Hierarchical atom type definitions and extensible all-atom force fields.

Science.gov (United States)

Jin, Zhao; Yang, Chunwei; Cao, Fenglei; Li, Feng; Jing, Zhifeng; Chen, Long; Shen, Zhe; Xin, Liang; Tong, Sijia; Sun, Huai

2016-03-15

The extensibility of force field is a key to solve the missing parameter problem commonly found in force field applications. The extensibility of conventional force fields is traditionally managed in the parameterization procedure, which becomes impractical as the coverage of the force field increases above a threshold. A hierarchical atom-type definition (HAD) scheme is proposed to make extensible atom type definitions, which ensures that the force field developed based on the definitions are extensible. To demonstrate how HAD works and to prepare a foundation for future developments, two general force fields based on AMBER and DFF functional forms are parameterized for common organic molecules. The force field parameters are derived from the same set of quantum mechanical data and experimental liquid data using an automated parameterization tool, and validated by calculating molecular and liquid properties. The hydration free energies are calculated successfully by introducing a polarization scaling factor to the dispersion term between the solvent and solute molecules. © 2015 Wiley Periodicals, Inc. © 2015 Wiley Periodicals, Inc.

Physico-Chemical and Structural Interpretation of Discrete Derivative Indices on N-Tuples Atoms

Science.gov (United States)

Martínez-Santiago, Oscar; Marrero-Ponce, Yovani; Barigye, Stephen J.; Le Thi Thu, Huong; Torres, F. Javier; Zambrano, Cesar H.; Muñiz Olite, Jorge L.; Cruz-Monteagudo, Maykel; Vivas-Reyes, Ricardo; Vázquez Infante, Liliana; Artiles Martínez, Luis M.

2016-01-01

This report examines the interpretation of the Graph Derivative Indices (GDIs) from three different perspectives (i.e., in structural, steric and electronic terms). It is found that the individual vertex frequencies may be expressed in terms of the geometrical and electronic reactivity of the atoms and bonds, respectively. On the other hand, it is demonstrated that the GDIs are sensitive to progressive structural modifications in terms of: size, ramifications, electronic richness, conjugation effects and molecular symmetry. Moreover, it is observed that the GDIs quantify the interaction capacity among molecules and codify information on the activation entropy. A structure property relationship study reveals that there exists a direct correspondence between the individual frequencies of atoms and Hückel’s Free Valence, as well as between the atomic GDIs and the chemical shift in NMR, which collectively validates the theory that these indices codify steric and electronic information of the atoms in a molecule. Taking in consideration the regularity and coherence found in experiments performed with the GDIs, it is possible to say that GDIs possess plausible interpretation in structural and physicochemical terms. PMID:27240357

An atomic model of brome mosaic virus using direct electron detection and real-space optimization

Science.gov (United States)

Wang, Zhao; Hryc, Corey F.; Bammes, Benjamin; Afonine, Pavel V.; Jakana, Joanita; Chen, Dong-Hua; Liu, Xiangan; Baker, Matthew L.; Kao, Cheng; Ludtke, Steven J.; Schmid, Michael F.; Adams, Paul D.; Chiu, Wah

2014-09-01

Advances in electron cryo-microscopy have enabled structure determination of macromolecules at near-atomic resolution. However, structure determination, even using de novo methods, remains susceptible to model bias and overfitting. Here we describe a complete workflow for data acquisition, image processing, all-atom modelling and validation of brome mosaic virus, an RNA virus. Data were collected with a direct electron detector in integrating mode and an exposure beyond the traditional radiation damage limit. The final density map has a resolution of 3.8 Å as assessed by two independent data sets and maps. We used the map to derive an all-atom model with a newly implemented real-space optimization protocol. The validity of the model was verified by its match with the density map and a previous model from X-ray crystallography, as well as the internal consistency of models from independent maps. This study demonstrates a practical approach to obtain a rigorously validated atomic resolution electron cryo-microscopy structure.

Atomic Reference Data for Electronic Structure Calculations

CERN Document Server

Kotochigova, S; Shirley, E L

We have generated data for atomic electronic structure calculations, to provide a standard reference for results of specified accuracy under commonly used approximations. Results are presented here for total energies and orbital energy eigenvalues for all atoms from H to U, at microHartree accuracy in the total energy, as computed in the local-density approximation (LDA) the local-spin-density approximation (LSD); the relativistic local-density approximation (RLDA); and scalar-relativistic local-density approximation (ScRLDA).

Atomic structure in black hole

International Nuclear Information System (INIS)

Nagatani, Yukinori

2006-01-01

We propose that any black hole has atomic structure in its inside and has no horizon as a model of black holes. Our proposal is founded on a mean field approximation of gravity. The structure of our model consists of a (charged) singularity at the center and quantum fluctuations of fields around the singularity, namely, it is quite similar to that of atoms. Any properties of black holes, e.g. entropy, can be explained by the model. The model naturally quantizes black holes. In particular, we find the minimum black hole, whose structure is similar to that of the hydrogen atom and whose Schwarzschild radius is approximately 1.1287 times the Planck length. Our approach is conceptually similar to Bohr's model of the atomic structure, and the concept of the minimum Schwarzschild radius is similar to that of the Bohr radius. The model predicts that black holes carry baryon number, and the baryon number is rapidly violated. This baryon number violation can be used as verification of the model. (author)

Physico-Chemical and Structural Interpretation of Discrete Derivative Indices on N-Tuples Atoms

Directory of Open Access Journals (Sweden)

Oscar Martínez-Santiago

2016-05-01

Full Text Available This report examines the interpretation of the Graph Derivative Indices (GDIs from three different perspectives (i.e., in structural, steric and electronic terms. It is found that the individual vertex frequencies may be expressed in terms of the geometrical and electronic reactivity of the atoms and bonds, respectively. On the other hand, it is demonstrated that the GDIs are sensitive to progressive structural modifications in terms of: size, ramifications, electronic richness, conjugation effects and molecular symmetry. Moreover, it is observed that the GDIs quantify the interaction capacity among molecules and codify information on the activation entropy. A structure property relationship study reveals that there exists a direct correspondence between the individual frequencies of atoms and Hückel’s Free Valence, as well as between the atomic GDIs and the chemical shift in NMR, which collectively validates the theory that these indices codify steric and electronic information of the atoms in a molecule. Taking in consideration the regularity and coherence found in experiments performed with the GDIs, it is possible to say that GDIs possess plausible interpretation in structural and physicochemical terms.

Direct experimental determination of the atomic structure at internal interfaces

Energy Technology Data Exchange (ETDEWEB)

Browning, N.D. [Oak Ridge National Lab., TN (United States)]|[Illinois Univ., Chicago, IL (United States); Pennycook, S.J. [Oak Ridge National Lab., TN (United States)

1995-07-01

A crucial first step in understanding the effect that internal interfaces have on the properties of materials is the ability to determine the atomic structure at the interface. As interfaces can contain atomic disorder, dislocations, segregated impurities and interphases, sensitivity to all of these features is essential for complete experimental characterization. By combining Z-contrast imaging and electron energy loss spectroscopy (EELS) in a dedicated scanning transmission electron microscope (STEM), the ability to probe the structure, bonding and composition at interfaces with the necessary atomic resolution has been obtained. Experimental conditions can be controlled to provide, simultaneously, both incoherent imaging and spectroscopy. This enables interface structures observed in the image to be interpreted intuitively and the bonding in a specified atomic column to be probed directly by EELS. The bonding and structure information can then be correlated using bond-valence sum analysis to produce structural models. This technique is demonstrated for 25{degrees}, 36{degrees} and 67{degrees} symmetric and 45{degrees} and 25{degrees} asymmetric [001] tilt grain boundaries in SrTiO{sub 3} The structures of both types of boundary were found to contain partially occupied columns in the boundary plane. From these experimental results, a series of structural units were identified which could be combined, using continuity of gain boundary structure principles, to construct all [001] tilt boundaries in SrTiO{sub 3}. Using these models, the ability of this technique to address the issues of vacancies and dopant segregation at grain boundaries in electroceramics is discussed.

2D-PES/XAS method for atomic-layer-resolved magnetic structure analysis

International Nuclear Information System (INIS)

Matsui, F.; Daimon, H.; Matsushita, T.; Guo, F.Z.

2008-01-01

Photoelectron and Auger electron angular distributions from a localized core level provide information on atomic configurations. Forward-focusing peaks indicate the directions of atoms surrounding the excited atom. X-ray absorption fine structure and X-ray magnetic circular dichroism measurements by Auger electron yield detection on the other hand are excellent methods for studying of the electronic and magnetic structures of surfaces, adsorbates, and thin films. However, all the information from atoms within the electron mean-free-path region is averaged into the obtained spectra. Here, we introduce a new method of X-ray absorption spectroscopy (XAS) combined with measurements of Auger electron angular distribution using a display-type analyzer. Taking advantage of the forward-focusing peak as an excellent element- and site-selective probe, 2D-XAS enables direct access to the individual electronic and magnetic structures of each atomic layer. This method was applied to studying the electronic and magnetic structures of Ni thin film at atomic level. (author)

Niels Bohr and the Atomic Structure

Indian Academy of Sciences (India)

IAS Admin

principle with the restriction that no more than two electrons occupy a given ... displacement laws. Early in his ... The only difference between them is their atomic weight. F Soddy ... validity, Bohr took his theory to Rutherford. Unfortunately,.

Energy landscape of all-atom protein-protein interactions revealed by multiscale enhanced sampling.

Directory of Open Access Journals (Sweden)

Kei Moritsugu

2014-10-01

Full Text Available Protein-protein interactions are regulated by a subtle balance of complicated atomic interactions and solvation at the interface. To understand such an elusive phenomenon, it is necessary to thoroughly survey the large configurational space from the stable complex structure to the dissociated states using the all-atom model in explicit solvent and to delineate the energy landscape of protein-protein interactions. In this study, we carried out a multiscale enhanced sampling (MSES simulation of the formation of a barnase-barstar complex, which is a protein complex characterized by an extraordinary tight and fast binding, to determine the energy landscape of atomistic protein-protein interactions. The MSES adopts a multicopy and multiscale scheme to enable for the enhanced sampling of the all-atom model of large proteins including explicit solvent. During the 100-ns MSES simulation of the barnase-barstar system, we observed the association-dissociation processes of the atomistic protein complex in solution several times, which contained not only the native complex structure but also fully non-native configurations. The sampled distributions suggest that a large variety of non-native states went downhill to the stable complex structure, like a fast folding on a funnel-like potential. This funnel landscape is attributed to dominant configurations in the early stage of the association process characterized by near-native orientations, which will accelerate the native inter-molecular interactions. These configurations are guided mostly by the shape complementarity between barnase and barstar, and lead to the fast formation of the final complex structure along the downhill energy landscape.

Multiscale approach for the construction of equilibrated all-atom models of a poly(ethylene glycol)-based hydrogel

Science.gov (United States)

Li, Xianfeng; Murthy, N. Sanjeeva; Becker, Matthew L.; Latour, Robert A.

2016-01-01

A multiscale modeling approach is presented for the efficient construction of an equilibrated all-atom model of a cross-linked poly(ethylene glycol) (PEG)-based hydrogel using the all-atom polymer consistent force field (PCFF). The final equilibrated all-atom model was built with a systematic simulation toolset consisting of three consecutive parts: (1) building a global cross-linked PEG-chain network at experimentally determined cross-link density using an on-lattice Monte Carlo method based on the bond fluctuation model, (2) recovering the local molecular structure of the network by transitioning from the lattice model to an off-lattice coarse-grained (CG) model parameterized from PCFF, followed by equilibration using high performance molecular dynamics methods, and (3) recovering the atomistic structure of the network by reverse mapping from the equilibrated CG structure, hydrating the structure with explicitly represented water, followed by final equilibration using PCFF parameterization. The developed three-stage modeling approach has application to a wide range of other complex macromolecular hydrogel systems, including the integration of peptide, protein, and/or drug molecules as side-chains within the hydrogel network for the incorporation of bioactivity for tissue engineering, regenerative medicine, and drug delivery applications. PMID:27013229

Structures of 38-atom gold-platinum nanoalloy clusters

Energy Technology Data Exchange (ETDEWEB)

Ong, Yee Pin; Yoon, Tiem Leong [School of Physics, Universiti Sains Malaysia, 11800 USM, Penang (Malaysia); Lim, Thong Leng [Faculty of Engineering and Technology, Multimedia University, Melaka Campus, 75450 Melaka (Malaysia)

2015-04-24

Bimetallic nanoclusters, such as gold-platinum nanoclusters, are nanomaterials promising wide range of applications. We perform a numerical study of 38-atom gold-platinum nanoalloy clusters, Au{sub n}Pt{sub 38−n} (0 ≤ n ≤ 38), to elucidate the geometrical structures of these clusters. The lowest-energy structures of these bimetallic nanoclusters at the semi-empirical level are obtained via a global-minimum search algorithm known as parallel tempering multi-canonical basin hopping plus genetic algorithm (PTMBHGA), in which empirical Gupta many-body potential is used to describe the inter-atomic interactions among the constituent atoms. The structures of gold-platinum nanoalloy clusters are predicted to be core-shell segregated nanoclusters. Gold atoms are observed to preferentially occupy the surface of the clusters, while platinum atoms tend to occupy the core due to the slightly smaller atomic radius of platinum as compared to gold’s. The evolution of the geometrical structure of 38-atom Au-Pt clusters displays striking similarity with that of 38-atom Au-Cu nanoalloy clusters as reported in the literature.

Local atomic structure in tetragonal pure ZrO{sub 2} nanopowders

Energy Technology Data Exchange (ETDEWEB)

Acuna, Leandro M.; Lamas, Diego G.; Fuentes, Rodolfo O.; Fabregas, Ismael O. [CITEFA-CONICET, Villa Martelli, Provincia de Buenos Aires (AR). CINSO (Centro de Investigaciones en Solidos); Fantini, Marcia C.A.; Craievich, Aldo F. [Universidade de Sao Paulo (Brazil). Inst. de Fisica; Prado, Rogerio J. [Universidade Federal de Mato Grosso (UFMT), Cuiaba (Brazil). Inst. de Fisica

2010-04-15

The local atomic structures around the Zr atom of pure (undoped) ZrO{sub 2} nanopowders with different average crystallite sizes, ranging from 7 to 40 nm, have been investigated. The nanopowders were synthesized by different wetchemical routes, but all exhibit the high-temperature tetragonal phase stabilized at room temperature, as established by synchrotron radiation X-ray diffraction. The extended X-ray absorption fine structure (EXAFS) technique was applied to analyze the local structure around the Zr atoms. Several authors have studied this system using the EXAFS technique without obtaining a good agreement between crystallographic and EXAFS data. In this work, it is shown that the local structure of ZrO{sub 2} nanopowders can be described by a model consisting of two oxygen subshells (4+4 atoms) with different Zr-O distances, in agreement with those independently determined by X-ray diffraction. However, the EXAFS study shows that the second oxygen subshell exhibits a Debye-Waller (DW) parameter much higher than that of the first oxygen subshell, a result that cannot be explained by the crystallographic model accepted for the tetragonal phase of zirconia-based materials. However, as proposed by other authors, the difference in the DW parameters between the two oxygen subshells around the Zr atoms can be explained by the existence of oxygen displacements perpendicular to the z direction; these mainly affect the second oxygen subshell because of the directional character of the EXAFS DW parameter, in contradiction to the crystallographic value. It is also established that this model is similar to another model having three oxygen subshells, with a 4+2+2 distribution of atoms, with only one DW parameter for all oxygen subshells. Both models are in good agreement with the crystal structure determined by X-ray diffraction experiments. (orig.)

Atomic structure of a decagonal Al-Pd-Mn phase

Science.gov (United States)

Mihalkovič, Marek; Roth, Johannes; Trebin, Hans-Rainer

2017-12-01

We present a detailed structure solution for the 16 -Å decagonal quasicrystal in the Al-Pd-Mn system by means of cluster decoration and ab initio energy minimization. It is based on structure models of the ɛ and other approximant phases. The ɛ phases can be represented as subsets of a hexagon-boat-star (HBS) tiling. The decagonal phase comprises further HBS tiles. We have constructed several fictitious HBS approximants and optimized their structures individually. All tiles are decorated by two types of atomic clusters: the pseudo-Mackay icosahedron (PMI) and the large bicapped pentagonal prism (LBPP). It turns out that, whereas the PMI clusters can be kept essentially unchanged, the LBPP clusters must be adjusted in occupancy with Al atoms depending on their positions in the various tiles. In this way we obtain cluster decorations for all tiles of the decagonal quasicrystal. The calculations were confirmed by evaluation of an effective tile Hamiltonian.

Influence of the atomic structure on the quantum state of sputtered Ir atoms

International Nuclear Information System (INIS)

Bastiaansen, J.; Philipsen, V.; Lievens, P.; Silverans, R.E.; Vandeweert, E.

2004-01-01

The probability of the ejection of a neutral atom in a specific quantum state after keV-ion beam sputtering is often interpreted in terms of the interaction between the atomic states of the escaping atom and the electronic states of the solid. In this work, we examined this interplay in the sputtering of iridium as this element has--unlike the elements employed in previous investigations--a complex atomic structure due to strong configuration interactions. Double-resonant two-photon laser ionization is used to probe the sputtered Ir atoms yielding information about the probability for an ejected atom to populate a specific atomic state and its escape velocity. The qualitative features of the corresponding population partition and state-selective velocity distributions show the influence of the excitation energy and the electronic structure of the different atomic states. A comparison is made between the experimental data and predictions from the resonant electron transfer description

Explicit all-atom modeling of realistically sized ligand-capped nanocrystals

KAUST Repository

Kaushik, Ananth P.; Clancy, Paulette

2012-01-01

We present a study of an explicit all-atom representation of nanocrystals of experimentally relevant sizes (up to 6 nm), capped with alkyl chain ligands, in vacuum. We employ all-atom molecular dynamics simulation methods in concert with a well

Self-consistent calculation of atomic structure for mixture

International Nuclear Information System (INIS)

Meng Xujun; Bai Yun; Sun Yongsheng; Zhang Jinglin; Zong Xiaoping

2000-01-01

Based on relativistic Hartree-Fock-Slater self-consistent average atomic model, atomic structure for mixture is studied by summing up component volumes in mixture. Algorithmic procedure for solving both the group of Thomas-Fermi equations and the self-consistent atomic structure is presented in detail, and, some numerical results are discussed

The atomic structure of transition metal clusters

International Nuclear Information System (INIS)

Riley, S.J.

1995-01-01

Chemical reactions are used to probe the atomic (geometrical) structure of isolated clusters of transition metal atoms. The number of adsorbate molecules that saturate a cluster, and/or the binding energy of molecules to cluster surfaces, are determined as a function of cluster size. Systematics in these properties often make it possible to propose geometrical structures consistent with the experimental observations. We will describe how studies of the reactions of cobalt and nickel clusters with ammonia, water, and nitrogen provide important and otherwise unavailable structural information. Specifically, small (less than 20 atoms) clusters of cobalt and nickel atoms adopt entirely different structures, the former having packing characteristic of the bulk and the latter having pentagonal symmetry. These observations provide important input for model potentials that attempt to describe the local properties of transition metals. In particular, they point out the importance of a proper treatment of d-orbital binding in these systems, since cobalt and nickel differ so little in their d-orbital occupancy

Temperature dependent XAFS studies of local atomic structure of the perovskite-type zirconates

International Nuclear Information System (INIS)

Vedrinskii, R. V.; Lemeshko, M. P.; Novakovich, A. A.; Nazarenko, E. S.; Nassif, V.; Proux, O.; Joly, Y.

2006-01-01

Temperature dependent preedge and extended x-ray absorption fine structure measurements at the Zr K edge for the perovskite-type zirconates PbZr 0.515 Ti 0.485 O 3 (PZT), PbZrO 3 (PZ), and BaZrO 3 are performed. To carry out a more accurate study of the weak reconstruction of the local atomic structure we employed a combination of two techniques: (i) analysis of the preedge fine structure, and (ii) analysis of the Fourier transform of the difference between χ(k) functions obtained at different temperatures. A detailed investigation of local atomic structure in the cubic phase for all the crystals is also performed. It is shown that neither the displacive nor the order-disorder model can describe correctly the changes of local atomic structure during phase transitions in PZ and PZT. A spherical model describing the local atomic structure of perovskite-type crystals suffering structural phase transitions is proposed

On-line system for investigation of atomic structure

International Nuclear Information System (INIS)

Amus'ya, M.Ya.; Chernysheva, L.V.

1983-01-01

A description of the on-line ATOM system is presented that enables to investigate the structure of atomic electron shells and their interactions with different scattering particles-electrons, positronse photons, mesons - with the use of computerized numerical solutions. The problem is stated along with mathematical description of atomic properties including theoretical and numerical models for each investigated physical process. The ATOM system structure is considered. The Hartree-Fock method is used to determine the wave functions of the ground and excited atomic states. The programs are written in the ALGOL langauge. Different atomic characteristics were possible to be calculated for the first time with an accuracy exceeding an experimental one

Atomic structure of graphene supported heterogeneous model catalysts

International Nuclear Information System (INIS)

Franz, Dirk

2017-04-01

Graphene on Ir(111) forms a moire structure with well defined nucleation centres. Therefore it can be utilized to create hexagonal metal cluster lattices with outstanding structural quality. At diffraction experiments these 2D surface lattices cause a coherent superposition of the moire cell structure factor, so that the measured signal intensity scales with the square of coherently scattering unit cells. This artificial signal enhancement enables the opportunity for X-ray diffraction to determine the atomic structure of small nano-objects, which are hardly accessible with any experimental technique. The uniform environment of every metal cluster makes the described metal cluster lattices on graphene/Ir(111) an attractive model system for the investigation of catalytic, magnetic and quantum size properties of ultra-small nano-objects. In this context the use of x-rays provides a maximum of flexibility concerning the possible sample environments (vacuum, selected gases, liquids, sample temperature) and allows in-situ/operando measurements. In the framework of the present thesis the structure of different metal clusters grown by physical vapor deposition in an UHV environment and after gas exposure have been investigated. On the one hand the obtained results will explore many aspects of the atomic structure of these small metal clusters and on the other hand the presented results will proof the capabilities of the described technique (SXRD on cluster lattices). For iridium, platinum, iridium/palladium and platinum/rhodium the growth on graphene/Ir(111) of epitaxial, crystalline clusters with an ordered hexagonal lattice arrangement has been confirmed using SXRD. The clusters nucleate at the hcp sites of the moire cell and bind via rehybridization of the carbon atoms (sp"2 → sp"3) to the Ir(111) substrate. This causes small displacements of the substrate atoms, which is revealed by the diffraction experiments. All metal clusters exhibit a fcc structure, whereupon

Atomic structure of graphene supported heterogeneous model catalysts

Energy Technology Data Exchange (ETDEWEB)

Franz, Dirk

2017-04-15

Graphene on Ir(111) forms a moire structure with well defined nucleation centres. Therefore it can be utilized to create hexagonal metal cluster lattices with outstanding structural quality. At diffraction experiments these 2D surface lattices cause a coherent superposition of the moire cell structure factor, so that the measured signal intensity scales with the square of coherently scattering unit cells. This artificial signal enhancement enables the opportunity for X-ray diffraction to determine the atomic structure of small nano-objects, which are hardly accessible with any experimental technique. The uniform environment of every metal cluster makes the described metal cluster lattices on graphene/Ir(111) an attractive model system for the investigation of catalytic, magnetic and quantum size properties of ultra-small nano-objects. In this context the use of x-rays provides a maximum of flexibility concerning the possible sample environments (vacuum, selected gases, liquids, sample temperature) and allows in-situ/operando measurements. In the framework of the present thesis the structure of different metal clusters grown by physical vapor deposition in an UHV environment and after gas exposure have been investigated. On the one hand the obtained results will explore many aspects of the atomic structure of these small metal clusters and on the other hand the presented results will proof the capabilities of the described technique (SXRD on cluster lattices). For iridium, platinum, iridium/palladium and platinum/rhodium the growth on graphene/Ir(111) of epitaxial, crystalline clusters with an ordered hexagonal lattice arrangement has been confirmed using SXRD. The clusters nucleate at the hcp sites of the moire cell and bind via rehybridization of the carbon atoms (sp{sup 2} → sp{sup 3}) to the Ir(111) substrate. This causes small displacements of the substrate atoms, which is revealed by the diffraction experiments. All metal clusters exhibit a fcc structure

Structural atlas of dynein motors at atomic resolution.

Science.gov (United States)

Toda, Akiyuki; Tanaka, Hideaki; Kurisu, Genji

2018-04-01

Dynein motors are biologically important bio-nanomachines, and many atomic resolution structures of cytoplasmic dynein components from different organisms have been analyzed by X-ray crystallography, cryo-EM, and NMR spectroscopy. This review provides a historical perspective of structural studies of cytoplasmic and axonemal dynein including accessory proteins. We describe representative structural studies of every component of dynein and summarize them as a structural atlas that classifies the cytoplasmic and axonemal dyneins. Based on our review of all dynein structures in the Protein Data Bank, we raise two important points for understanding the two types of dynein motor and discuss the potential prospects of future structural studies.

Kinetic-energy density functional: Atoms and shell structure

International Nuclear Information System (INIS)

Garcia-Gonzalez, P.; Alvarellos, J.E.; Chacon, E.

1996-01-01

We present a nonlocal kinetic-energy functional which includes an anisotropic average of the density through a symmetrization procedure. This functional allows a better description of the nonlocal effects of the electron system. The main consequence of the symmetrization is the appearance of a clear shell structure in the atomic density profiles, obtained after the minimization of the total energy. Although previous results with some of the nonlocal kinetic functionals have given incipient structures for heavy atoms, only our functional shows a clear shell structure for most of the atoms. The atomic total energies have a good agreement with the exact calculations. Discussion of the chemical potential and the first ionization potential in atoms is included. The functional is also extended to spin-polarized systems. copyright 1996 The American Physical Society

Diagnosing Students’ conception on atomic structure using open ended questions

Science.gov (United States)

Fitriza, Z.; Gazali, F.

2018-05-01

This study aims to diagnose students’ conception on atomic structure concepts using open ended questions. For this reason, a 7 items of assay test was administered to 135 senior high school students from different schools in West Sumatera. The data were collected using a an open ended test which is covering the concept used in the topic Atomic Structure. The open ended test of students’ conceptual was developed to identify the alternative conceptions that student might have regarding the concepts in Atomic Structure, to measure the level of students’ conceptions, and the way of students’ thinking concerning the concepts. The results showed that students find difficulties about some concepts of Atomic structure such as atom, atomic model, electron configuration, period and group.The result of this study illuminated the concepts to be underlined in developing teaching and learning approach concerning the topic of Atomic Structure.

Atomic structure of highly-charged ions. Final report

International Nuclear Information System (INIS)

Livingston, A. Eugene

2002-01-01

Atomic properties of multiply charged ions have been investigated using excitation of energetic heavy ion beams. Spectroscopy of excited atomic transitions has been applied from the visible to the extreme ultraviolet wavelength regions to provide accurate atomic structure and transition rate data in selected highly ionized atoms. High-resolution position-sensitive photon detection has been introduced for measurements in the ultraviolet region. The detailed structures of Rydberg states in highly charged beryllium-like ions have been measured as a test of long-range electron-ion interactions. The measurements are supported by multiconfiguration Dirac-Fock calculations and by many-body perturbation theory. The high-angular-momentum Rydberg transitions may be used to establish reference wavelengths and improve the accuracy of ionization energies in highly charged systems. Precision wavelength measurements in highly charged few-electron ions have been performed to test the most accurate relativistic atomic structure calculations for prominent low-lying excited states. Lifetime measurements for allowed and forbidden transitions in highly charged few-electron ions have been made to test theoretical transition matrix elements for simple atomic systems. Precision lifetime measurements in laser-excited alkali atoms have been initiated to establish the accuracy of relativistic atomic many-body theory in many-electron systems

Validation of Structures in the Protein Data Bank.

Science.gov (United States)

Gore, Swanand; Sanz García, Eduardo; Hendrickx, Pieter M S; Gutmanas, Aleksandras; Westbrook, John D; Yang, Huanwang; Feng, Zukang; Baskaran, Kumaran; Berrisford, John M; Hudson, Brian P; Ikegawa, Yasuyo; Kobayashi, Naohiro; Lawson, Catherine L; Mading, Steve; Mak, Lora; Mukhopadhyay, Abhik; Oldfield, Thomas J; Patwardhan, Ardan; Peisach, Ezra; Sahni, Gaurav; Sekharan, Monica R; Sen, Sanchayita; Shao, Chenghua; Smart, Oliver S; Ulrich, Eldon L; Yamashita, Reiko; Quesada, Martha; Young, Jasmine Y; Nakamura, Haruki; Markley, John L; Berman, Helen M; Burley, Stephen K; Velankar, Sameer; Kleywegt, Gerard J

2017-12-05

The Worldwide PDB recently launched a deposition, biocuration, and validation tool: OneDep. At various stages of OneDep data processing, validation reports for three-dimensional structures of biological macromolecules are produced. These reports are based on recommendations of expert task forces representing crystallography, nuclear magnetic resonance, and cryoelectron microscopy communities. The reports provide useful metrics with which depositors can evaluate the quality of the experimental data, the structural model, and the fit between them. The validation module is also available as a stand-alone web server and as a programmatically accessible web service. A growing number of journals require the official wwPDB validation reports (produced at biocuration) to accompany manuscripts describing macromolecular structures. Upon public release of the structure, the validation report becomes part of the public PDB archive. Geometric quality scores for proteins in the PDB archive have improved over the past decade. Copyright © 2017 The Authors. Published by Elsevier Ltd.. All rights reserved.

Atomic and electronic structure of exfoliated black phosphorus

International Nuclear Information System (INIS)

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

2015-01-01

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

Report on atomic structure research 1961-1990

International Nuclear Information System (INIS)

Fawcett, B.C.

1990-07-01

This report documents the atomic-structure research carried out during the period 1961-90. The contributions are in two main areas. The first comprises original line classifications of spectra of highly ionized atoms including identifications of a major proportion of newly observed lines in the solar far ultraviolet and soft X-ray spectrum. The second consists of theoretical calculations of atomic data such as oscillator strengths, wavelengths, energy levels and their composition. These were calculated with advanced atomic-structure codes and cover most solar abundant ions. A new method was applied to collision calculations. Research in this field, presently conducted at Rutherford Appleton Laboratory (RAL), was initiated in the United Kingdom Atomic Energy Authority (UKAEA) at Harwell in 1960. It continued under the UKAEA at Culham Laboratory in 1962 and until 1986 when staff were taken over by Science and Engineering Research Council (SERC) and later transferred to RAL in 1981. (author)

Validation of molecular crystal structures from powder diffraction data with dispersion-corrected density functional theory (DFT-D)

International Nuclear Information System (INIS)

Streek, Jacco van de; Neumann, Marcus A.

2014-01-01

The accuracy of 215 experimental organic crystal structures from powder diffraction data is validated against a dispersion-corrected density functional theory method. In 2010 we energy-minimized 225 high-quality single-crystal (SX) structures with dispersion-corrected density functional theory (DFT-D) to establish a quantitative benchmark. For the current paper, 215 organic crystal structures determined from X-ray powder diffraction (XRPD) data and published in an IUCr journal were energy-minimized with DFT-D and compared to the SX benchmark. The on average slightly less accurate atomic coordinates of XRPD structures do lead to systematically higher root mean square Cartesian displacement (RMSCD) values upon energy minimization than for SX structures, but the RMSCD value is still a good indicator for the detection of structures that deserve a closer look. The upper RMSCD limit for a correct structure must be increased from 0.25 Å for SX structures to 0.35 Å for XRPD structures; the grey area must be extended from 0.30 to 0.40 Å. Based on the energy minimizations, three structures are re-refined to give more precise atomic coordinates. For six structures our calculations provide the missing positions for the H atoms, for five structures they provide corrected positions for some H atoms. Seven crystal structures showed a minor error for a non-H atom. For five structures the energy minimizations suggest a higher space-group symmetry. For the 225 SX structures, the only deviations observed upon energy minimization were three minor H-atom related issues. Preferred orientation is the most important cause of problems. A preferred-orientation correction is the only correction where the experimental data are modified to fit the model. We conclude that molecular crystal structures determined from powder diffraction data that are published in IUCr journals are of high quality, with less than 4% containing an error in a non-H atom

Atomic parity nonconservation: Electroweak parameters and nuclear structure

International Nuclear Information System (INIS)

Pollock, S.J.; Fortson, E.N.; Wilets, L.

1992-01-01

There have been suggestions to measure atomic parity nonconservation (PNC) along an isotopic chain, by taking ratios of observables in order to cancel complicated atomic-structure effects. Precise atomic PNC measurements could make a significant contribution to tests of the standard model at the level of one-loop radiative corrections. However, the results also depend upon certain features of nuclear structure, such as the spatial distribution of neutrons in the nucleus. To examine the sensitivity to nuclear structure, we consider the case of Pb isotopes using various recent relativistic and nonrelativistic nuclear model calculations. Contributions from nucleon internal weak structure are included, but found to be fairly negligible. The spread among present models in predicted sizes of nuclear-structure effects may preclude using Pb isotope ratios to test the standard model at better than a 1% level, unless there are adequate independent tests of the nuclear models by various alternative strong and electroweak nuclear probes. On the other hand, sufficiently accurate atomic PNC experiments would provide a unique method to measure neutron distributions in heavy nuclei

Beyond Modeling: All-Atom Olfactory Receptor Model Simulations

Directory of Open Access Journals (Sweden)

Peter C Lai

2012-05-01

Full Text Available Olfactory receptors (ORs are a type of GTP-binding protein-coupled receptor (GPCR. These receptors are responsible for mediating the sense of smell through their interaction with odor ligands. OR-odorant interactions marks the first step in the process that leads to olfaction. Computational studies on model OR structures can validate experimental functional studies as well as generate focused and novel hypotheses for further bench investigation by providing a view of these interactions at the molecular level. Here we have shown the specific advantages of simulating the dynamic environment that is associated with OR-odorant interactions. We present a rigorous methodology that ranges from the creation of a computationally-derived model of an olfactory receptor to simulating the interactions between an OR and an odorant molecule. Given the ubiquitous occurrence of GPCRs in the membranes of cells, we anticipate that our OR-developed methodology will serve as a model for the computational structural biology of all GPCRs.

Evolution in time of an N-atom system. II. Calculation of the eigenstates

International Nuclear Information System (INIS)

Rudolph, Terry; Yavin, Itay; Freedhoff, Helen

2004-01-01

We calculate the energy eigenvalues and eigenstates corresponding to coherent single and multiple excitations of a number of different arrays of N identical two-level atoms (TLA's) or qubits, including polygons, 'diamond' structures, polygon multilayers, icosahedra, and dodecahedra. We assume only that the coupling occurs via an exchange interaction which depends on the separation between the atoms. We include the interactions between all pairs of atoms, and our results are valid for arbitrary separations relative to the radiation wavelength

Relativistic Collisions of Structured Atomic Particles

CERN Document Server

Voitkiv, Alexander

2008-01-01

The book reviews the progress achieved over the last decade in the study of collisions between an ion and an atom in which both the atomic particles carry electrons and can undergo transitions between their internal states -- including continua. It presents the detailed considerations of different theoretical approaches, that can be used to describe collisions of structured atomic particles for the very broad interval of impact energies ranging from 0.5--1 MeV/u till extreme relativistic energies where the collision velocity very closely approaches the speed of light.

Explicit all-atom modeling of realistically sized ligand-capped nanocrystals

KAUST Repository

Kaushik, Ananth P.

2012-01-01

We present a study of an explicit all-atom representation of nanocrystals of experimentally relevant sizes (up to 6 nm), capped with alkyl chain ligands, in vacuum. We employ all-atom molecular dynamics simulation methods in concert with a well-tested intermolecular potential model, MM3 (molecular mechanics 3), for the studies presented here. These studies include determining the preferred conformation of an isolated single nanocrystal (NC), pairs of isolated NCs, and (presaging studies of superlattice arrays) unit cells of NC superlattices. We observe that very small NCs (3 nm) behave differently in a superlattice as compared to larger NCs (6 nm and above) due to the conformations adopted by the capping ligands on the NC surface. Short ligands adopt a uniform distribution of orientational preferences, including some that lie against the face of the nanocrystal. In contrast, longer ligands prefer to interdigitate. We also study the effect of changing ligand length and ligand coverage on the NCs on the preferred ligand configurations. Since explicit all-atom modeling constrains the maximum system size that can be studied, we discuss issues related to coarse-graining the representation of the ligands, including a comparison of two commonly used coarse-grained models. We find that care has to be exercised in the choice of coarse-grained model. The data provided by these realistically sized ligand-capped NCs, determined using explicit all-atom models, should serve as a reference standard for future models of coarse-graining ligands using united atom models, especially for self-assembly processes. © 2012 American Institute of Physics.

Atomic and electronic structure of exfoliated black phosphorus

Energy Technology Data Exchange (ETDEWEB)

Wu, Ryan J.; Topsakal, Mehmet; Jeong, Jong Seok; Wentzcovitch, Renata M.; Mkhoyan, K. Andre, E-mail: mkhoyan@umn.edu [Department of Chemical Engineering and Materials Science, University of Minnesota, Minneapolis, Minnesota 55455 (United States); Low, Tony; Robbins, Matthew C.; Haratipour, Nazila; Koester, Steven J. [Department of Electrical and Computer Engineering, University of Minnesota, Minneapolis, Minnesota 55455 (United States)

2015-11-15

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

Kinetic theory of beam-induced plasmas generalised to sophisticated atomic structures

International Nuclear Information System (INIS)

Peyraud-Cuenca, Nelly

1987-01-01

We present an analytic kinetic model available for all particle-beam-induced atomic plasmas, without any restriction on the distribution of electronic levels. The method is an iteration of the already known solution available only for the distribution of atomic levels as in the rare gases. We recall a universal atomic kinetic model which, independently of its applications to the study of efficient laser systems, might be a first step in the analytic investigation of molecular problems. Then, the iteration is systematically applied to all possible atomic structures whose number is increased by the non-local character of inelastic processes. We deduce a general analytic representation of the 'tail' of the electron distribution function as a ratio between non-local source terms and a combination of inelastic cross sections, from which we exhibit a physical interpretation and essential scaling laws. The theory is applied to sodium which is an important element in the research of efficient laser systems. (author)

Structure and stability of semiconductor tip apexes for atomic force microscopy

International Nuclear Information System (INIS)

Pou, P; Perez, R; Ghasemi, S A; Goedecker, S; Jelinek, P; Lenosky, T

2009-01-01

The short range force between the tip and the surface atoms, that is responsible for atomic-scale contrast in atomic force microscopy (AFM), is mainly controlled by the tip apex. Thus, the ability to image, manipulate and chemically identify single atoms in semiconductor surfaces is ultimately determined by the apex structure and its composition. Here we present a detailed and systematic study of the most common structures that can be expected at the apex of the Si tips used in experiments. We tackle the determination of the structure and stability of Si tips with three different approaches: (i) first principles simulations of small tip apexes; (ii) simulated annealing of a Si cluster; and (iii) a minima hopping study of large Si tips. We have probed the tip apexes by making atomic contacts between the tips and then compared force-distance curves with the experimental short range forces obtained with dynamic force spectroscopy. The main conclusion is that although there are multiple stable solutions for the atomically sharp tip apexes, they can be grouped into a few types with characteristic atomic structures and properties. We also show that the structure of the last atomic layers in a tip apex can be both crystalline and amorphous. We corroborate that the atomically sharp tips are thermodynamically stable and that the tip-surface interaction helps to produce the atomic protrusion needed to get atomic resolution.

An intrinsic representation of atomic structure: From clusters to periodic systems

Science.gov (United States)

Li, Xiao-Tian; Xu, Shao-Gang; Yang, Xiao-Bao; Zhao, Yu-Jun

2017-10-01

We have improved our distance matrix and eigen-subspace projection function (EPF) [X.-T. Li et al., J. Chem. Phys. 146, 154108 (2017)] to describe the atomic structure for periodic systems. Depicting the local structure of an atom, the EPF turns out to be invariant with respect to the choices of the unit cell and coordinate frame, leading to an intrinsic representation of the crystal with a set of EPFs of the nontrivial atoms. The difference of EPFs reveals the difference of atoms in local structure, while the accumulated difference between two sets of EPFs can be taken as the distance between configurations. Exemplified with the cases of carbon allotropes and boron sheets, our EPF approach shows exceptional rationality and efficiency to distinguish the atomic structures, which is crucial in structure recognition, comparison, and analysis.

Dopant distributions in n-MOSFET structure observed by atom probe tomography

International Nuclear Information System (INIS)

Inoue, K.; Yano, F.; Nishida, A.; Takamizawa, H.; Tsunomura, T.; Nagai, Y.; Hasegawa, M.

2009-01-01

The dopant distributions in an n-type metal-oxide-semiconductor field effect transistor (MOSFET) structure were analyzed by atom probe tomography. The dopant distributions of As, P, and B atoms in a MOSFET structure (gate, gate oxide, channel, source/drain extension, and halo) were obtained. P atoms were segregated at the interface between the poly-Si gate and the gate oxide, and on the grain boundaries of the poly-Si gate, which had an elongated grain structure along the gate height direction. The concentration of B atoms was enriched near the edge of the source/drain extension where the As atoms were implanted.

Dopant distributions in n-MOSFET structure observed by atom probe tomography.

Science.gov (United States)

Inoue, K; Yano, F; Nishida, A; Takamizawa, H; Tsunomura, T; Nagai, Y; Hasegawa, M

2009-11-01

The dopant distributions in an n-type metal-oxide-semiconductor field effect transistor (MOSFET) structure were analyzed by atom probe tomography. The dopant distributions of As, P, and B atoms in a MOSFET structure (gate, gate oxide, channel, source/drain extension, and halo) were obtained. P atoms were segregated at the interface between the poly-Si gate and the gate oxide, and on the grain boundaries of the poly-Si gate, which had an elongated grain structure along the gate height direction. The concentration of B atoms was enriched near the edge of the source/drain extension where the As atoms were implanted.

A coarse-graining approach for molecular simulation that retains the dynamics of the all-atom reference system by implementing hydrodynamic interactions

Energy Technology Data Exchange (ETDEWEB)

Markutsya, Sergiy [Ames Laboratory, Iowa State University, Ames, Iowa 50011 (United States); Lamm, Monica H., E-mail: mhlamm@iastate.edu [Ames Laboratory, Iowa State University, Ames, Iowa 50011 (United States); Department of Chemical and Biological Engineering, Iowa State University, Ames, Iowa 50011 (United States)

2014-11-07

We report on a new approach for deriving coarse-grained intermolecular forces that retains the frictional contribution that is often discarded by conventional coarse-graining methods. The approach is tested for water and an aqueous glucose solution, and the results from the new implementation for coarse-grained molecular dynamics simulation show remarkable agreement with the dynamics obtained from reference all-atom simulations. The agreement between the structural properties observed in the coarse-grained and all-atom simulations is also preserved. We discuss how this approach may be applied broadly to any existing coarse-graining method where the coarse-grained models are rigorously derived from all-atom reference systems.

A coarse-graining approach for molecular simulation that retains the dynamics of the all-atom reference system by implementing hydrodynamic interactions

International Nuclear Information System (INIS)

Markutsya, Sergiy; Lamm, Monica H.

2014-01-01

We report on a new approach for deriving coarse-grained intermolecular forces that retains the frictional contribution that is often discarded by conventional coarse-graining methods. The approach is tested for water and an aqueous glucose solution, and the results from the new implementation for coarse-grained molecular dynamics simulation show remarkable agreement with the dynamics obtained from reference all-atom simulations. The agreement between the structural properties observed in the coarse-grained and all-atom simulations is also preserved. We discuss how this approach may be applied broadly to any existing coarse-graining method where the coarse-grained models are rigorously derived from all-atom reference systems

Big Atoms for Small Children: Building Atomic Models from Common Materials to Better Visualize and Conceptualize Atomic Structure

Science.gov (United States)

Cipolla, Laura; Ferrari, Lia A.

2016-01-01

A hands-on approach to introduce the chemical elements and the atomic structure to elementary/middle school students is described. The proposed classroom activity presents Bohr models of atoms using common and inexpensive materials, such as nested plastic balls, colored modeling clay, and small-sized pasta (or small plastic beads).

Understanding Atomic Structure: Is There a More Direct and Compelling Connection between Atomic Line Spectra and the Quantization of an Atom's Energy?

Science.gov (United States)

Rittenhouse, Robert C.

2015-01-01

The "atoms first" philosophy, adopted by a growing number of General Chemistry textbook authors, places greater emphasis on atomic structure as a key to a deeper understanding of the field of chemistry. A pivotal concept needed to understand the behavior of atoms is the restriction of an atom's energy to specific allowed values. However,…

Hydrogen atoms in protein structures: high-resolution X-ray diffraction structure of the DFPase

Science.gov (United States)

2013-01-01

Background Hydrogen atoms represent about half of the total number of atoms in proteins and are often involved in substrate recognition and catalysis. Unfortunately, X-ray protein crystallography at usual resolution fails to access directly their positioning, mainly because light atoms display weak contributions to diffraction. However, sub-Ångstrom diffraction data, careful modeling and a proper refinement strategy can allow the positioning of a significant part of hydrogen atoms. Results A comprehensive study on the X-ray structure of the diisopropyl-fluorophosphatase (DFPase) was performed, and the hydrogen atoms were modeled, including those of solvent molecules. This model was compared to the available neutron structure of DFPase, and differences in the protein and the active site solvation were noticed. Conclusions A further examination of the DFPase X-ray structure provides substantial evidence about the presence of an activated water molecule that may constitute an interesting piece of information as regard to the enzymatic hydrolysis mechanism. PMID:23915572

Theoretical atomic physics code development I: CATS: Cowan Atomic Structure Code

International Nuclear Information System (INIS)

Abdallah, J. Jr.; Clark, R.E.H.; Cowan, R.D.

1988-12-01

An adaptation of R.D. Cowan's Atomic Structure program, CATS, has been developed as part of the Theoretical Atomic Physics (TAPS) code development effort at Los Alamos. CATS has been designed to be easy to run and to produce data files that can interface with other programs easily. The CATS produced data files currently include wave functions, energy levels, oscillator strengths, plane-wave-Born electron-ion collision strengths, photoionization cross sections, and a variety of other quantities. This paper describes the use of CATS. 10 refs

Atomic-accuracy prediction of protein loop structures through an RNA-inspired Ansatz.

Directory of Open Access Journals (Sweden)

Rhiju Das

Full Text Available Consistently predicting biopolymer structure at atomic resolution from sequence alone remains a difficult problem, even for small sub-segments of large proteins. Such loop prediction challenges, which arise frequently in comparative modeling and protein design, can become intractable as loop lengths exceed 10 residues and if surrounding side-chain conformations are erased. Current approaches, such as the protein local optimization protocol or kinematic inversion closure (KIC Monte Carlo, involve stages that coarse-grain proteins, simplifying modeling but precluding a systematic search of all-atom configurations. This article introduces an alternative modeling strategy based on a 'stepwise ansatz', recently developed for RNA modeling, which posits that any realistic all-atom molecular conformation can be built up by residue-by-residue stepwise enumeration. When harnessed to a dynamic-programming-like recursion in the Rosetta framework, the resulting stepwise assembly (SWA protocol enables enumerative sampling of a 12 residue loop at a significant but achievable cost of thousands of CPU-hours. In a previously established benchmark, SWA recovers crystallographic conformations with sub-Angstrom accuracy for 19 of 20 loops, compared to 14 of 20 by KIC modeling with a comparable expenditure of computational power. Furthermore, SWA gives high accuracy results on an additional set of 15 loops highlighted in the biological literature for their irregularity or unusual length. Successes include cis-Pro touch turns, loops that pass through tunnels of other side-chains, and loops of lengths up to 24 residues. Remaining problem cases are traced to inaccuracies in the Rosetta all-atom energy function. In five additional blind tests, SWA achieves sub-Angstrom accuracy models, including the first such success in a protein/RNA binding interface, the YbxF/kink-turn interaction in the fourth 'RNA-puzzle' competition. These results establish all-atom enumeration as

Complete all-atom hydrodynamics of protein unfolding in uniform flow

International Nuclear Information System (INIS)

Wang, Guan M; Sandberg, William C

2010-01-01

The unfolding dynamics of a protein, ubiquitin, pinned in several uniform flows, was studied at low and high flow rates in an all-atom style through a non-equilibrium molecular dynamics approach with explicit water molecules included. Atomic hydrodynamic force components on individual amino acids, as a function of time, due to the collisional interactions with the flowing water molecules were calculated explicitly. The protein conformational change in response to those time-varying forces was computed completely at the high flow rate up to nanosecond until the fully stretched state was reached. The end-to-end length of the single ubiquitin protein molecule at high flow rate is smoothly increasing. The step-like jumps between metastable states that describe the μm ms -1 scale force pulling experiments conducted on polyubiquitins at low flow rates, are not seen at the high flow speeds necessary to computationally probe the ns nm -1 scale regime. No unfolding was observed in the low flow rate atomic computations at nanosecond scale while partial and complete unfolding was observed in the coarse-grained low flow rate computations at microsecond scale. Examination of the all-atom computation of the time variation of the hydrodynamic forces on, and the velocity components of, the protein molecule unveiled to some extent the details of the complexity of the hydrodynamic friction variation in the nm ns -1 regime of high rate flow-driven protein unfolding. This demonstrates quantitatively that all-atom computations are more suitable than the Langevin equation or Brownian dynamics methods for probing the interaction dynamics and resulting conformational dynamics of protein unfolding in strong flows on nm ns -1 time/length scales while the reverse is true for investigation of slow, diffusively driven systems.

Unraveling the atomic structure of ultrafine iron clusters

KAUST Repository

Wang, Hongtao

2012-12-18

Unraveling the atomic structures of ultrafine iron clusters is critical to understanding their size-dependent catalytic effects and electronic properties. Here, we describe the stable close-packed structure of ultrafine Fe clusters for the first time, thanks to the superior properties of graphene, including the monolayer thickness, chemical inertness, mechanical strength, electrical and thermal conductivity. These clusters prefer to take regular planar shapes with morphology changes by local atomic shuffling, as suggested by the early hypothesis of solid-solid transformation. Our observations differ from observations from earlier experimental study and theoretical model, such as icosahedron, decahedron or cuboctahedron. No interaction was observed between Fe atoms or clusters and pristine graphene. However, preferential carving, as observed by other research groups, can be realized only when Fe clusters are embedded in graphene. The techniques introduced here will be of use in investigations of other clusters or even single atoms or molecules.

Determination of atomic cluster structure with cluster fusion algorithm

DEFF Research Database (Denmark)

Obolensky, Oleg I.; Solov'yov, Ilia; Solov'yov, Andrey V.

2005-01-01

We report an efficient scheme of global optimization, called cluster fusion algorithm, which has proved its reliability and high efficiency in determination of the structure of various atomic clusters.......We report an efficient scheme of global optimization, called cluster fusion algorithm, which has proved its reliability and high efficiency in determination of the structure of various atomic clusters....

Validation and extraction of molecular-geometry information from small-molecule databases.

