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Sample records for dependent structure function

  1. Spin dependent proton structure functions

    Energy Technology Data Exchange (ETDEWEB)

    de Florian, D.; Garcia Canal, C.A. [Laboratorio de Fisica Teorica, Departamento de Fisica, Universidad Nacional de La Plata C.C. 67-1900 La Plata (Argentina); Sassot, R. [Departamento de Fisica, Universidad de Buenos Aires, Ciudad Universitaria, Pab. 1 1428 Bs.As. (Argentina)

    1996-02-01

    We address the issue of gluon contributions to the polarized deep inelastic asymmetries. Particularly, of their effects in the scale dependence induced by the usual leading order Altarelli-Parisi evolution equations and those arising from fixed order {alpha}{sub {ital s}} and {alpha}{sup 2}{sub {ital s}} evolution approximations. {copyright} {ital 1996 American Institute of Physics.}

  2. Significance tests for functional data with complex dependence structure

    KAUST Repository

    Staicu, Ana-Maria

    2015-01-01

    We propose an L (2)-norm based global testing procedure for the null hypothesis that multiple group mean functions are equal, for functional data with complex dependence structure. Specifically, we consider the setting of functional data with a multilevel structure of the form groups-clusters or subjects-units, where the unit-level profiles are spatially correlated within the cluster, and the cluster-level data are independent. Orthogonal series expansions are used to approximate the group mean functions and the test statistic is estimated using the basis coefficients. The asymptotic null distribution of the test statistic is developed, under mild regularity conditions. To our knowledge this is the first work that studies hypothesis testing, when data have such complex multilevel functional and spatial structure. Two small-sample alternatives, including a novel block bootstrap for functional data, are proposed, and their performance is examined in simulation studies. The paper concludes with an illustration of a motivating experiment.

  3. Precision measurement of the neutron spin dependent structure functions

    Energy Technology Data Exchange (ETDEWEB)

    Kolomensky, Y.G.

    1997-02-01

    In experiment E154 at the Stanford Linear Accelerator Center the spin dependent structure function g{sub 1}{sup n} (x, Q{sup 2}) of the neutron was measured by scattering longitudinally polarized 48.3 GeV electrons off a longitudinally polarized {sup 3}He target. The high beam energy allowed the author to extend the kinematic coverage compared to the previous SLAC experiments to 0.014 {le} x {le} 0.7 with an average Q{sup 2} of 5 GeV{sup 2}. The author reports the integral of the spin dependent structure function in the measured range to be {integral}{sub 0.014}{sup 0.7} dx g{sub 1}{sup n}(x, 5 GeV{sup 2}) = {minus}0.036 {+-} 0.004(stat.) {+-} 0.005(syst.). The author observes relatively large values of g{sub 1}{sup n} at low x that call into question the reliability of data extrapolation to x {r_arrow} 0. Such divergent behavior disagrees with predictions of the conventional Regge theory, but is qualitatively explained by perturbative QCD. The author performs a Next-to-Leading Order perturbative QCD analysis of the world data on the nucleon spin dependent structure functions g{sub 1}{sup p} and g{sub 1}{sup n} paying careful attention to the experimental and theoretical uncertainties. Using the parameterizations of the helicity-dependent parton distributions obtained in the analysis, the author evolves the data to Q{sup 2} = 5 GeV{sup 2}, determines the first moments of the polarized structure functions of the proton and neutron, and finds agreement with the Bjorken sum rule.

  4. Nucleon effective mass and the A dependence of structure functions

    Energy Technology Data Exchange (ETDEWEB)

    Garcia Canal, C.A.; Santangelo, E.M.; Vucetich, H.

    1984-10-08

    The nucleon effective mass was successfully used, as the only free parameter, to adjust the ratio R(A) of structure functions measured in a nucleus of mass number A and in the deuteron, for each A value in the SLAC set of experimental data. The resulting A dependence of the effective mass, being linear in A/sup -1/3/, is consistent with the behavior expected from nuclear structure considerations. The extrapolated value of the effective mass for nuclear matter agrees with previous estimations.

  5. Improved protein structure selection using decoy-dependent discriminatory functions

    Directory of Open Access Journals (Sweden)

    Levitt Michael

    2004-06-01

    Full Text Available Abstract Background A key component in protein structure prediction is a scoring or discriminatory function that can distinguish near-native conformations from misfolded ones. Various types of scoring functions have been developed to accomplish this goal, but their performance is not adequate to solve the structure selection problem. In addition, there is poor correlation between the scores and the accuracy of the generated conformations. Results We present a simple and nonparametric formula to estimate the accuracy of predicted conformations (or decoys. This scoring function, called the density score function, evaluates decoy conformations by performing an all-against-all Cα RMSD (Root Mean Square Deviation calculation in a given decoy set. We tested the density score function on 83 decoy sets grouped by their generation methods (4state_reduced, fisa, fisa_casp3, lmds, lattice_ssfit, semfold and Rosetta. The density scores have correlations as high as 0.9 with the Cα RMSDs of the decoy conformations, measured relative to the experimental conformation for each decoy. We previously developed a residue-specific all-atom probability discriminatory function (RAPDF, which compiles statistics from a database of experimentally determined conformations, to aid in structure selection. Here, we present a decoy-dependent discriminatory function called self-RAPDF, where we compiled the atom-atom contact probabilities from all the conformations in a decoy set instead of using an ensemble of native conformations, with a weighting scheme based on the density scores. The self-RAPDF has a higher correlation with Cα RMSD than RAPDF for 76/83 decoy sets, and selects better near-native conformations for 62/83 decoy sets. Self-RAPDF may be useful not only for selecting near-native conformations from decoy sets, but also for fold simulations and protein structure refinement. Conclusions Both the density score and the self-RAPDF functions are decoy-dependent

  6. Measuring spin-dependent structure functions at CEBAF

    Energy Technology Data Exchange (ETDEWEB)

    Schaefer, A. [Universitaet Frankfurt (Germany)

    1994-04-01

    The author analyses whether CEBAF with a 10 GeV beam could contribute significantly to the understanding of spin-dependent deep-inelastic scattering as well as semi-inclusive reactions. The main advantage of CEBAF is the much better attainable statistics, its great disadvantage its comparably low energy, which limits the accessible x-range to about 0.15 to 0.7. Within these constraints CEBAF could provide (1) high precision data which would be very valuable to understand the Q{sup 2} dependence of the spin-dependent structure functions g{sub 1}(x) and G{sub 2}(x) and (2) the by far most precise determination of the third moments of g{sub 1}(x) and g{sub 2}(x) the latter of which the author argues to be related to a fundamental property of the nucleon.

  7. TonB-dependent transporters: regulation, structure, and function.

    Science.gov (United States)

    Noinaj, Nicholas; Guillier, Maude; Barnard, Travis J; Buchanan, Susan K

    2010-01-01

    TonB-dependent transporters (TBDTs) are bacterial outer membrane proteins that bind and transport ferric chelates, called siderophores, as well as vitamin B(12), nickel complexes, and carbohydrates. The transport process requires energy in the form of proton motive force and a complex of three inner membrane proteins, TonB-ExbB-ExbD, to transduce this energy to the outer membrane. The siderophore substrates range in complexity from simple small molecules such as citrate to large proteins such as serum transferrin and hemoglobin. Because iron uptake is vital for almost all bacteria, expression of TBDTs is regulated in a number of ways that include metal-dependent regulators, σ/anti-σ factor systems, small RNAs, and even a riboswitch. In recent years, many new structures of TBDTs have been solved in various states, resulting in a more complete understanding of siderophore selectivity and binding, signal transduction across the outer membrane, and interaction with the TonB-ExbB-ExbD complex. However, the transport mechanism is still unclear. In this review, we summarize recent progress in understanding regulation, structure, and function in TBDTs and questions remaining to be answered.

  8. A-dependence of weak nuclear structure functions

    Energy Technology Data Exchange (ETDEWEB)

    Haider, H.; Athar, M. Sajjad [Department of Physics, Aligarh Muslim University, Aligarh-202 002 (India); Simo, I. Ruiz [Dipartimento di Fisica, Universitá degli studi di Trento Via Sommarive 14, Povo (Trento) I-38123 (Italy)

    2015-05-15

    Effect of nuclear medium on the weak structure functions F{sub 2}{sup A}(x, Q{sup 2}) and F{sub 3}{sup A}(x, Q{sup 2}) have been studied using charged current (anti)neutrino deep inelastic scattering on various nuclear targets. Relativistic nuclear spectral function which incorporate Fermi motion, binding and nucleon correlations are used for the calculations. We also consider the pion and rho meson cloud contributions calculated from a microscopic model for meson-nucleus self-energies. Using these structure functions, F{sub i}{sup A}/F{sub i}{sup proton} and F{sub i}{sup A}/F{sub i}{sup deuteron}(i=2,3, A={sup 12}C, {sup 16}O, CH and H{sub 2}O) are obtained.

  9. Effects of alcohol intake on brain structure and function in non-alcohol-dependent drinkers

    NARCIS (Netherlands)

    Bruin, Eveline Astrid de

    2005-01-01

    About 85% of the adult population in the Netherlands regularly drinks alcohol. Chronic excessive alcohol intake in alcohol-dependent individuals is known to have damaging effects on brain structure and function. Relatives of alcohol-dependent individuals display differences in brain function that ar

  10. Effects of alcohol intake on brain structure and function in non-alcohol-dependent drinkers

    NARCIS (Netherlands)

    Bruin, Eveline Astrid de

    2005-01-01

    About 85% of the adult population in the Netherlands regularly drinks alcohol. Chronic excessive alcohol intake in alcohol-dependent individuals is known to have damaging effects on brain structure and function. Relatives of alcohol-dependent individuals display differences in brain function that

  11. Origin of the Q^2-dependence of the DIS structure functions

    CERN Document Server

    Ermolaev, B I; Troyan, S I

    2012-01-01

    We consider in detail the Q^2 -dependence of the DIS structure functions, with Q being the virtual photon momentum. Quite often this dependence is claimed to be originated by the Q^2-dependence of the QCD coupling. This leads to the small-x asymptotics of the structure functions with Q^2 -dependent intercepts. We demonstrate that the DGLAP parametrization alpha_s = alpha_s (Q^2) is an approximation valid in the region of large x (where 2pq can be approximated by Q^2) only, providing the factorization scale is also large. Outside this region, the DGLAP parametrization fails, so alpha_s should be replaced by an effective coupling which is independent of Q^2 at small x. As a consequence, intercepts of the structure functions are independent of Q^2. Nevertheless, the small-x asymptotics of the structure functions explicitly depend on Q^2, even when the coupling does not depend on it. We also consider the structure functions at small Q^2 and give a comment on power-Q^2 corrections to the structure functions at lar...

  12. Structure dependence of photochromism and thermochromism of azobenzene-functionalized polythiophenes

    Directory of Open Access Journals (Sweden)

    2007-07-01

    Full Text Available Two novel azobenzene-functionalized polythiophenes, poly[4-((4-(phenylazophenoxybutyl-3-thienylacetate] (P4 and the copolymer of 3-hexylthiophene and 4-((4-(phenylazophenoxybutyl-3-thienylacetate (COP64 have been synthesized. The structure dependence of photoluminescence features and thermochromic behaviors of both azobenzene-functionalized polymers was investigated. The results show that polymer structure has a strong influence on the conformation and optical properties of the resulting polythiophene derivatives. The photochemical control of photoluminescence property was achieved with homopolymer P4 using photoactive azobenzene side chains.

  13. Nuclear uncertainties in the spin-dependent structure functions for direct dark matter detection

    CERN Document Server

    Cerdeno, David G; Huh, Ji-Haeng; Peiro, Miguel

    2012-01-01

    We study the effect that uncertainties in the nuclear spin-dependent structure functions have in the determination of the dark matter (DM) parameters in a direct detection experiment. We show that different nuclear models that describe the spin-dependent structure function of specific target nuclei can lead to variations in the reconstructed values of the DM mass and scattering cross-section. We propose a parametrization of the spin structure functions that allows us to treat these uncertainties as variations of three parameters, with a central value and deviation that depend on the specific nucleus. The method is illustrated for germanium and xenon detectors with an exposure of 300 kg yr, assuming a hypothetical detection of DM and studying a series of benchmark points for the DM properties. We find that the effect of these uncertainties can be similar in amplitude to that of astrophysical uncertainties, especially in those cases where the spin-dependent contribution to the elastic scattering cross-section i...

  14. Spin-dependent structure functions in nuclear matter and the polarized EMC effect.

    Science.gov (United States)

    Cloët, I C; Bentz, W; Thomas, A W

    2005-07-29

    An excellent description of both spin-independent and spin-dependent quark distributions and structure functions has been obtained with a modified Nambu--Jona-Lasinio model, which is free of unphysical thresholds for nucleon decay into quarks--hence incorporating an important aspect of confinement. We utilize this model to investigate nuclear medium modifications to structure functions and find that we are readily able to reproduce both nuclear matter saturation and the experimental F2N(A)/F2N ratio, that is, the European Muon Collaboration (EMC) effect. Applying this framework to determine g1p(A), we find that the ratio g1p(A)/g1p differs significantly from unity, with the quenching caused by the nuclear medium being about twice that of the spin-independent case. This represents an exciting result, which, if confirmed experimentally, will reveal much about the quark structure of nuclear matter.

  15. A NEW METHOD FOR EXTRACTING SPIN-DEPENDENT NEUTRON STRUCTURE FUNCTIONS FROM NUCLEAR DATA

    Energy Technology Data Exchange (ETDEWEB)

    Kahn, Y.F.; Melnitchouk, W.

    2009-01-01

    High-energy electrons are currently the best probes of the internal structure of nucleons (protons and neutrons). By collecting data on electrons scattering off light nuclei, such as deuterium and helium, one can extract structure functions (SFs), which encode information about the quarks that make up the nucleon. Spin-dependent SFs, which depend on the relative polarization of the electron beam and the target nucleus, encode quark spins. Proton SFs can be measured directly from electron-proton scattering, but those of the neutron must be extracted from proton data and deuterium or helium-3 data because free neutron targets do not exist. At present, there is no reliable method for accurately determining spin-dependent neutron SFs in the low-momentum-transfer regime, where nucleon resonances are prominent and the functions are not smooth. The focus of this study was to develop a new method for extracting spin-dependent neutron SFs from nuclear data. An approximate convolution formula for nuclear SFs reduces the problem to an integral equation, for which a recursive solution method was designed. The method was then applied to recent data from proton and deuterium scattering experiments to perform a preliminary extraction of spin-dependent neutron SFs in the resonance region. The extraction method was found to reliably converge for arbitrary test functions, and the validity of the extraction from data was verifi ed using a Bjorken integral, which relates integrals of SFs to a known quantity. This new information on neutron structure could be used to assess quark-hadron duality for the neutron, which requires detailed knowledge of SFs in all kinematic regimes.

  16. Scale-dependence of processes structuring dung beetle metacommunities using functional diversity and community deconstruction approaches.

    Science.gov (United States)

    Silva, Pedro Giovâni da; Hernández, Malva Isabel Medina

    2015-01-01

    Community structure is driven by mechanisms linked to environmental, spatial and temporal processes, which have been successfully addressed using metacommunity framework. The relative importance of processes shaping community structure can be identified using several different approaches. Two approaches that are increasingly being used are functional diversity and community deconstruction. Functional diversity is measured using various indices that incorporate distinct community attributes. Community deconstruction is a way to disentangle species responses to ecological processes by grouping species with similar traits. We used these two approaches to determine whether they are improvements over traditional measures (e.g., species composition, abundance, biomass) for identification of the main processes driving dung beetle (Scarabaeinae) community structure in a fragmented mainland-island landscape in southern Brazilian Atlantic Forest. We sampled five sites in each of four large forest areas, two on the mainland and two on the island. Sampling was performed in 2012 and 2013. We collected abundance and biomass data from 100 sampling points distributed over 20 sampling sites. We studied environmental, spatial and temporal effects on dung beetle community across three spatial scales, i.e., between sites, between areas and mainland-island. The γ-diversity based on species abundance was mainly attributed to β-diversity as a consequence of the increase in mean α- and β-diversity between areas. Variation partitioning on abundance, biomass and functional diversity showed scale-dependence of processes structuring dung beetle metacommunities. We identified two major groups of responses among 17 functional groups. In general, environmental filters were important at both local and regional scales. Spatial factors were important at the intermediate scale. Our study supports the notion of scale-dependence of environmental, spatial and temporal processes in the distribution

  17. On The $Q^2$ Dependence of The Spin Structure Function In The Resonance Region

    CERN Document Server

    Li, Z; Li, Zhenping; Li, Zhujun

    1994-01-01

    In this paper, we show what we can learn from the CEBAF experiments on spin-structure functions, and the transition from the Drell-Hearn-Gerasimov sum rule in the real photon limit to the spin dependent sum rules in the deep inelastic scattering, and how the asymmetry $A_1(x,Q^2)$ approaches the scaling limit in the resonance region. The spin structure function in the resonance region alone can not determine the spin-dependent sum rule due to the kinematic restriction of the resonance region. The integral $\\int_0^1 \\frac {A_1(x,Q^2)F_2(x,Q^2)}{2x(1+R(x,Q^2))}dx$ is estimated from $Q^2=0$ to $2.5$ GeV$^2$. The result shows that there is a region where both contributions from the baryon resonances and the deep inelastic scattering are important, thus provides important information on the high twist effects on the spin dependent sum rule.

  18. Aberrant default-mode functional and structural connectivity in heroin-dependent individuals.

    Directory of Open Access Journals (Sweden)

    Xiaofen Ma

    Full Text Available Little is known about connectivity within the default mode network (DMN in heroin-dependent individuals (HDIs. In the current study, diffusion-tensor imaging (DTI and resting-state functional MRI (rs-fMRI were combined to investigate both structural and functional connectivity within the DMN in HDIs.Fourteen HDIs and 14 controls participated in the study. Structural (path length, tracts count, (fractional anisotropy FA and (mean diffusivity MD derived from DTI tractographyand functional (temporal correlation coefficient derived from rs-fMRI DMN connectivity changes were examined in HDIs. Pearson correlation analysis was performed to compare the structural/functional indices and duration of heroin use/Iowa gambling task(IGT performance in HDIs.HDIs had lower FA and higher MD in the tract connecting the posterior cingulate cortex/precuneus (PCC/PCUN to right parahippocampal gyrus (PHG, compared to the controls. HDIs also had decreased FA and track count in the tract connecting the PCC/PCUN and medial prefrontal cortex (MPFC, as well as decreased functional connectivity between the PCC/PCUN and bilateral PHG and MPFC, compared to controls. FA values for the tract connecting PCC/PCUN to the right PHG and connecting PCC/PCUN to the MPFC were negatively correlated to the duration of heroin use. The temporal correlation coefficients between the PCC/PCUN and the MPFC, and the FA values for the tract connecting the PCC/PCUN to the MPFC were positively correlated to IGT performance in HDIs.Structural and functional connectivity within the DMN are both disturbed in HDIs. This disturbance progresses as duration of heroin use increases and is related to deficits in decision making in HDIs.

  19. Target mass corrections for spin-dependent structure functions in collinear factorization

    CERN Document Server

    Accardi, A

    2008-01-01

    We derive target mass corrections (TMC) for the spin-dependent nucleon structure function g1 and polarization asymmetry A1 in collinear factorization at leading twist. The TMCs are found to be significant for g1 at large xB, even at relatively high Q^2 values, but largely cancel in A1. A comparison of TMCs obtained from collinear factorization and from the operator product expansion shows that at low Q^2 the corrections drive the proton A1 in opposite directions.

  20. Structural and functional characterization of sapovirus RNA-dependent RNA polymerase.

    Science.gov (United States)

    Fullerton, Stephen W B; Blaschke, Martina; Coutard, Bruno; Gebhardt, Julia; Gorbalenya, Alexander; Canard, Bruno; Tucker, Paul A; Rohayem, Jacques

    2007-02-01

    Sapoviruses are one of the major agents of acute gastroenteritis in childhood. They form a tight genetic cluster (genus) in the Caliciviridae family that regroups both animal and human pathogenic strains. No permissive tissue culture has been developed for human sapovirus, limiting its characterization to surrogate systems. We report here on the first extensive characterization of the key enzyme of replication, the RNA-dependent RNA polymerase (RdRp) associated with the 3D(pol)-like protein. Enzymatically active sapovirus 3D(pol) and its defective mutant were expressed in Escherichia coli and purified. The overall structure of the sapovirus 3D(pol) was determined by X-ray crystallography to 2.32-A resolution. It revealed a right hand fold typical for template-dependent polynucleotide polymerases. The carboxyl terminus is located within the active site cleft, as observed in the RdRp of some (norovirus) but not other (lagovirus) caliciviruses. Sapovirus 3D(pol) prefers Mn(2+) over Mg(2+) but may utilize either as a cofactor in vitro. In a synthetic RNA template-dependent reaction, sapovirus 3D(pol) synthesizes a double-stranded RNA or labels the template 3' terminus by terminal transferase activity. Initiation of RNA synthesis occurs de novo on heteropolymeric templates or in a primer-dependent manner on polyadenylated templates. Strikingly, this mode of initiation of RNA synthesis was also described for norovirus, but not for lagovirus, suggesting structural and functional homologies in the RNA-dependent RNA polymerase of human pathogenic caliciviruses. This first experimental evidence makes sapovirus 3D(pol) an attractive target for developing drugs to control calicivirus infection in humans.

  1. Structural and Functional Characterization of Sapovirus RNA-Dependent RNA Polymerase▿

    Science.gov (United States)

    Fullerton, Stephen W. B.; Blaschke, Martina; Coutard, Bruno; Gebhardt, Julia; Gorbalenya, Alexander; Canard, Bruno; Tucker, Paul A.; Rohayem, Jacques

    2007-01-01

    Sapoviruses are one of the major agents of acute gastroenteritis in childhood. They form a tight genetic cluster (genus) in the Caliciviridae family that regroups both animal and human pathogenic strains. No permissive tissue culture has been developed for human sapovirus, limiting its characterization to surrogate systems. We report here on the first extensive characterization of the key enzyme of replication, the RNA-dependent RNA polymerase (RdRp) associated with the 3Dpol-like protein. Enzymatically active sapovirus 3Dpol and its defective mutant were expressed in Escherichia coli and purified. The overall structure of the sapovirus 3Dpol was determined by X-ray crystallography to 2.32-Å resolution. It revealed a right hand fold typical for template-dependent polynucleotide polymerases. The carboxyl terminus is located within the active site cleft, as observed in the RdRp of some (norovirus) but not other (lagovirus) caliciviruses. Sapovirus 3Dpol prefers Mn2+ over Mg2+ but may utilize either as a cofactor in vitro. In a synthetic RNA template-dependent reaction, sapovirus 3Dpol synthesizes a double-stranded RNA or labels the template 3′ terminus by terminal transferase activity. Initiation of RNA synthesis occurs de novo on heteropolymeric templates or in a primer-dependent manner on polyadenylated templates. Strikingly, this mode of initiation of RNA synthesis was also described for norovirus, but not for lagovirus, suggesting structural and functional homologies in the RNA-dependent RNA polymerase of human pathogenic caliciviruses. This first experimental evidence makes sapovirus 3Dpol an attractive target for developing drugs to control calicivirus infection in humans. PMID:17121797

  2. The Deuteron Spin-dependent Structure Function $g^{d}_1$ and its First Moment

    CERN Document Server

    Alexakhin, V.Yu.; Alexeev, G.D.; Alexeev, M.; Amoroso, A.; Balestra, F.; Ball, J.; Barth, J.; Baum, G.; Becker, M.; Bedfer, Y.; Bernet, C.; Bertini, R.; Bettinelli, M.; Birsa, R.; Bisplinghoff, J.; Bordalo, P.; Bradamante, F.; Bressan, A.; Brona, G.; Burtin, E.; Bussa, M.P.; Bytchkov, V.N.; Chapiro, A.; Cicuttin, A.; Colantoni, M.; Colavita, A.A.; Costa, S.; Crespo, M.L.; d'Hose, N.; Dalla Torre, S.; Das, S.; Dasgupta, S.S.; De Masi, R.; Dedek, N.; Demchenko, D.; Denisov, O.Yu.; Dhara, L.; Diaz, V.; Dinkelbach, A.M.; Donskov, S.V.; Dorofeev, V.A.; Doshita, N.; Duic, V.; Dunnweber, W.; Efremov, A.; Eversheim, P.D.; Eyrich, W.; Faessler, M.; Fauland, P.; Ferrero, A.; Ferrero, L.; Finger, M.; M. Finger jr.; Fischer, H.; Franz, J.; Friedrich, J.M.; Frolov, V.; Garfagnini, R.; Gautheron, F.; Gavrichtchouk, O.P.; Gerassimov, S.; Geyer, R.; Giorgi, M.; Gobbo, B.; Goertz, S.; Gorin, A.M.; Grajek, O.A.; Grasso, A.; Grube, B.; Guskov, A.; Haas, F.; Hannappel, J.; von Harrach, D.; Hasegawa, T.; Hedicke, S.; Heinsius, F.H.; Hermann, R.; Hess, C.; Hinterberger, F.; von Hodenberg, M.; Horikawa, N.; Horikawa, S.; Horn, I.; Ilgner, C.; Ioukaev, A.I.; Ivanchin, I.; Ivanov, O.; Iwata, T.; Jahn, R.; Janata, A.; Joosten, R.; Jouravlev, N.I.; Kabuss, E.; Kang, D.; Ketzer, B.; Khaustov, G.V.; Khokhlov, Yu. A.; Kisselev, Yu.; Klein, F.; Klimaszewski, K.; Koblitz, S.; Koivuniemi, J.H.; Kolosov, V.N.; Komissarov, E.V.; Kondo, K.; Konigsmann, K.; Konorov, I.; Konstantinov, V.F.; Korentchenko, A.S.; Korzenev, A.; Kotzinian, A.M.; Koutchinski, N.A.; Kouznetsov, O.; Kowalik, K.; Kramer, D.; Kravchuk, N.P.; Krivokhizhin, G.V.; Kroumchtein, Z.V.; Kubart, J.; Kuhn, R.; Kukhtin, V.; Kunne, F.; Kurek, K.; Ladygin, M.E.; Lamanna, M.; Le Goff, J.M.; Leberig, M.; Lednev, A.A.; Lehmann, A.; Lichtenstadt, J.; Liska, T.; Ludwig, I.; Maggiora, A.; Maggiora, M.; Magnon, A.; Mallot, G.K.; Marchand, C.; Marroncle, J.; Martin, A.; Marzec, J.; Masek, L.; Massmann, F.; Matsuda, T.; Matthia, D.; Maximov, A.N.; Meyer, W.; Mielech, A.; Mikhailov, Yu. V.; Moinester, M.A.; Nagel, T.; Nahle, O.; Nassalski, J.; Neliba, S.; Neyret, D.P.; Nikolaenko, V.I.; Nikolaev, K.; Nozdrin, A.A.; Obraztsov, V.F.; Olshevsky, A.G.; Ostrick, M.; Padee, A.; Pagano, P.; Panebianco, S.; Panzieri, D.; Paul, S.; Peshekhonov, D.V.; Peshekhonov, V.D.; Piragino, G.; Platchkov, S.; Pochodzalla, J.; Polak, J.; Polyakov, V.A.; Pontecorvo, G.; Popov, A.A.; Pretz, J.; Procureur, S.; Quintans, C.; Ramos, S.; Reicherz, G.; Rondio, E.; Rozhdestvensky, A.M.; Ryabchikov, D.; Samoylenko, V.D.; Sandacz, A.; Santos, H.; Sapozhnikov, M.G.; Savin, I.A.; Schiavon, P.; Schill, C.; Schmitt, L.; Schroeder, W.; Seeharsch, D.; Seimetz, M.; Setter, D.; Shevchenko, O.Yu.; Siebert, H.W.; Silva, L.; Sinha, L.; Sissakian, A.N.; Slunecka, M.; Smirnov, G.I.; Sozzi, F.; Srnka, A.; Stinzing, F.; Stolarski, M.; Sugonyaev, V.P.; Sulc, M.; Sulej, R.; Tchalishev, V.V.; Tessaro, S.; Tessarotto, F.; Teufel, A.; Tkatchev, L.G.; Trippel, S.; Venugopal, G.; Virius, M.; Vlassov, N.V.; Webb, R.; Weise, E.; Weitzel, Q.; Windmolders, R.; Wislicki, W.; Zaremba, K.; Zavertyaev, M.; Zemlyanichkina, E.; Zhao, J.; Zvyagin, A.

    2007-01-01

    We present a measurement of the deuteron spin-dependent structure function g^d_1 based on the data collected by the COMPASS experiment at CERN during the years 2002-2004. The data provide an accurate evaluation for \\Gamma^d_1, the first moment of g^d_1(x), and for the matrix element of the singlet axial current, a_0. The results of QCD fits in the next to leading order (NLO) on all g1 deep inelastic scattering data are also presented. They provide two solutions with the gluon spin distribution function \\Delta_G positive or negative, which describe the data equally well. In both cases, at Q^2 = 3(GeV/c)^2 the first moment of \\Delta G is found to be of the order of 0:2 - 0:3 in absolute value.

  3. Structural and functional characteristics of cGMP-dependent methionine oxidation in Arabidopsis thaliana proteins

    KAUST Repository

    Marondedze, Claudius

    2013-01-05

    Background: Increasing structural and biochemical evidence suggests that post-translational methionine oxidation of proteins is not just a result of cellular damage but may provide the cell with information on the cellular oxidative status. In addition, oxidation of methionine residues in key regulatory proteins, such as calmodulin, does influence cellular homeostasis. Previous findings also indicate that oxidation of methionine residues in signaling molecules may have a role in stress responses since these specific structural modifications can in turn change biological activities of proteins. Findings. Here we use tandem mass spectrometry-based proteomics to show that treatment of Arabidopsis thaliana cells with a non-oxidative signaling molecule, the cell-permeant second messenger analogue, 8-bromo-3,5-cyclic guanosine monophosphate (8-Br-cGMP), results in a time-dependent increase in the content of oxidised methionine residues. Interestingly, the group of proteins affected by cGMP-dependent methionine oxidation is functionally enriched for stress response proteins. Furthermore, we also noted distinct signatures in the frequency of amino acids flanking oxidised and un-oxidised methionine residues on both the C- and N-terminus. Conclusions: Given both a structural and functional bias in methionine oxidation events in response to a signaling molecule, we propose that these are indicative of a specific role of such post-translational modifications in the direct or indirect regulation of cellular responses. The mechanisms that determine the specificity of the modifications remain to be elucidated. 2013 Marondedze et al.; licensee BioMed Central Ltd.

  4. The spin dependent structure function g{sub 1} of the deuteron and the proton

    Energy Technology Data Exchange (ETDEWEB)

    Klostermann, L.

    1995-02-27

    This thesis presents a study on the spin structure of the nucleon, via deep inelastic scattering (DIS) of polarised nuons on polarised proton and deuterium targets. The work was done in the Spin Muon Collaboration (SMC) at CERN in Geneva. From the asymmetry in the scattering cross section for nucleon and lepton spins parallel and anti-parallel, one con determine the spin dependent structure function g{sub 1}, which contains information on the quark and gluon spin distribution functions. The interpretation in the frame work of the quark parton model (QPM) of earlier results on g{sub 1}{sup p} by the European Muon Collaboration (EMC), gave an indication that only a small fraction of the proton spin, compatible with zero, is carried by the spins of the constituent quarks. The SMC was set up to check this unexpected result with improved accuracy, and to combine measurements of g{sub 1}{sup p} and g{sub 1}{sup d} to test a fundamental sum rule in quantum chromodynamics (QCD), the Bjorken sum rule. (orig./WL).

  5. NADP-Dependent Aldehyde Dehydrogenase from Archaeon Pyrobaculum sp.1860: Structural and Functional Features

    Directory of Open Access Journals (Sweden)

    Ekaterina Yu. Bezsudnova

    2016-01-01

    Full Text Available We present the functional and structural characterization of the first archaeal thermostable NADP-dependent aldehyde dehydrogenase AlDHPyr1147. In vitro, AlDHPyr1147 catalyzes the irreversible oxidation of short aliphatic aldehydes at 60–85°С, and the affinity of AlDHPyr1147 to the NADP+ at 60°С is comparable to that for mesophilic analogues at 25°С. We determined the structures of the apo form of AlDHPyr1147 (3.04 Å resolution, three binary complexes with the coenzyme (1.90, 2.06, and 2.19 Å, and the ternary complex with the coenzyme and isobutyraldehyde as a substrate (2.66 Å. The nicotinamide moiety of the coenzyme is disordered in two binary complexes, while it is ordered in the ternary complex, as well as in the binary complex obtained after additional soaking with the substrate. AlDHPyr1147 structures demonstrate the strengthening of the dimeric contact (as compared with the analogues and the concerted conformational flexibility of catalytic Cys287 and Glu253, as well as Leu254 and the nicotinamide moiety of the coenzyme. A comparison of the active sites of AlDHPyr1147 and dehydrogenases characterized earlier suggests that proton relay systems, which were previously proposed for dehydrogenases of this family, are blocked in AlDHPyr1147, and the proton release in the latter can occur through the substrate channel.

  6. Temperature-dependent structural and functional features of a hyperthermostable enzyme using elastic neutron scattering

    NARCIS (Netherlands)

    Koutsopoulos, S; van der Oost, J; Norde, W

    2005-01-01

    The dynamic behavior of an endoglucanase from the hyperthermophilic microorganism Pyrococcus furiosus was investigated using elastic neutron scattering. The temperature dependence of the atomic motions was correlated with conformational. and functional characteristics of the enzyme. The onset of

  7. Temperature-dependent structural and functional features of a hyperthermostable enzyme using elastic neutron scattering

    NARCIS (Netherlands)

    Koutsopoulos, S.; Oost, van der J.; Norde, W.

    2005-01-01

    The dynamic behavior of an endoglucanase from the hyperthermophilic microorganism Pyrococcus furiosus was investigated using elastic neutron scattering. The temperature dependence of the atomic motions was correlated with conformational and functional characteristics of the enzyme. The onset of

  8. The relation between structural and functional connectivity depends on age and on task goals

    Directory of Open Access Journals (Sweden)

    Jaclyn Hennessey Ford

    2014-05-01

    Full Text Available The last decade has seen an increase in neuroimaging studies examining structural (i.e., structural integrity of white matter tracts and functional connectivity (e.g., correlations in neural activity throughout the brain. Although structural and functional connectivity changes have often been measured independently, examining the relation between these two measures is critical to understanding the specific function of neural networks and the ways they may differ across tasks and individuals. The current study addressed this question by examining the effect of age (treated as a continuous variable and emotional valence on the relation between functional and structural connectivity. As prior studies have suggested that prefrontal regions may guide and regulate emotional memory search via functional connections with the amygdala, the current analysis focused on functional connectivity between the left amygdala and the left prefrontal cortex, and structural integrity of the uncinate fasciculus, a white matter tract connecting prefrontal and temporal regions.Participants took part in a scanned retrieval task in which they recalled positive, negative, and neutral images associated with neutral titles. Aging was associated with a significant increase in the relation between measures of structural integrity (specifically, fractional anisotropy, or FA along the uncinate fasciculus and functional connectivity between the left ventral prefrontal cortex and amygdala during positive event retrieval, but not negative or neutral retrieval. Notably, during negative event retrieval, age was linked to stronger structure-function relations between the amygdala and the dorsal anterior cingulate cortex, such that increased structural integrity predicted strong negative functional connectivity in older adults only. These findings are consistent with theories that older adults may engage regulatory strategies if they have the structural pathways to allow them to do so.

  9. LDF (Lag Dependence Functions)

    DEFF Research Database (Denmark)

    2000-01-01

    LDF (Lag Dependence Functions) is an S-PLUS library for identification of non-linear dependencies in univariate time series. The methods can be considered generalizations of the tools applicable for linear time series.......LDF (Lag Dependence Functions) is an S-PLUS library for identification of non-linear dependencies in univariate time series. The methods can be considered generalizations of the tools applicable for linear time series....

  10. LDF (Lag Dependence Functions)

    DEFF Research Database (Denmark)

    2000-01-01

    LDF (Lag Dependence Functions) is an S-PLUS library for identification of non-linear dependencies in univariate time series. The methods can be considered generalizations of the tools applicable for linear time series.......LDF (Lag Dependence Functions) is an S-PLUS library for identification of non-linear dependencies in univariate time series. The methods can be considered generalizations of the tools applicable for linear time series....

  11. NCACO-score: An effective main-chain dependent scoring function for structure modeling

    Directory of Open Access Journals (Sweden)

    Dong Xiaoxi

    2011-05-01

    Full Text Available Abstract Background Development of effective scoring functions is a critical component to the success of protein structure modeling. Previously, many efforts have been dedicated to the development of scoring functions. Despite these efforts, development of an effective scoring function that can achieve both good accuracy and fast speed still presents a grand challenge. Results Based on a coarse-grained representation of a protein structure by using only four main-chain atoms: N, Cα, C and O, we develop a knowledge-based scoring function, called NCACO-score, that integrates different structural information to rapidly model protein structure from sequence. In testing on the Decoys'R'Us sets, we found that NCACO-score can effectively recognize native conformers from their decoys. Furthermore, we demonstrate that NCACO-score can effectively guide fragment assembly for protein structure prediction, which has achieved a good performance in building the structure models for hard targets from CASP8 in terms of both accuracy and speed. Conclusions Although NCACO-score is developed based on a coarse-grained model, it is able to discriminate native conformers from decoy conformers with high accuracy. NCACO is a very effective scoring function for structure modeling.

  12. Dielectric-dependent Density Functionals for Accurate Electronic Structure Calculations of Molecules and Solids

    Science.gov (United States)

    Skone, Jonathan; Govoni, Marco; Galli, Giulia

    Dielectric-dependent hybrid [DDH] functionals have recently been shown to yield highly accurate energy gaps and dielectric constants for a wide variety of solids, at a computational cost considerably less than standard GW calculations. The fraction of exact exchange included in the definition of DDH functionals depends (self-consistently) on the dielectric constant of the material. In the present talk we introduce a range-separated (RS) version of DDH functionals where short and long-range components are matched using material dependent, non-empirical parameters. Comparing with state of the art GW calculations and experiment, we show that such RS hybrids yield accurate electronic properties of both molecules and solids, including energy gaps, photoelectron spectra and absolute ionization potentials. This work was supported by NSF-CCI Grant Number NSF-CHE-0802907 and DOE-BES.

  13. Structure, biosynthesis, and function of bacterial capsular polysaccharides synthesized by ABC transporter-dependent pathways.

    Science.gov (United States)

    Willis, Lisa M; Whitfield, Chris

    2013-08-30

    Bacterial capsules are formed primarily from long-chain polysaccharides with repeat-unit structures. A given bacterial species can produce a range of capsular polysaccharides (CPSs) with different structures and these help distinguish isolates by serotyping, as is the case with Escherichia coli K antigens. Capsules are important virulence factors for many pathogens and this review focuses on CPSs synthesized via ATP-binding cassette (ABC) transporter-dependent processes in Gram-negative bacteria. Bacteria utilizing this pathway are often associated with urinary tract infections, septicemia, and meningitis, and E. coli and Neisseria meningitidis provide well-studied examples. CPSs from ABC transporter-dependent pathways are synthesized at the cytoplasmic face of the inner membrane through the concerted action of glycosyltransferases before being exported across the inner membrane and translocated to the cell surface. A hallmark of these CPSs is a conserved reducing terminal glycolipid composed of phosphatidylglycerol and a poly-3-deoxy-d-manno-oct-2-ulosonic acid (Kdo) linker. Recent discovery of the structure of this conserved lipid terminus provides new insights into the early steps in CPS biosynthesis.

  14. Nuclear Dependence in Weak Structure Functions and the Determination of Weak Mixing Angle

    CERN Document Server

    Athar, M Sajjad; Simo, I Ruiz; Vacas, M J Vicente

    2013-01-01

    We have studied nuclear medium effects in the weak structure functions $F^A_2(x)$ and $F^A_3(x)$ and in the extraction of weak mixing angle using Paschos Wolfenstein(PW) relation. We have modified the PW relation for nonisoscalar nuclear target. We have incorporated the medium effects like Pauli blocking, Fermi motion, nuclear binding energy, nucleon correlations, pion $\\&$ rho cloud contributions, and shadowing and antishadowing effects.

  15. Nongenomic STAT5-dependent effects on Golgi apparatus and endoplasmic reticulum structure and function.

    Science.gov (United States)

    Lee, Jason E; Yang, Yang-Ming; Liang, Feng-Xia; Gough, Daniel J; Levy, David E; Sehgal, Pravin B

    2012-03-01

    We report unexpected nongenomic functions of signal transducer and activator of transcription (STAT) 5 species in the cytoplasm aimed at preserving the structure and function of the Golgi apparatus and rough endoplasmic reticulum (ER) in vascular cells. Immunoimaging and green fluorescent protein-tagged-STAT5a protein localization studies showed the constitutive association of nonphosphorylated STAT5a, and to a lesser extent STAT5b, with the Golgi apparatus and of STAT5a with centrosomes in human pulmonary arterial endothelial and smooth muscle cells. Acute knockdown of STAT5a/b species using small interfering RNAs (siRNAs), including in the presence of an mRNA synthesis inhibitor (5,6-dichloro-1-β-d-ribofuranosylbenzimidazole), produced a dramatic phenotype within 1 day, consisting of dilatation and fragmentation of Golgi cisternae, a marked tubule-to-cyst change in the ER, increased accumulation of reticulon-4 (RTN4)/Nogo-B and atlastin-3 (ATL3) at cyst-zone boundaries, cystic separation of the outer and inner nuclear membranes, accompanied by scalloped/lunate distortion of the nucleus, with accumulation of RTN4 on convex sides of distorted nuclei. These cells showed inhibition of vesicular stomatitis virus G protein glycoprotein trafficking, mitochondrial fragmentation, and reduced mitochondrial function. STAT5a/b(-/-) mouse embryo fibroblasts also showed altered ER/Golgi dynamics. RTN4 knockdown using siRNA did not affect development of the cystic phenotype; ATL3 siRNA led to effacement of cyst-zone boundaries. In magnetic-bead cross-immunopanning assays, ATL3 bound both STAT5a and STAT5b. Remarkably, this novel cystic ER/lunate nucleus phenotype was characteristic of vascular cells in arterial lesions of idiopathic pulmonary hypertension, an unrelentingly fatal human disease. These data provide evidence of a STAT-family protein regulating the structure of a cytoplasmic organelle and implicate this mechanism in the pathogenesis of a human disease.

  16. Structure-dependent interatomic dispersion coefficients in oxides with maximally localized Wannier functions

    Science.gov (United States)

    Sukhomlinov, Sergey V.; Smirnov, Konstantin S.

    2012-11-01

    The interatomic C6 dispersion coefficients in crystalline and amorphous SiO2 and ZrO2 structures were obtained with the approach proposed by Silvestrelli (2008 Phys. Rev. Lett. 100 053002) and based on the use of maximally localized Wannier functions (MLWFs) for partitioning the electron density. Localization of Wannier functions close to the nuclei in oxide systems makes it possible to assign the MLWFs to the atoms in an unambiguous way and then to compute the C6 coefficients in an atom pairwise manner. A modification of the method is suggested in which the MLWFs are condensed to effective orbitals centred on the atoms and parameters of these effective orbitals are used for computing the interatomic dispersion coefficients. The obtained values of the dispersion coefficients were found to vary not only from one oxide to another, but also between different modifications of the same compound. The oxygen-oxygen coefficient {C}_{6}^{{OO}} reveals the largest variation and its value in ZrO2 structures is twice as large as that in SiO2 ones. Atomic characteristics obtained in the frame of the effective orbital method, such as the self-atom dispersion coefficient, and the oxide ion polarizability were found to correlate with the metal-oxygen bond length and the oxygen coordination number in the systems. This behaviour is attributed to the confinement of electrons by the electrostatic potential. The values of the coefficient and of the polarizability were related to charges of the oxygen atoms. In all studied systems the oxygen atoms having larger absolute values of charge were found to be less polarizable because of a stronger confinement effect. The obtained results can be used in the development of polarizable force fields for the atomistic modelling of oxide materials.

  17. Measurement of the Spin-Dependent \\\\ Structure Functions of the Proton and the Deuteron

    CERN Multimedia

    2002-01-01

    % NA47 %title \\\\ \\\\The physics motivation of the experiments of the Spin Muon Collaboration is to better understand how the nucleon spin is built-up by its partons and to test the fundamental Bjorken sum rule. \\\\ \\\\The spin-dependent stucture functions g$ _{1} $(x) of the proton and the deuteron are determined from the measured cross section asymmetries for deep inelastic scattering of longitudinally polarized muons from longitudinally polarized nucleons. The experiment is similar to the NA2 one of the European Muon Collaboration in which the violation of the Ellis-Jaffe sum rule for the proton was found. \\\\ \\\\The apparatus is the upgraded forward spectrometer which was used originally by the European and New Muon Collaborations. To minimize the systematic uncertainties the target contains two oppositely polarized cells, which were exposed to the muon beam simultaneously. For the experiments in 1991 and 1992 the original EMC polarized target was reinstalled. In 1993 a new polarized target was put into operati...

  18. Pollutant emissions from gasoline combustion. 1. Dependence on fuel structural functionalities.

    Science.gov (United States)

    Zhang, Hongzhi R; Eddings, Eric G; Sarofim, Adel F

    2008-08-01

    To study the formation of air pollutants and soot precursors (e.g., acetylene, 1,3-butadiene, benzene, and higher aromatics) from aliphatic and aromatic fractions of gasoline fuels, the Utah Surrogate Mechanisms is extended to include submechanisms of gasoline surrogate compounds using a set of mechanism generation techniques. The mechanism yields very good predictions of species concentrations in premixed flames of n-heptane, isooctane, benzene, cyclohexane, olefins, oxygenates, and gasoline using a 23-component surrogate formulation. The 1,3-butadiene emission comes mainly from minor fuel fractions of olefins and cyclohexane. The benzene formation potential of gasoline components shows the following trends as functions of (i) chemical class: n-paraffins < isoparaffins < olefins < naphthalenes < alkylbenzenes < cycloparaffins < toluene; (ii) carbon number: n-butane < n-pentane < n-hexane; and (iii) branching: n-hexane < isohexane < 2,2,4-trimethylpentane < 2,2,3,3-tetramethylbutane. In contrast, fuel structure is not the main factor in determining acetylene formation. Therefore, matching the benzene formation potential of the surrogate fuel to that produced by the real fuel should have priority when selecting candidate surrogate components for combustion simulations.

  19. Density Functional Study of the Carbon Dependence of the Structural, Mechanic, Thermodynamic, and Dynamic Properties of SiC Alloys

    Science.gov (United States)

    Langueur, H.; Kassali, K.

    2017-03-01

    Using a density functional scheme, for the first time the carbon dependence on the structural, dynamic, thermodynamic, and dynamic properties of Si_{1-x}Cx alloys (x=0.0 to 1.0 in steps of 0.125) has been investigated. The structural properties of these materials, in particular, the composition dependence of the lattice parameter and bulk modulus, are in excellent agreement with experimental data and follow a quadratic law in ( x). A nonlinear relationship is found between the elastic constants C_{11}, C_{12}, and C_{44} and the carbon concentration ( x). The behavior of the acoustical and optical phonon frequencies at high-symmetry points Γ, X, and L is predicted. Through the quasi-harmonic Debye model, in which the photonic effects are taken into account, the Debye temperature, the heat capacity, the Helmholtz free energy, the internal energy, and the entropy are determined for the Si_{1-x}C_{x } compounds.

  20. Modeling-dependent protein characterization of the rice aldehyde dehydrogenase (ALDH superfamily reveals distinct functional and structural features.

    Directory of Open Access Journals (Sweden)

    Simeon O Kotchoni

    Full Text Available The completion of the rice genome sequence has made it possible to identify and characterize new genes and to perform comparative genomics studies across taxa. The aldehyde dehydrogenase (ALDH gene superfamily encoding for NAD(P(+-dependent enzymes is found in all major plant and animal taxa. However, the characterization of plant ALDHs has lagged behind their animal- and prokaryotic-ALDH homologs. In plants, ALDHs are involved in abiotic stress tolerance, male sterility restoration, embryo development and seed viability and maturation. However, there is still no structural property-dependent functional characterization of ALDH protein superfamily in plants. In this paper, we identify members of the rice ALDH gene superfamily and use the evolutionary nesting events of retrotransposons and protein-modeling-based structural reconstitution to report the genetic and molecular and structural features of each member of the rice ALDH superfamily in abiotic/biotic stress responses and developmental processes. Our results indicate that rice-ALDHs are the most expanded plant ALDHs ever characterized. This work represents the first report of specific structural features mediating functionality of the whole families of ALDHs in an organism ever characterized.

  1. pH Dependence of Chlorophyll States, Protein Structures and Function of the PSII Membranes

    Institute of Scientific and Technical Information of China (English)

    李冬海; 阮翔; 许强; 王可玢; 公衍道; 匡廷云; 张秀芳; 赵南明

    2003-01-01

    The effect of varying pH on the photosystem II (PSII) membrane was studied using absorption and steady-state fluorescence spectroscopy, and using a variable fluorescence technique.pH variations induced significant changes in the chlorophyll states of the PSII membrane, but no effect was seen on the chlorophyll fluorescence parameter F′v/F′m.For acidic pH conditions, protein structures of the PSII membrane were slightly altered, whilst at alkaline pH levels, large changes in the protein structure of the PSII membrane were detected.The results indicate that the microenvironment around Cys in the PSII membrane is very susceptible to alkaline pH conditions, and that in the acid (4≤pH7) regions, pH variation has no effect on the protein structures of the PSII reaction center (RC).

  2. Characterisation of structure-dependent functional properties of lignin with infrared spectroscopy

    NARCIS (Netherlands)

    Boeriu, C.G.; Bravo, D.; Gosselink, R.J.A.; Dam, van J.E.G.

    2004-01-01

    Fourier-transformed infrared spectroscopy (FT-IR) was evaluated as an analytical technique for the estimation of the chemical composition and functional properties of lignin. A sample set containing various non-wood, hardwood and softwood lignins isolated by different processing technologies was use

  3. Neuroadaptive Changes Associated with Smoking: Structural and Functional Neural Changes in Nicotine Dependence

    Directory of Open Access Journals (Sweden)

    Chantal Martin-Soelch

    2013-02-01

    Full Text Available Tobacco smoking is the most frequent form of substance abuse. We provide a review of the neuroadaptive changes evidenced in human smokers with regard to the current neurobiological models of addiction. Addiction is thought to result from an interplay between positive and negative reinforcement. Positive reinforcing effects of the drugs are mediated by striatal dopamine release, while negative reinforcement involves the relief of withdrawal symptoms and neurobiological stress systems. In addition, drug-related stimuli are attributed with excessive motivational value and are thought to exert a control on the behavior. This mechanism plays a central role in drug maintenance and relapse. Further neuroadaptive changes associated with chronic use of the drug consist of reduced responses to natural rewards and in the activation of an antireward system, related to neurobiological stress systems. Reduced inhibitory cognitive control is believed to support the development and the maintenance of addiction. The findings observed in human nicotine dependence are generally in line with these models. The current state of the research indicates specific neuroadaptive changes associated with nicotine addiction that need to be further elucidated with regard to their role in the treatment of nicotine dependence.

  4. Chaperonin function depends on structure and disorder in co-chaperonin mobile loops.

    Science.gov (United States)

    Landry, S J; Steede, N K; Garaudy, A M; Maskos, K; Viitanen, P V

    1999-01-01

    Co-chaperonins from diverse organisms exhibit mobile loops which fold into a beta hairpin conformation upon binding to the chaperonin. GroES, Gp31, and human Hsp10 mobile loops exhibit a preference for the beta hairpin conformation in the free co-chaperonins, and the conformational dynamics of the human Hsp10 mobile loop appear to be restricted by nascent hairpin formation. Backbone conformational entropy must weigh against binding of co-chaperonins to chaperonins, and thus the conformational preferences of the loops may strongly influence chaperonin-binding affinity. Indeed, subtle mutations in the loops change GroEL-binding affinity and cause defects in chaperonin function, and these defects can be suppressed by mutations in GroEL which compensate for the changes in affinity. The fact that high-affinity co-chaperonin binding impairs chaperonin function has implications for the mechanism of chaperonin-assisted protein folding.

  5. Structural and functional markers of health depending on lifestyle in elderly women from Poland

    Directory of Open Access Journals (Sweden)

    Skrzek A

    2015-04-01

    Full Text Available Anna Skrzek,1 Zofia Ignasiak,2 Teresa Sławińska,2 Jarosław Domaradzki,2 Jarosław Fugiel,2 Anna Sebastjan,2 Krystyna Rożek11Faculty of Physiotherapy, 2Faculty of Physical Education, University School of Physical Education in Wroclaw, Wroclaw, PolandObjective: To comparatively analyze the rate and magnitude of age-related changes between two groups of elderly women with different lifestyles living in Poland: women attending a University of the Third Age (active lifestyle and less-active peers not involved in any seniors association.Methods: The study was conducted in 2010–2012. The study design was approved by the Senate Ethics Committee for Scientific Research of the University School of Physical Education. In total, 417 women were recruited. Basic somatic characteristics, body composition, bone mineral density, physical fitness, respiratory function, postural stability, and body posture were measured. Regression analysis and Student’s t-tests for independent samples were calculated.Results and conclusion: The best results among the tests assessing functional biological markers of health were found in the group of elderly women attending a University of the Third Age. The rate of change was larger in the group of seniors leading a less-active lifestyle, indicating the important role of a preventive gerontological approach and the participation of seniors in programs that accentuate the need for physical activity. Keywords: age-related changes, bone mineral density, markers of health, lifestyle, elderly women

  6. MT1-MMP-dependent remodeling of cardiac extracellular matrix structure and function following myocardial infarction.

    Science.gov (United States)

    Koenig, Gerald C; Rowe, R Grant; Day, Sharlene M; Sabeh, Farideh; Atkinson, Jeffrey J; Cooke, Kenneth R; Weiss, Stephen J

    2012-05-01

    The myocardial extracellular matrix (ECM), an interwoven meshwork of proteins, glycoproteins, proteoglycans, and glycosaminoglycans that is dominated by polymeric fibrils of type I collagen, serves as the mechanical scaffold on which myocytes are arrayed for coordinated and synergistic force transduction. Following ischemic injury, cardiac ECM remodeling is initiated via localized proteolysis, the bulk of which has been assigned to matrix metalloproteinase (MMP) family members. Nevertheless, the key effector(s) of myocardial type I collagenolysis both in vitro and in vivo have remained unidentified. In this study, using cardiac explants from mice deficient in each of the major type I collagenolytic MMPs, including MMP-13, MMP-8, MMP-2, MMP-9, or MT1-MMP, we identify the membrane-anchored MMP, MT1-MMP, as the dominant collagenase that is operative within myocardial tissues in vitro. Extending these observations to an in vivo setting, mice heterozygous for an MT1-MMP-null allele display a distinct survival advantage and retain myocardial function relative to wild-type littermates in an experimental model of myocardial infarction, effects associated with preservation of the myocardial type I collagen network as a consequence of the decreased collagenolytic potential of cardiac fibroblasts. This study identifies MT1-MMP as a key MMP responsible for effecting postinfarction cardiac ECM remodeling and cardiac dysfunction.

  7. Impact of graphene oxide on the structure and function of important multiple blood components by a dose-dependent pattern.

    Science.gov (United States)

    Feng, Ru; Yu, Yueping; Shen, Chaoxuan; Jiao, Yanpeng; Zhou, Changren

    2015-06-01

    Graphene and its derivatives have become great concern in biomedical fields. Though many investigations about their toxicity have been reported, systematic investigation on the interaction with multiple blood components is lacking. In this work, we studied the effects of the graphene oxide (GO) on the structure and function of the blood components, especially, on morphology and hemolysis of red blood cells (RBCs), bovine serum albumin (BSA) and fibrinogen conformation, complement activation, and blood coagulation function. Scanning electron microscopy observation and hemolysis test results showed that the GO can affect RBC morphology and membrane integrity in a concentration-dependent way. Fluorescence and circular dichroism spectra showed that GO could alter the secondary structures and conformation of BSA and fibrinogen. In addition, the presence of GO could also trigger complement activation by detecting their key biomarker molecules in plasma. In the blood clotting process, the GO showed significant adverse effect on the activated partial thromboplastin time but not on prothrombin time of the platelet-poor plasma. Meanwhile, the GO also caused abnormal thromboelastography parameters of the whole blood coagulation. The results obtained in this study provides good insight into understanding the biomedical application of GO in vivo.

