to the z axis and form a layer parallel to (100). Water molecules and K+ cations are located at the centre of the tubular silicate chain. The latter also occupy positions close to the centres of eight-membered rings in the silicate chains. The silicate chains are geometrically constrained by neighbouring octahedra walls and present an ambiguity with respect to their z position along these walls, with displacements between neighbouring layers being either Δz = c/4 or −c/4. Such behaviour is typical for polytypic sequences and leads to disorder along [100]. In fact, the diffraction pattern does not show any sharp reflections with l odd, but continuous diffuse streaks parallel to a* instead. Only reflections with l even are sharp. The diffuse scattering is caused by (100) nano­lamellae separated by stacking faults and twin boundaries. The structure can be described according to the order–disorder (OD) theory as a stacking of layers parallel to (100). PMID:28512570

Synthesis and CV Studies of Dithiol-terminated Metal Terpyridine Complexes

NASA Technical Reports Server (NTRS)

Asano, Sylvia; Fan, Wendy; Ng, Hou-Tee; Han, Jie; Meyyappan, M.

2003-01-01

Transition metal coordination complexes possess unique electronic structures that should be a good model for studying electronic transport behavior at a molecular level. The discrete, multiple redox states, low redox potential and the superb ability to establish contact with other molecular and electronic components by coordination chemistry have made this a subject of investigation for their possible application as active electronic components in molecular devices. We present the synthesis and electrochemical characterization of 4'-thioacetylphenyl-2'2:6',2"-terpyridine iron(II) complex and compare it with a model bis-terpyridine iron(II) complex by cyclic voltammetry. With the use of different working electrodes, the behavior of these complexes show different electron transfer rates.

A revised partiality model and post-refinement algorithm for X-ray free-electron laser data

DOE PAGES

Ginn, Helen Mary; Brewster, Aaron S.; Hattne, Johan; ...

2015-05-23

Research towards using X-ray free-electron laser (XFEL) data to solve structures using experimental phasing methods such as sulfur single-wavelength anomalous dispersion (SAD) has been hampered by shortcomings in the diffraction models for X-ray diffraction from FELs. Owing to errors in the orientation matrix and overly simple partiality models, researchers have required large numbers of images to converge to reliable estimates for the structure-factor amplitudes, which may not be feasible for all biological systems. Here, data for cytoplasmic polyhedrosis virus type 17 (CPV17) collected at 1.3 Å wavelength at the Linac Coherent Light Source (LCLS) are revisited. A previously published definitionmore » of a partiality model for reflections illuminated by self-amplified spontaneous emission (SASE) pulses is built upon, which defines a fraction between 0 and 1 based on the intersection of a reflection with a spread of Ewald spheres modelled by a super-Gaussian wavelength distribution in the X-ray beam. A method of post-refinement to refine the parameters of this model is suggested. This has generated a merged data set with an overall discrepancy (by calculating theR splitvalue) of 3.15% to 1.46 Å resolution from a 7225-image data set. The atomic numbers of C, N and O atoms in the structure are distinguishable in the electron-density map. There are 13 S atoms within the 237 residues of CPV17, excluding the initial disordered methionine. These only possess 0.42 anomalous scattering electrons each at 1.3 Å wavelength, but the 12 that have single predominant positions are easily detectable in the anomalous difference Fourier map. It is hoped that these improvements will lead towards XFEL experimental phase determination and structure determination by sulfur SAD and will generally increase the utility of the method for difficult cases.« less

FUSION++: A New Data Assimilative Model for Electron Density Forecasting

NASA Astrophysics Data System (ADS)

Bust, G. S.; Comberiate, J.; Paxton, L. J.; Kelly, M.; Datta-Barua, S.

2014-12-01

There is a continuing need within the operational space weather community, both civilian and military, for accurate, robust data assimilative specifications and forecasts of the global electron density field, as well as derived RF application product specifications and forecasts obtained from the electron density field. The spatial scales of interest range from a hundred to a few thousand kilometers horizontally (synoptic large scale structuring) and meters to kilometers (small scale structuring that cause scintillations). RF space weather applications affected by electron density variability on these scales include navigation, communication and geo-location of RF frequencies ranging from 100's of Hz to GHz. For many of these applications, the necessary forecast time periods range from nowcasts to 1-3 hours. For more "mission planning" applications, necessary forecast times can range from hours to days. In this paper we present a new ionosphere-thermosphere (IT) specification and forecast model being developed at JHU/APL based upon the well-known data assimilation algorithms Ionospheric Data Assimilation Four Dimensional (IDA4D) and Estimating Model Parameters from Ionospheric Reverse Engineering (EMPIRE). This new forecast model, "Forward Update Simple IONosphere model Plus IDA4D Plus EMPIRE (FUSION++), ingests data from observations related to electron density, winds, electric fields and neutral composition and provides improved specification and forecast of electron density. In addition, the new model provides improved specification of winds, electric fields and composition. We will present a short overview and derivation of the methodology behind FUSION++, some preliminary results using real observational sources, example derived RF application products such as HF bi-static propagation, and initial comparisons with independent data sources for validation.

Structure and Electronic Properties of Interface-Confined Oxide Nanostructures

DOE PAGES

Liu, Yun; Ning, Yanxiao; Yu, Liang; ...

2017-09-16

The controlled fabrication of nanostructures has often made use of a substrate template to mediate and control the growth kinetics. Electronic substrate-mediated interactions have been demonstrated to guide the assembly of organic molecules or the nucleation of metal atoms but usually at cryogenic temperatures, where the diffusion has been limited. Combining STM, STS, and DFT studies, we report that the strong electronic interaction between transition metals and oxides could indeed govern the growth of low-dimensional oxide nanostructures. As a demonstration, a series of FeO triangles, which are of the same structure and electronic properties but with different sizes (side lengthmore » >3 nm), are synthesized on Pt(111). The strong interfacial interaction confines the growth of FeO nanostructures, leading to a discrete size distribution and a uniform step structure. Given the same interfacial configuration, as-grown FeO nanostructures not only expose identical edge/surface structure but also exhibit the same electronic properties, as manifested by the local density of states and local work functions. We expect the interfacial confinement effect can be generally applied to control the growth of oxide nanostructures on transition metal surfaces. These oxide nanostructures of the same structure and electronic properties are excellent models for studies of nanoscale effects and applications.« less

Structure and Electronic Properties of Interface-Confined Oxide Nanostructures

DOE Office of Scientific and Technical Information (OSTI.GOV)

Liu, Yun; Ning, Yanxiao; Yu, Liang

The controlled fabrication of nanostructures has often made use of a substrate template to mediate and control the growth kinetics. Electronic substrate-mediated interactions have been demonstrated to guide the assembly of organic molecules or the nucleation of metal atoms but usually at cryogenic temperatures, where the diffusion has been limited. Combining STM, STS, and DFT studies, we report that the strong electronic interaction between transition metals and oxides could indeed govern the growth of low-dimensional oxide nanostructures. As a demonstration, a series of FeO triangles, which are of the same structure and electronic properties but with different sizes (side lengthmore » >3 nm), are synthesized on Pt(111). The strong interfacial interaction confines the growth of FeO nanostructures, leading to a discrete size distribution and a uniform step structure. Given the same interfacial configuration, as-grown FeO nanostructures not only expose identical edge/surface structure but also exhibit the same electronic properties, as manifested by the local density of states and local work functions. We expect the interfacial confinement effect can be generally applied to control the growth of oxide nanostructures on transition metal surfaces. These oxide nanostructures of the same structure and electronic properties are excellent models for studies of nanoscale effects and applications.« less

Orientation-dependent imaging of electronically excited quantum dots

NASA Astrophysics Data System (ADS)

Nguyen, Duc; Goings, Joshua J.; Nguyen, Huy A.; Lyding, Joseph; Li, Xiaosong; Gruebele, Martin

2018-02-01

We previously demonstrated that we can image electronic excitations of quantum dots by single-molecule absorption scanning tunneling microscopy (SMA-STM). With this technique, a modulated laser beam periodically saturates an electronic transition of a single nanoparticle, and the resulting tunneling current modulation ΔI(x0, y0) maps out the SMA-STM image. In this paper, we first derive the basic theory to calculate ΔI(x0, y0) in the one-electron approximation. For near-resonant tunneling through an empty orbital "i" of the nanostructure, the SMA-STM signal is approximately proportional to the electron density |φi) (x0,y0)|

Orientation-dependent imaging of electronically excited quantum dots.

PubMed

Nguyen, Duc; Goings, Joshua J; Nguyen, Huy A; Lyding, Joseph; Li, Xiaosong; Gruebele, Martin

2018-02-14

We previously demonstrated that we can image electronic excitations of quantum dots by single-molecule absorption scanning tunneling microscopy (SMA-STM). With this technique, a modulated laser beam periodically saturates an electronic transition of a single nanoparticle, and the resulting tunneling current modulation ΔI(x 0 , y 0 ) maps out the SMA-STM image. In this paper, we first derive the basic theory to calculate ΔI(x 0 , y 0 ) in the one-electron approximation. For near-resonant tunneling through an empty orbital "i" of the nanostructure, the SMA-STM signal is approximately proportional to the electron density φ i x 0 ,y 0 2 of the excited orbital in the tunneling region. Thus, the SMA-STM signal is approximated by an orbital density map (ODM) of the resonantly excited orbital at energy E i . The situation is more complex for correlated electron motion, but either way a slice through the excited electronic state structure in the tunneling region is imaged. We then show experimentally that we can nudge quantum dots on the surface and roll them, thus imaging excited state electronic structure of a single quantum dot at different orientations. We use density functional theory to model ODMs at various orientations, for qualitative comparison with the SMA-STM experiment. The model demonstrates that our experimentally observed signal monitors excited states, localized by defects near the surface of an individual quantum dot. The sub-nanometer super-resolution imaging technique demonstrated here could become useful for mapping out the three-dimensional structure of excited states localized by defects within nanomaterials.

Understanding valence-shell electron-pair repulsion (VSEPR) theory using origami molecular models

NASA Astrophysics Data System (ADS)

Endah Saraswati, Teguh; Saputro, Sulistyo; Ramli, Murni; Praseptiangga, Danar; Khasanah, Nurul; Marwati, Sri

2017-01-01

Valence-shell electron-pair repulsion (VSEPR) theory is conventionally used to predict molecular geometry. However, it is difficult to explore the full implications of this theory by simply drawing chemical structures. Here, we introduce origami modelling as a more accessible approach for exploration of the VSEPR theory. Our technique is simple, readily accessible and inexpensive compared with other sophisticated methods such as computer simulation or commercial three-dimensional modelling kits. This method can be implemented in chemistry education at both the high school and university levels. We discuss the example of a simple molecular structure prediction for ammonia (NH3). Using the origami model, both molecular shape and the scientific justification can be visualized easily. This ‘hands-on’ approach to building molecules will help promote understanding of VSEPR theory.

Electronic band structures and optical properties of type-II superlattice photodetectors with interfacial effect.

PubMed

Qiao, Peng-Fei; Mou, Shin; Chuang, Shun Lien

2012-01-30

The electronic band structures and optical properties of type-II superlattice (T2SL) photodetectors in the mid-infrared (IR) range are investigated. We formulate a rigorous band structure model using the 8-band k · p method to include the conduction and valence band mixing. After solving the 8 × 8 Hamiltonian and deriving explicitly the new momentum matrix elements in terms of envelope functions, optical transition rates are obtained through the Fermi's golden rule under various doping and injection conditions. Optical measurements on T2SL photodetectors are compared with our model and show good agreement. Our modeling results of quantum structures connect directly to the device-level design and simulation. The predicted doping effect is readily applicable to the optimization of photodetectors. We further include interfacial (IF) layers to study the significance of their effect. Optical properties of T2SLs are expected to have a large tunable range by controlling the thickness and material composition of the IF layers. Our model provides an efficient tool for the designs of novel photodetectors.

Efficient and accurate approach to modeling the microstructure and defect properties of LaCoO3

NASA Astrophysics Data System (ADS)

Buckeridge, J.; Taylor, F. H.; Catlow, C. R. A.

2016-04-01

Complex perovskite oxides are promising materials for cathode layers in solid oxide fuel cells. Such materials have intricate electronic, magnetic, and crystalline structures that prove challenging to model accurately. We analyze a wide range of standard density functional theory approaches to modeling a highly promising system, the perovskite LaCoO3, focusing on optimizing the Hubbard U parameter to treat the self-interaction of the B-site cation's d states, in order to determine the most appropriate method to study defect formation and the effect of spin on local structure. By calculating structural and electronic properties for different magnetic states we determine that U =4 eV for Co in LaCoO3 agrees best with available experiments. We demonstrate that the generalized gradient approximation (PBEsol +U ) is most appropriate for studying structure versus spin state, while the local density approximation (LDA +U ) is most appropriate for determining accurate energetics for defect properties.

Insight into mitochondrial structure and function from electron tomography.

PubMed

Frey, T G; Renken, C W; Perkins, G A

2002-09-10

In recent years, electron tomography has provided detailed three-dimensional models of mitochondria that have redefined our concept of mitochondrial structure. The models reveal an inner membrane consisting of two components, the inner boundary membrane (IBM) closely apposed to the outer membrane and the cristae membrane that projects into the matrix compartment. These two components are connected by tubular structures of relatively uniform size called crista junctions. The distribution of crista junction sizes and shapes is predicted by a thermodynamic model based upon the energy of membrane bending, but proteins likely also play a role in determining the conformation of the inner membrane. Results of structural studies of mitochondria during apoptosis demonstrate that cytochrome c is released without detectable disruption of the outer membrane or extensive swelling of the mitochondrial matrix, suggesting the formation of an outer membrane pore large enough to allow passage of holo-cytochrome c. The possible compartmentation of inner membrane function between the IBM and the cristae membrane is also discussed.

Influence of the plasma environment on atomic structure using an ion-sphere model

DOE PAGES

Belkhiri, Madeny Jean; Fontes, Christopher John; Poirier, Michel

2015-09-03

Plasma environment effects on atomic structure are analyzed using various atomic structure codes. To monitor the effect of high free-electron density or low temperatures, Fermi-Dirac and Maxwell-Boltzmann statistics are compared. After a discussion of the implementation of the Fermi-Dirac approach within the ion-sphere model, several applications are considered. In order to check the consistency of the modifications brought here to extant codes, calculations have been performed using the Los Alamos Cowan Atomic Structure (cats) code in its Hartree-Fock or Hartree-Fock-Slater form and the parametric potential Flexible Atomic Code (fac). The ground-state energy shifts due to the plasma effects for themore » six most ionized aluminum ions have been calculated using the fac and cats codes and fairly agree. For the intercombination resonance line in Fe 22+, the plasma effect within the uniform electron gas model results in a positive shift that agrees with the MCDF value of B. Saha et al.« less

Cholesterol oxidase: ultrahigh-resolution crystal structure and multipolar atom model-based analysis.

PubMed

Zarychta, Bartosz; Lyubimov, Artem; Ahmed, Maqsood; Munshi, Parthapratim; Guillot, Benoît; Vrielink, Alice; Jelsch, Christian

2015-04-01

Examination of protein structure at the subatomic level is required to improve the understanding of enzymatic function. For this purpose, X-ray diffraction data have been collected at 100 K from cholesterol oxidase crystals using synchrotron radiation to an optical resolution of 0.94 Å. After refinement using the spherical atom model, nonmodelled bonding peaks were detected in the Fourier residual electron density on some of the individual bonds. Well defined bond density was observed in the peptide plane after averaging maps on the residues with the lowest thermal motion. The multipolar electron density of the protein-cofactor complex was modelled by transfer of the ELMAM2 charge-density database, and the topology of the intermolecular interactions between the protein and the flavin adenine dinucleotide (FAD) cofactor was subsequently investigated. Taking advantage of the high resolution of the structure, the stereochemistry of main-chain bond lengths and of C=O···H-N hydrogen bonds was analyzed with respect to the different secondary-structure elements.

Influence of the plasma environment on atomic structure using an ion-sphere model

DOE Office of Scientific and Technical Information (OSTI.GOV)

Belkhiri, Madeny Jean; Fontes, Christopher John; Poirier, Michel

Plasma environment effects on atomic structure are analyzed using various atomic structure codes. To monitor the effect of high free-electron density or low temperatures, Fermi-Dirac and Maxwell-Boltzmann statistics are compared. After a discussion of the implementation of the Fermi-Dirac approach within the ion-sphere model, several applications are considered. In order to check the consistency of the modifications brought here to extant codes, calculations have been performed using the Los Alamos Cowan Atomic Structure (cats) code in its Hartree-Fock or Hartree-Fock-Slater form and the parametric potential Flexible Atomic Code (fac). The ground-state energy shifts due to the plasma effects for themore » six most ionized aluminum ions have been calculated using the fac and cats codes and fairly agree. For the intercombination resonance line in Fe 22+, the plasma effect within the uniform electron gas model results in a positive shift that agrees with the MCDF value of B. Saha et al.« less

X-ray absorption spectroscopy of LiBF 4 in propylene carbonate. A model lithium ion battery electrolyte

DOE PAGES

Smith, Jacob W.; Lam, Royce K.; Sheardy, Alex T.; ...

2014-08-20

Since their introduction into the commercial marketplace in 1991, lithium ion batteries have become increasingly ubiquitous in portable technology. Nevertheless, improvements to existing battery technology are necessary to expand their utility for larger-scale applications, such as electric vehicles. Advances may be realized from improvements to the liquid electrolyte; however, current understanding of the liquid structure and properties remains incomplete. X-ray absorption spectroscopy of solutions of LiBF 4 in propylene carbonate (PC), interpreted using first-principles electronic structure calculations within the eXcited electron and Core Hole (XCH) approximation, yields new insight into the solvation structure of the Li + ion in thismore » model electrolyte. By generating linear combinations of the computed spectra of Li +-associating and free PC molecules and comparing to the experimental spectrum, we find a Li +–solvent interaction number of 4.5. This result suggests that computational models of lithium ion battery electrolytes should move beyond tetrahedral coordination structures.« less

Ab initio modeling of complex amorphous transition-metal-based ceramics.

PubMed

Houska, J; Kos, S

2011-01-19

Binary and ternary amorphous transition metal (TM) nitrides and oxides are of great interest because of their suitability for diverse applications ranging from high-temperature machining to the production of optical filters or electrochromic devices. However, understanding of bonding in, and electronic structure of, these materials represents a challenge mainly due to the d electrons in their valence band. In the present work, we report ab initio calculations of the structure and electronic structure of ZrSiN materials. We focus on the methodology needed for the interpretation and automatic analysis of the bonding structure, on the effect of the length of the calculation on the convergence of individual quantities of interest and on the electronic structure of materials. We show that the traditional form of the Wannier function center-based algorithm fails due to the presence of d electrons in the valence band. We propose a modified algorithm, which allows one to analyze bonding structure in TM-based systems. We observe an appearance of valence p states of TM atoms in the electronic spectra of such systems (not only ZrSiN but also NbO(x) and WAuO), and examine the importance of the p states for the character of the bonding as well as for facilitating the bonding analysis. The results show both the physical phenomena and the computational methodology valid for a wide range of TM-based ceramics.

3D Printing of Plant Golgi Stacks from Their Electron Tomographic Models.

PubMed

Mai, Keith Ka Ki; Kang, Madison J; Kang, Byung-Ho

2017-01-01

Three-dimensional (3D) printing is an effective tool for preparing tangible 3D models from computer visualizations to assist in scientific research and education. With the recent popularization of 3D printing processes, it is now possible for individual laboratories to convert their scientific data into a physical form suitable for presentation or teaching purposes. Electron tomography is an electron microscopy method by which 3D structures of subcellular organelles or macromolecular complexes are determined at nanometer-level resolutions. Electron tomography analyses have revealed the convoluted membrane architectures of Golgi stacks, chloroplasts, and mitochondria. But the intricacy of their 3D organizations is difficult to grasp from tomographic models illustrated on computer screens. Despite the rapid development of 3D printing technologies, production of organelle models based on experimental data with 3D printing has rarely been documented. In this chapter, we present a simple guide to creating 3D prints of electron tomographic models of plant Golgi stacks using the two most accessible 3D printing technologies.

3D electron density distributions in the solar corona during solar minima: assessment for more realistic solar wind modeling

NASA Astrophysics Data System (ADS)

de Patoul, J.; Foullon, C.; Riley, P.

2015-12-01

Knowledge of the electron density distribution in the solar corona put constraints on the magnetic field configurations for coronal modeling, and on initial conditions for solar wind modeling. We work with polarized SOHO/LASCO-C2 images from the last two recent minima of solar activity (1996-1997 and 2008-2010), devoid of coronal mass ejections. We derive the 4D electron density distributions in the corona by applying a newly developed time-dependent tomographic reconstruction method. First we compare the density distributions obtained from tomography with magnetohydrodynamic (MHD) solutions. The tomography provides more accurate distributions of electron densities in the polar regions, and we find that the observed density varies with the solar cycle in both polar and equatorial regions. Second, we find that the highest-density structures do not always correspond to the predicted large-scale heliospheric current sheet or its helmet streamer but can follow the locations of pseudo-streamers. We conclude that tomography offers reliable density distribution in the corona, reproducing the slow time evolution of coronal structures, without prior knowledge of the coronal magnetic field over a full rotation. Finally, we suggest that the highest-density structures show a differential rotation well above the surface depending on how it is magnetically connected to the surface. Such valuable information on the rotation of large-scale structures could help to connect the sources of the solar wind to their in-situ counterparts in future missions such as Solar Orbiter and Solar Probe Plus. This research combined with the MHD coronal modeling efforts has the potential to increase the reliability for future space weather forecasting.

Semantic modeling and structural synthesis of onboard electronics protection means as open information system

NASA Astrophysics Data System (ADS)

Zhevnerchuk, D. V.; Surkova, A. S.; Lomakina, L. S.; Golubev, A. S.

2018-05-01

The article describes the component representation approach and semantic models of on-board electronics protection from ionizing radiation of various nature. Semantic models are constructed, the feature of which is the representation of electronic elements, protection modules, sources of impact in the form of blocks with interfaces. The rules of logical inference and algorithms for synthesizing the object properties of the semantic network, imitating the interface between the components of the protection system and the sources of radiation, are developed. The results of the algorithm are considered using the example of radiation-resistant microcircuits 1645RU5U, 1645RT2U and the calculation and experimental method for estimating the durability of on-board electronics.

Gravitational instantons as models for charged particle systems

NASA Astrophysics Data System (ADS)

Franchetti, Guido; Manton, Nicholas S.

2013-03-01

In this paper we propose ALF gravitational instantons of types A k and D k as models for charged particle systems. We calculate the charges of the two families. These are -( k + 1) for A k , which is proposed as a model for k + 1 electrons, and 2 - k for D k , which is proposed as a model for either a particle of charge +2 and k electrons or a proton and k - 1 electrons. Making use of preferred topological and metrical structures of the manifolds, namely metrically preferred representatives of middle dimension homology classes, we construct two different energy functionals which reproduce the Coulomb interaction energy for a system of charged particles.

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 stark shift, coherent coupling of electronic states in a quantum dot molecule etc.; (3) to assess the potential use of the quantum dots in real device implementation and to provide physical insight to the experimentalists. Full three dimensional strain and electronic structure simulations of quantum dot structures containing multi-million atoms are done using NEMO 3-D. Both single and vertically stacked quantum dot structures are analyzed in detail. The results show that the strain and the piezoelectricity significantly impact the electronic structure of these devices. This work shows that the InAs quantum dots when placed in the InGaAs quantum well red shifts the emission wavelength. Such InAs/GaAs-based optical devices can be used for optical-fiber based communication systems at longer wavelengths (1.3um -- 1.5um). Our atomistic simulations of InAs/InGaAs/GaAs quantum dots quantitatively match with the experiment and give the critical insight of the physics involved in these structures. A single quantum dot molecule is studied for coherent quantum coupling of electronic states under the influence of static electric field applied in the growth direction. Such nanostructures can be used in the implementation of quantum information technologies. A close quantitative match with the experimental optical measurements allowed us to get a physical insight into the complex physics of quantum tunnel couplings of electronic states as the device operation switches between atomic and molecular regimes. Another important aspect is to design the quantum dots for a desired isotropic polarization of the optical emissions. Both single and coupled quantum dots are studied for TE/TM ratio engineering. The atomistic study provides a detailed physical analysis of these computationally expensive large nanostructures and serves as a guide for the experimentalists for the design of the polarization independent devices for the optical communication systems.

Onion-like nanoscale structures and fullerene-type cages formed by electron irradiation on turbostratic B{sub x}C{sub 1{minus}x} (x<0.2)

DOE Office of Scientific and Technical Information (OSTI.GOV)

Golberg, D.; Bando, Y.; Kurashima, K.

Flakes of CVD grown B{sub x}C{sub 1{minus}x} (x<0.2) films were exposed to intense electron irradiation (flux density up to {approximately}100 A/cm{sup 2}) in a 300 kV high resolution electron microscope equipped with a field emission gun. The starting flakes revealed a turbostratic B{sub x}C{sub 1{minus}x} structure. The composition of the starting materials and irradiated products was determined by using electron energy loss spectroscopy (EELS). Depending on the electron dose applied, irradiation of the turbostratic material led to formation of soap-bubble-like irregularly-shaped objects (linear dimensions of {approximately}2--5 nm), onion- and semi-onion-like structures (d{approximately}10nm), nested fullerenes (3--14 shells) and elementary fullerene-type cagesmore » (d{approximately}0.7 nm). It is thought that these curled and closed nanostructures arise from a continuous bending of the hexagonal B{sub x}C{sub 1{minus}x} sheets under electron irradiation. Finally, some possible structural models of B{sub x}C{sub 1{minus}x} fullerenes are considered.« less

Electronic structure of negative charge transfer CaFeO3 across the metal-insulator transition

NASA Astrophysics Data System (ADS)

Rogge, Paul C.; Chandrasena, Ravini U.; Cammarata, Antonio; Green, Robert J.; Shafer, Padraic; Lefler, Benjamin M.; Huon, Amanda; Arab, Arian; Arenholz, Elke; Lee, Ho Nyung; Lee, Tien-Lin; Nemšák, Slavomír; Rondinelli, James M.; Gray, Alexander X.; May, Steven J.

2018-01-01

We investigated the metal-insulator transition for epitaxial thin films of the perovskite CaFeO3, a material with a significant oxygen ligand hole contribution to its electronic structure. We find that biaxial tensile and compressive strain suppress the metal-insulator transition temperature. By combining hard x-ray photoelectron spectroscopy, soft x-ray absorption spectroscopy, and density functional calculations, we resolve the element-specific changes to the electronic structure across the metal-insulator transition. We demonstrate that the Fe sites undergo no observable spectroscopic change between the metallic and insulating states, whereas the O electronic configuration undergoes significant changes. This strongly supports the bond-disproportionation model of the metal-insulator transition for CaFeO3 and highlights the importance of ligand holes in its electronic structure. By sensitively measuring the ligand hole density, however, we find that it increases by ˜5 -10 % in the insulating state, which we ascribe to a further localization of electron charge on the Fe sites. These results provide detailed insight into the metal-insulator transition of negative charge transfer compounds and should prove instructive for understanding metal-insulator transitions in other late transition metal compounds such as the nickelates.

Modelling Students' Visualisation of Chemical Reaction

ERIC Educational Resources Information Center

Cheng, Maurice M. W.; Gilbert, John K.

2017-01-01

This paper proposes a model-based notion of "submicro representations of chemical reactions". Based on three structural models of matter (the simple particle model, the atomic model and the free electron model of metals), we suggest there are two major models of reaction in school chemistry curricula: (a) reactions that are simple…

A Monte Carlo modeling on charging effect for structures with arbitrary geometries

NASA Astrophysics Data System (ADS)

Li, C.; Mao, S. F.; Zou, Y. B.; Li, Yong Gang; Zhang, P.; Li, H. M.; Ding, Z. J.

2018-04-01

Insulating materials usually suffer charging effects when irradiated by charged particles. In this paper, we present a Monte Carlo study on the charging effect caused by electron beam irradiation for sample structures with any complex geometry. When transporting in an insulating solid, electrons encounter elastic and inelastic scattering events; the Mott cross section and a Lorentz-type dielectric function are respectively employed to describe such scatterings. In addition, the band gap and the electron–long optical phonon interaction are taken into account. The electronic excitation in inelastic scattering causes generation of electron–hole pairs; these negative and positive charges establish an inner electric field, which in turn induces the drift of charges to be trapped by impurities, defects, vacancies etc in the solid, where the distributions of trapping sites are assumed to have uniform density. Under charging conditions, the inner electric field distorts electron trajectories, and the surface electric potential dynamically alters secondary electron emission. We present, in this work, an iterative modeling method for a self-consistent calculation of electric potential; the method has advantages in treating any structure with arbitrary complex geometry, in comparison with the image charge method—which is limited to a quite simple boundary geometry. Our modeling is based on: the combination of the finite triangle mesh method for an arbitrary geometry construction; a self-consistent method for the spatial potential calculation; and a full dynamic description for the motion of deposited charges. Example calculations have been done to simulate secondary electron yield of SiO2 for a semi-infinite solid, the charging for a heterostructure of SiO2 film grown on an Au substrate, and SEM imaging of a SiO2 line structure with rough surfaces and SiO2 nanoparticles with irregular shapes. The simulations have explored interesting interlaced charge layer distribution underneath the nanoparticle surface and the mechanism by which it is produced.

Demonstration of Anisotropic Fluid Closure Capturing the Kinetic Structure of Magnetic Reconnection

NASA Astrophysics Data System (ADS)

Ohia, Obioma

2012-10-01

Magnetic reconnection in collisionless plasmas plays an important role in space and laboratory plasmas. Allowing magnetic stress to be reduced by a rearrangement of magnetic line topology, this process is often accompanied by a large release of magnetic field energy, which can heat the plasma, drive large scale flows, or accelerate particles. Reconnection has been widely studied through fluid models and kinetic simulations. While two-fluid models often reproduce the fast reconnection that is observed in nature and seen in kinetic simulations, it is found that the structure surrounding the electron diffusion region and the electron current layer differ vastly between fluid models and kinetic simulations [1]. Recently, using an adiabatic solution of the Vlasov equation, a new fluid closure has been obtained for electrons that relate parallel and perpendicular pressures to the density and magnetic field [2]. Here we present the results of fluid simulation, developed using the HiFi framework [3], that implements new equations of state for guide-field reconnection. The new fluid closure accurately accounts for the anisotropic electron pressure that builds in the reconnection region due to electric and magnetic trapping of electrons. In contrast to previous fluid models, our fluid simulation reproduces the detailed reconnection region as observed in fully kinetic simulations [4]. We hereby demonstrate that the new fluid closure self-consistently captures all the physics relevant to the structure of the reconnection region, providing a gateway to a renewed and deeper theoretical understanding for reconnection in weakly collisional regimes.[4pt] [1] Daughton W et al., Phys. Plasmas 13, 072101 (2006).[0pt] [2] Le A et al., Phys. Rev. Lett. 102, 085001 (2009). [0pt] [3] Lukin VS, Linton MG, Nonlinear Proc. Geoph. 18, 871 (2011). [0pt] [4] Ohia O, et al., Phys. Rev. Lett. In Press (2012).