Science.gov (United States)

Long, Fei; Nicholls, Robert A; Emsley, Paul; Graǽulis, Saulius; Merkys, Andrius; Vaitkus, Antanas; Murshudov, Garib N

2017-02-01

A freely available small-molecule structure database, the Crystallography Open Database (COD), is used for the extraction of molecular-geometry information on small-molecule compounds. The results are used for the generation of new ligand descriptions, which are subsequently used by macromolecular model-building and structure-refinement software. To increase the reliability of the derived data, and therefore the new ligand descriptions, the entries from this database were subjected to very strict validation. The selection criteria made sure that the crystal structures used to derive atom types, bond and angle classes are of sufficiently high quality. Any suspicious entries at a crystal or molecular level were removed from further consideration. The selection criteria included (i) the resolution of the data used for refinement (entries solved at 0.84 Å resolution or higher) and (ii) the structure-solution method (structures must be from a single-crystal experiment and all atoms of generated molecules must have full occupancies), as well as basic sanity checks such as (iii) consistency between the valences and the number of connections between atoms, (iv) acceptable bond-length deviations from the expected values and (v) detection of atomic collisions. The derived atom types and bond classes were then validated using high-order moment-based statistical techniques. The results of the statistical analyses were fed back to fine-tune the atom typing. The developed procedure was repeated four times, resulting in fine-grained atom typing, bond and angle classes. The procedure will be repeated in the future as and when new entries are deposited in the COD. The whole procedure can also be applied to any source of small-molecule structures, including the Cambridge Structural Database and the ZINC database.

Surface structure investigations using noncontact atomic force microscopy

International Nuclear Information System (INIS)

Kolodziej, J.J.; Such, B.; Goryl, M.; Krok, F.; Piatkowski, P.; Szymonski, M.

2006-01-01

Surfaces of several A III B V compound semiconductors (InSb, GaAs, InP, InAs) of the (0 0 1) orientation have been studied with noncontact atomic force microscopy (NC-AFM). Obtained atomically resolved patterns have been compared with structural models available in the literature. It is shown that NC-AFM is an efficient tool for imaging complex surface structures in real space. It is also demonstrated that the recent structural models of III-V compound surfaces provide a sound base for interpretation of majority of features present in recorded patterns. However, there are also many new findings revealed by the NC-AFM method that is still new experimental technique in the context of surface structure determination

Electronic structure and magnetic properties of substitutional transition-metal atoms in GaN nanotubes

International Nuclear Information System (INIS)

Zhang Min; Shi Jun-Jie

2014-01-01

The electronic structure and magnetic properties of the transition-metal (TM) atoms (Sc—Zn, Pt and Au) doped zigzag GaN single-walled nanotubes (NTs) are investigated using first-principles spin-polarized density functional calculations. Our results show that the bindings of all TM atoms are stable with the binding energy in the range of 6–16 eV. The Sc- and V-doped GaN NTs exhibit a nonmagnetic behavior. The GaN NTs doped with Ti, Mn, Ni, Cu and Pt are antiferromagnetic. On the contrary, the Cr-, Fe-, Co-, Zn- and Au-doped GaN NTs show the ferromagnetic characteristics. The Mn- and Co-doped GaN NTs induce the largest local moment of 4μ B among these TM atoms. The local magnetic moment is dominated by the contribution from the substitutional TM atom and the N atoms bonded with it. (condensed matter: electronic structure, electrical, magnetic, and optical properties)

Modeling of the atomic and electronic structures of interfaces

International Nuclear Information System (INIS)

Sutton, A.P.

1988-01-01

Recent tight binding and Car-Parrinello simulations of grain boundaries in semiconductors are reviewed. A critique is given of some models of embrittlement that are based on electronic structure considerations. The structural unit model of grain boundary structure is critically assessed using some results for mixed tilt and twist grain boundaries. A new method of characterizing interfacial structure in terms of bond angle distribution functions is described. A new formulation of thermodynamic properties of interfaces is presented which focusses on the local atomic environment. Effective, temperature dependent N-body atomic interactions are derived for studying grain boundary structure at elevated temperature

Structural system identification: Structural dynamics model validation

Energy Technology Data Exchange (ETDEWEB)

Red-Horse, J.R.

1997-04-01

Structural system identification is concerned with the development of systematic procedures and tools for developing predictive analytical models based on a physical structure`s dynamic response characteristics. It is a multidisciplinary process that involves the ability (1) to define high fidelity physics-based analysis models, (2) to acquire accurate test-derived information for physical specimens using diagnostic experiments, (3) to validate the numerical simulation model by reconciling differences that inevitably exist between the analysis model and the experimental data, and (4) to quantify uncertainties in the final system models and subsequent numerical simulations. The goal of this project was to develop structural system identification techniques and software suitable for both research and production applications in code and model validation.

Diamond surface: atomic and electronic structure

International Nuclear Information System (INIS)

Pate, B.B.

1984-01-01

Experimental studies of the diamond surface (with primary emphasis on the (111) surface) are presented. Aspects of the diamond surface which are addressed include (1) the electronic structure, (2) the atomic structure, and (3) the effect of termination of the lattice by foreign atoms. Limited studies of graphite are discussed for comparison with the diamond results. Experimental results from valence band and core level photoemission spectroscopy (PES), Auger electron spectroscopy (AES), low energy electron diffraction (LEED), and carbon 1s near edge x-ray absorption fine structure (NEXAFS) spectroscopy (both the total electron yield (TEY) and Auger electron yield (AEY) techniques) are used to study and characterize both the clean and hydrogenated surface. In addition, the interaction of hydrogen with the diamond surface is examined using results from vibrational high resolution low energy electron loss spectroscopy (in collaboration with Waclawski, Pierce, Swanson, and Celotta at the National Bureau of Standards) and photon stimulated ion desorption (PSID) yield at photon energies near the carbon k-edge (hv greater than or equal to 280 eV). Both EELS and PSID verify that the mechanically polished 1 x 1 surface is hydrogen terminated and also that the reconstructed surface is hydrogen free. The (111) 2 x 2/2 x 1 reconstructed surface is obtained from the hydrogenated (111) 1 x 1:H surface by annealing to approx. = 1000 0 C. We observe occupied intrinsic surface states and a surface chemical shift (0.95 +- 0.1 eV) to lower binding energy of the carbon 1s level on the hydrogen-free reconstructed surface. Atomic hydrogen is found to be reactive with the reconstructed surface, while molecular hydrogen is relatively inert. Exposure of the reconstructed surface to atomic hydrogen results in chemisorption of hydrogen and removal of the intrinsic surface state emission in and near the band gap region

ValidatorDB: database of up-to-date validation results for ligands and non-standard residues from the Protein Data Bank.

Science.gov (United States)

Sehnal, David; Svobodová Vařeková, Radka; Pravda, Lukáš; Ionescu, Crina-Maria; Geidl, Stanislav; Horský, Vladimír; Jaiswal, Deepti; Wimmerová, Michaela; Koča, Jaroslav

2015-01-01

Following the discovery of serious errors in the structure of biomacromolecules, structure validation has become a key topic of research, especially for ligands and non-standard residues. ValidatorDB (freely available at http://ncbr.muni.cz/ValidatorDB) offers a new step in this direction, in the form of a database of validation results for all ligands and non-standard residues from the Protein Data Bank (all molecules with seven or more heavy atoms). Model molecules from the wwPDB Chemical Component Dictionary are used as reference during validation. ValidatorDB covers the main aspects of validation of annotation, and additionally introduces several useful validation analyses. The most significant is the classification of chirality errors, allowing the user to distinguish between serious issues and minor inconsistencies. Other such analyses are able to report, for example, completely erroneous ligands, alternate conformations or complete identity with the model molecules. All results are systematically classified into categories, and statistical evaluations are performed. In addition to detailed validation reports for each molecule, ValidatorDB provides summaries of the validation results for the entire PDB, for sets of molecules sharing the same annotation (three-letter code) or the same PDB entry, and for user-defined selections of annotations or PDB entries. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.

Relativistic many-body theory of atomic structures

International Nuclear Information System (INIS)

Cheng, K.T.

1983-01-01

The main objective of this program is to improve our understanding of the effect of relativity and electron correlations on atomic processes. Current efforts include hyperfine structure (hfs) studies using the multiconfiguration Dirac-Fock (MCDF) technique. Atomic hfs are known to be sensitive to relativity and electron correlations, and provide important tests of relativistic atomic many-body theories. Preliminary results on the hfs of the 4f 12 3 H ground state of 68 Er 167 are shown and are in good agreement with experiment. This shows that the MCDF technique can be an efficient and powerful method for atomic hfs studies. Further tests of this method are in progress. We are also studying the absorption spectra for Xe-like ions in the region of 4d → nf, epsilonf transitions

Examining the origins of the hydration force between lipid bilayers using all-atom simulations.

Science.gov (United States)

Gentilcore, Anastasia N; Michaud-Agrawal, Naveen; Crozier, Paul S; Stevens, Mark J; Woolf, Thomas B

2010-05-01

Using 237 all-atom double bilayer simulations, we examined the thermodynamic and structural changes that occur as a phosphatidylcholine lipid bilayer stack is dehydrated. The simulated system represents a micropatch of lipid multilayer systems that are studied experimentally using surface force apparatus, atomic force microscopy and osmotic pressure studies. In these experiments, the hydration level of the system is varied, changing the separation between the bilayers, in order to understand the forces that the bilayers feel as they are brought together. These studies have found a curious, strongly repulsive force when the bilayers are very close to each other, which has been termed the "hydration force," though the origins of this force are not clearly understood. We computationally reproduce this repulsive, relatively free energy change as bilayers come together and make qualitative conclusions as to the enthalpic and entropic origins of the free energy change. This analysis is supported by data showing structural changes in the waters, lipids and salts that have also been seen in experimental work. Increases in solvent ordering as the bilayers are dehydrated are found to be essential in causing the repulsion as the bilayers come together.

Advanced Kr Atomic Structure and Ionization Kinetics for Pinches on ZR

Science.gov (United States)

Dasgupta, Arati; Clark, Robert; Giuliani, John; Ouart, Nick; Davis, Jack; Jones, Brent; Ampleford, Dave; Hansen, Stephanie

2011-10-01

High fluence photon sources above 10 keV are a challenge for HED plasmas. This motivates Kr atomic modeling as its K-shell radiation starts at 13 keV. We have developed atomic structure and collisional-radiatve data for the full K-and L-shell and much of the M-shell using the the state-of-the-art Flexible Atomic Code. All relevant atomic collisional and radiative processes that affect ionization balance and are necessary to accurately model the pinch dynamics and the spectroscopic details of the emitted radiation are included in constructing the model. This non-LTE CRE model will be used to generate synthetic spectra for fixed densities and temperatures relevant for Kr gas-puff simulations in ZR. Work supported by DOE/NNSA. Sandia is a multi-program laboratory operated by Sandia Corporation, a Lockheed Martin Company, for the United States Department of Energy's National Nuclear Security Administration under contract DE-AC04-94AL85000.

Unraveling the atomic structure of ultrafine iron clusters

KAUST Repository

Wang, Hongtao; Li, Kun; Yao, Yingbang; Wang, Qingxiao; Cheng, Yingchun; Schwingenschlö gl, Udo; Zhang, Xixiang; Yang, Wei

2012-01-01

Unraveling the atomic structures of ultrafine iron clusters is critical to understanding their size-dependent catalytic effects and electronic properties. Here, we describe the stable close-packed structure of ultrafine Fe clusters for the first

Self-consistent average-atom scheme for electronic structure of hot and dense plasmas of mixture

International Nuclear Information System (INIS)

Yuan Jianmin

2002-01-01

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 (H 2 O), and CO 2 at a few temperatures and densities are presented

Self-consistent average-atom scheme for electronic structure of hot and dense plasmas of mixture.

Science.gov (United States)

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.

Vortex-ring-fractal Structure of Atom and Molecule

International Nuclear Information System (INIS)

Osmera, Pavel

2010-01-01

This chapter is an attempt to attain a new and profound model of the nature's structure using a vortex-ring-fractal theory (VRFT). Scientists have been trying to explain some phenomena in Nature that have not been explained so far. The aim of this paper is the vortex-ring-fractal modeling of elements in the Mendeleev's periodic table, which is not in contradiction to the known laws of nature. We would like to find some acceptable structure model of the hydrogen as a vortex-fractal-coil structure of the proton and a vortex-fractal-ring structure of the electron. It is known that planetary model of the hydrogen atom is not right, the classical quantum model is too abstract. Our imagination is that the hydrogen is a levitation system of the proton and the electron. Structures of helium, oxygen, and carbon atoms and a hydrogen molecule are presented too.

Nanoscale structure and atomic disorder in the iron-based chalcogenides

Directory of Open Access Journals (Sweden)

Naurang Lal Saini

2013-01-01

Full Text Available The multiband iron-based superconductors have layered structure with a phase diagram characterized by a complex interplay of charge, spin and lattice excitations, with nanoscale atomic structure playing a key role in their fundamental electronic properties. In this paper, we briefly review nanoscale structure and atomic disorder in iron-based chalcogenide superconductors. We focus on the Fe(Se,S1−xTex (11-type and K0.8Fe1.6Se2 (122-type systems, discussing their local structure obtained by extended x-ray absorption fine structure. Local structure studies on the Fe(Se,S1−xTex system reveal clear nanoscale phase separation characterized by coexisting components of different atomic configurations, similar to the case of random alloys. In fact, the Fe–Se/S and Fe–Te distances in the ternary Fe(Se,S1−xTex are found to be closer to the respective distances in the binary FeSe/FeS and FeTe systems, showing significant divergence of the local structure from the average one. The observed features are characteristic of ternary random alloys, indicating breaking of the local symmetry in these materials. On the other hand, K0.8Fe1.6Se2 is known for phase separation in an iron-vacancy ordered phase and an in-plane compressed lattice phase. The local structure of these 122-type chalcogenides shows that this system is characterized by a large local disorder. Indeed, the experiments suggest a nanoscale glassy phase in K0.8Fe1.6Se2, with the superconductivity being similar to the granular materials. While the 11-type structure has no spacer layer, the 122-type structure contains intercalated atoms unlike the 1111-type REFeAsO (RE = rare earth oxypnictides, having well-defined REO spacer layers. It is clear that the interlayer atomic correlations in these iron-based superconducting structures play an important role in structural stability as well as superconductivity and magnetism.

Software for relativistic atomic structure theory: The grasp project at oxford

International Nuclear Information System (INIS)

Parpia, F.A.; Grant, I.P.

1991-01-01

GRASP is an acronym for General-purpose Relativistic Atomic Structure Program. The objective of the GRASP project at Oxford is to produce user-friendly state-of-the-art multiconfiguration Dirac-Fock (MCDF) software packages for rleativistic atomic structure theory

Extending the validity of the Feeding Practices and Structure Questionnaire.

Science.gov (United States)

Jansen, Elena; Mallan, Kimberley M; Daniels, Lynne A

2015-06-30

Feeding practices are commonly examined as potentially modifiable determinants of children's eating behaviours and weight status. Although a variety of questionnaires exist to assess different feeding aspects, many lack thorough reliability and validity testing. The Feeding Practices and Structure Questionnaire (FPSQ) is a tool designed to measure early feeding practices related to non-responsive feeding and structure of the meal environment. Face validity, factorial validity, internal reliability and cross-sectional correlations with children's eating behaviours have been established in mothers with 2-year-old children. The aim of the present study was to further extend the validity of the FPSQ by examining factorial, construct and predictive validity, and stability. Participants were from the NOURISH randomised controlled trial which evaluated an intervention with first-time mothers designed to promote protective feeding practices. Maternal feeding practices (FP) and child eating behaviours were assessed when children were aged 2 years and 3.7 years (n = 388). Confirmatory Factor analysis, group differences, predictive relationships, and stability were tested. The original 9-factor structure was confirmed when children were aged 3.7 ± 0.3 years. Cronbach's alpha was above the recommended 0.70 cut-off for all factors except Structured Meal Timing, Over Restriction and Distrust in Appetite which were 0.58, 0.67 and 0.66 respectively. Allocated group differences reflected behaviour consistent with intervention content and all feeding practices were stable across both time points (range of r = 0.45-0.70). There was some evidence for the predictive validity of factors with 2 FP showing expected relationships, 2 FP showing expected and unexpected relationships and 5 FP showing no relationship. Reliability and validity was demonstrated for most subscales of the FPSQ. Future validation is warranted with culturally diverse samples and with fathers and

Quantum Mechanics/Molecular Mechanics Method Combined with Hybrid All-Atom and Coarse-Grained Model: Theory and Application on Redox Potential Calculations.

Science.gov (United States)

Shen, Lin; Yang, Weitao

2016-04-12

We developed a new multiresolution method that spans three levels of resolution with quantum mechanical, atomistic molecular mechanical, and coarse-grained models. The resolution-adapted all-atom and coarse-grained water model, in which an all-atom structural description of the entire system is maintained during the simulations, is combined with the ab initio quantum mechanics and molecular mechanics method. We apply this model to calculate the redox potentials of the aqueous ruthenium and iron complexes by using the fractional number of electrons approach and thermodynamic integration simulations. The redox potentials are recovered in excellent accordance with the experimental data. The speed-up of the hybrid all-atom and coarse-grained water model renders it computationally more attractive. The accuracy depends on the hybrid all-atom and coarse-grained water model used in the combined quantum mechanical and molecular mechanical method. We have used another multiresolution model, in which an atomic-level layer of water molecules around redox center is solvated in supramolecular coarse-grained waters for the redox potential calculations. Compared with the experimental data, this alternative multilayer model leads to less accurate results when used with the coarse-grained polarizable MARTINI water or big multipole water model for the coarse-grained layer.

Atomic-level structures and physical properties of magnetic CoSiB metallic glasses

International Nuclear Information System (INIS)

Shan, Guangcun; Liang Zhang, Ji; Li, Jiong; Zhang, Shuo; Jiang, Zheng; Huang, Yuying; Shek, Chan-Hung

2014-01-01

Two CoSiB metallic glasses of low Co contents, which consist of different clusters, have recently been developed by addition of solute atoms. In this work, the atomic structure and the magnetic properties of the two CoBSi metallic glasses were elucidated by state-of-the-art extended X-ray absorption fine structure spectroscopy (EXAFS) combining with ab initio molecular-dynamics (AIMD) computational techniques. Besides, the origin of these magnetic behaviors was discussed in view of the EXAFS results and atomic structures of the metallic glasses. - Graphical abstract: The atomic structure and the origins of the magnetic properties of two ternary CoBSi metallic glasses were elucidated by state-of-the-art extended X-ray absorption fine structure spectroscopy (EXAFS) combining with ab initio molecular-dynamics (AIMD) techniques. - Highlights: • The atomic structure and the origins of the magnetic properties of two ternary CoBSi metallic glasses were revealed. • The atomic structures were elucidated by state-of-the-art extended X-ray absorption fine structure spectroscopy (EXAFS) combining with ab initio molecular-dynamics (AIMD) techniques. • The experimental spectra were in good agreement with the predictions of ab initio full multiple scattering theory using the FEFF8.4 code. • The origin of these magnetic behaviors was discussed in view of the EXAFS results and atomic structures of the metallic glasses. • These two metallic glasses consist of different clusters, and hence different magnetic properties, which are dominated by short-range orders (SROs)

Atomic fine structure in a space of constant curvature

International Nuclear Information System (INIS)

Bessis, N.; Bessis, G.; Shamseddine, R.

1982-01-01

As a contribution to a tentative formulation of atomic physics in a curved space, the determination of atomic fine structure energies in a space of constant curvature is investigated. Starting from the Dirac equation in a curved space-time, the analogue of the Pauli equation in a general coordinate system is derived. The theoretical curvature induced shifts and splittings of the fine structure energy levels are put in evidence and examined for the particular case of the hydrogenic n=2 levels. (author)

Realizing high magnetic moments in fcc Fe nanoparticles through atomic structure stretch

International Nuclear Information System (INIS)

Baker, S H; Roy, M; Thornton, S C; Binns, C

2012-01-01

We describe the realization of a high moment state in fcc Fe nanoparticles through a controlled change in their atomic structure. Embedding Fe nanoparticles in a Cu 1-x Au x matrix causes their atomic structure to switch from bcc to fcc. Extended x-ray absorption fine structure (EXAFS) measurements show that the structure in both the matrix and the Fe nanoparticles expands as the amount of Au in the matrix is increased, with the data indicating a tetragonal stretch in the Fe nanoparticles. The samples were prepared directly from the gas phase by co-deposition, using a gas aggregation source and MBE-type sources respectively for the nanoparticle and matrix materials. The structure change in the Fe nanoparticles is accompanied by a sharp increase in atomic magnetic moment, ultimately to values of ∼2.5 ± 0.3 μ B /atom. (paper)

The cytotoxicity of organobismuth compounds with certain molecular structures can be diminished by replacing the bismuth atom with an antimony atom in the molecules.

Science.gov (United States)

Kohri, Kumiko; Yoshida, Eiko; Yasuike, Shuji; Fujie, Tomoya; Yamamoto, Chika; Kaji, Toshiyuki

2015-06-01

Organic-inorganic hybrid molecules, which are composed of an organic structure and metal(s), are indispensable for synthetic chemical reactions; however, their toxicity has been incompletely understood. In the present study, we discovered two cytotoxic organobismuth compounds whose cytotoxicity diminished upon replacement of the intramolecular bismuth atom with an antimony atom. The intracellular accumulation of the organobismuth compounds was much higher than that of the organoantimony compounds with the corresponding organic structures. We also showed that both the organic structure and bismuth atom are required for certain organobismuth compounds to exert their cytotoxic effect, suggesting that the cytotoxicity of such a compound is a result of an interaction between the organic structure and the bismuth atom. The present data suggest that organobismuth compounds with certain molecular structures exhibit cytotoxicity via an interaction between the molecular structure and the bismuth atom, and this cytotoxicity can be diminished by replacing the bismuth atom with an antimony atom, resulting in lower intracellular accumulation.

Atom-type-based AI topological descriptors: application in structure-boiling point correlations of oxo organic compounds.

Science.gov (United States)

Ren, Biye

2003-01-01

Structure-boiling point relationships are studied for a series of oxo organic compounds by means of multiple linear regression (MLR) analysis. Excellent MLR models based on the recently introduced Xu index and the atom-type-based AI indices are obtained for the two subsets containing respectively 77 ethers and 107 carbonyl compounds and a combined set of 184 oxo compounds. The best models are tested using the leave-one-out cross-validation and an external test set, respectively. The MLR model produces a correlation coefficient of r = 0.9977 and a standard error of s = 3.99 degrees C for the training set of 184 compounds, and r(cv) = 0.9974 and s(cv) = 4.16 degrees C for the cross-validation set, and r(pred) = 0.9949 and s(pred) = 4.38 degrees C for the prediction set of 21 compounds. For the two subsets containing respectively 77 ethers and 107 carbonyl compounds, the quality of the models is further improved. The standard errors are reduced to 3.30 and 3.02 degrees C, respectively. Furthermore, the results obtained from this study indicate that the boiling points of the studied oxo compound dominantly depend on molecular size and also depend on individual atom types, especially oxygen heteroatoms in molecules due to strong polar interactions between molecules. These excellent structure-boiling point models not only provide profound insights into the role of structural features in a molecule but also illustrate the usefulness of these indices in QSPR/QSAR modeling of complex compounds.

Characterization of iron ferromagnetism by the local atomic volume: from three-dimensional structures to isolated atoms.

Science.gov (United States)

Zhang, Lei; Sob, M; Wu, Zhe; Zhang, Ying; Lu, Guang-Hong

2014-02-26

We present a comprehensive study of the relationship between the ferromagnetism and the structural properties of Fe systems from three-dimensional ones to isolated atoms based on the spin-density functional theory. We have found a relation between the magnetic moment and the volume of the Voronoi polyhedron, determining, in most cases, the value of the total magnetic moment as a function of this volume with an average accuracy of ±0.28 μ(B) and of the 3d magnetic moment with an average accuracy of ±0.07 μ(B) when the atomic volume is larger than 22 ų. It is demonstrated that this approach is applicable for many three-dimensional systems, including high-symmetry structures of perfect body-centered cubic (bcc), face-centered cubic (fcc), hexagonal close-packed (hcp), double hexagonal close-packed (dhcp), and simple cubic (sc) crystals, as well as for lower-symmetry ones, for example atoms near a grain boundary (GB) or a surface, around a vacancy or in a linear chain (for low-dimensional cases, we provide a generalized definition of the Voronoi polyhedron). Also, we extend the validity of the Stoner model to low-dimensional structures, such as atomic chains, free-standing monolayers and surfaces, determining the Stoner parameter for these systems. The ratio of the 3d-exchange splitting to the magnetic moment, corresponding to the Stoner parameter, is found to be I(3d) = (0.998 ± 0.006) eV /μ(B) for magnetic moments up to 3.0 μ(B). Further, the 3d exchange splitting changes nearly linearly in the region of higher magnetic moments (3.0-4.0 μ(B)) and the corresponding Stoner exchange parameter equals I(h)(3d) = (0.272 ± 0.006) eV /μ(B). The existence of these two regions reflects the fact that, with increasing Voronoi volume, the 3d bands separate first and, consequently, the 3d magnetic moment increases. When the Voronoi volume is sufficiently large (≥22 ų), the separation of the 3d bands is complete and the magnetic moment reaches a value of 3.0 �

Characterization of iron ferromagnetism by the local atomic volume: from three-dimensional structures to isolated atoms

International Nuclear Information System (INIS)

Zhang, Lei; Šob, M; Wu, Zhe; Zhang, Ying; Lu, Guang-Hong

2014-01-01

We present a comprehensive study of the relationship between the ferromagnetism and the structural properties of Fe systems from three-dimensional ones to isolated atoms based on the spin-density functional theory. We have found a relation between the magnetic moment and the volume of the Voronoi polyhedron, determining, in most cases, the value of the total magnetic moment as a function of this volume with an average accuracy of ±0.28 μ B and of the 3d magnetic moment with an average accuracy of ±0.07 μ B when the atomic volume is larger than 22 Å 3 . It is demonstrated that this approach is applicable for many three-dimensional systems, including high-symmetry structures of perfect body-centered cubic (bcc), face-centered cubic (fcc), hexagonal close-packed (hcp), double hexagonal close-packed (dhcp), and simple cubic (sc) crystals, as well as for lower-symmetry ones, for example atoms near a grain boundary (GB) or a surface, around a vacancy or in a linear chain (for low-dimensional cases, we provide a generalized definition of the Voronoi polyhedron). Also, we extend the validity of the Stoner model to low-dimensional structures, such as atomic chains, free-standing monolayers and surfaces, determining the Stoner parameter for these systems. The ratio of the 3d-exchange splitting to the magnetic moment, corresponding to the Stoner parameter, is found to be I 3d = (0.998 ± 0.006) eV /μ B for magnetic moments up to 3.0 μ B . Further, the 3d exchange splitting changes nearly linearly in the region of higher magnetic moments (3.0–4.0 μ B ) and the corresponding Stoner exchange parameter equals I 3d h =(0.272±0.006) eV/μ B . The existence of these two regions reflects the fact that, with increasing Voronoi volume, the 3d bands separate first and, consequently, the 3d magnetic moment increases. When the Voronoi volume is sufficiently large (≥22 Å 3 ), the separation of the 3d bands is complete and the magnetic moment reaches a value of 3.0�

An optimized intermolecular force field for hydrogen-bonded organic molecular crystals using atomic multipole electrostatics

International Nuclear Information System (INIS)

Pyzer-Knapp, Edward O.; Thompson, Hugh P. G.; Day, Graeme M.

2016-01-01

An empirically parameterized intermolecular force field is developed for crystal structure modelling and prediction. The model is optimized for use with an atomic multipole description of electrostatic interactions. We present a re-parameterization of a popular intermolecular force field for describing intermolecular interactions in the organic solid state. Specifically we optimize the performance of the exp-6 force field when used in conjunction with atomic multipole electrostatics. We also parameterize force fields that are optimized for use with multipoles derived from polarized molecular electron densities, to account for induction effects in molecular crystals. Parameterization is performed against a set of 186 experimentally determined, low-temperature crystal structures and 53 measured sublimation enthalpies of hydrogen-bonding organic molecules. The resulting force fields are tested on a validation set of 129 crystal structures and show improved reproduction of the structures and lattice energies of a range of organic molecular crystals compared with the original force field with atomic partial charge electrostatics. Unit-cell dimensions of the validation set are typically reproduced to within 3% with the re-parameterized force fields. Lattice energies, which were all included during parameterization, are systematically underestimated when compared with measured sublimation enthalpies, with mean absolute errors of between 7.4 and 9.0%

Atomic structure of a metal-supported two-dimensional germania film

Science.gov (United States)

Lewandowski, Adrián Leandro; Schlexer, Philomena; Büchner, Christin; Davis, Earl M.; Burrall, Hannah; Burson, Kristen M.; Schneider, Wolf-Dieter; Heyde, Markus; Pacchioni, Gianfranco; Freund, Hans-Joachim

2018-03-01

The growth and microscopic characterization of two-dimensional germania films is presented. Germanium oxide monolayer films were grown on Ru(0001) by physical vapor deposition and subsequent annealing in oxygen. We obtain a comprehensive image of the germania film structure by combining intensity-voltage low-energy electron diffraction (I/V-LEED) and ab initio density functional theory (DFT) analysis with atomic-resolution scanning tunneling microscopy (STM) imaging. For benchmarking purposes, the bare Ru(0001) substrate and the (2 ×2 )3 O covered Ru(0001) were analyzed with I/V-LEED with respect to previous reports. STM topographic images of the germania film reveal a hexagonal network where the oxygen and germanium atom positions appear in different imaging contrasts. For quantitative LEED, the best agreement has been achieved with DFT structures where the germanium atoms are located preferentially on the top and fcc hollow sites of the Ru(0001) substrate. Moreover, in these atomically flat germania films, local site geometries, i.e., tetrahedral building blocks, ring structures, and domain boundaries, have been identified, indicating possible pathways towards two-dimensional amorphous networks.

Mechanical properties and electronic structure of edge-doped graphene nanoribbons with F, O, and Cl atoms.

Science.gov (United States)

Piriz, Sebastián; Fernández-Werner, Luciana; Pardo, Helena; Jasen, Paula; Faccio, Ricardo; Mombrú, Álvaro W

2017-08-16

In this study, we present the structural, electronic, and mechanical properties of edge-doped zigzag graphene nanoribbons (ZGNRs) doped with fluorine, oxygen, and chlorine atoms. To the best of our knowledge, to date, no experimental results concerning the mechanical properties of graphene-derived nanoribbons have been reported in the literature. Simulations indicate that Cl- and F-doped ZGNRs present an equivalent 2-dimensional Young's modulus E 2D , which seems to be higher than those of graphene and H-doped ZGNRs. This is a consequence of the electronic structure of the system, particularly originating from strong interactions between the dopant atoms localized at the edges. The interaction between dopant atoms located at the edges is higher for Cl and lower for F and O atoms. This is the origin of the observed trend, in which E > E > E for all the analyzed ZGNRs.

Local atomic structure of α-Pu

International Nuclear Information System (INIS)

Espinosa, F. J.; Villella, P.; Lashley, J. C.; Conradson, S. D.; Cox, L. E.; Martinez, R.; Martinez, B.; Morales, L.; Terry, J.; Pereyra, R. A.

2001-01-01

The local atomic structure of α-Pu was investigated using x-ray absorption fine structure (XAFS) spectroscopy. XAFS spectra were obtained for a zone-refined α-Pu and the results were compared to 32-year-old and Ce-doped (0.34 at.%) samples. X-ray diffraction (XRD) patterns were also measured for the zone-refined and 32-year-old materials. The extent of the Bragg peaks showed that amorphization of the 32-year-old sample had not occurred despite the prolonged exposure to self-radiation. Analogous to metastable δ-Pu alloys, the local atomic structure around Pu for the zone-refined material shows the possible presence of noncrystallographic Pu-Pu distances. Conversely, the Ce and the 32-year-old sample show no evidence for such noncrystallographic distances. Disorder in the Pu local environment was found to be impurity dependent. The Ce-doped sample presented a larger Pu-Pu nearest neighbor disorder than the aged sample, although the total amount of Am, U, and He impurities was actually higher in the aged sample. The local environment around U and Ce impurities is consistent with these elements being in substitutional lattice sites. In addition, U and Ce do not introduce significant lattice distortion to their nearest neighbors. This is consistent with disorder being more related to the perturbation of the coupling between the electronic and crystal structure, or the Peierls--Jahn-Teller distortion that generates the monoclinic α-Pu structure, and less to strain fields produced in the vicinity of the impurities

Finding the Atomic Configuration with a Required Physical Property in Multi-Atom Structures

International Nuclear Information System (INIS)

d'Avezac, M.; Zunger, A.

2007-01-01

In many problems in molecular and solid state structures one seeks to determine the energy-minimizing decoration of sites with different atom types. In other problems, one is interested in finding a decoration with a target physical property (e.g. alloy band gap) within a certain range. In both cases, the sheer size of the configurational space can be horrendous. We present two approaches which identify either the minimum-energy configuration or configurations with a target property for a fixed underlying Bravais lattice. We compare their efficiency at locating the deepest minimum energy configuration of face centered cubic Au-Pd alloy. We show that a global-search genetic-algorithm approach with diversity-enhancing constraints and reciprocal-space mating can efficiently find the global optimum, whereas the local-search virtual-atom approach presented here is more efficient at finding structures with a target property

Atomic structures and mechanical properties of single-crystal GaN nanotubes

International Nuclear Information System (INIS)

Xu, B.; Lu, A.J.; Pan, B.C.; Yu, Q.X.

2005-01-01

An approach is proposed to theoretically construct a realistic single-crystal GaN nanotube at atomic scale. The generated atomic structures of the single-crystal GaN nanotubes match the structural aspects from experiment very well. Our energetic calculations show that a single-crystal GaN nanotube with [100]-oriented lateral facets is more stable than that with [110]-oriented lateral facets, when they have around the same wall thickness. For a specified orientation of the lateral facets on the single-crystal GaN nanotubes, the energetic stabilities of the tubes obey a P rule, in which P is the ratio of the number of four-coordinated atoms to the number of three-coordinated atoms. Furthermore, the Young's modulus of the considered GaN nanotubes decrease with increasing the ratio of the number of bulk atoms to the number of surface atoms in each type of tube. Our calculations and analysis demonstrate that the surface effect of a single-crystal nanotube enhances its Young's modulus significantly

Atomic structure of self-organizing iridium induced nanowires on Ge(001)

Energy Technology Data Exchange (ETDEWEB)

Kabanov, N.S., E-mail: n.kabanov@utwente.nl [Faculty of Physics, Moscow State University, 119991 (Russian Federation); Physics of Interfaces and Nanomaterials, MESA+ Institute for Nanotechnology, University of Twente, P. O. Box 217, Enschede 7500 AE (Netherlands); Heimbuch, R.; Zandvliet, H.J.W. [Physics of Interfaces and Nanomaterials, MESA+ Institute for Nanotechnology, University of Twente, P. O. Box 217, Enschede 7500 AE (Netherlands); Saletsky, A.M.; Klavsyuk, A.L. [Faculty of Physics, Moscow State University, 119991 (Russian Federation)

2017-05-15

Highlights: • Ir/Ge(001) structure has been studied with DFT calculations and scanning tunneling microscopy. • Ir/Ge(001) nanowires are composed of Ge atoms and Ir atoms are located in subsurface positions. • The regions in the vicinity of the nanowires are very dynamic, even at temperatures as low as 77 K. - Abstract: The atomic structure of self-organizing iridium (Ir) induced nanowires on Ge(001) is studied by density functional theory (DFT) calculations and variable-temperature scanning tunneling microscopy. The Ir induced nanowires are aligned in a direction perpendicular to the Ge(001) substrate dimer rows, have a width of two atoms and are completely kink-less. Density functional theory calculations show that the Ir atoms prefer to dive into the Ge(001) substrate and push up the neighboring Ge substrate atoms. The nanowires are composed of Ge atoms and not Ir atoms as previously assumed. The regions in the vicinity of the nanowires are very dynamic, even at temperatures as low as 77 K. Time-resolved scanning tunneling microscopy measurements reveal that this dynamics is caused by buckled Ge substrate dimers that flip back and forth between their two buckled configurations.

Effect of Cu insertion on structural, local electronic/atomic structure and photocatalyst properties of TiO{sub 2}, ZnO and Ni(OH){sub 2} nanostructures: XANES-EXAFS study

Energy Technology Data Exchange (ETDEWEB)

Sharma, Aditya; Varshney, Mayora [Advanced Analysis Centre, Korea Institute of Science and Technology, Seoul, 02792 (Korea, Republic of); Shin, Hyun Joon, E-mail: shj001@postech.ac.kr [Pohang Accelerator Laboratory (POSTECH), Pohang, 37673 (Korea, Republic of); Lee, Byeong-Hyeon [Advanced Analysis Centre, Korea Institute of Science and Technology, Seoul, 02792 (Korea, Republic of); Chae, Keun Hwa, E-mail: khchae@kist.re.kr [Advanced Analysis Centre, Korea Institute of Science and Technology, Seoul, 02792 (Korea, Republic of); Won, Sung Ok, E-mail: sowon@kist.re.kr [Advanced Analysis Centre, Korea Institute of Science and Technology, Seoul, 02792 (Korea, Republic of)

2017-04-15

We report detailed investigations on the synthesis, structural, morphology, electronic/atomic structure and photocatalyst properties of Cu doped TiO{sub 2}, ZnO and Ni(OH){sub 2} nanostructures. All of the samples were synthesized by using the chemical precipitation method. Samples were characterized by X-ray diffraction (XRD), transmission electron microscope (TEM), X-ray absorption near edge structure (XANES), extended X-ray absorption fine structure (EXAFS) and photocatalyst measurements. XRD studies revealed single phase nature of the samples and omitted the presence of trivial metallic or binary oxide phases. TiO{sub 2} set of samples have shown nanorod kind of morphology, however TEM images of ZnO and Ni(OH){sub 2} set of samples depicted the spherical morphology of particles. XANES spectra at the Cu K-edge and Cu L-edge, along with the atomic multiplet calculations, revealed the predominance of Cu{sup 2+} ions in all of the samples, within the entire doping range. Ti L-edge and Ti K-edge XANES confirmed the existence of Ti{sup 4+} ions in the pure and Cu doped TiO{sub 2} samples with anatase local structure. Zn L-edge XANES results confirmed the divalent character of Zn ions in the pure and Cu doped ZnO, which is further validated by the Zn K-edge XANES. Ni L-edge and Ni K-edge XANES conveyed the +2 valence state of Ni ions in the pure and Cu doped Ni (OH){sub 2} samples. EXAFS analysis at the Cu K-edge nullifies the formation of Cu metallic clusters and other trivial phases, suggesting random distribution of Cu atoms in the oxide materials. Though, local atomic arrangement of Cu ions is disparate in the different oxide compounds. As an application of the pure and Cu doped TiO{sub 2}, ZnO and Ni(OH){sub 2} nanostructures, towards the degradation of water pollutant dyes, we demonstrate that all of the samples can serve as effective photocatalyst materials towards the degradation of methyl orange aqueous pollutant dye under the UV-light irradiation

Synthesis and atomic structure determination of Al8V5 gamma-brass

International Nuclear Information System (INIS)

Mizutani, Uichiro

2006-01-01

Many structurally complex compounds like quasicrystals and their approximants are known to be stabilized at a particular electron per atom ratio e/a, regardless of constituent elements involved. This has been often referred to as the Hume-Rothery electron concentration rule. We consider the understanding of the Hume-Rothery stabilization mechanism to be best deepened by performing both ab initio LMTO-ASA and FLAPW band calculations for the complex compound whose atomic structure is experimentally determined. Admittedly, however, a computing time increases rapidly beyond practical level with increasing the number of atoms in a unit cell. Among various candidates, we chose a series of gamma-brasses containing 52 atoms in a unit cell by taking a full advantage of the facts that it exists in as many as 24 binary alloy systems and that its unit cell is just in size to be handled even in more time-consuming FLAPW method. We have so far studied the stability mechanism of Cu 5 Zn 8 and Cu 9 Al 4 , both being regarded as its prototype, and TM 2 Zn 11 gamma-brasses containing late transition elements TM=Fe, Co, Ni and Pd. In the present work, we chose the gamma-brass consisting of early transition metal element V and trivalent element Al. An almost single phase Al 8 V 5 gamma-brass was ultimately synthesized by overcoming metallurgical difficulties encountered. Its atomic structure was determined by using the Brandon model as a starting structure in the Rietveld structure analysis for powdered diffraction spectra taken at the beam line BL02B2 of 8 GeV synchrotron radiation facility, SPring-8, Japan. The atomic structure suitable for band calculations was then proposed by eliminating quenched-in chemical disorder, i.e., partial mixing of Al and V atoms at given sites with minimum sacrifice. (author)

All-optical atom trap trace analysis for rare krypton isotopes

Energy Technology Data Exchange (ETDEWEB)

Woelk, Pablo; Kohler, Markus; Sieveke, Carsten; Hebel, Simon; Sahling, Peter [Carl Friedrich von Weizsaecker Centre for Science and Peace Research, University of Hamburg (Germany); Becker, Christoph; Sengstock, Klaus [Institut fuer Laser-Physik, University of Hamburg (Germany)

2016-07-01

The isotope Krypton-85 is an excellent indicator for the detection of nuclear reprocessing activities. However, for the analysis of atmospheric air samples, sensitive measuring methods down to the single atom level are required because of the small concentrations. Furthermore, for a practical and effective detection of clandestine reprocessing, small sample sizes and a high sample throughput rate are desirable. Established methods using Atom Trap Trace Analysis (ATTA) allow high sensitivity but have a limited throughput of about 200 samples per year, since the vacuum chambers have to be flushed for several hours after each measurement to avoid cross contamination due to the RF-driven excitation of metastable states. Here we present an enhanced ATTA apparatus, which in contrast to the established methods, produces metastable Kr all-optically. This avoids cross contamination, therefore allowing a much higher throughput rate. The apparatus is based on a self-made VUV-lamp and a 2D-3D magneto-optical trap setup. In the 2D trap metastable krypton is produced and a beam of atoms is formed by Doppler-cooling simultaneously.

The variational method in the atomic structure calcularion

International Nuclear Information System (INIS)

Tomimura, A.

1970-01-01

The importance and limitations of variational methods on the atomic structure calculations is set into relevance. Comparisons are made to the Perturbation Theory. Ilustrating it, the method is applied to the H - , H + and H + 2 simple atomic structure systems, and the results are analysed with basis on the study of the associated essential eigenvalue spectrum. Hydrogenic functions (where the screening constants are replaced by variational parameters) are combined to construct the wave function with proper symmetry for each one of the systems. This shows the existence of a bound state for H - , but no conclusions can be made for the others, where it may or may not be necessary to use more flexible wave functions, i.e., with greater number of terms and parameters. (author) [pt

Atomic structure of machined semiconducting chips: An x-ray absorption spectroscopy study

Energy Technology Data Exchange (ETDEWEB)

Paesler, M.; Sayers, D.

1988-12-01

X-ray absorption spectroscopy (XAS) has been used to examine the atomic structure of chips of germanium that were produced by single point diamond machining. It is demonstrated that although the local (nearest neighbor) atomic structure is experimentally quite similar to that of single crystal specimens information from more distant atoms indicates the presence of considerable stress. An outline of the technique is given and the strength of XAS in studying the machining process is demonstrated.

Atomic structure and formation of CuZrAl bulk metallic glasses and composites

International Nuclear Information System (INIS)

Kaban, I.; Jóvári, P.; Escher, B.; Tran, D.T.; Svensson, G.; Webb, M.A.; Regier, T.Z.; Kokotin, V.; Beuneu, B.; Gemming, T.; Eckert, J.

2015-01-01

Graphical abstract: Partial radial distribution functions for Cu 47.5 Zr 47.5 Al 5 metallic glass and relevant crystal structures. - Abstract: Cu 47.5 Zr 47.5 Al 5 metallic glass is studied experimentally by high-energy X-ray diffraction, neutron diffraction with isotopic substitution, electron diffraction and X-ray absorption spectroscopy. The atomic structure of the glass is modeled by reverse Monte-Carlo and molecular dynamics simulations. RMC modeling of seven experimental datasets enabled reliable separation of all partial pair distribution functions for Cu 47.5 Zr 47.5 Al 5 metallic glass. A peculiar structural feature of the ternary alloy is formation of the strong Al–Zr bonds, which are supposed to determine its high viscosity and enhanced bulk glass formation. Analysis of the local atomic order in Cu 47.5 Zr 47.5 Al 5 glass and Cu 10 Zr 7 , CuZr 2 and CuZr B2 crystalline structures elucidates their similarities and differences explaining the phase formation sequence by devitrification of the glass.

Computer Simulation of Atoms Nuclei Structure Using Information Coefficients of Proportionality

OpenAIRE

Labushev, Mikhail M.

2012-01-01

The latest research of the proportionality of atomic weights of chemical elements made it possible to obtain 3 x 3 matrices for the calculation of information coefficients of proportionality Ip that can be used for 3D modeling of the structure of atom nucleus. The results of computer simulation show high potential of nucleus structure research for the characterization of their chemical and physical properties.

Validation-driven protein-structure improvement

NARCIS (Netherlands)

Touw, W.G.

2016-01-01

High-quality protein structure models are essential for many Life Science applications, such as protein engineering, molecular dynamics, drug design, and homology modelling. The WHAT_CHECK model validation project and the PDB_REDO model optimisation project have shown that many structure models in

Fine structures of atomic excited states: precision atomic spectroscopy and electron-ion collision process

International Nuclear Information System (INIS)

Gao Xiang; Cheng Cheng; Li Jiaming

2011-01-01

Scientific research fields for future energies such as inertial confinement fusion researches and astrophysics studies especially with satellite observatories advance into stages of precision physics. The relevant atomic data are not only enormous but also of accuracy according to requirements, especially for both energy levels and the collision data. The fine structure of high excited states of atoms and ions can be measured by precision spectroscopy. Such precision measurements can provide not only knowledge about detailed dynamics of electron-ion interactions but also a bench mark examination of the accuracy of electron-ion collision data, especially incorporating theoretical computations. We illustrate that by using theoretical calculation methods which can treat the bound states and the adjacent continua on equal footing. The precision spectroscopic measurements of excited fine structures can be served as stringent tests of electron-ion collision data. (authors)

Distortion of Local Atomic Structures in Amorphous Ge-Sb-Te Phase Change Materials

Science.gov (United States)

Hirata, A.; Ichitsubo, T.; Guan, P. F.; Fujita, T.; Chen, M. W.

2018-05-01

The local atomic structures of amorphous Ge-Sb-Te phase-change materials have yet to be clarified and the rapid crystal-amorphous phase change resulting in distinct optical contrast is not well understood. We report the direct observation of local atomic structures in amorphous Ge2Sb2Te5 using "local" reverse Monte Carlo modeling dedicated to an angstrom-beam electron diffraction analysis. The results corroborated the existence of local structures with rocksalt crystal-like topology that were greatly distorted compared to the crystal symmetry. This distortion resulted in the breaking of ideal octahedral atomic environments, thereby forming local disordered structures that basically satisfied the overall amorphous structure factor. The crystal-like distorted octahedral structures could be the main building blocks in the formation of the overall amorphous structure of Ge-Sb-Te.

Atomic spectral-product representations of molecular electronic structure: metric matrices and atomic-product composition of molecular eigenfunctions.

Science.gov (United States)

Ben-Nun, M; Mills, J D; Hinde, R J; Winstead, C L; Boatz, J A; Gallup, G A; Langhoff, P W

2009-07-02

Recent progress is reported in development of ab initio computational methods for the electronic structures of molecules employing the many-electron eigenstates of constituent atoms in spectral-product forms. The approach provides a universal atomic-product description of the electronic structure of matter as an alternative to more commonly employed valence-bond- or molecular-orbital-based representations. The Hamiltonian matrix in this representation is seen to comprise a sum over atomic energies and a pairwise sum over Coulombic interaction terms that depend only on the separations of the individual atomic pairs. Overall electron antisymmetry can be enforced by unitary transformation when appropriate, rather than as a possibly encumbering or unnecessary global constraint. The matrix representative of the antisymmetrizer in the spectral-product basis, which is equivalent to the metric matrix of the corresponding explicitly antisymmetric basis, provides the required transformation to antisymmetric or linearly independent states after Hamiltonian evaluation. Particular attention is focused in the present report on properties of the metric matrix and on the atomic-product compositions of molecular eigenstates as described in the spectral-product representations. Illustrative calculations are reported for simple but prototypically important diatomic (H(2), CH) and triatomic (H(3), CH(2)) molecules employing algorithms and computer codes devised recently for this purpose. This particular implementation of the approach combines Slater-orbital-based one- and two-electron integral evaluations, valence-bond constructions of standard tableau functions and matrices, and transformations to atomic eigenstate-product representations. The calculated metric matrices and corresponding potential energy surfaces obtained in this way elucidate a number of aspects of the spectral-product development, including the nature of closure in the representation, the general redundancy or

Atomic-level structure and structure-property relationship in metallic glass

Science.gov (United States)

Cheng, Yongqiang

One of the key tasks in material science is to understand the structure and structure-property relationship. The recently emerging bulk metallic glasses (BMGs) have demonstrated unique properties, especially intriguing mechanical properties such as their high strength and high propensity to localize deformation in shear bands. However, a comprehensive understanding of the structure of BMGs has been hindered by the complexity of these amorphous materials. Even more challenging is the structure-property correlation, which has been well established in crystals but has been seriously lacking for BMGs. This thesis presents a systematic study of the atomic-level structures of two representative BMGs, Cu-Zr and Cu-Zr-Al. The interpenetrating Cu-centered icosahedral clusters have been identified to be the primary structural feature. The fraction of icosahedra increases with increasing Cu or Al contents, and with decreasing cooling rate. The effect of Al in improving the icosahedral order is two-fold: the geometric effect due to the atomic-size mismatch and the chemical effect originated from the Cu-Al bond shortening. The resolved structure is used to study the structure-property relationship. The full icosahedra are found to be responsible for the dynamical slowdown of the supercooled liquid, which underlies the non-Arrhenius behavior, and explains the composition dependence of glass transition temperature, glass forming ability, and the room temperature strength. By simulated deformation, the initiation of plasticity and tendency for strain localization are also investigated. The full icosahedra are found to be the most rigid and resistant cluster with solid-like character, while the unstable clusters with liquid-like character serve as the fertile sites for initiating shear transformations. In addition, the elastic moduli are calculated and analyzed, and the origins of the different configurational dependence of shear modulus (G) and bulk modulus ( B) are explained. The

Electronic and atomic structure of the AlnHn+2 clusters

DEFF Research Database (Denmark)

Martinez, Jose Ignacio; Alonso, J.A.

2008-01-01

The electronic and atomic structure of the family of hydrogenated Al clusters AlnHn+2 with n=4-11 has been studied using the density functional theory with the generalized gradient approximation (GGA) for exchange and correlation. All these clusters have substantial gaps between the highest...... a polyhedron of n vertices and n H atoms form strong H-Al terminal bonds; one pair of electrons is involved in each of those bonds. The remaining n+1 electron pairs form a delocalized cloud over the surface of the Al cage. The clusters fulfilling the Wade-Mingos rule have wider HOMO-LUMO gaps...... and are chemically more stable. The trends in the gap have some reflections in the form of the photoabsorption spectra, calculated in the framework of time-dependent density functional theory using the GGA single-particle energies and orbitals and a local density approximation exchange-correlation kernel....