  8. Final COMPASS results on the deuteron spin-dependent structure function g1d and the Bjorken sum rule

    Directory of Open Access Journals (Sweden)

    C. Adolph

    2017-06-01

    Full Text Available Final results are presented from the inclusive measurement of deep-inelastic polarised-muon scattering on longitudinally polarised deuterons using a 6LiD target. The data were taken at 160 GeV beam energy and the results are shown for the kinematic range 1(GeV/c24GeV/c2 in the mass of the hadronic final state. The deuteron double-spin asymmetry A1d and the deuteron longitudinal-spin structure function g1d are presented in bins of x and Q2. Towards lowest accessible values of x, g1d decreases and becomes consistent with zero within uncertainties. The presented final g1d values together with the recently published final g1p values of COMPASS are used to again evaluate the Bjorken sum rule and perform the QCD fit to the g1 world data at next-to-leading order of the strong coupling constant. In both cases, changes in central values of the resulting numbers are well within statistical uncertainties. The flavour-singlet axial charge a0, which is identified in the MS‾ renormalisation scheme with the total contribution of quark helicities to the nucleon spin, is extracted at next-to-leading order accuracy from only the COMPASS deuteron data: a0(Q2=3(GeV/c2=0.32±0.02stat±0.04syst±0.05evol. Together with the recent results on the proton spin structure function g1p, the results on g1d constitute the COMPASS legacy on the measurements of g1 through inclusive spin-dependent deep inelastic scattering.

  9. The Spin-dependent Structure Function of the Proton $g_{1}^p$ and a Test of the Bjorken Sum Rule

    CERN Document Server

    Alekseev, M G; Alexandrov, Yu; Alexeev, G D; Amoroso, A; Austregesilo, A; Badelek, B; Balestra, F; Ball, J; Barth, J; Baum, G; Bedfer, Y; Bernhard, J; Bertini, R; Bettinelli, M; Birsa, R; Bisplinghoff, J; Bordalo, P; Bradamante, F; Bravar, A; Bressan, A; Brona, G; Burtin, E; Bussa, M P; Chaberny, D; Cotic, D; Chiosso, M; Chung, S U; Cicuttin, A; Colantoni, M; Crespo, M L; Dalla Torre, S; Das, S; Dasgupta, S S; Denisov, O Yu; Dhara, L; Diaz, V; Donskov, S V; Doshita, N; Duic, V; Dünnweber, W; Efremov, A; El Alaoui, A; Eversheim, P D; Eyrich, W; Faessler, M; Ferrero, A; Filin, A; Finger, M; Finger, M Jr; Fischer, H; Franco, C; Friedrich, J M; Garfagnini, R; Gautheron, F; Gavrichtchouk, O P; Gazda, R; Gerassimov, S; Geyer, R; Giorgi, M; Gnesi, I; Gobbo, B; Goertz, S; Grabmüller, S; Grasso, A; Grube, B; Gushterski, R; Guskov, A; Haas, F; von Harrach, D; Hasegawa, T; Heinsius, F H; Hermann, R; Herrmann, F; Heß, C; Hinterberger, F; Horikawa, N; Höppner, Ch; d'Hose, N; Ilgner, C; Ishimoto, S; Ivanov, O; Ivanshin, Yu; Iwata, T; Jahn, R; Jasinski, P; Jegou, G; Joosten, R; Kabuß, E; Käfer, W; Kang, D; Ketzer, B; Khaustov, G V; Khokhlov, Yu A; Kisselev, Yu; Klein, F; Klimaszewski, K; Koblitz, S; Koivuniemi, J H; Kolosov, V N; Kondo, K; Königsmann, K; Konopka, R; Konorov, I; Konstantinov, V F; Korzenev, A; Kotzinian, A M; Kouznetsov, O; Kowalik, K; Krämer, M; Kral, A; Kroumchtein, Z V; Kuhn, R; Kunne, F; Kurek, K; Lauser, L; Le Goff, J M; Lednev, A A; Lehmann, A; Levorato, S; Lichtenstadt, J; Liska, T; Maggiora, A; Maggiora, M; Magnon, A; Mallot, G K; Mann, A; Marchand, C; Marroncle, J; Martin, A; Marzec, J; Massmann, F; Matsuda, T; Maximov, A N; W Meyer, W; Michigami, T; Mikhailov, Yu V; Moinester, M A; Mutter, A; Nagaytsev, A; Nagel, T; Nassalski, J; Negrini, T; Nerling, F; Neubert, S; Neyret, D; Nikolaenko, V I; Olshevsky, A G; Ostrick, M; Padee, A; Panknin, R; Panzieri, D; Parsamyan, B; Paul, S; Pawlukiewicz-Kaminska, B; Perevalova, E; Pesaro, G; Peshekhonov, D V; Piragino, G; Platchkov, S; Pochodzalla, J; Polak, J; Polyakov, V A; Pontecorvo, G; Pretz, J; Quintans, C; Rajotte, J F; Ramos, S; Rapatsky, V; Reicherz, G; Richter, A; Robinet, F; Rocco, E; Rondio, E; Ryabchikov, D I; Samoylenko, V D; Sandacz, A; Santos, H; Sapozhnikov, M G; Sarkar, S; Savin, I A; Sbrizzai, G; Schiavon, P; Schill, C; Schmitt, L; Schlüter, T; Schopferer, S; Schröder, W; Shevchenko, O Yu; Siebert, H W; Silva, L; Sinha, L; Sissakian, A N; Slunecka, M; Smirnov, G I; Sosio, S; Sozzi, F; Srnka, A; Stolarski, M; Sulc, M; Sulej, R; Takekawa, S; Tessaro, S; Tessarotto, F; Teufel, A; Tkatchev, L G; Uhl, S; Uman, I; Virius, M; Vlassov, N V; Vossen, A; Weitzel, Q; Windmolders, R; Wislicki, W; Wollny, H; Zaremba, K; Zavertyaev, M; Zemlyanichkina, E; Ziembicki, M; Zhao, J; Zhuravlev, N; Zvyagin, A

    2010-01-01

    The inclusive double-spin asymmetry, $A_{1}^{p}$, has been measured at COMPASS in deepinelastic polarised muon scattering off a large polarised NH3 target. The data, collected in the year 2007, cover the range Q2 > 1 (GeV/c)^2, 0.004 < x < 0.7 and improve the statistical precision of g_{1}^{p}(x) by a factor of two in the region x < 0.02. The new proton asymmetries are combined with those previously published for the deuteron to extract the non-singlet spin-dependent structure function g_1^NS(x,Q2). The isovector quark density, Delta_q_3(x,Q2), is evaluated from a NLO QCD fit of g_1^NS. The first moment of Delta_q3 is in good agreement with the value predicted by the Bjorken sum rule and corresponds to a ratio of the axial and vector coupling constants g_A/g_V = 1.28+-0.07(stat)+-0.10(syst).

  10. Tel2 structure and function in the Hsp90-dependent maturation of mTOR and ATR complexes

    Energy Technology Data Exchange (ETDEWEB)

    Takai, Hiroyuki; Xie, Yihu; de Lange, Titia; Pavletich, Nikola P. (Rockefeller); (SKI)

    2010-09-20

    We reported previously that the stability of all mammalian phosphatidylinositol 3-kinase-related protein kinases (PIKKs) depends on their interaction with Tel2, the ortholog of yeast Tel2 and Caenorhabditis elegans Clk-2. Here we provide evidence that Tel2 acts with Hsp90 in the maturation of PIKK complexes. Quantitative immunoblotting showed that the abundance of Tel2 is low compared with the PIKKs, and Tel2 preferentially bound newly synthesized ATM, ATR, mTOR, and DNA-PKcs. Tel2 complexes contained, in addition to Tti1-Tti2, the Hsp90 chaperone, and inhibition of Hsp90 interfered with the interaction of Tel2 with the PIKKs. Analysis of in vivo labeled nascent protein complexes showed that Tel2 and Hsp90 mediate the formation of the mTOR TORC1 and TORC2 complexes and the association of ATR with ATRIP. The structure of yeast Tel2, reported here, shows that Tel2 consists of HEAT-like helical repeats that assemble into two separate {alpha}-solenoids. Through mutagenesis, we identify a surface patch of conserved residues involved in binding to the Tti1-Tti2 complex in vitro. In vivo, mutation of this conserved patch affects cell growth, levels of PIKKs, and ATM/ATR-mediated checkpoint signaling, highlighting the importance of Tti1-Tti2 binding to the function of Tel2. Taken together, our data suggest that the Tel2-Tti1-Tti2 complex is a PIKK-specific cochaperone for Hsp90.

  11. Time-dependent effects of o-xylene on rat lung and liver microsomal membrane structure and function.

    Science.gov (United States)

    Park, S H; AuCoin, T A; Silverman, D M; Schatz, R A

    1994-12-01

    The present study investigates the time-dependent effect of acute intraperitoneal o-xylene administration (1 g/kg) on rat hepatic and pulmonary mixed-function oxidase (MFO) content and activity and microsomal membrane structural parameters for up to 12 h postadministration. The purpose of this study was to determine whether o-xylene has similar effects on these parameters as those previously observed for the m and p isomers. o-xylene decreased total pulmonary cytochrome P-450 content and aryl hydrocarbon hydroxylase (AHH) activity at all time points examined with maximal inhibition occurring at 3 h postdose. The isozyme-specific MFO activity responsible for AHH activity was examined using benzyloxyresorufin O-dealkylation (BROD) as a measure of CYP2B1 activity and ethoxyresorufin O-dealkylation (EROD) as a measure of CYP1A1 activity. Reduced pulmonary activity for both EROD and BROD was noted for the 12-h postexposure period, in agreement with the decreases in total cytochrome P-450 content and AHH activity data. In contrast, increased hepatic cytochrome P-450 content was noted at 6 and 12 h with slightly increased EROD activity and markedly increased BROD activity. Conjugated diene (CD) formation, and index of membrane peroxidation, and phospholipid (PL) and cholesterol (CL) content of the microsomal membranes were also examined in lung and liver to assess membrane structural integrity. Pulmonary CD formation was increased only at the 12-h time point, while hepatic CD formation was increased from 3 to 12 h. An increase in pulmonary microsomal PL and CL content was noted as early as 1 h postdose. In liver, PL content was increased as early as 3 h, with no change in CL content. An increase in the PL/CL ratio, suggesting an increase in membrane fluidity, was observed in pulmonary microsomes 12 h after dosing, and in hepatic microsomes at 3, 6, and 12 h postdose. There was no correlation between solvent tissue levels and MFO or membrane changes. It seems unlikely that

  12. Applying Alkyl-Chain Surface Functionalizations in Mesoporous Inorganic Structures: Their Impact on Gas Flow and Selectivity Depending on Temperature.

    Science.gov (United States)

    Besser, Benjamin; Ahmed, Atiq; Baune, Michael; Kroll, Stephen; Thöming, Jorg; Rezwan, Kurosch

    2016-10-12

    Porous inorganic capillary membranes are prepared to serve as model structures for the experimental investigation of the gas transport in functionalized mesopores. The porous structures possess a mean pore diameter of 23 nm which is slightly reduced to 20 nm after immobilizing C16-alkyl chains on the surface. Gas permeation measurements are performed at temperatures ranging from 0 to 80 °C using Ar, N2, and CO2. Nonfunctionalized structures feature a gas transport according to Knudsen diffusion with regard to gas flow and selectivity. After C16-functionalization, the gas flow is reduced by a factor of 10, and the ideal selectivities deviate from the Knudsen theory. CO2 adsorption measurements show a decrease in total amount of adsorbed gas and isosteric heat of adsorption. It is hypothesized that the immobilized C16-chains sterically influence the gas transport behavior without a contribution from adsorption effects. The reduced gas flow derives from an additional surface resistance caused by the C16-chains spacially limiting the adsorption and desorption directions for gas molecules propagating through the structure, resulting in longer diffusion paths. In agreement, the gas flow is found to correlate with the molecular diameter of the gas species (CO2 ideal selectivities with the relation [Formula: see text]. The influence on selectivity increases with increasing temperature which leads to the conclusion that the temperature induced movement of the C16-chains is responsible for the stronger interaction between gas molecules and surface functional groups.

  13. Dependence of the functional characteristics of thermomechanically processed titanium nickelide on the size of the structural elements of austenite

    Science.gov (United States)

    Polyakova-Vachiyan, K. A.; Ryklina, E. P.; Prokoshkin, S. D.; Dubinskii, S. M.

    2016-08-01

    Effect of the size of the elements of the mixed structure of B2 austenite, which consists of nanosized grains and subgrains of a polygonized substructure, on the functional properties of the Ti-50.7 at % Ni alloy preliminarily subjected to a low-temperature thermomechanical treatment (LTMT) and post-deformation annealing (PDA), has been investigated. The generation of the shape-memory effect (SME) and reversible two-way SME (TWSME) was performed using bending deformation. A maximum (for the Ti-Ni alloys) value of the recovery strain ɛr = 15.5 ± 0.5% has been obtained after annealing at 600°C for 1 h (recrystallized structure) and after LTMT + PDA at 430°C for 10 h (mixed nanocrystalline and nanosubgrain structure). The behavior of the parameters of the SME and TWSME in different structural states has been considered. A comparative study of the effect of the temperature and time of holding at a temperature upon the PDA on the formation of the microstructure and submicrostructure of the B2 austenite has been performed.

  14. Effect of pH on the structure, function, and stability of human calcium/calmodulin-dependent protein kinase IV: combined spectroscopic and MD simulation studies.

    Science.gov (United States)

    Naz, Huma; Shahbaaz, Mohd; Bisetty, Krishna; Islam, Asimul; Ahmad, Faizan; Hassan, Md Imtaiyaz

    2016-06-01

    Human calcium/calmodulin-dependent protein kinase IV (CAMKIV) is a member of Ser/Thr protein kinase family. It is regulated by the calcium-calmodulin dependent signal through a secondary messenger, Ca(2+), which leads to the activation of its autoinhibited form. The over-expression and mutation in CAMKIV as well as change in Ca(2+) concentration is often associated with numerous neurodegenerative diseases and cancers. We have successfully cloned, expressed, and purified a functionally active kinase domain of human CAMKIV. To observe the effect of different pH conditions on the structural and functional properties of CAMKIV, we have used spectroscopic techniques such as circular diachroism (CD) absorbance and fluorescence. We have observed that within the pH range 5.0-11.5, CAMKIV maintained both its secondary and tertiary structures, along with its function, whereas significant aggregation was observed at acidic pH (2.0-4.5). We have also performed ATPase activity assays under different pH conditions and found a significant correlation between the structure and enzymatic activities of CAMKIV. In-silico validations were further carried out by modeling the 3-dimensional structure of CAMKIV and then subjecting it to molecular dynamics (MD) simulations to understand its conformational behavior in explicit water conditions. A strong correlation between spectroscopic observations and the output of molecular dynamics simulation was observed for CAMKIV.

  15. Precision Measurement of the Neutron Spin Asymmetries and Spin-dependent Structure Functions in the Valence Quark Region

    CERN Document Server

    Zheng, X; Armstrong, D S; Averett, T D; Bertozzi, W; Binet, S; Burtin, E; Busato, E; Butuceanu, C; Calarco, J; Camsonne, A; Cates, G D; Chai, Z; Chen, J P; Seonho Choi; Chudakov, E; Cusanno, F; De Leo, R; Deur, A; Dieterich, S; Dutta, D; Finn, J M; Frullani, S; Gao, H; Gao, J; Garibaldi, F; Gilad, S; Gilman, R; Gómez, J; Hansen, J O; Higinbotham, D W; Hinton, W; Horn, T; De Jager, C W; Jiang, X; Kaufman, L; Kelly, J; Korsch, W; Krämer, K; Le Rose, J J; Lhuillier, D; Liyanage, N K; Margaziotis, D J; Marie, F; Markowitz, P; McCormick, K; Meziani, Z E; Michaels, R; Moffit, B; Nanda, S; Neyret, D; Phillips, S K; Powell, A; Pussieux, T; Reitz, B; Roche, J; Roché, R; Roedelbronn, M; Ron, G; Rvachev, M; Saha, A; Savvinov, N; Singh, J; Sirca, S; Slifer, K J; Solvignon, P; Souder, P A; Steiner, D J; Strauch, S; Sulkosky, V; Tobias, A; Urciuoli, G; Vacheret, A; Wojtsekhowski, B; Xiang, H; Xiao, Y; Xiong, F; Zhang, B; Zhu, L; Zhu, X

    2004-01-01

    We report on measurements of the neutron spin asymmetries $A_{1,2}^n$ and polarized structure functions $g_{1,2}^n$ at three kinematics in the deep inelastic region, with $x=0.33$, 0.47 and 0.60 and $Q^2=2.7$, 3.5 and 4.8 (GeV/c)$^2$, respectively. These measurements were performed using a 5.7 GeV longitudinally-polarized electron beam and a polarized $^3$He target. The results for $A_1^n$ and $g_1^n$ at $x=0.33$ are consistent with previous world data and, at the two higher $x$ points, have improved the precision of the world data by about an order of magnitude. The new $A_1^n$ data show a zero crossing around $x=0.47$ and the value at $x=0.60$ is significantly positive. These results agree with a next-to-leading order QCD analysis of previous world data. The trend of data at high $x$ agrees with constituent quark model predictions but disagrees with that from leading-order perturbative QCD (pQCD) assuming hadron helicity conservation. Results for $A_2^n$ and $g_2^n$ have a precision comparable to the best w...

  16. Time-dependent effect of graphene on the structure, abundance, and function of the soil bacterial community.

    Science.gov (United States)

    Ren, Wenjie; Ren, Gaidi; Teng, Ying; Li, Zhengao; Li, Lina

    2015-10-30

    The increased application of graphene raises concerns about its environmental impact, but little information is available on the effect of graphene on the soil microbial community. This study evaluated the impact of graphene on the structure, abundance and function of the soil bacterial community based on quantitative real-time polymerase chain reaction (qPCR), pyrosequencing and soil enzyme activities. The results show that the enzyme activities of dehydrogenase and fluorescein diacetate (FDA) esterase and the biomass of the bacterial populations were transiently promoted by the presence of graphene after 4 days of exposure, but these parameters recovered completely after 21 days. Pyrosequencing analysis suggested a significant shift in some bacterial populations after 4 days, and the shift became weaker or disappeared as the exposure time increased to 60 days. During the entire exposure process, the majority of bacterial phylotypes remained unaffected. Some bacterial populations involved in nitrogen biogeochemical cycles and the degradation of organic compounds can be affected by the presence of graphene.

  17. Precision Measurement of the Neutron Spin Asymmetries and Spin-dependent Structure Functions in the Valence Quark Region

    Energy Technology Data Exchange (ETDEWEB)

    Xiaochao Zheng; Konrad Aniol; David Armstrong; Todd Averett; William Bertozzi; Sebastien Binet; Etienne Burtin; Emmanuel Busato; Cornel Butuceanu; John Calarco; Alexandre Camsonne; Gordon Cates; Zhengwei Chai; Jian-ping Chen; Seonho Choi; Eugene Chudakov; Francesco Cusanno; Raffaele De Leo; Alexandre Deur; Sonja Dieterich; Dipangkar Dutta; John Finn; Salvatore Frullani; Haiyan Gao; Juncai Gao; Franco Garibaldi; Shalev Gilad; Ronald Gilman; Javier Gomez; Jens-ole Hansen; Douglas Higinbotham; Wendy Hinton; Tanja Horn; Cornelis De Jager; Xiaodong Jiang; Lisa Kaufman; James Kelly; Wolfgang Korsch; Kevin Kramer; John Lerose; David Lhuillier; Nilanga Liyanage; Demetrius Margaziotis; Frederic Marie; Pete Markowitz; Kathy Mccormick; Zein-eddine Meziani; Robert Michaels; Bryan Moffit; Sirish Nanda; Damien Neyret; Sarah Phillips; Anthony Powell; Thierry Pussieux; Bodo Reitz; Julie Roche; Michael Roedelbronn; Guy Ron; Marat Rvachev; Arunava Saha; Nikolai Savvinov; Jaideep Singh; Simon Sirca; Karl Slifer; Patricia Solvignon; Paul Souder; Daniel Steiner; Steffen Strauch; Vincent Sulkosky; William Tobias; Guido Urciuoli; Antonin Vacheret; Bogdan Wojtsekhowski; Hong Xiang; Yuan Xiao; Feng Xiong; Bin Zhang; Lingyan Zhu; Xiaofeng Zhu; Piotr Zolnierczuk

    2004-05-01

    We report on measurements of the neutron spin asymmetries A{sub 1,2}{sup n} and polarized structure functions g{sub 1,2}{sup n} at three kinematics in the deep inelastic region, with x = 0.33, 0.47 and .60 and Q{sub 2} = 2.7, 3.5 and 4.8 (GeV/c){sup 2}, respectively. These measurements were performed using a 5.7 GeV longitudinally-polarized electron beam and a polarized {sup 3}He target. The results for A{sub 1}{sup n} and g{sub 1}{sup n} at x = 0.33 are consistent with previous world data and, at the two higher x points, have improved the precision of the world data by about an order of magnitude. The new A{sub 1}{sup n} data show a zero crossing around x = 0.47 and the value at x = 0.60 is significantly positive. These results agree with a next-to-leading order QCD analysis of previous world data. The trend of data at high x agrees with constituent quark model predictions but disagrees with that from leading-order perturbative QCD (pQCD) assuming hadron helicity conservation. Results for A{sub 2}{sup n} and g{sub 2}{sup n} have a precision comparable to the best world data in this kinematic region. Combined with previous world data, the moment d{sub 2}{sup n} was evaluated and the new result has improved the precision of this quantity by about a factor of two. When combined with the world proton data, polarized quark distribution functions were extracted from the new g{sub 1}{sup n}/F{sub 1}{sup n} values based on the quark parton model. While results for {Delta}u/u agree well with predictions from various models, results for {Delta}d/d disagree with the leading-order pQCD prediction when hadron helicity conservation is imposed.

  18. J-dependence of s-wave neutron strength function and presence of intermediate structure in medium and heavy mass nuclides

    Science.gov (United States)

    Badola, Amit; Singhal, S. K.; Bhatnagar, Manoj; Agrawal, H. M.

    2017-01-01

    Neutron resonance structures of nuclides have been studied over a wide energy range as these parameters are used for regulating the inputs to optical and statistical model calculations. On the basis of high resolution data on resonance parameters (E0, Γn, Jπ), s-wave neutron strength functions (S0) for individual Jπ values are calculated and the J-dependence of it has been investigated for 79 odd nuclides. Our analysis of statistical properties shows the J-dependence of (S0) and this contribution should be included in the OM calculations. Our study well materializes the presence of intermediate structure (IS) for 24 odd nuclides within both data and information reported in literature.

  19. Structure-Function Relationships in the Gas-Sensing Heme-Dependent Transcription Factors RcoM and DNR

    Science.gov (United States)

    Bowman, Hannah E.

    Transition metals play an important role in many biological processes, however, they are also toxic at high concentrations. Therefore, the uptake and efflux of these metals must be tightly regulated by the cell. Bacteria have evolved a variety of pathways and regulatory systems to monitor the presence and concentration of metals in the cellular environment. A key component of those systems are transcription factors that either "sense metals" or use "metal sensors". The first class of these proteins have metals as their allosteric effector ligand. The second class of these proteins utilize transition metal containing cofactors to sense other environmental cues through the specific chemistry afforded by the cofactor. Chapter 1 reviews the current literature regarding both types of transcription factors. The focus of this work has been on two heme-containing, gas-sensing transcription factors found in bacteria, RcoM (regulator of CO metabolism) and DNR (dissimilative nitrate respiration regulator). RcoM is a CO-dependent protein found in Burkholderia xenovorans and sits upstream of the cox operon for oxidative CO metabolism. RcoM senses the presence of CO, as well as changes in redox potential, through a ligand switch process at its heme cofactor. Chapter 2 details spectroscopic characterization of several methionine mutants to identify the Fe(II) ligand trans to His 74. That study concludes that Met104 acts as the CO-replacable ligand. Met105, while not the ligand, does play an important role in reversibility of the ligand switch process. RcoM has a unique tertiary structure that combines a sensory domain and a DNA-binding domain normally found in two-component systems. Chapter 3 provides evidence that RcoM adopts a dimeric state. Further biophysical and structural characterization gives further insight into how the two domains are organized and the implications for the DNA-binding mechanism. DNR is a NO-sensing transcription factor from Pseudomonas aeruginosa and

  20. Dependency Structures for Statistical Machine Translation

    Science.gov (United States)

    Bach, Nguyen

    2012-01-01

    Dependency structures represent a sentence as a set of dependency relations. Normally the dependency structures from a tree connect all the words in a sentence. One of the most defining characters of dependency structures is the ability to bring long distance dependency between words to local dependency structures. Another the main attraction of…

  1. Measurements of the $Q^{2}$-Dependence of the Proton and Neutron Spin Structure Functions g1p and g1n

    CERN Document Server

    Anthony, P L; Averett, T; Band, H R; Berisso, M C; Borel, H; Bosted, P E; Bültmann, S; Buénerd, M; Chupp, T E; Churchwell, S; Court, G R; Crabb, D; Day, D; Decowski, P; De Pietro, P; Erbacher, R D; Erickson, R; Feltham, A; Fonvieille, H; Frlez, E; Gearhart, R A; Ghazikhanian, V; Gómez, J; Griffioen, K A; Harris, C; Houlden, M A; Hughes, E W; Hyde-Wright, C E; Igo, G; Incerti, S; Jensen, J; Johnson, J R; King, P M; Kolomensky, Yu G; Kuhn, S E; Lindgren, R; Lombard-Nelsen, R M; Marroncle, J; McCarthy, J; McKee, P M; Meyer, Werner T; Mitchell, G S; Mitchell, J; Olson, M N; Penttilä, S; Peterson, G A; Petratos, G G; Pitthan, R; Pocanic, D; Prepost, R; Prescott, C; Qin, L M; Raue, B A; Reyna, D; Rochester, L S; Rock, S E; Rondon-Aramayo, O A; Sabatié, F; Sick, I; Smith, T; Sorrell, L; Staley, F; Saint-Lorant, S; Stuart, L M; Szalata, Z M; Terrien, Y; Tobias, A; Todor, L; Toole, T; Trentalange, S; Walz, D; Welsh, R C; Wesselmann, F R; Wright, T R; Young, C C; Zeier, M; Zhu, H; Zihlmann, B

    2000-01-01

    The structure functions g1p and g1n have been measured over the range 0.014 < x < 0.9 and 1 < Q2 < 40 GeV2 using deep-inelastic scattering of 48 GeV longitudinally polarized electrons from polarized protons and deuterons. We find that the Q2 dependence of g1p (g1n) at fixed x is very similar to that of the spin-averaged structure function F1p (F1n). From a NLO QCD fit to all available data we find $\\Gamma_1^p - \\Gamma_1^n =0.176 \\pm 0.003 \\pm 0.007$ at Q2=5 GeV2, in agreement with the Bjorken sum rule prediction of 0.182 \\pm 0.005.

  2. Spin asymmetry $A^d_1$ and the spin-dependent structure function $g^d_1$ of the deuteron at low values of $x$ and $Q^2$

    CERN Document Server

    Ageev, E S; Alexandrov, Y; Alexeev, G D; Amoroso, A; Badelek, B; Balestra, F; Ball, J; Baum, G; Bedfer, Y; Berglund, P; Bernet, C; Bertini, R; Birsa, R; Bisplinghoff, J; Bordalo, P; Bradamante, Franco; Bravar, A; Bressan, A; Burtin, E; Bussa, M P; Bytchkov, V N; Cerini, L; Chapiro, A; Cicuttin, A; Colantoni, M L; Colavita, A A; Costa, S; Crespo, M L; D'Hose, N; Dalla Torre, S; Das-Gupta, S S; De Masi, R; Dedek, N; Denisov, O Yu; Dhara, L; Diáz-Kavka, V; Dinkelbach, A M; Dolgopolov, A V; Donskov, S V; Dorofeev, V A; Doshita, N; Duic, V; Dünnweber, W; Ehlers, J; Eversheim, P D; Eyrich, W; Fabro, M; Faessler, M; Falaleev, V; Fauland, P; Ferrero, A; Ferrero, L; Finger, M; Fischer, H; Franz, J; Friedrich, J M; Frolov, V; Fuchs, U; Garfagnini, R; Gautheron, F; Gavrichtchouk, O P; Gerassimov, S G; Geyer, R; Giorgi, M; Gobbo, B; Görtz, S; Gorin, A M; Grajek, O A; Grasso, A; Grube, B; Grünemaier, A; Hannappel, J; Von Harrach, D; Hasegawa, T; Hedicke, S; Heinsius, F H; Hermann, R; Hess, C; Hinterberger, F; Von Hodenberg, M; Horikawa, N; Horikawa, S; Ijaduola, R B; Ilgner, C; Ioukaev, A I; Ishimoto, S; Ivanov, O; Iwata, T; Jahn, R; Janata, A; Joosten, R; Jouravlev, N I; Kabu, E; Kalinnikov, V; Kang, D; Karstens, F; Kastaun, W; Ketzer, B; Khaustov, G V; Khokhlov, Yu A; Khomutov, N V; Kisselev, Yu V; Klein, F; Koblitz, S; Koivuniemi, J H; Kolosov, V N; Komissarov, E V; Kondo, K; Königsmann, K C; Konoplyannikov, A K; Konorov, I; Konstantinov, V F; Korentchenko, A S; Korzenev, A; Kotzinian, A M; Koutchinski, N A; Kowalik, K L; Kravchuk, N P; Krivokhizhin, V G; Krumshtein, Z; Kühn, R; Kunne, Fabienne; Kurek, K; Ladygin, M E; Lamanna, M; Le Goff, J M; Leberig, M; Lichtenstadt, J; Liska, T; Ludwig, I; Maggiora, A; Maggiora, M; Magnon, A; Mallot, G K; Manuilov, I V; Marchand, C; Marroncle, J; Martin, A; Marzec, J; Matsuda, T; Maximov, A N; Medved, K S; Meyer, W; Mielech, A; Mikhailov, Yu V; Moinester, M A; Nahle, O; Nassalski, J P; Neliba, S; Neyret, D P; Nikolaenko, V I; Nozdrin, A A; Obraztsov, V F; Olshevskii, A G; Ostrick, M; Padee, A; Pagano, P; Panebianco, S; Panzieri, D; Paul, S; Pereira, H D; Peshekhonov, V D; Piragino, G; Platchkov, S; Platzer, K; Pochodzalla, J; Polyakov, V A; Popov, A A; Pretz, J; Quintans, C; Ramos, S; Rebourgeard, P C; Reicherz, G; Reymann, J; Rith, K; Rozhdestvensky, A M; Rondio, E; Sadovski, A B; Saller, E; Samoylenko, V D; Sandacz, A; Sans, M; Sapozhnikov, M G; Savin, I A; Schiavon, Paolo; Schill, C; Schmidt, T; Schmitt, H; Schmitt, L; Shevchenko, O Yu; Shishkin, A A; Siebert, H W; Sinha, L; Sissakian, A N; Skachkova, A N; Slunecka, M; Smirnov, G I; Sozzi, F; Sugonyaev, V P; Srnka, A; Stinzing, F; Stolarski, M; Sulc, M; Sulej, R; Takabayashi, N; Tchalishev, V V; Tessarotto, F; Teufel, A; Thers, D; Tkatchev, L G; Toeda, T; Tretyak, V I; Trousov, S; Varanda, M; Virius, M; Vlassov, N V; Wagner, M; Webb, R; Weise, E; Weitzel, Q; Wiedner, U; Wiesmann, M; Windmolders, R; Wirth, S; Wilicki, W; Zanetti, A M; Zaremba, K; Zhao, J; Ziegler, R; Zvyagin, A

    2007-01-01

    We present a precise measurement of the deuteron longitudinal spin asymmetry $A_1^d$ and of the deuteron spin-dependent structure function $g_1^d$ at $Q^2 < $ 1~(GeV/$c$)$^2$ and $4\\cdot$10$^{-5} < x < $~2.5$\\cdot$10$^{-2}$ based on the data collected by the COMPASS experiment at CERN during the years 2002 and 2003. The statistical precision is tenfold better than that of the previous measurement in this region. The measured $A_1^d$ and $g_1^d$ are found to be consistent with zero in the whole range of $x$.

  3. Size dependent structural, electronic, and magnetic properties of Sc(N) (N=2-14) clusters investigated by density functional theory.

    Science.gov (United States)

    Bhunia, Snehasis; Vyas, Nidhi; Sahu, Chandan; Ojha, Animesh K

    2014-11-01

    Structural, electronic, and magnetic properties of ScN (N=2-14) clusters have been investigated using density functional theory (DFT) calculations. Different spin states isomer for each cluster size has been optimized with symmetry relaxation. The structural stability, dissociation energy, binding energy, spin stability, vertical ionization energy, electron affinity, chemical hardness, and size dependent magnetic moment per atom are calculated for the energetically most stable spin isomer for each size. The structural stability for a specific size cluster has been explained in terms of atomic shell closing effect, close packed symmetric structure, and chemical bonding. Spin stability of each cluster size is determined by calculating the value of spin gaps. The maximum value for second-order energy difference is observed for the clusters of size N = 2, 6, 11, and 13, which implies that these clusters are relatively more stable. The magnetic moment per atom corresponding to lowest energy structure has also been calculated. The magnetic moment per atom corresponding to lowest energy structures has been calculated. The calculated values of magnetic moment per atom vary in an oscillatory fashion with cluster size. The calculated results are compared with the available experimental data.

  4. Identification and structural-functional analysis of cyclin-dependent kinases of the cattle tick Rhipicephalus (Boophilus microplus.

    Directory of Open Access Journals (Sweden)

    Helga Gomes

    Full Text Available Cyclin-dependent kinases (CDKs are a family of serine/threonine kinases essential for cell cycle progression. Herein, we describe the participation of CDKs in the physiology of Rhipicephalus microplus, the southern cattle tick and an important disease vector. Firstly, amino acid sequences homologous with CDKs of other organisms were identified from a R. microplus transcriptome database in silico. The analysis of the deduced amino acid sequences of CDK1 and CDK10 from R. microplus showed that both have caspase-3/7 cleavage motifs despite their differences in motif position and length of encoded proteins. CDK1 has two motifs (DKRGD and SAKDA located opposite to the ATP binding site while CDK10 has only one motif (SLLDN for caspase 3-7 near the ATP binding site. Roscovitine (Rosco, a purine derivative that inhibits CDK/cyclin complexes by binding to the catalytic domain of the CDK molecule at the ATP binding site, which prevents the transfer of ATP's γphosphoryl group to the substrate. To determine the effect of Rosco on tick CDKs, BME26 cells derived from R. microplus embryo cells were utilized in vitro inhibition assays. Cell viability decreased in the Rosco-treated groups after 24 hours of incubation in a concentration-dependent manner and this was observed up to 48 hours following incubation. To our knowledge, this is the first report on characterization of a cell cycle protein in arachnids, and the sensitivity of BME26 tick cell line to Rosco treatment suggests that CDKs are potential targets for novel drug design to control tick infestation.

  5. Identification and Structural-Functional Analysis of Cyclin-Dependent Kinases of the Cattle Tick Rhipicephalus (Boophilus) microplus

    Science.gov (United States)

    Gomes, Helga; Romeiro, Nelilma C.; Braz, Gloria R. C.; de Oliveira, Eduardo Alves Gamosa; Rodrigues, Camilla; da Fonseca, Rodrigo Nunes; Githaka, Naftaly; Isezaki, Masayoshi; Konnai, Satoru; Ohashi, Kazuhiko; da Silva Vaz, Itabajara; Logullo, Carlos; Moraes, Jorge

    2013-01-01

    Cyclin-dependent kinases (CDKs) are a family of serine/threonine kinases essential for cell cycle progression. Herein, we describe the participation of CDKs in the physiology of Rhipicephalus microplus, the southern cattle tick and an important disease vector. Firstly, amino acid sequences homologous with CDKs of other organisms were identified from a R. microplus transcriptome database in silico. The analysis of the deduced amino acid sequences of CDK1 and CDK10 from R. microplus showed that both have caspase-3/7 cleavage motifs despite their differences in motif position and length of encoded proteins. CDK1 has two motifs (DKRGD and SAKDA) located opposite to the ATP binding site while CDK10 has only one motif (SLLDN) for caspase 3–7 near the ATP binding site. Roscovitine (Rosco), a purine derivative that inhibits CDK/cyclin complexes by binding to the catalytic domain of the CDK molecule at the ATP binding site, which prevents the transfer of ATP's γphosphoryl group to the substrate. To determine the effect of Rosco on tick CDKs, BME26 cells derived from R. microplus embryo cells were utilized in vitro inhibition assays. Cell viability decreased in the Rosco-treated groups after 24 hours of incubation in a concentration-dependent manner and this was observed up to 48 hours following incubation. To our knowledge, this is the first report on characterization of a cell cycle protein in arachnids, and the sensitivity of BME26 tick cell line to Rosco treatment suggests that CDKs are potential targets for novel drug design to control tick infestation. PMID:24146826

  6. The spin-dependent structure function $g_1(x)$ of the proton from polarized deep-inelastic muon scattering

    CERN Document Server

    Adeva, B; Arvidson, A; Badelek, B; Bardin, G; Baum, G; Berglund, P; Betev, L; Birsa, R; De Botton, N R; Bradamante, Franco; Bravar, A; Bressan, A; Bültmann, S; Burtin, E; Crabb, D; Cranshaw, J; Çuhadar-Dönszelmann, T; Dalla Torre, S; Van Dantzig, R; Derro, B R; Deshpande, A A; Dhawan, S K; Dulya, C M; Eichblatt, S; Fasching, D; Feinstein, F; Fernández, C; Forthmann, S; Frois, Bernard; Gallas, A; Garzón, J A; Gilly, H; Giorgi, M A; Görtz, S; Gracia, G; De Groot, N; Haft, K; Von Harrach, D; Hasegawa, T; Hautle, P; Hayashi, N; Heusch, C A; Horikawa, N; Hughes, V W; Igo, G; Ishimoto, S; Iwata, T; Kabuss, E M; Kageya, T; Karev, A G; Ketel, T; Kiryluk, J; Kiselev, Yu F; Krivokhizhin, V G; Kröger, W; Kukhtin, V V; Kurek, K; Kyynäräinen, J; Lamanna, M; Landgraf, U; Le Goff, J M; Lehár, F; de Lesquen, A; Lichtenstadt, J; Litmaath, M; Magnon, A; Mallot, G K; Marie, F; Martin, A; Martino, J; Matsuda, T; Mayes, B W; McCarthy, J S; Medved, K S; Meyer, W T; Van Middelkoop, G; Miller, D; Miyachi, Y; Mori, K; Moromisato, J H; Nassalski, J P; Naumann, Lutz; Niinikoski, T O; Oberski, J; Ogawa, A; Grosse-Perdekamp, M; Pereira, H; Perrot-Kunne, F; Peshekhonov, V D; Pinsky, L; Platchkov, S K; Pló, M; Pose, D; Postma, H; Pretz, J; Puntaferro, R; Rädel, G; Rijllart, A; Reicherz, G; Rodríguez, M; Rondio, Ewa; Roscherr, B; Sabo, I; Saborido, J; Sandacz, A; Savin, I A; Schiavon, R P; Schiller, A; Sichtermann, E P; Simeoni, F; Smirnov, G I; Staude, A; Steinmetz, A; Stiegler, U; Stuhrmann, H B; Szleper, M; Tessarotto, F; Thers, D; Tlaczala, W; Tripet, A; Ünel, G; Velasco, M; Vogt, J; Voss, Rüdiger; Whitten, C; Windmolders, R; Wislicki, W; Witzmann, A; Ylöstalo, J; Zanetti, A M; Zaremba, K

    1997-01-01

    We present a new measurement of the virtual photon proton asymmetry $A_1^{\\rm p}$ from deep inelastic scattering of polarized muons on polarized protons in the kinematic range $0.0008 1$ GeV$^{2}$. A perturbative QCD evolution in next-to-leading order is used to determine $g_1^{\\rm p}(x)$ at a constant $Q^2$. At $Q^{2} = 10$ GeV$^{2}$ we find, in the measured range, $\\int_{0.003}^{0.7} g_{1}^{\\rm p}(x){\\rm d}x = 0.139 \\pm 0.006~({\\rm stat})\\pm 0.008~({\\rm syst)} \\pm 0.006~({\\rm evol})$. The value of the first moment $\\Gamma_{1}^{\\rm p} = \\int_{0}^{1} g_{1}^{\\rm p}(x){\\rm d}x$ of $g_{1}^{\\rm p}$ depends on the approach used to describe the behaviour of $g_{1}^{\\rm p}$ at low $x$. We find that the Ellis-Jaffe sum rule is violated. With our published result for $\\Gamma_{1}^{\\rm d}$ we confirm the Bjorken sum rule with an accuracy of $\\approx 15\\%$ at the one standard deviation level.

  7. Purely Functional Structured Programming

    OpenAIRE

    Obua, Steven

    2010-01-01

    The idea of functional programming has played a big role in shaping today's landscape of mainstream programming languages. Another concept that dominates the current programming style is Dijkstra's structured programming. Both concepts have been successfully married, for example in the programming language Scala. This paper proposes how the same can be achieved for structured programming and PURELY functional programming via the notion of LINEAR SCOPE. One advantage of this proposal is that m...

  8. Structure function monitor

    Energy Technology Data Exchange (ETDEWEB)

    McGraw, John T [Placitas, NM; Zimmer, Peter C [Albuquerque, NM; Ackermann, Mark R [Albuquerque, NM

    2012-01-24

    Methods and apparatus for a structure function monitor provide for generation of parameters characterizing a refractive medium. In an embodiment, a structure function monitor acquires images of a pupil plane and an image plane and, from these images, retrieves the phase over an aperture, unwraps the retrieved phase, and analyzes the unwrapped retrieved phase. In an embodiment, analysis yields atmospheric parameters measured at spatial scales from zero to the diameter of a telescope used to collect light from a source.

  9. Structures and properties of electronically excited chromophores in solution from the polarizable continuum model coupled to the time-dependent density functional theory.

    Science.gov (United States)

    Mennucci, Benedetta; Cappelli, Chiara; Guido, Ciro Achille; Cammi, Roberto; Tomasi, Jacopo

    2009-04-02

    This paper provides an overview of recent research activities concerning the quantum-mechanical description of structures and properties of electronically excited chromophores in solution. The focus of the paper is on a specific approach to include solvent effects, namely the polarizable continuum model (PCM). Such a method represents an efficient strategy if coupled to proper quantum-mechanical descriptions such as the time-dependent density functional theory (TDDFT). As a result, the description of molecules in the condensed phase can be extended to excited states still maintaining the computational efficiency and the physical reliability of the ground-state calculations. The most important theoretical and computational aspects of the coupling between PCM and TDDFT are presented and discussed together with an example of application to the study of the low-lying electronic excited states of push-pull chromophores in different solvents.

  10. Chromatin Structure and Function

    CERN Document Server

    Wolffe, Alan P

    1999-01-01

    The Third Edition of Chromatin: Structure and Function brings the reader up-to-date with the remarkable progress in chromatin research over the past three years. It has been extensively rewritten to cover new material on chromatin remodeling, histone modification, nuclear compartmentalization, DNA methylation, and transcriptional co-activators and co-repressors. The book is written in a clear and concise fashion, with 60 new illustrations. Chromatin: Structure and Function provides the reader with a concise and coherent account of the nature, structure, and assembly of chromatin and its active

  11. Time-dependent density functional theory study on the electronic excited-state geometric structure, infrared spectra, and hydrogen bonding of a doubly hydrogen-bonded complex.

    Science.gov (United States)

    Liu, Yufang; Ding, Junxia; Liu, Ruiqiong; Shi, Deheng; Sun, Jinfeng

    2009-12-01

    The geometric structures and infrared (IR) spectra in the electronically excited state of a novel doubly hydrogen-bonded complex formed by fluorenone and alcohols, which has been observed by IR spectra in experimental study, are investigated by the time-dependent density functional theory (TDDFT) method. The geometric structures and IR spectra in both ground state and the S(1) state of this doubly hydrogen-bonded FN-2MeOH complex are calculated using the DFT and TDDFT methods, respectively. Two intermolecular hydrogen bonds are formed between FN and methanol molecules in the doubly hydrogen-bonded FN-2MeOH complex. Moreover, the formation of the second intermolecular hydrogen bond can make the first intermolecular hydrogen bond become slightly weak. Furthermore, it is confirmed that the spectral shoulder at around 1700 cm(-1) observed in the IR spectra should be assigned as the doubly hydrogen-bonded FN-2MeOH complex from our calculated results. The electronic excited-state hydrogen bonding dynamics is also studied by monitoring some vibraitonal modes related to the formation of hydrogen bonds in different electronic states. As a result, both the two intermolecular hydrogen bonds are significantly strengthened in the S(1) state of the doubly hydrogen-bonded FN-2MeOH complex. The hydrogen bond strengthening in the electronically excited state is similar to the previous study on the singly hydrogen-bonded FN-MeOH complex and play important role on the photophysics of fluorenone in solutions.

  12. Fuzzy Functional Dependencies and Bayesian Networks

    Institute of Scientific and Technical Information of China (English)

    LIU WeiYi(刘惟一); SONG Ning(宋宁)

    2003-01-01

    Bayesian networks have become a popular technique for representing and reasoning with probabilistic information. The fuzzy functional dependency is an important kind of data dependencies in relational databases with fuzzy values. The purpose of this paper is to set up a connection between these data dependencies and Bayesian networks. The connection is done through a set of methods that enable people to obtain the most information of independent conditions from fuzzy functional dependencies.

  13. Hartree potential dependent exchange functional

    CERN Document Server

    Constantin, L A; Della Sala, F

    2016-01-01

    We introduce a novel non-local ingredient for the construction of exchange density functionals: the reduced Hartree parameter, which is invariant under the uniform scaling of the density and represents the exact exchange enhancement factor for one- and two-electron systems. The reduced Hartree parameter is used together with the conventional meta-generalized gradient approximation (meta-GGA) semilocal ingredients (i.e. the electron density, its gradient and the kinetic energy density) to construct a new generation exchange functional, termed u-meta-GGA. This u-meta-GGA functional is exact for {the exchange of} any one- and two-electron systems, is size-consistent and non-empirical, satisfies the uniform density scaling relation, and recovers the modified gradient expansion derived from the semiclassical atom theory. For atoms, ions, jellium spheres, and molecules, it shows a good accuracy, being often better than meta-GGA exchange functionals. Our construction validates the use of the reduced Hartree ingredie...

  14. Structural homologues P(II) and P(Z) of Azospirillum brasilense provide intracellular signalling for selective regulation of various nitrogen-dependent functions.

    Science.gov (United States)

    de Zamaroczy, M

    1998-07-01

    P(II) (glnB) is a signal transduction protein that in Azospirillum brasilense is specifically required for nitrogen fixation. Little is known about whether and how its homologue P(Z) (glnZ) participates in the regulation of cellular functions. In this study, we have shown the regulatory action of the two proteins by analysing the relevant single and double null-mutant strains. The transcription of glnZ is monocistronic, and it starts mainly from a sigma54-dependent promoter, activated by NtrC. glnZ expression is dependent on the ntr system, even under conditions of nitrogen excess, and is greatly enhanced in the presence of aspartate. P(Z) is uridylylated in response to nitrogen limitation, like P(II), although different amounts of the two proteins are synthesized. P(II) is required for the dephosphorylation of NtrC. Thus, in the absence of P(II), the repression of nitrate assimilation is not promoted, which, in turn, leads to a high rate of ammonium excretion. Unexpectedly, P(II) and P(Z) proteins are not essential for the reversible modification of glutamine synthetase. (Methyl)ammonium transport into the cell is negatively regulated by P(Z). The growth of a double-mutant strain (glnB::kan; glnZ::omega) is drastically disabled, although wild-type growth is restored by complementation with either glnB or glnZ. We conclude that P(II) and P(Z), despite their structural similarity, are involved in different regulatory processes, except for that required for cell growth.

  15. Avian reovirus L2 genome segment sequences and predicted structure/function of the encoded RNA-dependent RNA polymerase protein

    Directory of Open Access Journals (Sweden)

    Xu Wanhong

    2008-12-01

    Full Text Available Abstract Background The orthoreoviruses are infectious agents that possess a genome comprised of 10 double-stranded RNA segments encased in two concentric protein capsids. Like virtually all RNA viruses, an RNA-dependent RNA polymerase (RdRp enzyme is required for viral propagation. RdRp sequences have been determined for the prototype mammalian orthoreoviruses and for several other closely-related reoviruses, including aquareoviruses, but have not yet been reported for any avian orthoreoviruses. Results We determined the L2 genome segment nucleotide sequences, which encode the RdRp proteins, of two different avian reoviruses, strains ARV138 and ARV176 in order to define conserved and variable regions within reovirus RdRp proteins and to better delineate structure/function of this important enzyme. The ARV138 L2 genome segment was 3829 base pairs long, whereas the ARV176 L2 segment was 3830 nucleotides long. Both segments were predicted to encode λB RdRp proteins 1259 amino acids in length. Alignments of these newly-determined ARV genome segments, and their corresponding proteins, were performed with all currently available homologous mammalian reovirus (MRV and aquareovirus (AqRV genome segment and protein sequences. There was ~55% amino acid identity between ARV λB and MRV λ3 proteins, making the RdRp protein the most highly conserved of currently known orthoreovirus proteins, and there was ~28% identity between ARV λB and homologous MRV and AqRV RdRp proteins. Predictive structure/function mapping of identical and conserved residues within the known MRV λ3 atomic structure indicated most identical amino acids and conservative substitutions were located near and within predicted catalytic domains and lining RdRp channels, whereas non-identical amino acids were generally located on the molecule's surfaces. Conclusion The ARV λB and MRV λ3 proteins showed the highest ARV:MRV identity values (~55% amongst all currently known ARV and MRV

  16. [Protein phosphatases: structure and function].

    Science.gov (United States)

    Bulanova, E G; Budagian, V M

    1994-01-01

    The process of protein and enzyme systems phosphorylation is necessary for cell growth, differentiation and preparation for division and mitosis. The conformation changes of protein as a result of phosphorylation lead to increased enzyme activity and enhanced affinity to substrates. A large group of enzymes--protein kinases--is responsible for phosphorylation process in cell, which are divided into tyrosine- and serine-threonine-kinases depending on their ability to phosphorylate appropriate amino acid residues. In this review has been considered the functional importance and structure of protein phosphatases--enzymes, which are functional antagonists of protein kinases.

  17. Functional and Dysfunctional rumination in alcohol dependence

    OpenAIRE

    Grynberg, Delphine; Briane, Yasmine; Timary, Philippe De; Maurage, Pierre; 16th International Society of Addiction Medicine Annual Meeting

    2014-01-01

    Previous findings have shown that rumination predicts alcohol abuse independently of depression. However, the literature does not inform about the relationships between alcohol dependence and functional and dysfunctional rumination. It has indeed been suggested that there exist a functional form of rumination(concrete thinking) and a dysfunctional form of rumination (abstract thinking). In this study, our aim is to evaluate if alcohol dependence is similarly associated with functional/constru...

  18. DNA: Structure and function

    DEFF Research Database (Denmark)

    Sinden, Richard R.; E. Pearson, Christopher; N. Potaman, Vladimir

    1998-01-01

    for a long period of time before its information is accessed by the cell. Although DNA plays a critical role as an informational storage molecule, it is by no means as unexciting as a computer tape or disk drive. The structure of the DNA described by Watson and Crick in 1953 is a right handed helix of two......This chapter discusses the structure and function of DNA. DNA occupies a critical role in cells, because it is the source of all intrinsic genetic information. Chemically, DNA is a very stable molecule, a characteristic important for a macromolecule that may have to persist in an intact form...... individual antiparallel DNA strands. Hydrogen bonds provide specificity that allows pairing between the complementary bases (A.T and G.C) in opposite strands. Base stacking occurs near the center of the DNA helix and provides a great deal of stability to the helix (in addition to hydrogen bonding). The sugar...

  19. Structural and Functional Plasticity within the Nucleus Accumbens and Prefrontal Cortex Associated with Time-Dependent Increases in Food Cue Seeking Behavior.

    Science.gov (United States)

    Dingess, Paige M; Darling, Rebecca A; Derman, Rifka C; Wulff, Shaun S; Hunter, Melissa L; Ferrario, Carrie R; Brown, Travis E

    2017-03-15

    Urges to consume food can be driven by stimuli in the environment that are associated with previous food experience. Identifying adaptations within brain reward circuits that facilitate cue-induced food seeking is critical for understanding and preventing the overconsumption of food and subsequent weight gain. Utilizing electrophysiological, biochemical, and DiI labeling we examined functional and structural changes in the nucleus accumbens (NAc) and prefrontal cortex (PFC) associated with time-dependent increases in food craving ('incubation of craving'). Rats self-administered 60% high-fat or chow 45 mg pellets and were then tested for incubation of craving either 1 or 30 days after training (1d, 30d). High-fat was chosen for comparison to determine if palatability differentially affected incubation and/or plasticity. Rats showed robust incubation of craving for both food rewards, although responding for cues previously associated with high-fat was greater than chow at both 1d and 30d. In addition, previous experience with high-fat consumption reduced dendritic spine density in the PFC at both time points. In contrast, incubation was associated with an increase in NAc spine density and α-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid receptor (AMPAR)-mediated transmission at 30d in both groups. Finally, incubation of craving for chow and high-fat was accompanied by an increase in calcium-permeable and calcium-impermeable AMPARs, respectively. Our results suggest that incubation of food craving alters brain reward circuitry and macronutrient composition specifically induces cortical changes in a way that may facilitate maladaptive food seeking behaviors.Neuropsychopharmacology accepted article preview online, 15 March 2017. doi:10.1038/npp.2017.57.

  20. Structure Function Estimated From Histological Tissue Sections.

    Science.gov (United States)

    Han, Aiguo; O'Brien, William D

    2016-09-01

    Ultrasonic scattering is determined by not only the properties of individual scatterers but also the correlation among scatterer positions. The role of scatterer spatial correlation is significant for dense medium, but has not been fully understood. The effect of scatterer spatial correlation may be modeled by the structure function as a frequency-dependent factor in the backscatter coefficient (BSC) expression. The structure function has been previously estimated from the BSC data. The aim of this study is to estimate the structure function from histology to test if the acoustically estimated structure function is indeed caused by the scatterer spatial distribution. Hematoxylin and eosin stained histological sections from dense cell pellet biophantoms were digitized. The scatterer positions were determined manually from the histological images. The structure function was calculated from the extracted scatterer positions. The structure function obtained from histology showed reasonable agreement in the shape but not in the amplitude, compared with the structure function previously estimated from the backscattered data. Fitting a polydisperse structure function model to the histologically estimated structure function yielded relatively accurate cell radius estimates ([Formula: see text]). Furthermore, two types of mouse tumors that have similar cell size and shape but distinct cell spatial distributions were studied, where the backscattered data were shown to be related to the cell spatial distribution through the structure function estimated from histology. In conclusion, the agreement between acoustically estimated and histologically estimated structure functions suggests that the acoustically estimated structure function is related to the scatterer spatial distribution.

  1. Structural dependence of the efficiency of functionalization of silica-coated FeOx magnetic nanoparticles studied by ATR-IR

    Science.gov (United States)

    Vargas, Angelo; Shnitko, Ivan; Teleki, Alexandra; Weyeneth, Stephen; Pratsinis, Sotiris E.; Baiker, Alfons

    2011-01-01

    The efficiency of propylamino functionalization of magnetic silica-coated FeOx nanoparticles prepared by different methods, including coprecipitation and flame aerosol synthesis, has been evaluated by attenuated total reflection infrared spectroscopy (ATR-IR) combined with a specific surface reaction, thus revealing the availability of the grafted functional groups. Large differences in the population of reactive groups were observed for the investigated materials, underlining the tight relation between the structure of nanoparticles and their suitability for organic functionalization. The materials possessed different core structure, surface area, and porosity, as evidenced by transmission electron microscopy and nitrogen adsorption-desorption isotherms. Grafting of aminopropyl groups using a standard procedure based on reaction with (3-aminopropyl)trimethoxysilane as source of the propylamino groups was performed, followed by classical dry analysis methods to determine the specific concentration of the organic functional groups (in mmol g-1 of material). ATR-IR spectroscopy in a specially constructed reactor cell was applied as wet methodology to determine the chemically available amount of such functional groups, showing that the materials possess largely different loading capacity, with a variability of up to 70% in the chemical availability of the organic functional group. The amount of (3-aminopropyl)trimethoxysilane used for functionalization was optimized, thus reaching a saturation limit characteristic of the material.

  2. Discovery of functional and approximate functional dependencies in relational databases

    Directory of Open Access Journals (Sweden)

    Ronald S. King

    2003-01-01

    Full Text Available This study develops the foundation for a simple, yet efficient method for uncovering functional and approximate functional dependencies in relational databases. The technique is based upon the mathematical theory of partitions defined over a relation's row identifiers. Using a levelwise algorithm the minimal non-trivial functional dependencies can be found using computations conducted on integers. Therefore, the required operations on partitions are both simple and fast. Additionally, the row identifiers provide the added advantage of nominally identifying the exceptions to approximate functional dependencies, which can be used effectively in practical data mining applications.

  3. Structural completeness in propositional logics of dependence

    NARCIS (Netherlands)

    Iemhoff, Rosalie; Yang, Fan

    2016-01-01

    In this paper we prove that three of the main propositional logics of dependence (including propositional dependence logic and inquisitive logic), none of which is structural, are structurally complete with respect to a class of substitutions under which the logics are closed. We obtain an analogous

  4. Functional structure of stomodeum

    Directory of Open Access Journals (Sweden)

    Chependyuk Т.А.