Collisional radiative model for Ar-O2 mixture plasma with fully relativistic fine structure cross sections

NASA Astrophysics Data System (ADS)

Priti, Gangwar, Reetesh Kumar; Srivastava, Rajesh

2018-04-01

A collisional radiative (C-R) model has been developed to diagnose the rf generated Ar-O2 (0%-5%) mixture plasma at low temperatures. Since in such plasmas the most dominant process is an electron impact excitation process, we considered several electron impact fine structure transitions in an argon atom from its ground as well as excited states. The cross-sections for these transitions have been obtained using the reliable fully relativistic distorted wave theory. Processes which account for the coupling of argon with the oxygen molecules have been further added to the model. We couple our model to the optical spectroscopic measurements reported by Jogi et al. [J. Phys. D: Appl. Phys. 47, 335206 (2014)]. The plasma parameters, viz. the electron density (ne) and the electron temperature (Te) as a function of O2 concentration have been obtained using thirteen intense emission lines out of 3p54p → 3p54s transitions observed in their spectroscopic measurements. It is found that as the content of O2 in Ar increases from 0%-5%, Te increases in the range 0.85-1.7 eV, while the electron density decreases from 2.76 × 1012-2.34 × 1011 cm-3. The Ar-3p54s (1si) fine-structure level populations at our extracted plasma parameters are found to be in very good agreement with those obtained from the measurements. Furthermore, we have estimated the individual contributions coming from the ground state, 1si manifolds and cascade contributions to the population of the radiating Ar-3p54p (2pi) states as a function of a trace amount of O2. Such information is very useful to understand the importance of various processes occurring in the plasma.

Tuning transport properties on graphene multiterminal structures by mechanical deformations

NASA Astrophysics Data System (ADS)

Latge, Andrea; Torres, Vanessa; Faria, Daiara

The realization of mechanical strain on graphene structures is viewed as a promise route to tune electronic and transport properties such as changing energy band-gaps and promoting localization of states. Using continuum models, mechanical deformations are described by effective gauge fields, mirrored as pseudomagnetic fields that may reach quite high values. Interesting symmetry features are developed due to out of plane deformations on graphene; lift sublattice symmetry was predicted and observed in centrosymmetric bumps and strained nanobubbles. Here we discuss the effects of Gaussian-like strain on a hexagonal graphene flake connected to three leads, modeled as perfect graphene nanoribbons. The Green function formalism is used within a tight-binding approximation. For this particular deformation sharp resonant states are achieved depending on the strained structure details. We also study a fold-strained structure in which the three leads are deformed extending up to the very center of the hexagonal flake. We show that conductance suppressions can be controlled by the strain intensity and important transport features are modeled by the electronic band structure of the leads.

Structural defects in GaN revealed by Transmission Electron Microscopy

DOE Office of Scientific and Technical Information (OSTI.GOV)

Liliental-Weber, Zuzanna

This paper reviews the various types of structural defects observed by Transmission Electron Microscopy in GaN heteroepitaxial layers grown on foreign substrates and homoepitaxial layers grown on bulk GaN substrates. The structural perfection of these layers is compared to the platelet self-standing crystals grown by High Nitrogen Pressure Solution. Defects in undoped and Mg doped GaN are discussed. Lastly, some models explaining the formation of inversion domains in heavily Mg doped layers that are possible defects responsible for the difficulties of p-doping in GaN are also reviewed.

Structural defects in GaN revealed by Transmission Electron Microscopy

DOE PAGES

Liliental-Weber, Zuzanna

2014-09-08

This paper reviews the various types of structural defects observed by Transmission Electron Microscopy in GaN heteroepitaxial layers grown on foreign substrates and homoepitaxial layers grown on bulk GaN substrates. The structural perfection of these layers is compared to the platelet self-standing crystals grown by High Nitrogen Pressure Solution. Defects in undoped and Mg doped GaN are discussed. Lastly, some models explaining the formation of inversion domains in heavily Mg doped layers that are possible defects responsible for the difficulties of p-doping in GaN are also reviewed.

Graphene: Nanostructure engineering and applications

NASA Astrophysics Data System (ADS)

Zhang, Tingting; Wu, Shuang; Yang, Rong; Zhang, Guangyu

2017-02-01

Graphene has attracted extensive research interest in recent years because of its fascinating physical properties and its potential for various applications. The band structure or electronic properties of graphene are very sensitive to its geometry, size, and edge structures, especially when the size of graphene is below the quantum confinement limit. Graphene nanoribbons (GNRs) can be used as a model system to investigate such structure-sensitive parameters. In this review, we examine the fabrication of GNRs via both top-down and bottom-up approaches. The edge-related electronic and transport properties of GNRs are also discussed.

Three-dimensional structure of basal body triplet revealed by electron cryo-tomography

PubMed Central

Li, Sam; Fernandez, Jose-Jesus; Marshall, Wallace F; Agard, David A

2012-01-01

Basal bodies and centrioles play central roles in microtubule (MT)-organizing centres within many eukaryotes. They share a barrel-shaped cylindrical structure composed of nine MT triplet blades. Here, we report the structure of the basal body triplet at 33 Å resolution obtained by electron cryo-tomography and 3D subtomogram averaging. By fitting the atomic structure of tubulin into the EM density, we built a pseudo-atomic model of the tubulin protofilaments at the core of the triplet. The 3D density map reveals additional densities that represent non-tubulin proteins attached to the triplet, including a large inner circular structure in the basal body lumen, which functions as a scaffold to stabilize the entire basal body barrel. We found clear longitudinal structural variations along the basal body, suggesting a sequential and coordinated assembly mechanism. We propose a model in which δ-tubulin and other components participate in the assembly of the basal body. PMID:22157822

Two-Electron Transfer Pathways.

PubMed

Lin, Jiaxing; Balamurugan, D; Zhang, Peng; Skourtis, Spiros S; Beratan, David N

2015-06-18

The frontiers of electron-transfer chemistry demand that we develop theoretical frameworks to describe the delivery of multiple electrons, atoms, and ions in molecular systems. When electrons move over long distances through high barriers, where the probability for thermal population of oxidized or reduced bridge-localized states is very small, the electrons will tunnel from the donor (D) to acceptor (A), facilitated by bridge-mediated superexchange interactions. If the stable donor and acceptor redox states on D and A differ by two electrons, it is possible that the electrons will propagate coherently from D to A. While structure-function relations for single-electron superexchange in molecules are well established, strategies to manipulate the coherent flow of multiple electrons are largely unknown. In contrast to one-electron superexchange, two-electron superexchange involves both one- and two-electron virtual intermediate states, the number of virtual intermediates increases very rapidly with system size, and multiple classes of pathways interfere with one another. In the study described here, we developed simple superexchange models for two-electron transfer. We explored how the bridge structure and energetics influence multielectron superexchange, and we compared two-electron superexchange interactions to single-electron superexchange. Multielectron superexchange introduces interference between singly and doubly oxidized (or reduced) bridge virtual states, so that even simple linear donor-bridge-acceptor systems have pathway topologies that resemble those seen for one-electron superexchange through bridges with multiple parallel pathways. The simple model systems studied here exhibit a richness that is amenable to experimental exploration by manipulating the multiple pathways, pathway crosstalk, and changes in the number of donor and acceptor species. The features that emerge from these studies may assist in developing new strategies to deliver multiple electrons in condensed-phase redox systems, including multiple-electron redox species, multimetallic/multielectron redox catalysts, and multiexciton excited states.

Electronic structure and bonding of intergranular glassy films in polycrystalline Si3 N4 : Ab initio studies and classical molecular dynamics simulations

NASA Astrophysics Data System (ADS)

Rulis, P.; Chen, J.; Ouyang, L.; Ching, W.-Y.; Su, X.; Garofalini, S. H.

2005-06-01

The electronic structure and bonding of a realistic model of an intergranular glassy film (IGF) was studied with multiple computational methods. The model has a Si-O-N glassy region sandwiched between crystalline basal planes of β-Si3N4 and contains a total of 798 atoms. It was constructed with periodic boundary conditions via classical molecular dynamics (MD) techniques using an accurate multibody atomic potential. The model was then further relaxed by the VASP (Vienna ab initio simulation package) program. It is shown that the VASP-relaxed structure reduces the total energy from the MD-relaxed structure by only 47.38eV , validating the accuracy of the multiatom potential used. The calculated electronic structure shows the IGF model to be an insulator with a sizable gap of almost 3eV . Quasidefectlike states can be identified near the band edges arising from the more strained Si-N and Si-O bonds at the interface. Calculation of the Mulliken effective charge and bond order values indicates that the bonds in the glassy region and at the interface can be enhanced and weakened by distortions in the bond length and bond angle. The states at the top of the valence band are derived mostly from the crystalline part of the Si-N bonding while the states at the bottom of the conduction band are dominated by the Si-O bonding in the glassy region. Calculation of the electrostatic potential across the interface shows an average band offset of about 1.5eV between the crystalline β-Si3N4 and the glassy Si-O-N region which could be related to the space charge model for IGF.

The [(AI 2O 3) 2] - Anion Cluster: Electron Localization-Delocalization Isomerism

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sierka, Marek; Dobler, Jens; Sauer, Joachim

2009-10-05

Three-dimensional bulk alumina and its two-dimensional thin films show great structural diversity, posing considerable challenges to their experimental structural characterization and computational modeling. Recently, structural diversity has also been demonstrated for zerodimensional gas phase aluminum oxide clusters. Mass-selected clusters not only make systematic studies of the structural and electronic properties as a function of size possible, but lately have also emerged as powerful molecular models of complex surfaces and solid catalysts. In particular, the [(Al 2O 3) 3-5] + clusters were the first example of polynuclear maingroup metal oxide cluster that are able to thermally activate CH 4. Over themore » past decades gas phase aluminum oxide clusters have been extensively studied both experimentally and computationally, but definitive structural assignments were made for only a handful of them: the planar [Al 3O 3] - and [Al 5O 4] - cluster anions, and the [(Al 2O 3) 1-4(AlO)] + cluster cations. For stoichiometric clusters only the atomic structures of [(Al 2O 3) 4] +/0 have been nambiguously resolved. Here we report on the structures of the [(Al 2O 3) 2] -/0 clusters combining photoelectron spectroscopy (PES) and quantum chemical calculations employing a genetic algorithm as a global optimization technique. The [(Al 2O 3) 2] - cluster anion show energetically close lying but structurally distinct cage and sheet-like isomers which differ by delocalization/localization of the extra electron. The experimental results are crucial for benchmarking the different computational methods applied with respect to a proper description of electron localization and the relative energies for the isomers which will be of considerable value for future computational studies of aluminum oxide and related systems.« less

Theoretical study of the elasticity, mechanical behavior, electronic structure, interatomic bonding, and dielectric function of an intergranular glassy film model in prismatic β-Si3N4

NASA Astrophysics Data System (ADS)

Ching, W. Y.; Rulis, Paul; Ouyang, Lizhi; Aryal, Sitaram; Misra, Anil.

2010-06-01

Microstructures such as intergranular glassy films (IGFs) are ubiquitous in many structural ceramics. They control many of the important physical properties of polycrystalline ceramics and can be influenced during processing to modify the performance of devices that contain them. In recent years, there has been intense research, both experimentally and computationally, on the structure and properties of IGFs. Unlike grain boundaries or dislocations with well-defined crystalline planes, the atomic scale structure of IGFs, their fundamental electronic interactions, and their bonding characteristics are far more complicated and not well known. In this paper, we present the results of theoretical simulations using ab initio methods on an IGF model in β-Si3N4 with prismatic crystalline planes. The 907-atom model has a dimension of 14.533Å×15.225Å×47.420Å . The IGF layer is perpendicular to the z axis, 16.4Å wide, and contains 72 Si, 32 N, and 124 O atoms. Based on this model, the mechanical and elastic properties, the electronic structure, the interatomic bonding, the localization of defective states, the distribution of electrostatic potential, and the optical dielectric function are evaluated and compared with crystalline β-Si3N4 . We have also performed a theoretical tensile experiment on this model by incrementally extending the structure in the direction perpendicular to the IGF plane until the model fully separated. It is shown that fracture occurs at a strain of 9.42% with a maximum stress of 13.9 GPa. The fractured segments show plastic behavior and the formation of surfacial films on the β-Si3N4 . These results are very different from those of a previously studied basal plane model [J. Chen , Phys. Rev. Lett. 95, 256103 (2005)10.1103/PhysRevLett.95.256103] and add insights to the structure and behavior of IGFs in polycrystalline ceramics. The implications of these results and the need for further investigations are discussed.

Electronic structure and partial charge distribution of doxorubicin under different molecular environments

NASA Astrophysics Data System (ADS)

Poudel, Lokendra

Doxorubicin (trade name Adriamycin, abbreviated DOX) is a well-known an- thracyclic chemotherapeutic used in treating a variety of cancers including acute leukemia, lymphoma, multiple myeloma, and a range of stomach, lung, bladder, bone, breast, and ovarian cancers. The purpose of the present work is to study electronic structure, partial charge distribution and interaction energy of DOX under different environments. It provides a framework for better understanding of bioactivity of DOX with DNA. While in this work, we focus on DOX -- DNA interactions; the obtained knowledge could be translated to other drug -- target interactions or biomolecular interactions. The electronic structure and partial charge distribution of DOX in three dierent molecular environments: isolated, solvated, and intercalated into a DNA complex,were studied by rst principles density functional methods. It is shown that the addition of solvating water molecules to DOX and the proximity and interaction with DNA has a signicant impact on the electronic structure as well as the partial charge distribution. The calculated total partial charges for DOX in the three models are 0.0, +0.123 and -0.06 electrons for the isolated, solvated, and intercalated state, respectively. Furthermore, by using the more accurate ab initio partial charge values on every atom in the models, signicant improvement in estimating the DOX-DNA interaction energy is obtained in conjunction with the NAnoscale Molecular Dynamics (NAMD) code. The electronic structure of the DOX-DNA is further elucidated by resolving the total density of states (TDOS) into dierent functional groups of DOX, DNA, water, co-crystallized Spermine molecule, and Na ions. The surface partial charge distribution in the DOX-DNA is calculated and displayed graphically. We conclude that the presence of the solvent as well as the details of the interaction geometry matter greatly in the determination of the stability of the DOX complexion. Ab initio calculations on realistic models are an important step towards a more accurate description of biomolecular interaction and in the eventual understanding of long-range interactions in biomolecular systems.

Electron and proton absorption calculations for a graphite/epoxy composite model. [large space structures

NASA Technical Reports Server (NTRS)

Long, E. R., Jr.

1979-01-01

The Bethe-Bloch stopping power relations for inelastic collisions were used to determine the absorption of electron and proton energy in cured neat epoxy resin and the absorption of electron energy in a graphite/epoxy composite. Absorption of electron energy due to bremsstrahlung was determined. Electron energies from 0.2 to 4.0 MeV and proton energies from 0.3 to 1.75 MeV were used. Monoenergetic electron energy absorption profiles for models of pure graphite, cured neat epoxy resin, and graphite/epoxy composites are reported. A relation is determined for depth of uniform energy absorption in a composite as a function of fiber volume fraction and initial electron energy. Monoenergetic proton energy absorption profiles are reported for the neat resin model. A relation for total proton penetration in the epoxy resin as a function of initial proton energy is determined. Electron energy absorption in the composite due to bremsstrahlung is reported. Electron and proton energy absorption profiles in cured neat epoxy resin are reported for environments approximating geosynchronous earth orbit.

Detailed Modeling of Physical Processes in Electron Sources for Accelerator Applications

NASA Astrophysics Data System (ADS)

Chubenko, Oksana; Afanasev, Andrei

2017-01-01

At present, electron sources are essential in a wide range of applications - from common technical use to exploring the nature of matter. Depending on the application requirements, different methods and materials are used to generate electrons. State-of-the-art accelerator applications set a number of often-conflicting requirements for electron sources (e.g., quantum efficiency vs. polarization, current density vs. lifetime, etc). Development of advanced electron sources includes modeling and design of cathodes, material growth, fabrication of cathodes, and cathode testing. The detailed simulation and modeling of physical processes is required in order to shed light on the exact mechanisms of electron emission and to develop new-generation electron sources with optimized efficiency. The purpose of the present work is to study physical processes in advanced electron sources and develop scientific tools, which could be used to predict electron emission from novel nano-structured materials. In particular, the area of interest includes bulk/superlattice gallium arsenide (bulk/SL GaAs) photo-emitters and nitrogen-incorporated ultrananocrystalline diamond ((N)UNCD) photo/field-emitters. Work supported by The George Washington University and Euclid TechLabs LLC.

Integration of QSAR and SAR methods for the mechanistic interpretation of predictive models for carcinogenicity

PubMed Central

Fjodorova, Natalja; Novič, Marjana

2012-01-01

The knowledge-based Toxtree expert system (SAR approach) was integrated with the statistically based counter propagation artificial neural network (CP ANN) model (QSAR approach) to contribute to a better mechanistic understanding of a carcinogenicity model for non-congeneric chemicals using Dragon descriptors and carcinogenic potency for rats as a response. The transparency of the CP ANN algorithm was demonstrated using intrinsic mapping technique specifically Kohonen maps. Chemical structures were represented by Dragon descriptors that express the structural and electronic features of molecules such as their shape and electronic surrounding related to reactivity of molecules. It was illustrated how the descriptors are correlated with particular structural alerts (SAs) for carcinogenicity with recognized mechanistic link to carcinogenic activity. Moreover, the Kohonen mapping technique enables one to examine the separation of carcinogens and non-carcinogens (for rats) within a family of chemicals with a particular SA for carcinogenicity. The mechanistic interpretation of models is important for the evaluation of safety of chemicals. PMID:24688639

Theoretical calculations of Electron Paramagnetic Resonance parameters of liquid phase Orotic acid radical

NASA Astrophysics Data System (ADS)

Sarikaya, Ebru Karakaş; Dereli, Ömer

2017-02-01

To obtain liquid phase molecular structure, conformational analysis of Orotic acid was performed and six conformers were determined. For these conformations, eight possible radicals were modelled by using Density Functional Theory computations with respect to molecular structure. Electron Paramagnetic Resonance parameters of these model radicals were calculated and then they were compared with the experimental ones. Geometry optimizations of the molecule and modeled radicals were performed using Becke's three-parameter hybrid-exchange functional combined with the Lee-Yang-Parr correlation functional of Density Functional Theory and 6-311++G(d,p) basis sets in p-dioxane solution. Because Orotic acid can be mutagenic in mammalian somatic cells and it is also mutagenic for bacteria and yeast, it has been studied.

Magnetic Local Time Dependant Low Energy Electron Flux Models at Geostationary Earth Orbit

NASA Astrophysics Data System (ADS)

Boynton, R.; Balikhin, M. A.; Walker, S. N.

2017-12-01

The low energy electron fluxes in the outer radiation belts at Geostationary Earth Orbit (GEO) can vary widely in Magnetic Local Time (MLT). This spatial variation is due to the convective and substorm-associated electric fields and can take place on short time scales. This makes it difficult to deduce a data based model of the low energy electrons. For higher energies, where there is negligible spatial variation at a particular L-star, data based models employ averaged fluxes over the orbit. This removes the diurnal variation as GEO passes through various L-star due to the structure of Earth's magnetic field. This study develops a number of models for the low energy electron fluxes measured by GOES 13 and 15 for different MLT to capture the dynamics of the spatial variations.

A minimalistic approach to static and dynamic electron correlations: Amending generalized valence bond method with extended random phase approximation correlation correction

DOE Office of Scientific and Technical Information (OSTI.GOV)

Chatterjee, Koushik; Jawulski, Konrad; Pastorczak, Ewa

A perfect-pairing generalized valence bond (GVB) approximation is known to be one of the simplest approximations, which allows one to capture the essence of static correlation in molecular systems. In spite of its attractive feature of being relatively computationally efficient, this approximation misses a large portion of dynamic correlation and does not offer sufficient accuracy to be generally useful for studying electronic structure of molecules. We propose to correct the GVB model and alleviate some of its deficiencies by amending it with the correlation energy correction derived from the recently formulated extended random phase approximation (ERPA). On the examples ofmore » systems of diverse electronic structures, we show that the resulting ERPA-GVB method greatly improves upon the GVB model. ERPA-GVB recovers most of the electron correlation and it yields energy barrier heights of excellent accuracy. Thanks to a balanced treatment of static and dynamic correlation, ERPA-GVB stays reliable when one moves from systems dominated by dynamic electron correlation to those for which the static correlation comes into play.« less

Model for Generation of Neutrons in a Compact Diode with Laser-Plasma Anode and Suppression of Electron Conduction Using a Permanent Cylindrical Magnet

NASA Astrophysics Data System (ADS)

Shikanov, A. E.; Vovchenko, E. D.; Kozlovskii, K. I.; Rashchikov, V. I.; Shatokhin, V. L.

2018-04-01

A model for acceleration of deuterons and generation of neutrons in a compact laser-plasma diode with electron isolation using magnetic field generated by a hollow cylindrical permanent magnet is presented. Experimental and computer-simulated neutron yields are compared for the diode structure under study. An accelerating neutron tube with a relatively high neutron generation efficiency can be constructed using suppression of electron conduction with the aid of a magnet placed in the vacuum volume.

QEDMOD: Fortran program for calculating the model Lamb-shift operator

NASA Astrophysics Data System (ADS)

Shabaev, V. M.; Tupitsyn, I. I.; Yerokhin, V. A.

2018-02-01

We present Fortran package QEDMOD for computing the model QED operator hQED that can be used to account for the Lamb shift in accurate atomic-structure calculations. The package routines calculate the matrix elements of hQED with the user-specified one-electron wave functions. The operator can be used to calculate Lamb shift in many-electron atomic systems with a typical accuracy of few percent, either by evaluating the matrix element of hQED with the many-electron wave function, or by adding hQED to the Dirac-Coulomb-Breit Hamiltonian.

Dynamic molecular structure retrieval from low-energy laser-induced electron diffraction spectra

NASA Astrophysics Data System (ADS)

Vu, Dinh-Duy T.; Phan, Ngoc-Loan T.; Hoang, Van-Hung; Le, Van-Hoang

2017-12-01

A recently developed quantitative rescattering theory showed that a laser-free elastic cross section can be separated from laser-induced electron diffraction (LIED) spectra. Based upon this idea, Blaga et al investigated the possibility of reconstructing molecular structure from LIED spectra (2012 Nature 483 7388). In the above study, an independent atoms model (IAM) was used to interpret high-energy electron-molecule collisions induced by a mid-infrared laser. Our research aims to extend the application range of this structural retrieval method to low-energy spectra induced by more common near-infrared laser sources. The IAM is insufficient in this case, so we switch to a more comprehensive model—the multiple scattering (MS) theory. From the original version concerning only neutral targets, we upgrade the model so that it is compatible with electron-ion collisions at low energy. With available LIED experiment data of CO2 and O2, the upgraded MS is shown to be greatly effective as a tool for molecular imaging from spectra induced by a near-infrared laser. The captured image is at about 2 fs after the ionization, shorter than the period 4-6 fs by using the mid-infrared laser in Blaga’s experiment.

Towards a First-Principles Determination of Effective Coulomb Interactions in Correlated Electron Materials: Role of Intershell Interactions

NASA Astrophysics Data System (ADS)

Seth, Priyanka; Hansmann, Philipp; van Roekeghem, Ambroise; Vaugier, Loig; Biermann, Silke

2017-08-01

The determination of the effective Coulomb interactions to be used in low-energy Hamiltonians for materials with strong electronic correlations remains one of the bottlenecks for parameter-free electronic structure calculations. We propose and benchmark a scheme for determining the effective local Coulomb interactions for charge-transfer oxides and related compounds. Intershell interactions between electrons in the correlated shell and ligand orbitals are taken into account in an effective manner, leading to a reduction of the effective local interactions on the correlated shell. Our scheme resolves inconsistencies in the determination of effective interactions as obtained by standard methods for a wide range of materials, and allows for a conceptual understanding of the relation of cluster model and dynamical mean field-based electronic structure calculations.

Towards a First-Principles Determination of Effective Coulomb Interactions in Correlated Electron Materials: Role of Intershell Interactions.

PubMed

Seth, Priyanka; Hansmann, Philipp; van Roekeghem, Ambroise; Vaugier, Loig; Biermann, Silke

2017-08-04

The determination of the effective Coulomb interactions to be used in low-energy Hamiltonians for materials with strong electronic correlations remains one of the bottlenecks for parameter-free electronic structure calculations. We propose and benchmark a scheme for determining the effective local Coulomb interactions for charge-transfer oxides and related compounds. Intershell interactions between electrons in the correlated shell and ligand orbitals are taken into account in an effective manner, leading to a reduction of the effective local interactions on the correlated shell. Our scheme resolves inconsistencies in the determination of effective interactions as obtained by standard methods for a wide range of materials, and allows for a conceptual understanding of the relation of cluster model and dynamical mean field-based electronic structure calculations.

Theoretical Modeling of Electromagnetic Field from Electron Bunches in Periodic Wire Medium

DOE Office of Scientific and Technical Information (OSTI.GOV)

Chuchurka, S.; Benediktovitch, A.; Galyamin, S. N.

The interaction of relativistic electrons with periodic conducting structures results in radiation via a number of mechanisms. In case of crystals one obtains parametric X-ray radiation, its frequency is determined by the distance between crystallographic planes and the direction of electron beam. If instead of a crystal one considers a periodic structure of metallic wires with the spacing of the order of mm, it is plausible to expect the emission of radiation of a similar nature (“diffraction response”) at THz frequencies. Additionally, a “long-wave” radiation will occur in this case with wavelengths much larger then structure periods. In this contribution,more » we present different theoretical approaches for describing the electromagnetic radiation field from prolonged electron bunch propagated in the lattice of metallic wires. The validity of these analytical descriptions is checked by numerical simulations. We discuss the possible applications of aforementioned structure as sources of coherent THz radiation.« less

MMM: A toolbox for integrative structure modeling.

PubMed

Jeschke, Gunnar

2018-01-01

Structural characterization of proteins and their complexes may require integration of restraints from various experimental techniques. MMM (Multiscale Modeling of Macromolecules) is a Matlab-based open-source modeling toolbox for this purpose with a particular emphasis on distance distribution restraints obtained from electron paramagnetic resonance experiments on spin-labelled proteins and nucleic acids and their combination with atomistic structures of domains or whole protomers, small-angle scattering data, secondary structure information, homology information, and elastic network models. MMM does not only integrate various types of restraints, but also various existing modeling tools by providing a common graphical user interface to them. The types of restraints that can support such modeling and the available model types are illustrated by recent application examples. © 2017 The Protein Society.

Preparing for Electronic Medical Record Implementation: Carolina Care Communication in an Electronic Environment.

PubMed

Carroll, Tracy; Tonges, Mary; Ray, Joel

2017-11-01

This article describes 1 organization's successful approach to mitigating the potential negative effects of a new electronic medical record on patient experience. The Carolina Care model, developed at the University of North Carolina Hospitals to actualize caring theory in practice, helped to structure and greatly facilitate this work. Seven focus areas were integrated to create the "Communication in an Electronic Environment" program with a strong emphasis on nurse-patient communication.

Growth process, characterization, and modeling of electronic properties of coupled InAsSbP nanostructures

NASA Astrophysics Data System (ADS)

Marquardt, Oliver; Hickel, Tilmann; Neugebauer, Jörg; Gambaryan, Karen M.; Aroutiounian, Vladimir M.

2011-08-01

Quaternary III-V InAsSbP quantum dots (QDs) have been grown in the form of cooperative InAsSb/InAsP structures using a modified version of the liquid phase epitaxy. High resolution scanning electron microscopy, atomic force microscopy, and Fourier-transform infrared spectrometry were used to investigate these so-called nano-camomiles, mainly consisting of a central InAsSb QD surrounded by six InAsP-QDs, that shall be referred to as leaves in the following. The observed QDs average density ranges from 0.8 to 2 × 109 cm-2, with heights and widths dimensions from 2 to 20 nm and 5 to 45 nm, respectively. The average density of the leaves is equal to (6-10) × 109 cm-2 with dimensions of approx. 5 to 40 nm in width and depth. To achieve a first basic understanding of the electronic properties, we have modeled these novel nanostructures using second-order continuum elasticity theory and an eight-band k .p model to calculate the electronic structure. Our calculations found a clear localization of hole states in the central InAsSb dot. The localization of electron states, however, was found to be weak and might thus be easily influenced by external electric fields or strain.

Crystal structure stability and electronic properties of the layered nickelate La4Ni3O10

NASA Astrophysics Data System (ADS)

Puggioni, Danilo; Rondinelli, James M.

2018-03-01

We investigate the crystal structure and the electronic properties of the trilayer nickelate La4Ni3O10 by means of quantum-mechanical calculations in the framework of the density-functional theory. We find that, at low temperature, La4Ni3O10 undergoes a hitherto unreported structural phase transition and transforms to a new monoclinic P 21/a phase. This phase exhibits electronic properties in agreement with recent angle-resolved photoemission spectroscopy data reported in H. Li et al., [Nat. Commun. 8, 704 (2017), 10.1038/s41467-017-00777-0] and should be considered in models focused on explaining the observed ˜140 K metal-to-metal phase transition.

Figure Control of Lightweight Optical Structures

NASA Technical Reports Server (NTRS)

Main, John A.; Song, Haiping

2005-01-01

The goal of this paper is to demonstrate the use of fuzzy logic controllers in modifying the figure of a piezoceramic bimorph mirror. Non-contact electron actuation technology is used to actively control a bimorph mirror comprised two PZT-5H wafers by varying the electron flux and electron voltages. Due to electron blooming generated by the electron flux, it is difficult to develop an accurate control model for the bimorph mirror through theoretical analysis alone. The non-contact shape control system with electron flux blooming can be approximately described with a heuristic model based on experimental data. Two fuzzy logic feedback controllers are developed to control the shape of the bimorph mirror according to heuristic fuzzy inference rules generated from previous experimental results. Validation of the proposed fuzzy logic controllers is also discussed.

Imprints of the Molecular Electronic Structure in the Photoelectron Spectra of Strong-Field Ionized Asymmetric Triatomic Model Molecules

NASA Astrophysics Data System (ADS)

Paul, Matthias; Yue, Lun; Gräfe, Stefanie

2018-06-01

We examine the circular dichroism in the angular distribution of photoelectrons of triatomic model systems ionized by strong-field ionization. Following our recent work on this effect [Paul, Yue, and Gräfe, J. Mod. Opt. 64, 1104 (2017), 10.1080/09500340.2017.1299883], we demonstrate how the symmetry and electronic structure of the system is imprinted into the photoelectron momentum distribution. We use classical trajectories to reveal the origin of the threefolded pattern in the photoelectron momentum distribution, and show how an asymmetric nuclear configuration of the triatomic system effects the photoelectron spectra.

Construction and validation of an atomic model for bacterial TSPO from electron microscopy density, evolutionary constraints, and biochemical and biophysical data.

PubMed

Hinsen, Konrad; Vaitinadapoule, Aurore; Ostuni, Mariano A; Etchebest, Catherine; Lacapere, Jean-Jacques

2015-02-01

The 18 kDa protein TSPO is a highly conserved transmembrane protein found in bacteria, yeast, animals and plants. TSPO is involved in a wide range of physiological functions, among which the transport of several molecules. The atomic structure of monomeric ligand-bound mouse TSPO in detergent has been published recently. A previously published low-resolution structure of Rhodobacter sphaeroides TSPO, obtained from tubular crystals with lipids and observed in cryo-electron microscopy, revealed an oligomeric structure without any ligand. We analyze this electron microscopy density in view of available biochemical and biophysical data, building a matching atomic model for the monomer and then the entire crystal. We compare its intra- and inter-molecular contacts with those predicted by amino acid covariation in TSPO proteins from evolutionary sequence analysis. The arrangement of the five transmembrane helices in a monomer of our model is different from that observed for the mouse TSPO. We analyze possible ligand binding sites for protoporphyrin, for the high-affinity ligand PK 11195, and for cholesterol in TSPO monomers and/or oligomers, and we discuss possible functional implications. Copyright © 2014 Elsevier B.V. All rights reserved.

Applications of large-scale density functional theory in biology

NASA Astrophysics Data System (ADS)

Cole, Daniel J.; Hine, Nicholas D. M.