Atomic structure of non-stoichiometric transition metal carbides

International Nuclear Information System (INIS)

Moisy-Maurice, Virginie.

1981-10-01

Different kinds of experimental studies of the atomic arrangement in non-stoichiometric transition metal carbides are proposed: the ordering of carbon vacancies and the atomic static displacements are the main subjects studied. Powder neutron diffraction on TiCsub(1-x) allowed us to determine the order-disorder transition critical temperature -Tsub(c) approximately 770 0 C- in the TiCsub(0.52-0.67) range, and to analyze at 300 K the crystal structure of long-range ordered samples. A neutron diffuse scattering quantitative study at 300 K of short-range order in TiCsub(0.76), TiCsub(0.79) and NbCsub(0.73) single crystals is presented: as in Ti 2 Csub(1+x) and Nb 6 C 5 superstructures, vacancies avoid to be on each side of a metal atom. Besides, the mean-square carbon atom displacements from their sites are small, whereas metal atoms move radially about 0.03 A away from vacancies. These results are in qualitative agreement with EXAFS measurements at titanium-K edge of TiCsub(1-x). An interpretation of ordering in term of short-range interaction pair potentials between vacancies is proposed [fr

All-gas-phase synthesis of UiO-66 through modulated atomic layer deposition

Science.gov (United States)

Lausund, Kristian Blindheim; Nilsen, Ola

2016-11-01

Thin films of stable metal-organic frameworks (MOFs) such as UiO-66 have enormous application potential, for instance in microelectronics. However, all-gas-phase deposition techniques are currently not available for such MOFs. We here report on thin-film deposition of the thermally and chemically stable UiO-66 in an all-gas-phase process by the aid of atomic layer deposition (ALD). Sequential reactions of ZrCl4 and 1,4-benzenedicarboxylic acid produce amorphous organic-inorganic hybrid films that are subsequently crystallized to the UiO-66 structure by treatment in acetic acid vapour. We also introduce a new approach to control the stoichiometry between metal clusters and organic linkers by modulation of the ALD growth with additional acetic acid pulses. An all-gas-phase synthesis technique for UiO-66 could enable implementations in microelectronics that are not compatible with solvothermal synthesis. Since this technique is ALD-based, it could also give enhanced thickness control and the possibility to coat irregular substrates with high aspect ratios.

Three-Dimensional Atomic Structure of Metastable Nanoclusters in Doped Semiconductors

Science.gov (United States)

Couillard, Martin; Radtke, Guillaume; Knights, Andrew P.; Botton, Gianluigi A.

2011-10-01

Aberration-corrected scanning transmission electron microscopy is used to determine the atomic structure of nanoclusters of cerium dopant atoms embedded in silicon. By channeling electrons along two crystallographic orientations, we identify a characteristic zinc-blende chemical ordering within CeSi clusters coherent with the silicon host matrix. Strain energy limits the size of these ordered arrangements to just above 1 nm. With the local order identified, we then determine the atomic configuration of an individual subnanometer cluster by quantifying the scattering intensity under weak channeling condition in terms of the number of atoms. Analysis based on single-atom visualization also evidences the presence of split-vacancy impurity complexes, which supports the hypothesis of a vacancy-assisted formation of these metastable CeSi nanophases.

Structural analysis of γ radiation-induced chromosomal aberrations observed by atomic force microscopy

International Nuclear Information System (INIS)

Qu Shuang; Chen Ying; Ge Shili; Liu Xiulin; Zhou Pingkun; Zhang Sa; Zhang Detian

2003-01-01

Objective: To find a new method for the measurement of radiation-induced damage, the structures of normal chromosomes and 60 Co γ-ray-induced chromosomal aberration were analyzed by atomic force microscopy. Methods: Normal and irradiated chromosomes of human peripheral blood lymphocytes were prepared, then three-dimensional structure and height of chromosomes were analyzed by atomic force microscopy. Results: Three-dimensional structures of normal chromosomes and dicentric aberration in irradiated chromosomes were observed clearly. The data of chromosome height were helpful to recognizing the dicentric aberrations. Conclusion: Atomic force microscopy providing three-dimension image and linear measurement is a new and valuable tool for structural analysis of radiation-induced chromosomal aberrations

Probing the folded state and mechanical unfolding pathways of T4 lysozyme using all-atom and coarse-grained molecular simulation

Energy Technology Data Exchange (ETDEWEB)

Zheng, Wenjun, E-mail: wjzheng@buffalo.edu; Glenn, Paul [Department of Physics, University at Buffalo, Buffalo, New York 14260 (United States)

2015-01-21

The Bacteriophage T4 Lysozyme (T4L) is a prototype modular protein comprised of an N-terminal and a C-domain domain, which was extensively studied to understand the folding/unfolding mechanism of modular proteins. To offer detailed structural and dynamic insights to the folded-state stability and the mechanical unfolding behaviors of T4L, we have performed extensive equilibrium and steered molecular dynamics simulations of both the wild-type (WT) and a circular permutation (CP) variant of T4L using all-atom and coarse-grained force fields. Our all-atom and coarse-grained simulations of the folded state have consistently found greater stability of the C-domain than the N-domain in isolation, which is in agreement with past thermostatic studies of T4L. While the all-atom simulation cannot fully explain the mechanical unfolding behaviors of the WT and the CP variant observed in an optical tweezers study, the coarse-grained simulations based on the Go model or a modified elastic network model (mENM) are in qualitative agreement with the experimental finding of greater unfolding cooperativity in the WT than the CP variant. Interestingly, the two coarse-grained models predict different structural mechanisms for the observed change in cooperativity between the WT and the CP variant—while the Go model predicts minor modification of the unfolding pathways by circular permutation (i.e., preserving the general order that the N-domain unfolds before the C-domain), the mENM predicts a dramatic change in unfolding pathways (e.g., different order of N/C-domain unfolding in the WT and the CP variant). Based on our simulations, we have analyzed the limitations of and the key differences between these models and offered testable predictions for future experiments to resolve the structural mechanism for cooperative folding/unfolding of T4L.

The method of intersecting spheres for determination of coordination numbers of atoms in crystal structures

International Nuclear Information System (INIS)

Serezhkin, V.N.; Buslaev, Yu.A.; Mikhajlov, Yu.N.

1997-01-01

New method for determination of coordination numbers (CN) of atoms in crystal structures, based on the model of interatomic interaction, within the frames whereof each atom is approximated by two spheres with the common center in the atom nuclei, is proposed. One of the spheres specifies conditionally isolated (chemically unbound) atom and its radius is a constant, which for atoms of the given chemical sort in the structure of any compound is equal to quasi-orbital Sleiter radius. The sphere of the other radius specifies chemically bound atom and coincides with the sphere, the volume whereof is equal to the volume of the Voronoj-Dirichlet polyhedron of the corresponding atom in the structure of the concrete crystal. Using a series of examples, workability of the given method for CN determination of atoms in structures of both simple substances and chemical compounds (alkali, transition metals, U, Th). Good agreement of the obtained results with the generally accepted CN s of atoms for the considered crystals is noted and a number of principal advantages of the new method, as compared to classical one of the CNs evaluation, is demonstrated

Internal structure of reactor building for Madras Atomic Power Project

International Nuclear Information System (INIS)

Pandit, D.P.

1975-01-01

The structural configuration and analysis of structural elements of the internal structure of reactor building for the Madras Atomic Power Project has been presented. Two methods of analysis of the internal structure, viz. Equivalent Plane Frame and Finite Element Method, are explained and compared with the use of bending moments obtained. (author)

Relativistic atomic structure: past, present and future

International Nuclear Information System (INIS)

Grant, I P

2010-01-01

Developments in a relativistic atomic structure have been driven by a combination of advances in experimental methods, in the theory of quantum electrodynamics, in numerical algorithms, computer hardware and software. Today's programs are still in many respects 'legacy codes' containing many features going back nearly half a century. It is time for a rethink.

Adhesion and Atomic Structures of Gold on Ceria Nanostructures:The Role of Surface Structure and Oxidation State of Ceria Supports

Energy Technology Data Exchange (ETDEWEB)

Lin, Yuyuan [Northwestern University, Evanston; Wu, Zili [ORNL; Wen, Jianguo [Argonne National Laboratory (ANL); Poeppelmeier, Kenneth R [Northwestern University, Evanston; Marks, Laurence D [Northwestern University, Evanston

2015-01-01

Recent advances in heterogeneous catalysis have demonstrated that oxides supports with the same material but different shapes can result in metal catalysts with distinct catalytic properties. The shape-dependent catalysis was not well-understood owing to the lack of direct visualization of the atomic structures at metal-oxide interface. Herein, we utilized aberration-corrected electron microscopy and revealed the atomic structures of gold particles deposited on ceria nanocubes and nanorods with {100} or {111} facets exposed. For the ceria nanocube support, gold nanoparticles have extended atom layers at the metal-support interface. In contrast, regular gold nanoparticles and rafts are present on the ceria nanorod support. After hours of water gas shift reaction, the extended gold atom layers and rafts vanish, which is associated with the decrease of the catalytic activities. By understanding the atomic structures of the support surfaces, metal-support interfaces, and morphologies of the gold particles, a direct structure-property relationship is established.

An Atomic Data and Analysis Structure

International Nuclear Information System (INIS)

Summers, Hugh P.

2000-01-01

The Atomic Data and Analysis Structure (ADAS) Project is a shared activity of a world-wide consortium of fusion and astrophysical laboratories directed at developing and maintaining a common approach to analysing and modelling the radiating properties of plasmas. The origin and objectives of ADAS and the organization of its codes and data collections outlined. Current special projects in the ADAS Project work-plans are listed and an illustration given of ADAS at work. (author)

Structural reliability of atomic power plant

International Nuclear Information System (INIS)

Klemin, A.I.; Polyakov, E.F.

1980-01-01

In 1978 the first specialized technical manual ''Technique of Calculating the Structural Reliability of an Atomic Power Plant and Its Systems in the Design Stage'' was developed. The present article contains information about the main characteristics and capabilities of the manual. The manual gives recommendations concerning the calculations of the reliability of such specific systems as the reactor control and safety system, the system of instrumentation and automatic control, and safety systems. 2 refs

Max Auwaerter Price lecture: building and probing atomic structures

International Nuclear Information System (INIS)

Ternes, M.

2008-01-01

Full text: The control of the geometric, electronic, and magnetic properties of atomic-scale nanostructures is a prerequisite for the understanding and fabrication of new materials and devices. Two routes lead towards this goal: Atomic manipulation of single atoms and molecules by scanning probe microscopy, or patterning using self-assembly. Atomic manipulation has been performed since almost 20 years, but it has been difficult to answer the simple question: how much force does it take to manipulate atoms and molecules on surfaces? To address this question, we used a combined atomic force and scanning tunneling microscope to simultaneously measure the force and the current between an adsorbate and a tip during atomic manipulation. We found that the force it takes to move an atom depends crucially on the binding between adsorbate and surface. Our results indicate that for moving metal atoms on metal surfaces, the lateral force component plays the dominant role. Measuring the forces during manipulation yielded the full potential energy landscape of the tip-sample interaction. Surprisingly, the potential energy barriers are comparable to diffusion barriers, which are obtained in the absence of a probe tip. Furthermore, we used the scanning tunneling microscope to assemble magnetic structures on a thin insulator. We found, that the spin of the atom is influenced by the magnetocrystalline anisotropy of the supporting surface which lifts the spin degeneracy of the ground state and enables the identification of individual atoms. The ground state of atoms with half-integer spin remains always degenerated at zero field due to Kramers theorem. We found that if these states differ by an orbital momentum of m = ±1 the localized spin is screened by the surrounding conducting electrons of the non-magnetic host and form a many-electron spin-singlet at sufficiently low temperature. (author)

Geometric stability and electronic structure of infinite and finite phosphorus atomic chains

International Nuclear Information System (INIS)

Qiao Jingsi; Zhou Linwei; Ji Wei

2017-01-01

One-dimensional mono- or few-atomic chains were successfully fabricated in a variety of two-dimensional materials, like graphene, BN, and transition metal dichalcogenides, which exhibit striking transport and mechanical properties. However, atomic chains of black phosphorus (BP), an emerging electronic and optoelectronic material, is yet to be investigated. Here, we comprehensively considered the geometry stability of six categories of infinite BP atomic chains, transitions among them, and their electronic structures. These categories include mono- and dual-atomic linear, armchair, and zigzag chains. Each zigzag chain was found to be the most stable in each category with the same chain width. The mono-atomic zigzag chain was predicted as a Dirac semi-metal. In addition, we proposed prototype structures of suspended and supported finite atomic chains. It was found that the zigzag chain is, again, the most stable form and could be transferred from mono-atomic armchair chains. An orientation dependence was revealed for supported armchair chains that they prefer an angle of roughly 35 ° –37 ° perpendicular to the BP edge, corresponding to the [110] direction of the substrate BP sheet. These results may promote successive research on mono- or few-atomic chains of BP and other two-dimensional materials for unveiling their unexplored physical properties. (special topic)

Electronic structure of graphene nanoribbons doped with nitrogen atoms: a theoretical insight.

Science.gov (United States)

Torres, A E; Fomine, S

2015-04-28

The electronic structure of graphene nanoribbons doped with a graphitic type of nitrogen atoms has been studied using B3LYP, B2PLYP and CAS methods. In all but one case the restricted B3LYP solutions were unstable and the CAS calculations provided evidence for the multiconfigurational nature of the ground state with contributions from two dominant configurations. The relative stability of the doped nanoribbons depends mostly on the mutual position of the dopant atoms and notably less on the position of nitrogen atoms within the nanoribbon. N-graphitic doping affects cationic states much more than anionic ones due the participation of the nitrogen atoms in the stabilization of the positive charge, resulting in a drop in ionization energies (IPs) for N-graphitic doped systems. Nitrogen atoms do not participate in the negative charge stabilization of anionic species and, therefore, the doping does not affect the electron affinities (EAs). The unrestricted B3LYP method is the method of choice for the calculation of IPs and EAs. Restricted B3LYP and B2PLYP produces unreliable results for both IPs and EAs while CAS strongly underestimates the electron affinities. This is also true for the reorganization energies where restricted B3LYP produces qualitatively incorrect results. Doping changes the reorganization energy of the nanoribbons; the hole reorganization energy is generally higher than the corresponding electron reorganization energy due to the participation of nitrogen atoms in the stabilization of the positive charge.

Large-angle illumination STEM: Toward three-dimensional atom-by-atom imaging

Energy Technology Data Exchange (ETDEWEB)

Ishikawa, Ryo, E-mail: ishikawa@sigma.t.u-tokyo.ac.jp [Institute of Engineering Innovation, University of Tokyo, Tokyo 113-8656 (Japan); Lupini, Andrew R. [Materials Science & Technology Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831 (United States); Hinuma, Yoyo [Department of Materials Science and Engineering, Kyoto University, Kyoto 606-8501 (Japan); Pennycook, Stephen J. [Department of Materials Science and Engineering, The University of Tennessee, 328 Ferris Hall, Knoxville, TN 37996 (United States)

2015-04-15

To fully understand and control materials and their properties, it is of critical importance to determine their atomic structures in all three dimensions. Recent revolutionary advances in electron optics – the inventions of geometric and chromatic aberration correctors as well as electron source monochromators – have provided fertile ground for performing optical depth sectioning at atomic-scale dimensions. In this study we theoretically demonstrate the imaging of top/sub-surface atomic structures and identify the depth of single dopants, single vacancies and the other point defects within materials by large-angle illumination scanning transmission electron microscopy (LAI-STEM). The proposed method also allows us to measure specimen properties such as thickness or three-dimensional surface morphology using observations from a single crystallographic orientation. - Highlights: • We theoretically demonstrate 3D near-atomic depth resolution imaging by large-angle illumination STEM. • This method can be useful to identify the depth of single dopants, single vacancies within materials. • This method can be useful to determine reconstructed surface atomic structures.

Atomic structure and phason modes of the Sc–Zn icosahedral quasicrystal

Directory of Open Access Journals (Sweden)

Tsunetomo Yamada

2016-07-01

Full Text Available The detailed atomic structure of the binary icosahedral (i ScZn7.33 quasicrystal has been investigated by means of high-resolution synchrotron single-crystal X-ray diffraction and absolute scale measurements of diffuse scattering. The average atomic structure has been solved using the measured Bragg intensity data based on a six-dimensional model that is isostructural to the i-YbCd5.7 one. The structure is described with a quasiperiodic packing of large Tsai-type rhombic triacontahedron clusters and double Friauf polyhedra (DFP, both resulting from a close-packing of a large (Sc and a small (Zn atom. The difference in chemical composition between i-ScZn7.33 and i-YbCd5.7 was found to lie in the icosahedron shell and the DFP where in i-ScZn7.33 chemical disorder occurs on the large atom sites, which induces a significant distortion to the structure units. The intensity in reciprocal space displays a substantial amount of diffuse scattering with anisotropic distribution, located around the strong Bragg peaks, that can be fully interpreted as resulting from phason fluctuations, with a ratio of the phason elastic constants K2/K1 = −0.53, i.e. close to a threefold instability limit. This induces a relatively large perpendicular (or phason Debye–Waller factor, which explains the vanishing of `high-Qperp' reflections.

Student perception and conceptual development as represented by student mental models of atomic structure

Science.gov (United States)

Park, Eun Jung

The nature of matter based upon atomic theory is a principal concept in science; hence, how to teach and how to learn about atoms is an important subject for science education. To this end, this study explored student perceptions of atomic structure and how students learn about this concept by analyzing student mental models of atomic structure. Changes in student mental models serve as a valuable resource for comprehending student conceptual development. Data was collected from students who were taking the introductory chemistry course. Responses to course examinations, pre- and post-questionnaires, and pre- and post-interviews were used to analyze student mental models of atomic structure. First, this study reveals that conceptual development can be achieved, either by elevating mental models toward higher levels of understanding or by developing a single mental model. This study reinforces the importance of higher-order thinking skills to enable students to relate concepts in order to construct a target model of atomic structure. Second, Bohr's orbital structure seems to have had a strong influence on student perceptions of atomic structure. With regard to this finding, this study suggests that it is instructionally important to teach the concept of "orbitals" related to "quantum theory." Third, there were relatively few students who had developed understanding at the level of the target model, which required student understanding of the basic ideas of quantum theory. This study suggests that the understanding of atomic structure based on the idea of quantum theory is both important and difficult. Fourth, this study included different student assessments comprised of course examinations, questionnaires, and interviews. Each assessment can be used to gather information to map out student mental models. Fifth, in the comparison of the pre- and post-interview responses, this study showed that high achieving students moved toward more improved models or to advanced

Antiprotonic Radioactive Atom for Nuclear Structure Studies

International Nuclear Information System (INIS)

Wada, M.; Yamazaki, Y.

2005-01-01

A future experiment to synthesize antiprotonic radioactive nuclear ions is proposed for nuclear structure studies. Antiprotonic radioactive nuclear atom can be synthesized in a nested Penning trap where a cloud of antiprotons is prestored and slow radioactive nuclear ions are bunch-injected into the trap. By observing of the ratio of π+ and π- produced in the annihilation process, we can deduce the different abundance of protons and neutrons at the surface of the nuclei. The proposed method would provide a unique probe for investigating the nuclear structure of unstable nuclei

Hirshfeld atom refinement.

Science.gov (United States)

Capelli, Silvia C; Bürgi, Hans-Beat; Dittrich, Birger; Grabowsky, Simon; Jayatilaka, Dylan

2014-09-01

Hirshfeld atom refinement (HAR) is a method which determines structural parameters from single-crystal X-ray diffraction data by using an aspherical atom partitioning of tailor-made ab initio quantum mechanical molecular electron densities without any further approximation. Here the original HAR method is extended by implementing an iterative procedure of successive cycles of electron density calculations, Hirshfeld atom scattering factor calculations and structural least-squares refinements, repeated until convergence. The importance of this iterative procedure is illustrated via the example of crystalline ammonia. The new HAR method is then applied to X-ray diffraction data of the dipeptide Gly-l-Ala measured at 12, 50, 100, 150, 220 and 295 K, using Hartree-Fock and BLYP density functional theory electron densities and three different basis sets. All positions and anisotropic displacement parameters (ADPs) are freely refined without constraints or restraints - even those for hydrogen atoms. The results are systematically compared with those from neutron diffraction experiments at the temperatures 12, 50, 150 and 295 K. Although non-hydrogen-atom ADPs differ by up to three combined standard uncertainties (csu's), all other structural parameters agree within less than 2 csu's. Using our best calculations (BLYP/cc-pVTZ, recommended for organic molecules), the accuracy of determining bond lengths involving hydrogen atoms from HAR is better than 0.009 Å for temperatures of 150 K or below; for hydrogen-atom ADPs it is better than 0.006 Å(2) as judged from the mean absolute X-ray minus neutron differences. These results are among the best ever obtained. Remarkably, the precision of determining bond lengths and ADPs for the hydrogen atoms from the HAR procedure is comparable with that from the neutron measurements - an outcome which is obtained with a routinely achievable resolution of the X-ray data of 0.65 Å.

Formation and structural phase transition in Co atomic chains on a Cu(775) surface

International Nuclear Information System (INIS)

Syromyatnikov, A. G.; Kabanov, N. S.; Saletsky, A. M.; Klavsyuk, A. L.

2017-01-01

The formation of Co atomic chains on a Cu(775) surface is investigated by the kinetic Monte Carlo method. It is found that the length of Co atomic chains formed as a result of self-organization during epitaxial growth is a random quantity and its mean value depends on the parameters of the experiment. The existence of two structural phases in atomic chains is detected using the density functional theory. In the first phase, the separations between an atom and its two nearest neighbors in a chain are 0.230 and 0.280 nm. In the second phase, an atomic chain has identical atomic spacings of 0.255 nm. It is shown that the temperature of the structural phase transition depends on the length of the atomic chain.

Formation and structural phase transition in Co atomic chains on a Cu(775) surface

Energy Technology Data Exchange (ETDEWEB)

Syromyatnikov, A. G.; Kabanov, N. S.; Saletsky, A. M.; Klavsyuk, A. L., E-mail: klavsyuk@physics.msu.ru [Moscow State University (Russian Federation)

2017-01-15

The formation of Co atomic chains on a Cu(775) surface is investigated by the kinetic Monte Carlo method. It is found that the length of Co atomic chains formed as a result of self-organization during epitaxial growth is a random quantity and its mean value depends on the parameters of the experiment. The existence of two structural phases in atomic chains is detected using the density functional theory. In the first phase, the separations between an atom and its two nearest neighbors in a chain are 0.230 and 0.280 nm. In the second phase, an atomic chain has identical atomic spacings of 0.255 nm. It is shown that the temperature of the structural phase transition depends on the length of the atomic chain.

The Atom in a Molecule: Implications for Molecular Structure and Properties

Science.gov (United States)

2016-05-23

Briefing Charts 3. DATES COVERED (From - To) 01 February 2016 – 23 May 2016 4. TITLE AND SUBTITLE The atom in a molecule: Implications for molecular...For presentation at American Physical Society - Division of Atomic , Molecular, and Optical Physics (May 2016) PA Case Number: #16075; Clearance Date...10 Energy (eV) R C--H (au) R C--H(au) The Atom in a Molecule: Implications for Molecular Structures and Properties P. W. Langhoff, Chemistry

Structured mirror array for two-dimensional collimation of a chromium beam in atom lithography

International Nuclear Information System (INIS)

Zhang Wan-Jing; Ma Yan; Li Tong-Bao; Zhang Ping-Ping; Deng Xiao; Chen Sheng; Xiao Sheng-Wei

2013-01-01

Direct-write atom lithography, one of the potential nanofabrication techniques, is restricted by some difficulties in producing optical masks for the deposition of complex structures. In order to make further progress, a structured mirror array is developed to transversely collimate the chromium atomic beam in two dimensions. The best collimation is obtained when the laser red detunes by natural line-width of transition 7 S 3 → 7 P 0 4 of the chromium atom. The collimation ratio is 0.45 vertically (in x axis), and it is 0.55 horizontally (in y axis). The theoretical model is also simulated, and success of our structured mirror array is achieved. (atomic and molecular physics)

DFT computations of the lattice constant, stable atomic structure and ...

African Journals Online (AJOL)

This paper presents the most stable atomic structure and lattice constant of Fullerenes (C60). FHI-aims DFT code was used to predict the stable structure and the computational lattice constant of C60. These were compared with known experimental structures and lattice constants of C60. The results obtained showed that ...

Rapid increase of near atomic resolution virus capsid structures determined by cryo-electron microscopy.

Science.gov (United States)

Ho, Phuong T; Reddy, Vijay S

2018-01-01

The recent technological advances in electron microscopes, detectors, as well as image processing and reconstruction software have brought single particle cryo-electron microscopy (cryo-EM) into prominence for determining structures of bio-molecules at near atomic resolution. This has been particularly true for virus capsids, ribosomes, and other large assemblies, which have been the ideal specimens for structural studies by cryo-EM approaches. An analysis of time series metadata of virus structures on the methods of structure determination, resolution of the structures, and size of the virus particles revealed a rapid increase in the virus structures determined by cryo-EM at near atomic resolution since 2010. In addition, the data highlight the median resolution (∼3.0 Å) and size (∼310.0 Å in diameter) of the virus particles determined by X-ray crystallography while no such limits exist for cryo-EM structures, which have a median diameter of 508 Å. Notably, cryo-EM virus structures in the last four years have a median resolution of 3.9 Å. Taken together with minimal sample requirements, not needing diffraction quality crystals, and being able to achieve similar resolutions of the crystal structures makes cryo-EM the method of choice for current and future virus capsid structure determinations. Copyright © 2017 Elsevier Inc. All rights reserved.

Atomic structure of large angle grain boundaries determined by quantitative X-ray diffraction techniques

International Nuclear Information System (INIS)

Fitzsimmons, M.R.; Sass, S.L.

1988-01-01

Quantitative X-ray diffraction techniques have been used to determine the atomic structure of the Σ = 5 and 13 [001] twist boundaries in Au with a resolution of 0.09 Angstrom or better. The reciprocal lattices of these boundaries were mapped out using synchrotron radiation. The atomic structures were obtained by testing model structures against the intensity observations with a chi square analysis. The boundary structure were modeled using polyhedra, including octahedra, special configurations of tetrahedra and Archimedian anti-prisms, interwoven together by the boundary symmetry. The results of this work point to the possibility of obtaining general rules for grain boundary structure based on X-ray diffraction observations that give the atomic positions with high resolution

Update on nuclear structure effects in light muonic atoms

Energy Technology Data Exchange (ETDEWEB)

Hernandez, Oscar Javier, E-mail: javierh@triumf.ca; Dinur, Nir Nevo; Ji, Chen; Bacca, Sonia [TRIUMF (Canada); Barnea, Nir [The Hebrew University, Racah Institute of Physics (Israel)

2016-12-15

We present calculations of the nuclear structure corrections to the Lamb shift in light muonic atoms, using state-of-the-art nuclear potentials. We outline updated results on finite nucleon size contributions.

On the atomic shell structure calculation (1)

International Nuclear Information System (INIS)

Choe Sun Chol

1986-01-01

We have considered the problem of atomic shell structure calculation using operator technique. We introduce reduced matrix elements of annihilation operators according to eg. (4). The normalized basis function is denoted as || ...>. The reduced matrix elements of the pair annihilation operators are expressed throw one-electron matrix elements. Some numerical results are represented and the problem of sign assignment is discussed. (author)

Atomic oxygen fine-structure splittings with tunable far-infrared spectroscopy

Science.gov (United States)

Zink, Lyndon R.; Evenson, Kenneth M.; Matsushima, Fusakazu; Nelis, Thomas; Robinson, Ruth L.

1991-01-01

Fine-structure splittings of atomic oxygen (O-16) in the ground state have been accurately measured using a tunable far-infrared spectrometer. The 3P0-3pl splitting is 2,060,069.09 (10) MHz, and the 3Pl-3P2 splitting is 4,744,777.49 (16) MHz. These frequencies are important for measuring atomic oxygen concentration in earth's atmosphere and the interstellar medium.

Electron structure of atoms in laser plasma: The Debye shielding model

International Nuclear Information System (INIS)

Sako, Tokuei; Okutsu, Hiroshi; Yamanouchi, Kaoru

2005-01-01

The electronic structure and the energy spectra of multielectron atoms in laser plasmas are examined by the Debye shielding model. The effect of the plasma environment on the electrons bound in an atom is taken into account by introducing the screened Coulomb-type potentials into the electronic Hamiltonian of an atom in place of the standard nuclear attraction and electron repulsion potentials. The capabilities of this new Hamiltonian are demonstrated for He and Li in laser plasmas. (author)

Clustered atom-replaced structure in single-crystal-like metal oxide

Science.gov (United States)

Araki, Takeshi; Hayashi, Mariko; Ishii, Hirotaka; Yokoe, Daisaku; Yoshida, Ryuji; Kato, Takeharu; Nishijima, Gen; Matsumoto, Akiyoshi

2018-06-01

By means of metal organic deposition using trifluoroacetates (TFA-MOD), we replaced and localized two or more atoms in a single-crystalline structure having almost perfect orientation. Thus, we created a new functional structure, namely, clustered atom-replaced structure (CARS), having single-crystal-like metal oxide. We replaced metals in the oxide with Sm and Lu and localized them. Energy dispersive x-ray spectroscopy results, where the Sm signal increases with the Lu signal in the single-crystalline structure, confirm evidence of CARS. We also form other CARS with three additional metals, including Pr. The valence number of Pr might change from 3+ to approximately 4+, thereby reducing the Pr–Ba distance. We directly observed the structure by a high-angle annular dark-field image, which provided further evidence of CARS. The key to establishing CARS is an equilibrium chemical reaction and a combination of additional larger and smaller unit cells to matrix cells. We made a new functional metal oxide with CARS and expect to realize CARS in other metal oxide structures in the future by using the above-mentioned process.

Atomic ionization of germanium by neutrinos from an ab initio approach

International Nuclear Information System (INIS)

Chen, Jiunn-Wei; Chi, Hsin-Chang; Huang, Keh-Ning; Liu, C.-P.; Shiao, Hao-Tse; Singh, Lakhwinder; Wong, Henry T.; Wu, Chih-Liang; Wu, Chih-Pan

2014-01-01

An ab initio calculation of atomic ionization of germanium by neutrinos was carried out in the framework of multiconfiguration relativistic random phase approximation and benchmarked by related atomic structure and photoabsorption data. This improves over the conventional approach based on scattering off free electrons whose validity at sub-keV energy transfer is questionable. Limits on neutrino magnetic moments are derived using reactor neutrino data taken with low threshold germanium detectors. Future applications of these atomic techniques will greatly reduce the atomic uncertainties in low-energy neutrino and dark matter detections.

Effects of Al addition on atomic structure of Cu-Zr metallic glass

Science.gov (United States)

Li, Feng; Zhang, Huajian; Liu, Xiongjun; Dong, Yuecheng; Yu, Chunyan; Lu, Zhaoping

2018-02-01

The atomic structures of Cu52Zr48 and Cu45Zr48Al7 metallic glasses (MGs) have been studied by molecular dynamic simulations. The results reveal that the molar volume of the Cu45Zr48Al7 MG is smaller than that of the Cu52Zr48 MG, although the size of the Al atom is larger than that of the Cu atom, implying an enhanced atomic packing density achieved by introducing Al into the ternary MG. Bond shortening in unlike atomic pairs Zr-Al and Cu-Al is observed in the Cu45Zr48Al7 MG, which is attributed to strong interactions between Al and (Zr, Cu) atoms. Meanwhile, the atomic packing efficiency is enhanced by the minor addition of Al. Compared with the Cu52Zr48 binary MG, the potential energy of the ternary MG decreases and the glass transition temperature increases. Structural analyses indicate that more Cu- and Al-centered full icosahedral clusters emerge in the Cu45Zr48Al7 MG as some Cu atoms are substituted by Al. Furthermore, the addition of Al leads to more icosahedral medium-range orders in the ternary MG. The increase of full icosahedral clusters and the enhancement of the packing density are responsible for the improved glass-forming ability of Cu45Zr48Al7.

Atomic structures of a monolayer of AlAs, GaAs, and InAs on Si(111)

International Nuclear Information System (INIS)

Lee, Geunjung; Yoon, Younggui

2010-01-01

We study atomic structures of a monolayer of AlAs, GaAs, and InAs on a Si(111) substrate from first-principles. The surface with the stacking sequence of ...SiSiMAsSiAs is energetically more stable than the surface with the stacking sequence of ...SiSiSiAsMAs, where M is Al, Ga, or In. The atomic structure of the three top layers of the low-energy surfaces are quite robust, irrespective of M, and the atomic structure of the AlAsSiAs terminated surface and that of the GaAsSiAs terminated surface are very similar. For the high-energy AsMAs terminated surfaces, the broken local tetrahedral symmetry plays an important role in the atomic structures. The calculated atomic structures of InAs on the Si(111) substrate depart most from the structure of crystalline Si.

Exploring the atomic structure of 1.8 nm monolayer-protected gold clusters with aberration-corrected STEM

Energy Technology Data Exchange (ETDEWEB)

Liu, Jian; Jian, Nan; Ornelas, Isabel; Pattison, Alexander J. [Nanoscale Physics Research Laboratory, School of Physics and Astronomy, University of Birmingham, Birmingham B15 2TT (United Kingdom); Lahtinen, Tanja; Salorinne, Kirsi [Department of Chemistry, Nanoscience Center, University of Jyväskylä, FI-40014 Jyväskylä (Finland); Häkkinen, Hannu [Department of Chemistry, Nanoscience Center, University of Jyväskylä, FI-40014 Jyväskylä (Finland); Department of Physics, Nanoscience Center, University of Jyväskylä, FI-40014 Jyväskylä (Finland); Palmer, Richard E., E-mail: richardepalmerwork@yahoo.com [Nanoscale Physics Research Laboratory, School of Physics and Astronomy, University of Birmingham, Birmingham B15 2TT (United Kingdom)

2017-05-15

Monolayer-protected (MP) Au clusters present attractive quantum systems with a range of potential applications e.g. in catalysis. Knowledge of the atomic structure is needed to obtain a full understanding of their intriguing physical and chemical properties. Here we employed aberration-corrected scanning transmission electron microscopy (ac-STEM), combined with multislice simulations, to make a round-robin investigation of the atomic structure of chemically synthesised clusters with nominal composition Au{sub 144}(SCH{sub 2}CH{sub 2}Ph){sub 60} provided by two different research groups. The MP Au clusters were “weighed” by the atom counting method, based on their integrated intensities in the high angle annular dark field (HAADF) regime and calibrated exponent of the Z dependence. For atomic structure analysis, we compared experimental images of hundreds of clusters, with atomic resolution, against a variety of structural models. Across the size range 123–151 atoms, only 3% of clusters matched the theoretically predicted Au{sub 144}(SR){sub 60} structure, while a large proportion of the clusters were amorphous (i.e. did not match any model structure). However, a distinct ring-dot feature, characteristic of local icosahedral symmetry, was observed in about 20% of the clusters. - Highlights: • Chemically synthesised gold clusters were “weighed” by atom counting to get true size. • Image simulations show a few percent of clusters have the predicted atomic structure. • But a specific ring-dot feature indicates local icosahedral order in many clusters.

A hierarchical coarse-grained (all-atom to all residue) approach to peptides (P1, P2) binding with a graphene sheet

Science.gov (United States)

Pandey, Ras; Kuang, Zhifeng; Farmer, Barry; Kim, Sang; Naik, Rajesh

2012-02-01

Recently, Kim et al. [1] have found that peptides P1: HSSYWYAFNNKT and P2: EPLQLKM bind selectively to graphene surfaces and edges respectively which are critical in modulating both the mechanical as well as electronic transport properties of graphene. Such distinctions in binding sites (edge versus surface) observed in electron micrographs were verified by computer simulation by an all-atomic model that captures the pi-pi bonding. We propose a hierarchical approach that involves input from the all-atom Molecular Dynamics (MD) study (with atomistic detail) into a coarse-grained Monte Carlo simulation to extend this study further to a larger scale. The binding energy of a free amino acid with the graphene sheet from all-atom simulation is used in the interaction parameter for the coarse-grained approach. Peptide chain executes its stochastic motion with the Metropolis algorithm. We investigate a number of local and global physical quantities and find that peptide P1 is likely to bind more strongly to graphene sheet than P2 and that it is anchored by three residues ^4Y^5W^6Y. [1] S.N. Kim et al J. Am. Chem. Soc. 133, 14480 (2011).

Atomic Resolution Imaging of Nanoscale Structural Ordering in a Complex Metal Oxide Catalyst

KAUST Repository

Zhu, Yihan

2012-08-28

The determination of the atomic structure of a functional material is crucial to understanding its "structure-to-property" relationship (e.g., the active sites in a catalyst), which is however challenging if the structure possesses complex inhomogeneities. Here, we report an atomic structure study of an important MoVTeO complex metal oxide catalyst that is potentially useful for the industrially relevant propane-based BP/SOHIO process. We combined aberration-corrected scanning transmission electron microscopy with synchrotron powder X-ray crystallography to explore the structure at both nanoscopic and macroscopic scales. At the nanoscopic scale, this material exhibits structural and compositional order within nanosized "domains", while the domains show disordered distribution at the macroscopic scale. We proposed that the intradomain compositional ordering and the interdomain electric dipolar interaction synergistically induce the displacement of Te atoms in the Mo-V-O channels, which determines the geometry of the multifunctional metal oxo-active sites.

Validation of the Dyadic Coping Inventory with Chinese couples: Factorial structure, measurement invariance, and construct validity.

Science.gov (United States)

Xu, Feng; Hilpert, Peter; Randall, Ashley K; Li, Qiuping; Bodenmann, Guy

2016-08-01

The Dyadic Coping Inventory (DCI, Bodenmann, 2008) assesses how couples support each other when facing individual (e.g., workload) and common (e.g., parenting) stressors. Specifically, the DCI measures partners' perceptions of their own (Self) and their partners' behaviors (Partner) when facing individual stressors, and partners' common coping behaviors when facing common stressors (Common). To date, the DCI has been validated in 6 different languages from individualistic Western cultures; however, because culture can affect interpersonal interactions, it is unknown whether the DCI is a reliable measure of coping behaviors for couples living in collectivistic Eastern cultures. Based on data from 474 Chinese couples (N = 948 individuals), the current study examined the Chinese version of the DCI's factorial structure, measurement invariance (MI), and construct validity of test scores. Using 3 cultural groups (China, Switzerland, and the United States [U.S.]), confirmatory factor analysis revealed a 5-factor structure regarding Self and Partner and a 2-factor structure regarding Common dyadic coping (DC). Results from analyses of MI indicated that the DCI subscales met the criteria for configural, metric, and full/partial scalar invariance across cultures (Chinese-Swiss and Chinese-U.S.) and genders (Chinese men and women). Results further revealed good construct validity of the DCI test scores. In all, the Chinese version of the DCI can be used for measuring Chinese couples' coping behaviors, and is available for cross-cultural studies examining DC behaviors between Western and Eastern cultures. (PsycINFO Database Record (c) 2016 APA, all rights reserved).

Ab initio study of the structural, magnetic, and electronic properties of copper and silver clusters and their alloys with one palladium atom

Directory of Open Access Journals (Sweden)

S. J Hashemifar

2015-01-01

Full Text Available In this paper, the structural, magnetic, and electronic properties of two- to nine-atom copper and silver clusters and their alloys with one palladium atom are investigated by using full-potential all-electron density functional computations. After calculating minimized energy of several structural isomers of every nanocluster, it is argued that the small size nanoclusters (up to size of 6, ‎ prefer planar structures, while by increasing size a 2D-3D structural transformation is observed. The structural transformation of pure and copper-palladium clusters occurs in the size of seven and that of silver-palladium cluster in happens at the size of six. The calculated second difference and dissociation energies confirm that the two- and eight- atom pure clusters and three- and seven- atom alloyed clusters are magic clusters. The electronic and magnetic properties of stable isomers are calculated and considered after applying many body based GW correction.

Calculation of atom displacement cross section for structure material

International Nuclear Information System (INIS)

Liu Ping; Xu Yiping

2015-01-01

The neutron radiation damage in material is an important consideration of the reactor design. The radiation damage of materials mainly comes from atom displacements of crystal structure materials. The reaction cross sections of charged particles, cross sections of displacements per atom (DPA) and KERMA are the basis of radiation damage calculation. In order to study the differences of DPA cross sections with different codes and different evaluated nuclear data libraries, the DPA cross sections for structure materials were calculated with UNF and NJOY codes, and the comparisons of results were given. The DPA cross sections from different evaluated nuclear data libraries were compared. And the comparison of DPA cross sections between NJOY and Monte Carlo codes was also done. The results show that the differences among these evaluated nuclear data libraries exist. (authors)

Classroom: inexpensive models for teaching atomic structure and ...

African Journals Online (AJOL)

Classroom: inexpensive models for teaching atomic structure and compounds at junior secondary school level of education. WHK Hordzi, BA Mensah. Abstract. No Abstract. Global Journal of Educational Research Vol. 2(1&2) 2003: 33-40. Full Text: EMAIL FREE FULL TEXT EMAIL FREE FULL TEXT · DOWNLOAD FULL ...

Local atomic structure inheritance in Ag50Sn50 melt

International Nuclear Information System (INIS)

Bai, Yanwen; Bian, Xiufang; Qin, Jingyu; Hu, Lina; Yang, Jianfei; Zhang, Kai; Zhao, Xiaolin; Yang, Chuncheng; Zhang, Shuo; Huang, Yuying

2014-01-01

Local structure inheritance signatures were observed during the alloying process of the Ag 50 Sn 50 melt, using high-temperature X-ray diffraction and ab initio molecular dynamics simulations. The coordination number N m around Ag atom is similar in the alloy and in pure Ag melts (N m  ∼ 10), while, during the alloying process, the local structure around Sn atoms rearranges. Sn-Sn covalent bonds were substituted by Ag-Sn chemical bonds, and the total coordination number around Sn increases by about 70% as compared with those in the pure Sn melt. Changes in the electronic structure of the alloy have been studied by Ag and Sn K-edge X-ray absorption spectroscopy, as well as by calculations of the partial density of states. We propose that a leading mechanism for local structure inheritance in Ag 50 Sn 50 is due to s-p dehybridization of Sn and to the interplay between Sn-s and Ag-d electrons

Structural and electronic properties of isovalent boron atoms in GaAs

Science.gov (United States)

Krammel, C. M.; Nattermann, L.; Sterzer, E.; Volz, K.; Koenraad, P. M.

2018-04-01

Boron containing GaAs, which is grown by metal organic vapour phase epitaxy, is studied at the atomic level by cross-sectional scanning tunneling microscopy (X-STM) and spectroscopy (STS). In topographic X-STM images, three classes of B related features are identified, which are attributed to individual B atoms on substitutional Ga sites down to the second layer below the natural {110} cleavage planes. The X-STM contrast of B atoms below the surface reflects primarily the structural modification of the GaAs matrix by the small B atoms. However, B atoms in the cleavage plane have in contrast to conventional isovalent impurities, such as Al and In, a strong influence on the local electronic structure similar to donors or acceptors. STS measurements show that B in the GaAs {110} surfaces gives rise to a localized state short below the conduction band (CB) edge while in bulk GaAs, the B impurity state is resonant with the CB. The analysis of BxGa1-xAs/GaAs quantum wells reveals a good crystal quality and shows that the incorporation of B atoms in GaAs can be controlled along the [001] growth direction at the atomic level. Surprisingly, the formation of the first and fourth nearest neighbor B pairs, which are oriented along the directions, is strongly suppressed at a B concentration of 1% while the third nearest neighbor B pairs are found more than twice as often than expected for a completely spatially random pattern.

Validating Westinghouse atom 16 x 16 and 18 x 18 PWR fuel performance

International Nuclear Information System (INIS)

Andersson, S.; Gustafson, J.; Jourdain, P.; Lindstroem, L.; Hallstadius, L.; Hofling, C.G.

2001-01-01

Westinghouse Atom designs and fabricates PWR fuel for all major European fuel types: 17 x 17 standard (12 ft) and 17 x 17 XL (14 ft) for Westinghouse type PWRs, and 16 x 16 and 18 x 18 fuel for Siemens type PWRs. The W Atom PWR fuel designs are based on the extensive Westinghouse CE PWR fuel experience from combustion engineering type PWRs. The W atom designs utilise basic design features from the W CE fuel tradition, such as all-Zircaloy mid grids and the proven ( 6 rod years) Guardian TM debris catcher, which is integrated in the bottom Inconel grid. Several new features have been developed to meet with stringent European requirements originating from requirements on very high burnup, in combination with low-leakage core operating strategies and high coolant temperatures. The overall reliability of the Westinghouse Atom PWR fuel is very high; no fuel failure has been detected since 1997. (orig.)

All-Optical Atom Trap Trace Analysis: Potential Use of 85Kr in Safeguards Activities

International Nuclear Information System (INIS)

Kohler, M.; Sahling, P.; Sieveke, C.; Kirchner, G.

2015-01-01

Sensitive measurement techniques for the detection of anthropogenic tracers demand measurement resolutions down to single atoms, as it has been demonstrated by the first atom trap trace analysis experiments. However, technical limitations had lowered the sample throughput to about 200 per year per machine. We have developed an all-optical apparatus which allows higher sample throughput and small sample sizes at the same time. Krypton-85 as anthropogenic isotope is an ideal tracer for nuclear activities since the only relevant source term is fission. An increased 85Kr concentration in an air sample indicates, that a plume was passing by during sampling. In practice, however, its applicability may be limited by the global and regional background concentrations caused by the emissions of nuclear fuel reprocessing plants. The potential of 85Kr monitoring for safeguards applications has been discussed extensively. Among these is the short range detection of elevated concentrations of 85Kr in the vicinity of reprocessing plants. Our ATTA technique needs sample sizes of about 1 l of air only and thus for the first time will allow simple environmental sampling of 85Kr with high spatial and temporal resolution. The design of such a study including local sampling and tracer transport modelling in proximity to a reprocessing plants is outlined. In addition, such a study could be used also for validating near-field atmospheric dispersion models if the 85Kr source term is known. The potential of environmental analyzes of 85Kr during an IAEA short-notice access is discussed. It is shown that it crucially depends on the emission dynamics after shut-down of fuel dissolution which needs further study. (author)

All-optical atom trap as a target for MOTRIMS-like collision experiments

Science.gov (United States)

Sharma, S.; Acharya, B. P.; De Silva, A. H. N. C.; Parris, N. W.; Ramsey, B. J.; Romans, K. L.; Dorn, A.; de Jesus, V. L. B.; Fischer, D.

2018-04-01

Momentum-resolved scattering experiments with laser-cooled atomic targets have been performed since almost two decades with magneto-optical trap recoil ion momentum spectroscopy (MOTRIMS) setups. Compared to experiments with gas-jet targets, MOTRIMS features significantly lower target temperatures allowing for an excellent recoil ion momentum resolution. However, the coincident and momentum-resolved detection of electrons was long rendered impossible due to incompatible magnetic field requirements. Here we report on an experimental approach which is based on an all-optical 6Li atom trap that—in contrast to magneto-optical traps—does not require magnetic field gradients in the trapping region. Atom temperatures of about 2 mK and number densities up to 109 cm-3 make this trap ideally suited for momentum-resolved electron-ion coincidence experiments. The overall configuration of the trap is very similar to conventional magneto-optical traps. It mainly requires small modifications of laser beam geometries and polarization which makes it easily implementable in other existing MOTRIMS experiments.

Evolution of local atomic structure during solidification of Al2Au liquid: An ab initio study

Energy Technology Data Exchange (ETDEWEB)

Xiong, L H; Lou, H B; Wang, X D; Debela, T T; Cao, Q P; Zhang, D X; Wang, S Y; Wang, C Z; Jiang, J Z

2014-04-01

The local atomic structure evolution in Al2Au alloy during solidification from 2000 K to 400 K was studied by ab initio molecular dynamics simulations and analyzed using the structure factor, pair correlation functions, bond angle distributions, the Honeycutt-Anderson (HA) index and Voronoi tessellation methods. It was found that the icosahedral-like clusters are negligible in the Al2Au stable liquid and supercooled liquid states, and the most abundant clusters are those having HA indices of 131 and 120 or Voronoi indices of < 0,4,4,0 >, < 0,3, 6,0 > and < 0,4,4,2 > with coordination numbers of 8, 9 and 10, respectively. These clusters are similar to the local atomic structures in the CaF2-type Al2Au crystal, revealing the existence of structure heredity between liquid and crystalline phase in Al2Au alloy. (C) 2014 Acta Materialia Inc. Published by Elsevier Ltd. All rights reserved.

Energy-related atomic and molecular structure and scattering studies: Final report

International Nuclear Information System (INIS)

1987-01-01

The general goals of the DOE research concerned the use of molecular beams techniques in the study of atomic and molecular polarizabilities and the study of the interactions between electrons and highly polar molecules. Both of these goals are directly relevant to the general problem of the role played by long-range forces in atomic and molecular physics. Details related to this motivation can be found in the published literature. Here we will describe in general terms the work performed under DOE sponsorship in the atomic beams laboratory at NYU. Our original intent was to exploit techniques developed at NYU, mainly in the study of simple atomic systems, to the more complex atomic and molecular systems that are related to DOE interests. These included the developing understanding of the structure of molecular systems, particularly of alkali halide molecules, and the study of the interactions of electrons with such molecules. The structure experiments would serve as critical experimental benchmarks for computational techniques on molecular properties, including both molecular wave functions and derivative properties of them, such as vibrational and rotational constants, but in particular of molecular electric dipole polarizabilities. We believe that we have at least to some extent fulfilled these goals. 16 refs., 1 fig

Asymptotic Structure in the Classically Forbidden Region of the Hooke's Atoms

International Nuclear Information System (INIS)

Wang Xuemei

2013-01-01

The two-electron Hooke's atom — a quantum mechanical system with two electrons bound in a harmonic potential — is well known for its exact analytical properties at certain oscillator strengths. The Hooke's atoms with more than two electrons offer more scope for valuable practical applications. In this work, we study the asymptotic structure of these Hooke's atoms in the classically forbidden region. The leading-order term of the long-range expression for the KS exchange-correlation potential v xc (r) is shown to be −1/r. The second and third higher order terms are also exactly obtained. Various components of v xc (r) are also studied. It is shown that the leading term of O(1/r) in v xc (r) is due to the pure Pauli correlation, while the leading contribution of the Coulomb correlation is of O(1/r 3 ). Neither of them makes contribution to the term of O(1/r 2 ), which is shown to be solely due to the kinetic correlation effect. Results for the two-electron Hooke's atom were obtained before in the literature. Our results reduce to those of the two-electron Hooke's atom as a special case. (condensed matter: electronic structure, electrical, magnetic, and optical properties)

xMDFF: molecular dynamics flexible fitting of low-resolution X-ray structures.