    2014-06-01

    Full Text Available Purpose: identification of the structure providing outflow of liquid from stomodeum in the process of formation. Material and Methods. 150 stomodea have been investigated for the ways of removal of liquid by the following methods: stage-by-stage freezing, contrasting and macerations. Result. One of the ways of removal of liquid from enamel of a being formed tooth is the crypt canal. Conclusion. Function of the channel of a crypt of developing teeth consists of removal of biological specific dental fluid from a surface of enamel of stomodeum in a mouth in the following options: on an oral surface of alveolar processes, near a periodontal fissure, or directly in a periodontium of a milk tooth — predecessor.

  5. Synthesis, structure, and spectroscopic properties of chiral oxorhenium(V) complexes incorporating polydentate ligands derived from L-amino acids: a density functional theory/time-dependent density functional theory investigation.

    Science.gov (United States)

    Basak, Sucharita; Rajak, Kajal Krishna

    2008-10-06

    The oxorhenium(V) complexes [Re (V)O(L A)Cl 2] bearing the (N-2-pyridylmethyl) of l-valine (HL A (1)), l-leucine (HL A (2)), and l-phenylalanine (HL A (3)) and [Re (V)O(L B)Cl] containing the {(N-2pyridylmethyl)-(N-(5-nitro-2-hydroxybenzyl)} of l-valine (H 2L B (1)), l-leucine (H 2L B (2)), and l-phenylalanine (H 2L B (3)) are presented in this article. The complexes are isolated in enantiomeric pure form examined from X-ray structure determination. The complexes are characterized by spectroscopic and electrochemical methods. The molecular structures observed in the solid state are grossly preserved in solution ( (1)H, (13)C, and circular dichroism spectra). Gas-phase geometry optimization and the electronic structures of [Re (V)O(L A (1))Cl 2], [Re (V)O(L A (2))Cl 2], and [Re (V)O(L B (2))Cl] have been investigated with the framework of density functional theory. The absorption and circular dichroism spectra of the complexes were also calculated applying time-dependent density functional theory (TDDFT) using the conductor-like polarizable continuum solvent model to understand the origin of the electronic excitations. The chemical shift ( (1)H and (13)C) as well as (1)H- (1)H spin-spin coupling constant were also computed by the gauge-independent atomic orbital method, and the computed values are consistent with the experimental data.

  6. Hybrid density functional based study on the band structure of trioctahedral mica and its dependence on the variation of Fe(2+) content.

    Science.gov (United States)

    Timón, V; Praveen, C S; Escamilla-Roa, E; Valant, M

    2013-07-01

    A hybrid density functional based study of a phyllosilicate (PS) is presented here for the first time. Using all-electron electronic structure calculations with the B3LYP hybrid functional, we have investigated the electronic and structural properties of a series of trioctahedral 1M-polytype K-bearing micas starting from phlogopite (the Mg-end member), ending with the annite (the Fe-end member), and passing through the biotite (a solid solution of the end members). Electronic band gap is calculated for all the compositions and nature of the electronic transition is discussed with the aid of band structure and density of states plots. An excellent agreement with the available experimental data has been observed. An insulator to semiconductor transition is explained on the basis of orbital hybridization. A further comparison is made using the pure GGA functional. For the completeness of the study, the dielectric properties of phlogopite are calculated using the coupled perturbed Kohn-Sham scheme, as implemented within the CRYSTAL09 code.

  7. Multi-functional composite structures

    Energy Technology Data Exchange (ETDEWEB)

    Mulligan, Anthony C.; Halloran, John; Popovich, Dragan; Rigali, Mark J.; Sutaria, Manish P.; Vaidyanathan, K. Ranji; Fulcher, Michael L.; Knittel, Kenneth L.

    2010-04-27

    Fibrous monolith processing techniques to fabricate multifunctional structures capable of performing more than one discrete function such as structures capable of bearing structural loads and mechanical stresses in service and also capable of performing at least one additional non-structural function.

  8. Multi-functional composite structures

    Energy Technology Data Exchange (ETDEWEB)

    Mulligan, Anthony C.; Halloran, John; Popovich, Dragan; Rigali, Mark J.; Sutaria, Manish P.; Vaidyanathan, K. Ranji; Fulcher, Michael L.; Knittel, Kenneth L.

    2004-10-19

    Fibrous monolith processing techniques to fabricate multifunctional structures capable of performing more than one discrete function such as structures capable of bearing structural loads and mechanical stresses in service and also capable of performing at least one additional non-structural function.

  9. The Crystal Structure of the RNA-Dependent RNA Polymerase from Human Rhinovirus: A Dual Function Target for Common Cold Antiviral Therapy

    Energy Technology Data Exchange (ETDEWEB)

    Love, Robert A.; Maegley, Karen A.; Yu, Xiu; Ferre, RoseAnn; Lingardo, Laura K.; Diehl, Wade; Parge, Hans E.; Dragovich, Peter S.; Fuhrman, Shella A. (Pfizer)

    2010-11-16

    Human rhinoviruses (HRV), the predominant members of the Picornaviridae family of positive-strand RNA viruses, are the major causative agents of the common cold. Given the lack of effective treatments for rhinoviral infections, virally encoded proteins have become attractive therapeutic targets. The HRV genome encodes an RNA-dependent RNA polymerase (RdRp) denoted 3D{sup pol}, which is responsible for replicating the viral genome and for synthesizing a protein primer used in the replication. Here the crystal structures for three viral serotypes (1B, 14, and 16) of HRV 3D{sup pol} have been determined. The three structures are very similar to one another, and to the closely related poliovirus (PV) 3D{sup pol} enzyme. Because the reported PV crystal structure shows significant disorder, HRV 3D{sup pol} provides the first complete view of a picornaviral RdRp. The folding topology of HRV 3D{sup pol} also resembles that of RdRps from hepatitis C virus (HCV) and rabbit hemorrhagic disease virus (RHDV) despite very low sequence homology.

  10. The crystal structure of the RNA-dependent RNA polymerase from human rhinovirus: a dual function target for common cold antiviral therapy.

    Science.gov (United States)

    Love, Robert A; Maegley, Karen A; Yu, Xiu; Ferre, Rose Ann; Lingardo, Laura K; Diehl, Wade; Parge, Hans E; Dragovich, Peter S; Fuhrman, Shella A

    2004-08-01

    Human rhinoviruses (HRV), the predominant members of the Picornaviridae family of positive-strand RNA viruses, are the major causative agents of the common cold. Given the lack of effective treatments for rhinoviral infections, virally encoded proteins have become attractive therapeutic targets. The HRV genome encodes an RNA-dependent RNA polymerase (RdRp) denoted 3Dpol, which is responsible for replicating the viral genome and for synthesizing a protein primer used in the replication. Here the crystal structures for three viral serotypes (1B, 14, and 16) of HRV 3Dpol have been determined. The three structures are very similar to one another, and to the closely related poliovirus (PV) 3Dpol enzyme. Because the reported PV crystal structure shows significant disorder, HRV 3Dpol provides the first complete view of a picornaviral RdRp. The folding topology of HRV 3Dpol also resembles that of RdRps from hepatitis C virus (HCV) and rabbit hemorrhagic disease virus (RHDV) despite very low sequence homology.

  11. Longitudial observation of dynamic changes in cortical function and white matter fibrous structure of patients with visual pathway lesions by blood oxygenation level dependent-functional magnetic resonance imaging combined with diffusion tensor imaging

    Institute of Scientific and Technical Information of China (English)

    2007-01-01

    BACKGROUND: Functional magnetic resonance imaging (fMRI) is initially used for visual cortex location.However, the application of fMRI in investigating the development of visual pathway lesions needs to be further observed.OBJECTIVE: This study is to longitudially observe the dynamic changes in cortical function and white matter fibrous structure of patients with visual pathway lesions by blood oxygenation level dependent-functional magnetic resonance imaging (BOLD-fMRI) combined with diffusion tensor imaging (DTI), and to analyze the characteristics of brain function and structural recombination at convalescent period of lesions.DESIGN: Randomized controlled observation.SETTING: Department of Radiology, the General Hospital of Nanjing Military Area Command of Chinese PLA.PARTICIPANTS: Eight patients with unilateral or bilateral visual disorder caused by visual pathway lesions,who admitted to Department of Radiology, the General Hospital of Nanjing Military Area Command of Chinese PLA from January to September 2006 were involved, and served as experimental subjects. The patients, 6 males and 2 females, were aged 16 - 67 years. They had visual disorder confirmed by clinical examination, i.e. visual pathway lesion, which was further diagnosed by MR or CT. Another 12 subjects generally matching to those patients of experimental group in gender, age and sight, who received health examination in synchronization were involved and served as controls. The subjects had no history of eye diseases. Their binocular visual acuity (or corrected visual acuity) was over 1.0. Both routine examination of ophthalmology and examination of fundus were normal. Informed consents of detected items were obtained from all the subjects.METHODS: Signa Excite HD 1.5T magnetic resonance imaging system with 16 passages (GE Company,USA) and coil with 8 passages were used; brain functional stimulus apparatus (SAV-8800. Meide Company) was used for showing experimental mission. At the early stage

  12. The structure and UV spectroscopy of benzene-water (Bz-W6) clusters using time-dependent density functional theory.

    Science.gov (United States)

    Sharma, Divya; Paterson, Martin J

    2014-11-01

    DFT and MP2 calculations are performed to obtain optimized ground state geometries and binding energies of the cage and the prism conformers of water W6 clusters and Bz-W6 clusters using the aug-cc-pVDZ basis set. The cage conformer of Bz-W6 system is found to be more stable than prism conformer for all range of DFT functionals and MP2. Time dependent-DFT is then used to study UV spectroscopy of Bz, water W6 clusters and Bz-W6 clusters at both the MP2 and wB97XD optimized ground state geometries using the B3LYP, CAM-B3LYP and M06-2X functionals with 6-31++G(d,p) and aug-cc-pVTZ basis sets. Our results predict minor differences in the UV spectroscopy of cage and prism conformers W6 and Bz-W6 clusters that may be observable with high-resolution spectroscopy. The M06-2X and CAM-B3LYP functionals perform consistently with each other. Benzene-mediated excitations of the water W6 cluster towards longer wavelengths above 170 nm are noticed in both the cage and prism geometries of Bz-W6. Benzene is found to be influenced after interacting with the cage and prism W6 geometries, and is seen to undergo a red shift in the main π→π* electronic transition, in which the degeneracy is slightly broken. Charge transfer (CT) states and diffuse Rydberg-type states are also found to play an important role in the spectroscopy of such systems.

  13. Beneficial Effects of Tianeptine on Hippocampus-Dependent Long-Term Memory and Stress-Induced Alterations of Brain Structure and Function

    Directory of Open Access Journals (Sweden)

    Carmen Muñoz

    2010-10-01

    Full Text Available Tianeptine is a well-described antidepressant which has been shown to prevent stress from producing deleterious effects on brain structure and function. Preclinical studies have shown that tianeptine blocks stress-induced alterations of neuronal morphology and synaptic plasticity. Moreover, tianeptine prevents stress from impairing learning and memory, and, importantly, demonstrates memory-enhancing properties in the absence of stress. Recent research has indicated that tianeptine works by normalizing glutamatergic neurotransmission, a mechanism of action that may underlie its effectiveness as an antidepressant. These findings emphasize the value in focusing on the mechanisms of action of tianeptine, and specifically, the glutamatergic system, in the development of novel pharmacotherapeutic strategies in the treatment of depression.

  14. On the structure and function of the phytoene desaturase CRTI from Pantoea ananatis, a membrane-peripheral and FAD-dependent oxidase/isomerase.

    Directory of Open Access Journals (Sweden)

    Patrick Schaub

    Full Text Available CRTI-type phytoene desaturases prevailing in bacteria and fungi can form lycopene directly from phytoene while plants employ two distinct desaturases and two cis-tans isomerases for the same purpose. This property renders CRTI a valuable gene to engineer provitamin A-formation to help combat vitamin A malnutrition, such as with Golden Rice. To understand the biochemical processes involved, recombinant CRTI was produced and obtained in homogeneous form that shows high enzymatic activity with the lipophilic substrate phytoene contained in phosphatidyl-choline (PC liposome membranes. The first crystal structure of apo-CRTI reveals that CRTI belongs to the flavoprotein superfamily comprising protoporphyrinogen IX oxidoreductase and monoamine oxidase. CRTI is a membrane-peripheral oxidoreductase which utilizes FAD as the sole redox-active cofactor. Oxygen, replaceable by quinones in its absence, is needed as the terminal electron acceptor. FAD, besides its catalytic role also displays a structural function by enabling the formation of enzymatically active CRTI membrane associates. Under anaerobic conditions the enzyme can act as a carotene cis-trans isomerase. In silico-docking experiments yielded information on substrate binding sites, potential catalytic residues and is in favor of single half-site recognition of the symmetrical C(40 hydrocarbon substrate.

  15. From networks of protein interactions to networks of functional dependencies

    Directory of Open Access Journals (Sweden)

    Luciani Davide

    2012-05-01

    Full Text Available Abstract Background As protein-protein interactions connect proteins that participate in either the same or different functions, networks of interacting and functionally annotated proteins can be converted into process graphs of inter-dependent function nodes (each node corresponding to interacting proteins with the same functional annotation. However, as proteins have multiple annotations, the process graph is non-redundant, if only proteins participating directly in a given function are included in the related function node. Results Reasoning that topological features (e.g., clusters of highly inter-connected proteins might help approaching structured and non-redundant understanding of molecular function, an algorithm was developed that prioritizes inclusion of proteins into the function nodes that best overlap protein clusters. Specifically, the algorithm identifies function nodes (and their mutual relations, based on the topological analysis of a protein interaction network, which can be related to various biological domains, such as cellular components (e.g., peroxisome and cellular bud or biological processes (e.g., cell budding of the model organism S. cerevisiae. Conclusions The method we have described allows converting a protein interaction network into a non-redundant process graph of inter-dependent function nodes. The examples we have described show that the resulting graph allows researchers to formulate testable hypotheses about dependencies among functions and the underlying mechanisms.

  16. The antioxidant behaviour of melatonin and structural analogues during lipid peroxidation depends not only on their functional groups but also on the assay system.

    Science.gov (United States)

    Fagali, Natalia; Catalá, Angel

    2012-07-13

    There is no general agreement yet on the antioxidant effect of pineal indoles against lipid peroxidation. Accordingly, the main goal of the present work was to study the antioxidant activity of melatonin (MLT), N-acetylserotonin (NAS), 5-HO-tryptophan (5HO-TRP) and 5-methoxytryptamine (5MTP) in two different lipid systems with high content of polyunsaturated fatty acids (PUFAs): triglycerides (rich in 20:5 n-3, 22:6 n-3) dissolved in chloroform and sonicated liposomes made of retinal lipids (rich in 22:6 n-3). In the triglyceride-chloroform-system the peroxidation reaction was initiated by cumene hydroperoxide (CHP) whereas liposomes were peroxidized with Fe(2+). The techniques employed at the present work were: (1) TBARS production, (2) DPPH assay, (3) determination of conjugated dienes production and (4) analysis of fatty acid profile by GC-MS. Butylated hydroxytoluene (BHT) was employed as a reference because of its well known antioxidant capacity. Our results showed that MLT and 5MTP were unable to protect PUFAs against lipid peroxidation in both systems, whereas NAS and 5HO-TRP were better antioxidants that BHT in the triglyceride-system but ineffective in the liposome-system. We conclude that the antioxidant behaviour of pineal indoles depends not only on their functional groups but also on the assay system and could be explained by the polar paradox theory.

  17. Copula-based measures of dependence structure in assets returns

    Science.gov (United States)

    Fernandez, Viviana

    2008-06-01

    Copula modeling has become an increasingly popular tool in finance to model assets returns dependency. In essence, copulas enable us to extract the dependence structure from the joint distribution function of a set of random variables and, at the same time, to isolate such dependence structure from the univariate marginal behavior. In this study, based on US stock data, we illustrate how tail-dependency tests may be misleading as a tool to select a copula that closely mimics the dependency structure of the data. This problem becomes more severe when the data is scaled by conditional volatility and/or filtered out for serial correlation. The discussion is complemented, under more general settings, with Monte Carlo simulations and portfolio management implications.

  18. A density functional theory study on size-dependent structures, stabilities, and electronic properties of bimetallic MnAgm (M=Na, Li; n + m ≤ 7) clusters

    Institute of Scientific and Technical Information of China (English)

    Sun Hao-Ran; Kuang Xiao-Yu; Li Yan-Fang; Shao Peng; Zhao Ya-Ru

    2012-01-01

    The equilibrium geometries,relative stabilities,and electronic properties of MnAgm(M=-Na,Li; n +-m ≤ 7) as well as pure Agn,Nan,Lin (n ≤ 7) clusters are systematically investigated by means of the density functional theory.The optimized geometries reveal that for 2 ≤ n ≤ 7,there are significant similarities in geometry among pure Agn,Nan,and Lin clusters,and the transitions from planar to three-dimensional configurations occur at n =7,7,and 6,respectively.In contrast,the first three-dimensional (3D) structures are observed at n + m =5 for both NanAgm and LinAgm clusters.When n + m ≥ 5,a striking feature is that the trigonal bipyramid becomes the main subunit of LinAgm.Furthermore,dramatic odd-even alternative behaviours are obtained in the fragmentation energies,secondorder difference energies,highest occupied and lowest unoccupied molecular orbital energy gaps,and chemical hardness for both pure and doped clusters.The analytic results exhibit that clusters with an even electronic configuration (2,4,6) possess the weakest chemical reactivity and more enhanced stability.

  19. Structure functions at large x

    CERN Document Server

    Zhang, Z

    2002-01-01

    Structure function data together with other measurements from fixed-target deep inelastic scattering and hadron-hadron collider experiments which contribute to our knowledge of the parton density functions are reviewed. The inclusive cross-section measurements of neutral and charged current interactions at HERA are presented and their impact on the parton density functions is discussed. Future prospects for an improved knowledge of the parton density functions at large x are briefly mentioned.

  20. The multiplex dependency structure of financial markets

    CERN Document Server

    Musmeci, Nicoló; Aste, Tomaso; Di Matteo, Tiziana; Latora, Vito

    2016-01-01

    We propose here a multiplex network approach to investigate simultaneously different types of dependency in complex data sets. In particular, we consider multiplex networks made of four layers corresponding respectively to linear, non-linear, tail, and partial correlations among a set of financial time series. We construct the sparse graph on each layer using a standard network filtering procedure, and we then analyse the structural properties of the obtained multiplex networks. The study of the time evolution of the multiplex constructed from financial data uncovers important changes in intrinsically multiplex properties of the network, and such changes are associated with periods of financial stress. We observe that some features are unique to the multiplex structure and would not be visible otherwise by the separate analysis of the single-layer networks corresponding to each dependency measure.

  1. Structural Chemistry of Functional Materials

    Institute of Scientific and Technical Information of China (English)

    2011-01-01

    @@ This innovative research group on structural chemistry of functional materials was approved by NSFC in 2005.Headed by Prof.HONG Maochun, the team consists of several young research scientists from the CAS Fujian Institute of Research on the Structures of Matter, including Profs CAO Rong, LU Canzhong, GUO Guocong, CHEN Zhongning, MAO Jianggao Mao and CHEN Ling.

  2. Unbiased spin-dependent Parton Distribution Functions

    CERN Document Server

    Nocera, Emanuele Roberto

    2014-01-01

    We present the first unbiased determination of spin-dependent, or polarized, Parton Distribution Functions (PDFs) of the proton. A statistically sound representation of the corresponding uncertainties is achieved by means of the NNPDF methodology: this was formerly developed for unpolarized distributions and is now generalized to the polarized here for the first time. The features of the procedure, based on robust statistical tools (Monte Carlo sampling for error propagation, neural networks for PDF parametrization, genetic algorithm for their minimization, and possibly reweighting for including new data samples without refitting), are illustrated in detail. Different sets of polarized PDFs are obtained at next-to-leading order accuracy in perturbative quantum chromodynamics, based on both fixed-target inclusive deeply-inelastic scattering data and the most recent polarized collider data. A quantitative appraisal on the potential role of future measurements at an Electron-Ion Collider is also presented. We st...

  3. Structured Functional Principal Component Analysis

    Science.gov (United States)

    Shou, Haochang; Zipunnikov, Vadim; Crainiceanu, Ciprian M.; Greven, Sonja

    2015-01-01

    Summary Motivated by modern observational studies, we introduce a class of functional models that expand nested and crossed designs. These models account for the natural inheritance of the correlation structures from sampling designs in studies where the fundamental unit is a function or image. Inference is based on functional quadratics and their relationship with the underlying covariance structure of the latent processes. A computationally fast and scalable estimation procedure is developed for high-dimensional data. Methods are used in applications including high-frequency accelerometer data for daily activity, pitch linguistic data for phonetic analysis, and EEG data for studying electrical brain activity during sleep. PMID:25327216

  4. Cocaine dependence and thalamic functional connectivity: a multivariate pattern analysis

    Directory of Open Access Journals (Sweden)

    Sheng Zhang

    2016-01-01

    Full Text Available Cocaine dependence is associated with deficits in cognitive control. Previous studies demonstrated that chronic cocaine use affects the activity and functional connectivity of the thalamus, a subcortical structure critical for cognitive functioning. However, the thalamus contains nuclei heterogeneous in functions, and it is not known how thalamic subregions contribute to cognitive dysfunctions in cocaine dependence. To address this issue, we used multivariate pattern analysis (MVPA to examine how functional connectivity of the thalamus distinguishes 100 cocaine-dependent participants (CD from 100 demographically matched healthy control individuals (HC. We characterized six task-related networks with independent component analysis of fMRI data of a stop signal task and employed MVPA to distinguish CD from HC on the basis of voxel-wise thalamic connectivity to the six independent components. In an unbiased model of distinct training and testing data, the analysis correctly classified 72% of subjects with leave-one-out cross-validation (p < 0.001, superior to comparison brain regions with similar voxel counts (p < 0.004, two-sample t test. Thalamic voxels that form the basis of classification aggregate in distinct subclusters, suggesting that connectivities of thalamic subnuclei distinguish CD from HC. Further, linear regressions provided suggestive evidence for a correlation of the thalamic connectivities with clinical variables and performance measures on the stop signal task. Together, these findings support thalamic circuit dysfunction in cognitive control as an important neural marker of cocaine dependence.

  5. Structure functions and parton distributions

    Energy Technology Data Exchange (ETDEWEB)

    Martin, A.D.; Stirling, W.J. [Univ. of Durham (United Kingdom); Roberts, R.G. [Rutherford Appleton Lab., Chilton, Didcot (United Kingdom)

    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.

  6. Proton structure functions at HERA

    Science.gov (United States)

    Stella, Bruno

    2001-10-01

    The electron-proton collider HERA, like an electron-mycroscope, explores the structure of the proton down to 10-16 cm and up to the situation of very high parton densities. The proton energy was upgraded from 820 to 920 GeV in the Fall of '98 and the luminosity has also substantially improved, with another factor of 3 upgrade expected to follow this year. Inclusive proton structure functions have been studied with incident e+ and e- of 27 GeV in the neutral (NC) and charged (CC) current interactions as functions of the squared four-momentum transfer, Q2, and of the fractional proton momentum carried by partons, x. The structure function F2, as well as the γ-Z0 interference term xF3, have been measured in a range of Q2 and 1/x that extends by orders of magnitude that reached by fixed target experiments. The DGLAP evolution equations [1] allow for a perturbative NLO QCD fit of the measured non-perturbative structure functions in the available kinematic range: αS and the gluon density at low x are fitted at the same time with good precision. The longitudinal structure function, FL, can be determined within the DGLAP formalism. With CC, the electroweak unification has been tested; at high x, a first flavor decomposition of the light quarks is achieved. The contribution to F2 of the charm quark has been measured and results to be relevant. Bounds on the radius of quarks and on compositeness are derived from the data at the highest Q2, 100

  7. General Structures of Block Based Interpolational Function

    Institute of Scientific and Technical Information of China (English)

    ZOU LE; TANG SHUO; Ma Fu-ming

    2012-01-01

    We construct general structures of one and two variable interpolation function,without depending on the existence of divided difference or inverse differences,and we also discuss the block based osculatory interpolation in one variable case.Clearly,our method offers many flexible interpolation schemes for choices.Error terms for the interpolation are determined and numerical examples are given to show the effectiveness of the results.

  8. Anisotropic nanomaterials: structure, growth, assembly, and functions

    OpenAIRE

    Panikkanvalappil R. Sajanlal; Theruvakkattil S. Sreeprasad; Samal, Akshaya K.; Thalappil Pradeep

    2011-01-01

    Comprehensive knowledge over the shape of nanomaterials is a critical factor in designing devices with desired functions. Due to this reason, systematic efforts have been made to synthesize materials of diverse shape in the nanoscale regime. Anisotropic nanomaterials are a class of materials in which their properties are direction-dependent and more than one structural parameter is needed to describe them. Their unique and fine-tuned physical and chemical properties make them ideal candidates...

  9. Nonlinear Structure Formation with the Environmentally Dependent Dilaton

    CERN Document Server

    Brax, Phil; Davis, Anne-C; Li, Baojiu; Shaw, Douglas J

    2011-01-01

    We have studied the nonlinear structure formation of the environmentally dependent dilaton model using $N$-body simulations. We find that the mechanism of suppressing the scalar fifth force in high-density regions works very well. Within the parameter space allowed by the solar system tests, the dilaton model predicts small deviations of the matter power spectrum and the mass function from their $\\Lambda$CDM counterparts. The importance of taking full account of the nonlinearity of the model is also emphasized.

  10. Concentration Dependent Structure of Block Copolymer Solutions

    Science.gov (United States)

    Choi, Soohyung; Bates, Frank S.; Lodge, Timothy P.

    2015-03-01

    Addition of solvent molecules into block copolymer can induce additional interactions between the solvent and both blocks, and therefore expands the range of accessible self-assembled morphologies. In particular, the distribution of solvent molecules plays a key role in determining the microstructure and its characteristic domain spacing. In this study, concentration dependent structures formed by poly(styrene-b-ethylene-alt-propylene) (PS-PEP) solution in squalane are investigated using small-angle X-ray scattering. This reveals that squalane is essentially completely segregated into the PEP domains. In addition, the conformation of the PS block changes from stretched to nearly fully relaxed (i.e., Gaussian conformation) as amounts of squalane increases. NRF

  11. Temperature dependent spin structures in Hexaferrite crystal

    Energy Technology Data Exchange (ETDEWEB)

    Chao, Y.C. [Center for Condensed Matter Sciences, National Taiwan University, Taipei 106, Taiwan (China); Lin, J.G., E-mail: jglin@ntu.edu.tw [Center for Condensed Matter Sciences, National Taiwan University, Taipei 106, Taiwan (China); Chun, S.H.; Kim, K.H. [Department of Physics and Astronomy, Seoul National University, Seoul 151-747 (Korea, Republic of)

    2016-01-01

    In this work, the Hexaferrite Ba{sub 0.5}Sr{sub 1.5}Zn{sub 2}Fe{sub 12}O{sub 22} (BSZFO) is studied due to its interesting characteristics of long-wavelength spin structure. Ferromagnetic resonance (FMR) is used to probe the magnetic states of BSZFO single crystal and its temperature dependence behavior is analyzed by decomposing the multiple lines of FMR spectra into various phases. Distinguished phase transition is observed at 110 K for one line, which is assigned to the ferro(ferri)-magnetic transition from non-collinear to collinear spin state. - Highlights: • For the first time Ferromagnetic Resonance is used to probe the local magnetic structure of Ba{sub 0.5}Sr{sub 1.5}Zn{sub 2}Fe{sub 12}O{sub 22.} • The multiphases in the single crystal is identified, which provides important information toward its future application for the magnetoelectric devices.

  12. A comparison of dependence function estimators in multivariate extremes

    KAUST Repository

    Vettori, Sabrina

    2017-05-11

    Various nonparametric and parametric estimators of extremal dependence have been proposed in the literature. Nonparametric methods commonly suffer from the curse of dimensionality and have been mostly implemented in extreme-value studies up to three dimensions, whereas parametric models can tackle higher-dimensional settings. In this paper, we assess, through a vast and systematic simulation study, the performance of classical and recently proposed estimators in multivariate settings. In particular, we first investigate the performance of nonparametric methods and then compare them with classical parametric approaches under symmetric and asymmetric dependence structures within the commonly used logistic family. We also explore two different ways to make nonparametric estimators satisfy the necessary dependence function shape constraints, finding a general improvement in estimator performance either (i) by substituting the estimator with its greatest convex minorant, developing a computational tool to implement this method for dimensions $$D\\\\ge 2$$D≥2 or (ii) by projecting the estimator onto a subspace of dependence functions satisfying such constraints and taking advantage of Bernstein–Bézier polynomials. Implementing the convex minorant method leads to better estimator performance as the dimensionality increases.

  13. Structure and Function of Glucansucrases

    Science.gov (United States)

    Dijkstra, B. W.; Vujičić-Žagar, A.

    2008-03-01

    Glucansucrases are relatively large (~160 kDa) extracellular enzymes produced by lactic acid bacteria. Using sucrose as a substrate they synthesize high molecular mass glucose polymers, called α-glucans, which allow the bacteria to adhere to surfaces and create a biofilm. The glucan polymers are of importance for the food and dairy industry as thickening and jellying agents. An overview is given of the current insights into the structure and functioning of these and related enzymes.

  14. Measurements of the Q{sup 2}-Dependence of the Proton and Neutron Spin Structure Functions g{sub 1}{sup p} and g{sub 1}{sup n}

    Energy Technology Data Exchange (ETDEWEB)

    Perry Anthony; R.G. Arnold; Todd Averett; H.R. Band; M.C. Berisso; H. Borel; Peter Bosted; Stephen Bueltmann; M. Buenerd; T. Chupp; Steve Churchwell; G.R. Court; Donald Crabb; Donal Day; Piotr Decowski; P. DePietro; Robin D. Erbacher; R. Erickson; A. Feltham; Helene Fonvieille; Emil Frlez; R. Gearhart; V. Ghazikhanian; Javier Gomez; Keith Griffioen; C. Harris; M.A. Houlden; Emlyn Hughes; Charles Hyde-wright; G. Igo; Sebastien Incerti; John Jensen; J.R. Johnson; Paul King; Yu.G. Kolomensky; Sebastian Kuhn; Richard Lindgren; R.M. Lombard-Nelsen; Jacques Marroncle; James Mccarthy; Paul Mckee; Werner Meyer; Gregory Mitchell; Joseph Mitchell; Michael Olson; Seppo Penttila; Gerald Peterson; Gerassimos Petratos; R. Pitthan; Dinko Pocanic; R. Prepost; C. Prescott; Liming Qin; Brian Raue; D. Reyna; L.S. Rochester; Stephen Rock; Oscar Rondon-aramayo; Franck Sabatie; Ingo Sick; Tim Smith; Lee Sorrell; F. Staley; S. St. Lorant; L.M. Stuart; Z. Szalata; Y. Terrien; William Tobias; Luminita Todor; T. Toole; S. Trentalange; D. Walz; Robert Welsh; Frank Wesselmann; T.R. Wright; C.C. Young; Markus Zeier; Hong Guo Zhu; Benedikt Zihlmann

    2000-11-09

    The structure functions g{sub 1}{sup p} and g{sub 1}{sup n} have been measured over the range 0.014 < x < 0.9 and 1 < Q{sup 2} < 40 GeV{sup 2} using deep-inelastic scattering of 48 GeV longitudinally polarized electrons from polarized protons and deuterons. We find that the Q{sup 2} dependence of g{sub 1}{sup p} (g{sub 1}{sup n}) at fixed x is very similar to that of the spin-averaged structure function F{sub 1}{sup p} (F{sub 1}{sup n}). From a NLO QCD fit to all available data we find {Gamma}{sub 1}{sup p} - {Gamma}{sub 1}{sup n} = 0.176 {+-} 0.003 {+-} 0.007 at Q{sup 2} = 5 GeV{sup 2}, in agreement with the Bjorken sum rule prediction of 0.182 {+-} 0.005.

  15. Longitudinal double-spin asymmetry $A_1^{\\rm p}$ and spin dependent structure function $g_1^{\\rm p}$ of the proton at small values of $x$ and $Q^2$

    CERN Document Server

    Aghasyan, M; The COMPASS collaboration; Alexeev, M G; Alexeev, G D; Amoroso, A; Andrieux, V; Anfimov, N V; Anosov, V; Antoshkin, A; Augsten, K; Augustyniak, W; Austregesilo, A; Azevedo, C D R; Badelek, B; Balestra, F; Ball, M; Barth, J; Beck, R; Bedfer, Y; Bernhard, J; Bicker, K; Bielert, E R; Birsa, R; Bodlak, M; Bordalo, P; Bradamante, F; Bressan, A; Buechele, M; Burtsev, V E; Chang, W -C; Chatterjee, C; Chiosso, M; Choi, I; Chumakov, A G; Chung, S -U; Cicuttin, A; Crespo, M L; Dalla Torre, S; Dasgupta, S S; Dasgupta, S; Denisov, O Yu; Dhara, L; Donskov, S V; Doshita, N; Dreisbach, Ch; Duennweber, W; Dusaev, R R; Dziewiecki, M; Efremov, A; Eversheim, P D; Faessler, M; Ferrero, A; Finger, M; Finger jr, M; Fischer, H; Franco, C; du Fresne von Hohenesche, N; Friedrich, J M; Frolov, V; Fuchey, E; Gautheron, F; Gavrichtchouk, O P; Gerassimov, S; Giarra, J; Giordano, F; Gnesi, I; Gorzellik, M; Grasso, A; Gridin, A; Grosse Perdekamp, M; Grube, B; Grussenmeyer, T; Guskov, A; Hahne, D; Hamar, G; von Harrach, D; Heinsius, F H; Heitz, R; Herrmann, F; Horikawa, N; d'Hose, N; Hsieh, C -Y; Huber, S; Ishimoto, S; Ivanov, A; Ivanshin, Yu; Iwata, T; Jary, V; Joosten, R; Joerg, P; Kabuss, E; Kerbizi, A; Ketzer, B; Khaustov, G V; Khokhlov, Yu A; Kisselev, Yu; Klein, F; Koivuniemi, J H; Kolosov, V N; Kondo, K; Koenigsmann, K; Konorov, I; Konstantinov, V F; Kotzinian, A M; Kouznetsov, O M; Kral, Z; Kraemer, M; Kremser, P; Krinner, F; Kroumchtein, Z V; Kulinich, Y; Kunne, F; Kurek, K; Kurjata, R P; Kuznetsov, I I; Kveton, A; Lednev, A A; Levchenko, E A; Levillain, M; Levorato, S; Lian, Y -S; Lichtenstadt, J; Longo, R; Lyubovitskij, V E; Maggiora, A; Magnon, A; Makins, N; Makke, N; Mallot, G K; Mamon, S A; Marianski, B; Martin, A; Marzec, J; Matousek, J; Matsuda, H; Matsuda, T; Meshcheryakov, G V; Meyer, M; Meyer, W; Mikhailov, Yu V; Mikhasenko, M; Mitrofavov, E; Mitrofanov, N; Miyachi, Y; Moretti, A; Nagaytsev, A; Nerling, F; Neyret, D; Novy, J; Nowak, W -D; Nukazuka, G; Nunes, A S; Olshevsky, A G; Orlov, I; Ostrick, M; Panzieri, D; Parsamyan, B; Paul, S; Peng, J -C; Pereira, F; Pesek, M; Peskova, M; Peshekhonov, D V; Pierre, N; Platchkov, S; Pochodzalla, J; Polyakov, V A; Pretz, J; Quaresma, M; Quintans, C; Ramos, S; Regali, C; Reicherz, G; Riedl, C; Rogacheva, N; Ryabchikov, D I; Rybnikov, A; Rychter, A; Salac, R; Samoylenko, V D; Sandacz, A; Santos, C; Sarkar, S; Savin, I A; Sawada, T; Sbrizzai, G; Schiavon, P; Schmidt, K; Schmieden, H; Schoenning, K; Seder, E; Selyunin, A; Silva, L; Sinha, L; Sirtl, S; Slunecka, M; Smolik, J; Srnka, A; Steffen, D; Stolarski, M; Subrt, O; Sulc, M; Suzuki, H; Szabelski, A; Szameitat, T; Sznajder, P; Tasevsky, M; Tessaro, S; Tessarotto, F; Thiel, A; Tomsa, J; Tosello, F; Tskhay, V; Uhl, S; Vasilishin, B I; Vauth, A; Veloso, J; Vidon, A; Virius, M; Wallner, S; Weisrock, T; Wilfert, M; ter Wolbeek, J; Zaremba, K; Zavada, P; Zavertyaev, M; Zemlyanichkina, E; Zhuravlev, N; Ziembicki, M

    2017-01-01

    We present a precise measurement of the proton longitudinal double-spin asymmetry $A_1^{\\rm p}$ and the proton spin-dependent structure function $g_1^{\\rm p}$ at photon virtualities $0.006~({\\rm GeV}/c)^2< Q^2< 1~ ({\\rm GeV}/c)^2$ in the Bjorken $x$ range of $4 \\times 10^{-5} < x < 4 \\times 10^{-2}$. The results are based on data collected by the COMPASS Collaboration at CERN using muon beam energies of $160~{\\rm GeV}$ and $200~ {\\rm GeV}$. The statistical precision is more than tenfold better than that of the previous measurement in this region. In the whole range of $x$, the measured values of $A_1^{\\rm p}$ and $g_1^{\\rm p}$ are found to be positive. It is for the first time that spin effects are found at such low values of $x$.

  16. Sodium-dependent phosphate transporters in osteoclast differentiation and function.

    Directory of Open Access Journals (Sweden)

    Giuseppe Albano

    Full Text Available Osteoclasts are multinucleated bone degrading cells. Phosphate is an important constituent of mineralized bone and released in significant quantities during bone resorption. Molecular contributors to phosphate transport during the resorptive activity of osteoclasts have been controversially discussed. This study aimed at deciphering the role of sodium-dependent phosphate transporters during osteoclast differentiation and bone resorption. Our studies reveal RANKL-induced differential expression of sodium-dependent phosphate transport protein IIa (NaPi-IIa transcript and protein during osteoclast development, but no expression of the closely related NaPi-IIb and NaPi-IIc SLC34 family isoforms. In vitro studies employing NaPi-IIa-deficient osteoclast precursors and mature osteoclasts reveal that NaPi-IIa is dispensable for bone resorption and osteoclast differentiation. These results are supported by the analysis of structural bone parameters by high-resolution microcomputed tomography that yielded no differences between adult NaPi-IIa WT and KO mice. By contrast, both type III sodium-dependent phosphate transporters Pit-1 and Pit-2 were abundantly expressed throughout osteoclast differentiation, indicating that they are the relevant sodium-dependent phosphate transporters in osteoclasts and osteoclast precursors. We conclude that phosphate transporters of the SLC34 family have no role in osteoclast differentiation and function and propose that Pit-dependent phosphate transport could be pivotal for bone resorption and should be addressed in further studies.

  17. Bounds on transverse momentum dependent distribution functions

    CERN Document Server

    Henneman, A A

    2001-01-01

    When more than one hadron takes part in a hard process, an extended set of quark distribution and fragmentation functions becomes relevant. In this talk, the derivation of Soffer-like bounds for these functions, in the case of a spin-1/2 target, is sketched and some of their aspects are discussed.

  18. Bounds on transverse momentum dependent distribution functions

    OpenAIRE

    Henneman, A.

    2000-01-01

    When more than one hadron takes part in a hard process, an extended set of quark distribution and fragmentation functions becomes relevant. In this talk, the derivation of Soffer-like bounds for these functions, in the case of a spin-1/2 target, is sketched and some of their aspects are discussed.

  19. Bounds on transverse momentum dependent distribution functions

    Science.gov (United States)

    Henneman, A.

    2001-01-01

    When more than one hadron takes part in a hard process, an extended set of quark distribution and fragmentation functions becomes relevant. In this talk, the derivation of Soffer-like bounds for these functions, in the case of a spin-1/2 target [1], is sketched and some of their aspects are discussed.

  20. 时滞相关Logistic函数浮点数据模糊加密稀疏集构造%Sparse Set Structure of Floating-point Data Fuzzy Encryption Based on Delay Dependent Logistic Function

    Institute of Scientific and Technical Information of China (English)

    李晓靖

    2015-01-01

    提出一种基于时滞相关Logistic函数线性调频采样的浮点数据模糊加密算法优化技术,给出时滞相关Logistic函数及相关定义,研究了浮点数据的模糊编码算法,设计实时交互网络的浮点数据模糊加密方案,实现密钥稀疏集构造,采用基于稀疏矩阵的存储格式下的时滞相关Logistic函数浮点数据加密运算,构造密钥稀疏集,优化了算法性能。仿真结果表明,算法数据加密和解密性能较好,具有较高的数据吞吐量,能实现对大数据库的数据加密,提高了密文的不可预测性。%A sample Logistic function linear frequency based on the delay of floating-point data encryption algorithm for fuzzy optimization techniques is proposed, given the delay dependent Logistic function and definition of fuzzy coding algo⁃rithm, floating-point data, floating-point data design of real-time interactive network fuzzy encryption scheme is obtained. Realize the key sparse set structure, using encryption delay dependent Logistic function point data storage format based on the sparse matrix, key sparse sets are constructed, the performance of the algorithm is optimized. The simulation results show that, the algorithm of data encryption and decryption performance is good, the data throughput is higher, it can realize the data encryption of database, the cipher text is unpredictable.

  1. Mitochondria: isolation, structure and function.

    Science.gov (United States)

    Picard, Martin; Taivassalo, Tanja; Gouspillou, Gilles; Hepple, Russell T

    2011-09-15

    Mitochondria are complex organelles constantly undergoing processes of fusion and fission, processes that not only modulate their morphology, but also their function. Yet the assessment of mitochondrial function in skeletal muscle often involves mechanical isolation of the mitochondria, a process which disrupts their normally heterogeneous branching structure and yields relatively homogeneous spherical organelles. Alternatively, methods have been used where the sarcolemma is permeabilized and mitochondrial morphology is preserved, but both methods face the downside that they remove potential influences of the intracellular milieu on mitochondrial function. Importantly, recent evidence shows that the fragmented mitochondrial morphology resulting from routine mitochondrial isolation procedures used with skeletal muscle alters key indices of function in a manner qualitatively similar to mitochondria undergoing fission in vivo. Although these results warrant caution when interpreting data obtained with mitochondria isolated from skeletal muscle, they also suggest that isolated mitochondrial preparations might present a useful way of interrogating the stress resistance of mitochondria. More importantly, these new findings underscore the empirical value of studying mitochondrial function in minimally disruptive experimental preparations. In this review, we briefly discuss several considerations and hypotheses emerging from this work.

  2. The structure and function of fungal cells

    Science.gov (United States)

    Nozawa, Y.

    1984-01-01

    The structure and function of fungal cell walls were studied with particular emphasis on dermatophytes. Extraction, isolation, analysis, and observation of the cell wall structure and function were performed. The structure is described microscopically and chemically.

  3. Tissue Factor Structure and Function

    Directory of Open Access Journals (Sweden)

    Saulius Butenas

    2012-01-01

    Full Text Available Tissue factor (TF is an integral membrane protein that is essential to life. It is a component of the factor VIIa-TF complex enzyme and plays a primary role in both normal hemostasis and thrombosis. With a vascular injury, TF becomes exposed to blood and binds plasma factor VIIa, and the resulting complex initiates a series of enzymatic reactions leading to clot formation and vascular sealing. Many cells, both healthy, and tumor cells, produce detectable amounts of TF, especially when they are stimulated by various agents. Despite the relative simplicity and small size of TF, there are numerous contradictory reports about the synthesis and presentation of TF on blood cells and circulation in normal blood either on microparticles or as a soluble protein. Another subject of controversy is related to the structure/function of TF. It has been almost commonly accepted that cell-surface-associated TF has low (if any activity, that is, is “encrypted” and requires specific conditions/reagents to become active, that is, “decrypted.” However there is a lack of agreement related to the mechanism and processes leading to alterations in TF function. In this paper TF structure, presentation, and function, and controversies concerning these features are discussed.

  4. REVIEW: STRUCTURE AND FUNCTIONS OF RNA-DEPENDENT RNA POLYMERASE OF POSITIVE-STRAND RNA VIRUSES%正链RNA病毒复制酶结构与功能研究进展

    Institute of Scientific and Technical Information of China (English)

    王超; 吴润; 刘光清

    2011-01-01

    The positive-strand RNA viruses are composed of a large family that infect various animals,plants and human beings.Understanding on the replication and regulation mechanisms of RNA viruses is important to investigate pathogenesis and develop antiviral drugs and vaccines.The RNA-dependent RNA polymerase(RdRp) is a key enzyme responsible for the replication of positive-strand RNA viruses.This review focused on recent progress in research on structure and functions of RdRp.%正链RNA病毒是家族非常庞大,可以感染多种动、植物及人的一类病毒。研究这类病毒的复制机理和调控方式对于阐明病毒的致病机制,以及研制新型抗病毒药物和疫苗等具有重要意义。RNA依赖性RNA聚合酶(RNA-dependent RNA polymerase,RdRp)是正链RNA病毒进行复制的关键蛋白酶,研究其结构与功能是了解病毒复制机理的前提和基础。本文即对近年来关于正链RNA病毒RdRp的结构与功能研究进展情况进行综述。

  5. The Functions of RNA-Dependent RNA Polymerases in Arabidopsis

    Science.gov (United States)

    Willmann, Matthew R.; Endres, Matthew W.; Cook, Rebecca T.; Gregory, Brian D.

    2011-01-01

    One recently identified mechanism that regulates mRNA abundance is RNA silencing, and pioneering work in Arabidopsis thaliana and other genetic model organisms helped define this process. RNA silencing pathways are triggered by either self-complementary fold-back structures or the production of double-stranded RNA (dsRNA) that gives rise to small RNAs (smRNAs) known as microRNAs (miRNAs) or small-interfering RNAs (siRNAs). These smRNAs direct sequence-specific regulation of various gene transcripts, repetitive sequences, viruses, and mobile elements via RNA cleavage, translational inhibition, or transcriptional silencing through DNA methylation and heterochromatin formation. Early genetic screens in Arabidopsis were instrumental in uncovering numerous proteins required for these important regulatory pathways. Among the factors identified by these studies were RNA-dependent RNA polymerases (RDRs), which are proteins that synthesize siRNA-producing dsRNA molecules using a single-stranded RNA (ssRNA) molecule as a template. Recently, a growing body of evidence has implicated RDR-dependent RNA silencing in many different aspects of plant biology ranging from reproductive development to pathogen resistance. Here, we focus on the specific functions of the six Arabidopsis RDRs in RNA silencing, their ssRNA substrates and resulting RDR-dependent smRNAs, and the numerous biological functions of these proteins in plant development and stress responses. PMID:22303271

  6. Cocrystal Structures of Antibody N60-i3 and Antibody JR4 in Complex with gp120 Define More Cluster A Epitopes Involved in Effective Antibody-Dependent Effector Function against HIV-1.

    Science.gov (United States)

    Gohain, Neelakshi; Tolbert, William D; Acharya, Priyamvada; Yu, Lei; Liu, Tongyun; Zhao, Pingsen; Orlandi, Chiara; Visciano, Maria L; Kamin-Lewis, Roberta; Sajadi, Mohammad M; Martin, Loïc; Robinson, James E; Kwong, Peter D; DeVico, Anthony L; Ray, Krishanu; Lewis, George K; Pazgier, Marzena

    2015-09-01

    Accumulating evidence indicates a role for Fc receptor (FcR)-mediated effector functions of antibodies, including antibody-dependent cell-mediated cytotoxicity (ADCC), in prevention of human immunodeficiency virus type 1 (HIV-1) acquisition and in postinfection control of viremia. Consequently, an understanding of the molecular basis for Env epitopes that constitute effective ADCC targets is of fundamental interest for humoral anti-HIV-1 immunity and for HIV-1 vaccine design. A substantial portion of FcR effector function of potentially protective anti-HIV-1 antibodies is directed toward nonneutralizing, transitional, CD4-inducible (CD4i) epitopes associated with the gp41-reactive region of gp120 (cluster A epitopes). Our previous studies defined the A32-like epitope within the cluster A region and mapped it to the highly conserved and mobile layers 1 and 2 of the gp120 inner domain within the C1-C2 regions of gp120. Here, we elucidate additional cluster A epitope structures, including an A32-like epitope, recognized by human monoclonal antibody (MAb) N60-i3, and a hybrid A32-C11-like epitope, recognized by rhesus macaque MAb JR4. These studies define for the first time a hybrid A32-C11-like epitope and map it to elements of both the A32-like subregion and the seven-layered β-sheet of the gp41-interactive region of gp120. These studies provide additional evidence that effective antibody-dependent effector function in the cluster A region depends on precise epitope targeting--a combination of epitope footprint and mode of antibody attachment. All together these findings help further an understanding of how cluster A epitopes are targeted by humoral responses. HIV/AIDS has claimed the lives of over 30 million people. Although antiretroviral drugs can control viral replication, no vaccine has yet been developed to prevent the spread of the disease. Studies of natural HIV-1 infection, simian immunodeficiency virus (SIV)- or simian-human immunodeficiency virus (SHIV

  7. Supramolecular Structure and Function 9

    CERN Document Server

    Pifat-Mrzljak, Greta

    2007-01-01

    The book is based on International Summer Schools on Biophysics held in Croatia which, contrary to other workshops centered mainly on one topic or technique, has very broad scope providing advanced training in areas related to biophysics. This volume is presenting papers in the field of biophysics for studying biological phenomena by using physical methods (NMR, EPR, FTIR, Mass Spectrometry, etc.) and/or concepts (predictions of protein-protein interactions, virtual ligand screening etc.). The interrelationship of supramolecular structures and there functions is enlightened by applications of principals of these physical methods in the biophysical and molecular biology context.

  8. Molecular and vibrational structure of tetroxo d0 metal complexes in their excited states. a study based on time-dependent density functional calculations and Franck-Condon theory.

    Science.gov (United States)

    Jose, Linta; Seth, Michael; Ziegler, Tom

    2012-02-23

    We have applied time dependent density functional theory to study excited state structures of the tetroxo d(0) transition metal complexes MnO(4)(-), TcO(4)(-), RuO(4), and OsO(4). The excited state geometry optimization was based on a newly implemented scheme [Seth et al. Theor. Chem. Acc. 2011, 129, 331]. The first excited state has a C(3v) geometry for all investigated complexes and is due to a "charge transfer" transition from the oxygen based HOMO to the metal based LUMO. The second excited state can uniformly be characterized by "charge transfer" from the oxygen HOMO-1 to the metal LUMO with a D(2d) geometry for TcO(4)(-), RuO(4), and OsO(4) and two C(2v) geometries for MnO(4)(-). It is finally found that the third excited state of MnO(4)(-) representing the HOMO to metal based LUMO+1 orbital transition has a D(2d) geometry. On the basis of the calculated excited state structures and vibrational modes, the Franck-Condon method was used to simulate the vibronic structure of the absorption spectra for the tetroxo d(0) transition metal complexes. The Franck-Condon scheme seems to reproduce the salient features of the experimental spectra as well as the simulated vibronic structure for MnO(4)(-) generated from an alternative scheme [Neugebauer J. J. Phys. Chem. A 2005, 109, 1168] that does not apply the Franck-Condon approximation.

  9. Structural and functional insights into Mimivirus ORFans

    Directory of Open Access Journals (Sweden)

    Fischer Daniel

    2007-05-01

    Full Text Available Abstract Background Mimivirus isolated from A. polyphaga is the largest virus discovered so far. It is unique among all the viruses in having genes related to translation, DNA repair and replication which bear close homology to eukaryotic genes. Nevertheless, only a small fraction of the proteins (33% encoded in this genome has been assigned a function. Furthermore, a large fraction of the unassigned protein sequences bear no sequence similarity to proteins from other genomes. These sequences are referred to as ORFans. Because of their lack of sequence similarity to other proteins, they can not be assigned putative functions using standard sequence comparison methods. As part of our genome-wide computational efforts aimed at characterizing Mimivirus ORFans, we have applied fold-recognition methods to predict the structure of these ORFans and further functions were derived based on conservation of functionally important residues in sequence-template alignments. Results Using fold recognition, we have identified highly confident computational 3D structural assignments for 21 Mimivirus ORFans. In addition, highly confident functional predictions for 6 of these ORFans were derived by analyzing the conservation of functional motifs between the predicted structures and proteins of known function. This analysis allowed us to classify these 6 previously unannotated ORFans into their specific protein families: carboxylesterase/thioesterase, metal-dependent deacetylase, P-loop kinases, 3-methyladenine DNA glycosylase, BTB domain and eukaryotic translation initiation factor eIF4E. Conclusion Using stringent fold recognition criteria we have assigned three-dimensional structures for 21 of the ORFans encoded in the Mimivirus genome. Further, based on the 3D models and an analysis of the conservation of functionally important residues and motifs, we were able to derive functional attributes for 6 of the ORFans. Our computational identification of important

  10. Anthocyanin kinetics are dependent on anthocyanin structure.

    Science.gov (United States)

    Novotny, Janet A; Clevidence, Beverly A; Kurilich, Anne C

    2012-02-01

    The kinetics of anthocyanin metabolism was investigated in a human feeding trial. Volunteers (n 12) consumed purple carrots containing five anthocyanin forms: cyanidin-3-(xylose-glucose-galactoside), cyanidin-3-(xylose-galactoside), cyanidin-3-(xylose-sinapoyl-glucose-galactoside), cyanidin-3-(xylose-feruloyl-glucose-galactoside) and cyanidin-3-(xylose-coumuroyl-glucose-galactoside). The purple carrots were served as three different treatments in a crossover design with a 3-week washout between treatments. Purple carrot treatments were 250 g raw carrots, 250 g cooked carrots and 500 g cooked carrots. Serial blood and urine samples were collected for 8 and 24 h after the dose, respectively, and analysed for anthocyanins. Of the anthocyanin forms ingested, four were detected in plasma and urine: cyanidin-3-(xylose-glucose-galactoside), cyanidin-3-(xylose-galactoside), cyanidin-3-(xylose-sinapoyl-glucose-galactoside) and cyanidin-3-(xylose-feruloyl-glucose-galactoside). The time courses of plasma and urine anthocyanin contents were evaluated with compartmental modelling. Results showed that absorption, gastrointestinal transit and plasma elimination are dependent on anthocyanin structure. Absorption efficiencies of acylated compounds (cyanidin-3-(xylose-sinapoyl-glucose-galactoside) and cyanidin-3-(xylose-feruloyl-glucose-galactoside)) were less than those for non-acylated anthocyanins (cyanidin-3-(xylose-glucose-galactoside) and cyanidin-3-(xylose-galactoside)). The acylated anthocyanins exhibited a shorter half-life for gastrointestinal absorption than the non-acylated anthocyanins. Fractional elimination of non-acylated compounds was slower than that for acylated anthocyanins. These results provide the first information about the kinetics of individual anthocyanins in human beings.

  11. Functional Dependencies and Its Axiom System in XML

    Institute of Scientific and Technical Information of China (English)

    ZHAO Xiangguo; WANG Guoren; HOU Huan; DING Dabin

    2007-01-01

    According to the analysis of existing complicated functional dependencies constraint, we conclude the conditions of defining functional dependency in XML, and then we introduce the concept of the node value equality. Anew path language and a new definition of functional dependencies in XML (XFD) are proposed.XFD includes the relative XFD and the absolute XFD, in which absolute key and relative key are the particular cases. We focus on the logical implication and the closure problems, and propose a group of inference rules. Finally, some proofs of the correctness and completeness are given. XFD is powerful on expressing functional dependencies in XML causing data redundancy, and has a complete axiom system.

  12. Age dependence of rat liver function measurements

    DEFF Research Database (Denmark)

    Fischer-Nielsen, A; Poulsen, H E; Hansen, B A

    1989-01-01

    Changes in the galactose elimination capacity, the capacity of urea-N synthesis and antipyrine clearance were studied in male Wistar rats at the age of 8, 20 and 44 weeks. Further, liver tissue concentrations of microsomal cytochrome P-450, microsomal protein and glutathione were measured. All...... liver function measurements increased from the age of 8 to 44 weeks when expressed in absolute values. In relation to body weight, these function measurements were unchanged or reduced from week 8 to week 20. At week 44, galactose elimination capacity and capacity of urea-N synthesis related to body...... weight were increased by 10% and 36%, respectively, and antipyrine plasma clearance was reduced to 50%. Liver tissue concentrations of microsomal cytochrome P-450 and microsomal protein increased with age when expressed in absolute values, but were unchanged per g liver, i.e., closely related to liver...