2016-10-01

Density functional theory (DFT) has become a routine tool for the computation of electronic structure in the physics, materials and chemistry fields. Yet the application of traditional DFT to problems in the biological sciences is hindered, to a large extent, by the unfavourable scaling of the computational effort with system size. Here, we review some of the major software and functionality advances that enable insightful electronic structure calculations to be performed on systems comprising many thousands of atoms. We describe some of the early applications of large-scale DFT to the computation of the electronic properties and structure of biomolecules, as well as to paradigmatic problems in enzymology, metalloproteins, photosynthesis and computer-aided drug design. With this review, we hope to demonstrate that first principles modelling of biological structure-function relationships are approaching a reality.

UV absorption spectrum and photodissociation channels of the simplest Criegee intermediate (CH2OO).

PubMed

Dawes, Richard; Jiang, Bin; Guo, Hua

2015-01-14

The lowest-lying singlet states of the simplest Criegee intermediate (CH2OO) have been characterized along the O-O dissociation coordinate using explicitly correlated MRCI-F12 electronic structure theory and large active spaces. It is found that a high-level treatment of dynamic electron-correlation is essential to accurately describe these states. A significant well on the B-state is identified at the MRCI-F12 level with an equilibrium structure that differs substantially from that of the ground X-state. This well is presumably responsible for the apparent vibrational structure in some experimental UV absorption spectra, analogous to the structured Huggins band of the iso-electronic ozone. The B-state potential in the Franck-Condon region is sufficiently accurate that an absorption spectrum calculated with a one-dimensional model agrees remarkably well with experiment.

The impact of recent improvements in cryo-electron microscopy technology on the understanding of bacterial ribosome assembly

PubMed Central

Razi, Aida; Britton, Robert A.

2017-01-01

Abstract Cryo-electron microscopy (cryo-EM) had played a central role in the study of ribosome structure and the process of translation in bacteria since the development of this technique in the mid 1980s. Until recently cryo-EM structures were limited to ∼10 Å in the best cases. However, the recent advent of direct electron detectors has greatly improved the resolution of cryo-EM structures to the point where atomic resolution is now achievable. This improved resolution will allow cryo-EM to make groundbreaking contributions in essential aspects of ribosome biology, including the assembly process. In this review, we summarize important insights that cryo-EM, in combination with chemical and genetic approaches, has already brought to our current understanding of the ribosomal assembly process in bacteria using previous detector technology. More importantly, we discuss how the higher resolution structures now attainable with direct electron detectors can be leveraged to propose precise testable models regarding this process. These structures will provide an effective platform to develop new antibiotics that target this fundamental cellular process. PMID:28180306

The role of chemical structure on the magnetic and electronic properties of Co{sub 2}FeAl{sub 0.5}Si{sub 0.5}/Si(111) interface

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kuerbanjiang, Balati; Nedelkoski, Zlatko; Ghasemi, Arsham

2016-04-25

We show that Co{sub 2}FeAl{sub 0.5}Si{sub 0.5} film deposited on Si(111) has a single crystal structure and twin related epitaxial relationship with the substrate. Sub-nanometer electron energy loss spectroscopy shows that in a narrow interface region there is a mutual inter-diffusion dominated by Si and Co. Atomic resolution aberration-corrected scanning transmission electron microscopy reveals that the film has B2 ordering. The film lattice structure is unaltered even at the interface due to the substitutional nature of the intermixing. First-principles calculations performed using structural models based on the aberration corrected electron microscopy show that the increased Si incorporation in the filmmore » leads to a gradual decrease of the magnetic moment as well as significant spin-polarization reduction. These effects can have significant detrimental role on the spin injection from the Co{sub 2}FeAl{sub 0.5}Si{sub 0.5} film into the Si substrate, besides the structural integrity of this junction.« less

Features of the electronic structure of FeTe compounds

NASA Astrophysics Data System (ADS)

Grechnev, G. E.; Lyogenkaya, A. A.; Panfilov, A. S.; Logosha, A. V.; Kotlyar, O. V.; Gnezdilov, V. P.; Makarova, I. P.; Chareev, D. A.; Mitrofanova, E. S.

2015-12-01

A theoretical and experimental study of the electronic structure and nature of the chemical bonds in FeTe compounds in antiferromagnetic (AFM) and paramagnetic phases was carried out. It is established that the nature of the chemical bonds is mainly metallic, and the presence of covalent bonds Fe-Te and Te-Te helps to stabilize the structural distortions of the tetragonal phase of FeTe in the low-temperature region. It is found that the bicollinear AFM structure corresponds to the ground state of the FeTe compound and the calculated value of the magnetic moment MFe = -2.4μB is in good agreement with the data from neutron diffraction measurements. At the same time, the Fermi surface (FS) of the low-temperature AFM phase is radically different from the FS of the paramagnetic FeTe. Reconstructing the FS can lead to a sign change of the Hall coefficient observed in FeTe. The calculation results serve as evidence of the fact that the electronic structures and magnetic properties of FeTe are well-described by the model of itinerant d-electrons and the density functional theory (DFT-GGA).

Machine learning of molecular electronic properties in chemical compound space

NASA Astrophysics Data System (ADS)

Montavon, Grégoire; Rupp, Matthias; Gobre, Vivekanand; Vazquez-Mayagoitia, Alvaro; Hansen, Katja; Tkatchenko, Alexandre; Müller, Klaus-Robert; Anatole von Lilienfeld, O.

2013-09-01

The combination of modern scientific computing with electronic structure theory can lead to an unprecedented amount of data amenable to intelligent data analysis for the identification of meaningful, novel and predictive structure-property relationships. Such relationships enable high-throughput screening for relevant properties in an exponentially growing pool of virtual compounds that are synthetically accessible. Here, we present a machine learning model, trained on a database of ab initio calculation results for thousands of organic molecules, that simultaneously predicts multiple electronic ground- and excited-state properties. The properties include atomization energy, polarizability, frontier orbital eigenvalues, ionization potential, electron affinity and excitation energies. The machine learning model is based on a deep multi-task artificial neural network, exploiting the underlying correlations between various molecular properties. The input is identical to ab initio methods, i.e. nuclear charges and Cartesian coordinates of all atoms. For small organic molecules, the accuracy of such a ‘quantum machine’ is similar, and sometimes superior, to modern quantum-chemical methods—at negligible computational cost.

Atomic and electronic properties of quasi-one-dimensional MOS2 nanowires

PubMed Central

Seivane, Lucas Fernandez; Barron, Hector; Botti, Silvana; Marques, Miguel Alexandre Lopes; Rubio, Ángel; López-Lozano, Xóchitl

2013-01-01

The structural, electronic and magnetic properties of quasi-one-dimensional MoS2 nanowires, passivated by extra sulfur, have been determined using ab initio density-functional theory. The nanostructures were simulated using several different models based on experimental electron microscopy images. It is found that independently of the geometrical details and the coverage of extra sulfur at the Mo-edge, quasi-one-dimensional metallic states are predominant in all the low-energy model structures despite their reduced dimensionality. These metallic states are localized mainly at the edges. However, the electronic and magnetic character of the NWs does not depend only on the S saturation but also on the symmetry configuration of the S edge atoms. Our results show that for the same S saturation the magnetization can be decreased by increasing the pairing of the S and Mo edge atoms. In spite of the observed pairing of S dimers at the Mo-edge, the nanowires do not experience a Peierls-like metal-insulator transition PMID:25429189

Hydrodynamic electronic fluid instability in GaAs MESFETs at terahertz frequencies

NASA Astrophysics Data System (ADS)

Li, Kang; Hao, Yue; Jin, Xiaoqi; Lu, Wu

2018-01-01

III-V compound semiconductor field effect transistors (FETs) are potential candidates as solid state THz emitters and detectors due to plasma wave instability in these devices. Using a 2D hydrodynamic model, here we present the numerical studies of electron fluid instability in a FET structure. The model is implemented in a GaAs MESFET structure with a gate length of 0.2 µm as a testbed by taking into account the non-equilibrium transport and multi-valley non-parabolicity energy bands. The results show that the electronic density instability in the channel can produce stable periodic oscillations at THz frequencies. Along with stable oscillations, negative differential resistance in output characteristics is observed. The THz emission energy density increases monotonically with the drain bias. The emission frequency of electron density oscillations can be tuned by both gate and drain biases. The results suggest that III-V FETs can be a kind of versatile THz devices with good tunability on both radiative power and emission frequency.

Research Update: Spatially resolved mapping of electronic structure on atomic level by multivariate statistical analysis

DOE PAGES

Belianinov, Alex; Panchapakesan, G.; Lin, Wenzhi; ...

2014-12-02

Atomic level spatial variability of electronic structure in Fe-based superconductor FeTe0.55Se0.45 (Tc = 15 K) is explored using current-imaging tunneling-spectroscopy. Multivariate statistical analysis of the data differentiates regions of dissimilar electronic behavior that can be identified with the segregation of chalcogen atoms, as well as boundaries between terminations and near neighbor interactions. Subsequent clustering analysis allows identification of the spatial localization of these dissimilar regions. Similar statistical analysis of modeled calculated density of states of chemically inhomogeneous FeTe1 x Sex structures further confirms that the two types of chalcogens, i.e., Te and Se, can be identified by their electronic signaturemore » and differentiated by their local chemical environment. This approach allows detailed chemical discrimination of the scanning tunneling microscopy data including separation of atomic identities, proximity, and local configuration effects and can be universally applicable to chemically and electronically inhomogeneous surfaces.« less

Universal interaction-driven gap in metallic carbon nanotubes

NASA Astrophysics Data System (ADS)

Senger, Mitchell J.; McCulley, Daniel R.; Lotfizadeh, Neda; Deshpande, Vikram V.; Minot, Ethan D.

2018-02-01

Suspended metallic carbon nanotubes (m-CNTs) exhibit a remarkably large transport gap that can exceed 100 meV. Both experiment and theory suggest that strong electron-electron interactions play a crucial role in generating this electronic structure. To further understand this strongly interacting system, we have performed electronic measurements of suspended m-CNTs with known diameter and chiral angle. Spectrally resolved photocurrent microscopy was used to determine m-CNT structure. The room-temperature electrical characteristics of 18 individually contacted m-CNTs were compared to their respective diameter and chiral angle. At the charge neutrality point, we observe a peak in m-CNT resistance that scales exponentially with inverse diameter. Using a thermally activated transport model, we estimate that the transport gap is (450 meV nm)/D , where D is CNT diameter. We find no correlation between the gap and the CNT chiral angle. Our results add important constraints to theories attempting to describe the electronic structure of m-CNTs.

Research Update: Spatially resolved mapping of electronic structure on atomic level by multivariate statistical analysis

DOE Office of Scientific and Technical Information (OSTI.GOV)

Belianinov, Alex, E-mail: belianinova@ornl.gov; Ganesh, Panchapakesan; Lin, Wenzhi

2014-12-01

Atomic level spatial variability of electronic structure in Fe-based superconductor FeTe{sub 0.55}Se{sub 0.45} (T{sub c} = 15 K) is explored using current-imaging tunneling-spectroscopy. Multivariate statistical analysis of the data differentiates regions of dissimilar electronic behavior that can be identified with the segregation of chalcogen atoms, as well as boundaries between terminations and near neighbor interactions. Subsequent clustering analysis allows identification of the spatial localization of these dissimilar regions. Similar statistical analysis of modeled calculated density of states of chemically inhomogeneous FeTe{sub 1−x}Se{sub x} structures further confirms that the two types of chalcogens, i.e., Te and Se, can be identified bymore » their electronic signature and differentiated by their local chemical environment. This approach allows detailed chemical discrimination of the scanning tunneling microscopy data including separation of atomic identities, proximity, and local configuration effects and can be universally applicable to chemically and electronically inhomogeneous surfaces.« less

Valence Band Control of Metal Silicide Films via Stoichiometry.

PubMed

Streller, Frank; Qi, Yubo; Yang, Jing; Mangolini, Filippo; Rappe, Andrew M; Carpick, Robert W

2016-07-07

The unique electronic and mechanical properties of metal silicide films render them interesting for advanced materials in plasmonic devices, batteries, field-emitters, thermoelectric devices, transistors, and nanoelectromechanical switches. However, enabling their use requires precisely controlling their electronic structure. Using platinum silicide (PtxSi) as a model silicide, we demonstrate that the electronic structure of PtxSi thin films (1 ≤ x ≤ 3) can be tuned between metallic and semimetallic by changing the stoichiometry. Increasing the silicon content in PtxSi decreases the carrier density according to valence band X-ray photoelectron spectroscopy and theoretical density of states (DOS) calculations. Among all PtxSi phases, Pt3Si offers the highest DOS due to the modest shift of the Pt5d manifold away from the Fermi edge by only 0.5 eV compared to Pt, rendering it promising for applications. These results, demonstrating tunability of the electronic structure of thin metal silicide films, suggest that metal silicides can be designed to achieve application-specific electronic properties.

On the inversion of the 1 Bu and 2 Ag electronic states in α,ω-diphenylpolyenes

NASA Astrophysics Data System (ADS)

Catalán, J.

2003-07-01

An alternative model to that of the inversion of the states 1Bu and 2Ag is proposed for interpreting the photophysics of the α,ω-diphenylpolyenes. This model is based upon the existence of two chemical structures with Bu symmetry, which may be ascribed to the same excited electronic state 1Bu. One of the two chemical structures corresponds to the Franck-Condon structure with conjugated single and double bonds for the polyene chain, and another consists of a nearly equivalent series of partial double bonds along the polyene chain. The latter relaxed structure is consistent with the observation of high torsional energy barriers and low photoisomerization quantum yields for diphenylhexatriene in the singlet excited state manifold. Interestingly, such a simple quantum model as that of the particle in a one-dimensional box provides quite an accurate description of the absorption spectroscopic properties of these major compounds. This is partly the result of the most stable structures for these compounds being of the all-trans type; such structures increase in length as additional ethylene units are added, which makes them very similar to a one-dimensional box becoming increasingly longer.

Electromigration and the structure of metallic nanocontacts

NASA Astrophysics Data System (ADS)

Hoffmann-Vogel, R.

2017-09-01

This article reviews efforts to structurally characterize metallic nanocontacts. While the electronic characterization of such junctions is relatively straight forward, usually it is technically challenging to study the nanocontact's structure at small length scales. However, knowing that the structure is the basis for understanding the electronic properties of the nanocontact, for example, it is necessary to explain the electronic properties by calculations based on structural models. Besides using a gate electrode, controlling the structure is an important way of understanding how the electronic transport properties can be influenced. A key to make structural information directly accessible is to choose a fabrication method that is adapted to the structural characterization method. Special emphasis is given to transmission electron microscopy fabrication and to thermally assisted electromigration methods due to their potential for obtaining information on both electrodes of the forming nanocontact. Controlled electromigration aims at studying the contact at constant temperature of the contact during electromigration compared to studies at constant temperature of the environment as done previously. We review efforts to calculate electromigration forces. We describe how hot spots are formed during electromigration. We summarize implications for the structure obtained from studies of the ballistic transport regime, tunneling, and Coulomb-blockade. We review the structure of the nanocontacts known from direct structural characterization. Single-crystalline wires allow suppressing grain boundary electromigration. In thin films, the substrate plays an important role in influencing the defect and temperature distribution. Hot-spot formation and recrystallization are observed. We add information on the local temperature and current density and on alloys important for microelectronic interconnects.

Phason space analysis and structure modelling of 100 Å-scale dodecagonal quasicrystal in Mn-based alloy

NASA Astrophysics Data System (ADS)

Ishimasa, Tsutomu; Iwami, Shuhei; Sakaguchi, Norihito; Oota, Ryo; Mihalkovič, Marek

2015-11-01

The dodecagonal quasicrystal classified into the five-dimensional space group P126/mmc, recently discovered in a Mn-Cr-Ni-Si alloy, has been analysed using atomic-resolution spherical aberration-corrected electron microscopy, i.e. high-angle annular dark-field scanning transmission electron microscopy (HAADF-STEM) and conventional transmission electron microscopy. By observing along the 12-fold axis, non-periodic tiling consisting of an equilateral triangle and a square has been revealed, of which common edge length is a = 4.560 Å. These tiles tend to form a network of dodecagons of which size is ?a ≈ 17 Å in diameter. The tiling was interpreted as an aggregate of 100 Å-scale oriented domains of high- and low-quality quasicrystals with small crystallites appearing at their boundaries. The quasicrystal domains exhibited a densely filled circular acceptance region in the phason space. This is the first observation of the acceptance region in an actual dodecagonal quasicrystal. Atomic structure model consistent with the electron microscopy images is a standard Frank-Kasper decoration of the triangle and square tiles that can be inferred from the crystal structures of Zr4Al3 and Cr3Si. Four kinds of layers located at z = 0, ±1/4 and 1/2 are stacked periodically along the 12-fold axis, and the atoms at z = 0 and 1/2 form hexagonal anti-prisms consistently with the 126-screw axis. The validity of this structure model was examined by means of powder X-ray diffraction.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lin, Jiusheng; van den Bedem, Henry; Brunger, Axel T.

Calmodulin (CaM) is the primary calcium signaling protein in eukaryotes and has been extensively studied using various biophysical techniques. Prior crystal structures have noted the presence of ambiguous electron density in both hydrophobic binding pockets of Ca 2+-CaM, but no assignment of these features has been made. In addition, Ca 2+-CaM samples many conformational substates in the crystal and accurately modeling the full range of this functionally important disorder is challenging. In order to characterize these features in a minimally biased manner, a 1.0 Å resolution single-wavelength anomalous diffraction data set was measured for selenomethionine-substituted Ca 2+-CaM. Density-modified electron-density mapsmore » enabled the accurate assignment of Ca 2+-CaM main-chain and side-chain disorder. These experimental maps also substantiate complex disorder models that were automatically built using low-contour features of model-phased electron density. Furthermore, experimental electron-density maps reveal that 2-methyl-2,4-pentanediol (MPD) is present in the C-terminal domain, mediates a lattice contact between N-terminal domains and may occupy the N-terminal binding pocket. The majority of the crystal structures of target-free Ca 2+-CaM have been derived from crystals grown using MPD as a precipitant, and thus MPD is likely to be bound in functionally critical regions of Ca 2+-CaM in most of these structures. The adventitious binding of MPD helps to explain differences between the Ca 2+-CaM crystal and solution structures and is likely to favor more open conformations of the EF-hands in the crystal.« less

One-Dimensional Hybrid Satellite Track Model for the Dynamics Explorer 2 (DE 2) Satellite

NASA Technical Reports Server (NTRS)

Deng, Wei; Killeen, T. L.; Burns, A. G.; Johnson, R. M.; Emery, B. A.; Roble, R. G.; Winningham, J. D.; Gary, J. B.

1995-01-01

A one-dimensional hybrid satellite track model has been developed to calculate the high-latitude thermospheric/ionospheric structure below the satellite altitude using Dynamics Explorer 2 (DE 2) satellite measurements and theory. This model is based on Emery et al. satellite track code but also includes elements of Roble et al. global mean thermosphere/ionosphere model. A number of parameterizations and data handling techniques are used to input satellite data from several DE 2 instruments into this model. Profiles of neutral atmospheric densities are determined from the MSIS-90 model and measured neutral temperatures. Measured electron precipitation spectra are used in an auroral model to calculate particle impact ionization rates below the satellite. These rates are combined with a solar ionization rate profile and used to solve the O(+) diffusion equation, with the measured electron density as an upper boundary condition. The calculated O(+) density distribution, as well as the ionization profiles, are then used in a photochemical equilibrium model to calculate the electron and molecular ion densities. The electron temperature is also calculated by solving the electron energy equation with an upper boundary condition determined by the DE 2 measurement. The model enables calculations of altitude profiles of conductivity and Joule beating rate along and below the satellite track. In a first application of the new model, a study is made of thermospheric and ionospheric structure below the DE 2 satellite for a single orbit which occurred on October 25, 1981. The field-aligned Poynting flux, which is independently obtained for this orbit, is compared with the model predictions of the height-integrated energy conversion rate. Good quantitative agreement between these two estimates has been reached. In addition, measurements taken at the incoherent scatter radar site at Chatanika (65.1 deg N, 147.4 deg W) during a DE 2 overflight are compared with the model calculations. A good agreement was found in lower thermospheric conductivities and Joule heating rate.

A Chemical Approach to Understanding Oxide Surface Structure and Reactivity

NASA Astrophysics Data System (ADS)

Enterkin, James Andrew

Transmission electron microscopy and diffraction are powerful tools for solving complex structural problems. They complement other analytical techniques, such as x-ray diffraction, elucidating problems which cannot be solved by other techniques. One area where they are of particularly great value is in the determination of surface structures. The research presented herein uses electron microscopy and diffraction as the primary experimental techniques in the development of a chemistry of surface structures. High-resolution electron microscopy revealed that the La4Cu 3MoO12 structure has turbostratic disorder and a lower symmetry space group (Pm) than was previously found. The refinement of the x-ray data was significantly improved by using a disordered model and the Pm space group. A bond valence analysis confirmed that the disordered structure is the superior model. Strontium titanate, SrTiO3, single crystal surfaces were examined principally via transmission electron diffraction. A homologous series with intergrowths was discovered on the (110) surface of strontium titanate, marking the first time that these important concepts of solid state chemistry have been found at the surface. Atmospheric adsorbates, such as H2O and CO2, were found to help to stabilize undercoordinated surface structures on the (100) surface. It was shown that chemical bonding, bond valence, atomic coordination, and stoichiometry greatly influence the development of surface structures. Additionally, such chemistry based analysis was demonstrated to be able to predict surface structure stability and reactivity. Application of a modified Wulff construction to the observed shape of strontium titanate nanocuboids revealed that the surface structure and particle stoichiometry are interlinked, with control over one allowing equally precise control over the other. Platinum nanoparticles on the strontium titanate nanocuboids were shown via high resolution electron microscopy to have cube-on-cube epitaxy, with the shape of the platinum nanoparticles governed by the Winterbottom construction. Precise modification of the support surface will therefore allow engineering of supported metal particles with precise control over which facets are exposed. These results suggest that control over the support surface chemistry can be used to engineer thermodynamically stable, face selective catalysts.

Ne matrix spectra of the sym-C6Br3F3+ radical cation

USGS Publications Warehouse

Bondybey, V.E.; Sears, T.J.; Miller, T.A.; Vaughn, C.; English, J.H.; Shiley, R.S.

1981-01-01

The electronic absorption and laser excited, wavelength resolved fluorescence spectra of the title cation have been observed in solid Ne matrix and vibrationally analysed. The vibrational structure of the excited B2A2??? state shows close similarity to the parent compound. The X2E??? ground state structure is strongly perturbed and irregular owing to a large Jahn-Teller distortion. The data are analysed in terms of a recently developed, sophisticated multimode Jahn-Teller theoretical model. We have generated the sym-C6Br3F3+ cations in solid Ne matrix and obtained their wavelength resolved emission and absorption spectra. T ground electronic X2E??? state exhibits an irregular and strongly perturbed vibrational structure, which can be successfully modeled using sophisticated multimode Jahn-Teller theory. ?? 1981.

Electronic bandstructure of semiconductor dilute bismide structures

NASA Astrophysics Data System (ADS)

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

2017-02-01

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

Atomic and electronic structure of the CdTe(111)B–(2√3 × 4) orthogonal surface

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bekenev, V. L., E-mail: bekenev@ipms.kiev.ua; Zubkova, S. M.

2017-01-15

The atomic and electronic structure of four variants of Te-terminated CdTe(111)B–(2√3 × 4) orthogonal polar surface (ideal, relaxed, reconstructed, and reconstructed with subsequent relaxation) are calculated ab initio for the first time. The surface is modeled by a film composed of 12 atomic layers with a vacuum gap of ~16 Å in the layered superlattice approximation. To close Cd dangling bonds on the opposite side of the film, 24 fictitious hydrogen atoms with a charge of 1.5 electrons each are added. Ab initio calculations are performed using the Quantum Espresso program based on density functional theory. It is demonstrated thatmore » relaxation leads to splitting of the four upper layers. The band energy structures and total and layer-by-layer densities of electronic states for the four surface variants are calculated and analyzed.« less

Ferromagnetism in the Hubbard Model with a Gapless Nearly-Flat Band

NASA Astrophysics Data System (ADS)

Tanaka, Akinori

2018-01-01

We present a version of the Hubbard model with a gapless nearly-flat lowest band which exhibits ferromagnetism in two or more dimensions. The model is defined on a lattice obtained by placing a site on each edge of the hypercubic lattice, and electron hopping is assumed to be only between nearest and next nearest neighbor sites. The lattice, where all the sites are identical, is simple, and the corresponding single-electron band structure, where two cosine-type bands touch without an energy gap, is also simple. We prove that the ground state of the model is unique and ferromagnetic at half-filling of the lower band, if the lower band is nearly flat and the strength of on-site repulsion is larger than a certain value which is independent of the lattice size. This is the first example of ferromagnetism in three dimensional non-singular models with a gapless band structure.

Oblique ion-acoustic cnoidal waves in two temperature superthermal electrons magnetized plasma

NASA Astrophysics Data System (ADS)

Panwar, A.; Ryu, C. M.; Bains, A. S.

2014-12-01

A study is presented for the oblique propagation of ion acoustic cnoidal waves in a magnetized plasma consisting of cold ions and two temperature superthermal electrons modelled by kappa-type distributions. Using the reductive perturbation method, the nonlinear Korteweg de-Vries equation is derived, which further gives the solutions with a special type of cnoidal elliptical functions. Both compressive and rarefactive structures are found for these cnoidal waves. Nonlinear periodic cnoidal waves are explained in terms of plasma parameters depicting the Sagdeev potential and the phase curves. It is found that the density ratio of hot electrons to ions μ significantly modifies compressive/refractive wave structures. Furthermore, the combined effects of superthermality of cold and hot electrons κ c , κ h , cold to hot electron temperature ratio σ, angle of propagation and ion cyclotron frequency ωci have been studied in detail to analyze the height and width of compressive/refractive cnoidal waves. The findings in the present study could have important implications in understanding the physics of electrostatic wave structures in the Saturn's magnetosphere where two temperature superthermal electrons are present.

Microstructure and mechanical properties of porous titanium structures fabricated by electron beam melting for cranial implants.

PubMed

Moiduddin, Khaja

2018-02-01

The traditional methods of metallic bone implants are often dense and suffer from adverse reactions, biomechanical mismatch and lack of adequate space for new bone tissue to grow into the implant. The objective of this study is to evaluate the customized porous cranial implant with mechanical properties closer to that of bone and to improve the aesthetic outcome in cranial surgery with precision fitting for a better quality of life. Two custom cranial implants (bulk and porous) are digitally designed based on the Digital Imaging and Communications in Medicine files and fabricated using additive manufacturing. Initially, the defective skull model and the implant were fabricated using fused deposition modeling for the purpose of dimensional validation. Subsequently, the implant was fabricated using titanium alloy (Ti6Al4V extra low interstitial) by electron beam melting technology. The electron beam melting-produced body diagonal node structure incorporated in cranial implant was evaluated based on its mechanical strength and structural characterization. The results show that the electron beam melting-produced porous cranial implants provide the necessary framework for the bone cells to grow into the pores and mimic the architecture and mechanical properties closer to the region of implantation. Scanning electron microscope and micro-computed tomography scanning confirm that the produced porous implants have a highly regular pattern of porous structure with a fully interconnected network channel without any internal defect and voids. The physical properties of the titanium porous structure, containing the compressive strength of 61.5 MPa and modulus of elasticity being 1.20 GPa, represent a promising means of reducing stiffness and stress-shielding effect on the surrounding bone. This study reveals that the use of porous structure in cranial reconstruction satisfies the need of lighter implants with an adequate mechanical strength and structural characteristics, thus restoring better functionality and aesthetic outcomes for the patients.

Self-consistent average-atom scheme for electronic structure of hot and dense plasmas of mixture.

PubMed

Yuan, Jianmin

2002-10-01

An average-atom model is proposed to treat the electronic structures of hot and dense plasmas of mixture. It is assumed that the electron density consists of two parts. The first one is a uniform distribution with a constant value, which is equal to the electron density at the boundaries between the atoms. The second one is the total electron density minus the first constant distribution. The volume of each kind of atom is proportional to the sum of the charges of the second electron part and of the nucleus within each atomic sphere. By this way, one can make sure that electrical neutrality is satisfied within each atomic sphere. Because the integration of the electron charge within each atom needs the size of that atom in advance, the calculation is carried out in a usual self-consistent way. The occupation numbers of electron on the orbitals of each kind of atom are determined by the Fermi-Dirac distribution with the same chemical potential for all kinds of atoms. The wave functions and the orbital energies are calculated with the Dirac-Slater equations. As examples, the electronic structures of the mixture of Au and Cd, water (H2O), and CO2 at a few temperatures and densities are presented.

Advances in Structural Biology and the Application to Biological Filament Systems.

PubMed

Popp, David; Koh, Fujiet; Scipion, Clement P M; Ghoshdastider, Umesh; Narita, Akihiro; Holmes, Kenneth C; Robinson, Robert C

2018-04-01

Structural biology has experienced several transformative technological advances in recent years. These include: development of extremely bright X-ray sources (microfocus synchrotron beamlines and free electron lasers) and the use of electrons to extend protein crystallography to ever decreasing crystal sizes; and an increase in the resolution attainable by cryo-electron microscopy. Here we discuss the use of these techniques in general terms and highlight their application for biological filament systems, an area that is severely underrepresented in atomic resolution structures. We assemble a model of a capped tropomyosin-actin minifilament to demonstrate the utility of combining structures determined by different techniques. Finally, we survey the methods that attempt to transform high resolution structural biology into more physiological environments, such as the cell. Together these techniques promise a compelling decade for structural biology and, more importantly, they will provide exciting discoveries in understanding the designs and purposes of biological machines. © 2018 The Authors. BioEssays Published by WILEY Periodicals, Inc.