Science.gov (United States)

McGreevy, Ryan; Singharoy, Abhishek; Li, Qufei; Zhang, Jingfen; Xu, Dong; Perozo, Eduardo; Schulten, Klaus

2014-09-01

X-ray crystallography remains the most dominant method for solving atomic structures. However, for relatively large systems, the availability of only medium-to-low-resolution diffraction data often limits the determination of all-atom details. A new molecular dynamics flexible fitting (MDFF)-based approach, xMDFF, for determining structures from such low-resolution crystallographic data is reported. xMDFF employs a real-space refinement scheme that flexibly fits atomic models into an iteratively updating electron-density map. It addresses significant large-scale deformations of the initial model to fit the low-resolution density, as tested with synthetic low-resolution maps of D-ribose-binding protein. xMDFF has been successfully applied to re-refine six low-resolution protein structures of varying sizes that had already been submitted to the Protein Data Bank. Finally, via systematic refinement of a series of data from 3.6 to 7 Å resolution, xMDFF refinements together with electrophysiology experiments were used to validate the first all-atom structure of the voltage-sensing protein Ci-VSP.

Structure sensitivity in CO oxidation by a single Au atom supported on ceria

NARCIS (Netherlands)

Song, W.; Hensen, E.J.M.

2013-01-01

The mechanism of CO oxidation by a CeO2(110)-supported gold atom has been investigated by DFT calculations. A novel stable surface structure has been identified in which one surface O atom of ceria migrates toward the isolated Au atom, resulting in a surface Au–O species that can react with CO.

Validity of the independent-processes approximation for resonance structures in electron-ion scattering cross sections

International Nuclear Information System (INIS)

Badnell, N.R.; Pindzola, M.S.; Griffin, D.C.

1991-01-01

The total inelastic cross section for electron-ion scattering may be found in the independent-processes approximation by adding the resonant cross section to the nonresonant background cross section. We study the validity of this approximation for electron excitation of multiply charged ions. The resonant-excitation cross section is calculated independently using distorted waves for various Li-like and Na-like ions using (N+1)-electron atomic-structure methods previously developed for the calculation of dielectronic-recombination cross sections. To check the effects of interference between the two scattering processes, we also carry out detailed close-coupling calculations for the same atomic ions using the R-matrix method. For low ionization stages, interference effects manifest themselves sometimes as strong window features in the close-coupling cross section, which are not present in the independent-processes cross section. For higher ionization stages, however, the resonance features found in the independent-processes approximation are found to be in good agreement with the close-coupling results

Development of atomic spectroscopy technologies - Hyperfine structure of 2 period atoms using optogalvanic effects

Energy Technology Data Exchange (ETDEWEB)

Kwon, Nam Ic [Hankuk University of foreign studies, Seoul (Korea)

2000-03-01

The source of anomalous broad linewidth of 3{sup 3}P{sub 1},{sub 2},{sub 3}-3{sup 3}D{sub 2},{sub 3},4(3s') transition was explained. The broad optogalvanic spectrum was consisted of two gaussian peaks of different linewidths, and they are separated by 250 MHz. The Narrow peak, which has linewidth of room temperature, is from oxygen atoms already separated, and the shifted broad peak, which has linewidth corresponding to a temperature of 9000 K, is from weakly bound molecular ions. Obtained hyperfine spectrum of fluorine atom at the expected frequency, was too weak to analyze hyperfine structure constants. Microwave discharge might be necessary for higher density of excited state. 16 refs., 11 figs. (Author)

Robust procedure for creating and characterizing the atomic structure of scanning tunneling microscope tips.

Science.gov (United States)

Tewari, Sumit; Bastiaans, Koen M; Allan, Milan P; van Ruitenbeek, Jan M

2017-01-01

Scanning tunneling microscopes (STM) are used extensively for studying and manipulating matter at the atomic scale. In spite of the critical role of the STM tip, procedures for controlling the atomic-scale shape of STM tips have not been rigorously justified. Here, we present a method for preparing tips in situ while ensuring the crystalline structure and a reproducibly prepared tip structure up to the second atomic layer. We demonstrate a controlled evolution of such tips starting from undefined tip shapes.

On the way to unveiling the atomic structure of superheavy elements

International Nuclear Information System (INIS)

Laatiaoui, Mustapha

2016-01-01

Optical spectroscopy of the transfermium elements (atomic number Z > 100) is nowadays one of the most fascinating and simultaneously challenging tasks in atomic physics. On the one hand, key atomic and even nuclear ground-state properties may be obtained by studying the spectral lines of these heaviest elements. On the other hand, these elements have to be produced “online” by heavy-ion induced fusion-evaporation reactions yielding rates on the order of a few atoms per second at most, which renders their optical spectroscopy extremely difficult. Only recently, a first foray of laser spectroscopy into this heaviest element region was reported. Several atomic transitions in the element nobelium (Z = 102) were observed and characterized, using an ultra-sensitive and highly efficient resonance ionization technique. The findings confirm the predictions and additionally provide a benchmark for theoretical modelling. The work represents an important stepping stone towards experimental studies of the atomic structure of superheavy elements.

Selecting the "Best" Factor Structure and Moving Measurement Validation Forward: An Illustration.

Science.gov (United States)

Schmitt, Thomas A; Sass, Daniel A; Chappelle, Wayne; Thompson, William

2018-04-09

Despite the broad literature base on factor analysis best practices, research seeking to evaluate a measure's psychometric properties frequently fails to consider or follow these recommendations. This leads to incorrect factor structures, numerous and often overly complex competing factor models and, perhaps most harmful, biased model results. Our goal is to demonstrate a practical and actionable process for factor analysis through (a) an overview of six statistical and psychometric issues and approaches to be aware of, investigate, and report when engaging in factor structure validation, along with a flowchart for recommended procedures to understand latent factor structures; (b) demonstrating these issues to provide a summary of the updated Posttraumatic Stress Disorder Checklist (PCL-5) factor models and a rationale for validation; and (c) conducting a comprehensive statistical and psychometric validation of the PCL-5 factor structure to demonstrate all the issues we described earlier. Considering previous research, the PCL-5 was evaluated using a sample of 1,403 U.S. Air Force remotely piloted aircraft operators with high levels of battlefield exposure. Previously proposed PCL-5 factor structures were not supported by the data, but instead a bifactor model is arguably more statistically appropriate.

Fluorescence detection of white-beam X-ray absorption anisotropy: towards element-sensitive projections of local atomic structure

International Nuclear Information System (INIS)

Korecki, P.; Tolkiehn, M.; Dąbrowski, K. M.; Novikov, D. V.

2011-01-01

A method for a direct measurement of X-ray projections of the atomic structure is described. Projections of the atomic structure around Nb atoms in a LiNbO 3 single crystal were obtained from a white-beam X-ray absorption anisotropy pattern detected using Nb K fluorescence. Projections of the atomic structure around Nb atoms in a LiNbO 3 single crystal were obtained from a white-beam X-ray absorption anisotropy (XAA) pattern detected using Nb K fluorescence. This kind of anisotropy results from the interference of X-rays inside a sample and, owing to the short coherence length of a white beam, is visible only at small angles around interatomic directions. Consequently, the main features of the recorded XAA corresponded to distorted real-space projections of dense-packed atomic planes and atomic rows. A quantitative analysis of XAA was carried out using a wavelet transform and allowed well resolved projections of Nb atoms to be obtained up to distances of 10 Å. The signal of nearest O atoms was detected indirectly by a comparison with model calculations. The measurement of white-beam XAA using characteristic radiation indicates the possibility of obtaining element-sensitive projections of the local atomic structure in more complex samples

Atomic Structure of Type VI Contractile Sheath from Pseudomonas aeruginosa.

Science.gov (United States)

Salih, Osman; He, Shaoda; Planamente, Sara; Stach, Lasse; MacDonald, James T; Manoli, Eleni; Scheres, Sjors H W; Filloux, Alain; Freemont, Paul S

2018-02-06

Pseudomonas aeruginosa has three type VI secretion systems (T6SSs), H1-, H2-, and H3-T6SS, each belonging to a distinct group. The two T6SS components, TssB/VipA and TssC/VipB, assemble to form tubules that conserve structural/functional homology with tail sheaths of contractile bacteriophages and pyocins. Here, we used cryoelectron microscopy to solve the structure of the H1-T6SS P. aeruginosa TssB1C1 sheath at 3.3 Å resolution. Our structure allowed us to resolve some features of the T6SS sheath that were not resolved in the Vibrio cholerae VipAB and Francisella tularensis IglAB structures. Comparison with sheath structures from other contractile machines, including T4 phage and R-type pyocins, provides a better understanding of how these systems have conserved similar functions/mechanisms despite evolution. We used the P. aeruginosa R2 pyocin as a structural template to build an atomic model of the TssB1C1 sheath in its extended conformation, allowing us to propose a coiled-spring-like mechanism for T6SS sheath contraction. Copyright © 2017 The Authors. Published by Elsevier Ltd.. All rights reserved.

Robust procedure for creating and characterizing the atomic structure of scanning tunneling microscope tips

Directory of Open Access Journals (Sweden)

Sumit Tewari

2017-11-01

Full Text Available Scanning tunneling microscopes (STM are used extensively for studying and manipulating matter at the atomic scale. In spite of the critical role of the STM tip, procedures for controlling the atomic-scale shape of STM tips have not been rigorously justified. Here, we present a method for preparing tips in situ while ensuring the crystalline structure and a reproducibly prepared tip structure up to the second atomic layer. We demonstrate a controlled evolution of such tips starting from undefined tip shapes.

Visions of Atomic Scale Tomography

International Nuclear Information System (INIS)

Kelly, T.F.; Miller, Michael K.; Rajan, Krishna; Ringer, S.P.

2012-01-01

A microscope, by definition, provides structural and analytical information about objects that are too small to see with the unaided eye. From the very first microscope, efforts to improve its capabilities and push them to ever-finer length scales have been pursued. In this context, it would seem that the concept of an ultimate microscope would have received much attention by now; but has it really ever been defined? Human knowledge extends to structures on a scale much finer than atoms, so it might seem that a proton-scale microscope or a quark-scale microscope would be the ultimate. However, we argue that an atomic-scale microscope is the ultimate for the following reason: the smallest building block for either synthetic structures or natural structures is the atom. Indeed, humans and nature both engineer structures with atoms, not quarks. So far as we know, all building blocks (atoms) of a given type are identical; it is the assembly of the building blocks that makes a useful structure. Thus, would a microscope that determines the position and identity of every atom in a structure with high precision and for large volumes be the ultimate microscope? We argue, yes. In this article, we consider how it could be built, and we ponder the answer to the equally important follow-on questions: who would care if it is built, and what could be achieved with it?

Structural Validation of the Holistic Wellness Assessment

Science.gov (United States)

Brown, Charlene; Applegate, E. Brooks; Yildiz, Mustafa

2015-01-01

The Holistic Wellness Assessment (HWA) is a relatively new assessment instrument based on an emergent transdisciplinary model of wellness. This study validated the factor structure identified via exploratory factor analysis (EFA), assessed test-retest reliability, and investigated concurrent validity of the HWA in three separate samples. The…

Synthesis, crystal structure and charge-distribution validation of β-Na4Cu(MoO43 adopting the alluadite structure-type

Directory of Open Access Journals (Sweden)

Wassim Dridi

2016-08-01

Full Text Available Single crystals of a new variety of tetrasodium copper(II tris[molybdate(VI], Na4Cu(MoO43, have been synthesized by solid-state reactions and characterized by single-crystal X-ray diffraction. This alluaudite structure-type is characterized by the presence of infinite layers of composition (Cu/Na2Mo3O14 parallel to the (100 plane, which are linked by MoO4 tetrahedra, forming a three-dimensional framework containing two types of hexagonal channels in which Na+ cations reside. The Cu2+ and Na2+ cations are located at the same general site with occupancies of 0.5. All atoms are on general positions except for one Mo, two Na (site symmetry 2 and another Na (site symmetry -1 atom. One O atom is split into two separate positions with occupancies of 0.5. The title compound is isotypic with Na5Sc(MoO44 and Na3In2As3O12. The structure model is supported by bond-valence-sum (BVS and charge-distribution CHARDI methods. β-Na4Cu(MoO43 is compared and discussed with the K4Cu(MoO43 and α-Na4Cu(MoO43 structures.

Atomic layer deposition of lithium phosphates as solid-state electrolytes for all-solid-state microbatteries

International Nuclear Information System (INIS)

Wang, Biqiong; Liu, Jian; Sun, Qian; Li, Ruying; Sun, Xueliang; Sham, Tsun-Kong

2014-01-01

Atomic layer deposition (ALD) has been shown as a powerful technique to build three-dimensional (3D) all-solid-state microbattery, because of its unique advantages in fabricating uniform and pinhole-free thin films in 3D structures. The development of solid-state electrolyte by ALD is a crucial step to achieve the fabrication of 3D all-solid-state microbattery by ALD. In this work, lithium phosphate solid-state electrolytes were grown by ALD at four different temperatures (250, 275, 300, and 325 °C) using two precursors (lithium tert-butoxide and trimethylphosphate). A linear dependence of film thickness on ALD cycle number was observed and uniform growth was achieved at all four temperatures. The growth rate was 0.57, 0.66, 0.69, and 0.72 Å/cycle at deposition temperatures of 250, 275, 300, and 325 °C, respectively. Furthermore, x-ray photoelectron spectroscopy confirmed the compositions and chemical structures of lithium phosphates deposited by ALD. Moreover, the lithium phosphate thin films deposited at 300 °C presented the highest ionic conductivity of 1.73 × 10 −8 S cm −1 at 323 K with ∼0.51 eV activation energy based on the electrochemical impedance spectroscopy. The ionic conductivity was calculated to be 3.3 × 10 −8 S cm −1 at 26 °C (299 K). (paper)

The development of high-resolution spectroscopic methods and their use in atomic structure studies

International Nuclear Information System (INIS)

Poulsen, O.

1984-01-01

This thesis discusses work performed during the last nine years in the field of atomic spectroscopy. Several high-resolution techniques, ranging from quantum beats, level crossings, rf-laser double resonances to nonlinear field atom interactions, have been employed. In particular, these methods have been adopted and developed to deal with fast accelerated atomic or ionic beams, allowing studies of problems in atomic-structure theory. Fine- and hyperfine-structure determinations in the He I and Li I isoelectronic sequences, in 51 V I, and in 235 U I, II have permitted a detailed comparison with ab initio calculations, demonstrating the change in problems when going towards heavier elements or higher ionization stage. The last part of the thesis is concerned with the fundamental question of obtaining very high optical resolution in the interaction between a fast accelerated atom or ion beam and a laser field, this problem being the core in the continuing development of atomic spectroscopy necessary to challenge the more precise and sophisticated theories advanced. (Auth.)

Structural Interpretation of the Large Slowdown of Water Dynamics at Stacked Phospholipid Membranes for Decreasing Hydration Level: All-Atom Molecular Dynamics

Directory of Open Access Journals (Sweden)

Carles Calero

2016-04-01

Full Text Available Hydration water determines the stability and function of phospholipid membranes as well as the interaction of membranes with other molecules. Experiments and simulations have shown that water dynamics slows down dramatically as the hydration decreases, suggesting that the interfacial water that dominates the average dynamics at low hydration is slower than water away from the membrane. Here, based on all-atom molecular dynamics simulations, we provide an interpretation of the slowdown of interfacial water in terms of the structure and dynamics of water–water and water–lipid hydrogen bonds (HBs. We calculate the rotational and translational slowdown of the dynamics of water confined in stacked phospholipid membranes at different levels of hydration, from completely hydrated to poorly hydrated membranes. For all hydrations, we analyze the distribution of HBs and find that water–lipids HBs last longer than water–water HBs and that at low hydration most of the water is in the interior of the membrane. We also show that water–water HBs become more persistent as the hydration is lowered. We attribute this effect (i to HBs between water molecules that form, in turn, persistent HBs with lipids; (ii to the hindering of the H-bonding switching between water molecules due to the lower water density at the interface; and (iii to the higher probability of water–lipid HBs as the hydration decreases. Our interpretation of the large dynamic slowdown in water under dehydration is potentially relevant in understanding membrane biophysics at different hydration levels.

Atomic structure of Fe thin-films on Cu(0 0 1) studied with stereoscopic photography

International Nuclear Information System (INIS)

Hattori, Azusa N.; Fujikado, M.; Uchida, T.; Okamoto, S.; Fukumoto, K.; Guo, F.Z.; Matsui, F.; Nakatani, K.; Matsushita, T.; Hattori, K.; Daimon, H.

2004-01-01

The complex magnetic properties of Fe films epitaxially grown on Cu(0 0 1) have been discussed in relation to their atomic structure. We have studied the Fe films on Cu(0 0 1) by a new direct method for three-dimensional (3D) atomic structure analysis, so-called 'stereoscopic photography'. The forward-focusing peaks in the photoelectron angular distribution pattern excited by the circularly polarized light rotate around the light axis in either clockwise or counterclockwise direction depending on the light helicity. By using a display-type spherical mirror analyzer for this phenomenon, we can obtain stereoscopic photographs of atomic structure. The photographs revealed that the iron structure changes from bcc to fcc and almost bcc structure with increasing iron film thickness

Transition metal atoms absorbed on MoS2/h-BN heterostructure: stable geometries, band structures and magnetic properties.

Science.gov (United States)

Wu, Yanbing; Huang, Zongyu; Liu, Huating; He, Chaoyu; Xue, Lin; Qi, Xiang; Zhong, Jianxin

2018-06-15

We have studied the stable geometries, band structures and magnetic properties of transition-metal (V, Cr, Mn, Fe, Co and Ni) atoms absorbed on MoS2/h-BN heterostructure systems by first-principles calculations. By comparing the adsorption energies, we find that the adsorbed transition metal (TM) atoms prefer to stay on the top of Mo atoms. The results of the band structure without spin-orbit coupling (SOC) interaction indicate that the Cr-absorbed systems behave in a similar manner to metals, and the Co-absorbed system exhibits a half-metallic state. We also deduce that the V-, Mn-, Fe-absorbed systems are semiconductors with 100% spin polarization at the HOMO level. The Ni-absorbed system is a nonmagnetic semiconductor. In contrast, the Co-absorbed system exhibits metallic state, and the bandgap of V-absorbed system decreases slightly according to the SOC calculations. In addition, the magnetic moments of all the six TM atoms absorbed on the MoS2/h-BN heterostructure systems decrease when compared with those of their free-standing states.

Local atomic structure of Zr-Cu and Zr-Cu-Al amorphous alloys investigated by EXAFS method

International Nuclear Information System (INIS)

Antonowicz, J.; Pietnoczka, A.; Zalewski, W.; Bacewicz, R.; Stoica, M.; Georgarakis, K.; Yavari, A.R.

2011-01-01

Research highlights: → Coordination number, interatomic distances and mean square atomic displacement in Zr-Cu and Zr-Cu-Al glasses. → Icosahedral symmetry in local atomic structure. → Deviation from random mixing behavior resulting from Al addition. - Abstract: We report on extended X-ray absorption fine structure (EXAFS) study of rapidly quenched Zr-Cu and Zr-Cu-Al glassy alloys. The local atomic order around Zr and Cu atoms was investigated. From the EXAFS data fitting the values of coordination number, interatomic distances and mean square atomic displacement were obtained for wide range of compositions. It was found that icosahedral symmetry rather than that of corresponding crystalline analogs dominates in the local atomic structure of Zr-Cu and Zr-Cu-Al amorphous alloys. Judging from bonding preferences we conclude that addition of Al as an alloying element results in considerable deviation from random mixing behavior observed in binary Zr-Cu alloys.

Polarization-gradient laser cooling as a way to create strongly localized structures for atom lithography

International Nuclear Information System (INIS)

Prudnikov, O. N.; Taichenachev, A. V.; Tumaikin, A. M.; Yudin, V. I.

2007-01-01

Generally, conditions for deep sub-Doppler laser cooling do not match conditions for strong atomic localization, that takes place in a deeper optical potential and leads to higher temperature. Moreover, for a given detuning in a deep optical potential the secular approximation, which is frequently used for a quantum description of laser cooling, fails. Here we investigate the atomic localization in optical potential, using a full quantum approach for atomic density matrix beyond the secular approximation. It is shown that laser cooling in a deep optical potential, created by a light field with polarization gradients, can be used as an alternative method for the formation of high contrast spatially localized structures of atoms for the purposes of atom lithography and atomic nanofabrication. Finally, we analyze possible limits for the width and contrast of localized atomic structures that can be reached in this type of light mask

Mechanical instability in non-uniform atomic structure: Application to amorphous metal

International Nuclear Information System (INIS)

Umeno, Yoshitaka; Kitamura, Takayuki; Tagawa, Motoki

2007-01-01

It is important to reveal the deformation of amorphous metal in the atomistic scale level as materials with non-crystal structure have been attracting attention with their prominent functions. In this paper atomistic simulations of tensile deformation of an amorphous model are conducted and local mechanical instability is analyzed to clarify the deformation mechanism of the amorphous structure. Instability causing sharp stress drop is associated with unstable motion of atoms within local region. The size of the region where the unstable atomic motion occurs corresponds to the magnitude of total stress decrease. At instability with large stress decrease the deformation at the onset of the instability propagates to surrounding region, which gives rise to a hysteresis loop in the stress-strain relation. This manifests the microscopic mechanism of the plasticity of amorphous structure

Atom-by-atom assembly

International Nuclear Information System (INIS)

Hla, Saw Wai

2014-01-01

Atomic manipulation using a scanning tunneling microscope (STM) tip enables the construction of quantum structures on an atom-by-atom basis, as well as the investigation of the electronic and dynamical properties of individual atoms on a one-atom-at-a-time basis. An STM is not only an instrument that is used to ‘see’ individual atoms by means of imaging, but is also a tool that is used to ‘touch’ and ‘take’ the atoms, or to ‘hear’ their movements. Therefore, the STM can be considered as the ‘eyes’, ‘hands’ and ‘ears’ of the scientists, connecting our macroscopic world to the exciting atomic world. In this article, various STM atom manipulation schemes and their example applications are described. The future directions of atomic level assembly on surfaces using scanning probe tips are also discussed. (review article)

Local electronic and geometric structures of silicon atoms implanted in graphite

International Nuclear Information System (INIS)

Baba, Yuji; Sekiguchi, Tetsuhiro; Shimoyama, Iwao

2002-01-01

Low-energy Si + ions were implanted in highly oriented pyrolitic graphite (HOPG) up to 1% of surface atomic concentration, and the local electronic and geometric structures around the silicon atoms were in situ investigated by means of the Si K-edge X-ray absorption near-edge structure (XANES) and X-ray photoelectron spectroscopy using linearly polarized synchrotron radiation. The resonance peak appeared at 1839.5 eV in the Si K-edge XANES spectra for Si + -implanted HOPG. This energy is lower than those of the Si 1s→σ * resonance peaks in any other Si-containing materials. The intensity of the resonance peak showed strong polarization dependence, which suggests that the final state orbitals around the implanted Si atoms have π * -like character. It is concluded that the σ-type Si-C bonds produced by the Si + -ion implantation are nearly parallel to the graphite plane, and Si x C phase forms two-dimensionally spread graphite-like layer with sp 2 bonds

Atomic Structure Control of Silica Thin Films on Pt(111)

KAUST Repository

Crampton, Andrew S

2015-05-27

Metal oxide thin films grown on metal single crystals are commonly used to model heterogeneous catalyst supports. The structure and properties of thin silicon dioxide films grown on metal single crystals have only recently been thoroughly characterized and their spectral properties well established. We report the successful growth of a three- dimensional, vitreous silicon dioxide thin film on the Pt(111) surface and reproduce the closed bilayer structure previously reported. The confirmation of the three dimensional nature of the film is unequivocally shown by the infrared absorption band at 1252 cm−1. Temperature programmed desorption was used to show that this three-dimensional thin film covers the Pt(111) surface to such an extent that its application as a catalyst support for clusters/nanoparticles is possible. The growth of a three-dimensional film was seen to be directly correlated with the amount of oxygen present on the surface after the silicon evaporation process. This excess of oxygen is tentatively attributed to atomic oxygen being generated in the evaporator. The identification of atomic oxygen as a necessary building block for the formation of a three-dimensional thin film opens up new possibilities for thin film growth on metal supports, whereby simply changing the type of oxygen enables thin films with different atomic structures to be synthesized. This is a novel approach to tune the synthesis parameters of thin films to grow a specific structure and expands the options for modeling common amorphous silica supports under ultra high vacuum conditions.

Atomic structure calculations of Mo XV-XL

International Nuclear Information System (INIS)

Kubo, Hirotaka; Sugie, Tatsuo; Shiho, Makoto; Suzuki, Yasuo; Ishii, Keishi; Maeda, Hikosuke.

1986-06-01

Energy levels and oscillator strengths were calculated for Mo XV - Mo XL. The computer program for atomic structure calculation, developed by Dr. Robert D. Cowan, Los Alamos National Laboratory, was used in the present work. The scaled energy parameters were empirically determined from the observed spectral data. We present wavelengths and transition probabilities of Mo XV-XL. Energy levels and spectral patterns are presented in figures that are useful for the identification of spectral lines. (author)

Prediction of reacting atoms for the major biotransformation reactions of organic xenobiotics.

Science.gov (United States)

Rudik, Anastasia V; Dmitriev, Alexander V; Lagunin, Alexey A; Filimonov, Dmitry A; Poroikov, Vladimir V

2016-01-01

The knowledge of drug metabolite structures is essential at the early stage of drug discovery to understand the potential liabilities and risks connected with biotransformation. The determination of the site of a molecule at which a particular metabolic reaction occurs could be used as a starting point for metabolite identification. The prediction of the site of metabolism does not always correspond to the particular atom that is modified by the enzyme but rather is often associated with a group of atoms. To overcome this problem, we propose to operate with the term "reacting atom", corresponding to a single atom in the substrate that is modified during the biotransformation reaction. The prediction of the reacting atom(s) in a molecule for the major classes of biotransformation reactions is necessary to generate drug metabolites. Substrates of the major human cytochromes P450 and UDP-glucuronosyltransferases from the Biovia Metabolite database were divided into nine groups according to their reaction classes, which are aliphatic and aromatic hydroxylation, N- and O-glucuronidation, N-, S- and C-oxidation, and N- and O-dealkylation. Each training set consists of positive and negative examples of structures with one labelled atom. In the positive examples, the labelled atom is the reacting atom of a particular reaction that changed adjacency. Negative examples represent non-reacting atoms of a particular reaction. We used Labelled Multilevel Neighbourhoods of Atoms descriptors for the designation of reacting atoms. A Bayesian-like algorithm was applied to estimate the structure-activity relationships. The average invariant accuracy of prediction obtained in leave-one-out and 20-fold cross-validation procedures for five human isoforms of cytochrome P450 and all isoforms of UDP-glucuronosyltransferase varies from 0.86 to 0.99 (0.96 on average). We report that reacting atoms may be predicted with reasonable accuracy for the major classes of metabolic reactions

Weather and atmosphere observation with the ATOM all-sky camera

Directory of Open Access Journals (Sweden)

Jankowsky Felix

2015-01-01

Full Text Available The Automatic Telescope for Optical Monitoring (ATOM for H.E.S.S. is an 75 cm optical telescope which operates fully automated. As there is no observer present during observation, an auxiliary all-sky camera serves as weather monitoring system. This device takes an all-sky image of the whole sky every three minutes. The gathered data then undergoes live-analysis by performing astrometric comparison with a theoretical night sky model, interpreting the absence of stars as cloud coverage. The sky monitor also serves as tool for a meteorological analysis of the observation site of the the upcoming Cherenkov Telescope Array. This overview covers design and benefits of the all-sky camera and additionally gives an introduction into current efforts to integrate the device into the atmosphere analysis programme of H.E.S.S.

Interaction and dynamics of add-atoms with 2-dimensional structures

CERN Multimedia

The interaction and dynamics of add-atoms with graphene, graphene-derivate structures and, later, MoSi$_2$, two-dimensional – single and few – atomic layers will be studied with the Perturbed Angular Correlation – PAC – technique. Graphene is also envisaged as new platform for growing semiconductor nanostructure devices, such as quantum dots and as a particularly powerful catalyst. Understanding nucleation of nanostructures and clusters on graphene and related phases in wet conditions as they are used in chemical methods in research and industry require complementary studies. These systems will therefore be studied systematically using radioactive probe atoms attaching via a transfer media (e.g., water in catalysis process) or being deposited with soft-landing techniques under vacuum and UHV conditions, as put in place at the ASPIC setup at ISOLDE. The hyperfine fields obtained under different environments are expected to reveal basic information on the rich atomic and physical mechanisms associated w...

Unambiguous Determination of Intermolecular Hydrogen Bond of NMR Structure by Molecular Dynamics Refinement Using All-Atom Force Field and Implicit Solvent Model

International Nuclear Information System (INIS)

Jee, Jun Goo

2010-01-01

It has been shown that AMD refinement is very useful for defining an intermolecular hydrogen bond in NMR structure calculation. The refined structure also provides a clue for explaining the pH dependence in Ub and UIM complexes. As reported by Choi et al., serine-mediated hydrogen bonds are the third most populated hydrogen bonds found in protein-protein intermolecular interactions, after the backbone-backbone and backbone-aspartate ones. The abundance imposes the requirement of an method to determine the interface of protein-protein complexes. The precise geometry is particularly important in the complex structures between Ub and UBDs. Ub recognizes various targets with the same surface, where both hydrophobic and hydrophobic interactions are involved. Hence, the details of the hydrophilic interactions are necessary to find the common binding modes. The structure determination of a biomolecule by NMR depends heavily on the distance restraints derived by the NOE cross peaks that are observed between two protons within 6 A through space. Therefore, the existence of the NOE peaks and their correct assignments to two corresponding protons are essential for an accurate and precise structure determination. Recent developments of NOE assignment and calculation algorithms have enabled the determination of protein 3D structures without any manual interpretation, provided chemical shifts are assigned in most atoms and sufficient NOE peaks exist. Along with these advances, the necessity of determining complicated structures such as complexes is increasing

The structure of filled skutterudites and the local vibration behavior of the filling atom

Energy Technology Data Exchange (ETDEWEB)

Zhou, Xiaojuan [Institute of High Energy Physics, Chinese Academy of Sciences, Beijing 100049 (China); Dongguan Institute of Neutron Science, Dongguan 523808 (China); University of Chinese Academy of Sciences, Beijing 100049 (China); Zong, Peng-an [State Key Laboratory of New Ceramics and Fine Processing, School of Materials Science and Engineering, Tsinghua University, Beijing 100084 (China); Shanghai Institute of Ceramics, Chinese Academy of Sciences, Shanghai 200050 (China); Chen, Xihong [Shanghai Institute of Ceramics, Chinese Academy of Sciences, Shanghai 200050 (China); Tao, Juzhou, E-mail: taoj@ihep.ac.cn [Institute of High Energy Physics, Chinese Academy of Sciences, Beijing 100049 (China); Dongguan Institute of Neutron Science, Dongguan 523808 (China); Lin, He, E-mail: linhe@sinap.ac.cn [Shanghai Institute of Applied Physics, Chinese Academy of Science, Shanghai 201204 (China)

2017-02-15

Both of atomic pair distribution function (PDF) and extended x-ray absorption fine structure (EXAFS) experiments have been carried out on unfilled and Yb-filled skutterudites Yb{sub x}Co{sub 4}Sb{sub 12} (x=0, 0.15, 0.2 and 0.25) samples. The structure refinements on PDF data confirm the large amplitude vibration of Yb atom and the dependence of Yb vibration amplitude on the filling content. Temperature dependent EXAFS experiment on filled skutterudites have been carried out at Yb L{sub Ⅲ}-edge in order to explore the local vibration behavior of filled atom. EXAFS experiments show that the Einstein temperature of the filled atom is very low (70.9 K) which agrees with the rattling behavior.

Atomic Structure of Au−Pd Bimetallic Alloyed Nanoparticles

KAUST Repository

Ding, Yong

2010-09-08

Using a two-step seed-mediated growth method, we synthesized bimetallic nanoparticles (NPs) having a gold octahedron core and a palladium epitaxial shell with controlled Pd-shell thickness. The mismatch-release mechanism between the Au core and Pd shell of the NPs was systematically investigated by high-resolution transmission electron microscopy. In the NPs coated with a single atomic layer of Pd, the strain between the surface Pd layer and the Au core is released by Shockley partial dislocations (SPDs) accompanied by the formation of stacking faults. For NPs coated with more Pd (>2 nm), the stacking faults still exist, but no SPDs are found. This may be due to the diffusion of Au atoms into the Pd shell layers to eliminate the SPDs. At the same time, a long-range ordered L11 AuPd alloy phase has been identified in the interface area, supporting the assumption of the diffusion of Au into Pd to release the interface mismatch. With increasing numbers of Pd shell layers, the shape of the Au-Pd NP changes, step by step, from truncated-octahedral to cubic. After the bimetallic NPs were annealed at 523 K for 10 min, the SPDs at the surface of the NPs coated with a single atomic layer of Pd disappeared due to diffusion of the Au atoms into the surface layer, while the stacking faults and the L11 Au-Pd alloyed structure remained. When the annealing temperature was increased to 800 K, electron diffraction patterns and diffraction contrast images revealed that the NPs became a uniform Au-Pd alloy, and most of the stacking faults disappeared as a result of the annealing. Even so, some clues still support the existence of the L11 phase, which suggests that the L11 phase is a stable, long-range ordered structure in Au-Pd bimetallic NPs. © 2010 American Chemical Society.

Higher order structure of short immunostimulatory oligonucleotides studied by atomic force microscopy

International Nuclear Information System (INIS)

Klein, Dionne C.G.; Latz, Eicke; Espevik, Terje; Stokke, Bjorn T.

2010-01-01

Immunostimulatory CpG-DNA activates the innate immune system by binding to Toll-like receptor 9. Structurally different CpG-containing oligonucleotides trigger a different type of immune response while activating the same receptor. We therefore investigated the higher order structure of two different classes of immunostimulatory CpG-DNA. Class A, which contains a partly self-complementary sequence and poly-G ends, forms duplexes and nanoparticles in salt solution, while class B, which does not contain these features and is purely linear, does not form a duplex or nanoparticles. Results obtained here by high-resolution atomic force microscopy of classes A and B CpG-DNA, reflect these differences in secondary structure. Detailed structural analysis of the atomic force microscopy topographs is presented for two different sample preparation methods.

Higher order structure of short immunostimulatory oligonucleotides studied by atomic force microscopy

Energy Technology Data Exchange (ETDEWEB)

Klein, Dionne C.G., E-mail: dionne.c.g.klein@ntnu.no [Department of Physics, Norwegian University of Science and Technology, N-7491, Trondheim (Norway); Department of Cancer Research and Molecular Medicine, Norwegian University of Science and Technology, N-7489, Trondheim (Norway); Latz, Eicke [Department of Cancer Research and Molecular Medicine, Norwegian University of Science and Technology, N-7489, Trondheim (Norway); Division of Infectious Diseases and Immunology, University of Massachusetts Medical School, 364 Plantation Street, Worcester, MA 01605 (United States); Institute of Innate Immunity, University Hospitals, University of Bonn, Sigmund-Freud-Str. 25, 53127 Bonn (Germany); Espevik, Terje [Department of Cancer Research and Molecular Medicine, Norwegian University of Science and Technology, N-7489, Trondheim (Norway); Stokke, Bjorn T. [Department of Physics, Norwegian University of Science and Technology, N-7491, Trondheim (Norway)

2010-05-15

Immunostimulatory CpG-DNA activates the innate immune system by binding to Toll-like receptor 9. Structurally different CpG-containing oligonucleotides trigger a different type of immune response while activating the same receptor. We therefore investigated the higher order structure of two different classes of immunostimulatory CpG-DNA. Class A, which contains a partly self-complementary sequence and poly-G ends, forms duplexes and nanoparticles in salt solution, while class B, which does not contain these features and is purely linear, does not form a duplex or nanoparticles. Results obtained here by high-resolution atomic force microscopy of classes A and B CpG-DNA, reflect these differences in secondary structure. Detailed structural analysis of the atomic force microscopy topographs is presented for two different sample preparation methods.

Principle for possible memory structures with extra high density by using the electron sharing mechanisms of atoms in an inflective orbit

Science.gov (United States)

Sengor, T.

2014-10-01

Both of the qualitative and quantitative knowledge of electromagnetic fields in the inter-atomic scale bring useful applications. From this point of view, bringing some possible new sights and solutions to atom-electron-photon-atom and/or molecule interactions is aimed in the near-field at inter atomic scale and their potential applications. The electron sharing processes between neighbor atoms are considered as an inflective surface system and an inflective guiding processes. The critical pass and transition structures are derived. The structures involving trigging that transition mechanisms may be suitable to design extra high density and fast data storage processes. The electron sharing processes between two near atomic system are modelled with gate mechanisms involving two distinct passages: continuous pass and discontinuous pass. Even if the stochastic processes are applicable at these cases theoretical approach putting an influence like inner and external dipole mechanisms fits best to the situation and provides almost deterministic scheme, which has potential to estimate some processes being able to design new electronics structures and devices. We call orbitron all of such structures and/or devices. The boundary value problem of atomic system sharing an electron in the way of electron passage model is formulated in inflective spherical coordinate system. The wave phenomenon is studied near spherically inflection points. The analytical essentials are derived for the solution of Helmholtz's equation when inflective boundaries are included. The evaluation is obtained by the extracted separation method. The results are given by using the spherically inflective wave series. The method is reshaped for the solution of Schrödinger equation.

New Equations for Calculating Principal and Fine-Structure Atomic Spectra for Single and Multi-Electron Atoms

Energy Technology Data Exchange (ETDEWEB)

Surdoval, Wayne A. [National Energy Technology Lab. (NETL), Pittsburgh, PA, (United States); Berry, David A. [National Energy Technology Lab. (NETL), Morgantown, WV (United States); Shultz, Travis R. [National Energy Technology Lab. (NETL), Morgantown, WV (United States)

2018-03-09

A set of equations are presented for calculating atomic principal spectral lines and fine-structure energy splits for single and multi-electron atoms. Calculated results are presented and compared to the National Institute of Science and Technology database demonstrating very good accuracy. The equations do not require fitted parameters. The only experimental parameter required is the Ionization energy for the electron of interest. The equations have comparable accuracy and broader applicability than the single electron Dirac equation. Three Appendices discuss the origin of the new equations and present calculated results. New insights into the special relativistic nature of the Dirac equation and its relationship to the new equations are presented.

Ultracold atoms in a cavity-mediated double-well system

International Nuclear Information System (INIS)

Larson, Jonas; Martikainen, Jani-Petri

2010-01-01

We study ground-state properties and dynamics of a dilute ultracold atomic gas in a double-well potential. The Gaussian barrier separating the two wells derives from the interaction between the atoms and a quantized field of a driven Fabry-Perot cavity. Due to intrinsic atom-field nonlinearity, several interesting phenomena arise which are the focus of this work. For the ground state, there is a critical pumping amplitude in which the atoms self-organize and the intra-cavity-field amplitude drastically increases. In the dynamical analysis, we show that the Josephson oscillations depend strongly on the atomic density and may be greatly suppressed within certain regimes, reminiscent of self-trapping of Bose-Einstein condensates in double-well setups. This pseudo-self-trapping effect is studied within a mean-field treatment valid for large atom numbers. For small numbers of atoms, we consider the analogous many-body problem and demonstrate a collapse-revival structure in the Josephson oscillations.

A theoretical inquiry into the question of W and Ta (100) atomic structures

International Nuclear Information System (INIS)

Treglia, G.; Spanjaard, D.

1983-01-01

In spite of the very large number of experiments (LEED, AES, UPS, MeV He + scattering, work function, FIM) carried out on W (100), no structural model consistent with all the data has been proposed yet: in particular, the question of the reconstruction thermally induced when the sample is cooled below room temperature remains a puzzling problem. Furthermore, from a theoretical point of view, no definitive answer has been given. Actually, either the mechanism invoked for the reconstruction is too weak, or some contributions are omitted or calculated without sufficient care. The surface energy of W (100) is computed taking into account the band term treated in the tight binding approximation, a pairwise repulsive potential of the Born-Mayer type and the electronic correlation contribution obtained from a perturbation treatment of the Hubbard model in the band limit. This energy is then fully minimised with respect to all coordinates of surface atoms, keeping all atoms neutral for any displace,ment. It is found that the unreconstructed surface is the most stable at T = 0 K and discuss this unexpected result. A similar calculation for Ta (100) leads to opposite conclusions. (author)

Atomic and magnetic structure of MnF3

International Nuclear Information System (INIS)

Hunter, B.A.; Kennedy, B.J.; Vogt, T.

2003-01-01

Full text: The magnetic and atomic structure of MnF 3 has been determined from 4K to 300K using neutron powder diffraction. The MnF 3 compound is the archetypical Mn-based colossal magnetoresistive compound. A Neel temperature of approximately 40K was observed from the temperature variation of the magnetic moment. Below the Neel temperature a large negative thermal expansion was observed, in striking similarity to other Mn-based colossal magnetoresistive compounds. The variation in structure is discussed in relation to other Mn-based compounds, particularly as this compound cannot support charge ordering

The atomic structure of Fe100-xCux nanoalloys: X-ray absorption analysis

International Nuclear Information System (INIS)

Kravtsova, A.N.; Yalovega, G.E.; Soldatov, A.V.; Yan, W.S.; Wei, S.Q.

2009-01-01

The local atomic structure of Fe 100-x Cu x nanoalloys (x = 0, 10, 20, 40, 60, 70, 80 and 100%) has been investigated by X-ray absorption near edge structure (XANES) analysis. Local environment around copper and iron atoms in Fe 100-x Cu x has been studied by comparing the experimental XANES with corresponding theoretical spectra calculated for several structural models. It has been established that the most probable structure of the Fe 100-x Cu x nanoalloys for a low concentration of copper (x = 10-20%) is a homogenous bcc structure, for a high copper concentration (x = 60-80%)-a homogenous fcc structure, while at an intermediate copper concentration (about 40%) the nanoalloys have an inhomogeneous structure consisting of clusters of fcc solid solution (90%) and of clusters of bcc solid solution (10%)

Bloch oscillations of ultracold atoms and measurement of the fine structure constant; Oscillations de Bloch d'atomes ultrafroids et mesure de la constante de structure fine

Energy Technology Data Exchange (ETDEWEB)

Clade, P

2005-10-15

From a measurement of the recoil velocity of an atom absorbing a photon, it is possible to deduce a determination of the ratio h/m between the Planck constant and the mass of the atoms and then to deduce a value of the fine structure constant alpha. To do this measurement, we use the technique of Bloch oscillations, which allows us to transfer a large number of recoils to atoms. A velocity sensor, based on velocity selective Raman transition, enables us to measure the momentum transferred to the atoms. A measurement with a statistical uncertainty of 4.4 10{sup -9}, in conjunction with a careful study of systematic effects (5 10{sup -9}), has led us to a determination of alpha with an uncertainty of 6.7 10{sup -9}: {alpha}{sup -1}(Rb) = 137.03599878 (91). This uncertainty is similar to the uncertainty of the best determinations of alpha based on atom interferometry. (author)

Microtraps for neutral atoms using superconducting structures in the critical state

International Nuclear Information System (INIS)

Emmert, A.; Brune, M.; Raimond, J.-M.; Nogues, G.; Lupascu, A.; Haroche, S.

2009-01-01

Recently demonstrated superconducting atom chips provide a platform for trapping atoms and coupling them to solid-state quantum systems. Controlling these devices requires a full understanding of the supercurrent distribution in the trapping structures. For type-II superconductors, this distribution is hysteretic in the critical state due to the partial penetration of the magnetic field in the thin superconducting film through pinned vortices. We report here an experimental observation of this memory effect. Our results are in good agreement with the predictions of the Bean model of the critical state without adjustable parameters. The memory effect allows to write and store permanent currents in micron-sized superconducting structures and paves the way toward engineered trapping potentials.

Atomic disorder and amorphization of B2-structure CoZr by ball milling

International Nuclear Information System (INIS)

Zhou, G.F.; Bakker, H.

1996-01-01

For a considerable number of intermetallic compounds it has been found that ball milling introduces atomic (chemical) disorder. Disorder due to milling was demonstrated by x-ray diffraction in AlRu, crystallizing in the B2 structure (ordered b.c.c.) by a decrease of the intensity of superlattice reflections relative to fundamental reflections. The same technique was used to investigate disordering by milling in Ni 3 Al, crystallizing in the L1 2 structure (ordered f.c.c.). In both cases the disorder is anti-site disorder of both components, i.e. both atomic species substitute on the wrong sublattices. Besides x-ray diffraction measurements of magnetic properties turned out to be useful in monitoring structural changes due to milling. The change in the superconducting transition temperature, measured by magnetic a.c. susceptibility, was used to demonstrate atomic disordering by milling in Nb 3 Sn and Nb 3 Au. The type of disorder turned out to be anti-site disorder. Such a type of disorder occurs in the same materials also at high temperatures or after irradiation by neutrons. The disordering was accompanied by an increase of the lattice parameter. An increase in high-field magnetization accompanied by a decrease of the lattice parameter during milling was found in B2 CoGa and B2 CoAl. In principle in the completely ordered state both compounds are non-magnetic, because the CO atoms are shielded from one another by Ga and Al atoms, respectively. However, when a Co atom is transferred to the wrong sublattice, it is surrounded by Co atoms as nearest neighbors and bears a magnetic moment. This explains the strong increase of the magnetization due to milling

Refined OPLS All-Atom Force Field for Saturated Phosphatidylcholine Bilayers at Full Hydration

DEFF Research Database (Denmark)

Maciejewski, A.; Pasenkiewicz-Gierula, M.; Cramariuc, O.

2014-01-01

validation, and it is also one of the highly important and abundant lipid types, e.g., in lung surfactant. Overall, PCs have not been previously parametrized in the OPLS-AA force field; thus, there is a need to derive its bonding and nonbonding parameters for both the polar and nonpolar parts of the molecule....... In the present study, we determined the parameters for torsion angles in the phosphatidylcholine and glycerol moieties and in the acyl chains, as well the partial atomic charges. In these calculations, we used three methods: (1) Hartree-Fock (HF), (2) second order Moller-Plesset perturbation theory (MP2), and (3...... one was found to be able to satisfactorily reproduce experimental data for the lipid bilayer. The successful DPPC model was obtained from MP2 calculations in an implicit polar environment (PCM)....

Atomic Resolution Imaging of Nanoscale Structural Ordering in a Complex Metal Oxide Catalyst

KAUST Repository

Zhu, Yihan; Wang, Qingxiao; Zhao, Lan; Teng, Baiyang; Lu, Weimin; Han, Yu

2012-01-01

The determination of the atomic structure of a functional material is crucial to understanding its "structure-to-property" relationship (e.g., the active sites in a catalyst), which is however challenging if the structure possesses complex

Rayleigh-Plesset equation of the bubble stable cavitation in water: A nonequilibrium all-atom molecular dynamics simulation study

Science.gov (United States)

Man, Viet Hoang; Li, Mai Suan; Derreumaux, Philippe; Nguyen, Phuong H.

2018-03-01

The Rayleigh-Plesset (RP) equation was derived from the first principles to describe the bubble cavitation in liquids in terms of macroscopic hydrodynamics. A number of nonequilibrium molecular dynamics studies have been carried out to validate this equation in describing the bubble inertial cavitation, but their results are contradictory and the applicability of the RP equation still remains to be examined, especially for the stable cavitation. In this work, we carry out nonequilibrium all-atom simulation to validate the applicability of the RP equation in the description of the stable cavitation of nano-sized bubbles in water. We show that although microscopic effects are not explicitly included, this equation still describes the dynamics of subnano-bubbles quite well as long as the contributions of various terms including inertial, surface tension, and viscosity are correctly taken into account. These terms are directly and inversely proportional to the amplitude and period of the cavitation, respectively. Thus, their contributions to the RP equation depend on these two parameters. This may explain the discrepancy between the current results obtained using different parameters. Finally, the accuracy of the RP equation in the current mathematical modeling studies of the ultrasound-induced blood-brain-barrier experiments is discussed in some detail.

Dye-sensitized solar cells: Atomic scale investigation of interface structure and dynamics

International Nuclear Information System (INIS)

Ma Wei; Zhang Fan; Meng Sheng

2014-01-01

Recent progress in dye-sensitized solar cells (DSC) research is reviewed, focusing on atomic-scale investigations of the interface electronic structures and dynamical processes, including the structure of dye adsorption onto TiO 2 , ultrafast electron injection, hot-electron injection, multiple-exciton generation, and electron—hole recombination. Advanced experimental techniques and theoretical approaches are briefly summarized, and then progressive achievements in photovoltaic device optimization based on insights from atomic scale investigations are introduced. Finally, some challenges and opportunities for further improvement of dye solar cells are presented. (invited review — international conference on nanoscience and technology, china 2013)

Study of the Adsorption of Atoms and Molecules on Silicon Surfaces: Crystallographics and Electronic Structure

International Nuclear Information System (INIS)

Bengio, Silvina

2003-01-01

This thesis work has been concerned with adsorption properties of silicon surfaces.The atomic and electronic structure of molecules and atoms adsorbed on Si has been investigated by means of photoemission experiments combined with synchrotron radiation.The quantitative atomic structure determination was held applying the photoelectron diffraction technique.This technique is sensible to the local structure of a reference atomic specie and has elemental and chemical-state specificity.This approach has been applied to three quite different systems with different degrees of complexity, Sb/Si(111) √3x √3R30 0 , H 2 O/Si(100)2x1 and NH 3 /Si(111)7x7.Our results show that Sb which forms a ( √3√3)R30 0 phase produces a bulklike-terminated Si(111)1x1 substrate free of stacking faults.Regarding the atomic structure of its interface, this study strongly favours the T4-site milkstool model over the H3 one.An important aspect regarding the H 2 O/Si(100)(2x1) system was establishing the limits of precision with which one can determine not only the location of the adsorbed hydroxyl (OH) species, but also the extent to which this adsorption modifes the asymmetric dimers of the clean surface to which it is bonded.On the Si(111)(7x7) surface the problem is particularly complex because there are several different potentially active sites for NH3 adsorption and fragmentation.The application of the PhD method, however, has shown that the majority of the N atoms are on so-called 'rest atom' sites when deposited at RT.This is consistent with the N in the NH2 chemical state.This investigation represents the first quantitative structural study of any molecular adsorbate on the complex Si(111)(7x7) surface.This atomic structures determination shows the PhD is a powerful tool for the atomic structure determination.The molecular systems interacting with the active sites of the substrate fragments producing a short-range order surface.This long-range disorder is produced by the

The role of electron localization in the atomic structure of transition-metal 13-atom clusters: the example of Co13, Rh13, and Hf13.