  13. Structure and function of aggrecan

    Institute of Scientific and Technical Information of China (English)

    2002-01-01

    Aggrecan is the major proteoglycan in the articular cartilage. This molecule is important in the proper functioning of articular cartilage because it provides a hydrated gel structure (via its interaction with hyaluronan and link protein) that endows the cartilage with load-bearing properties. It is also crucial in chondroskeletal morphogenesis during development. Aggrecan is a multimodular molecule expressed by chondrocytes. Its core protein is composed of three globular domains (Gl, G2, and G3) and a large extended region (CS) between G2 and G3 for glycosaminoglycan chain attachment. G1 comprises the amino terminus of the core protein. This domain has the same structural motif as link protein. Functionally, the G1 domain interacts with hyaluronan acid and link protein, forming stable ternary complexes in the extracellular matrix.G2 is homologous to the tandem repeats of G1 and of link protein and is involved in product processing. G3makes up the carboxyl terminus of the core protein. It enhances glycosaminoglycan modification and product secretion. Aggrecan plays an important role in mediating chondrocyte-chondrocyte and chondrocyte-matrix interactions through its ability to bind hyaluronan.

  14. Structures and Functions of Oligosaccharins

    Energy Technology Data Exchange (ETDEWEB)

    Albersheim, Peter

    1995-12-01

    We have made considerable progress during the 2.5 year funding period just ending in our studies of the structures and functions of oligosaccharide signal molecules (oligosaccharins). We have emphasized studies of the enzymes that solubilize, process, and degrade oligosaccharins and of the proteins that inhibit those enzymes. We have been especially interested in elucidating how oligosaccharins and their processing enzymes participate in determining the outcome of challenges to plants by pathogenic microbes. We have studied, to a lesser extent, the roles of oligosaccharins in plant growth and development. Abstracts of papers describing results acquired with support from this grant that have been published, submitted, or in preparation are presented to summarize the progress made during the last two and one half years. The report highlights the most important contributions made in our oiigosaccharin research during this time period, and the corresponding abstract is referenced. Results of work in progress are described primarily in conjunction with our application for continued support.

  15. Functional evolution of nuclear structure

    Science.gov (United States)

    Dawson, Scott C.

    2011-01-01

    The evolution of the nucleus, the defining feature of eukaryotic cells, was long shrouded in speculation and mystery. There is now strong evidence that nuclear pore complexes (NPCs) and nuclear membranes coevolved with the endomembrane system, and that the last eukaryotic common ancestor (LECA) had fully functional NPCs. Recent studies have identified many components of the nuclear envelope in living Opisthokonts, the eukaryotic supergroup that includes fungi and metazoan animals. These components include diverse chromatin-binding membrane proteins, and membrane proteins with adhesive lumenal domains that may have contributed to the evolution of nuclear membrane architecture. Further discoveries about the nucleoskeleton suggest that the evolution of nuclear structure was tightly coupled to genome partitioning during mitosis. PMID:22006947

  16. STRUCTURE AND GRAMMATICAL FUNCTION OF LEO LANGUAGE

    Directory of Open Access Journals (Sweden)

    I Ketut Yudha

    2015-01-01

    Full Text Available Lio language is a language spoken in Central Flores. Having limited morphological process in general and affixation process involving verbs (head marking and nouns (dependent marking in particular, it is classified into an isolating language. The studies exploring the languages spoken in the eastern part of Indonesia using Lexical Functional Grammar and the theory of typology are highly limited. In addition, Lio language is merely an isolating one and does not have cross referencing. It is this which inspired the writer to conduct research in syntax. This study aims at investigating the canonic structure, the types of verbs used as predicates, the grammatical function, the alternate of clausal structure, the mapping and the pivotance in Lio language. The results of analysis show that the clauses in Lio language can be divided into basic clauses with verbal and nonverbal predicates. The  predicates of the verbal clauses are classified into simple, serial, and causative.  The serial verbal constructions are distinguished based on the semantic features of the verbal components forming the serial verbal constructions. These types can be observed from the nature of the relationships among the components forming the serial verbal constructions. A serial verbal construction is made up of more than one verbs and behaves as a simple predicate. There is no dependence marker among the components forming the serial verb.  The causative structure also forms monoclause and biclause. The functional mapping uses the features [+/-r] and [+/-o], the argument uses the features [-r] and [-o] which are mapped to  SUBJ, [-r] and [+o] are mapped to OBJ, [+r] and [+o] are mapped to OBJ2 or OBJ? and [+r] and [-o] are mapped to OBL (Oblique. Lio language has GF SUBJ and OBJ as the nuclear GF (nuclear grammatical function, and OBL, COMP, and ADJ as the nonnuclear grammatical functions. The SUBJ appears before the verb (preverbal position and the OBJ appears after the

  17. Some Lower Valence Vanadium Fluorides: Their Crystal Distortions, Domain Structures, Modulated Structures, Ferrimagnetism, and Composition Dependence.

    Science.gov (United States)

    Hong, Y. S.; And Others

    1980-01-01

    Describes some contemporary concepts unique to the structure of advanced solids, i.e., their crystal distortions, domain structures, modulated structures, ferrimagnetism, and composition dependence. (Author/CS)

  18. Investigating the Dependence Structure between Real Estate and Finance Industries Based on the Copula Function%基于Copula房地产与金融行业的股票相关性研究

    Institute of Scientific and Technical Information of China (English)

    刘琼芳; 张宗益

    2011-01-01

    房地产市场和金融市场的关系多数文献从相互影响的角度研究,而本文以房地产与金融行业的股票收益率数据,引入Copula方法定量刻画两个行业股票之间的相关关系.实证结果表明,双参数结构的Copula拟合度普遍高于单参数结构的Copula;如果仅考虑单参数或双参数Copula函数结构,可能会得出错误的结论.本文同时选取单参数和双参数的Copula拟合房地产与金融行业的股票收益率之间相关性结构,通过AIC、BIC最小原则应为BB3 Copula,说明两个行业股票在市场低迷时期的尾部相关性高于活跃时期的尾部相关性.因此,在投资股票时,不能通过对这两个行业股票的组合投资降低风险.%Real estate markets and financial markets play essential roles for the continuous growth of developing economies. The development of these two markets has an interrelated influence on one other. Recent studies show that real estate and financial markets are linearly correlated with each other. However, the nonlinear Graner causality between these two markets does not exist. Most of these studies are qualitative and have paid little attention to using stock data to analyze the dependence structure between the real estate and financial industries.This paper applies the Copulas theory to investigate the dependence structure between real estate and financial industries. The Copula theory can capture nonlinear, asymmetric and tail dependence. Our analysis is based on the stock database of Tsinghua Financial Data from July 2, 2001 to August 5, 2009. We are able to use 1,953 pairs of data. Univariate distribution method is based on a symmeparametric extreme value model. EV Copulas, Archimedean Copulas and Archimax Copulas simulate the correlation between real estate and financial markets.The first part of this study estimates the parameters of the Copula function. We adopt the margin inference method by estimating the parameters for the

  19. Structural and functional neuroimaging in intractable epilepsy

    Directory of Open Access Journals (Sweden)

    Chinchure Swati

    2010-01-01

    Full Text Available Medical management remains unsatisfactory in about a third of patients with epilepsy and some of them are candidates for resective epilepsy surgery. Structural and functional neuroimaging plays an important role in the identification of the precise cortical region responsible for seizures and is very crucial for a good surgical outcome. Furthermore, identification of eloquent cortical areas near the region to be resected is essential to avoid postoperative neurologic deficit. The magnetic resonance imaging (MRI protocol for epilepsy can be individually tailored depending on the seizure semiology and possibly electroencephalography. New MRI techniques demonstrate the structure of the brain in fine detail, help in understanding the underlying pathology, and demonstrate functional activity of the brain with high spatial and temporal resolution. Metabolic imaging techniques, such as positron emission tomography (PET and single photon emission tomography (SPECT visualize metabolic alterations of the brain in the ictal and interictal states. In MR-negative epilepsy patients, these techniques may have localizing value. The proper use and interpretation of the findings provided by these new technologies is crucial. In this review article, we discuss various conventional and advanced MRI techniques, interpretation of various findings, and the role of functional imaging modalities, such as functional MRI, PET, and SPECT in the localization of epileptogenic substrate as well as for understanding the pathophysiology, propagation, and neurochemical correlates of epilepsy.

  20. Shaping inhibition: activity dependent structural plasticity of GABAergic synapses

    Directory of Open Access Journals (Sweden)

    Carmen E Flores

    2014-10-01

    Full Text Available Inhibitory transmission through the neurotransmitter Ɣ-aminobutyric acid (GABA shapes network activity in the mammalian cerebral cortex by filtering synaptic incoming information and dictating the activity of principal cells. The incredibly diverse population of cortical neurons that use GABA as neurotransmitter shows an equally diverse range of mechanisms that regulate changes in the strength of GABAergic synaptic transmission and allow them to dynamically follow and command the activity of neuronal ensembles. Similarly to glutamatergic synaptic transmission, activity-dependent functional changes in inhibitory neurotransmission are accompanied by alterations in GABAergic synapse structure that range from morphological reorganization of postsynaptic density to de novo formation and elimination of inhibitory contacts. Here we review several aspects of structural plasticity of inhibitory synapses, including its induction by different forms of neuronal activity, behavioral and sensory experience and the molecular mechanisms and signaling pathways involved. We discuss the functional consequences of GABAergic synapse structural plasticity for information processing and memory formation in view of the heterogenous nature of the structural plasticity phenomena affecting inhibitory synapses impinging on somatic and dendritic compartments of cortical and hippocampal neurons.

  1. Transverse momentum-dependent parton distribution functions in lattice QCD

    Energy Technology Data Exchange (ETDEWEB)

    Engelhardt, Michael G. [New Mexico State University; Musch, Bernhard U. [Tech. University Munich; Haegler, Philipp G. [Tech. University Munich; Negele, John W. [MIT; Schaefer, Andreas [Regensburg

    2013-08-01

    A fundamental structural property of the nucleon is the distribution of quark momenta, both parallel as well as perpendicular to its propagation. Experimentally, this information is accessible via selected processes such as semi-inclusive deep inelastic scattering (SIDIS) and the Drell-Yan process (DY), which can be parametrized in terms of transversemomentum-dependent parton distributions (TMDs). On the other hand, these distribution functions can be extracted from nucleon matrix elements of a certain class of bilocal quark operators in which the quarks are connected by a staple-shaped Wilson line serving to incorporate initial state (DY) or final state (SIDIS) interactions. A scheme for evaluating such matrix elements within lattice QCD is developed. This requires casting the calculation in a particular Lorentz frame, which is facilitated by a parametrization of the matrix elements in terms of invariant amplitudes. Exploratory results are presented for the time-reversal odd Sivers and Boer-Mulders transverse momentum shifts.

  2. Decay of autoionizing states in time-dependent density functional and reduced density matrix functional theory

    Energy Technology Data Exchange (ETDEWEB)

    Kapoor, Varun; Brics, Martins; Bauer, Dieter [Institut fuer Physik, Universitaet Rostock, 18051 Rostock (Germany)

    2013-07-01

    Autoionizing states are inaccessible to time-dependent density functional theory (TDDFT) using known, adiabatic Kohn-Sham (KS) potentials. We determine the exact KS potential for a numerically exactly solvable model Helium atom interacting with a laser field that is populating an autoionizing state. The exact single-particle density of the population in the autoionizing state corresponds to that of the energetically lowest quasi-stationary state in the exact KS potential. We describe how this exact potential controls the decay by a barrier whose height and width allows for the density to tunnel out and decay with the same rate as in the ab initio time-dependent Schroedinger calculation. However, devising a useful exchange-correlation potential that is capable of governing such a scenario in general and in more complex systems is hopeless. As an improvement over TDDFT, time-dependent reduced density matrix functional theory has been proposed. We are able to obtain for the above described autoionization process the exact time-dependent natural orbitals (i.e., the eigenfunctions of the exact, time-dependent one-body reduced density matrix) and study the potentials that appear in the equations of motion for the natural orbitals and the structure of the two-body density matrix expanded in them.

  3. Structure and functions of fungal cell surfaces

    Science.gov (United States)

    Nozawa, Y.

    1984-01-01

    A review with 24 references on the biochemistry, molecular structure, and function of cell surfaces of fungi, especially dermatophytes: the chemistry and structure of the cell wall, the effect of polyene antibiotics on the morphology and function of cytoplasmic membranes, and the chemical structure and function of pigments produced by various fungi are discussed.

  4. Tropomyosin structure and function new insights.

    Science.gov (United States)

    Muthuchamy, M; Rethinasamy, P; Wieczorek, D F

    1997-05-01

    Cardiac muscle contraction is dependent upon a cooperative interaction between thick and thin filament sarcomeric proteins. Tropomyosin (TM), an essential thin filament protein, interacts with actin and the troponin complex to regulate contractile activity. During muscle contraction, an increase of calcium (Ca(2+)) in the myofilament space promotes binding of Ca(2+) to troponin C, which alters the conformational state of TM and facilitates acto-myosin interactions. By coupling classic genetic approaches with recent developments in transgenic animal model systems, new insights have been provided on the functional role of TM isoforms in both normal and disease states. The focus of this article is to review the current state of knowledge on TM structure and function, with a particular emphasis on myocardial expression in transgenic mouse model systems. (Trends Cardiovasc Med 1997;7:124-128). © 1997, Elsevier Science Inc.

  5. Calculation of the Gluon Distribution Function Using Alternative Method for the Proton Structure Function

    Institute of Scientific and Technical Information of China (English)

    N.Ghahramany; G.R.Boroun

    2003-01-01

    A calculation of the proton structure function F2(x,Q2) is reported with an approximation method that relates the reduced cross section derivative and the F2(x, Q2) scaling violation at low x by using quadratic form for the structure function. This quadratic form approximation method can be used to determine the structure function F2 (x, Q2) from the HERA reduced cross section data taken at low x. This new approach can determine the structure functions F2(x,Q2) with reasonable precision even for low x values which have not been investigated. We observe that the Q2 dependence is quadratic over the full kinematic covered range. To test the validity of our new determined structure functions, we find the gluon distribution function in the leading order approximation with our new calculation for the structure functions and compare them with the QCD parton distribution functions.

  6. Calculation of the Gluon Distribution Function Using Alternative Method for the Proton Structure Function

    Institute of Scientific and Technical Information of China (English)

    N. Ghahramany; G.R. Boroun

    2003-01-01

    A calculation of the proton structure function F2(x,Q2) is reported with an approximation method that relates the reduced cross section derivative and the F2(x, Q2) scaling violation at low x by using quadratic form for the structure function. This quadratic form approximation method can be used to determine the structure function F2 (x, Q2)from the HERA reduced cross section data taken at low x. This new approach can determine the structure functions F2(x,Q2) with reasonable precision even for low x values which have not been investigated. We observe that the Q2 dependence is quadratic over the full kinematic covered range. To test the validity of our new determined structure functions, wefind the gluon distribution function in the leading order approximation with our new calculation for the structure functions and compare them with the QCD parton distribution functions.

  7. Novel Structure and Function of Typhoid Toxin

    Science.gov (United States)

    ... Matters NIH Research Matters July 29, 2013 Novel Structure and Function of Typhoid Toxin Structure of typhoid toxin, showing the 2 A subunits ( ... to cultured cells. The scientists next determined the structure of the typhoid toxin. The toxin was already ...

  8. Structure and Function of Lipase

    DEFF Research Database (Denmark)

    Skjold-Jørgensen, Jakob

    Lipases are triacylglycerol hydrolases (EC 3.1.1.3) which are able to act on water-insoluble esters, butdisplay very low activity towards water-soluble, monomeric substrates. This is ascribed to theircharacteristic activation mechanism occurring at the boundary between water and lipid, i.e. the w......Lipases are triacylglycerol hydrolases (EC 3.1.1.3) which are able to act on water-insoluble esters, butdisplay very low activity towards water-soluble, monomeric substrates. This is ascribed to theircharacteristic activation mechanism occurring at the boundary between water and lipid, i.......e. the waterlipidinterface. For Thermomyces lanuginosus lipase (TlL) and related lipases, activation of the enzymeinvolves a rearrangement of a structural domain, called the “lid”, which covers the active site inhomogenous aqueous solution. At the water-lipid interface, the lid is displaced from the active site andmoves...... towards an open conformation enabling the substrate to gain access, thus initiating catalysis.Lipases have been studied for decades and their functional features have drawn much attention withinindustrial applications since their first discovery. However, given that their molecular action takes placeat...

  9. Soft nanotechnology: "structure" vs. "function".

    Science.gov (United States)

    Whitesides, George M; Lipomi, Darren J

    2009-01-01

    This paper offers a perspective on "soft nanotechnology"; that is, the branch of nanotechnology concerned with the synthesis and properties of organic and organometallic nanostructures, and with nanofabrication using techniques in which soft components play key roles. It begins with a brief history of soft nanotechnology. This history has followed a path involving a gradual shift from the promise of revolutionary electronics, nanorobotics, and other futuristic concepts, to the realization of evolutionary improvements in the technology for current challenges in information technology, medicine, and sustainability. Soft nanoscience is an area that is occupied principally by chemists, and is in many ways indistinguishable from "nanochemistry". The paper identifies the natural tendency of its practitioners--exemplified by the speakers at this Faraday Discussion--to focus on synthesis and structure, rather than on function and application, of nanostructures. Soft nanotechnology has the potential to apply to a wide variety of large-scale applied (information technology, healthcare cost reduction, sustainability, energy) and fundamental (molecular biochemistry, cell biology, charge transport in organic matter) problems.

  10. Structural Response Analysis under Dependent Variables Based on Probability Boxes

    National Research Council Canada - National Science Library

    Xiao, Z; Yang, G

    2015-01-01

      This paper considers structural response analysis when structural uncertainty parameters distribution cannot be specified precisely due to lack of information and there are complex dependencies in the variables...

  11. The Dependence of All-Atom Statistical Potentials on Structural Training Database

    OpenAIRE

    Zhang, Chi; Liu, Song; Zhou, Hongyi; Zhou, Yaoqi

    2004-01-01

    An accurate statistical energy function that is suitable for the prediction of protein structures of all classes should be independent of the structural database used for energy extraction. Here, two high-resolution, low-sequence-identity structural databases of 333 α-proteins and 271 β-proteins were built for examining the database dependence of three all-atom statistical energy functions. They are RAPDF (residue-specific all-atom conditional probability discriminatory function), atomic KBP ...

  12. Structure-function analysis of CYP27B1 and CYP27A1. Studies on mutants from patients with vitamin D-dependent rickets type I (VDDR-I) and cerebrotendinous xanthomatosis (CTX).

    Science.gov (United States)

    Sawada, N; Sakaki, T; Kitanaka, S; Kato, S; Inouye, K

    2001-12-01

    We have determined eight types of missense mutants of CYP27B1 from Japanese vitamin D-dependent rickets type I (VDDR-I) patients [Kitanaka, S., Takeyama, K., Murayama, A., Sato, T., Okumura, K., Nogami, M., Hasegawa, Y., Niimi, H., Yanagisawa, J., Tanaka, T. & Kato, S. (1998) New England J. Med., 338, 653-661 and Kitanaka, S., Murayama, A., Sakaki, T., Inouye, K., Seino, Y., Fukumoto, S., Shima, M., Yukizane, S., Takayanagi, M., Niimi, H., Takeyama, K. & Kato, S. (1999) J. Clin. Endocrine Metab., 84, 4111-4117]. None of the CYP27B1 mutants showed 1alpha-hydroxylase activity towards 25-hydroxyvitamin D3. Thus, it was assumed that the mutated amino-acid residues play important roles in the 1alpha-hydroxylase activity, such as substrate binding, activation of molecular oxygen, interaction with adrenodoxin, and folding of the cytochrome P450 structure. To examine our hypothesis, we generated various mutants of CYP27B1 and studied their enzymatic properties. In addition, the corresponding mutations were introduced to CYP27A1, which belongs to the same family as CYP27B1. As CYP27A1 showed much higher expression level than CYP27B1 in Escherichia coli, further analysis including heme-binding and substrate-binding was performed with CYP27A1 in place of CYP27B1. Western blot analysis, spectral analysis including reduced CO-difference spectra and substrate-induced difference spectra, and enzymatic analysis of the mutant CYP27A1 gave information on the structure-function relationships of both CYP27A1 and CYP27B1. Although the sequence alignment suggested that Arg107, Gly125, and Pro497 of CYP27B1 might be involved in substrate binding, the experimental data strongly suggested that mutations of these amino-acid residues destroyed the tertiary structure of the substrate-heme pocket. It was also suggested that Arg389 and Arg453 of CYP27B1 were involved in heme-propionate binding, and Asp164 stabilized the four-helix bundle consisting of D, E, I and J helices, possibly by forming

  13. BALANCE FUNCTIONS : Multiplicity and transverse momentum dependence of the charge dependent correlations in ALICE

    NARCIS (Netherlands)

    Rodriguez Manso, A.

    2015-01-01

    The measurement of charge-dependent correlations between positively and negatively charged particles as a function of pseudorapidity and azimuthal angle, known as the \\emph{balance functions}, provide insight to the properties of matter created in high-energy collisions. The balance functions are ar

  14. Ubiquitination-dependent mechanisms regulate synaptic growth and function.

    Science.gov (United States)

    DiAntonio, A; Haghighi, A P; Portman, S L; Lee, J D; Amaranto, A M; Goodman, C S

    2001-07-26

    The covalent attachment of ubiquitin to cellular proteins is a powerful mechanism for controlling protein activity and localization. Ubiquitination is a reversible modification promoted by ubiquitin ligases and antagonized by deubiquitinating proteases. Ubiquitin-dependent mechanisms regulate many important processes including cell-cycle progression, apoptosis and transcriptional regulation. Here we show that ubiquitin-dependent mechanisms regulate synaptic development at the Drosophila neuromuscular junction (NMJ). Neuronal overexpression of the deubiquitinating protease fat facets leads to a profound disruption of synaptic growth control; there is a large increase in the number of synaptic boutons, an elaboration of the synaptic branching pattern, and a disruption of synaptic function. Antagonizing the ubiquitination pathway in neurons by expression of the yeast deubiquitinating protease UBP2 (ref. 5) also produces synaptic overgrowth and dysfunction. Genetic interactions between fat facets and highwire, a negative regulator of synaptic growth that has structural homology to a family of ubiquitin ligases, suggest that synaptic development may be controlled by the balance between positive and negative regulators of ubiquitination.

  15. Modeling of the structure-specific kinetics of abiotic, dark reduction of Hg(II) complexed by O/N and S functional groups in humic acids while accounting for time-dependent structural rearrangement

    Science.gov (United States)

    Jiang, Tao; Skyllberg, Ulf; Wei, Shiqiang; Wang, Dingyong; Lu, Song; Jiang, Zhenmao; Flanagan, Dennis C.

    2015-04-01

    Dark reduction of Hg(II) to Hg(0) in deep waters, soils and sediments accounts for a large part of legacy Hg recycling back to the atmosphere. Natural organic matter (NOM) plays a dual role in the process, acting as an electron donor and complexation agent of Hg(II). Experimental determination of rates of dark Hg(II) reduction is complicated by the simultaneously ongoing kinetics of Hg(II) rearrangement from the abundant, relatively weakly bonding RO/N (carboxyl, amino) groups in NOM to the much stronger bonding RSH (thiol) group. In this study, kinetics of the rearrangement are accounted for and we report rates of dark Hg(II) reduction for two molecular structures in presence of humic acids (HA) extracted from three different sources. Values on the pseudo first-order rate constant for the proposed structure Hg(OR)2 (kredHg(OR)2) were 0.18, 0.22 and 0.35 h-1 for Peat, Coal and Soil HA, respectively, and values on the constant for the proposed structure RSHgOR (kred RSHgOR) were 0.003 and 0.006 h-1 for Peat and Soil HA, respectively. The Hg(SR)2 structure is the thermodynamically most stable, but the limited time of the experiment (53 h) did not allow for a determination of the rate of the very slow reduction of Hg(II) in this structure. For two out of three HA samples the concentration of RSH groups optimized by the kinetic model (0.6 × 10-3 RSH groups per C atoms) was in good agreement with independent estimates provided by sulfur X-ray absorption near-edge spectroscopy (S XANES). Experiments conducted at varying concentrations of Hg(II) and HA demonstrated a positive relationship between Hg(II) reduction and concentrations of specific Hg(II) structures and electron donor groups, suggesting first order in each of these two components. The limitation of the Hg(II) reduction by electron donating groups of HA, as represented by the native reducing capacity (NRC), was demonstrated for the Coal HA sample. Normalization to NRC resulted in pseudo second-order rate

  16. Extracting nucleon spin structure functions from nuclear data

    Energy Technology Data Exchange (ETDEWEB)

    Thomas, A.W.; Afnan, I.R.; Bissey, F. [CSSM, University of Adelaide (Australia)

    2000-05-01

    The determination of the spin-dependent structure functions of the nucleons from nuclear data requires a knowledge of the changes induced by the nuclear medium. This is especially important for the neutron because there are no free neutron targets. We present the results of a study of the accuracy with which one can extract the neutron spin structure function from data on polarized {sup 3}He. This study is based on a three-body calculation of the wave function of the A=3 system, which is then used to calculate the nuclear structure functions including binding and off-shell effects. (author)

  17. Generalization of Dielectric-Dependent Hybrid Functionals to Finite Systems

    Science.gov (United States)

    Brawand, Nicholas P.; Vörös, Márton; Govoni, Marco; Galli, Giulia

    2016-10-01

    The accurate prediction of electronic and optical properties of molecules and solids is a persistent challenge for methods based on density functional theory. We propose a generalization of dielectric-dependent hybrid functionals to finite systems where the definition of the mixing fraction of exact and semilocal exchange is physically motivated, nonempirical, and system dependent. The proposed functional yields ionization potentials, and fundamental and optical gaps of many, diverse molecular systems in excellent agreement with experiments, including organic and inorganic molecules and semiconducting nanocrystals. We further demonstrate that this hybrid functional gives the correct alignment between energy levels of the exemplary TTF-TCNQ donor-acceptor system.

  18. Work function of elemental metals and its face dependence ...

    African Journals Online (AJOL)

    Journal of the Nigerian Association of Mathematical Physics. Journal Home ... Open Access DOWNLOAD FULL TEXT Subscription or Fee Access. Work function of elemental metals and its face dependence: Stabilized Jellium approach.

  19. State dependent matrices and balanced energy functions for nonlinear systems

    NARCIS (Netherlands)

    Scherpen, Jacquelien M.A.; Gray, W. Steven

    2000-01-01

    The nonlinear extension of the balancing procedure requires the case of state dependent quadratic forms for the energy functions, i.e., the nonlinear extensions of the linear Gramians are state dependent matrices. These extensions have some interesting ambiguities that do not occur in the linear cas

  20. Oppor tunistic maintenance for multi-component systems considering structural dependence and economic dependence

    Institute of Scientific and Technical Information of China (English)

    Junbao Geng; Michael Azarian; Michael Pecht

    2015-01-01

    Although opportunistic maintenance strategies are widely used for multi-component systems, al opportunistic mainte-nance strategies only consider economic dependence and do not take structural dependence into account. An opportunistic main-tenance strategy is presented for a multi-component system that considers both structural dependence and economic dependence. The cost relation and time relation among components based on structural dependence are developed. The maintenance strategy for each component of a multi-component system involves one of five maintenance actions, namely, no-maintenance, a minimal maintenance action, an imperfect maintenance action, a perfect maintenance action, and a replacement action. The maintenance action is determined by the virtual age of the component, the life expectancy of the component, and the age threshold values. Monte Carlo simulation is designed to obtain the optimal oppor-tunistic maintenance strategy of the system over its lifetime. The simulation result reveals that the minimum maintenance cost with a strategy that considers structural dependence is less than that with a strategy that does not consider structural dependence. The availability with a strategy that considers structural dependence is greater than that with a strategy that does not consider structural dependence under the same conditions.

  1. Random Time Dependent Resistance Analysis on Reinforced Concrete Structures

    Institute of Scientific and Technical Information of China (English)

    GUAN Chang-sheng; WU Ling

    2002-01-01

    The analysis method on random time dependence of reinforced concrete material is introduced,the effect mechanism on reinforced concrete are discussed, and the random time dependence resistance of reinforced concrete is studied. Furthermore, the corrosion of steel bar in reinforced concrete structures is analyzed. A practical statistical method of evaluating the random time dependent resistance, which includes material, structural size and calculation influence, is also established. In addition, an example of predicting random time dependent resistance of reinforced concrete structural element is given.

  2. The effect of oxide shell thickness on the structural, electronic, and optical properties of Si-SiO2 core-shell nano-crystals: A (time dependent)density functional theory study

    Science.gov (United States)

    Nazemi, Sanaz; Pourfath, Mahdi; Soleimani, Ebrahim Asl; Kosina, Hans

    2016-04-01

    Due to their tunable properties, silicon nano-crystals (NC) are currently being investigated. Quantum confinement can generally be employed for size-dependent band-gap tuning at dimensions smaller than the Bohr radius (˜5 nm for silicon). At the nano-meter scale, however, increased surface-to-volume ratio makes the surface effects dominant. Specifically, in Si-SiO2 core-shell semiconductor NCs the interfacial transition layer causes peculiar electronic and optical properties, because of the co-existence of intermediate oxidation states of silicon (Sin+, n = 0-4). Due to the presence of the many factors involved, a comprehensive understanding of the optical properties of these NCs has not yet been achieved. In this work, Si-SiO2 NCs with a diameter of 1.1 nm and covered by amorphous oxide shells with thicknesses between 2.5 and 4.75 Å are comprehensively studied, employing density functional theory calculations. It is shown that with increased oxide shell thickness, the low-energy part of the optical transition spectrum of the NC is red shifted and attenuated. Moreover, the absorption coefficient is increased in the high-energy part of the spectrum which corresponds to SiO2 transitions. Structural examinations indicate a larger compressive stress on the central silicon cluster with a thicker oxide shell. Examination of the local density of states reveals the migration of frontier molecular orbitals from the oxide shell into the silicon core with the increase of silica shell thickness. The optical and electrical properties are explained through the analysis of the density of states and the spatial distribution of silicon sub-oxide species.

  3. Executive Functions in Tobacco Dependence: Importance of Inhibitory Capacities.

    Directory of Open Access Journals (Sweden)

    Valentin Flaudias

    Full Text Available Executive functions are linked to tobacco dependence and craving. In this cross-sectional study, we assessed the impact of three executive functions: updating, inhibition and shifting processes on tobacco craving and dependence.134 tobacco consumers were included in this study: 81 moderately (Fagerström score 7. Dependence was assessed with the Fagerström test and craving with the tobacco craving questionnaire (TCQ 12. We used the Stroop test and the Hayling test to measure inhibition, the Trail Making Test to measure shifting processes and the n-back test to measure updating processes. A multivariate logistic model was used to assess which variables explained best the level of nicotine dependence.Inhibition (p = 0.002 and updating (p = 0.014 processes, but not shifting processes, were associated with higher tobacco dependence. Inhibition capacity had a significant effect on the nicotine dependence level independently of age, education, time since last cigarette, intellectual quotient, craving, updating and shifting process.Nicotine dependence level seems better explained by inhibition capacities than by craving and updating effects. The capacity to inhibit our behaviours is a good predictor of the severity of tobacco dependence. Our results suggest a prefrontal cortex dysfunction affecting the inhibitory capacities of heavy tobacco dependent smokers. Further studies are needed to investigate the application of these findings in the treatment of tobacco dependence.

  4. Sensitive Dependence of Mental Function on Prefrontal Cortex

    OpenAIRE

    Alen J Salerian

    2015-01-01

    This study offers evidence to suggest that both normalcy and psychiatric illness are sensitively dependent upon prefrontal cortex function. In general, the emergence of psychiatric symptoms coincide with diminished influence of prefrontal cortex function. The mediating influence of prefrontal cortex may be independent of molecular and regional brain dysfunctions contributory to psychiatric illness.

  5. Conformation of repaglinide: A solvent dependent structure

    Science.gov (United States)

    Chashmniam, Saeed; Tafazzoli, Mohsen

    2017-09-01

    Experimental and theoretical conformational study of repaglinide in chloroform and dimethyl sulfoxide was investigated. By applying potential energy scanning (PES) at B3LYP/6-311++g** and B3LYP-D3/6-311++g** level of theory on rotatable single bonds, four stable conformers (R1-R4) were identified. Spin-spin coupling constant values were obtained from a set of 2D NMR spectra (Hsbnd H COSY, Hsbnd C HMQC and Hsbnd C HMBC) and compared to its calculated values. Interestingly, from 1HNMR and 2D-NOESY NMR, it has been found that repaglinide structure is folded in CDCl3 and cause all single bonds to rotate at an extremely slow rate. On the other hand, in DMSO-d6, with strong solvent-solute intermolecular interactions, the single bonds rotate freely. Also, energy barrier and thermodynamic parameters for chair to chair interconversion was measured (13.04 kcal mol-1) in CDCl3 solvent by using temperature dynamic NMR.

  6. Ran-dependent nuclear export mediators: a structural perspective.

    Science.gov (United States)

    Güttler, Thomas; Görlich, Dirk

    2011-08-31

    Nuclear export is an essential eukaryotic activity. It proceeds through nuclear pore complexes (NPCs) and is mediated by soluble receptors that shuttle between nucleus and cytoplasm. RanGTPase-dependent export mediators (exportins) constitute the largest class of these carriers and are functionally highly versatile. All of these exportins load their substrates in response to RanGTP binding in the nucleus and traverse NPCs as ternary RanGTP-exportin-cargo complexes to the cytoplasm, where GTP hydrolysis leads to export complex disassembly. The different exportins vary greatly in their substrate range. Recent structural studies of both protein- and RNA-specific exporters have illuminated how exportins bind their cargoes, how Ran triggers cargo loading and how export complexes are disassembled in the cytoplasm. Here, we review the current state of knowledge and highlight emerging principles as well as prevailing questions.

  7. Survivability Specification Framework for Dependability- Functionality Codesign of ERTS

    Institute of Scientific and Technical Information of China (English)

    JIN Yong-xian

    2005-01-01

    In order to maintain the dependability of system and meet the functional need of users desire, this paper introduces a survivability mechanism into embedded real-time system, and proposes a general comprehensive approach based on a rigorous definition of survivability. This approach permits a trade-off between the function and the cost of system development. It emphasizes the ultradependable implementation of crucial function without demanding that of entire system.

  8. Nuclear effects in the structure functions

    Indian Academy of Sciences (India)

    E Marco; E Oset; S K Singh

    2003-11-01

    By using a relativistic framework and accurate nuclear spectral function the structure functions 2 and 3 of deep inelastic charged lepton and neutrino scattering are calculated in nuclei and results are presented.

  9. Mutant p53 accumulation in human breast cancer is not an intrinsic property or dependent on structural or functional disruption but is regulated by exogenous stress and receptor status.

    Science.gov (United States)

    Bouchalova, Pavla; Nenutil, Rudolf; Muller, Petr; Hrstka, Roman; Appleyard, M Virginia; Murray, Karen; Jordan, Lee B; Purdie, Colin A; Quinlan, Philip; Thompson, Alastair M; Vojtesek, Borivoj; Coates, Philip J

    2014-07-01

    Many human cancers contain missense TP53 mutations that result in p53 protein accumulation. Although generally considered as a single class of mutations that abrogate wild-type function, individual TP53 mutations may have specific properties and prognostic effects. Tumours that contain missense TP53 mutations show variable p53 stabilization patterns, which may reflect the specific mutation and/or aspects of tumour biology. We used immunohistochemistry on cell lines and human breast cancers with known TP53 missense mutations and assessed the effects of each mutation with four structure-function prediction methods. Cell lines with missense TP53 mutations show variable percentages of cells with p53 stabilization under normal growth conditions, ranging from approximately 50% to almost 100%. Stabilization is not related to structural or functional disruption, but agents that stabilize wild-type p53 increase the percentages of cells showing missense mutant p53 accumulation in cell lines with heterogeneous stabilization. The same heterogeneity of p53 stabilization occurs in primary breast cancers, independent of the effect of the mutation on structural properties or functional disruption. Heterogeneous accumulation is more common in steroid receptor-positive or HER2-positive breast cancers and cell lines than in triple-negative samples. Immunohistochemcal staining patterns associate with Mdm2 levels, proliferation, grade and overall survival, whilst the type of mutation reflects downstream target activity. Inhibiting Mdm2 activity increases the extent of p53 stabilization in some, but not all, breast cancer cell lines. The data indicate that missense mutant p53 stabilization is a complex and variable process in human breast cancers that associates with disease characteristics but is unrelated to structural or functional properties. That agents which stabilize wild-type p53 also stabilize mutant p53 has implications for patients with heterogeneous mutant p53 accumulation

  10. The structure and function of cartilage proteoglycans

    Directory of Open Access Journals (Sweden)

    P J Roughley

    2006-11-01

    Full Text Available Cartilage contains a variety of proteoglycans that are essential for its normal function. These include aggrecan, decorin, biglycan, fibromodulin and lumican. Each proteoglycan serves several functions that are determined by both its core protein and its glycosaminoglycan chains. This review discusses the structure/function relationships of the cartilage proteoglycans, and the manner in which perturbations in proteoglycan structure or abundance can adversely affect tissue function.

  11. Parametric dependence of ocean wave-radar modulation transfer functions

    Science.gov (United States)

    Plant, W. J.; Keller, W. C.; Cross, A.

    1983-01-01

    Microwave techniques at X and L band were used to determine the dependence of ocean-wave radar modulation transfer functions (MTFs) on various environmental and radar parameters during the Marine Remote Sensing experiment of 1979 (MARSEN 79). These MIF are presented, as are coherence functions between the AM and FM parts of the backscattered microwave signal. It is shown that they both depend on several of these parameters. Besides confirming many of the properties of transfer functions reported by previous authors, indications are found that MTFs decrease with increasing angle between wave propagation and antenna-look directions but are essentially independent of small changes in air-sea temperature difference. However, coherence functions are much smaller when the antennas are pointed perpendicular to long waves. It is found that X band transfer functions measured with horizontally polarized microwave radiation have larger magnitudes than those obtained by using vertical polarization.

  12. Angle-dependent strong-field molecular ionization rates with tuned range-separated time-dependent density functional theory.

    Science.gov (United States)

    Sissay, Adonay; Abanador, Paul; Mauger, François; Gaarde, Mette; Schafer, Kenneth J; Lopata, Kenneth

    2016-09-07

    Strong-field ionization and the resulting electronic dynamics are important for a range of processes such as high harmonic generation, photodamage, charge resonance enhanced ionization, and ionization-triggered charge migration. Modeling ionization dynamics in molecular systems from first-principles can be challenging due to the large spatial extent of the wavefunction which stresses the accuracy of basis sets, and the intense fields which require non-perturbative time-dependent electronic structure methods. In this paper, we develop a time-dependent density functional theory approach which uses a Gaussian-type orbital (GTO) basis set to capture strong-field ionization rates and dynamics in atoms and small molecules. This involves propagating the electronic density matrix in time with a time-dependent laser potential and a spatial non-Hermitian complex absorbing potential which is projected onto an atom-centered basis set to remove ionized charge from the simulation. For the density functional theory (DFT) functional we use a tuned range-separated functional LC-PBE*, which has the correct asymptotic 1/r form of the potential and a reduced delocalization error compared to traditional DFT functionals. Ionization rates are computed for hydrogen, molecular nitrogen, and iodoacetylene under various field frequencies, intensities, and polarizations (angle-dependent ionization), and the results are shown to quantitatively agree with time-dependent Schrödinger equation and strong-field approximation calculations. This tuned DFT with GTO method opens the door to predictive all-electron time-dependent density functional theory simulations of ionization and ionization-triggered dynamics in molecular systems using tuned range-separated hybrid functionals.

  13. Angle-dependent strong-field molecular ionization rates with tuned range-separated time-dependent density functional theory

    Science.gov (United States)

    Sissay, Adonay; Abanador, Paul; Mauger, François; Gaarde, Mette; Schafer, Kenneth J.; Lopata, Kenneth

    2016-09-01

    Strong-field ionization and the resulting electronic dynamics are important for a range of processes such as high harmonic generation, photodamage, charge resonance enhanced ionization, and ionization-triggered charge migration. Modeling ionization dynamics in molecular systems from first-principles can be challenging due to the large spatial extent of the wavefunction which stresses the accuracy of basis sets, and the intense fields which require non-perturbative time-dependent electronic structure methods. In this paper, we develop a time-dependent density functional theory approach which uses a Gaussian-type orbital (GTO) basis set to capture strong-field ionization rates and dynamics in atoms and small molecules. This involves propagating the electronic density matrix in time with a time-dependent laser potential and a spatial non-Hermitian complex absorbing potential which is projected onto an atom-centered basis set to remove ionized charge from the simulation. For the density functional theory (DFT) functional we use a tuned range-separated functional LC-PBE*, which has the correct asymptotic 1/r form of the potential and a reduced delocalization error compared to traditional DFT functionals. Ionization rates are computed for hydrogen, molecular nitrogen, and iodoacetylene under various field frequencies, intensities, and polarizations (angle-dependent ionization), and the results are shown to quantitatively agree with time-dependent Schrödinger equation and strong-field approximation calculations. This tuned DFT with GTO method opens the door to predictive all-electron time-dependent density functional theory simulations of ionization and ionization-triggered dynamics in molecular systems using tuned range-separated hybrid functionals.

  14. Factor structure of functional state of primary school age children

    Directory of Open Access Journals (Sweden)

    Davidenko O.V.

    2011-02-01

    Full Text Available The examination of primary school children to determine the ranking of significant factors that determine the structure of their functional state depending on the level of physical health. It is shown that the main factor in the structure of the functional state of younger schoolchildren in low-and lower-middle level of physical fitness is selected morpho-functional status, which characterizes the functions of the body at rest. For children with average or above average level of physical fitness is a leading factor in physical fitness of schoolchildren.

  15. Energy Dependence of String Fragmentation Function and φ Meson Production

    Institute of Scientific and Technical Information of China (English)

    SA Ben-Hao; CAI Xu; Chinorat Kobdaj; WANG Zhong-Qi; YAN Yu-Peng; ZHOU Dai-Mei

    2004-01-01

    The φ meson productions in A u+A u and/or P b+Pb collisions at AGS, SPS, RHIC, and LHC energies have been studied systematically with a hadron and string cascade model LUCIAE.After considering the energy dependence of the model parameter α in string fragmentation function and adjusting it to the experimental data of charged multiplicity to a certain extent, the model predictions for φ meson yield, rapidity, and transverse mass distributions are compatible with the experimental data at AGS, SPS and RHIC energies. A calculation for Pb+Pb collisions at LHC energy is given as well. The obtained fractional variable in string fragmentation function shows a saturation in energy dependence. It is discussed that the saturation of fractional variable in string fragmentation function might be a qualitative representation of the energy dependence of nuclear transparency.

  16. Spin Structure Functions in a Covariant Spectator Quark Model

    Energy Technology Data Exchange (ETDEWEB)

    G. Ramalho, Franz Gross and M. T. Peña

    2010-12-01

    We apply the covariant spectator quark–diquark model, already probed in the description of the nucleon elastic form factors, to the calculation of the deep inelastic scattering (DIS) spin-independent and spin-dependent structure functions of the nucleon. The nucleon wave function is given by a combination of quark–diquark orbital states, corresponding to S, D and P-waves. A simple form for the quark distribution function associated to the P and D waves is tested.

  17. Functional and Structural Brain Changes Associated with Methamphetamine Abuse

    Directory of Open Access Journals (Sweden)

    Bruce R. Russell

    2012-10-01

    Full Text Available Methamphetamine (MA is a potent psychostimulant drug whose abuse has become a global epidemic in recent years. Firstly, this review article briefly discusses the epidemiology and clinical pharmacology of methamphetamine dependence. Secondly, the article reviews relevant animal literature modeling methamphetamine dependence and discusses possible mechanisms of methamphetamine-induced neurotoxicity. Thirdly, it provides a critical review of functional and structural neuroimaging studies in human MA abusers; including positron emission tomography (PET and functional and structural magnetic resonance imaging (MRI. The effect of abstinence from methamphetamine, both short- and long-term within the context of these studies is also reviewed.

  18. Photon structure function in supersymmetric QCD revisited

    Energy Technology Data Exchange (ETDEWEB)

    Sahara, Ryo, E-mail: sahara@scphys.kyoto-u.ac.jp [Department of Physics, Graduate School of Science, Kyoto University, Kitashirakawa, Kyoto 606-8502 (Japan); Uematsu, Tsuneo, E-mail: uematsu@scphys.kyoto-u.ac.jp [Department of Physics, Graduate School of Science, Kyoto University, Kitashirakawa, Kyoto 606-8502 (Japan); Kitadono, Yoshio, E-mail: kitadono@phys.sinica.edu.tw [Institute of Physics, Academia Sinica, Taipei, Taiwan (China)

    2012-02-07

    We investigate the virtual photon structure function in the supersymmetric QCD (SQCD), where we have squarks and gluinos in addition to the quarks and gluons. Taking into account the heavy particle mass effects to the leading order in QCD and SQCD we evaluate the photon structure function and numerically study its behavior for the QCD and SQCD cases.

  19. Photon Structure Function in Supersymmetric QCD Revisited

    CERN Document Server

    Sahara, Ryo; Kitadono, Yoshio

    2011-01-01

    We investigate the virtual photon structure function in the supersymmetric QCD (SQCD), where we have squarks and gluinos in addition to the quarks and gluons. Taking into account the heavy particle mass effects to the leading order in QCD and SQCD we evaluate the photon structure function and numerically study its behavior for the QCD and SQCD cases.

  20. Structure-function clustering in multiplex brain networks

    Science.gov (United States)

    Crofts, J. J.; Forrester, M.; O'Dea, R. D.

    2016-10-01

    A key question in neuroscience is to understand how a rich functional repertoire of brain activity arises within relatively static networks of structurally connected neural populations: elucidating the subtle interactions between evoked “functional connectivity” and the underlying “structural connectivity” has the potential to address this. These structural-functional networks (and neural networks more generally) are more naturally described using a multilayer or multiplex network approach, in favour of standard single-layer network analyses that are more typically applied to such systems. In this letter, we address such issues by exploring important structure-function relations in the Macaque cortical network by modelling it as a duplex network that comprises an anatomical layer, describing the known (macro-scale) network topology of the Macaque monkey, and a functional layer derived from simulated neural activity. We investigate and characterize correlations between structural and functional layers, as system parameters controlling simulated neural activity are varied, by employing recently described multiplex network measures. Moreover, we propose a novel measure of multiplex structure-function clustering which allows us to investigate the emergence of functional connections that are distinct from the underlying cortical structure, and to highlight the dependence of multiplex structure on the neural dynamical regime.

  1. Exact response functions within the time-dependent Gutzwiller approach

    Science.gov (United States)

    Bünemann, J.; Wasner, S.; Oelsen, E. v.; Seibold, G.

    2015-02-01

    We investigate the applicability of the two existing versions of a time-dependent Gutzwiller approach (TDGA) beyond the frequently used limit of infinite spatial dimensions. To this end, we study the two-particle response functions of a two-site Hubbard model where we can compare the exact results and those derived from the TDGA. It turns out that only the more recently introduced version of the TDGA can be combined with a diagrammatic approach which allows for the evaluation of Gutzwiller wave functions in finite dimensions. For this TDGA method, we derive the time-dependent Lagrangian for general single-band Hubbard models.

  2. The transverse momentum dependent distribution functions in the bag model

    Energy Technology Data Exchange (ETDEWEB)

    Avakian, Harut; Efremov, Anatoly; Schweitzer, Peter; Yuan, Feng

    2010-01-29

    Leading and subleading twist transverse momentum dependent parton distribution functions (TMDs) are studied in a quark model framework provided by the bag model. A complete set of relations among different TMDs is derived, and the question is discussed how model-(in)dependent such relations are. A connection of the pretzelosity distribution and quark orbital angular momentum is derived. Numerical results are presented, and applications for phenomenology discussed. In particular, it is shown that in the valence-x region the bag model supports a Gaussian Ansatz for the transverse momentum dependence of TMDs.

  3. Transverse momentum dependent distribution functions in the bag model

    Energy Technology Data Exchange (ETDEWEB)

    Avakian, Harut A. [Thomas Jefferson National Accelerator Facility (TJNAF), Newport News, VA (United States); Efremov, A. V. [Joint Inst. for Nuclear Research (JINR), Dubna (Russian Federation); Schweitzer, P. [Univ. of Connecticut, Storrs, CT (United States); Yuan, F. [Brookhaven National Lab. (BNL), Upton, NY (United States). RIKEN Research Center; Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)

    2010-04-01

    Leading and subleading twist transverse momentum dependent parton distribution functions (TMDs) are studied in a quark model framework provided by the bag model. A complete set of relations among different TMDs is derived, and the question is discussed how model-(in)dependent such relations are. A connection of the pretzelosity distribution and quark orbital angular momentum is derived. Numerical results are presented, and applications for phenomenology discussed. In particular, it is shown that in the valence-x region the bag model supports a Gaussian Ansatz for the transverse momentum dependence of TMDs.

  4. Temperature dependence of the magnetization of canted spin structures

    DEFF Research Database (Denmark)

    Jacobsen, Henrik; Lefmann, Kim; Brok, Erik;

    2012-01-01

    Numerous studies of the low-temperature saturation magnetization of ferrimagnetic nanoparticles and diamagnetically substituted ferrites have shown an anomalous temperature dependence. It has been suggested that this is related to freezing of canted magnetic structures. We present models for the ......Numerous studies of the low-temperature saturation magnetization of ferrimagnetic nanoparticles and diamagnetically substituted ferrites have shown an anomalous temperature dependence. It has been suggested that this is related to freezing of canted magnetic structures. We present models...

  5. Modeling the Dependency Structure of Integrated Intensity Processes.

    Directory of Open Access Journals (Sweden)

    Yong-Ki Ma

    Full Text Available This paper studies an important issue of dependence structure. To model this structure, the intensities within the Cox processes are driven by dependent shot noise processes, where jumps occur simultaneously and their sizes are correlated. The joint survival probability of the integrated intensities is explicitly obtained from the copula with exponential marginal distributions. Subsequently, this result can provide a very useful guide for credit risk management.

  6. WAY TO DETERMINE STIFFNESS FUNCTION OF STRUCTURE

    Institute of Scientific and Technical Information of China (English)

    WANG De-ming; GAI Bing-zheng

    2005-01-01

    For calculating the stiffness function of a structure, the differential equation of the vibration of the structure was divided into the differential equation on the original stiffness function that was known, and Fredholm integral equation of the first kind on the undetermined stiffness function that was unknown. And the stable solutions of the integral equation, when the smooth factor was equal to zero, was solved by the extrapolation with p smooth factors. So the stiffness function of the structure is obtained. Applied examples show that the method is feasible and effective.

  7. Functional evolution of nuclear structure

    OpenAIRE

    Wilson, Katherine L.; Dawson, Scott C.

    2011-01-01

    The evolution of the nucleus, the defining feature of eukaryotic cells, was long shrouded in speculation and mystery. There is now strong evidence that nuclear pore complexes (NPCs) and nuclear membranes coevolved with the endomembrane system, and that the last eukaryotic common ancestor (LECA) had fully functional NPCs. Recent studies have identified many components of the nuclear envelope in living Opisthokonts, the eukaryotic supergroup that includes fungi and metazoan animals. These compo...

  8. Time-dependent density functional theory: Causality and other problems

    Energy Technology Data Exchange (ETDEWEB)

    Ruggenthaler, Michael; Bauer, Dieter [Max-Planck-Inst. fuer Kernphysik, Heidelberg (Germany)

    2007-07-01

    Time-dependent density functional theory (TDDFT) is a reformulation of the time dependent many-body problem in quantum mechanics which is capable of reducing the computational cost to calculate, e.g., strongly driven many-electron systems enormously. Recent developments were able to overcome fundamental problems associated with ionization processes. Still vital issues have to be clarified. Besides the construction of the underlying functionals we investigate the causality problem of TDDFT by general considerations and by studying a exactly solvable system of two correlated electrons in an intense laser-pulse. For the latter system, the two alternative approaches to the construction of the action functional or a constrained functional derivative by van Leeuwen and Gal, respectively, are explored.

  9. Structure and function in flow networks

    CERN Document Server

    Rubido, Nicolás; Baptista, Murilo S

    2013-01-01

    This Letter presents a unified approach for the fundamental relationship between structure and function in flow networks by solving analytically the voltages in a resistor network, transforming the network structure to an effective all-to-all topology, and then measuring the resultant flows. Moreover, it defines a way to study the structural resilience of the graph and to detect possible communities.

  10. Light-dependent structural change of chicken retinal Cryptochrome4.

    Science.gov (United States)

    Watari, Ryuji; Yamaguchi, Chiaki; Zemba, Wataru; Kubo, Yoko; Okano, Keiko; Okano, Toshiyuki

    2012-12-14

    Animals have several classes of cryptochromes (CRYs), some of which function as core elements of circadian clockwork, circadian photoreceptors, and/or light-dependent magnetoreceptors. In addition to the circadian clock genes Cry1 and Cry2, nonmammalian vertebrates have the Cry4 gene, the molecular function of which remains unknown. Here we analyzed chicken CRY4 (cCRY4) expression in the retina with in situ hybridization and found that cCRY4 was likely transcribed in the visual pigment cells, cells in the inner nuclear layer, and retinal ganglion cells. We further developed several monoclonal antibodies to the carboxyl-terminal extension of cCRY4 and localized cCRY4 protein with immunohistochemistry. Consistent with the results of in situ hybridization, cCRY4 immunoreactivity was found in visual pigment cells and cells located at the inner nuclear layer and the retinal ganglion cell layer. Among the antibodies, one termed C1-mAb had its epitope within the carboxyl-terminal 14-amino acid sequence (QLTRDDADDPMEMK) and associated with cCRY4 in the retinal soluble fraction more strongly in the dark than under blue light conditions. Immunoprecipitation experiments under various light conditions indicated that cCRY4 from the immunocomplex formed in the dark dissociated from C1-mAb during blue light illumination as weak as 25 μW/cm(2) and that the release occurred with not only blue but also near UV light. These results suggest that cCRY4 reversibly changes its structure within the carboxyl-terminal region in a light-dependent manner and operates as a photoreceptor or magnetoreceptor with short wavelength sensitivity in the retina.

  11. Structure-function relationships in calpains.

    Science.gov (United States)

    Campbell, Robert L; Davies, Peter L

    2012-11-01

    Calpains are a family of complex multi-domain intracellular enzymes that share a calcium-dependent cysteine protease core. These are not degradative enzymes, but instead carry out limited cleavage of target proteins in response to calcium signalling. Selective cutting of cytoskeletal proteins to facilitate cell migration is one such function. The two most abundant and extensively studied members of this family in mammals, calpains 1 and 2, are heterodimers of an isoform-specific 80 kDa large subunit and a common 28 kDa small subunit. Structures of calpain-2, both Ca2+-free and bound to calpastatin in the activated Ca2+-bound state, have provided a wealth of information about the enzyme's structure-function relationships and activation. The main association between the subunits is the pairing of their C-terminal penta-EF-hand domains through extensive intimate hydrophobic contacts. A lesser contact is made between the N-terminal anchor helix of the large subunit and the penta-EF-hand domain of the small subunit. Up to ten Ca2+ ions are co-operatively bound during activation. The anchor helix is released and individual domains change their positions relative to each other to properly align the active site. Because calpains 1 and 2 require ~30 and ~350 μM Ca2+ ions for half-maximal activation respectively, it has long been argued that autoproteolysis, subunit dissociation, post-translational modifications or auxiliary proteins are needed to activate the enzymes in the cell, where Ca2+ levels are in the nanomolar range. In the absence of robust support for these mechanisms, it is possible that under normal conditions calpains are transiently activated by high Ca2+ concentrations in the microenvironment of a Ca2+ influx, and then return to an inactive state ready for reactivation.

  12. Effective Maxwell Equations from Time-dependent Density Functional Theory

    Institute of Scientific and Technical Information of China (English)

    Weinan E; Jianfeng LU; Xu YANG

    2011-01-01

    The behavior of interacting electrons in a perfect crystal under macroscopic external electric and magnetic fields is studied. Effective Maxwell equations for the macroscopic electric and magnetic fields are derived starting from time-dependent density functional theory. Effective permittivity and permeability coefficients are obtained.

  13. Bias-corrected estimation of stable tail dependence function

    DEFF Research Database (Denmark)

    Beirlant, Jan; Escobar-Bach, Mikael; Goegebeur, Yuri

    2016-01-01

    We consider the estimation of the stable tail dependence function. We propose a bias-corrected estimator and we establish its asymptotic behaviour under suitable assumptions. The finite sample performance of the proposed estimator is evaluated by means of an extensive simulation study where...

  14. Bias-corrected estimation of stable tail dependence function

    DEFF Research Database (Denmark)

    Beirlant, Jan; Escobar-Bach, Mikael; Goegebeur, Yuri

    2016-01-01

    We consider the estimation of the stable tail dependence function. We propose a bias-corrected estimator and we establish its asymptotic behaviour under suitable assumptions. The finite sample performance of the proposed estimator is evaluated by means of an extensive simulation study where...

  15. Pay-as-you-go data integration using functional dependencies

    NARCIS (Netherlands)

    Ayat, N.; Afsarmanesh, H.; Akbarinia, R.; Valduriez, P.

    2012-01-01

    Setting up a full data integration system for many application contexts, e.g. web and scientific data management, requires significant human effort which prevents it from being really scalable. In this paper, we propose IFD (Integration based on Functional Dependencies), a pay-as-you-go data integra

  16. Multicomponent density-functional theory for time-dependent systems

    NARCIS (Netherlands)

    Butriy, O.; Ebadi, H.; de Boeij, P. L.; van Leeuwen, R.; Gross, E. K. U.

