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Sample records for pair distribution functions

  1. Local structure studies of materials using pair distribution function analysis

    NASA Astrophysics Data System (ADS)

    Peterson, Joseph W.

    A collection of pair distribution function studies on various materials is presented in this dissertation. In each case, local structure information of interest pushes the current limits of what these studies can accomplish. The goal is to provide insight into the individual material behaviors as well as to investigate ways to expand the current limits of PDF analysis. Where possible, I provide a framework for how PDF analysis might be applied to a wider set of material phenomena. Throughout the dissertation, I discuss 0 the capabilities of the PDF method to provide information pertaining to a material's structure and properties, ii) current limitations in the conventional approach to PDF analysis, iii) possible solutions to overcome certain limitations in PDF analysis, and iv) suggestions for future work to expand and improve the capabilities PDF analysis.

  2. Temperature effects on atomic pair distribution functions of melts

    NASA Astrophysics Data System (ADS)

    Ding, J.; Xu, M.; Guan, P. F.; Deng, S. W.; Cheng, Y. Q.; Ma, E.

    2014-02-01

    Using molecular dynamics simulations, we investigate the temperature-dependent evolution of the first peak position/shape in pair distribution functions of liquids. For metallic liquids, the peak skews towards the left (shorter distance side) with increasing temperature, similar to the previously reported anomalous peak shift. Making use of constant-volume simulations in the absence of thermal expansion and change in inherent structure, we demonstrate that the apparent shift of the peak maximum can be a result of the asymmetric shape of the peak, as the asymmetry increases with temperature-induced spreading of neighboring atoms to shorter and longer distances due to the anharmonic nature of the interatomic interaction potential. These findings shed light on the first-shell expansion/contraction paradox for metallic liquids, aside from possible changes in local topological or chemical short-range ordering. The melts of covalent materials are found to exhibit an opposite trend of peak shift, which is attributed to an effect of the directionality of the interatomic bonds.

  3. Algorithm for systematic peak extraction from atomic pair distribution functions.

    PubMed

    Granlund, L; Billinge, S J L; Duxbury, P M

    2015-07-01

    The study presents an algorithm, ParSCAPE, for model-independent extraction of peak positions and intensities from atomic pair distribution functions (PDFs). It provides a statistically motivated method for determining parsimony of extracted peak models using the information-theoretic Akaike information criterion (AIC) applied to plausible models generated within an iterative framework of clustering and chi-square fitting. All parameters the algorithm uses are in principle known or estimable from experiment, though careful judgment must be applied when estimating the PDF baseline of nanostructured materials. ParSCAPE has been implemented in the Python program SrMise. Algorithm performance is examined on synchrotron X-ray PDFs of 16 bulk crystals and two nanoparticles using AIC-based multimodeling techniques, and particularly the impact of experimental uncertainties on extracted models. It is quite resistant to misidentification of spurious peaks coming from noise and termination effects, even in the absence of a constraining structural model. Structure solution from automatically extracted peaks using the Liga algorithm is demonstrated for 14 crystals and for C60. Special attention is given to the information content of the PDF, theory and practice of the AIC, as well as the algorithm's limitations. PMID:26131896

  4. Temperature effects on atomic pair distribution functions of melts

    SciTech Connect

    Ding, J. Ma, E.; Xu, M.; Guan, P. F.; Deng, S. W.; Cheng, Y. Q.

    2014-02-14

    Using molecular dynamics simulations, we investigate the temperature-dependent evolution of the first peak position/shape in pair distribution functions of liquids. For metallic liquids, the peak skews towards the left (shorter distance side) with increasing temperature, similar to the previously reported anomalous peak shift. Making use of constant-volume simulations in the absence of thermal expansion and change in inherent structure, we demonstrate that the apparent shift of the peak maximum can be a result of the asymmetric shape of the peak, as the asymmetry increases with temperature-induced spreading of neighboring atoms to shorter and longer distances due to the anharmonic nature of the interatomic interaction potential. These findings shed light on the first-shell expansion/contraction paradox for metallic liquids, aside from possible changes in local topological or chemical short-range ordering. The melts of covalent materials are found to exhibit an opposite trend of peak shift, which is attributed to an effect of the directionality of the interatomic bonds.

  5. Pair distribution function study on compression of liquid gallium

    SciTech Connect

    Luo, Shengnian; Yu, Tony; Chen, Jiuhua; Ehm, Lars; Guo, Quanzhong; Parise, John

    2008-01-01

    Integrating a hydrothermal diamond anvil cell (HDAC) and focused high energy x-ray beam from the superconductor wiggler X17 beamline at the National Synchrotron Light Source (NSLS) at the Brookhaven National Laboratory (BNL), we have successfully collected high quality total x-ray scattering data of liquid gallium. The experiments were conducted at a pressure range from 0.1GPa up to 2GPa at ambient temperature. For the first time, pair distribution functions (PDF) for liquid gallium at high pressure were derived up to 10 {angstrom}. Liquid gallium structure has been studied by x-ray absorption (Di Cicco & Filipponi, 1993; Wei et al., 2000; Comez et al., 2001), x-ray diffraction studies (Waseda & Suzuki, 1972), and molecular dynamics simulation (Tsay, 1993; Hui et al., 2002). These previous reports have focused on the 1st nearest neighbor structure, which tells us little about the atomic arrangement outside the first shell in non- crystalline materials. This study focuses on the structure of liquid gallium and the atomic structure change due to compression. The PDF results show that the observed atomic distance of the first nearest neighbor at 2.78 {angstrom} (first G(r) peak and its shoulder at the higher Q position) is consistent with previous studies by x-ray absorption (2.76 {angstrom}, Comez et al., 2001). We have also observed that the first nearest neighbor peak position did not change with pressure increasing, while the farther peaks positions in the intermediate distance range decreased with pressure increasing. This leads to a conclusion of the possible existence of 'locally rigid units' in the liquid. With the addition of reverse Monte Carlo modeling, we have observed that the coordination number in the local rigit unit increases with pressure. The bulk modulus of liquid gallium derived from the volume compression curve at ambient temperature (300K) is 12.1(6) GPa.

  6. Atom Pair Distribution Functions of Liquid Water at 25circC from Neutron Diffraction

    NASA Astrophysics Data System (ADS)

    Narten, A. H.; Thiessen, W. E.; Blum, L.

    1982-09-01

    The structure of liquid water is described by three atom pair distribution functions gOO(r), gOH(r), and gHH(r). These functions have now been derived from neutron diffraction data on four mixtures of light and heavy water. They will provide a crucial and sensitive test for proposed models of liquid water.

  7. Uncovering the intrinsic geometry from the atomic pair distribution function of nanomaterials

    NASA Astrophysics Data System (ADS)

    Lei, Ming; de Graff, Adam M. R.; Thorpe, M. F.; Wells, Stephen A.; Sartbaeva, Asel

    2009-07-01

    Atomic pair distribution functions are useful because they have an easy intuitive interpretation and can be obtained both experimentally and from computer-generated structure models. For bulk materials, atomic pair distribution functions are solely determined by the intrinsic atomic geometry, i.e., how atoms are positioned with respect to one another. For a nanomaterial, however, the atomic pair distribution function also depends on the shape and size of the nanomaterial. A modified form of the radial distribution function is discussed that decouples shape and size effects from intrinsic effects so that nanomaterials of any shape and size, sharing a common atomic geometry, map onto a universal curve, by using a form factor. Mapping onto this universal curve allows differences in the intrinsic atomic geometry of nanomaterials of various shapes and sizes to be directly compared. This approach is demonstrated on nanoscale amorphous and crystalline silica models. It is shown how form factors can be computed for arbitrary shapes and this is illustrated for tetrahedral nanoparticles of vitreous silica.

  8. Ultrasound-driven preparation and pair distribution function-assisted structure solution of a copper-based layered coordination polymer.

    PubMed

    Mohideen, M Infas; Allan, Phoebe K; Chapman, Karena W; Hriljac, Joseph A; Morris, Russell E

    2014-07-21

    Nanoparticles of a copper-based layered coordination polymer, STAM-2, have been prepared via an ultrasound mediated transformation from a layered metal-organic framework, STAM-1. The structure of the material was then solved using pair distribution function analysis to identify the structural units present and the final structural model refined against the pair distribution function data. PMID:24310447

  9. Local Atomic Structure of Semiconductor Alloys Using Pair Distribution Function Analysis

    SciTech Connect

    Billinge, S.J.L.; Thorpe, M.F.

    2002-06-24

    We have been taking advantage of recent experimental developments, which involve utilizing diffraction data from x-rays or neutrons out to very large wave-vectors, to obtain a detailed structural characterization of semiconductor alloys. This approach allows an accurate Pair Distribution Function (PDF) to be obtained to 20A and beyond and reveals the local structure of the alloy directly. These data can be modeled explicitly to learn about local correlations and short-range order in materials. We are combining theory, modeling and experiments to study a range of materials from semiconductors to thermoelectrics and proton conductors.

  10. Finite Size Effects on the Real-Space Pair Distribution Function of Nanoparticles

    SciTech Connect

    Gilbert, Benjamin

    2008-10-01

    The pair distribution function (PDF) method is a powerful approach for the analysis of the structure of nanoparticles. An important approximation used in nanoparticle PDF simulations is the incorporation of a form factor describing nanoparticle size and shape. The precise effect of the form factor on the PDF is determined by both particle shape and structure if these characteristics are both anisotropic and correlated. The correct incorporation of finite size effects is important for distinguishing and quantifying the structural consequences of small particle size in nanomaterials.

  11. Calibration and data collection protocols for reliable lattice parameter values in electron pair distribution function studies

    SciTech Connect

    Abeykoon, A. M. Milinda; Hu, Hefei; Wu, Lijun; Zhu, Yimei; Billinge, Simon J. L.

    2015-01-30

    Different protocols for calibrating electron pair distribution function (ePDF) measurements are explored and described for quantitative studies on nanomaterials. It is found that the most accurate approach to determine the camera length is to use a standard calibration sample of Au nanoparticles from the National Institute of Standards and Technology. Different protocols for data collection are also explored, as are possible operational errors, to find the best approaches for accurate data collection for quantitative ePDF studies.

  12. Directional pair distribution function for diffraction line profile analysis of atomistic models

    PubMed Central

    Leonardi, Alberto; Leoni, Matteo; Scardi, Paolo

    2013-01-01

    The concept of the directional pair distribution function is proposed to describe line broadening effects in powder patterns calculated from atomistic models of nano-polycrystalline microstructures. The approach provides at the same time a description of the size effect for domains of any shape and a detailed explanation of the strain effect caused by the local atomic displacement. The latter is discussed in terms of different strain types, also accounting for strain field anisotropy and grain boundary effects. The results can in addition be directly read in terms of traditional line profile analysis, such as that based on the Warren–Averbach method. PMID:23396818

  13. Quantitative Nanostructure Characterization Using Atomic Pair Distribution Functions Obtained From Laboratory Electron Microscopes

    SciTech Connect

    Abeykoon M.; Billinge S.; Malliakas, C.D.; Juhas, P.; Bozin, E.S.; Kanatzidis, M.G.

    2012-05-01

    Quantitatively reliable atomic pair distribution functions (PDFs) have been obtained from nanomaterials in a straightforward way from a standard laboratory transmission electron microscope (TEM). The approach looks very promising for making electron derived PDFs (ePDFs) a routine step in the characterization of nanomaterials because of the ubiquity of such TEMs in chemistry and materials laboratories. No special attachments such as energy filters were required on the microscope. The methodology for obtaining the ePDFs is described as well as some opportunities and limitations of the method.

  14. Differential Pair Distribution Function Study of the Structure of Arsenate Adsorbed on Nanocrystalline [gamma]-Alumina

    SciTech Connect

    Li, Wei; Harrington, Richard; Tang, Yuanzhi; Kubicki, James D.; Aryanpour, Masoud; Reeder, Richard J.; Parise, John B.; Phillips, Brian L.

    2012-03-15

    Structural information is important for understanding surface adsorption mechanisms of contaminants on metal (hydr)oxides. In this work, a novel technique was employed to study the interfacial structure of arsenate oxyanions adsorbed on {gamma}-alumina nanoparticles, namely, differential pair distribution function (d-PDF) analysis of synchrotron X-ray total scattering. The d-PDF is the difference of properly normalized PDFs obtained for samples with and without arsenate adsorbed, otherwise identically prepared. The real space pattern contains information on atomic pair correlations between adsorbed arsenate and the atoms on {gamma}-alumina surface (Al, O, etc.). PDF results on the arsenate adsorption sample on {gamma}-alumina prepared at 1 mM As concentration and pH 5 revealed two peaks at 1.66 {angstrom} and 3.09 {angstrom}, corresponding to As-O and As-Al atomic pair correlations. This observation is consistent with those measured by extended X-ray absorption fine structure (EXAFS) spectroscopy, which suggests a first shell of As-O at 1.69 {+-} 0.01 {angstrom} with a coordination number of 4 and a second shell of As-Al at 3.13 {+-} 0.04 {angstrom} with a coordination number of 2. These results are in agreement with a bidentate binuclear coordination environment to the octahedral Al of {gamma}-alumina as predicted by density functional theory (DFT) calculation.

  15. Novel trends in pair distribution function approaches on bulk systems with nanoscale heterogeneities

    DOE PAGESBeta

    Emil S. Bozin; Billinge, Simon J. L.

    2016-07-29

    Novel materials for high performance applications increasingly exhibit structural order on the nanometer length scale; a domain where crystallography, the basis of Rietveld refinement, fails [1]. In such instances the total scattering approach, which treats Bragg and diffuse scattering on an equal basis, is a powerful approach. In recent years, the analysis of the total scattering data became an invaluable tool and the gold standard for studying nanocrystalline, nanoporous, and disordered crystalline materials. The data may be analyzed in reciprocal space directly, or Fourier transformed to the real-space atomic pair distribution function (PDF) and this intuitive function examined for localmore » structural information. Here we give a number of illustrative examples, for convenience picked from our own work, of recent developments and applications of total scattering and PDF analysis to novel complex materials. There are many other wonderful examples from the work of others.« less

  16. Organic-modified and biological silica studied by synchrotron x-ray pair distribution function measurements

    NASA Astrophysics Data System (ADS)

    Dimasi, Elaine; Jeffryes, Clayton; Rorrer, Gregory; Belton, David; Perry, Carole

    2007-03-01

    Biomineralization is a process by which living organisms create composite organic/mineral tissues which have hierarchical structures on micron and submicron scales. Fine control over mineral phase and morphology make biomineralization an important inspiration for materials science. It is often not appreciated that even amorphous minerals such as silica can exhibit hierarchical structure and special properties. One difficulty is that the molecular structures of amorphous phases can be hard to elucidate. We are exploring the use of pair distribution function measurements from synchrotron x-ray scattering to study silica structures, comparing both synthetic organic-modifed silicas and germanium-containing biosilica from diatoms. The raw scattering patterns show clear differences. We will discuss how these data can be scrutinized to determine what differences may be created at the molecular level by different silicification processes.

  17. Total-scattering pair-distribution function of organic material from powder electron diffraction data.

    PubMed

    Gorelik, Tatiana E; Schmidt, Martin U; Kolb, Ute; Billinge, Simon J L

    2015-04-01

    This paper shows that pair-distribution function (PDF) analyses can be carried out on organic and organometallic compounds from powder electron diffraction data. Different experimental setups are demonstrated, including selected area electron diffraction and nanodiffraction in transmission electron microscopy or nanodiffraction in scanning transmission electron microscopy modes. The methods were demonstrated on organometallic complexes (chlorinated and unchlorinated copper phthalocyanine) and on purely organic compounds (quinacridone). The PDF curves from powder electron diffraction data, called ePDF, are in good agreement with PDF curves determined from X-ray powder data demonstrating that the problems of obtaining kinematical scattering data and avoiding beam damage of the sample are possible to resolve. PMID:25510245

  18. The total scattering atomic pair distribution function: New methodology for nanostructure analysis

    NASA Astrophysics Data System (ADS)

    Masadeh, Ahmad

    The conventional xray diffration (XRD) methods probe for the presence of long-range order (periodic structure) which are reflected in the Bragg peaks. Local structural deviations or disorder mainly affect the diffuse scattering intensity. In order to obtain structural information about both long-range order and local structure disorder, a technique that takes in account both Bragg and diffuse scattering need to be employed, such as the atomic pair distribution function (PDF) technique. This work introduces a PDF based methodology to quantitatively investigate nanostructure materials in general. The introduced methodology can be applied to extract quantitatively structural information about structure, crystallinity level, core/shell size, nanoparticle size, and inhomogeneous internal strain in the measured nanoparticles. This method is generally applicable to the characterization of the nano-scale solid, many of which may exhibit complex disorder and strain

  19. Total-scattering pair-distribution function of organic material from powder electron diffraction data

    SciTech Connect

    Gorelik, Tatiana E.; Billinge, Simon J. L.; Schmidt, Martin U.; Kolb, Ute

    2015-04-01

    This paper shows for the first time that pair-distribution function analyses can be carried out on organic and organo-metallic compounds from powder electron diffraction data. Different experimental setups are demonstrated, including selected area electron diffraction (SAED) and nanodiffraction in transmission electron microscopy (TEM) or nanodiffraction in scanning transmission electron microscopy (STEM) modes. The methods were demonstrated on organo-metallic complexes (chlorinated and unchlorinated copper-phthalocyanine) and on purely organic compounds (quinacridone). The PDF curves from powder electron diffraction data, called ePDF, are in good agreement with PDF curves determined from X-ray powder data demonstrating that the problems of obtaining kinematical scattering data and avoiding beam-damage of the sample are possible to resolve.

  20. Total-scattering pair-distribution function of organic material from powder electron diffraction data

    DOE PAGESBeta

    Gorelik, Tatiana E.; Billinge, Simon J. L.; Schmidt, Martin U.; Kolb, Ute

    2015-04-01

    This paper shows for the first time that pair-distribution function analyses can be carried out on organic and organo-metallic compounds from powder electron diffraction data. Different experimental setups are demonstrated, including selected area electron diffraction (SAED) and nanodiffraction in transmission electron microscopy (TEM) or nanodiffraction in scanning transmission electron microscopy (STEM) modes. The methods were demonstrated on organo-metallic complexes (chlorinated and unchlorinated copper-phthalocyanine) and on purely organic compounds (quinacridone). The PDF curves from powder electron diffraction data, called ePDF, are in good agreement with PDF curves determined from X-ray powder data demonstrating that the problems of obtaining kinematical scattering datamore » and avoiding beam-damage of the sample are possible to resolve.« less

  1. Expansions of the pair distribution function and the second-order density matrix in terms of homogeneous functionals

    NASA Astrophysics Data System (ADS)

    Liu, Shubin

    1996-12-01

    It has been shown previously that under certain circumstances the correlation energy density functional Ec[ρ] and its kinetic Tc[ρ] and potential Vc[ρ] components can be expanded in terms of homogeneous functionals An[ρ], with n=1,2,3,..., and where An[ρ] is homogeneous of degree (1-n) with respect to coordinate scaling. In this paper, we extend the analysis to expand similarly the pair distribution function gxc([ρ]r1,r2) and the second-order density matrix ρ2(r1,r2). It is found that both of them can be expanded under certain circumstances in terms of functionals an([ρ]r1,r2), with n=1,2,3,..., that are homogeneous of degree -n in coordinate scaling. The An[ρ] are explicitly obtained in terms of the an([ρ]r1,r2).

  2. High pressure pair distribution function studies of Green River oil shale.

    SciTech Connect

    Chapman, K. W.; Chupas, P. J.; Locke, D. R.; Winans, R. E.; Pugmire, R. J.; Univ. of Utah

    2008-01-01

    The compression behavior of a silicate-rich oil shale from the Green River formation in the pressure range 0.0-2.4 GPa was studied using in situ high pressure X-ray pair distribution function (PDF) measurements for the sample contained within a Paris-Edinburgh cell. The real-space local structural information in the PDF, G(r), was used to evaluate the compressibility of the oil shale. Specifically, the pressure-induced reduction in the medium- to long-range atom distances ({approx}6-20 {angstrom}) yielded an average sample compressibility corresponding to a bulk modulus of ca. 61-67 GPa. A structural model consisting of a three phase mixture of the principal crystalline oil shale components (quartz, albite and Illite) provided a good fit to the ambient pressure PDF data (R {approx} 30.7%). Indeed the features in the PDF beyond {approx} {angstrom}, were similarly well fit by a single phase model of the highest symmetry, highly crystalline quartz component. The factors influencing the observed compression behavior are discussed.

  3. Synthesis and structural characterisation using Rietveld and pair distribution function analysis of layered mixed titaniumzirconium phosphates

    SciTech Connect

    Burnell, Victoria A.; Readman, Jennifer E.; Tang, Chiu C; Parker, Julia E.; Thompson, Stephen P.; Hriljac, Joseph A.

    2010-07-24

    Crystalline metal (IV) phosphates with variable zirconium-to-titanium molar ratios of general formula (Ti1-xZrx)(HPO4)2 • H2O have been prepared by precipitation of soluble salts of the metals with phosphoric acid and heating the amorphous solids in 12 M H3PO4 in an autoclave. The new materials are structurally characterised by Rietveld analysis of synchrotron X-ray powder diffraction data and pair distribution function (PDF) analysis of high energy synchrotron X-ray total scattering data. A broad range of zirconium-titanium phosphate solid solutions were formed showing isomorphous substitution of titanium by zirconium in the α-titanium phosphate lattice and vice versa for titanium substitution into the α-zirconium phosphate lattice. In both cases the solubility is partial with the coexistence of two substituted phases observed in samples with nominal compositions between the solubility limits.

  4. Towards solution and refinement of organic crystal structures by fitting to the atomic pair distribution function.

    PubMed

    Prill, Dragica; Juhás, Pavol; Billinge, Simon J L; Schmidt, Martin U

    2016-01-01

    A method towards the solution and refinement of organic crystal structures by fitting to the atomic pair distribution function (PDF) is developed. Approximate lattice parameters and molecular geometry must be given as input. The molecule is generally treated as a rigid body. The positions and orientations of the molecules inside the unit cell are optimized starting from random values. The PDF is obtained from carefully measured X-ray powder diffraction data. The method resembles `real-space' methods for structure solution from powder data, but works with PDF data instead of the diffraction pattern itself. As such it may be used in situations where the organic compounds are not long-range-ordered, are poorly crystalline, or nanocrystalline. The procedure was applied to solve and refine the crystal structures of quinacridone (β phase), naphthalene and allopurinol. In the case of allopurinol it was even possible to successfully solve and refine the structure in P1 with four independent molecules. As an example of a flexible molecule, the crystal structure of paracetamol was refined using restraints for bond lengths, bond angles and selected torsion angles. In all cases, the resulting structures are in excellent agreement with structures from single-crystal data. PMID:26697868

  5. Towards solution and refinement of organic crystal structures by fitting to the atomic pair distribution function

    DOE PAGESBeta

    Prill, Dragica; Juhas, Pavol; Billinge, Simon J. L.; Schmidt, Martin U.

    2016-01-01

    In this study, a method towards the solution and refinement of organic crystal structures by fitting to the atomic pair distribution function (PDF) is developed. Approximate lattice parameters and molecular geometry must be given as input. The molecule is generally treated as a rigid body. The positions and orientations of the molecules inside the unit cell are optimized starting from random values. The PDF is obtained from carefully measured X-ray powder diffraction data. The method resembles `real-space' methods for structure solution from powder data, but works with PDF data instead of the diffraction pattern itself. As such it may bemore » used in situations where the organic compounds are not long-range-ordered, are poorly crystalline, or nanocrystalline. The procedure was applied to solve and refine the crystal structures of quinacridone (β phase), naphthalene and allopurinol. In the case of allopurinol it was even possible to successfully solve and refine the structure in P1 with four independent molecules. As an example of a flexible molecule, the crystal structure of paracetamol was refined using restraints for bond lengths, bond angles and selected torsion angles. In all cases, the resulting structures are in excellent agreement with structures from single-crystal data.« less

  6. Total Scattering and Pair Distribution Function Analysis in Modelling Disorder in PZN

    DOE PAGESBeta

    Whitfield, Ross E.; Goossens, Darren J; Welberry, T. R.

    2016-01-01

    The ability of the pair distribution function (PDF) analysis of total scattering (TS) from a powder to determine the local ordering in ferroelectric PZN (PbZn1/3Nb2/3O3) has been explored by comparison with a model established using single-crystal diffuse scattering (SCDS). While X-ray PDF analysis is discussed, the focus is on neutron diffraction results because of the greater extent of the data and the sensitivity of the neutron to oxygen atoms, the behaviour of which is important in PZN. The PDF was shown to be sensitive to many effects not apparent in the average crystal structure, including variations in the B-site—O separationmore » distances and the fact that (110) Pb2+ displacements are most likely. A qualitative comparison between SCDS and the PDF shows that some features apparent in SCDS were not apparent in the PDF. These tended to pertain to short-range correlations in the structure, rather than to interatomic separations. For example, in SCDS the short-range alternation of the B-site cations was quite apparent in diffuse scattering at (½ ½ ½), whereas it was not apparent in the PDF.« less

  7. Atomic Structure of a Cesium Aluminosilicate Geopolymer: A Pair Distribution Function Study

    SciTech Connect

    Bell, J.; Sarin, P; Provis, J; Haggerty, R; Driemeyer, P; Chupas, P; van Deventer, J; Kriven, W

    2008-01-01

    The atomic pair distribution function (PDF) method was used to study the structure of cesium aluminosilicate geopolymer. The geopolymer was prepared by reacting metakaolin with cesium silicate solution followed by curing at 50C for 24 h in a sealed container. Heating of Cs-geopolymer above 1000C resulted in formation of crystalline pollucite (CsAlSi{sub 2}O{sub 6}). PDF refinement of the pollucite phase formed displayed an excellent fit over the 10-30 {angstrom} range when compared with a cubic pollucite model. A poorer fit was attained from 1-10 {angstrom} due to an additional amorphous phase present in the heated geopolymer. On the basis of PDF analysis, unheated Cs-geopolymer displayed structural ordering similar to pollucite up to a length scale of 9 {angstrom}, despite some differences. Our results suggest that hydrated Cs{sup +} ions were an integral part of the Cs-geopolymer structure and that most of the water present was not associated with Al-OH or Si-OH bonds.

  8. Towards solution and refinement of organic crystal structures by fitting to the atomic pair distribution function

    SciTech Connect

    Prill, Dragica; Juhas, Pavol; Billinge, Simon J. L.; Schmidt, Martin U.

    2016-01-01

    In this study, a method towards the solution and refinement of organic crystal structures by fitting to the atomic pair distribution function (PDF) is developed. Approximate lattice parameters and molecular geometry must be given as input. The molecule is generally treated as a rigid body. The positions and orientations of the molecules inside the unit cell are optimized starting from random values. The PDF is obtained from carefully measured X-ray powder diffraction data. The method resembles `real-space' methods for structure solution from powder data, but works with PDF data instead of the diffraction pattern itself. As such it may be used in situations where the organic compounds are not long-range-ordered, are poorly crystalline, or nanocrystalline. The procedure was applied to solve and refine the crystal structures of quinacridone (β phase), naphthalene and allopurinol. In the case of allopurinol it was even possible to successfully solve and refine the structure in P1 with four independent molecules. As an example of a flexible molecule, the crystal structure of paracetamol was refined using restraints for bond lengths, bond angles and selected torsion angles. In all cases, the resulting structures are in excellent agreement with structures from single-crystal data.

  9. Total Scattering and Pair Distribution Function Analysis in Modelling Disorder in PZN

    SciTech Connect

    Whitfield, Ross E.; Goossens, Darren J; Welberry, T. R.

    2016-01-01

    The ability of the pair distribution function (PDF) analysis of total scattering (TS) from a powder to determine the local ordering in ferroelectric PZN (PbZn1/3Nb2/3O3) has been explored by comparison with a model established using single-crystal diffuse scattering (SCDS). While X-ray PDF analysis is discussed, the focus is on neutron diffraction results because of the greater extent of the data and the sensitivity of the neutron to oxygen atoms, the behaviour of which is important in PZN. The PDF was shown to be sensitive to many effects not apparent in the average crystal structure, including variations in the B-site—O separation distances and the fact that (110) Pb2+ displacements are most likely. A qualitative comparison between SCDS and the PDF shows that some features apparent in SCDS were not apparent in the PDF. These tended to pertain to short-range correlations in the structure, rather than to interatomic separations. For example, in SCDS the short-range alternation of the B-site cations was quite apparent in diffuse scattering at (½ ½ ½), whereas it was not apparent in the PDF.

  10. X-ray Pair Distribution Function Analysis of Potassium Based Geopolymer

    SciTech Connect

    Bell, J.; Sarin, P; Driemeyer, P; Haggerty, R; Chupas, P; Kriven, W

    2008-01-01

    The atomic structure of geopolymers is often described as amorphous with a local structure that is equivalent to that of crystalline zeolites. However, this structural relationship has never been quantified beyond a first-nearest-neighbor bonding environment. In this study, the short to medium range (1 nm) structural order of metakaolin-based KAlSi{sub 2}O{sub 6}{center_dot}5.5H{sub 2}O geopolymer was quantified and compared to zeolitic tetragonal leucite (KAlSi2O6) using the X-ray atomic pair distribution function technique. Unheated KAlSi{sub 2}O{sub 6}{center_dot}5.5H{sub 2}O was found to be structurally similar to leucite out to a length of 8 {angstrom}, but had increased medium range disorder over the 4.5 {angstrom} < r < 8 {angstrom} range. On heating to >300 C, changes in the short to medium range structure were observed due to dehydration and removal of chemically bound water. Crystallization of leucite occurred in samples heated beyond 1050 C. Refinements of a leucite model against the PDF data for geopolymer heated to 1100 C for 24 h yielded a good fit.

  11. In situ X-ray pair distribution function analysis of geopolymer gel nanostructure formation kinetics.

    PubMed

    White, Claire E; Provis, John L; Bloomer, Breaunnah; Henson, Neil J; Page, Katharine

    2013-06-14

    With the ever-increasing environmentally-driven demand for technologically advanced structural materials, geopolymer cement is fast becoming a viable alternative to traditional cements due to its proven engineering characteristics and the reduction in CO2 emitted during manufacturing (as much as 80% less CO2 emitted in manufacture, compared to ordinary Portland cement). Nevertheless, much remains unknown regarding the kinetics of reaction responsible for nanostructural evolution during the geopolymerisation process. Here, in situ X-ray total scattering measurements and pair distribution function (PDF) analysis are used to quantify the extent of reaction as a function of time for alkali-activated metakaolin/slag geopolymer binders, including the impact of various activators (alkali hydroxide/silicate) on the kinetics of the geopolymerisation reaction. Quantifying the reaction process in situ from X-ray PDF data collected during the initial ten hours can provide an estimate of the total reaction extent, but when combined with data obtained at longer times (128 days here) enables more accurate determination of the overall rate of reaction. To further assess the initial stages of the geopolymerisation reaction process, a pseudo-single step first order rate equation is fitted to the extent of reaction data, which reveals important mechanistic information regarding the role of free silica in the activators in the evolution of the binder systems. Hence, it is shown that in situ X-ray PDF analysis is an ideal experimental local structure tool to probe the reaction kinetics of complex reacting systems involving transitions between disordered/amorphous phases, of which geopolymerisation is an important example. PMID:23450172

  12. Solid state NMR and pair distribution function studies of silicon electrodes for lithium-ion batteries

    NASA Astrophysics Data System (ADS)

    Key, Baris

    The universally used negative electrode material in a LIB is carbon, because of its moderate capacity (372 mAhg-1 for graphite), cyclability and high rate capability. However, new, low cost, safe electrode materials with higher capacities are still urgently required for both portable and transportation applications. Silicon anodes are particularly attractive alternatives to carbon with extremely high gravimetric energy densities (3572 mAhg-1). Compared to graphite, silicon has a massive volumetric capacity of 8322 mAhcm-3 (calculated based on the original volume of silicon) which is approximately ten times that graphite. At room temperature, upon electrochemical lithiation, silicon undergoes a crystalline to amorphous phase transition forming a lithiated amorphous silicide phase. Unfortunately, due to the amorphous nature of the lithiated silicides, it is not possible to monitor all the structural changes that occur during lithium insertion/removal with conventional methods such as diffraction. The short range order of the amorphous materials remains unknown, preventing attempts to optimize performance based on electrochemical-structure correlations. In this work, a combination of local structure probes, ex-situ 7Li nuclear magnetic resonance (NMR) studies and pair distribution function (PDF) analysis of X-ray data was applied to investigate the changes in short range order that occur during the initial charge and discharge cycles. The distinct electrochemical profiles observed subsequent to the 1 st discharge have been shown to be associated with the formation of distinct amorphous lithiated silicide structures. A (de)lithiation model consisting of four different mechanisms, each being valid for regions of the charge or discharge process is proposed to explain the hysteresis and the steps in the electrochemical profile observed during lithiation and delithiation of Si. A spontaneous reaction of the fully lithiated lithium silicide with the electrolyte is directly

  13. Pair distribution function analysis of La(Fe{sub 1−x}Ru{sub x})AsO compounds

    SciTech Connect

    Martinelli, A.; Palenzona, A.; Ferdeghini, C.; Mazzani, M.; Bonfa', P.; Allodi, G.

    2014-12-15

    The local structures of La(Fe{sub 1−x}Ru{sub x})AsO (0.00≤x≤0.80) compounds were investigated by means of pair distribution function analysis at room temperature; as a result, no phase separation or clustering takes place. Local distortions are no longer correlated beyond ∼15 Å for both pure and substituted samples, indicating that the presence of Ru atoms does not determine a notable variation in the length scale of the local distortion. Different types of short range correlation between Fe and Ru atoms do not produce significant changes in the pair distribution function. - Graphical abstract: Fe–As and Ru–As bond length distributions as obtained by pair distribution function analysis of La(Fe{sub 0.70}Ru{sub 0.30})AsO; As atoms (purple spheres) undergo a random shifting around their crystallographic positions (red spheres: Fe/Ru atoms). - Highlights: • No phase separation or clustering takes place in La(Fe{sub 1−x}Ru{sub x})AsO solid solutions. • Local distortions are no longer correlated beyond ∼15 Å. • Ru displays a tendency towards local enrichment in the transition metal sublattice.