Science.gov (United States)

Piotrowski, Maurício J; Piquini, Paulo; Cândido, Ladir; Da Silva, Juarez L F

2011-10-14

The crystalline structure of transition-metals (TM) has been widely known for several decades, however, our knowledge on the atomic structure of TM clusters is still far from satisfactory, which compromises an atomistic understanding of the reactivity of TM clusters. For example, almost all density functional theory (DFT) calculations for TM clusters have been based on local (local density approximation--LDA) and semilocal (generalized gradient approximation--GGA) exchange-correlation functionals, however, it is well known that plain DFT fails to correct the self-interaction error, which affects the properties of several systems. To improve our basic understanding of the atomic and electronic properties of TM clusters, we report a DFT study within two nonlocal functionals, namely, the hybrid HSE (Heyd, Scuseria, and Ernzerhof) and GGA+U functionals, of the structural and electronic properties of the Co(13), Rh(13), and Hf(13) clusters. For Co(13) and Rh(13), we found that improved exchange-correlation functionals decrease the stability of open structures such as the hexagonal bilayer (HBL) and double simple-cubic (DSC) compared with the compact icosahedron (ICO) structure, however, DFT-GGA, DFT-GGA+U, and DFT-HSE yield very similar results for Hf(13). Thus, our results suggest that the DSC structure obtained by several plain DFT calculations for Rh(13) can be improved by the use of improved functionals. Using the sd hybridization analysis, we found that a strong hybridization favors compact structures, and hence, a correct description of the sd hybridization is crucial for the relative energy stability. For example, the sd hybridization decreases for HBL and DSC and increases for ICO in the case of Co(13) and Rh(13), while for Hf(13), the sd hybridization decreases for all configurations, and hence, it does not affect the relative stability among open and compact configurations.

[Factor structure validity of the social capital scale used at baseline in the ELSA-Brasil study].

Science.gov (United States)

Souto, Ester Paiva; Vasconcelos, Ana Glória Godoi; Chor, Dora; Reichenheim, Michael E; Griep, Rosane Härter

2016-07-21

This study aims to analyze the factor structure of the Brazilian version of the Resource Generator (RG) scale, using baseline data from the Brazilian Longitudinal Health Study in Adults (ELSA-Brasil). Cross-validation was performed in three random subsamples. Exploratory factor analysis using exploratory structural equation models was conducted in the first two subsamples to diagnose the factor structure, and confirmatory factor analysis was used in the third to corroborate the model defined by the exploratory analyses. Based on the 31 initial items, the model with the best fit included 25 items distributed across three dimensions. They all presented satisfactory convergent validity (values greater than 0.50 for the extracted variance) and precision (values greater than 0.70 for compound reliability). All factor correlations were below 0.85, indicating full discriminative factor validity. The RG scale presents acceptable psychometric properties and can be used in populations with similar characteristics.

Bottom-up Approach Design, Band Structure, and Lithium Storage Properties of Atomically Thin γ-FeOOH Nanosheets.

Science.gov (United States)

Song, Yun; Cao, Yu; Wang, Jing; Zhou, Yong-Ning; Fang, Fang; Li, Yuesheng; Gao, Shang-Peng; Gu, Qin-Fen; Hu, Linfeng; Sun, Dalin

2016-08-24

As a novel class of soft matter, two-dimensional (2D) atomic nanosheet-like crystals have attracted much attention for energy storage devices due to the fact that nearly all of the atoms can be exposed to the electrolyte and involved in redox reactions. Herein, atomically thin γ-FeOOH nanosheets with a thickness of ∼1.5 nm are synthesized in a high yield, and the band and electronic structures of the γ-FeOOH nanosheet are revealed using density-functional theory calculations for the first time. The rationally designed γ-FeOOH@rGO composites with a heterostacking structure are used as an anode material for lithium-ion batteries (LIBs). A high reversible capacity over 850 mAh g(-1) after 100 cycles at 200 mA g(-1) is obtained with excellent rate capability. The remarkable performance is attributed to the ultrathin nature of γ-FeOOH nanosheets and 2D heterostacking structure, which provide the minimized Li(+) diffusion length and buffer zone for volume change. Further investigation on the Li storage electrochemical mechanism of γ-FeOOH@rGO indicates that the charge-discharge processes include both conversion reaction and capacitive behavior. This synergistic effect of conversion reaction and capacitive behavior originating from 2D heterostacking structure casts new light on the development of high-energy anode materials.

Observation of atomic arrangement by using photoelectron holography and atomic stereo-photograph

International Nuclear Information System (INIS)

Matsushita, Tomohiro; Guo, Fang Zhun; Agui, Akane; Matsui, Fumihiko; Daimon, Hiroshi

2006-01-01

Both a photoelectron holography and atomic stereo-photograph are the atomic structure analysis methods on the basis of photoelectron diffraction. They have six special features such as 1) direct determination of atomic structure, 2) measurement of three dimensional atomic arrangements surrounding of specific element in the sample, 3) determination of position of atom in spite of electron cloud, 4) unnecessary of perfect periodic structure, 5) good sensitivity of structure in the neighborhood of surface and 6) information of electron structure. Photoelectron diffraction, the principle and measurement system of photoelectron holography and atomic stereo-photograph is explained. As application examples of atomic stereo-photograph, the single crystal of cupper and graphite are indicated. For examples of photoelectron holography, Si(001)2p and Ge(001)3s are explained. (S.Y.)

Towards atomically resolved EELS elemental and fine structure mapping via multi-frame and energy-offset correction spectroscopy.

Science.gov (United States)

Wang, Yi; Huang, Michael R S; Salzberger, Ute; Hahn, Kersten; Sigle, Wilfried; van Aken, Peter A

2018-01-01

Electron energy-loss spectroscopy and energy-dispersive X-ray spectroscopy are two of the most common means for chemical analysis in the scanning transmission electron microscope. The marked progress of the instrumentation hardware has made chemical analysis at atomic resolution readily possible nowadays. However, the acquisition and interpretation of atomically resolved spectra can still be problematic due to image distortions and poor signal-to-noise ratio of the spectra, especially for investigation of energy-loss near-edge fine structures. By combining multi-frame spectrum imaging and automatic energy-offset correction, we developed a spectrum imaging technique implemented into customized DigitalMicrograph scripts for suppressing image distortions and improving the signal-to-noise ratio. With practical examples, i.e. SrTiO 3 bulk material and Sr-doped La 2 CuO 4 superlattices, we demonstrate the improvement of elemental mapping and the EELS spectrum quality, which opens up new possibilities for atomically resolved EELS fine structure mapping. Copyright © 2017 The Authors. Published by Elsevier B.V. All rights reserved.

'Seeing' Atoms: The Crystallographic Revolution.

Science.gov (United States)

Schwarzenbach, Dieter

2014-02-26

Laue's experiment in 1912 of the diffraction of X-rays by crystals led to one of the most influential discoveries in the history of science: the first determinations of crystal structures, NaCl and diamond in particular, by W. L. Bragg in 1913. For the first time, the visualisation of the structure of matter at the atomic level became possible. X-ray diffraction provided a sort of microscope with atomic resolution, atoms became observable physical objects and their relative positions in space could be seen. All branches of science concerned with matter, solid-state physics, chemistry, materials science, mineralogy and biology, could now be firmly anchored on the spatial arrangement of atoms. During the ensuing 100 years, structure determination by diffraction methods has matured into an indispensable method of chemical analysis. We trace the history of the development of 'small-structure' crystallography (excepting macromolecular structures) in Switzerland. Among the pioneers figure Peter Debye and Paul Scherrer with powder diffraction, and Paul Niggli and his Zurich School with space group symmetry and geometrical crystallography. Diffraction methods were applied early on by chemists at the Universities of Bern and Geneva. By the 1970s, X-ray crystallography was firmly established at most Swiss Universities, directed by full professors. Today, chemical analysis by structure determination is the task of service laboratories. However, the demand of diffraction methods to solve problems in all disciplines of science is still increasing and powerful radiation sources and detectors are being developed in Switzerland and worldwide.

Novel low-dose imaging technique for characterizing atomic structures through scanning transmission electron microscope

Science.gov (United States)

Su, Chia-Ping; Syu, Wei-Jhe; Hsiao, Chien-Nan; Lai, Ping-Shan; Chen, Chien-Chun

2017-08-01

To investigate dislocations or heterostructures across interfaces is now of great interest to condensed matter and materials scientists. With the advances in aberration-corrected electron optics, the scanning transmission electron microscope has demonstrated its excellent capability of characterizing atomic structures within nanomaterials, and well-resolved atomic-resolution images can be obtained through long-exposure data acquisition. However, the sample drifting, carbon contamination, and radiation damage hinder further analysis, such as deriving three-dimensional (3D) structures from a series of images. In this study, a method for obtaining atomic-resolution images with significantly reduced exposure time was developed, using which an original high-resolution image with approximately one tenth the electron dose can be obtained by combining a fast-scan high-magnification image and a slow-scan low-magnification image. The feasibility of obtaining 3D atomic structures using the proposed approach was demonstrated through multislice simulation. Finally, the feasibility and accuracy of image restoration were experimentally verified. This general method cannot only apply to electron microscopy but also benefit to image radiation-sensitive materials using various light sources.

Efficient evaluation of atom tunneling combined with electronic structure calculations.

Science.gov (United States)

Ásgeirsson, Vilhjálmur; Arnaldsson, Andri; Jónsson, Hannes

2018-03-14

Methodology for finding optimal tunneling paths and evaluating tunneling rates for atomic rearrangements is described. First, an optimal JWKB tunneling path for a system with fixed energy is obtained using a line integral extension of the nudged elastic band method. Then, a calculation of the dynamics along the path is used to determine the temperature at which it corresponds to an optimal Feynman path for thermally activated tunneling (instanton) and a harmonic approximation is used to estimate the transition rate. The method is illustrated with calculations for a modified two-dimensional Müller-Brown surface but is efficient enough to be used in combination with electronic structure calculations of the energy and atomic forces in systems containing many atoms. An example is presented where tunneling is the dominant mechanism well above room temperature as an H 3 BNH 3 molecule dissociates to form H 2 . Also, a solid-state example is presented where density functional theory calculations of H atom tunneling in a Ta crystal give close agreement with experimental measurements on hydrogen diffusion over a wide range in temperature.

Atomic physics. Introduction to quantum physics and structure of the atomic system. 2. ed.

International Nuclear Information System (INIS)

Cagnac, Bernard; Pebay-Peyroula, J.-C.

1975-01-01

This lecture is intended for providing experimental foundations to the basic principles of quantum mechanics, from descriptions of some characteristic experiments which emphasize the limitations of the classical theory. The basic laws that govern the internal structure of atomic systems are exposed (waves and photons, the planetary model and principal quantum number, and the spatial classification of kinetic momenta and magnetic moments). Experimental studies presently in progress are reviewed and their aims are outlined [fr

Atomic structure of diamond {111} surfaces etched in oxygen water vapor

International Nuclear Information System (INIS)

Theije, F.K. de; Reedijk, M.F.; Arsic, J.; Enckevort, W.J.P. van; Vlieg, E.

2001-01-01

The atomic structure of the {111} diamond face after oxygen-water-vapor etching is determined using x-ray scattering. We find that a single dangling bond diamond {111} surface model, terminated by a full monolayer of -OH fits our data best. To explain the measurements it is necessary to add an ordered water layer on top of the -OH terminated surface. The vertical contraction of the surface cell and the distance between the oxygen atoms are generally in agreement with model calculations and results on similar systems. The OH termination is likely to be present during etching as well. This model experimentally confirms the atomic-scale mechanism we proposed previously for this etching system

Structurally uniform and atomically precise carbon nanostructures

Science.gov (United States)

Segawa, Yasutomo; Ito, Hideto; Itami, Kenichiro

2016-01-01

Nanometre-sized carbon materials consisting of benzene units oriented in unique geometric patterns, hereafter named nanocarbons, conduct electricity, absorb and emit light, and exhibit interesting magnetic properties. Spherical fullerene C60, cylindrical carbon nanotubes and sheet-like graphene are representative forms of nanocarbons, and theoretical simulations have predicted several exotic 3D nanocarbon structures. At present, synthetic routes to nanocarbons mainly lead to mixtures of molecules with a range of different structures and properties, which cannot be easily separated or refined into pure forms. Some researchers believe that it is impossible to synthesize these materials in a precise manner. Obtaining ‘pure’ nanocarbons is a great challenge in the field of nanocarbon science, and the construction of structurally uniform nanocarbons, ideally as single molecules, is crucial for the development of functional materials in nanotechnology, electronics, optics and biomedical applications. This Review highlights the organic chemistry approach — more specifically, bottom-up construction with atomic precision — that is currently the most promising strategy towards this end.

Role of atom--atom inelastic collisions in two-temperature nonequilibrium plasmas

International Nuclear Information System (INIS)

Kunc, J.A.

1987-01-01

The contribution of inelastic atom--atom collisions to the production of electrons and excited atoms in two-temperature (with electron temperature T/sub e/, atomic temperature T/sub a/, and atomic density N/sub a/), steady-state, nonequilibrium atomic hydrogen plasma is investigated. The results are valid for plasmas having large amounts of atomic hydrogen as one of the plasma components, so that e--H and H--H inelastic collisions and interaction of these atoms with radiation dominate the production of electrons and excited hydrogen atoms. Densities of electrons and excited atoms are calculated in low-temperature plasma, with T/sub e/ and T/sub a/≤8000 K and 10 16 cm -3 ≤N/sub a/≤10 18 cm -3 , and with different degrees of the reabsorption of radiation. The results indicate that inelastic atom--atom collisions are important for production of electrons and excited atoms in partially ionized plasmas with medium and high atomic density and temperatures below 8000 K

Workshop on foundations of the relativistic theory of atomic structure

International Nuclear Information System (INIS)

1981-03-01

The conference is an attempt to gather state-of-the-art information to understand the theory of relativistic atomic structure beyond the framework of the original Dirac theory. Abstracts of twenty articles from the conference were prepared separately for the data base

Density functional theory calculations establish the experimental evidence of the DX center atomic structure in CdTe.

Science.gov (United States)

Lany, Stephan; Wolf, Herbert; Wichert, Thomas

2004-06-04

The In DX center and the DX-like configuration of the Cd host atom in CdTe are investigated using density functional theory. The simultaneous calculation of the atomic structure and the electric field gradient (EFG) allows one to correlate the theoretically predicted structure of the DX center with an experimental observable, namely, the EFG obtained from radioactive 111In/111Cd probe atoms in In doped CdTe. In this way, the experimental identification of the DX center structure is established.

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

Science.gov (United States)

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.

Principle and Reconstruction Algorithm for Atomic-Resolution Holography

Science.gov (United States)

Matsushita, Tomohiro; Muro, Takayuki; Matsui, Fumihiko; Happo, Naohisa; Hosokawa, Shinya; Ohoyama, Kenji; Sato-Tomita, Ayana; Sasaki, Yuji C.; Hayashi, Kouichi

2018-06-01

Atomic-resolution holography makes it possible to obtain the three-dimensional (3D) structure around a target atomic site. Translational symmetry of the atomic arrangement of the sample is not necessary, and the 3D atomic image can be measured when the local structure of the target atomic site is oriented. Therefore, 3D local atomic structures such as dopants and adsorbates are observable. Here, the atomic-resolution holography comprising photoelectron holography, X-ray fluorescence holography, neutron holography, and their inverse modes are treated. Although the measurement methods are different, they can be handled with a unified theory. The algorithm for reconstructing 3D atomic images from holograms plays an important role. Although Fourier transform-based methods have been proposed, they require the multiple-energy holograms. In addition, they cannot be directly applied to photoelectron holography because of the phase shift problem. We have developed methods based on the fitting method for reconstructing from single-energy and photoelectron holograms. The developed methods are applicable to all types of atomic-resolution holography.

Extending the validity of the Feeding Practices and Structure Questionnaire

OpenAIRE

Jansen, Elena; Mallan, Kimberley M.; Daniels, Lynne A.

2015-01-01

Background Feeding practices are commonly examined as potentially modifiable determinants of children?s eating behaviours and weight status. Although a variety of questionnaires exist to assess different feeding aspects, many lack thorough reliability and validity testing. The Feeding Practices and Structure Questionnaire (FPSQ) is a tool designed to measure early feeding practices related to non-responsive feeding and structure of the meal environment. Face validity, factorial validity, inte...

Quantitative characterization of the atomic-scale structure of oxyhydroxides in rusts formed on steel surfaces

International Nuclear Information System (INIS)

Saito, M.; Suzuki, S.; Kimura, M.; Suzuki, T.; Kihira, H.; Waseda, Y.

2005-01-01

Quantitative X-ray structural analysis coupled with anomalous X-ray scattering has been used for characterizing the atomic-scale structure of rust formed on steel surfaces. Samples were prepared from rust layers formed on the surfaces of two commercial steels. X-ray scattered intensity profiles of the two samples showed that the rusts consisted mainly of two types of ferric oxyhydroxide, α-FeOOH and γ-FeOOH. The amounts of these rust components and the realistic atomic arrangements in the components were estimated by fitting both the ordinary and the environmental interference functions with a model structure calculated using the reverse Monte Carlo simulation technique. The two rust components were found to be the network structure formed by FeO 6 octahedral units, the network structure itself deviating from the ideal case. The present results also suggest that the structural analysis method using anomalous X-ray scattering and the reverse Monte Carlo technique is very successful in determining the atomic-scale structure of rusts formed on the steel surfaces

Atomic structure calculations for F-like tungsten

Science.gov (United States)

Sunny, Aggarwal

2014-09-01

Energy levels, wavefunction compositions and lifetimes have been computed for all levels of 1s22s22p5, 1s22s2p6, 1s22s22p43s, 1s22s22p43p, and 1s22s22p43d configurations in highly charged F-like tungsten ion. The multiconfigurational Dirac—Fock method (MCDF) is adopted to generate the wavefunctions. We have also presented the transition wavelengths, oscillator strengths, transition probabilities, and line strengths for the electric dipole (E1) and magnetic quadrupole (M2) transition from the 1s22s22p5 ground configuration. We have performed parallel calculations with the flexible atomic code (FAC) for comparing the atomic data. The reliability of present data is assessed by comparison with other theoretical and experimental data available in the literature. Good agreement is found between our results and those obtained using different approaches confirm the quality of our results. Additionally, we have predicted some new atomic data for F-like W that were not available so far and may be important for plasma diagnostic analysis in fusion plasma.

Pre-service physics teachers' ideas on size, visibility and structure of the atom

International Nuclear Information System (INIS)

Uenlue, Pervin

2010-01-01

Understanding the atom gives the opportunity to both understand and conceptually unify the various domains of science, such as physics, chemistry, biology, astronomy and geology. Among these disciplines, physics teachers are expected to be particularly well educated in this topic. It is important that pre-service physics teachers know what sort of theories regarding the atom they will bring into their own classrooms. Six tasks were developed, comprising size, visibility and structure of the atom. These tasks carried out by pre-service physics teachers were examined by content analysis and six categories were determined. These are size, visibility, subatomic particles, atom models, electron orbit and electron features. Pre-service physics teachers' ideas about the atom were clarified under these categories.

Theoretical and experimental investigation of atomic radiative lifetimes and hyperfine structures

International Nuclear Information System (INIS)

Joensson, Per.

1992-01-01

Atomic radiative lifetimes and hyperfine structures as well as other properties, such as total energy and specific mass shift, have been studied theoretically and experimentally. Computer programs to calculate hyperfine structure constants from non-relativistic multiconfiguration Hartree-Fock (MCHF) and relativistic multi-configuration Dirac-Fock (MCDF) wavefunctions have been written. Using these programs large-scale calculations of hyperfine structures in lithium and sodium have been performed. It is shown, that the MCHF method is able to predict hyperfine structures to an accuracy of a few per mille in lithium, whereas for the more complex hyperfine structures to an accuracy of a few per mille in lithium, whereas for the more complex sodium atom an accuracy of a few per cent is obtainable. For lithium convergence of the total energy, ionization energy, specific mass shift and hyperfine parameters has been studied with the MCHF method. Radiative lifetimes and hyperfine structures of excited states in sodium and silver have been experimentally determined using time-resolved laser spectroscopy. By recording the fluorescence light decay curves following VUV excitation, the radiative lifetimes and hyperfine structures of the 7p 2 P states in silver were measured. The delayed-coincidence technique has been used to make very accurate measurements of the radiative lifetimes and hyperfine structures of the lowest P states in sodium and silver

Cross validation for the classical model of structured expert judgment

International Nuclear Information System (INIS)

Colson, Abigail R.; Cooke, Roger M.

2017-01-01

We update the 2008 TU Delft structured expert judgment database with data from 33 professionally contracted Classical Model studies conducted between 2006 and March 2015 to evaluate its performance relative to other expert aggregation models. We briefly review alternative mathematical aggregation schemes, including harmonic weighting, before focusing on linear pooling of expert judgments with equal weights and performance-based weights. Performance weighting outperforms equal weighting in all but 1 of the 33 studies in-sample. True out-of-sample validation is rarely possible for Classical Model studies, and cross validation techniques that split calibration questions into a training and test set are used instead. Performance weighting incurs an “out-of-sample penalty” and its statistical accuracy out-of-sample is lower than that of equal weighting. However, as a function of training set size, the statistical accuracy of performance-based combinations reaches 75% of the equal weight value when the training set includes 80% of calibration variables. At this point the training set is sufficiently powerful to resolve differences in individual expert performance. The information of performance-based combinations is double that of equal weighting when the training set is at least 50% of the set of calibration variables. Previous out-of-sample validation work used a Total Out-of-Sample Validity Index based on all splits of the calibration questions into training and test subsets, which is expensive to compute and includes small training sets of dubious value. As an alternative, we propose an Out-of-Sample Validity Index based on averaging the product of statistical accuracy and information over all training sets sized at 80% of the calibration set. Performance weighting outperforms equal weighting on this Out-of-Sample Validity Index in 26 of the 33 post-2006 studies; the probability of 26 or more successes on 33 trials if there were no difference between performance

Pattern recognition approach to quantify the atomic structure of graphene

DEFF Research Database (Denmark)

Kling, Jens; Vestergaard, Jacob Schack; Dahl, Anders Bjorholm

2014-01-01

We report a pattern recognition approach to detect the atomic structure in high-resolution transmission electron microscopy images of graphene. The approach provides quantitative information such as carbon-carbon bond lengths and bond length variations on a global and local scale alike. © 2014...

Brazilian Portuguese version of the Revised Fibromyalgia Impact Questionnaire (FIQR-Br): cross-cultural validation, reliability, and construct and structural validation.

Science.gov (United States)

Lupi, Jaqueline Basilio; Carvalho de Abreu, Daniela Cristina; Ferreira, Mariana Candido; Oliveira, Renê Donizeti Ribeiro de; Chaves, Thais Cristina

2017-08-01

This study aimed to culturally adapt and validate the Revised Fibromyalgia Impact Questionnaire (FIQR) to Brazilian Portuguese, by the use of analysis of internal consistency, reliability, and construct and structural validity. A total of 100 female patients with fibromyalgia participated in the validation process of the Brazilian Portuguese version of the FIQR (FIQR-Br).The intraclass correlation coefficient (ICC) was used for statistical analysis of reliability (test-retest), Cronbach's alpha for internal consistency, Pearson's rank correlation for construct validity, and confirmatory factor analysis (CFA) for structural validity. It was verified excellent levels of reliability, with ICC greater than 0.75 for all questions and domains of the FIQR-Br. For internal consistency, alpha values greater than 0.70 for the items and domains of the questionnaire were observed. Moderate (0.40  0.70) correlations were observed for the scores of domains and total score between the FIQR-Br and FIQ-Br. The structure of the three domains of the FIQR-Br was confirmed by CFA. The results of this study suggest that that the FIQR-Br is a reliable and valid instrument for assessing fibromyalgia-related impact, and supports its use in clinical settings and research. The structure of the three domains of the FIQR-Br was also confirmed. Implications for Rehabilitation Fibromyalgia is a chronic musculoskeletal disorder characterized by widespread and diffuse pain, fatigue, sleep disturbances, and depression. The disease significantly impairs patients' quality of life and can be highly disabling. To be used in multicenter research efforts, the Revised Fibromyalgia Impact Questionnaire (FIQR) must be cross-culturally validated and psychometrically tested. This paper will make available a new version of the FIQR-Br since another version already exists, but there are concerns about its measurement properties. The availability of an instrument adapted to and validated for Brazilian

Analysis and validation of carbohydrate three-dimensional structures

International Nuclear Information System (INIS)

Lütteke, Thomas

2009-01-01

The article summarizes the information that is gained from and the errors that are found in carbohydrate structures in the Protein Data Bank. Validation tools that can locate these errors are described. Knowledge of the three-dimensional structures of the carbohydrate molecules is indispensable for a full understanding of the molecular processes in which carbohydrates are involved, such as protein glycosylation or protein–carbohydrate interactions. The Protein Data Bank (PDB) is a valuable resource for three-dimensional structural information on glycoproteins and protein–carbohydrate complexes. Unfortunately, many carbohydrate moieties in the PDB contain inconsistencies or errors. This article gives an overview of the information that can be obtained from individual PDB entries and from statistical analyses of sets of three-dimensional structures, of typical problems that arise during the analysis of carbohydrate three-dimensional structures and of the validation tools that are currently available to scientists to evaluate the quality of these structures

Atomic structure of a peptide coated gold nanocluster identified using theoretical and experimental studies

Science.gov (United States)

Wang, Hui; Li, Xu; Gao, Liang; Zhai, Jiao; Liu, Ru; Gao, Xueyun; Wang, Dongqi; Zhao, Lina

2016-06-01

, in Au24(Cys-Cys)8 and Au24(SR)20 cause the different Au/S ratios in the coated Au24. The reason is that the Au/S ratio is crucial in determining the size of the Au core of the ligand protected AuNC, and the size of the Au core corresponds to a specific electronic structure. By the adjustment of ligand coatings from alkylthiolate to peptide, the Au/S ratio could be controlled to generate different AuNCs with versatile electronic structures, optical properties and reaction stabilities. Therefore, we propose a universal approach to obtain a specific Au/S ratio of ligand coated AuNCs by adjusting the ligand composition, thus controlling the chemicophysical properties of AuNCs with ultimately the same number of Au atoms. Electronic supplementary information (ESI) available: The MALDI-TOF-MS identification of Au24Peptide8, the structural divisions of Au24(Cys-Cys)8 obtained based on the ``divide and protect'' approach, the structure of level-1 and -3 staple motifs, the relative energies of all stable configurations of Au24(Cys-Cys)8, orbital components of Iso1 of Au24(Cys-Cys)8, electronic structure comparison between Au24(Cys-Cys)8 and Au24(SR)20, and the coordination of Iso1. See DOI: 10.1039/c5nr08727a

Atomic structure of the APC/C and its mechanism of protein ubiquitination

Science.gov (United States)

Yang, Jing; McLaughlin, Stephen H.; Barford, David

2015-01-01

The anaphase-promoting complex (APC/C) is a multimeric RING E3 ubiquitin ligase that controls chromosome segregation and mitotic exit. Its regulation by coactivator subunits, phosphorylation, the mitotic checkpoint complex, and interphase inhibitor Emi1 ensures the correct order and timing of distinct cell cycle transitions. Here, we used cryo-electron microscopy to determine atomic structures of APC/C-coactivator complexes with either Emi1 or a UbcH10-ubiquitin conjugate. These structures define the architecture of all APC/C subunits, the position of the catalytic module, and explain how Emi1 mediates inhibition of the two E2s UbcH10 and Ube2S. Definition of Cdh1 interactions with the APC/C indicates how they are antagonized by Cdh1 phosphorylation. The structure of the APC/C with UbcH10-ubiquitin reveals insights into the initiating ubiquitination reaction. Our results provide a quantitative framework for the design of experiments to further investigate APC/C functions in vivo. PMID:26083744

Atomic-scale structure of dislocations revealed by scanning tunneling microscopy and molecular dynamics

DEFF Research Database (Denmark)

Christiansen, Jesper; Morgenstern, K.; Schiøtz, Jakob

2002-01-01

The intersection between dislocations and a Ag(111) surface has been studied using an interplay of scanning tunneling microscopy (STM) and molecular dynamics. Whereas the STM provides atomically resolved information about the surface structure and Burgers vectors of the dislocations, the simulati......The intersection between dislocations and a Ag(111) surface has been studied using an interplay of scanning tunneling microscopy (STM) and molecular dynamics. Whereas the STM provides atomically resolved information about the surface structure and Burgers vectors of the dislocations......, the simulations can be used to determine dislocation structure and orientation in the near-surface region. In a similar way, the subsurface structure of other extended defects can be studied. The simulations show dislocations to reorient the partials in the surface region leading to an increased splitting width...

All-atom simulation study of protein PTH(1-34) by using the Wang-Landau sampling method

Energy Technology Data Exchange (ETDEWEB)

Kim, Seung-Yeon [Korea National University of Transportation, Chungju (Korea, Republic of); Kwak, Woo-Seop [Chosun University, Gwangju (Korea, Republic of)

2014-12-15

We perform simulations of the N-terminal 34-residue protein fragment PTH(1-34), consisting of 581 atoms, of the 84-residue human parathyroid hormone by using the all-atom ECEPP/3 force field and the Wang-Landau sampling method. Through a massive high-performance computation, the density of states and the partition function Z(T), as a continuous function of T, are obtained for PTH(1-34). From the continuous partition function Z(T), the partition function zeros of PTH(1-34) are evaluated for the first time. From both the specific heat and the partition function zeros, two characteristic transition temperatures are obtained for the all-atom protein PTH(1-34). The higher transition temperature T{sub 1} and the lower transition temperature T{sub 2} of PTH(1-34) can be interpreted as the collapse temperature T{sub θ} and the folding temperature T{sub f} , respectively.

Relaxation volumes of self-interstitial-atoms and vacancies in metals

International Nuclear Information System (INIS)

Ehrhart, P.

1983-01-01

Experimental results for the relaxation volumes of self-interstitial-atoms and vacancies as obtained after low temperature irradiation of different metals are reviewed. For fcc metals the relaxation volumes of the SIA's are very similar: ΔVsup(rel) = 1.6 +- 0.3 atomic volumes. This value is valid as well for the pure fcc metals (Al, Cu, Ni) as for different alloys. Vacancy relaxation volumes are small and vary between: ΔVsup(rel) = -0.05 and -0.25 atomic volumes. For bcc metals (Fe, Mo) the relaxation volume of the SIA is significantly smaller: ΔVsup(rel) = 1.1 +- 0.2 atomic volumes. In spite of the obvious similarity of the close-packed fcc and hcp structures, the SIA parameters for hcp metals are much different: ΔVsup(rel) = 3.5 for Zn, ΔVsup(rel) = 1.5 for Co and ΔVsup(rel) = 0.6 at. vol. for Zr. Vacancy relaxation volumes seem to be small as in cubic metals. The influence of lattice nonharmonicity on the validity of an extrapolation of the values determined at 6 K to higher temperatures is discussed. (author)

Bloch oscillations of ultracold atoms and measurement of the fine structure constant

International Nuclear Information System (INIS)

Clade, P.

2005-10-01

From a measurement of the recoil velocity of an atom absorbing a photon, it is possible to deduce a determination of the ratio h/m between the Planck constant and the mass of the atoms and then to deduce a value of the fine structure constant alpha. To do this measurement, we use the technique of Bloch oscillations, which allows us to transfer a large number of recoils to atoms. A velocity sensor, based on velocity selective Raman transition, enables us to measure the momentum transferred to the atoms. A measurement with a statistical uncertainty of 4.4 10 -9 , in conjunction with a careful study of systematic effects (5 10 -9 ), has led us to a determination of alpha with an uncertainty of 6.7 10 -9 : α -1 (Rb) = 137.03599878 (91). This uncertainty is similar to the uncertainty of the best determinations of alpha based on atom interferometry. (author)

The atomic and electronic structure of amorphous silicon nitride

International Nuclear Information System (INIS)

Alvarez, F.; Valladares, A.A.

2002-01-01

Using a novel approach to the ab initio generation of random networks we constructed two nearly stoichiometric samples of amorphous silicon nitride with the same content x= 1.29. The two 64-atom periodically-continued cubic diamond-like cells contain 28 silicons and 36 nitrogens randomly substituted, and were amorphized with a 6 f s time step by heating them to just below their melting temperature with a Harris-functional based, molecular dynamics code in the LDA approximation. The averaged total radial distribution function (RDF) obtained is compared with some existing Tersoff-like potential simulations and with experiment; ours agree with experiment. All the partial radial features are calculated and the composition of the second peak also agrees with experiment. The electronic structure is calculated and the optical gaps obtained using both a HOMO-LUMO approach and the Tauc-like procedure developed recently that gives reasonable gaps. (Author)

Automatic kinetic Monte-Carlo modeling for impurity atom diffusion in grain boundary structure of tungsten material

Directory of Open Access Journals (Sweden)

Atsushi M. Ito

2017-08-01

Full Text Available The diffusion process of hydrogen and helium in plasma-facing material depends on the grain boundary structures. Whether a grain boundary accelerates or limits the diffusion speed of these impurity atoms is not well understood. In the present work, we proposed the automatic modeling of a kinetic Monte-Carlo (KMC simulation to treat an asymmetric grain boundary structure that corresponds to target samples used in fusion material experiments for retention and permeation. In this method, local minimum energy sites and migration paths for impurity atoms in the grain boundary structure are automatically found using localized molecular dynamics. The grain boundary structure was generated with the Voronoi diagram. Consequently, we demonstrate that the KMC simulation for the diffusion process of impurity atoms in the generated grain boundary structure of tungsten material can be performed.

Validation of molecular crystal structures from powder diffraction data with dispersion-corrected density functional theory (DFT-D).

Science.gov (United States)

van de Streek, Jacco; Neumann, Marcus A

2014-12-01

In 2010 we energy-minimized 225 high-quality single-crystal (SX) structures with dispersion-corrected density functional theory (DFT-D) to establish a quantitative benchmark. For the current paper, 215 organic crystal structures determined from X-ray powder diffraction (XRPD) data and published in an IUCr journal were energy-minimized with DFT-D and compared to the SX benchmark. The on average slightly less accurate atomic coordinates of XRPD structures do lead to systematically higher root mean square Cartesian displacement (RMSCD) values upon energy minimization than for SX structures, but the RMSCD value is still a good indicator for the detection of structures that deserve a closer look. The upper RMSCD limit for a correct structure must be increased from 0.25 Å for SX structures to 0.35 Å for XRPD structures; the grey area must be extended from 0.30 to 0.40 Å. Based on the energy minimizations, three structures are re-refined to give more precise atomic coordinates. For six structures our calculations provide the missing positions for the H atoms, for five structures they provide corrected positions for some H atoms. Seven crystal structures showed a minor error for a non-H atom. For five structures the energy minimizations suggest a higher space-group symmetry. For the 225 SX structures, the only deviations observed upon energy minimization were three minor H-atom related issues. Preferred orientation is the most important cause of problems. A preferred-orientation correction is the only correction where the experimental data are modified to fit the model. We conclude that molecular crystal structures determined from powder diffraction data that are published in IUCr journals are of high quality, with less than 4% containing an error in a non-H atom.

GRASP92: a package for large-scale relativistic atomic structure calculations

Science.gov (United States)

Parpia, F. A.; Froese Fischer, C.; Grant, I. P.

2006-12-01

of CSFs sharing the same quantum numbers is determined using the configuration-interaction (CI) procedure that results upon varying the expansion coefficients to determine the extremum of a variational functional. Radial functions may be determined by numerically solving the multiconfiguration Dirac-Fock (MCDF) equations that result upon varying the orbital radial functions or some subset thereof so as to obtain an extremum of the variational functional. Radial wavefunctions may also be determined using a screened hydrogenic or Thomas-Fermi model, although these schemes generally provide initial estimates for MCDF self-consistent-field (SCF) calculations. Transition properties for pairs of ASFs are computed from matrix elements of multipole operators of the electromagnetic field. All matrix elements of CSFs are evaluated using the Racah algebra. Reasons for the new version: During recent studies using the general relativistic atomic structure package (GRASP92), several errors were found, some of which might have been present already in the earlier GRASP92 version (program ABJN_v1_0, Comput. Phys. Comm. 55 (1989) 425). These errors were reported and discussed by Froese Fischer, Gaigalas, and Ralchenko in a separate publication [C. Froese Fischer, G. Gaigalas, Y. Ralchenko, Comput. Phys. Comm. 175 (2006) 738-744. [7

Atomic structures and compositions of internal interfaces

Energy Technology Data Exchange (ETDEWEB)

Seidman, D.N. (Northwestern Univ., Evanston, IL (United States). Dept. of Materials Science and Engineering); Merkle, K.L. (Argonne National Lab., IL (United States))

1992-03-01

This research program addresses fundamental questions concerning the relationships between atomic structures and chemical compositions of metal/ceramic heterophase interfaces. The chemical composition profile across a Cu/MgO {l brace}111{r brace}-type heterophase interface, produced by the internal oxidation of a Cu(Mg) single phase alloy, is measured via atom-probe field-ion microscopy with a spatial resolution of 0.121 nm; this resolution is equal to the interplanar space of the {l brace}222{r brace} MgO planes. In particular, we demonstrate for the first time that the bonding across a Cu/MgO {l brace}111{r brace}-type heterophase interface, along a <111> direction common to both the Cu matrix and an MgO precipitate, has the sequence Cu{vert bar}O{vert bar}Mg{hor ellipsis} and not Cu{vert bar}Mg{vert bar}O{hor ellipsis}; this result is achieved without any deconvolution of the experimental data. Before determining this chemical sequence it was established, via high resolution electron microscopy, that the morphology of an MgO precipitate in a Cu matrix is an octahedron faceted on {l brace}111{r brace} planes with a cube-on-cube relationship between a precipitate and the matrix. First results are also presented for the Ni/Cr{sub 2}O{sub 4} interface; for this system selected area atom probe microscopy was used to analyze this interface; Cr{sub 2}O{sub 4} precipitates are located in a field-ion microscope tip and a precipitate is brought into the tip region via a highly controlled electropolishing technique.

5. All-Russian (international) scientific conference. Physicochemical processes during selection of atoms and molecules. Collection of reports

International Nuclear Information System (INIS)

Baranov, V.Yu.; Kolesnikov, Yu.A.

2000-01-01

The materials of the 5. All-Russian (international) scientific conference: Physicochemical processes during selection of atoms and molecules, are presented. The conference took place in Zvenigorod, 2-6 October, 2000. A wide range of items connected with uranium enrichment, selection of atoms and molecules by isotopic composition: laser methods, ion cyclotron-resonance method, are discussed. The selection of molecules and atoms by rectification and chemical isotopic exchange methods, the selection in the field of centrifugal forces are treated. The questions of search for the new advanced methods for selection of atoms and molecules were discussed at the conference, the problems of radioisotope production were represented. The subject matter of the use of stable isotopes and radionuclides is demonstrated widely. The subjects connected with experimental and engineering equipment for selection of atoms and molecules are embodied in the paper [ru

Paramyxovirus membrane fusion: Lessons from the F and HN atomic structures

International Nuclear Information System (INIS)

Lamb, Robert A.; Paterson, Reay G.; Jardetzky, Theodore S.

2006-01-01

Paramyxoviruses enter cells by fusion of their lipid envelope with the target cell plasma membrane. Fusion of the viral membrane with the plasma membrane allows entry of the viral genome into the cytoplasm. For paramyxoviruses, membrane fusion occurs at neutral pH, but the trigger mechanism that controls the viral entry machinery such that it occurs at the right time and in the right place remains to be elucidated. Two viral glycoproteins are key to the infection process-an attachment protein that varies among different paramyxoviruses and the fusion (F) protein, which is found in all paramyxoviruses. For many of the paramyxoviruses (parainfluenza viruses 1-5, mumps virus, Newcastle disease virus and others), the attachment protein is the hemagglutinin/neuraminidase (HN) protein. In the last 5 years, atomic structures of paramyxovirus F and HN proteins have been reported. The knowledge gained from these structures towards understanding the mechanism of viral membrane fusion is described

Studying the Atomic Nucleus - A New Era in Nuclear Structure Studies

International Nuclear Information System (INIS)

Casten, R. F.

2011-01-01

The study of atomic nuclei is part of the fascinating quest to understand the fundamental nature and origins of matter. This field, nuclear structure, is undergoing a revolutionary transformation that is breaking cherished paradigms, opening new vistas of nuclear matter for study, and which has the promise of leading to a new comprehensive understanding. The advent of new facilities for the production and study of exotic nuclei provides access to an entirely new territory of nuclei, and advances in extreme computing are enabling similar advances in the theory of atomic nuclei.

Molecular dynamic simulation of the atomic structure of aluminum solid–liquid interfaces

International Nuclear Information System (INIS)

Men, H; Fan, Z

2014-01-01

In this paper, molecular dynamic (MD) simulation was used to investigate the equilibrium atomic arrangement at aluminum solid–liquid (S/L) interfaces with {111}, {110} and {100} orientations. The simulation results reveal that the aluminum S/L interfaces are diffuse for all the orientations, and extend up to 7 atomic layers. Within the diffuse interfaces there exists substantial atomic ordering, which is manifested by atomic layering perpendicular to the interface and in-plane atomic ordering parallel to the interface. Atomic layering can be quantified by the atomic density profile (ρ(z)) while the in-plane atomic ordering can be described by the in-plane ordering parameter (S(z)). The detailed MD simulation suggests that atomic layering at the interface always occurs within 7 atomic layers independent of the interface orientation while the in-plane ordering is highly dependent on the interface orientations, with the {111} interface being less diffuse than the {100} and {110} interfaces. This study demonstrates clearly that the physical origin of the diffuse interface is atomic layering and in-plane atomic ordering at the S/L interfaces. It is suggested that the difference in atomic layering and in-plane ordering at the S/L interface with different orientations is responsible for the observed growth anisotropy. (papers)

Vivaldi: Visualization and validation of biomacromolecular NMR structures from the PDB

Science.gov (United States)

Hendrickx, Pieter M S; Gutmanas, Aleksandras; Kleywegt, Gerard J

2013-01-01

We describe Vivaldi (VIsualization and VALidation DIsplay; http://pdbe.org/vivaldi), a web-based service for the analysis, visualization, and validation of NMR structures in the Protein Data Bank (PDB). Vivaldi provides access to model coordinates and several types of experimental NMR data using interactive visualization tools, augmented with structural annotations and model-validation information. The service presents information about the modeled NMR ensemble, validation of experimental chemical shifts, residual dipolar couplings, distance and dihedral angle constraints, as well as validation scores based on empirical knowledge and databases. Vivaldi was designed for both expert NMR spectroscopists and casual non-expert users who wish to obtain a better grasp of the information content and quality of NMR structures in the public archive. © Proteins 2013. © 2012 Wiley Periodicals, Inc. PMID:23180575

Multiconfiguration Dirac-Fock method for atomic structure

International Nuclear Information System (INIS)

Sasaki, Ken

1982-02-01

The multiconfiguration Dirac-Fock method for calculating the atomic structure is reviewed in some detail. Being more comprehensive than the ones introduced in Desclaux's paper, the mathematical formulae derived in this review are more helpful to trace the thread of ideas and understand the algorithm in Desclaux's computer program which embodied the method. A detailed analysis is made on the restrictions on how the program is used, that is, on the fact that it does not apply to the problem where the configuration mixing occurs via the one-electron Hamiltonian. Finally, in conclusion, a way to overcome the difficulty is suggested. (author)

Michael Faraday and the concept of atomic structure

International Nuclear Information System (INIS)

Pocock, R.F.

1991-01-01

Written to commemorate the bicentenary of Faraday's birth, this article surveys his influence on atomic theory during the 19th and early 20th centuries. It identifies which developments were derived from projects which he had started; it shows that his ideas and methods determined the direction of researches which he had not himself initiated. The account is in the form of a chronological narrative. This is based entirely on published sources, and the treatment is non-mathematical. In consequence it contains no new factual data. The presentation of Faraday's work in this particular context is, however, original. Although not covering studies of the nucleus - which were mostly later than the period considered -this article describes the origins of modern theories of atomic structure reasonably completely. It is a useful overview for engineers unfamiliar with details of the history of physics. In addition, it is a case-study of the persistence of scientific ideas in researches occupying a century or more. (author)

ZnO: Hydroquinone superlattice structures fabricated by atomic/molecular layer deposition

International Nuclear Information System (INIS)

Tynell, Tommi; Karppinen, Maarit

2014-01-01

Here we employ atomic layer deposition in combination with molecular layer deposition to deposit crystalline thin films of ZnO interspersed with single layers of hydroquinone in an effort to create hybrid inorganic–organic superlattice structures. The ratio of the ZnO and hydroquinone deposition cycles is varied between 199:1 and 1:1, and the structure of the resultant thin films is verified with X-ray diffraction and reflectivity techniques. Clear evidence of the formation of a superlattice-type structure is observed in the X-ray reflectivity patterns and the presence of organic bonds in the films corresponding to the structure of hydroquinone is confirmed with Fourier transform infrared spectroscopy measurements. We anticipate that hybrid superlattice structures such as the ones described in this work have the potential to be of great importance for future applications where the precise control of different inorganic and organic layers in hybrid superlattice materials is required. - Highlights: • Inorganic–organic superlattices can be made by atomic/molecular layer deposition. • This is demonstrated here for ZnO and hydroquinone (HQ). • The ratio of the ZnO and HQ layers is varied between 199:1 and 14:1. • The resultant thin films are crystalline

ZnO: Hydroquinone superlattice structures fabricated by atomic/molecular layer deposition

Energy Technology Data Exchange (ETDEWEB)

Tynell, Tommi; Karppinen, Maarit, E-mail: maarit.karppinen@aalto.fi

2014-01-31

Here we employ atomic layer deposition in combination with molecular layer deposition to deposit crystalline thin films of ZnO interspersed with single layers of hydroquinone in an effort to create hybrid inorganic–organic superlattice structures. The ratio of the ZnO and hydroquinone deposition cycles is varied between 199:1 and 1:1, and the structure of the resultant thin films is verified with X-ray diffraction and reflectivity techniques. Clear evidence of the formation of a superlattice-type structure is observed in the X-ray reflectivity patterns and the presence of organic bonds in the films corresponding to the structure of hydroquinone is confirmed with Fourier transform infrared spectroscopy measurements. We anticipate that hybrid superlattice structures such as the ones described in this work have the potential to be of great importance for future applications where the precise control of different inorganic and organic layers in hybrid superlattice materials is required. - Highlights: • Inorganic–organic superlattices can be made by atomic/molecular layer deposition. • This is demonstrated here for ZnO and hydroquinone (HQ). • The ratio of the ZnO and HQ layers is varied between 199:1 and 14:1. • The resultant thin films are crystalline.

QMCPACK: an open source ab initio quantum Monte Carlo package for the electronic structure of atoms, molecules and solids

Science.gov (United States)

Kim, Jeongnim; Baczewski, Andrew D.; Beaudet, Todd D.; Benali, Anouar; Chandler Bennett, M.; Berrill, Mark A.; Blunt, Nick S.; Josué Landinez Borda, Edgar; Casula, Michele; Ceperley, David M.; Chiesa, Simone; Clark, Bryan K.; Clay, Raymond C., III; Delaney, Kris T.; Dewing, Mark; Esler, Kenneth P.; Hao, Hongxia; Heinonen, Olle; Kent, Paul R. C.; Krogel, Jaron T.; Kylänpää, Ilkka; Li, Ying Wai; Lopez, M. Graham; Luo, Ye; Malone, Fionn D.; Martin, Richard M.; Mathuriya, Amrita; McMinis, Jeremy; Melton, Cody A.; Mitas, Lubos; Morales, Miguel A.; Neuscamman, Eric; Parker, William D.; Pineda Flores, Sergio D.; Romero, Nichols A.; Rubenstein, Brenda M.; Shea, Jacqueline A. R.; Shin, Hyeondeok; Shulenburger, Luke; Tillack, Andreas F.; Townsend, Joshua P.; Tubman, Norm M.; Van Der Goetz, Brett; Vincent, Jordan E.; ChangMo Yang, D.; Yang, Yubo; Zhang, Shuai; Zhao, Luning

2018-05-01

QMCPACK is an open source quantum Monte Carlo package for ab initio electronic structure calculations. It supports calculations of metallic and insulating solids, molecules, atoms, and some model Hamiltonians. Implemented real space quantum Monte Carlo algorithms include variational, diffusion, and reptation Monte Carlo. QMCPACK uses Slater–Jastrow type trial wavefunctions in conjunction with a sophisticated optimizer capable of optimizing tens of thousands of parameters. The orbital space auxiliary-field quantum Monte Carlo method is also implemented, enabling cross validation between different highly accurate methods. The code is specifically optimized for calculations with large numbers of electrons on the latest high performance computing architectures, including multicore central processing unit and graphical processing unit systems. We detail the program’s capabilities, outline its structure, and give examples of its use in current research calculations. The package is available at http://qmcpack.org.

Low energy atom-atom collisions

International Nuclear Information System (INIS)

Child, M.S.

1980-01-01

The semiclassical theory of atom-atom potential scattering and of low energy inelastic atom-atom scattering is reviewed. Particular attention is given to the origin and interpretation of rainbow structure, diffraction oscillations and exchange oscillations in the potential scattering differential cross-section, and to the glory structure and symmetry oscillations in the integral cross-section. Available methods for direct inversion of the cross-section data to recover the potential are reviewed in some detail. The theory of non-adiabatic transitions is introduced by a short discussion of interaction mechanisms and of diabetic and adiabatic representations. Analytical S matrix elements are presented for two state curve-crossing (Landau-Zener-Stuckelberg), Demkov and Nikitin models. The relation between Stuckelberg oscillations in the S matrix and in the differential cross-section is discussed in terms of interference between trajectories belonging to two different classical deflection functions. The energy dependences of the inelastic integral cross-section for curve-crossing and Demkov type transitions are also discussed. Finally the theory is reviewed in relation to a recent close-coupled study of fine structure transitions in F( 2 P) + Xe( 2 S) scattering

Atomic-scale structure of single-layer MoS2 nanoclusters

DEFF Research Database (Denmark)

Helveg, S.; Lauritsen, J. V.; Lægsgaard, E.

2000-01-01

We have studied using scanning tunneling microscopy (STM) the atomic-scale realm of molybdenum disulfide (MoS2) nanoclusters, which are of interest as a model system in hydrodesulfurization catalysis. The STM gives the first real space images of the shape and edge structure of single-layer MoS2...

Matrix Methods for Solving Hartree-Fock Equations in Atomic Structure Calculations and Line Broadening

Directory of Open Access Journals (Sweden)

Thomas Gomez

2018-04-01

Full Text Available Atomic structure of N-electron atoms is often determined by solving the Hartree-Fock equations, which are a set of integro-differential equations. The integral part of the Hartree-Fock equations treats electron exchange, but the Hartree-Fock equations are not often treated as an integro-differential equation. The exchange term is often approximated as an inhomogeneous or an effective potential so that the Hartree-Fock equations become a set of ordinary differential equations (which can be solved using the usual shooting methods. Because the Hartree-Fock equations are an iterative-refinement method, the inhomogeneous term relies on the previous guess of the wavefunction. In addition, there are numerical complications associated with solving inhomogeneous differential equations. This work uses matrix methods to solve the Hartree-Fock equations as an integro-differential equation. It is well known that a derivative operator can be expressed as a matrix made of finite-difference coefficients; energy eigenvalues and eigenvectors can be obtained by using linear-algebra packages. The integral (exchange part of the Hartree-Fock equation can be approximated as a sum and written as a matrix. The Hartree-Fock equations can be solved as a matrix that is the sum of the differential and integral matrices. We compare calculations using this method against experiment and standard atomic structure calculations. This matrix method can also be used to solve for free-electron wavefunctions, thus improving how the atoms and free electrons interact. This technique is important for spectral line broadening in two ways: it improves the atomic structure calculations, and it improves the motion of the plasma electrons that collide with the atom.