Structural and electronic features of binary Li2S-P2S5 glasses

PubMed Central

Ohara, Koji; Mitsui, Akio; Mori, Masahiro; Onodera, Yohei; Shiotani, Shinya; Koyama, Yukinori; Orikasa, Yuki; Murakami, Miwa; Shimoda, Keiji; Mori, Kazuhiro; Fukunaga, Toshiharu; Arai, Hajime; Uchimoto, Yoshiharu; Ogumi, Zempachi

2016-01-01

The atomic and electronic structures of binary Li2S-P2S5 glasses used as solid electrolytes are modeled by a combination of density functional theory (DFT) and reverse Monte Carlo (RMC) simulation using synchrotron X-ray diffraction, neutron diffraction, and Raman spectroscopy data. The ratio of PSx polyhedral anions based on the Raman spectroscopic results is reflected in the glassy structures of the 67Li2S-33P2S5, 70Li2S-30P2S5, and 75Li2S-25P2S5 glasses, and the plausible structures represent the lithium ion distributions around them. It is found that the edge sharing between PSx and LiSy polyhedra increases at a high Li2S content, and the free volume around PSx polyhedra decreases. It is conjectured that Li+ ions around the face of PSx polyhedra are clearly affected by the polarization of anions. The electronic structure of the DFT/RMC model suggests that the electron transfer between the P ion and the bridging sulfur (BS) ion weakens the positive charge of the P ion in the P2S7 anions. The P2S7 anions of the weak electrostatic repulsion would causes it to more strongly attract Li+ ions than the PS4 and P2S6 anions, and suppress the lithium ionic conduction. Thus, the control of the edge sharing between PSx and LiSy polyhedra without the electron transfer between the P ion and the BS ion is expected to facilitate lithium ionic conduction in the above solid electrolytes. PMID:26892385

High-Performance First-Principles Molecular Dynamics for Predictive Theory and Modeling

DOE Office of Scientific and Technical Information (OSTI.GOV)

Gygi, Francois; Galli, Giulia; Schwegler, Eric

This project focused on developing high-performance software tools for First-Principles Molecular Dynamics (FPMD) simulations, and applying them in investigations of materials relevant to energy conversion processes. FPMD is an atomistic simulation method that combines a quantum-mechanical description of electronic structure with the statistical description provided by molecular dynamics (MD) simulations. This reliance on fundamental principles allows FPMD simulations to provide a consistent description of structural, dynamical and electronic properties of a material. This is particularly useful in systems for which reliable empirical models are lacking. FPMD simulations are increasingly used as a predictive tool for applications such as batteries, solarmore » energy conversion, light-emitting devices, electro-chemical energy conversion devices and other materials. During the course of the project, several new features were developed and added to the open-source Qbox FPMD code. The code was further optimized for scalable operation of large-scale, Leadership-Class DOE computers. When combined with Many-Body Perturbation Theory (MBPT) calculations, this infrastructure was used to investigate structural and electronic properties of liquid water, ice, aqueous solutions, nanoparticles and solid-liquid interfaces. Computing both ionic trajectories and electronic structure in a consistent manner enabled the simulation of several spectroscopic properties, such as Raman spectra, infrared spectra, and sum-frequency generation spectra. The accuracy of the approximations used allowed for direct comparisons of results with experimental data such as optical spectra, X-ray and neutron diffraction spectra. The software infrastructure developed in this project, as applied to various investigations of solids, liquids and interfaces, demonstrates that FPMD simulations can provide a detailed, atomic-scale picture of structural, vibrational and electronic properties of complex systems relevant to energy conversion devices.« less

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

NASA Astrophysics Data System (ADS)

Ding, Feizhi

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

Inner reorganization limiting electron transfer controlled hydrogen bonding: intra- vs. intermolecular effects.

PubMed

Martínez-González, Eduardo; Frontana, Carlos

2014-05-07

In this work, experimental evidence of the influence of the electron transfer kinetics during electron transfer controlled hydrogen bonding between anion radicals of metronidazole and ornidazole, derivatives of 5-nitro-imidazole, and 1,3-diethylurea as the hydrogen bond donor, is presented. Analysis of the variations of voltammetric EpIcvs. log KB[DH], where KB is the binding constant, allowed us to determine the values of the binding constant and also the electron transfer rate k, confirmed by experiments obtained at different scan rates. Electronic structure calculations at the BHandHLYP/6-311++G(2d,2p) level for metronidazole, including the solvent effect by the Cramer/Truhlar model, suggested that the minimum energy conformer is stabilized by intramolecular hydrogen bonding. In this structure, the inner reorganization energy, λi,j, contributes significantly (0.5 eV) to the total reorganization energy of electron transfer, thus leading to a diminishment of the experimental k.

The atmosphere of a dirty-clathrate cometary nucleus - A two-phase, multifluid model

NASA Astrophysics Data System (ADS)

Marconi, M. L.; Mendis, D. A.

1983-10-01

The dynamical and thermal structure of a dirty-clathrate cometary nucleus' gas atmosphere is presently given a self-consistent, transonic multifluid solution in which, although the heavy neutron and ion species are treated as a single fluid in the collision-dominated region, the photoproduced H is treated separately. The thermal profile of the atmosphere thus obtained is entirely different from those predicted by the earlier, single-fluid models as well as the multifluid models which assumed equipartition of energy between electrons and ions. While the electron gas, like the neutrals and the ions, cools due to expansion, its main mode of energy loss in the inner coma is by way of inelastic collisions with the predominant H2O molecule. The high electron temperature in the outer coma also decreases the efficiency of electron removal by dissociative recombination, thereby increasing electron density throughout the coma.

Structure determination of Ba5AlF13 by coupling electron, synchrotron and neutron powder diffraction, solid-state NMR and ab initio calculations.

PubMed

Martineau, Charlotte; Allix, Mathieu; Suchomel, Matthew R; Porcher, Florence; Vivet, François; Legein, Christophe; Body, Monique; Massiot, Dominique; Taulelle, Francis; Fayon, Franck

2016-10-04

The room temperature structure of Ba 5 AlF 13 has been investigated by coupling electron, synchrotron and neutron powder diffraction, solid-state high-resolution NMR ( 19 F and 27 Al) and first principles calculations. An initial structural model has been obtained from electron and synchrotron powder diffraction data, and its main features have been confirmed by one- and two-dimensional NMR measurements. However, DFT GIPAW calculations of the 19 F isotropic shieldings revealed an inaccurate location of one fluorine site (F3, site 8a), which exhibited unusual long F-Ba distances. The atomic arrangement was reinvestigated using neutron powder diffraction data. Subsequent Fourier maps showed that this fluorine atom occupies a crystallographic site of lower symmetry (32e) with partial occupancy (25%). GIPAW computations of the NMR parameters validate the refined structural model, ruling out the presence of local static disorder and indicating that the partial occupancy of this F site reflects a local motional process. Visualisation of the dynamic process was then obtained from the Rietveld refinement of neutron diffraction data using an anharmonic description of the displacement parameters to account for the thermal motion of the mobile fluorine. The whole ensemble of powder diffraction and NMR data, coupled with first principles calculations, allowed drawing an accurate structural model of Ba 5 AlF 13 , including site-specific dynamical disorder in the fluorine sub-network.

Study of electronic structure of liquid Pb

NASA Astrophysics Data System (ADS)

Vora, A. M.; Gajjar, P. N.

2018-04-01

The Fiolhais et al.'s universal model potential in conjunction with the hard sphere technique of Percus and Yevick has been used for the study of electronic structure, Fermi energy and density of states of liquid Pb. The screening influence of the different forms of the local field correction functions proposed by Hartree (H) and Taylor (T) on the afore said properties is studied, which replicates the changing effects of screening and found suitable for the present study.

Non-destructive detection of cross-sectional strain and defect structure in an individual Ag five-fold twinned nanowire by 3D electron diffraction mapping.

PubMed

Fu, Xin; Yuan, Jun

2017-07-24

Coherent x-ray diffraction investigations on Ag five-fold twinned nanowires (FTNWs) have drawn controversial conclusions concerning whether the intrinsic 7.35° angular gap could be compensated homogeneously through phase transformation or inhomogeneously by forming disclination strain field. In those studies, the x-ray techniques only provided an ensemble average of the structural information from all the Ag nanowires. Here, using three-dimensional (3D) electron diffraction mapping approach, we non-destructively explore the cross-sectional strain and the related strain-relief defect structures of an individual Ag FTNW with diameter about 30 nm. The quantitative analysis of the fine structure of intensity distribution combining with kinematic electron diffraction simulation confirms that for such a Ag FTNW, the intrinsic 7.35° angular deficiency results in an inhomogeneous strain field within each single crystalline segment consistent with the disclination model of stress-relief. Moreover, the five crystalline segments are found to be strained differently. Modeling analysis in combination with system energy calculation further indicates that the elastic strain energy within some crystalline segments, could be partially relieved by the creation of stacking fault layers near the twin boundaries. Our study demonstrates that 3D electron diffraction mapping is a powerful tool for the cross-sectional strain analysis of complex 1D nanostructures.

Solution to the Boltzmann equation for layered systems for current perpendicular to the planes

DOE Office of Scientific and Technical Information (OSTI.GOV)

Butler, W. H.; Zhang, X.-G.; MacLaren, J. M.

2000-05-01

Present theories of giant magnetoresistance (GMR) for current perpendicular to the planes (CPP) are based on an extremely restricted solution to the Boltzmann equation that assumes a single free electron band structure for all layers and all spin channels. Within this model only the scattering rate changes from one layer to the next. This model leads to the remarkable result that the resistance of a layered material is simply the sum of the resistances of each layer. We present a solution to the Boltzmann equation for CPP for the case in which the electronic structure can be different for differentmore » layers. The problem of matching boundary conditions between layers is much more complicated than in the current in the planes (CIP) geometry because it is necessary to include the scattering-in term of the Boltzmann equation even for the case of isotropic scattering. This term couples different values of the momentum parallel to the planes. When the electronic structure is different in different layers there is an interface resistance even in the absence of intermixing of the layers. The size of this interface resistance is affected by the electronic structure, scattering rates, and thicknesses of nearby layers. For Co-Cu, the calculated interface resistance and its spin asymmetry is comparable to that measured at low temperature in sputtered samples. (c) 2000 American Institute of Physics.« less

Developing sensor activity relationships for the JPL electronic nose sensors using molecular modeling and QSAR techniques

NASA Technical Reports Server (NTRS)

Shevade, A. V.; Ryan, M. A.; Homer, M. L.; Jewell, A. D.; Zhou, H.; Manatt, K.; Kisor, A. K.

2005-01-01

We report a Quantitative Structure-Activity Relationships (QSAR) study using Genetic Function Approximations (GFA) to describe the polymer-carbon composite sensor activities in the JPL Electronic Nose, when exposed to chemical vapors at parts-per-million concentration levels.

Model for intensity calculation in electron guns

NASA Astrophysics Data System (ADS)

Doyen, O.; De Conto, J. M.; Garnier, J. P.; Lefort, M.; Richard, N.

2007-04-01

The calculation of the current in an electron gun structure is one of the main investigations involved in the electron gun physics understanding. In particular, various simulation codes exist but often present some important discrepancies with experiments. Moreover, those differences cannot be reduced because of the lack of physical information in these codes. We present a simple physical three-dimensional model, valid for all kinds of gun geometries. This model presents a better precision than all the other simulation codes and models encountered and allows the real understanding of the electron gun physics. It is based only on the calculation of the Laplace electric field at the cathode, the use of the classical Child-Langmuir's current density, and a geometrical correction to this law. Finally, the intensity versus voltage characteristic curve can be precisely described with only a few physical parameters. Indeed, we have showed that only the shape of the electric field at the cathode without beam, and a distance of an equivalent infinite planar diode gap, govern mainly the electron gun current generation.

Investigating molecule-semiconductor interfaces with nonlinear spectroscopies

NASA Astrophysics Data System (ADS)

Giokas, Paul George

Knowledge of electronic structures and transport mechanisms at molecule-semiconductor interfaces is motivated by their ubiquity in photoelectrochemical cells. In this dissertation, optical spectroscopies are used uncover the influence of electronic coupling, coherent vibrational motion, and molecular geometry, and other factors on dynamics initiated by light absorption at such interfaces. These are explored for a family of ruthenium bipyridyl chromophores bound to titanium dioxide. Transient absorption measurements show molecular singlet state electron injection in 100 fs or less. Resonance Raman intensity analysis suggests the electronic excitations possess very little charge transfer character. The connections drawn in this work between molecular structure and photophysical behavior contribute to the general understanding of photoelectrochemical cells. Knowledge of binding geometry in nanocrystalline films is challenged by heterogeneity of semiconductor surfaces. Polarized resonance Raman spectroscopy is used to characterize the ruthenium chromophore family on single crystal titanium dioxide . Chromophores display a broad distribution of molecular geometries at the interface, with increased variation in binding angle due to the presence of a methylene bridge, as well as additional phosphonate anchors. This result implies multiple binding configurations for chromophores which incorporate multiple phosphonate ligands, and indicates the need for careful consideration when developing surface-assembled chromophore-catalyst cells. Electron transfer transitions occurring on the 100 fs time scale challenge conventional second-order approximations made when modeling these reactions. A fourth-order perturbative model which includes the relationship between coincident electron transfer and nuclear relaxation processes is presented. Insights provided by the model are illustrated for a two-level donor molecule. The presented fourth-order rate formula constitutes a rigorous and intuitive framework for understanding sub-picosecond photoinduced electron transfer dynamics. Charge transfer systems fit by this model include catechol-sensitized titanium dioxide nanoparticles and a closely-related molecular complex. These systems exhibit vibrational coherence coincident with back-electron transfer in the first picosecond after excitation, which suggests that intramolecular nuclear motion strongly influences the electronic transfer process and plays an important role in the dynamics of interfacial systems following light absorption.

Spin fluctuations and superconductivity in a 3D tight-binding model for BaFe2As2

DOE Office of Scientific and Technical Information (OSTI.GOV)

Graser, Siegfried; Kemper, Alexander F; Maier, Thomas A

2010-01-01

Despite the wealth of experimental data on the Fe-pnictide compounds of the KFe2As2 type, K=Ba, Ca, or Sr, the main theoretical work based on multiorbital tight-binding models has been restricted so far to the study of the related 1111 compounds. This can be ascribed to the more three-dimensional electronic structure found by ab initio calculations for the 122 materials, making this system less amenable to model development. In addition, the more complicated Brillouin zone BZ of the body-centered tetragonal symmetry does not allow a straightforward unfolding of the electronic band structure into an effective 1Fe/unit cell BZ. Here we presentmore » an effective five-orbital tight-binding fit of the full density functional theory band structure for BaFe2As2 including the kz dispersions. We compare the five-orbital spin fluctuation model to one previously studied for LaOFeAs and calculate the random-phase approximation enhanced susceptibility. Using the fluctuation ex- change approximation to determine the leading pairing instability, we then examine the differences between a strictly two-dimensional model calculation over a single kz cut of the BZ and a completely three-dimensional approach. We find pairing states quite similar to the 1111 materials, with generic quasi-isotropic pairing on the hole sheets and nodal states on the electron sheets at kz=0, which however are gapped as the system is hole doped. On the other hand, a substantial kz dependence of the order parameter remains, with most of the pairing strength deriving from processes near kz=?. These states exhibit a tendency for an enhanced anisotropy on the hole sheets and a reduced anisotropy on the electron sheets near the top of the BZ.« less

The role of amino acid electron-donor/acceptor atoms in host-cell binding peptides is associated with their 3D structure and HLA-binding capacity in sterile malarial immunity induction

DOE Office of Scientific and Technical Information (OSTI.GOV)

Patarroyo, Manuel E., E-mail: mepatarr@mail.com; Universidad Nacional de Colombia, Bogota; Almonacid, Hannia

Highlights: Black-Right-Pointing-Pointer Fundamental residues located in some HABPs are associated with their 3D structure. Black-Right-Pointing-Pointer Electron-donor atoms present in {beta}-turn, random, distorted {alpha}-helix structures. Black-Right-Pointing-Pointer Electron-donor atoms bound to HLA-DR53. Black-Right-Pointing-Pointer Electron-acceptor atoms present in regular {alpha}-helix structure bound to HLA-DR52. -- Abstract: Plasmodium falciparum malaria continues being one of the parasitic diseases causing the highest worldwide mortality due to the parasite's multiple evasion mechanisms, such as immunological silence. Membrane and organelle proteins are used during invasion for interactions mediated by high binding ability peptides (HABPs); these have amino acids which establish hydrogen bonds between them in some of theirmore » critical binding residues. Immunisation assays in the Aotus model using HABPs whose critical residues had been modified have revealed a conformational change thereby enabling a protection-inducing response. This has improved fitting within HLA-DR{beta}1{sup Asterisk-Operator} molecules where amino acid electron-donor atoms present in {beta}-turn, random or distorted {alpha}-helix structures preferentially bound to HLA-DR53 molecules, whilst HABPs having amino acid electron-acceptor atoms present in regular {alpha}-helix structure bound to HLA-DR52. This data has great implications for vaccine development.« less

Structural and electronic engineering of 3DOM WO3 by alkali metal doping for improved NO2 sensing performance

NASA Astrophysics Data System (ADS)

Wang, Zhihua; Fan, Xiaoxiao; Han, Dongmei; Gu, Fubo

2016-05-01

Novel alkali metal doped 3DOM WO3 materials were prepared using a simple colloidal crystal template method. Raman, XRD, SEM, TEM, XPS, PL, Hall and UV-Vis techniques were used to characterize the structural and electronic properties of all the products, while the corresponding sensing performances targeting ppb level NO2 were determined at different working temperatures. For the overall goal of structural and electronic engineering, the co-effect of structural and electronic properties on the improved NO2 sensing performance of alkali metal doped 3DOM WO3 was studied. The test results showed that the gas sensing properties of 3DOM WO3/Li improved the most, with the fast response-recovery time and excellent selectivity. More importantly, the response of 3DOM WO3/Li to 500 ppb NO2 was up to 55 at room temperature (25 °C). The especially high response to ppb level NO2 at room temperature (25 °C) in this work has a very important practical significance. The best sensing performance of 3DOM WO3/Li could be ascribed to the most structure defects and the highest carrier mobility. And the possible gas sensing mechanism based on the model of the depletion layer was proposed to demonstrate that both structural and electronic properties are responsible for the NO2 sensing behavior.Novel alkali metal doped 3DOM WO3 materials were prepared using a simple colloidal crystal template method. Raman, XRD, SEM, TEM, XPS, PL, Hall and UV-Vis techniques were used to characterize the structural and electronic properties of all the products, while the corresponding sensing performances targeting ppb level NO2 were determined at different working temperatures. For the overall goal of structural and electronic engineering, the co-effect of structural and electronic properties on the improved NO2 sensing performance of alkali metal doped 3DOM WO3 was studied. The test results showed that the gas sensing properties of 3DOM WO3/Li improved the most, with the fast response-recovery time and excellent selectivity. More importantly, the response of 3DOM WO3/Li to 500 ppb NO2 was up to 55 at room temperature (25 °C). The especially high response to ppb level NO2 at room temperature (25 °C) in this work has a very important practical significance. The best sensing performance of 3DOM WO3/Li could be ascribed to the most structure defects and the highest carrier mobility. And the possible gas sensing mechanism based on the model of the depletion layer was proposed to demonstrate that both structural and electronic properties are responsible for the NO2 sensing behavior. Electronic supplementary information (ESI) available: Raman, SEM, TEM, mapping, XPS and PL images; transient plot; response of 3DOM WO3/Li to NO2 concentration, sensing stability and the corresponding log (Sg - 1) versus log Cg curves. See DOI: 10.1039/c6nr00858e

The Jupiter ONERA Electron (JOE) and Jupiter ONERA Proton (JOP) specification models

NASA Astrophysics Data System (ADS)

Bourdarie, S.; Sicard-Piet, A.

2008-09-01

The use of recent improvement in the understanding of the Jovian radiation belt structure has allowed to develop a more accurate engineering model of the Jovian electron and proton radiation belts. The basic idea was to combine the results of the Salammbô code when available (for proton and electron species) with the Divine and Garret model 1983 and/or with GIRE. The advantage of such an approach was that the resulting model is global in term of spatial and energy coverage, is optimised inside Europa orbit (the Divine and Garret model is not accurate inside Io orbit due to poor in-situ data there - note that inside Io is the region where ionizing radiation fluxes are maximum) and take advantage of the two models. The resulting JOE-JOP models will be presented, pro and cons will be listed and commented. Finally future plans to upgrade these models will be given.

Using the Job Burden-Capital Model of Occupational Stress to Predict Depression and Well-Being among Electronic Manufacturing Service Employees in China

PubMed Central

Wang, Chao; Li, Shuang; Li, Tao; Yu, Shanfa; Dai, Junming; Liu, Xiaoman; Zhu, Xiaojun; Ji, Yuqing; Wang, Jin

2016-01-01

Background: This study aimed to identify the association between occupational stress and depression-well-being by proposing a comprehensive and flexible job burden-capital model with its corresponding hypotheses. Methods: For this research, 1618 valid samples were gathered from the electronic manufacturing service industry in Hunan Province, China; self-rated questionnaires were administered to participants for data collection after obtaining their written consent. The proposed model was fitted and tested through structural equation model analysis. Results: Single-factor correlation analysis results indicated that coefficients between all items and dimensions had statistical significance. The final model demonstrated satisfactory global goodness of fit (CMIN/DF = 5.37, AGFI = 0.915, NNFI = 0.945, IFI = 0.952, RMSEA = 0.052). Both the measurement and structural models showed acceptable path loadings. Job burden and capital were directly associated with depression and well-being or indirectly related to them through personality. Multi-group structural equation model analyses indicated general applicability of the proposed model to basic features of such a population. Gender, marriage and education led to differences in the relation between occupational stress and health outcomes. Conclusions: The job burden-capital model of occupational stress-depression and well-being was found to be more systematic and comprehensive than previous models. PMID:27529267

Using the Job Burden-Capital Model of Occupational Stress to Predict Depression and Well-Being among Electronic Manufacturing Service Employees in China.

PubMed

Wang, Chao; Li, Shuang; Li, Tao; Yu, Shanfa; Dai, Junming; Liu, Xiaoman; Zhu, Xiaojun; Ji, Yuqing; Wang, Jin

2016-08-12

This study aimed to identify the association between occupational stress and depression-well-being by proposing a comprehensive and flexible job burden-capital model with its corresponding hypotheses. For this research, 1618 valid samples were gathered from the electronic manufacturing service industry in Hunan Province, China; self-rated questionnaires were administered to participants for data collection after obtaining their written consent. The proposed model was fitted and tested through structural equation model analysis. Single-factor correlation analysis results indicated that coefficients between all items and dimensions had statistical significance. The final model demonstrated satisfactory global goodness of fit (CMIN/DF = 5.37, AGFI = 0.915, NNFI = 0.945, IFI = 0.952, RMSEA = 0.052). Both the measurement and structural models showed acceptable path loadings. Job burden and capital were directly associated with depression and well-being or indirectly related to them through personality. Multi-group structural equation model analyses indicated general applicability of the proposed model to basic features of such a population. Gender, marriage and education led to differences in the relation between occupational stress and health outcomes. The job burden-capital model of occupational stress-depression and well-being was found to be more systematic and comprehensive than previous models.

Magnetospheric electrons

NASA Technical Reports Server (NTRS)

Coroniti, F. V.; Thorne, R. M.

1972-01-01

Coupling of source, transport, and sink processes produces a fairly accurate model for the macroscopic structure and dynamics of magnetospheric electrons. Auroral electrons are controlled by convective transport from a plasma sheet source coupled with a precipitation loss due to whistler and electrostatic plasma turbulence. Outer and inner zone electrons are governed by radial diffusion transport from convection and acceleration sources external to the plasmapause and by parasitic precipitation losses arising from cyclotron and Landau interactions with whistler and ion cyclotron turbulence.

Temperature-dependent band structure of SrTiO3 interfaces

NASA Astrophysics Data System (ADS)

Raslan, Amany; Lafleur, Patrick; Atkinson, W. A.

2017-02-01

We build a theoretical model for the electronic properties of the two-dimensional (2D) electron gas that forms at the interface between insulating SrTiO3 and a number of polar cap layers, including LaTiO3, LaAlO3, and GdTiO3. The model treats conduction electrons within a tight-binding approximation and the dielectric polarization via a Landau-Devonshire free energy that incorporates strontium titanate's strongly nonlinear, nonlocal, and temperature-dependent dielectric response. The self-consistent band structure comprises a mix of quantum 2D states that are tightly bound to the interface and quasi-three-dimensional (3D) states that extend hundreds of unit cells into the SrTiO3 substrate. We find that there is a substantial shift of electrons away from the interface into the 3D tails as temperature is lowered from 300 K to 10 K. This shift is least important at high electron densities (˜1014cm-2 ) but becomes substantial at low densities; for example, the total electron density within 4 nm of the interface changes by a factor of two for 2D electron densities ˜1013cm-2 . We speculate that the quasi-3D tails form the low-density high-mobility component of the interfacial electron gas that is widely inferred from magnetoresistance measurements.

Topology of the electron density of d0 transition metal compounds at subatomic resolution.

PubMed

Batke, Kilian; Eickerling, Georg

2013-11-14

Accurate X-ray diffraction experiments allow for a reconstruction of the electron density distribution of solids and molecules in a crystal. The basis for the reconstruction of the electron density is in many cases a multipolar expansion of the X-ray scattering factors in terms of spherical harmonics, a so-called multipolar model. This commonly used ansatz splits the total electron density of each pseudoatom in the crystal into (i) a spherical core, (ii) a spherical valence, and (iii) a nonspherical valence contribution. Previous studies, for example, on diamond and α-silicon have already shown that this approximation is no longer valid when ultrahigh-resolution diffraction data is taken into account. We report here the results of an analysis of the calculated electron density distribution in the d(0) transition metal compounds [TMCH3](2+) (TM = Sc, Y, and La) at subatomic resolution. By a detailed molecular orbital analysis, it is demonstrated that due to the radial nodal structure of the 3d, 4d, and 5d orbitals involved in the TM-C bond formation a significant polarization of the electron density in the inner electronic shells of the TM atoms is observed. We further show that these polarizations have to be taken into account by an extended multipolar model in order to recover accurate electron density distributions from high-resolution structure factors calculated for the title compounds.

T-gate geometric (solution for submicrometer gate length) HEMT: Physical analysis, modeling and implementation as parasitic elements and its usage as dual gate for variable gain amplifiers

NASA Astrophysics Data System (ADS)

Gupta, Ritesh; Rathi, Servin; Kaur, Ravneet; Gupta, Mridula; Gupta, R. S.

2009-03-01

In order to achieve superior RF performance, short gate length is required for the compound semiconductor field effect transistors, but the limitation in lithography for submicrometer gate lengths leads to the formation of various metal-insulator geometries like T-gate [Sandeep R. Bahl, Jesus A. del Alamo, Physics of breakdown in InAlAs/ n +-InGaAs heterostructure field-effect transistors, IEEE Trans. Electron Devices 41 (12) (1994) 2268-2275]. These geometries are the combination of various Metal-Semiconductor (MS)/Metal-Air-Semiconductor (MAS) contacts. Moreover, field plates [S. Karmalkar, M.S. Shur, G. Simin, M. Asif Khan, Field-plate engineering for HFETs, IEEE Trans. Electron Devices 52 (2005) 2534-2540] are also being fabricated these days, mainly at the drain end ( Γ-gate) having Metal-Insulator-Semiconductor (MIS) instead of MAS contact with the intention of increasing the breakdown voltage of the device. To realize the effect of upper gate electrode in the T-gate structure and field plates, an analytical model has been proposed in the present article by dividing the whole structure into MS/MIS contact regions, applying current continuity among them and solving iteratively. The model proposed for Metal-Insulator Semiconductor High Electron Mobility Transistor (MISHEMT) [R. Gupta, S.K. Aggarwal, M. Gupta, R.S. Gupta, Analytical model for metal insulator semiconductor high electron mobility transistor (MISHEMT) for its high frequency and high power applications, J. Semicond. Technol. Sci. 6 (3) (2006) 189-198], is equally applicable to High Electron Mobility Transistors (HEMT) and has been used to formulate this model. In this paper, various structures and geometries have been compared to anticipate the need of T-gate modeling. The effect of MIS contacts has been implemented as parasitic resistance and capacitance and has also been studied to control the middle conventional gate as in dual gate technology by applying separate voltages across it. The results obtained using the proposed analytical scheme has been compared with simulated and experimental results, to prove the validity of our model.

Small amplitude Kinetic Alfven waves in a superthermal electron-positron-ion plasma

NASA Astrophysics Data System (ADS)

Adnan, Muhammad; Mahmood, Sahahzad; Qamar, Anisa; Tribeche, Mouloud

2016-11-01

We are investigating the propagating properties of coupled Kinetic Alfven-acoustic waves in a low beta plasma having superthermal electrons and positrons. Using the standard reductive perturbation method, a nonlinear Korteweg-de Vries (KdV) type equation is derived which describes the evolution of Kinetic Alfven waves. It is found that nonlinearity and Larmor radius effects can compromise and give rise to solitary structures. The parametric role of superthermality and positron content on the characteristics of solitary wave structures is also investigated. It is found that only sub-Alfvenic and compressive solitons are supported in the present model. The present study may find applications in a low β electron-positron-ion plasma having superthermal electrons and positrons.

Landau-level spectroscopy of massive Dirac fermions in single-crystalline ZrTe5 thin flakes

NASA Astrophysics Data System (ADS)

Jiang, Y.; Dun, Z. L.; Zhou, H. D.; Lu, Z.; Chen, K.-W.; Moon, S.; Besara, T.; Siegrist, T. M.; Baumbach, R. E.; Smirnov, D.; Jiang, Z.

2017-07-01

We report infrared magnetospectroscopy studies on thin crystals of an emerging Dirac material ZrTe5 near the intrinsic limit. The observed structure of the Landau-level transitions and zero-field infrared absorption indicate a two-dimensional Dirac-like electronic structure, similar to that in graphene but with a small relativistic mass corresponding to a 9.4-meV energy gap. Measurements with circularly polarized light reveal a significant electron-hole asymmetry, which leads to splitting of the Landau-level transitions at high magnetic fields. Our model, based on the Bernevig-Hughes-Zhang effective Hamiltonian, quantitatively explains all observed transitions, determining the values of the Fermi velocity, Dirac mass (or gap), electron-hole asymmetry, and electron and hole g factors.

Amyloid Structure and Assembly: Insights from Scanning Transmission Electron Microscopy

PubMed Central

Goldsbury, Claire; Baxa, Ulrich; Simon, Martha N.; Steven, Alasdair C.; Engel, Andreas; Wall, Joseph S.; Aebi, Ueli; Müller, Shirley A.

2010-01-01

Amyloid fibrils are filamentous protein aggregates implicated in several common diseases like Alzheimer’s disease and type II diabetes. Similar structures are also the molecular principle of the infectious spongiform encephalopathies like Creutzfeldt-Jakob disease in humans, scrapie in sheep, and of the so-called yeast prions, inherited non-chromosomal elements found in yeast and fungi. Scanning transmission electron microscopy (STEM) is often used to delineate the assembly mechanism and structural properties of amyloid aggregates. In this review we consider specifically contributions and limitations of STEM for the investigation of amyloid assembly pathways, fibril polymorphisms and structural models of amyloid fibrils. This type of microscopy provides the only method to directly measure the mass-per-length (MPL) of individual filaments. Made on both in vitro assembled and ex vivo samples, STEM mass measurements have illuminated the hierarchical relationships between amyloid fibrils and revealed that polymorphic fibrils and various globular oligomers can assemble simultaneously from a single polypeptide. The MPLs also impose strong constraints on possible packing schemes, assisting in molecular model building when combined with high-resolution methods like solid-state nuclear magnetic resonance (NMR) and electron paramagnetic resonance (EPR). PMID:20868754

The Effect of Electronic Structure on the Phases Present in High Entropy Alloys

PubMed Central

Leong, Zhaoyuan; Wróbel, Jan S.; Dudarev, Sergei L.; Goodall, Russell; Todd, Iain; Nguyen-Manh, Duc

2017-01-01

Multicomponent systems, termed High Entropy Alloys (HEAs), with predominantly single solid solution phases are a current area of focus in alloy development. Although different empirical rules have been introduced to understand phase formation and determine what the dominant phases may be in these systems, experimental investigation has revealed that in many cases their structure is not a single solid solution phase, and that the rules may not accurately distinguish the stability of the phase boundaries. Here, a combined modelling and experimental approach that looks into the electronic structure is proposed to improve accuracy of the predictions of the majority phase. To do this, the Rigid Band model is generalised for magnetic systems in prediction of the majority phase most likely to be found. Good agreement is found when the predictions are confronted with data from experiments, including a new magnetic HEA system (CoFeNiV). This also includes predicting the structural transition with varying levels of constituent elements, as a function of the valence electron concentration, n, obtained from the integrated spin-polarised density of states. This method is suitable as a new predictive technique to identify compositions for further screening, in particular for magnetic HEAs. PMID:28059106

The Effect of Electronic Structure on the Phases Present in High Entropy Alloys.