  14. Direct assignment of molecular vibrations via normal mode analysis of the neutron dynamic pair distribution function technique

    SciTech Connect

    Fry-Petit, A. M. E-mail: afry@fullerton.edu; Sheckelton, J. P.; McQueen, T. M. E-mail: afry@fullerton.edu; Rebola, A. F.; Fennie, C. J.; Mourigal, M.; Valentine, M.; Drichko, N.

    2015-09-28

    For over a century, vibrational spectroscopy has enhanced the study of materials. Yet, assignment of particular molecular motions to vibrational excitations has relied on indirect methods. Here, we demonstrate that applying group theoretical methods to the dynamic pair distribution function analysis of neutron scattering data provides direct access to the individual atomic displacements responsible for these excitations. Applied to the molecule-based frustrated magnet with a potential magnetic valence-bond state, LiZn{sub 2}Mo{sub 3}O{sub 8}, this approach allows direct assignment of the constrained rotational mode of Mo{sub 3}O{sub 13} clusters and internal modes of MoO{sub 6} polyhedra. We anticipate that coupling this well known data analysis technique with dynamic pair distribution function analysis will have broad application in connecting structural dynamics to physical properties in a wide range of molecular and solid state systems.

  15. Direct assignment of molecular vibrations via normal mode analysis of the neutron dynamic pair distribution function technique.

    PubMed

    Fry-Petit, A M; Rebola, A F; Mourigal, M; Valentine, M; Drichko, N; Sheckelton, J P; Fennie, C J; McQueen, T M

    2015-09-28

    For over a century, vibrational spectroscopy has enhanced the study of materials. Yet, assignment of particular molecular motions to vibrational excitations has relied on indirect methods. Here, we demonstrate that applying group theoretical methods to the dynamic pair distribution function analysis of neutron scattering data provides direct access to the individual atomic displacements responsible for these excitations. Applied to the molecule-based frustrated magnet with a potential magnetic valence-bond state, LiZn2Mo3O8, this approach allows direct assignment of the constrained rotational mode of Mo3O13 clusters and internal modes of MoO6 polyhedra. We anticipate that coupling this well known data analysis technique with dynamic pair distribution function analysis will have broad application in connecting structural dynamics to physical properties in a wide range of molecular and solid state systems. PMID:26429001

  16. Relationship Between the Atomic Pair Distribution Function and Small-Angle Scattering: Implications for Modeling of Nanoparticles

    SciTech Connect

    Billinge, S.; Farrowa, C.L.

    2009-05-01

    The relationship between the equations used in the atomic pair distribution function (PDF) method and those commonly used in small-angle-scattering (SAS) analyses is explicitly shown. The origin of the sloping baseline, -4{pi}r{rho}{sub 0}, in PDFs of bulk materials is identified as originating from the SAS intensity that is neglected in PDF measurements. The nonlinear baseline in nanoparticles has the same origin, and contains information about the shape and size of the nanoparticles.

  17. Calibration and data collection protocols for reliable lattice parameter values in electron pair distribution function (ePDF) studies

    DOE PAGESBeta

    Abeykoon, A. M. Milinda; Hu, Hefei; Wu, Lijun; Zhu, Yimei; Billinge, Simon J. L.

    2015-02-01

    We explore and describe different protocols for calibrating electron pair distribution function (ePDF) measurements for quantitative studies on nano-materials. We find the most accurate approach to determine the camera-length is to use a standard calibration sample of Au nanoparticles from National Institute of Standards and Technology. Different protocols for data collection are also explored, as are possible operational errors, to find the best approaches for accurate data collection for quantitative ePDF studies.

  18. Nyquist-Shannon sampling theorem applied to refinements of the atomic pair distribution function

    SciTech Connect

    Farrow, Christopher L.; Shaw, Margaret; Kim, Hyunjeong; Juhás, Pavol; Billinge, Simon J.L.

    2011-12-07

    We have systematically studied the optimal real-space sampling of atomic pair distribution (PDF) data by comparing refinement results from oversampled and resampled data. Based on nickel and a complex perovskite system, we show that not only is the optimal sampling bounded by the Nyquist interval described by the Nyquist-Shannon (NS) sampling theorem as expected, but near this sampling interval, the data points in the PDF are minimally correlated, which results in more reliable uncertainty estimates in the modeling. Surprisingly, we find that PDF refinements quickly become unstable for data on coarser grids. Although the Nyquist-Shannon sampling theorem is well known, it has not been applied to PDF refinements, despite the growing popularity of the PDF method and its adoption in a growing number of communities. Here, we give explicit expressions for the application of NS sampling theorem to the PDF case, and establish through modeling that it is working in practice, which lays the groundwork for this to become more widely adopted. This has implications for the speed and complexity of possible refinements that can be carried out many times faster than currently with no loss of information, and it establishes a theoretically sound limit on the amount of information contained in the PDF that will prevent over-parametrization during modeling.

  19. DShaper: An approach for handling missing low-Q data in pair distribution function analysis of nanostructured systems

    DOE PAGESBeta

    Olds, Daniel; Wang, Hsiu -Wen; Page, Katharine

    2015-01-01

    This study discusses the potential problems and currently available solutions in modeling powder-diffraction-based pair distribution function (PDF) data from systems where morphological feature information content includes distances in the nanometre length scale, such as finite nanoparticles, nanoporous networks and nanoscale precipitates in bulk materials. The implications of an experimental finite minimumQvalue are reviewed by simulation, which also demonstrates the advantages of combining PDF data with small-angle scattering data. A simple Fortran90 code, DShaper, is introduced, which may be incorporated into PDF data fitting routines in order to approximate the so-called `shape function' for any atomistic model.

  20. Pair distribution function (PDF) analysis of mesoporous α-Fe2O3 and Cr2O3.

    PubMed

    Hill, Adrian H; Allieta, Mattia

    2013-06-14

    We have measured atomic pair distribution functions of novel mesoporous metal oxides, α-Fe2O3 and Cr2O3. These have an ordered pore mosaic as well as crystalline structure within the pore walls, making them an interesting class of materials to characterise. Comparison of "bulk" and mesoporous data sets has allowed an estimate of long range structural coherence to be derived; ≈125 Å and ≈290 Å for α-Fe2O3 and Cr2O3 respectively. Further "box-car" analysis has shown that above ≈40 Å both mesoporous samples deviate greatly from their bulk counterparts. This is attributed to the pores of the mesoporous structure creating voids in the pair-correlations, disrupting long range order. PMID:23619834

  1. Kinetic Equation for Two-Particle Distribution Function in Boltzmann Gas Mixtures and Equation of Motion for Quasiparticle Pairs

    NASA Astrophysics Data System (ADS)

    Saveliev, V. L.

    2011-05-01

    Pair collisions is the main interaction process in the Boltzmann gas dynamics. By making use of exactly the same physical assumptions as was used by Ludwig Boltzmann we write the kinetic equation for two-particle distribution function of molecules in the gas mixtures. Instead of the collision integral, there are the linear scattering operator and the chaos projector in the right part of this equation. Because the scattering operator is more simple then Boltzmann collision integral this equation opens new opportunities for mathematical description of the Boltzmann gas dynamics.

  2. DShaper: An approach for handling missing low-Q data in pair distribution function analysis of nanostructured systems

    DOE PAGESBeta

    Olds, Daniel; Wang, Hsiu -Wen; Page, Katharine L.

    2015-09-04

    In this work we discuss the potential problems and currently available solutions in modeling powder-diffraction based pair-distribution function (PDF) data from systems where morphological feature information content includes distances in the nanometer length scale, such as finite nanoparticles, nanoporous networks, and nanoscale precipitates in bulk materials. The implications of an experimental finite minimum Q-value are addressed by simulation, which also demonstrates the advantages of combining PDF data with small angle scattering data (SAS). In addition, we introduce a simple Fortran90 code, DShaper, which may be incorporated into PDF data fitting routines in order to approximate the so-called shape-function for anymore » atomistic model.« less

  3. DShaper: An approach for handling missing low-Q data in pair distribution function analysis of nanostructured systems

    SciTech Connect

    Olds, Daniel; Wang, Hsiu -Wen; Page, Katharine L.

    2015-09-04

    In this work we discuss the potential problems and currently available solutions in modeling powder-diffraction based pair-distribution function (PDF) data from systems where morphological feature information content includes distances in the nanometer length scale, such as finite nanoparticles, nanoporous networks, and nanoscale precipitates in bulk materials. The implications of an experimental finite minimum Q-value are addressed by simulation, which also demonstrates the advantages of combining PDF data with small angle scattering data (SAS). We introduce a simple Fortran90 code, DShaper, which may be incorporated into PDF data fitting routines in order to approximate the so-called shape-function for any atomistic model.

  4. Resolving the structure of Ti3C2Tx MXenes through multilevel structural modeling of the atomic pair distribution function

    DOE PAGESBeta

    Wesolowski, David J.; Wang, Hsiu -Wen; Page, Katharine L.; Naguib, Michael; Gogotsi, Yury

    2015-12-08

    MXenes are a recently discovered family of two-dimensional (2D) early transition metal carbides and carbonitrides, which have already shown many attractive properties and a great promise in energy storage and many other applications. However, a complex surface chemistry and small coherence length has been an obstacle in some applications of MXenes, also limiting accuracy of predictions of their properties. In this study, we describe and benchmark a novel way of modeling layered materials with real interfaces (diverse surface functional groups and stacking order between the adjacent monolayers) against experimental data. The structures of three kinds of Ti3C2Tx MXenes (T standsmore » for surface terminating species, including O, OH, and F) produced under different synthesis conditions were resolved for the first time using atomic pair distribution function obtained by high-quality neutron total scattering. The true nature of the material can be easily captured with the sensitivity of neutron scattering to the surface species of interest and the detailed third-generation structure model we present. The modeling approach leads to new understanding of MXene structural properties and can replace the currently used idealized models in predictions of a variety of physical, chemical and functional properties of Ti3C2-based MXenes. Furthermore, the developed models can be employed to guide the design of new MXene materials with selected surface termination and controlled contact angle, catalytic, optical, electrochemical and other properties. We suggest that the multi-level structural modeling should form the basis for a generalized methodology on modeling diffraction and pair distribution function data for 2D and layered materials.« less

  5. Pair distribution function of the spin-polarized electron gas: A first-principles analytic model for all uniform densities

    NASA Astrophysics Data System (ADS)

    Gori-Giorgi, Paola; Perdew, John P.

    2002-10-01

    We construct analytic formulas that represent the coupling-constant-averaged pair distribution function gxc(rs,ζ,kFu) of a three-dimensional nonrelativistic ground-state electron gas constrained to a uniform density with density parameter rs=(9π/4)1/3/kF and relative spin polarization ζ over the whole range 0∞) oscillations averaged out. The pair distribution function gxc at the physical coupling constant is then given by differentiation with respect to rs. Our formulas are constructed using only known theoretical constraints plus the correlation energy ɛc(rs,ζ), and accurately reproduce the gxc of the quantum Monte Carlo method and of the fluctuation-dissipation theorem with the Richardson-Ashcroft dynamical local-field factor. Our gxc is correct even in the high-density (rs-->0) and low-density (rs-->∞) limits. When the spin resolution of ɛc into ↑↑, ↓↓, and ↑↓ contributions is known, as it is in the high- and low-density limits, our formulas also yield the spin resolution of gxc. Because of these features, our formulas may be useful for the construction of density functionals for nonuniform systems. We also analyze the kinetic energy of correlation into contributions from density fluctuations of various wave vectors. The exchange and long-range correlation parts of our gxc(rs,ζ,kFu)-1 are analytically Fourier transformable, so that the static structure factor Sxc(rs,ζ,k/kF) is easily evaluated.

  6. Confirmation of disordered structure of ultrasmall CdSe nanoparticles from X-ray atomic pair distribution function analysis.

    PubMed

    Yang, Xiaohao; Masadeh, Ahmad S; McBride, James R; Božin, Emil S; Rosenthal, Sandra J; Billinge, Simon J L

    2013-06-14

    The atomic pair distribution function (PDF) analysis of X-ray powder diffraction data has been used to study the structure of small and ultra-small CdSe nanoparticles. A method is described that uses a wurtzite and zinc-blende mixed phase model to account for stacking faults in CdSe particles. The mixed-phase model successfully describes the structure of nanoparticles larger than 2 nm yielding a stacking fault density of about 30%. However, for ultrasmall nanoparticles smaller than 2 nm, the models cannot fit the experimental PDF showing that the structure is significantly modified from that of larger particles and the bulk. The observation of a significant change in the average structure at ultra-small size is likely to explain the unusual properties of the ultrasmall particles such as their white light emitting ability. PMID:23525376

  7. Association constants and distribution functions for ion pairs in binary solvent mixtures: Application to a cyanine dye system

    NASA Astrophysics Data System (ADS)

    Odinokov, A. V.; Basilevsky, M. V.; Nikitina, E. A.

    2011-10-01

    The computations of the association constants Kass were performed at the microscopic level for the ion pair Cy+I- composed of the complex cyanine dye cation Cy+ coupled to the negative iodine counterion. The wide array of Kass values is arranged by a variation of the composition of the binary solvent mixtures toluene/dimethylsulfoxide with the accompanying change of the solvent polarity. The potentials of mean force (PMFs) are calculated for a set of interionic separations R in the Cy+I- by a methodology which combines the quantum-chemical techniques for the treatment of the electronic structure of the Cy+I- system with the recent dielectric continuum approach which accounts for the solvation effects. For a given solute/solvent system the probability function P(R), which describes the distribution of interionic separations, is constructed in terms of the PMFs and implemented for the evaluation of the Kass.

  8. Investigation of surface structures by powder diffraction : a differential pair distribution function study on arsenate sorption on ferrihydrite.

    SciTech Connect

    Harrington, R.; Hausner, D. B.; Bhandari, N.; Strongin, D. R.; Chapman, K. W.; Chupas, P. J.; Middlemiss, D. S.; Grey, C. P.; Parise, J. B.; X-Ray Science Division; Stony Brook Univ.; Temple Univ.

    2010-01-01

    Differential pair distribution function (d-PDF) analysis of high energy powder X-ray diffraction data was carried out on 2-line ferrihydrite nanoparticles with arsenate oxyanions adsorbed on the surface to investigate the binding mechanism. In this analysis, a PDF of ferrihydrite is subtracted from a PDF of ferrihydrite with arsenate sorbed on the surface, leaving only correlations from within the surface layer and between the surface and the particle. As-O and As-Fe correlations were observed at 1.68 and 3.29 {angstrom}, respectively, in good agreement with previously published EXAFS data, confirming a bidentate binuclear binding mechanism. Further peaks are observed in the d-PDF which are not present in EXAFS, corresponding to correlations between As and O in the particle and As-2nd Fe.

  9. Structural study of biotic and abiotic poorly-crystalline manganese oxides using atomic pair distribution function analysis

    SciTech Connect

    Zhu, Mengqiang; Farrow, Christopher L.; Post, Jeffrey E.; Livi, Kenneth J.T.; Billinge, Simon J.L.; Ginder-Vogel, Matthew; Sparks, Donald L.

    2012-03-15

    Manganese (Mn) oxides are among the most reactive natural minerals and play an important role in elemental cycling in oceanic and terrestrial environments. A large portion of naturally-occurring Mn oxides tend to be poorly-crystalline and/or nanocrystalline, with not fully resolved crystal structures. In this study, the crystal structures of their synthetic analogs including acid birnessite (AcidBir), {delta}-MnO{sub 2}, polymeric MnO{sub 2} (PolyMnO{sub 2}) and a bacteriogenic Mn oxide (BioMnO{sub x}), have been revealed using atomic pair distribution function (PDF) analysis. Results unambiguously verify that these Mn oxides are layered materials. The best models that accurately allow simulation of pair distribution functions (PDFs) belong to the monoclinic C12/m1 space group with a disk-like shape. The single MnO{sub 6} layers in the average structures deviate significantly from hexagonal symmetry, in contrast to the results of previous studies based on X-ray diffraction analysis in reciprocal space. Manganese occupancies in MnO{sub 6} layers are estimated to be 0.936, 0.847, 0.930 and 0.935, for AcidBir, BioMnOx, {delta}-MnO{sub 2} and PolyMnO{sub 2}, respectively; however, occupancies of interlayer cations and water molecules cannot be accurately determined using the models in this study. The coherent scattering domains (CSDs) of PolyMnO{sub 2}, {delta}-MnO{sub 2} and BioMnO{sub x} are at the nanometer scale, comprising one to three MnO{sub 6} layers stacked with a high disorder in the crystallographic c-axis direction. Overall, the results of this study advance our understanding of the mineralogy of Mn oxide minerals in the environment.

  10. Structural Study of Biotic and Abiotic Poorly-crystalline Manganese Oxides Using Atomic Pair Distribution Function Analysis

    SciTech Connect

    Billinge S. J.; Zhu, M.; Farrow, C.L.; Post, J.E.; Livi, K.J.T.; Ginder-Vogel, M.; Sparks, D.L.

    2012-03-15

    Manganese (Mn) oxides are among the most reactive natural minerals and play an important role in elemental cycling in oceanic and terrestrial environments. A large portion of naturally-occurring Mn oxides tend to be poorly-crystalline and/or nanocrystalline, with not fully resolved crystal structures. In this study, the crystal structures of their synthetic analogs including acid birnessite (AcidBir), {delta}-MnO{sub 2}, polymeric MnO{sub 2} (PolyMnO{sub 2}) and a bacteriogenic Mn oxide (BioMnO{sub x}), have been revealed using atomic pair distribution function (PDF) analysis. Results unambiguously verify that these Mn oxides are layered materials. The best models that accurately allow simulation of pair distribution functions (PDFs) belong to the monoclinic C12/m1 space group with a disk-like shape. The single MnO{sub 6} layers in the average structures deviate significantly from hexagonal symmetry, in contrast to the results of previous studies based on X-ray diffraction analysis in reciprocal space. Manganese occupancies in MnO{sub 6} layers are estimated to be 0.936, 0.847, 0.930 and 0.935, for AcidBir, BioMnO{sub x}, {delta}-MnO{sub 2} and PolyMnO{sub 2}, respectively; however, occupancies of interlayer cations and water molecules cannot be accurately determined using the models in this study. The coherent scattering domains (CSDs) of PolyMnO{sub 2}, {delta}-MnO{sub 2} and BioMnO{sub x} are at the nanometer scale, comprising one to three MnO{sub 6} layers stacked with a high disorder in the crystallographic c-axis direction. Overall, the results of this study advance our understanding of the mineralogy of Mn oxide minerals in the environment.

  11. Verification of Anderson superexchange in MnO via magnetic pair distribution function analysis and ab initio theory

    DOE PAGESBeta

    Benjamin A. Frandsen; Brunelli, Michela; Page, Katharine; Uemura, Yasutomo J.; Staunton, Julie B.; Billinge, Simon J. L.

    2016-05-11

    Here, we present a temperature-dependent atomic and magnetic pair distribution function (PDF) analysis of neutron total scattering measurements of antiferromagnetic MnO, an archetypal strongly correlated transition-metal oxide. The known antiferromagnetic ground-state structure fits the low-temperature data closely with refined parameters that agree with conventional techniques, confirming the reliability of the newly developed magnetic PDF method. The measurements performed in the paramagnetic phase reveal significant short-range magnetic correlations on a ~1 nm length scale that differ substantially from the low-temperature long-range spin arrangement. Ab initio calculations using a self-interaction-corrected local spin density approximation of density functional theory predict magnetic interactions dominatedmore » by Anderson superexchange and reproduce the measured short-range magnetic correlations to a high degree of accuracy. Further calculations simulating an additional contribution from a direct exchange interaction show much worse agreement with the data. Furthermore, the Anderson superexchange model for MnO is thus verified by experimentation and confirmed by ab initio theory.« less

  12. Verification of Anderson Superexchange in MnO via Magnetic Pair Distribution Function Analysis and ab initio Theory

    NASA Astrophysics Data System (ADS)

    Frandsen, Benjamin A.; Brunelli, Michela; Page, Katharine; Uemura, Yasutomo J.; Staunton, Julie B.; Billinge, Simon J. L.

    2016-05-01

    We present a temperature-dependent atomic and magnetic pair distribution function (PDF) analysis of neutron total scattering measurements of antiferromagnetic MnO, an archetypal strongly correlated transition-metal oxide. The known antiferromagnetic ground-state structure fits the low-temperature data closely with refined parameters that agree with conventional techniques, confirming the reliability of the newly developed magnetic PDF method. The measurements performed in the paramagnetic phase reveal significant short-range magnetic correlations on a ˜1 nm length scale that differ substantially from the low-temperature long-range spin arrangement. Ab initio calculations using a self-interaction-corrected local spin density approximation of density functional theory predict magnetic interactions dominated by Anderson superexchange and reproduce the measured short-range magnetic correlations to a high degree of accuracy. Further calculations simulating an additional contribution from a direct exchange interaction show much worse agreement with the data. The Anderson superexchange model for MnO is thus verified by experimentation and confirmed by ab initio theory.

  13. Investigating short-range magnetism in strongly correlated materials via magnetic pair distribution function analysis and ab initio theory

    NASA Astrophysics Data System (ADS)

    Frandsen, Benjamin; Page, Katharine; Brunelli, Michela; Staunton, Julie; Billinge, Simon

    Short-range magnetic correlations are known to exist in a variety of strongly correlated electron systems, but our understanding of the role they play is challenged by the difficulty of experimentally probing such correlations. Magnetic pair distribution function (mPDF) analysis is a newly developed neutron total scattering method that can reveal short-range magnetic correlations directly in real space, and may therefore help ameliorate this difficulty. We present temperature-dependent mPDF measurements of the short-range magnetic correlations in the paramagnetic phase of antiferromagnetic MnO, an archetypal strongly correlated transition-metal oxide. We observe significant correlations on a ~1 nm length scale that differ substantially from the low-temperature long-range-ordered spin arrangement. With no free parameters, ab initio calculations using the self-interaction-corrected local spin density approximation of density functional theory quantitatively reproduce the magnetic correlations to a high degree of accuracy. These results yield valuable insight into the magnetic exchange in MnO and showcase the utility of the mPDF technique for studying magnetic properties of strongly correlated electron systems.

  14. Verification of Anderson Superexchange in MnO via Magnetic Pair Distribution Function Analysis and ab initio Theory.

    PubMed

    Frandsen, Benjamin A; Brunelli, Michela; Page, Katharine; Uemura, Yasutomo J; Staunton, Julie B; Billinge, Simon J L

    2016-05-13

    We present a temperature-dependent atomic and magnetic pair distribution function (PDF) analysis of neutron total scattering measurements of antiferromagnetic MnO, an archetypal strongly correlated transition-metal oxide. The known antiferromagnetic ground-state structure fits the low-temperature data closely with refined parameters that agree with conventional techniques, confirming the reliability of the newly developed magnetic PDF method. The measurements performed in the paramagnetic phase reveal significant short-range magnetic correlations on a ∼1  nm length scale that differ substantially from the low-temperature long-range spin arrangement. Ab initio calculations using a self-interaction-corrected local spin density approximation of density functional theory predict magnetic interactions dominated by Anderson superexchange and reproduce the measured short-range magnetic correlations to a high degree of accuracy. Further calculations simulating an additional contribution from a direct exchange interaction show much worse agreement with the data. The Anderson superexchange model for MnO is thus verified by experimentation and confirmed by ab initio theory. PMID:27232042

  15. Combining the pair distribution function and computational methods to understand lithium insertion in Brookite (TiO2).

    PubMed

    Dambournet, Damien; Chapman, Karena W; Koudriachova, Marina V; Chupas, Peter J; Belharouak, Ilias; Amine, Khalil

    2011-07-01

    X-ray pair distribution function (PDF) methods and first-principles calculations have been combined to probe the structure of electrochemically lithiated TiO(2) Brookite. Traditional powder diffraction studies suggest that Brookite amorphizes upon lithium insertion, with the Bragg reflections disappearing. However, PDF analysis indicates that the TiO(2) framework connectivity is maintained throughout lithium intercalation, with expansions along the a and b axes. The Li(+) ions within the framework are poorly observed in the X-ray PDF, which is dominated by contributions from the more strongly scattering Ti and O atoms. First-principles calculations were used to identify energetically favorable Li(+) sites within the Brookite lattice and to develop a complete structural model of the lithiated material. This model replicates the local structure and decreased intermediate range order observed in the PDF data. The analysis suggests that local structural distortions of the TiO(2) lattice accommodate lithium in five-coordinate sites. This structural model is consistent with the observed electrochemical behavior. PMID:21627151

  16. Combining pair distribution function and computational methods to understand lithium insertion in brookite (TiO{sub 2}).

    SciTech Connect

    Dambournet, D.; Chapman, K. W.; Koudriachova, M. V.; Chupas, P. J.; Belharouak, I.; Amine, K.

    2011-07-04

    X-ray pair distribution function (PDF) methods and first-principles calculations have been combined to probe the structure of electrochemically lithiated TiO{sub 2} Brookite. Traditional powder diffraction studies suggest that Brookite amorphizes upon lithium insertion, with the Bragg reflections disappearing. However, PDF analysis indicates that the TiO{sub 2} framework connectivity is maintained throughout lithium intercalation, with expansions along the a and b axes. The Li{sup +} ions within the framework are poorly observed in the X-ray PDF, which is dominated by contributions from the more strongly scattering Ti and O atoms. First-principles calculations were used to identify energetically favorable Li{sup +} sites within the Brookite lattice and to develop a complete structural model of the lithiated material. This model replicates the local structure and decreased intermediate range order observed in the PDF data. The analysis suggests that local structural distortions of the TiO{sub 2} lattice accommodate lithium in five-coordinate sites. This structural model is consistent with the observed electrochemical behavior.

  17. Magnetic structure determination from the magnetic pair distribution function (mPDF): ground state of MnO.

    PubMed

    Frandsen, Benjamin A; Billinge, Simon J L

    2015-05-01

    An experimental determination of the magnetic pair distribution function (mPDF) defined in an earlier paper [Frandsen et al. (2014). Acta Cryst. A70, 3-11] is presented for the first time. The mPDF was determined from neutron powder diffraction data from a reactor and a neutron time-of-flight total scattering source on a powder sample of the antiferromagnetic oxide MnO. A description of the data treatment that allowed the measured mPDF to be extracted and then modelled is provided and utilized to investigate the low-temperature structure of MnO. Atomic and magnetic co-refinements support the scenario of a locally monoclinic ground-state atomic structure, despite the average structure being rhombohedral, with the mPDF analysis successfully recovering the known antiferromagnetic spin configuration. The total scattering data suggest a preference for the spin axis to lie along the pseudocubic [10{\\overline 1}] direction. Finally, r-dependent PDF refinements indicate that the local monoclinic structure tends toward the average rhombohedral R{\\overline 3}m symmetry over a length scale of approximately 100 Å. PMID:25921501

  18. Inversion of radial distribution functions to pair forces by solving the Yvon-Born-Green equation iteratively.

    PubMed

    Cho, Hyung Min; Chu, Jhih-Wei

    2009-10-01

    We develop a new method to invert the target profiles of radial distribution functions (RDFs) to the pair forces between particles. The target profiles of RDFs can be obtained from all-atom molecular dynamics (MD) simulations or experiments and the inverted pair forces can be used in molecular simulations at a coarse-grained (CG) scale. Our method is based on a variational principle that determines the mean forces between CG sites after integrating out the unwanted degrees of freedom. The solution of this variational principle has been shown to correspond to the Yvon-Born-Green (YBG) equation [Noid et al., J. Phys. Chem. B 111, 4116 (2007)]. To invert RDFs, we solve the YBG equation iteratively by running a CG MD simulation at each step of iteration. A novelty of the iterative-YBG method is that during iteration, CG forces are updated according to the YBG equation without imposing any approximation as is required by other methods. As a result, only three to ten iterations are required to achieve convergence for all cases tested in this work. Furthermore, we show that not only are the target RDFs reproduced by the iterative solution; the profiles of the three-body correlation function in the YBG equation computed from all-atom and CG simulations also have a better agreement. The iterative-YBG method is applied to compute the CG forces of four molecular liquids to illustrate its efficiency and robustness: water, ethane, ethanol, and a water/methanol mixture. Using the resulting CG forces, all of the target RDFs observed in all-atom MD simulations are reproduced. We also show that the iterative-YBG method can be applied with a virial constraint to expand the representability of a CG force field. The iterative-YBG method thus provides a general and robust framework for computing CG forces from RDFs and could be systematically generalized to go beyond pairwise forces and to include higher-body interactions in a CG force field by applying the aforementioned variational

  19. In situ X-ray pair distribution function analysis of accelerated carbonation of a synthetic calcium-silicate-hydrate gel

    SciTech Connect

    Morandeau, Antoine E.; White, Claire E.

    2015-04-21

    Calcium–silicate–hydrate (C–S–H) gel is the main binder component in hydrated ordinary Portland cement (OPC) paste, and is known to play a crucial role in the carbonation of cementitious materials, especially for more sustainable alternatives containing supplementary cementitious materials. However, the exact atomic structural changes that occur during carbonation of C–S–H gel remain unknown. Here, we investigate the local atomic structural changes that occur during carbonation of a synthetic calcium–silicate–hydrate gel exposed to pure CO₂ vapour, using in situ X-ray total scattering measurements and subsequent pair distribution function (PDF) analysis. By analysing both the reciprocal and real-space scattering data as the C–S–H carbonation reaction progresses, all phases present during the reaction (crystalline and non-crystalline) have been identified and quantified, with the results revealing the emergence of several polymorphs of crystalline calcium carbonate (vaterite and calcite) in addition to the decalcified C–S–H gel. Furthermore, the results point toward residual calcium being present in the amorphous decalcified gel, potentially in the form of an amorphous calcium carbonate phase. As a result of the quantification process, the reaction kinetics for the evolution of the individual phases have been obtained, revealing new information on the rate of growth/dissolution for each phase associated with C–S–H gel carbonation. Moreover, the investigation reveals that the use of real space diffraction data in the form of PDFs enables more accurate determination of the phases that develop during complex reaction processes such as C–S–H gel carbonation in comparison to the conventional reciprocal space Rietveld analysis approach.

  20. Detection and characterization of nanoparticles in suspension at low concentrations using the X-ray total scattering pair distribution function technique.

    PubMed

    Terban, Maxwell W; Johnson, Matthew; Di Michiel, Marco; Billinge, Simon J L

    2015-03-12

    Difference atomic pair distribution function methods have been applied to detect and characterize nanoparticles suspended in a solvent at very dilute concentrations. We specifically consider nanoparticles of a pharmaceutical compound in aqueous solution using X-ray PDF methods, a challenging case due to the low atomic number of the nanoparticle species. The nanoparticles were unambiguously detected at the level of 0.25 wt%. Even at these low concentrations the signals were highly reproducible, allowing for reliable detection and quantitative analysis of the nanoparticle structure. PMID:25732228

  1. Pair distribution function analysis: The role of structural degrees of freedom in the high-pressure insulator to metal transition of VO2

    NASA Astrophysics Data System (ADS)

    Baldini, M.; Postorino, P.; Malavasi, L.; Marini, C.; Chapman, K. W.; Mao, Ho-kwang

    2016-06-01

    The evolution of the local structure of VO2 was investigated across the pressure-induced insulator to metal transition (IMT) by means of pair distribution function measurements. The pressure behavior of the V-V and V-O bond lengths have been determined. The data demonstrated that the pressure-driven IMT is not activated by the suppression of the Peierls-type distortion. A clear octahedra symmetrization is observed in the metallic phase, suggesting a link between structural degree of freedom and the metallization process.

  2. Study of the reaction products of SF6 and C in the laser heated diamond anvil cell by pair distribution function analysis and micro-Raman spectroscopy

    NASA Astrophysics Data System (ADS)

    Rademacher, N.; Bayarjargal, L.; Morgenroth, W.; Bauer, J. D.; Milman, V.; Winkler, B.

    2015-05-01

    The decomposition of SF6 in the presence of glassy carbon was induced in laser heated diamond anvil cells at 10-11 GPa and 2000-2500 K. The reaction products were characterised by synchrotron X-ray diffraction, including high pressure pair distribution function analysis, and micro-Raman spectroscopy combined with atomistic model calculations. The decomposition leads to elemental amorphous helical sulfur and crystalline CF4-III. Two different sulfur phases, namely helical Sμ and crystalline α-S8, were observed after recovering the laser heated samples of different experiments at ambient conditions.

  3. DShaper : an approach for handling missing low- Q data in pair distribution function analysis of nanostructured systems

    SciTech Connect

    Olds, Daniel; Wang, Hsiu-Wen; Page, Katharine

    2015-10-13

    This article discusses the potential problems and currently available solutions in modeling powder-diffraction-based pair distribution function (PDF) data from systems where morphological feature information content includes distances in the nanometre length scale, such as finite nanoparticles, nanoporous networks and nanoscale precipitates in bulk materials. The implications of an experimental finite minimumQvalue are reviewed by simulation, which also demonstrates the advantages of combining PDF data with small-angle scattering data. A simple Fortran90 code,DShaper, is introduced, which may be incorporated into PDF data fitting routines in order to approximate the so-called `shape function' for any atomistic model.

  4. DShaper: An approach for handling missing low-Q data in pair distribution function analysis of nanostructured systems

    SciTech Connect

    Olds, Daniel; Wang, Hsiu -Wen; Page, Katharine

    2015-01-01

    This study discusses the potential problems and currently available solutions in modeling powder-diffraction-based pair distribution function (PDF) data from systems where morphological feature information content includes distances in the nanometre length scale, such as finite nanoparticles, nanoporous networks and nanoscale precipitates in bulk materials. The implications of an experimental finite minimumQvalue are reviewed by simulation, which also demonstrates the advantages of combining PDF data with small-angle scattering data. A simple Fortran90 code, DShaper, is introduced, which may be incorporated into PDF data fitting routines in order to approximate the so-called `shape function' for any atomistic model.

  5. Distributed processing; distributed functions?

    PubMed Central

    Fox, Peter T.; Friston, Karl J.