    2007-01-01

    We derive the basic formalism of density functional theory for time-dependent electron-nuclear systems. The basic variables of this theory are the electron density in body-fixed frame coordinates and the diagonal of the nuclear N-body density matrix. The body-fixed frame transformation is carried ou

  17. Linear-response thermal time-dependent density functional theory

    CERN Document Server

    Pribram-Jones, Aurora; Burke, Kieron

    2015-01-01

    The van Leeuwen proof of linear-response time-dependent density functional theory (TDDFT) is generalized to thermal ensembles. This allows generalization to finite temperatures of the Gross-Kohn relation, the exchange-correlation kernel of TDDFT, and fluctuation dissipation theorem for DFT. This produces a natural method for generating new thermal exchange-correlation (XC) approximations.

  18. Structure and Function of Lipase

    DEFF Research Database (Denmark)

    Skjold-Jørgensen, Jakob

    out to calculate the energydifference between the open and closed lid conformation for TlL and a selection of lid-variants (PaperIII). Here, a correlation between experimental and theoretical data was discovered supporting the notionlid plays a key role in governing activation at the interface...... towards an open conformation enabling the substrate to gain access, thus initiating catalysis.Lipases have been studied for decades and their functional features have drawn much attention withinindustrial applications since their first discovery. However, given that their molecular action takes placeat...... onthe activation mechanism. From characterization studies of these variants we have shown (Paper I) thatthe lid-region plays a crucial role in governing interfacial activation and enzymatic activity. Specifically,using a combination of spectroscopic and enzymatic activity-based methods we have...

  19. Nitrogenase structure and function relationships by density functional theory.

    Science.gov (United States)

    Harris, Travis V; Szilagyi, Robert K

    2011-01-01

    Modern density functional theory has tremendous potential with matching popularity in metalloenzymology to reveal the unseen atomic and molecular details of structural data, spectroscopic measurements, and biochemical experiments by providing insights into unobservable structures and states, while also offering theoretical justifications for observed trends and differences. An often untapped potential of this theoretical approach is to bring together diverse experimental structural and reactivity information and allow for these to be critically evaluated at the same level. This is particularly applicable for the tantalizingly complex problem of the structure and molecular mechanism of biological nitrogen fixation. In this chapter we provide a review with extensive practical details of the compilation and evaluation of experimental data for an unbiased and systematic density functional theory analysis that can lead to remarkable new insights about the structure-function relationships of the iron-sulfur clusters of nitrogenase.

  20. Perspective: Fundamental aspects of time-dependent density functional theory

    Science.gov (United States)

    Maitra, Neepa T.

    2016-06-01

    In the thirty-two years since the birth of the foundational theorems, time-dependent density functional theory has had a tremendous impact on calculations of electronic spectra and dynamics in chemistry, biology, solid-state physics, and materials science. Alongside the wide-ranging applications, there has been much progress in understanding fundamental aspects of the functionals and the theory itself. This Perspective looks back to some of these developments, reports on some recent progress and current challenges for functionals, and speculates on future directions to improve the accuracy of approximations used in this relatively young theory.

  1. Density-functional perturbation theory goes time-dependent

    OpenAIRE

    Gebauer, Ralph; Rocca, Dario; Baroni, Stefano

    2009-01-01

    The scope of time-dependent density-functional theory (TDDFT) is limited to the lowest portion of the spectrum of rather small systems (a few tens of atoms at most). In the static regime, density-functional perturbation theory (DFPT) allows one to calculate response functions of systems as large as currently dealt with in ground-state simulations. In this paper we present an effective way of combining DFPT with TDDFT. The dynamical polarizability is first expressed as an off-diagonal matrix e...

  2. Functional materials discovery using energy-structure-function maps

    Science.gov (United States)

    Pulido, Angeles; Chen, Linjiang; Kaczorowski, Tomasz; Holden, Daniel; Little, Marc A.; Chong, Samantha Y.; Slater, Benjamin J.; McMahon, David P.; Bonillo, Baltasar; Stackhouse, Chloe J.; Stephenson, Andrew; Kane, Christopher M.; Clowes, Rob; Hasell, Tom; Cooper, Andrew I.; Day, Graeme M.

    2017-03-01

    Molecular crystals cannot be designed in the same manner as macroscopic objects, because they do not assemble according to simple, intuitive rules. Their structures result from the balance of many weak interactions, rather than from the strong and predictable bonding patterns found in metal-organic frameworks and covalent organic frameworks. Hence, design strategies that assume a topology or other structural blueprint will often fail. Here we combine computational crystal structure prediction and property prediction to build energy-structure-function maps that describe the possible structures and properties that are available to a candidate molecule. Using these maps, we identify a highly porous solid, which has the lowest density reported for a molecular crystal so far. Both the structure of the crystal and its physical properties, such as methane storage capacity and guest-molecule selectivity, are predicted using the molecular structure as the only input. More generally, energy-structure-function maps could be used to guide the experimental discovery of materials with any target function that can be calculated from predicted crystal structures, such as electronic structure or mechanical properties.

  3. Orientation-dependent backbone-only residue pair scoring functions for fixed backbone protein design

    Directory of Open Access Journals (Sweden)

    Bordner Andrew J

    2010-04-01

    Full Text Available Abstract Background Empirical scoring functions have proven useful in protein structure modeling. Most such scoring functions depend on protein side chain conformations. However, backbone-only scoring functions do not require computationally intensive structure optimization and so are well suited to protein design, which requires fast score evaluation. Furthermore, scoring functions that account for the distinctive relative position and orientation preferences of residue pairs are expected to be more accurate than those that depend only on the separation distance. Results Residue pair scoring functions for fixed backbone protein design were derived using only backbone geometry. Unlike previous studies that used spherical harmonics to fit 2D angular distributions, Gaussian Mixture Models were used to fit the full 3D (position only and 6D (position and orientation distributions of residue pairs. The performance of the 1D (residue separation only, 3D, and 6D scoring functions were compared by their ability to identify correct threading solutions for a non-redundant benchmark set of protein backbone structures. The threading accuracy was found to steadily increase with increasing dimension, with the 6D scoring function achieving the highest accuracy. Furthermore, the 3D and 6D scoring functions were shown to outperform side chain-dependent empirical potentials from three other studies. Next, two computational methods that take advantage of the speed and pairwise form of these new backbone-only scoring functions were investigated. The first is a procedure that exploits available sequence data by averaging scores over threading solutions for homologs. This was evaluated by applying it to the challenging problem of identifying interacting transmembrane alpha-helices and found to further improve prediction accuracy. The second is a protein design method for determining the optimal sequence for a backbone structure by applying Belief Propagation

  4. Identifying microproduction inaccuracies with Knudsen number depending correction functions

    Science.gov (United States)

    Groll, R.; Gomez, J.

    2016-11-01

    The pressure drop of a transonic Laval nozzle depends on the rarefaction of the gas flow. So relative deviations of the numerical data are a measure for describing the influence of the rarefaction of the gas flow. This deviation is predicted by using a second-order modeling approximation for the Knudsen number depending correction function in the slip-flow regime. The production accuracy is able to be read in these deviation functions because of a deviation from the analytical solutions of the slip-flow influence. With the usage of experimental data the correction function can be calibrated through elimination of the error resulting from the accuracy. The investigated case is a micronozzle flow with Knudsen numbers of slip-flow regime near the nozzle throat in vacuum environment. Compared gases are neon, argon, krypton and xenon.

  5. Functional-dependent and size-dependent uptake of nanoparticles in PC12

    Energy Technology Data Exchange (ETDEWEB)

    Sakai, N; Matsui, Y; Nakayama, A; Yoneda, M [Department of Environment Engineering, Graduate School of Engineering, Kyoto University, 4 Kyotodaigaku Katsura, Nishikyo-ku, Kyoto 6158540 (Japan); Tsuda, A, E-mail: sakai@risk.env.kyoto-u.ac.jp [Department of Environmental Health, Harvard School of Public Health, 665 Huntington Avenue, Boston, MA 02115 (United States)

    2011-07-06

    It is suggested that the uptake of nanoparticles is changed by the particle size or the surface modification. In this study, we quantified the uptake of nanoparticles in PC12 cells exposed Quantum Dots with different surface modification or fluorescent polystyrene particles with different particle size. The PC12 cells were exposed three types of the Quantum Dots (carboxyl base-functionalized, amino base-functionalized or non-base-functionalized) or three types of the fluorescent particles (22 nm, 100 nm or 1000 nm) for 3 hours. The uptake of the nanoparticles was quantified with a spectrofluorophotometer. The carboxyl base-functionalized Quantum Dots were considerably taken up by the cells than the non-base-functionalized Quantum Dots. Conversely, the amino base-functionalized Quantum Dots were taken up by the cells less frequently than the non-base-functionalized Quantum Dots. The particle number of the 22 nm-nanoparticles taken up by the cells was about 53 times higher than the 100 nm-particles. However, the particle weight of the 100 nm-particles taken up by the cells was higher than that of the 22 nm-nanoparticles. The 1000 nm-particles were adhered to the cell membrane, but they were little taken up by the cells. We concluded that nanoparticles can be taken up nerve cells in functional-dependent and size-dependent manners.

  6. Extensions of PDZ domains as important structural and functional elements

    OpenAIRE

    Wang, Conan K.; Pan, Lifeng; Chen, Jia; Zhang, Mingjie

    2010-01-01

    ‘Divide and conquer’ has been the guiding strategy for the study of protein structure and function. Proteins are divided into domains with each domain having a canonical structural definition depending on its type. In this review, we push forward with the interesting observation that many domains have regions outside of their canonical definition that affect their structure and function; we call these regions ‘extensions’. We focus on the highly abundant PDZ (PSD-95, DLG1 and ZO-1) domain. Us...

  7. Exploration of a modified density dependence in the Skyrme functional

    CERN Document Server

    Erler, J; Reinhard, P -G

    2010-01-01

    A variant of the basic Skyrme-Hartree-Fock (SHF) functional is considered dealing with a new form of density dependence. It employs only integer powers and thus will allow a more sound basis for projection schemes (particle number, angular momentum). We optimize the new functional with exactly the same adjustment strategy as used in an earlier study with a standard Skyrme functional. This allows direct comparisons of the performance of the new functional relative to the standard one. We discuss various observables: bulk properties of finite nuclei, nuclear matter, giant resonances, super-heavy elements, and energy systematics. The new functional performs at least as well as the standard one, but offers a wider range of applicability (e.g. for projection) and more flexibility in the regime of high densities.

  8. Concentration dependent structural parameters of liquid Al-Fe alloys

    Science.gov (United States)

    Lalnuntluanga, C.; Mishra, Raj Kumar

    2016-10-01

    Square well potential is perturbed over Lebowtiz solution of hard sphere mixtures to determine direct correlation function,C(0) ij(r) in repulsive and attractive regions under Mean Spherical Model Approximation [1]. Obtained direct correlation functions were employed to derive partial structure factors and then total structure factor, S(k) in liquid Al-Fe alloy at different atomic percent of Al. Fourier transform of partial and total structure factors gives partial and total radial distribution functions, g(r) from which partial and total coordination numbers and the partial nearest-neighbor distances were computed.

  9. Intercepts of the non-singlet structure functions

    CERN Document Server

    Ermolaev, B I; Troyan, S I

    2001-01-01

    Infrared evolution equations for small-$x$ behaviour of the non-singlet structure functions $f_1^{NS}$ and $g_1^{NS}$ are obtained and solved in the next-to-leading approximation, to all orders in $\\alpha_s$, and including running $\\alpha_s$ effects. The intercepts of these structure functions, i.e. the exponents of the power-like small-$x$ behaviour, are calculated. A detailed comparison with the leading logarithmic approximation (LLA) and DGLAP is made. We explain why the LLA predictions for the small-$x$ dependence of the structure functions may be more reliable than the prediction for the $Q^2$ dependence in the range of $Q^2$ explored at HERA.

  10. Direction-dependent learning approach for radial basis function networks.

    Science.gov (United States)

    Singla, Puneet; Subbarao, Kamesh; Junkins, John L

    2007-01-01

    Direction-dependent scaling, shaping, and rotation of Gaussian basis functions are introduced for maximal trend sensing with minimal parameter representations for input output approximation. It is shown that shaping and rotation of the radial basis functions helps in reducing the total number of function units required to approximate any given input-output data, while improving accuracy. Several alternate formulations that enforce minimal parameterization of the most general radial basis functions are presented. A novel "directed graph" based algorithm is introduced to facilitate intelligent direction based learning and adaptation of the parameters appearing in the radial basis function network. Further, a parameter estimation algorithm is incorporated to establish starting estimates for the model parameters using multiple windows of the input-output data. The efficacy of direction-dependent shaping and rotation in function approximation is evaluated by modifying the minimal resource allocating network and considering different test examples. The examples are drawn from recent literature to benchmark the new algorithm versus existing methods.

  11. The Polarized Structure Function $g_{2} A Lattice Study Revisited

    CERN Document Server

    Göckeler, M; Kürzinger, W; Oelrich, H; Rakow, P; Schierholz, G

    1999-01-01

    A recent lattice calculation of the spin-dependent structure function g_2 is revisited. It has been recognized that the twist-three operator, which gives rise to d_2, mixes non-perturbatively with operators of lower dimensions under renormalization. This changes the results substantially.

  12. Structural and functional properties of designed globins

    Indian Academy of Sciences (India)

    Yasuhiro Isogai; Anna Ishii; Manabu Ishida; Masahiro Mukai; Motonori Ota; Ken Nishikawa; Tetsutaro Iizuka

    2000-06-01

    De novo design of artificial proteins is an essential approach to elucidate the principles of protein architecture and to understand specific functions of natural proteins and also to yield novel molecules for medical and industrial aims. We have designed artificial sequences of 153 amino acids to fit the main-chain framework of the sperm whale myoglobin structure based on the knowledge-based energy functions to evaluate the compatibility between protein tertiary structures and amino acid sequences. The synthesized artificial globins bind a single heme per protein molecule as designed, which show well-defined electrochemical and spectroscopic features characteristic of proteins with a low-spin heme. Redox and ligand binding reactions of the artificial heme proteins were investigated and these heme-related functions were found to vary with their structural uniqueness. Relationships between the structural and functional properties are discussed.

  13. Progress on nuclear modifications of structure functions

    CERN Document Server

    Kumano, S

    2016-01-01

    We report progress on nuclear structure functions, especially on their nuclear modifications and a new tensor structure function for the deuteron. To understand nuclear structure functions is an important step toward describing nuclei and QCD matters from low to high densities and from low to high energies in terms of fundamental quark and gluon degrees of freedom beyond conventional hadron and nuclear physics. It is also practically important for understanding new phenomena in high-energy heavy-ion collisions at RHIC and LHC. Furthermore, since systematic errors of current neutrino-oscillation experiments are dominated by uncertainties of neutrino-nucleus interactions, such studies are valuable for finding new physics beyond current framework. Next, a new tensor-polarized structure function $b_1$ is discussed for the deuteron. There was a measurement by HERMES; however, its data are inconsistent with the conventional convolution estimate based on the standard deuteron model with D-state admixture. This fact ...

  14. Understanding Microbial Communities: Function, Structure and Dynamics

    Science.gov (United States)

    2015-02-11

    microbial communities: Function, structure and dynamics’, at the Isaac Newton Institute, University of Cambridge, United Kingdom, from August to...dynamics’, at the Isaac Newton Institute, University of Cambridge, United Kingdom, from August to December 2014. The programme involved over 150...Communities: Function, Structure and Dynamics’, at the Isaac Newton Institute, Cambridge University, UK, from 19th August 2014 – 19th December 2014

  15. Recent Structure Function Results from CCFR

    CERN Document Server

    Fleming, B T; Alton, A; Arroyo, C G; Avvakumov, S; De Barbaro, L; De Barbaro, P; Bazarko, A O; Bernstein, R H; Bodek, Arie; Bolton, T; Brau, J E; Buchholz, D; Budd, H S; Bugel, L; Conrad, J; Drucker, R B; Formaggio, J A; Frey, R; Goldman, J; Goncharov, M; Harris, D A; Johnson, R A; Kim, J H; King, B J; Kinnel, T; Koutsoliotas, S; Lamm, M J; Marsh, W; Mason, D; McFarland, K S; McNulty, C; Mishra, S R; Naples, D; Nienaber, P; Romosan, A; Sakumoto, W K; Schellman, H; Sciulli, F J; Seligman, W G; Shaevitz, M H; Smith, W H; Spentzouris, P; Stern, E G; Vakili, M; Vaitaitis, A G; Yang, U K; Yu, J; Zeller, G P; Zimmerman, E D

    2000-01-01

    A new structure function analysis of CCFR deep inelastic nu-N and nubar-N scattering data is presented for previously unexplored kinematic regions down to Bjorken x=0.0045 and Q^2=0.3 GeV^2. Comparisons to charged lepton scattering data from NMC and E665 experiments are made and the behavior of the structure function F2_nu is studied in the limit Q^2 -> 0

  16. Polarized deuteron structure functions at small x

    CERN Document Server

    Edelmann, J; Weise, W

    1997-01-01

    We investigate shadowing corrections to the polarized deuteron structure functions g_1^d and b_1. In the kinematic domain of current fixed target experiments we observe that shadowing effects in g_1^d are approximately twice as large as for the unpolarized structure function F_2^d. Furthermore, we find that b_1 is surprisingly large at x < 0.1 and receives dominant contributions from coherent double scattering.

  17. Structure and Structure-activity Relationship of Functional Organic Molecules

    Institute of Scientific and Technical Information of China (English)

    2011-01-01

    @@ Research theme The group is made up of junior scientists from the State Key Laboratory of Elemento-organic Chemistry, Nankai University.The scientists focus their studis on the structure and structure-activity relationship of functional organic molecules not only because it has been the basis of their research, but also because the functional study of organic compounds is now a major scientific issue for organic chemists around the world.

  18. Next-order structure-function equations

    Science.gov (United States)

    Hill, Reginald J.; Boratav, Olus N.

    2001-01-01

    Kolmogorov's equation [Dokl. Akad. Nauk SSSR 32, 16 (1941)] relates the two-point second- and third-order velocity structure functions and the energy dissipation rate. The analogous next higher-order two-point equation relates the third- and fourth-order velocity structure functions and the structure function of the product of pressure-gradient difference and two factors of velocity difference, denoted Tijk. The equation is simplified on the basis of local isotropy. Laboratory and numerical simulation data are used to evaluate and compare terms in the equation, examine the balance of the equation, and evaluate components of Tijk. Atmospheric surface-layer data are used to evaluate Tijk in the inertial range. Combined with the random sweeping hypothesis, the equation relates components of the fourth-order velocity structure function. Data show the resultant error of this application of random sweeping. The next-order equation constrains the relationships that have been suggested among components of the fourth-order velocity structure function. The pressure structure function, pressure-gradient correlation, and mean-squared pressure gradient are related to Tijk. Inertial range formulas are discussed.

  19. Zinc finger structure-function in Ikaros

    Institute of Scientific and Technical Information of China (English)

    Marvin; A; Payne

    2011-01-01

    The zinc finger motif was used as a vehicle for the initial discovery of Ikaros in the context of T-cell differentiation and has been central to all subsequent analyses of Ikaros function.The Ikaros gene is alternately spliced to produce several isoforms that confer diversity of function and consequently have complicated analysis of the function of Ikaros in vivo.Key features of Ikaros in vivo function are associated with six C2H2 zinc fingers;four of which are alternately incorporated in the production of the various Ikaros isoforms.Although no complete structures are available for the Ikaros protein or any of its family members,considerable evidence has accumulated about the structure of zinc fingers and the role that this structure plays in the functions of the Ikaros family of proteins.This review summarizes the structural aspects of Ikaros zinc fingers,individually,and in tandem to provide a structural context for Ikaros function and to provide a structural basis to inform the design of future experiments with Ikaros and its family members.

  20. Anisotropic nanomaterials: structure, growth, assembly, and functions.

    Science.gov (United States)

    Sajanlal, Panikkanvalappil R; Sreeprasad, Theruvakkattil S; Samal, Akshaya K; Pradeep, Thalappil

    2011-01-01

    Comprehensive knowledge over the shape of nanomaterials is a critical factor in designing devices with desired functions. Due to this reason, systematic efforts have been made to synthesize materials of diverse shape in the nanoscale regime. Anisotropic nanomaterials are a class of materials in which their properties are direction-dependent and more than one structural parameter is needed to describe them. Their unique and fine-tuned physical and chemical properties make them ideal candidates for devising new applications. In addition, the assembly of ordered one-dimensional (1D), two-dimensional (2D), and three-dimensional (3D) arrays of anisotropic nanoparticles brings novel properties into the resulting system, which would be entirely different from the properties of individual nanoparticles. This review presents an overview of current research in the area of anisotropic nanomaterials in general and noble metal nanoparticles in particular. We begin with an introduction to the advancements in this area followed by general aspects of the growth of anisotropic nanoparticles. Then we describe several important synthetic protocols for making anisotropic nanomaterials, followed by a summary of their assemblies, and conclude with major applications.

  1. Anisotropic nanomaterials: structure, growth, assembly, and functions

    Directory of Open Access Journals (Sweden)

    Panikkanvalappil R. Sajanlal

    2011-02-01

    Full Text Available Comprehensive knowledge over the shape of nanomaterials is a critical factor in designing devices with desired functions. Due to this reason, systematic efforts have been made to synthesize materials of diverse shape in the nanoscale regime. Anisotropic nanomaterials are a class of materials in which their properties are direction-dependent and more than one structural parameter is needed to describe them. Their unique and fine-tuned physical and chemical properties make them ideal candidates for devising new applications. In addition, the assembly of ordered one-dimensional (1D, two-dimensional (2D, and three-dimensional (3D arrays of anisotropic nanoparticles brings novel properties into the resulting system, which would be entirely different from the properties of individual nanoparticles. This review presents an overview of current research in the area of anisotropic nanomaterials in general and noble metal nanoparticles in particular. We begin with an introduction to the advancements in this area followed by general aspects of the growth of anisotropic nanoparticles. Then we describe several important synthetic protocols for making anisotropic nanomaterials, followed by a summary of their assemblies, and conclude with major applications.

  2. [Snake venom metalloproteinases: structure, biosynthesis and function(s)].

    Science.gov (United States)

    Limam, I; El Ayeb, M; Marrakchi, N

    2010-01-01

    The biochemical and the pharmacological characterization of snake venoms revealed an important structural and functional polymorphism of proteins which they contain. Among them, snake venom metalloproteases (SVMPs) constitute approximatively 20 to 60% of the whole venom proteins. During the last decades, a significant progress was performed against structure studies and the biosynthesis of the SVMPs. Indeed, several metalloproteases were isolated and characterized against their structural and pharmacological properties. In this review, we report the most important properties concerning the classification, the structure of the various domains of the SVMPs as well as their biosynthesis and their activities as potential therapeutic agents.

  3. Comorbid functional shoulder pain and zolpidem dependence treated with pramipexole

    Directory of Open Access Journals (Sweden)

    Dhiraj Kandre

    2015-01-01

    Full Text Available Pramipexole is a dopamine agonist with higher affinity for D3 receptors. Treatment with pramipexole in clinical conditions such as restless legs syndrome, fibromyalgia, and parkinsonism has been found to significantly improve measures of pain and sleep along with the other symptoms. There is no research data available that explores the usefulness of pramipexole in somatoform/functional pain syndromes. We report a case of a 65-year-old male with bilateral functional shoulder pain associated with insomnia and zolpidem dependence effectively treated with pramipexole.

  4. Time-dependent density-functional theory concepts and applications

    CERN Document Server

    Ullrich, Carsten A

    2011-01-01

    Time-dependent density-functional theory (TDDFT) describes the quantum dynamics of interacting electronic many-body systems formally exactly and in a practical and efficient manner. TDDFT has become the leading method for calculating excitation energies and optical properties of large molecules, with accuracies that rival traditional wave-function based methods, but at a fraction of the computational cost.This book is the first graduate-level text on the concepts and applications of TDDFT, including many examples and exercises, and extensive coverage of the literature. The book begins with a s

  5. Time-dependent density functional theory for quantum transport.

    Science.gov (United States)

    Zheng, Xiao; Chen, GuanHua; Mo, Yan; Koo, SiuKong; Tian, Heng; Yam, ChiYung; Yan, YiJing

    2010-09-21

    Based on our earlier works [X. Zheng et al., Phys. Rev. B 75, 195127 (2007); J. S. Jin et al., J. Chem. Phys. 128, 234703 (2008)], we propose a rigorous and numerically convenient approach to simulate time-dependent quantum transport from first-principles. The proposed approach combines time-dependent density functional theory with quantum dissipation theory, and results in a useful tool for studying transient dynamics of electronic systems. Within the proposed exact theoretical framework, we construct a number of practical schemes for simulating realistic systems such as nanoscopic electronic devices. Computational cost of each scheme is analyzed, with the expected level of accuracy discussed. As a demonstration, a simulation based on the adiabatic wide-band limit approximation scheme is carried out to characterize the transient current response of a carbon nanotube based electronic device under time-dependent external voltages.

  6. Lyapunov functions and global stability for SIR and SEIR models with age-dependent susceptibility

    KAUST Repository

    Korobeinikov, Andrei

    2013-01-01

    We consider global asymptotic properties for the SIR and SEIR age structured models for infectious diseases where the susceptibility depends on the age. Using the direct Lyapunov method with Volterra type Lyapunov functions, we establish conditions for the global stability of a unique endemic steady state and the infection-free steady state.

  7. Lyapunov functions and global stability for SIR and SEIR models with age-dependent susceptibility.

    Science.gov (United States)

    Melnik, Andrey V; Korobeinikov, Andrei

    2013-04-01

    We consider global asymptotic properties for the SIR and SEIR age structured models for infectious diseases where the susceptibility depends on the age. Using the direct Lyapunov method with Volterra type Lyapunov functions, we establish conditions for the global stability of a unique endemic steady state and the infection-free steady state.

  8. Huntington's disease : functional and structural biomarkers

    NARCIS (Netherlands)

    Dumas, Eve Marie

    2012-01-01

    The aims of this thesis were to gain insight into specific disease processes in Huntington’s Disease (HD) and to identify biomarkers. To achieve these aims, cognitive functioning, structural brain characteristics and intrinstic functional brain connectivity of premanifest and early HD subjects were

  9. 2004 Structural, Function and Evolutionary Genomics

    Energy Technology Data Exchange (ETDEWEB)

    Douglas L. Brutlag Nancy Ryan Gray

    2005-03-23

    This Gordon conference will cover the areas of structural, functional and evolutionary genomics. It will take a systematic approach to genomics, examining the evolution of proteins, protein functional sites, protein-protein interactions, regulatory networks, and metabolic networks. Emphasis will be placed on what we can learn from comparative genomics and entire genomes and proteomes.

  10. Time dependent density functional calculation of plasmon response in clusters

    Institute of Scientific and Technical Information of China (English)

    Wang Feng(王锋); Zhang Feng-Shou(张丰收); Eric Suraud

    2003-01-01

    We have introduced a theoretical scheme for the efficient description of the optical response of a cluster based on the time-dependent density functional theory. The practical implementation is done by means of the fully fledged timedependent local density approximation scheme, which is solved directly in the time domain without any linearization.As an example we consider the simple Na2 cluster and compute its surface plasmon photoabsorption cross section, which is in good agreement with the experiments.

  11. Charge transfer in time-dependent density functional theory

    Science.gov (United States)

    Maitra, Neepa T.

    2017-10-01

    Charge transfer plays a crucial role in many processes of interest in physics, chemistry, and bio-chemistry. In many applications the size of the systems involved calls for time-dependent density functional theory (TDDFT) to be used in their computational modeling, due to its unprecedented balance between accuracy and efficiency. However, although exact in principle, in practise approximations must be made for the exchange-correlation functional in this theory, and the standard functional approximations perform poorly for excitations which have a long-range charge-transfer component. Intense progress has been made in developing more sophisticated functionals for this problem, which we review. We point out an essential difference between the properties of the exchange-correlation kernel needed for an accurate description of charge-transfer between open-shell fragments and between closed-shell fragments. We then turn to charge-transfer dynamics, which, in contrast to the excitation problem, is a highly non-equilibrium, non-perturbative, process involving a transfer of one full electron in space. This turns out to be a much more challenging problem for TDDFT functionals. We describe dynamical step and peak features in the exact functional evolving over time, that are missing in the functionals currently used. The latter underestimate the amount of charge transferred and manifest a spurious shift in the charge transfer resonance position. We discuss some explicit examples.

  12. Structure functions in the chiral bag model

    Energy Technology Data Exchange (ETDEWEB)

    Sanjose, V.; Vento, V.

    1989-07-13

    We calculate the structure functions of an isoscalar nuclear target for the deep inelastic scattering by leptons in an extended version of the chiral bag model which incorporates the qanti q structure of the pions in the cloud. Bjorken scaling and Regge behavior are satisfied. The model calculation reproduces the low-x behavior of the data but fails to explain the medium- to large-x behavior. Evolution of the quark structure functions seem inevitable to attempt a connection between the low-energy models and the high-energy behavior of quantum chromodynamics. (orig.).

  13. Clustering aspects in nuclear structure functions

    CERN Document Server

    Hirai, M; Saito, K; Watanabe, T

    2010-01-01

    For understanding an anomalous nuclear effect experimentally observed for the beryllium-9 nucleus at the Thomas Jefferson National Accelerator Facility (JLab), clustering aspects are studied in structure functions of deep inelastic lepton-nucleus scattering by using momentum distributions calculated in antisymmetrized (or fermionic) molecular dynamics (AMD) and also in a simple shell model for comparison. According to the AMD, the Be-9 nucleus consists of two alpha-like clusters with a surrounding neutron. The clustering produces high-momentum components in nuclear wave functions, which affects nuclear modifications of the structure functions. We investigated whether clustering features could appear in the structure function F_2 of Be-9 along with studies for other light nuclei. We found that nuclear modifications of F_2 are similar in both AMD and shell models within our simple convolution description although there are slight differences in Be-9. It indicates that the anomalous Be-9 result should be explain...

  14. Predicting protein structure classes from function predictions

    DEFF Research Database (Denmark)

    Sommer, I.; Rahnenfuhrer, J.; de Lichtenberg, Ulrik;

    2004-01-01

    We introduce a new approach to using the information contained in sequence-to-function prediction data in order to recognize protein template classes, a critical step in predicting protein structure. The data on which our method is based comprise probabilities of functional categories; for given...... query sequences these probabilities are obtained by a neural net that has previously been trained on a variety of functionally important features. On a training set of sequences we assess the relevance of individual functional categories for identifying a given structural family. Using a combination...... of the most relevant categories, the likelihood of a query sequence to belong to a specific family can be estimated. Results: The performance of the method is evaluated using cross-validation. For a fixed structural family and for every sequence, a score is calculated that measures the evidence for family...

  15. Magnetism and Structure in Functional Materials

    CERN Document Server

    Planes, Antoni; Saxena, Avadh

    2005-01-01

    Magnetism and Structure in Functional Materials addresses three distinct but related topics: (i) magnetoelastic materials such as magnetic martensites and magnetic shape memory alloys, (ii) the magnetocaloric effect related to magnetostructural transitions, and (iii) colossal magnetoresistance (CMR) and related magnanites. The goal is to identify common underlying principles in these classes of materials that are relevant for optimizing various functionalities. The emergence of apparently different magnetic/structural phenomena in disparate classes of materials clearly points to a need for common concepts in order to achieve a broader understanding of the interplay between magnetism and structure in this general class of new functional materials exhibiting ever more complex microstructure and function. The topic is interdisciplinary in nature and the contributors correspondingly include physicists, materials scientists and engineers. Likewise the book will appeal to scientists from all these areas.

  16. The proteome: structure, function and evolution.

    Science.gov (United States)

    Fleming, Keiran; Kelley, Lawrence A; Islam, Suhail A; MacCallum, Robert M; Muller, Arne; Pazos, Florencio; Sternberg, Michael J E

    2006-03-29

    This paper reports two studies to model the inter-relationships between protein sequence, structure and function. First, an automated pipeline to provide a structural annotation of proteomes in the major genomes is described. The results are stored in a database at Imperial College, London (3D-GENOMICS) that can be accessed at www.sbg.bio.ic.ac.uk. Analysis of the assignments to structural superfamilies provides evolutionary insights. 3D-GENOMICS is being integrated with related proteome annotation data at University College London and the European Bioinformatics Institute in a project known as e-protein (http://www.e-protein.org/). The second topic is motivated by the developments in structural genomics projects in which the structure of a protein is determined prior to knowledge of its function. We have developed a new approach PHUNCTIONER that uses the gene ontology (GO) classification to supervise the extraction of the sequence signal responsible for protein function from a structure-based sequence alignment. Using GO we can obtain profiles for a range of specificities described in the ontology. In the region of low sequence similarity (around 15%), our method is more accurate than assignment from the closest structural homologue. The method is also able to identify the specific residues associated with the function of the protein family.

  17. A dependent stress-strength interference model based on mixed copula function

    Energy Technology Data Exchange (ETDEWEB)

    Gao, Jian Xiong; An, Zong Wen; Liu, Bo [School of Mechatronics Engineering, Lanzhou University of Technology, Lanzhou (China)

    2016-10-15

    In the traditional Stress-strength interference (SSI) model, stress and strength must satisfy the basic assumption of mutual independence. However, a complex dependence between stress and strength exists in practical engineering. To evaluate structural reliability under the case that stress and strength are dependent, a mixed copula function is introduced to a new dependent SSI model. This model can fully characterize the dependence between stress and strength. The residual square sum method and genetic algorithm are also used to estimate the unknown parameters of the model. Finally, the validity of the proposed model is demonstrated via a practical case. Results show that traditional SSI model ignoring the dependence between stress and strength more easily overestimates product reliability than the new dependent SSI model.

  18. Structure and Functions of Linker Histones.

    Science.gov (United States)

    Lyubitelev, A V; Nikitin, D V; Shaytan, A K; Studitsky, V M; Kirpichnikov, M P

    2016-03-01

    Linker histones such as variants H1, H5, and other similar proteins play an important role in regulation of chromatin structure and dynamics. However, interactions of linker histones with DNA and proteins, as well as specific functions of their different variants, are poorly studied. This is because they acquire tertiary structure only when interacting with a nucleosome, and because of limitations of currently available methods. However, deeper investigation of linker histones and their interactions with other proteins will address a number of important questions - from structure of compacted chromatin to regulation of early embryogenesis. In this review, structures of histone H1 variants and its interaction with chromatin DNA are considered. A possible functional significance of different H1 variants, a role of these proteins in maintaining interphase chromatin structure, and interactions of linker histones with other cellular proteins are also discussed.

  19. The Transverse Momentum Dependent Fragmentation Function at NNLO

    CERN Document Server

    Echevarria, Miguel G; Vladimirov, Alexey

    2016-01-01

    We calculate the unpolarized non-singlet transverse momentum dependent fragmentation function (TMDFF) at next-to-next-to-leading order (NNLO), evaluating separately TMD soft factor and TMD collinear correlator. For the first time the cancellation of spurious rapidity divergences in a properly defined individual TMD beyond the first non-trivial order is shown. This represents a strong check of the given TMD definition. We extract the matching coefficient necessary to perform the transverse momentum resummation at next-to-next-to-next-to-leading-logarithmic accuracy. The universal character of the soft function, which enters the definition of all (un)polarized TMD distribution/fragmentation functions, facilitates the future calculation of all the other TMDs and their coefficients at NNLO, pushing forward the accuracy of theoretical predictions for the current and next generation of high energy colliders.

  20. Evaluation of sexual functions in Turkish alcohol-dependent males.

    Science.gov (United States)

    Dişsiz, Melike; Oskay, Ümran Yeşiltepe

    2011-11-01

    It was reported that long-term and high amount of alcohol consumption cause sexual dysfunction in men. There is a lack of descriptive studies focusing on the sexual dysfunction of alcohol dependent men in Turkey. This study was conducted to evaluate sexual functions of alcohol dependent men. This descriptive study was performed at the Alcohol and Substance Research Treatment and Education Center (ASRTEC). The data was collected between 26 December 2007 and 26 December 2008. As research instruments, an interview form of 30 questions that questioned personal characteristics and was developed by researchers, and IIEF (International Index of Erectile Dysfunction) with 15 items that evaluated sexual dysfunction were used. Mean age of men was 41.22 ± 8.19; 36.5% of participants were graduated from primary school, and 57.5% were unemployed. Average daily alcohol consumption was 16.41 ± 4.90 standard alcohol. We found that 47% of alcohol-dependent men had their first sexual experience before they were 18 years old, 64.4% had multiple partners, 1.7% experienced a sexually transmitted disease, 7.7% had a chronic disease, and 18.3% had pain during intercourse. Mean total IIEF scores of alcohol-dependent men was 57 ± 9.23 (mean ED scores 23.41 ± 3.91). Therefore, 70.3% of participants had a mild (17-25), and 4.4% had a moderate (11-16) erectile dysfunction. With a multivariate analysis, predictors of erectile dysfunction in chronic alcohol dependent male were determined as age of subject, age of onset for alcohol, duration of alcoholism, and cigarette use. Chronic alcoholism affects sexual functions in men. Sexual dysfunction in alcohol addicted males is related with education level and unemployment and starting alcohol consumption at an early age and long-term cigarette smoking. © 2010 International Society for Sexual Medicine.

  1. SLC6 Neurotransmitter Transporters: Structure, Function, and Regulation

    DEFF Research Database (Denmark)

    Kristensen, Anders S; Andersen, Jacob; Jørgensen, Trine N

    2011-01-01

    The neurotransmitter transporters (NTTs) belonging to the solute carrier 6 (SLC6) gene family (also referred to as the neurotransmitter-sodium-symporter family or Na(+)/Cl(-)-dependent transporters) comprise a group of nine sodium- and chloride-dependent plasma membrane transporters for the monoa......The neurotransmitter transporters (NTTs) belonging to the solute carrier 6 (SLC6) gene family (also referred to as the neurotransmitter-sodium-symporter family or Na(+)/Cl(-)-dependent transporters) comprise a group of nine sodium- and chloride-dependent plasma membrane transporters....... Furthermore, psychostimulants such as cocaine and amphetamines have the SLC6 NTTs as primary targets. Beginning with the determination of a high-resolution structure of a prokaryotic homolog of the mammalian SLC6 transporters in 2005, the understanding of the molecular structure, function, and pharmacology...

  2. The Universal Transverse Momentum Dependent Soft Function at NNLO

    CERN Document Server

    Echevarria, Miguel G; Vladimirov, Alexey

    2015-01-01

    All (un)polarized transverse momentum dependent functions (TMDs), both distribution and fragmentation functions, are defined with the same universal soft function, which cancels spurious rapidity divergences within an individual TMD and renders them well-defined hadronic quantities. Moreover, it is independent of the kinematics, whether it is Drell-Yan ($e^+e^-\\rightarrow 2$ hadrons) or deep inelastic scattering. In this paper we provide this soft function at next-to-next-to-leading order (NNLO), necessary for the calculation of all TMDs at the same order, and to perform the resummation of large logarithms at next-to-next-to-next-to-leading-logarithmic accuracy. From the results we obtain the $D$ function at NNLO, which governs the evolution of all TMDs. This work represents the first independent and direct calculation of this quantity. Given the all order relation through a Casimir scaling between the soft function relevant for gluon TMDs and the one for quark TMDs, we also obtain the first at NNLO. The used...

  3. Time Variation in Asset Return Dependence: Strength or Structure?

    NARCIS (Netherlands)

    T.D. Markwat (Thijs); H.J.W.G. Kole (Erik); D.J.C. van Dijk (Dick)

    2009-01-01

    textabstractThe dependence between asset returns varies. Its strength can become stronger or weaker. Also, its structure can change, for example, when asymmetries related to bull and bear markets become more or less pronounced. To analyze these different types of variations, we develop a model that

  4. Dynamic structure evolution of time-dependent network

    Science.gov (United States)

    Zhang, Beibei; Zhou, Yadong; Xu, Xiaoyan; Wang, Dai; Guan, Xiaohong

    2016-08-01

    In this paper, we research the long-voided problem of formulating the time-dependent network structure evolution scheme, it focus not only on finding new emerging vertices in evolving communities and new emerging communities over the specified time range but also formulating the complex network structure evolution schematic. Previous approaches basically applied to community detection on time static networks and thus failed to consider the potentially crucial and useful information latently embedded in the dynamic structure evolution process of time-dependent network. To address these problems and to tackle the network non-scalability dilemma, we propose the dynamic hierarchical method for detecting and revealing structure evolution schematic of the time-dependent network. In practice and specificity, we propose an explicit hierarchical network evolution uncovering algorithm framework originated from and widely expanded from time-dependent and dynamic spectral optimization theory. Our method yields preferable results compared with previous approaches on a vast variety of test network data, including both real on-line networks and computer generated complex networks.

  5. A Structural Equation Approach to Models with Spatial Dependence

    NARCIS (Netherlands)

    Oud, J.H.L.; Folmer, H.

    2008-01-01

    We introduce the class of structural equation models (SEMs) and corresponding estimation procedures into a spatial dependence framework. SEM allows both latent and observed variables within one and the same (causal) model. Compared with models with observed variables only, this feature makes it poss

  6. A structural equation approach to models with spatial dependence

    NARCIS (Netherlands)

    Oud, J.H.L.; Folmer, H.

    2008-01-01

    We introduce the class of structural equation models (SEMs) and corresponding estimation procedures into a spatial dependence framework. SEM allows both latent and observed variables within one and the same (causal) model. Compared with models with observed variables only, this feature makes it poss

  7. Structural requirements of pyrroloquinoline quinone dependent enzymatic reactions

    NARCIS (Netherlands)

    Oubrie, Arthur; Dijkstra, Bauke W.

    2000-01-01

    On the basis of crystal structures of the pyrroloquinoline quinone (PQQ) dependent enzymes methanol dehydrogenase (MDH) and soluble glucose dehydrogenase (s-GDH), different catalytic mechanisms have been proposed. However, several lines of biochemical and kinetic evidence are strikingly similar for

  8. Balance functions: Multiplicity and transverse momentum dependence of the charge dependent correlations in ALICE

    CERN Document Server

    AUTHOR|(CDS)2078856; Snellings, Raimond; Christakoglou, Panos

    The measurement of charge-dependent correlations between positively and negatively charged particles as a function of pseudorapidity and azimuthal angle, known as the balance functions, provide insight to the properties of matter created in high-energy collisions. The balance functions are argued to probe the creation time of the particles and are also sensitive to the collective motion of the system. In this thesis, I present the results of the measured balance functions in p--Pb collisions at √sNN = 5.02~TeV obtained with the ALICE detector at the LHC. The results are compared with balance functions measured in pp and Pb--Pb collisions at √s=7~TeV and √sNN = 2.76~TeV$, respectively. The width of the balance functions in both pseudorapidity and azimuthal angle for non-identified charged particles decreases with increasing multiplicity in all three systems, for particles with low transverse momentum value pT < 2~GeV/c. For higher values of transverse momentum the balance functions become narrower and...

  9. The role of the Schizosaccharomyces pombe gar2 protein in nucleolar structure and function depends on the concerted action of its highly charged N terminus and its RNA-binding domains.

    Science.gov (United States)

    Sicard, H; Faubladier, M; Noaillac-Depeyre, J; Léger-Silvestre, I; Gas, N; Caizergues-Ferrer, M

    1998-08-01

    Nonribosomal nucleolar protein gar2 is required for 18S rRNA and 40S ribosomal subunit production in Schizosaccharomyces pombe. We have investigated the consequences of the absence of each structural domain of gar2 on cell growth, 18S rRNA production, and nucleolar structure. Deletion of gar2 RNA-binding domains (RBDs) causes stronger inhibition of growth and 18S rRNA accumulation than the absence of the whole protein, suggesting that other factors may be titrated by its remaining N-terminal basic/acidic serine-rich domain. These drastic functional defects correlate with striking nucleolar hypertrophy. Point mutations in the conserved RNP1 motifs of gar2 RBDs supposed to inhibit RNA-protein interactions are sufficient to induce severe nucleolar modifications but only in the presence of the N-terminal domain of the protein. Gar2 and its mutants also distribute differently in glycerol gradients: gar2 lacking its RBDs is found either free or assembled into significantly larger complexes than the wild-type protein. We propose that gar2 helps the assembly on rRNA of factors necessary for 40S subunit synthesis by providing a physical link between them. These factors may be recruited by the N-terminal domain of gar2 and may not be released if interaction of gar2 with rRNA is impaired.

  10. Structural study of surfactant-dependent interaction with protein

    Energy Technology Data Exchange (ETDEWEB)

    Mehan, Sumit; Aswal, Vinod K., E-mail: vkaswal@barc.gov.in [Solid State Physics Division, Bhabha Atomic Research Centre, Mumbai 400 085 (India); Kohlbrecher, Joachim [Laboratory for Neutron Scattering, Paul Scherrer Institut, CH-5232 PSI Villigen (Switzerland)

    2015-06-24

    Small-angle neutron scattering (SANS) has been used to study the complex structure of anionic BSA protein with three different (cationic DTAB, anionic SDS and non-ionic C12E10) surfactants. These systems form very different surfactant-dependent complexes. We show that the structure of protein-surfactant complex is initiated by the site-specific electrostatic interaction between the components, followed by the hydrophobic interaction at high surfactant concentrations. It is also found that hydrophobic interaction is preferred over the electrostatic interaction in deciding the resultant structure of protein-surfactant complexes.

  11. Crystalline structure and symmetry dependence of acoustic nonlinearity parameters

    Science.gov (United States)

    Cantrell, John H.

    1994-01-01

    A quantitative measure of elastic wave nonlinearity in crystals is provided by the acoustic nonlinearity parameters. The nonlinearity parameters are defined for arbitrary propagation modes for solids of arbitrary crystalline symmetry and are determined along the pure mode propagation directions for 33 crystals of cubic symmetry from data reported in the literature. The magnitudes of the nonlinearity parameters are found to exhibit a strong dependence on the crystalline structure and symmetries associated with the modal direction in the solid. Calculations based on the Born-Mayer potential for crystals having a dominant repulsive contribution to the elastic constants from the interatomic pair potential suggest that the origin of the structure dependence is associated with the shape rather than the strength of the potential. Considerations based on variations in crystal symmetry during loading along pure mode propagation directions of face-centered-cubic solids provide a qualitative explanation for the dependence of the acoustic nonlinearity parameters on modal direction.

  12. Functionally diverse biotin-dependent enzymes with oxaloacetate decarboxylase activity.

    Science.gov (United States)

    Lietzan, Adam D; St Maurice, Martin

    2014-02-15

    Biotin-dependent enzymes catalyze carboxylation, decarboxylation and transcarboxylation reactions that participate in the primary metabolism of a wide range of organisms. In all cases, the overall reaction proceeds via two half reactions that take place in physically distinct active sites. In the first half-reaction, a carboxyl group is transferred to the 1-N' of a covalently tethered biotin cofactor. The tethered carboxybiotin intermediate subsequently translocates to a second active site where the carboxyl group is either transferred to an acceptor substrate or, in some bacteria and archaea, is decarboxylated to biotin and CO2 in order to power the export of sodium ions from the cytoplasm. A homologous carboxyltransferase domain is found in three enzymes that catalyze diverse overall reactions: carbon fixation by pyruvate carboxylase, decarboxylation and sodium transport by the biotin-dependent oxaloacetate decarboxylase complex, and transcarboxylation by transcarboxylase from Propionibacterium shermanii. Over the past several years, structural data have emerged which have greatly advanced the mechanistic description of these enzymes. This review assembles a uniform description of the carboxyltransferase domain structure and catalytic mechanism from recent studies of pyruvate carboxylase, oxaloacetate decarboxylase and transcarboxylase, three enzymes that utilize an analogous carboxyltransferase domain to catalyze the biotin-dependent decarboxylation of oxaloacetate.

  13. A measurement of the photon structure function F sub 2

    Energy Technology Data Exchange (ETDEWEB)

    Sasaki, T.; Ishi, Y.; Miyano, K.; Miyata, H. (Niigata Univ. (Japan)); Yamagishi, Y.; Tanaka, R.; Kojima, T.; Matsumoto, S.; Yasuda, T. (Chuo Univ., Tokyo (Japan)); Kirk, P.; Lim, J.; McNeil, R.R.; Metcalf, W.; Myung, S.S. (Louisiana State Univ., Baton Rouge (USA)); Cheng, C.P.; Gu, P.; Ye, M.H.; Zhu, Y.C. (Academia Sinica, Beijing (China). Inst. of High Energy Physics); Abashian, A.; Gotow, K.; Hu, K.P.; Lai, A.Z.; Low, E.H.; Mattson, M.E.; Piilonen, L.; Sterner, K.L. (Virginia Polytechnic Inst. and State Univ., Blacksburg (USA)); Li, Y.K.; Lusin, S.; Rosenfeld, C.; Wang, A.T.M.; Wilson, S. (South Carolina Univ., Columbia (USA)); Frautschi, M.; Kagan, H.; Kass, R. (Ohio State Univ., Columbus (USA)); Breedon, R.E.; Kim, G.N. (California Univ., Davis (USA) National Lab. for High Energy Physics, Tsukuba, Ibaraki (Japan)); Ko, W.; Lander, R.L.; Maeshima, K.; Malchow, R.L.; Rowe, J.; Smith, J.R.; Stuart, D. (California Univ., Davis (USA)); Abe, K.; Fujii, Y.; Higashi, Y.; Kim, S.K.; AMY Collaboration

    1990-12-20

    The photon structure function F{sub 2} has been measured at average Q{sup 2} values of 73, 160 and 390 (GeV/c){sup 2}. We compare the x dependence of the Q{sup 2}=73(GeV/c){sup 2} data with thereotical expectations based on QCD. In addition we present results on the Q{sup 2} evolution of the structure function for the intermediate x range (0.3{le}x{le}0.8). The results are consistent with QCD. (orig.).

  14. The Structure, Functions, and Mechanical Properties of Keratin

    Science.gov (United States)

    McKittrick, J.; Chen, P.-Y.; Bodde, S. G.; Yang, W.; Novitskaya, E. E.; Meyers, M. A.

    2012-04-01

    Keratin is one of the most important structural proteins in nature and is widely found in the integument in vertebrates. It is classified into two types: α-helices and β-pleated sheets. Keratinized materials can be considered as fiber-reinforced composites consisting of crystalline intermediate filaments embedded in an amorphous protein matrix. They have a wide variety of morphologies and properties depending on different functions. Here, we review selected keratin-based materials, such as skin, hair, wool, quill, horn, hoof, feather, and beak, focusing on the structure-mechanical property-function relationships and finally give some insights on bioinspired composite design based on keratinized materials.

  15. Fungal NRPS-dependent siderophores: From function to prediction

    DEFF Research Database (Denmark)

    Sørensen, Jens Laurids; Knudsen, Michael; Hansen, Frederik Teilfeldt

    2014-01-01

    discuss the function of siderophores in relation to fungal iron uptake mechanisms and their importance for coexistence with host organisms. The chemical nature of the major groups of siderophores and their regulation is described along with the function and architecture of the large multi-domain enzymes...... responsible for siderophore synthesis, namely the non-ribosomal peptide synthetases (NRPSs). Finally, we present the most recent advances in our understanding of the structural biology of fungal NRPSs and discuss opportunities for the development of a fungal NRPS prediction server...

  16. Fungal NRPS-dependent siderophores: From function to prediction

    DEFF Research Database (Denmark)

    Sørensen, Jens Laurids; Knudsen, Michael; Hansen, Frederik Teilfeldt

    2014-01-01

    discuss the function of siderophores in relation to fungal iron uptake mechanisms and their importance for coexistence with host organisms. The chemical nature of the major groups of siderophores and their regulation is described along with the function and architecture of the large multi-domain enzymes...... responsible for siderophore synthesis, namely the non-ribosomal peptide synthetases (NRPSs). Finally, we present the most recent advances in our understanding of the structural biology of fungal NRPSs and discuss opportunities for the development of a fungal NRPS prediction server...

  17. GRASPs in Golgi Structure and Function

    Directory of Open Access Journals (Sweden)

    Xiaoyan eZhang

    2016-01-01

    Full Text Available The Golgi apparatus is a central intracellular membrane organelle for trafficking and modification of proteins and lipids. Its basic structure is a stack of tightly aligned flat cisternae. In mammalian cells, dozens of stacks are concentrated in the pericentriolar region and laterally connected to form a ribbon. Despite extensive research in the last decades, how this unique structure is formed and why its formation is important for proper Golgi functioning remain largely unknown. The Golgi ReAssembly Stacking Proteins, GRASP65 and GRASP55, are so far the only proteins shown to function in Golgi stacking. They are peripheral membrane proteins on the cytoplasmic face of the Golgi cisternae that form trans-oligomers through their N-terminal GRASP domain, and thereby function as the glue to stick adjacent cisternae together into a stack and to link Golgi stacks into a ribbon. Depletion of GRASPs in cells disrupts the Golgi structure and results in accelerated protein trafficking and defective glycosylation. In this minireview we summarize our current knowledge on how GRASPs function in Golgi structure formation and discuss why Golgi structure formation is important for its function.

  18. Time-dependent density-functional theory for extended systems

    Energy Technology Data Exchange (ETDEWEB)

    Botti, Silvana [European Theoretical Spectroscopy Facility (ETSF) (Country Unknown); Schindlmayr, Arno [European Theoretical Spectroscopy Facility (ETSF) (Country Unknown); Del Sole, Rodolfo [European Theoretical Spectroscopy Facility (ETSF) (Country Unknown); Reining, Lucia [European Theoretical Spectroscopy Facility (ETSF) (Country Unknown)

    2007-03-15

    For the calculation of neutral excitations, time-dependent density functional theory (TDDFT) is an exact reformulation of the many-body time-dependent Schroedinger equation, based on knowledge of the density instead of the many-body wavefunction. The density can be determined in an efficient scheme by solving one-particle non-interacting Schroedinger equations-the Kohn-Sham equations. The complication of the problem is hidden in the-unknown-time-dependent exchange and correlation potential that appears in the Kohn-Sham equations and for which it is essential to find good approximations. Many approximations have been suggested and tested for finite systems, where even the very simple adiabatic local-density approximation (ALDA) has often proved to be successful. In the case of solids, ALDA fails to reproduce optical absorption spectra, which are instead well described by solving the Bethe-Salpeter equation of many-body perturbation theory (MBPT). On the other hand, ALDA can lead to excellent results for loss functions (at vanishing and finite momentum transfer). In view of this and thanks to recent successful developments of improved linear-response kernels derived from MBPT, TDDFT is today considered a promising alternative to MBPT for the calculation of electronic spectra, even for solids. After reviewing the fundamentals of TDDFT within linear response, we discuss different approaches and a variety of applications to extended systems.

  19. Structural and functional state of heart left ventricle depending on polymorphism rs966221 phosphodiesterase 4D gene in emergency workers of the Chornobyl NPP suffering from coronary heart disease.

    Science.gov (United States)

    Nastina, O; Pleskach, G; Kursina, N; Bazyka, O; Makarevich, O; Abramenko, I; Chumak, A; Belyi, D

    2016-12-01

    This study consisted in examination the features of structural and functional state of the cardiovascular system in emergency workers (EW) of the Chernobyl nuclear power plant (ChNPP) who suffered from coronary heart disease (CHD) and having different genotypes due to polymorphism rs966221 phosphodiesterase 4D (PDE4D) gene. The study involved 121 EW and 63 non irradiated patients with CHD. Standardized survey included echo doppler cardiography (EchoCG) that was done by Diagnostic Ultrasound System DS N3 (Mindray). Polymorphism rs966221 PDE4D determined by polymerase chain reaction followed by restriction reaction products. The distribution of genotypes PDE4D in EW was as follows: CC - 42, CT - 49 and TT - 30 patients. In the con trol group, carriers of the same genotypes were 27, 21 and 15 persons respectively. All echocardiographic parame ters in EW workers and non irradiated patients did not differ significantly. Amongst TT genotype carriers of both groups the proportion of patients with increased myocardial mass index was the highest (82.9%) compared to CC genotype (78.4%) and CT (71.4%). The concentric type of left ventricular (LV) hypertrophy was found in 54.9% of patients with CC genotype, in 51.8% with CT genotype and 45.7% with TT genotype, while the eccentric type in 23.5, 21.4 and 37.1% respectively. The relative number of people with high LV end diastolic volume (EDV) normalized by body surface area (BSA) was 27.5% in CC genotype carriers, 26.8% in CT genotype and 40% in TT genotype carriers (p > 0.05). The increase of BSA indexed LV end systolic volume (ESV) was found in 27.5, 30.4 and 28.6%, and the ejection fraction in 15.7, 23.2 and 22.9% respectively. The largest number of CHD patients with inadequate dias tolic function was in carriers of TT genotype (75%) compared with the data in CC (66.7%) and CT genotypes (42.9%) carriers. In patients with the same genotype, both EW and non irradiated persons there were virtually no dif ferences in indicators

  20. Sensitive dependence of network dynamics on network structure

    CERN Document Server

    Nishikawa, Takashi; Motter, Adilson E

    2016-01-01

    The relation between network structure and dynamics is determinant for the behavior of complex systems in numerous domains. An important longstanding problem concerns the properties of the networks that optimize the dynamics with respect to a given performance measure. Here we show that such optimization can lead to sensitive dependence of the dynamics on the structure of the network. Specifically, we demonstrate that the stability of the dynamical state, as determined by the maximum Lyapunov exponent, can exhibit a cusp-like dependence on the number of nodes and links as well as on the size of perturbations applied to the network structure. As mechanisms underlying this sensitivity, we identify discontinuous transitions occurring in the complement of optimal networks and the prevalence of eigenvector degeneracy in these networks. These findings establish a unified characterization of networks optimized for dynamical stability in diffusively coupled systems, which we illustrate using Turing instability in act...