PubMed

Leong, Zhaoyuan; Wróbel, Jan S; Dudarev, Sergei L; Goodall, Russell; Todd, Iain; Nguyen-Manh, Duc

2017-01-06

Multicomponent systems, termed High Entropy Alloys (HEAs), with predominantly single solid solution phases are a current area of focus in alloy development. Although different empirical rules have been introduced to understand phase formation and determine what the dominant phases may be in these systems, experimental investigation has revealed that in many cases their structure is not a single solid solution phase, and that the rules may not accurately distinguish the stability of the phase boundaries. Here, a combined modelling and experimental approach that looks into the electronic structure is proposed to improve accuracy of the predictions of the majority phase. To do this, the Rigid Band model is generalised for magnetic systems in prediction of the majority phase most likely to be found. Good agreement is found when the predictions are confronted with data from experiments, including a new magnetic HEA system (CoFeNiV). This also includes predicting the structural transition with varying levels of constituent elements, as a function of the valence electron concentration, n, obtained from the integrated spin-polarised density of states. This method is suitable as a new predictive technique to identify compositions for further screening, in particular for magnetic HEAs.

Atomic structures of B20 FeGe thin films grown on the Si(111) surface

NASA Astrophysics Data System (ADS)

Kim, Wondong; Noh, Seungkyun; Yoon, Jisoo; Kim, Young Heon; Lee, Inho; Kim, Jae-Sung; Hwang, Chanyong

We investigated the growth and atomic structures of FeGe thin films on the Si (111) surface by using scanning tunneling microscopy (STM) and transmission electron microscopy (TEM). The 2 5nm- thick FeGe thin films were prepared on the clean Si(111) 7x7 surface by co-deposition of Fe and Ge from separated electron-beam evaporators. With direct deposition on the substrate at the temperature above 550 K, the surface of FeGe films was not smooth and consisted of coarse grains. By the combination of room-temperature annealing and post-annealing process around 800 K, the structure of FeGe thin films evolved into the well crystalized structures. Atom-resolved STM images revealed that there are at least four different surface terminations. We constructed atomic models for each surface terminations based on the bulk atomic arrangement of a B20 chiral structure and confirmed that the observed STM images are successfully reproduced by using computational simulations employing Vienna Ab Initio Simulation package (VASP) with a B20 chiral structure model. TEM cross-sectional images also support our atomic models by revealing clearly the characteristic zigzag features of B20 structures of FeGe(111) thin films.

Microgravity

NASA Image and Video Library

2001-06-06

X-rays diffracted from a well-ordered protein crystal create sharp patterns of scattered light on film. A computer can use these patterns to generate a model of a protein molecule. To analyze the selected crystal, an X-ray crystallographer shines X-rays through the crystal. Unlike a single dental X-ray, which produces a shadow image of a tooth, these X-rays have to be taken many times from different angles to produce a pattern from the scattered light, a map of the intensity of the X-rays after they diffract through the crystal. The X-rays bounce off the electron clouds that form the outer structure of each atom. A flawed crystal will yield a blurry pattern; a well-ordered protein crystal yields a series of sharp diffraction patterns. From these patterns, researchers build an electron density map. With powerful computers and a lot of calculations, scientists can use the electron density patterns to determine the structure of the protein and make a computer-generated model of the structure. The models let researchers improve their understanding of how the protein functions. They also allow scientists to look for receptor sites and active areas that control a protein's function and role in the progress of diseases. From there, pharmaceutical researchers can design molecules that fit the active site, much like a key and lock, so that the protein is locked without affecting the rest of the body. This is called structure-based drug design.

Multigrid based First-Principles Molecular Dynamics

DOE Office of Scientific and Technical Information (OSTI.GOV)

Fattebert, Jean-Luc; Osei-Kuffuor, Daniel; Dunn, Ian

2017-06-01

MGmol ls a First-Principles Molecular Dynamics code. It relies on the Born-Oppenheimer approximation and models the electronic structure using Density Functional Theory, either LDA or PBE. Norm-conserving pseudopotentials are used to model atomic cores.

Fine structural features of nanoscale zero-valent iron characterized by spherical aberration corrected scanning transmission electron microscopy (Cs-STEM).

PubMed

Liu, Airong; Zhang, Wei-xian

2014-09-21

An angstrom-resolution physical model of nanoscale zero-valent iron (nZVI) is generated with a combination of spherical aberration corrected scanning transmission electron microscopy (Cs-STEM), selected area electron diffraction (SAED), energy-dispersive X-ray spectroscopy (EDS) and electron energy-loss spectroscopy (EELS) on the Fe L-edge. Bright-field (BF), high-angle annular dark-field (HAADF) and secondary electron (SE) imaging of nZVI acquired by a Hitachi HD-2700 STEM show near atomic resolution images and detailed morphological and structural information of nZVI. The STEM-EDS technique confirms that the fresh nZVI comprises of a metallic iron core encapsulated with a thin layer of iron oxides or oxyhydroxides. SAED patterns of the Fe core suggest the polycrystalline structure in the metallic core and amorphous nature of the oxide layer. Furthermore, Fe L-edge of EELS shows varied structural features from the innermost Fe core to the outer oxide shell. A qualitative analysis of the Fe L(2,3) edge fine structures reveals that the shell of nZVI consists of a mixed Fe(II)/Fe(III) phase close to the Fe (0) interface and a predominantly Fe(III) at the outer surface of nZVI.

Phase-space perspective on the wavelength-dependent electron correlation of strong-field double ionization of Xe

NASA Astrophysics Data System (ADS)

Shao, Yun; Yuan, Zongqiang; Ye, Difa; Fu, Libin; Liu, Ming-Ming; Sun, Xufei; Wu, Chengyin; Liu, Jie; Gong, Qihuang; Liu, Yunquan

2017-12-01

We measure the wavelength-dependent correlated-electron momentum (CEM) spectra of strong-field double ionization of Xe atoms, and observe a significant change from a roughly nonstructured (uncorrelated) pattern at 795 nm to an elongated distribution with V-shaped structure (correlated) at higher wavelengths of 1320 and 1810 nm, pointing to the transition of the ionization dynamics imprinted in the momentum distributions. These observations are well reproduced by a semiclassical model using Green-Sellin-Zachor potential to take into account the screening effect. We show that the momentum distribution of Xe2+ undergoes a bifurcation structure emerging from single-hump to double-hump structure as the laser wavelength increases, which is dramatically different from that of He2+, indicating the complex multi-electron effect. By back analyzing the double ionization trajectories in the phase space (the initial transverse momentum and the laser phase at the tunneling exit) of the first tunneled electrons, we provide deep insight into the physical origin for electron correlation dynamics. We find that a random distribution in phase-space is responsible for a less distinct structured CEM spectrum at shorter wavelength. While increasing the laser wavelength, a topology-invariant pattern in phase-space appears, leading to the clearly visible V-shaped structures.

Iterative model building, structure refinement and density modification with the PHENIX AutoBuild wizard.

PubMed

Terwilliger, Thomas C; Grosse-Kunstleve, Ralf W; Afonine, Pavel V; Moriarty, Nigel W; Zwart, Peter H; Hung, Li Wei; Read, Randy J; Adams, Paul D

2008-01-01

The PHENIX AutoBuild wizard is a highly automated tool for iterative model building, structure refinement and density modification using RESOLVE model building, RESOLVE statistical density modification and phenix.refine structure refinement. Recent advances in the AutoBuild wizard and phenix.refine include automated detection and application of NCS from models as they are built, extensive model-completion algorithms and automated solvent-molecule picking. Model-completion algorithms in the AutoBuild wizard include loop building, crossovers between chains in different models of a structure and side-chain optimization. The AutoBuild wizard has been applied to a set of 48 structures at resolutions ranging from 1.1 to 3.2 A, resulting in a mean R factor of 0.24 and a mean free R factor of 0.29. The R factor of the final model is dependent on the quality of the starting electron density and is relatively independent of resolution.

FAST TRACK COMMUNICATION: Modelling of streamer propagation in atmospheric-pressure helium plasma jets

NASA Astrophysics Data System (ADS)

Naidis, G. V.

2010-10-01

The results of a two-dimensional numerical simulation of positive streamer propagation in atmospheric-pressure helium jets injected into ambient air are presented. It is shown that depending on the jet width and the initial radial distribution of electron number density streamer structures of two types can be formed: one with maxima of electric field and electron density at the jet axis and another with maxima of these parameters near the boundary between the jet and surrounding air. The latter structure is similar to the observed ring-shaped structures of plasma bullets.

Comparative study of electronic structure and microscopic model of SrMn3P4O14 and Sr3Cu3(PO4)4

NASA Astrophysics Data System (ADS)

Khanam, Dilruba; Rahaman, Badiur

2018-05-01

We present the first principle density functional calculations to figure out the comparative study of the underlying spin model SrMn3P4O14 and Sr3Cu3(PO4)4. We explicitly discuss the nature of the exchange paths and provide quantitative estimates of magnetic exchange couplings for both compounds. A microscopic modeling based on analysis of the electronic structure of both systems puts them in the interesting class of weakly coupled trimer units, which makes chains S=5/2 for SrMn3P4O14 and S=1/2 for Sr3Cu3(PO4)4 that are in turn weakly coupled to each other.

Improved electron collisional line broadening for low-temperature ions and neutrals in plasma modeling

DOE Office of Scientific and Technical Information (OSTI.GOV)

Johns, H. M.; Kilcrease, D. P.; Colgan, J.

In this study, electron collisional broadening of observed spectral lines depends on plasma electron temperature and density. Including this effect in models of measured spectra is necessary to determine plasma conditions; however, computational limits make accurate line broadening treatments difficult to implement in large-scale plasma modeling efforts. In this paper, we report on improvements to the treatment of electron collisional line broadening and illustrate this with calculations using the Los Alamos ATOMIC code. We implement the Dimitrijevic and Konjevic modified semi-empirical model Dimitrijevic and Konjevic (1986 Astron. and Astrophy. 163 297 and 1987 Astron. Astrophys. 172 345), which we amendmore » by employing oscillator strengths from Hartree–Fock calculations. This line broadening model applies to near-neutral plasmas with electron temperatures of Te ~ 1 eV and electron densities of N e ~10 17 cm -3. We evaluate the D.K.-inspired model against the previous hydrogenic approach in ATOMIC through comparison to NIST-rated measurements for selected neutral and singly-ionized Ca, O, Fe, and Sn lines using both fine-structure and configuration-averaged oscillator strengths. The new D.K.-inspired model is significantly more accurate than the previous hydrogenic model and we find the use of configuration-averaged oscillator strengths a good approximation for applications such as LIBS (laser induced breakdown spectroscopy), for which we demonstrate the use of the D.K.-inspired model.« less

Improved electron collisional line broadening for low-temperature ions and neutrals in plasma modeling

DOE PAGES

Johns, H. M.; Kilcrease, D. P.; Colgan, J.; ...

2015-09-29

In this study, electron collisional broadening of observed spectral lines depends on plasma electron temperature and density. Including this effect in models of measured spectra is necessary to determine plasma conditions; however, computational limits make accurate line broadening treatments difficult to implement in large-scale plasma modeling efforts. In this paper, we report on improvements to the treatment of electron collisional line broadening and illustrate this with calculations using the Los Alamos ATOMIC code. We implement the Dimitrijevic and Konjevic modified semi-empirical model Dimitrijevic and Konjevic (1986 Astron. and Astrophy. 163 297 and 1987 Astron. Astrophys. 172 345), which we amendmore » by employing oscillator strengths from Hartree–Fock calculations. This line broadening model applies to near-neutral plasmas with electron temperatures of Te ~ 1 eV and electron densities of N e ~10 17 cm -3. We evaluate the D.K.-inspired model against the previous hydrogenic approach in ATOMIC through comparison to NIST-rated measurements for selected neutral and singly-ionized Ca, O, Fe, and Sn lines using both fine-structure and configuration-averaged oscillator strengths. The new D.K.-inspired model is significantly more accurate than the previous hydrogenic model and we find the use of configuration-averaged oscillator strengths a good approximation for applications such as LIBS (laser induced breakdown spectroscopy), for which we demonstrate the use of the D.K.-inspired model.« less

Injection locking of an electronic maser in the hard excitation mode

NASA Astrophysics Data System (ADS)

Yakunina, K. A.; Kuznetsov, A. P.; Ryskin, N. M.

2015-11-01

The phenomenon of hard excitation is natural for many electronic oscillators. In particular, in a gyrotron, a maximal efficiency is often attained in the hard excitation regime. In this paper, we study the injection-locking phenomena using two models of an electronic maser in the hard excitation mode. First, bifurcation analysis is performed for the quasilinear model described by ordinary differential equations for the slow amplitude and phase. Two main scenarios of transition to the injection-locked mode are described, which are generalizations of the well-known phase-locking and suppression mechanisms. The results obtained for the quasilinear model are confirmed by numerical simulations of a gyrotron with fixed Gaussian structure of the RF field.

Exact Time-Dependent Exchange-Correlation Potential in Electron Scattering Processes

NASA Astrophysics Data System (ADS)

Suzuki, Yasumitsu; Lacombe, Lionel; Watanabe, Kazuyuki; Maitra, Neepa T.

2017-12-01

We identify peak and valley structures in the exact exchange-correlation potential of time-dependent density functional theory that are crucial for time-resolved electron scattering in a model one-dimensional system. These structures are completely missed by adiabatic approximations that, consequently, significantly underestimate the scattering probability. A recently proposed nonadiabatic approximation is shown to correctly capture the approach of the electron to the target when the initial Kohn-Sham state is chosen judiciously, and it is more accurate than standard adiabatic functionals but ultimately fails to accurately capture reflection. These results may explain the underestimation of scattering probabilities in some recent studies on molecules and surfaces.

Imaging the atomic structure and local chemistry of platelets in natural type Ia diamond

NASA Astrophysics Data System (ADS)

Olivier, E. J.; Neethling, J. H.; Kroon, R. E.; Naidoo, S. R.; Allen, C. S.; Sawada, H.; van Aken, P. A.; Kirkland, A. I.

2018-03-01

In the past decades, many efforts have been devoted to characterizing {001} platelet defects in type Ia diamond. It is known that N is concentrated at the defect core. However, an accurate description of the atomic structure of the defect and the role that N plays in it is still unknown. Here, by using aberration-corrected transmission electron microscopy and electron energy-loss spectroscopy we have determined the atomic arrangement within platelet defects in a natural type Ia diamond and matched it to a prevalent theoretical model. The platelet has an anisotropic atomic structure with a zigzag ordering of defect pairs along the defect line. The electron energy-loss near-edge fine structure of both carbon K- and nitrogen K-edges obtained from the platelet core is consistent with a trigonal bonding arrangement at interstitial sites. The experimental observations support an interstitial aggregate mode of formation for platelet defects in natural diamond.

Imaging the atomic structure and local chemistry of platelets in natural type Ia diamond.

PubMed

Olivier, E J; Neethling, J H; Kroon, R E; Naidoo, S R; Allen, C S; Sawada, H; van Aken, P A; Kirkland, A I

2018-03-01

In the past decades, many efforts have been devoted to characterizing {001} platelet defects in type Ia diamond. It is known that N is concentrated at the defect core. However, an accurate description of the atomic structure of the defect and the role that N plays in it is still unknown. Here, by using aberration-corrected transmission electron microscopy and electron energy-loss spectroscopy we have determined the atomic arrangement within platelet defects in a natural type Ia diamond and matched it to a prevalent theoretical model. The platelet has an anisotropic atomic structure with a zigzag ordering of defect pairs along the defect line. The electron energy-loss near-edge fine structure of both carbon K- and nitrogen K-edges obtained from the platelet core is consistent with a trigonal bonding arrangement at interstitial sites. The experimental observations support an interstitial aggregate mode of formation for platelet defects in natural diamond.

High-resolution Single Particle Analysis from Electron Cryo-microscopy Images Using SPHIRE

PubMed Central

Moriya, Toshio; Saur, Michael; Stabrin, Markus; Merino, Felipe; Voicu, Horatiu; Huang, Zhong; Penczek, Pawel A.; Raunser, Stefan; Gatsogiannis, Christos

2017-01-01

SPHIRE (SPARX for High-Resolution Electron Microscopy) is a novel open-source, user-friendly software suite for the semi-automated processing of single particle electron cryo-microscopy (cryo-EM) data. The protocol presented here describes in detail how to obtain a near-atomic resolution structure starting from cryo-EM micrograph movies by guiding users through all steps of the single particle structure determination pipeline. These steps are controlled from the new SPHIRE graphical user interface and require minimum user intervention. Using this protocol, a 3.5 Å structure of TcdA1, a Tc toxin complex from Photorhabdus luminescens, was derived from only 9500 single particles. This streamlined approach will help novice users without extensive processing experience and a priori structural information, to obtain noise-free and unbiased atomic models of their purified macromolecular complexes in their native state. PMID:28570515

Influence of Al grain boundaries segregations and La-doping on embrittlement of intermetallic NiAl

NASA Astrophysics Data System (ADS)

Kovalev, Anatoly I.; Wainstein, Dmitry L.; Rashkovskiy, Alexander Yu.

2015-11-01

The microscopic nature of intergranular fracture of NiAl was experimentally investigated by the set of electron spectroscopy techniques. The paper demonstrates that embrittlement of NiAl intermetallic compound is caused by ordering of atomic structure that leads to formation of structural aluminum segregations at grain boundaries (GB). Such segregations contain high number of brittle covalent interatomic bonds. The alloying by La increases the ductility of material avoiding Al GB enrichment and disordering GB atomic structure. The influence of La alloying on NiAl mechanical properties was investigated. GB chemical composition, atomic and electronic structure transformations after La doping were investigated by AES, XPS and EELFS techniques. To qualify the interatomic bonds metallicity the Fermi level (EF) position and electrons density (neff) in conduction band were determined in both undoped and doped NiAl. Basing on experimental results the physical model of GB brittleness formation was proposed.

Structural and electronic phase transitions of MoTe2 induced by Li ionic gating

NASA Astrophysics Data System (ADS)

Hwang, Jeongwoon; Zhang, Chenxi; Cho, Kyeongjae

2017-12-01

Monolayer MoTe2 has semiconducting and semimetallic phases with small energy difference, and the relative stability is readily reversed by gating. By first-principles calculations, we investigate the changes in atomic structure, electronic structure, and relative stability of two phases induced by Li ionic gating. To model Li ionic gating, we employ two approaches; one is direct adsorption of Li on MoTe2 and the other is introducing non-contacting Li plate over MoTe2. We show phonon instability in H-phase of MoTe2 with increasing the amount of charge transfer from Li, which implies a large electron-phonon coupling in the system resulting in a charge density wave state. Structural distortion is also observed in highly doped T d phase. The transition energy barrier from distorted H phase to distorted T d phase is reduced considerably compared to that of pristine MoTe2.

Atomic structure and electronic properties of MgO grain boundaries in tunnelling magnetoresistive devices

PubMed Central

Bean, Jonathan J.; Saito, Mitsuhiro; Fukami, Shunsuke; Sato, Hideo; Ikeda, Shoji; Ohno, Hideo; Ikuhara, Yuichi; McKenna, Keith P.

2017-01-01

Polycrystalline metal oxides find diverse applications in areas such as nanoelectronics, photovoltaics and catalysis. Although grain boundary defects are ubiquitous their structure and electronic properties are very poorly understood since it is extremely challenging to probe the structure of buried interfaces directly. In this paper we combine novel plan-view high-resolution transmission electron microscopy and first principles calculations to provide atomic level understanding of the structure and properties of grain boundaries in the barrier layer of a magnetic tunnel junction. We show that the highly [001] textured MgO films contain numerous tilt grain boundaries. First principles calculations reveal how these grain boundaries are associated with locally reduced band gaps (by up to 3 eV). Using a simple model we show how shunting a proportion of the tunnelling current through grain boundaries imposes limits on the maximum magnetoresistance that can be achieved in devices. PMID:28374755

Electronic structure of scandium-doped MgB2

NASA Astrophysics Data System (ADS)

de La Peña, Omar; Agrestini, Stefano

2005-03-01

Recently has been reported the synthesis of a new superconducting alloy based on MgB2, where Mg is partially substituted with Sc. In order to analyze the effect of Sc doping on the structural and superconducting properties of Mg1-xScxB2, we have performed a detailed study of the electronic structure for this new diboride. The calculations have been done using the first-principles LAPW method, within the supercell approach for modeling the doping. In this work we report results for the electronic band structure, Fermi surface, and density of states. The effect of the Sc-d orbitals on the structural and electronic properties of Mg1-xScxB2 is analyzed. Increasing the Sc concentration (x) the σ-band is gradually filled, because Sc have one valence electron more than Mg. Interestingly, the analysis of the band structure shows that even for ScB2 the top of the σ-band remain above the Fermi level, nevertheless the σ-band presents high dispersion and has an important contribution of d states. In this way, in addition to the band filling effect, Sc doping gradually reduces the two-dimensional character of the σ- band in Mg1-xScxB2 as a result of increasing the sp(B)-d(Sc) hybridization. This research was partially supported by Consejo Nacional de Ciencia y Tecnolog'ia (CONACYT, M'exico) under Grant. No. 43830-F

Electron-density descriptors as predictors in quantitative structure--activity/property relationships and drug design.

PubMed

Matta, Chérif F; Arabi, Alya A

2011-06-01

The use of electron density-based molecular descriptors in drug research, particularly in quantitative structure--activity relationships/quantitative structure--property relationships studies, is reviewed. The exposition starts by a discussion of molecular similarity and transferability in terms of the underlying electron density, which leads to a qualitative introduction to the quantum theory of atoms in molecules (QTAIM). The starting point of QTAIM is the topological analysis of the molecular electron-density distributions to extract atomic and bond properties that characterize every atom and bond in the molecule. These atomic and bond properties have considerable potential as bases for the construction of robust quantitative structure--activity/property relationships models as shown by selected examples in this review. QTAIM is applicable to the electron density calculated from quantum-chemical calculations and/or that obtained from ultra-high resolution x-ray diffraction experiments followed by nonspherical refinement. Atomic and bond properties are introduced followed by examples of application of each of these two families of descriptors. The review ends with a study whereby the molecular electrostatic potential, uniquely determined by the density, is used in conjunction with atomic properties to elucidate the reasons for the biological similarity of bioisosteres.

Electronic structure of the benzene dimer cation

NASA Astrophysics Data System (ADS)

Pieniazek, Piotr A.; Krylov, Anna I.; Bradforth, Stephen E.

2007-07-01

The benzene and benzene dimer cations are studied using the equation-of-motion coupled-cluster model with single and double substitutions for ionized systems. The ten lowest electronic states of the dimer at t-shaped, sandwich, and displaced sandwich configurations are described and cataloged based on the character of the constituent fragment molecular orbitals. The character of the states, bonding patterns, and important features of the electronic spectrum are explained using qualitative dimer molecular orbital linear combination of fragment molecular orbital framework. Relaxed ground state geometries are obtained for all isomers. Calculations reveal that the lowest energy structure of the cation has a displaced sandwich structure and a binding energy of 20kcal/mol, while the t-shaped isomer is 6kcal/mol higher. The calculated electronic spectra agree well with experimental gas phase action spectra and femtosecond transient absorption in liquid benzene. Both sandwich and t-shaped structures feature intense charge resonance bands, whose location is very sensitive to the interfragment distance. Change in the electronic state ordering was observed between σ and πu states, which correlate to the B˜ and C˜ bands of the monomer, suggesting a reassignment of the local excitation peaks in the gas phase experimental spectrum.

Quadrupolar Kondo effect in uranium heavy-electron materials?

NASA Technical Reports Server (NTRS)

Cox, D. L.

1987-01-01

The possibility of an electric quadrupole Kondo effect for a non-Kramers doublet on a uranium (U) ion is a cubic metallic host is demonstrated by model calculations showing a Kondo upturn in the resistivity, universal quenching of the quadrupolar moment, and a heavy-electron anomaly in the electronic specific heat. With inclusion of excited crystal-field levels, some of the unusual magnetic-response data in the heavy-electron superconductor UBe13 may be understood. Structural phase transitions at unprecedented low temperatures may occur in U-based heavy-electron materials.

Micro-wrinkling and delamination-induced buckling of stretchable electronic structures

DOE Office of Scientific and Technical Information (OSTI.GOV)

Oyewole, O. K.; Department of Materials Science and Engineering, Kwara State University, Malete, P.M.B 1530, Ilorin, Kwara State; Yu, D.

This paper presents the results of experimental and theoretical/computational micro-wrinkles and buckling on the surfaces of stretchable poly-dimethylsiloxane (PDMS) coated with nano-scale Gold (Au) layers. The wrinkles and buckles are formed by the unloading of pre-stretched PDMS/Au structure after the evaporation of nano-scale Au layers. They are then characterized using atomic force microscopy and scanning electron microscopy. The critical stresses required for wrinkling and buckling are analyzed using analytical models. The possible interfacial cracking that can occur along with film buckling is also studied using finite element simulations of the interfacial crack growth. The implications of the results are discussedmore » for potential applications of micro-wrinkles and micro-buckles in stretchable electronic structures and biomedical devices.« less

Electronic structure and optical properties of Si, Ge and diamond in the lonsdaleite phase.

PubMed

De, Amrit; Pryor, Craig E

2014-01-29

Crystalline semiconductors may exist in different polytypic phases with significantly different electronic and optical properties. In this paper, we calculate the electronic structure and optical properties of diamond, Si and Ge in the lonsdaleite (hexagonal diamond) phase using a transferable model empirical pseudopotential method with spin–orbit interactions. We calculate their band structures and extract various relevant parameters. Differences between the cubic and hexagonal phases are highlighted by comparing their densities of states. While diamond and Si remain indirect gap semiconductors in the lonsdaleite phase, Ge transforms into a direct gap semiconductor with a much smaller bandgap. We also calculate complex dielectric functions for different optical polarizations and find strong optical anisotropy. We further provide expansion parameters for the dielectric functions in terms of Lorentz oscillators.

Model systems in heterogeneous catalysis: towards the design and understanding of structure and electronic properties.

PubMed

Pan, Q; Li, L; Shaikhutdinov, S; Fujimori, Y; Hollerer, M; Sterrer, M; Freund, H-J

2018-05-29

We discuss in this paper two case studies related to nano-particle catalyst systems. One concerns a model system for the Cr/SiO2 Phillips catalyst for ethylene polymerization and here we present XPS data to complement the previously published TPD, IRAS and reactivity studies to elucidate the electronic structure of the system in some detail. The second case study provides additional information on Au nano-particles supported on ultrathin MgO(100)/Ag(100) films where we had observed a specific activity of the particle's rim at the metal-oxide interface with respect to CO2 activation and oxalate formation, obviously connected to electron transfer through the MgO film from the metal substrate underneath. Here we present XPS and Auger data, which allows detailed analysis of the observed chemical shifts. This analysis corroborates previous findings deduced via STM.

Electronic structure and equation of state of Sm2Co17 from first-principles DFT+ U

NASA Astrophysics Data System (ADS)

Huang, Patrick; Butch, Nicholas P.; Jeffries, Jason R.; McCall, Scott K.

2013-03-01

Rare-earth intermetallics have important applications as permanent magnet materials, and the rational optimization of their properties would benefit greatly from guidance from ab initio modeling. However, these systems are particularly challenging for current electronic structure methods. Here, we present an ab initio study of the prototype material Sm2Co17 and related compounds, using density functional theory with a Hubbard correction for the Sm 4 f-electrons (DFT+ U method) and ultrasoft pseudopotentials. The Hubbard U parameter is derived from first principles [Cococcioni and de Gironcoli, PRB 71, 035105 (2005)], not fit to experiment. Our calculations are in good agreement with recent photoemission measurements at ambient pressure and the equation of state up to 40 GPa, thus supporting the validity of our DFT+ U model. Prepared by LLNL under Contract DE-AC52-07NA27344.

Effective lattice Hamiltonian for monolayer tin disulfide: Tailoring electronic structure with electric and magnetic fields

NASA Astrophysics Data System (ADS)

Yu, Jin; van Veen, Edo; Katsnelson, Mikhail I.; Yuan, Shengjun

2018-06-01

The electronic properties of monolayer tin dilsulfide (ML -Sn S2 ), a recently synthesized metal dichalcogenide, are studied by a combination of first-principles calculations and tight-binding (TB) approximation. An effective lattice Hamiltonian based on six hybrid s p -like orbitals with trigonal rotation symmetry are proposed to calculate the band structure and density of states for ML -Sn S2 , which demonstrates good quantitative agreement with relativistic density-functional-theory calculations in a wide energy range. We show that the proposed TB model can be easily applied to the case of an external electric field, yielding results consistent with those obtained from full Hamiltonian results. In the presence of a perpendicular magnetic field, highly degenerate equidistant Landau levels are obtained, showing typical two-dimensional electron gas behavior. Thus, the proposed TB model provides a simple way in describing properties in ML -Sn S2 .

Modeling of Diamond Field-Emitter-Arrays for high brightness photocathode applications

NASA Astrophysics Data System (ADS)

Kwan, Thomas; Huang, Chengkun; Piryatinski, Andrei; Lewellen, John; Nichols, Kimberly; Choi, Bo; Pavlenko, Vitaly; Shchegolkov, Dmitry; Nguyen, Dinh; Andrews, Heather; Simakov, Evgenya

2017-10-01

We propose to employ Diamond Field-Emitter-Arrays (DFEAs) as high-current-density ultra-low-emittance photocathodes for compact laser-driven dielectric accelerators capable of generating ultra-high brightness electron beams for advanced applications. We develop a semi-classical Monte-Carlo photoemission model for DFEAs that includes carriers' transport to the emitter surface and tunneling through the surface under external fields. The model accounts for the electronic structure size quantization affecting the transport and tunneling process within the sharp diamond tips. We compare this first principle model with other field emission models, such as the Child-Langmuir and Murphy-Good models. By further including effects of carrier photoexcitation, we perform simulations of the DFEAs' photoemission quantum yield and the emitted electron beam. Details of the theoretical model and validation against preliminary experimental data will be presented. Work ssupported by LDRD program at LANL.

Dissociation kinetics of metal clusters on multiple electronic states including electronic level statistics into the vibronic soup

NASA Astrophysics Data System (ADS)

Shvartsburg, Alexandre A.; Siu, K. W. Michael

2001-06-01

Modeling the delayed dissociation of clusters had been over the last decade a frontline development area in chemical physics. It is of fundamental interest how statistical kinetics methods previously validated for regular molecules and atomic nuclei may apply to clusters, as this would help to understand the transferability of statistical models for disintegration of complex systems across various classes of physical objects. From a practical perspective, accurate simulation of unimolecular decomposition is critical for the extraction of true thermochemical values from measurements on the decay of energized clusters. Metal clusters are particularly challenging because of the multitude of low-lying electronic states that are coupled to vibrations. This has previously been accounted for assuming the average electronic structure of a conducting cluster approximated by the levels of electron in a cavity. While this provides a reasonable time-averaged description, it ignores the distribution of instantaneous electronic structures in a "boiling" cluster around that average. Here we set up a new treatment that incorporates the statistical distribution of electronic levels around the average picture using random matrix theory. This approach faithfully reflects the completely chaotic "vibronic soup" nature of hot metal clusters. We found that the consideration of electronic level statistics significantly promotes electronic excitation and thus increases the magnitude of its effect. As this excitation always depresses the decay rates, the inclusion of level statistics results in slower dissociation of metal clusters.

Modelling and simulation of parallel triangular triple quantum dots (TTQD) by using SIMON 2.0

DOE Office of Scientific and Technical Information (OSTI.GOV)

Fathany, Maulana Yusuf, E-mail: myfathany@gmail.com; Fuada, Syifaul, E-mail: fsyifaul@gmail.com; Lawu, Braham Lawas, E-mail: bram-labs@rocketmail.com

2016-04-19

This research presents analysis of modeling on Parallel Triple Quantum Dots (TQD) by using SIMON (SIMulation Of Nano-structures). Single Electron Transistor (SET) is used as the basic concept of modeling. We design the structure of Parallel TQD by metal material with triangular geometry model, it is called by Triangular Triple Quantum Dots (TTQD). We simulate it with several scenarios using different parameters; such as different value of capacitance, various gate voltage, and different thermal condition.