    2016-01-01

    After more than twenty years busily mapping the human brain, what have we learned from neuroimaging? This review (coda) considers this question from the point of view of structure–function relationships and the two cornerstones of functional neuroimaging; functional segregation and integration. Despite remarkable advances and insights into the brain’s functional architecture, the earliest and simplest challenge in human brain mapping remains unresolved: We do not have a principled way to map brain function onto its structure in a way that speaks directly to cognitive neuroscience. Having said this, there are distinct clues about how this might be done: First, there is a growing appreciation of the role of functional integration in the distributed nature of neuronal processing. Second, there is an emerging interest in data-driven cognitive ontologies, i.e., that are internally consistent with functional anatomy. We will focus this review on the growing momentum in the fields of functional connectivity and distributed brain responses and consider this in the light of meta-analyses that use very large data sets to disclose large-scale structure–function mappings in the human brain. PMID:22245638

  6. The functional significance of density and distribution of outgrowths on co-opted contact pairs in biological arresting systems.

    PubMed

    Filippov, Alexander E; Popov, Valentin L; Gorb, Stanislav N

    2015-02-01

    Microstructures responsible for temporary arresting of contacting surfaces are widely distributed on surfaces in different organisms. Recent morphological studies show that these structures have different density of outgrowths and not ideal distribution pattern on both complementary parts of the contact. One can suggest that this difference is optimized by natural selection to get stronger mechanical arrest within the system. In this paper, we simulate such a system numerically, both in the frames of continuous contact and discrete dynamical models to prove this hypothesis and elucidate other aspects of optimization of such mechanical adhesive systems. PMID:25533090

  7. Manifestation of Negative Compressibility in Low-Density Electron Liquids: Anomaly in the Ion-Pair Distribution Function in Supercritical Fluid Rb

    NASA Astrophysics Data System (ADS)

    Takada, Yasutami

    2006-03-01

    It is a well-known fact that the electronic compressibility κ diverges in the 3D electron gas as the density parameter rs approaches 5.25. A recent investigation clarifies that this divergence is due to the excitonic effect in the electron-hole pair excitation, in particular, to its zero-energy excitation [1]. For rs>5.25, κ becomes negative, leading to the negative static dielectric function ɛ(q,0) for at least small q owing to the compressibility sum rule. Then we can expect that two positive test charges do not repel but attract to each other in such a system. Keeping this situation in mind, we have calculated the ion-pair distribution function g(R) in the expanded Rb liquid metal by using the Monte Carlo method and found interesting features in g(R) characteristic to the negative ɛ(q,0) [2]. Such features have been observed by the recent measurement of g(R) in the supercritical fluid Rb metal with continuously increasing rs from 5.25 [3]. This confirms the situation of κ<0 in the low-density 3D electron gas for the first time. [1] YT, J. Superconductivity 18, No.3 (2005). [2] H. Maebashi and YT, to be submitted. [3] K. Matsuda and K. Tamura, private communication.

  8. Pair-distribution function analysis of the structural valence transition in Cp{sub 2}{sup *}Yb(4,4'-Me{sub 2}-bipy)

    SciTech Connect

    Booth, C H; Bauer, E D; Bozin, E S; Billinge, S J L; Walter, M D

    2010-07-20

    The Cp{sup *}{sub 2} Yb(L) class of compounds, where Cp{sup *}=pentamethylcyclopentadienyl = C{sub 5}Me{sub 5} and L is either a 1,4-diazabutadiene or bipy = 2,2'bipyridine related ligand, have provided excellent analogies to the Kondo state on the nanoscale. Cp{sup *}{sub 2} Yb(4,4'-Me{sub 2}-bipy) furthers this analogy by demonstrating a valence transition as the sample is cooled below 200 K. Here, pair-distribution function (PDF) analysis of x-ray powder diffraction data demonstrate that the Cp{sup *}{sub 2}Yb(4,4'Me{sub 2}-bipy) molecule is virtually unchanged through the valence transition. However, the molecule’s stacking arrangement is altered through the valence transition.

  9. Benchmark oxygen-oxygen pair-distribution function of ambient water from x-ray diffraction measurements with a wide Q-range

    SciTech Connect

    Skinner, Lawrie B.; Huang, Congcong; Schlesinger, Daniel; Pettersson, Lars G. M.; Nilsson, Anders; Benmore, Chris J.

    2013-02-21

    Four recent x-ray diffraction measurements of ambient liquid water are reviewed here. Each of these measurements represents a significant development of the x-ray diffraction technique applied to the study of liquid water. Sources of uncertainty from statistical noise, Q-range, Compton scattering, and self-scattering are discussed. The oxygen-hydrogen contribution to the measured x-ray scattering pattern was subtracted using literature data to yield an experimental determination, with error bars, of the oxygen-oxygen pair-distribution function, g{sub OO}(r), which essentially describes the distribution of molecular centers. The extended Q-range and low statistical noise of these measurements has significantly reduced truncation effects and related errors in the g{sub OO}(r) functions obtained. From these measurements and error analysis, the position and height of the nearest neighbor maximum in g{sub OO}(r) were found to be 2.80(1) A and 2.57(5) respectively. Numerical data for the coherent differential x-ray scattering cross-section I{sub X}(Q), the oxygen-oxygen structure factor S{sub OO}(Q), and the derived g{sub OO}(r) are provided as benchmarks for calibrating force-fields for water.

  10. Structural characterization of Green River oil-shale at high-pressure using pair distribution function analysis and small angle x-ray scattering.

    SciTech Connect

    Locke, D. R.; Chupas, P. J.; Chapman, K. W.; Pugmire, R. J.; Winans, R. E.; Univ. of Utah

    2008-01-01

    The compression behavior of a silicate-rich oil shale from the Green River formation in the pressure range 0.0-2.4 GPa was studied using in situ high pressure X-ray pair distribution function (PDF) measurements for the sample contained within a Paris-Edinburgh cell. The real-space local structural information in the PDF, G(r), was used to evaluate the compressibility of the oil shale. Specifically, the pressure-induced reduction in the medium- to long-range atom distances (6-20 {angstrom}) yielded an average sample compressibility corresponding to a bulk modulus of ca. 61-67 GPa. A structural model consisting of a three phase mixture of the principal crystalline oil shale components (quartz, albite and Illite) provided a good fit to the ambient pressure PDF data (R 30.7%). Indeed the features in the PDF beyond 6 {angstrom}, were similarly well fit by a single phase model of the highest symmetry, highly crystalline quartz component.

  11. High-energy X-ray focusing and applications to pair distribution function investigation of Pt and Au nanoparticles at high pressures.

    PubMed

    Hong, Xinguo; Ehm, Lars; Zhong, Zhong; Ghose, Sanjit; Duffy, Thomas S; Weidner, Donald J

    2016-01-01

    We report development of micro-focusing optics for high-energy x-rays by combining a sagittally bent Laue crystal monchromator with Kirkpatrick-Baez (K-B) X-ray focusing mirrors. The optical system is able to provide a clean, high-flux X-ray beam suitable for pair distribution function (PDF) measurements at high pressure using a diamond anvil cell (DAC). A focused beam of moderate size (10-15 μm) has been achieved at energies of 66 and 81 keV. PDF data for nanocrystalline platinum (n-Pt) were collected at 12.5 GPa with a single 5 s X-ray exposure, showing that the in-situ compression, decompression, and relaxation behavior of samples in the DAC can be investigated with this technique. PDFs of n-Pt and nano Au (n-Au) under quasi-hydrostatic loading to as high as 71 GPa indicate the existence of substantial reduction of grain or domain size for Pt and Au nanoparticles at pressures below 10 GPa. The coupling of sagittally bent Laue crystals with K-B mirrors provides a useful means to focus high-energy synchrotron X-rays from a bending magnet or wiggler source. PMID:26902122

  12. High-energy X-ray focusing and applications to pair distribution function investigation of Pt and Au nanoparticles at high pressures

    PubMed Central

    Hong, Xinguo; Ehm, Lars; Zhong, Zhong; Ghose, Sanjit; Duffy, Thomas S.; Weidner, Donald J.

    2016-01-01

    We report development of micro-focusing optics for high-energy x-rays by combining a sagittally bent Laue crystal monchromator with Kirkpatrick-Baez (K–B) X-ray focusing mirrors. The optical system is able to provide a clean, high-flux X-ray beam suitable for pair distribution function (PDF) measurements at high pressure using a diamond anvil cell (DAC). A focused beam of moderate size (10–15 μm) has been achieved at energies of 66 and 81 keV. PDF data for nanocrystalline platinum (n-Pt) were collected at 12.5 GPa with a single 5 s X-ray exposure, showing that the in-situ compression, decompression, and relaxation behavior of samples in the DAC can be investigated with this technique. PDFs of n-Pt and nano Au (n-Au) under quasi-hydrostatic loading to as high as 71 GPa indicate the existence of substantial reduction of grain or domain size for Pt and Au nanoparticles at pressures below 10 GPa. The coupling of sagittally bent Laue crystals with K–B mirrors provides a useful means to focus high-energy synchrotron X-rays from a bending magnet or wiggler source. PMID:26902122

  13. Amorphous Analogs of Martian Global Soil: Pair Distribution Function Analyses and Implications for Scattering Models of Chemin X-ray Diffraction Data

    NASA Technical Reports Server (NTRS)

    Achilles, C. N.; Bish, D. L.; Rampe, E. B.; Morris, R. V.

    2015-01-01

    Soils on Mars have been analyzed by the Mars Exploration Rovers (MER) and most recently by the Mars Science Laboratory (MSL) rover. Chemical analyses from a majority of soil samples suggest that there is a relatively uniform global soil composition across much of the planet. A soil site, Rocknest, was sampled by the MSL science payload including the CheMin X-ray diffractometer and the Alpha Particle X-ray Spectrometer (APXS). Che- Min X-ray diffraction (XRD) data revealed crystalline phases and a broad, elevated background, indicating the presence of amorphous or poorly ordered materials (Fig 1). Based on the chemical composition of the bulk soil measured by APXS and the composition of crystalline phases derived from unit-cell parameters determined with CheMin data, the percentages of crystalline and amorphous phases were calculated at 51% and 49%, respectively. Attempts to model the amorphous contribution to CheMin XRD patterns were made using amorphous standards and full-pattern fitting methods and show that the broad, elevated background region can be fitted by basaltic glass, allophane, and palagonite. However, the modeling shows only that these phases have scattering patterns similar to that for the soil, not that they represent unique solutions. Here, we use pair distribution function (PDF) analysis to determine the short-range order of amorphous analogs in martian soils and better constrain the amorphous material detected by CheMin.

  14. Total scattering and pair distribution function analysis in modelling disorder in PZN (PbZn1/3Nb2/3O3)

    PubMed Central

    Whitfield, Ross E.; Goossens, Darren J.; Welberry, T. Richard

    2016-01-01

    The ability of the pair distribution function (PDF) analysis of total scattering (TS) from a powder to determine the local ordering in ferroelectric PZN (PbZn1/3Nb2/3O3) has been explored by comparison with a model established using single-crystal diffuse scattering (SCDS). While X-ray PDF analysis is discussed, the focus is on neutron diffraction results because of the greater extent of the data and the sensitivity of the neutron to oxygen atoms, the behaviour of which is important in PZN. The PDF was shown to be sensitive to many effects not apparent in the average crystal structure, including variations in the B-site—O separation distances and the fact that 〈110〉 Pb2+ displacements are most likely. A qualitative comparison between SCDS and the PDF shows that some features apparent in SCDS were not apparent in the PDF. These tended to pertain to short-range correlations in the structure, rather than to interatomic separations. For example, in SCDS the short-range alternation of the B-site cations was quite apparent in diffuse scattering at (½ ½ ½), whereas it was not apparent in the PDF. PMID:26870378

  15. High-energy X-ray focusing and applications to pair distribution function investigation of Pt and Au nanoparticles at high pressures

    NASA Astrophysics Data System (ADS)

    Hong, Xinguo; Ehm, Lars; Zhong, Zhong; Ghose, Sanjit; Duffy, Thomas S.; Weidner, Donald J.

    2016-02-01

    We report development of micro-focusing optics for high-energy x-rays by combining a sagittally bent Laue crystal monchromator with Kirkpatrick-Baez (K-B) X-ray focusing mirrors. The optical system is able to provide a clean, high-flux X-ray beam suitable for pair distribution function (PDF) measurements at high pressure using a diamond anvil cell (DAC). A focused beam of moderate size (10-15 μm) has been achieved at energies of 66 and 81 keV. PDF data for nanocrystalline platinum (n-Pt) were collected at 12.5 GPa with a single 5 s X-ray exposure, showing that the in-situ compression, decompression, and relaxation behavior of samples in the DAC can be investigated with this technique. PDFs of n-Pt and nano Au (n-Au) under quasi-hydrostatic loading to as high as 71 GPa indicate the existence of substantial reduction of grain or domain size for Pt and Au nanoparticles at pressures below 10 GPa. The coupling of sagittally bent Laue crystals with K-B mirrors provides a useful means to focus high-energy synchrotron X-rays from a bending magnet or wiggler source.

  16. High-energy X-ray focusing and applications to pair distribution function investigation of Pt and Au nanoparticles at high pressures

    DOE PAGESBeta

    Hong, Xinguo; Ehm, Lars; Zhong, Zhong; Ghose, Sanjit; Duffy, Thomas S.; Weidner, Donald J.

    2016-02-23

    We report development of micro-focusing optics for high-energy x-rays by combining a sagittally bent Laue crystal monchromator with Kirkpatrick-Baez (K–B) X-ray focusing mirrors. The optical system is able to provide a clean, high-flux X-ray beam suitable for pair distribution function (PDF) measurements at high pressure using a diamond anvil cell (DAC). A focused beam of moderate size (10–15 μm) has been achieved at energies of 66 and 81keV. PDF data for nanocrystalline platinum (n-Pt) were collected at 12.5 GPa with a single 5 s X-ray exposure, showing that the in-situ compression, decompression, and relaxation behavior of samples in the DACmore » can be investigated with this technique. PDFs of n-Pt and nano Au (n-Au) under quasi-hydrostatic loading to as high as 71GPa indicate the existence of substantial reduction of grain or domain size for Pt and Au nanoparticles at pressures below 10 GPa. In conclusion, the coupling of sagittally bent Laue crystals with K–B mirrors provides a useful means to focus high-energy synchrotron X-rays from a bending magnet or wiggler source.« less

  17. Pair distribution function-derived mechanism of a single-crystal to disordered to single-crystal transformation in a hemilabile metal-organic framework

    SciTech Connect

    Allan, P. K.; Chapman, K. W.; Chupas, P. J.; Hriljac, J. A.; Renouf, C. L.; Lucas, T. C. A.; Morris, R. E.

    2012-01-01

    Flexible metal-organic frameworks (MOFs) are materials of great current interest. A small class of MOFs show flexibility driven by reversible bonding rearrangements that lead directly to unusual properties. Cu-SIP-3 is a MOF based on the 5-sulfoisophthalate ligand, where the strong copper-carboxylate bonds ensure that the three-dimensional integrity of the structure is retained while allowing bonding changes to occur at the more weakly bonding sulfonate group leading to unusual properties such as the ultra-selective adsorption of only certain gases. While the integrity of the framework remains intact during bonding changes, crystalline order is not retained at all times during the transformations. X-Ray diffraction reveals that highly crystalline single crystals lose order during the transformation before regaining crystallinity once it is complete. Here we show how X-ray pair distribution function analysis can be used to reveal the mechanism of the transformations in Cu-SIP-3, identifying the sequence of atomic displacements that occur in the disordered phase. A similar approach reveals the underlying mechanism of Cu-SIP-3's ultra-selective gas adsorption.

  18. A linked electron pair functional.

    PubMed

    Knowles, Peter J; Cooper, Bridgette

    2010-12-14

    A modification of the variational configuration interaction functional in the first-order interacting space for molecular electronic structure is presented. The modified functional is a fully linked expression that by construction is extensive and invariant to transformations of the underlying orbital basis and is exact for an ensemble of separated two-electron subsystems. In addition, an approximation to variational coupled cluster is generated through truncation of the exponential cluster operator. When combined, these methods demonstrate accuracy that exceeds that of the standard coupled-cluster method, in particular in situations where the reference Slater determinant is not a good approximation. PMID:21171682

  19. What Can We Learn From a Detailed Study of the Temperature Dependence of Omega, the Width of the Pair Distribution Function?

    SciTech Connect

    Bridges, F.; Downward, L.; Jiang, Y.; O'Brien, T.

    2009-06-04

    In many systems there is a significant coupling between the local structure and other properties of the system such as magnetism, electrical and thermal transport, metal/insulator transitions etc. In such materials, a detailed temperature-dependent study of the width of the Pair Distribution Function (PDF), {sigma}, can separate different contributions and provide a connection between the observed macroscopic observations and the underlying atomic interactions that produce them. The usual model for simple systems is that the T-dependence of {sigma}{sup 2} is described by an Einstein or Correlated Debye model, with one characteristic temperature for the system; in such models {sigma}{sup 2}(T) increases smoothly with T and has a slowly increasing slope. However that is not always the case: in structures with large unit cells containing several types of atoms, some atoms in the crystal can have a low Einstein temperature while others have a very high correlated Debye temperature as observed in a number of thermoelectric systems (skutterudites and clathrates). In others systems such as the negative thermal expansion material ZrW{sub 2}O{sub 8}, the same atom cam be involved in both low and high temperature Einstein modes. Vibrations of atoms (or molecular unit) described by a low Einstein temperature often control/determine the lattice properties. In other systems there are deviations from the T-dependence expected for either the Einstein or correlated Debye models -- such as a small increase in {sigma}{sup 2} at low temperatures for the Ru-Ru pair in PrRu{sub 4}Sb{sub 12} which has a metal/insulator transition near 60K, or a very sharp step in {sigma}{sup 2}(T) observed in the bilayer colossal magnetoresistance system La{sub 2-2x}Sr{sub 1+2x}Mn{sub 2}O{sub 7} at the ferromagnetic transition. We discuss broadening of the PDF in more complex systems, show some simulations and then present several recent examples.

  20. Demonstration of thin film pair distribution function analysis (tfPDF) for the study of local structure in amorphous and crystalline thin films.

    PubMed

    Jensen, Kirsten M Ø; Blichfeld, Anders B; Bauers, Sage R; Wood, Suzannah R; Dooryhée, Eric; Johnson, David C; Iversen, Bo B; Billinge, Simon J L

    2015-09-01

    By means of normal-incidence, high-flux and high-energy X-rays, total scattering data for pair distribution function (PDF) analysis have been obtained from thin films (tf), suitable for local structure analysis. By using amorphous substrates as support for the films, the standard Rapid Acquisition PDF setup can be applied and the scattering signal from the film can be isolated from the total scattering data through subtraction of an independently measured background signal. No angular corrections to the data are needed, as would be the case for grazing incidence measurements. The 'tfPDF' method is illustrated through studies of as-deposited (i.e. amorphous) and crystalline FeSb3 films, where the local structure analysis gives insight into the stabilization of the metastable skutterudite FeSb3 phase. The films were prepared by depositing ultra-thin alternating layers of Fe and Sb, which interdiffuse and after annealing crystallize to form the FeSb3 structure. The tfPDF data show that the amorphous precursor phase consists of corner-sharing FeSb6 octahedra with motifs highly resembling the local structure in crystalline FeSb3. Analysis of the amorphous structure allows the prediction of whether the final crystalline product will form the FeSb3 phase with or without excess Sb present. The study thus illustrates how analysis of the local structure in amorphous precursor films can help to understand crystallization processes of metastable phases and opens for a range of new local structure studies of thin films. PMID:26306190

  1. Demonstration of thin film pair distribution function analysis (tfPDF) for the study of local structure in amorphous and crystalline thin films

    DOE PAGESBeta

    Jensen, K. M.Ø.; Blichfeld, A. B.; Bauers, S. R.; Wood, S. R.; Dooryhee, E.; Johnson, D. C.; Iversen, B. B.; Billinge, S.

    2015-07-05

    By means of normal incidence, high flux and high energy x-rays, we have obtained total scattering data for Pair Distribution Function (PDF) analysis from thin films (tf), suitable for local structure analysis. By using amorphous substrates as support for the films, the standard Rapid Acquisition PDF setup can be applied and the scattering signal from the film can be isolated from the total scattering data through subtraction of an independently measured background signal. No angular corrections to the data are needed, as would be the case for grazing incidence measurements. We illustrate the ‘tfPDF’ method through studies of as depositedmore » (i.e. amorphous) and crystalline FeSb3 films, where the local structure analysis gives insight into the stabilization of the metastable skutterudite FeSb3 phase. The films were prepared by depositing ultra-thin alternating layers of Fe and Sb, which interdiffuse and after annealing crystallize to form the FeSb3 structure. The tfPDF data show that the amorphous precursor phase consists of corner-sharing FeSb6 octahedra with motifs highly resembling the local structure in crystalline FeSb3. Analysis of the amorphous structure allows predicting whether the final crystalline product will form the FeSb3 phase with or without excess Sb present. The study thus illustrates how analysis of the local structure in amorphous precursor films can help to understand crystallization processes of metastable phases and opens for a range of new local structure studies of thin films.« less

  2. Demonstration of thin film pair distribution function analysis (tfPDF) for the study of local structure in amorphous and crystalline thin films

    SciTech Connect

    Jensen, K. M.Ø.; Blichfeld, A. B.; Bauers, S. R.; Wood, S. R.; Dooryhee, E.; Johnson, D. C.; Iversen, B. B.; Billinge, S.

    2015-07-05

    By means of normal incidence, high flux and high energy x-rays, we have obtained total scattering data for Pair Distribution Function (PDF) analysis from thin films (tf), suitable for local structure analysis. By using amorphous substrates as support for the films, the standard Rapid Acquisition PDF setup can be applied and the scattering signal from the film can be isolated from the total scattering data through subtraction of an independently measured background signal. No angular corrections to the data are needed, as would be the case for grazing incidence measurements. We illustrate the ‘tfPDF’ method through studies of as deposited (i.e. amorphous) and crystalline FeSb3 films, where the local structure analysis gives insight into the stabilization of the metastable skutterudite FeSb3 phase. The films were prepared by depositing ultra-thin alternating layers of Fe and Sb, which interdiffuse and after annealing crystallize to form the FeSb3 structure. The tfPDF data show that the amorphous precursor phase consists of corner-sharing FeSb6 octahedra with motifs highly resembling the local structure in crystalline FeSb3. Analysis of the amorphous structure allows predicting whether the final crystalline product will form the FeSb3 phase with or without excess Sb present. The study thus illustrates how analysis of the local structure in amorphous precursor films can help to understand crystallization processes of metastable phases and opens for a range of new local structure studies of thin films.

  3. Oxyanion Induced Variations in Domain Structure for Amorphous Cobalt Oxide Oxygen Evolving Catalysts, Resolved by X-ray Pair Distribution Function Analysis

    DOE PAGESBeta

    Kwon, Gihan; Kokhan, Oleksandr; Han, Ali; Chapman, Karena W.; Chupas, Peter J.; Du, Pingwu; Tiede, David M.

    2015-12-01

    Amorphous thin film oxygen evolving catalysts, OECs, of first-row transition metals show promise to serve as self-assembling photoanode materials in solar-driven, photoelectrochemical `artificial leaf' devices. This report demonstrates the ability to use high-energy X-ray scattering and atomic pair distribution function analysis, PDF, to resolve structure in amorphous metal oxide catalyst films. The analysis is applied here to resolve domain structure differences induced by oxyanion substitution during the electrochemical assembly of amorphous cobalt oxide catalyst films, Co-OEC. PDF patterns for Co-OEC films formed using phosphate, Pi, methylphosphate, MPi, and borate, Bi, electrolyte buffers show that the resulting domains vary in sizemore » following the sequence Pi < MPi < Bi. The increases in domain size for CoMPi and CoBi were found to be correlated with increases in the contributions from bilayer and trilayer stacked domains having structures intermediate between those of the LiCoOO and CoO(OH) mineral forms. The lattice structures and offset stacking of adjacent layers in the partially stacked CoMPi and CoBi domains were best matched to those in the LiCoOO layered structure. The results demonstrate the ability of PDF analysis to elucidate features of domain size, structure, defect content and mesoscale organization for amorphous metal oxide catalysts that are not readily accessed by other X-ray techniques. Finally, PDF structure analysis is shown to provide a way to characterize domain structures in different forms of amorphous oxide catalysts, and hence provide an opportunity to investigate correlations between domain structure and catalytic activity.« less

  4. Oxyanion Induced Variations in Domain Structure for Amorphous Cobalt Oxide Oxygen Evolving Catalysts, Resolved by X-ray Pair Distribution Function Analysis

    SciTech Connect

    Kwon, Gihan; Kokhan, Oleksandr; Han, Ali; Chapman, Karena W.; Chupas, Peter J.; Du, Pingwu; Tiede, David M.

    2015-12-01

    Amorphous thin film oxygen evolving catalysts, OECs, of first-row transition metals show promise to serve as self-assembling photoanode materials in solar-driven, photoelectrochemical `artificial leaf' devices. This report demonstrates the ability to use high-energy X-ray scattering and atomic pair distribution function analysis, PDF, to resolve structure in amorphous metal oxide catalyst films. The analysis is applied here to resolve domain structure differences induced by oxyanion substitution during the electrochemical assembly of amorphous cobalt oxide catalyst films, Co-OEC. PDF patterns for Co-OEC films formed using phosphate, Pi, methylphosphate, MPi, and borate, Bi, electrolyte buffers show that the resulting domains vary in size following the sequence Pi < MPi < Bi. The increases in domain size for CoMPi and CoBi were found to be correlated with increases in the contributions from bilayer and trilayer stacked domains having structures intermediate between those of the LiCoOO and CoO(OH) mineral forms. The lattice structures and offset stacking of adjacent layers in the partially stacked CoMPi and CoBi domains were best matched to those in the LiCoOO layered structure. The results demonstrate the ability of PDF analysis to elucidate features of domain size, structure, defect content and mesoscale organization for amorphous metal oxide catalysts that are not readily accessed by other X-ray techniques. Finally, PDF structure analysis is shown to provide a way to characterize domain structures in different forms of amorphous oxide catalysts, and hence provide an opportunity to investigate correlations between domain structure and catalytic activity.

  5. Oxyanion induced variations in domain structure for amorphous cobalt oxide oxygen evolving catalysts, resolved by X-ray pair distribution function analysis

    PubMed Central

    Kwon, Gihan; Kokhan, Oleksandr; Han, Ali; Chapman, Karena W.; Chupas, Peter J.; Du, Pingwu; Tiede, David M.

    2015-01-01

    Amorphous thin film oxygen evolving catalysts, OECs, of first-row transition metals show promise to serve as self-assembling photoanode materials in solar-driven, photoelectrochemical ‘artificial leaf’ devices. This report demonstrates the ability to use high-energy X-ray scattering and atomic pair distribution function analysis, PDF, to resolve structure in amorphous metal oxide catalyst films. The analysis is applied here to resolve domain structure differences induced by oxyanion substitution during the electrochemical assembly of amorphous cobalt oxide catalyst films, Co-OEC. PDF patterns for Co-OEC films formed using phosphate, Pi, methylphosphate, MPi, and borate, Bi, electrolyte buffers show that the resulting domains vary in size following the sequence Pi < MPi < Bi. The increases in domain size for CoMPi and CoBi were found to be correlated with increases in the contributions from bilayer and trilayer stacked domains having structures intermediate between those of the LiCoOO and CoO(OH) mineral forms. The lattice structures and offset stacking of adjacent layers in the partially stacked CoMPi and CoBi domains were best matched to those in the LiCoOO layered structure. The results demonstrate the ability of PDF analysis to elucidate features of domain size, structure, defect content and mesoscale organization for amorphous metal oxide catalysts that are not readily accessed by other X-ray techniques. PDF structure analysis is shown to provide a way to characterize domain structures in different forms of amorphous oxide catalysts, and hence provide an opportunity to investigate correlations between domain structure and catalytic activity. PMID:26634728

  6. Demonstration of thin film pair distribution function analysis (tfPDF) for the study of local structure in amorphous and crystalline thin films

    PubMed Central

    Jensen, Kirsten M. Ø.; Blichfeld, Anders B.; Bauers, Sage R.; Wood, Suzannah R.; Dooryhée, Eric; Johnson, David C.; Iversen, Bo B.; Billinge, Simon J. L.

    2015-01-01

    By means of normal-incidence, high-flux and high-energy X-rays, total scattering data for pair distribution function (PDF) analysis have been obtained from thin films (tf), suitable for local structure analysis. By using amorphous substrates as support for the films, the standard Rapid Acquisition PDF setup can be applied and the scattering signal from the film can be isolated from the total scattering data through subtraction of an independently measured background signal. No angular corrections to the data are needed, as would be the case for grazing incidence measurements. The ‘tfPDF’ method is illustrated through studies of as-deposited (i.e. amorphous) and crystalline FeSb3 films, where the local structure analysis gives insight into the stabilization of the metastable skutterudite FeSb3 phase. The films were prepared by depositing ultra-thin alternating layers of Fe and Sb, which interdiffuse and after annealing crystallize to form the FeSb3 structure. The tfPDF data show that the amorphous precursor phase consists of corner-sharing FeSb6 octahedra with motifs highly resembling the local structure in crystalline FeSb3. Analysis of the amorphous structure allows the prediction of whether the final crystalline product will form the FeSb3 phase with or without excess Sb present. The study thus illustrates how analysis of the local structure in amorphous precursor films can help to understand crystallization processes of metastable phases and opens for a range of new local structure studies of thin films. PMID:26306190

  7. Fingerprinting analysis of non-crystalline pharmaceutical compounds using high energy X-rays and the total scattering pair distribution function

    NASA Astrophysics Data System (ADS)

    Davis, Timur D.

    2011-12-01

    In the development of new medicinal products, poor oral bioavailability, due to the low solubilities of many active pharmaceutical ingredients (APIs), is increasingly a barrier for treatments to be administered using tablet or capsule formulations and one of the main challenges facing the pharmaceutical industry. Non-crystalline phases such as the amorphous and nanostructured states can confer increased solubility to a drug, and therefore, have recently garnered a lot of interest from pharmaceutical researchers. However, little is known about local ordering in non-crystalline pharmaceuticals due to the lack of reliable experimental probes, hindering the clinical application of these compounds. The powerful tools of crystallography begin to lose their potency for structures on the nanoscale; conventional X-ray powder diffraction (XRPD) patterns become broad and featureless in these cases and are not useful for differentiating between different local molecular packing arrangements. In this thesis, we introduce the use of high energy X-rays coupled with total scattering pair distribution function (TSPDF) and fingerprinting analysis to investigate the local structures of non-crystalline pharmaceutical compounds. The high energy X-rays allow us to experimentally collect diffuse scattering intensities, which contain information about a sample's local ordering, in addition to the Bragg scattering available in conventional XRPD experiments, while the TSPDF allows us to view the intra- and inter-molecular correlations in real space. The goal of this study was to address some fundamental problems involving fingerprinting non-crystalline APIs using TSPDF in order to lay the groundwork for the proper use of the technique by the pharmaceutical community. We achieved this by developing the methodology as well as the exploring the scientific implications. On the methodology side, we introduced PDFGetX3, a new software program for calculating TSPDFs that simplifies the procedure

  8. Tracking Sodium-Antimonide Phase Transformations in Sodium-Ion Anodes: Insights from Operando Pair Distribution Function Analysis and Solid-State NMR Spectroscopy

    PubMed Central

    2016-01-01

    Operando pair distribution function (PDF) analysis and ex situ 23Na magic-angle spinning solid-state nuclear magnetic resonance (MAS ssNMR) spectroscopy are used to gain insight into the alloying mechanism of high-capacity antimony anodes for sodium-ion batteries. Subtraction of the PDF of crystalline NaxSb phases from the total PDF, an approach constrained by chemical phase information gained from 23Na ssNMR in reference to relevant model compounds, identifies two previously uncharacterized intermediate species formed electrochemically; a-Na3–xSb (x ≈ 0.4–0.5), a structure locally similar to crystalline Na3Sb (c-Na3Sb) but with significant numbers of sodium vacancies and a limited correlation length, and a-Na1.7Sb, a highly amorphous structure featuring some Sb–Sb bonding. The first sodiation breaks down the crystalline antimony to form first a-Na3–xSb and, finally, crystalline Na3Sb. Desodiation results in the formation of an electrode formed of a composite of crystalline and amorphous antimony networks. We link the different reactivity of these networks to a series of sequential sodiation reactions manifesting as a cascade of processes observed in the electrochemical profile of subsequent cycles. The amorphous network reacts at higher voltages reforming a-Na1.7Sb, then a-Na3–xSb, whereas lower potentials are required for the sodiation of crystalline antimony, which reacts to form a-Na3–xSb without the formation of a-Na1.7Sb. a-Na3–xSb is converted to crystalline Na3Sb at the end of the second discharge. We find no evidence of formation of NaSb. Variable temperature 23Na NMR experiments reveal significant sodium mobility within c-Na3Sb; this is a possible contributing factor to the excellent rate performance of Sb anodes. PMID:26824406

  9. Tracking Sodium-Antimonide Phase Transformations in Sodium-Ion Anodes: Insights from Operando Pair Distribution Function Analysis and Solid-State NMR Spectroscopy.