  1. Time-dependent reliability analysis and condition assessment of structures

    Energy Technology Data Exchange (ETDEWEB)

    Ellingwood, B.R. [Johns Hopkins Univ., Baltimore, MD (United States)

    1997-01-01

    Structures generally play a passive role in assurance of safety in nuclear plant operation, but are important if the plant is to withstand the effect of extreme environmental or abnormal events. Relative to mechanical and electrical components, structural systems and components would be difficult and costly to replace. While the performance of steel or reinforced concrete structures in service generally has been very good, their strengths may deteriorate during an extended service life as a result of changes brought on by an aggressive environment, excessive loading, or accidental loading. Quantitative tools for condition assessment of aging structures can be developed using time-dependent structural reliability analysis methods. Such methods provide a framework for addressing the uncertainties attendant to aging in the decision process.

  2. Using computational models to relate structural and functional brain connectivity.

    Science.gov (United States)

    Hlinka, Jaroslav; Coombes, Stephen

    2012-07-01

    Modern imaging methods allow a non-invasive assessment of both structural and functional brain connectivity. This has lead to the identification of disease-related alterations affecting functional connectivity. The mechanism of how such alterations in functional connectivity arise in a structured network of interacting neural populations is as yet poorly understood. Here we use a modeling approach to explore the way in which this can arise and to highlight the important role that local population dynamics can have in shaping emergent spatial functional connectivity patterns. The local dynamics for a neural population is taken to be of the Wilson-Cowan type, whilst the structural connectivity patterns used, describing long-range anatomical connections, cover both realistic scenarios (from the CoComac database) and idealized ones that allow for more detailed theoretical study. We have calculated graph-theoretic measures of functional network topology from numerical simulations of model networks. The effect of the form of local dynamics on the observed network state is quantified by examining the correlation between structural and functional connectivity. We document a profound and systematic dependence of the simulated functional connectivity patterns on the parameters controlling the dynamics. Importantly, we show that a weakly coupled oscillator theory explaining these correlations and their variation across parameter space can be developed. This theoretical development provides a novel way to characterize the mechanisms for the breakdown of functional connectivity in diseases through changes in local dynamics.

  3. Free flexural vibration of functionally graded size-dependent nanoplates

    CERN Document Server

    Natarajan, S; Thangavel, M

    2012-01-01

    In this paper, the linear free flexural vibration behaviour of functionally graded (FG) size-dependent nanoplates are investigated using the finite element method. The field variables are approximated by non-uniform rational B-splines. The size-dependent FG nanoplate is investigated by using Eringen's differential form of nonlocal elasticity theory. The material properties are assumed to vary only in the thickness direction and the effective properties for FG nanoplate are computed using Mori-Tanaka homogenization scheme. The accuracy of the present formulation is tested considering the problems for which solutions are available. A detailed numerical study is carried out to examine the effect of material gradient index, the characteristic internal length, the plate thickness, the plate aspect ratio and the boundary conditions on the global response of FG nanoplate.

  4. Lung morphometry: the link between structure and function.

    Science.gov (United States)

    Weibel, Ewald R

    2017-03-01

    The study of the structural basis of gas exchange function in the lung depends on the availability of quantitative information that concerns the structures establishing contact between the air in the alveoli and the blood in the alveolar capillaries, which can be entered into physiological equations for predicting oxygen uptake. This information is provided by morphometric studies involving stereological methods and allows estimates of the pulmonary diffusing capacity of the human lung that agree, in experimental studies, with the maximal oxygen consumption. The basis for this "machine lung" structure lies in the complex design of the cells building an extensive air-blood barrier with minimal cell mass.

  5. Structure and function of the archaeal exosome.

    Science.gov (United States)

    Evguenieva-Hackenberg, Elena; Hou, Linlin; Glaeser, Stefanie; Klug, Gabriele

    2014-01-01

    The RNA-degrading exosome in archaea is structurally very similar to the nine-subunit core of the essential eukaryotic exosome and to bacterial polynucleotide phosphorylase (PNPase). In contrast to the eukaryotic exosome, PNPase and the archaeal exosome exhibit metal ion-dependent, phosphorolytic activities and synthesize heteropolymeric RNA tails in addition to the exoribonucleolytic RNA degradation in 3' → 5' direction. The archaeal nine-subunit exosome consists of four orthologs of eukaryotic exosomal subunits: the RNase PH-domain-containing subunits Rrp41 and Rrp42 form a hexameric ring with three active sites, whereas the S1-domain-containing subunits Rrp4 and Csl4 form an RNA-binding trimeric cap on the top of the ring. In vivo, this cap contains Rrp4 and Csl4 in variable amounts. Rrp4 confers poly(A) specificity to the exosome, whereas Csl4 is involved in the interaction with the archaea-specific subunit of the complex, the homolog of the bacterial primase DnaG. The archaeal DnaG is a highly conserved protein and its gene is present in all sequenced archaeal genomes, although the exosome was lost in halophilic archaea and some methanogens. In exosome-containing archaea, DnaG is tightly associated with the exosome. It functions as an additional RNA-binding subunit with poly(A) specificity in the reconstituted exosome of Sulfolobus solfataricus and enhances the degradation of adenine-rich transcripts in vitro. Not only the RNA-binding cap but also the hexameric Rrp41-Rrp42 ring alone shows substrate selectivity and prefers purines over pyrimidines. This implies a coevolution of the exosome and its RNA substrates resulting in 3'-ends with different affinities to the exosome.

  6. Surface structure of polymer Gels and emerging functions

    CERN Document Server

    Kobiki, Y

    1999-01-01

    We report the surface structure of polymer gels on a submicrometer scale during the volume phase transition. Sponge-like domains with a mesoscopic scale were directly observed in water by using at atomic force microscope (AFM). The surface structure characterized by the domains is discussed in terms of the root-mean-square roughness and the auto-correlation function, which were calculated from the AFM images. In order to demonstrate the role of surface structure in determining the macroscopic properties of film-like poly (N-isopropylacrylamide: NIPA) gels. It was found that the temperature dependence, as well as the absolute values of the static contact angle, were strongly dependent on the bulk network inhomogeneities. The relation between the mesoscopic structure and the macroscopic properties is qualitatively discussed in terms of not only the changes in the chemical, but also in the physical, surface properties of the NIPA gels in response to a temperature change.

  7. Deep Inelastic Structure Functions at small x

    CERN Document Server

    Ermolaev, B I; Troyan, S I

    2006-01-01

    Explicit expressions for the non-singlet and singlet structure functions g_1 in the small-x region are obtained. They include the total resummation of the double- and single- logarithms of x and account for the running QCD coupling effects. Both the non-singlet and singlet structure functions are Regge behavied asymptotically, with the intercepts predicted in agreement with experiments. A detailed comparison with the DGLAP evolution equations for different values of x and Q^2 is performed. Finally, the role played by singular terms in DGLAP fits is discussed and explicitly shown to mimic the resummation of leading logarithms at small x.

  8. Transverse Momentum Dependent Parton Distribution Functions through SIDIS and Drell-Yan at COMPASS

    CERN Document Server

    AUTHOR|(CDS)2079419; Ramos, Sérgio; Quintans, Catarina

    The spin structure of the nucleon has been studied at the COMPASS experiment at CERN. The Semi-Inclusive Deep Inelastic Scattering (SIDIS) measurements are a powerful tool to access the Parton Distribution Functions (PDFs) and the Transverse Momentum Dependent Parton Distribution Functions (TMD PDFs). The COMPASS polarised target gives the opportunity to measure the azimuthal modulations depending on the spin orientation and the extraction of the transverse spin asymmetries, which are convolutions of TMD PDFs of the nucleon and Fragmentation Functions (FF). The analysis of these data is done in several kinematic bins, which provides a vast input for the theoreticians to extract the TMDs and the FFs and their kinematic dependence. The TMD PDFs are also accessible through the measurement of the Drell-Yan process, in this case the transverse spin asymmetries are convolutions of two TMD PDFs, one corresponding to the annihilating quark from the beam hadron and the other to the annihilating quark from the target h...

  9. Computing the partition function for kinetically trapped RNA secondary structures.

    Directory of Open Access Journals (Sweden)

    William A Lorenz

    Full Text Available An RNA secondary structure is locally optimal if there is no lower energy structure that can be obtained by the addition or removal of a single base pair, where energy is defined according to the widely accepted Turner nearest neighbor model. Locally optimal structures form kinetic traps, since any evolution away from a locally optimal structure must involve energetically unfavorable folding steps. Here, we present a novel, efficient algorithm to compute the partition function over all locally optimal secondary structures of a given RNA sequence. Our software, RNAlocopt runs in O(n3 time and O(n2 space. Additionally, RNAlocopt samples a user-specified number of structures from the Boltzmann subensemble of all locally optimal structures. We apply RNAlocopt to show that (1 the number of locally optimal structures is far fewer than the total number of structures--indeed, the number of locally optimal structures approximately equal to the square root of the number of all structures, (2 the structural diversity of this subensemble may be either similar to or quite different from the structural diversity of the entire Boltzmann ensemble, a situation that depends on the type of input RNA, (3 the (modified maximum expected accuracy structure, computed by taking into account base pairing frequencies of locally optimal structures, is a more accurate prediction of the native structure than other current thermodynamics-based methods. The software RNAlocopt constitutes a technical breakthrough in our study of the folding landscape for RNA secondary structures. For the first time, locally optimal structures (kinetic traps in the Turner energy model can be rapidly generated for long RNA sequences, previously impossible with methods that involved exhaustive enumeration. Use of locally optimal structure leads to state-of-the-art secondary structure prediction, as benchmarked against methods involving the computation of minimum free energy and of maximum expected

  10. Time-dependent density-functional description of nuclear dynamics

    CERN Document Server

    Nakatsukasa, Takashi; Matsuo, Masayuki; Yabana, Kazuhiro

    2016-01-01

    We present the basic concepts and recent developments in the time-dependent density functional theory (TDDFT) for describing nuclear dynamics at low energy. The symmetry breaking is inherent in nuclear energy density functionals (EDFs), which provides a practical description of important correlations at the ground state. Properties of elementary modes of excitation are strongly influenced by the symmetry breaking and can be studied with TDDFT. In particular, a number of recent developments in the linear response calculation have demonstrated their usefulness in description of collective modes of excitation in nuclei. Unrestricted real-time calculations have also become available in recent years, with new developments for quantitative description of nuclear collision phenomena. There are, however, limitations in the real-time approach; for instance, it cannot describe the many-body quantum tunneling. Thus, we treat the quantum fluctuations associated with slow collective motions assuming that time evolution of...

  11. Studies of Spuriously Time-dependent Resonances in Time-dependent Density Functional Theory

    CERN Document Server

    Luo, Kai; Maitra, Neepa T

    2016-01-01

    Adiabatic approximations in time-dependent density functional theory (TDDFT) will in general yield unphysical time-dependent shifts in the resonance positions of a system driven far from its ground-state. This spurious time-dependence is rationalized in [J. I. Fuks, K. Luo, E. D. Sandoval and N. T. Maitra, Phys. Rev. Lett. {\\bf 114}, 183002 (2015)] in terms of the violation of an exact condition by the non-equilibrium exchange-correlation kernel of TDDFT. Here we give details on the derivation and discuss reformulations of the exact condition that apply in special cases. In its most general form, the condition states that when a system is left in an arbitrary state, in the absence of time-dependent external fields nor ionic motion, the TDDFT resonance position for a given transition is independent of the state. Special cases include the invariance of TDDFT resonances computed with respect to any reference interacting stationary state of a fixed potential, and with respect to any choice of appropriate stationa...

  12. New insights into plastid nucleoid structure and functionality.

    Science.gov (United States)

    Krupinska, Karin; Melonek, Joanna; Krause, Kirsten

    2013-03-01

    Investigations over many decades have revealed that nucleoids of higher plant plastids are highly dynamic with regard to their number, their structural organization and protein composition. Membrane attachment and environmental cues seem to determine the activity and functionality of the nucleoids and point to a highly regulated structure-function relationship. The heterogeneous composition and the many functions that are seemingly associated with the plastid nucleoids could be related to the high number of chromosomes per plastid. Recent proteomic studies have brought novel nucleoid-associated proteins into the spotlight and indicated that plastid nucleoids are an evolutionary hybrid possessing prokaryotic nucleoid features and eukaryotic (nuclear) chromatin components, several of which are dually targeted to the nucleus and chloroplasts. Future studies need to unravel if and how plastid-nucleus communication depends on nucleoid structure and plastid gene expression.

  13. Hippocampal-dependent learning requires a functional circadian system.

    Science.gov (United States)

    Ruby, Norman F; Hwang, Calvin E; Wessells, Colin; Fernandez, Fabian; Zhang, Pei; Sapolsky, Robert; Heller, H Craig

    2008-10-01

    Decades of studies have shown that eliminating circadian rhythms of mammals does not compromise their health or longevity in the laboratory in any obvious way. These observations have raised questions about the functional significance of the mammalian circadian system, but have been difficult to address for lack of an appropriate animal model. Surgical ablation of the suprachiasmatic nucleus (SCN) and clock gene knockouts eliminate rhythms, but also damage adjacent brain regions or cause developmental effects that may impair cognitive or other physiological functions. We developed a method that avoids these problems and eliminates rhythms by noninvasive means in Siberian hamsters (Phodopus sungorus). The present study evaluated cognitive function in arrhythmic animals by using a hippocampal-dependent learning task. Control hamsters exhibited normal circadian modulation of performance in a delayed novel-object recognition task. By contrast, arrhythmic animals could not discriminate a novel object from a familiar one only 20 or 60 min after training. Memory performance was not related to prior sleep history as sleep manipulations had no effect on performance. The GABA antagonist pentylenetetrazol restored learning without restoring circadian rhythms. We conclude that the circadian system is involved in memory function in a manner that is independent of sleep. Circadian influence on learning may be exerted via cyclic GABA output from the SCN to target sites involved in learning. Arrhythmic hamsters may have failed to perform this task because of chronic inhibitory signaling from the SCN that interfered with the plastic mechanisms that encode learning in the hippocampus.

  14. Implementation Strategies for Orbital-dependent Density Functionals

    Science.gov (United States)

    Bento, Marsal E.; Vieira, Daniel

    2016-12-01

    The development of density functional theory (DFT) has been focused primarily on two main pillars: (1) the pursuit of more accurate exchange-correlation (XC) density functionals; (2) the feasibility of computational implementation when dealing with many-body systems. In this context, this work is aimed on using one-dimensional quantum systems as theoretical laboratories to investigate the implementation of orbital functionals (OFs) of density. By definition, OFs are those which depend only implicitly on the density, via an explicit formulation in terms of Kohn-Sham orbitals. Typical examples are the XC functionals arising from the Perdew-Zunger self-interaction correction (PZSIC). Formally, via Kohn-Sham equations, the implementation of OFs must be performed by means of the optimized effective potential method (OEP), which is known by requiring an excessive computational effort even when dealing with few electrons systems. Here, we proceed a systematical investigation aiming to simplify or avoid the OEP procedure, taking as reference the implementation of the PZSIC correction applied to one-dimensional Hubbard chains.

  15. Density-functional perturbation theory goes time-dependent

    Directory of Open Access Journals (Sweden)

    Gebauer, Ralph

    2008-05-01

    Full Text Available The scope of time-dependent density-functional theory (TDDFT is limited to the lowest portion of the spectrum of rather small systems (a few tens of atoms at most. In the static regime, density-functional perturbation theory (DFPT allows one to calculate response functions of systems as large as currently dealt with in ground-state simulations. In this paper we present an effective way of combining DFPT with TDDFT. The dynamical polarizability is first expressed as an off-diagonal matrix element of the resolvent of the Kohn-Sham Liouvillian super-operator. A DFPT representation of response functions allows one to avoid the calculation of unoccupied Kohn-Sham orbitals. The resolvent of the Liouvillian is finally conveniently evaluated using a newly developed non-symmetric Lanczos technique, which allows for the calculation of the entire spectrum with a single Lanczos recursion chain. Each step of the chain essentially requires twice as many operations as a single step of the iterative diagonalization of the unperturbed Kohn-Sham Hamiltonian or, for that matter, as a single time step of a Car-Parrinello molecular dynamics run. The method will be illustrated with a few case molecular applications.

  16. Implementation Strategies for Orbital-dependent Density Functionals

    Science.gov (United States)

    Bento, Marsal E.; Vieira, Daniel

    2016-10-01

    The development of density functional theory (DFT) has been focused primarily on two main pillars: (1) the pursuit of more accurate exchange-correlation (XC) density functionals; (2) the feasibility of computational implementation when dealing with many-body systems. In this context, this work is aimed on using one-dimensional quantum systems as theoretical laboratories to investigate the implementation of orbital functionals (OFs) of density. By definition, OFs are those which depend only implicitly on the density, via an explicit formulation in terms of Kohn-Sham orbitals. Typical examples are the XC functionals arising from the Perdew-Zunger self-interaction correction (PZSIC). Formally, via Kohn-Sham equations, the implementation of OFs must be performed by means of the optimized effective potential method (OEP), which is known by requiring an excessive computational effort even when dealing with few electrons systems. Here, we proceed a systematical investigation aiming to simplify or avoid the OEP procedure, taking as reference the implementation of the PZSIC correction applied to one-dimensional Hubbard chains.

  17. The structure of bivariate rational hypergeometric functions

    CERN Document Server

    Cattani, Eduardo; Villegas, Fernando Rodriguez

    2009-01-01

    We describe the structure of all codimension-two lattice configurations $A$ which admit a stable rational $A$-hypergeometric function, that is a rational function $F$ all whose partial derivatives are non zero, and which is a solution of the $A$-hypergeometric system of partial differential equations defined by Gel'fand, Kapranov and Zelevinsky. We show, moreover, that all stable rational $A$-hypergeometric functions may be described by toric residues and apply our results to study the rationality of bivariate series whose coefficients are quotients of factorials of linear forms.

  18. Unified approach to partition functions of RNA secondary structures.

    Science.gov (United States)

    Bundschuh, Ralf

    2014-11-01

    RNA secondary structure formation is a field of considerable biological interest as well as a model system for understanding generic properties of heteropolymer folding. This system is particularly attractive because the partition function and thus all thermodynamic properties of RNA secondary structure ensembles can be calculated numerically in polynomial time for arbitrary sequences and homopolymer models admit analytical solutions. Such solutions for many different aspects of the combinatorics of RNA secondary structure formation share the property that the final solution depends on differences of statistical weights rather than on the weights alone. Here, we present a unified approach to a large class of problems in the field of RNA secondary structure formation. We prove a generic theorem for the calculation of RNA folding partition functions. Then, we show that this approach can be applied to the study of the molten-native transition, denaturation of RNA molecules, as well as to studies of the glass phase of random RNA sequences.

  19. Hemodynamics, functional state of endothelium and renal function, platelets depending on the body mass index in patients with chronic heart failure and preserved systolic function

    Directory of Open Access Journals (Sweden)

    Kushnir Yu.

    2014-03-01

    Full Text Available The aim of the study was to evaluate hemodynamics, endothelium function of kidneys and platelets depending on the body mass index (BMI in patients with chronic heart failure (CHF and preserved systolic function. 42 patients (mean age - 76,690,83 years with CHF II-III FC NYHA with preserved systolic function (LVEF>45% were enrolled. Echocardiography was performed, endothelial function, serum creatinine levels and microalbuminuria were determined in patients. BMI and glomerulation filtration rate were calculated by formulas. The morphological and functional status of platelets was estimated by electronic microscopy. It was defined that increased BMI in patients with CHF and preserved systolic function determines the structural and functional changes of the myocardium and leads to the endothelial and renal functional changes. An increased risk of thrombogenesis was established in patients with overweight and obesity.

  20. Application of Time-Dependent Density-Functional Theory to C6

    Institute of Scientific and Technical Information of China (English)

    ZHOU Xiao-Lin; BAI Yu-Lin; CHEN Xiang-Rong; YANG Xiang-Dong

    2004-01-01

    @@ We employ a real-space pseudopotential method to determine the ground state structure of the carbon cluster C6 via simulated annealing and the corresponding optical absorption spectra from the adiabatic time-dependent density-functional theory (TDDFT) and the local density approximation (TDLDA). It is found that the ground state structure of the carbon cluster C6 belongs to a monocyclic D3h structure and the calculated spectra exhibit a variety of features that can be used for comparison against future experimental investigations.

  1. Progress on nuclear modifications of structure functions

    Directory of Open Access Journals (Sweden)

    Kumano S.

    2016-01-01

    Full Text Available We report progress on nuclear structure functions, especially on their nuclear modifications and a new tensor structure function for the deuteron. To understand nuclear structure functions is an important step toward describing nuclei and QCD matters from low to high densities and from low to high energies in terms of fundamental quark and gluon degrees of freedom beyond conventional hadron and nuclear physics. It is also practically important for understanding new phenomena in high-energy heavy-ion collisions at RHIC and LHC. Furthermore, since systematic errors of current neutrinooscillation experiments are dominated by uncertainties of neutrino-nucleus interactions, such studies are valuable for finding new physics beyond current framework. Next, a new tensor-polarized structure function b1 is discussed for the deuteron. There was a measurement by HERMES; however, its data are inconsistent with the conventional convolution estimate based on the standard deuteron model with D-state admixture. This fact suggests that a new hadronic phenomenon should exist in the tensor-polarized deuteron at high energies, and it will be experimentally investigated at JLab from the end of 2010’s.

  2. Structure and functions of glutathione transferases

    Directory of Open Access Journals (Sweden)

    O. M. Fedets

    2014-06-01

    Full Text Available Data about classification, nomenclature, structure, substrate specificity and role of many glutathione transferase’s isoenzymes in cell functions have been summarised. The enzyme has been discovered more than 50 years ago. This family of proteins is updated continuously. It has very different composition and will have demand for system analysis for many years.

  3. [Structure and functions of glutathione transferases].

    Science.gov (United States)

    Fedets, O M

    2014-01-01

    Data about classification, nomenclature, structure, substrate specificity and role of many glutathione transferase's isoenzymes in cell functions have been summarised. The enzyme has been discovered more than 50 years ago. This family of proteins is updated continuously. It has very different composition and will have demand for system analysis for many years.

  4. The Refined Function-Behaviour-Structure Framework

    NARCIS (Netherlands)

    Diertens, B.

    2013-01-01

    We refine the function-behaviour-structure framework for design introduced by John Gero in order to deal with complexity. We do this by connecting the frameworks for the desing of two models, one the refinement of the other. The result is a refined framework for the design of an object on two levels

  5. Structural Functionalism as a Heuristic Device.

    Science.gov (United States)

    Chilcott, John H.

    1998-01-01

    Argues that structural functionalism as a method for conducting fieldwork and as a format for the analysis of ethnographic data remains a powerful model, one that is easily understood by professional educators. As a heuristic device, functionalist theory can help in the solution of a problem that is otherwise incapable of theoretical…

  6. Structure and Function of Your Skin

    Science.gov (United States)

    ... Favorite Name: Category: Share: Yes No, Keep Private Structure & Function of Your Skin Share | What It Looks Like . . . Skin is a waterproof, flexible, but tough protective covering for your body. Normally the surface is smooth, punctuated only with hair and pores for sweat. A cross-section of ...

  7. Body Structure and Function. Teacher Edition.

    Science.gov (United States)

    Oklahoma State Dept. of Vocational and Technical Education, Stillwater. Curriculum and Instructional Materials Center.

    This curriculum guide contains the materials required to teach a course in body structure and function. The following topics are covered in the course's 17 instructional units: basic concepts of physical and life sciences; microbiology and bacteriology; the integumentary, skeletal, muscular, digestive, circulatory, respiratory, urinary, central…

  8. Polynomial Structure of Topological String Partition Functions

    CERN Document Server

    Zhou, Jie

    2015-01-01

    We review the polynomial structure of the topological string partition functions as solutions to the holomorphic anomaly equations. We also explain the connection between the ring of propagators defined from special K\\"ahler geometry and the ring of almost-holomorphic modular forms defined on modular curves.

  9. Cosmological parameter dependence in local string theories of structure formation

    CERN Document Server

    Copeland, E J; Steer, D A; Magueijo, Joao

    2000-01-01

    We perform the most accurate study to date of the dependence on cosmological parameters of structure formation with local cosmic strings. The crucial new ingredients are the inclusion of the effects of gravitational backreaction on the evolution of the network, and the accurate evolution of the network through the radiation to matter transition. Our work re-iterates the fact that expanding Universe numerical simulations only probe a transient regime, and we incorporate our results into the unequal time correlators recently measured. We then compute the CMB and CDM fluctuations' power spectra for various values of the Hubble constant $H_0$ and baryon fraction $\\Omega_b$. We find that, whereas the dependence on $\\Omega_b$ is negligible, there is still a strong dependence on $H_0$.

  10. Doping-dependent quasiparticle band structure in cuprate superconductors

    NARCIS (Netherlands)

    Eder, R; Ohta, Y.; Sawatzky, G.A

    1997-01-01

    We present an exact diagonalization study of the single-particle spectral function in the so-called t-t'-t ''-J model in two dimensions. As a key result, we find that hole doping leads to a major reconstruction of the quasiparticle band structure near (pi,0): whereas for the undoped system the quasi

  11. Dependence of thermal conductivity on structural parameters in porous samples

    OpenAIRE

    L. Miettinen; Kekäläinen, P; T. Turpeinen; Hyväluoma, J; Merikoski, J.; J. Timonen

    2012-01-01

    The in-plane thermal conductivity of porous sintered bronze plates was studied both experimentally and numerically. We developed and validated an experimental setup, where the sample was placed in vacuum and heated while its time-dependent temperature field was measured with an infrared camera. The porosity and detailed three-dimensional structure of the samples were determined by X-ray microtomography. Lattice-Boltzmann simulations of thermal conductivity in the tomographic reconstructions o...

  12. Generalized functions, convergence structures, and their applications

    CERN Document Server

    Pap, Endre; Pilipović, Stevan; Vladimirov, Vasilij; International Conference "Generalized functions, convergence structures and their applications" (GFCA-87)

    1988-01-01

    This Proceedings consists of a collection of papers presented at the International Conference "Generalized functions, convergence structures and their applications" held from June 23-27, 1987 in Dubrovnik, Yugoslavia (GFCA-87): 71 participants from 21 countr~es from allover the world took part in the Conference. Proceedings reflects the work of the Conference. Plenary lectures of J. Burzyk, J. F. Colombeau, W. Gahler, H. Keiter, H. Komatsu, B. Stankovic, H. G. Tillman, V. S. Vladimirov provide an up-to-date account of the cur­ rent state of the subject. All these lectures, except H. G. Tillman's, are published in this volume. The published communications give the contemporary problems and achievements in the theory of generalized functions, in the theory of convergence structures and in their applications, specially in the theory of partial differential equations and in the mathematical physics. New approaches to the theory of generalized functions are presented, moti­ vated by concrete problems of applicat...

  13. Size-dependent structure of silver nanoparticles under high pressure

    Energy Technology Data Exchange (ETDEWEB)

    Koski, Kristie Jo [Univ. of California, Berkeley, CA (United States)

    2008-12-31

    Silver noble metal nanoparticles that are<10 nm often possess multiply twinned grains allowing them to adopt shapes and atomic structures not observed in bulk materials. The properties exhibited by particles with multiply twinned polycrystalline structures are often far different from those of single-crystalline particles and from the bulk. I will present experimental evidence that silver nanoparticles<10 nm undergo a reversible structural transformation under hydrostatic pressures up to 10 GPa. Results for nanoparticles in the intermediate size range of 5 to 10 nm suggest a reversible linear pressure-dependent rhombohedral distortion which has not been previously observed in bulk silver. I propose a mechanism for this transitiion that considers the bond-length distribution in idealized multiply twinned icosahedral particles. Results for nanoparticles of 3.9 nm suggest a reversible linear pressure-dependent orthorhombic distortion. This distortion is interpreted in the context of idealized decahedral particles. In addition, given these size-dependent measurements of silver nanoparticle compression with pressure, we have constructed a pressure calibration curve. Encapsulating these silver nanoparticles in hollow metal oxide nanospheres then allows us to measure the pressure inside a nanoshell using x-ray diffraction. We demonstrate the measurement of pressure gradients across nanoshells and show that these nanoshells have maximum resolved shear strengths on the order of 500 MPa to IGPa.

  14. Crystal structures of phosphoketolase: thiamine diphosphate-dependent dehydration mechanism.

    Science.gov (United States)

    Suzuki, Ryuichiro; Katayama, Takane; Kim, Byung-Jun; Wakagi, Takayoshi; Shoun, Hirofumi; Ashida, Hisashi; Yamamoto, Kenji; Fushinobu, Shinya

    2010-10-29

    Thiamine diphosphate (ThDP)-dependent enzymes are ubiquitously present in all organisms and catalyze essential reactions in various metabolic pathways. ThDP-dependent phosphoketolase plays key roles in the central metabolism of heterofermentative bacteria and in the pentose catabolism of various microbes. In particular, bifidobacteria, representatives of beneficial commensal bacteria, have an effective glycolytic pathway called bifid shunt in which 2.5 mol of ATP are produced per glucose. Phosphoketolase catalyzes two steps in the bifid shunt because of its dual-substrate specificity; they are phosphorolytic cleavage of fructose 6-phosphate or xylulose 5-phosphate to produce aldose phosphate, acetyl phosphate, and H(2)O. The phosphoketolase reaction is different from other well studied ThDP-dependent enzymes because it involves a dehydration step. Although phosphoketolase was discovered more than 50 years ago, its three-dimensional structure remains unclear. In this study we report the crystal structures of xylulose 5-phosphate/fructose 6-phosphate phosphoketolase from Bifidobacterium breve. The structures of the two intermediates before and after dehydration (α,β-dihydroxyethyl ThDP and 2-acetyl-ThDP) and complex with inorganic phosphate give an insight into the mechanism of each step of the enzymatic reaction.

  15. Protein tyrosine phosphatases: structure-function relationships.

    Science.gov (United States)

    Tabernero, Lydia; Aricescu, A Radu; Jones, E Yvonne; Szedlacsek, Stefan E

    2008-03-01

    Structural analysis of protein tyrosine phosphatases (PTPs) has expanded considerably in the last several years, producing more than 200 structures in this class of enzymes (from 35 different proteins and their complexes with ligands). The small-medium size of the catalytic domain of approximately 280 residues plus a very compact fold makes it amenable to cloning and overexpression in bacterial systems thus facilitating crystallographic analysis. The low molecular weight PTPs being even smaller, approximately 150 residues, are also perfect targets for NMR analysis. The availability of different structures and complexes of PTPs with substrates and inhibitors has provided a wealth of information with profound effects in the way we understand their biological functions. Developments in mammalian expression technology recently led to the first crystal structure of a receptor-like PTP extracellular region. Altogether, the PTP structural work significantly advanced our knowledge regarding the architecture, regulation and substrate specificity of these enzymes. In this review, we compile the most prominent structural traits that characterize PTPs and their complexes with ligands. We discuss how the data can be used to design further functional experiments and as a basis for drug design given that many PTPs are now considered strategic therapeutic targets for human diseases such as diabetes and cancer.

  16. The structure function as a metric for roughness and figure

    Science.gov (United States)

    Parks, Robert E.; Tuell, Michael T.

    2016-09-01

    As optical designs become more sophisticated and incorporate aspheric and free form surfaces, the need to specify limits on mid-spatial frequency manufacturing errors becomes more critical, particularly as we better understand the effects of these errors on image quality. While there already exist methods based on Fourier analysis to specify these errors in most commercial interferometry software, the method of calculation and the power spectral density (PSD) results remain obscure to many in the optical design and manufacturing field. We suggest that the structure functions (SF) contains the same information as in the Fourier based PSD but in a way that is much more transparent to analysis, interpretation and application as a specification. The units of measure are more familiar and the concept behind the analysis is simpler to understand. Further, the information contained in the structure function (or PSD) allows a complete specification of an optical surface from the finest measurable detail of roughness to the overall figure. We discuss the origin of the structure function in the field of astronomy to describe the effects of air turbulence on image quality, the simple mathematical definition of the structure function and its easy means of calculation and how its results should be scaled depending on the location of the optical surface in a system from pupil to image plane. Finally, we give an example of how to write a specification of an optical surface using the structure function.

  17. In Medium Nucleon Structure Functions, SRC, and the EMC effect

    CERN Document Server

    Hen, O; Gilad, S; Wood, S A

    2014-01-01

    A proposal approved by the Jefferson Lab PAC to study semi-inclusive deep inelastic scattering (DIS) off the deuteron, tagged with high momentum recoiling protons or neutrons emitted at large angle relative to the momentum transfer. This experiment aims at studying the virtuality dependence of the bound nucleon structure function as a possible cause to the EMC effect and the EMC-SRC correlations. The experiment was approved in 2011 for a total run time of 40 days.

  18. Generating function approach to reliability analysis of structural systems

    Institute of Scientific and Technical Information of China (English)

    2009-01-01

    The generating function approach is an important tool for performance assessment in multi-state systems. Aiming at strength reliability analysis of structural systems, generating function approach is introduced and developed. Static reliability models of statically determinate, indeterminate systems and fatigue reliability models are built by constructing special generating functions, which are used to describe probability distributions of strength (resistance), stress (load) and fatigue life, by defining composite operators of generating functions and performance structure functions thereof. When composition operators are executed, computational costs can be reduced by a big margin by means of collecting like terms. The results of theoretical analysis and numerical simulation show that the generating function approach can be widely used for probability modeling of large complex systems with hierarchical structures due to the unified form, compact expression, computer program realizability and high universality. Because the new method considers twin loads giving rise to component failure dependency, it can provide a theoretical reference and act as a powerful tool for static, dynamic reliability analysis in civil engineering structures and mechanical equipment systems with multi-mode damage coupling.

  19. [Structure and function of histone chaperone FACT].

    Science.gov (United States)

    Bondarenko, M T; Maluchenko, N V; Valieva, M E; Gerasimova, N S; Kulaeva, O I; Georgiev, P G; Studitsky, V M

    2015-01-01

    FACT is heterodimer protein complex and histone chaperone that plays an important role in maintaining and modifying chromatin structure during various DNA-dependent processes. FACT is involved in nucleosome assembly de novo and in the preservation and recovery of the nucleosome structure during and after transcription, replication and repair of DNA. During transcript elongation FACT reduces the height of the nucleosome barrier and supports survival of the nucleosomes during and after passage of RNA polymerase II. In this process FACT interacts with histone H2A-H2B dimer in nucleosomes, thus facilitating uncoiling of nucleosomal DNA from the octamer of histones; it also facilitates subsequent recovery of the canonical structure of the nucleosome after transcription. FACT also plays an important role in transformation of human cells and in maintaining the viability of the tumor cells.

  20. Structured scale dependence in the Lyapunov exponent of a Boolean chaotic map.

    Science.gov (United States)

    Cohen, Seth D

    2015-04-01

    We report on structures in a scale-dependent Lyapunov exponent of an experimental chaotic map that arise due to discontinuities in the map. The chaos is realized in an autonomous Boolean network, which is constructed using asynchronous logic gates to form a map operator that outputs an unclocked pulse-train of varying widths. The map operator executes pulse-width stretching and folding and the operator's output is fed back to its input to continuously iterate the map. Using a simple model, we show that the structured scale-dependence in the system's Lyapunov exponent is the result of the discrete logic elements in the map operator's stretching function.

  1. Relativistic Spin-Isospin Dependent Response Function of Nucleus

    Institute of Scientific and Technical Information of China (English)

    LIU Liang-Gang; CHEN Wei; AI Bao-Quan; ZHENG Xiao-Ping; Masahiro Nakano

    2000-01-01

    A full relativistic formalism is employed to derive the relativistic particle-hole and delta-hole excitation polariza tion insertion of pion propagator in nuclear matter. The spin-isospin-dependent response function of nucleus at high energy-momentum transfer is calculated with the nuclear matter approximation. The short range correlation effect, two-nucleon absorption and nucleus form factor effects are included in the calculation. The position and width of the resonance peak of the spin-isospin mode are reproduced and found to be coincident with experiment data. The position of the peak and its width is sensitive to Landau-Migdal parameter g' which is about 0.6.

  2. Pollen structure and function in caesalpinioid legumes.

    Science.gov (United States)

    Banks, Hannah; Rudall, Paula J

    2016-03-01

    A diverse range of pollen morphologies occurs within the large, paraphyletic legume subfamily Caesalpinioideae, especially among early-branching lineages. Previous studies have hypothesized an association between surface ornamentation and pollination syndrome or other aspects of pollen function such as desiccation tolerance and adaptations to accommodate volume changes. We reviewed caesalpinioid pollen morphology using light microscopy, scanning and transmission electron microscopy, in combination with a literature survey of pollination vectors. Pollen structural diversity is greatest in the early-branching tribes Cercideae and Detarieae, whereas Cassieae and Caesalpinieae are relatively low in pollen diversity. Functional structures to counter desiccation include opercula (lids) covering apertures and reduced aperture size. Structures preventing wall rupture during dehydration and rehydration include different forms of colpi (syncolpi, parasyncolpi, pseudocolpi), striate supratectal ornamentation, and columellate or granular wall structures that resist tensile or compressive forces respectively. Specialized aperture structures (Zwischenkörper) may be advantageous for efficient germination of the pollen tube. In Detarieae and Cercideae in particular, there is potential to utilize pollen characters to estimate pollination systems where these are unknown. Supratectal verrucae and gemmae have apparently evolved iteratively in Cercideae and Detarieae. At the species level, there is a potential correlation between striate/verrucate patterns and vertebrate pollination. © 2016 Botanical Society of America.

  3. Nuclear Structure Functions from Constituent Quark Model

    CERN Document Server

    Arash, F; Arash, Firooz; Atashbar-Tehrani, Shahin

    1999-01-01

    We have used the notion of the constituent quark model of nucleon, where a constituent quark carries its own internal structure, and applied it to determine nuclear structure functions ratios. It is found that the description of experimental data require the inclusion of strong shadowing effect for $x<0.01$. Using the idea of vector meson dominance model and other ingredients this effect is calculated in the context of the constituent quark model. It is rather striking that the constituent quark model, used here, gives a good account of the data for a wide range of atomic mass number from A=4 to A=204.

  4. Community structure in time-dependent, multiscale, and multiplex networks.

    Science.gov (United States)

    Mucha, Peter J; Richardson, Thomas; Macon, Kevin; Porter, Mason A; Onnela, Jukka-Pekka

    2010-05-14

    Network science is an interdisciplinary endeavor, with methods and applications drawn from across the natural, social, and information sciences. A prominent problem in network science is the algorithmic detection of tightly connected groups of nodes known as communities. We developed a generalized framework of network quality functions that allowed us to study the community structure of arbitrary multislice networks, which are combinations of individual networks coupled through links that connect each node in one network slice to itself in other slices. This framework allows studies of community structure in a general setting encompassing networks that evolve over time, have multiple types of links (multiplexity), and have multiple scales.

  5. Dynamics of Buyer-Supplier Co-dependency for Optimizing Functional Efficiency

    OpenAIRE

    Rajagopal, MR

    2007-01-01

    The performance related issues of buyer-supplier relationship have attracted both the academic and corporate managers. The study attempts to make theoretical contributions to the literature on relationships in marketing channels. Compared with the impact of the often-investigated construct of dependence structure, the impact of channel function performance on relationship quality is relatively large. This study has been conducted in reference to the suppliers of office equipments serving to t...

  6. Longitudinal Structure Function FL from Charm Structure Function F2c

    Institute of Scientific and Technical Information of China (English)

    B.Rezaei; G.R.Boroun

    2013-01-01

    We predict the effect of the charm structure function on the longitudinal structure function at small x.In NLO analysis we find that the hard Pomeron behavior gives a good description of FL and Fkc (k =2,L) at small x values.We conclude that a direct relation between FL∝ F2c would provide useful information on how to measure longitudinal structure function at high Q2 values.Having checked that this model gives a good description of the data,when compared with other models.

  7. Proteins with Novel Structure, Function and Dynamics

    Science.gov (United States)

    Pohorille, Andrew

    2014-01-01

    Recently, a small enzyme that ligates two RNA fragments with the rate of 10(exp 6) above background was evolved in vitro (Seelig and Szostak, Nature 448:828-831, 2007). This enzyme does not resemble any contemporary protein (Chao et al., Nature Chem. Biol. 9:81-83, 2013). It consists of a dynamic, catalytic loop, a small, rigid core containing two zinc ions coordinated by neighboring amino acids, and two highly flexible tails that might be unimportant for protein function. In contrast to other proteins, this enzyme does not contain ordered secondary structure elements, such as alpha-helix or beta-sheet. The loop is kept together by just two interactions of a charged residue and a histidine with a zinc ion, which they coordinate on the opposite side of the loop. Such structure appears to be very fragile. Surprisingly, computer simulations indicate otherwise. As the coordinating, charged residue is mutated to alanine, another, nearby charged residue takes its place, thus keeping the structure nearly intact. If this residue is also substituted by alanine a salt bridge involving two other, charged residues on the opposite sides of the loop keeps the loop in place. These adjustments are facilitated by high flexibility of the protein. Computational predictions have been confirmed experimentally, as both mutants retain full activity and overall structure. These results challenge our notions about what is required for protein activity and about the relationship between protein dynamics, stability and robustness. We hypothesize that small, highly dynamic proteins could be both active and fault tolerant in ways that many other proteins are not, i.e. they can adjust to retain their structure and activity even if subjected to mutations in structurally critical regions. This opens the doors for designing proteins with novel functions, structures and dynamics that have not been yet considered.

  8. Interplay between histone H1 structure and function.

    Science.gov (United States)

    Roque, Alicia; Ponte, Inma; Suau, Pedro

    2016-03-01

    H1 linker histones are involved both in the maintenance of higher-order chromatin structure and in gene regulation. Histone H1 exists in multiple isoforms, is evolutionarily variable and undergoes a large variety of post-translational modifications. We review recent progress in the understanding of the folding and structure of histone H1 domains with an emphasis on the interactions with DNA. The importance of intrinsic disorder and hydrophobic interactions in the folding and function of the carboxy-terminal domain (CTD) is discussed. The induction of a molten globule-state in the CTD by macromolecular crowding is also considered. The effects of phosphorylation by cyclin-dependent kinases on the structure of the CTD, as well as on chromatin condensation and oligomerization, are described. We also address the extranuclear functions of histone H1, including the interaction with the β-amyloid peptide. Copyright © 2015 Elsevier B.V. All rights reserved.

  9. Phosphatidylinositol 4-kinases: Function, structure, and inhibition

    Energy Technology Data Exchange (ETDEWEB)

    Boura, Evzen, E-mail: boura@uochb.cas.cz; Nencka, Radim, E-mail: nencka@uochb.cas.cz

    2015-10-01

    The phosphatidylinositol 4-kinases (PI4Ks) synthesize phosphatidylinositol 4-phosphate (PI4P), a key member of the phosphoinositide family. PI4P defines the membranes of Golgi and trans-Golgi network (TGN) and regulates trafficking to and from the Golgi. Humans have two type II PI4Ks (α and β) and two type III enzymes (α and β). Recently, the crystal structures were solved for both type II and type III kinase revealing atomic details of their function. Importantly, the type III PI4Ks are hijacked by +RNA viruses to create so-called membranous web, an extensively phosphorylated and modified membrane system dedicated to their replication. Therefore, selective and potent inhibitors of PI4Ks have been developed as potential antiviral agents. Here we focus on the structure and function of PI4Ks and their potential in human medicine.

  10. Multimodality imaging of structure and function

    Energy Technology Data Exchange (ETDEWEB)

    Townsend, D W [Departments of Medicine and Radiology, University of Tennessee Medical Center, 1924 Alcoa Highway, Knoxville, TN 37920 (United States)], E-mail: dtownsend@mc.utmck.edu

    2008-02-21

    Historically, medical devices to image either anatomical structure or functional processes have developed along somewhat independent paths. The recognition that combining images from different modalities can nevertheless offer significant diagnostic advantages gave rise to sophisticated software techniques to coregister structure and function. Recently, alternatives to retrospective software-based fusion have become available through instrumentation that combines two imaging modalities within a single device, an approach that has since been termed hardware fusion. As a result, following their recent introduction into the clinic, combined PET/CT and SPECT/CT devices are now playing an increasingly important role in the diagnosis and staging of human disease. Recently, although limited to the brain, the first clinical MR scanner with a PET insert, a technically-challenging design, has been undergoing evaluation. This review will follow the development of multimodality instrumentation for clinical use from conception to present-day technology and assess the status and future potential for such devices. (topical review)

  11. Optimized distance-dependent atom-pair-based potential DOOP for protein structure prediction.

    Science.gov (United States)

    Chae, Myong-Ho; Krull, Florian; Knapp, Ernst-Walter

    2015-05-01

    The DOcking decoy-based Optimized Potential (DOOP) energy function for protein structure prediction is based on empirical distance-dependent atom-pair interactions. To optimize the atom-pair interactions, native protein structures are decomposed into polypeptide chain segments that correspond to structural motives involving complete secondary structure elements. They constitute near native ligand-receptor systems (or just pairs). Thus, a total of 8609 ligand-receptor systems were prepared from 954 selected proteins. For each of these hypothetical ligand-receptor systems, 1000 evenly sampled docking decoys with 0-10 Å interface root-mean-square-deviation (iRMSD) were generated with a method used before for protein-protein docking. A neural network-based optimization method was applied to derive the optimized energy parameters using these decoys so that the energy function mimics the funnel-like energy landscape for the interaction between these hypothetical ligand-receptor systems. Thus, our method hierarchically models the overall funnel-like energy landscape of native protein structures. The resulting energy function was tested on several commonly used decoy sets for native protein structure recognition and compared with other statistical potentials. In combination with a torsion potential term which describes the local conformational preference, the atom-pair-based potential outperforms other reported statistical energy functions in correct ranking of native protein structures for a variety of decoy sets. This is especially the case for the most challenging ROSETTA decoy set, although it does not take into account side chain orientation-dependence explicitly. The DOOP energy function for protein structure prediction, the underlying database of protein structures with hypothetical ligand-receptor systems and their decoys are freely available at http://agknapp.chemie.fu-berlin.de/doop/.

  12. Nuclear medium modification of the F2 structure function

    CERN Document Server

    Athar, M Sajjad; Vacas, M J Vicente

    2009-01-01

    We study the nuclear effects in the electromagnetic structure function $F_{2}(x, Q^2)$ in nuclei in the deep inelastic lepton nucleus scattering process by taking into account Fermi motion, binding, pion and rho meson cloud contributions. Calculations have been done in a local density approximation using relativistic nuclear spectral functions which include nucleon correlations for nuclear matter. The ratios $R_{F2}^A(x,Q^2)=\\frac{2F_2^A(x,Q^2)}{AF_{2}^{Deut}(x,Q^2)}$ are obtained and compared with the recent JLAB results for light nuclei that show a non trivial A dependence.

  13. [Structural and functional neuroimaging of the pathophysiology of apraxia].

    Science.gov (United States)

    Weiss, P H; Fink, G R

    2010-12-01

    A better understanding of the neural bases of apraxia is an important prerequisite to develop new therapeutic strategies for the disabling apraxic deficits after left-hemisphere stroke, like disturbed imitation of gestures, deficient pantomime, and object use deficits. Recently, functional and structural imaging methods allowed deeper insights into the pathophysiology of apraxia: While apraxic object use deficits result from the dysfunction of an extended fronto-parietal network within the left hemisphere, pantomime deficits are caused by impaired functioning of the left inferior frontal cortex. Further apraxia-related, motor cognitive processes (i.e., gesture imitation, integration of temporal and spatial movement information, and intentional movement planning) depend on the integrity of the left parietal cortex. Newly developed functional and structural imaging methods, like dynamic causal modelling (DCM) and diffusion tensor imaging (DTI), promise to further elucidate the pathophysiology of apraxia at the network level.

  14. Correlation function as a measure of the structure

    CERN Document Server

    Buryak, O E

    1995-01-01

    Geometrical model of structure of the universe is examined to obtain analytical expression for the two points nonlinear correlation function. According to the model the objects (galaxies) are concentrated into two types of structure elements - filaments and sheets. We considered the filaments ( similar to galaxy filaments ) simply as straight lines and the sheets ( similar to superclusters of galaxies ) simply as planes. The homogeneously distributed objects are also taken into consideration. The spatial distribution of lines, planes and points is uncorrelated. The nonlinear correlation function depends on four parameters and is similar to the observed and simulated ones for different samples. It describes quite well the correlation of galaxies, clusters of galaxies and dark matter distribution. Possible interpretation of the parameters of nonlinear correlation function is discussed.

  15. R-ratios and moments of nuclear structure functions

    CERN Document Server

    Rinat, A S

    2000-01-01

    We study implications of a model, which links nuclear and nucleon structure functions. Computed Callen-Gross functions $\\kappa^A(x,Q^2)= 2xF_1^A(x,Q^2)/F_2^A(x,Q^2)$ appear for finite $Q^2$ to be close to their asymptotic value 1. Using those $\\kappa$, we compure $R$ ratios for $Q^2\\ge 5 GeV^2$. We review approximate methods in use for the extraction of $R$ from inclusive scattering and ENC data. Further we calcuate ratios of the moments of $F_k$ and find these to describe the data, in particular their $Q^2$ dependence. The above observables, as well as inclusive cross sections, are sensitive tests for the underlying relation between nucleonic and nuclear structure functions. In view of the overall agreement, we speculate that the above relation effectively circumvents a QCD calculation.

  16. Modelling the statistical dependence of rainfall event variables by a trivariate copula function

    Directory of Open Access Journals (Sweden)

    M. Balistrocchi

    2011-01-01

    Full Text Available In many hydrological models, such as those derived by analytical probabilistic methods, the precipitation stochastic process is represented by means of individual storm random variables which are supposed to be independent of each other. However, several proposals were advanced to develop joint probability distributions able to account for the observed statistical dependence. The traditional technique of the multivariate statistics is nevertheless affected by several drawbacks, whose most evident issue is the unavoidable subordination of the dependence structure assessment to the marginal distribution fitting. Conversely, the copula approach can overcome this limitation, by splitting the problem in two distinct items. Furthermore, goodness-of-fit tests were recently made available and a significant improvement in the function selection reliability has been achieved. Herein a trivariate probability distribution of the rainfall event volume, the wet weather duration and the interevent time is proposed and verified by test statistics with regard to three long time series recorded in different Italian climates. The function was developed by applying a mixing technique to bivariate copulas, which were formerly obtained by analyzing the random variables in pairs. A unique probabilistic model seems to be suitable for representing the dependence structure, despite the sensitivity shown by the dependence parameters towards the threshold utilized in the procedure for extracting the independent events. The joint probability function was finally developed by adopting a Weibull model for the marginal distributions.

  17. Dependability of the Exemplary Technical System for Assumed Functions of Defect Density

    Directory of Open Access Journals (Sweden)

    Stępień Sławomir

    2016-12-01

    Full Text Available The analysis of structural dependability of technical system, especially determining the change in dependability over time, requires knowledge on density function or the understanding of cumulative distribution function of components belonging to the structure. Based on previously registered data concerning component defect, it is relatively easy to establish the average uptime of component as well as the standard deviation for this time. However, defining distribution shape gives rise to some difficulties. Usually, we do not have the sufficient number of data at our disposal to verify the hypothesis regarding the distribution shape. Due to this fact, it is a common practice, depending on the case under consideration, to apply the function of defect density. However, the question arises: Does the incorrect determination of types of distributions of components leads to the big error of estimation results of dependability and system durability? This article will not respond to this question in whole, but one will conduct a comparison of calculation results for a few cases. The calculations were conducted for the exemplary technical system.

  18. Stochastic Time-Dependent Current-Density Functional Theory

    Science.gov (United States)

    D'Agosta, Roberto

    2008-03-01

    Static and dynamical density functional methods have been applied with a certain degree of success to a variety of closed quantum mechanical systems, i.e., systems that can be described via a Hamiltonian dynamics. However, the relevance of open quantum systems - those coupled to external environments, e.g., baths or reservoirs - cannot be overestimated. To investigate open quantum systems with DFT methods we have introduced a new theory, we have named Stochastic Time-Dependent Current Density Functional theory (S-TDCDFT) [1]: starting from a suitable description of the system dynamics via a stochastic Schrödinger equation [2], we have proven that given an initial quantum state and the coupling between the system and the environment, there is a one-to-one correspondence between the ensemble-averaged current density and the external vector potential applied to the system.In this talk, I will introduce the stochastic formalism needed for the description of open quantum systems, discuss in details the theorem of Stochastic TD-CDFT, and provide few examples of its applicability like the dissipative dynamics of excited systems, quantum-measurement theory and other applications relevant to charge and energy transport in nanoscale systems.[1] M. Di Ventra and R. D'Agosta, Physical Review Letters 98, 226403 (2007)[2] N.G. van Kampen, Stochastic processes in Physics and Chemistry, (North Holland, 2001), 2nd ed.

  19. Sex Dependence of Cognitive Functions in Bipolar Disorder

    Directory of Open Access Journals (Sweden)

    Aleksandra Suwalska

    2014-01-01

    Full Text Available The objective of the present study was to assess the performance of lithium treated euthymic bipolar patients in tests measuring spatial working memory (SWM, planning, and verbal fluency and to delineate the influence of gender on cognitive functioning. Fifty-nine euthymic bipolar patients, treated with lithium carbonate for at least 5 yr, were studied. Patients and controls underwent a neuropsychological assessment. Bipolar patients had significantly worse results than the healthy controls in the spatial memory and planning as well as verbal fluency tests. We detected a gender-related imbalance in the SWM results. Deficits in SWM were observed in male-only comparisons but not in female-only comparisons. The SWM scores were significantly poorer in male patients than in male controls. In female-only comparisons, female patients did not have significantly poorer SWM results in any category than their controls. Bipolar women scored worse in some other tests. The present study points to the different patterns of neuropsychological disturbances in female and male patients and suggests that sex-dependent differences should be taken into account in order to tailor the therapeutic intervention aimed at the improvement of cognitive functions.

  20. Functional assessment of ubiquitin-depended processes under microgravity conditions

    Science.gov (United States)

    Zhabereva, Anastasia; Shenkman, Boris S.; Gainullin, Murat; Gurev, Eugeny; Kondratieva, Ekaterina; Kopylov, Arthur

    , were separated by SDS-PAGE and subjected for mass spectrometry-based analysis.With the described workflow, we identified more than 200 proteins including of 26S proteasome subunits, members of SUMO (Small Ubiquitin-like Modifier) family and ubiquitylated substrates. On the whole, our results provide an unbiased view of ubiquitylation state under microgravity conditions and thereby demonstrate the utility of proposed combination of analytical methods for functional assessment of ubiquitin-depended processes. Acknowledgment - We thank teams of Institute of Biomedical Problems of Russian Academy of Sciences and TsSKB “Progress” Samara for organization and preparation for spaceflight. This work is partially supported by the Russian Foundation for Basic Research (grant12-04-01836).

  1. Truncated Moment Analysis of Nucleon Structure Functions

    Energy Technology Data Exchange (ETDEWEB)

    A. Psaker; W. Melnitchouk; M. E. Christy; C. E. Keppel

    2007-11-16

    We employ a novel new approach using "truncated" moments, or integrals of structure functions over restricted regions of x, to study local quark-hadron duality, and the degree to which individual resonance regions are dominated by leading twists. Because truncated moments obey the same Q^2 evolution equations as the leading twist parton distributions, this approach makes possible for the first time a description of resonance region data and the phenomenon of quark-hadron duality directly from QCD.

  2. Structure and function of mammalian cilia

    DEFF Research Database (Denmark)

    Satir, Peter; Christensen, Søren T

    2008-01-01

    In the past half century, beginning with electron microscopic studies of 9 + 2 motile and 9 + 0 primary cilia, novel insights have been obtained regarding the structure and function of mammalian cilia. All cilia can now be viewed as sensory cellular antennae that coordinate a large number...... of cellular signaling pathways, sometimes coupling the signaling to ciliary motility or alternatively to cell division and differentiation. This view has had unanticipated consequences for our understanding of developmental processes and human disease....

  3. Non-Stationary Dependence Structures for Spatial Extremes

    KAUST Repository

    Huser, Raphaël

    2016-03-03

    Max-stable processes are natural models for spatial extremes because they provide suitable asymptotic approximations to the distribution of maxima of random fields. In the recent past, several parametric families of stationary max-stable models have been developed, and fitted to various types of data. However, a recurrent problem is the modeling of non-stationarity. In this paper, we develop non-stationary max-stable dependence structures in which covariates can be easily incorporated. Inference is performed using pairwise likelihoods, and its performance is assessed by an extensive simulation study based on a non-stationary locally isotropic extremal t model. Evidence that unknown parameters are well estimated is provided, and estimation of spatial return level curves is discussed. The methodology is demonstrated with temperature maxima recorded over a complex topography. Models are shown to satisfactorily capture extremal dependence.