Electronic structure of PPP@ZnO from all-electron quasiarticle calculations

NASA Astrophysics Data System (ADS)

Höffling, Benjamin; Nabok, Dimitri; Draxl, Claudia; Condensed Matter Theory Group, Humboldt University Berlin Team

We investigate the electronic properties of poly(para-phenylene) (PPP) adsorbed on the non-polar (001) surface of rocksalt (rs) ZnO using all-electron density functional theory (DFT) as well as quasiparticle (QP) calculations within the GW approach. A particular focus is put on the electronic band discontinuities at the interface, where we investigate the impact of quantum confinement, molecular polarization, and charge rearrangement. For our prototypical system, PPP@ZnO, we find a type-I heterostructure. Comparison of the band offsets derived from a QP-treatment of the hybrid system with predictions based on mesoscopic methods, like the Shockley-Anderson model or alignment via the electrostatic potential, reveals the inadequacy of these simple approaches for the prediction of the electronic structure of such inorganic/organic heterosystems. Finally, we explore the optical excitations of the interface compared to the features of the pristine components and discuss the methodological implications for the ab-initio treatment of interface electronics.

High-resolution structure of the Shigella type-III secretion needle by solid-state NMR and cryo-electron microscopy

NASA Astrophysics Data System (ADS)

Demers, Jean-Philippe; Habenstein, Birgit; Loquet, Antoine; Kumar Vasa, Suresh; Giller, Karin; Becker, Stefan; Baker, David; Lange, Adam; Sgourakis, Nikolaos G.

2014-09-01

We introduce a general hybrid approach for determining the structures of supramolecular assemblies. Cryo-electron microscopy (cryo-EM) data define the overall envelope of the assembly and rigid-body orientation of the subunits while solid-state nuclear magnetic resonance (ssNMR) chemical shifts and distance constraints define the local secondary structure, protein fold and inter-subunit interactions. Finally, Rosetta structure calculations provide a general framework to integrate the different sources of structural information. Combining a 7.7-Å cryo-EM density map and 996 ssNMR distance constraints, the structure of the type-III secretion system needle of Shigella flexneri is determined to a precision of 0.4 Å. The calculated structures are cross-validated using an independent data set of 691 ssNMR constraints and scanning transmission electron microscopy measurements. The hybrid model resolves the conformation of the non-conserved N terminus, which occupies a protrusion in the cryo-EM density, and reveals conserved pore residues forming a continuous pattern of electrostatic interactions, thereby suggesting a mechanism for effector protein translocation.

InN/GaN quantum dot superlattices: Charge-carrier states and surface electronic structure

NASA Astrophysics Data System (ADS)

Kanouni, F.; Brezini, A.; Djenane, M.; Zou, Q.

2018-03-01

We have theoretically investigated the electron energy spectra and surface states energy in the three dimensionally ordered quantum dot superlattices (QDSLs) made of InN and GaN semiconductors. The QDSL is assumed in this model to be a matrix of GaN containing cubic dots of InN of the same size and uniformly distributed. For the miniband’s structure calculation, the resolution of the effective mass Schrödinger equation is done by decoupling it in the three directions within the framework of Kronig-Penney model. We found that the electrons minibands in infinite ODSLs are clearly different from those in the conventional quantum-well superlattices. The electrons localization and charge-carrier states are very dependent on the quasicrystallographic directions, the size and the shape of the dots which play a role of the artificial atoms in such QD supracrystal. The energy spectrum of the electron states localized at the surface of InN/GaN QDSL is represented by Kronig-Penney like-model, calculated via direct matching procedure. The calculation results show that the substrate breaks symmetrical shape of QDSL on which some localized electronic surface states can be produced in minigap regions. Furthermore, we have noticed that the surface states degeneracy is achieved in like very thin bands located in the minigaps, identified by different quantum numbers nx, ny, nz. Moreover, the surface energy bands split due to the reduction of the symmetry of the QDSL in z-direction.

Existence domains of arbitrary amplitude nonlinear structures in two-electron temperature space plasmas. II. High-frequency electron-acoustic solitons

DOE Office of Scientific and Technical Information (OSTI.GOV)

Maharaj, S. K.; Bharuthram, R.; Singh, S. V.

2012-12-15

A three-component plasma model composed of ions, cool electrons, and hot electrons is adopted to investigate the existence of large amplitude electron-acoustic solitons not only for the model for which inertia and pressure are retained for all plasma species which are assumed to be adiabatic but also neglecting inertial effects of the hot electrons. Using the Sagdeev potential formalism, the Mach number ranges supporting the existence of large amplitude electron-acoustic solitons are presented. The limitations on the attainable amplitudes of electron-acoustic solitons having negative potentials are attributed to a number of different physical reasons, such as the number density ofmore » either the cool electrons or hot electrons ceases to be real valued beyond the upper Mach number limit, or, alternatively, a negative potential double layer occurs. Electron-acoustic solitons having positive potentials are found to be supported only if inertial effects of the hot electrons are retained and these are found to be limited only by positive potential double layers.« less

Electronic structure of the high-temperature oxide superconductors

NASA Astrophysics Data System (ADS)

Pickett, Warren E.

1989-04-01

Since the discovery of superconductivity above 30 K by Bednorz and Müller in the La copper oxide system, the critical temperature has been raised to 90 K in YBa2Cu3O7 and to 110 and 125 K in Bi-based and Tl-based copper oxides, respectively. In the two years since this Nobel-prize-winning discovery, a large number of electronic structure calculations have been carried out as a first step in understanding the electronic properties of these materials. In this paper these calculations (mostly of the density-functional type) are gathered and reviewed, and their results are compared with the relevant experimental data. The picture that emerges is one in which the important electronic states are dominated by the copper d and oxygen p orbitals, with strong hybridization between them. Photon, electron, and positron spectroscopies provide important information about the electronic states, and comparison with electronic structure calculations indicates that, while many features can be interpreted in terms of existing calculations, self-energy corrections ("correlations") are important for a more detailed understanding. The antiferromagnetism that occurs in some regions of the phase diagram poses a particularly challenging problem for any detailed theory. The study of structural stability, lattice dynamics, and electron-phonon coupling in the copper oxides is also discussed. Finally, a brief review is given of the attempts so far to identify interaction constants appropriate for a model Hamiltonian treatment of many-body interactions in these materials.

Molecular and electronic structure of the peptide subunit of Geobacter sulfurreducens conductive pili from first principles.

PubMed

Feliciano, Gustavo T; da Silva, Antonio J R; Reguera, Gemma; Artacho, Emilio

2012-08-02

The respiration of metal oxides by the bacterium Geobacter sulfurreducens requires the assembly of a small peptide (the GS pilin) into conductive filaments termed pili. We gained insights into the contribution of the GS pilin to the pilus conductivity by developing a homology model and performing molecular dynamics simulations of the pilin peptide in vacuo and in solution. The results were consistent with a predominantly helical peptide containing the conserved α-helix region required for pilin assembly but carrying a short carboxy-terminal random-coiled segment rather than the large globular head of other bacterial pilins. The electronic structure of the pilin was also explored from first principles and revealed a biphasic charge distribution along the pilin and a low electronic HOMO-LUMO gap, even in a wet environment. The low electronic band gap was the result of strong electrostatic fields generated by the alignment of the peptide bond dipoles in the pilin's α-helix and by charges from ions in solution and amino acids in the protein. The electronic structure also revealed some level of orbital delocalization in regions of the pilin containing aromatic amino acids and in spatial regions of high resonance where the HOMO and LUMO states are, which could provide an optimal environment for the hopping of electrons under thermal fluctuations. Hence, the structural and electronic features of the pilin revealed in these studies support the notion of a pilin peptide environment optimized for electron conduction.

Electron-acoustic solitary waves in dense quantum electron-ion plasmas

DOE Office of Scientific and Technical Information (OSTI.GOV)

Misra, A. P.; Shukla, P. K.; Bhowmik, C.

2007-08-15

A quantum hydrodynamic (QHD) model is used to investigate the propagation characteristics of nonlinear electron-acoustic solitary waves (EASWs) in a dense quantum plasma whose constituents are two groups of electrons: one inertial cold electrons and other inertialess hot electrons, and the stationary ions which form the neutralizing background. By using the standard reductive perturbation technique, a Kadomtsev-Petviashvili (KP) equation, which governs the dynamics of EASWs, is derived in both spherical and cylindrical geometry. The effects of cold electrons and the density correlations due to quantum fluctuations on the profiles of the amplitudes and widths of the solitary structures are examinedmore » numerically. The nondimensional parameter {delta}=n{sub c0}/n{sub h0}, which is the equilibrium density ratio of the cold to hot electron component, is shown to play a vital role in the formation of both bright and dark solitons. It is also found that the angular dependence of the physical quantities and the presence of cold electrons in a quantum plasma lead to the coexistence of some new interesting novel solitary structures quite distinctive from the classical ones.« less

Alfven Waves Underlying Ionospheric Destabilization: Ground-Based Observations

NASA Astrophysics Data System (ADS)

Hirsch, Michael

During geomagnetic storms, terawatts of power in the million mile-per-hour solar wind pierce the Earth's magnetosphere. Geomagnetic storms and substorms create transverse magnetic waves known as Alfven waves. In the auroral acceleration region, Alfven waves accelerate electrons up to one-tenth the speed of light via wave-particle interactions. These inertial Alfven wave (IAW) accelerated electrons are imbued with sub-100 meter structure perpendicular to geomagnetic field B. The IAW electric field parallel to B accelerates electrons up to about 10 keV along B. The IAW dispersion relation quantifies the precipitating electron striation observed with high-speed cameras as spatiotemporally dynamic fine structured aurora. A network of tightly synchronized tomographic auroral observatories using model based iterative reconstruction (MBIR) techniques were developed in this dissertation. The TRANSCAR electron penetration model creates a basis set of monoenergetic electron beam eigenprofiles of auroral volume emission rate for the given location and ionospheric conditions. Each eigenprofile consists of nearly 200 broadband line spectra modulated by atmospheric attenuation, bandstop filter and imager quantum efficiency. The L-BFGS-B minimization routine combined with sub-pixel registered electron multiplying CCD video stream at order 10 ms cadence yields estimates of electron differential number flux at the top of the ionosphere. Our automatic data curation algorithm reduces one terabyte/camera/day into accurate MBIR-processed estimates of IAW-driven electron precipitation microstructure. This computer vision structured auroral discrimination algorithm was developed using a multiscale dual-camera system observing a 175 km and 14 km swath of sky simultaneously. This collective behavior algorithm exploits the "swarm" behavior of aurora, detectable even as video SNR approaches zero. A modified version of the algorithm is applied to topside ionospheric radar at Mars and broadcast FM passive radar. The fusion of data from coherent radar backscatter and optical data at order 10 ms cadence confirms and further quantifies the relation of strong Langmuir turbulence and streaming plasma upflows in the ionosphere with the finest spatiotemporal auroral dynamics associated with IAW acceleration. The software programs developed in this dissertation solve the century-old problem of automatically discriminating finely structured aurora from other forms and pushes the observational wave-particle science frontiers forward.

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

PubMed Central

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

DOE Office of Scientific and Technical Information (OSTI.GOV)

Thompson, M.A.; Zerner, M.C.

Photosynthetic electron transfer is arguably the most important series of chemical transformations for life on this planet. In recent years the structure of the reaction centers (RC) from the photosynthetic bacteria Rhodopseudomonas viridis and Rhodobacter sphaeroides have been presented. On the basis of these structures, several mechanisms have been proposed to explain the primary electron-transfer event with as yet no consensus. The authors report here INDO/S calculations of the excited states of a model of the RC of Rps. viridis in both the absence and presence of a polarizable medium.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Starrett, C. E.; Saumon, D.

Here, we present an approximation for calculating the equation of state (EOS) of warm and hot dense matter that is built on the previously published pseudoatom molecular dynamics (PAMD) model of dense plasmas [Starrett et al., Phys. Rev. E 91, 013104 (2015)]. And while the EOS calculation with PAMD was previously limited to orbital-free density functional theory (DFT), the new approximation presented here allows a Kohn-Sham DFT treatment of the electrons. The resulting EOS thus includes a quantum mechanical treatment of the electrons with a self-consistent model of the ionic structure, while remaining tractable at high temperatures. The method ismore » validated by comparisons with pressures from ab initio simulations of Be, Al, Si, and Fe. The EOS in the Thomas-Fermi approximation shows remarkable thermodynamic consistency over a wide range of temperatures for aluminum. We also calculate the principal Hugoniots of aluminum and silicon up to 500 eV. We find that the ionic structure of the plasma has a modest effect that peaks at temperatures of a few eV and that the features arising from the electronic structure agree well with ab initio simulations.« less

Computational thermochemistry: Automated generation of scale factors for vibrational frequencies calculated by electronic structure model chemistries

NASA Astrophysics Data System (ADS)

Yu, Haoyu S.; Fiedler, Lucas J.; Alecu, I. M.; Truhlar, Donald G.

2017-01-01

We present a Python program, FREQ, for calculating the optimal scale factors for calculating harmonic vibrational frequencies, fundamental vibrational frequencies, and zero-point vibrational energies from electronic structure calculations. The program utilizes a previously published scale factor optimization model (Alecu et al., 2010) to efficiently obtain all three scale factors from a set of computed vibrational harmonic frequencies. In order to obtain the three scale factors, the user only needs to provide zero-point energies of 15 or 6 selected molecules. If the user has access to the Gaussian 09 or Gaussian 03 program, we provide the option for the user to run the program by entering the keywords for a certain method and basis set in the Gaussian 09 or Gaussian 03 program. Four other Python programs, input.py, input6, pbs.py, and pbs6.py, are also provided for generating Gaussian 09 or Gaussian 03 input and PBS files. The program can also be used with data from any other electronic structure package. A manual of how to use this program is included in the code package.

Nitrogen-related intermediate band in P-rich GaN xP yAs 1-x-y alloys

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zelazna, K.; Gladysiewicz, M.; Polak, M. P.

The electronic band structure of phosphorus-rich GaN xP yAs 1-x-y alloys (x ~ 0.025 and y ≥ 0.6) is studied experimentally using optical absorption, photomodulated transmission, contactless electroreflectance, and photoluminescence. Here, it is shown that incorporation of a few percent of N atoms has a drastic effect on the electronic structure of the alloys. The change of the electronic band structure is very well described by the band anticrossing (BAC) model in which localized nitrogen states interact with the extended states of the conduction band of GaAsP host. The BAC interaction results in the formation of a narrow intermediate bandmore » (E - band in BAC model) with the minimum at the Γ point of the Brillouin zone resulting in a change of the nature of the fundamental band gap from indirect to direct. The splitting of the conduction band by the BAC interaction is further confirmed by a direct observation of the optical transitions to the E + band using contactless electroreflectance spectroscopy.« less

Nitrogen-related intermediate band in P-rich GaN xP yAs 1-x-y alloys

DOE PAGES

Zelazna, K.; Gladysiewicz, M.; Polak, M. P.; ...

2017-11-16

The electronic band structure of phosphorus-rich GaN xP yAs 1-x-y alloys (x ~ 0.025 and y ≥ 0.6) is studied experimentally using optical absorption, photomodulated transmission, contactless electroreflectance, and photoluminescence. Here, it is shown that incorporation of a few percent of N atoms has a drastic effect on the electronic structure of the alloys. The change of the electronic band structure is very well described by the band anticrossing (BAC) model in which localized nitrogen states interact with the extended states of the conduction band of GaAsP host. The BAC interaction results in the formation of a narrow intermediate bandmore » (E - band in BAC model) with the minimum at the Γ point of the Brillouin zone resulting in a change of the nature of the fundamental band gap from indirect to direct. The splitting of the conduction band by the BAC interaction is further confirmed by a direct observation of the optical transitions to the E + band using contactless electroreflectance spectroscopy.« less

Review of electronic transport models for thermoelectric materials

NASA Astrophysics Data System (ADS)

Bulusu, A.; Walker, D. G.

2008-07-01

Thermoelectric devices have gained importance in recent years as viable solutions for applications such as spot cooling of electronic components, remote power generation in space stations and satellites etc. These solid-state devices have long been known for their reliability rather than their efficiency; they contain no moving parts, and their performance relies primarily on material selection, which has not generated many excellent candidates. Research in recent years has been focused on developing both thermoelectric structures and materials that have high efficiency. In general, thermoelectric research is two-pronged with (1) experiments focused on finding new materials and structures with enhanced thermoelectric performance and (2) analytical models that predict thermoelectric behavior to enable better design and optimization of materials and structures. While numerous reviews have discussed the importance of and dependence on materials for thermoelectric performance, an overview of how to predict the performance of various materials and structures based on fundamental quantities is lacking. In this paper we present a review of the theoretical models that were developed since thermoelectricity was first observed in 1821 by Seebeck and how these models have guided experimental material search for improved thermoelectric devices. A new quantum model is also presented, which provides opportunities for the optimization of nanoscale materials to enhance thermoelectric performance.

Effects of micro-structure on aerodynamics of Coccinella septempunctata elytra (ladybird) in forward flight as assessed via electron microscopy.

PubMed

Xiang, Jinwu; Liu, Kai; Li, Daochun; Du, Jianxun

2017-11-01

The effects of micro-structure on aerodynamics of Coccinella septempunctata (Coleoptera: Coccinellidae) elytra in forward flight were investigated. The micro-structure was examined by a scanning electron microscope and a digital microscope. Based on the experimental results, five elytron models were constructed to separately investigate the effects of the camber and the local corrugation in both leading edge and trailing edge on aerodynamics. Computational fluid dynamic simulations of five elytron models were conducted by solving the Reynolds-Averaged Navier-Stokes equations with the Reynolds number of 245. The results show that camber and the local corrugation in the leading edge play significant roles in improving the aerodynamic performance, while the local corrugation in the trailing edge has little effect on aerodynamics. Copyright © 2017 Elsevier Ltd. All rights reserved.

Quantum Entanglement in Double Quantum Systems and Jaynes-Cummings Model.

PubMed

Jakubczyk, Paweł; Majchrowski, Klaudiusz; Tralle, Igor

2017-12-01

In the paper, we proposed a new approach to producing the qubits in electron transport in low-dimensional structures such as double quantum wells or double quantum wires (DQW). The qubit could arise as a result of quantum entanglement of two specific states of electrons in DQW structure. These two specific states are the symmetric and antisymmetric (with respect to inversion symmetry) states arising due to tunneling across the structure, while entanglement could be produced and controlled by means of the source of nonclassical light. We examined the possibility to produce quantum entanglement in the framework of Jaynes-Cummings model and have shown that at least in principle, the entanglement can be achieved due to series of "revivals" and "collapses" in the population inversion due to the interaction of a quantized single-mode EM field with a two-level system.

Antisymmetric Spin-Orbit Coupling in a d-p Model on a Zigzag Chain

DOE PAGES

Sugita, Yusuke; Hayami, Satoru; Motome, Yukitoshi

2015-12-29

In this paper, we theoretically investigate how an antisymmetric spin-orbit coupling emerges in electrons moving on lattice structures which are centrosymmetric but break the spatial inversion symme- try at atomic positions. We construct an effective d-p model on the simplest lattice structure, a zigzag chain of edge-sharing octahedra, with taking into account the crystalline electric field, the spin-orbit coupling, and on-site and inter-site d-p hybridizations. We show that an effective antisymmetric spin-orbit coupling arises in the sublattice-dependent form, which results in a hidden spin polarization in the band structure. Finally, we explicitly derive the effective antisymmetric spin-orbit coupling for dmore » electrons, which not only explains the hidden spin polarization but also indicates how to enhance it.« less

Antisymmetric Spin-Orbit Coupling in a d-p Model on a Zigzag Chain

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sugita, Yusuke; Hayami, Satoru; Motome, Yukitoshi

In this paper, we theoretically investigate how an antisymmetric spin-orbit coupling emerges in electrons moving on lattice structures which are centrosymmetric but break the spatial inversion symme- try at atomic positions. We construct an effective d-p model on the simplest lattice structure, a zigzag chain of edge-sharing octahedra, with taking into account the crystalline electric field, the spin-orbit coupling, and on-site and inter-site d-p hybridizations. We show that an effective antisymmetric spin-orbit coupling arises in the sublattice-dependent form, which results in a hidden spin polarization in the band structure. Finally, we explicitly derive the effective antisymmetric spin-orbit coupling for dmore » electrons, which not only explains the hidden spin polarization but also indicates how to enhance it.« less

Ultrafast electronic dynamics in unipolar n-doped indium gallium arsenide/gallium arsenide self-assembled quantum dots

NASA Astrophysics Data System (ADS)

Wu, Zong-Kwei J.

2006-12-01

Photodetectors based on intraband infrared absorption in the quantum dots have demonstrated improved performance over its quantum well counterpart by lower dark current, relative temperature insensitivity, and its ability for normal incidence operation. Various scattering processes, including phonon emission/absorption and carrier-carrier scattering, are critical in understanding device operation on the fundamental level. In previous studies, our group has investigated carrier dynamics in both low- and high-density regime. Ultrafast electron-hole scattering and the predicted phonon bottleneck effect in intrinsic quantum dots have been observed. Further examination on electron dynamics in unipolar structures is presented in this thesis. We used n-doped quantum dot in mid-infrared photodetector device structure to study the electron dynamics in unipolar structure. Differential transmission spectroscopy with mid-infrared intraband pump and optical interband probe was implemented to measure the electron dynamics directly without creating extra electron-hole pair, Electron relaxation after excitation was measured under various density and temperature conditions. Rapid capture into quantum dot within ˜ 10 ps was observed due to Auger-type electron-electron scattering. Intradot relaxation from the quantum dot excited state to the ground state was also observed on the time scale of 100 ps. With highly doped electron density in the structure, the inter-sublevel relaxation is dominated by Auger-type electron-electron scattering and the phonon bottleneck effect is circumvented. Nanosecond-scale recovery in larger-sized quantum dots was observed, not intrinsic to electron dynamics but due to band-bending and built-in voltage drift. An ensemble Monte Carlo simulation was also established to model the dynamics in quantum dots and in goad agreement with the experimental results. We presented a comprehensive picture of electron dynamics in the unipolar quantum dot structure. Although the phonon bottleneck is circumvented with high doped electron density, relaxation processes in unipolar quantum dots have been measured with time scales longer than that of bipolar systems. The results explain the operation principles of the quantum dot infrared photodetector on a microscopic level and provide basic understanding for future applications and designs.

Defining Electron Bifurcation in the Electron-Transferring Flavoprotein Family.

PubMed

Garcia Costas, Amaya M; Poudel, Saroj; Miller, Anne-Frances; Schut, Gerrit J; Ledbetter, Rhesa N; Fixen, Kathryn R; Seefeldt, Lance C; Adams, Michael W W; Harwood, Caroline S; Boyd, Eric S; Peters, John W

2017-11-01

Electron bifurcation is the coupling of exergonic and endergonic redox reactions to simultaneously generate (or utilize) low- and high-potential electrons. It is the third recognized form of energy conservation in biology and was recently described for select electron-transferring flavoproteins (Etfs). Etfs are flavin-containing heterodimers best known for donating electrons derived from fatty acid and amino acid oxidation to an electron transfer respiratory chain via Etf-quinone oxidoreductase. Canonical examples contain a flavin adenine dinucleotide (FAD) that is involved in electron transfer, as well as a non-redox-active AMP. However, Etfs demonstrated to bifurcate electrons contain a second FAD in place of the AMP. To expand our understanding of the functional variety and metabolic significance of Etfs and to identify amino acid sequence motifs that potentially enable electron bifurcation, we compiled 1,314 Etf protein sequences from genome sequence databases and subjected them to informatic and structural analyses. Etfs were identified in diverse archaea and bacteria, and they clustered into five distinct well-supported groups, based on their amino acid sequences. Gene neighborhood analyses indicated that these Etf group designations largely correspond to putative differences in functionality. Etfs with the demonstrated ability to bifurcate were found to form one group, suggesting that distinct conserved amino acid sequence motifs enable this capability. Indeed, structural modeling and sequence alignments revealed that identifying residues occur in the NADH- and FAD-binding regions of bifurcating Etfs. Collectively, a new classification scheme for Etf proteins that delineates putative bifurcating versus nonbifurcating members is presented and suggests that Etf-mediated bifurcation is associated with surprisingly diverse enzymes. IMPORTANCE Electron bifurcation has recently been recognized as an electron transfer mechanism used by microorganisms to maximize energy conservation. Bifurcating enzymes couple thermodynamically unfavorable reactions with thermodynamically favorable reactions in an overall spontaneous process. Here we show that the electron-transferring flavoprotein (Etf) enzyme family exhibits far greater diversity than previously recognized, and we provide a phylogenetic analysis that clearly delineates bifurcating versus nonbifurcating members of this family. Structural modeling of proteins within these groups reveals key differences between the bifurcating and nonbifurcating Etfs. Copyright © 2017 American Society for Microbiology.

Defining Electron Bifurcation in the Electron-Transferring Flavoprotein Family

PubMed Central

Garcia Costas, Amaya M.; Poudel, Saroj; Miller, Anne-Frances; Schut, Gerrit J.; Ledbetter, Rhesa N.; Seefeldt, Lance C.; Adams, Michael W. W.

2017-01-01

ABSTRACT Electron bifurcation is the coupling of exergonic and endergonic redox reactions to simultaneously generate (or utilize) low- and high-potential electrons. It is the third recognized form of energy conservation in biology and was recently described for select electron-transferring flavoproteins (Etfs). Etfs are flavin-containing heterodimers best known for donating electrons derived from fatty acid and amino acid oxidation to an electron transfer respiratory chain via Etf-quinone oxidoreductase. Canonical examples contain a flavin adenine dinucleotide (FAD) that is involved in electron transfer, as well as a non-redox-active AMP. However, Etfs demonstrated to bifurcate electrons contain a second FAD in place of the AMP. To expand our understanding of the functional variety and metabolic significance of Etfs and to identify amino acid sequence motifs that potentially enable electron bifurcation, we compiled 1,314 Etf protein sequences from genome sequence databases and subjected them to informatic and structural analyses. Etfs were identified in diverse archaea and bacteria, and they clustered into five distinct well-supported groups, based on their amino acid sequences. Gene neighborhood analyses indicated that these Etf group designations largely correspond to putative differences in functionality. Etfs with the demonstrated ability to bifurcate were found to form one group, suggesting that distinct conserved amino acid sequence motifs enable this capability. Indeed, structural modeling and sequence alignments revealed that identifying residues occur in the NADH- and FAD-binding regions of bifurcating Etfs. Collectively, a new classification scheme for Etf proteins that delineates putative bifurcating versus nonbifurcating members is presented and suggests that Etf-mediated bifurcation is associated with surprisingly diverse enzymes. IMPORTANCE Electron bifurcation has recently been recognized as an electron transfer mechanism used by microorganisms to maximize energy conservation. Bifurcating enzymes couple thermodynamically unfavorable reactions with thermodynamically favorable reactions in an overall spontaneous process. Here we show that the electron-transferring flavoprotein (Etf) enzyme family exhibits far greater diversity than previously recognized, and we provide a phylogenetic analysis that clearly delineates bifurcating versus nonbifurcating members of this family. Structural modeling of proteins within these groups reveals key differences between the bifurcating and nonbifurcating Etfs. PMID:28808132

Standards for the Analysis and Processing of Surface-Water Data and Information Using Electronic Methods

USGS Publications Warehouse

Sauer, Vernon B.

2002-01-01

Surface-water computation methods and procedures are described in this report to provide standards from which a completely automated electronic processing system can be developed. To the greatest extent possible, the traditional U. S. Geological Survey (USGS) methodology and standards for streamflow data collection and analysis have been incorporated into these standards. Although USGS methodology and standards are the basis for this report, the report is applicable to other organizations doing similar work. The proposed electronic processing system allows field measurement data, including data stored on automatic field recording devices and data recorded by the field hydrographer (a person who collects streamflow and other surface-water data) in electronic field notebooks, to be input easily and automatically. A user of the electronic processing system easily can monitor the incoming data and verify and edit the data, if necessary. Input of the computational procedures, rating curves, shift requirements, and other special methods are interactive processes between the user and the electronic processing system, with much of this processing being automatic. Special computation procedures are provided for complex stations such as velocity-index, slope, control structures, and unsteady-flow models, such as the Branch-Network Dynamic Flow Model (BRANCH). Navigation paths are designed to lead the user through the computational steps for each type of gaging station (stage-only, stagedischarge, velocity-index, slope, rate-of-change in stage, reservoir, tide, structure, and hydraulic model stations). The proposed electronic processing system emphasizes the use of interactive graphics to provide good visual tools for unit values editing, rating curve and shift analysis, hydrograph comparisons, data-estimation procedures, data review, and other needs. Documentation, review, finalization, and publication of records are provided for with the electronic processing system, as well as archiving, quality assurance, and quality control.

Optical bistability and second-harmonic generation in thin film coupled cavity photonic crystal structures

NASA Astrophysics Data System (ADS)

Diao, Liyong

This thesis deals with design, fabrication and modeling of bistable and multi-stable switching dynamics and second-harmonic generation in two groups of thin film coupled cavity photonic crystal structures. The first component studies optical bistability and multistability in such structures. Optical bistability and multistability are modelled by a nonlinear transfer matrix method. The second component is focused on the modelling and experimental measurement of second-harmonic generation in such structures. It is found that coupled cavity structures can reduce the threshold and index change for bistable operation, but single cavity structures can do the same. However, there is a clear advantage in using coupled cavity structures for multistability in that the threshold for multistability can be reduced. Second-harmonic generation is enhanced by field localization due to the resonant effect at the fundamental wavelength in single and coupled cavity structures by simulated and measured results. The work in this thesis makes three significant contributions. First, in the successful fabrication of thin film coupled cavity structures, the simulated linear transmissions of such structures match those of the fabricated structures almost exactly. Second, the newly defined figure of merit at the maximum transmission point on the bistable curve can be used to compare the material damage tolerance to any other Kerr effect nonlinear gate. Third, the simulated second-harmonic generation agrees excellently with experimental results. More generally optical thin film fabrication has commercial applications in many industry sections, such as electronics, opto-electronics, optical coating, solar cell and MEMS.

In situ characterization of cofacial Co(IV) centers in Co4O4 cubane: Modeling the high-valent active site in oxygen-evolving catalysts.

PubMed

Brodsky, Casey N; Hadt, Ryan G; Hayes, Dugan; Reinhart, Benjamin J; Li, Nancy; Chen, Lin X; Nocera, Daniel G

2017-04-11

The Co 4 O 4 cubane is a representative structural model of oxidic cobalt oxygen-evolving catalysts (Co-OECs). The Co-OECs are active when residing at two oxidation levels above an all-Co(III) resting state. This doubly oxidized Co(IV) 2 state may be captured in a Co(III) 2 (IV) 2 cubane. We demonstrate that the Co(III) 2 (IV) 2 cubane may be electrochemically generated and the electronic properties of this unique high-valent state may be probed by in situ spectroscopy. Intervalence charge-transfer (IVCT) bands in the near-IR are observed for the Co(III) 2 (IV) 2 cubane, and spectroscopic analysis together with electrochemical kinetics measurements reveal a larger reorganization energy and a smaller electron transfer rate constant for the doubly versus singly oxidized cubane. Spectroelectrochemical X-ray absorption data further reveal systematic spectral changes with successive oxidations from the cubane resting state. Electronic structure calculations correlated to experimental data suggest that this state is best represented as a localized, antiferromagnetically coupled Co(IV) 2 dimer. The exchange coupling in the cofacial Co(IV) 2 site allows for parallels to be drawn between the electronic structure of the Co 4 O 4 cubane model system and the high-valent active site of the Co-OEC, with specific emphasis on the manifestation of a doubly oxidized Co(IV) 2 center on O-O bond formation.