    PubMed

    Allan, Phoebe K; Griffin, John M; Darwiche, Ali; Borkiewicz, Olaf J; Wiaderek, Kamila M; Chapman, Karena W; Morris, Andrew J; Chupas, Peter J; Monconduit, Laure; Grey, Clare P

    2016-02-24

    Operando pair distribution function (PDF) analysis and ex situ (23)Na magic-angle spinning solid-state nuclear magnetic resonance (MAS ssNMR) spectroscopy are used to gain insight into the alloying mechanism of high-capacity antimony anodes for sodium-ion batteries. Subtraction of the PDF of crystalline NaxSb phases from the total PDF, an approach constrained by chemical phase information gained from (23)Na ssNMR in reference to relevant model compounds, identifies two previously uncharacterized intermediate species formed electrochemically; a-Na(3-x)Sb (x ≈ 0.4-0.5), a structure locally similar to crystalline Na3Sb (c-Na3Sb) but with significant numbers of sodium vacancies and a limited correlation length, and a-Na(1.7)Sb, a highly amorphous structure featuring some Sb-Sb bonding. The first sodiation breaks down the crystalline antimony to form first a-Na(3-x)Sb and, finally, crystalline Na3Sb. Desodiation results in the formation of an electrode formed of a composite of crystalline and amorphous antimony networks. We link the different reactivity of these networks to a series of sequential sodiation reactions manifesting as a cascade of processes observed in the electrochemical profile of subsequent cycles. The amorphous network reacts at higher voltages reforming a-Na(1.7)Sb, then a-Na(3-x)Sb, whereas lower potentials are required for the sodiation of crystalline antimony, which reacts to form a-Na(3-x)Sb without the formation of a-Na(1.7)Sb. a-Na(3-x)Sb is converted to crystalline Na3Sb at the end of the second discharge. We find no evidence of formation of NaSb. Variable temperature (23)Na NMR experiments reveal significant sodium mobility within c-Na3Sb; this is a possible contributing factor to the excellent rate performance of Sb anodes. PMID:26824406

  10. Local structure and lattice dynamics study of low dimensional materials using atomic pair distribution function and high energy resolution inelastic x-ray scattering

    NASA Astrophysics Data System (ADS)

    Shi, Chenyang

    Structure and dynamics lie at the heart of the materials science. A detailed knowledge of both subjects would be foundational in understanding the materials' properties and predicting their potential applications. However, the task becomes increasingly dicult as the particle size is reduced to the nanometer scale. For nanostructured materials their laboratory x-ray scattering patterns are overlapped and broadened, making structure determination impossible. Atomic pair distribution function technique based on either synchrotron x-ray or neutron scattering data is known as the tool of choice for probing local structures. However, to solve the "structure problem" in low-dimensional materials with PDF is still challenging. For example for 2D materials of interest in this thesis the crystallographic modeling approach often yields unphysical thermal factors along stacking direction where new chemical intuitions about their actual structures and new modeling methodology/program are needed. Beyond this, lattice dynamical investigations on nanosized particles are extremely dicult. Laboratory tools such as Raman and infra-red only probe phonons at Brillouin zone center. Although in literature there are a great number of theoretical studies of their vibrational properties based on either empirical force elds or density functional theory, various approximations made in theories make the theoretical predictions less reliable. Also, there lacks the direct experiment result to validate the theory against. In this thesis, we studied the structure and dynamics of a wide variety of technologically relevant low-dimensional materials through synchrotron based x-ray PDF and high energy resolution inelastic x-ray scattering (HERIX) techniques. By collecting PDF data and employing advanced modeling program such as DiPy-CMI, we successfully determined the atomic structures of (i) emerging Ti3C2, Nb4C3 MXenes (transition metal carbides and/or nitrides) that are promising for energy storage

  11. Pair correlation function integrals: Computation and use

    NASA Astrophysics Data System (ADS)

    Wedberg, Rasmus; O'Connell, John P.; Peters, Günther H.; Abildskov, Jens

    2011-08-01

    We describe a method for extending radial distribution functions obtained from molecular simulations of pure and mixed molecular fluids to arbitrary distances. The method allows total correlation function integrals to be reliably calculated from simulations of relatively small systems. The long-distance behavior of radial distribution functions is determined by requiring that the corresponding direct correlation functions follow certain approximations at long distances. We have briefly described the method and tested its performance in previous communications [R. Wedberg, J. P. O'Connell, G. H. Peters, and J. Abildskov, Mol. Simul. 36, 1243 (2010);, 10.1080/08927020903536366 Fluid Phase Equilib. 302, 32 (2011)], 10.1016/j.fluid.2010.10.004, but describe here its theoretical basis more thoroughly and derive long-distance approximations for the direct correlation functions. We describe the numerical implementation of the method in detail, and report numerical tests complementing previous results. Pure molecular fluids are here studied in the isothermal-isobaric ensemble with isothermal compressibilities evaluated from the total correlation function integrals and compared with values derived from volume fluctuations. For systems where the radial distribution function has structure beyond the sampling limit imposed by the system size, the integration is more reliable, and usually more accurate, than simple integral truncation.

  12. Resolving the structure of Ti3C2Tx MXenes through multilevel structural modeling of the atomic pair distribution function

    SciTech Connect

    Wesolowski, David J.; Wang, Hsiu -Wen; Page, Katharine L.; Naguib, Michael; Gogotsi, Yury

    2015-12-08

    MXenes are a recently discovered family of two-dimensional (2D) early transition metal carbides and carbonitrides, which have already shown many attractive properties and a great promise in energy storage and many other applications. However, a complex surface chemistry and small coherence length has been an obstacle in some applications of MXenes, also limiting accuracy of predictions of their properties. In this study, we describe and benchmark a novel way of modeling layered materials with real interfaces (diverse surface functional groups and stacking order between the adjacent monolayers) against experimental data. The structures of three kinds of Ti3C2Tx MXenes (T stands for surface terminating species, including O, OH, and F) produced under different synthesis conditions were resolved for the first time using atomic pair distribution function obtained by high-quality neutron total scattering. The true nature of the material can be easily captured with the sensitivity of neutron scattering to the surface species of interest and the detailed third-generation structure model we present. The modeling approach leads to new understanding of MXene structural properties and can replace the currently used idealized models in predictions of a variety of physical, chemical and functional properties of Ti3C2-based MXenes. Furthermore, the developed models can be employed to guide the design of new MXene materials with selected surface termination and controlled contact angle, catalytic, optical, electrochemical and other properties. We suggest that the multi-level structural modeling should form the basis for a generalized methodology on modeling diffraction and pair distribution function data for 2D and layered materials.

  13. Multi-user distribution of polarization entangled photon pairs

    NASA Astrophysics Data System (ADS)

    Trapateau, J.; Ghalbouni, J.; Orieux, A.; Diamanti, E.; Zaquine, I.

    2015-10-01

    We experimentally demonstrate multi-user distribution of polarization entanglement using commercial telecom wavelength division demultiplexers. The entangled photon pairs are generated from a broadband source based on spontaneous parametric down conversion in a periodically poled lithium niobate crystal using a double path setup employing a Michelson interferometer and active phase stabilisation. We test and compare demultiplexers based on various technologies and analyze the effect of their characteristics, such as losses and polarization dependence, on the quality of the distributed entanglement for three channel pairs of each demultiplexer. In all cases, we obtain a Bell inequality violation, whose value depends on the demultiplexer features. This demonstrates that entanglement can be distributed to at least three user pairs of a network from a single source. Additionally, we verify for the best demultiplexer that the violation is maintained when the pairs are distributed over a total channel attenuation corresponding to 20 km of optical fiber. These techniques are therefore suitable for resource-efficient practical implementations of entanglement-based quantum key distribution and other quantum communication network applications.

  14. Multi-user distribution of polarization entangled photon pairs

    SciTech Connect

    Trapateau, J.; Orieux, A.; Diamanti, E.; Zaquine, I.; Ghalbouni, J.

    2015-10-14

    We experimentally demonstrate multi-user distribution of polarization entanglement using commercial telecom wavelength division demultiplexers. The entangled photon pairs are generated from a broadband source based on spontaneous parametric down conversion in a periodically poled lithium niobate crystal using a double path setup employing a Michelson interferometer and active phase stabilisation. We test and compare demultiplexers based on various technologies and analyze the effect of their characteristics, such as losses and polarization dependence, on the quality of the distributed entanglement for three channel pairs of each demultiplexer. In all cases, we obtain a Bell inequality violation, whose value depends on the demultiplexer features. This demonstrates that entanglement can be distributed to at least three user pairs of a network from a single source. Additionally, we verify for the best demultiplexer that the violation is maintained when the pairs are distributed over a total channel attenuation corresponding to 20 km of optical fiber. These techniques are therefore suitable for resource-efficient practical implementations of entanglement-based quantum key distribution and other quantum communication network applications.

  15. Detailed mapping of the local Ir4+ dimers through the metal-insulator transitions of CuIr2S4 thiospinel by X-ray atomic pair distribution function measurements.

    PubMed

    Božin, E S; Masadeh, A S; Hor, Y S; Mitchell, J F; Billinge, S J L

    2011-01-28

    The evolution of the short-range structural signature of the Ir4+ dimer state in CuIr2S4 thiospinel has been studied across the metal-insulator phase transitions as the metallic state is induced by temperature, Cr doping, and x-ray fluence. An atomic pair distribution function (PDF) approach reveals that there are no local dimers that survive into the metallic phase when this is invoked by temperature and doping. The PDF shows Ir4+ dimers when they exist, regardless of whether or not they are long-range ordered. At 100 K, exposure to a 98 keV x-ray beam melts the long-range dimer order within a few seconds, though the local dimers remain intact. This shows that the metallic state accessed on warming and doping is qualitatively different from the state obtained under x-ray irradiation. PMID:21405330

  16. Distributed wireless quantum communication networks with partially entangled pairs

    NASA Astrophysics Data System (ADS)

    Yu, Xu-Tao; Zhang, Zai-Chen; Xu, Jin

    2014-01-01

    Wireless quantum communication networks transfer quantum state by teleportation. Existing research focuses on maximal entangled pairs. In this paper, we analyse the distributed wireless quantum communication networks with partially entangled pairs. A quantum routing scheme with multi-hop teleportation is proposed. With the proposed scheme, is not necessary for the quantum path to be consistent with the classical path. The quantum path and its associated classical path are established in a distributed way. Direct multi-hop teleportation is conducted on the selected path to transfer a quantum state from the source to the destination. Based on the feature of multi-hop teleportation using partially entangled pairs, if the node number of the quantum path is even, the destination node will add another teleportation at itself. We simulated the performance of distributed wireless quantum communication networks with a partially entangled state. The probability of transferring the quantum state successfully is statistically analyzed. Our work shows that multi-hop teleportation on distributed wireless quantum networks with partially entangled pairs is feasible.

  17. Correlating size and composition-dependent effects with magnetic, Mössbauer, and pair distribution function measurements in a family of catalytically active ferrite nanoparticles

    DOE PAGESBeta

    Wong, Stanislaus; Papaefthymiou, Georgia C.; Lewis, Crystal S.; Han, Jinkyu; Zhang, Cheng; Li, Qiang; Shi, Chenyang; Abeykoon, A. M.Milinda; Billinge, Simon J.L.; Stach, Eric; et al

    2015-05-06

    The magnetic spinel ferrites, MFe₂O₄ (wherein 'M' = a divalent metal ion such as but not limited to Mn, Co, Zn, and Ni), represent a unique class of magnetic materials in which the rational introduction of different 'M's can yield correspondingly unique and interesting magnetic behaviors. Herein we present a generalized hydrothermal method for the synthesis of single-crystalline ferrite nanoparticles with 'M' = Mg, Fe, Co, Ni, Cu, and Zn, respectively, which can be systematically and efficaciously produced simply by changing the metal precursor. Our protocol can moreover lead to reproducible size control by judicious selection of various surfactants. Asmore » such, we have probed the effects of both (i) size and (ii) chemical composition upon the magnetic properties of these nanomaterials using complementary magnetometry and Mössbauer spectroscopy techniques. The structure of the samples was confirmed by atomic PDF analysis of X-ray and electron powder diffraction data as a function of particle size. These materials retain the bulk spinel structure to the smallest size (i.e., 3 nm). In addition, we have explored the catalytic potential of our ferrites as both (a) magnetically recoverable photocatalysts and (b) biological catalysts, and noted that many of our as-prepared ferrite systems evinced intrinsically higher activities as compared with their iron oxide analogues.« less

  18. Correlating size and composition-dependent effects with magnetic, Mössbauer, and pair distribution function measurements in a family of catalytically active ferrite nanoparticles

    SciTech Connect

    Wong, Stanislaus; Papaefthymiou, Georgia C.; Lewis, Crystal S.; Han, Jinkyu; Zhang, Cheng; Li, Qiang; Shi, Chenyang; Abeykoon, A. M.Milinda; Billinge, Simon J.L.; Stach, Eric; Thomas, Justin; Guerrero, Kevin; Munayco, Pablo; Munayco, Jimmy; Scorzelli, Rosa B.; Burnham, Philip; Viescas, Arthur J; Tiano, Amanda L.

    2015-05-06

    The magnetic spinel ferrites, MFe₂O₄ (wherein 'M' = a divalent metal ion such as but not limited to Mn, Co, Zn, and Ni), represent a unique class of magnetic materials in which the rational introduction of different 'M's can yield correspondingly unique and interesting magnetic behaviors. Herein we present a generalized hydrothermal method for the synthesis of single-crystalline ferrite nanoparticles with 'M' = Mg, Fe, Co, Ni, Cu, and Zn, respectively, which can be systematically and efficaciously produced simply by changing the metal precursor. Our protocol can moreover lead to reproducible size control by judicious selection of various surfactants. As such, we have probed the effects of both (i) size and (ii) chemical composition upon the magnetic properties of these nanomaterials using complementary magnetometry and Mössbauer spectroscopy techniques. The structure of the samples was confirmed by atomic PDF analysis of X-ray and electron powder diffraction data as a function of particle size. These materials retain the bulk spinel structure to the smallest size (i.e., 3 nm). In addition, we have explored the catalytic potential of our ferrites as both (a) magnetically recoverable photocatalysts and (b) biological catalysts, and noted that many of our as-prepared ferrite systems evinced intrinsically higher activities as compared with their iron oxide analogues.

  19. Distance distributions of photogenerated charge pairs in organic photovoltaic cells.

    PubMed

    Barker, Alex J; Chen, Kai; Hodgkiss, Justin M

    2014-08-27

    Strong Coulomb interactions in organic photovoltaic cells dictate that charges must separate over relatively long distances in order to circumvent geminate recombination and produce photocurrent. In this article, we measure the distance distributions of thermalized charge pairs by accessing a regime at low temperature where charge pairs are frozen out following the primary charge separation step and recombine monomolecularly via tunneling. The exponential attenuation of tunneling rate with distance provides a sensitive probe of the distance distribution of primary charge pairs, reminiscent of electron transfer studies in proteins. By fitting recombination dynamics to distributions of recombination rates, we identified populations of charge-transfer states and well-separated charge pairs. For the wide range of materials we studied, the yield of separated charges in the tunneling regime is strongly correlated with the yield of free charges measured via their intensity-dependent bimolecular recombination dynamics at room temperature. We therefore conclude that populations of free charges are established via long-range charge separation within the thermalization time scale, thus invoking early branching between free and bound charges across an energetic barrier. Subject to assumed values of the electron tunneling attenuation constant, we estimate critical charge separation distances of ∼3-4 nm in all materials. In some blends, large fullerene crystals can enhance charge separation yields; however, the important role of the polymers is also highlighted in blends that achieved significant charge separation with minimal fullerene concentration. We expect that our approach of isolating the intrinsic properties of primary charge pairs will be of considerable value in guiding new material development and testing the validity of proposed mechanisms for long-range charge separation. PMID:25102389

  20. Unraveling the Hydrogenation of TiO 2 and Graphene Oxide/TiO 2 Composites in Real Time by in Situ Synchrotron X-ray Powder Diffraction and Pair Distribution Function Analysis

    DOE PAGESBeta

    Nguyen-Phan, Thuy-Duong; Liu, Zongyuan; Luo, Si; Gamalski, Andrew D.; Vovchok, Dimitry; Xu, Wenqian; Stach, Eric A.; Polyansky, Dmitry E.; Fujita, Etsuko; Rodriguez, José A.; et al

    2016-02-18

    The functionalization of graphene oxide (GO) and graphene by TiO2 and other metal oxides has attracted considerable attention due to numerous promising applications in catalysis, energy conversion, and storage. We propose hydrogenation of this class of materials as a promising way to tune catalytic properties by altering the structural and chemical transformations that occur upon H incorporation. We also investigate the structural changes that occur during the hydrogenation process using in situ powder X-ray diffraction and pair distribution function analysis of GO–TiO2 and TiO2 under H2 reduction. Sequential Rietveld refinement was employed to gain insight into the evolution of crystalmore » growth of TiO2 nanoparticles in the presence of two-dimensional (2D) GO nanosheets. GO sheets not only significantly retarded the nucleation and growth of rutile impurities, stabilizing the anatase structure, but was also partially reduced to hydrogenated graphene by the introduction of atomic hydrogen into the honeycomb lattice. We discuss the hydrogenation processes and the resulting composite structure that occurs during the incorporation of atomic H and the dynamic structural transformations that leads to a highly active photocatalyst.« less

  1. Pairing Nambu-Goldstone Modes within Nuclear Density Functional Theory.

    PubMed

    Hinohara, Nobuo; Nazarewicz, Witold

    2016-04-15

    We show that the Nambu-Goldstone formalism of the broken gauge symmetry in the presence of the T=1 pairing condensate offers a quantitative description of the binding-energy differences of open-shell superfluid nuclei. We conclude that the pairing-rotational moments of inertia are excellent pairing indicators, which are free from ambiguities attributed to odd-mass systems. We offer a new, unified interpretation of the binding-energy differences traditionally viewed in the shell model picture as signatures of the valence nucleon properties. We present the first systematic analysis of the off-diagonal pairing-rotational moments of inertia and demonstrate the mixing of the neutron and proton pairing-rotational modes in the ground states of even-even nuclei. Finally, we discuss the importance of mass measurements of neutron-rich nuclei for constraining the pairing energy density functional. PMID:27127964

  2. Pairing Nambu-Goldstone Modes within Nuclear Density Functional Theory

    NASA Astrophysics Data System (ADS)

    Hinohara, Nobuo; Nazarewicz, Witold

    2016-04-01

    We show that the Nambu-Goldstone formalism of the broken gauge symmetry in the presence of the T =1 pairing condensate offers a quantitative description of the binding-energy differences of open-shell superfluid nuclei. We conclude that the pairing-rotational moments of inertia are excellent pairing indicators, which are free from ambiguities attributed to odd-mass systems. We offer a new, unified interpretation of the binding-energy differences traditionally viewed in the shell model picture as signatures of the valence nucleon properties. We present the first systematic analysis of the off-diagonal pairing-rotational moments of inertia and demonstrate the mixing of the neutron and proton pairing-rotational modes in the ground states of even-even nuclei. Finally, we discuss the importance of mass measurements of neutron-rich nuclei for constraining the pairing energy density functional.

  3. Three-dimensional structure of nanocomposites from atomic pair distribution function analysis: study of polyaniline and (polyaniline)(0.5)V(2)O(5) x 1.0 H(2)O.

    PubMed

    Petkov, Valeri; Parvanov, Vencislav; Trikalitis, Pantelis; Malliakas, Christos; Vogt, Tom; Kanatzidis, Mercouri G

    2005-06-22

    The three-dimensional structures of emeraldine base polyaniline (PANI) and (polyaniline)(0.5)V(2)O(5) x 1.0 H(2)O have been determined by total X-ray scattering experiments. Atomic pair distribution functions (PDF) were measured to obtain experimental observables against which structural models were tested and refined. The PDF approach is necessary because of the limited structural coherence in these nanostructured materials. Polyaniline possesses a well-defined local atomic arrangement that can be described in terms of an 84-atom orthorhombic unit cell. The nanocomposite (PANI)(0.5)V(2)O(5) x 1.0 H(2)O too is locally well ordered and may be described in terms of a small number of structure-sensible parameters. The PDF approach allows the construction of structure models of PANI and (PANI)(0.5)V(2)O(5) x 1.0 H(2)O on the basis of which important materials' properties can be explained predicted and possibly improved. PMID:15954787

  4. Probing local structure in the yellow phosphor LaSr[subscript 2]AlO[subscript 5]:Ce[superscript 3+], by the maximum entropy method and pair distribution function analysis

    SciTech Connect

    Im, Won Bin; Page, Katharine; DenBaars, Steven P.; Seshadri, Ram

    2011-08-04

    The compound LaSr{sub 2}AlO{sub 5} was recently introduced as a competitive Ce{sup 3+} host material for blue-pumped yellow phosphors for use in white light emitting diodes. A crucial feature of the crystal structure of LaSr{sub 2}AlO{sub 5} is that La, which is the host site for Ce{sup 3+}, is located in the 8h positions of the I4/mcm crystal structure, a site equally shared with Sr. While the average crystal structure of LaSr{sub 2}AlO{sub 5} as revealed by Rietveld analysis of laboratory and synchrotron X-ray diffraction data suggests nothing untoward, maximum entropy method analysis of the synchrotron X-ray data reveals the existence of conspicuous non-sphericity of the electron density. Pair distribution function analysis of the data suggests that despite their occupying the same crystallographic site, La and Sr possess distinct coordination environments, and the environment around La is more compact and regular than the environment suggested by the Rietveld refinement of the average structure. The absorption and emission from Ce{sup 3+} centers is controlled by the local coordination and symmetry, and the use of powerful new tools in unraveling details of these strengthens the rational search for new phosphors for solid state white lighting.

  5. Element-specific structure of materials with intrinsic disorder by high-energy resonant x-ray diffraction and differential atomic pair-distribution functions : a study of PtPd nanosized catalysts.

    SciTech Connect

    Petkov, V.; Shastri, S. D.; X-Ray Science Division; Central Michigan Univ.

    2010-01-01

    We demonstrate how high-energy resonant x-ray diffraction (XRD) and differential atomic-pair-distribution function (PDF) analysis can be used to characterize the atomic ordering in materials of limited structural coherence with both excellent spatial resolution and element specificity. First we prove that this experimental approach is feasible by probing the K-absorption edge of Au({approx}81 keV) atoms in chemically ordered and disordered bulk Cu3Au alloys. The resulting Au-differential PDFs show very clearly the different ways Au atoms are known to occupy the sites of otherwise identical cubic lattices of those materials. Next we apply it to a more complex material: PtPd alloy and core-shell nanosized ({approx}2-4 nm) particles by probing the K-absorption edge of Pt({approx}78 keV). The resulting Pt-differential atomic PDFs reveal how exactly the atomic ordering of catalytically active Pt atoms is affected by the nanoparticles design, thus providing a firm structural basis for understanding their properties. The work is a step forward in expanding the limits of applicability of nontraditional XRD to the rapidly growing field of materials of unusual structural complexity.

  6. Element-specific structure of materials with intrinsic disorder by high-energy resonant x-ray diffraction and differential atomic pair-distribution functions: A study of PtPd nanosized catalysts

    NASA Astrophysics Data System (ADS)

    Petkov, V.; Shastri, S. D.

    2010-04-01

    We demonstrate how high-energy resonant x-ray diffraction (XRD) and differential atomic-pair-distribution function (PDF) analysis can be used to characterize the atomic ordering in materials of limited structural coherence with both excellent spatial resolution and element specificity. First we prove that this experimental approach is feasible by probing the K -absorption edge of Au(˜81keV) atoms in chemically ordered and disordered bulk Cu3Au alloys. The resulting Au-differential PDFs show very clearly the different ways Au atoms are known to occupy the sites of otherwise identical cubic lattices of those materials. Next we apply it to a more complex material: PtPd alloy and core-shell nanosized (˜2-4nm) particles by probing the K -absorption edge of Pt(˜78keV) . The resulting Pt-differential atomic PDFs reveal how exactly the atomic ordering of catalytically active Pt atoms is affected by the nanoparticles’ design, thus providing a firm structural basis for understanding their properties. The work is a step forward in expanding the limits of applicability of nontraditional XRD to the rapidly growing field of materials of unusual structural complexity.

  7. Synergy between pair coupled cluster doubles and pair density functional theory

    SciTech Connect

    Garza, Alejandro J.; Bulik, Ireneusz W.; Henderson, Thomas M.; Scuseria, Gustavo E.

    2015-01-28

    Pair coupled cluster doubles (pCCD) has been recently studied as a method capable of accounting for static correlation with low polynomial cost. We present three combinations of pCCD with Kohn–Sham functionals of the density and on-top pair density (the probability of finding two electrons on top of each other) to add dynamic correlation to pCCD without double counting. With a negligible increase in computational cost, these pCCD+DFT blends greatly improve upon pCCD in the description of typical problems where static and dynamic correlations are both important. We argue that—as a black-box method with low scaling, size-extensivity, size-consistency, and a simple quasidiagonal two-particle density matrix—pCCD is an excellent match for pair density functionals in this type of fusion of multireference wavefunctions with DFT.

  8. Nucleon and nucleon-pair momentum distributions in A≤12 nuclei

    SciTech Connect

    Wiringa, Robert B.; Schiavilla, Rocco; Pieper, Steven C.; Carlson, Joseph A.

    2014-02-10

    We report variational Monte Carlo calculations of single-nucleon momentum distributions for A≤12 nuclei and nucleon-pair and nucleon-cluster momentum distributions for A≤8. The wave functions have been generated for a Hamiltonian containing the Argonne ν18 two-nucleon and Urbana X three-nucleon potentials. The single-nucleon and nucleon-pair momentum distributions exhibit universal features attributable to the one-pion-exchange tensor interaction The single-nucleon distributions are broken down into proton and neutron components and spin-up and spin-down components where appropriate. The nucleon-pair momentum distributions are given separately for pp and pn pairs. The nucleon-cluster momentum distributions include dp in 3He, tp and dd in S4He, αd in 6Li,αt in 7Li, and αα in 8Be. Detailed tables are provided on-line for download.

  9. Nucleon and nucleon-pair momentum distributions in A≤12 nuclei

    DOE PAGESBeta

    Wiringa, Robert B.; Schiavilla, Rocco; Pieper, Steven C.; Carlson, Joseph A.

    2014-02-10

    We report variational Monte Carlo calculations of single-nucleon momentum distributions for A≤12 nuclei and nucleon-pair and nucleon-cluster momentum distributions for A≤8. The wave functions have been generated for a Hamiltonian containing the Argonne ν18 two-nucleon and Urbana X three-nucleon potentials. The single-nucleon and nucleon-pair momentum distributions exhibit universal features attributable to the one-pion-exchange tensor interaction The single-nucleon distributions are broken down into proton and neutron components and spin-up and spin-down components where appropriate. The nucleon-pair momentum distributions are given separately for pp and pn pairs. The nucleon-cluster momentum distributions include dp in 3He, tp and dd in S4He, αd inmore » 6Li,αt in 7Li, and αα in 8Be. Detailed tables are provided on-line for download.« less

  10. Cation Ordering in Li[NixMnxCo(1-2x)]O2-Layered Cathode Materials: A Nuclear Magnetic Resonance (NMR), Pair Distribution Function, X-ray Absorption Spectroscopy, and Electrochemical Study

    SciTech Connect

    Zeng,D.; Cabana, J.; Breger, J.; Yoon, W.; Grey, C.

    2007-01-01

    Several members of the compositional series Li[NixMnxCo(1-2x)]O2 (0.01 = x = 1/3) were synthesized and characterized. X-ray diffraction results confirm the presence of the layered a-NaFeO2-type structure, while X-ray absorption near-edge spectroscopy experiments verify the presence of Ni2+, Mn4+, and Co3+. Their local environment and short-range ordering were investigated by using a combination of 6Li magic angle spinning (MAS) nuclear magnetic resonance (NMR) spectroscopy and neutron pair distribution function (PDF) analysis, associated with reverse Monte Carlo (RMC) calculations. The 6Li MAS NMR spectra of compounds with low Ni/Mn contents (x = 0.10) show several well-resolved resonances, which start to merge when the amount of Ni and Mn increases, finally forming a broad resonance at high Ni/Mn contents. Analysis of the 6Li MAS NMR 6Li[Ni0.02Mn0.02Co0.96]O2 spectrum, is consistent with the formation of Ni2+ and Mn4+ clusters within the transition-metal layers, even at these low-doping levels. The oxidation state of Ni in this high Co content sample strongly depends upon the Li/transition metal ratio of the starting materials. Neutron PDF analysis of the highest Ni/Mn content sample Li[Ni1/3Mn1/3Co1/3]O2 shows a tendency for Ni cations to be close to Mn cations in the first coordination shell; however, the Co3+ ions are randomly distributed. Analysis of the intensity of the 'LiCoO2' resonance, arising from Li surrounded by Co3+ in its first two cation coordination shells, for the whole series provides further evidence for a nonrandom distribution of the transition-metal cations. The presence of the insulator-to-metal transition seen in the electrochemical profiles of these materials upon charging correlates strongly with the concentration of the 'LiCoO2' resonance.

  11. Nuclear Parton Distribution Functions

    SciTech Connect

    I. Schienbein, J.Y. Yu, C. Keppel, J.G. Morfin, F. Olness, J.F. Owens

    2009-06-01

    We study nuclear effects of charged current deep inelastic neutrino-iron scattering in the framework of a {chi}{sup 2} analysis of parton distribution functions (PDFs). We extract a set of iron PDFs which are used to compute x{sub Bj}-dependent and Q{sup 2}-dependent nuclear correction factors for iron structure functions which are required in global analyses of free nucleon PDFs. We compare our results with nuclear correction factors from neutrino-nucleus scattering models and correction factors for charged-lepton--iron scattering. We find that, except for very high x{sub Bj}, our correction factors differ in both shape and magnitude from the correction factors of the models and charged-lepton scattering.

  12. An efficient algorithm for generating random number pairs drawn from a bivariate normal distribution

    NASA Technical Reports Server (NTRS)

    Campbell, C. W.

    1983-01-01

    An efficient algorithm for generating random number pairs from a bivariate normal distribution was developed. Any desired value of the two means, two standard deviations, and correlation coefficient can be selected. Theoretically the technique is exact and in practice its accuracy is limited only by the quality of the uniform distribution random number generator, inaccuracies in computer function evaluation, and arithmetic. A FORTRAN routine was written to check the algorithm and good accuracy was obtained. Some small errors in the correlation coefficient were observed to vary in a surprisingly regular manner. A simple model was developed which explained the qualities aspects of the errors.

  13. Interactions in 1-ethyl-3-methyl imidazolium tetracyanoborate ion pair: Spectroscopic and density functional study

    SciTech Connect

    Mao, James X; Lee, Anita S; Kitchin, John R; Nulwala, Hunaid B; Luebke, David R; Damodaran, Krishnan

    2013-04-24

    Density Functional Theory is used to investigate a weakly coordinating room-temperature ionic liquid, 1-ethyl-3-methyl imidazolium tetracyanoborate ([Emim]{sup +}[TCB]{sup -}). Four locally stable conformers of the ion pair were located. Atoms-in-molecules (AIM) and electron density analysis indicated the existence of several hydrogen bonds. Further investigation through the Natural Bond Orbital (NBO) and Natural Energy Decomposition Analysis (NEDA) calculations provided insight into the origin of interactions in the [Emim]{sup +}[TCB]{sup -} ion pair. Strength of molecular interactions in the ionic liquid was correlated with frequency shifts of the characteristic vibrations of the ion pair. Harmonic vibrations of the ion pair were also compared with the experimental Raman and Infrared spectra. Vibrational frequencies were assigned by visualizing displacements of atoms around their equilibrium positions and through Potential Energy Distribution (PED) analysis.

  14. Cluster pair correlation function of simple fluids: energetic connectivity criteria.

    PubMed

    Pugnaloni, Luis A; Zarragoicoechea, Guillermo J; Vericat, Fernando

    2006-11-21

    We consider the clustering of Lennard-Jones particles by using an energetic connectivity criterion proposed long ago by Hill [J. Chem. Phys. 32, 617 (1955)] for the bond between pairs of particles. The criterion establishes that two particles are bonded (directly connected) if their relative kinetic energy is less than minus their relative potential energy. Thus, in general, it depends on the direction as well as on the magnitude of the velocities and positions of the particles. An integral equation for the pair connectedness function, proposed by two of the authors [Phys. Rev. E 61, R6067 (2000)], is solved for this criterion and the results are compared with those obtained from molecular dynamics simulations and from a connectedness Percus-Yevick-type integral equation for a velocity-averaged version of Hill's energetic criterion. PMID:17129128

  15. The partial pair correlation functions of dense supercritical water

    NASA Astrophysics Data System (ADS)

    Tassaing, T.; Bellissent-Funel, M.-C.; Guillot, B.; Guissani, Y.

    1998-05-01

    Neutron diffraction measurements of heavy water and of two isotopic H2O/D2O mixtures at supercritical state (T = 380 °C and ρD2O = 0.73 g/cm3) are presented. In combining the set of neutron diffraction data with previous X-rays measurements of Yamanaka et al. (J. Chem. Phys., 101 (1994) 9830), it has been possible by using a Monte Carlo method to reach the partial pair correlation functions gOH(r), gHH(r) and gOO(r). The results are compared with molecular-dynamics simulations using the SPCE pair potential for water. These new results confirm that hydrogen bonding is still present in dense supercritical water.

  16. Hyperdimensional analysis of amino acid pair distributions in proteins.

    PubMed

    Henriksen, Svend B; Mortensen, Rasmus J; Geertz-Hansen, Henrik M; Neves-Petersen, Maria Teresa; Arnason, Omar; Söring, Jón; Petersen, Steffen B

    2011-01-01

    Our manuscript presents a novel approach to protein structure analyses. We have organized an 8-dimensional data cube with protein 3D-structural information from 8706 high-resolution non-redundant protein-chains with the aim of identifying packing rules at the amino acid pair level. The cube contains information about amino acid type, solvent accessibility, spatial and sequence distance, secondary structure and sequence length. We are able to pose structural queries to the data cube using program ProPack. The response is a 1, 2 or 3D graph. Whereas the response is of a statistical nature, the user can obtain an instant list of all PDB-structures where such pair is found. The user may select a particular structure, which is displayed highlighting the pair in question. The user may pose millions of different queries and for each one he will receive the answer in a few seconds. In order to demonstrate the capabilities of the data cube as well as the programs, we have selected well known structural features, disulphide bridges and salt bridges, where we illustrate how the queries are posed, and how answers are given. Motifs involving cysteines such as disulphide bridges, zinc-fingers and iron-sulfur clusters are clearly identified and differentiated. ProPack also reveals that whereas pairs of Lys residues virtually never appear in close spatial proximity, pairs of Arg are abundant and appear at close spatial distance, contrasting the belief that electrostatic repulsion would prevent this juxtaposition and that Arg-Lys is perceived as a conservative mutation. The presented programs can find and visualize novel packing preferences in proteins structures allowing the user to unravel correlations between pairs of amino acids. The new tools allow the user to view statistical information and visualize instantly the structures that underpin the statistical information, which is far from trivial with most other SW tools for protein structure analysis. PMID:22174733

  17. Distribution functions of probabilistic automata

    NASA Technical Reports Server (NTRS)

    Vatan, F.