  4. Industrial entrepreneurial network: Structural and functional analysis

    Science.gov (United States)

    Medvedeva, M. A.; Davletbaev, R. H.; Berg, D. B.; Nazarova, J. J.; Parusheva, S. S.

    2016-12-01

    Structure and functioning of two model industrial entrepreneurial networks are investigated in the present paper. One of these networks is forming when implementing an integrated project and consists of eight agents, which interact with each other and external environment. The other one is obtained from the municipal economy and is based on the set of the 12 real business entities. Analysis of the networks is carried out on the basis of the matrix of mutual payments aggregated over the certain time period. The matrix is created by the methods of experimental economics. Social Network Analysis (SNA) methods and instruments were used in the present research. The set of basic structural characteristics was investigated: set of quantitative parameters such as density, diameter, clustering coefficient, different kinds of centrality, and etc. They were compared with the random Bernoulli graphs of the corresponding size and density. Discovered variations of random and entrepreneurial networks structure are explained by the peculiarities of agents functioning in production network. Separately, were identified the closed exchange circuits (cyclically closed contours of graph) forming an autopoietic (self-replicating) network pattern. The purpose of the functional analysis was to identify the contribution of the autopoietic network pattern in its gross product. It was found that the magnitude of this contribution is more than 20%. Such value allows using of the complementary currency in order to stimulate economic activity of network agents.

  5. Orbital-Dependent-Functionals within Density Functional Theory: Methodology and Applications

    Science.gov (United States)

    Makmal, Adi

    I have designed and implemented a new numerical scheme for solving Kohn-Sham (KS) equations for diatomic systems, together with a full solution of the OEP equation. The equations are solved on a real-space prolate spheroidal coordinate grid, such that all the system's electrons are taken into account. The OEP equation is solved via the S-iteration scheme. This newly developed software package is called DARSEC (DiAtomic Real-Space Electronic structure Calculations). It involves no approximation except for the one inherent in the XC functional. Thus it is especially suitable for examining new functionals of any kind, and ODFs in particular. It is also an ideal tool for assessing the validity of commonly used approximations, for the same reasons. One case for which this uniqueness of DARSEC was exploited in this thesis is the examination of the validity of the pseudopotential approximation for KS gaps that are calculated with EXX OEP (xOEP). Before this study, use of the pseudopotential approximation in such calculations was called into question. I have shown that KS gaps obtained with pseudopotentials that have been constructed in a manner consistent with the exact-exchange functional agree with the all-electron results (i.e. without the pseudopotential approximation), for the cases studied. This confirmed the reliability of the pseudopotential approximation for ODFs such as EXX. Explicit density-dependent XC functionals traditionally fail to obtain atomization-energy as well as charge-dissociation curves that are, at least qualitatively, correct for diatomic systems. On the other hand, Hartree-Fock (HF) theory encounters no such problem. Hence, an additional goal of this research was to study the performances of the EXX functional (being the DFT counterpart of HF) in describing binding energies and charge dissociations for stretched diatomic molecules. Moreover, I wanted to investigate the special features of the resulting single and local EXX KS potential, as

  6. Linking community size structure and ecosystem functioning using metabolic theory.

    Science.gov (United States)

    Yvon-Durocher, Gabriel; Allen, Andrew P

    2012-11-05

    Understanding how biogeochemical cycles relate to the structure of ecological communities is a central research question in ecology. Here we approach this problem by focusing on body size, which is an easily measured species trait that has a pervasive influence on multiple aspects of community structure and ecosystem functioning. We test the predictions of a model derived from metabolic theory using data on ecosystem metabolism and community size structure. These data were collected as part of an aquatic mesocosm experiment that was designed to simulate future environmental warming. Our analyses demonstrate significant linkages between community size structure and ecosystem functioning, and the effects of warming on these links. Specifically, we show that carbon fluxes were significantly influenced by seasonal variation in temperature, and yielded activation energies remarkably similar to those predicted based on the temperature dependencies of individual-level photosynthesis and respiration. We also show that community size structure significantly influenced fluxes of ecosystem respiration and gross primary production, particularly at the annual time-scale. Assessing size structure and the factors that control it, both empirically and theoretically, therefore promises to aid in understanding links between individual organisms and biogeochemical cycles, and in predicting the responses of key ecosystem functions to future environmental change.

  7. Temperature dependence of crystal structure and digestibility of roasted diaspore

    Institute of Scientific and Technical Information of China (English)

    周秋生; 李小斌; 彭志宏; 刘桂华

    2004-01-01

    Through X-ray diffraction patterns and scanning electronic micrographs, temperature dependence of the crystal structure of roasted diasporic bauxite at different temperatures and the digestibility of roasting production were investigated systematically. The lattice parameters of unit cell for chemically purified diaspore and unequilibrium alumina-contained oxide obtained from the diaspore roasted at different temperatures were determined. It is found that, with roasting temperature increasing, the roasting production changes from the original dense and perfect diaspore crystal into imperfect corundum with many microcracks and small pores on its surface and then into perfect corundum with low digestibility. The optimum roasting temperature with best digestibility is approximately 525 ℃ when residence time is about 25 min. It is thought that the change of crystal structure, formation of microcracks and small pores in the temperature field are the main essential reasons for improving digestibility of diasporic bauxite and its roasting production.

  8. Oxidative stress and redox regulation on hippocampal-dependent cognitive functions.

    Science.gov (United States)

    Huang, Ting-Ting; Leu, David; Zou, Yani

    2015-06-15

    Hippocampal-dependent cognitive functions rely on production of new neurons and maintenance of dendritic structures to provide the synaptic plasticity needed for learning and formation of new memories. Hippocampal formation is exquisitely sensitive to patho-physiological changes, and reduced antioxidant capacity and exposure to low dose irradiation can significantly impede hippocampal-dependent functions of learning and memory by reducing the production of new neurons and alter dendritic structures in the hippocampus. Although the mechanism leading to impaired cognitive functions is complex, persistent oxidative stress likely plays an important role in the SOD-deficient and radiation-exposed hippocampal environment. Aging is associated with increased production of pro-oxidants and accumulation of oxidative end products. Similar to the hippocampal defects observed in SOD-deficient mice and mice exposed to low dose irradiation, reduced capacity in learning and memory, diminishing hippocampal neurogenesis, and altered dendritic network are universal in the aging brains. Given the similarities in cellular and structural changes in the aged, SOD-deficient, and radiation-exposed hippocampal environment and the corresponding changes in cognitive decline, understanding the shared underlying mechanism will provide more flexible and efficient use of SOD deficiency or irradiation to model age-related changes in cognitive functions and identify potential therapeutic or intervention methods.

  9. Gender-dependent negative correlation of peripheral E2 estradiol levels with ventricular diastolic functions.

    Science.gov (United States)

    Tan, Bo; Zhao, Lili; FaweiHE, Fawei

    2016-08-01

    The aim of this study to investigate the correlation of the peripheral concentrations of one representative estrogen, E2 estradiol, with various indicators reflecting different aspects of cardiac structures and functions. A total of 84 typical patients with hypertrophic cardiomyopathy (HCM) and 77 healthy subjects were enrolled. Venous blood samples were taken to test E2 estradiol contents. Echocardiographic imaging was performed to record various indices of cardiac structures and functions. Concentrations of peripheral E2 estradiol were decreased in female HCM patients, compared to female normal controls; after medical treatment, peripheral E2 estradiol levels were elevated, nearly to normal levels. Peripheral E2 estradiol concentrations were negatively correlated with LAV (r2=0.5078, Pnegatively correlated with ventricular diastolic functions and this correlation was gender-dependent. Our study could provide clues to explore the molecular mechanisms of HCM, and clinic evidence for the diagnosis and prognostic management of HCM patients, as well as medical intervening for HCM.

  10. Intracellular mediators of JAM-A-dependent epithelial barrier function.

    Science.gov (United States)

    Monteiro, Ana C; Parkos, Charles A

    2012-06-01

    Junctional adhesion molecule-A (JAM-A) is a critical signaling component of the apical junctional complex, a structure composed of several transmembrane and scaffold molecules that controls the passage of nutrients and solutes across epithelial surfaces. Observations from JAM-A-deficient epithelial cells and JAM-A knockout animals indicate that JAM-A is an important regulator of epithelial paracellular permeability; however, the mechanism(s) linking JAM-A to barrier function are not understood. This review highlights recent findings relevant to JAM-A-mediated regulation of epithelial permeability, focusing on the role of upstream and downstream signaling candidates. We draw on what is known about proteins reported to associate with JAM-A in other pathways and on known modulators of barrier function to propose candidate effectors that may mediate JAM-A regulation of epithelial paracellular permeability. Further investigation of pathways highlighted in this review may provide ideas for novel therapeutics that target debilitating conditions associated with barrier dysfunction, such as inflammatory bowel disease.

  11. Dependence of thermal conductivity on structural parameters in porous samples

    Science.gov (United States)

    Miettinen, L.; Kekäläinen, P.; Turpeinen, T.; Hyväluoma, J.; Merikoski, J.; Timonen, J.

    2012-03-01

    The in-plane thermal conductivity of porous sintered bronze plates was studied both experimentally and numerically. We developed and validated an experimental setup, where the sample was placed in vacuum and heated while its time-dependent temperature field was measured with an infrared camera. The porosity and detailed three-dimensional structure of the samples were determined by X-ray microtomography. Lattice-Boltzmann simulations of thermal conductivity in the tomographic reconstructions of the samples were used to correct the contact area between bronze particles as determined by image analysis from the tomographic reconstructions. Small openings in the apparent contacts could not be detected with the imaging resolution used, and they caused an apparent thermal contact resistance between particles. With this correction included, the behavior of the measured thermal conductivity was successfully explained by an analytical expression, originally derived for regular structures, which involves three structural parameters of the porous structures. There was no simple relationship between heat conductivity and porosity.

  12. Dependence of thermal conductivity on structural parameters in porous samples

    Directory of Open Access Journals (Sweden)

    L. Miettinen

    2012-03-01

    Full Text Available The in-plane thermal conductivity of porous sintered bronze plates was studied both experimentally and numerically. We developed and validated an experimental setup, where the sample was placed in vacuum and heated while its time-dependent temperature field was measured with an infrared camera. The porosity and detailed three-dimensional structure of the samples were determined by X-ray microtomography. Lattice-Boltzmann simulations of thermal conductivity in the tomographic reconstructions of the samples were used to correct the contact area between bronze particles as determined by image analysis from the tomographic reconstructions. Small openings in the apparent contacts could not be detected with the imaging resolution used, and they caused an apparent thermal contact resistance between particles. With this correction included, the behavior of the measured thermal conductivity was successfully explained by an analytical expression, originally derived for regular structures, which involves three structural parameters of the porous structures. There was no simple relationship between heat conductivity and porosity.

  13. Crystalline structure-dependent growth of bimetallic nanostructures.

    Science.gov (United States)

    Li, Qian; Jiang, Ruibin; Ming, Tian; Fang, Caihong; Wang, Jianfang

    2012-11-21

    Morphological control of multimetallic nanostructures is crucial for obtaining shape-dependent physical and chemical properties. Up to date, control of the shapes of multimetallic nanostructures has remained largely empirical. Multimetallic nanostructures have been produced mostly through seed-mediated growth. Understanding the role played by starting nanocrystal seeds can help in controlling the shape and in turn the plasmonic and catalytic properties of multimetallic nanostructures. In this work, we have studied the effect of the crystalline structure and shape of Au nanocrystal seeds on the morphology of the resultant bimetallic nanostructures. Single-crystalline Au nanorods, multiply twinned Au nanorods, and multiply twinned Au nanobipyramids were employed as the starting seeds. Both silver and palladium exhibit highly preferential growth on the side surfaces of the single-crystalline Au nanorods, giving rise to bimetallic cuboids, whereas they prefer to grow at the ends of the multiply twinned Au nanorods and nanobipyramids, giving rise to bimetallic nanorods. These results indicate that the morphology of the bimetallic nanostructures is highly dependent on the crystalline structure of the Au nanocrystal seeds. Our results will be useful for guiding the preparation of multimetallic nanostructures with desired shapes and therefore plasmonic properties for various plasmon-based applications.

  14. Ferromagnetism and temperature-dependent electronic structure in metallic films

    CERN Document Server

    Herrmann, T

    1999-01-01

    reduced at the surface compared to the inner layers. This observation clearly contradicts the well-known Stoner picture of band magnetism and can be explained in terms of general arguments which are based on exact results in the limit of strong Coulomb interaction. The magnetic behavior of the Hubbard films can be analyzed in detail by inspecting the local quasi particle density of states as well as the wave vector dependent spectral density. The electronic structure is found to be strongly spin-, layer-, and temperature-dependent. The last part of this work is concerned about the temperature-driven reorientation transition in thin metallic films. For the description of the magnetic anisotropy in thin films the dipole interaction as well as the spin-orbit interaction have to be included in the model. By calculating the temperature-dependence of the magnetic anisotropy energy it is found that both types of temperature-driven reorientation transitions, from out-of-plane to in-plane (''Fe-type'') and from in-pla...

  15. Phenylalanine hydroxylase: function, structure, and regulation.

    Science.gov (United States)

    Flydal, Marte I; Martinez, Aurora

    2013-04-01

    Mammalian phenylalanine hydroxylase (PAH) catalyzes the rate-limiting step in the phenylalanine catabolism, consuming about 75% of the phenylalanine input from the diet and protein catabolism under physiological conditions. In humans, mutations in the PAH gene lead to phenylketonuria (PKU), and most mutations are mainly associated with PAH misfolding and instability. The established treatment for PKU is a phenylalanine-restricted diet and, recently, supplementation with preparations of the natural tetrahydrobiopterin cofactor also shows effectiveness for some patients. Since 1997 there has been a significant increase in the understanding of the structure, catalytic mechanism, and regulation of PAH by its substrate and cofactor, in addition to improved correlations between genotype and phenotype in PKU. Importantly, there has also been an increased number of studies on the structure and function of PAH from bacteria and lower eukaryote organisms, revealing an additional anabolic role of the enzyme in the synthesis of melanin-like pigments. In this review, we discuss these recent studies, which contribute to define the evolutionary adaptation of the PAH structure and function leading to sophisticated regulation for effective catabolic processing of phenylalanine in mammalian organisms.

  16. Detailed Measurements of Structure Functions from Nucleons and Nuclei

    CERN Multimedia

    2002-01-01

    The experiment will study deep inelastic muon nucleon scattering in a wide range of Q|2~(1-200 (GeV/c)|2) and x~(0.005-0.75). The main aims of the experiment are: \\item a)~~~~Detailed measurements of the nuclear dependence of the structure function F^2|A, of R~=~@s^L/@s^T and of the cross-section for J/@y production. They will provide a basis for the understanding of the EMC effect: the modification of quark and gluon distributions due to the nuclear environment. \\item b)~~~~A simultaneous high luminosity measurement of the structure function F^2 on hydrogen and deuterium. This will provide substantially improved accuracy in the knowledge of the neutron structure function F^2|n, of F^2|p-F^2|n and F^2|n/F^2|p and their Q|2 dependence. Furthermore, the data will allow a determination of the strong coupling constant @a^s(Q|2) with reduced experimental and theoretical uncertainties as well as of the ratio of the down to up quark distributions in the valence region. Due to the large x range covered by the experim...

  17. The structure and function of presynaptic endosomes

    Energy Technology Data Exchange (ETDEWEB)

    Jähne, Sebastian, E-mail: sebastian.jaehne1@stud.uni-goettingen.de [Department of Neuro- and Sensory Physiology, University of Göttingen Medical Center, Cluster of Excellence Nanoscale Microscopy and Molecular Physiology of the Brain, Humboldtallee 23, 37073 Göttingen (Germany); International Max Planck Research School for Neurosciences, 37077 Göttingen (Germany); Rizzoli, Silvio O. [Department of Neuro- and Sensory Physiology, University of Göttingen Medical Center, Cluster of Excellence Nanoscale Microscopy and Molecular Physiology of the Brain, Humboldtallee 23, 37073 Göttingen (Germany); Helm, Martin S., E-mail: martin.helm@med.uni-goettingen.de [Department of Neuro- and Sensory Physiology, University of Göttingen Medical Center, Cluster of Excellence Nanoscale Microscopy and Molecular Physiology of the Brain, Humboldtallee 23, 37073 Göttingen (Germany); International Max Planck Research School for Molecular Biology, 37077 Göttingen (Germany)

    2015-07-15

    The function of endosomes and of endosome-like structures in the presynaptic compartment is still controversial. This is in part due to the absence of a consensus on definitions and markers for these compartments. Synaptic endosomes are sometimes seen as stable organelles, permanently present in the synapse. Alternatively, they are seen as short-lived intermediates in synaptic vesicle recycling, arising from the endocytosis of large vesicles from the plasma membrane, or from homotypic fusion of small vesicles. In addition, the potential function of the endosome is largely unknown in the synapse. Some groups have proposed that the endosome is involved in the sorting of synaptic vesicle proteins, albeit others have produced data that deny this possibility. In this review, we present the existing evidence for synaptic endosomes, we discuss their potential functions, and we highlight frequent technical pitfalls in the analysis of this elusive compartment. We also sketch a roadmap to definitely determine the role of synaptic endosomes for the synaptic vesicle cycle. Finally, we propose a common definition of synaptic endosome-like structures.

  18. From Protein Structure to Function via Single Crystal Optical Spectroscopy

    Directory of Open Access Journals (Sweden)

    Luca eRonda

    2015-04-01

    Full Text Available The more than 100.000 protein structures determined by X-ray crystallography provide a wealth of information for the characterization of biological processes at the molecular level. However, several crystallographic artifacts, including conformational selection, crystallization conditions and radiation damages, may affect the quality and the interpretation of the electron density map, thus limiting the relevance of structure determinations. Moreover, for most of these structures no functional data have been obtained in the crystalline state, thus posing serious questions on their validity in the inference for protein mechanisms. In order to solve these issues, spectroscopic methods have been applied for the determination of equilibrium and kinetic properties of proteins in the crystalline state. These methods are UV-vis spectrophotometry, spectrofluorimetry, IR, EPR, Raman and resonance Raman spectroscopy. Some of these approaches have been implemented with on-line instruments at X-ray synchrotron beamlines. Here, we provide an overview of investigations predominantly carried out in our laboratory by single crystal polarized absorption UV-vis microspectrophotometry, the most applied technique for the functional characterization of proteins in the crystalline state. Studies on hemoglobins, pyridoxal 5’-phosphate dependent enzymes and green fluorescent protein in the crystalline state have addressed key biological issues, leading to either straightforward structure-function correlations or limitations to structure-based mechanisms.

  19. Functional Characterization of Pseudomonas Contact Dependent Growth Inhibition (CDI) Systems.

    Science.gov (United States)

    Mercy, Chryslène; Ize, Bérengère; Salcedo, Suzana P; de Bentzmann, Sophie; Bigot, Sarah

    2016-01-01

    Contact-dependent inhibition (CDI) toxins, delivered into the cytoplasm of target bacterial cells, confer to host strain a significant competitive advantage. Upon cell contact, the toxic C-terminal region of surface-exposed CdiA protein (CdiA-CT) inhibits the growth of CDI- bacteria. CDI+ cells express a specific immunity protein, CdiI, which protects from autoinhibition by blocking the activity of cognate CdiA-CT. CdiA-CT are separated from the rest of the protein by conserved peptide motifs falling into two distinct classes, the "E. coli"- and "Burkholderia-type". CDI systems have been described in numerous species except in Pseudomonadaceae. In this study, we identified functional toxin/immunity genes linked to CDI systems in the Pseudomonas genus, which extend beyond the conventional CDI classes by the variability of the peptide motif that delimits the polymorphic CdiA-CT domain. Using P. aeruginosa PAO1 as a model, we identified the translational repressor RsmA as a negative regulator of CDI systems. Our data further suggest that under conditions of expression, P. aeruginosa CDI systems are implicated in adhesion and biofilm formation and provide an advantage in competition assays. All together our data imply that CDI systems could play an important role in niche adaptation of Pseudomonadaceae.

  20. Size Bounds for Conjunctive Queries with General Functional Dependencies

    CERN Document Server

    Valiant, Gregory

    2009-01-01

    This paper resolves the main open question left by Gottlob, Lee, and Valiant (PODS 2009)[GLV09], establishing tight worst-case bounds for the size of the result Q(D) of a conjunctive query Q to a database D given an arbitrary set of functional dependencies. We show that the lower bound presented in [GLV09] in which the variables of the query are "colored" so as to yield a coloring number C(Q) for each query Q is, in fact, also an upper bound. To show this, we formalize the original intuition that each color used represents some possible entropy of that variable, and express the maximum possible size increase as a linear program that seeks to maximize how much more entropy is in the result of the query than the input. Although this linear program has exponentially many variables, we also show that we can decide in polynomial time whether the result can be any larger than the input database.

  1. Functional Fixedness in Creative Thinking Tasks Depends on Stimulus Modality.

    Science.gov (United States)

    Chrysikou, Evangelia G; Motyka, Katharine; Nigro, Cristina; Yang, Song-I; Thompson-Schill, Sharon L

    2016-11-01

    Pictorial examples during creative thinking tasks can lead participants to fixate on these examples and reproduce their elements even when yielding suboptimal creative products. Semantic memory research may illuminate the cognitive processes underlying this effect. Here, we examined whether pictures and words differentially influence access to semantic knowledge for object concepts depending on whether the task is close- or open-ended. Participants viewed either names or pictures of everyday objects, or a combination of the two, and generated common, secondary, or ad hoc uses for them. Stimulus modality effects were assessed quantitatively through reaction times and qualitatively through a novel coding system, which classifies creative output on a continuum from top-down-driven to bottom-up-driven responses. Both analyses revealed differences across tasks. Importantly, for ad hoc uses, participants exposed to pictures generated more top-down-driven responses than those exposed to object names. These findings have implications for accounts of functional fixedness in creative thinking, as well as theories of semantic memory for object concepts.

  2. Simple preconditioning for time-dependent density functional perturbation theory

    Science.gov (United States)

    Lehtovaara, Lauri; Marques, Miguel A. L.

    2011-07-01

    By far, the most common use of time-dependent density functional theory is in the linear-reponse regime, where it provides information about electronic excitations. Ideally, the linear-response equations should be solved by a method that avoids the use of the unoccupied Kohn-Sham states — such as the Sternheimer method — as this reduces the complexity and increases the precision of the calculation. However, the Sternheimer equation becomes ill-conditioned near and indefinite above the first resonant frequency, seriously hindering the use of efficient iterative solution methods. To overcome this serious limitation, and to improve the general convergence properties of the iterative techniques, we propose a simple preconditioning strategy. In our method, the Sternheimer equation is solved directly as a linear equation using an iterative Krylov subspace method, i.e., no self-consistent cycle is required. Furthermore, the preconditioner uses the information of just a few unoccupied states and requires simple and minimal modifications to existing implementations. In this way, convergence can be reached faster and in a considerably wider frequency range than the traditional approach.

  3. Quantum Drude friction for time-dependent density functional theory

    Science.gov (United States)

    Neuhauser, Daniel; Lopata, Kenneth

    2008-10-01

    way to very simple finite grid description of scattering and multistage conductance using time-dependent density functional theory away from the linear regime, just as absorbing potentials and self-energies are useful for noninteracting systems and leads.

  4. Dose-dependent deterioration of swallowing function after induction chemotherapy and definitive chemoradiotherapy for laryngopharyngeal cancer

    Energy Technology Data Exchange (ETDEWEB)

    Haderlein, M.; Semrau, S.; Ott, O.; Speer, S.; Fietkau, R. [University Hospital Erlangen, Department of Radiation Oncology, Erlangen (Germany); Bohr, C. [University Hospital Erlangen, Department of Otorhinolaryngology, Head and Neck Surgery, Erlangen (Germany)

    2014-02-15

    To evaluate the influence of clinical, treatment- and dose-dependent factors on posttreatment swallowing function after induction chemotherapy and definitive chemoradiotherapy in a group of homogeneously treated laryngopharyngeal cancer patients. From 28 May 2008 to 15 February 2013, 45 patients with borderline inoperable laryngopharyngeal cancer that had responded well to induction chemotherapy were treated with definitive chemoradiotherapy. Median follow-up was 22 months. Swallowing function and clinical data were prospectively analyzed using the EORTC QLQ-C30 questionnaire. Swallowing structures were retrospectively delineated on the original treatment planning CT. Dose-volume histograms were calculated for swallowing structures and D{sub mean}, D{sub max} and V50-V64 values (in 2 Gy increments) were determined for each patient. Tumor volume and infiltration of the swallowing apparatus was defined by CT before induction chemotherapy. Of the 45 patients, 26 (57.8 %) fully regained swallowing function after chemoradiotherapy. A further 12 patients (26.7 %) were able to manage soft, pureed and/or liquid foods; the remaining 7 (15.6 %) were completely dependent on percutaneous endoscopic gastrostomy (PEG). Posttreatment swallowing function was significantly influenced by D{sub mean} to the superior pharyngeal constrictor muscle (PCM, p = 0.041). Correlations between late dysphagia and dose-volume relationships in the superior PCM and soft palate were also observed, which were significant from V60 (p = 0.043) and V58 for the soft palate and superior PCM, respectively. Of the evaluated clinical and tumor-related factors, only alcohol abuse (p = 0.024) had an influence on posttreatment swallowing function. Almost 50 % of patients had deterioration of swallowing function after definitive chemoradiotherapy for laryngopharyngeal cancer. The dose to anatomical structures responsible for swallowing function appears to play a role. Therefore, in selected patients, target

  5. Nuclear matrix - structure, function and pathogenesis.

    Science.gov (United States)

    Wasąg, Piotr; Lenartowski, Robert

    2016-12-20

    The nuclear matrix (NM), or nuclear skeleton, is the non-chromatin, ribonucleoproteinaceous framework that is resistant to high ionic strength buffers, nonionic detergents, and nucleolytic enzymes. The NM fulfills a structural role in eukaryotic cells and is responsible for maintaining the shape of the nucleus and the spatial organization of chromatin. Moreover, the NM participates in several cellular processes, such as DNA replication/repair, gene expression, RNA transport, cell signaling and differentiation, cell cycle regulation, apoptosis and carcinogenesis. Short nucleotide sequences called scaffold/matrix attachment regions (S/MAR) anchor the chromatin loops to the NM proteins (NMP). The NMP composition is dynamic and depends on the cell type and differentiation stage or metabolic activity. Alterations in the NMP composition affect anchoring of the S/MARs and thus alter gene expression. This review aims to systematize information about the skeletal structure of the nucleus, with particular emphasis on the organization of the NM and its role in selected cellular processes. We also discuss several diseases that are caused by aberrant NM structure or dysfunction of individual NM elements.

  6. MRI in Optic Neuritis: Structure, Function, Interactions

    DEFF Research Database (Denmark)

    Fuglø, Dan

    2011-01-01

    resonance imaging (MRI), and the visual evoked potential (VEP) continues to show a delayed P100 indicating persistent demyelination. The explanation for this apparent discrepancy between structure and function could be due to either a redundancy in the visual pathways so that some degree of signal loss...... are low. Functional MRI (fMRI) is a non-invasive technique that can measure brain activity with a high spatial resolution. Recently, technical and methodological advancements have made it feasible to record VEPs and fMRI simultaneously and the relationship between averaged VEPs and averaged fMRI signals...... have been described. Still, to take full advantage of simultaneously recorded VEP-fMRI one would ideally want to track single-trial changes in the VEP and use this information in the fMRI analysis. In order to do this we examined 10 healthy volunteers with simultaneous VEP-fMRI. Different measures...

  7. Soft matter nanotechnology from structure to function

    CERN Document Server

    Chen, Xiaodong

    2015-01-01

    Using the well-honed tools of nanotechnology, this book presents breakthrough results in soft matter research, benefitting from the synergies between the chemistry, physics, biology, materials science, and engineering communities. The team of international authors delves beyond mere structure-making and places the emphasis firmly on imparting functionality to soft nanomaterials with a focus on devices and applications. Alongside reviewing the current level of knowledge, they also put forward novel ideas to foster research and development in such expanding fields as nanobiotechnology and nanom

  8. Surface Appendages of Archaea: Structure, Function, Genetics and Assembly

    Directory of Open Access Journals (Sweden)

    Sarah Siu

    2013-01-01

    Full Text Available Organisms representing diverse subgroupings of the Domain Archaea are known to possess unusual surface structures. These can include ones unique to Archaea such as cannulae and hami as well as archaella (archaeal flagella and various types of pili that superficially resemble their namesakes in Bacteria, although with significant differences. Major advances have occurred particularly in the study of archaella and pili using model organisms with recently developed advanced genetic tools. There is common use of a type IV pili-model of assembly for several archaeal surface structures including archaella, certain pili and sugar binding structures termed bindosomes. In addition, there are widespread posttranslational modifications of archaellins and pilins with N-linked glycans, with some containing novel sugars. Archaeal surface structures are involved in such diverse functions as swimming, attachment to surfaces, cell to cell contact resulting in genetic transfer, biofilm formation, and possible intercellular communication. Sometimes functions are co-dependent on other surface structures. These structures and the regulation of their assembly are important features that allow various Archaea, including thermoacidophilic, hyperthermophilic, halophilic, and anaerobic ones, to survive and thrive in the extreme environments that are commonly inhabited by members of this domain.

  9. Nuclear structure functions in carbon near x=1

    Energy Technology Data Exchange (ETDEWEB)

    Benvenuti, A.C.; Bollini, D.; Camporesi, T.; Monari, L.; Navarria, F.L. (Dipt. di Fisica, Univ. Bologna (Italy) INFN, Sezione di Bologna (Italy)); Argento, A.; Cvach, J.; Lohmann, W.; Piemontese, L. (CERN, Geneva (Switzerland)); Genchev, V.I.; Hladky, J.; Golutvin, I.A.; Kiryushin, Yu.T.; Kiselev, V.S.; Krivokhizhin, V.G.; Kukhtin, V.V.; Nemecek, S.; Peshekhonov, D.V.; Reimer, P.; Savin, I.A.; Smirnov, G.I.; Sultanov, S.; Volodko, A.G.; Zacek, J. (Joint Inst. for Nuclear Research, Dubna (Russian Federation)); Jamnik, D.; Kopp, R.; Meyer-Berkhout, U.; Staude, A.; Teichert, K.M.; Tirler, R.; Voss, R.; Zupancic, C. (Sektion Physik, Univ. Muenchen (Germany)); Feltesse, J.; Misztajn, A.; Ouraou, A.; Rich-Hennion, P.; Sacquin, Y.; Smadja, G.; Verrecchia, P.; Virchaux, M. (DAPNIA-SPP, Centre d' Etudes de Saclay, CEA, Gif-sur-Yvette (France)); BCDMS Collaboration

    1994-07-01

    Data from deep inelastic scattering of 200 GeV muons on a carbon target with squared four-momentum transfer 52 GeV[sup 2][<=]Q[sup 2][<=]200 GeV[sup 2] were analysed in the region of the Bjorken variable close to x=1, which is the kinematic limit for scattering on a free nucleon. At this value of x, the carbon structure function is found to be F[sub 2][sup C][approx]1.2.10[sup -4]. The x dependence of the structure function for x>0.8 is well described by an exponential F[sub 2][sup C][proportional to]exp(-sx) with s=16.5[+-]0.6. (orig.)

  10. Alu element-containing RNAs maintain nucleolar structure and function.

    Science.gov (United States)

    Caudron-Herger, Maïwen; Pankert, Teresa; Seiler, Jeanette; Németh, Attila; Voit, Renate; Grummt, Ingrid; Rippe, Karsten

    2015-11-12

    Non-coding RNAs play a key role in organizing the nucleus into functional subcompartments. By combining fluorescence microscopy and RNA deep-sequencing-based analysis, we found that RNA polymerase II transcripts originating from intronic Alu elements (aluRNAs) were enriched in the nucleolus. Antisense-oligo-mediated depletion of aluRNAs or drug-induced inhibition of RNA polymerase II activity disrupted nucleolar structure and impaired RNA polymerase I-dependent transcription of rRNA genes. In contrast, overexpression of a prototypic aluRNA sequence increased both nucleolus size and levels of pre-rRNA, suggesting a functional link between aluRNA, nucleolus integrity and pre-rRNA synthesis. Furthermore, we show that aluRNAs interact with nucleolin and target ectopic genomic loci to the nucleolus. Our study suggests an aluRNA-based mechanism that links RNA polymerase I and II activities and modulates nucleolar structure and rRNA production.

  11. Time dependent couplings in the dark sector: from background evolution to nonlinear structure formation

    CERN Document Server

    Baldi, Marco

    2010-01-01

    We present a complete numerical study of cosmological models with a time dependent coupling between the dark energy component driving the present accelerated expansion of the Universe and the Cold Dark Matter (CDM) fluid. Depending on the functional form of the coupling strength, these models show a range of possible intermediate behaviors between the standard LCDM background evolution and the widely studied case of interacting dark energy models with a constant coupling. These different background evolutions play a crucial role in the growth of cosmic structures, and determine strikingly different effects of the coupling on the internal dynamics of nonlinear objects. By means of a suitable modification of the cosmological N-body code GADGET-2 we have performed a series of high-resolution N-body simulations of structure formation in the context of interacting dark energy models with variable couplings. Depending on the type of background evolution, the halo density profiles are found to be either less or more...

  12. Changes in bird functional diversity across multiple land uses: interpretations of functional redundancy depend on functional group identity.

    Science.gov (United States)

    Luck, Gary W; Carter, Andrew; Smallbone, Lisa

    2013-01-01

    Examinations of the impact of land-use change on functional diversity link changes in ecological community structure driven by land modification with the consequences for ecosystem function. Yet, most studies have been small-scale, experimental analyses and primarily focussed on plants. There is a lack of research on fauna communities and at large-scales across multiple land uses. We assessed changes in the functional diversity of bird communities across 24 land uses aligned along an intensification gradient. We tested the hypothesis that functional diversity is higher in less intensively used landscapes, documented changes in diversity using four diversity metrics, and examined how functional diversity varied with species richness to identify levels of functional redundancy. Functional diversity, measured using a dendogram-based metric, increased from high to low intensity land uses, but observed values did not differ significantly from randomly-generated expected values. Values for functional evenness and functional divergence did not vary consistently with land-use intensification, although higher than expected values were mostly recorded in high intensity land uses. A total of 16 land uses had lower than expected values for functional dispersion and these were mostly low intensity native vegetation sites. Relations between functional diversity and bird species richness yielded strikingly different patterns for the entire bird community vs. particular functional groups. For all birds and insectivores, functional evenness, divergence and dispersion showed a linear decline with increasing species richness suggesting substantial functional redundancy across communities. However, for nectarivores, frugivores and carnivores, there was a significant hump-shaped or non-significant positive linear relationship between these functional measures and species richness indicating less redundancy. Hump-shaped relationships signify that the most functionally diverse

  13. ORPHA, ORPHIC FUNCTIONS, AND THE ORPHIC ANALYST: WINNICOTT'S "REGRESSION TO DEPENDENCE" IN THE LANGUAGE OF FERENCZI().

    Science.gov (United States)

    Gurevich, Hayuta

    2016-12-01

    Early developmental trauma is imprinted in the psyche by survival fragmentation and dissociation. Traumatized patients need the analyst to be actively involved and allow for regression to dependence in order to strengthen, create and construct their psychic functioning and structure so that environmental failures will be contained and not rupture continuity of being. I suggest that Ferenczi's and Winnicott's ideas about regression to dependence in analysis are fundamental contributions to these quests, and that Ferenczi set the foundation, which Winnicott further explored and developed. I would like to focus on their clinical theory of treating early developmental trauma of the psyche, describing it in the less known language of Ferenczi, reviving his concept of Orpha and its functions. The complementarities of the two approaches can enrich and broaden our understanding of the clinical complications that arise in the analysis of such states.

  14. RNA病毒RNA依赖的RNA聚合酶的结构与功能%The Structures and Functions of the RNA-dependent RNA Polymerase of RNA Viruses

    Institute of Scientific and Technical Information of China (English)

    王明连; 李劲松

    2004-01-01

    RNA病毒一般传播迅速,给人类和自然造成巨大危害和威胁。许多RNA病毒的结构蛋白在基础研究和应用方面已日趋完善。相比之下,就非结构蛋白(NS)所做的研究较少,存在许多未知问题。在这些非结构蛋白中,病毒自身编码的RNA依赖的RNA聚合酶(RNA-dependent RNA polymerase.RdRP)对病毒的复制起关键作用。

  15. Structure, expression and functions of MTA genes.

    Science.gov (United States)

    Kumar, Rakesh; Wang, Rui-An

    2016-05-15

    Metastatic associated proteins (MTA) are integrators of upstream regulatory signals with the ability to act as master coregulators for modifying gene transcriptional activity. The MTA family includes three genes and multiple alternatively spliced variants. The MTA proteins neither have their own enzymatic activity nor have been shown to directly interact with DNA. However, MTA proteins interact with a variety of chromatin remodeling factors and complexes with enzymatic activities for modulating the plasticity of nucleosomes, leading to the repression or derepression of target genes or other extra-nuclear and nucleosome remodeling and histone deacetylase (NuRD)-complex independent activities. The functions of MTA family members are driven by the steady state levels and subcellular localization of MTA proteins, the dynamic nature of modifying signals and enzymes, the structural features and post-translational modification of protein domains, interactions with binding proteins, and the nature of the engaged and resulting features of nucleosomes in the proximity of target genes. In general, MTA1 and MTA2 are the most upregulated genes in human cancer and correlate well with aggressive phenotypes, therapeutic resistance, poor prognosis and ultimately, unfavorable survival of cancer patients. Here we will discuss the structure, expression and functions of the MTA family of genes in the context of cancer cells.

  16. Condition dependence of male and female genital structures in the seed beetle Callosobruchus maculatus (Coleoptera: Bruchidae).

    Science.gov (United States)

    Cayetano, L; Bonduriansky, R

    2015-07-01

    Theory predicts that costly secondary sexual traits will evolve heightened condition dependence, and many studies have reported strong condition dependence of signal and weapon traits in a variety of species. However, although genital structures often play key roles in intersexual interactions and appear to be subject to sexual or sexually antagonistic selection, few studies have examined the condition dependence of genital structures, especially in both sexes simultaneously. We investigated the responses of male and female genital structures to manipulation of larval diet quality (new versus once-used mung beans) in the bruchid seed beetle Callosobruchus maculatus. We quantified effects on mean relative size and static allometry of the male aedeagus, aedeagal spines, flap and paramere and the female reproductive tract and bursal spines. None of the male traits showed a significant effect of diet quality. In females, we found that longer bursal spines (relative to body size) were expressed on low-quality diet. Although the function of bursal spines is poorly understood, we suggest that greater bursal spine length in low-condition females may represent a sexually antagonistic adaptation. Overall, we found no evidence that genital traits in C. maculatus are expressed to a greater extent when nutrients are more abundant. This suggests that, even though some genital traits appear to function as secondary sexual traits, genital traits do not exhibit heightened condition dependence in this species. We discuss possible reasons for this finding.

  17. CONSOLIDATING BATCH AND TRANSACTIONAL WORKLOADS USING DEPENDENCY STRUCTURE PRIORITIZATION

    Directory of Open Access Journals (Sweden)

    S.NIVETHITHA

    2013-04-01

    Full Text Available Organizations offer efficient services to their customers through cloud. These services can either be a batch or transactional workloads. To offer a real-time service, there comes a need to schedule these workloads in an efficient way. An idea to consolidate these workloads enables us to cut down the energy consumption and infrastructure cost. It will be harder to consolidate both these workloads due to the difference in their nature, performance goals and control mechanisms. The proposed work implements the concept of Dependency Structure Prioritization (DSP to assign priority to the job. This work tends to make effective resource utilization through reducing the number of job migration and missed deadline jobs by considering the deadline and the priority of the job as the most important evaluation factor.

  18. Structural insight into the sequence dependence of nucleosome positioning.

    Science.gov (United States)

    Wu, Bin; Mohideen, Kareem; Vasudevan, Dileep; Davey, Curt A

    2010-03-14

    Nucleosome positioning displays sequence dependency and contributes to genomic regulation in a site-specific manner. We solved the structures of nucleosome core particle composed of strong positioning TTTAA elements flanking the nucleosome center. The positioning strength of the super flexible TA dinucleotide is consistent with its observed central location within minor groove inward regions, where it can contribute maximally to energetically challenging minor groove bending, kinking and compression. The marked preference for TTTAA and positioning power of the site 1.5 double helix turns from the nucleosome center relates to a unique histone protein motif at this location, which enforces a sustained, extremely narrow minor groove via a hydrophobic "sugar clamp." Our analysis sheds light on the basis of nucleosome positioning and indicates that the histone octamer has evolved not to fully minimize sequence discrimination in DNA binding.

  19. Water Contact Angle Dependence with Hydroxyl Functional Groups on Silica Surfaces under CO2 Sequestration Conditions.

    Science.gov (United States)

    Chen, Cong; Zhang, Ning; Li, Weizhong; Song, Yongchen

    2015-12-15

    Functional groups on silica surfaces under CO2 sequestration conditions are complex due to reactions among supercritical CO2, brine and silica. Molecular dynamics simulations have been performed to investigate the effects of hydroxyl functional groups on wettability. It has been found that wettability shows a strong dependence on functional groups on silica surfaces: silanol number density, space distribution, and deprotonation/protonation degree. For neutral silica surfaces with crystalline structure (Q(3), Q(3)/Q(4), Q(4)), as silanol number density decreases, contact angle increases from 33.5° to 146.7° at 10.5 MPa and 318 K. When Q(3) surface changes to an amorphous structure, water contact angle increases 20°. Water contact angle decreases about 12° when 9% of silanol groups on Q(3) surface are deprotonated. When the deprotonation degree increases to 50%, water contact angle decreases to 0. The dependence of wettability on silica surface functional groups was used to analyze contact angle measurement ambiguity in literature. The composition of silica surfaces is complicated under CO2 sequestration conditions, the results found in this study may help to better understand wettability of CO2/brine/silica system.

  20. Relativistic Adiabatic Time-Dependent Density Functional Theory Using Hybrid Functionals and Noncollinear Spin Magnetization

    DEFF Research Database (Denmark)

    Bast, Radovan; Jensen, Hans Jørgen Aagaard; Saue, Trond

    2009-01-01

    We report an implementation of adiabatic time-dependent density functional theory based on the 4-component relativistic Dirac-Coulomb Hamiltonian and a closed-shell reference. The implementation includes noncollinear spin magnetization and full derivatives of functionals, including hybrid...... and time reversal symmetry on trial vectors to obtain even better reductions in terms of memory and run time, and without invoking approximations. Further reductions are obtained by exploiting point group symmetries for D2h and subgroups in a symmetry scheme where symmetry reductions translate...... into reduction of algebra from quaternion to complex or real. For hybrid GGAs with noncollinear spin magnetization we derive a new computationally advantageous equation for the full second variational derivatives of such exchange-correlation functionals. We apply our implementation to calculations on the ns2...

  1. FAK dimerization controls its kinase-dependent functions at focal adhesions

    KAUST Repository

    Brami-Cherrier, Karen

    2014-01-30

    Focal adhesion kinase (FAK) controls adhesion-dependent cell motility, survival, and proliferation. FAK has kinase-dependent and kinase-independent functions, both of which play major roles in embryogenesis and tumor invasiveness. The precise mechanisms of FAK activation are not known. Using x-ray crystallography, small angle x-ray scattering, and biochemical and functional analyses, we show that the key step for activation of FAK\\'s kinase-dependent functions-autophosphorylation of tyrosine-397-requires site-specific dimerization of FAK. The dimers form via the association of the N-terminal FERM domain of FAK and are stabilized by an interaction between FERM and the C-terminal FAT domain. FAT binds to a basic motif on FERM that regulates co-activation and nuclear localization. FAK dimerization requires local enrichment, which occurs specifically at focal adhesions. Paxillin plays a dual role, by recruiting FAK to focal adhesions and by reinforcing the FAT:FERM interaction. Our results provide a structural and mechanistic framework to explain how FAK combines multiple stimuli into a site-specific function. The dimer interfaces we describe are promising targets for blocking FAK activation. © 2014 The Authors.

  2. Structure-function investigations of bacterial photosynthetic reaction centers.

    Science.gov (United States)

    Leonova, M M; Fufina, T Yu; Vasilieva, L G; Shuvalov, V A

    2011-12-01

    During photosynthesis light energy is converted into energy of chemical bonds through a series of electron and proton transfer reactions. Over the first ultrafast steps of photosynthesis that take place in the reaction center (RC) the quantum efficiency of the light energy transduction is nearly 100%. Compared to the plant and cyanobacterial photosystems, bacterial RCs are well studied and have relatively simple structure. Therefore they represent a useful model system both for manipulating of the electron transfer parameters to study detailed mechanisms of its separate steps as well as to investigate the common principles of the photosynthetic RC structure, function, and evolution. This review is focused on the research papers devoted to chemical and genetic modifications of the RCs of purple bacteria in order to study principles and mechanisms of their functioning. Investigations of the last two decades show that the maximal rates of the electron transfer reactions in the RC depend on a number of parameters. Chemical structure of the cofactors, distances between them, their relative orientation, and interactions to each other are of great importance for this process. By means of genetic and spectral methods, it was demonstrated that RC protein is also an essential factor affecting the efficiency of the photochemical charge separation. Finally, some of conservative water molecules found in RC not only contribute to stability of the protein structure, but are directly involved in the functioning of the complex.

  3. Structure and Function of the LmbE-like Superfamily

    Directory of Open Access Journals (Sweden)

    Shane Viars

    2014-05-01

    Full Text Available The LmbE-like superfamily is comprised of a series of enzymes that use a single catalytic metal ion to catalyze the hydrolysis of various substrates. These substrates are often key metabolites for eukaryotes and prokaryotes, which makes the LmbE-like enzymes important targets for drug development. Herein we review the structure and function of the LmbE-like proteins identified to date. While this is the newest superfamily of metallohydrolases, a growing number of functionally interesting proteins from this superfamily have been characterized. Available crystal structures of LmbE-like proteins reveal a Rossmann fold similar to lactate dehydrogenase, which represented a novel fold for (zinc metallohydrolases at the time the initial structure was solved. The structural diversity of the N-acetylglucosamine containing substrates affords functional diversity for the LmbE-like enzyme superfamily. The majority of enzymes identified to date are metal-dependent deacetylases that catalyze the hydrolysis of a N-acetylglucosamine moiety on substrate using a combination of amino acid side chains and a single bound metal ion, predominantly zinc. The catalytic zinc is coordinated to proteins via His2-Asp-solvent binding site. Additionally, studies indicate that protein dynamics play important roles in regulating access to the active site and facilitating catalysis for at least two members of this protein superfamily.

  4. Structural models of vanadate-dependent haloperoxidases and their reactivity

    Indian Academy of Sciences (India)

    Mannar R Maurya

    2006-11-01

    Vanadium(V) complexes with hydrazone-based ONO and ONN donor ligands that partly model active-site structures of vanadate-dependent haloperoxidases have been reported. On reaction with [VO(acac)2] (Hacac = acetylacetone) under nitrogen, these ligands generally provide oxovanadium(IV) complexes [VO(ONO)X] (X = solvent or nothing) and [VO(acac)(ONN)], respectively. Under aerobic conditions, these oxovanadium(IV) species undergo oxidation to give oxovanadium(V), dioxovanadium (V) or -oxobis{oxovanadium(V)} species depending upon the nature of the ligand. Anionic and neutral dioxovanadium(V) complexes slowly deoxygenate in methanol to give monooxo complexes [VO(OMe)(MeOH)(ONO)]. The anionic complexes [VO2(ONO)]- can also be converted in situ on acidification to oxohydroxo complexes [VO(OH)(HONO)]+ and to peroxo complexes [VO(O2)(ONO)]-, and thus to the species assumed to be intermediates in the haloperoxidases activity of the enzymes. In the presence of catechol (H2cat) and benzohydroxamic acid (H2bha), oxovanadium (IV) complexes, [VO (acac)(ONN)] gave mixed-chelate oxovanadium(V) complexes [VO(cat)(ONN)] and [VO(bha)(ONN)] respectively. These complexes are not very stable in solution and slowly convert to the corresponding dioxo species [VO2(ONN)] as observed by 51V NMR and electronic absorption spectroscopic studies.

  5. Origins, structures, and functions of circulating DNA in oncology.

    Science.gov (United States)

    Thierry, A R; El Messaoudi, S; Gahan, P B; Anker, P; Stroun, M

    2016-09-01

    While various clinical applications especially in oncology are now in progress such as diagnosis, prognosis, therapy monitoring, or patient follow-up, the determination of structural characteristics of cell-free circulating DNA (cirDNA) are still being researched. Nevertheless, some specific structures have been identified and cirDNA has been shown to be composed of many "kinds." This structural description goes hand-in-hand with the mechanisms of its origins such as apoptosis, necrosis, active release, phagocytosis, and exocytose. There are multiple structural forms of cirDNA depending upon the mechanism of release: particulate structures (exosomes, microparticles, apoptotic bodies) or macromolecular structures (nucleosomes, virtosomes/proteolipidonucleic acid complexes, DNA traps, links with serum proteins or to the cell-free membrane parts). In addition, cirDNA concerns both nuclear and/or mitochondrial DNA with both species exhibiting different structural characteristics that potentially reveal different forms of biological stability or diagnostic significance. This review focuses on the origins, structures and functional aspects that are paradoxically less well described in the literature while numerous reviews are directed to the clinical application of cirDNA. Differentiation of the various structures and better knowledge of the fate of cirDNA would considerably expand the diagnostic power of cirDNA analysis especially with regard to the patient follow-up enlarging the scope of personalized medicine. A better understanding of the subsequent fate of cirDNA would also help in deciphering its functional aspects such as their capacity for either genometastasis or their pro-inflammatory and immunological effects.

  6. Time-dependent density functional theory for open systems with a positivity-preserving decomposition scheme for environment spectral functions

    Energy Technology Data Exchange (ETDEWEB)

    Wang, RuLin [Beijing Computational Science Research Center, No. 3 He-Qing Road, Beijing 100084 (China); Zheng, Xiao, E-mail: xz58@ustc.edu.cn [Hefei National Laboratory for Physical Sciences at the Microscale, University of Science and Technology of China, Hefei, Anhui 230026 (China); Synergetic Innovation Center of Quantum Information and Quantum Physics, University of Science and Technology of China, Hefei, Anhui 230026 (China); Kwok, YanHo; Xie, Hang; Chen, GuanHua [Department of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong (China); Yam, ChiYung, E-mail: yamcy@csrc.ac.cn [Beijing Computational Science Research Center, No. 3 He-Qing Road, Beijing 100084 (China); Department of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong (China)

    2015-04-14

    Understanding electronic dynamics on material surfaces is fundamentally important for applications including nanoelectronics, inhomogeneous catalysis, and photovoltaics. Practical approaches based on time-dependent density functional theory for open systems have been developed to characterize the dissipative dynamics of electrons in bulk materials. The accuracy and reliability of such approaches depend critically on how the electronic structure and memory effects of surrounding material environment are accounted for. In this work, we develop a novel squared-Lorentzian decomposition scheme, which preserves the positive semi-definiteness of the environment spectral matrix. The resulting electronic dynamics is guaranteed to be both accurate and convergent even in the long-time limit. The long-time stability of electronic dynamics simulation is thus greatly improved within the current decomposition scheme. The validity and usefulness of our new approach are exemplified via two prototypical model systems: quasi-one-dimensional atomic chains and two-dimensional bilayer graphene.

  7. Time-dependent density functional theory for open systems with a positivity-preserving decomposition scheme for environment spectral functions

    Science.gov (United States)

    Wang, RuLin; Zheng, Xiao; Kwok, YanHo; Xie, Hang; Chen, GuanHua; Yam, ChiYung

    2015-04-01

    Understanding electronic dynamics on material surfaces is fundamentally important for applications including nanoelectronics, inhomogeneous catalysis, and photovoltaics. Practical approaches based on time-dependent density functional theory for open systems have been developed to characterize the dissipative dynamics of electrons in bulk materials. The accuracy and reliability of such approaches depend critically on how the electronic structure and memory effects of surrounding material environment are accounted for. In this work, we develop a novel squared-Lorentzian decomposition scheme, which preserves the positive semi-definiteness of the environment spectral matrix. The resulting electronic dynamics is guaranteed to be both accurate and convergent even in the long-time limit. The long-time stability of electronic dynamics simulation is thus greatly improved within the current decomposition scheme. The validity and usefulness of our new approach are exemplified via two prototypical model systems: quasi-one-dimensional atomic chains and two-dimensional bilayer graphene.

  8. Time-dependent density functional theory for open systems with a positivity-preserving decomposition scheme for environment spectral functions.

    Science.gov (United States)

    Wang, RuLin; Zheng, Xiao; Kwok, YanHo; Xie, Hang; Chen, GuanHua; Yam, ChiYung

    2015-04-14

    Understanding electronic dynamics on material surfaces is fundamentally important for applications including nanoelectronics, inhomogeneous catalysis, and photovoltaics. Practical approaches based on time-dependent density functional theory for open systems have been developed to characterize the dissipative dynamics of electrons in bulk materials. The accuracy and reliability of such approaches depend critically on how the electronic structure and memory effects of surrounding material environment are accounted for. In this work, we develop a novel squared-Lorentzian decomposition scheme, which preserves the positive semi-definiteness of the environment spectral matrix. The resulting electronic dynamics is guaranteed to be both accurate and convergent even in the long-time limit. The long-time stability of electronic dynamics simulation is thus greatly improved within the current decomposition scheme. The validity and usefulness of our new approach are exemplified via two prototypical model systems: quasi-one-dimensional atomic chains and two-dimensional bilayer graphene.

  9. Latent structures of female sexual functioning.

    Science.gov (United States)

    Carvalho, Joana; Vieira, Armando Luís; Nobre, Pedro

    2012-08-01

    For the last three decades, male and female sexual responses have been conceptualized as similar, based on separated and sequential phases as proposed by the models of Masters and Johnson (1966) and Kaplan (1979) model. However, there is a growing debate around the need to conceptualize female sexual response and the classification of sexual dysfunction in women, in view of the upcoming editions of the DSM and ICD. The aim of this study was to test, using structural equation modeling, five conceptual, alternative models of female sexual function, using a sample of women with sexual difficulties and a sample of women without sexual problems. A total of 1993 Portuguese women participated in the study and completed a modified version of the Female Sexual Function Index. Findings suggested a four-factor solution as the model that best fit the data regarding women presenting sexual difficulties: (1) desire/arousal; (2) lubrication; (3) orgasm; (4) pain/vaginismus. In relation to sexually healthy women, the best model was a five-factor solution comprising of (1) desire; (2) arousal; (3) lubrication; (4) orgasm; and (5) pain/vaginismus. Discriminant validity between factors was supported, suggesting that these dimensions measure distinct phenomena. Model fit to the data significantly decreased in both samples, as models began to successively consider greater levels of overlap among phases of sexual function, towards a single-factor solution. By suggesting the overlap between pain and vaginismus, results partially support the new classification that is currently being discussed regarding DSM-5. Additionally, results on the relationship between sexual desire and arousal were inconclusive as sexually healthy women were better characterized by a five-factor model that considered the structural independence among these factors, whereas women with sexual difficulties better fit with a four-factor model merging sexual desire and subjective sexual arousal.

  10. Annexin A2 Heterotetramer: Structure and Function

    Directory of Open Access Journals (Sweden)

    David Waisman

    2013-03-01

    Full Text Available Annexin A2 is a pleiotropic calcium- and anionic phospholipid-binding protein that exists as a monomer and as a heterotetrameric complex with the plasminogen receptor protein, S100A10. Annexin A2 has been proposed to play a key role in many processes including exocytosis, endocytosis, membrane organization, ion channel conductance, and also to link F-actin cytoskeleton to the plasma membrane. Despite an impressive list of potential binding partners and regulatory activities, it was somewhat unexpected that the annexin A2-null mouse should show a relatively benign phenotype. Studies with the annexin A2-null mouse have suggested important functions for annexin A2 and the heterotetramer in fibrinolysis, in the regulation of the LDL receptor and in cellular redox regulation. However, the demonstration that depletion of annexin A2 causes the depletion of several other proteins including S100A10, fascin and affects the expression of at least sixty-one genes has confounded the reports of its function. In this review we will discuss the annexin A2 structure and function and its proposed physiological and pathological roles.

  11. Microenvironment Dependent Photobiomodulation on Function-Specific Signal Transduction Pathways

    Directory of Open Access Journals (Sweden)

    Timon Cheng-Yi Liu

    2014-01-01

    Full Text Available Cellular photobiomodulation on a cellular function has been shown to be homeostatic. Its function-specific pathway mechanism would be further discussed in this paper. The signal transduction pathways maintaining a normal function in its function-specific homeostasis (FSH, resisting the activation of many other irrelative signal transduction pathways, are so sparse that it can be supposed that there may be normal function-specific signal transduction pathways (NSPs. A low level laser irradiation or monochromatic light may promote the activation of partially activated NSP and/or its redundant NSP so that it may induce the second-order phase transition of a function from its dysfunctional one far from its FSH to its normal one in a function-specific microenvironment and may also induce the first-order functional phase transition of the normal function from low level to high level.