In situ characterization of cofacial Co(IV) centers in Co 4O 4 cubane: Modeling the high-valent active site in oxygen-evolving catalysts

DOE PAGES

Brodsky, Casey N.; Hadt, Ryan G.; Hayes, Dugan; ...

2017-03-27

The Co 4O 4 cubane is a representative structural model of oxidic cobalt oxygen evolving catalysts (Co-OECs). The Co-OECs are active when residing at two oxidation levels above an all Co(III) resting state. This doubly oxidized Co(IV) 2 state may be captured in a Co(III) 2(IV) 2 cubane. We demonstrate that the Co(III) 2(IV) 2 cubane may be electrochemically generated and the electronic properties of this unique high-valent state may be probed by in situ spectroscopy. Intervalence charge transfer (IVCT) bands in the near-IR are observed for the Co(III) 2(IV) 2 cubane, and spectroscopic analysis together with electrochemical kinetics measurementsmore » reveal a larger reorganization energy and a smaller electron transfer rate constant for the doubly versus singly oxidized cubane. Spectroelectrochemical X-ray absorption data further reveal systematic spectral changes with successive oxidations from the cubane resting state. Electronic structure calculations correlated to experimental data suggest that this state is best represented as a localized, antiferromagnetically coupled Co(IV) 2 dimer. The exchange coupling in the cofacial Co(IV) 2 site allows for parallels to be drawn between the electronic structure of the Co 4O 4 cubane model system and the high valent active site of the Co-OEC, with specific emphasis on the manifestation of a doubly oxidized Co(IV) 2 center on O–O bond formation.« less

3DIANA: 3D Domain Interaction Analysis: A Toolbox for Quaternary Structure Modeling

PubMed Central

Segura, Joan; Sanchez-Garcia, Ruben; Tabas-Madrid, Daniel; Cuenca-Alba, Jesus; Sorzano, Carlos Oscar S.; Carazo, Jose Maria

2016-01-01

Electron microscopy (EM) is experiencing a revolution with the advent of a new generation of Direct Electron Detectors, enabling a broad range of large and flexible structures to be resolved well below 1 nm resolution. Although EM techniques are evolving to the point of directly obtaining structural data at near-atomic resolution, for many molecules the attainable resolution might not be enough to propose high-resolution structural models. However, accessing information on atomic coordinates is a necessary step toward a deeper understanding of the molecular mechanisms that allow proteins to perform specific tasks. For that reason, methods for the integration of EM three-dimensional maps with x-ray and NMR structural data are being developed, a modeling task that is normally referred to as fitting, resulting in the so called hybrid models. In this work, we present a novel application—3DIANA—specially targeted to those cases in which the EM map resolution is medium or low and additional experimental structural information is scarce or even lacking. In this way, 3DIANA statistically evaluates proposed/potential contacts between protein domains, presents a complete catalog of both structurally resolved and predicted interacting regions involving these domains and, finally, suggests structural templates to model the interaction between them. The evaluation of the proposed interactions is computed with DIMERO, a new method that scores physical binding sites based on the topology of protein interaction networks, which has recently shown the capability to increase by 200% the number of domain-domain interactions predicted in interactomes as compared to previous approaches. The new application displays the information at a sequence and structural level and is accessible through a web browser or as a Chimera plugin at http://3diana.cnb.csic.es. PMID:26772592

Criticality of the electron-nucleus cusp condition to local effective potential-energy theories

DOE Office of Scientific and Technical Information (OSTI.GOV)

Pan Xiaoyin; Sahni, Viraht; Graduate School of the City University of New York, 360 Fifth Avenue, New York, New York 10016

2003-01-01

Local(multiplicative) effective potential energy-theories of electronic structure comprise the transformation of the Schroedinger equation for interacting Fermi systems to model noninteracting Fermi or Bose systems whereby the equivalent density and energy are obtained. By employing the integrated form of the Kato electron-nucleus cusp condition, we prove that the effective electron-interaction potential energy of these model fermions or bosons is finite at a nucleus. The proof is general and valid for arbitrary system whether it be atomic, molecular, or solid state, and for arbitrary state and symmetry. This then provides justification for all prior work in the literature based on themore » assumption of finiteness of this potential energy at a nucleus. We further demonstrate the criticality of the electron-nucleus cusp condition to such theories by an example of the hydrogen molecule. We show thereby that both model system effective electron-interaction potential energies, as determined from densities derived from accurate wave functions, will be singular at the nucleus unless the wave function satisfies the electron-nucleus cusp condition.« less

Counterintuitive electron localisation from density-functional theory with polarisable solvent models

DOE Office of Scientific and Technical Information (OSTI.GOV)

Dale, Stephen G., E-mail: sdale@ucmerced.edu; Johnson, Erin R., E-mail: erin.johnson@dal.ca

2015-11-14

Exploration of the solvated electron phenomena using density-functional theory (DFT) generally results in prediction of a localised electron within an induced solvent cavity. However, it is well known that DFT favours highly delocalised charges, rendering the localisation of a solvated electron unexpected. We explore the origins of this counterintuitive behaviour using a model Kevan-structure system. When a polarisable-continuum solvent model is included, it forces electron localisation by introducing a strong energetic bias that favours integer charges. This results in the formation of a large energetic barrier for charge-hopping and can cause the self-consistent field to become trapped in local minimamore » thus converging to stable solutions that are higher in energy than the ground electronic state. Finally, since the bias towards integer charges is caused by the polarisable continuum, these findings will also apply to other classical polarisation corrections, as in combined quantum mechanics and molecular mechanics (QM/MM) methods. The implications for systems beyond the solvated electron, including cationic DNA bases, are discussed.« less

Valley density-wave (VDW) and Superconductivity in Iron-Pnictides

NASA Astrophysics Data System (ADS)

Cvetkovic, Vladimir; Tesanovic, Zlatko

2009-03-01

One of the experimentally observed features of iron-pnictide superconductors is the structural transition and SDW ordering occurring at almost the same temperature. Starting from a tight-binding model [1], we construct an effective theory for iron-pnictides with the distinctive two hole and two electron Fermi surfaces. This theory is then mapped onto a negative-U Hubbard model with additional orbital and spin flavors [2]. We demonstrate that the superconducting instability of the attractive Hubbard model --- valley density-wave (VDW) --- corresponds to the observed structural and SDW orders. The deviations from perfect nesting between the hole and electron Fermi surfaces are mapped onto the Zeeman field which causes portions of Fermi surface to remain ungapped. The origin of pnictide superconductivity in this model, and its ties to the VDW are discussed. [1] V. Cvetkovic and Z. Tesanovic, http://arxiv.org/abs/0804.4678. [2] V. Cvetkovic and Z. Tesanovic, http://arxiv.org/abs/0808.3742.

Prediction on electronic structure of CH3NH3PbI3/Fe3O4 interfaces

NASA Astrophysics Data System (ADS)

Hou, Xueyao; Wang, Xiaocha; Mi, Wenbo; Du, Zunfeng

2018-01-01

The interfacial electronic structures of CH3NH3PbI3(MAPbI3)/Fe3O4 heterostructures are predicted by density functional theory. Four models (MAI/FeBO, PbI2/FeBO, MAI/FeA and PbI2/FeA) are included. Especially, a half-metal to semiconductor transition of Fe3O4 appears in PbI2/FeA model. A series of electric field is added to PbI2/FeA model, and a direct-indirect bandgap transition of Fe3O4 appears at a 500-kV/cm field. The electric field can control the bandgap of Fe3O4 in PbI2/FeA model by modulating the hybridization. The prediction of spin-related bandgap characteristic in MAPbI3/Fe3O4 is meaningful for further study.

Polaronic transport in Ag-based quaternary chalcogenides

NASA Astrophysics Data System (ADS)

Wei, Kaya; Khabibullin, Artem R.; Stedman, Troy; Woods, Lilia M.; Nolas, George S.

2017-09-01

Low temperature resistivity measurements on dense polycrystalline quaternary chalcogenides Ag2+xZn1-xSnSe4, with x = 0, 0.1, and 0.3, indicate polaronic type transport which we analyze employing a two-component Holstein model based on itinerant and localized polaron contributions. Electronic structure property calculations via density functional theory simulations on Ag2ZnSnSe4 for both energetically similar kesterite and stannite structure types were also performed in order to compare our results to those of the compositionally similar but well known Cu2ZnSnSe4. This theoretical comparison is crucial in understanding the bonding that results in polaronic type transport for Ag2ZnSnSe4, as well as the structural and electronic properties of both crystal structure types. In addition to possessing this unique electronic transport, the thermal conductivity of Ag2ZnSnSe4 is low and decreases with increasing silver content. This work reveals unique structure-property relationships in materials that continue to be of interest for thermoelectric and photovoltaic applications.

The Physiological Molecular Shape of Spectrin: A Compact Supercoil Resembling a Chinese Finger Trap.

PubMed

Brown, Jeffrey W; Bullitt, Esther; Sriswasdi, Sira; Harper, Sandra; Speicher, David W; McKnight, C James

2015-06-01

The primary, secondary, and tertiary structures of spectrin are reasonably well defined, but the structural basis for the known dramatic molecular shape change, whereby the molecular length can increase three-fold, is not understood. In this study, we combine previously reported biochemical and high-resolution crystallographic data with structural mass spectroscopy and electron microscopic data to derive a detailed, experimentally-supported quaternary structure of the spectrin heterotetramer. In addition to explaining spectrin's physiological resting length of ~55-65 nm, our model provides a mechanism by which spectrin is able to undergo a seamless three-fold extension while remaining a linear filament, an experimentally observed property. According to the proposed model, spectrin's quaternary structure and mechanism of extension is similar to a Chinese Finger Trap: at shorter molecular lengths spectrin is a hollow cylinder that extends by increasing the pitch of each spectrin repeat, which decreases the internal diameter. We validated our model with electron microscopy, which demonstrated that, as predicted, spectrin is hollow at its biological resting length of ~55-65 nm. The model is further supported by zero-length chemical crosslink data indicative of an approximately 90 degree bend between adjacent spectrin repeats. The domain-domain interactions in our model are entirely consistent with those present in the prototypical linear antiparallel heterotetramer as well as recently reported inter-strand chemical crosslinks. The model is consistent with all known physical properties of spectrin, and upon full extension our Chinese Finger Trap Model reduces to the ~180-200 nm molecular model currently in common use.

Block-diagonalization as a tool for the robust diabatization of high-dimensional potential energy surfaces

DOE Office of Scientific and Technical Information (OSTI.GOV)

Venghaus, Florian; Eisfeld, Wolfgang, E-mail: wolfgang.eisfeld@uni-bielefeld.de

2016-03-21

Robust diabatization techniques are key for the development of high-dimensional coupled potential energy surfaces (PESs) to be used in multi-state quantum dynamics simulations. In the present study we demonstrate that, besides the actual diabatization technique, common problems with the underlying electronic structure calculations can be the reason why a diabatization fails. After giving a short review of the theoretical background of diabatization, we propose a method based on the block-diagonalization to analyse the electronic structure data. This analysis tool can be used in three different ways: First, it allows to detect issues with the ab initio reference data and ismore » used to optimize the setup of the electronic structure calculations. Second, the data from the block-diagonalization are utilized for the development of optimal parametrized diabatic model matrices by identifying the most significant couplings. Third, the block-diagonalization data are used to fit the parameters of the diabatic model, which yields an optimal initial guess for the non-linear fitting required by standard or more advanced energy based diabatization methods. The new approach is demonstrated by the diabatization of 9 electronic states of the propargyl radical, yielding fully coupled full-dimensional (12D) PESs in closed form.« less

Enhanced vibronic interaction caused by local lattice symmetry lowering in the (Fe, Mg)As2 ternary system

NASA Astrophysics Data System (ADS)

Pishtshev, A.; Rubin, P.

2018-04-01

By means of periodic density functional theory (DFT) electronic structure calculations, we investigate iron-site doping effects in a structural model of bulk FeAs2. Simulations performed within the projector augmented-wave method-Perdew-Burke-Ernzerhof (PBE) generalized gradient approximation (GGA) functional scheme reveal that the impacts of the two stoichiometric substitutions Fe → Mg and Fe → Ni are radically different with respect to the structural and electronic behavior of the dopants. In particular, unlike the Ni dopant, the Mg dopant incorporated in FeAs2 occupies a noncentral equilibrium position characterized by an off-center displacement from the reference higher-symmetry position. Analysis of the respective electron and vibrational factors allows us to explain this result in terms of the local pseudo Jahn-Teller effect (pJTE). On the basis of DFT calculations, we deduce which electron orbitals and lattice vibrational modes are appropriate for promoting the local instability at the origin of the pJTE. Quantitative evaluations of the pJTE parameters performed within the polyatomic formalism of an effective tight-binding model show that it is just the enhanced vibronic interaction in the Mg-[FeAs6] cluster that is responsible for the local lattice symmetry breaking.

Chiral helimagnetic state in a Kondo lattice model with the Dzyaloshinskii-Moriya interaction

NASA Astrophysics Data System (ADS)

Okumura, Shun; Kato, Yasuyuki; Motome, Yukitoshi

2018-05-01

Monoaxial chiral magnets can form a noncollinear twisted spin structure called the chiral helimagnetic state. We study magnetic properties of such a chiral helimagnetic state, with emphasis on the effect of itinerant electrons. Modeling a monoaxial chiral helimagnet by a one-dimensional Kondo lattice model with the Dzyaloshinskii-Moriya interaction, we perform a variational calculation to elucidate the stable spin configuration in the ground state. We obtain a chiral helimagnetic state as a candidate for the ground state, whose helical pitch is modulated by the model parameters: the Kondo coupling, the Dzyaloshinski-Moriya interaction, and electron filling.

The MOLLER Experiment: ``An Ultra-precise Measurement of the Weak Charge of the Electron using moller Scattering''

NASA Astrophysics Data System (ADS)

Beminiwattha, Rakitha; Moller Collaboration

2017-09-01

Parity Violating Electron Scattering (PVES) is an extremely successful precision frontier tool that has been used for testing the Standard Model (SM) and understanding nucleon structure. Several generations of highly successful PVES programs at SLAC, MIT-Bates, MAMI-Mainz, and Jefferson Lab have contributed to the understanding of nucleon structure and testing the SM. But missing phenomena like matter-antimatter asymmetry, neutrino flavor oscillations, and dark matter and energy suggest that the SM is only a `low energy' effective theory. The MOLLER experiment at Jefferson Lab will measure the weak charge of the electron, QWe = 1 - 4sin2θW , with a precision of 2.4 % by measuring the parity violating asymmetry in electron-electron () scattering and will be sensitive to subtle but measurable deviations from precisely calculable predictions from the SM. The MOLLER experiment will provide the best contact interaction search for leptons at low OR high energy makes it a probe of physics beyond the Standard Model with sensitivities to mass-scales of new PV physics up to 7.5 TeV. Overview of the experiment and recent pre-R&D progress will be reported.

Vanadium fine-structure K-shell electron impact ionization cross sections for fast-electron diagnostic in laser–solid experiments

DOE Office of Scientific and Technical Information (OSTI.GOV)

Palmeri, P., E-mail: patrick.palmeri@umons.ac.be; Quinet, P., E-mail: pascal.quinet@umons.ac.be; IPNAS, Université de Liège, B-4000 Liège

2015-09-15

The K-shell electron impact ionization (EII) cross section, along with the K-shell fluorescence yield, is one of the key atomic parameters for fast-electron diagnostic in laser–solid experiments through the K-shell emission cross section. In addition, in a campaign dedicated to the modeling of the K lines of astrophysical interest (Palmeri et al. (2012)), the K-shell fluorescence yields for the K-vacancy fine-structure atomic levels of all the vanadium isonuclear ions have been calculated. In this study, the K-shell EII cross sections connecting the ground and the metastable levels of the parent vanadium ions to the daughter ions K-vacancy levels considered in Palmerimore » et al. (2012) have been determined. The relativistic distorted-wave (DW) approximation implemented in the FAC atomic code has been used for the incident electron kinetic energies up to 20 times the K-shell threshold energies. Moreover, the resulting DW cross sections have been extrapolated at higher energies using the asymptotic behavior of the modified relativistic binary encounter Bethe model (MRBEB) of Guerra et al. (2012) with the density-effect correction proposed by Davies et al. (2013)« less

On the inapplicability of electron-hopping models for the organic semiconductor Phenyl-C61-butyric Acid Methyl Ester (PCBM)

DOE Office of Scientific and Technical Information (OSTI.GOV)

Gajdos, Fruzsina; Oberhofer, Harald; Dupuis, Michel

2013-03-21

Phenyl-C61-butyric Acid Methyl Ester (PCBM) is one of the most popular semiconductors in organic photovoltaic cells, but the electron transport mechanism in the microcrystalline domains of this material as well as its preferred packing structure remains unclear. Here we use density functional theory to calculate electronic coupling matrix elements, reorganization energies and activation energies for available experimental and model crystal structures. We find that the picture of an excess electron hopping from one fullerene to another does not apply for any of the crystalline phases, rendering traditional rate equations inappropriate. We also find that the cohesive energy increases in themore » order body-centred-cubic < hexagonal < simple cubic < monoclinic < triclinic, independently on the type of dispersion correction used. Our results indicate that the electron-ion dynamics needs to be solved explicitly in order to obtain a realistic description of charge transfer in this material. M.D. was supported by the U.S. Department of Energy (DOE), Office of Basic Energy Sciences (BES), Division of Chemical Sciences, Geosciences and Biosciences. PNNL is a multiprogram national laboratory operated for DOE by Battelle.« less

Geometrical effects on the electron residence time in semiconductor nano-particles.

PubMed

Koochi, Hakimeh; Ebrahimi, Fatemeh

2014-09-07

We have used random walk (RW) numerical simulations to investigate the influence of the geometry on the statistics of the electron residence time τ(r) in a trap-limited diffusion process through semiconductor nano-particles. This is an important parameter in coarse-grained modeling of charge carrier transport in nano-structured semiconductor films. The traps have been distributed randomly on the surface (r(2) model) or through the whole particle (r(3) model) with a specified density. The trap energies have been taken from an exponential distribution and the traps release time is assumed to be a stochastic variable. We have carried out (RW) simulations to study the effect of coordination number, the spatial arrangement of the neighbors and the size of nano-particles on the statistics of τ(r). It has been observed that by increasing the coordination number n, the average value of electron residence time, τ̅(r) rapidly decreases to an asymptotic value. For a fixed coordination number n, the electron's mean residence time does not depend on the neighbors' spatial arrangement. In other words, τ̅(r) is a porosity-dependence, local parameter which generally varies remarkably from site to site, unless we are dealing with highly ordered structures. We have also examined the effect of nano-particle size d on the statistical behavior of τ̅(r). Our simulations indicate that for volume distribution of traps, τ̅(r) scales as d(2). For a surface distribution of traps τ(r) increases almost linearly with d. This leads to the prediction of a linear dependence of the diffusion coefficient D on the particle size d in ordered structures or random structures above the critical concentration which is in accordance with experimental observations.

Nuclear structure and weak rates of heavy waiting point nuclei under rp-process conditions

NASA Astrophysics Data System (ADS)

Nabi, Jameel-Un; Böyükata, Mahmut

2017-01-01

The structure and the weak interaction mediated rates of the heavy waiting point (WP) nuclei 80Zr, 84Mo, 88Ru, 92Pd and 96Cd along N = Z line were studied within the interacting boson model-1 (IBM-1) and the proton-neutron quasi-particle random phase approximation (pn-QRPA). The energy levels of the N = Z WP nuclei were calculated by fitting the essential parameters of IBM-1 Hamiltonian and their geometric shapes were predicted by plotting potential energy surfaces (PESs). Half-lives, continuum electron capture rates, positron decay rates, electron capture cross sections of WP nuclei, energy rates of β-delayed protons and their emission probabilities were later calculated using the pn-QRPA. The calculated Gamow-Teller strength distributions were compared with previous calculation. We present positron decay and continuum electron capture rates on these WP nuclei under rp-process conditions using the same model. For the rp-process conditions, the calculated total weak rates are twice the Skyrme HF+BCS+QRPA rates for 80Zr. For remaining nuclei the two calculations compare well. The electron capture rates are significant and compete well with the corresponding positron decay rates under rp-process conditions. The finding of the present study supports that electron capture rates form an integral part of the weak rates under rp-process conditions and has an important role for the nuclear model calculations.

Molecular dynamics-based refinement and validation for sub-5 Å cryo-electron microscopy maps.

PubMed

Singharoy, Abhishek; Teo, Ivan; McGreevy, Ryan; Stone, John E; Zhao, Jianhua; Schulten, Klaus

2016-07-07

Two structure determination methods, based on the molecular dynamics flexible fitting (MDFF) paradigm, are presented that resolve sub-5 Å cryo-electron microscopy (EM) maps with either single structures or ensembles of such structures. The methods, denoted cascade MDFF and resolution exchange MDFF, sequentially re-refine a search model against a series of maps of progressively higher resolutions, which ends with the original experimental resolution. Application of sequential re-refinement enables MDFF to achieve a radius of convergence of ~25 Å demonstrated with the accurate modeling of β-galactosidase and TRPV1 proteins at 3.2 Å and 3.4 Å resolution, respectively. The MDFF refinements uniquely offer map-model validation and B-factor determination criteria based on the inherent dynamics of the macromolecules studied, captured by means of local root mean square fluctuations. The MDFF tools described are available to researchers through an easy-to-use and cost-effective cloud computing resource on Amazon Web Services.

Ontology aided modeling of organic reaction mechanisms with flexible and fragment based XML markup procedures.

PubMed

Sankar, Punnaivanam; Aghila, Gnanasekaran

2007-01-01

The mechanism models for primary organic reactions encoding the structural fragments undergoing substitution, addition, elimination, and rearrangements are developed. In the proposed models, each and every structural component of mechanistic pathways is represented with flexible and fragment based markup technique in XML syntax. A significant feature of the system is the encoding of the electron movements along with the other components like charges, partial charges, half bonded species, lone pair electrons, free radicals, reaction arrows, etc. needed for a complete representation of reaction mechanism. The rendering of reaction schemes described with the proposed methodology is achieved with a concise XML extension language interoperating with the structure markup. The reaction scheme is visualized as 2D graphics in a browser by converting them into SVG documents enabling the desired layouts normally perceived by the chemists conventionally. An automatic representation of the complex patterns of the reaction mechanism is achieved by reusing the knowledge in chemical ontologies and developing artificial intelligence components in terms of axioms.

A combined experimental and theoretical spectroscopic protocol for determination of the structure of heterogeneous catalysts: developing the information content of the resonance Raman spectra of M1 MoVOx † †Electronic supplementary information (ESI) available. See DOI: 10.1039/c7sc01771e Click here for additional data file.

PubMed Central

Kubas, Adam; Noak, Johannes

2017-01-01

Absorption and multiwavelength resonance Raman spectroscopy are widely used to investigate the electronic structure of transition metal centers in coordination compounds and extended solid systems. In combination with computational methodologies that have predictive accuracy, they define powerful protocols to study the spectroscopic response of catalytic materials. In this work, we study the absorption and resonance Raman spectra of the M1 MoVOx catalyst. The spectra were calculated by time-dependent density functional theory (TD-DFT) in conjunction with the independent mode displaced harmonic oscillator model (IMDHO), which allows for detailed bandshape predictions. For this purpose cluster models with up to 9 Mo and V metallic centers are considered to represent the bulk structure of MoVOx. Capping hydrogens were used to achieve valence saturation at the edges of the cluster models. The construction of model structures was based on a thorough bonding analysis which involved conventional DFT and local coupled cluster (DLPNO-CCSD(T)) methods. Furthermore the relationship of cluster topology to the computed spectral features is discussed in detail. It is shown that due to the local nature of the involved electronic transitions, band assignment protocols developed for molecular systems can be applied to describe the calculated spectral features of the cluster models as well. The present study serves as a reference for future applications of combined experimental and computational protocols in the field of solid-state heterogeneous catalysis. PMID:28989667

3D ELECTRON DENSITY DISTRIBUTIONS IN THE SOLAR CORONA DURING SOLAR MINIMA: ASSESSMENT FOR MORE REALISTIC SOLAR WIND MODELING

DOE Office of Scientific and Technical Information (OSTI.GOV)

Patoul, Judith de; Foullon, Claire; Riley, Pete, E-mail: j.depatoul@exeter.ac.uk, E-mail: c.foullon@exeter.ac.uk, E-mail: rileype@saic.com

Knowledge of the electron density distribution in the solar corona put constraints on the magnetic field configurations for coronal modeling and on initial conditions for solar wind modeling. We work with polarized SOHO/LASCO-C2 images from the last two recent minima of solar activity (1996–1997 and 2008–2010), devoid of coronal mass ejections. The goals are to derive the 4D electron density distributions in the corona by applying a newly developed time-dependent tomographic reconstruction method and to compare the results between the two solar minima and with two magnetohydrodynamic models. First, we confirm that the values of the density distribution in thermodynamic models aremore » more realistic than in polytropic ones. The tomography provides more accurate distributions in the polar regions, and we find that the density in tomographic and thermodynamic solutions varies with the solar cycle in both polar and equatorial regions. Second, we find that the highest-density structures do not always correspond to the predicted large-scale heliospheric current sheet or its helmet streamer but can follow the locations of pseudo-streamers. We deduce that tomography offers reliable density distributions in the corona, reproducing the slow time evolution of coronal structures, without prior knowledge of the coronal magnetic field over a full rotation. Finally, we suggest that the highest-density structures show a differential rotation well above the surface depending on how they are magnetically connected to the surface. Such valuable information on the rotation of large-scale structures could help to connect the sources of the solar wind to their in situ counterparts in future missions such as Solar Orbiter and Solar Probe Plus.« less

8-band and 14-band kp modeling of electronic band structure and material gain in Ga(In)AsBi quantum wells grown on GaAs and InP substrates

DOE Office of Scientific and Technical Information (OSTI.GOV)

Gladysiewicz, M.; Wartak, M. S.; Department of Physics and Computer Science, Wilfrid Laurier University, Waterloo, Ontario N2L 3C5

The electronic band structure and material gain have been calculated for GaAsBi/GaAs quantum wells (QWs) with various bismuth concentrations (Bi ≤ 15%) within the 8-band and 14-band kp models. The 14-band kp model was obtained by extending the standard 8-band kp Hamiltonian by the valence band anticrossing (VBAC) Hamiltonian, which is widely used to describe Bi-related changes in the electronic band structure of dilute bismides. It has been shown that in the range of low carrier concentrations n < 5 × 10{sup 18 }cm{sup −3}, material gain spectra calculated within 8- and 14-band kp Hamiltonians are similar. It means that the 8-band kp model can be usedmore » to calculate material gain in dilute bismides QWs. Therefore, it can be applied to analyze QWs containing new dilute bismides for which the VBAC parameters are unknown. Thus, the energy gap and electron effective mass for Bi-containing materials are used instead of VBAC parameters. The electronic band structure and material gain have been calculated for 8 nm wide GaInAsBi QWs on GaAs and InP substrates with various compositions. In these QWs, Bi concentration was varied from 0% to 5% and indium concentration was tuned in order to keep the same compressive strain (ε = 2%) in QW region. For GaInAsBi/GaAs QW with 5% Bi, gain peak was determined to be at about 1.5 μm. It means that it can be possible to achieve emission at telecommunication windows (i.e., 1.3 μm and 1.55 μm) for GaAs-based lasers containing GaInAsBi/GaAs QWs. For GaInAsBi/Ga{sub 0.47}In{sub 0.53}As/InP QWs with 5% Bi, gain peak is predicted to be at about 4.0 μm, i.e., at the wavelengths that are not available in current InP-based lasers.« less

Theoretical Modeling of Various Spectroscopies for Cuprates and Topological Insulators

NASA Astrophysics Data System (ADS)

Basak, Susmita

Spectroscopies resolved highly in momentum, energy and/or spatial dimensions are playing an important role in unraveling key properties of wide classes of novel materials. However, spectroscopies do not usually provide a direct map of the underlying electronic spectrum, but act as a complex 'filter' to produce a 'mapping' of the underlying energy levels, Fermi surfaces (FSs) and excitation spectra. The connection between the electronic spectrum and the measured spectra is described as a generalized 'matrix element effect'. The nature of the matrix element involved differs greatly between different spectroscopies. For example, in angle-resolved photoemission (ARPES) an incoming photon knocks out an electron from the sample and the energy and momentum of the photoemitted electron is measured. This is quite different from what happens in K-edge resonant inelastic X-ray scattering (RIXS), where an X-ray photon is scattered after inducing electronic transitions near the Fermi energy through an indirect second order process, or in Compton scattering where the incident X-ray photon is scattered inelastically from an electron transferring energy and momentum to the scattering electron. For any given spectroscopy, the matrix element is, in general, a complex function of the phase space of the experiment, e.g. energy/polarization of the incoming photon and the energy/momentum/spin of the photoemitted electron in the case of ARPES. The matrix element can enhance or suppress signals from specific states, or merge signals of groups of states, making a good understanding of the matrix element effects important for not only a robust interpretation of the spectra, but also for ascertaining optimal regions of the experimental phase space for zooming in on states of the greatest interest. In this thesis I discuss a comprehensive scheme for modeling various highly resolved spectroscopies of the cuprates and topological insulators (TIs) where effects of matrix element, crystal structure, strong electron correlations (for cuprates) and spin-orbit coupling (for TIs) are included realistically in material-specific detail. Turning to the cuprates, in order to obtain a realistic description of various spectroscopies, one must include not only the effects of the matrix elements and the complexity of the crystal structure, but also of strong electronic correlations beyond the local density approximation (LDA)-based conventional picture, so that the physics of kinks, pseudogaps and superconductivity can be taken into account properly. In this connection, a self-consistent, intermediate coupling scheme informed by material-specific, first-principles band structures has been developed, where electron correlation effects beyond the LDA are incorporated via appropriate self-energy corrections to the electron and hole one-particle Green's functions. Here the antiferromagnetic (AFM) order is used as the simplest model of a competing order. A number of salient features of the resulting electronic spectrum and its energy, momentum and doping dependencies are in accord with experimental observations in electron as well as hole doped cuprates. This scheme thus provides a reasonable basis for undertaking a comprehensive, beyond-LDA level of modeling of various spectroscopies. The specific topics considered here are: (i) Origin of high-energy kink or the waterfall effect found in ARPES; (ii) Identification of the three energy scales observed in RIXS spectra as the pseudogap, charge transfer gap, and Mott gap; (iii) Evolution of the electron momentum densities with holedoping as seen in Compton scattering experiments. For three dimensional topological insulators, the ARPES and scanning tunneling microscopy (STM) spectra has been analyzed using a tight-binding model as well as a k · p model. The spin-orbit coupling, which is essential to produce the characteristic features of the surface states of a TI, is included realistically in the above models. In our generalized k · p model Dresselhaus spin-orbit coupling term extends up to fifth order to reproduce the correct spin-polarization of the surface electrons. These model calculations explain a number of important features associated with the energy and spins of the surface electrons of the first and second generations of TIs. The specific issues addressed in this article are: (i) Non-orthogonality between spin and momentum of the surface electrons; (ii) Electron dynamics at the TI-metal interface; (iii) Origin of the broken time-reversal symmetry observed in the Fourier transform scanning tunneling spectroscopy.