    2001-01-01

    Each probabilistic automaton M over an alphabet A defines a probability measure Prob sub(M) on the set of all finite and infinite words over A. We can identify a k letter alphabet A with the set {0, 1,..., k-1}, and, hence, we can consider every finite or infinite word w over A as a radix k expansion of a real number X(w) in the interval [0, 1]. This makes X(w) a random variable and the distribution function of M is defined as usual: F(x) := Prob sub(M) { w: X(w) < x }. Utilizing the fixed-point semantics (denotational semantics), extended to probabilistic computations, we investigate the distribution functions of probabilistic automata in detail. Automata with continuous distribution functions are characterized. By a new, and much more easier method, it is shown that the distribution function F(x) is an analytic function if it is a polynomial. Finally, answering a question posed by D. Knuth and A. Yao, we show that a polynomial distribution function F(x) on [0, 1] can be generated by a prob abilistic automaton iff all the roots of F'(x) = 0 in this interval, if any, are rational numbers. For this, we define two dynamical systems on the set of polynomial distributions and study attracting fixed points of random composition of these two systems.

  18. Valence quark spin distribution functions

    SciTech Connect

    Nathan Isgur

    1998-09-01

    The hyperfine interactions of the constituent quark model provide a natural explanation for many nucleon properties, including the {Delta} - N splitting, the charge radius of the neutron, and the observation that the proton's quark distribution function ratio d(x)/u(x) {r_arrow} 0 as x {r_arrow} 1. The hyperfine-perturbed quark model also makes predictions for the nucleon spin-dependent distribution functions. Precision measurements of the resulting asymmetries A{sub 1}{sup p}(x) and A{sub 1}{sup n}(x) in the valence region can test this model and thereby the hypothesis that the valence quark spin distributions are ''normal''.

  19. Distributed Pair Programming Using Collaboration Scripts: An Educational System and Initial Results

    ERIC Educational Resources Information Center

    Tsompanoudi, Despina; Satratzemi, Maya; Xinogalos, Stelios

    2015-01-01

    Since pair programming appeared in the literature as an effective method of teaching computer programming, many systems were developed to cover the application of pair programming over distance. Today's systems serve personal, professional and educational purposes allowing distributed teams to work together on the same programming project. The…

  20. Kinematic distributions for electron pair production by muons

    NASA Technical Reports Server (NTRS)

    Linsker, R.

    1972-01-01

    Cross sections and kinematic distributions for the trident production process plus or negative muon plus charge yields plus or minus muon plus electron plus positron plus charge (with charge = dipion moment and Fe) are given for beam energies of 100 to 300 GeV at fixed (electron positron) masses from 5 to 15 GeV. This process is interesting as a test of quantum electrodynamics at high energies, and in particular as a test of the form of the photon propagator at large timelike (four-momentum) squared. For this purpose, it is desirable to impose kinematic cuts that favor those Bethe-Heitler graphs which contain a timelike photon propagator. It is found that there are substantial differences between the kinematic distributions for the full Bethe-Heitler matrix element and the distributions for the two timelike-photon graphs alone; these differences can be exploited in the selection of appropriate kinematic cuts.

  1. Structure functions and parton distributions

    SciTech Connect

    Martin, A.D.; Stirling, W.J.; Roberts, R.G.

    1995-07-01

    The MRS parton distribution analysis is described. The latest sets are shown to give an excellent description of a wide range of deep-inelastic and other hard scattering data. Two important theoretical issues-the behavior of the distributions at small x and the flavor structure of the quark sea-are discussed in detail. A comparison with the new structure function data from HERA is made, and the outlook for the future is discussed.

  2. Modeling the Pauli potential in the pair density functional theory.

    PubMed

    Amovilli, C; Nagy, A

    2008-11-28

    In the ground state the pair density can be determined by solving a single auxiliary equation of a two-particle problem. A novel method for determining the Pauli potential entering this equation is presented and, starting from a reliable description of the pair density, an analytical expression is derived for atomic systems. Test calculations are presented for Be and isoelectronic C(2+) and O(4+) ions. PMID:19045853

  3. Yield, variance and spatial distribution of electron-hole pairs in CsI

    SciTech Connect

    Gao, Fei; Xie, Y.; Kerisit, S.; Campbell, L. W.; Weber, William J

    2011-01-01

    A Monte Carlo method previously developed has been applied to simulate the interaction of photons with CsI over the energy range from 50 eV to ~ 1 MeV and the subsequent electron cascades, as well as various quantum mechanical processes. The MC model has been employed to investigate the creation and nano-scale spatial distribution of electron-hole pairs and to calculate important intrinsic properties, including the W value, which is the mean energy required to produce an electron-hole pair, and the Fano factor. At energies lower than 10 keV, W generally decreases with increasing photon energy from 19 to 15 eV, whereas it saturates to 15 eV for higher energies. However, W exhibits a sawtooth variation, and discontinuities at the shell edges that follow the photoionization cross sections. The Fano factor, F, generally increases with increasing energy, and has a value of 0.28 at energies higher than 10 keV. The decrease of W value up to 10 keV may account for the initial rise in relative light yield with incident energy, as observed in experiments in CsI, and this suggests that the nonlinearity at low energy range may be associated with intrinsic properties of materials. Also, the spatial distribution of e-h pairs shows that the e-h pairs are primarily distributed along fast electron tracks in CsI, but the density of electron-hole pairs is low. A significant number of electron-hole pairs are produced through the different ionization channels of core shells and corresponding relaxation processes, which may provide an explanation why the Fano factor in CsI is larger than that in Si or Ge. The spatial distribution and density of thermalized electron-hole pairs along the primary and secondary tracks are important for large scale simulations of electron-hole pair transport.

  4. High-energy X-ray powder diffraction and atomic-pair distribution-function studies of charged/discharged structures in carbon-hybridized Li2MnSiO4 nanoparticles as a cathode material for lithiumion batteries

    SciTech Connect

    Moriya, Maki; Miyahara, Masahiko; Hokazono, Mana; Sasaki, Hirokazu; Nemoto, Atsushi; Katayama, Shingo; Akimoto, Yuji; Hirano, Shin-ichi; Ren, Yang

    2014-10-01

    The stable cycling performance with a high discharge capacity of similar to 190 mAh g(-1) in a carbon-hybridized Li2MnSiO4 nanostructured powder has prompted an experimental investigation of the charged/discharged structures using synchrotron-based and laboratory-based X-rays and atomic-pair distributionfunction (PDF) analyses. A novel method of in-situ spray pyrolysis of a precursor solution with glucose as a carbon source enabled the successful synthesis of the carbon-hybridized Li2(M)nSiO(4) nanoparticles. The XRD patters of the discharged (lithiated) samples exhibit a long-range ordered structure characteristic of the (beta) Li2MnSiO4 crystalline phase (space group Pmn2(1)) which dissipates in the charged (delithiated) samples. However, upon discharging the long-range ordered structure recovers in each cycle. The disordered structure, according to the PDF analysis, is mainly due to local distortions of the MnO4 tetrahedra which show a mean Mn-O nearest neighbor distance shorter than that of the long-range ordered phase. These results corroborate the notion of the smaller Mn3+/Mn4+ ionic radii in the Li extracted phase versus the larger Mn2+ ionic radius in Li inserted phase. Thus Li extraction/insertion drives the fluctuation between the disordered and the long-range ordered structures. (C) 2014 Elsevier B.V. All rights reserved.

  5. Yield, variance and spatial distribution of electron–hole pairs in CsI

    SciTech Connect

    Gao, Fei; Xie, YuLong; Kerisit, Sebastien N.; Campbell, Luke W.; Weber, William J.

    2011-10-01

    A Monte Carlo (MC) method previously developed has been applied to simulate the interaction of photons, with energies ranging from 50 eV to ~ 1 MeV, with CsI and the subsequent electron cascades. The MC model has been employed to compute nano-scale spatial distributions of electron-hole pairs and important intrinsic properties, including W, the mean energy per electron-hole pair, and the Fano factor, F. W exhibits discontinuities at the shell edges that follow the photoionization cross sections and decreases with increasing photon energy (from ~19 to 15 eV), with an asymptotic value of 15.2 eV at high energy. This decrease may contribute the initial rise in relative light yield with incident energy observed experimentally for CsI, thus suggesting that nonlinearity may be associated with intrinsic properties of the material at low energies. F is calculated to increase with increasing energy and has an asymptotic value of 0.28. A significant number of electron-hole pairs are produced through the different ionization channels of core shells and corresponding relaxation processes, which may explain why F is larger for CsI than for Si or Ge. Finally, the calculated spatial distributions show that the electron-hole pairs are primarily distributed along fast electron tracks. These spatial distributions constitute important input for large-scale simulations of electron-hole pair transport.

  6. The counterbalance theory for evolution and function of paired receptors.

    PubMed

    Barclay, A Neil; Hatherley, Deborah

    2008-11-14

    Paired receptors are families of membrane proteins containing similar extracellular regions but differing in their potential for signaling with one type able to give inhibitory signals and the other activating. Inhibitory receptors could be good targets for pathogens to restrict immune responses against them. Here we suggest that activating members may have evolved to counterbalance pathogens utilizing the inhibitory pathway. Thus, if a pathogen utilizes any part of the inhibitory receptor to downregulate responses against itself, it may, because of similarities in structure, also bind the activating receptor and give an opposing signal. We evaluate recent structural data on SIRPalpha (signal regulatory protein) and LILRB1 (leukocyte immunoglobulin-like receptor subfamily B member 1) showing evidence of pathogen pressure in nonligand-binding regions of these receptors together with data on pathogen binding to PIRs (paired Ig-like receptors) to provide support for this theory. PMID:19006692

  7. Unbiased estimators for spatial distribution functions of classical fluids.

    PubMed

    Adib, Artur B; Jarzynski, Christopher

    2005-01-01

    We use a statistical-mechanical identity closely related to the familiar virial theorem, to derive unbiased estimators for spatial distribution functions of classical fluids. In particular, we obtain estimators for both the fluid density rho(r) in the vicinity of a fixed solute and the pair correlation g(r) of a homogeneous classical fluid. We illustrate the utility of our estimators with numerical examples, which reveal advantages over traditional histogram-based methods of computing such distributions. PMID:15638649

  8. Familial Clustering of Executive Functioning in Affected Sibling Pair Families with ADHD

    ERIC Educational Resources Information Center

    Slaats-Willemse, Dorine; Swaab-Barneveld, Hanna; De Sonneville, Leo; Buitelaar, Jan

    2005-01-01

    Objective: To investigate familial clustering of executive functioning (i.e., response inhibition, fine visuomotor functioning, and attentional control) in attention-deficit/hyperactivity disorder (ADHD)-affected sibling pairs. Method: Fifty-two affected sibling pairs aged 6 to 18 years and diagnosed with ADHD according to DSM-IV performed the…

  9. Variational derivation of equation for generalized pair correlation function

    NASA Technical Reports Server (NTRS)

    Malik, F. Bary

    1992-01-01

    The wavefunction of a system is explicitly written down in a fully anti-symmetric way between a fermion pair and a medium, and the equations for each one of them are derived from the variation of total energy for bound systems and by forming appropriate scalar products for continuum states. High-energy particles, such as protons, electrons, and nuclei impinging upon spacecraft, produce secondary radiations. In order to protect the internal environment of spacecraft from these radiations, their intensities are determined in many instances theoretically, and an appropriate program has been developed in the High Energy Science Branch. The purpose of this research is to investigate the problem of indistinguishability of an incident projectile with one of the same in a target.

  10. Multiconfiguration Pair-Density Functional Theory Spectral Calculations Are Stable to Adding Diffuse Basis Functions.

    PubMed

    Hoyer, Chad E; Gagliardi, Laura; Truhlar, Donald G

    2015-11-01

    Time-dependent Kohn-Sham density functional theory (TD-KS-DFT) is useful for calculating electronic excitation spectra of large systems, but the low-energy spectra are often complicated by artificially lowered higher-energy states. This affects even the lowest energy excited states. Here, by calculating the lowest energy spin-conserving excited state for atoms from H to K and for formaldehyde, we show that this problem does not occur in multiconfiguration pair-density functional theory (MC-PDFT). We use the tPBE on-top density functional, which is a translation of the PBE exchange-correlation functional. We compare to a robust multireference method, namely, complete active space second-order perturbation theory (CASPT2), and to TD-KS-DFT with two popular exchange-correlation functionals, PBE and PBE0. We find for atoms that the mean unsigned error (MUE) of MC-PDFT with the tPBE functional improves from 0.42 to 0.40 eV with a double set of diffuse functions, whereas the MUEs for PBE and PBE0 drastically increase from 0.74 to 2.49 eV and from 0.45 to 1.47 eV, respectively. PMID:26722961

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

    NASA Astrophysics Data System (ADS)

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

    2016-05-01

    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.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

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

    PubMed

    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. PMID:27160891

  13. Function transfer in human operant experiments: the role of stimulus pairings.

    PubMed Central

    Tonneau, François; González, Carmen

    2004-01-01

    Although function transfer often has been studied in complex operant procedures (such as matching to sample), whether operant reinforcement actually produces function transfer in such settings has not been established. The present experiments, with high school students as subjects, suggest that stimulus pairings can promote function transfer in conditions that closely approximate those of matching to sample. In Experiment 1, the subjects showed transfer of operant responding from three geometric figures (C1, C2, C3) to three colored shapes (B1, B2, B3) when the latter were paired with the former. Experiment 2 involved two groups of subjects. In the matching group, subjects matched the colored shapes with the geometric figures; in the yoked group, the shapes were merely paired with the geometric figures, and the schedule of stimulus pairing was yoked to the performance of the subjects in the matching group. Both groups of subjects showed function transfer. Experiment 3 documented function transfer from C stimuli to B stimuli through indirect stimulus pairings (A-B, A-C). In Experiment 4, function transfer was obtained even though the subjects vocalized continuously during the pairing trials, presumably preventing covert verbalization that might mediate transfer effects. Our results are consistent with a Pavlovian account and raise difficulties for current operant theories of function transfer. PMID:15357508

  14. The Differential cross section distribution of Drell-Yan dielectron pairs in the z boson mass region

    SciTech Connect

    Han, Jiyeon; /Rochester U.

    2008-11-01

    We report on a measurement of the rapidity distribution, d{sigma}/dy, for Z=Drell-Yan {yields} ee events produced in p{bar p} collisions at {radical}s = 1.96 TeV. The data sample consists of 2.13 fb{sup -1} corresponding to about 160,000 Z/Drell-Yan {yields} ee candidates in the Z boson mass region collected by the Collider Detector at Fermilab. The d{sigma}/dy distribution, which is measured over the full kinematic range for e{sup +}e{sup -} pairs in the invariant mass range 66 < M{sub ee} < 116 GeV/c{sup 2}, is compared with theory predictions. There is good agreement between the data and predictions of Quantum Chromodynamics in Next to Leading Order with the CTEQ6.1M Parton Distribution Functions.

  15. Sweet complementarity: the functional pairing of glycans with lectins.

    PubMed

    Gabius, H-J; Manning, J C; Kopitz, J; André, S; Kaltner, H

    2016-05-01

    Carbohydrates establish the third alphabet of life. As part of cellular glycoconjugates, the glycans generate a multitude of signals in a minimum of space. The presence of distinct glycotopes and the glycome diversity are mapped by sugar receptors (antibodies and lectins). Endogenous (tissue) lectins can read the sugar-encoded information and translate it into functional aspects of cell sociology. Illustrated by instructive examples, each glycan has its own ligand properties. Lectins with different folds can converge to target the same epitope, while intrafamily diversification enables functional cooperation and antagonism. The emerging evidence for the concept of a network calls for a detailed fingerprinting. Due to the high degree of plasticity and dynamics of the display of genes for lectins the validity of extrapolations between different organisms of the phylogenetic tree yet is inevitably limited. PMID:26956894

  16. Function Transfer in Human Operant Experiments: The Role of Stimulus Pairings

    ERIC Educational Resources Information Center

    Tonneau, Francois; Gonzalez, Carmen

    2004-01-01

    Although function transfer often has been studied in complex operant procedures (such as matching to sample), whether operant reinforcement actually produces function transfer in such settings has not been established. The present experiments, with high school students as subjects, suggest that stimulus pairings can promote function transfer in…

  17. Symmetric time warping, Boltzmann pair probabilities and functional genomics.

    PubMed

    Clote, Peter; Straubhaar, Jürg

    2006-07-01

    Given two time series, possibly of different lengths, time warping is a method to construct an optimal alignment obtained by stretching or contracting time intervals. Unlike pairwise alignment of amino acid sequences, classical time warping, originally introduced for speech recognition, is not symmetric in the sense that the time warping distance between two time series is not necessarily equal to the time warping distance of the reversal of the time series. Here we design a new symmetric version of time warping, and present a formal proof of symmetry for our algorithm as well as for one of the variants of Aach and Church [1]. We additionally design quadratic time dynamic programming algorithms to compute both the forward and backward Boltzmann partition functions for symmetric time warping, and hence compute the Boltzmann probability that any two time series points are aligned. In the future, with the availability of increasingly long and accurate time series gene expression data, our algorithm can provide a sense of biological significance for aligned time points - e.g. our algorithm could be used to provide evidence that expression values of two genes have higher Boltzmann probability (say) in the G1 and S phase than in G2 and M phases. Algorithms, source code and web interface, developed by the first author, are made publicly available via the Boltzmann Time Warping web server at bioinformatics.bc.edu/clotelab/. PMID:16791652

  18. Measurement of Vertical Temperature Distribution Using a Single Pair of Loudspeaker and Microphone with Acoustic Reflection

    NASA Astrophysics Data System (ADS)

    Saito, Ikumi; Mizutani, Koichi; Wakatsuki, Naoto; Kawabe, Satoshi

    2009-07-01

    It is important to maintain an adequate indoor temperature for comfortable working conditions, improvement of the rate of production of farm goods grown in greenhouses, and for saving energy. Thus, it is necessary to measure the temperature distribution to realize efficient air-conditioning systems. However, we have to use many conventional instruments to measure the temperature distribution. We proposed a measurement system for vertical temperature distribution using a single pair of loudspeaker (SP) and microphone (MIC), and acoustic reflectors. This system consists of SP, MIC, and multiple acoustic reflectors, and it can be used to determine the temperature distribution from the mean temperature of the area bounded by two reflectors. In experiments, the vertical temperature distribution was measured using five sound probes in a large facility every 20 s for 24 h. From the results of this experiment, it was verified that this system can be used to measure the vertical temperature distribution from the mean temperature of each area bounded by two reflectors. This system could be used to measure the change in the temperature distribution over time. We constructed a simple system to measure the vertical temperature distribution.

  19. Meiotic Telomere Protein Ndj1p Is Required for Meiosis-Specific Telomere Distribution, Bouquet Formation and Efficient Homologue Pairing

    PubMed Central

    Trelles-Sticken, Edgar; Dresser, Michael E.; Scherthan, Harry

    2000-01-01

    We have investigated the requirements for NDJ1 in meiotic telomere redistribution and clustering in synchronized cultures of Saccharomyces cerevisiae. On induction of wild-type meiosis, telomeres disperse from premeiotic aggregates over the nuclear periphery, and then cluster near the spindle pole body (bouquet arrangement) before dispersing again. In ndj1Δ meiocytes, telomeres are scattered throughout the nucleus and fail to form perinuclear meiosis-specific distribution patterns, suggesting that Ndj1p may function to tether meiotic telomeres to the nuclear periphery. Since ndj1Δ meiocytes fail to cluster their telomeres at any prophase stage, Ndj1p is the first protein shown to be required for bouquet formation in a synaptic organism. Analysis of homologue pairing by two-color fluorescence in situ hybridization with cosmid probes to regions on III, IX, and XI revealed that disruption of bouquet formation is associated with a significant delay (>2 h) of homologue pairing. An increased and persistent fraction of ndj1Δ meiocytes with Zip1p polycomplexes suggests that chromosome polarization is important for synapsis progression. Thus, our observations support the hypothesis that meiotic telomere clustering contributes to efficient homologue alignment and synaptic pairing. Under naturally occurring conditions, bouquet formation may allow for rapid sporulation and confer a selective advantage. PMID:11018056

  20. The Mass-Radius-Eccentricity Distribution of Near-Resonant Transiting Exoplanet Pairs Detected by Kepler

    NASA Astrophysics Data System (ADS)

    Shabram, Megan; Jontof-Hutter, Daniel; Ford, Eric B.

    2015-12-01

    We characterize the mass-radius-eccentricity distribution of transiting planets near first-order mean motion resonances using Transit Timing Variation (TTV) observations from NASA's Kepler mission. Kepler's precise measurements of transit times (Mazeh et al. 2014; Rowe et al. 2015) constrain the planet-star mass ratio, eccentricity and pericenter directions for hundreds of planets. Strongly-interacting planetary systems allow TTVs to provide precise measurements of masses and orbital eccentricities separately (e.g., Kepler-36, Carter et al. 2012). In addition to these precisely characterized planetary systems, there are several systems harboring at least two planets near a mean motion resonance (MMR) for which TTVs provide a joint constraint on planet masses, eccentricities and pericenter directions (Hadden et al. 2015). Unfortunately, a near degeneracy between these parameters leads to a posterior probability density with highly correlated uncertainties. Nevertheless, the population encodes valuable information about the distribution of planet masses, orbital eccentricities and the planet mass-radius relationship. We characterize the distribution of masses and eccentricities for near-resonant transiting planets by combining a hierarchical Bayesian model with an analytic model for the TTV signatures of near-resonant planet pairs (Lithwick & Wu 2012). By developing a rigorous statistical framework for analyzing the TTV signatures of a population of planetary systems, we significantly improve upon previous analyses. For example, our analysis includes transit timing measurements of near-resonant transiting planet pairs regardless of whether there is a significant detection of TTVs, thereby avoiding biases due to only including TTV detections.

  1. Linear Response Calculation using Canonical-basis TDHFB with a schematic pairing functional

    SciTech Connect

    Ebata, S.; Nakatsukasa, T.; Inakura, T.; Hashimoto, Y.; Yabana, K.

    2010-08-12

    We derive the Canonical-basis Time-Dependent Hartree-Fock-Bogoliubov (CbTDHFB) equations using time-dependent variational principle with a special pairing energy functional. We obtain the isoscalar quadrupole strength functions for Neon isotopes with small-amplitude CbTDHFB calculation in the three-dimensional coordinate-space representation.

  2. A Photographic View of Cumulative Distribution Functions

    ERIC Educational Resources Information Center

    Jernigan, Robert W.

    2008-01-01

    This article shows a concrete and easy recognizable view of a cumulative distribution function(cdf). Photograph views of the search tabs on dictionaries are used to increase students' understanding and facility with the concept of a cumulative distribution function. Projects for student investigations are also given. This motivation and view helps…

  3. Wigner distribution function in nonlinear optics.

    PubMed

    Dragoman, D

    1996-07-20

    Transformation laws for the Wigner distribution function, the radiant intensity, the radiant emittance, and the first- and second-order moments of the Wigner distribution function through an inhomogeneous, Kerr-type medium have been derived as well as for the beam quality factor and the kurtosis parameter. It is shown that the inhomogeneous Kerr-type medium can be approximated from the Wigner-distribution-function transformation-law point of view with a symplectic ABCD matrix with elements depending on the field distribution. PMID:21102821

  4. Angular distribution of positrons in coherent pair production in deformed crystals

    NASA Astrophysics Data System (ADS)

    Parazian, V. V.

    2009-05-01

    We investigate the angular distribution of positrons in the coherent process electron-positron pair creation process by high-energy photons in a periodically deformed single crystal with a complex base. The formula for the corresponding differential cross section is derived for an arbitrary deformation field. The case is considered in detail when the photon enters into the crystal at small angles with respect to a crystallographic axis. The results of the numerical calculations are presented for SiO2 and diamond single crystals and Moliere parameterization of the screened atomic potentials in the case of the deformation field generated by an acoustic wave of S-type.

  5. d sigma/dy Distribution of Drell-Yan Dielectron Pairs

    SciTech Connect

    Han, Jiyeon; Bodek, A.; Sakumoto, W.; Chung, Y.; /Rochester U.

    2007-11-01

    The authors report on the measurement of the rapidity distribution, d{sigma}/dY, over the full kinematic range for e{sup +}e{sup -} pairs produced in p{bar p} collisions at {radical}s = 1.96 TeV in the Z boson region of 66 < M{sub ee} < 116 GeV/c{sup 2}. The data sample consists of 1.1 fb{sup -1} of p{bar p} collisions at {radical}s = 1.96 TeV taken by the Collider Detector at Fermilab (CDF). The d{sigma}/dy is compared with the NLO theory prediction.

  6. The parton distribution function library

    SciTech Connect

    Plothow-Besch, H.

    1995-07-01

    This article describes an integrated package of Parton Density Functions called PDFLIB which has been added to the CERN Program Library Pool W999 and is labelled as W5051. In this package all the different sets of parton density functions of the Nucleon, Pion and the Photon which are available today have been put together. All these sets have been combined in a consistent way such that they all have similar calling sequences and no external data files have to be read in anymore. A default set has been prepared, although those preferring their own set or wanting to test a new one may do so within the package. The package also offers a program to calculate the strong coupling constant {alpha}, to first or second order. The correct {Lambda}{sub QCD} associated to the selected set of structure functions and the number of allowed flavours with respect to the given Q{sup 2} is automatically used in the calculation. The selection of sets, the program parameters as well as the possibilities to modify the defaults and to control errors occurred during execution are described.

  7. Synthesis and characterization of bifunctional surfaces with tunable functional group pairs

    NASA Astrophysics Data System (ADS)

    Galloway, John M.; Kung, Mayfair; Kung, Harold H.

    2016-06-01

    Grafting of pairs of functional groups onto a silica surface was demonstrated by tethering both terminals of an organochlorosilane precursor molecule, Cl2(CH3)Si(CH2)4(CO)(OSi(i-Pr)2)(CH2)2Si(CH3)Cl2, that possess a cleavable silyl ester bond, onto a silica surface. Hydrolytic cleavage of the silyl ester bond of the grafted molecule resulted in the generation of organized pairs of carboxylic acid and organosilanol groups. This organosilanol moiety was easily transformed into other functional groups through condensation reactions to form, together with the neighboring acid group, pairs such as carboxylic acid/secondary amine, carboxylic acid/pyridine, and carboxylic acid/phosphine. In the case of carboxylic acid/amine pairing, there was evidence of the formation of amide. A sample grafted with amine-carboxylic acid pairs was three times more active (per free amine) than a sample without such pairs for the nitroaldol condensation of 4-nitrobenzaldehyde and nitromethane.

  8. Photophysical properties of charge transfer pairs encapsulated inside macrocycle cage: A density functional theory study

    NASA Astrophysics Data System (ADS)

    Bandyopadhyay, Arkamita; Pati, Swapan K.

    2015-03-01

    Density functional theory calculations have been performed on three charge transfer donor-acceptor (D-A) molecular pairs, i.e. naphthalene-diamine (Naph) and tetrathiafulvalene (TTF) molecules as electron donors and benzene-diimide (Diimide) and tetracyanoquinodimethane (TCNQ) as electron acceptors. Structural, charge transfer and optical properties of the systems have been studied. The D-A pairs then has been considered inside a macrocycle (cucurbit[8]uril) cavity and Naph-Diimide and TTF-Diimide pairs have been shown to exhibit changes in their structures and orientations, TTF-TCNQ pair does not show any significant structural change. Our work suggests that these changes in structures or orientations are result of electronic repulsion between the keto group oxygen atoms and it can lead to tuning of charge transfer and optical properties of the systems.

  9. Separation of photo-induced radical pair in cryptochrome to a functionally critical distance

    NASA Astrophysics Data System (ADS)

    Solov'yov, Ilia A.; Domratcheva, Tatiana; Schulten, Klaus

    2014-01-01

    Cryptochrome is a blue light receptor that acts as a sensor for the geomagnetic field and assists many animals in long-range navigation. The magnetoreceptor function arises from light-induced formation of a radical pair through electron transfer between a flavin cofactor (FAD) and a triad of tryptophan residues. Here, this electron transfer is investigated by quantum chemical and classical molecular dynamics calculations. The results reveal how sequential electron transfer, assisted by rearrangement of polar side groups in the cryptochrome interior, can yield a FAD-Trp radical pair state with the FAD and Trp partners separated beyond a critical distance. The large radical pair separation reached establishes cryptochrome's sensitivity to the geomagnetic field through weakening of distance-dependent exchange and dipole-dipole interactions. It is estimated that the key secondary electron transfer step can overcome in speed both recombination (electron back-transfer) and proton transfer involving the radical pair reached after primary electron transfer.

  10. Measurement device-independent quantum key distribution with heralded pair coherent state

    NASA Astrophysics Data System (ADS)

    Chen, Dong; Shang-Hong, Zhao; Lei, Shi

    2016-07-01

    The original measurement device-independent quantum key distribution is reviewed, and a modified protocol using heralded pair coherent state (HPCS) is proposed to overcome the quantum bit error rate associated with the dark count rate of the detectors in long-distance quantum key distribution. Our simulation indicates that the secure transmission distance can be improved evidently with HPCS owing to the lower probability of vacuum events when compared with weak coherent source scenario, while the secure key rate can be increased with HPCS due to the higher probability of single-photon events when compared with heralded single-photon source scenario. Furthermore, we apply the finite key analysis to the decoy state MDI-QKD with HPCS and obtain a practical key rate.

  11. Plasma Dispersion Function for the Kappa Distribution

    NASA Technical Reports Server (NTRS)

    Podesta, John J.

    2004-01-01

    The plasma dispersion function is computed for a homogeneous isotropic plasma in which the particle velocities are distributed according to a Kappa distribution. An ordinary differential equation is derived for the plasma dispersion function and it is shown that the solution can be written in terms of Gauss' hypergeometric function. Using the extensive theory of the hypergeometric function, various mathematical properties of the plasma dispersion function are derived including symmetry relations, series expansions, integral representations, and closed form expressions for integer and half-integer values of K.

  12. Particulate distribution function evolution for ejecta transport

    SciTech Connect

    Hammerberg, James Edward; Plohr, Bradley J

    2010-01-01

    The time evolution of the ejecta distribution function in a gas is discussed in the context of the recent experiments of W. Buttler and M. Zellner for well characterized Sn surfaces. Evolution equations are derived for the particulate distribution function when the dominant gas-particle interaction in is particulate drag. In the approximation of separability of the distribution function in velocity and size, the solution for the time dependent distribution function is a Fredholm integral equation of the first kind whose kernel is expressible in terms of the vacuum time dependent velocity distribution function measured with piezo probes or Asay foils. The solution of this equation in principle gives the size distribution function. We discuss the solution of this equation and the results of the Buttler - Zellner experiments. These suggest that correlations in velocity and size are necessary for a complete description of the transport dala. The solutions presented also represent an analytic test problem for the calculated distribution function in ejecta transport implementations.

  13. An unnatural base pair system for efficient PCR amplification and functionalization of DNA molecules

    PubMed Central

    Kimoto, Michiko; Kawai, Rie; Mitsui, Tsuneo; Yokoyama, Shigeyuki; Hirao, Ichiro

    2009-01-01

    Toward the expansion of the genetic alphabet, we present an unnatural base pair system for efficient PCR amplification, enabling the site-specific incorporation of extra functional components into DNA. This system can be applied to conventional PCR protocols employing DNA templates containing unnatural bases, natural and unnatural base triphosphates, and a 3′→5′ exonuclease-proficient DNA polymerase. For highly faithful and efficient PCR amplification involving the unnatural base pairing, we identified the natural-base sequences surrounding the unnatural bases in DNA templates by an in vitro selection technique, using a DNA library containing the unnatural base. The system facilitates the site-specific incorporation of a variety of modified unnatural bases, linked with functional groups of interest, into amplified DNA. DNA fragments (0.15 amol) containing the unnatural base pair can be amplified 107-fold by 30 cycles of PCR, with <1% total mutation rate of the unnatural base pair site. Using the system, we demonstrated efficient PCR amplification and functionalization of DNA fragments for the extremely sensitive detection of zeptomol-scale target DNA molecules from mixtures with excess amounts (pmol scale) of foreign DNA species. This unnatural base pair system will be applicable to a wide range of DNA/RNA-based technologies. PMID:19073696

  14. Fog droplet distribution functions for lidar

    SciTech Connect

    Mallow, J.V.

    1982-04-15

    The interpretation of lidar data on fog has been limited by two obstacles: approximations in the form of the Mie scattering cross sections for water droplets, and droplet size distribution functions whose relationship to the experiment has not been clear. This paper develops a method for generating distribution functions from experimental data. These functions are then used with newly available Mie cross sections to obtain backscattering and extinction coefficients for singly scattered ruby laser pulses in fog. The results show what experimental lidar accuracies are needed to uniquely determine fog droplet size distribution.

  15. Description of pairing correlation in many-body finite systems with density functional theory

    NASA Astrophysics Data System (ADS)

    Hupin, Guillaume; Lacroix, Denis

    2011-02-01

    Different steps leading to the new functional for pairing based on natural orbitals and occupancies proposed earlier [D. Lacroix and G. Hupin, Phys. Rev. BPLRBAQ1098-012110.1103/PhysRevB.82.144509 82, 144509 (2010)] are carefully analyzed. Properties of quasiparticle states projected onto good particle numbers are first reviewed. These properties are used to (i) prove the existence of such a functional, (ii) provide an explicit functional through a 1/N expansion starting from the BCS approach, and (iii) give a compact form of the functional summing up all orders in the expansion. The functional is benchmarked in the case of the picket-fence pairing Hamiltonian where even and odd systems are studied, using the blocking technique, at various particle numbers and coupling strengths, with uniform and random single-particle level spacing. In all cases, very good agreement is found, with a deviation of <1% compared to the exact energy.

  16. Fully self-consistent calculations of momentum distributions of annihilating electron-positron pairs in SiC

    NASA Astrophysics Data System (ADS)

    Wiktor, Julia; Jomard, Gérald; Torrent, Marc; Barthe, Marie-France; Bertolus, Marjorie

    2016-05-01

    We performed calculations of momentum distributions of annihilating electron-positron pairs in various fully relaxed vacancy defects in SiC. We used self-consistent two-component density functional theory schemes to find the electronic and positronic densities and wave functions in the considered systems. Using the one-dimensional momentum distributions (Doppler-broadened annihilation radiation line shapes) we calculated the line-shape parameters S and W . We emphasize the effect of the experimental resolution and the choice of the integration ranges for the S and W parameters on the distributions of the points corresponding to different defects in the S (W ) plot. We performed calculation for two polytypes of SiC, 3 C , and 6 H and showed that for silicon vacancies and clusters containing this defect there were no significant differences between the Doppler spectra. The results of the Doppler spectra calculations were compared with experimental data obtained for n -type 6 H -SiC samples irradiated with 4-MeV Au ions. We observed a good general agreement between the measured and calculated points.