Raman spectroscopy as a tool to investigate the structure and electronic properties of carbon-atom wires

Directory of Open Access Journals (Sweden)

Alberto Milani

2015-02-01

Full Text Available Graphene, nanotubes and other carbon nanostructures have shown potential as candidates for advanced technological applications due to the different coordination of carbon atoms and to the possibility of π-conjugation. In this context, atomic-scale wires comprised of sp-hybridized carbon atoms represent ideal 1D systems to potentially downscale devices to the atomic level. Carbon-atom wires (CAWs can be arranged in two possible structures: a sequence of double bonds (cumulenes, resulting in a 1D metal, or an alternating sequence of single–triple bonds (polyynes, expected to show semiconducting properties. The electronic and optical properties of CAWs can be finely tuned by controlling the wire length (i.e., the number of carbon atoms and the type of termination (e.g., atom, molecular group or nanostructure. Although linear, sp-hybridized carbon systems are still considered elusive and unstable materials, a number of nanostructures consisting of sp-carbon wires have been produced and characterized to date. In this short review, we present the main CAW synthesis techniques and stabilization strategies and we discuss the current status of the understanding of their structural, electronic and vibrational properties with particular attention to how these properties are related to one another. We focus on the use of vibrational spectroscopy to provide information on the structural and electronic properties of the system (e.g., determination of wire length. Moreover, by employing Raman spectroscopy and surface enhanced Raman scattering in combination with the support of first principles calculations, we show that a detailed understanding of the charge transfer between CAWs and metal nanoparticles may open the possibility to tune the electronic structure from alternating to equalized bonds.

On the effect of atomic structure on the deactivation of catalytic gold nanoparticles

International Nuclear Information System (INIS)

Walsh, M J; Gai, P L; Boyes, E D

2012-01-01

Here we present atomic scale studies into the nature of both the internal structure and external surfaces of catalytic Au nanoparticles using aberration corrected in-situ electron microscopy. The activity of catalytic nanoparticles is thought to be highly sensitive to the particles' structure, meaning typical local atomic rearrangements are likely to significantly affect the overall performance of the catalyst. As-deposited Au nanoparticles are found to exhibit a variety of morphologies, with many being internally strained or highly stepped at the surface. Upon heating, surface atoms are observed to minimise the particles' surface energy by restructuring towards planar (111) facets, resulting in the removal of low co-ordinated sites thought to be crucial in catalysis by Au nanoparticles. These results suggest the process of surface energy minimisation made possible by heating may lead to a loss of active sites and consequently contribute to the deactivation of the catalyst.

The all-too-flexible abductive method: ATOM's normative status.

Science.gov (United States)

Romeijn, Jan-Willem

2008-09-01

The author discusses the abductive theory of method (ATOM) by Brian Haig from a philosophical perspective, connecting his theory with a number of issues and trends in contemporary philosophy of science. It is argued that as it stands, the methodology presented by Haig is too permissive. Both the use of analogical reasoning and the application of exploratory factor analysis leave us with too many candidate theories to choose from, and explanatory coherence cannot be expected to save the day. The author ends with some suggestions to remedy the permissiveness and lack of normative force in ATOM, deriving from the experimental practice within which psychological data are produced.

Atomic structure calculations on the CRAY X-MP

International Nuclear Information System (INIS)

Fischer, C.F.

1989-01-01

Atomic structure calculations require both radial and angular integrations, where the latter are often based on Racah algebra. With relatively minor modifications, good performance is obtained on vector machines for radial integrations. Angular integrations, however, present the bottleneck. In this paper some recent improvements in the algorithms for angular integrations are described, as well as some multitasking experiments on the CRAY X-MP and CRAY 2. These show that the workload can easily be distributed evenly among available processors with dynamic scheduling

Atom exchange between aqueous Fe(II) and structural Fe in clay minerals.

Science.gov (United States)

Neumann, Anke; Wu, Lingling; Li, Weiqiang; Beard, Brian L; Johnson, Clark M; Rosso, Kevin M; Frierdich, Andrew J; Scherer, Michelle M

2015-03-03

Due to their stability toward reductive dissolution, Fe-bearing clay minerals are viewed as a renewable source of Fe redox activity in diverse environments. Recent findings of interfacial electron transfer between aqueous Fe(II) and structural Fe in clay minerals and electron conduction in octahedral sheets of nontronite, however, raise the question whether Fe interaction with clay minerals is more dynamic than previously thought. Here, we use an enriched isotope tracer approach to simultaneously trace Fe atom movement from the aqueous phase to the solid ((57)Fe) and from the solid into the aqueous phase ((56)Fe). Over 6 months, we observed a significant decrease in aqueous (57)Fe isotope fraction, with a fast initial decrease which slowed after 3 days and stabilized after about 50 days. For the aqueous (56)Fe isotope fraction, we observed a similar but opposite trend, indicating that Fe atom movement had occurred in both directions: from the aqueous phase into the solid and from the solid into aqueous phase. We calculated that 5-20% of structural Fe in clay minerals NAu-1, NAu-2, and SWa-1 exchanged with aqueous Fe(II), which significantly exceeds the Fe atom layer exposed directly to solution. Calculations based on electron-hopping rates in nontronite suggest that the bulk conduction mechanism previously demonstrated for hematite1 and suggested as an explanation for the significant Fe atom exchange observed in goethite2 may be a plausible mechanism for Fe atom exchange in Fe-bearing clay minerals. Our finding of 5-20% Fe atom exchange in clay minerals indicates that we need to rethink how Fe mobility affects the macroscopic properties of Fe-bearing phyllosilicates and its role in Fe biogeochemical cycling, as well as its use in a variety of engineered applications, such as landfill liners and nuclear repositories.

Feature Extraction for Structural Dynamics Model Validation

Energy Technology Data Exchange (ETDEWEB)

Farrar, Charles [Los Alamos National Laboratory; Nishio, Mayuko [Yokohama University; Hemez, Francois [Los Alamos National Laboratory; Stull, Chris [Los Alamos National Laboratory; Park, Gyuhae [Chonnam Univesity; Cornwell, Phil [Rose-Hulman Institute of Technology; Figueiredo, Eloi [Universidade Lusófona; Luscher, D. J. [Los Alamos National Laboratory; Worden, Keith [University of Sheffield

2016-01-13

As structural dynamics becomes increasingly non-modal, stochastic and nonlinear, finite element model-updating technology must adopt the broader notions of model validation and uncertainty quantification. For example, particular re-sampling procedures must be implemented to propagate uncertainty through a forward calculation, and non-modal features must be defined to analyze nonlinear data sets. The latter topic is the focus of this report, but first, some more general comments regarding the concept of model validation will be discussed.

Contribution to viscosity from the structural relaxation via the atomic scale Green-Kubo stress correlation function

Science.gov (United States)

Levashov, V. A.

2017-11-01

We studied the connection between the structural relaxation and viscosity for a binary model of repulsive particles in the supercooled liquid regime. The used approach is based on the decomposition of the macroscopic Green-Kubo stress correlation function into the correlation functions between the atomic level stresses. Previously we used the approach to study an iron-like single component system of particles. The role of vibrational motion has been addressed through the demonstration of the relationship between viscosity and the shear waves propagating over large distances. In our previous considerations, however, we did not discuss the role of the structural relaxation. Here we suggest that the contribution to viscosity from the structural relaxation can be taken into account through the consideration of the contribution from the atomic stress auto-correlation term only. This conclusion, however, does not mean that only the auto-correlation term represents the contribution to viscosity from the structural relaxation. Previously the role of the structural relaxation for viscosity has been addressed through the considerations of the transitions between inherent structures and within the mode-coupling theory by other authors. In the present work, we study the structural relaxation through the considerations of the parent liquid and the atomic level stress correlations in it. The comparison with the results obtained on the inherent structures also is made. Our current results suggest, as our previous observations, that in the supercooled liquid regime, the vibrational contribution to viscosity extends over the times that are much larger than the Einstein's vibrational period and much larger than the times that it takes for the shear waves to propagate over the model systems. Besides addressing the atomic level shear stress correlations, we also studied correlations between the atomic level pressure elements.

The local atomic quasicrystal structure of the icosahedral Mg25Y11Zn64 alloy

International Nuclear Information System (INIS)

Bruehne, S; Uhrig, E; Gross, C; Assmus, W; Masadeh, A S; Billinge, S J L

2005-01-01

A local and medium range atomic structure model for the face centred icosahedral (fci) Mg 25 Y 11 Zn 64 alloy has been established in a sphere of r = 27 A. The model was refined by least squares techniques using the atomic pair distribution (PDF) function obtained from synchrotron powder diffraction. Three hierarchies of the atomic arrangement can be found: (i) five types of local coordination polyhedra for the single atoms, four of which are of Frank-Kasper type. In turn, they (ii) form a three-shell (Bergman) cluster containing 104 atoms, which is condensed sharing its outer shell with its neighbouring clusters, and (iii) a cluster connecting scheme corresponding to a three-dimensional tiling leaving space for a few glue atoms. Inside adjacent clusters, Y 8 cubes are tilted with respect to each other and thus allow for overall icosahedral symmetry. It is shown that the title compound is essentially isomorphic to its holmium analogue. Therefore, fci-Mg-Y-Zn can be seen as the representative structure type for the other rare earth analogues fci-Mg-Zn-RE (RE = Dy, Er, Ho, Tb) reported in the literature

Fluorescence detection of white-beam X-ray absorption anisotropy: towards element-sensitive projections of local atomic structure

Science.gov (United States)

Korecki, P.; Tolkiehn, M.; Dąbrowski, K. M.; Novikov, D. V.

2011-01-01

Projections of the atomic structure around Nb atoms in a LiNbO3 single crystal were obtained from a white-beam X-ray absorption anisotropy (XAA) pattern detected using Nb K fluorescence. This kind of anisotropy results from the interference of X-rays inside a sample and, owing to the short coherence length of a white beam, is visible only at small angles around interatomic directions. Consequently, the main features of the recorded XAA corresponded to distorted real-space projections of dense-packed atomic planes and atomic rows. A quantitative analysis of XAA was carried out using a wavelet transform and allowed well resolved projections of Nb atoms to be obtained up to distances of 10 Å. The signal of nearest O atoms was detected indirectly by a comparison with model calculations. The measurement of white-beam XAA using characteristic radiation indicates the possibility of obtaining element-sensitive projections of the local atomic structure in more complex samples. PMID:21997909

NMR structure calculation for all small molecule ligands and non-standard residues from the PDB Chemical Component Dictionary

Energy Technology Data Exchange (ETDEWEB)

Yilmaz, Emel Maden; Güntert, Peter, E-mail: guentert@em.uni-frankfurt.de [Goethe University Frankfurt am Main, Center for Biomolecular Magnetic Resonance, Institute of Biophysical Chemistry (Germany)

2015-09-15

An algorithm, CYLIB, is presented for converting molecular topology descriptions from the PDB Chemical Component Dictionary into CYANA residue library entries. The CYANA structure calculation algorithm uses torsion angle molecular dynamics for the efficient computation of three-dimensional structures from NMR-derived restraints. For this, the molecules have to be represented in torsion angle space with rotations around covalent single bonds as the only degrees of freedom. The molecule must be given a tree structure of torsion angles connecting rigid units composed of one or several atoms with fixed relative positions. Setting up CYANA residue library entries therefore involves, besides straightforward format conversion, the non-trivial step of defining a suitable tree structure of torsion angles, and to re-order the atoms in a way that is compatible with this tree structure. This can be done manually for small numbers of ligands but the process is time-consuming and error-prone. An automated method is necessary in order to handle the large number of different potential ligand molecules to be studied in drug design projects. Here, we present an algorithm for this purpose, and show that CYANA structure calculations can be performed with almost all small molecule ligands and non-standard amino acid residues in the PDB Chemical Component Dictionary.

Atomic imaging of an InSe single-crystal surface with atomic force microscope

OpenAIRE

Uosaki, Kohei; Koinuma, Michio

1993-01-01

The atomic force microscope was employed to observed in air the surface atomic structure of InSe, one of III-VI compound semiconductors with layered structures. Atomic arrangements were observed in both n-type and p-type materials. The observed structures are in good agreement with those expected from bulk crystal structures. The atomic images became less clear by repeating the imaging process. Wide area imaging after the imaging of small area clearly showed that a mound was created at the sp...

Simulation of the Atomic and Electronic Structure of Oxygen Vacancies and Polyvacancies in ZrO2

Science.gov (United States)

Perevalov, T. V.

2018-03-01

Cubic, tetragonal, and monoclinic phases of zirconium oxide with oxygen vacancies and polyvacancies are studied by quantum chemical modeling of the atomic and electronic structure. It is demonstrated that an oxygen vacancy in ZrO2 may act as both an electron trap and a hole one. An electron added to the ZrO2 structure with an oxygen vacancy is distributed between two neighboring Zr atoms and is a bonding orbital by nature. It is advantageous for each subsequent O vacancy to form close to the already existing ones; notably, one Zr atom has no more than two removed O atoms related to it. Defect levels from oxygen polyvacancies are distributed in the bandgap with preferential localization in the vicinity of the oxygen monovacancy level.

Sub-Angstrom Atomic-Resolution Imaging of Heavy Atoms to Light Atoms

Energy Technology Data Exchange (ETDEWEB)

O' Keefe, Michael A.; Shao-Horn, Yang

2003-05-23

Three decades ago John Cowley and his group at ASU achieved high-resolution electron microscope images showing the crystal unit cell contents at better than 4Angstrom resolution. Over the years, this achievement has inspired improvements in resolution that have enabled researchers to pinpoint the positions of heavy atom columns within the cell. More recently, this ability has been extended to light atoms as resolution has improved. Sub-Angstrom resolution has enabled researchers to image the columns of light atoms (carbon, oxygen and nitrogen) that are present in many complex structures. By using sub-Angstrom focal-series reconstruction of the specimen exit surface wave to image columns of cobalt, oxygen, and lithium atoms in a transition metal oxide structure commonly used as positive electrodes in lithium rechargeable batteries, we show that the range of detectable light atoms extends to lithium. HRTEM at sub-Angstrom resolution will provide the essential role of experimental verification for the emergent nanotech revolution. Our results foreshadow those to be expected from next-generation TEMs with Cs-corrected lenses and monochromated electron beams.

Li-atoms-induced structure changes of Guinier–Preston–Bagaryatsky zones in AlCuLiMg alloys

Energy Technology Data Exchange (ETDEWEB)

Duan, S.Y.; Le, Z.; Chen, Z.K.; Gao, Z. [Center for High-Resolution Electron Microscopy, College of Materials Science and Engineering, Hunan University, Changsha, Hunan 410082 (China); Chen, J.H., E-mail: jhchen123@hnu.edu.cn [Center for High-Resolution Electron Microscopy, College of Materials Science and Engineering, Hunan University, Changsha, Hunan 410082 (China); Advanced Research Center, Central South University, Changsha 410083 (China); Ming, W.Q.; Li, S.Y.; Wu, C.L. [Center for High-Resolution Electron Microscopy, College of Materials Science and Engineering, Hunan University, Changsha, Hunan 410082 (China); Yan, N. [Advanced Research Center, Central South University, Changsha 410083 (China)

2016-11-15

Guinier–Preston–Bagaryatsky (GPB) zones are the well-known strengthening precipitates of AlCuMg alloys formed upon thermal ageing. Here we report that when formed in AlCuLiMg alloys the GPB zones can change significantly in morphology and structure. It is shown that though they do still consist of Al, Cu and Mg elements fundamentally, the GPB zones in AlCuLiMg alloys have a rather different structure due to a featured Li-segregation at their interfaces with the matrix and possible Li-replacement of partial Mg atoms in the structure. As such the Li-containing GPB zones often develop from one-dimensional to quasi-two-dimensional precipitates. - Highlights: • We observe Guinier–Preston–Bagaryatsky zone variants in AlCuLiMg alloys. • We obtain atomic-resolution images of the precipitates and model their structures. • Li-atoms play a key role in modifying the structure of these precipitate variants.

Construction of the energy matrix for complex atoms. Part VIII: Hyperfine structure HPC calculations for terbium atom

Science.gov (United States)

Elantkowska, Magdalena; Ruczkowski, Jarosław; Sikorski, Andrzej; Dembczyński, Jerzy

2017-11-01

A parametric analysis of the hyperfine structure (hfs) for the even parity configurations of atomic terbium (Tb I) is presented in this work. We introduce the complete set of 4fN-core states in our high-performance computing (HPC) calculations. For calculations of the huge hyperfine structure matrix, requiring approximately 5000 hours when run on a single CPU, we propose the methods utilizing a personal computer cluster or, alternatively a cluster of Microsoft Azure virtual machines (VM). These methods give a factor 12 performance boost, enabling the calculations to complete in an acceptable time.

Ab initio random structure search for 13-atom clusters of fcc elements

International Nuclear Information System (INIS)

Chou, J P; Hsing, C R; Wei, C M; Cheng, C; Chang, C M

2013-01-01

The 13-atom metal clusters of fcc elements (Al, Rh, Ir, Ni, Pd, Pt, Cu, Ag, Au) were studied by density functional theory calculations. The global minima were searched for by the ab initio random structure searching method. In addition to some new lowest-energy structures for Pd 13 and Au 13 , we found that the effective coordination numbers of the lowest-energy clusters would increase with the ratio of the dimer-to-bulk bond length. This correlation, together with the electronic structures of the lowest-energy clusters, divides the 13-atom clusters of these fcc elements into two groups (except for Au 13 , which prefers a two-dimensional structure due to the relativistic effect). Compact-like clusters that are composed exclusively of triangular motifs are preferred for elements without d-electrons (Al) or with (nearly) filled d-band electrons (Ni, Pd, Cu, Ag). Non-compact clusters composed mainly of square motifs connected by some triangular motifs (Rh, Ir, Pt) are favored for elements with unfilled d-band electrons. (paper)

Atoms

International Nuclear Information System (INIS)

Fuchs, Alain; Villani, Cedric; Guthleben, Denis; Leduc, Michele; Brenner, Anastasios; Pouthas, Joel; Perrin, Jean

2014-01-01

Completed by recent contributions on various topics (atoms and the Brownian motion, the career of Jean Perrin, the evolution of atomic physics since Jean Perrin, relationship between scientific atomism and philosophical atomism), this book is a reprint of a book published at the beginning of the twentieth century in which the author addressed the relationship between atomic theory and chemistry (molecules, atoms, the Avogadro hypothesis, molecule structures, solutes, upper limits of molecular quantities), molecular agitation (molecule velocity, molecule rotation or vibration, molecular free range), the Brownian motion and emulsions (history and general features, statistical equilibrium of emulsions), the laws of the Brownian motion (Einstein's theory, experimental control), fluctuations (the theory of Smoluchowski), light and quanta (black body, extension of quantum theory), the electricity atom, the atom genesis and destruction (transmutations, atom counting)

All solid-state polymer electrolytes prepared from a hyper-branched graft polymer using atom transfer radical polymerization

International Nuclear Information System (INIS)

Higa, Mitsuru; Fujino, Yukiko; Koumoto, Taihei; Kitani, Ryousuke; Egashira, Satsuki

2005-01-01

We propose an all solid-state (liquid free) polymer electrolyte (SPE) prepared from a hyper-branched graft copolymer. The graft copolymer consisting of a poly(methyl methacrylate) main chain and poly(ethylene glycol) methyl ether methacrylate side chains was synthesized by atom transfer radical polymerization changing the average chain distance between side chains, side chain length and branched chain length of the proposed structure of the graft copolymer. The ionic conductivity of the SPEs increases with increasing the side chain length, branched chain length and/or average distance between the side chains. The ionic conductivity of the SPE prepared from POEM 9 whose POEM content = 51 wt% shows 2 x 10 -5 S/cm at 30 deg. C. The tensile strength of the SPEs decreases with increases the side chain length, branched chain length and/or average distance between the side chains. These results indicate that a SPE prepared from the hyper-branched graft copolymer has potential to be applied to an all-solid polymer electrolyte

Atomic physics

CERN Document Server

Born, Max

1969-01-01

The Nobel Laureate's brilliant exposition of the kinetic theory of gases, elementary particles, the nuclear atom, wave-corpuscles, atomic structure and spectral lines, electron spin and Pauli's principle, quantum statistics, molecular structure and nuclear physics. Over 40 appendices, a bibliography, numerous figures and graphs.

Structure of ordered polyelectrolyte films from atomic-force microscopy and X-ray reflectivity data

International Nuclear Information System (INIS)

Belyaev, V.V.; Tolstikhina, A.L.; Stepina, N.D.; Kayushina, R.L.

1998-01-01

The possible application of atomic-force microscopy and X-ray reflectometry methods to structural studies of polyelectrolyte films obtained due to alternating adsorption of oppositely charged polyanion [sodium polysterenesulfonate (PSS)] and polycation [poly(allylamine) hydrochloride (PAA)] layers on solid substrates has been considered. The atomic-force microscopy study has revealed the characteristic features of the surface topography of samples consisting of different numbers of polyelectrolyte layers deposited from solutions characterized by different ionic strength values. It is shown that the shape of the reflectivity curves obtained from thin polyelectrolyte films depends on their surface structure

Prospects of linear reconstruction in atomic resolution electron holographic tomography

International Nuclear Information System (INIS)

Krehl, Jonas; Lubk, Axel

2015-01-01

Tomography commonly requires a linear relation between the measured signal and the underlying specimen property; for Electron Holographic Tomography this is given by the Phase Grating Approximation (PGA). While largely valid at medium resolution, discrepancies arise at high resolution imaging conditions. We set out to investigate the artefacts that are produced if the reconstruction still assumes the PGA even with an atomic resolution tilt series. To forego experimental difficulties the holographic tilt series was simulated. The reconstructed electric potential clearly shows peaks at the positions of the atoms. These peaks have characterisitic deformations, which can be traced back to the defocus a particular atom has in the holograms of the tilt series. Exchanging an atom for one of a different atomic number results in a significant change in the reconstructed potential that is well contained within the atom's peak. - Highlights: • We simulate a holographic tilt series of a nanocrystal with atomic resolution. • Using PGA-based Holographic Tomography we reconstruct the atomic structure. • The reconstruction shows characteristic artefacts, chiefly caused by defocus. • Changing one atom's Z produces a well localised in the reconstruction

Prospects of linear reconstruction in atomic resolution electron holographic tomography

Energy Technology Data Exchange (ETDEWEB)

Krehl, Jonas, E-mail: Jonas.Krehl@triebenberg.de; Lubk, Axel

2015-03-15

Tomography commonly requires a linear relation between the measured signal and the underlying specimen property; for Electron Holographic Tomography this is given by the Phase Grating Approximation (PGA). While largely valid at medium resolution, discrepancies arise at high resolution imaging conditions. We set out to investigate the artefacts that are produced if the reconstruction still assumes the PGA even with an atomic resolution tilt series. To forego experimental difficulties the holographic tilt series was simulated. The reconstructed electric potential clearly shows peaks at the positions of the atoms. These peaks have characterisitic deformations, which can be traced back to the defocus a particular atom has in the holograms of the tilt series. Exchanging an atom for one of a different atomic number results in a significant change in the reconstructed potential that is well contained within the atom's peak. - Highlights: • We simulate a holographic tilt series of a nanocrystal with atomic resolution. • Using PGA-based Holographic Tomography we reconstruct the atomic structure. • The reconstruction shows characteristic artefacts, chiefly caused by defocus. • Changing one atom's Z produces a well localised in the reconstruction.

Hybrid inorganic–organic superlattice structures with atomic layer deposition/molecular layer deposition

Energy Technology Data Exchange (ETDEWEB)

Tynell, Tommi; Yamauchi, Hisao; Karppinen, Maarit, E-mail: maarit.karppinen@aalto.fi [Department of Chemistry, Aalto University, FI-00076 Aalto (Finland)

2014-01-15

A combination of the atomic layer deposition (ALD) and molecular layer deposition (MLD) techniques is successfully employed to fabricate thin films incorporating superlattice structures that consist of single layers of organic molecules between thicker layers of ZnO. Diethyl zinc and water are used as precursors for the deposition of ZnO by ALD, while three different organic precursors are investigated for the MLD part: hydroquinone, 4-aminophenol and 4,4′-oxydianiline. The successful superlattice formation with all the organic precursors is verified through x-ray reflectivity studies. The effects of the interspersed organic layers/superlattice structure on the electrical and thermoelectric properties of ZnO are investigated through resistivity and Seebeck coefficient measurements at room temperature. The results suggest an increase in carrier concentration for small concentrations of organic layers, while higher concentrations seem to lead to rather large reductions in carrier concentration.

Visualization and automatic detection of defect distribution in GaN atomic structure from sampling Moiré phase.

Science.gov (United States)

Wang, Qinghua; Ri, Shien; Tsuda, Hiroshi; Kodera, Masako; Suguro, Kyoichi; Miyashita, Naoto

2017-09-19

Quantitative detection of defects in atomic structures is of great significance to evaluating product quality and exploring quality improvement process. In this study, a Fourier transform filtered sampling Moire technique was proposed to visualize and detect defects in atomic arrays in a large field of view. Defect distributions, defect numbers and defect densities could be visually and quantitatively determined from a single atomic structure image at low cost. The effectiveness of the proposed technique was verified from numerical simulations. As an application, the dislocation distributions in a GaN/AlGaN atomic structure in two directions were magnified and displayed in Moire phase maps, and defect locations and densities were detected automatically. The proposed technique is able to provide valuable references to material scientists and engineers by checking the effect of various treatments for defect reduction. © 2017 IOP Publishing Ltd.

AtomPy: an open atomic-data curation environment

Science.gov (United States)

Bautista, Manuel; Mendoza, Claudio; Boswell, Josiah S; Ajoku, Chukwuemeka

2014-06-01

We present a cloud-computing environment for atomic data curation, networking among atomic data providers and users, teaching-and-learning, and interfacing with spectral modeling software. The system is based on Google-Drive Sheets, Pandas (Python Data Analysis Library) DataFrames, and IPython Notebooks for open community-driven curation of atomic data for scientific and technological applications. The atomic model for each ionic species is contained in a multi-sheet Google-Drive workbook, where the atomic parameters from all known public sources are progressively stored. Metadata (provenance, community discussion, etc.) accompanying every entry in the database are stored through Notebooks. Education tools on the physics of atomic processes as well as their relevance to plasma and spectral modeling are based on IPython Notebooks that integrate written material, images, videos, and active computer-tool workflows. Data processing workflows and collaborative software developments are encouraged and managed through the GitHub social network. Relevant issues this platform intends to address are: (i) data quality by allowing open access to both data producers and users in order to attain completeness, accuracy, consistency, provenance and currentness; (ii) comparisons of different datasets to facilitate accuracy assessment; (iii) downloading to local data structures (i.e. Pandas DataFrames) for further manipulation and analysis by prospective users; and (iv) data preservation by avoiding the discard of outdated sets.

All Validity Is Construct Validity. Or Is It?

Science.gov (United States)

Kane, Michael

2012-01-01

Paul E. Newton's article on the consensus definition of validity tackles a number of big issues and makes a number of strong claims. I agreed with much of what he said, and I disagreed with a number of his claims, but I found his article to be consistently interesting and thought provoking (whether I agreed or not). I will focus on three general…

Atomic-scale structure of irradiated GaN compared to amorphised GaP and GaAs

International Nuclear Information System (INIS)

Ridgway, M.C.; Everett, S.E.; Glover, C.J.; Kluth, S.M.; Kluth, P.; Johannessen, B.; Hussain, Z.S.; Llewellyn, D.J.; Foran, G.J.; Azevedo, G. de M.

2006-01-01

We have compared the atomic-scale structure of ion irradiated GaN to that of amorphised GaP and GaAs. While continuous and homogenous amorphised layers were easily achieved in GaP and GaAs, ion irradiation of GaN yielded both structural and chemical inhomogeneities. Transmission electron microscopy revealed GaN crystallites and N 2 bubbles were interspersed within an amorphous GaN matrix. The crystallite orientation was random relative to the unirradiated epitaxial structure, suggesting their formation was irradiation-induced, while the crystallite fraction was approximately constant for all ion fluences beyond the amorphisation threshold, consistent with a balance between amorphisation and recrystallisation processes. Extended X-ray absorption fine structure measurements at the Ga K-edge showed short-range order was retained in the amorphous phase for all three binary compounds. For ion irradiated GaN, the stoichiometric imbalance due to N 2 bubble formation was not accommodated by Ga-Ga bonding in the amorphous phase or precipitation of metallic Ga but instead by a greater reduction in Ga coordination number

Atomic probes of surface structure and dynamics

International Nuclear Information System (INIS)

Heller, E.J.; Jonsson, H.

1992-01-01

The following were studied: New semiclassical method for scattering calculations, He atom scattering from defective Pt surfaces, He atom scattering from Xe overlayers, thermal dissociation of H 2 on Cu(110), spin flip scattering of atoms from surfaces, and Car-Parrinello simulations of surface processes

Development of a microlesson in teaching energy levels of atoms

Science.gov (United States)

Rodriguez, Cherilyn A.; Buan, Amelia T.

2018-01-01

Energy levels of atoms is one of the difficult topics in understanding atomic structure of matter. It appears tobe abstract, theoretical and needs visual representation and images. Hence, in this study a microlesson in teaching the high school chemistry concept on the energy levels of atoms is developed and validated. The researchers utilized backward curriculum design in planning the microlesson to meet the standards of the science K-12 curriculum. The planning process of the microlesson involved a) Identifying the learning competencies in K-12 science curriculum b) write learning objectives c) planning of assessment tools d) making a storyboard e) designing the microlesson and validate and revise the microlesson. The microlesson made use of varied resources in the internet from which the students accessed and collected information about energy levels of atoms. Working in groups, the students synthesized the information on how and why fireworks produce various colors of light through a post card. Findings of the study showed that there was an increase of achievement in learning the content and the students were highly motivated to learn chemistry. Furthermore, the students perceived that the microlesson helped them to understand the chemistry concept through the use of appropriate multimedia activities.

Validation of missed space-group symmetry in X-ray powder diffraction structures with dispersion-corrected density functional theory.

Science.gov (United States)

Hempler, Daniela; Schmidt, Martin U; van de Streek, Jacco

2017-08-01

More than 600 molecular crystal structures with correct, incorrect and uncertain space-group symmetry were energy-minimized with dispersion-corrected density functional theory (DFT-D, PBE-D3). For the purpose of determining the correct space-group symmetry the required tolerance on the atomic coordinates of all non-H atoms is established to be 0.2 Å. For 98.5% of 200 molecular crystal structures published with missed symmetry, the correct space group is identified; there are no false positives. Very small, very symmetrical molecules can end up in artificially high space groups upon energy minimization, although this is easily detected through visual inspection. If the space group of a crystal structure determined from powder diffraction data is ambiguous, energy minimization with DFT-D provides a fast and reliable method to select the correct space group.

Chemical Structure and Properties: A Modified Atoms-First, One-Semester Introductory Chemistry Course

Science.gov (United States)

Schaller, Chris P.; Graham, Kate J.; Johnson, Brian J.; Jakubowski, Henry V.; McKenna, Anna G.; McIntee, Edward J.; Jones, T. Nicholas; Fazal, M. A.; Peterson, Alicia A.

2015-01-01

A one-semester, introductory chemistry course is described that develops a primarily qualitative understanding of structure-property relationships. Starting from an atoms-first approach, the course examines the properties and three-dimensional structure of metallic and ionic solids before expanding into a thorough investigation of molecules. In…

Local atomic and crystal structure rearrangement during the martensitic transformation in Ti50Ni25Cu25 shape memory alloy

International Nuclear Information System (INIS)

Menushenkov, Alexey; Grishina, Olga; Shelyakov, Alexander; Yaroslavtsev, Alexander; Zubavichus, Yan; Veligzhanin, Alexey; Bednarcik, Jozef; Chernikov, Roman; Sitnikov, Nikolay

2014-01-01

Highlights: • Local crystalline structure of TiNiCu SMA is investigated using EXAFS. • Peculiarities of Ni and Cu local environment are found. • Ti atoms show greater mobility relative to Ni atoms. • Ni local environment change is significant for shape memory effect. -- Abstract: The changes of crystal structure and local crystalline environment of Ti, Ni and Cu atoms in Ti 50 Ni 25 Cu 25 shape memory alloy are investigated using X-ray diffraction and extended X-ray absorption fine structure spectroscopy (EXAFS) in temperature range of martensite transformation. The analysis of the EXAFS-spectra shows that the bonds involving Ni atoms have the highest degree of disorder and the change in the local environment around Ni atoms is significant for the occurrence of the shape memory effect, while Cu atoms occupy the normal positions in the crystallographic structure and have the lowest displacement amplitude leading to the stabilization of both phases

Structure formation in atom lithography using geometric collimation

NARCIS (Netherlands)

Meijer, T.; Beardmore, J.P.; Fabrie, C.G.C.H.M.; van Lieshout, J.P.; Notermans, R.P.M.J.W.; Sang, R.T.; Vredenbregt, E.J.D.; Leeuwen, van K.A.H.

2011-01-01

Atom lithography uses standing wave light fields as arrays of lenses to focus neutral atom beams into line patterns on a substrate. Laser cooled atom beams are commonly used, but an atom beam source with a small opening placed at a large distance from a substrate creates atom beams which are locally

Non-Markovian decay of a three-level cascade atom in a structured reservoir

International Nuclear Information System (INIS)

Dalton, B.J.; Garraway, B.M.

2003-01-01

The dynamics of a three-level atom in a cascade (or ladder) configuration with both transitions coupled to a single structured reservoir of quantized electromagnetic field modes is treated using Laplace transform methods applied to the coupled amplitude equations. In this system two-photon excitation of the reservoir occurs, and both sequences for emitting the two photons are allowed and included in the theory. An integral equation is found to govern the complex amplitudes of interest. It is shown that the dynamics of the atomic system is completely determined in terms of reservoir structure functions, which are products of the mode density with the coupling constant squared. This dependence on reservoir structure functions rather than on the mode density or coupling constants alone, shows that it may be possible to extend pseudomode theory to treat multiphoton excitation of a structured reservoir--pseudomodes being introduced in one-one correspondence with the poles of reservoir structure functions in the complex frequency plane. A general numerical method for solving the integral equations based on discretizing frequency space, and applicable to different structured reservoirs such as high-Q cavities and photonic band-gap systems, is presented. An application to a high-Q-cavity case with identical Lorentzian reservoir structure functions is made, and the non-Markovian decay of the excited state shown. A formal solution to the integral equations in terms of right and left eigenfunctions of a non-Hermitian kernel is also given. The dynamics of the cascade atom, with the two transitions coupled to two separate structured reservoirs of quantized electromagnetic field modes, is treated similarly to the single structured reservoir situation. Again the dynamics only depends on reservoir structure functions. As only one sequence of emitting the two photons now occurs, the integral equation for the amplitudes can be solved analytically. The non-Markovian decay of the

Atomic level structural modulation during the structural relaxation and its effect on magnetic properties of Fe81Si4B10P4Cu1 nanocrystalline alloy

Science.gov (United States)

Cao, C. C.; Zhu, L.; Meng, Y.; Zhai, X. B.; Wang, Y. G.

2018-06-01

The evolution of local structure and defects in the Fe81Si4B10P4Cu1 amorphous alloy during the structural relaxation has been investigated by Mössbauer spectroscopy, positron annihilation lifetime spectroscopy and transmission electron microscopy to explore their effects on magnetic properties of the nanocrystalline. The atomic rearrangements at the early stage of the structural relaxation cause the density increase of the amorphous matrix, but the subsequent atomic rearrangements contribute to the transformation of Fe3B-like atomic arrangements to FeB-like ones with the temperature increasing. As the structural relaxation processes, the released Fe atoms both from Fe3B- and Fe3P-like atomic arrangements result in the formation of new Fe clusters and the increase of Fe-Fe coordination number in the existing Fe clusters and the nucleation sites for α-Fe gradually increase, both of which promote the crystallization. However, the homogeneity of amorphous matrix will be finally destroyed under excessive relaxation temperature, which coarsens nanograins during the crystallization instead. Therefore, soft magnetic properties of the Fe81Si4B10P4Cu1 nanocrystalline alloy can be improved by pre-annealing the amorphous precursor at an appropriate temperature due to the atomic level structural optimization.

Autoionizing states of atoms calculated using generalized sturmians

DEFF Research Database (Denmark)

Avery, James Emil; Avery, John Scales

2005-01-01

The generalized Sturmian method is applied to autoionizing states of atoms and ions. If the Goscinskian basis sets allow for a sufficient amount of angular correletion, the calculated energies of doubly-excited (autoionizing) states are found to agree well with the few available experimental...... energies. A large-Z approximation is discussed, and simple formulas are derived which are valid not only for autoionizing states, but for all states of an isoelectronic atomic series. Diagonalization of a small block of the interelectron repulsion matrix yields roots that can be used for a wide range of Z...

Structure of the Balmer jump. The isolated hydrogen atom

Science.gov (United States)

Calvo, F.; Belluzzi, L.; Steiner, O.

2018-06-01

Context. The spectrum of the hydrogen atom was explained by Bohr more than one century ago. We revisit here some of the aspects of the underlying quantum structure, with a modern formalism, focusing on the limit of the Balmer series. Aims: We investigate the behaviour of the absorption coefficient of the isolated hydrogen atom in the neighbourhood of the Balmer limit. Methods: We analytically computed the total cross-section arising from bound-bound and bound-free transitions in the isolated hydrogen atom at the Balmer limit, and established a simplified semi-analytical model for the surroundings of that limit. We worked within the framework of the formalism of Landi Degl'Innocenti & Landolfi (2004, Astrophys. Space Sci. Lib., 307), which permits an almost straight-forward generalization of our results to other atoms and molecules, and which is perfectly suitable for including polarization phenomena in the problem. Results: We analytically show that there is no discontinuity at the Balmer limit, even though the concept of a "Balmer jump" is still meaningful. Furthermore, we give a possible definition of the location of the Balmer jump, and we check that this location is dependent on the broadening mechanisms. At the Balmer limit, we compute the cross-section in a fully analytical way. Conclusions: The Balmer jump is produced by a rapid drop of the total Balmer cross-section, yet this variation is smooth and continuous when both bound-bound and bound-free processes are taken into account, and its shape and location is dependent on the broadening mechanisms.

Forging Fast Ion Conducting Nanochannels with Swift Heavy Ions: The Correlated Role of Local Electronic and Atomic Structure

Energy Technology Data Exchange (ETDEWEB)

Sachan, Ritesh [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States). Material Science and Technology Division; Cooper, Valentino R. [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States). Material Science and Technology Division; Liu, Bin [Univ. of Tennessee, Knoxville, TN (United States). Dept. of Materials Science and Engineering; Aidhy, Dilpuneet S. [Univ. of Wyoming, Laramie, WY (United States). Dept. of Mechanical Engineering; Voas, Brian K. [Iowa State Univ., Ames, IA (United States). Dept. of Materials Science and Engineering; Lang, Maik [Univ. of Tennessee, Knoxville, TN (United States). Dept. of Nuclear Engineering; Ou, Xin [Chinese Academy of Sciences (CAS), Shanghai (China). State Key Lab. of Functional Material for Informatics; Trautmann, Christina [GSI Helmholtz Centre for Heavy Ion Research, Darmstadt (Germany); Technical Univ. of Darmstadt (Germany). Dept. of Materials Science; Zhang, Yanwen [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States). Material Science and Technology Division; Univ. of Tennessee, Knoxville, TN (United States). Dept. of Materials Science and Engineering; Chisholm, Matthew F. [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States). Material Science and Technology Division; Weber, William J. [Univ. of Tennessee, Knoxville, TN (United States). Dept. of Materials Science and Engineering; Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States). Material Science and Technology Division

2016-12-19

Atomically disordered oxides have attracted significant attention in recent years due to the possibility of enhanced ionic conductivity. However, the correlation between atomic disorder, corresponding electronic structure, and the resulting oxygen diffusivity is not well understood. The disordered variants of the ordered pyrochlore structure in gadolinium titanate (Gd₂Ti₂O₇) are seen as a particularly interesting prospect due to intrinsic presence of a vacant oxygen site in the unit atomic structure, which could provide a channel for fast oxygen conduction. In this paper, we provide insights into the subangstrom scale on the disordering-induced variations in the local atomic environment and its effect on the electronic structure in high-energy ion irradiation-induced disordered nanochannels, which can be utilized as pathways for fast oxygen ion transport. With the help of an atomic plane-by-plane-resolved analyses, the work shows how the presence of various types of TiO_x polyhedral that exist in the amorphous and disordered crystalline phase modify the electronic structures relative to the ordered pyrochlore phase in Gd₂Ti₂O₇. Finally, the correlated molecular dynamics simulations on the disordered structures show a remarkable enhancement in oxygen diffusivity as compared with ordered pyrochlore lattice and make that a suitable candidate for applications requiring fast oxygen conduction.

Fine structure and analytical quantum-defect wave functions

International Nuclear Information System (INIS)

Kostelecky, V.A.; Nieto, M.M.; Truax, D.R.

1988-01-01

We investigate the domain of validity of previously proposed analytical wave functions for atomic quantum-defect theory. This is done by considering the fine-structure splitting of alkali-metal and singly ionized alkaline-earth atoms. The Lande formula is found to be naturally incorporated. A supersymmetric-type integer is necessary for finite results. Calculated splittings correctly reproduce the principal features of experimental values for alkali-like atoms

Study of atomic and condensed atomic indices for reactive sites of ...

Indian Academy of Sciences (India)

Unknown

function indices in the framework of the AIM method of Bader.15 The atomic and group ... P Kolandaivel et al. 592. FF values. One of the reasons, they have argued, is that according to the analytic definition of FF it is valid only when ∆N → 0. In that case, the fluctuation in ..... In their work, they have concluded that the N atom ...

Local Atomic Structure and Discommensurations in the Charge Density Wave of CeTe3

International Nuclear Information System (INIS)

Kim, H.J.; Tomic, A.T.; Tessmer, S.H.; Billinge, S.J.L.; Malliakas, C.D.; Kanatzidis, M.G.

2006-01-01

The local structure of CeTe 3 in the incommensurate charge density wave (IC-CDW) state has been obtained using atomic pair distribution function analysis of x-ray diffraction data. Local atomic distortions in the Te nets due to the CDW are larger than observed crystallographically, resulting in distinct short and long Te-Te bonds. Observation of different distortion amplitudes in the local and average structures is explained by the discommensurated nature of the CDW, since the pair distribution function is sensitive to the local displacements within the commensurate regions, whereas the crystallographic result averages over many discommensurated domains. The result is supported by STM data. This is the first quantitative local structural study within the commensurate domains in an IC-CDW system

Local atomic structure of Fe/Cr multilayers: Depth-resolved method

Science.gov (United States)

Babanov, Yu. A.; Ponomarev, D. A.; Devyaterikov, D. I.; Salamatov, Yu. A.; Romashev, L. N.; Ustinov, V. V.; Vasin, V. V.; Ageev, A. L.

2017-10-01

A depth-resolved method for the investigation of the local atomic structure by combining data of X-ray reflectivity and angle-resolved EXAFS is proposed. The solution of the problem can be divided into three stages: 1) determination of the element concentration profile with the depth z from X-ray reflectivity data, 2) determination of the X-ray fluorescence emission spectrum of the element i absorption coefficient μia (z,E) as a function of depth and photon energy E using the angle-resolved EXAFS data Iif (E , ϑl) , 3) determination of partial correlation functions gij (z , r) as a function of depth from μi (z , E) . All stages of the proposed method are demonstrated on a model example of a multilayer nanoheterostructure Cr/Fe/Cr/Al2O3. Three partial pair correlation functions are obtained. A modified Levenberg-Marquardt algorithm and a regularization method are applied.

Neutral-helium-atom diffraction from a micron-scale periodic structure: Photonic-crystal-membrane characterization

Science.gov (United States)

Nesse, Torstein; Eder, Sabrina D.; Kaltenbacher, Thomas; Grepstad, Jon Olav; Simonsen, Ingve; Holst, Bodil

2017-06-01

Surface scattering of neutral helium beams created by supersonic expansion is an established technique for measuring structural and dynamical properties of surfaces on the atomic scale. Helium beams have also been used in Fraunhofer and Fresnel diffraction experiments. Due to the short wavelength of the atom beams of typically 0.1 nm or less, Fraunhofer diffraction experiments in transmission have so far been limited to grating structures with a period (pitch) of up to 200 nm. However, larger periods are of interest for several applications, for example, for the characterization of photonic-crystal-membrane structures, where the period is typically in the micron to high submicron range. Here we present helium atom diffraction measurements of a photonic-crystal-membrane structure with a two-dimensional square lattice of 100 ×100 circular holes. The nominal period and the hole radius were 490 and 100 nm, respectively. To our knowledge this is the largest period that has been measured with helium diffraction. The helium diffraction measurements are interpreted using a model based on the helium beam characteristics. It is demonstrated how to successfully extract values from the experimental data for the average period of the grating, the hole diameter, and the width of the virtual source used to model the helium beam.

Feelings about culture scales: development, factor structure, reliability, and validity.

Science.gov (United States)

Maffini, Cara S; Wong, Y Joel

2015-04-01

Although measures of cultural identity, values, and behavior exist in the multicultural psychological literature, there is currently no measure that explicitly assesses ethnic minority individuals' positive and negative affect toward culture. Therefore, we developed 2 new measures called the Feelings About Culture Scale--Ethnic Culture and Feelings About Culture Scale--Mainstream American Culture and tested their psychometric properties. In 6 studies, we piloted the measures, conducted factor analyses to clarify their factor structure, and examined reliability and validity. The factor structure revealed 2 dimensions reflecting positive and negative affect for each measure. Results provided evidence for convergent, discriminant, criterion-related, and incremental validity as well as the reliability of the scales. The Feelings About Culture Scales are the first known measures to examine both positive and negative affect toward an individual's ethnic culture and mainstream American culture. The focus on affect captures dimensions of psychological experiences that differ from cognitive and behavioral constructs often used to measure cultural orientation. These measures can serve as a valuable contribution to both research and counseling by providing insight into the nuanced affective experiences ethnic minority individuals have toward culture. (c) 2015 APA, all rights reserved).

Variable temperature investigation of the atomic structure of gold nanoparticles

International Nuclear Information System (INIS)

Young, N P; Kirkland, A I; Huis, M A van; Zandbergen, H W; Xu, H

2010-01-01

The characterisation of nanoparticle structures is the first step towards understanding and optimising their utility in important technological applications such as catalysis. Using newly developed in-situ transmission electron microscopy (TEM) specimen holders, the temperature dependent atomic structure of gold nanoparticles in the size range 5-12 nm has been investigated. In this size interval, the decahedral morphology has been identified as the most favourable structure at or above room temperature, while particle surface roughening becomes evident above 600 0 C. An icosahedral transition has also been identified at low temperature in particles under 9 nm in diameter. These experimental results are consistent with recently published temperature dependent equilibrium phase maps for gold nanoparticles.

Variable temperature investigation of the atomic structure of gold nanoparticles

Energy Technology Data Exchange (ETDEWEB)

Young, N P; Kirkland, A I [Department of Materials, University of Oxford, Parks Road, Oxford OX1 3PH (United Kingdom); Huis, M A van; Zandbergen, H W [Kavli Insitute of Nanoscience, Delft University of Technolgy, Lorentzweg 1, NL-2628CJ, Delft (Netherlands); Xu, H, E-mail: neil.young@materials.ox.ac.u [Department of Geology and Geophysics, and Materials Science Program, University of Wisconsin-Madison, Madison, Wisconsin (United States)

2010-07-01

The characterisation of nanoparticle structures is the first step towards understanding and optimising their utility in important technological applications such as catalysis. Using newly developed in-situ transmission electron microscopy (TEM) specimen holders, the temperature dependent atomic structure of gold nanoparticles in the size range 5-12 nm has been investigated. In this size interval, the decahedral morphology has been identified as the most favourable structure at or above room temperature, while particle surface roughening becomes evident above 600{sup 0}C. An icosahedral transition has also been identified at low temperature in particles under 9 nm in diameter. These experimental results are consistent with recently published temperature dependent equilibrium phase maps for gold nanoparticles.

The influence of nuclear structure on the Lamb shift in hydrogenlike heavy atoms

International Nuclear Information System (INIS)

Beier, T.; Plunien, G.; Soff, G.

1997-01-01

We evaluate and list the various contributions to the Lamb shift in hydrogenlike heavy atoms which arise from parameters describing shape, size and structure of the nucleus. We compare these contributions with those obtained from quantum electrodynamics. It is found that in heavy nuclei, nuclear contributions depending on experimental parameters and nuclear models are of the same size as QED contributions of order a 2 . Therefore, in these systems the theoretical predictions for binding energies are limited by the exact knowledge of the nuclear parameters. In addition, we tabulate all corrections contributing to the 1s 1/2 Lamb shift in hydrogenlike Pb and U. (orig.)

Atomic Scale Structure-Chemistry Relationships at Oxide Catalyst Surfaces and Interfaces

Science.gov (United States)

McBriarty, Martin E.

Oxide catalysts are integral to chemical production, fuel refining, and the removal of environmental pollutants. However, the atomic-scale phenomena which lead to the useful reactive properties of catalyst materials are not sufficiently understood. In this work, the tools of surface and interface science and electronic structure theory are applied to investigate the structure and chemical properties of catalytically active particles and ultrathin films supported on oxide single crystals. These studies focus on structure-property relationships in vanadium oxide, tungsten oxide, and mixed V-W oxides on the surfaces of alpha-Al2O3 and alpha-Fe2O 3 (0001)-oriented single crystal substrates, two materials with nearly identical crystal structures but drastically different chemical properties. In situ synchrotron X-ray standing wave (XSW) measurements are sensitive to changes in the atomic-scale geometry of single crystal model catalyst surfaces through chemical reaction cycles, while X-ray photoelectron spectroscopy (XPS) reveals corresponding chemical changes. Experimental results agree with theoretical calculations of surface structures, allowing for detailed electronic structure investigations and predictions of surface chemical phenomena. The surface configurations and oxidation states of V and W are found to depend on the coverage of each, and reversible structural shifts accompany chemical state changes through reduction-oxidation cycles. Substrate-dependent effects suggest how the choice of oxide support material may affect catalytic behavior. Additionally, the structure and chemistry of W deposited on alpha-Fe 2O3 nanopowders is studied using X-ray absorption fine structure (XAFS) measurements in an attempt to bridge single crystal surface studies with real catalysts. These investigations of catalytically active material surfaces can inform the rational design of new catalysts for more efficient and sustainable chemistry.

Theoretical Atomic Physics code development II: ACE: Another collisional excitation code

International Nuclear Information System (INIS)

Clark, R.E.H.; Abdallah, J. Jr.; Csanak, G.; Mann, J.B.; Cowan, R.D.