Direct Visualization of Orbital Flipping in Volborthite by Charge Density Analysis Using Detwinned Data

NASA Astrophysics Data System (ADS)

Sugawara, Kento; Sugimoto, Kunihisa; Fujii, Tatsuya; Higuchi, Takafumi; Katayama, Naoyuki; Okamoto, Yoshihiko; Sawa, Hiroshi

2018-02-01

The distribution of d-orbital valence electrons in volborthite [Cu3V2O7(OH)2 • 2H2O] was investigated by charge density analysis of the multipole model refinement. Diffraction data were obtained by synchrotron radiation single-crystal X-ray diffraction experiments. Data reduction by detwinning of the multiple structural domains was performed using our developed software. In this study, using high-quality data, we demonstrated that the water molecules in volborthite can be located by the hydrogen bonding in cavities that consist of Kagome lattice layers of CuO4(OH)2 and pillars of V2O7. Final multipole refinements before and after the structural phase transition directly visualized the deformation electron density of the valence electrons. We successfully directly visualized the orbital flipping of the d-orbital dx2-y2, which is the highest level of 3d orbitals occupied by d9 electrons in volborthite. The developed techniques and software can be employed for investigations of structural properties of systems with multiple structural domains.

All-electron quasiparticle self-consistent GW band structures for SrTiO 3 including lattice polarization corrections in different phases

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bhandari, Churna; van Schilfgaarde, Mark; Kotani, Takao

The electronic band structure of SrTiO3 is investigated in the all-electron quasiparticle self-consistent GW (QSGW) approximation. Unlike previous pseudopotential-based QSGW or single-shot G0W0 calculations, the gap is found to be significantly overestimated compared to experiment. After putting in a correction for the underestimate of the screening by the random phase approximation in terms of a 0.8Σ approach, the gap is still overestimated. The 0.8Σ approach is discussed and justified in terms of various recent literature results including electron-hole corrections. Adding a lattice polarization correction (LPC) in the q→0 limit for the screening of W, agreement with experiment is recovered. Themore » LPC is alternatively estimated using a polaron model. Here, we apply our approach to the cubic and tetragonal phases as well as a hypothetical layered postperovskite structure and find that the local density approximation (LDA) to GW gap correction is almost independent of structure.« less

All-electron quasiparticle self-consistent GW band structures for SrTiO 3 including lattice polarization corrections in different phases

DOE PAGES

Bhandari, Churna; van Schilfgaarde, Mark; Kotani, Takao; ...

2018-01-23

The electronic band structure of SrTiO3 is investigated in the all-electron quasiparticle self-consistent GW (QSGW) approximation. Unlike previous pseudopotential-based QSGW or single-shot G0W0 calculations, the gap is found to be significantly overestimated compared to experiment. After putting in a correction for the underestimate of the screening by the random phase approximation in terms of a 0.8Σ approach, the gap is still overestimated. The 0.8Σ approach is discussed and justified in terms of various recent literature results including electron-hole corrections. Adding a lattice polarization correction (LPC) in the q→0 limit for the screening of W, agreement with experiment is recovered. Themore » LPC is alternatively estimated using a polaron model. Here, we apply our approach to the cubic and tetragonal phases as well as a hypothetical layered postperovskite structure and find that the local density approximation (LDA) to GW gap correction is almost independent of structure.« less

Theoretical study of orbital ordering induced structural phase transition in iron pnictides

DOE Office of Scientific and Technical Information (OSTI.GOV)

Jena, Sushree Sangita, E-mail: sushree@iopb.res.in; Rout, G. C., E-mail: gcr@iopb.res.in; Panda, S. K., E-mail: skp@iopb.res.in

2016-05-06

We attribute the structural phase transition (SPT) in the parent compounds of the iron pnictides to orbital ordering. Due to anisotropy of the d{sub xz} and d{sub yz} orbitals in the xy plane, orbital ordering makes the orthorhombic structure more favorable and thus inducing the SPT. We consider a one band model Hamiltonian consisting of first and second-nearest-neighbor hopping of the electrons. We introduce Jahn-Tellar (JT) distortion in the system arising due to the orbital ordering present in this system. We calculate the electron Green’s function by using Zuvareb’s Green’s function technique and hence calculate an expression for the temperaturemore » dependent lattice strain which is computed numerically and self-consistently. The temperature dependent electron specific heat is calculated by minimizing the free energy of the system. The lattice strain is studied by varying the JT coupling and elastic constant of the system. The structural anomaly is studied through the electron occupation number and the specific heat by varying the physical parameters like JT coupling, lattice constant, chemical potential and hopping integrals of the system.« less

Effective mass and Fermi surface complexity factor from ab initio band structure calculations

NASA Astrophysics Data System (ADS)

Gibbs, Zachary M.; Ricci, Francesco; Li, Guodong; Zhu, Hong; Persson, Kristin; Ceder, Gerbrand; Hautier, Geoffroy; Jain, Anubhav; Snyder, G. Jeffrey

2017-02-01

The effective mass is a convenient descriptor of the electronic band structure used to characterize the density of states and electron transport based on a free electron model. While effective mass is an excellent first-order descriptor in real systems, the exact value can have several definitions, each of which describe a different aspect of electron transport. Here we use Boltzmann transport calculations applied to ab initio band structures to extract a density-of-states effective mass from the Seebeck Coefficient and an inertial mass from the electrical conductivity to characterize the band structure irrespective of the exact scattering mechanism. We identify a Fermi Surface Complexity Factor: Nv*K* from the ratio of these two masses, which in simple cases depends on the number of Fermi surface pockets (Nv* ) and their anisotropy K*, both of which are beneficial to high thermoelectric performance as exemplified by the high values found in PbTe. The Fermi Surface Complexity factor can be used in high-throughput search of promising thermoelectric materials.

Lateral terahertz hot-electron bolometer based on an array of Sn nanothreads in GaAs

NASA Astrophysics Data System (ADS)

Ponomarev, D. S.; Lavrukhin, D. V.; Yachmenev, A. E.; Khabibullin, R. A.; Semenikhin, I. E.; Vyurkov, V. V.; Ryzhii, M.; Otsuji, T.; Ryzhii, V.

2018-04-01

We report on the proposal and the theoretical and experimental studies of the terahertz hot-electron bolometer (THz HEB) based on a gated GaAs structure like the field-effect transistor with the array of parallel Sn nanothreads (Sn-NTs). The operation of the HEB is associated with an increase in the density of the delocalized electrons due to their heating by the incoming THz radiation. The quantum and the classical device models were developed, the quantum one was based on the self-consistent solution of the Poisson and Schrödinger equations, the classical model involved the Poisson equation and density of states omitting quantization. We calculated the electron energy distributions in the channels formed around the Sn-NTs for different gate voltages and found the fraction of the delocalized electrons propagating across the energy barriers between the NTs. Since the fraction of the delocalized electrons strongly depends on the average electron energy (effective temperature), the proposed THz HEB can exhibit an elevated responsivity compared with the HEBs based on more standard heterostructures. Due to a substantial anisotropy of the device structure, the THz HEB may demonstrate a noticeable polarization selectivity of the response to the in-plane polarized THz radiation. The features of the THz HEB might be useful in their practical applications in biology, medicine and material science.

A minimal model for the structural energetics of VO2

NASA Astrophysics Data System (ADS)

Kim, Chanul; Marianetti, Chris; The Marianetti Group Team

Resolving the structural, magnetic, and electronic structure of VO2 from the first-principles of quantum mechanics is still a forefront problem despite decades of attention. Hybrid functionals have been shown to qualitatively ruin the structural energetics. While density functional theory (DFT) combined with cluster extensions of dynamical mean-field theory (DMFT) have demonstrated promising results in terms of the electronic properties, structural phase stability has not yet been addressed. In order to capture the basic physics of the structural transition, we propose a minimal model of VO2 based on the one dimensional Peierls-Hubbard model and parameterize this based on DFT calculations of VO2. The total energy versus dimerization in the minimal mode is then solved numerically exactly using density matrix renormalization group (DMRG) and compared to the Hartree-Fock solution. We demonstrate that the Hartree-Fock solution exhibits the same pathologies as DFT+U, and spin density functional theory for that matter, while the DMRG solution is consistent with experimental observation. Our results demonstrate the critical role of non-locality in the total energy, and this will need to be accounted for to obtain a complete description of VO2 from first-principles. The authors acknowledge support from FAME, one of six centers of STARnet, a Semiconductor Research Corporation program sponsored by MARCO and DARPA.

A high-level object-oriented model for representing relationships in an electronic medical record.

PubMed Central

Dolin, R. H.

1994-01-01

The importance of electronic medical records to improve the quality and cost-effectiveness of medical care continues to be realized. This growing importance has spawned efforts at defining the structure and content of medical data, which is heterogeneous, highly inter-related, and complex. Computer-assisted data modeling tools have greatly facilitated the process of representing medical data, however the complex inter-relationships of medical information can result in data models that are large and cumbersome to manipulate and view. This report presents a high-level object-oriented model for representing the relationships between objects or entities that might exist in an electronic medical record. By defining the relationship between objects at a high level and providing for inheritance, this model enables relating any medical entity to any other medical entity, even though the relationships were not directly specified or known during data model design. PMID:7949981

Amp: A modular approach to machine learning in atomistic simulations

NASA Astrophysics Data System (ADS)

Khorshidi, Alireza; Peterson, Andrew A.

2016-10-01

Electronic structure calculations, such as those employing Kohn-Sham density functional theory or ab initio wavefunction theories, have allowed for atomistic-level understandings of a wide variety of phenomena and properties of matter at small scales. However, the computational cost of electronic structure methods drastically increases with length and time scales, which makes these methods difficult for long time-scale molecular dynamics simulations or large-sized systems. Machine-learning techniques can provide accurate potentials that can match the quality of electronic structure calculations, provided sufficient training data. These potentials can then be used to rapidly simulate large and long time-scale phenomena at similar quality to the parent electronic structure approach. Machine-learning potentials usually take a bias-free mathematical form and can be readily developed for a wide variety of systems. Electronic structure calculations have favorable properties-namely that they are noiseless and targeted training data can be produced on-demand-that make them particularly well-suited for machine learning. This paper discusses our modular approach to atomistic machine learning through the development of the open-source Atomistic Machine-learning Package (Amp), which allows for representations of both the total and atom-centered potential energy surface, in both periodic and non-periodic systems. Potentials developed through the atom-centered approach are simultaneously applicable for systems with various sizes. Interpolation can be enhanced by introducing custom descriptors of the local environment. We demonstrate this in the current work for Gaussian-type, bispectrum, and Zernike-type descriptors. Amp has an intuitive and modular structure with an interface through the python scripting language yet has parallelizable fortran components for demanding tasks; it is designed to integrate closely with the widely used Atomic Simulation Environment (ASE), which makes it compatible with a wide variety of commercial and open-source electronic structure codes. We finally demonstrate that the neural network model inside Amp can accurately interpolate electronic structure energies as well as forces of thousands of multi-species atomic systems.

The derivative discontinuity of the exchange-correlation functional.

PubMed

Mori-Sánchez, Paula; Cohen, Aron J

2014-07-28

The derivative discontinuity is a key concept in electronic structure theory in general and density functional theory in particular. The electronic energy of a quantum system exhibits derivative discontinuities with respect to different degrees of freedom that are a consequence of the integer nature of electrons. The classical understanding refers to the derivative discontinuity of the total energy as a function of the total number of electrons (N), but it can also manifest at constant N. Examples are shown in models including several hydrogen systems with varying numbers of electrons or nuclear charge (Z), as well as the 1-dimensional Hubbard model (1DHM). Two sides of the problem are investigated: first, the failure of currently used approximate exchange-correlation functionals in DFT and, second, the importance of the derivative discontinuity in the exact electronic structure of molecules, as revealed by full configuration interaction (FCI). Currently, all approximate functionals, including hybrids, miss the derivative discontinuity, leading to basic errors that can be seen in many ways: from the complete failure to give the total energy of H2 and H2(+), to the missing gap in Mott insulators such as stretched H2 and the thermodynamic limit of the 1DHM, or a qualitatively incorrect density in the HZ molecule with two electrons and incorrect electron transfer processes. Description of the exact particle behaviour of electrons is emphasised, which is key to many important physical processes in real systems, especially those involving electron transfer, and offers a challenge for the development of new exchange-correlation functionals.

Electronics reliability fracture mechanics. Volume 2: Fracture mechanics

NASA Astrophysics Data System (ADS)

Kallis, J.; Duncan, L.; Buechler, D.; Backes, P.; Sandkulla, D.

1992-05-01

This is the second of two volumes. The other volume (WL-TR-92-3015) is 'Causes of Failures of Shop Replaceable Units and Hybrid Microcircuits.' The objective of the Electronics Reliability Fracture Mechanics (ERFM) program was to develop and demonstrate a life prediction technique for electronic assemblies, when subjected to environmental stresses of vibration and thermal cycling, based upon the mechanical properties of the materials and packaging configurations which make up an electronic system. The application of fracture mechanics to microscale phenomena in electronic assemblies was a pioneering research effort. The small scale made the experiments very difficult; for example, the 1-mil-diameter bond wires in microelectronic devices are 1/3 the diameter of a human hair. A number of issues had to be resolved to determine whether a fracture mechanics modelling approach is correct for the selected failures; specifically, the following two issues had to be resolved: What fraction of the lifetime is spent in crack initiation? Are macro fracture mechanics techniques, used in large structures such as bridges, applicable to the tiny structures in electronic equipment? The following structural failure mechanisms were selected for modelling: bondwire fracture from mechanical cycling; bondwire fracture from thermal (power) cycling; plated through hole (PTH) fracture from thermal cycling. The bondwire fracture test specimens were A1-1 percent Si wires, representative of wires used in the parts in the modules selected for detailed investigation in this program (see Vol. 1 of this report); 1-mil-diameter wires were tested in this program. The PTH test specimens were sections of 14-layer printed wiring boards of the type used.

Langmuir Probe Measurements in an Inductively Coupled GEC Reference Cell Plasma

NASA Technical Reports Server (NTRS)

Ji, J. S.; Kim, J. S.; Cappelli, M. A.; Sharma, S. P.; Arnold, J. O. (Technical Monitor)

1998-01-01

Measurements of electron number density, electron temperature, and electron energy distribution function (EEDF) using a compensated Langmuir probe have been performed on an inductively (transformer ) coupled Gaseous Electronics Conference (GEC) reference cell plasma. The plasma source is operated with CH4, CF4, or their mixtures with argon. The effect of independently driving the electrode supporting the wafer on the probe data is studied. In particular, we find that the plasma structure depends on the phase in addition to the magnitude of the power coupled to the electrode relative to that of the transformer coil. The Langmuir probe is translated in a plane parallel to the electrode to investigate the spatial structure of the plasma. The probe data is also compared with fluid model predictions.

Ion Streaming Instabilities in Pair Ion Plasma and Localized Structure with Non-Thermal Electrons

NASA Astrophysics Data System (ADS)

Nasir Khattak, M.; Mushtaq, A.; Qamar, A.

2015-12-01

Pair ion plasma with a fraction of non-thermal electrons is considered. We investigate the effects of the streaming motion of ions on linear and nonlinear properties of unmagnetized, collisionless plasma by using the fluid model. A dispersion relation is derived, and the growth rate of streaming instabilities with effect of streaming motion of ions and non-thermal electrons is calculated. A qausi-potential approach is adopted to study the characteristics of ion acoustic solitons. An energy integral equation involving Sagdeev potential is derived during this process. The presence of the streaming term in the energy integral equation affects the structure of the solitary waves significantly along with non-thermal electrons. Possible application of the work to the space and laboratory plasmas are highlighted.

Electron transfer flavoprotein domain II orientation monitored using double electron-electron resonance between an enzymatically reduced, native FAD cofactor, and spin labels

PubMed Central

Swanson, Michael A; Kathirvelu, Velavan; Majtan, Tomas; Frerman, Frank E; Eaton, Gareth R; Eaton, Sandra S

2011-01-01

Human electron transfer flavoprotein (ETF) is a soluble mitochondrial heterodimeric flavoprotein that links fatty acid β-oxidation to the main respiratory chain. The crystal structure of human ETF bound to medium chain acyl-CoA dehydrogenase indicates that the flavin adenine dinucleotide (FAD) domain (αII) is mobile, which permits more rapid electron transfer with donors and acceptors by providing closer access to the flavin and allows ETF to accept electrons from at least 10 different flavoprotein dehydrogenases. Sequence homology is high and low-angle X-ray scattering is identical for Paracoccus denitrificans (P. denitrificans) and human ETF. To characterize the orientations of the αII domain of P. denitrificans ETF, distances between enzymatically reduced FAD and spin labels in the three structural domains were measured by double electron-electron resonance (DEER) at X- and Q-bands. An FAD to spin label distance of 2.8 ± 0.15 nm for the label in the FAD-containing αII domain (A210C) agreed with estimates from the crystal structure (3.0 nm), molecular dynamics simulations (2.7 nm), and rotamer library analysis (2.8 nm). Distances between the reduced FAD and labels in αI (A43C) were between 4.0 and 4.5 ± 0.35 nm and for βIII (A111C) the distance was 4.3 ± 0.15 nm. These values were intermediate between estimates from the crystal structure of P. denitrificans ETF and a homology model based on substrate-bound human ETF. These distances suggest that the αII domain adopts orientations in solution that are intermediate between those which are observed in the crystal structures of free ETF (closed) and ETF bound to a dehydrogenase (open). PMID:21308847

Visualizing the global secondary structure of a viral RNA genome with cryo-electron microscopy

PubMed Central

Garmann, Rees F.; Gopal, Ajaykumar; Athavale, Shreyas S.; Knobler, Charles M.; Gelbart, William M.; Harvey, Stephen C.

2015-01-01

The lifecycle, and therefore the virulence, of single-stranded (ss)-RNA viruses is regulated not only by their particular protein gene products, but also by the secondary and tertiary structure of their genomes. The secondary structure of the entire genomic RNA of satellite tobacco mosaic virus (STMV) was recently determined by selective 2′-hydroxyl acylation analyzed by primer extension (SHAPE). The SHAPE analysis suggested a single highly extended secondary structure with much less branching than occurs in the ensemble of structures predicted by purely thermodynamic algorithms. Here we examine the solution-equilibrated STMV genome by direct visualization with cryo-electron microscopy (cryo-EM), using an RNA of similar length transcribed from the yeast genome as a control. The cryo-EM data reveal an ensemble of branching patterns that are collectively consistent with the SHAPE-derived secondary structure model. Thus, our results both elucidate the statistical nature of the secondary structure of large ss-RNAs and give visual support for modern RNA structure determination methods. Additionally, this work introduces cryo-EM as a means to distinguish between competing secondary structure models if the models differ significantly in terms of the number and/or length of branches. Furthermore, with the latest advances in cryo-EM technology, we suggest the possibility of developing methods that incorporate restraints from cryo-EM into the next generation of algorithms for the determination of RNA secondary and tertiary structures. PMID:25752599

Structure-property relationships in cubic cuprous iodide: A novel view on stability, chemical bonding, and electronic properties

NASA Astrophysics Data System (ADS)

Pishtshev, A.; Karazhanov, S. Zh.

2017-02-01

Based on the combination of density functional theory and theory-group methods, we performed systematic modeling of γ-CuI structural design at the atomistic level. Being started from the metallic copper lattice, we treated a crystal assembly as a stepwise iodination process characterized in terms of a sequence of intermediate lattice geometries. These geometries were selected and validated via screening of possible structural transformations. The genesis of chemical bonding was studied for three structural transformations by analyzing the relevant changes in the topology of valence electron densities. We determined structural trends driven by metal-ligand coupling. This allowed us to suggest the improved scenario of chemical bonding in γ-CuI. In particular, the unconventional effect of spatial separation of metallic and covalent interactions was found to be very important with respect to the preferred arrangements of valence electrons in the iodination process. We rigorously showed that useful electronic and optical properties of γ-CuI originate from the combination of two separated bonding patterns—strong covalency established in I-Cu tetrahedral connections and noncovalent interactions of copper cores is caused by the 3d10 closed-shell electron configurations. The other finding of ours is that the self-consistency of the GW calculations is crucial for correctly determining the dynamic electronic correlations in γ-CuI. Detail reinvestigation of the quasi-particle energy structure by means of the self-consistent GW approach allowed us to explain how p-type electrical conductivity can be engineered in the material.

Rechargeable magnesium-ion battery based on a TiSe2-cathode with d-p orbital hybridized electronic structure

PubMed Central

Gu, Yunpeng; Katsura, Yukari; Yoshino, Takafumi; Takagi, Hidenori; Taniguchi, Kouji

2015-01-01

Rechargeable ion-batteries, in which ions such as Li+ carry charges between electrodes, have been contributing to the improvement of power-source performance in a wide variety of mobile electronic devices. Among them, Mg-ion batteries are recently attracting attention due to possible low cost and safety, which are realized by abundant natural resources and stability of Mg in the atmosphere. However, only a few materials have been known to work as rechargeable cathodes for Mg-ion batteries, owing to strong electrostatic interaction between Mg2+ and the host lattice. Here we demonstrate rechargeable performance of Mg-ion batteries at ambient temperature by selecting TiSe2 as a model cathode by focusing on electronic structure. Charge delocalization of electrons in a metal-ligand unit through d-p orbital hybridization is suggested as a possible key factor to realize reversible intercalation of Mg2+ into TiSe2. The viewpoint from the electronic structure proposed in this study might pave a new way to design electrode materials for multivalent-ion batteries. PMID:26228263

Analytical and numerical analysis of imaging mechanism of dynamic scanning electron microscopy.

PubMed

Schröter, M-A; Holschneider, M; Sturm, H

2012-11-02

The direct observation of small oscillating structures with the help of a scanning electron beam is a new approach to study the vibrational dynamics of cantilevers and microelectromechanical systems. In the scanning electron microscope, the conventional signal of secondary electrons (SE, dc part) is separated from the signal response of the SE detector, which is correlated to the respective excitation frequency for vibration by means of a lock-in amplifier. The dynamic response is separated either into images of amplitude and phase shift or into real and imaginary parts. Spatial resolution is limited to the diameter of the electron beam. The sensitivity limit to vibrational motion is estimated to be sub-nanometer for high integration times. Due to complex imaging mechanisms, a theoretical model was developed for the interpretation of the obtained measurements, relating cantilever shapes to interaction processes consisting of incident electron beam, electron-lever interaction, emitted electrons and detector response. Conclusions drawn from this new model are compared with numerical results based on the Euler-Bernoulli equation.

Black Box Real-Time Transient Absorption Spectroscopy and Electron Correlation

NASA Astrophysics Data System (ADS)

Parkhill, John

2017-06-01

We introduce an atomistic, all-electron, black-box electronic structure code to simulate transient absorption (TA) spectra and apply it to simulate pyrazole and a GFP- chromophore derivative1. The method is an application of OSCF2, our dissipative exten- sion of time-dependent density-functional theory. We compare our simulated spectra directly with recent ultra-fast spectroscopic experiments. We identify features in the TA spectra to Pauli-blocking which may be missed without a first-principles model. An important ingredient in this method is the stationary-TDDFT correction scheme recently put forwards by Fischer, Govind, and Cramer which allows us to overcome a limitation of adiabatic TDDFT. We demonstrate that OSCF2 is able to reproduce the energies of bleaches and induced absorptions, as well as the decay of the transient spectrum, with only the molecular structure as input. We show that the treatment of electron correlation is the biggest hurdle for TA simulations, which motivates the second half of the talk a new method for realtime electron correlation. We continue to derive and propagate self-consistent electronic dynamics. Extending our derivation of OSCF2 to include electron correlation we obtain a non-linear correlated one-body equation of motion which corrects TDHF. Similar equations are known in quantum kinetic theory, but rare in electronic structure. We introduce approximations that stabilize the theory and reduce its computational cost. We compare the resulting dynamics with well-known exact and approximate theories showing improvements over TDHF. When propagated EE2 changes occupation numbers like exact theory, an important feature missing from TDHF or TDDFT. We introduce a rotating wave approximation to reduce the scaling of the model to O(N^4), and enable propagation on realistically large systems. The equation-of-motion does not rely on a pure-state model for the electronic state, and could be used to study the relationship between electron correlation and relaxation/dephasing or as a non-adiabatic kernel for TDDFT. We show that a quasi-thermal Fermi-Dirac population of one-particle states is a stationary state of the method reached as the endpoint of propagation in some limits. We discuss this 'thermalization' of an isolated quantum many-body system in the context of the eigenstate thermalization hypothesis.

Electronic structure of dense Pb overlayers on Si(111) investigated using angle-resolved photoemission

NASA Astrophysics Data System (ADS)

Choi, W. H.; Koh, H.; Rotenberg, E.; Yeom, H. W.

2007-02-01

Dense Pb overlayers on Si(111) are important as the wetting layer for anomalous Pb island growth as well as for their own complex “devil’s-staircase” phases. The electronic structures of dense Pb overlayers on Si(111) were investigated in detail by angle-resolved photoemission. Among the series of ordered phases found recently above one monolayer, the low-coverage 7×3 and the high-coverage 14×3 phases are studied; they are well ordered and form reproducibly in large areas. The band dispersions and Fermi surfaces of the two-dimensional (2D) electronic states of these overlayers are mapped out. A number of metallic surface-state bands are identified for both phases with complex Fermi contours. The basic features of the observed Fermi contours can be explained by overlapping 2D free-electron-like Fermi circles. This analysis reveals that the 2D electrons near the Fermi level of the 7×3 and 14×3 phases are mainly governed by strong 1×1 and 3×3 potentials, respectively. The origins of the 2D electronic states and their apparent Fermi surface shapes are discussed based on recent structure models.

Electronic structures of 1-ML C84/Ag(111): Energy level alignment and work function variation

NASA Astrophysics Data System (ADS)

Wang, Peng; Zhao, Li-Li; Zhang, Jin-Juan; Li, Wen-Jie; Liu, Wei-Hui; Chen, Da; Sheng, Chun-Qi; Wang, Jia-Ou; Qian, Hai-Jie; Ibrahim, Kurash; Li, Hong-Nian

2017-12-01

The electronic structures of fullerene/metal interface are critical to the performance of devices based on fullerene in molecular electronics and organic electronics. Herein, we investigate the electronic structures at the interface between C84 and Ag(111) by photoelectron spectroscopy and soft X-ray absorption spectroscopy techniques. It is observed that C84 monolayer on Ag(111) surface (1-ML C84/Ag(111)) has metallic nature. A charge transfer from substrate to the unoccupied states of C84 is determined to be 1.3 electrons per molecule. However, the work function of 1-ML C84 (4.72 eV) is observed slightly larger than that of the clean Ag(111) substrate (4.50 eV). A bidirectional charge transfer model is introduced to understand the work function variation of the fullerene/metal system. In addition to the charge transfer from substrate to the adsorbate's unoccupied states, there exists non-negligible back charge transfer from fullerene occupied molecular orbital to the metal substrate through interfacial hybridization. The Fermi level will be pinned at ∼4.72 eV for C84 monolayer on coinage metal substrate.

Insights on energy selective contacts for thermal energy harvesting using double resonant tunneling contacts and numerical modeling

NASA Astrophysics Data System (ADS)

Julian, A.; Jehl, Z.; Miyashita, N.; Okada, Y.; Guillemoles, J.-F.

2016-12-01

Energy selective electrical contacts have been proposed as a way to approach ultimate efficiencies both for thermoelectric and photovoltaic devices as they allow a reduction of the entropy production during the energy conversion process. A self-consistent numerical model based on the transfer matrix approach in the effective mass and envelope function approximation has been developed to calculate the electronic properties of double resonant tunneling barriers used as energy selective contacts in hot carrier solar cells. It is found that the application of an external electric bias significantly degrades the electronic transmission of the structure, and thus the tunneling current in the current-voltage characteristic. This is due to a symmetry breaking which can be offset using finely tuned asymmetric double resonant tunneling barriers, leading to a full recovery of the tunneling current in our model. Moreover, we model the heterostructure using electrons temperature in the emitter higher than that of the lattice, providing insights on the interpretation of experimental devices functioning in hot carrier conditions, especially regarding the previously reported shift of the resonance peak (negative differential resistance), which we interpret as related to a shift in the hot electron distribution while the maximum remains at the conduction band edge of the emitter. Finally, experimental results are presented using asymmetric structure showing significantly improved resonant properties at room temperature with very sharp negative differential resistance.

Many-particle-effects in the theory of the extended X-ray absorption fine structure

NASA Astrophysics Data System (ADS)

Tran Thoai, D. B.; Ekardt, W.

1981-10-01

The Lee-Beni-procedure for the calculation of the extended X-ray absorption fine structure (EXAFS) is extended so as to include the effects of the electronic charge density outside the localized muffin-tin potentials. In our scheme EXAFS is caused by back-scattering of an elementary excitation of a homogeneous electron gas by localized energy dependent many-particle muffin-tin potentials. The difference between the two schemes is negligible at large k's, as expected from physical grounds. However, at small and intermediate k-values the difference is quite large. The effect of the outer electrons as compared to the Lee-Beni-model is twofold. First, they renormalize the scattered electron in the usual way. Second, they are missing within the scattering muffin-tins. Hence, we avoid to count some of the electrons twice. Results are presented for Cu as an example.

Electronically decoupled stacking fault tetrahedra embedded in Au(111) films

PubMed Central

Schouteden, Koen; Amin-Ahmadi, Behnam; Li, Zhe; Muzychenko, Dmitry; Schryvers, Dominique; Van Haesendonck, Chris

2016-01-01

Stacking faults are known as defective structures in crystalline materials that typically lower the structural quality of the material. Here, we show that a particular type of defect, that is, stacking fault tetrahedra (SFTs), exhibits pronounced quantized electronic behaviour, revealing a potential synthetic route to decoupled nanoparticles in metal films. We report on the electronic properties of SFTs that exist in Au(111) films, as evidenced by scanning tunnelling microscopy and confirmed by transmission electron microscopy. We find that the SFTs reveal a remarkable decoupling from their metal surroundings, leading to pronounced energy level quantization effects within the SFTs. The electronic behaviour of the SFTs can be described well by the particle-in-a-box model. Our findings demonstrate that controlled preparation of SFTs may offer an alternative way to achieve well-decoupled nanoparticles of high crystalline quality in metal thin films without the need of thin insulating layers. PMID:28008910

Electronically decoupled stacking fault tetrahedra embedded in Au(111) films.

PubMed

Schouteden, Koen; Amin-Ahmadi, Behnam; Li, Zhe; Muzychenko, Dmitry; Schryvers, Dominique; Van Haesendonck, Chris

2016-12-23

Stacking faults are known as defective structures in crystalline materials that typically lower the structural quality of the material. Here, we show that a particular type of defect, that is, stacking fault tetrahedra (SFTs), exhibits pronounced quantized electronic behaviour, revealing a potential synthetic route to decoupled nanoparticles in metal films. We report on the electronic properties of SFTs that exist in Au(111) films, as evidenced by scanning tunnelling microscopy and confirmed by transmission electron microscopy. We find that the SFTs reveal a remarkable decoupling from their metal surroundings, leading to pronounced energy level quantization effects within the SFTs. The electronic behaviour of the SFTs can be described well by the particle-in-a-box model. Our findings demonstrate that controlled preparation of SFTs may offer an alternative way to achieve well-decoupled nanoparticles of high crystalline quality in metal thin films without the need of thin insulating layers.

The World as Viewed by and with Unpaired Electrons

PubMed Central

Eaton, Sandra S.; Eaton, Gareth R.

2012-01-01

Recent advances in electron paramagnetic resonance (EPR) include capabilities for applications to areas as diverse as archeology, beer shelf life, biological structure, dosimetry, in vivo imaging, molecular magnets, and quantum computing. Enabling technologies include multifrequency continuous wave, pulsed, and rapid scan EPR. Interpretation is enhanced by increasingly powerful computational models. PMID:22975244