  17. The uniqueness theorems of meromorphic functions sharing three values and one pair of values

    NASA Astrophysics Data System (ADS)

    Li, Xiao-Min; Yi, Hong-Xun

    2008-03-01

    In this paper, we deal with a uniqueness theorem of two meromorphic functions that have three weighted sharing values and one pair of values. The results in this paper improve those given by G.G. Gundersen, G. Brosch, T.C. Alzahary, T.C. Alzahary and H.X. Yi, I. Lahiri and P. Sahoo, and other authors.

  18. Transversity distribution functions in the valon model

    NASA Astrophysics Data System (ADS)

    Alizadeh Yazdi, Z.; Taghavi-Shahri, F.; Arash, F.; Zomorrodian, M. E.

    2014-05-01

    We use the valon model to calculate the transversity distribution functions inside the nucleon. Transversity distributions indicate the probability to find partons with spin aligned (antialigned) to the transversely polarized nucleon. The results are in good agreement with all available experimental data and also global fits.

  19. Extracting the kaon Collins function from e+e- hadron pair production data

    NASA Astrophysics Data System (ADS)

    Anselmino, M.; Boglione, M.; D'Alesio, U.; Hernandez, J. O. Gonzalez; Melis, S.; Murgia, F.; Prokudin, A.

    2016-02-01

    The latest data released by the BABAR Collaboration on azimuthal correlations measured for pion-kaon and kaon-kaon pairs produced in e+e- annihilations allow, for the first time, a direct extraction of the kaon Collins functions. These functions are then used to compute the kaon Collins asymmetries in semi-inclusive deep inelastic scattering processes, which result in good agreement with the measurements performed by the HERMES and COMPASS collaborations.

  20. Generating functions for generalized binomial distributions

    NASA Astrophysics Data System (ADS)

    Bergeron, H.; Curado, E. M. F.; Gazeau, J. P.; Rodrigues, Ligia M. C. S.

    2012-10-01

    In a recent article generalization of the binomial distribution associated with a sequence of positive numbers was examined. The analysis of the nonnegativeness of the formal probability distributions was a key point to allow to give them a statistical interpretation in terms of probabilities. In this article we present an approach based on generating functions that solves the previous difficulties. Our main theorem makes explicit the conditions under which those formal probability distributions are always non-negative. Therefore, the constraints of non-negativeness are automatically fulfilled giving a complete characterization in terms of generating functions. A large number of analytical examples becomes available.

  1. Sum Rules for the Pair-Correlation Functions of Inhomogeneous Fluids: Results for the Hard-Sphere-Hard-Wall System

    NASA Astrophysics Data System (ADS)

    Henderson, D.; Plischke, M.

    1987-04-01

    Starting from well-known relations for the derivatives of the radial distribution functions of a mixture of fluids, and allowing the diameter of one particle to become exceedingly large, three sum rules for a fluid with density inhomogeneities are obtained. None of these sum rules are new. However, the relation between the Lovett-Mou-Buff-Wertheim and the Born-Green hierarchy of equations seems not well known. The accuracy of a recent parametrization of the pair correlation of hard spheres near a hard wall and of the solutions of the Percus-Yevick and hypernetted-chain equation for this same function are examined by determination of how well these functions satisfy these sum rules and the accuracy of their surface tension, calculated from the sum rule of Triezenberg and Zwanzig. Generally speaking, the Percus-Yevick theory gives the best results and the hypernetted-chain approximation gives the worst results with the parametrization being intermediate.

  2. Measurement-device-independent quantum key distribution with pairs of vector vortex beams

    NASA Astrophysics Data System (ADS)

    Chen, Dong; Zhao, Shang-Hong; Shi, Lei; Liu, Yun

    2016-03-01

    The vector vortex (VV) beam, originally introduced to exhibit a form of single-particle quantum entanglement between different degrees of freedom, has specific applications for quantum-information protocols. In this paper, by combining measurement-device-independent quantum key distribution (MDIQKD) with a spontaneous parametric-downconversion source (SPDCS), we present a modified MDIQKD scheme with pairs of VV beams, which shows a structure of hybrid entangled entanglement corresponding to intrasystem entanglement and intersystem entanglement. The former entanglement, which is entangled between polarization and orbit angular momentum within each VV beam, is adopted to overcome the polarization misalignment associated with random rotations in quantum key distribution. The latter entanglement, which is entangled between the two VV beams, is used to perform the MDIQKD protocol with SPDCS to inherit the merit of the heralded process. The numerical simulations show that our modified scheme has apparent advances both in transmission distance and key-generation rate compared to the original MDIQKD. Furthermore, our modified protocol only needs to insert q plates in a practical experiment.

  3. Pair-flowered cymes in the Lamiales: structure, distribution and origin

    PubMed Central

    Weber, Anton

    2013-01-01

    Background and Aims In the Lamiales, indeterminate thyrses (made up of axillary cymes) represent a significant inflorescence type. However, it has been largely overlooked that there occur two types of cymes: (1) ordinary cymes, and (2) ‘pair-flowered cymes’ (PFCs), with a flower pair (terminal and front flower) topping each cyme unit. PFCs are unique to the Lamiales and their distribution, origin and phylogeny are not well understood. Methods The Lamiales are screened as to the occurrence of PFCs, ordinary cymes and single flowers (constituting racemic inflorescences). Key Results PFCs are shown to exhibit a considerable morphological and developmental diversity and are documented to occur in four neighbouring taxa of Lamiales: Calceolariaceae, Sanango, Gesneriaceae and Plantaginaceae. They are omnipresent in the Calceolariaceae and almost so in the Gesneriaceae. In the Plantaginaceae, PFCs are restricted to the small sister tribes Russelieae and Cheloneae (while the large remainder has single flowers in the leaf/bract axils; ordinary cymes do not occur). Regarding the origin of PFCs, the inflorescences of the genus Peltanthera (unplaced as to family; sister to Calceolariaceae, Sanango and Gesneriaceae in most molecular phylogenies) support the idea that PFCs have originated from paniculate systems, with the front-flowers representing remnant flowers. Conclusions From the exclusive occurrence of PFCs in the Lamiales and the proximity of the respective taxa in molecular phylogenies it may be expected that PFCs have originated once, representing a synapomorphy for this group of taxa and fading out within the Plantaginaceae. However, molecular evidence is ambiguous. Depending on the position of Peltanthera (depending in turn on the kind and number of genes and taxa analysed) a single, a double (the most probable scenario) or a triple origin appears conceivable. PMID:23884395

  4. Pairing and rotational properties of actinides and superheavy nuclei in covariant density functional theory

    NASA Astrophysics Data System (ADS)

    Afanasjev, A. V.; Abdurazakov, O.

    2013-07-01

    The cranked relativistic Hartree-Bogoliubov theory has been applied for a systematic study of pairing and rotational properties of actinides and light superheavy nuclei. Pairing correlations are taken into account by the Brink-Booker part of finite-range Gogny D1S force. For the first time, in the covariant density functional theory (CDFT) framework, the pairing properties of deformed nuclei are studied via the quantities (such as three-point Δ(3) indicators) related to odd-even mass staggerings. The investigation of the moments of inertia at low spin and the Δ(3) indicators shows the need for an attenuation of the strength of the Brink-Booker part of the Gogny D1S force in pairing channel. The investigation of rotational properties of even-even and odd-mass nuclei at normal deformation, performed in the density functional theory framework in such a systematic way for the first time, reveals that in the majority of the cases the experimental data are well described. These include the evolution of the moments of inertia with spin, band crossings in the A≥242 nuclei, the impact of the particle in specific orbital on the moments of inertia in odd-mass nuclei. The analysis of the discrepancies between theory and experiment in the band crossing region of A≤240 nuclei suggests the stabilization of octupole deformation at high spin, not included in the present calculations. The evolution of pairing with deformation, which is important for the fission barriers, has been investigated via the analysis of the moments of inertia in the superdeformed minimum. The dependence of the results on the CDFT parametrization has been studied by comparing the results of the calculations obtained with the NL1 and NL3* parametrizations.

  5. Multiconfiguration pair-density functional theory: barrier heights and main group and transition metal energetics.

    PubMed

    Carlson, Rebecca K; Li Manni, Giovanni; Sonnenberger, Andrew L; Truhlar, Donald G; Gagliardi, Laura

    2015-01-13

    Kohn-Sham density functional theory, resting on the representation of the electronic density and kinetic energy by a single Slater determinant, has revolutionized chemistry, but for open-shell systems, the Kohn-Sham Slater determinant has the wrong symmetry properties as compared to an accurate wave function. We have recently proposed a theory, called multiconfiguration pair-density functional theory (MC-PDFT), in which the electronic kinetic energy and classical Coulomb energy are calculated from a multiconfiguration wave function with the correct symmetry properties, and the rest of the energy is calculated from a density functional, called the on-top density functional, that depends on the density and the on-top pair density calculated from this wave function. We also proposed a simple way to approximate the on-top density functional by translation of Kohn-Sham exchange-correlation functionals. The method is much less expensive than other post-SCF methods for calculating the dynamical correlation energy starting with a multiconfiguration self-consistent-field wave function as the reference wave function, and initial tests of the theory were quite encouraging. Here, we provide a broader test of the theory by applying it to bond energies of main-group molecules and transition metal complexes, barrier heights and reaction energies for diverse chemical reactions, proton affinities, and the water dimerization energy. Averaged over 56 data points, the mean unsigned error is 3.2 kcal/mol for MC-PDFT, as compared to 6.9 kcal/mol for Kohn-Sham theory with a comparable density functional. MC-PDFT is more accurate on average than complete active space second-order perturbation theory (CASPT2) for main-group small-molecule bond energies, alkyl bond dissociation energies, transition-metal-ligand bond energies, proton affinities, and the water dimerization energy. PMID:26574206

  6. Electron energy-distribution functions in gases

    SciTech Connect

    Pitchford, L.C.

    1981-01-01

    Numerical calculation of the electron energy distribution functions in the regime of drift tube experiments is discussed. The discussion is limited to constant applied fields and values of E/N (ratio of electric field strength to neutral density) low enough that electron growth due to ionization can be neglected. (GHT)

  7. Probability distribution functions in turbulent convection

    NASA Technical Reports Server (NTRS)

    Balachandar, S.; Sirovich, L.

    1991-01-01

    Results of an extensive investigation of probability distribution functions (pdfs) for Rayleigh-Benard convection, in hard turbulence regime, are presented. It is shown that the pdfs exhibit a high degree of internal universality. In certain cases this universality is established within two Kolmogorov scales of a boundary. A discussion of the factors leading to the universality is presented.

  8. Calculation of the Poisson cumulative distribution function

    NASA Technical Reports Server (NTRS)

    Bowerman, Paul N.; Nolty, Robert G.; Scheuer, Ernest M.

    1990-01-01

    A method for calculating the Poisson cdf (cumulative distribution function) is presented. The method avoids computer underflow and overflow during the process. The computer program uses this technique to calculate the Poisson cdf for arbitrary inputs. An algorithm that determines the Poisson parameter required to yield a specified value of the cdf is presented.

  9. Weibel instability with semirelativistic Maxwellian distribution function

    SciTech Connect

    Zaheer, S.; Murtaza, G.

    2007-07-15

    A macroscopic description of the linear Weibel instability, based on semirelativistic distribution in an unmagnetized plasma is presented. In particular, analytical expressions are derived for the real and imaginary parts of the dielectric constant for the Maxwellian and semirelativistic Maxwellian distribution functions under the conditions of {xi}=({omega}/k{sub parallel}{theta}{sub parallel})>>1 and <<1. The real frequency and the growth rate of the instability for the semirelativistic case now depends upon the factor {chi} generated from the relativistic term in the distribution function. The presence of {chi} which is always greater than unity favors the Weibel instability to occur even for the small anisotropy of temperature. As we increase the value of {chi} large enough that it dominates over other terms, the damping changes into growth. In the limiting case, i.e., {chi}=1, the results approach the Maxwellian situation.

  10. A modified coupled pair functional approach. [for dipole moment calculation of metal hydride ground states

    NASA Technical Reports Server (NTRS)

    Chong, D. P.; Langhoff, S. R.

    1986-01-01

    A modified coupled pair functional (CPF) method is presented for the configuration interaction problem that dramatically improves properties for cases where the Hartree-Fock reference configuration is not a good zeroth-order wave function description. It is shown that the tendency for CPF to overestimate the effect of higher excitations arises from the choice of the geometric mean for the partial normalization denominator. The modified method is demonstrated for ground state dipole moment calculations of the NiH, CuH, and ZnH transition metal hydrides, and compared to singles-plus-doubles configuration interaction and the Ahlrichs et al. (1984) CPF method.

  11. Distribution of elements in biotite-hornblende pairs and in an orthopyroxene-clinopyroxene pair from zoned plutons, northern Sierra Nevada, California

    USGS Publications Warehouse

    Hietanen, A.

    1971-01-01

    Distribution of major and minor elements has been determined for five hornblende-biotite pairs from hornblende-biotite quartz diorite and monzotonalite and for a clinopyroxene-orthopyroxene pair from pyroxene diorite collected from the border zones and centers of zoned plutons in the northern Sierra Nevada, California. The distribution coefficients Kd [Mg/Fe] for biotite/hornblende are of the same magnitude (0.61-0.67) for both the mafic border zone and the silicic center. For comparison, KD [Mg/Fe] values for biotite/hornblende from plutonic rocks of the central Sierra Nevada and the southern California batholith were calculated from data published by others. Rocks of the oldest age group (ca. 150 m.y.) in the central Sierra Nevada have an average distribution coefficient, KD, of 0.64, close to the average KD in the study area, where K-Ar dates are 143 to 129 m.y. The intermediate age group has an average KD=0.81, and the youngest group has KD=0.77. KD [Mg/Fe] for biotite/hornblende from the southern California batholith is 0.83, close to the average of the intermediate age group in the central Sierra Nevada. The calculated difference in pressure of crystallization between rocks of the Feather River area and the southern California batholith is 1 kb; the rocks of the Feather River area being crystallized at a higher pressure. This is in good agreement with the low-pressure contact metamorphism in the south (pyroxene hornfels facies), as compared with a medium-pressure metamorphism around the northern plutons, where andalusitesillimanite-cordierite and andalusite-staurolite subfacies of the amphibolite facies indicate pressures of about 4 kb. Trace elements Cr, V, Ni, Co, Ga are distributed equally between biotite and hornblende, whereas Ba and possibly Cu are concentrated in biotite and Sr and Sc and possibly Zr in hornblende. ?? 1971 Springer-Verlag.

  12. Recent progress on nuclear parton distribution functions

    NASA Astrophysics Data System (ADS)

    Hirai, M.; Kumano, S.; Saito, K.

    2011-09-01

    We report current status of global analyses on nuclear parton distribution functions (NPDFs). The optimum NPDFs are determined by analyzing high-energy nuclear reaction data. Due to limited experimental measurements, antiquark modifications have large uncertainties at x > 0.2 and gluon modifications cannot be determined. A nuclear modification difference between u and d quark distributions could be an origin of the long-standing NuTeV sin2θw anomaly. There is also an issue of nuclear modification differences between the structure functions of charged-lepton and neutrino reactions. Next, nuclear clustering effects are discussed in structure functions F2A as a possible explanation for an anomalous result in the 9Be nucleus at the Thomas Jefferson National Accelerator Facility (JLab). Last, tensor-polarized quark and antiquark distribution functions are extracted from HERMES data on the polarized structure function b1 of the deuteron, and they could be used for testing theoretical models and for proposing future experiments, for example, the one at JLab. Such measurements could open a new field of spin physics in spin-one hadrons.

  13. Wigner distribution function for finite signals

    NASA Astrophysics Data System (ADS)

    Wolf, Kurt B.; Atakishiyev, Natig M.; Chumakov, Sergey M.

    1997-07-01

    We construct a bilinear form with the properties of the Wigner distribution function for a model of finite optics: the multimodal linear waveguide. This is a guide that can carry a finite number of oscillator modes, and sends/reads the data by an equal number of sensors. The Wigner distribution function is a function of the classical observables of position and momentum, as well as the mode content; it provides a visual image corresponding to the (`musical') score of the signal. The dynamical group for this model is SU(2) and the wavefunctions span the space of a finite-dimensional irreducible representation of this group. Phase space is a sphere and the linear optical transformations are: translations along the waveguide, refractive wedges and inclined slabs, which correspond to rotations around the 3-, 1-, and 2-axes, respectively. Coherent and Schrodinger cat states are readily identified.

  14. Molecular Interactions in 1-Ethyl-3-methylimidazolium Acetate Ion Pair: A Density Functional Study

    NASA Astrophysics Data System (ADS)

    Dhumal, Nilesh R.; Kim, Hyung J.; Kiefer, Johannes

    2009-08-01

    The density functional method is used to obtain the molecular structure, electron density topography, and vibrational frequencies of the ion pair 1-ethyl-3-methylimidazolium acetate. Different conformers are simulated on the basis of molecular interactions between the 1-ethyl-3-methylimidazolium cation and acetate anion. The lowest energy conformers exhibit strong C-H···O interionic interactions compared with other conformers. Characteristic vibrational frequencies of the ion pair and their shifts with respect to free ions are analyzed via the natural bond orbitals and difference electron density maps coupled with molecular electron density topology. Theoretically scaled vibrational frequencies are also compared with the spontaneous Raman scattering and attenuated total reflection infrared absorption measurements.

  15. Metal-ligand multiple bonds as frustrated Lewis pairs for C-H functionalization.

    PubMed

    Whited, Matthew T

    2012-01-01

    The concept of frustrated Lewis pairs (FLPs) has received considerable attention of late, and numerous reports have demonstrated the power of non- or weakly interacting Lewis acid-base pairs for the cooperative activation of small molecules. Although most studies have focused on the use of organic or main-group FLPs that utilize steric encumbrance to prevent adduct formation, a related strategy can be envisioned for both organic and inorganic complexes, in which "electronic frustration" engenders reactivity consistent with both nucleophilic (basic) and electrophilic (acidic) character. Here we propose that such a description is consistent with the behavior of many coordinatively unsaturated transition-metal species featuring metal-ligand multiple bonds, and we further demonstrate that the resultant reactivity may be a powerful tool for the functionalization of C-H and E-H bonds. PMID:23209486

  16. Functional research and cognitive-process research in behavioural science: An unequal but firmly connected pair.

    PubMed

    Fiedler, Klaus

    2016-02-01

    Drawing on illustrative examples of the functional and cognitive psychology in contemporary research, the present article emphasizes the primacy of functional relationships, which provide the fundament for all attempts to uncover invisible cognitive processes. Cognitive research is not only inherently more difficult and much more ambitious than functional research. It also suffers from several home-made problems, such as unwarranted inferences from model fitting, the mediation-analysis cult and the failure to take environmental influences into account. However, despite the primacy of functional psychology and the problems associated with the ambitious goals of cognitive research, the two partners in this unequal pair are firmly connected and jointly responsible for the most impressive examples of progress in behavioural science. PMID:25921294

  17. Representations and uses of light distribution functions

    NASA Astrophysics Data System (ADS)

    Lalonde, Paul Albert

    1998-11-01

    At their lowest level, all rendering algorithms depend on models of local illumination to define the interplay of light with the surfaces being rendered. These models depend both on the representations of light scattering at a surface due to reflection and to an equal extent on the representation of light sources and light fields. Both emission and reflection have in common that they describe how light leaves a surface as a function of direction. Reflection also depends on an incident light direction. Emission can depend on the position on the light source We call the functions representing emission and reflection light distribution functions (LDF's). There are some difficulties to using measured light distribution functions. The data sets are very large-the size of the data grows with the fourth power of the sampling resolution. For example, a bidirectional reflectance distribution function (BRDF) sampled at five degrees angular resolution, which is arguably insufficient to capture highlights and other high frequency effects in the reflection, can easily require one and a half million samples. Once acquired this data requires some form of interpolation to use them. Any compression method used must be efficient, both in space and in the time required to evaluate the function at a point or over a range of points. This dissertation examines a wavelet representation of light distribution functions that addresses these issues. A data structure is presented that allows efficient reconstruction of LDFs for a given set of parameters, making the wavelet representation feasible for rendering tasks. Texture mapping methods that take advantage of our LDF representations are examined, as well as techniques for filtering LDFs, and methods for using wavelet compressed bidirection reflectance distribution functions (BRDFs) and light sources with Monte Carlo path tracing algorithms. The wavelet representation effectively compresses BRDF and emission data while inducing only a

  18. S-pairing in neutron matter: I. Correlated basis function theory

    NASA Astrophysics Data System (ADS)

    Fabrocini, Adelchi; Fantoni, Stefano; Illarionov, Alexey Yu.; Schmidt, Kevin E.

    2008-05-01

    S-wave pairing in neutron matter is studied within an extension of correlated basis function (CBF) theory to include the strong, short range spatial correlations due to realistic nuclear forces and the pairing correlations of the Bardeen, Cooper and Schrieffer (BCS) approach. The correlation operator contains central as well as tensor components. The correlated BCS scheme of [S. Fantoni, Nucl. Phys. A 363 (1981) 381], developed for simple scalar correlations, is generalized to this more realistic case. The energy of the correlated pair condensed phase of neutron matter is evaluated at the two-body order of the cluster expansion, but considering the one-body density and the corresponding energy vertex corrections at the first order of the Power Series expansion. Based on these approximations, we have derived a system of Euler equations for the correlation factors and for the BCS amplitudes, resulting in correlated nonlinear gap equations, formally close to the standard BCS ones. These equations have been solved for the momentum independent part of several realistic potentials (Reid, Argonne v and Argonne v) to stress the role of the tensor correlations and of the many-body effects. Simple Jastrow correlations and/or the lack of the density corrections enhance the gap with respect to uncorrelated BCS, whereas it is reduced according to the strength of the tensor interaction and following the inclusion of many-body contributions.

  19. Functional neuroimaging study in identical twin pairs discordant for regular cigarette smoking.

    PubMed

    Lessov-Schlaggar, Christina N; Lepore, Rebecca L; Kristjansson, Sean D; Schlaggar, Bradley L; Barnes, Kelly Anne; Petersen, Steven E; Madden, Pamela A F; Heath, Andrew C; Barch, Deanna M

    2013-01-01

    Despite the tremendous public health and financial burden of cigarette smoking, relatively little is understood about brain mechanisms that subserve smoking behavior. This study investigated the effect of lifetime regular smoking on brain processing in a reward guessing task using functional magnetic resonance imaging and a co-twin control study design in monozygotic (MZ) twin pairs that maximally controls for genetic and family background factors. Young adult (24-34 years) MZ female twin pairs (n = 15 pairs), discordant for regular smoking defined using Centers for Disease Control criteria as having smoked ≥100 cigarettes in their lifetime, were recruited from an ongoing genetic epidemiological longitudinal study of substance use and psychopathology. We applied hypothesis-driven region of interest (ROI) and whole-brain analyses to investigate the effect of regular smoking on reward processing. Reduced response to reward and punishment in regular compared with never-regular smokers was seen in hypothesis-driven ROI analysis of bilateral ventral striatum. Whole-brain analysis identified bilateral reward-processing regions that showed activation differences in response to winning or losing money but no effect of regular smoking; and frontal/parietal regions, predominantly in the right hemisphere, that showed robust effect of regular smoking but no effect of winning or losing money. Altogether, using a study design that maximally controls for group differences, we found that regular smoking had modest effects on striatal reward processing regions but robust effects on cognitive control/attentional systems. PMID:22340136

  20. TRANSVERSE POLARIZATION DISTRIBUTION AND FRAGMENTATION FUNCTIONS

    SciTech Connect

    BOER,D.

    2000-04-11

    The authors discuss transverse polarization distribution and fragmentation functions, in particular, T-odd functions with transverse momentum dependence, which might be relevant for the description of single transverse spin asymmetries. The role of intrinsic transverse momentum in the expansion in inverse powers of the hard scale is elaborated upon. The sin {phi} single spin asymmetry in the process e {rvec p} {r_arrow} e{prime} {pi}{sup +} X as recently reported by the HERMES Collaboration is investigated, in particular, by using the bag model.

  1. Selected topics on parton distribution functions

    SciTech Connect

    Hirai, M.; Saito, K.; Kawamura, H.; Kumano, S.

    2011-12-14

    We report recent studies on structure functions of the nucleon and nuclei. First, clustering effects are investigated in the structure function F{sub 2} of {sup 9}Be for explaining an unusual nuclear correction found in a JLab experiment. We propose that high densities created by formation of clustering structure like 2{alpha}+neutron in {sup 9}Be is the origin of the unexpected JLab result by using the antisymmetrized molecular dynamics (AMD). There is an approved proposal at JLab to investigate the structure functions of light nuclei including the cluster structure, so that much details will become clear in a few years. Second, tensor-polarized quark and antiquark distributions are obtained by analyzing HERMES measurements on the structure function b{sub 1} for the deuteron. The result suggests a finite tensor polarization for antiquark distributions, which is an interesting topic for further theoretical and experimental investigations. An experimental proposal exists at JLab for measuring b{sub 1} of the deuteron as a new tensor-structure study in 2010's. Furthermore, the antiquark tensor polarization could be measured by polarized deuteron Drell-Yan processes at hadron facilities such as J-PARC and GSI-FAIR. Third, the recent CDF dijet anomaly is investigated within the standard model by considering possible modifications of the strange-quark distribution. We find that the shape of a dijet-mass spectrum changes depending on the strange-quark distribution. It indicates that the CDF excess could be partially explained as a PDF effect, particularly by the strangeness in the nucleon, within the standard model if the excess at m{sub jj}{approx_equal}140 GeV is not a sharp peak.

  2. Nuclear parton distribution functions and their uncertainties

    SciTech Connect

    Hirai, M.; Kumano, S.; Nagai, T.-H.

    2004-10-01

    We analyze experimental data of nuclear structure-function ratios F{sub 2}{sup A}/F{sub 2}{sup A{sup '}} and Drell-Yan cross section ratios for obtaining optimum parton distribution functions (PDFs) in nuclei. Then, uncertainties of the nuclear PDFs are estimated by the Hessian method. Valence-quark distributions are determined by the F{sub 2} data at large x; however, the small-x part is not obvious from the data. On the other hand, the antiquark distributions are determined well at x{approx}0.01 from the F{sub 2} data and at x{approx}0.1 by the Drell-Yan data; however, the large-x behavior is not clear. Gluon distributions cannot be fixed by the present data and they have large uncertainties in the whole x region. Parametrization results are shown in comparison with the data. We provide a useful code for calculating nuclear PDFs at given x and Q{sup 2}.

  3. Electron distribution functions in electric field environments

    NASA Technical Reports Server (NTRS)

    Rudolph, Terence H.

    1991-01-01

    The amount of current carried by an electric discharge in its early stages of growth is strongly dependent on its geometrical shape. Discharges with a large number of branches, each funnelling current to a common stem, tend to carry more current than those with fewer branches. The fractal character of typical discharges was simulated using stochastic models based on solutions of the Laplace equation. Extension of these models requires the use of electron distribution functions to describe the behavior of electrons in the undisturbed medium ahead of the discharge. These electrons, interacting with the electric field, determine the propagation of branches in the discharge and the way in which further branching occurs. The first phase in the extension of the referenced models , the calculation of simple electron distribution functions in an air/electric field medium, is discussed. Two techniques are investigated: (1) the solution of the Boltzmann equation in homogeneous, steady state environments, and (2) the use of Monte Carlo simulations. Distribution functions calculated from both techniques are illustrated. Advantages and disadvantages of each technique are discussed.

  4. Dynamical correlation effects on pair-correlation functions of spin polarized two-dimensional electron gas

    NASA Astrophysics Data System (ADS)

    Kumar, Krishan; Garg, Vinayak; Moudgil, R. K.

    2013-06-01

    We report a theoretical study on the spin-resolved pair-correlation functions gσσ'(r) of a two-dimensional electron gas having arbitrary spin polarization ζ by including the dynamics of exchange-correlations within the dynamical self-consistent mean-field theory of Hasegawa and Shimizu. The calculated g↑↑(r), g↓↓(r) and g↑↓(r) exhibit a nice agreement with the recent quantum Monte Carlo simulation data of Gori-Giorgi et al. However, the agreement for the minority spin correlation function g↓↓(r) decreases with increase in ζ and/or decrease in electron density. Nevertheless, the spin-summed correlation function remains close to the simulation data.

  5. Differential Selection within the Drosophila Retinal Determination Network and Evidence for Functional Divergence between Paralog Pairs

    PubMed Central

    Datta, Rhea R.; Cruickshank, Tami; Kumar, Justin P.

    2011-01-01

    The retinal determination (RD) network in Drosophila comprises fourteen known nuclear proteins that include DNA binding proteins, transcriptional co-activators, kinases and phosphatases. The composition of the network varies considerably throughout the animal kingdom, with the network in several basal insects having fewer members and with vertebrates having potentially significantly higher numbers of retinal determination genes. One important contributing factor for the variation in gene number within the network is gene duplication. For example, ten members of the RD network in Drosophila are derived from duplication events. Here we present an analysis of the coding regions of the five pairs of duplicate genes from within the retinal determination network of several different Drosophila species. We demonstrate that there is differential selection across the coding regions of all RD genes. Additionally, some of the most significant differences in ratios of non-silent to silent site substitutions (dN/dS) between paralog pairs are found within regions that have no ascribed function. Previous structure/function analyses of several duplicate genes have identified areas within one gene that contain novel activities when compared to its paralog. The evolutionary analysis presented here identifies these same areas in the paralogs as being under high levels of relaxed selection. We suggest that sequence divergence between paralogs and selection signatures can be used as a reasonable predictor of functional changes in rapidly evolving motifs. PMID:21210943

  6. Comparing Functional Analysis and Paired-choice Assessment Results in Classroom Settings

    PubMed Central

    Berg, Wendy K; Wacker, David P; Cigrand, Karla; Merkle, Steve; Wade, Jeanie; Henry, Kim; Wang, Yu-Chia

    2007-01-01

    The results of a functional analysis of problem behavior and a paired-choice assessment were compared to determine whether the same social reinforcers were identified for problem behavior and an appropriate response (time allocation). The two assessments were conducted in classroom settings with 4 adolescents with mental retardation who engaged in severe problem behavior. Each student's classroom teacher served as the therapist for all phases of assessment. The two assessment procedures identified the same social reinforcers for problem and appropriate behavior for 3 of 4 participants. PMID:17970268

  7. Functional connectivity of paired default mode network subregions in primary insomnia

    PubMed Central

    Nie, Xiao; Shao, Yi; Liu, Si-yu; Li, Hai-jun; Wan, Ai-lan; Nie, Si; Peng, De-chang; Dai, Xi-jian

    2015-01-01

    Objective The aim of this study is to explore the resting-state functional connectivity (FC) differences between the paired default mode network (DMN) subregions in patients with primary insomnia (PIs). Methods Forty-two PIs and forty-two age- and sex-matched good sleepers (GSs) were recruited. All subjects underwent the resting-state functional magnetic resonance imaging scans. The seed-based region-to-region FC method was used to evaluate the abnormal connectivity within the DMN subregions between the PIs and the GSs. Pearson correlation analysis was used to investigate the relationships between the abnormal FC strength within the paired DMN subregions and the clinical features in PIs. Results Compared with the GSs, the PIs showed higher Pittsburgh Sleep Quality Index score, Hamilton Anxiety Rating Scale score, Hamilton Depression Rating Scale score, Self-Rating Depression Scale score, Self Rating Anxiety Scale score, Self-Rating Scale of Sleep score, and Profile of Mood States score (P<0.001). Compared with the GSs, the PIs showed significant decreased region-to-region FC between the medial prefrontal cortex and the right medial temporal lobe (t=−2.275, P=0.026), and between the left medial temporal lobe and the left inferior parietal cortices (t=−3.32, P=0.001). The abnormal FC strengths between the DMN subregions did not correlate with the clinical features. Conclusion PIs showed disrupted FC within the DMN subregions. PMID:26719693

  8. Estimation and optimization of loss-of-pair uncertainties based on PIV correlation functions

    NASA Astrophysics Data System (ADS)

    Scharnowski, Sven; Kähler, Christian J.

    2016-02-01

    The uncertainty quantification of particle image velocimetry (PIV) measurements is still an open problem, and to date, no consensus exists about the best suited approach. When the spatial resolution is not appropriate, the largest uncertainties are usually caused by flow gradients. But also the amount of loss-of-pairs due to out-of-plane flow motion and insufficient light-sheet overlap causes strong uncertainties in real experiments. In this paper, we show how the amount of loss-of-pairs can be quantified using the volume of the correlation function normalized by the volume of the autocorrelation function. The findings are an important step toward a reliable uncertainty estimation of instantaneous planar velocity fields computed from PIV and stereo-PIV data. Another important consequence of the analysis is that the results allow for the optimization of PIV and stereo-PIV setups in view of minimizing the total error. In particular, it is shown that the best results (concerning the relative uncertainty) can be achieved if the out-of-plane loss-of-correlation is smaller than one ( F o ). The only exception is the case where the out-of-plane motion is exactly zero. The predictions are confirmed experimentally in the last part of the paper.

  9. Exact Green's function of the reversible diffusion-influenced reaction for an isolated pair in two dimensions

    NASA Astrophysics Data System (ADS)

    Prüstel, Thorsten; Meier-Schellersheim, Martin

    2012-08-01

    We derive an exact Green's function of the diffusion equation for a pair of disk-shaped interacting particles in two dimensions subject to a backreaction boundary condition. Furthermore, we use the obtained function to calculate exact expressions for the survival probability and the time-dependent rate coefficient for the initially unbound pair and the survival probability of the bound state. The derived expressions will be of particular utility for the description of reversible membrane-bound reactions in cell biology.

  10. Spaceflight alters immune cell function and distribution

    NASA Technical Reports Server (NTRS)

    Sonnenfeld, Gerald; Mandel, Adrian D.; Konstantinova, Irina V.; Berry, Wallace D.; Taylor, Gerald R.; Lesniak, A. T.; Fuchs, Boris B.; Rakhmilevich, Alexander L.

    1992-01-01

    Experiments are described which were performed onboard Cosmos 2044 to determine spaceflight effects on immunologically important cell function and distribution. Results indicate that bone marrow cells from flown and suspended rats exhibited a decreased response to a granulocyte/monocyte colony-stimulating factor compared with the bone marrow cells from control rats. Bone marrow cells showed an increase in the percentage of cells expressing markers for helper T-cells in the myelogenous population and increased percentages of anti-asialo granulocyte/monocyte-1-bearing interleulin-2 receptor bearing pan T- and helper T-cells in the lymphocytic population.