1988-12-01

A new computer code for calculating collisional excitation data (collision strengths or cross sections) using a variety of models is described. The code uses data generated by the Cowan Atomic Structure code or CATS for the atomic structure. Collisional data are placed on a random access file and can be displayed in a variety of formats using the Theoretical Atomic Physics Code or TAPS. All of these codes are part of the Theoretical Atomic Physics code development effort at Los Alamos. 15 refs., 10 figs., 1 tab

Atomic diffusion in stars

CERN Document Server

Michaud, Georges; Richer, Jacques

2015-01-01

This book gives an overview of atomic diffusion, a fundamental physical process, as applied to all types of stars, from the main sequence to neutron stars. The superficial abundances of stars as well as their evolution can be significantly affected. The authors show where atomic diffusion plays an essential role and how it can be implemented in modelling.  In Part I, the authors describe the tools that are required to include atomic diffusion in models of stellar interiors and atmospheres. An important role is played by the gradient of partial radiative pressure, or radiative acceleration, which is usually neglected in stellar evolution. In Part II, the authors systematically review the contribution of atomic diffusion to each evolutionary step. The dominant effects of atomic diffusion are accompanied by more subtle effects on a large number of structural properties throughout evolution. One of the goals of this book is to provide the means for the astrophysicist or graduate student to evaluate the importanc...

All-Atom Molecular Dynamics Simulation of Protein Translocation through an α-Hemolysin Nanopore

KAUST Repository

Di Marino, Daniele

2015-08-06

© 2015 American Chemical Society. Nanopore sensing is attracting the attention of a large and varied scientific community. One of the main issues in nanopore sensing is how to associate the measured current signals to specific features of the molecule under investigation. This is particularly relevant when the translocating molecule is a protein and the pore is sufficiently narrow to necessarily involve unfolding of the translocating protein. Recent experimental results characterized the cotranslocational unfolding of Thioredoxin (Trx) passing through an α-hemolisin pore, providing evidence for the existence of a multistep process. In this study we report the results of all-atom molecular dynamics simulations of the same system. Our data indicate that Trx translocation involves two main barriers. The first one is an unfolding barrier associated with a translocation intermediate where the N-terminal region of Trx is stuck at the pore entrance in a conformation that strongly resembles the native one. After the abrupt unfolding of the N-terminal region, the Trx enters the α-hemolisin vestibule. During this stage, the constriction is occupied not only by the translocating residue but also by a hairpin-like structure forming a tangle in the constriction. The second barrier is associated with the disentangling of this region.

All-Atom Molecular Dynamics Simulation of Protein Translocation through an α-Hemolysin Nanopore

KAUST Repository

Di Marino, Daniele; Bonome, Emma Letizia; Tramontano, Anna; Chinappi, Mauro

2015-01-01

© 2015 American Chemical Society. Nanopore sensing is attracting the attention of a large and varied scientific community. One of the main issues in nanopore sensing is how to associate the measured current signals to specific features of the molecule under investigation. This is particularly relevant when the translocating molecule is a protein and the pore is sufficiently narrow to necessarily involve unfolding of the translocating protein. Recent experimental results characterized the cotranslocational unfolding of Thioredoxin (Trx) passing through an α-hemolisin pore, providing evidence for the existence of a multistep process. In this study we report the results of all-atom molecular dynamics simulations of the same system. Our data indicate that Trx translocation involves two main barriers. The first one is an unfolding barrier associated with a translocation intermediate where the N-terminal region of Trx is stuck at the pore entrance in a conformation that strongly resembles the native one. After the abrupt unfolding of the N-terminal region, the Trx enters the α-hemolisin vestibule. During this stage, the constriction is occupied not only by the translocating residue but also by a hairpin-like structure forming a tangle in the constriction. The second barrier is associated with the disentangling of this region.

Atomic and electronic structures of divacancy in graphene nanoribbons

Energy Technology Data Exchange (ETDEWEB)

Zhao Jun [College of Physical Science and Technology, Yangtze University, Jingzhou, Hubei 434023 (China); Zeng Hui, E-mail: zenghui@yangtzeu.edu.cn [College of Physical Science and Technology, Yangtze University, Jingzhou, Hubei 434023 (China); Wei Jianwei [School of Mathematics and Physics, Chongqing University of Technology, Chongqing 400054 (China)

2012-01-15

First principles calculations have been performed to investigate the electronic structures and transport properties of defective graphene nanoribbons (GNRs) in the presence of pentagon-octagon-pentagon (5-8-5) defects. Electronic band structure results reveal that 5-8-5 defects in the defective zigzag graphene nanoribbon (ZGNR) is unfavorable for electronic transport. However, such defects in the defective armchair graphene nanoribbon (AGNR) give rise to smaller band gap than that in the pristine AGNR, and eventually results in semiconductor to metal-like transition. The distinct roles of 5-8-5 defects in two kinds of edged-GNR are attributed to the different coupling between {pi}{sup Low-Asterisk} and {pi} subbands influenced by the defects. Our findings indicate the possibility of a new route to improve the electronic transport properties of graphene nanoribbons via tailoring the atomic structures by ion irradiation.

4. All-Russian (international) scientific conference. Physicochemical processes during selection of atoms and molecules. Collection of reports

International Nuclear Information System (INIS)

Baranov, V.Yu.; Kolesnikov, Yu.A.

1999-01-01

The reports of the 4. All-Russian (international) scientific conference: Physicochemical processes during selection of atoms and molecules, are presented. The conference took place in Zvenigorod, 4-8 October, 1999. Contents of the reports are the following: laser isotope separation of molecules and atoms; isotopic selection of molecules and atoms in the field of centrifugal forces; selection of molecules by means of rectification and isotopic exchange methods; separation of isotopes by ion cyclotron-resonance method, in electric discharge and electromagnetic field; change in physical properties of substances which variation of their natural isotopic composition; use of isotopes in pharmacy preparation; status of experimental and diagnostic technique; certain promising methods of selection of atoms and molecules. The problems of laser separation of uranium isotopes, separation of carbon isotopes by multi-photon selective dissociation are discussed. The procedures permitting production of isotopes with high concentration and efficiency are developed [ru

Design and development of high-resolution atomic beam fluorescence spectroscopy facility for isotope shift and hyperfine structure measurements

International Nuclear Information System (INIS)

Acharyulu, G.V.S.G.; Sankari, M.; Kiran Kumar, P.V.; Suryanarayana, M.V.

2012-01-01

A high-resolution atomic beam fluorescence spectroscopy facility for the determination of isotope shifts and hyperfine structure in atomic species has been designed and developed. A resistively heated graphite tube atomic beam source was designed, tested and integrated into a compact interaction chamber for atomic beam fluorescence experiments. The design of the laser-atom interaction chamber and the source has been modified in a phased manner so as to achieve sub-Doppler resolution. The system has been used to record the hyperfine spectrum of the D2 transitions of Rb and K isotopes. The spectral resolution achieved is ∼ 26 MHz and is adequate to carry out high resolution measurement of isotope shifts and hyperfine structure of various atomic species. The other major advantage of the source is that it requires very small amounts of sample for achieving very good signal to noise ratio. (author)

Hexapole-compensated magneto-optical trap on a mesoscopic atom chip

DEFF Research Database (Denmark)

Jöllenbeck, S.; Mahnke, J.; Randoll, R.

2011-01-01

Magneto-optical traps on atom chips are usually restricted to small atomic samples due to a limited capture volume caused primarily by distorted field configurations. Here we present a magneto-optical trap based on a millimeter-sized wire structure which generates a magnetic field with minimized...... distortions. Together with the loading from a high-flux two-dimensional magneto-optical trap, we achieve a loading rate of 8.4×1010 atoms/s and maximum number of 8.7×109 captured atoms. The wire structure is placed outside of the vacuum to enable a further adaptation to new scientific objectives. Since all...

Laser-assisted atom-atom collisions

International Nuclear Information System (INIS)

Roussel, F.

1984-01-01

The basic layer-assisted atom-atom collision processes are reviewed in order to get a simpler picture of the main physical facts. The processes can be separated into two groups: optical collisions where only one atom is changing state during the collision, the other acting as a spectator atom, and radiative collisions where the states of the two atoms are changing during the collision. All the processes can be interpreted in terms of photoexcitation of the quasimolecule formed during the collisional process. (author)

Accelerating all-atom MD simulations of lipids using a modified virtual-sites technique

DEFF Research Database (Denmark)

Loubet, Bastien; Kopec, Wojciech; Khandelia, Himanshu

2014-01-01

We present two new implementations of the virtual sites technique which completely suppresses the degrees of freedom of the hydrogen atoms in a lipid bilayer allowing for an increased time step of 5 fs in all-atom simulations of the CHARMM36 force field. One of our approaches uses the derivation...... of the virtual sites used in GROMACS while the other uses a new definition of the virtual sites of the CH2 groups. Our methods is tested on a DPPC (no unsaturated chain), a POPC (one unsaturated chain), and a DOPC (two unsaturated chains) lipid bilayers. We calculate various physical properties of the membrane...... of our simulations with and without virtual sites and explain the differences and similarity observed. The best agreements are obtained for the GROMACS original virtual sites on the DOPC bilayer where we get an area per lipid of 67.3 ± 0.3 A˚2 without virtual sites and 67.6 ± 0.3 A˚2 with virtual sites...

PubChem atom environments.

Science.gov (United States)

Hähnke, Volker D; Bolton, Evan E; Bryant, Stephen H

2015-01-01

Atom environments and fragments find wide-spread use in chemical information and cheminformatics. They are the basis of prediction models, an integral part in similarity searching, and employed in structure search techniques. Most of these methods were developed and evaluated on the relatively small sets of chemical structures available at the time. An analysis of fragment distributions representative of most known chemical structures was published in the 1970s using the Chemical Abstracts Service data system. More recently, advances in automated synthesis of chemicals allow millions of chemicals to be synthesized by a single organization. In addition, open chemical databases are readily available containing tens of millions of chemical structures from a multitude of data sources, including chemical vendors, patents, and the scientific literature, making it possible for scientists to readily access most known chemical structures. With this availability of information, one can now address interesting questions, such as: what chemical fragments are known today? How do these fragments compare to earlier studies? How unique are chemical fragments found in chemical structures? For our analysis, after hydrogen suppression, atoms were characterized by atomic number, formal charge, implicit hydrogen count, explicit degree (number of neighbors), valence (bond order sum), and aromaticity. Bonds were differentiated as single, double, triple or aromatic bonds. Atom environments were created in a circular manner focused on a central atom with radii from 0 (atom types) up to 3 (representative of ECFP_6 fragments). In total, combining atom types and atom environments that include up to three spheres of nearest neighbors, our investigation identified 28,462,319 unique fragments in the 46 million structures found in the PubChem Compound database as of January 2013. We could identify several factors inflating the number of environments involving transition metals, with many

Atomic Scale Structural Studies of Macromolecular Assemblies by Solid-state Nuclear Magnetic Resonance Spectroscopy.

Science.gov (United States)

Loquet, Antoine; Tolchard, James; Berbon, Melanie; Martinez, Denis; Habenstein, Birgit

2017-09-17

Supramolecular protein assemblies play fundamental roles in biological processes ranging from host-pathogen interaction, viral infection to the propagation of neurodegenerative disorders. Such assemblies consist in multiple protein subunits organized in a non-covalent way to form large macromolecular objects that can execute a variety of cellular functions or cause detrimental consequences. Atomic insights into the assembly mechanisms and the functioning of those macromolecular assemblies remain often scarce since their inherent insolubility and non-crystallinity often drastically reduces the quality of the data obtained from most techniques used in structural biology, such as X-ray crystallography and solution Nuclear Magnetic Resonance (NMR). We here present magic-angle spinning solid-state NMR spectroscopy (SSNMR) as a powerful method to investigate structures of macromolecular assemblies at atomic resolution. SSNMR can reveal atomic details on the assembled complex without size and solubility limitations. The protocol presented here describes the essential steps from the production of 13 C/ 15 N isotope-labeled macromolecular protein assemblies to the acquisition of standard SSNMR spectra and their analysis and interpretation. As an example, we show the pipeline of a SSNMR structural analysis of a filamentous protein assembly.

Atomic probes of surface structure and dynamics

International Nuclear Information System (INIS)

Heller, E.J.; Jonsson, H.

1992-01-01

Progress for the period Sept. 15, 1992 to Sept. 14, 1993 is discussed. Semiclassical methods that will allow much faster and more accurate three-dimensional atom--surface scattering calculations, both elastic and inelastic, are being developed. The scattering of He atoms from buckyballs is being investigated as a test problem. Somewhat more detail is given on studies of He atom scattering from defective Pt surfaces. Molecular dynamics simulations of He + and Ar + ion sputtering of Pt surfaces are also being done. He atom scattering from Xe overlayers on metal surfaces and the thermalized dissociation of H 2 on Cu(110) are being studied. (R.W.R.) 64 refs

Enrichment of true positives from structural alerts through the use of novel atomic fragment based descriptors

DEFF Research Database (Denmark)

Long, A.; Rydberg, Patrik

2013-01-01

To enhance the discrimination rate for methods applying structural alerts and biotransformation rules in the prediction of toxicity and drug metabolism we have developed a set of novel fragment based atomic descriptors. These atomic descriptors encode the properties of the fragments separating an...

Core-electron binding energies from self-consistent field molecular orbital theory using a mixture of all-electron real atoms and valence-electron model atoms

International Nuclear Information System (INIS)

Quinn, C.M.; Schwartz, M.E.

1981-01-01

The chemistry of large systems such as clusters may be readily investigated by valence-electron theories based on model potentials, but such an approach does not allow for the examination of core-electron binding energies which are commonly measured experimentally for such systems. Here we merge our previously developed Gaussian based valence-electron model potential theory with all-electron ab initio theory to allow for the calculation of core orbital binding energies when desired. For the atoms whose cores are to be examined, we use the real nuclear changes, all of the electrons, and the appropriate many-electron basis sets. For the rest of the system we use reduced nuclear charges, the Gaussian based model potentials, only the valence electrons, and appropriate valence-electron basis sets. Detailed results for neutral Al 2 are presented for the cases of all-electron, mixed real--model, and model--model SCF--MO calculations. Several different all-electron and valence electron calculations have been done to test the use of the model potential per se, as well as the effect of basis set choice. The results are in all cases in excellent agreement with one another. Based on these studies, a set of ''double-zeta'' valence and all-electron basis functions have been used for further SCF--MO studies on Al 3 , Al 4 , AlNO, and OAl 3 . For a variety of difference combinations of real and model atoms we find excellent agreement for relative total energies, orbital energies (both core and valence), and Mulliken atomic populations. Finally, direct core-hole-state ionic calculations are reported in detail for Al 2 and AlNO, and noted for Al 3 and Al 4 . Results for corresponding frozen-orbital energy differences, relaxed SCF--MO energy differences, and relaxation energies are in all cases in excellent agreement (never differing by more than 0.07 eV, usually by somewhat less). The study clearly demonstrates the accuracy of the mixed real--model theory

Dislocations in AlGaN: Core Structure, Atom Segregation, and Optical Properties.

Science.gov (United States)

Massabuau, Fabien C-P; Rhode, Sneha L; Horton, Matthew K; O'Hanlon, Thomas J; Kovács, András; Zielinski, Marcin S; Kappers, Menno J; Dunin-Borkowski, Rafal E; Humphreys, Colin J; Oliver, Rachel A

2017-08-09

We conducted a comprehensive investigation of dislocations in Al 0.46 Ga 0.54 N. Using aberration-corrected scanning transmission electron microscopy and energy dispersive X-ray spectroscopy, the atomic structure and atom distribution at the dislocation core have been examined. We report that the core configuration of dislocations in AlGaN is consistent with that of other materials in the III-Nitride system. However, we observed that the dissociation of mixed-type dislocations is impeded by alloying GaN with AlN, which is confirmed by our experimental observation of Ga and Al atom segregation in the tensile and compressive parts of the dislocations, respectively. Investigation of the optical properties of the dislocations shows that the atom segregation at dislocations has no significant effect on the intensity recorded by cathodoluminescence in the vicinity of the dislocations. These results are in contrast with the case of dislocations in In 0.09 Ga 0.91 N where segregation of In and Ga atoms also occurs but results in carrier localization limiting non-radiative recombination at the dislocation. This study therefore sheds light on why InGaN-based devices are generally more resilient to dislocations than their AlGaN-based counterparts.

Structures, stability, magnetic moments and growth strategies of the Fe_nN (n = 1–7) clusters: All-electron density functional theory calculations

International Nuclear Information System (INIS)

Li, Zhi; Zhao, Zhen

2017-01-01

The geometries, electronic properties, magnetic moments and growth strategies of the Fe_nN (n = 1–7) clusters are investigated using all-electron density functional theory. The results show that N doping significantly distorts the Fe_n clusters. Fe_4N and Fe_6N clusters are more stable structures than other considered Fe_nN clusters. Local peaks of HOMO-LUMO gap curve are found at n = 3, 7, implying that the chemical stability of the Fe_3N and Fe_7N clusters is higher. Fe_2N, Fe_4N and Fe_6N clusters have larger magnetic moments compared to other considered Fe_nN (n = 1–7) clusters. It can be seen that the Fe_5 clusters are easier to adsorb a Fe atom while the Fe_4 clusters are easier to adsorb a N atom. The considered Fe_mN clusters prefer to adsorb a Fe atom and larger Fe_mN clusters are easier to grow. - Highlights: • The structural stability of the Fe_4N and Fe_6N clusters is higher. • The chemical stability of the Fe_3N and Fe_7N clusters is higher. • Fe_5 clusters are easier to adsorb a Fe atom while Fe_4 clusters are easier to adsorb a N atom. • Fe_nN clusters prefer to adsorb a Fe atom.

Electronic structure of super heavy atoms revisited

International Nuclear Information System (INIS)

Gitman, D M; Levin, A D; Tyutin, I V; Voronov, B L

2013-01-01

The electronic structure of an atom with Z ⩽ Z c = 137 can be described by the Dirac equation with the Coulomb field of a point charge Ze. It was believed that the Dirac equation with Z > Z c poses difficulties because the formula for the lower energy level of the Dirac Hamiltonian formally gives imaginary eigenvalues. But a strict mathematical consideration shows that difficulties with the electronic spectrum for Z > Z c do not arise if the Dirac Hamiltonian is correctly defined as a self-adjoint operator. In this paper, we briefly summarize the main physical results of that consideration in a form suitable for physicists with some additional new details and numerical calculations of the electronic spectra. (comment)

The effect of the electronic structure, phase transition, and localized dynamics of atoms in the formation of tiny particles of gold

Energy Technology Data Exchange (ETDEWEB)

Ali, Mubarak, E-mail: mubarak74@comsats.edu.pk, E-mail: mubarak74@mail.com [COMSATS Institute of Information Technology, Department of Physics (Pakistan); Lin, I-Nan [Tamkang University, Department of Physics (China)

2017-01-15

In addition to self-governing properties, tiny-sized particles of metallic colloids are the building blocks of large-sized particles; thus, their study has been the subject of a large number of publications. In the present work, it has been discussed that geometry structure of tiny particle made through atom-to-atom amalgamation depends on attained dynamics of gold atoms along with protruded orientations. The localized process conditions direct two-dimensional structure of a tiny particle at atomically flat air-solution interface while heating locally dynamically approached atoms, thus, negate the role of van der Waals interactions. At electronphoton-solution interface, impinging electrons stretch or deform atoms of tiny particles depending on the mechanism of impingement. In addition, to strike regular grid of electrons ejected on split of atoms not executing excitations and de-excitations of their electrons, atoms of tiny particles also deform or stretch while occupying various sites depending on the process of synergy. Under suitable impinging electron streams, those tiny particles in monolayer two-dimensional structure electron states of their atoms are diffused in the direction of transferred energy, thus, coincide to the next adjacent atoms in each one-dimensional array dealing the same sort of behavior. Instantaneously, photons of adequate energy propagate on the surfaces of such electronic structures and modify those into smooth elements, thus, disregard the phenomenon of localized surface plasmons. This study highlights the fundamental process of formation of tiny particles where the role of localized dynamics of atoms and their electronic structure along with interaction to light are discussed. Such a tool of processing materials, in nonequilibrium pulse-based process, opens a number of possibilities to develop engineered materials with specific chemical, optical, and electronic properties.

Phasons modulate the atomic Debye-Waller factors in incommensurate structures: Experimental evidence in ThBr4 at 55 K

International Nuclear Information System (INIS)

Madariaga, G.; Perez-Mato, J.M.; Aramburu, I.

1993-01-01

The incommensurate displacive structure of β-ThBr 4 at 55 K has been determined from a neutron diffraction data set including main reflections and first-order satellites. The superspace group is Psub(s anti 1 s1)sup(I4 1 /amd). Final agreement factors are 0.0193, 0.0186 and 0.045 for all, main and satellite reflections, respectively. It is shown that the effect of phasons on the atomic Debye-Waller factors can be quantified by two additional structural parameters: The modulus β 11,2 Br and the phase χ 11,2 Br of a second harmonic that spatially modulates the temperature factors of Br atoms. Results are in good agreement, within the resolution of the experimental data, with the theoretically expected value for χ 11,2 Br . Crystal data for the average structure: M r =551.65, tetragonal, I4 1 /amd, a=8.919(1), c=7.902(1) A, V=628.6(2) A 3 , Z=4, D x =5.82 Mg m -3 , λ=0.84 A, wavevector q=0.32c*. (orig.)

Magnetic atom optics: mirrors, guides, traps, and chips for atoms

Energy Technology Data Exchange (ETDEWEB)

Hinds, E.A.; Hughes, I.G. [Sussex Centre for Optical and Atomic Physics, University of Sussex, Brighton (United Kingdom)

1999-09-21

For the last decade it has been possible to cool atoms to microkelvin temperatures ({approx}1 cm s{sup -1}) using a variety of optical techniques. Light beams provide the very strong frictional forces required to slow atoms from room temperature ({approx}500 m s{sup -1}). However, once the atoms are cold, the relatively weak conservative forces of static electric and magnetic fields play an important role. In our group we have been studying the interaction of cold rubidium atoms with periodically magnetized data storage media. Here we review the underlying principles of the forces acting on atoms above a suitably magnetized substrate or near current-carrying wires. We also summarize the status of experiments. These structures can be used as smooth or corrugated reflectors for controlling the trajectories of cold atoms. Alternatively, they may be used to confine atoms to a plane, a line, or a dot and in some cases to reach the quantum limit of confinement. Atoms levitated above a magnetized surface can be guided electrostatically by wires deposited on the surface. The flow and interaction of atoms in such a structure may form the basis of a new technology, 'integrated atom optics' which might ultimately be capable of realizing a quantum computer. (author)

Collinear laser spectroscopy of atomic cadmium

CERN Document Server

Frömmgen, Nadja; Bissell, Mark L.; Bieroń, Jacek; Blaum, Klaus; Cheal, Bradley; Flanagan, Kieran; Fritzsche, Stephan; Geppert, Christopher; Hammen, Michael; Kowalska, Magdalena; Kreim, Kim; Krieger, Andreas; Neugart, Rainer; Neyens, Gerda; Rajabali, Mustafa M.; Nörtershäuser, Wilfried; Papuga, Jasna; Yordanov, Deyan T.

2015-01-01

Hyperfine structure $A$ and $B$ factors of the atomic $5s\\,5p\\,\\; ^3\\rm{P}_2 \\rightarrow 5s\\,6s\\,\\; ^3\\rm{S}_1$ transition are determined from collinear laser spectroscopy data of $^{107-123}$Cd and $^{111m-123m}$Cd. Nuclear magnetic moments and electric quadrupole moments are extracted using reference dipole moments and calculated electric field gradients, respectively. The hyperfine structure anomaly for isotopes with $s_{1/2}$ and $d_{5/2}$ nuclear ground states and isomeric $h_{11/2}$ states is evaluated and a linear relationship is observed for all nuclear states except $s_{1/2}$. This corresponds to the Moskowitz-Lombardi rule that was established in the mercury region of the nuclear chart but in the case of cadmium the slope is distinctively smaller than for mercury. In total four atomic and ionic levels were analyzed and all of them exhibit a similar behaviour. The electric field gradient for the atomic $5s\\,5p\\,\\; ^3\\mathrm{P}_2$ level is derived from multi-configuration Dirac-Hartree-Fock calculatio...

Structures of adsorbed CO on atomically smooth and on stepped sngle crystal surfaces

International Nuclear Information System (INIS)

Madey, T.E.; Houston, J.E.

1980-01-01

The structures of molecular CO adsorbed on atomically smooth surfaces and on surfaces containing monatomic steps have been studied using the electron stimulated desorption ion angular distribution (ESDIAD) method. For CO adsorbed on the close packed Ru(001) and W(110) surfaces, the dominant bonding mode is via the carbon atom, with the CO molecular axis perpendicular to the plane of the surface. For CO on atomicaly rough Pd(210), and for CO adsorbed at step sites on four different surfaces vicinal to W(110), the axis of the molecule is tilted or inclined away from the normal to the surface. The ESDIAD method, in which ion desorption angles are related to surface bond angles, provides a direct determination of the structures of adsorbed molecules and molecular complexes on surfaces

Multipolar electrostatics for proteins: atom-atom electrostatic energies in crambin.

Science.gov (United States)

Yuan, Yongna; Mills, Matthew J L; Popelier, Paul L A

2014-02-15

Accurate electrostatics necessitates the use of multipole moments centered on nuclei or extra point charges centered away from the nuclei. Here, we follow the former alternative and investigate the convergence behavior of atom-atom electrostatic interactions in the pilot protein crambin. Amino acids are cut out from a Protein Data Bank structure of crambin, as single amino acids, di, or tripeptides, and are then capped with a peptide bond at each side. The atoms in the amino acids are defined through Quantum Chemical Topology (QCT) as finite volume electron density fragments. Atom-atom electrostatic energies are computed by means of a multipole expansion with regular spherical harmonics, up to a total interaction rank of L = ℓA+ ℓB + 1 = 10. The minimum internuclear distance in the convergent region of all the 15 possible types of atom-atom interactions in crambin that were calculated based on single amino acids are close to the values calculated from di and tripeptides. Values obtained at B3LYP/aug-cc-pVTZ and MP2/aug-cc-pVTZ levels are only slightly larger than those calculated at HF/6-31G(d,p) level. This convergence behavior is transferable to the well-known amyloid beta polypeptide Aβ1-42. Moreover, for a selected central atom, the influence of its neighbors on its multipole moments is investigated, and how far away this influence can be ignored is also determined. Finally, the convergence behavior of AMBER becomes closer to that of QCT with increasing internuclear distance. Copyright © 2013 Wiley Periodicals, Inc.

Structural dynamics and activity of nanocatalysts inside fuel cells by in operando atomic pair distribution studies.

Science.gov (United States)

Petkov, Valeri; Prasai, Binay; Shan, Shiyao; Ren, Yang; Wu, Jinfang; Cronk, Hannah; Luo, Jin; Zhong, Chuan-Jian

2016-05-19

Here we present the results from a study aimed at clarifying the relationship between the atomic structure and activity of nanocatalysts for chemical reactions driving fuel cells, such as the oxygen reduction reaction (ORR). In particular, using in operando high-energy X-ray diffraction (HE-XRD) we tracked the evolution of the atomic structure and activity of noble metal-transition metal (NM-TM) nanocatalysts for ORR as they function at the cathode of a fully operational proton exchange membrane fuel cell (PEMFC). Experimental HE-XRD data were analysed in terms of atomic pair distribution functions (PDFs) and compared to the current output of the PEMFC, which was also recorded during the experiments. The comparison revealed that under actual operating conditions, NM-TM nanocatalysts can undergo structural changes that differ significantly in both length-scale and dynamics and so can suffer losses in their ORR activity that differ significantly in both character and magnitude. Therefore we argue that strategies for reducing ORR activity losses should implement steps for achieving control not only over the length but also over the time-scale of the structural changes of NM-TM NPs that indeed occur during PEMFC operation. Moreover, we demonstrate how such a control can be achieved and thereby the performance of PEMFCs improved considerably. Last but not least, we argue that the unique capabilities of in operando HE-XRD coupled to atomic PDF analysis to characterize active nanocatalysts inside operating fuel cells both in a time-resolved manner and with atomic level resolution, i.e. in 4D, can serve well the ongoing search for nanocatalysts that deliver more with less platinum.

Atomic physics

CERN Document Server

Foot, Christopher J

2007-01-01

This text will thoroughly update the existing literature on atomic physics. Intended to accompany an advanced undergraduate course in atomic physics, the book will lead the students up to the latest advances and the applications to Bose-Einstein Condensation of atoms, matter-wave inter-ferometry and quantum computing with trapped ions. The elementary atomic physics covered in the early chapters should be accessible to undergraduates when they are first introduced to the subject. To complement. the usual quantum mechanical treatment of atomic structure the book strongly emphasizes the experimen

Atomic Structure of Salutaridine Reductase from the Opium Poppy (Papaver somniferum)

Energy Technology Data Exchange (ETDEWEB)

Higashi, Yasuhiro; Kutchan, Toni M.; Smith, Thomas J. (Danforth)

2011-11-18

The opium poppy (Papaver somniferum L.) is one of the oldest known medicinal plants. In the biosynthetic pathway for morphine and codeine, salutaridine is reduced to salutaridinol by salutaridine reductase (SalR; EC 1.1.1.248) using NADPH as coenzyme. Here, we report the atomic structure of SalR to a resolution of {approx}1.9 {angstrom} in the presence of NADPH. The core structure is highly homologous to other members of the short chain dehydrogenase/reductase family. The major difference is that the nicotinamide moiety and the substrate-binding pocket are covered by a loop (residues 265-279), on top of which lies a large 'flap'-like domain (residues 105-140). This configuration appears to be a combination of the two common structural themes found in other members of the short chain dehydrogenase/reductase family. Previous modeling studies suggested that substrate inhibition is due to mutually exclusive productive and nonproductive modes of substrate binding in the active site. This model was tested via site-directed mutagenesis, and a number of these mutations abrogated substrate inhibition. However, the atomic structure of SalR shows that these mutated residues are instead distributed over a wide area of the enzyme, and many are not in the active site. To explain how residues distal to the active site might affect catalysis, a model is presented whereby SalR may undergo significant conformational changes during catalytic turnover.

Atomic and electronic structure transformations of silver nanoparticles under rapid cooling conditions

OpenAIRE

Lobato, I.; Rojas, J.; Landauro, C. V.; Torres, J.

2008-01-01

The structural evolution and dynamics of silver nanodrops Ag${}_{2896}$ (4.4 nm in diameter) during rapid cooling conditions has been studied by means of molecular dynamics simulations and electronic density of state calculations. The interaction of silver atoms is modeled by a tight-binding semiempirical interatomic potential proposed by Cleri and Rosato. The pair correlation functions and the pair analysis technique is applied to reveal the structural transition in the process of solidifica...

Polarization-induced interference within electromagnetically induced transparency for atoms of double-V linkage

Science.gov (United States)

Sun, Yuan; Liu, Chang; Chen, Ping-Xing; Liu, Liang

2018-02-01

People have been paying attention to the role of atoms' complex internal level structures in the research of electromagnetically induced transparency (EIT) for a long time, where the various degenerate Zeeman levels usually generate complex linkage patterns for the atomic transitions. It turns out, with special choices of the atomic states and the atomic transitions' linkage structure, clear signatures of quantum interference induced by the probe and coupling light's polarizations can emerge from a typical EIT phenomena. We propose to study a four-state system with double-V linkage pattern for the transitions and analyze the polarization-induced interference under the EIT condition. We show that such interference arises naturally under mild conditions on the optical field and atom manipulation techniques. Moreover, we construct a variation form of double-M linkage pattern where the polarization-induced interference enables polarization-dependent cross modulation between incident weak lights that can be effective even at the few-photon level. The theme is to gain more insight into the essential question: how can we build a nontrivial optical medium where incident lights experience polarization-dependent nonlinear optical interactions, valid for a wide range of incidence intensities down to the few-photon level?

Validity and factor structure of the bodybuilding dependence scale.

Science.gov (United States)

Smith, D; Hale, B

2004-04-01

To investigate the factor structure, validity, and reliability of the bodybuilding dependence scale and to investigate differences in bodybuilding dependence between men and women and competitive and non-competitive bodybuilders. Seventy two male competitive bodybuilders, 63 female competitive bodybuilders, 87 male non-competitive bodybuilders, and 63 non-competitive female bodybuilders completed the bodybuilding dependence scale (BDS), the exercise dependence questionnaire (EDQ), and the muscle dysmorphia inventory (MDI). Confirmatory factor analysis of the BDS supported a three factor model of bodybuilding dependence, consisting of social dependence, training dependence, and mastery dependence (Q = 3.16, CFI = 0.98, SRMR = 0.04). Internal reliability of all three subscales was high (Cronbach's alpha = 0.92, 0.92, and 0.93 respectively). Significant (pbodybuilders scored significantly (pbodybuilders. However, there were no significant sex differences on any of the BDS subscales (p>0.05). The three factor BDS appears to be a reliable and valid measure of bodybuilding dependence. Symptoms of bodybuilding dependence are more prevalent in competitive bodybuilders than non-competitive ones, but there are no significant sex differences in bodybuilding dependence.

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

Science.gov (United States)

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.

Local Atomic Structure and Discommensurations in the Charge Density Wave of CeTe{sub 3}

Energy Technology Data Exchange (ETDEWEB)

Kim, H J; Tomic, A T; Tessmer, S H; Billinge, S J.L. [Department of Physics and Astronomy, Michigan State University, East Lansing, Michigan 48824 (United States); Malliakas, C D; Kanatzidis, M G [Department of Chemistry, Michigan State University, East Lansing, Michigan 48824 (United States)

2006-06-09

The local structure of CeTe{sub 3} in the incommensurate charge density wave (IC-CDW) state has been obtained using atomic pair distribution function analysis of x-ray diffraction data. Local atomic distortions in the Te nets due to the CDW are larger than observed crystallographically, resulting in distinct short and long Te-Te bonds. Observation of different distortion amplitudes in the local and average structures is explained by the discommensurated nature of the CDW, since the pair distribution function is sensitive to the local displacements within the commensurate regions, whereas the crystallographic result averages over many discommensurated domains. The result is supported by STM data. This is the first quantitative local structural study within the commensurate domains in an IC-CDW system.

Atomic and electronic structures of an extremely fragile liquid.

Science.gov (United States)

Kohara, Shinji; Akola, Jaakko; Patrikeev, Leonid; Ropo, Matti; Ohara, Koji; Itou, Masayoshi; Fujiwara, Akihiko; Yahiro, Jumpei; Okada, Junpei T; Ishikawa, Takehiko; Mizuno, Akitoshi; Masuno, Atsunobu; Watanabe, Yasuhiro; Usuki, Takeshi

2014-12-18

The structure of high-temperature liquids is an important topic for understanding the fragility of liquids. Here we report the structure of a high-temperature non-glass-forming oxide liquid, ZrO2, at an atomistic and electronic level. The Bhatia-Thornton number-number structure factor of ZrO2 does not show a first sharp diffraction peak. The atomic structure comprises ZrO5, ZrO6 and ZrO7 polyhedra with a significant contribution of edge sharing of oxygen in addition to corner sharing. The variety of large oxygen coordination and polyhedral connections with short Zr-O bond lifetimes, induced by the relatively large ionic radius of zirconium, disturbs the evolution of intermediate-range ordering, which leads to a reduced electronic band gap and increased delocalization in the ionic Zr-O bonding. The details of the chemical bonding explain the extremely low viscosity of the liquid and the absence of a first sharp diffraction peak, and indicate that liquid ZrO2 is an extremely fragile liquid.

Band structure of one-dimensional doped photonic crystal with three level atoms using the Fresnel coefficients method

Science.gov (United States)

Jafari, A.; Rahmat, A.; Bakkeshizadeh, S.

2018-01-01

We consider a one-dimensional photonic crystal (1DPC) composed of double-layered dielectrics. Electric permittivity and magnetic permeability of this crystal depends on the incident electromagnetic wave frequency. We suppose that three level atoms have been added to the second layer of each dielectric and this photonic crystal (PC) has been doped. These atoms can be added to the layer with different rates. In this paper, we have calculated and compared the band structure of the mentioned PC considering the effect of added atoms to the second layer with different rates through the Fresnel coefficients method. We find out that according to the effective medium theory, the electric permittivity of the second layer changes. Also the band structure of PC for both TE and TM polarizations changes, too. The width of bandgaps related to “zero averaged refractive index” and “Bragg” increases. Moreover, new gap branches appear in new frequencies at both TE and TM polarizations. In specific state, two branches of “zero permittivity” gap appear in the PC band structure related to TM polarization. With increasing the amount of the filling rate of total volume with three level atoms, we observe a lot of changes in the PC band structure.

Effective stopping of relativistic structural heavy ions at collisions with atoms

International Nuclear Information System (INIS)

Matveev, V.I.

2002-01-01

One develops the unperturbed theory of energy losses at collision of atoms with structural high-charged heavy ions moving with relativistic velocity. One derived a simple formula for efficient braking. The structural ions in terms of this paper are considered to mean partially ionized ions of heavy elements compressing ion nucleus and some bound electrons compensating partially for ion nucleus charge. Account of ion charge magnitude is determined to result in essential increase of efficient braking of ion in contrast to braking of point nucleus of Z* charge [ru

Atomic-layer-resolved analysis of surface magnetism by diffraction spectroscopy

International Nuclear Information System (INIS)

Matsui, Fumihiko; Matsushita, Tomohiro; Daimon, Hiroshi

2010-01-01

X-ray absorption near edge structure (XANES) and X-ray magnetic circular dichroism (XMCD) measurements by Auger-electron-yield detection are powerful analysis tools for the electronic and magnetic structures of surfaces, but all the information from atoms within the electron mean-free-path range is summed into the obtained spectrum. In order to investigate the electronic and magnetic structures of each atomic layer at subsurface, we have proposed a new method, diffraction spectroscopy, which is the combination of X-ray absorption spectroscopy and Auger electron diffraction (AED). From a series of measured thickness dependent AED patterns, we deduced a set of atomic-layer-specific AED patterns arithmetically. Based on these AED patterns, we succeeded in disentangling obtained XANES and XMCD spectra into those from different atomic layers.

Electronic structure of fractionally nuclear charged atoms

International Nuclear Information System (INIS)

Pavao, Antonio C.; Bastos, Cristiano C.; Ferreira, Joacy V.

2008-01-01

Different properties of quark chemistry are studied by performing accurate ab initio Hartree- Fock calculations on fractionally nuclear charged atoms. Ground and first excited states of sodium atoms with quarks attached to the nucleus are obtained using CI calculations. It is suggested that the sodium 2 P -> 2 S electronic transition can be used as a guide in searching for unconfined quarks. Also, the variation of the binding electronic energy with nuclear charge in the isoelectronic series of fractionally nuclear charged atoms A ±2/3 and A ±1/3 (A = H, Li, Na, P and Ca) is analyzed. The present calculations suggest that unconfined colored particles have large appetite for heavy nuclei and that quark-antiquark pairs could be stabilized in presence of the atomic matter. (author)

Equilibrium structure and atomic vibrations of Nin clusters

Science.gov (United States)

Borisova, Svetlana D.; Rusina, Galina G.

2017-12-01

The equilibrium bond lengths and binding energy, second differences in energy and vibrational frequencies of free clusters Nin (2 ≤ n ≤ 20) were calculated with the use of the interaction potential obtained in the tight-binding approximation (TBA). The results show that the minimum vibration frequency plays a significant role in the evaluation of the dynamic stability of the clusters. A nonmonotonic dependence of the minimum vibration frequency of clusters on their size and the extreme values for the number of atoms in a cluster n = 4, 6, 13, and 19 are demonstrated. This result agrees with the theoretical and experimental data on stable structures of small metallic clusters.

Microfabricated Waveguide Atom Traps.

Energy Technology Data Exchange (ETDEWEB)

Jau, Yuan-Yu [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States)

2017-09-01

A nanoscale , microfabricated waveguide structure can in - principle be used to trap atoms in well - defined locations and enable strong photon-atom interactions . A neutral - atom platform based on this microfabrication technology will be prealigned , which is especially important for quantum - control applications. At present, there is still no reported demonstration of evanescent - field atom trapping using a microfabricated waveguide structure. We described the capabilities established by our team for future development of the waveguide atom - trapping technology at SNL and report our studies to overcome the technical challenges of loading cold atoms into the waveguide atom traps, efficient and broadband optical coupling to a waveguide, and the waveguide material for high - power optical transmission. From the atomic - physics and the waveguide modeling, w e have shown that a square nano-waveguide can be utilized t o achieve better atomic spin squeezing than using a nanofiber for first time.

Agreement between Ukraine and the International Atomic Energy Agency for the application of safeguards to all nuclear material in all peaceful nuclear activities of Ukraine

International Nuclear Information System (INIS)

1995-02-01

The text of the Agreement between Ukraine and the International Atomic Energy Agency for the Application of Safeguards to all Nuclear Material in all Peaceful Nuclear Activities of Ukraine is reproduced in this document for the information of all Members. The Agreement was approved by the Agency's Board of Governors on 12 September 1994 and signed in Vienna on 28 September 1994. The Agreement entered into force, pursuant to Article 24, on 13 January 1995

Electronic structure engineering in silicene via atom substitution and a new two-dimensional Dirac structure Si3C

Science.gov (United States)

Yin, Na; Dai, Ying; Wei, Wei; Huang, Baibiao

2018-04-01

A lot of efforts have been made towards the band gap opening in two-dimensional silicene, the silicon version of graphene. In the present work, the electronic structures of single atom doped (B, N, Al and P) and codoped (B/N and Al/P) silicene monolayers are systematically examined on the base of density functional electronic calculations. Our results demonstrate that single atom doping can realize electron or hole doping in the silicene; while codoping, due to the syergistic effects, results in finite band gap in silicene at the Dirac point without significantly degrading the electronic properties. In addition, the characteristic of band gap shows dependence on the doping concentration. Importantly, we predict a new two-dimensional Dirac structure, the graphene-like Si3C, which also shows linear band dispersion relation around the Fermi level. Our results demonstrates an important perspective to engineer the electronic and optical properties of silicene.

Exchange and polarization effects in the elementary excitation spectrum of a hydrogen atom immersed in a hot plasma

International Nuclear Information System (INIS)

Dharma-wardana, M.W.C.; Grimaldi, F.; Lecourt, A.; Pellissier, J.

1980-01-01

The one-particle hydrogenic Green's function has been calculated for a partially ionized plasma consisting of hydrogen atoms, electrons, and protons at high temperatures. The theoretical method extends a previous publication and involves an evaluation of the mass operator in the Dyson equation to include proper self-energy parts to ''all orders'' in the screened interaction. This mass operator characterizes the effective micropotential felt by the atom in the plasma and determines all of the one-particle properties and some two-particle properties associated with the atomic subsystem. The first-order mass operator is nonzero only for exchange scattering, which leads to a frequency-independent exchange shift. This temperature- and density-dependent theory of the exchange shift replaces the usual semiphenomenological schemes based on the Slater-Kohn-Sham type of theory. The exchange-shifted Green's functions are used in evaluating the higher-order contributions. Computer calculations and the resolution of the poles of the Green's function lead to level shifts, widths, and spectral functions. These are calculated within both the second-order and the all-order theory. The second-order theory, which may be valid at sufficiently high densities and in turbulent plasmas, overemphasises the atom-plasmon coupling and shows new structures. The inclusion of contributions beyond second order removes these structures and produces a more ''conventional'' spectral-intensity function. The effects of center-of-mass motion on the level shifts and level profiles are investigated and the onset of plasma instabilities touched upon. These calculations make contact with the work on ''plasma-polarization shifts'' and provide an approach to q,ω-dependent plasma microfields

Artificial Atoms: from Quantum Physics to Applications

International Nuclear Information System (INIS)

2014-01-01

The primary objective of this workshop is to survey the most recent advances of technologies enabling single atom- and artificial atom-based devices. These include the assembly of artificial molecular structures with magnetic dipole and optical interactions between engineered atoms embedded in solid-state lattices. The ability to control single atoms in diamond or similar solids under ambient operating conditions opens new perspectives for technologies based on nanoelectronics and nanophotonics. The scope of the workshop is extended towards the physics of strong coupling between atoms and radiation field modes. Beyond the traditional atom-cavity systems, artificial dipoles coupled to microwave radiation in circuit quantum electrodynamics is considered. All these technologies mutually influence each other in developing novel devices for sensing at the quantum level and for quantum information processing.

Near-Atomic Resolution Structure of a Plant Geminivirus Determined by Electron Cryomicroscopy.

Science.gov (United States)

Hipp, Katharina; Grimm, Clemens; Jeske, Holger; Böttcher, Bettina

2017-08-01

African cassava mosaic virus is a whitefly-transmitted geminivirus which forms unique twin particles of incomplete icosahedra that are joined at five-fold vertices, building an unusual waist. How its 22 capsomers interact within a half-capsid or across the waist is unknown thus far. Using electron cryo-microscopy and image processing, we determined the virion structure with a resolution of 4.2 Å and built an atomic model for its capsid protein. The inter-capsomer contacts mediated by the flexible N termini and loop regions differed within the half-capsids and at the waist, explaining partly the unusual twin structure. The tip of the pentameric capsomer is sealed by a plug formed by a turn region harboring the evolutionary conserved residue Y193. Basic amino acid residues inside the capsid form a positively charged pocket next to the five-fold axis of the capsomer suitable for binding DNA. Within this pocket, density most likely corresponding to DNA was resolved. Copyright © 2017 Elsevier Ltd. All rights reserved.

Highly excited atoms

International Nuclear Information System (INIS)

Kleppner, D.; Littman, M.G.; Zimmerman, M.L.

1981-01-01

Highly excited atoms are often called Rydberg atoms. These atoms have a wealth of exotic properties which are discussed. Of special interest, are the effects of electric and magnetic fields on Rydberg atoms. Ordinary atoms are scarcely affected by an applied electric or magnetic field; Rydberg atoms can be strongly distorted and even pulled apart by a relatively weak electric field, and they can be squeezed into unexpected shapes by a magnetic field. Studies of the structure of Rydberg atoms in electric and magnetic fields have revealed dramatic atomic phenomena that had not been observed before

External validation of structure-biodegradation relationship (SBR) models for predicting the biodegradability of xenobiotics.

Science.gov (United States)

Devillers, J; Pandard, P; Richard, B

2013-01-01

Biodegradation is an important mechanism for eliminating xenobiotics by biotransforming them into simple organic and inorganic products. Faced with the ever growing number of chemicals available on the market, structure-biodegradation relationship (SBR) and quantitative structure-biodegradation relationship (QSBR) models are increasingly used as surrogates of the biodegradation tests. Such models have great potential for a quick and cheap estimation of the biodegradation potential of chemicals. The Estimation Programs Interface (EPI) Suite™ includes different models for predicting the potential aerobic biodegradability of organic substances. They are based on different endpoints, methodologies and/or statistical approaches. Among them, Biowin 5 and 6 appeared the most robust, being derived from the largest biodegradation database with results obtained only from the Ministry of International Trade and Industry (MITI) test. The aim of this study was to assess the predictive performances of these two models from a set of 356 chemicals extracted from notification dossiers including compatible biodegradation data. Another set of molecules with no more than four carbon atoms and substituted by various heteroatoms and/or functional groups was also embodied in the validation exercise. Comparisons were made with the predictions obtained with START (Structural Alerts for Reactivity in Toxtree). Biowin 5 and Biowin 6 gave satisfactorily prediction results except for the prediction of readily degradable chemicals. A consensus model built with Biowin 1 allowed the diminution of this tendency.

Fast automated placement of polar hydrogen atoms in protein-ligand complexes

Directory of Open Access Journals (Sweden)

Lippert Tobias

2009-08-01

Full Text Available Abstract Background Hydrogen bonds play a major role in the stabilization of protein-ligand complexes. The ability of a functional group to form them depends on the position of its hydrogen atoms. An accurate knowledge of the positions of hydrogen atoms in proteins is therefore important to correctly identify hydrogen bonds and their properties. The high mobility of hydrogen atoms introduces several degrees of freedom: Tautomeric states, where a hydrogen atom alters its binding partner, torsional changes where the position of the hydrogen atom is rotated around the last heavy-atom bond in a residue, and protonation states, where the number of hydrogen atoms at a functional group may change. Also, side-chain flips in glutamine and asparagine and histidine residues, which are common crystallographic ambiguities must be identified before structure-based calculations can be conducted. Results We have implemented a method to determine the most probable hydrogen atom positions in a given protein-ligand complex. Optimality of hydrogen bond geometries is determined by an empirical scoring function which is used in molecular docking. This allows to evaluate protein-ligand interactions with an established model. Also, our method allows to resolve common crystallographic ambiguities such as as flipped amide groups and histidine residues. To ensure high speed, we make use of a dynamic programming approach. Conclusion Our results were checked against selected high-resolution structures from an external dataset, for which the positions of the hydrogen atoms have been validated manually. The quality of our results is comparable to that of other programs, with the advantage of being fast enough to be applied on-the-fly for interactive usage or during score evaluation.

Short- and medium-range order of atomic structure and electronic properties of arsenic salinide and sulphide amorphous films

International Nuclear Information System (INIS)

Sarsembinov, Sh.Sh.; Prikhodko, O.Yu.; Ryaguzov, A.P.; Maksimova, S.Ya.; Ushanov, V.Zh.

2004-01-01

Full text: The relationship between short- and medium-range order of atomic structure and electronic properties is the object of invariable attention of disordered matter physics. This problem is the most important for non-crystalline semiconductors, and specifically for chalcogenide glassy semiconductors (ChGS) films due to low co-ordination of atoms, which leads to lability of their structure. In this report we present results of atomic structure, electric, optical properties and carrier drift investigation in amorphous films of As 2 Se 3 and As 2 S 3 prepared by thermal evaporation in a vacuum (TE films) and by RF ion-plasma sputtering (RF films). These techniques strongly differing in the conditions of substance vaporization and condensation atoms on a substrate. The short- and medium-range order of the films atomic structure has been studied by X-ray diffraction analysis using the CuKα radiation (λ=1.5418 Angstrom) and by Raman spectroscopy. Raman spectra were measured at room temperature on Perkin-Elmer Spectrum GX Raman FT-IR Spectrometer (180 deg. backscattering). Vibrational modes were excited vertically polarized light of DPY Nd:YAG laser (1.064 μm). The radii of the first and second coordination spheres, number of the nearest neighbours of As and Se (S) atoms in the first coordination sphere, dimension of the medium-range order domain and 'quasi-period' in that region have been determined for the studied samples. The identification of the structural units in matrix of the film has been carried out, too. It is established that the films prepared by different methods have differences in the parameters of short- and medium range orders. It follows from the comparative analysis of Raman spectra that spectrum of RF films is significantly more complex than that of glass and TE films. The matrix of RF films contains, along with the structural units AsSe 3/2 (AsS 3/2 ) inherent in TE films and glass, other structural units with As and Se (S) excess. It may be

Structure of the SH3 domain of human osteoclast-stimulating factor at atomic resolution

International Nuclear Information System (INIS)

Chen, Liqing; Wang, Yujun; Wells, David; Toh, Diana; Harold, Hunt; Zhou, Jing; DiGiammarino, Enrico; Meehan, Edward J.

2006-01-01

The crystal structure of the SH3 domain of human osteoclast-stimulating factor has been determined and refined to the ultrahigh resolution of 1.07 Å. The structure at atomic resolution provides an accurate framework for structure-based design of its inhibitors. Osteoclast-stimulating factor (OSF) is an intracellular signaling protein, produced by osteoclasts themselves, that enhances osteoclast formation and bone resorption. It is thought to act via an Src-related signaling pathway and contains SH3 and ankyrin-repeat domains which are involved in protein–protein interactions. As part of a structure-based anti-bone-loss drug-design program, the atomic resolution X-ray structure of the recombinant human OSF SH3 domain (hOSF-SH3) has been determined. The domain, residues 12–72, yielded crystals that diffracted to the ultrahigh resolution of 1.07 Å. The overall structure shows a characteristic SH3 fold consisting of two perpendicular β-sheets that form a β-barrel. Structure-based sequence alignment reveals that the putative proline-rich peptide-binding site of hOSF-SH3 consists of (i) residues that are highly conserved in the SH3-domain family, including residues Tyr21, Phe23, Trp49, Pro62, Asn64 and Tyr65, and (ii) residues that are less conserved and/or even specific to hOSF, including Thr22, Arg26, Thr27, Glu30, Asp46, Thr47, Asn48 and Leu60, which might be key to designing specific inhibitors for hOSF to fight osteoporosis and related bone-loss diseases. There are a total of 13 well defined water molecules forming hydrogen bonds with the above residues in and around the peptide-binding pocket. Some of those water molecules might be important for drug-design approaches. The hOSF-SH3 structure at atomic resolution provides an accurate framework for structure-based design of its inhibitors

The Selective Mutism Questionnaire: Measurement Structure and Validity

Science.gov (United States)

Letamendi, Andrea M.; Chavira, Denise A.; Hitchcock, Carla A.; Roesch, Scott C.; Shipon-Blum, Elisa; Stein, Murray B.; Roesch, Scott C.

2010-01-01

Objective To evaluate the factor structure, reliability, and validity of the 17-item Selective Mutism Questionnaire. Method Diagnostic interviews were administered via telephone to 102 parents of children identified with selective mutism (SM) and 43 parents of children without SM from varying U.S. geographic regions. Children were between the ages of 3 and 11 inclusive and comprised 58% girls and 42% boys. SM diagnoses were determined using the Anxiety Disorders Interview Schedule for Children - Parent Version (ADIS-C/P); SM severity was assessed using the 17-item Selective Mutism Questionnaire (SMQ); and behavioral and affective symptoms were assessed using the Child Behavior Checklist (CBCL). An exploratory factor analysis (EFA) was conducted to investigate the dimensionality of the SMQ and a modified parallel analysis procedure was used to confirm EFA results. Internal consistency, construct validity, and incremental validity were also examined. Results The EFA yielded a 13-item solution consisting of three factors: a) Social Situations Outside of School, b) School Situations, and c) Home and Family Situations. Internal consistency of SMQ factors and total scale ranged from moderate to high. Convergent and incremental validity were also well supported. Conclusions Measure structure findings are consistent with the 3-factor solution found in a previous psychometric evaluation of the SMQ. Results also suggest that the SMQ provides useful and unique information in the prediction of SM phenomenon beyond other child anxiety measures. PMID:18698268

xMDFF: molecular dynamics flexible fitting of low-resolution X-ray structures

International Nuclear Information System (INIS)

McGreevy, Ryan; Singharoy, Abhishek; Li, Qufei; Zhang, Jingfen; Xu, Dong; Perozo, Eduardo; Schulten, Klaus

2014-01-01

A new real-space refinement method for low-resolution X-ray crystallography is presented. The method is based on the molecular dynamics flexible fitting protocol targeted at addressing large-scale deformations of the search model to achieve refinement with minimal manual intervention. An explanation of the method is provided, augmented by results from the refinement of both synthetic and experimental low-resolution data, including an independent electrophysiological verification of the xMDFF-refined crystal structure of a voltage-sensor protein. X-ray crystallography remains the most dominant method for solving atomic structures. However, for relatively large systems, the availability of only medium-to-low-resolution diffraction data often limits the determination of all-atom details. A new molecular dynamics flexible fitting (MDFF)-based approach, xMDFF, for determining structures from such low-resolution crystallographic data is reported. xMDFF employs a real-space refinement scheme that flexibly fits atomic models into an iteratively updating electron-density map. It addresses significant large-scale deformations of the initial model to fit the low-resolution density, as tested with synthetic low-resolution maps of d-ribose-binding protein. xMDFF has been successfully applied to re-refine six low-resolution protein structures of varying sizes that had already been submitted to the Protein Data Bank. Finally, via systematic refinement of a series of data from 3.6 to 7 Å resolution, xMDFF refinements together with electrophysiology experiments were used to validate the first all-atom structure of the voltage-sensing protein Ci-VSP

xMDFF: molecular dynamics flexible fitting of low-resolution X-ray structures

Energy Technology Data Exchange (ETDEWEB)

McGreevy, Ryan; Singharoy, Abhishek [University of Illinois at Urbana-Champaign, Urbana, IL 61801 (United States); Li, Qufei [The University of Chicago, Chicago, IL 60637 (United States); Zhang, Jingfen; Xu, Dong [University of Missouri, Columbia, MO 65211 (United States); Perozo, Eduardo [The University of Chicago, Chicago, IL 60637 (United States); Schulten, Klaus, E-mail: kschulte@ks.uiuc.edu [University of Illinois at Urbana-Champaign, Urbana, IL 61801 (United States); University of Illinois at Urbana-Champaign, Urbana, IL 61801 (United States)

2014-09-01

A new real-space refinement method for low-resolution X-ray crystallography is presented. The method is based on the molecular dynamics flexible fitting protocol targeted at addressing large-scale deformations of the search model to achieve refinement with minimal manual intervention. An explanation of the method is provided, augmented by results from the refinement of both synthetic and experimental low-resolution data, including an independent electrophysiological verification of the xMDFF-refined crystal structure of a voltage-sensor protein. X-ray crystallography remains the most dominant method for solving atomic structures. However, for relatively large systems, the availability of only medium-to-low-resolution diffraction data often limits the determination of all-atom details. A new molecular dynamics flexible fitting (MDFF)-based approach, xMDFF, for determining structures from such low-resolution crystallographic data is reported. xMDFF employs a real-space refinement scheme that flexibly fits atomic models into an iteratively updating electron-density map. It addresses significant large-scale deformations of the initial model to fit the low-resolution density, as tested with synthetic low-resolution maps of d-ribose-binding protein. xMDFF has been successfully applied to re-refine six low-resolution protein structures of varying sizes that had already been submitted to the Protein Data Bank. Finally, via systematic refinement of a series of data from 3.6 to 7 Å resolution, xMDFF refinements together with electrophysiology experiments were used to validate the first all-atom structure of the voltage-sensing protein Ci-VSP.

Predicting and validating protein interactions using network structure.

Directory of Open Access Journals (Sweden)

Pao-Yang Chen

2008-07-01

Full Text Available Protein interactions play a vital part in the function of a cell. As experimental techniques for detection and validation of protein interactions are time consuming, there is a need for computational methods for this task. Protein interactions appear to form a network with a relatively high degree of local clustering. In this paper we exploit this clustering by suggesting a score based on triplets of observed protein interactions. The score utilises both protein characteristics and network properties. Our score based on triplets is shown to complement existing techniques for predicting protein interactions, outperforming them on data sets which display a high degree of clustering. The predicted interactions score highly against test measures for accuracy. Compared to a similar score derived from pairwise interactions only, the triplet score displays higher sensitivity and specificity. By looking at specific examples, we show how an experimental set of interactions can be enriched and validated. As part of this work we also examine the effect of different prior databases upon the accuracy of prediction and find that the interactions from the same kingdom give better results than from across kingdoms, suggesting that there may be fundamental differences between the networks. These results all emphasize that network structure is important and helps in the accurate prediction of protein interactions. The protein interaction data set and the program used in our analysis, and a list of predictions and validations, are available at http://www.stats.ox.ac.uk/bioinfo/resources/PredictingInteractions.

Study on atomic and electronic structures of ceramic materials using spectroscopy, microscopy, and first principles calculation

International Nuclear Information System (INIS)

Mizoguchi, Teruyasu

2011-01-01

In this review, following two topics are introduced: 1) experimental and theoretical electron energy loss (EEL) near edge structures (ELNES) and X-ray absorption near edge structures (XANES), and 2) atomic and electronic structure analysis of ceramic interface by combing spectroscopy, microscopy, and first principles calculation. In the ELNES/XANES calculation, it is concluded that inclusion of core-hole effect in the calculation is essential. By combining high energy resolution observation and theoretical calculation, detailed analysis of the electronic structure is achieved. In addition, overlap population (OP) diagram is used to interpret the spectrum. In the case of AlN, sharp and intense first peak of N-K edge is found to reflect narrow dispersion of the conduction band bottom. By applying ELNES and the OP diagram to Cu/Al 2 O 3 heterointerface, it is revealed that intensity of prepeak in O-K edge is inverse proportional to interface strength. The relationships between atomic structure and defect energetics at SrTiO 3 grain boundary are also investigated, and reveal that the formation behavior of Ti vacancy is sensitive to the structural distortion. In addition, by using state-of-the-art spectroscopy, microscopy, and first principles calculations, atomic scale visualization of fluorine dopant in LaFeOAs and first principles calculation of HfO 2 phase transformation are demonstrated. (author)

Atoms - molecules - nuclei. Vol. 1

International Nuclear Information System (INIS)

Otter, G.; Honecker, R.

1993-01-01

This first volume covers the following topics: Wave-particle dualism, classical atomic physics; the Schroedinger equation, angular momentum in quantum physics, one-electron atoms and many-electron atoms with atomic structure, atomic spectra, exotic atoms, influence of electric and magnetic fields

Structural Dynamics and Activity of Nanocatalysts Inside Fuel Cells by in-operando Atomic Pair Distribution Studies

Science.gov (United States)

Prasai, Binay

We present the results from a study aimed at clarifying the relationship between the atomic structure and activity of nanocatalysts for chemical reactions driving fuel cells, such as the oxygen reduction reaction (ORR). Using in-operando high-energy X-ray diffraction we tracked the evolution of the atomic structure and activity of noble metal-transition metal(NM-TM) nanocatalysts for ORR as they function at the cathode of a fully operational proton exchange membrane fuel cell (PEMFC). Data were analyzed in terms of atomic pair distribution functions and compared to the current output of the PEMFC, which was also recorded during the experiments. The comparison revealed that under actual operating conditions, NM-TM nanocatalysts can undergo structural changes that differ significantly in both length-scale and dynamics and so can suffer losses in their ORR activity that differ significantly in both character and magnitude. Therefore, we argue that strategies for reducing ORR activity losses should implement steps for achieving control not only over the length but also over the time-scale of the structural changes of NM-TM NPs that indeed occur during PEMFC operation.

Molecular dynamics simulation of chemical sputtering of hydrogen atom on layer structured graphite

International Nuclear Information System (INIS)

Ito, A.; Wang, Y.; Irle, S.; Morokuma, K.; Nakamura, H.

2008-10-01

Chemical sputtering of hydrogen atom on graphite was simulated using molecular dynamics. Especially, the layer structure of the graphite was maintained by interlayer intermolecular interaction. Three kinds of graphite surfaces, flat (0 0 0 1) surface, armchair (1 1 2-bar 0) surface and zigzag (1 0 1-bar 0) surface, are dealt with as targets of hydrogen atom bombardment. In the case of the flat surface, graphene layers were peeled off one by one and yielded molecules had chain structures. On the other hand, C 2 H 2 and H 2 are dominant yielded molecules on the armchair and zigzag surfaces, respectively. In addition, the interaction of a single hydrogen isotope on a single graphene is investigated. Adsorption, reflection and penetration rates are obtained as functions of incident energy and explain hydrogen retention on layered graphite. (author)

Anomaly in shape of resonance absorption lines of atoms with large fine-structure splitting of levels

International Nuclear Information System (INIS)

Parkhomenko, A.I.; yachev, S.P."" >Podyachev, S.P.; Privalov, T.I.; Shalagin, A.M.

1997-01-01

Absorption line of monochromatic radiation by atoms nonselective excitation by velocities under conditions of optical excitation of components of superfine structure of the basic electron state is considered. It is shown that the absorption line has unusual substructures for certain values of the basic state superfine desintegration. These substructures in the absorption spectrum may be pointed out by accounting the superfine structure of the electron excited state. The absorption spectra of monochromatic radiation close tot he D 1 - and D 2 -lines of the atomic rubidium are calculated

Atomic structure of shear bands in Cu64Zr36 metallic glasses studied by molecular dynamics simulations

International Nuclear Information System (INIS)

Feng, Shidong; Qi, Li; Wang, Limin; Pan, Shaopeng; Ma, Mingzhen; Zhang, Xinyu; Li, Gong; Liu, Riping

2015-01-01

Graphical abstract: Figure shows that atoms in the shear band (SB) moved desultorily compared with those in the matrix. These atoms seriously interacted with each other similar to the grain boundary in crystalline materials. Figuratively, if these atoms wanted to “pass” the shear band, they should arrange their irritations. However, stress concentrations and high energy were observed in SB, which resulted in instability in the deformation process and finally led to a disastrously brittle fracture. - Abstract: Molecular dynamics simulations on the atomic structure of shear bands (SBs) in Cu 64 Zr 36 metallic glasses are presented. Results show that the atoms in the SB move desultorily, in contrast to those in the matrix. The saturated degree of bonded pairs considering the “liquid-like” character of SB quantitatively provides important details in extending earlier studies on SBs. Zr-centered 〈0, 2, 8, 5〉 clusters exhibit strong spatial correlations and tendency to connect with each other in short-range order. The 〈0, 2, 8, 5〉 cluster-type medium-range order is the main feature inside the SB relative to the matrix. The fractal results demonstrate the planar-like fashion of the 〈0, 2, 8, 5〉 network in SB, forming an interpenetrating solid-like backbone. Such heterogeneous structure provides a fundamental structural perspective of mechanical instability in SB

Relativistic correlations in atoms

International Nuclear Information System (INIS)

Dietz, K.

1987-01-01

Atoms are particularly well-suited objects when it comes to testing certain concepts of many-body theories. They play a unique role in this respect because of two constructively interfering reasons: first of all, the laws describing the interactions of their constituents are the ones best known in all of Physics; secondly, their structure is comparatively simple and amenable to concise theoretical treatment. Because of these two reasons, physically motivated many-body approximation schemes, ordered in a systematic hierarchy of precision, can be carefully tested; discrepancies between theory and experiment are due to many-body effects and are never masked by uncertainties in the constituent-interaction (needless to say, the very small hadronic contributions to atomic structure is left out. Many-body effects in atoms are solely produced by the electron-electron interaction which derives from the laws of Quantum Electrodynamics or, in a very good approximation from the repulsive Coulomb potential; in the general nomenclature they are named correlations. The material is organized in two chapters: chapter 1 deals with a general introduction and discussion of g-Hartree mean-field theories, chapter 2 deals with applications. The role of vacuum fluctuations and deformations of the Dirac sea in a consistent construction of mean-fields is emphasized and their explicit form in the g-Hartree theory is given. 21 references, 5 figures, 3 tables

Use of pseudopotentials in atom-atom (or molecule) collisions

International Nuclear Information System (INIS)

Pascale, J.

1985-09-01

Knowledge of interactions between ions, atoms or molecules is fundamental for interpretating or predicting collisional processes which may occur under various circumstances. The aim of this paper is to demonstrate the usefulness of using semiempirical effective interactions (more particularly, emphasis will be put on the pseudopotential approach) in the study of atom-atom (or molecule) collisions. We would like to show that if the semiempirical effective interactions are carefully defined, their use in molecular-structure calculations and in collision problems can give quite accurate results. We will limit our examples to one-electron systems. We consider the M-atom-He systems as a first example. For these systems, recent molecular-structure calculations have been carried out using an 1-dependent semiempirical pseudopotential approach and they have been tested against numerous experimental data in extensive calculations of cross sections for intra-and-inter-doublet transitions in the M-atom in collisions with He. Our second example will concern the M-H 2 systems, for which semiempirical pseudopotential molecular-structure calculations have been performed very recently using an one-electron two-center model. The results of these calculations are quite encouraging and we foresee the use of the pseudopotential approach in future studies of some reactive scattering processes

Agreement between Ukraine and the International Atomic Energy Agency for the application of safeguards to all nuclear material in all peaceful nuclear activities of Ukraine

Energy Technology Data Exchange (ETDEWEB)

NONE

1995-02-01

The text of the Agreement between Ukraine and the International Atomic Energy Agency for the Application of Safeguards to all Nuclear Material in all Peaceful Nuclear Activities of Ukraine is reproduced in this document for the information of all Members. The Agreement was approved by the Agency`s Board of Governors on 12 September 1994 and signed in Vienna on 28 September 1994. The Agreement entered into force, pursuant to Article 24, on 13 January 1995.

Structural exploration for the refinement of anticancer matrix metalloproteinase-2 inhibitor designing approaches through robust validated multi-QSARs

Science.gov (United States)

Adhikari, Nilanjan; Amin, Sk. Abdul; Saha, Achintya; Jha, Tarun

2018-03-01

Matrix metalloproteinase-2 (MMP-2) is a promising pharmacological target for designing potential anticancer drugs. MMP-2 plays critical functions in apoptosis by cleaving the DNA repair enzyme namely poly (ADP-ribose) polymerase (PARP). Moreover, MMP-2 expression triggers the vascular endothelial growth factor (VEGF) having a positive influence on tumor size, invasion, and angiogenesis. Therefore, it is an urgent need to develop potential MMP-2 inhibitors without any toxicity but better pharmacokinetic property. In this article, robust validated multi-quantitative structure-activity relationship (QSAR) modeling approaches were attempted on a dataset of 222 MMP-2 inhibitors to explore the important structural and pharmacophoric requirements for higher MMP-2 inhibition. Different validated regression and classification-based QSARs, pharmacophore mapping and 3D-QSAR techniques were performed. These results were challenged and subjected to further validation to explain 24 in house MMP-2 inhibitors to judge the reliability of these models further. All these models were individually validated internally as well as externally and were supported and validated by each other. These results were further justified by molecular docking analysis. Modeling techniques adopted here not only helps to explore the necessary structural and pharmacophoric requirements but also for the overall validation and refinement techniques for designing potential MMP-2 inhibitors.

Lamb shift and fine structure at n =2 in a hydrogenlike muonic atom with the nuclear spin I =0

Science.gov (United States)

Korzinin, Evgeny Yu.; Shelyuto, Valery A.; Ivanov, Vladimir G.; Karshenboim, Savely G.

2018-01-01

The paper is devoted to the Lamb shift and fine structure in a hydrogenlike muonic atom with a spinless nucleus up to the order α5m with all the recoil corrections included. Enhanced contributions of a higher order are also considered. We present the results on the pure QED contribution and on the finite-nuclear-size contribution, proportional to RN2, with the higher-order corrections included. We also consider the consistency of the pure QED theory and the evaluation of the nuclear-structure effects. Most of the QED theory is the same as the theory for the case of the nuclear spin 1/2. Additional nuclear-spin-dependent terms are considered in detail. The issue of the difference for the theories with a spinor nucleus and a scalar one is discussed for the recoil contributions in the order (Zα ) 4m ,α (Zα ) 4m , and (Zα ) 5m . The numerical results are presented for the muonic atoms with two lightest scalar nuclei, helium-4 and beryllium-10. We compare the theory of those muonic atoms with theory for the muonic hydrogen. Some higher-order finite-nuclear-size corrections for the Lamb shift in muonic hydrogen are revisited.

One Size Fits All? The Validity of a Composite Poverty Index Across Urban and Rural Households in South Africa.

Science.gov (United States)

Steinert, Janina Isabel; Cluver, Lucie Dale; Melendez-Torres, G J; Vollmer, Sebastian

2018-01-01

Composite indices have been prominently used in poverty research. However, validity of these indices remains subject to debate. This paper examines the validity of a common type of composite poverty indices using data from a cross-sectional survey of 2477 households in urban and rural KwaZulu-Natal, South Africa. Multiple-group comparisons in structural equation modelling were employed for testing differences in the measurement model across urban and rural groups. The analysis revealed substantial variations between urban and rural respondents both in the conceptualisation of poverty as well as in the weights and importance assigned to individual poverty indicators. The validity of a 'one size fits all' measurement model can therefore not be confirmed. In consequence, it becomes virtually impossible to determine a household's poverty level relative to the full sample. Findings from our analysis have important practical implications in nuancing how we can sensitively use composite poverty indices to identify poor people.

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

International Nuclear Information System (INIS)

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

2016-01-01

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. (paper)

Growth mechanisms for Si epitaxy on O atomic layers: Impact of O-content and surface structure

Energy Technology Data Exchange (ETDEWEB)

Jayachandran, Suseendran, E-mail: suseendran.jayachandran@imec.be [Imec, Kapeldreef 75, 3001 Leuven (Belgium); KU Leuven (University of Leuven), Department of Metallurgy and Materials, Castle Arenberg 44, B-3001 Leuven (Belgium); Billen, Arne [Imec, Kapeldreef 75, 3001 Leuven (Belgium); KU Leuven (University of Leuven), Department of Chemistry, Celestijnenlaan 200F, B-3001 Leuven (Belgium); Douhard, Bastien; Conard, Thierry; Meersschaut, Johan; Moussa, Alain; Caymax, Matty; Bender, Hugo [Imec, Kapeldreef 75, 3001 Leuven (Belgium); Vandervorst, Wilfried [Imec, Kapeldreef 75, 3001 Leuven (Belgium); KU Leuven (University of Leuven), Department of Physics and Astronomy, Celestijnenlaan 200D, B-3001 Leuven (Belgium); Heyns, Marc [Imec, Kapeldreef 75, 3001 Leuven (Belgium); KU Leuven (University of Leuven), Department of Metallurgy and Materials, Castle Arenberg 44, B-3001 Leuven (Belgium); Delabie, Annelies [Imec, Kapeldreef 75, 3001 Leuven (Belgium); KU Leuven (University of Leuven), Department of Chemistry, Celestijnenlaan 200F, B-3001 Leuven (Belgium)

2016-10-30

Highlights: • O{sub 3} or O{sub 2} exposures on H-Si(100) result in O ALs with different surface structures. • Si-EPI on O AL using O{sub 3} process is by direct epitaxial growth mechanism. • Si-EPI on O AL using O{sub 2} process is by epitaxial lateral overgrowth mechanism. • Distortions by O AL, SiH{sub 4} flux rate and Si thickness has an impact on Si-EPI quality. - Abstract: The epitaxial growth of Si layers on Si substrates in the presence of O atoms is generally considered a challenge, as O atoms degrade the epitaxial quality by generating defects. Here, we investigate the growth mechanisms for Si epitaxy on O atomic layers (ALs) with different O-contents and structures. O ALs are deposited by ozone (O{sub 3}) or oxygen (O{sub 2}) exposure on H-terminated Si at 50 °C and 300 °C respectively. Epitaxial Si is deposited by chemical vapor deposition using silane (SiH{sub 4}) at 500 °C. After O{sub 3} exposure, the O atoms are uniformly distributed in Si-Si dimer/back bonds. This O layer still allows epitaxial seeding of Si. The epitaxial quality is enhanced by lowering the surface distortions due to O atoms and by decreasing the arrival rate of SiH{sub 4} reactants, allowing more time for surface diffusion. After O{sub 2} exposure, the O atoms are present in the form of SiO{sub x} clusters. Regions of hydrogen-terminated Si remain present between the SiO{sub x} clusters. The epitaxial seeding of Si in these structures is realized on H-Si regions, and an epitaxial layer grows by a lateral overgrowth mechanism. A breakdown in the epitaxial ordering occurs at a critical Si thickness, presumably by accumulation of surface roughness.

Probing the atomic structure of metallic nanoclusters with the tip of a scanning tunneling microscope.

Science.gov (United States)

Schouteden, Koen; Lauwaet, Koen; Janssens, Ewald; Barcaro, Giovanni; Fortunelli, Alessandro; Van Haesendonck, Chris; Lievens, Peter

2014-02-21

Preformed Co clusters with an average diameter of 2.5 nm are produced in the gas phase and are deposited under controlled ultra-high vacuum conditions onto a thin insulating NaCl film on Au(111). Relying on a combined experimental and theoretical investigation, we demonstrate visualization of the three-dimensional atomic structure of the Co clusters by high-resolution scanning tunneling microscopy (STM) using a Cl functionalized STM tip that can be obtained on the NaCl surface. More generally, use of a functionalized STM tip may allow for systematic atomic structure determination with STM of nanoparticles that are deposited on metal surfaces.

Salient design features of secondary containment structure of Narora Atomic Power Project

International Nuclear Information System (INIS)

Rahalkar, B.D.

1975-01-01

Design of the secondary containment structure for Narora Atomic Power Project is an improvement over the two earlier structures at of Rajasthan and Kalpakkam wherein Candu-type of reactors are involved. The major improvements envisaged are : to limit the leakage through the double containment envelope to 0.1% of volume of the building per day as against 0.1% per hour achieved for earlier stations; to separate heavy water atmosphere from that of light water for effective heavy water recovery; and better man-rem budgetting by limiting inner containment structure upto boiler room floor level and making boiler room area accessible during normal operation for servicing of light water system equipment. Narora Atomic Power Station is located in the Indo-Gangetic alluvial plains in seismically active zone IV. Comprehensive soil investigation, including dynamic properties of soil is required to be undertaken as the foundation level of the containment structure is 17 M below the ground level. The salient results of this investigation relevant to the foundations as well as type of foundation proposed are presented in brief. Double containment concept similar to that adopted for Kalpakkam station is provided for this station also. However, necessary changes in design to withstand large earthquake forces are required to be made. These design problems are discussed in brief. (author)

Application of empirical hydration distribution functions around polar atoms for assessing hydration structures of proteins

International Nuclear Information System (INIS)

Matsuoka, Daisuke; Nakasako, Masayoshi

2013-01-01

Highlights: ► Empirical distribution functions of water molecules in protein hydration are made. ► The functions measure how hydrogen-bond geometry in hydration deviate from ideal. ► The functions assess experimentally identified hydration structures of protein. - Abstract: To quantitatively characterize hydrogen-bond geometry in local hydration structures of proteins, we constructed a set of empirical hydration distribution functions (EHDFs) around polar protein atoms in the main and side chains of 11 types of hydrophilic amino acids (D. Matsuoka, M. Nakasako, Journal of Physical Chemistry B 113 (2009) 11274). The functions are the ensemble average of possible hydration patterns around the polar atoms, and describe the anisotropic deviations from ideal hydrogen bond geometry. In addition, we defined probability distribution function of hydration water molecules (PDFH) over the hydrophilic surface of a protein as the sum of EHDFs of solvent accessible polar protein atoms. The functions envelop most of hydration sites identified in crystal structures of proteins (D. Matsuoka, M. Nakasako, Journal of Physical Chemistry B 114 (2010) 4652). Here we propose the application of EHDFs and PDFHs for assessing crystallographically identified hydration structures of proteins. First, hydration water molecules are classified with respect to the geometry in hydrogen bonds in referring EHDFs. Difference Fourier electron density map weighted by PDFH of protein is proposed to identify easily density peaks as candidates of hydration water molecules. A computer program implementing those ideas was developed and used for assessing hydration structures of proteins

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

International Nuclear Information System (INIS)

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

2014-01-01

Atomic level spatial variability of electronic structure in Fe-based superconductor FeTe 0.55 Se 0.45 (T 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 1−x Se x 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

Investigation of the atomic interface structure of mesotaxial Si/CoSi2(100) layers formed by high-dose implantation

International Nuclear Information System (INIS)

Bulle-Lieuwma, C.W.T.; Jong, A.F. de; Vandenhoudt, D.E.W.

1991-01-01

Aligned mesotaxial films of CoSi 2 in monocrystalline (100) oriented Si substrates have been formed by high-dose ion implantation of Co, followed by a high temperature treatment. The atomic structures of both the lower and upper Si/CoSi 2 (100) interfaces of the buried CoSi 2 layer have been investigated by high-resolution electron microscopy (HREM) combined with image simulations. A domain-like structure is observed consisting of areas with different interfaces. In order to derive the atomic configuration, image simulations of different proposed models are presented. By comparing simulated images and HREM images, two different atomic structure models for the Si/CoSi 2 (100) interface have been found. In the first model the interfacial Co atoms are six-fold coordinated and the tetrahedral coordination and bond lengths of silicon atoms are everywhere maintained. In the second model we found evidence for a 2 x 1 interface reconstruction, involving a difference in composition. The interfacial Co atoms are seven-fold coordinated. It is shown that the boundaries between the domains are associated with interfacial dislocations of edge-type with Burgers vectors b a/4 inclined and b = a/2 parallel to the interfacial plane. (author)

Quantitative structure-property relationships for octanol-water partition coefficients of polybrominated diphenyl ethers.

Science.gov (United States)

Li, Linnan; Xie, Shaodong; Cai, Hao; Bai, Xuetao; Xue, Zhao

2008-08-01

Theoretical molecular descriptors were tested against logK(OW) values for polybrominated diphenyl ethers (PBDEs) using the Partial Least-Squares Regression method which can be used to analyze data with many variables and few observations. A quantitative structure-property relationship (QSPR) model was successfully developed with a high cross-validated value (Q(cum)(2)) of 0.961, indicating a good predictive ability and stability of the model. The predictive power of the QSPR model was further cross-validated. The values of logK(OW) for PBDEs are mainly governed by molecular surface area, energy of the lowest unoccupied molecular orbital and the net atomic charges on the oxygen atom. All these descriptors have been discussed to interpret the partitioning mechanism of PBDE chemicals. The bulk property of the molecules represented by molecular surface area is the leading factor, and K(OW) values increase with the increase of molecular surface area. Higher energy of the lowest unoccupied molecular orbital and higher net atomic charge on the oxygen atom of PBDEs result in smaller K(OW). The energy of the lowest unoccupied molecular orbital and the net atomic charge on PBDEs oxygen also play important roles in affecting the partition of PBDEs between octanol and water by influencing the interactions between PBDEs and solvent molecules.

Formation, atomic structure, and electronic properties of GaSb quantum dots in GaAs

Energy Technology Data Exchange (ETDEWEB)

Timm, R.

2007-12-14

In this work, cross-sectional scanning tunneling microscopy and spectroscopy are used for the first time to study the shape, size, strain, chemical composition, and electronic properties of capped GaSb/GaAs QDs at the atomic scale. By evaluating such structural results on a variety of nanostructures built using different epitaxy methods and growth conditions, details on the underlying QD formation processes can be revealed. A cross-over from flat quantum wells (QWs) to optically active QDs can be observed in samples grown by metalorganic chemical vapor deposition (MOCVD) with increasing amount of GaSb, including self-assembled Sb accumulations within a still two-dimensional layer and tiny three-dimensional GaSb islands probably acting as precursor structures. The QWs consist of significantly intermixed material with stoichiometries of maximally 50% GaSb, additionally exhibiting small gaps filled with GaAs. A higher GaSb content up to nearly pure material is found in the QDs, being characterized by small sizes of up to 8 nm baselength and about 2 nm height. In spite of the intermixing, all nanostructures have rather abrupt interfaces, and no significant Sb segregation in growth direction is observed. This changes completely when molecular beam epitaxy (MBE) is used as growth method, in which case individual Sb atoms are found to be distributed over several nm above the nanostructures. Massive group-V atomic exchange processes are causing this strong inter-mixing and Sb segregation during GaAs overgrowth. In combination with the large strain inherent to GaSb/GaAs QDs, this segregation upon overgrowth is assumed to be the reason for a unique structural phenomenon: All MBE-grown QDs, independent of the amount of deposited GaSb, exhibit a ring structure, consisting of a ring body of high GaSb content and a more or less extended central gap filled with GaAs. These rings have formed in a self-assembled way even when the initial GaSb layer was overgrown considerably fast

Accurate atom-mapping computation for biochemical reactions.

Science.gov (United States)

Latendresse, Mario; Malerich, Jeremiah P; Travers, Mike; Karp, Peter D

2012-11-26

The complete atom mapping of a chemical reaction is a bijection of the reactant atoms to the product atoms that specifies the terminus of each reactant atom. Atom mapping of biochemical reactions is useful for many applications of systems biology, in particular for metabolic engineering where synthesizing new biochemical pathways has to take into account for the number of carbon atoms from a source compound that are conserved in the synthesis of a target compound. Rapid, accurate computation of the atom mapping(s) of a biochemical reaction remains elusive despite significant work on this topic. In particular, past researchers did not validate the accuracy of mapping algorithms. We introduce a new method for computing atom mappings called the minimum weighted edit-distance (MWED) metric. The metric is based on bond propensity to react and computes biochemically valid atom mappings for a large percentage of biochemical reactions. MWED models can be formulated efficiently as Mixed-Integer Linear Programs (MILPs). We have demonstrated this approach on 7501 reactions of the MetaCyc database for which 87% of the models could be solved in less than 10 s. For 2.1% of the reactions, we found multiple optimal atom mappings. We show that the error rate is 0.9% (22 reactions) by comparing these atom mappings to 2446 atom mappings of the manually curated Kyoto Encyclopedia of Genes and Genomes (KEGG) RPAIR database. To our knowledge, our computational atom-mapping approach is the most accurate and among the fastest published to date. The atom-mapping data will be available in the MetaCyc database later in 2012; the atom-mapping software will be available within the Pathway Tools software later in 2012.

Structural and incremental validity of the Wechsler Adult Intelligence Scale-Fourth Edition with a clinical sample.

Science.gov (United States)

Nelson, Jason M; Canivez, Gary L; Watkins, Marley W

2013-06-01

Structural and incremental validity of the Wechsler Adult Intelligence Scale-Fourth Edition (WAIS-IV; Wechsler, 2008a) was examined with a sample of 300 individuals referred for evaluation at a university-based clinic. Confirmatory factor analysis indicated that the WAIS-IV structure was best represented by 4 first-order factors as well as a general intelligence factor in a direct hierarchical model. The general intelligence factor accounted for the most common and total variance among the subtests. Incremental validity analyses indicated that the Full Scale IQ (FSIQ) generally accounted for medium to large portions of academic achievement variance. For all measures of academic achievement, the first-order factors combined accounted for significant achievement variance beyond that accounted for by the FSIQ, but individual factor index scores contributed trivial amounts of achievement variance. Implications for interpreting WAIS-IV results are discussed. (PsycINFO Database Record (c) 2013 APA, all rights reserved).

Structural and Dynamical Properties of 2:1 Phyllosilicates Edges and Nanoparticles

Science.gov (United States)

Newton, A. G.; Sposito, G.

2012-12-01

Classical mechanics simulations of bulk 2:1 phyllosilicate minerals provide atomic scale perspectives of the macroscopic sorption and diffusion phenomena in interlayer nanopores. An equivalent perspective of these interfacial phenomena in macropores bounded by the edges of stacked phyllosilicate particles is not possible due to the absence of a forcefield for the edges of phyllosilicate minerals. A valid forcefield to describe the phyllosilicate edge is essential to link the quantum and continuum mechanical models. The inherently disordered edge of 2:1 phyllosilicate minerals and rarity of well-crystallized samples further complicates the task of validating a forcefield for the phyllosilicate edge. Periodic bond chain theory identifies three tetrahedral-octahedral-tetrahedral (TOT) structures that parallel the edge faces of pseudohexagonal phyllosilicate particles. These TOT structures are the basis of atomistic models of the dominant edge interface and nanoparticles. The CLAYFF forcefield describes all pairwise atomic interactions with only minimal partial charge adjustments to maintain model neutrality, where necessary. Atomistic simulations in the isobaric-isothermal ensemble at nanosecond timescales predict equilibrium edge structures and dynamical properties of the aqueous interface. The CLAYFF forcefield and the limited adjustments to parameters predict edge and particle structures that are consistent with the results of ab initio MD simulations, support macroscopic observations of phyllosilicate reactivity, and provide legitimacy for disordered models of 2:1 phyllosilicates. The heterogeneous edge structures can be explained by the chemistry of the octahedral cation and surface charge anisotropy. In the plane of the octahedral sheet, the cations of the octahedral layer can assume four-, five-, and six-coordinate polyhedral geometries at the edge interface. These disordered edge structures create alternate alignments in the tetrahedral sheet. The structural

Atomic interactions in precision interferometry using Bose-Einstein condensates

International Nuclear Information System (INIS)

Jamison, Alan O.; Gupta, Subhadeep; Kutz, J. Nathan

2011-01-01

We present theoretical tools for predicting and reducing the effects of atomic interactions in Bose-Einstein condensate (BEC) interferometry experiments. To address mean-field shifts during free propagation, we derive a robust scaling solution that reduces the three-dimensional Gross-Pitaevskii equation to a set of three simple differential equations valid for any interaction strength. To model the other common components of a BEC interferometer--condensate splitting, manipulation, and recombination--we generalize the slowly varying envelope reduction, providing both analytic handles and dramatically improved simulations. Applying these tools to a BEC interferometer to measure the fine structure constant, α[S. Gupta, K. Dieckmann, Z. Hadzibabic, and D. E. Pritchard, Phys. Rev. Lett. 89, 140401 (2002)], we find agreement with the results of the original experiment and demonstrate that atomic interactions do not preclude measurement to better than part-per-billion accuracy, even for atomic species with relatively large scattering lengths. These tools help make BEC interferometry a viable choice for a broad class of precision measurements.

Directed Atom-by-Atom Assembly of Dopants in Silicon.

Science.gov (United States)

Hudak, Bethany M; Song, Jiaming; Sims, Hunter; Troparevsky, M Claudia; Humble, Travis S; Pantelides, Sokrates T; Snijders, Paul C; Lupini, Andrew R

2018-05-17

The ability to controllably position single atoms inside materials is key for the ultimate fabrication of devices with functionalities governed by atomic-scale properties. Single bismuth dopant atoms in silicon provide an ideal case study in view of proposals for single-dopant quantum bits. However, bismuth is the least soluble pnictogen in silicon, meaning that the dopant atoms tend to migrate out of position during sample growth. Here, we demonstrate epitaxial growth of thin silicon films doped with bismuth. We use atomic-resolution aberration-corrected imaging to view the as-grown dopant distribution and then to controllably position single dopants inside the film. Atomic-scale quantum-mechanical calculations corroborate the experimental findings. These results indicate that the scanning transmission electron microscope is of particular interest for assembling functional materials atom-by-atom because it offers both real-time monitoring and atom manipulation. We envision electron-beam manipulation of atoms inside materials as an achievable route to controllable assembly of structures of individual dopants.

Atomic structures of the rare-earths and actinides via relativistic current- and spin-density functional theory

International Nuclear Information System (INIS)

Higuchi, M.; Onuki, Y.; Osaka Univ., Toyonaka; Hasegawa, A.

1998-01-01

A new single-particle equation of the Kohn-Sham-Dirac type is derived from a relativistic current- and spin-density functional theory (RCSDFT), and is here applied to the calculations of the atomic structures of the rare-earth elements. Both the relativistic effects and the magnetic effects are taken into account on an equal footing, and the numerical calculation is carried out by modifying the method of Cortona et al. Because of the presence of the effective magnetic field, the degeneracies in all orbits are completely resolved like the Zeeman splittings. Total spin and orbital angular momenta over all the occupied states are shown to agree reasonably well with the Hund's rules for the rare-earth ions. (orig.)

Tailoring atomic structure to control the electronic transport in zigzag graphene nanoribbon

International Nuclear Information System (INIS)

Zeng, Hui; Zhao, Jun; Wei, Jianwei; Zeng, Xianliang; Xu, Yang

2012-01-01

We have performed ab initio density functional theory calculation to study the electronic transport properties of the tailored zigzag-edged graphene nanoribbon (ZGNR) with particular electronic transport channels. Our results demonstrated that tailoring the atomic structure had significantly influenced the electronic transport of the defective nanostructures, and could lead to the metal-semiconducting transition when sufficient atoms are tailored. The asymmetric I–V characteristics as a result of symmetry breaking have been exhibited, which indicates the route to utilize GNR as a basic component for novel nanoelectronics. -- Highlights: ► M–S transition induced by tailoring nanostructure. ► Asymmetric I–V curve due to symmetry breaking. ► Controllable electron transport by designing nanofiguration.

Tailoring atomic structure to control the electronic transport in zigzag graphene nanoribbon

Energy Technology Data Exchange (ETDEWEB)

Zeng, Hui [College of Physical Science and Technology, Yangtze University, Jingzhou, Hubei 434023 (China); Zhao, Jun, E-mail: zhaojun@yangtzeu.edu.cn [College of Physical Science and Technology, Yangtze University, Jingzhou, Hubei 434023 (China); Wei, Jianwei [College of Optoelectronic Information, Chongqing University of Technology, Chongqing 400054 (China); Zeng, Xianliang [College of Physical Science and Technology, Yangtze University, Jingzhou, Hubei 434023 (China); Xu, Yang [Department of Information Science and Electronic Engineering, Zhejiang University, Hangzhou, Zhejiang 310027 (China)

2012-10-01

We have performed ab initio density functional theory calculation to study the electronic transport properties of the tailored zigzag-edged graphene nanoribbon (ZGNR) with particular electronic transport channels. Our results demonstrated that tailoring the atomic structure had significantly influenced the electronic transport of the defective nanostructures, and could lead to the metal-semiconducting transition when sufficient atoms are tailored. The asymmetric I–V characteristics as a result of symmetry breaking have been exhibited, which indicates the route to utilize GNR as a basic component for novel nanoelectronics. -- Highlights: ► M–S transition induced by tailoring nanostructure. ► Asymmetric I–V curve due to symmetry breaking. ► Controllable electron transport by designing nanofiguration.

Structure of Alzheimer’s disease amyloid precursor protein copper-binding domain at atomic resolution

Energy Technology Data Exchange (ETDEWEB)

Kong, Geoffrey Kwai-Wai; Adams, Julian J. [Biota Structural Biology Laboratory, St Vincent’s Institute, 9 Princes Street, Fitzroy, Victoria 3065 (Australia); Cappai, Roberto [Department of Pathology and Centre for Neuroscience, The University of Melbourne, Victoria 3010 (Australia); The Mental Health Research Institute of Victoria, Parkville, Victoria 3052 (Australia); Bio21 Institute, The University of Melbourne, Victoria 3010 (Australia); Parker, Michael W., E-mail: mparker@svi.edu.au [Biota Structural Biology Laboratory, St Vincent’s Institute, 9 Princes Street, Fitzroy, Victoria 3065 (Australia); Bio21 Institute, The University of Melbourne, Victoria 3010 (Australia)

2007-10-01

An atomic resolution structure of the copper-binding domain of the Alzheimer’s disease amyloid precursor protein is presented. Amyloid precursor protein (APP) plays a central role in the pathogenesis of Alzheimer’s disease, as its cleavage generates the Aβ peptide that is toxic to cells. APP is able to bind Cu{sup 2+} and reduce it to Cu{sup +} through its copper-binding domain (CuBD). The interaction between Cu{sup 2+} and APP leads to a decrease in Aβ production and to alleviation of the symptoms of the disease in mouse models. Structural studies of CuBD have been undertaken in order to better understand the mechanism behind the process. Here, the crystal structure of CuBD in the metal-free form determined to ultrahigh resolution (0.85 Å) is reported. The structure shows that the copper-binding residues of CuBD are rather rigid but that Met170, which is thought to be the electron source for Cu{sup 2+} reduction, adopts two different side-chain conformations. These observations shed light on the copper-binding and redox mechanisms of CuBD. The structure of CuBD at atomic resolution provides an accurate framework for structure-based design of molecules that will deplete Aβ production.

All-loops calculation of the structure function x→0 in perturbative QCD

International Nuclear Information System (INIS)

Catani, S.

1991-01-01

We study in perturbative QCD the initial-state radiation associated to hadron processes in the semi-hard region of small x (x is the Bjorken variable). A recent analysis of the exclusive multi-gluon distributions to double (infrared and collinear) logarithmic accuracy is extended to the case of inclusive distributions, which we evaluate to single (infrared) logarithmic accuracy. Thus the resulting x→0 structure function or N→1 gluon anomalous dimension is computed to all-loops accuracy. For the inclusive distributions we are able to perform a calculation to such an accuracy by extensively using cancellations which originate from coherence of QCD radiation and the infrared regularity of real-virtual singularities. We find that the x→0 structure function satisfies the Lipatov equation. With the present study we therefore provide a new derivation of the Lipatov result in the context of hard collisions together with a fully exclusive description. We discuss the structure of the Lipatov equation in relation with the x→0 exclusive distributions previously obtained and with the Altarelli-Parisi equation valid for finite values of x. (orig.)

Validation of a method to quantify chromium, cadmium, manganese, nickel and lead in human whole blood, urine, saliva and hair samples by electrothermal atomic absorption spectrometry

Energy Technology Data Exchange (ETDEWEB)

Olmedo, P.; Pla, A.; Hernandez, A.F.; Lopez-Guarnido, O.; Rodrigo, L. [Department of Legal Medicine and Toxicology, University of Granada, School of Medicine (Spain); Gil, F., E-mail: fgil@ugr.es [Department of Legal Medicine and Toxicology, University of Granada, School of Medicine (Spain)

2010-02-05

For biological monitoring of heavy metal exposure in occupational toxicology, usually whole blood and urine samples are the most widely used and accepted matrix to assess internal xenobiotic exposure. Hair samples and saliva are also of interest in occupational and environmental health surveys but procedures for the determination of metals in saliva and hair are very scarce and to our knowledge there is no validation of a method to quantify Cr, Cd, Mn, Ni and Pb in four different human biological materials (whole blood, urine, saliva and axilary hair) by electrothermal atomization atomic absorption spectrometry (ETAAS). In the present study, quantification methods for the determination of Cr, Cd, Mn, Ni and Pb in whole blood, urine, saliva and axilary hair were validated according to the EU common standards. Pyrolisis and atomization temperatures have been determined. The main parameters evaluated were: detection and quantification limits, linearity range, repeatability, reproducibility, recovery and uncertainty. Accuracy of the methods was tested with the whole blood, urine and hair certified reference materials and recoveries of the spiked samples were acceptable ranged from 96.3 to 107.8%.

Validation of a method to quantify chromium, cadmium, manganese, nickel and lead in human whole blood, urine, saliva and hair samples by electrothermal atomic absorption spectrometry

International Nuclear Information System (INIS)

Olmedo, P.; Pla, A.; Hernandez, A.F.; Lopez-Guarnido, O.; Rodrigo, L.; Gil, F.

2010-01-01

For biological monitoring of heavy metal exposure in occupational toxicology, usually whole blood and urine samples are the most widely used and accepted matrix to assess internal xenobiotic exposure. Hair samples and saliva are also of interest in occupational and environmental health surveys but procedures for the determination of metals in saliva and hair are very scarce and to our knowledge there is no validation of a method to quantify Cr, Cd, Mn, Ni and Pb in four different human biological materials (whole blood, urine, saliva and axilary hair) by electrothermal atomization atomic absorption spectrometry (ETAAS). In the present study, quantification methods for the determination of Cr, Cd, Mn, Ni and Pb in whole blood, urine, saliva and axilary hair were validated according to the EU common standards. Pyrolisis and atomization temperatures have been determined. The main parameters evaluated were: detection and quantification limits, linearity range, repeatability, reproducibility, recovery and uncertainty. Accuracy of the methods was tested with the whole blood, urine and hair certified reference materials and recoveries of the spiked samples were acceptable ranged from 96.3 to 107.8%.

Spectroscopy of highly ionized atoms

International Nuclear Information System (INIS)

Livingston, A.E.

1987-01-01

The atomic structure and decay characteristics of excited states in multiply ionized atoms represent a fertile testing ground for atomic calculations ranging from accurate ab initio theory for few-electron systems to practical semi-empirical approaches for many-electron species. Excitation of fast ions by thin foils generally produces the highest ionization stages for heavy ions in laboratory sources. The associated characteristics of spectroscopic purity and high time resolution provide unique capabilities for studying the atomic properties of highly-ionized atoms. This report is limited to a brief discussion of three classes of atomic systems that are experiencing current theoretical and experimental interest: precision structure of helium-like ions, fine structure of doubly-excited states, and lifetimes of metastable states. Specific measurements in each of these types of systems are mentioned, with emphasis on the relation to studies involving slow, highly-charged ions

Validity and factor structure of the bodybuilding dependence scale

OpenAIRE

Smith, D; Hale, B

2004-01-01

Objectives: To investigate the factor structure, validity, and reliability of the bodybuilding dependence scale and to investigate differences in bodybuilding dependence between men and women and competitive and non-competitive bodybuilders.

Micropore Structure Representation of Sandstone in Petroleum Reservoirs Using an Atomic Force Microscope

International Nuclear Information System (INIS)

Bai Yong-Qiang; Zhu Xing; Wu Jun-Zheng; Bai Wen-Guang

2011-01-01

The pore structure of sandstone in an oil reservoir is investigated using atomic force microscopy (AFM). At nanoscale resolution, AFM images of sandstone show us the fine structure. The real height data of images display the three-dimensional space structure of sandstone effectively. The three-dimensional analysis results show that the AFM images of sandstone have unique characteristics that, like fingerprints, can identify different structural properties of sandstones. The results demonstrate that AFM is an effective method used to represent original sandstone in petroleum reservoirs, and may help geologists to appreciate the sandstone in oil reservoirs fully. (general)

Observations of resonance-like structures for positron-atom scattering at intermediate energies

International Nuclear Information System (INIS)

Dou, L.

1993-01-01

Absolute values of elastic differential cross sections (DCS's) are measured for position (e + ) scattering by argon (8.7-300 eV) krypton (6.7-400 eV) and also neon (13.6-400 eV) using a crossed-beam experimental setup. When the DCS's are plotted at fixed scattering angles of 30 degrees, 60 degrees, 90 degrees and 120 degrees versus energy it has been found that well-defined resonance-like structures are found at an energy of 55-60 eV for argon and at 25 and 200 eV for krypton, with a broader structure found between 100-200 eV for neon. These observed resonance-like structures are unusual because they occur at energies well above the known inelastic thresholds for these atoms. They may represent examples of open-quotes coupled channel shape resonancesclose quotes, first predicted by Higgins and Burke [1] for e + -H scattering in the vicinity of 36 eV (width ∼ 4 eV), which occurs only when both the elastic and positronium formation scattering channels are considered together. A more recent e + -H calculation by Hewitt et al. [2] supports the Higgins and Burke prediction. These predictions and the present observations suggest the existence of a new type of atomic scattering resonance

Thermal stability of atom configurations around Er atoms doped in InP by OMVPE

International Nuclear Information System (INIS)

Ofuchi, Hironori; Ito, Takashi; Kawamoto, Takeshi; Tabuchi, Masao; Fujiwara, Yasufumi; Takeda, Yoshikazu

1999-01-01

It has been found that there is a threshold growth temperature between 550 deg C and 580 deg C for the change of local structure around Er atoms in InP doped Er atoms grown by organometallic vapor phase epitaxy (OMVPE). To understand whether the structure change is induced at the growing surface or during the growth as an in situ annealing, the thermal stability of the local structures around the Er atoms doped in InP by the OMVPE at 530 deg C has been investigated by the extended X-ray absorption fine structure (EXAFS). The EXAFS analysis revealed that the local structure around the Er atoms, which existed substitutionally on In sites in the InP lattice, was stable against the post-growth annealing even for 1 h at 650 deg C. Therefore, it is concluded that the local structures are formed on the growth front, and not in the volume of InP by thermal annealing during or after the growth. (author)