  11. Momentum Distribution of Cooper Pairs and Strong-Coupling Effects in a Two-Dimensional Fermi Gas Near the Berezinskii-Kosterlitz-Thouless Transition

    NASA Astrophysics Data System (ADS)

    Matsumoto, M.; Inotani, D.; Ohashi, Y.

    2016-05-01

    We investigate strong-coupling properties of a two-dimensional ultracold Fermi gas in the normal state. Including pairing fluctuations within the framework of a T-matrix approximation, we calculate the distribution function n({\\varvec{Q}}) of Cooper pairs in terms of the center of mass momentum {\\varvec{Q}}. In the strong-coupling regime, n({\\varvec{Q}}=0) is shown to exhibit a remarkable increase with decreasing the temperature in the low temperature region, which agrees well with the recent experiment on a two-dimensional ^6Li Fermi gas (Ries et al. in Phys Rev Lett 114:230401, 2015). Our result indicates that the observed remarkable increase of the number of Cooper pairs with zero center of mass momentum can be explained without assuming the Berezinskii-Kosterlitz-Thouless (BKT) transition, when one properly includes pairing fluctuations that are enhanced by the low-dimensionality of the system. Since the BKT transition is a crucial topic in two-dimensional Fermi systems, our results would be useful for the study toward the realization of this quasi-long-range order in an ultracold Fermi gas.

  12. Structural and functional characterization of a conserved pair of bacterial cellulose-oxidizing lytic polysaccharide monooxygenases.

    PubMed

    Forsberg, Zarah; Mackenzie, Alasdair K; Sørlie, Morten; Røhr, Åsmund K; Helland, Ronny; Arvai, Andrew S; Vaaje-Kolstad, Gustav; Eijsink, Vincent G H

    2014-06-10

    For decades, the enzymatic conversion of cellulose was thought to rely on the synergistic action of hydrolytic enzymes, but recent work has shown that lytic polysaccharide monooxygenases (LPMOs) are important contributors to this process. We describe the structural and functional characterization of two functionally coupled cellulose-active LPMOs belonging to auxiliary activity family 10 (AA10) that commonly occur in cellulolytic bacteria. One of these LPMOs cleaves glycosidic bonds by oxidation of the C1 carbon, whereas the other can oxidize both C1 and C4. We thus demonstrate that C4 oxidation is not confined to fungal AA9-type LPMOs. X-ray crystallographic structures were obtained for the enzyme pair from Streptomyces coelicolor, solved at 1.3 Å (ScLPMO10B) and 1.5 Å (CelS2 or ScLPMO10C) resolution. Structural comparisons revealed differences in active site architecture that could relate to the ability to oxidize C4 (and that also seem to apply to AA9-type LPMOs). Despite variation in active site architecture, the two enzymes exhibited similar affinities for Cu(2+) (12-31 nM), redox potentials (242 and 251 mV), and electron paramagnetic resonance spectra, with only the latter clearly different from those of chitin-active AA10-type LPMOs. We conclude that substrate specificity depends not on copper site architecture, but rather on variation in substrate binding and orientation. During cellulose degradation, the members of this LPMO pair act in synergy, indicating different functional roles and providing a rationale for the abundance of these enzymes in biomass-degrading organisms. PMID:24912171

  13. Structural and functional characterization of a conserved pair of bacterial cellulose-oxidizing lytic polysaccharide monooxygenases

    PubMed Central

    Forsberg, Zarah; Mackenzie, Alasdair K.; Sørlie, Morten; Røhr, Åsmund K.; Helland, Ronny; Arvai, Andrew S.; Vaaje-Kolstad, Gustav; Eijsink, Vincent G. H.

    2014-01-01

    For decades, the enzymatic conversion of cellulose was thought to rely on the synergistic action of hydrolytic enzymes, but recent work has shown that lytic polysaccharide monooxygenases (LPMOs) are important contributors to this process. We describe the structural and functional characterization of two functionally coupled cellulose-active LPMOs belonging to auxiliary activity family 10 (AA10) that commonly occur in cellulolytic bacteria. One of these LPMOs cleaves glycosidic bonds by oxidation of the C1 carbon, whereas the other can oxidize both C1 and C4. We thus demonstrate that C4 oxidation is not confined to fungal AA9-type LPMOs. X-ray crystallographic structures were obtained for the enzyme pair from Streptomyces coelicolor, solved at 1.3 Å (ScLPMO10B) and 1.5 Å (CelS2 or ScLPMO10C) resolution. Structural comparisons revealed differences in active site architecture that could relate to the ability to oxidize C4 (and that also seem to apply to AA9-type LPMOs). Despite variation in active site architecture, the two enzymes exhibited similar affinities for Cu2+ (12–31 nM), redox potentials (242 and 251 mV), and electron paramagnetic resonance spectra, with only the latter clearly different from those of chitin-active AA10-type LPMOs. We conclude that substrate specificity depends not on copper site architecture, but rather on variation in substrate binding and orientation. During cellulose degradation, the members of this LPMO pair act in synergy, indicating different functional roles and providing a rationale for the abundance of these enzymes in biomass-degrading organisms. PMID:24912171

  14. Threshold resummation and the determination of parton distribution functions

    NASA Astrophysics Data System (ADS)

    Westmark, David

    Precise knowledge of parton distribution functions (PDFs) is necessary to the accurate calculation of QCD observables initiated by hadrons. The deep inelastic scattering (DIS) and lepton pair production (LPP) processes are primary sources of information on PDFs. Recent global fits for PDFs have used DIS data from the large Bjorken x, moderate Q 2 region. It is known that there are large logarithms in this kinematic region that can be resummed using threshold resummation techniques. The purpose of this study is to investigate the effects of simultaneously including DIS and LPP threshold resummation in the determinations of PDFs. The analysis includes a study of the effects of the choice of resummation prescription and of current resummation methods used in the LPP rapidity and x F distributions. It is demonstrated theoretically and phenomenologically that the current resummation methods for such distributions are approximations that lose accuracy at high rapidities or xF. The unapproximated resummation formalism is extended to the MS scheme in the minimal and Borel prescriptions and used in conjunction with resummation in DIS to perform a global fit. The resultant PDF sets that correspond to two choices of resummation prescription are analyzed to determine the effect of threshold resummation on PDF fits and its theoretical uncertainties.

  15. Actinide chemistry using singlet-paired coupled cluster and its combinations with density functionals.

    PubMed

    Garza, Alejandro J; Sousa Alencar, Ana G; Scuseria, Gustavo E

    2015-12-28

    Singlet-paired coupled cluster doubles (CCD0) is a simplification of CCD that relinquishes a fraction of dynamic correlation in order to be able to describe static correlation. Combinations of CCD0 with density functionals that recover specifically the dynamic correlation missing in the former have also been developed recently. Here, we assess the accuracy of CCD0 and CCD0+DFT (and variants of these using Brueckner orbitals) as compared to well-established quantum chemical methods for describing ground-state properties of singlet actinide molecules. The f(0) actinyl series (UO2(2+), NpO2(3+), PuO2(4+)), the isoelectronic NUN, and thorium (ThO, ThO(2+)) and nobelium (NoO, NoO2) oxides are studied. PMID:26723650

  16. Pair mobility functions for rigid spheres in concentrated colloidal dispersions: Force, torque, translation, and rotation.

    PubMed

    Zia, Roseanna N; Swan, James W; Su, Yu

    2015-12-14

    The formulation of detailed models for the dynamics of condensed soft matter including colloidal suspensions and other complex fluids requires accurate description of the physical forces between microstructural constituents. In dilute suspensions, pair-level interactions are sufficient to capture hydrodynamic, interparticle, and thermodynamic forces. In dense suspensions, many-body interactions must be considered. Prior analytical approaches to capturing such interactions such as mean-field approaches replace detailed interactions with averaged approximations. However, long-range coupling and effects of concentration on local structure, which may play an important role in, e.g., phase transitions, are smeared out in such approaches. An alternative to such approximations is the detailed modeling of hydrodynamic interactions utilizing precise couplings between moments of the hydrodynamic traction on a suspended particle and the motion of that or other suspended particles. For two isolated spheres, a set of these functions was calculated by Jeffrey and Onishi [J. Fluid Mech. 139, 261-290 (1984)] and Jeffrey [J. Phys. Fluids 4, 16-29 (1992)]. Along with pioneering work by Batchelor, these are the touchstone for low-Reynolds-number hydrodynamic interactions and have been applied directly in the solution of many important problems related to the dynamics of dilute colloidal dispersions [G. K. Batchelor and J. T. Green, J. Fluid Mech. 56, 375-400 (1972) and G. K. Batchelor, J. Fluid Mech. 74, 1-29 (1976)]. Toward extension of these functions to concentrated systems, here we present a new stochastic sampling technique to rapidly calculate an analogous set of mobility functions describing the hydrodynamic interactions between two hard spheres immersed in a suspension of arbitrary concentration, utilizing accelerated Stokesian dynamics simulations. These mobility functions provide precise, radially dependent couplings of hydrodynamic force and torque to particle translation

  17. Pair mobility functions for rigid spheres in concentrated colloidal dispersions: Force, torque, translation, and rotation

    SciTech Connect

    Zia, Roseanna N. Su, Yu; Swan, James W.

    2015-12-14

    The formulation of detailed models for the dynamics of condensed soft matter including colloidal suspensions and other complex fluids requires accurate description of the physical forces between microstructural constituents. In dilute suspensions, pair-level interactions are sufficient to capture hydrodynamic, interparticle, and thermodynamic forces. In dense suspensions, many-body interactions must be considered. Prior analytical approaches to capturing such interactions such as mean-field approaches replace detailed interactions with averaged approximations. However, long-range coupling and effects of concentration on local structure, which may play an important role in, e.g., phase transitions, are smeared out in such approaches. An alternative to such approximations is the detailed modeling of hydrodynamic interactions utilizing precise couplings between moments of the hydrodynamic traction on a suspended particle and the motion of that or other suspended particles. For two isolated spheres, a set of these functions was calculated by Jeffrey and Onishi [J. Fluid Mech. 139, 261–290 (1984)] and Jeffrey [J. Phys. Fluids 4, 16–29 (1992)]. Along with pioneering work by Batchelor, these are the touchstone for low-Reynolds-number hydrodynamic interactions and have been applied directly in the solution of many important problems related to the dynamics of dilute colloidal dispersions [G. K. Batchelor and J. T. Green, J. Fluid Mech. 56, 375–400 (1972) and G. K. Batchelor, J. Fluid Mech. 74, 1–29 (1976)]. Toward extension of these functions to concentrated systems, here we present a new stochastic sampling technique to rapidly calculate an analogous set of mobility functions describing the hydrodynamic interactions between two hard spheres immersed in a suspension of arbitrary concentration, utilizing accelerated Stokesian dynamics simulations. These mobility functions provide precise, radially dependent couplings of hydrodynamic force and torque to particle

  18. Pair mobility functions for rigid spheres in concentrated colloidal dispersions: Force, torque, translation, and rotation

    NASA Astrophysics Data System (ADS)

    Zia, Roseanna N.; Swan, James W.; Su, Yu

    2015-12-01

    The formulation of detailed models for the dynamics of condensed soft matter including colloidal suspensions and other complex fluids requires accurate description of the physical forces between microstructural constituents. In dilute suspensions, pair-level interactions are sufficient to capture hydrodynamic, interparticle, and thermodynamic forces. In dense suspensions, many-body interactions must be considered. Prior analytical approaches to capturing such interactions such as mean-field approaches replace detailed interactions with averaged approximations. However, long-range coupling and effects of concentration on local structure, which may play an important role in, e.g., phase transitions, are smeared out in such approaches. An alternative to such approximations is the detailed modeling of hydrodynamic interactions utilizing precise couplings between moments of the hydrodynamic traction on a suspended particle and the motion of that or other suspended particles. For two isolated spheres, a set of these functions was calculated by Jeffrey and Onishi [J. Fluid Mech. 139, 261-290 (1984)] and Jeffrey [J. Phys. Fluids 4, 16-29 (1992)]. Along with pioneering work by Batchelor, these are the touchstone for low-Reynolds-number hydrodynamic interactions and have been applied directly in the solution of many important problems related to the dynamics of dilute colloidal dispersions [G. K. Batchelor and J. T. Green, J. Fluid Mech. 56, 375-400 (1972) and G. K. Batchelor, J. Fluid Mech. 74, 1-29 (1976)]. Toward extension of these functions to concentrated systems, here we present a new stochastic sampling technique to rapidly calculate an analogous set of mobility functions describing the hydrodynamic interactions between two hard spheres immersed in a suspension of arbitrary concentration, utilizing accelerated Stokesian dynamics simulations. These mobility functions provide precise, radially dependent couplings of hydrodynamic force and torque to particle translation

  19. Recognition Memory for Pairs of Words as a Function of Associative Context.

    ERIC Educational Resources Information Center

    Underwood, Benton J.

    The purpose of these studies was to test a theory of associative context (defined as the association between two words in a pair) on recognition memory. The theory states that culturally associated words in a pair and nonassociated words in a pair differ after a single study trial in terms of their frequency representation in memory. Two…

  20. Properties of the cosmological density distribution function

    NASA Astrophysics Data System (ADS)

    Bernardeau, Francis; Kofman, Lev

    1995-04-01

    The properties of the probability distribution function (PDF) of the cosmological continuous density field are studied. We focus our analysis on the quasi-linear regime where various calculations, based on dynamically motivated methods, have been presented: either by using the Zel'dovich approximation (ZA) or by using the perturbation theory to evaluate the behavior of the moments of the distribution function. We show how these two approaches are related to each other and that they can be used in a complementary way. For that respect, the one-dimensional dynamics, where the ZA is exact solution, has first been used as a testing ground. In particular, we show that, when the density PDF obtained with the ZA is regularized, its various moments exhibit the behavior expected by the perturbation theory applied to the ZA. We show that ZA approach can be used for arbitrary initial conditions (not only Gaussian) and that the nonlinear evolution of the moments can be obtained. The perturbation theory can be used for the exact dynamics. We take into account the final filtering of the density field both for ZA and perturbation theory. Applying these techniques, we got the generating function of the moments for the one-dimensional dynamics, the three-dimensional ZA, with and without smoothing effects. We also suggest methods to build PDFs. One is based on the Laplace inverse transform of the moment generating function. The other, the Edgeworth expansion, is obtained when the previous generating function is truncated at a given order and allows evaluation of the PDF out of limited number of moments. It provides insight on the relationship between the moments and the shape of the density PDF. In particular, it provides an alternative method to evaluate the skewness and kurtosis by measuring the PDF around its maximum. Eventually, results obtained from a numerical simulation with cold dark matter initial conditions have been used to validate the accuracy of the considered

  1. Distribution function approach to redshift space distortions

    SciTech Connect

    Seljak, Uroš; McDonald, Patrick E-mail: pvmcdonald@lbl.gov

    2011-11-01

    We develop a phase space distribution function approach to redshift space distortions (RSD), in which the redshift space density can be written as a sum over velocity moments of the distribution function. These moments are density weighted and have well defined physical interpretation: their lowest orders are density, momentum density, and stress energy density. The series expansion is convergent if kμu/aH < 1, where k is the wavevector, H the Hubble parameter, u the typical gravitational velocity and μ = cos θ, with θ being the angle between the Fourier mode and the line of sight. We perform an expansion of these velocity moments into helicity modes, which are eigenmodes under rotation around the axis of Fourier mode direction, generalizing the scalar, vector, tensor decomposition of perturbations to an arbitrary order. We show that only equal helicity moments correlate and derive the angular dependence of the individual contributions to the redshift space power spectrum. We show that the dominant term of μ{sup 2} dependence on large scales is the cross-correlation between the density and scalar part of momentum density, which can be related to the time derivative of the matter power spectrum. Additional terms contributing to μ{sup 2} and dominating on small scales are the vector part of momentum density-momentum density correlations, the energy density-density correlations, and the scalar part of anisotropic stress density-density correlations. The second term is what is usually associated with the small scale Fingers-of-God damping and always suppresses power, but the first term comes with the opposite sign and always adds power. Similarly, we identify 7 terms contributing to μ{sup 4} dependence. Some of the advantages of the distribution function approach are that the series expansion converges on large scales and remains valid in multi-stream situations. We finish with a brief discussion of implications for RSD in galaxies relative to dark matter

  2. Audio feature extraction using probability distribution function

    NASA Astrophysics Data System (ADS)

    Suhaib, A.; Wan, Khairunizam; Aziz, Azri A.; Hazry, D.; Razlan, Zuradzman M.; Shahriman A., B.

    2015-05-01

    Voice recognition has been one of the popular applications in robotic field. It is also known to be recently used for biometric and multimedia information retrieval system. This technology is attained from successive research on audio feature extraction analysis. Probability Distribution Function (PDF) is a statistical method which is usually used as one of the processes in complex feature extraction methods such as GMM and PCA. In this paper, a new method for audio feature extraction is proposed which is by using only PDF as a feature extraction method itself for speech analysis purpose. Certain pre-processing techniques are performed in prior to the proposed feature extraction method. Subsequently, the PDF result values for each frame of sampled voice signals obtained from certain numbers of individuals are plotted. From the experimental results obtained, it can be seen visually from the plotted data that each individuals' voice has comparable PDF values and shapes.

  3. Pion valence-quark parton distribution function

    NASA Astrophysics Data System (ADS)

    Chang, Lei; Thomas, Anthony W.

    2015-10-01

    Within the Dyson-Schwinger equation formulation of QCD, a rainbow ladder truncation is used to calculate the pion valence-quark distribution function (PDF). The gap equation is renormalized at a typical hadronic scale, of order 0.5 GeV, which is also set as the default initial scale for the pion PDF. We implement a corrected leading-order expression for the PDF which ensures that the valence-quarks carry all of the pion's light-front momentum at the initial scale. The scaling behavior of the pion PDF at a typical partonic scale of order 5.2 GeV is found to be (1 - x) ν, with ν ≃ 1.6, as x approaches one.

  4. Nuclear modifications of Parton Distribution Functions

    NASA Astrophysics Data System (ADS)

    Adeluyi, Adeola Adeleke

    This dissertation addresses a central question of modern nuclear physics: how does the behavior of fundamental degrees of freedom (quarks and gluons) change in the nuclear environment? This is an important aspect of experimental studies at current facilities such as the Relativistic Heavy Ion Collider (RHIC) at Brookhaven National Laboratory and the Continuous Electron Beam Accelerator Facility (CEBAF) at the Thomas Jefferson National Laboratory (JLAB). It is also highly relevant to planned experimental efforts at the Large Hadron Collider (LHC) and the future Electron Ion Collider (EIC). All these facilities probe matter via collisions involving nuclei; thus complications arise due to the presence of the attendant nuclear medium. Theoretical efforts to understand and interpret experimental results from such collisions are therefore largely dependent on the resolution of this question. The development of nuclear physics demonstrates that theoretical description is most efficient in terms of the effective degrees of freedom relevant to the scale (energy) being probed. Thus at low energies, nuclei are described as bound states of protons and neutrons (nucleons). At higher energies, the nucleons are no longer elementary, but are revealed to possess an underlying substructure: they are made up of quarks and gluons, collectively termed partons. The mometum distributions of these partons in the nucleon are referred to as Parton Distribution Functions (PDFs). Parton distributions can be determined from experimental measurements of structure functions. The ratio of nuclear structure functions to nucleon structure functions (generically referred to as nuclear ratio) is a measure of the nuclear modifications of the free nucleon PDFs. Thus a study of the nuclear ratio suffices to gain an understanding of nuclear modifications. In this dissertation we aim to describe theoretically nuclear modifications in a restricted region where the nuclear ratio is less than unity, the so

  5. Linear dispersion properties of ring velocity distribution functions

    SciTech Connect

    Vandas, Marek

    2015-06-15

    Linear properties of ring velocity distribution functions are investigated. The dispersion tensor in a form similar to the case of a Maxwellian distribution function, but for a general distribution function separable in velocities, is presented. Analytical forms of the dispersion tensor are derived for two cases of ring velocity distribution functions: one obtained from physical arguments and one for the usual, ad hoc ring distribution. The analytical expressions involve generalized hypergeometric, Kampé de Fériet functions of two arguments. For a set of plasma parameters, the two ring distribution functions are compared. At the parallel propagation with respect to the ambient magnetic field, the two ring distributions give the same results identical to the corresponding bi-Maxwellian distribution. At oblique propagation, the two ring distributions give similar results only for strong instabilities, whereas for weak growth rates their predictions are significantly different; the two ring distributions have different marginal stability conditions.

  6. Pretzelosity distribution function h(1T)**perpendicular

    SciTech Connect

    Avagyan, Harutyun; V. Efremov, A.; Schweitzer, Peter; Yuan, Feng

    2009-01-01

    The 'pretzelosity' distribution is discussed. Theoretical properties, model results, and perspectives to access experimental information on this leading twist, transverse momentum dependent parton distribution function are reviewed. Its relation to helicity and transversity distributions is highlighted.

  7. Measurements of Correlated Pair Momentum Distributions in {sup 3}He(e,e{prime}pp)n with CLAS

    SciTech Connect

    Rustam Niyazov

    2003-05-01

    We have measured the {sup 3}He(e,e{prime}pp)n reaction at 2.2 and 4.4 GeV over a wide kinematic range. The kinetic energy distribution for ''fast'' nucleons (p > 250 MeV/c) peaks where two nucleons each have 20% or less and the third or ''leading'' nucleon carries most of the transferred energy. These fast nucleon pairs (both pp and pn) are back-to-back and carry very little momentum along {rvec q}, indicating that they are spectators. Experimental and theoretical evidence indicates that we have measured NN correlations in {sup 3}He(e,e{prime}pp)n by striking the third nucleon and detecting the spectator correlated pair.

  8. Functionalization of Intramolecular Frustrated Lewis Pairs by 1,1-Carboboration with Conjugated Enynes.

    PubMed

    Feldmann, Andreas; Kehr, Gerald; Daniliuc, Constantin G; Mück-Lichtenfeld, Christian; Erker, Gerhard

    2015-08-24

    The vicinal P/B frustrated Lewis pair (FLP) Mes2PCH2CH2B(C6F5)2 undergoes 1,1-carboboration reactions with the Me3Si-substituted enynes to give ring-enlarged functionalized C3-bridged P/B FLPs. These serve as active FLPs in the activation of dihydrogen to give the respective zwitterionic [P]H(+)/[B]H(-) products. One such product shows activity as a metal-free catalyst for the hydrogenation of enamines or a bulky imine. The ring-enlarged FLPs contain dienylborane functionalities that undergo "bora-Nazarov"-type ring-closing rearrangements upon photolysis. A DFT study had shown that the dienylborane cyclization of such systems itself is endothermic, but a subsequent C6F5 migration is very favorable. Furthermore, substituted 2,5-dihydroborole products are derived from cyclization and C6F5 migration from the photolysis reaction. In the case of the six-membered annulation product, a subsequent stereoisomerization reaction takes place and the resultant compound undergoes a P/B FLP 1,2-addition reaction with a terminal alkyne with rearrangement. PMID:26284948

  9. Increasing Occurrences and Functional Roles for High Energy Purine-Pyrimidine Base-Pairs in Nucleic Acids

    PubMed Central

    Kimsey, Isaac; Al-Hashimi, Hashim M.

    2014-01-01

    There are a growing number of studies reporting the observation of purine-pyrimidine base-pairs that are seldom observed in unmodified nucleic acids because they entail the loss of energetically favorable interactions or require energetically costly base ionization or tautomerization. These high energy purine-pyrimidine base-pairs include G•C+ and A•T Hoogsteen base-pairs, which entail ~180° rotation of the purine base in a Watson-Crick base-pair, protonation of cytosine N3, and constriction of the C1′–C1′ distance by ~2.5 Å. Other high energy pure-pyrimidine base-pairs include G•T, G•U, and A•C mispairs that adopt Watson-Crick like geometry through either base ionization or tautomerization. Although difficult to detect and characterize using biophysical methods, high energy purine-pyrimidine base-pairs appear to be more common than once thought. They further expand the structural and functional diversity of canonical and noncanonical nucleic acid base-pairs. PMID:24721455

  10. Productivity of Pair Programming in a Distributed Environment - Results from Two Controlled Case Studies

    NASA Astrophysics Data System (ADS)

    Pietinen, Sami; Tenhunen, Vesa; Tukiainen, Markku

    Several methods and techniques have surfaced to address the ongoing concerns of quality and productivity of software development. Among these is the Pair Programming (PP) method, which has gained a lot off attention through being an essential part of an agile software development methodology called the eXtreme Programming (XP). In this paper, we present the results of two controlled case studies that investigate the possible productivity improvement through the incorporation of PP over solo programming. The main focus is on implementation task, more specifically in programming, although PP is suitable for other tasks too. Our results show that very high level of PP use might be difficult to achieve in a very tightly scheduled software development project, but some of the benefits can be seen to come true even with proportional use of PP. In our case, PP added the additional effort of 13% over solo programming.

  11. Tests of structure functions using lepton pairs: W-charge asymmetry at CDF

    NASA Astrophysics Data System (ADS)

    Sakumoto, W. K.

    1994-09-01

    Large asymmetry of W-bosons produced in p(bar-p) collisions has been measured using 19 039 W yields e nu and W yields mu nu decays recorded by the CDF detector during the 1992-1993 Tevatron collider run. The asymmetry is sensitive to the slope of the proton's d/u quark distribution ratio down to x less than 0.01 at Q(exp 2) approximately M(sub w)(exp 2), where nonperturbative QCD effects are minimal. Of recent parton distribution functions, those of Martin, Roberts, and Stirling are favored over those of the CTEQ collaboration. This difference is seen even though both sets agree, at the level of the nuclear shadowing corrections, with the recent NMC measurements of F(sub 2)(sup mu n)/F(sub 2)(sup mu p).

  12. Tests of structure functions using lepton pairs: W-charge asymmetry at CDF

    SciTech Connect

    Sakumoto, W.K.; CDF Collaboration

    1994-09-01

    Large asymmetry of W-bosons produced in p{bar p} collisions has been measured using 19 039 W {yields} e{nu} and W {yields} {mu}{nu} decays recorded by the CDF detector during the 1992--1993 Tevatron collider run. The asymmetry is sensitive to the slope of the proton`s d/u quark distribution ratio down to x < 0.01 at Q{sup 2} {approx} M{sub w}{sup 2}, where nonperturbative QCD effects are minimal. Of recent parton distribution functions, those of Martin, Roberts and Stirling are favored over those of the CTEQ collaboration. This difference is seen even though both sets agree, at the leval of the nuclear shadowing corrections, with the recent NMC measurements of F{sub 2}{sup mu}n/F{sub 2}{sup mu}p.

  13. Visualization and functional dissection of coaxial paired SpoIIIE channels across the sporulation septum

    DOE PAGESBeta

    Shin, Jae Yen; Lopez-Garrido, Javier; Lee, Sang-Hyuk; Diaz-Celis, Cesar; Fleming, Tinya; Bustamante, Carlos; Pogliano, Kit

    2015-05-07

    SpoIIIE is a membrane-anchored DNA translocase that localizes to the septal midpoint to mediate chromosome translocation and membrane fission during Bacillus subtilis sporulation. Here we use cell-specific protein degradation and quantitative photoactivated localization microscopy in strains with a thick sporulation septum to investigate the architecture and function of the SpoIIIE DNA translocation complex in vivo. We were able to visualize SpoIIIE complexes with approximately equal numbers of molecules in the mother cell and the forespore. Cell-specific protein degradation showed that only the mother cell complex is required to translocate DNA into the forespore, whereas degradation in either cell reversesmore » membrane fission. Our data suggest that SpoIIIE assembles a coaxially paired channel for each chromosome arm comprised of one hexamer in each cell to maintain membrane fission during DNA translocation. We show that SpoIIIE can operate, in principle, as a bi-directional motor that exports DNA.« less

  14. Soft and collinear factorization and transverse momentum dependent parton distribution functions

    NASA Astrophysics Data System (ADS)

    Echevarría, Miguel G.; Idilbi, Ahmad; Scimemi, Ignazio

    2013-11-01

    In this work we consider how a parton distribution function, with an explicit transverse momentum dependence can be properly defined in a regularization-scheme independent manner. We argue that by considering a factorized form of the transverse momentum dependent spectrum for the production of a heavy lepton pair in Drell-Yan reaction, one should first split the relevant soft function into two boost invariant contributions. When those soft contributions are added to the pure collinear contributions, well-defined hadronic matrix elements emerge, i.e., the transverse momentum dependent distributions. We also perform a comparison with Collins' definition.

  15. Functional model for the [Fe] hydrogenase inspired by the frustrated Lewis pair concept.

    PubMed

    Kalz, Kai F; Brinkmeier, Alexander; Dechert, Sebastian; Mata, Ricardo A; Meyer, Franc

    2014-11-26

    [Fe] hydrogenase (Hmd) catalyzes the heterolytic splitting of H2 by using, in its active site, a unique organometallic iron-guanylylpyridinol (FeGP) cofactor and, as a hydride acceptor, the substrate methenyltetrahydromethanopterin (methenyl-H4MPT(+)). The combination FeGP/methenyl-H4MPT(+) and its reactivity bear resemblance to the concept of frustrated Lewis pairs (FLPs), some of which have been shown to heterolytically activate H2. The present work exploits this interpretation of Hmd reactivity by using the combination of Lewis basic ruthenium metalates, namely K[CpRu(CO)2] (KRp) and a related polymeric Cp/Ru/CO compound (Rs), with the new imidazolinium salt 1,3-bis(2,6-difluorophenyl)-2-(4-tolyl)imidazolinium bromide ([(Tol)Im(F4)](+)Br(-)) that was designed to emulate the hydride acceptor properties of methenyl-H4MPT(+). Solid-state structures of [(Tol)Im(F4)](+)Br(-) and the corresponding imidazolidine H(Tol)Im(F4) reveal that the heterocycle undergoes similar structural changes as in the biological substrate. DFT calculations indicate that heterolytic splitting of dihydrogen by the FLP Rp(-)/[(Tol)Im(F4)](+) is exothermic, but the formation of the initial Lewis pair should be unfavorable in polar solvents. Consequently the combination Rp(-)/[(Tol)Im(F4)](+) does not react with H2 but leads instead to side products from nucleophilic substitution (k = 4 × 10(-2) L mol (-1) s(-1) at room temperature). In contrast, the heterogeneous combination Rs/[(Tol)Im(F4)](+) does split H2 heterolytically to give H(Tol)Im(F4) and HRuCp(CO)2 (HRp) or D(Tol)Im(F4) and DRp when using D2. The reaction has been followed by (1)H/(2)H and (19)F NMR spectroscopy as well as by IR spectroscopy and reaches 96% conversion after 1 d. Formation of H(Tol)Im(F4) under these conditions demonstrates that superelectrophilic activation by protonation, which has been proposed for methenyl-H4MPT(+) to increase its carbocationic character, is not necessarily required for an imidazolinium ion to

  16. A critical base pair in k-turns determines the conformational class adopted, and correlates with biological function.

    PubMed

    Huang, Lin; Wang, Jia; Lilley, David M J

    2016-06-20

    k-turns are commonly-occurring motifs that introduce sharp kinks into duplex RNA, thereby facilitating tertiary contacts. Both the folding and conformation of k-turns are determined by their local sequence. k-turns fall into two conformational classes, called N3 and N1, that differ in the pattern of hydrogen bonding in the core. We show here that this is determined by the basepair adjacent to the critical G•A pairs. We determined crystal structures of a series of Kt-7 variants in which this 3b,3n position has been systematically varied, showing that this leads to a switch in the conformation. We have previously shown that the 3b,3n position also determines the folding characteristics of the k-turn, i.e. whether or not the k-turn can fold in the presence of metal ions alone. We have analyzed the distribution of 3b,3n sequences from four classes of k-turns from ribosomes, riboswitches and U4 snRNA, finding a strong conservation of properties for a given k-turn type. We thus demonstrate a strong association between biological function, 3b,3n sequence and k-turn folding and conformation. This has strong predictive power, and can be applied to the modeling of large RNA architectures. PMID:27016741

  17. A critical base pair in k-turns determines the conformational class adopted, and correlates with biological function

    PubMed Central

    Huang, Lin; Wang, Jia; Lilley, David M. J.

    2016-01-01

    k-turns are commonly-occurring motifs that introduce sharp kinks into duplex RNA, thereby facilitating tertiary contacts. Both the folding and conformation of k-turns are determined by their local sequence. k-turns fall into two conformational classes, called N3 and N1, that differ in the pattern of hydrogen bonding in the core. We show here that this is determined by the basepair adjacent to the critical G•A pairs. We determined crystal structures of a series of Kt-7 variants in which this 3b,3n position has been systematically varied, showing that this leads to a switch in the conformation. We have previously shown that the 3b,3n position also determines the folding characteristics of the k-turn, i.e. whether or not the k-turn can fold in the presence of metal ions alone. We have analyzed the distribution of 3b,3n sequences from four classes of k-turns from ribosomes, riboswitches and U4 snRNA, finding a strong conservation of properties for a given k-turn type. We thus demonstrate a strong association between biological function, 3b,3n sequence and k-turn folding and conformation. This has strong predictive power, and can be applied to the modeling of large RNA architectures. PMID:27016741

  18. Measurement-device-independent quantum key distribution with heralded pair coherent state

    NASA Astrophysics Data System (ADS)

    Wang, Xiang; Wang, Yang; Chen, Rui-Ke; Zhou, Chun; Li, Hong-Wei; Bao, Wan-Su

    2016-06-01

    Measurement-device-independent QKD (MDI-QKD) can solve security loophole problems brought by imperfections of detectors and provide enhanced practical security compared to traditional QKD. We propose an active-passive-combined decoy state MDI-QKD protocol with heralded pair coherent state (HPCS) source. By calculating the lower bound of the single-photon counting rate and the upper bound of the single-photon error rate, we present formulas of the secure key rate in our protocol. Based on the linear lossy channel model, we present calculation methods of estimating the overall gain and quantum bit error rate for HPCS source with full phase randomization. We numerically compare secure key rates for different decoy MDI-QKD protocol with different sources. The result shows that the active-passive-combined decoy state MDI-QKD protocol with HPCS source has certain superiority in the secure key rate. It can provide an important theoretical reference for practical implementations of MDI-QKD.

  19. Experimental triplet and quadruplet fluctuation densities and spatial distribution function integrals for liquid mixtures

    SciTech Connect

    Ploetz, Elizabeth A.; Smith, Paul E.

    2015-03-07

    Kirkwood-Buff or Fluctuation Solution Theory can be used to provide experimental pair fluctuations, and/or integrals over the pair distribution functions, from experimental thermodynamic data on liquid mixtures. Here, this type of approach is used to provide triplet and quadruplet fluctuations, and the corresponding integrals over the triplet and quadruplet distribution functions, in a purely thermodynamic manner that avoids the use of structure factors. The approach is then applied to binary mixtures of water + methanol and benzene + methanol over the full composition range under ambient conditions. The observed correlations between the different species vary significantly with composition. The magnitude of the fluctuations and integrals appears to increase as the number of the most polar molecule involved in the fluctuation or integral also increases. A simple physical picture of the fluctuations is provided to help rationalize some of these variations.

  20. Thermodynamically self-consistent integral equation theory for pair-correlation functions of molecular fluids-II

    NASA Astrophysics Data System (ADS)

    Singh, Ram Chandra; Ram, Jokhan

    2006-09-01

    A closure for the pair-correlation functions of molecular fluids is described in which the hypernetted-chain and the Percus-Yevick approximations are “mixed” as a function of interparticle separation. An adjustable parameter α in the mixing function is used to enforce thermodynamic consistency, by which it is meant that identical results are obtained when the equations of state are calculated via the virial and compressibility routes, respectively. The mixed integral equation for the pair-correlation functions has been solved for two model fluids: (i) a fluid of the hard Gaussian overlap model, and (ii) a fluid the molecules of which interact via a modified Gay-Berne model potential. For the modified Gay-Berne fluid we have slightly modified the original Gay-Berne potential to study the effect of attraction on hard core systems. The pair-correlation functions of the isotropic phase which enter in the density-functional theory as input informations have been calculated from the integral equation theories for these model fluids. We have used two different versions of the density-functional theory known as the second order and modified weighted-density-functional theory to locate the isotropic-nematic (I-N) transitions and calculate the values of transition parameters for the hard Gaussian overlap and modified Gay-Berne model fluids. We have compared our results with those of computer simulations wherever they are available. We find that the density-functional theory is good to study the I-N transition in molecular fluids if the values of the pair-correlation functions in the isotropic phase are accurately known.

  1. Bright integrated photon-pair source for practical passive decoy-state quantum key distribution

    NASA Astrophysics Data System (ADS)

    Krapick, S.; Stefszky, M. S.; Jachura, M.; Brecht, B.; Avenhaus, M.; Silberhorn, C.

    2014-01-01

    We report on a bright, nondegenerate type-I parametric down-conversion source, which is well suited for passive decoy-state quantum key distribution. We show the photon-number-resolved analysis over a broad range of pump powers and we prove heralded higher-order n-photon states up to n =4. The inferred photon click statistics exhibit excellent agreements to the theoretical predictions. From our measurement results we conclude that our source meets the requirements to avert photon-number-splitting attacks.

  2. The determination of pair-distance distribution by double electron-electron resonance: regularization by the length of distance discretization with Monte Carlo calculations.

    PubMed

    Dzuba, Sergei A

    2016-08-01

    Pulsed double electron-electron resonance technique (DEER, or PELDOR) is applied to study conformations and aggregation of peptides, proteins, nucleic acids, and other macromolecules. For a pair of spin labels, experimental data allows for the determination of their distance distribution function, P(r). P(r) is derived as a solution of a first-kind Fredholm integral equation, which is an ill-posed problem. Here, we suggest regularization by increasing the distance discretization length to its upper limit where numerical integration still provides agreement with experiment. This upper limit is found to be well above the lower limit for which the solution instability appears because of the ill-posed nature of the problem. For solving the integral equation, Monte Carlo trials of P(r) functions are employed; this method has an obvious advantage of the fulfillment of the non-negativity constraint for P(r). The regularization by the increasing of distance discretization length for the case of overlapping broad and narrow distributions may be employed selectively, with this length being different for different distance ranges. The approach is checked for model distance distributions and for experimental data taken from literature for doubly spin-labeled DNA and peptide antibiotics. PMID:27289419

  3. The determination of pair-distance distribution by double electron-electron resonance: regularization by the length of distance discretization with Monte Carlo calculations

    NASA Astrophysics Data System (ADS)

    Dzuba, Sergei A.

    2016-08-01

    Pulsed double electron-electron resonance technique (DEER, or PELDOR) is applied to study conformations and aggregation of peptides, proteins, nucleic acids, and other macromolecules. For a pair of spin labels, experimental data allows for the determination of their distance distribution function, P(r). P(r) is derived as a solution of a first-kind Fredholm integral equation, which is an ill-posed problem. Here, we suggest regularization by increasing the distance discretization length to its upper limit where numerical integration still provides agreement with experiment. This upper limit is found to be well above the lower limit for which the solution instability appears because of the ill-posed nature of the problem. For solving the integral equation, Monte Carlo trials of P(r) functions are employed; this method has an obvious advantage of the fulfillment of the non-negativity constraint for P(r). The regularization by the increasing of distance discretization length for the case of overlapping broad and narrow distributions may be employed selectively, with this length being different for different distance ranges. The approach is checked for model distance distributions and for experimental data taken from literature for doubly spin-labeled DNA and peptide antibiotics.

  4. Detection of prokaryotic promoters from the genomic distribution of hexanucleotide pairs

    PubMed Central

    Jacques, Pierre-Étienne; Rodrigue, Sébastien; Gaudreau, Luc; Goulet, Jean; Brzezinski, Ryszard

    2006-01-01

    Background In bacteria, sigma factors and other transcriptional regulatory proteins recognize DNA patterns upstream of their target genes and interact with RNA polymerase to control transcription. As a consequence of evolution, DNA sequences recognized by transcription factors are thought to be enriched in intergenic regions (IRs) and depleted from coding regions of prokaryotic genomes. Results In this work, we report that genomic distribution of transcription factors binding sites is biased towards IRs, and that this bias is conserved amongst bacterial species. We further take advantage of this observation to develop an algorithm that can efficiently identify promoter boxes by a distribution-dependent approach rather than a direct sequence comparison approach. This strategy, which can easily be combined with other methodologies, allowed the identification of promoter sequences in ten species and can be used with any annotated bacterial genome, with results that rival with current methodologies. Experimental validations of predicted promoters also support our approach. Conclusion Considering that complete genomic sequences of over 1000 bacteria will soon be available and that little transcriptional information is available for most of them, our algorithm constitutes a promising tool for the prediction of promoter sequences. Importantly, our methodology could also be adapted to identify DNA sequences recognized by other regulatory proteins. PMID:17014715

  5. Relation between transverse momentum dependent distribution functions and parton distribution functions in the covariant parton model approach

    SciTech Connect

    Efremov, A. V.; Teryaev, O. V.; Schweitzer, P.; Zavada, P.

    2011-03-01

    We derive relations between transverse momentum dependent distribution functions and the usual parton distribution functions in the 3D covariant parton model, which follow from Lorentz invariance and the assumption of a rotationally symmetric distribution of parton momenta in the nucleon rest frame. Using the known parton distribution functions f{sub 1}{sup a}(x) and g{sub 1}{sup a}(x) as input we predict the x- and p{sub T}-dependence of all twist-2 T-even transverse momentum dependent distribution functions.

  6. DETERMINATION OF THE POINT-SPREAD FUNCTION FOR THE FERMI LARGE AREA TELESCOPE FROM ON-ORBIT DATA AND LIMITS ON PAIR HALOS OF ACTIVE GALACTIC NUCLEI

    SciTech Connect

    Ackermann, M.; Ajello, M.; Allafort, A.; Bechtol, K.; Bloom, E. D.; Borgland, A. W.; Bottacini, E.; Buehler, R.; Asano, K.; Atwood, W. B.; Baldini, L.; Bellazzini, R.; Bregeon, J.; Ballet, J.; Bastieri, D.; Bonamente, E.; Brandt, T. J.; Brigida, M.; Bruel, P. E-mail: mar0@uw.edu [Laboratoire Leprince-Ringuet, Ecole polytechnique, CNRS and others

    2013-03-01

    The Large Area Telescope (LAT) on the Fermi Gamma-ray Space Telescope is a pair-conversion telescope designed to detect photons with energies from Almost-Equal-To 20 MeV to >300 GeV. The pre-launch response functions of the LAT were determined through extensive Monte Carlo simulations and beam tests. The point-spread function (PSF) characterizing the angular distribution of reconstructed photons as a function of energy and geometry in the detector is determined here from two years of on-orbit data by examining the distributions of {gamma} rays from pulsars and active galactic nuclei (AGNs). Above 3 GeV, the PSF is found to be broader than the pre-launch PSF. We checked for dependence of the PSF on the class of {gamma}-ray source and observation epoch and found none. We also investigated several possible spatial models for pair-halo emission around BL Lac AGNs. We found no evidence for a component with spatial extension larger than the PSF and set upper limits on the amplitude of halo emission in stacked images of low- and high-redshift BL Lac AGNs and the TeV blazars 1ES0229+200 and 1ES0347-121.

  7. Spin-correlation functions in ultracold paired atomic-fermion systems: Sum rules, self-consistent approximations, and mean fields

    NASA Astrophysics Data System (ADS)

    Yu, Z.; Baym, G.

    2006-06-01

    The spin response functions measured in multicomponent fermion gases by means of rf transitions between hyperfine states are strongly constrained by the symmetry of the interatomic interactions. Such constraints are reflected in the spin f -sum rule that the response functions must obey. In particular, only if the effective interactions are not fully invariant in SU(2) spin space, are the response functions sensitive to mean field and pairing effects. We demonstrate, via a self-consistent calculation of the spin-spin correlation function within the framework of Hartree-Fock-BCS theory, how one can derive a correlation function explicitly obeying the f -sum rule. By contrast, simple one-loop approximations to the spin response functions do not satisfy the sum rule, except in special cases. As we show, the emergence of a second peak at higher frequency in the rf spectrum, as observed in a recent experiment in trapped Li6 , can be understood as the contribution from the paired fermions, with a shift of the peak from the normal particle response proportional to the square of the BCS pairing gap.

  8. Quantum key distribution using a series of quantum correlated photon pairs

    SciTech Connect

    Inoue, Kyo

    2005-03-01

    The differential-phase-shift quantum key distribution (DPS-QKD) is a recently proposed QKD scheme in which a pulse train is transmitted through a quantum channel. This paper extends the ideal of the DPS-QKD to entanglement-based systems. Two schemes are presented. In one, an entanglement source sends pulse trains of signal and idler to two parties (Alice and Bob), respectively, who phase-modulate the incoming pulses and receive them after one-bit delay interferometers. In the other, two entanglement sources are prepared, one between Alice and a repeating node (Charlie) and one between Charlie and Bob, which send signal and idler pulse trains to Alice and Bob and Charlie, respectively. These schemes offer a longer distance between Alice and Bob than the conventional DPS-QKD.

  9. Extractions of polarized and unpolarized parton distribution functions

    SciTech Connect

    Jimenez-Delgado, Pedro

    2014-01-01

    An overview of our ongoing extractions of parton distribution functions of the nucleon is given. First JAM results on the determination of spin-dependent parton distribution functions from world data on polarized deep-inelastic scattering are presented first, and followed by a short report on the status of the JR unpolarized parton distributions. Different aspects of PDF analysis are briefly discussed, including effects of the nuclear structure of targets, target-mass corrections and higher twist contributions to the structure functions.

  10. Relationship between pairing symmetries and interaction parameters in iron-based superconductors from functional renormalization group calculations

    NASA Astrophysics Data System (ADS)

    Yuan, Jing; Hu, Jiangping

    2016-03-01

    Pairing symmetries of iron-based superconductors are investigated systematically in a five-orbital model within the different regions of interaction parameters by functional renormalization group (FRG). Even for a fixed Fermi surface with both hole and electron pockets, it is found that depending on interaction parameters, a variety of pairing symmetries, including two types of d-wave and two types of s-wave pairing symmetries, can emerge. Only the dx^2-y^2 - and the s±-waves are robustly supported by the nearest-neighbor (NN) intra-orbital J 1 and the next-nearest-neighbor (NNN) intra-orbital J 2 antiferromagnetic (AFM) exchange couplings, respectively. This study suggests that the accurate initial input of the interaction parameters is essential to make FRG a useful method to determine the leading channel of superconducting instability.

  11. Self-Energy Correction to Momentum-Density Distribution of Positron-Electron Pairs

    NASA Astrophysics Data System (ADS)

    Tang, Z.; Nagai, Y.; Inoue, K.; Toyama, T.; Chiba, T.; Saito, M.; Hasegawa, M.

    2005-03-01

    Positron two-dimensional angular correlation of annihilation radiation (2D ACAR), i.e., the 2D projection of the electron momentum densities sampled by positron, in Si is employed to verify the prediction of the density functional theory within the local-density approximation (LDA). Carefully conducted test shows that the LDA introduces small but definite discrepancies to the 2D-ACAR anisotropies. Self-energy calculation using the GW method indicates that density-fluctuation contributes anisotropic momentum-density correction and thus improves the agreement between theory and experiment. These results provide valuable annotations to the arguments concerning the accuracy and validity of the LDA and GW schemes.

  12. The function of one-word mediators in the recall of word pairs.

    PubMed

    Bellezza, F S; Poplawsky, A J

    1974-05-01

    The problem of demonstrating that natural language mediators play a role in learning and are not epiphenomena resulting from learning is an important problem in cognitive learning theories. Using a cued-recall and a free-recall learning task, Ss were requested to add a one-word mediator to some of the pairs of concrete nouns presented, The mediated pairs were learned better than the control pairs in both tasks. Both words were recalled only when the mediator was also recalled. Also, one-word mediators were the most effective recall cues and were the best recalled words in free recall. A two-stage learning model adequately described the data. However, a counterargument can be made which considers the mediator to be a high associate of one of the words presented and actually has no direct link to the other presented word. A possible experimental resolution of the problem is discussed. PMID:21274772

  13. Exclusive muon-pair production in ultrarelativistic heavy-ion collisions: Realistic nucleus charge form factor and differential distributions

    SciTech Connect

    Klusek-Gawenda, M.; Szczurek, A.

    2010-07-15

    The cross sections for exclusive muon-pair production in nucleus-nucleus collisions are calculated and several differential distributions are shown. Realistic (Fourier transform of charge density) charge form factors of nuclei are used and the corresponding results are compared with the cross sections calculated with monopole form factor often used in the literature and discussed recently in the context of higher-order QED corrections. Absorption effects are discussed and quantified. The cross sections obtained with realistic form factors are significantly smaller than those obtained with the monopole form factor. The effect is bigger for large muon rapidities and/or large muon transverse momenta. The predictions for the STAR and PHENIX collaboration measurements at RHIC as well as the ALICE and CMS collaborations at LHC are presented.

  14. Parametric Probability Distribution Functions for Axon Diameters of Corpus Callosum

    PubMed Central

    Sepehrband, Farshid; Alexander, Daniel C.; Clark, Kristi A.; Kurniawan, Nyoman D.; Yang, Zhengyi; Reutens, David C.

    2016-01-01

    Axon diameter is an important neuroanatomical characteristic of the nervous system that alters in the course of neurological disorders such as multiple sclerosis. Axon diameters vary, even within a fiber bundle, and are not normally distributed. An accurate distribution function is therefore beneficial, either to describe axon diameters that are obtained from a direct measurement technique (e.g., microscopy), or to infer them indirectly (e.g., using diffusion-weighted MRI). The gamma distribution is a common choice for this purpose (particularly for the inferential approach) because it resembles the distribution profile of measured axon diameters which has been consistently shown to be non-negative and right-skewed. In this study we compared a wide range of parametric probability distribution functions against empirical data obtained from electron microscopy images. We observed that the gamma distribution fails to accurately describe the main characteristics of the axon diameter distribution, such as location and scale of the mode and the profile of distribution tails. We also found that the generalized extreme value distribution consistently fitted the measured distribution better than other distribution functions. This suggests that there may be distinct subpopulations of axons in the corpus callosum, each with their own distribution profiles. In addition, we observed that several other distributions outperformed the gamma distribution, yet had the same number of unknown parameters; these were the inverse Gaussian, log normal, log logistic and Birnbaum-Saunders distributions. PMID:27303273

  15. Optimal Reward Functions in Distributed Reinforcement Learning

    NASA Technical Reports Server (NTRS)

    Wolpert, David H.; Tumer, Kagan

    2000-01-01

    We consider the design of multi-agent systems so as to optimize an overall world utility function when (1) those systems lack centralized communication and control, and (2) each agents runs a distinct Reinforcement Learning (RL) algorithm. A crucial issue in such design problems is to initialize/update each agent's private utility function, so as to induce best possible world utility. Traditional 'team game' solutions to this problem sidestep this issue and simply assign to each agent the world utility as its private utility function. In previous work we used the 'Collective Intelligence' framework to derive a better choice of private utility functions, one that results in world utility performance up to orders of magnitude superior to that ensuing from use of the team game utility. In this paper we extend these results. We derive the general class of private utility functions that both are easy for the individual agents to learn and that, if learned well, result in high world utility. We demonstrate experimentally that using these new utility functions can result in significantly improved performance over that of our previously proposed utility, over and above that previous utility's superiority to the conventional team game utility.

  16. Casimir dependence of transverse distribution of pairs produced from a strong constant chromo-electric background field

    SciTech Connect

    Cooper, Fred M; Mihaila, Bogdan; Dawson, John F

    2008-01-01

    Recently the transverse distribution of particle production from strong constant chromo-electric fields has been explicitly calculated in Ref. 1 for soft-gluon production and in Ref. 2 for quark (antiquark) production. This particle production method, originally discussed by Heisenberg and Euler, Schwinger and Weisskopf, has a long history as a model of the production of the quark gluon plasma following a relativistic heavy ion collision. The physical picture considered here is that of two relativistic heavy nuclei colliding and leaving behind a semi-classical gluon field which then non-perturbatively produces gluon and quark-antiquark pairs via the Schwinger mechanism. At high energy large hadron colliders, such as RHIC (Au-Au collisions at {radical}{ovr s} = 200 GeV) and LHC (Pb-Pb collisions at {radical}{ovr s} = 5.5 TeV), about half the total center-of-mass energy, E{sub cm}, goes into the production of a semi-classical gluon field, which can be thought to be initially in a Lorentz contracted disc. The gluon field in SU(3) is described by two Casimir invariants, the first one, C{sub 1} = E{sup a}E{sup a}, being related to the energy density of the initial field, where the second one, C{sub 2} = [d{sub abc}E{sup a}E{sup b}E{sup c}]{sup 2}, is related to the SU(3) color hypercharge left behind by the leading particles. So the question we want to study in this short note is how sensitive the transverse distribution is to this second Casimir invariant C{sub 2}. We have considered the dependence of the pair production rate of quarks and gluons from a strong chromo-electric field and have discovered that the effect of the second Casimir invariant of SU(3), which was not present in the electric field problem, effects the distribution by less than 15%. This event by event dependence of the transverse momentum distribution of jets on C{sub 2} may be something of interest at heavy ion colliders.

  17. A new family of distribution functions for spherical galaxies

    NASA Astrophysics Data System (ADS)

    Gerhard, Ortwin E.

    1991-06-01

    The present study describes a new family of anisotropic distribution functions for stellar systems designed to keep control of the orbit distribution at fixed energy. These are quasi-separable functions of energy and angular momentum, and they are specified in terms of a circularity function h(x) which fixes the distribution of orbits on the potential's energy surfaces outside some anisotropy radius. Detailed results are presented for a particular set of radially anisotropic circularity functions h-alpha(x). In the scale-free logarithmic potential, exact analytic solutions are shown to exist for all scale-free circularity functions. Intrinsic and projected velocity dispersions are calculated and the expected properties are presented in extensive tables and graphs. Several applications of the quasi-separable distribution functions are discussed. They include the effects of anisotropy or a dark halo on line-broadening functions, the radial orbit instability in anisotropic spherical systems, and violent relaxation in spherical collapse.

  18. A reference standard for bidirectional reflection distribution function and bidirectional transmission distribution function measurement

    NASA Technical Reports Server (NTRS)

    Witherow, William K. (Inventor)

    1988-01-01

    A Lambertian reference standard for uniformly scattering a beam of light is constructed of a plate having a planar surface with a layer of glue disposed on the surface. An evenly packed layer of monodisperse spheres is set in the layer, and when the standard is used for bi-directional (BRDF) measurements, the spheres are coated with a layer of highly relective substance, such as gold or silver. When the standard is used for bi-directional transmittance distribution function (BTDF) measurements, the spheres are of a transparent material and are provided with a roughened surface, as by acid etching. In this case, the layer of glue is an optical cement, and the plate is of glass, with the spheres, the layer, and the plate all possessing a similar refractive index.

  19. Self-Organizing Maps and Parton Distribution Functions

    SciTech Connect

    K. Holcomb, Simonetta Liuti, D. Z. Perry

    2011-05-01

    We present a new method to extract parton distribution functions from high energy experimental data based on a specific type of neural networks, the Self-Organizing Maps. We illustrate the features of our new procedure that are particularly useful for an anaysis directed at extracting generalized parton distributions from data. We show quantitative results of our initial analysis of the parton distribution functions from inclusive deep inelastic scattering.

  20. Messenger RNA modifications: Form, distribution, and function.

    PubMed

    Gilbert, Wendy V; Bell, Tristan A; Schaening, Cassandra

    2016-06-17

    RNA contains more than 100 distinct modifications that promote the functions of stable noncoding RNAs in translation and splicing. Recent technical advances have revealed widespread and sparse modification of messenger RNAs with N(6)-methyladenosine (m(6)A), 5-methylcytosine (m(5)C), and pseudouridine (Ψ). Here we discuss the rapidly evolving understanding of the location, regulation, and function of these dynamic mRNA marks, collectively termed the epitranscriptome. We highlight differences among modifications and between species that could instruct ongoing efforts to understand how specific mRNA target sites are selected and how their modification is regulated. Diverse molecular consequences of individual m(6)A modifications are beginning to be revealed, but the effects of m(5)C and Ψ remain largely unknown. Future work linking molecular effects to organismal phenotypes will broaden our understanding of mRNA modifications as cell and developmental regulators. PMID:27313037

  1. Finding of a highly efficient ZFN pair for Aqpep gene functioning in murine zygotes

    PubMed Central

    FUJII, Wataru; ONUMA, Asuka; YOSHIOKA, Shin; NAGASHIMA, Keisuke; SUGIURA, Koji; NAITO, Kunihiko

    2015-01-01

    The generation efficiencies of mutation-induced mice when using engineered zinc-finger nucleases (ZFNs) have been generally 10 to 20% of obtained pups in previous studies. The discovery of high-affinity DNA-binding modules can contribute to the generation of various kinds of novel artificial chromatin-targeting tools, such as zinc-finger acetyltransferases, zinc-finger histone kinases and so on, as well as improvement of reported zinc-finger recombinases and zinc-finger methyltransferases. Here, we report a novel ZFN pair that has a highly efficient mutation-induction ability in murine zygotes. The ZFN pair induced mutations in all obtained mice in the target locus, exon 17 of aminopeptidase Q gene, and almost all of the pups had biallelic mutations. This high efficiency was also shown in the plasmid DNA transfected in a cultured human cell line. The induced mutations were inherited normally in the next generation. The zinc-finger modules of this ZFN pair are expected to contribute to the development of novel ZF-attached chromatin-targeting tools. PMID:26460691

  2. Rationalisation of distribution functions for models of nanoparticle magnetism

    NASA Astrophysics Data System (ADS)

    El-Hilo, M.; Chantrell, R. W.

    2012-08-01

    A formalism is presented which reconciles the use of different distribution functions of particle diameter in analytical models of the magnetic properties of nanoparticle systems. For the lognormal distribution a transformation is derived which shows that a distribution of volume fraction transforms into a lognormal distribution of particle number albeit with a modified median diameter. This transformation resolves an apparent discrepancy reported in Tournus and Tamion [Journal of Magnetism and Magnetic Materials 323 (2011) 1118].

  3. Distributed implementation of functional program evaluation

    SciTech Connect

    Fasel, J.H.; Douglass, R.J.; Michelsen, R.; Hudak, P.

    1985-01-01

    In this paper, we explore the potential of the functional model, particularly as it pertains to architecture. In Section 2, we describe the graph-reduction operational model of computation and its relation to AI problems. In Section 3, we discuss a class of architectures that implement graph reduction and a prototype implementation in this class being developed at Los Alamos. Finally, we speculate on the applicability of graph reduction to some other classes of architecture.

  4. Computer routines for probability distributions, random numbers, and related functions

    USGS Publications Warehouse

    Kirby, W.

    1983-01-01

    Use of previously coded and tested subroutines simplifies and speeds up program development and testing. This report presents routines that can be used to calculate various probability distributions and other functions of importance in statistical hydrology. The routines are designed as general-purpose Fortran subroutines and functions to be called from user-written main progress. The probability distributions provided include the beta, chi-square, gamma, Gaussian (normal), Pearson Type III (tables and approximation), and Weibull. Also provided are the distributions of the Grubbs-Beck outlier test, Kolmogorov 's and Smirnov 's D, Student 's t, noncentral t (approximate), and Snedecor F. Other mathematical functions include the Bessel function, I sub o, gamma and log-gamma functions, error functions, and exponential integral. Auxiliary services include sorting and printer-plotting. Random number generators for uniform and normal numbers are provided and may be used with some of the above routines to generate numbers from other distributions. (USGS)

  5. Computer routines for probability distributions, random numbers, and related functions

    USGS Publications Warehouse

    Kirby, W.H.

    1980-01-01

    Use of previously codes and tested subroutines simplifies and speeds up program development and testing. This report presents routines that can be used to calculate various probability distributions and other functions of importance in statistical hydrology. The routines are designed as general-purpose Fortran subroutines and functions to be called from user-written main programs. The probability distributions provided include the beta, chisquare, gamma, Gaussian (normal), Pearson Type III (tables and approximation), and Weibull. Also provided are the distributions of the Grubbs-Beck outlier test, Kolmogorov 's and Smirnov 's D, Student 's t, noncentral t (approximate), and Snedecor F tests. Other mathematical functions include the Bessel function I (subzero), gamma and log-gamma functions, error functions and exponential integral. Auxiliary services include sorting and printer plotting. Random number generators for uniform and normal numbers are provided and may be used with some of the above routines to generate numbers from other distributions. (USGS)

  6. An Orientation Distribution Function for Trabecular Bone

    SciTech Connect

    Lawrence Livermore National Laboratory

    2004-10-08

    We describe a new method for quantifying the orientation of trabecular bone from three-dimensional images. Trabecular lattices from five human vertebrae were decomposed into individual trabecular elements, and the orientation, mass, and thickness of each element were recorded. Continuous functions that described the total mass (M({var_phi},{theta})) and mean thickness ({tau}({var_phi},{theta})) of all trabeculae as a function of orientation were derived. The results were compared with experimental measurements of the elastic modulus in the three principal anatomic directions. A power law scaling relationship between the anisotropies in mass and elastic modulus was observed; the scaling exponent was 1.41 (R{sup 2} = 0.88). As expected, the preponderance of trabecular mass was oriented along the cranial-caudal direction; on average, there was 3.4 times more mass oriented vertically than horizontally. Moreover, the vertical trabeculae were 30% thicker, on average, than the horizontal trabeculae. The vertical trabecular thickness was inversely related to the connectivity (R{sup 2} = 0.70; p = 0.07), suggesting a possible organization into either few, thick trabeculae or many thin trabeculae. The method, which accounts for the mechanical connectedness of the lattice, provides a rapid way to both visualize and quantify the three-dimensional organization of trabecular bone.

  7. Relation between transverse momentum dependent distribution functions and parton distribution functions in the covariant parton model approach

    SciTech Connect

    A.V. Efremov, P. Schweitzer, O.V. Teryaev, P. Zavada

    2011-03-01

    We derive relations between transverse momentum dependent distribution functions (TMDs) and the usual parton distribution functions (PDFs) in the 3D covariant parton model, which follow from Lorentz invariance and the assumption of a rotationally symmetric distribution of parton momenta in the nucleon rest frame. Using the known PDFs f_1(x) and g_1(x) as input we predict the x- and pT-dependence of all twist-2 T-even TMDs.

  8. Systematic mapping of WNT-FZD protein interactions reveals functional selectivity by distinct WNT-FZD pairs.

    PubMed

    Dijksterhuis, Jacomijn P; Baljinnyam, Bolormaa; Stanger, Karen; Sercan, Hakki O; Ji, Yun; Andres, Osler; Rubin, Jeffrey S; Hannoush, Rami N; Schulte, Gunnar

    2015-03-13

    The seven-transmembrane-spanning receptors of the FZD1-10 class are bound and activated by the WNT family of lipoglycoproteins, thereby inducing a complex network of signaling pathways. However, the specificity of the interaction between mammalian WNT and FZD proteins and the subsequent signaling cascade downstream of the different WNT-FZD pairs have not been systematically addressed to date. In this study, we determined the binding affinities of various WNTs for different members of the FZD family by using bio-layer interferometry and characterized their functional selectivity in a cell system. Using purified WNTs, we show that different FZD cysteine-rich domains prefer to bind to distinct WNTs with fast on-rates and slow off-rates. In a 32D cell-based system engineered to overexpress FZD2, FZD4, or FZD5, we found that WNT-3A (but not WNT-4, -5A, or -9B) activated the WNT-β-catenin pathway through FZD2/4/5 as measured by phosphorylation of LRP6 and β-catenin stabilization. Surprisingly, different WNT-FZD pairs showed differential effects on phosphorylation of DVL2 and DVL3, revealing a previously unappreciated DVL isoform selectivity by different WNT-FZD pairs in 32D cells. In summary, we present extensive mapping of WNT-FZD cysteine-rich domain interactions complemented by analysis of WNT-FZD pair functionality in a unique cell system expressing individual FZD isoforms. Differential WNT-FZD binding and selective functional readouts suggest that endogenous WNT ligands evolved with an intrinsic natural bias toward different downstream signaling pathways, a phenomenon that could be of great importance in the design of FZD-targeting drugs. PMID:25605717

  9. Systematic Mapping of WNT-FZD Protein Interactions Reveals Functional Selectivity by Distinct WNT-FZD Pairs*

    PubMed Central

    Dijksterhuis, Jacomijn P.; Baljinnyam, Bolormaa; Stanger, Karen; Sercan, Hakki O.; Ji, Yun; Andres, Osler; Rubin, Jeffrey S.; Hannoush, Rami N.; Schulte, Gunnar

    2015-01-01

    The seven-transmembrane-spanning receptors of the FZD1–10 class are bound and activated by the WNT family of lipoglycoproteins, thereby inducing a complex network of signaling pathways. However, the specificity of the interaction between mammalian WNT and FZD proteins and the subsequent signaling cascade downstream of the different WNT-FZD pairs have not been systematically addressed to date. In this study, we determined the binding affinities of various WNTs for different members of the FZD family by using bio-layer interferometry and characterized their functional selectivity in a cell system. Using purified WNTs, we show that different FZD cysteine-rich domains prefer to bind to distinct WNTs with fast on-rates and slow off-rates. In a 32D cell-based system engineered to overexpress FZD2, FZD4, or FZD5, we found that WNT-3A (but not WNT-4, -5A, or -9B) activated the WNT-β-catenin pathway through FZD2/4/5 as measured by phosphorylation of LRP6 and β-catenin stabilization. Surprisingly, different WNT-FZD pairs showed differential effects on phosphorylation of DVL2 and DVL3, revealing a previously unappreciated DVL isoform selectivity by different WNT-FZD pairs in 32D cells. In summary, we present extensive mapping of WNT-FZD cysteine-rich domain interactions complemented by analysis of WNT-FZD pair functionality in a unique cell system expressing individual FZD isoforms. Differential WNT-FZD binding and selective functional readouts suggest that endogenous WNT ligands evolved with an intrinsic natural bias toward different downstream signaling pathways, a phenomenon that could be of great importance in the design of FZD-targeting drugs. PMID:25605717

  10. Postmenopausal hormone replacement therapy modifies skeletal muscle composition and function: a study with monozygotic twin pairs.

    PubMed

    Ronkainen, Paula H A; Kovanen, Vuokko; Alén, Markku; Pöllänen, Eija; Palonen, Eeva-Maija; Ankarberg-Lindgren, Carina; Hämäläinen, Esa; Turpeinen, Ursula; Kujala, Urho M; Puolakka, Jukka; Kaprio, Jaakko; Sipilä, Sarianna

    2009-07-01

    We investigated whether long-term hormone replacement therapy (HRT) is associated with mobility and lower limb muscle performance and composition in postmenopausal women. Fifteen 54- to 62-yr-old monozygotic female twin pairs discordant for HRT were recruited from the Finnish Twin Cohort. Habitual (HWS) and maximal (MWS) walking speeds over 10 m, thigh muscle composition, lower body muscle power assessed as vertical jumping height, and maximal isometric hand grip and knee extension strengths were measured. Intrapair differences (IPD%) with 95% confidence intervals (CI) were calculated. The mean duration of HRT use was 6.9 +/- 4.1 yr. MWS was on average 7% (0.9 to 13.1%, P = 0.019) and muscle power 16% (-0.8 to 32.8%, P = 0.023) greater in HRT users than in their cotwins. Thigh muscle cross-sectional area tended to be larger (IPD% = 6%, 95% CI: -0.07 to 12.1%, P = 0.065), relative muscle area greater (IPD% = 8%, CI: 0.8 to 15.0%, P = 0.047), and relative fat area smaller (IPD% = -5%, CI: -11.3 to 1.2%, P = 0.047) in HRT users than in their sisters. There were no significant differences in maximal isometric strengths or HWS between users and nonusers. Subgroup analyses revealed that estrogen-containing therapies (11 pairs) significantly decreased total body and thigh fat content, whereas tibolone (4 pairs) tended to increase muscle cross-sectional area. This study showed that long-term HRT was associated with better mobility, greater muscle power, and favorable body and muscle composition among 54- to 62-yr-old women. The results indicate that HRT is a potential agent in preventing muscle weakness and mobility limitation in older women. PMID:19246654