  12. Time-dependent density functional theory study on direction-dependent electron and hole transfer processes in molecular systems.

    Science.gov (United States)

    Partovi-Azar, Pouya; Kaghazchi, Payam

    2017-04-15

    We report on real-time time-dependent density functional theory calculations on direction-dependent electron and hole transfer processes in molecular systems. As a model system, we focus on α-sulfur. It is shown that time scale of the electron transfer process from a negatively charged S8 molecule to a neighboring neutral monomer is comparable to that of a strong infrared-active molecular vibrations of the dimer with one negatively charged monomer. This results in a strong coupling between the electrons and the nuclei motion which eventually leads to S8 ring opening before the electron transfer process is completed. The open-ring structure is found to be stable. The similar infrared-active peak in the case of hole transfer, however, is shown to be very weak and hence no significant scattering by the nuclei is possible. The presented approach to study the charge transfer processes in sulfur has direct applications in the increasingly growing research field of charge transport in molecular systems. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

  13. Tensor polarization dependent fragmentation functions and e+e-→V π X at high energies

    Science.gov (United States)

    Chen, Kai-bao; Yang, Wei-hua; Wei, Shu-yi; Liang, Zuo-tang

    2016-08-01

    We present the systematic results for three-dimensional fragmentation functions of spin-1 hadrons defined via the quark-quark correlator. There are totally 72 such fragmentation functions, among them 18 are twist-2, 36 are twist-3 and 18 are twist-4. We also present the relationships between the twist-3 parts and those defined via the quark-gluon-quark correlator obtained from the QCD equation of motion. We show that the two particle semi-inclusive hadron production process e+e-→V π X at high energies is one of the best places to study the three-dimensional tensor polarization dependent fragmentation functions. We present the general kinematic analysis of this process and show that the cross section should be expressed in terms of 81 independent structure functions. After that we present parton model results for the hadronic tensor, the structure functions, and the azimuthal and spin asymmetries in terms of these gauge invariant fragmentation functions at the leading order perturbative quantum chromodynamics up to twist-3.

  14. Tensor polarization dependent fragmentation functions and e+e-\\to V \\pi X at high energies

    CERN Document Server

    Chen, Kai-bao; Wei, Shu-yi; Liang, Zuo-tang

    2016-01-01

    We present the systematic results for three dimensional fragmentation functions of spin one hadrons defined via quark-quark correlator. There are totally 72 such fragmentation functions, among them 18 are twist-2, 36 are twist-3 and 18 are twist-4. We also present the relationships between the twist-3 parts and those defined via quark-gluon-quark correlator obtained from the QCD equation of motion. We show that two particle semi-inclusive hadron production process $e^+e^-\\to V\\pi X$ at high energies is one of the best places to study the three-dimensional tensor polarization dependent fragmentation functions. We present the general kinematic analysis of this process and show that the cross section should be expressed in terms of 81 independent structure functions. After that we present parton model results for the hadronic tensor, the structure functions, the azimuthal and spin asymmetries in terms of these gauge invariant fragmentation functions at the leading order pQCD up to twist-3.

  15. Optimal pinning controllability of complex networks: dependence on network structure.

    Science.gov (United States)

    Jalili, Mahdi; Askari Sichani, Omid; Yu, Xinghuo

    2015-01-01

    Controlling networked structures has many applications in science and engineering. In this paper, we consider the problem of pinning control (pinning the dynamics into the reference state), and optimally placing the driver nodes, i.e., the nodes to which the control signal is fed. Considering the local controllability concept, a metric based on the eigenvalues of the Laplacian matrix is taken into account as a measure of controllability. We show that the proposed optimal placement strategy considerably outperforms heuristic methods including choosing hub nodes with high degree or betweenness centrality as drivers. We also study properties of optimal drivers in terms of various centrality measures including degree, betweenness, closeness, and clustering coefficient. The profile of these centrality values depends on the network structure. For homogeneous networks such as random small-world networks, the optimal driver nodes have almost the mean centrality value of the population (much lower than the centrality value of hub nodes), whereas the centrality value of optimal drivers in heterogeneous networks such as scale-free ones is much higher than the average and close to that of hub nodes. However, as the degree of heterogeneity decreases in such networks, the profile of centrality approaches the population mean.

  16. State-dependent Jastrow correlation functions for $^{4}He$ nuclei

    CERN Document Server

    Guardiola, R

    1998-01-01

    We calculate the ground-state energy for the nucleus 4He with V4 nucleon interactions, making use of a Jastrow description of the corresponding wavefunction with state-dependent correlation factors. The effect related to the state dependence of the correlation is quite important, lowering the upper bound for the ground-state energy by some 2 MeV.

  17. Structural and functional diversity of native brain neuronal nicotinic receptors.

    Science.gov (United States)

    Gotti, Cecilia; Clementi, Francesco; Fornari, Alice; Gaimarri, Annalisa; Guiducci, Stefania; Manfredi, Irene; Moretti, Milena; Pedrazzi, Patrizia; Pucci, Luca; Zoli, Michele

    2009-10-01

    Neuronal nicotinic acetylcholine receptors (nAChRs) are a family of ligand-gated ion channels present in the central and peripheral nervous systems, that are permeable to mono- and divalent cations. They share a common basic structure but their pharmacological and functional properties arise from the wide range of different subunit combinations making up distinctive subtypes. nAChRs are involved in many physiological functions in the central and peripheral nervous systems, and are the targets of the widely used drug of abuse nicotine. In addition to tobacco dependence, changes in their number and/or function are associated with neuropsychiatric disorders, ranging from epilepsy to dementia. Although some of the neural circuits involved in the acute and chronic effects of nicotine have been identified, much less is known about which native nAChR subtypes are involved in specific physiological functions and pathophysiological conditions. We briefly review some recent findings concerning the structure and function of native nAChRs, focusing on the subtypes identified in the mesostriatal and habenulo-interpeduncular pathways, two systems involved in nicotine reinforcement and withdrawal. We also discuss recent findings concerning the effect of chronic nicotine on the expression of native subtypes.

  18. [Age-related characteristics of structural support for ovarian function].

    Science.gov (United States)

    Koval'skiĭ, G B

    1984-12-01

    Histoenzymological assay was used to investigate various structures of the ovaries of rats of two groups aged 3-4 and 12-14 months during estral cycle. The activity of 3 beta-, 17 beta- and 20 alpha-steroid dehydrogenases, glucose-6-phosphate dehydrogenase, NAD and NADP-diaphorases, esterase, acid and alkaline phosphatases was studied. It has been shown that transport alterations in the microcirculation including the hematofollicular barrier play, the leading part in age-dependent depression of reproductive and endocrine functions. Ageing rats demonstrated no linkage between endothelial, thecal and granular cells, which points to the injury of the histophysiological mechanisms of the follicular system integration.

  19. Evolution of transverse momentum dependent distribution and fragmentation functions

    CERN Document Server

    Henneman, A A; Mulders, P J; Boer, Daniel

    2002-01-01

    We use Lorentz invariance and the QCD equations of motion to study the evolution of functions that appear at leading order in a 1/Q expansion in azimuthal asymmetries. This includes the evolution equation of the Collins fragmentation function. The moments of these functions are matrix elements of known twist two and twist three operators. We present the evolution in the large N_c limit, restricting to non-singlet for the chiral-even functions.

  20. Evolution of transverse momentum dependent distribution and fragmentation functions

    Energy Technology Data Exchange (ETDEWEB)

    Henneman, A.A. E-mail: alex@nat.vu.nl; Boer, Danieel; Mulders, P.J

    2002-01-07

    We use Lorentz invariance and the QCD equations of motion to study the evolution of functions that appear at leading order in a 1/Q expansion in azimuthal asymmetries. This includes the evolution equation of the Collins fragmentation function. The moments of these functions are matrix elements of known twist two and twist three operators. We present the evolution in the large N{sub c} limit, restricting to non-singlet for the chiral-even functions.

  1. Evolution of transverse momentum dependent distribution and fragmentation functions

    Science.gov (United States)

    Henneman, A. A.; Boer, Daniël; Mulders, P. J.

    2002-01-01

    We use Lorentz invariance and the QCD equations of motion to study the evolution of functions that appear at leading order in a 1/ Q expansion in azimuthal asymmetries. This includes the evolution equation of the Collins fragmentation function. The moments of these functions are matrix elements of known twist two and twist three operators. We present the evolution in the large Nc limit, restricting to non-singlet for the chiral-even functions.

  2. Evolution of transverse momentum dependent distribution and fragmentation functions

    NARCIS (Netherlands)

    Henneman, AA; Boer, D; Mulders, PJ

    2002-01-01

    We use Lorentz invariance and the QCD equations of motion to study the evolution of functions that appear at leading order in a I / Q expansion in azimuthal asymmetries. This includes the evolution equation of the Collins fragmentation function. The moments of these functions are matrix elements of

  3. Exact conditions on the temperature dependence of density functionals

    CERN Document Server

    Burke, Kieron; Grabowski, Paul E; Pribram-Jones, Aurora

    2015-01-01

    Universal exact conditions guided the construction of most ground-state density functional approximations in use today. We derive the relation between the entropy and Mermin free energy density functionals for thermal density functional theory. Both the entropy and sum of kinetic and electron-electron repulsion functionals are shown to be monotonically increasing with temperature, while the Mermin functional is concave downwards. Analogous relations are found for both exchange and correlation. The importance of these conditions is illustrated in two extremes: the Hubbard dimer and the uniform gas.

  4. Exact conditions on the temperature dependence of density functionals

    Science.gov (United States)

    Burke, K.; Smith, J. C.; Grabowski, P. E.; Pribram-Jones, A.

    2016-05-01

    Universal exact conditions guided the construction of most ground-state density functional approximations in use today. We derive the relation between the entropy and Mermin free energy density functionals for thermal density functional theory. Both the entropy and sum of kinetic and electron-electron repulsion functionals are shown to be monotonically increasing with temperature, while the Mermin functional is concave downwards. Analogous relations are found for both exchange and correlation. The importance of these conditions is illustrated in two extremes: the Hubbard dimer and the uniform gas.

  5. Structural and functional diversity of desmosomes.

    Science.gov (United States)

    Harmon, Robert M; Green, Kathleen J

    2013-12-01

    Desmosomes anchor intermediate filaments at sites of cell contact established by the interaction of cadherins extending from opposing cells. The incorporation of cadherins, catenin adaptors, and cytoskeletal elements resembles the closely related adherens junction. However, the recruitment of intermediate filaments distinguishes desmosomes and imparts a unique function. By linking the load-bearing intermediate filaments of neighboring cells, desmosomes create mechanically contiguous cell sheets and, in so doing, confer structural integrity to the tissues they populate. This trait and a well-established role in human disease have long captured the attention of cell biologists, as evidenced by a publication record dating back to the mid-1860s. Likewise, emerging data implicating the desmosome in signaling events pertinent to organismal development, carcinogenesis, and genetic disorders will secure a prominent role for desmosomes in future biological and biomedical investigations.

  6. Structure and function of histone acetyltransferase MOF.

    Science.gov (United States)

    Chen, Qiao Yi; Costa, Max; Sun, Hong

    2015-01-01

    MOF was first identified in Drosophila melanogaster as an important component of the dosage compensation complex. As a member of MYST family of histone acetyltransferase, MOF specifically deposits the acetyl groups to histone H4 lysine 16. Throughout evolution, MOF and its mammalian ortholog have retained highly conserved substrate specificity and similar enzymatic activities. MOF plays important roles in dosage compensation, ESC self-renewal, DNA damage and repair, cell survival, and gene expression regulation. Dysregulation of MOF has been implicated in tumor formation and progression of many types of human cancers. This review will discuss the structure and activity of mammalian hMOF as well as its function in H4K16 acetylation, DNA damage response, stem cell pluripotency, and carcinogenesis.

  7. Structural and Functional Views of Mechatronic Products

    DEFF Research Database (Denmark)

    Nielsen, Kjeld; Petersen, Thomas Ditlev; Jørgensen, Kaj Asbjørn

    2011-01-01

    The development and subsequent production of industrial products are often complicated tasks. The complication increases with combined product as mechatronic products and is further complicated when large variety is required. Modularity is often used to achieve optimum in these complications both...... in the costumer view as well in the production view. In this paper, the relationships in mechatronic products between the functional and structural levels are explored in relation to modularity. A list of commonly used module drivers is presented and a qualitative survey is used to explore significance...... of influence on these module drivers when applying mechatronic product technology and view levels. The result is summarized in a list of which drivers should be addressed in a mechatronic product approach to modularity. Keywords:...

  8. Evolution: functional evolution of nuclear structure.

    Science.gov (United States)

    Wilson, Katherine L; Dawson, Scott C

    2011-10-17

    The evolution of the nucleus, the defining feature of eukaryotic cells, was long shrouded in speculation and mystery. There is now strong evidence that nuclear pore complexes (NPCs) and nuclear membranes coevolved with the endomembrane system, and that the last eukaryotic common ancestor (LECA) had fully functional NPCs. Recent studies have identified many components of the nuclear envelope in living Opisthokonts, the eukaryotic supergroup that includes fungi and metazoan animals. These components include diverse chromatin-binding membrane proteins, and membrane proteins with adhesive lumenal domains that may have contributed to the evolution of nuclear membrane architecture. Further discoveries about the nucleoskeleton suggest that the evolution of nuclear structure was tightly coupled to genome partitioning during mitosis.

  9. Angle-dependent discoloration structures in wing scales of Morpho menelaus butterfly

    Institute of Scientific and Technical Information of China (English)

    NIU ShiChao; LI Bo; YE JunFeng; MU ZhengZhi; ZHANG JunQiu; LIU Yan; HAN ZhiWu

    2016-01-01

    The Morpho butterfly is famous for its typical structural color and has increasingly attracted the interest of scholars in a wide variety of research fields.Herein,it was found that the color of Morpho menelaus butterfly wings is not only structure-based but also viewing-angle-dependent.Firstly,the discoloration effect of this typical butterfly was confirmed by a series of experiments.Then,the general form,arrangements,and geometrical dimensions of the scales were observed using a stereomicroscope.Scanning electron microscopy was also used to examine the two-dimensional morphologies and structures of a single scale.Afterwards,one model with the optimized three-dimensional profile of the structure was described using Pro-engineer software.The associate model was then analyzed to reconstruct the process between the incident light and the model surface.Finally,the mechanism of the angle-dependent discoloration effect was analyzed by theoretical calculation and optical simulation.Different light propagation paths and the length of the incident light at different angles caused destructive or constructive interference between the light reflected from the different layers.The different spectra of the reflected light make the wings appear with different structural colors,thereby endowing the angle-dependent discoloration effect.The consistency of the calculation and simulation results confirms that these structures possess an excellent angle-dependent discoloration effect.This functional "biomimetic structure" would not only be of great scientific interest but could also have a great impact in a wide range of applications such as reflective displays,credit card security,and military stealth technology.

  10. Wigner function studies of spin transport in dilute magnetic semiconductor barrier structures

    Science.gov (United States)

    Grubin, Harold L.

    2004-12-01

    The spin dependent Wigner function is implemented to obtain the IV characteristics of a double barrier resonant tunneling diode with DMS layers. The structure distinguishes between spin-up and spin-down carriers, each of which experiences resonance at different magnetic field dependent bias levels. The results demonstrate the magnetic field dependence of the IV characteristics and illustrate the magnetic field dependence of relative spin-up and spin-down carriers.

  11. Bromodomains: Structure, function and pharmacology of inhibition.

    Science.gov (United States)

    Ferri, Elena; Petosa, Carlo; McKenna, Charles E

    2016-04-15

    Bromodomains are epigenetic readers of histone acetylation involved in chromatin remodeling and transcriptional regulation. The human proteome comprises 46 bromodomain-containing proteins with a total of 61 bromodomains, which, despite highly conserved structural features, recognize a wide array of natural peptide ligands. Over the past five years, bromodomains have attracted great interest as promising new epigenetic targets for diverse human diseases, including inflammation, cancer, and cardiovascular disease. The demonstration in 2010 that two small molecule compounds, JQ1 and I-BET762, potently inhibit proteins of the bromodomain and extra-terminal (BET) family with translational potential for cancer and inflammatory disease sparked intense efforts in academia and pharmaceutical industry to develop novel bromodomain antagonists for therapeutic applications. Several BET inhibitors are already in clinical trials for hematological malignancies, solid tumors and cardiovascular disease. Currently, the field faces the challenge of single-target selectivity, especially within the BET family, and of overcoming problems related to the development of drug resistance. At the same time, new trends in bromodomain inhibitor research are emerging, including an increased interest in non-BET bromodomains and a focus on drug synergy with established antitumor agents to improve chemotherapeutic efficacy. This review presents an updated view of the structure and function of bromodomains, traces the development of bromodomain inhibitors and their potential therapeutic applications, and surveys the current challenges and future directions of this vibrant new field in drug discovery. Copyright © 2015 Elsevier Inc. All rights reserved.

  12. Intrinsically disordered proteins: structural and functional dynamics

    Directory of Open Access Journals (Sweden)

    Wallin S

    2017-02-01

    Full Text Available Stefan Wallin Department of Physics and Physical Oceanography, Memorial University of Newfoundland, St. John’s, NL, Canada Abstract: The classical view holds that proteins fold into essentially unique three-dimensional structures before becoming biologically active. However, studies over the last several years have provided broad and convincing evidence that some proteins do not adopt a single structure and yet are fully functional. These intrinsically disordered proteins (IDPs have been found to be highly prevalent in many genomes, including human, and play key roles in central cellular processes, such as regulation of transcription and translation, cell cycle, and cell signaling. Moreover, IDPs are overrepresented among proteins implicated in disease, including various cancers and neurodegenerative disorders. Intense efforts, by using both experimental and computational approaches, are consequently under way to uncover the molecular mechanisms that underpin the roles of IDPs in biology and disease. This review provides an introduction to the general biophysical properties of IDPs and discusses some of the recent emerging areas in IDP research, including the roles of IDPs in allosteric regulation, regulatory unfolding, and formation of intracellular membrane-less organelles. In addition, recent attempts at therapeutic targeting of IDPs by small molecules, noting in particular that IDPs represent a potentially important source of new drug targets in light of their central role in protein–protein interaction networks, are also reviewed. Keywords: natively unfolded proteins, unstructured proteins, protein folding, protein–protein interaction, cell regulation, signaling, drug development, inhibitors

  13. Structure and functionality of bromine doped graphite.

    Science.gov (United States)

    Hamdan, Rashid; Kemper, A F; Cao, Chao; Cheng, H P

    2013-04-28

    First-principles calculations are used to study the enhanced in-plane conductivity observed experimentally in Br-doped graphite, and to study the effect of external stress on the structure and functionality of such systems. The model used in the numerical calculations is that of stage two doped graphite. The band structure near the Fermi surface of the doped systems with different bromine concentrations is compared to that of pure graphite, and the charge transfer between carbon and bromine atoms is analyzed to understand the conductivity change along different high symmetry directions. Our calculations show that, for large interlayer separation between doped graphite layers, bromine is stable in the molecular form (Br2). However, with increased compression (decreased layer-layer separation) Br2 molecules tend to dissociate. While in both forms, bromine is an electron acceptor. The charge exchange between the graphite layers and Br atoms is higher than that with Br2 molecules. Electron transfer to the Br atoms increases the number of hole carriers in the graphite sheets, resulting in an increase of conductivity.

  14. Structure and biological functions of fungal cerebrosides

    Directory of Open Access Journals (Sweden)

    Barreto-Bergter Eliana

    2004-01-01

    Full Text Available Ceramide monohexosides (CMHs, cerebrosides are glycosphingolipids composed of a hydrophobic ceramide linked to one sugar unit. In fungal cells, CMHs are very conserved molecules consisting of a ceramide moiety containing 9-methyl-4,8-sphingadienine in amidic linkage to 2-hydroxyoctadecanoic or 2-hydroxyhexadecanoic acids, and a carbohydrate portion consisting of one residue of glucose or galactose. 9-Methyl 4,8-sphingadienine-containing ceramides are usually glycosylated to form fungal cerebrosides, but the recent description of a ceramide dihexoside (CDH presenting phytosphingosine in Magnaporthe grisea suggests the existence of alternative pathways of ceramide glycosylation in fungal cells. Along with their unique structural characteristics, fungal CMHs have a peculiar subcellular distribution and striking biological properties. In Pseudallescheria boydii, Candida albicans, Cryptococcus neoformans, Aspergillus nidulans, A. fumigatus, and Schizophyllum commune, CMHs are apparently involved in morphological transitions and fungal growth. The elucidation of structural and functional aspects of fungal cerebrosides may therefore contribute to the design of new antifungal agents inhibiting growth and differentiation of pathogenic species.

  15. Wavelets and Geometric Structure for Function Spaces

    Institute of Scientific and Technical Information of China (English)

    Qi Xiang YANG

    2004-01-01

    With Littlewood-Paley analysis, Peetre and Triebel classified, systematically, almost all the usual function spaces into two classes of spaces: Besov spaces (B)s,q p(s ∈ R,0 < p,q ≤∞) and Triebel-Lizorkin spaces (F)s,q p(s∈R,0<p<∞,0<q≤∞); but the structure of dual spaces (D)s,q p of (F)s,q p(s∈R, 0<p≤1≤q≤∞) is very different from that of Besov spaces or that of Triebel-Lizorkin spaces, and their structure cannot be analysed easily in the Littlewood-Paley analysis. Our main goal is to characterize (D)s,q p (s ∈ R, 0<p= 1≤q≤∞) in tent spaces with wavelets. By the way, some applications are given: (i) Triebel-Lizorkin spaces for p = ∞ defined by Littlewood-Paley analysis cannot serve as the dual spaces of Triebel-Lizorkin spaces for p = 1; (ii) Some inclusion relations among these above spaces and some relations among(B)o,q1,(F)o,q1 and L1 are studied.

  16. Temperature dependence of the electronic structure of semiconductors and insulators

    Energy Technology Data Exchange (ETDEWEB)

    Poncé, S., E-mail: samuel.pon@gmail.com; Gillet, Y.; Laflamme Janssen, J.; Gonze, X. [European Theoretical Spectroscopy Facility and Institute of Condensed Matter and Nanosciences, Université catholique de Louvain, Chemin des étoiles 8, bte L07.03.01, B-1348 Louvain-la-neuve (Belgium); Marini, A. [Consiglio Nazionale delle Ricerche (CNR), Via Salaria Km 29.3, CP 10, 00016 Monterotondo Stazione (Italy); Verstraete, M. [European Theoretical Spectroscopy Facility and Physique des matériaux et nanostructures, Université de Liège, Allée du 6 Août 17, B-4000 Liège (Belgium)

    2015-09-14

    The renormalization of electronic eigenenergies due to electron-phonon coupling (temperature dependence and zero-point motion effect) is sizable in many materials with light atoms. This effect, often neglected in ab initio calculations, can be computed using the perturbation-based Allen-Heine-Cardona theory in the adiabatic or non-adiabatic harmonic approximation. After a short description of the recent progresses in this field and a brief overview of the theory, we focus on the issue of phonon wavevector sampling convergence, until now poorly understood. Indeed, the renormalization is obtained numerically through a slowly converging q-point integration. For non-zero Born effective charges, we show that a divergence appears in the electron-phonon matrix elements at q → Γ, leading to a divergence of the adiabatic renormalization at band extrema. This problem is exacerbated by the slow convergence of Born effective charges with electronic wavevector sampling, which leaves residual Born effective charges in ab initio calculations on materials that are physically devoid of such charges. Here, we propose a solution that improves this convergence. However, for materials where Born effective charges are physically non-zero, the divergence of the renormalization indicates a breakdown of the adiabatic harmonic approximation, which we assess here by switching to the non-adiabatic harmonic approximation. Also, we study the convergence behavior of the renormalization and develop reliable extrapolation schemes to obtain the converged results. Finally, the adiabatic and non-adiabatic theories, with corrections for the slow Born effective charge convergence problem (and the associated divergence) are applied to the study of five semiconductors and insulators: α-AlN, β-AlN, BN, diamond, and silicon. For these five materials, we present the zero-point renormalization, temperature dependence, phonon-induced lifetime broadening, and the renormalized electronic band structure.

  17. The Structural and Functional Organisation of Cognition.

    Directory of Open Access Journals (Sweden)

    Peter John Snow

    2016-10-01

    Full Text Available This paper proposes that what have been historically and contemporarily defined as different domains of human cognition are served by one of four functionally- and structurally-distinct areas of the prefrontal cortex. Their contributions to human intelligence are as follows: (a BA9, enables our emotional intelligence, engaging the psychosocial domain, (b BA47, enables our practical intelligence, engaging the material domain, (c BA46 (or BA46-9/46, enables our abstract intelligence, engaging the hypothetical domain and (d BA10, enables our temporal intelligence, engaging in planning within any of the other three domains. Given their unique contribution to human cognition, it is proposed that these areas be called the, social (BA9, material (BA47, abstract (BA46-9/46 and temporal (BA10 mind. The evidence that BA47 participates strongly in verbal and gestural communication suggests that language evolved primarily as a consequence of the extreme selective pressure for practicality; an observation supported by the functional connectivity between BA47 and orbital areas that negatively reinforce lying. It is further proposed that the abstract mind (BA46-9/46 is the primary seat of metacognition charged with creating adaptive behavioral strategies by generating higher-order concepts (hypotheses from lower-order concepts originating both from our perceptual representations and the other three domains of cognition.

  18. The Structural and Functional Organization of Cognition.

    Science.gov (United States)

    Snow, Peter J

    2016-01-01

    This article proposes that what have been historically and contemporarily defined as different domains of human cognition are served by one of four functionally- and structurally-distinct areas of the prefrontal cortex (PFC). Their contributions to human intelligence are as follows: (a) BA9, enables our emotional intelligence, engaging the psychosocial domain; (b) BA47, enables our practical intelligence, engaging the material domain; (c) BA46 (or BA46-9/46), enables our abstract intelligence, engaging the hypothetical domain; and (d) BA10, enables our temporal intelligence, engaging in planning within any of the other three domains. Given their unique contribution to human cognition, it is proposed that these areas be called the, social (BA9), material (BA47), abstract (BA46-9/46) and temporal (BA10) mind. The evidence that BA47 participates strongly in verbal and gestural communication suggests that language evolved primarily as a consequence of the extreme selective pressure for practicality; an observation supported by the functional connectivity between BA47 and orbital areas that negatively reinforce lying. It is further proposed that the abstract mind (BA46-9/46) is the primary seat of metacognition charged with creating adaptive behavioral strategies by generating higher-order concepts (hypotheses) from lower-order concepts originating from the other three domains of cognition.

  19. Structure, Function, and Evolution of Rice Centromeres

    Energy Technology Data Exchange (ETDEWEB)

    Jiang, Jiming

    2010-02-04

    The centromere is the most characteristic landmark of eukaryotic chromosomes. Centromeres function as the site for kinetochore assembly and spindle attachment, allowing for the faithful pairing and segregation of sister chromatids during cell division. Characterization of centromeric DNA is not only essential to understand the structure and organization of plant genomes, but it is also a critical step in the development of plant artificial chromosomes. The centromeres of most model eukaryotic species, consist predominantly of long arrays of satellite DNA. Determining the precise DNA boundary of a centromere has proven to be a difficult task in multicellular eukaryotes. We have successfully cloned and sequenced the centromere of rice chromosome 8 (Cen8), representing the first fully sequenced centromere from any multicellular eukaryotes. The functional core of Cen8 spans ~800 kb of DNA, which was determined by chromatin immunoprecipitation (ChIP) using an antibody against the rice centromere-specific H3 histone. We discovered 16 actively transcribed genes distributed throughout the Cen8 region. In addition to Cen8, we have characterized eight additional rice centromeres using the next generation sequencing technology. We discovered four subfamilies of the CRR retrotransposon that is highly enriched in rice centromeres. CRR elements are constitutively transcribed and different CRR subfamilies are differentially processed by RNAi. These results suggest that different CRR subfamilies may play different roles in the RNAi-mediated pathway for formation and maintenance of centromeric chromatin.

  20. Quinohemoprotein alcohol dehydrogenases: structure, function, and physiology.

    Science.gov (United States)

    Toyama, Hirohide; Mathews, F Scott; Adachi, Osao; Matsushita, Kazunobu

    2004-08-01

    Quino(hemo)protein alcohol dehydrogenases (ADH) that have pyrroloquinoline quinone (PQQ) as the prosthetic group are classified into 3 groups, types I, II, and III. Type I ADH is a simple quinoprotein having PQQ as the only prosthetic group, while type II and type III ADHs are quinohemoprotein having heme c as well as PQQ in the catalytic polypeptide. Type II ADH is a soluble periplasmic enzyme and is widely distributed in Proteobacteria such as Pseudomonas, Ralstonia, Comamonas, etc. In contrast, type III ADH is a membrane-bound enzyme working on the periplasmic surface solely in acetic acid bacteria. It consists of three subunits that comprise a quinohemoprotein catalytic subunit, a triheme cytochrome c subunit, and a third subunit of unknown function. The catalytic subunits of all the quino(hemo)protein ADHs have a common structural motif, a quinoprotein-specific superbarrel domain, where PQQ is deeply embedded in the center. In addition, in the type II and type III ADHs this subunit contains a unique heme c domain. Various type II ADHs each have a unique substrate specificity, accepting a wide variety of alcohols, as is discussed on the basis of recent X-ray crystallographic analyses. Electron transfer within both type II and III ADHs is discussed in terms of the intramolecular reaction from PQQ to heme c and also from heme to heme, and in terms of the intermolecular reaction with azurin and ubiquinone, respectively. Unique physiological functions of both types of quinohemoprotein ADHs are also discussed.

  1. Existence of time-dependent density-functional theory for open electronic systems: time-dependent holographic electron density theorem.

    Science.gov (United States)

    Zheng, Xiao; Yam, ChiYung; Wang, Fan; Chen, GuanHua

    2011-08-28

    We present the time-dependent holographic electron density theorem (TD-HEDT), which lays the foundation of time-dependent density-functional theory (TDDFT) for open electronic systems. For any finite electronic system, the TD-HEDT formally establishes a one-to-one correspondence between the electron density inside any finite subsystem and the time-dependent external potential. As a result, any electronic property of an open system in principle can be determined uniquely by the electron density function inside the open region. Implications of the TD-HEDT on the practicality of TDDFT are also discussed.

  2. Functional Brain Networks: Does the Choice of Dependency Estimator and Binarization Method Matter?

    Science.gov (United States)

    Jalili, Mahdi

    2016-07-01

    The human brain can be modelled as a complex networked structure with brain regions as individual nodes and their anatomical/functional links as edges. Functional brain networks are constructed by first extracting weighted connectivity matrices, and then binarizing them to minimize the noise level. Different methods have been used to estimate the dependency values between the nodes and to obtain a binary network from a weighted connectivity matrix. In this work we study topological properties of EEG-based functional networks in Alzheimer’s Disease (AD). To estimate the connectivity strength between two time series, we use Pearson correlation, coherence, phase order parameter and synchronization likelihood. In order to binarize the weighted connectivity matrices, we use Minimum Spanning Tree (MST), Minimum Connected Component (MCC), uniform threshold and density-preserving methods. We find that the detected AD-related abnormalities highly depend on the methods used for dependency estimation and binarization. Topological properties of networks constructed using coherence method and MCC binarization show more significant differences between AD and healthy subjects than the other methods. These results might explain contradictory results reported in the literature for network properties specific to AD symptoms. The analysis method should be seriously taken into account in the interpretation of network-based analysis of brain signals.

  3. Small catalytic RNA: Structure, function and application

    Energy Technology Data Exchange (ETDEWEB)

    Monforte, J.A.

    1991-04-01

    We have utilized a combination of photochemical cross-linking techniques and site-directed mutagenesis to obtain secondary and tertiary structure information for the self-cleaving, self-ligating subsequence of RNA from the negative strand of Satellite Tobacco Ringspot Virus. We have found that the helical regions fold about a hinge to promoting four different possible tertiary interactions, creating a molecular of similar shape to a paperclip. A model suggesting that the ``paperclip`` and ``hammerhead`` RNAs share a similar three dimensional structure is proposed. We have used a self-cleaving RNA molecule related to a subsequence of plant viroids, a ``hammerhead,`` to study the length-dependent folding of RNA produced during transcription by RNA polymerase. We have used this method to determine the length of RNA sequestered within elongating E. coli and T7 RNA polymerase complexes. The data show that for E. coli RNA polymerase 12{plus_minus}1 nucleotides are sequestered within the ternary complex, which is consistent with the presence of an RNA-DNA hybrid within the transcription bubble, as proposed by others. The result for T7 RNA polymerase differs from E. coli RNA polymerase, with only 10{plus_minus}1 nucleotides sequestered within the ternary complex, setting a new upper limit for the minimum RNA-DNA required for a stable elongating complex. Comparisons between E. coli and T7 RNA polymerase are made. The relevance of the results to models or transcription termination, abortive initiation, and initiation to elongation mode transitions are discussed.

  4. Small catalytic RNA: Structure, function and application

    Energy Technology Data Exchange (ETDEWEB)

    Monforte, J.A.

    1991-04-01

    We have utilized a combination of photochemical cross-linking techniques and site-directed mutagenesis to obtain secondary and tertiary structure information for the self-cleaving, self-ligating subsequence of RNA from the negative strand of Satellite Tobacco Ringspot Virus. We have found that the helical regions fold about a hinge to promoting four different possible tertiary interactions, creating a molecular of similar shape to a paperclip. A model suggesting that the paperclip'' and hammerhead'' RNAs share a similar three dimensional structure is proposed. We have used a self-cleaving RNA molecule related to a subsequence of plant viroids, a hammerhead,'' to study the length-dependent folding of RNA produced during transcription by RNA polymerase. We have used this method to determine the length of RNA sequestered within elongating E. coli and T7 RNA polymerase complexes. The data show that for E. coli RNA polymerase 12{plus minus}1 nucleotides are sequestered within the ternary complex, which is consistent with the presence of an RNA-DNA hybrid within the transcription bubble, as proposed by others. The result for T7 RNA polymerase differs from E. coli RNA polymerase, with only 10{plus minus}1 nucleotides sequestered within the ternary complex, setting a new upper limit for the minimum RNA-DNA required for a stable elongating complex. Comparisons between E. coli and T7 RNA polymerase are made. The relevance of the results to models or transcription termination, abortive initiation, and initiation to elongation mode transitions are discussed.

  5. In silico predicted structural and functional robustness of piscine steroidogenesis.

    Science.gov (United States)

    Hala, D; Huggett, D B

    2014-03-21

    Assessments of metabolic robustness or susceptibility are inherently dependent on quantitative descriptions of network structure and associated function. In this paper a stoichiometric model of piscine steroidogenesis was constructed and constrained with productions of selected steroid hormones. Structural and flux metrics of this in silico model were quantified by calculating extreme pathways and optimal flux distributions (using linear programming). Extreme pathway analysis showed progestin and corticosteroid synthesis reactions to be highly participant in extreme pathways. Furthermore, reaction participation in extreme pathways also fitted a power law distribution (degree exponent γ=2.3), which suggested that progestin and corticosteroid reactions act as 'hubs' capable of generating other functionally relevant pathways required to maintain steady-state functionality of the network. Analysis of cofactor usage (O2 and NADPH) showed progestin synthesis reactions to exhibit high robustness, whereas estrogen productions showed highest energetic demands with low associated robustness to maintain such demands. Linear programming calculated optimal flux distributions showed high heterogeneity of flux values with a near-random power law distribution (degree exponent γ≥2.7). Subsequently, network robustness was tested by assessing maintenance of metabolite flux-sum subject to targeted deletions of rank-ordered (low to high metric) extreme pathway participant and optimal flux reactions. Network robustness was susceptible to deletions of extreme pathway participant reactions, whereas minimal impact of high flux reaction deletion was observed. This analysis shows that the steroid network is susceptible to perturbation of structurally relevant (extreme pathway) reactions rather than those carrying high flux.

  6. Transverse momentum dependence in gluon distribution and fragmentation functions

    CERN Document Server

    Mulders, P J

    2001-01-01

    We investigate the twist two gluon distribution functions for spin 1/2 hadrons, emphasizing intrinsic transverse momentum of the gluons. These functions are relevant in leading order in the inverse hard scale in scattering processes such as inclusive leptoproduction or Drell-Yan scattering, or more general in hard processes in which at least two hadrons are involved. They show up in azimuthal asymmetries. For future estimates of such observables, we discuss specific bounds on these functions.

  7. Structure-dependent optical and electrical transport properties of nanostructured Al-doped ZnO.

    Science.gov (United States)

    Gondoni, P; Ghidelli, M; Di Fonzo, F; Carminati, M; Russo, V; Li Bassi, A; Casari, C S

    2012-09-14

    The structure-property relation of nanostructured Al-doped ZnO thin films has been investigated in detail through a systematic variation of structure and morphology, with particular emphasis on how they affect optical and electrical properties. A variety of structures, ranging from compact polycrystalline films to mesoporous, hierarchically organized cluster assemblies, are grown by pulsed laser deposition at room temperature at different oxygen pressures. We investigate the dependence of functional properties on structure and morphology and show how the correlation between electrical and optical properties can be studied to evaluate energy gap, conduction band effective mass and transport mechanisms. Understanding these properties opens up opportunities for specific applications in photovoltaic devices, where optimized combinations of conductivity, transparency and light scattering are required.

  8. Orbital-dependent exchange-correlation functionals in density-functional theory realized by the FLAPW method

    Energy Technology Data Exchange (ETDEWEB)

    Betzinger, Markus

    2011-12-14

    In this thesis, we extended the applicability of the full-potential linearized augmented-plane-wave (FLAPW) method, one of the most precise, versatile and generally applicable electronic structure methods for solids working within the framework of density-functional theory (DFT), to orbital-dependent functionals for the exchange-correlation (xc) energy. Two different schemes that deal with orbital-dependent functionals, the Kohn-Sham (KS) and the generalized Kohn-Sham (gKS) formalism, have been realized. Hybrid functionals, combining some amount of the orbital-dependent exact exchange energy with local or semi-local functionals of the density, are implemented within the gKS scheme. We work in particular with the PBE0 hybrid of Perdew, Burke, and Ernzerhof. Our implementation relies on a representation of the non-local exact exchange potential - its calculation constitutes the most time consuming step in a practical calculation - by an auxiliary mixed product basis (MPB). In this way, the matrix elements of the Hamiltonian corresponding to the non-local potential become a Brillouin-zone (BZ) sum over vector-matrix-vector products. Several techniques are developed and explored to further accelerate our numerical scheme. We show PBE0 results for a variety of semiconductors and insulators. In comparison with experiment, the PBE0 functional leads to improved band gaps and an improved description of localized states. Even for the ferromagnetic semiconductor EuO with localized 4f electrons, the electronic and magnetic properties are correctly described by the PBE0 functional. Subsequently, we discuss the construction of the local, multiplicative exact exchange (EXX) potential from the non-local, orbital-dependent exact exchange energy. For this purpose we employ the optimized effective potential (OEP) method. Central ingredients of the OEP equation are the KS wave-function response and the single-particle density response function. We show that a balance between the LAPW

  9. Social network types and functional dependency in older adults in Mexico

    Directory of Open Access Journals (Sweden)

    Espinosa-Alarcón Patricia

    2010-02-01

    Full Text Available Abstract Background Social networks play a key role in caring for older adults. A better understanding of the characteristics of different social networks types (TSNs in a given community provides useful information for designing policies to care for this age group. Therefore this study has three objectives: 1 To derive the TSNs among older adults affiliated with the Mexican Institute of Social Security; 2 To describe the main characteristics of the older adults in each TSN, including the instrumental and economic support they receive and their satisfaction with the network; 3 To determine the association between functional dependency and the type of social network. Methods Secondary data analysis of the 2006 Survey of Autonomy and Dependency (N = 3,348. The TSNs were identified using the structural approach and cluster analysis. The association between functional dependency and the TSNs was evaluated with Poisson regression with robust variance analysis in which socio-demographic characteristics, lifestyle and medical history covariates were included. Results We identified five TSNs: diverse with community participation (12.1%, diverse without community participation (44.3%; widowed (32.0%; nonfriends-restricted (7.6%; nonfamily-restricted (4.0%. Older adults belonging to widowed and restricted networks showed a higher proportion of dependency, negative self-rated health and depression. Older adults with functional dependency more likely belonged to a widowed network (adjusted prevalence ratio 1.5; 95%CI: 1.1-2.1. Conclusion The derived TSNs were similar to those described in developed countries. However, we identified the existence of a diverse network without community participation and a widowed network that have not been previously described. These TSNs and restricted networks represent a potential unmet need of social security affiliates.

  10. Emergence of ratio-dependent and predator-dependent functional responses for pollination mutualism and seed parasitism

    Science.gov (United States)

    DeAngelis, Donald L.; Holland, J. Nathaniel

    2006-01-01

    Prey (N) dependence [g(N)], predator (P) dependence [g(P) or g(N,P)], and ratio dependence [f(P/N)] are often seen as contrasting forms of the predator's functional response describing predator consumption rates on prey resources in predator–prey and parasitoid–host interactions. Analogously, prey-, predator-, and ratio-dependent functional responses are apparently alternative functional responses for other types of consumer–resource interactions. These include, for example, the fraction of flowers pollinated or seeds parasitized in pollination (pre-dispersal) seed-parasitism mutualisms, such as those between fig wasps and fig trees or yucca moths and yucca plants. Here we examine the appropriate functional responses for how the fraction of flowers pollinated and seeds parasitized vary with the density of pollinators (predator dependence) or the ratio of pollinator and flower densities (ratio dependence). We show that both types of functional responses can emerge from minor, but biologically important variations on a single model. An individual-based model was first used to describe plant–pollinator interactions. Conditional upon on whether the number of flowers visited by the pollinator was limited by factors other than search time (e.g., by the number of eggs it had to lay, if it was also a seed parasite), and on whether the pollinator could directly find flowers on a plant, or had to search, the simulation results lead to either a predator-dependent or a ratio-dependent functional response. An analytic model was then used to show mathematically how these two cases can arise.

  11. The rhodopsins: structure and function. Introduction

    Science.gov (United States)

    Lanyi, J. K.

    1992-01-01

    Nature makes use of the propensity of retinal for light-dependent double-bond isomerization in a number of systems and in a variety of ways. The common theme for light receptors based on this kind of chemistry is that (1) the retinal is bound in most cases to a small membrane protein via a protonated lysine-retinal Schiff base, (2) the absorption maximum in the visible is tuned to a suitable wavelength largely by electrostatic interaction with polar protein residues, and (3) the light-induced bond rotations and strains in the retinal set off reaction chains during which at least part of the excess free energy acquired is transferred to the protein and causes pK shifts of acidic residues and/or backbone conformational changes. The physiological consequence of the process initiated by absorption of light is either the activation of an information transfer chain (sensory and visual rhodopsins) or energy transduction which drives the electrogenic movement of ions across the membrane (ion-motive rhodopsins). Rhodopsins with these functions occur in bacteria and in higher organisms; from an evolutionary standpoint they are not related to one another. Nevertheless, all of these proteins are remarkably similar and form a distinct family.

  12. Engineering structure and function using thermoresponsive biopolymers.

    Science.gov (United States)

    Pastuszka, Martha K; MacKay, J Andrew

    2016-01-01

    Self-assembly enables exquisite control at the smallest scale and generates order among macromolecular-building blocks that remain too small to be manipulated individually. Environmental cues, such as heating, can trigger the organization of these materials from individual molecules to multipartixcle assemblies with a variety of compositions and functions. Synthetic as well as biological polymers have been engineered for these purposes; however, biological strategies can offer unparalleled control over the composition of these macromolecular-building blocks. Biologic polymers are macromolecules composed of monomeric units that can be precisely tailored at the genetic level; furthermore, they can often utilize endogenous biodegradation pathways, which may enhance their potential clinical applications. DNA (nucleotides), polysaccharides (carbohydrates), and proteins (amino acids) have all been engineered to self-assemble into nanostructures in response to a change in temperature. This focus article reviews the growing body of literature exploring temperature-dependent nano-assembly of these biological macromolecules, summarizes some of their physical properties, and discusses future directions.

  13. Nucleus-Dependent Valence-Space Approach to Nuclear Structure

    Science.gov (United States)

    Stroberg, S. R.; Calci, A.; Hergert, H.; Holt, J. D.; Bogner, S. K.; Roth, R.; Schwenk, A.

    2017-01-01

    We present a nucleus-dependent valence-space approach for calculating ground and excited states of nuclei, which generalizes the shell-model in-medium similarity renormalization group to an ensemble reference with fractionally filled orbitals. Because the ensemble is used only as a reference, and not to represent physical states, no symmetry restoration is required. This allows us to capture three-nucleon (3 N ) forces among valence nucleons with a valence-space Hamiltonian specifically targeted to each nucleus of interest. Predicted ground-state energies from carbon through nickel agree with results of other large-space ab initio methods, generally to the 1% level. In addition, we show that this new approach is required in order to obtain convergence for nuclei in the upper p and s d shells. Finally, we address the 1+/3+ inversion problem in 22Na and 46V. This approach extends the reach of ab initio nuclear structure calculations to essentially all light- and medium-mass nuclei.

  14. Density-dependent prophylaxis and condition-dependent immune function in Lepidopteran larvae: a multivariate approach

    OpenAIRE

    Cotter, Sheena; Hails, R. S.; Cory, J S; Wilson, K.

    2004-01-01

    1. The risk of parasitism and infectious disease is expected to increase with population density as a consequence of positive density-dependent transmission rates. Therefore, species that encounter large fluctuations in population density are predicted to exhibit plasticity in their immune system, such that investment in costly immune defences is adjusted to match the probability of exposure to parasites and pathogens (i.e. density-dependent prophylaxis).

  15. Loop-length-dependent SVM prediction of domain linkers for high-throughput structural proteomics.

    Science.gov (United States)

    Ebina, Teppei; Toh, Hiroyuki; Kuroda, Yutaka

    2009-01-01

    The prediction of structural domains in novel protein sequences is becoming of practical importance. One important area of application is the development of computer-aided techniques for identifying, at a low cost, novel protein domain targets for large-scale functional and structural proteomics. Here, we report a loop-length-dependent support vector machine (SVM) prediction of domain linkers, which are loops separating two structural domains. (DLP-SVM is freely available at: http://www.tuat.ac.jp/ approximately domserv/cgi-bin/DLP-SVM.cgi.) We constructed three loop-length-dependent SVM predictors of domain linkers (SVM-All, SVM-Long and SVM-Short), and also built SVM-Joint, which combines the results of SVM-Short and SVM-Long into a single consolidated prediction. The performances of SVM-Joint were, in most aspects, the highest, with a sensitivity of 59.7% and a specificity of 43.6%, which indicated that the specificity and the sensitivity were improved by over 2 and 3% respectively, when loop-length-dependent characteristics were taken into account. Furthermore, the sensitivity and specificity of SVM-Joint were, respectively, 37.6 and 17.4% higher than those of a random guess, and also superior to those of previously reported domain linker predictors. These results indicate that SVMs can be used to predict domain linkers, and that loop-length-dependent characteristics are useful for improving SVM prediction performances.

  16. Covariant density functional theory: Reexamining the structure of superheavy nuclei

    CERN Document Server

    Agbemava, S E; Nakatsukasa, T; Ring, P

    2015-01-01

    A systematic investigation of even-even superheavy elements in the region of proton numbers $100 \\leq Z \\leq 130$ and in the region of neutron numbers from the proton-drip line up to neutron number $N=196$ is presented. For this study we use five most up-to-date covariant energy density functionals of different types, with a non-linear meson coupling, with density dependent meson couplings, and with density-dependent zero-range interactions. Pairing correlations are treated within relativistic Hartree-Bogoliubov (RHB) theory based on an effective separable particle-particle interaction of finite range and deformation effects are taken into account. This allows us to assess the spread of theoretical predictions within the present covariant models for the binding energies, deformation parameters, shell structures and $\\alpha$-decay half-lives. Contrary to the previous studies in covariant density functional theory, it was found that the impact of $N=172$ spherical shell gap on the structure of superheavy elemen...

  17. Hantaviral proteins: structure, functions and role in hantavirus infection

    Directory of Open Access Journals (Sweden)

    Musalwa eMuyangwa

    2015-11-01

    Full Text Available Hantaviruses are the members of the family Bunyaviridae that are naturally maintained in the populations of small mammals, mostly rodents. Most of these viruses can easily infect humans through contact with aerosols or dust generated by contaminated animal waste products. Depending on the particular hantavirus involved, human infection could result in either Hemorrhagic Fever with Renal Syndrome (HFRS or in Hantavirus Cardiopulmonary Syndrome (HCPS. In the past few years, clinical cases of the hantavirus caused diseases have been on the rise. Understanding structure of the hantavirus genome and the functions of the key viral proteins is critical for the therapeutic agents’ research. This paper gives a brief overview of the current knowledge on the structure and properties of the hantavirus nucleoprotein and the glycoproteins.

  18. Structural Analysis of Monomeric RNA-Dependent Polymerases: Evolutionary and Therapeutic Implications.

    Directory of Open Access Journals (Sweden)

    Rodrigo Jácome

    Full Text Available The crystal structures of monomeric RNA-dependent RNA polymerases and reverse transcriptases of more than 20 different viruses are available in the Protein Data Bank. They all share the characteristic right-hand shape of DNA- and RNA polymerases formed by the fingers, palm and thumb subdomains, and, in many cases, "fingertips" that extend from the fingers towards the thumb subdomain, giving the viral enzyme a closed right-hand appearance. Six conserved structural motifs that contain key residues for the proper functioning of the enzyme have been identified in all these RNA-dependent polymerases. These enzymes share a two divalent metal-ion mechanism of polymerization in which two conserved aspartate residues coordinate the interactions with the metal ions to catalyze the nucleotidyl transfer reaction. The recent availability of crystal structures of polymerases of the Orthomyxoviridae and Bunyaviridae families allowed us to make pairwise comparisons of the tertiary structures of polymerases belonging to the four main RNA viral groups, which has led to a phylogenetic tree in which single-stranded negative RNA viral polymerases have been included for the first time. This has also allowed us to use a homology-based structural prediction approach to develop a general three-dimensional model of the Ebola virus RNA-dependent RNA polymerase. Our model includes several of the conserved structural motifs and residues described in other viral RNA-dependent RNA polymerases that define the catalytic and highly conserved palm subdomain, as well as portions of the fingers and thumb subdomains. The results presented here help to understand the current use and apparent success of antivirals, i.e. Brincidofovir, Lamivudine and Favipiravir, originally aimed at other types of polymerases, to counteract the Ebola virus infection.

  19. Temperature dependent electrical characteristics of Zn/ZnSe/n-GaAs/In structure

    Science.gov (United States)

    Sağlam, M.; Güzeldir, B.

    2016-04-01

    We have reported a study of the I-V characteristics of Zn/ZnSe/n-GaAs/In sandwich structure in a wide temperature range of 80-300 K by a step of 20 K, which are prepared by Successive Ionic Layer Adsorption and Reaction (SILAR) method. The main electrical parameters, such as ideality factor and zero-bias barrier height determined from the forward bias I-V characteristics were found strongly depend on temperature and when the increased, the n decreased with increasing temperature. The ideality factor and barrier height values as a function of the sample temperature have been attributed to the presence of the lateral inhomogeneities of the barrier height. Furthermore, the series resistance have been calculated from the I-V measurements as a function of temperature dependent.

  20. The influence of gravity on structure and function of animals

    Science.gov (United States)

    Ross, M. D.

    1984-01-01

    Gravity is the only environmental parameter that has remained constant during the period of evolution of living matter on earth. Thus, it must have been a major force in shaping living things. The influence of gravitational loading on evolution of the vertebrate skeleton is well recognized, and scale effects have been studied. This paper, however, considers in addition four pivotal events in early evolution that would seem to have been significant for the later success and diversifcation of animal life. These are evolution of the cytoskeleton, cell motility (flagellae and cilia), gravity detecting devices (accelerometers), and biomineralization. All are functionally calcium dependent in eukaryotes and all occurred or were foreshadowed in prokaryotes. A major question is why calcium was selected as an ion of great importance to the structure and function of living matter; another is whether gravity played a role in its selection.

  1. Objective function for municipal heat supply systems’ structural optimization

    Directory of Open Access Journals (Sweden)

    Sergiy V. Babich

    2015-03-01

    Full Text Available Modern heat supply systems in urban areas have the potential to heat supply cost reduction when using various alternative thermal energy sources. Availability of possible alternatives allows to select the source that generates a cheaper heat. At that arises the question of expressing such different sources’ characteristics as capital cost, reliability and efficiency in the consistent measurement units. This paper proposes an objective function representing all the factors affecting the thermal energy final cost in monetary units. It is shown that depending on external factors the range of prime cost for heat from various sources does vary considerably. Expected is that the proposed objective function application for managing the heat supply systems structure in urban areas will significantly reduce the operating costs.

  2. Galaxy And Mass Assembly (GAMA): the wavelength dependence of galaxy structure versus redshift and luminosity

    CERN Document Server

    Kennedy, Rebecca; Baldry, Ivan; Holwerda, Boris Häußler Benne W; Hopkins, Andrew M; Kelvin, Lee S; Lange, Rebecca; Moffett, Amanda J; Popescu, Cristina C; Taylor, Edward N; Tuffs, Richard J; Vika, Marina; Vulcani, Benedetta

    2015-01-01

    We study how the sizes and radial profiles of galaxies vary with wavelength, by fitting S\\'ersic functions simultaneously to imaging in nine optical and near-infrared bands. To quantify the wavelength dependence of effective radius we use the ratio, $\\mathcal{R}$, of measurements in two restframe bands. The dependence of S\\'ersic index on wavelength, $\\mathcal{N}$, is computed correspondingly. Vulcani et al. (2014) have demonstrated that different galaxy populations present sharply contrasting behaviour in terms of $\\mathcal{R}$ and $\\mathcal{N}$. Here we study the luminosity dependence of this result. We find that at higher luminosities, early-type galaxies display a more substantial decrease in effective radius with wavelength, whereas late-types present a more pronounced increase in S\\'ersic index. The structural contrast between types thus increases with luminosity. By considering samples at different redshifts, we demonstrate that lower data quality reduces the apparent difference between the main galaxy...

  3. Functional proteomics on zinc-dependent metalloproteinases using inhibitor probes

    NARCIS (Netherlands)

    Klein, Theo; Geurink, Paul P.; Overkleeft, Hermen S.; Kauffman, Henk K.; Bischoff, Rainer

    2009-01-01

    Metzincins ore a family of zinc(II)-dependent metolloproteinases with well known members such as the matrix metalloproteinases (MMPs) and A disintegrin and metalloproteinases (ADAMs). Metzincins are largely responsible for the modulation and regulation of the extracellular matrix by proteolytic degr

  4. Functional proteomics on zinc-dependent metalloproteinases using inhibitor probes

    NARCIS (Netherlands)

    Klein, Theo; Geurink, Paul P.; Overkleeft, Hermen S.; Kauffman, Henk K.; Bischoff, Rainer

    Metzincins ore a family of zinc(II)-dependent metolloproteinases with well known members such as the matrix metalloproteinases (MMPs) and A disintegrin and metalloproteinases (ADAMs). Metzincins are largely responsible for the modulation and regulation of the extracellular matrix by proteolytic

  5. Statistical mechanics-based method to extract atomic distance-dependent potentials from protein structures.

    Science.gov (United States)

    Huang, Sheng-You; Zou, Xiaoqin

    2011-09-01

    In this study, we have developed a statistical mechanics-based iterative method to extract statistical atomic interaction potentials from known, nonredundant protein structures. Our method circumvents the long-standing reference state problem in deriving traditional knowledge-based scoring functions, by using rapid iterations through a physical, global convergence function. The rapid convergence of this physics-based method, unlike other parameter optimization methods, warrants the feasibility of deriving distance-dependent, all-atom statistical potentials to keep the scoring accuracy. The derived potentials, referred to as ITScore/Pro, have been validated using three diverse benchmarks: the high-resolution decoy set, the AMBER benchmark decoy set, and the CASP8 decoy set. Significant improvement in performance has been achieved. Finally, comparisons between the potentials of our model and potentials of a knowledge-based scoring function with a randomized reference state have revealed the reason for the better performance of our scoring function, which could provide useful insight into the development of other physical scoring functions. The potentials developed in this study are generally applicable for structural selection in protein structure prediction.

  6. Comparative metabolomics and structural characterizations illuminate colibactin pathway-dependent small molecules.

    Science.gov (United States)

    Vizcaino, Maria I; Engel, Philipp; Trautman, Eric; Crawford, Jason M

    2014-07-02

    The gene cluster responsible for synthesis of the unknown molecule "colibactin" has been identified in mutualistic and pathogenic Escherichia coli. The pathway endows its producer with a long-term persistence phenotype in the human bowel, a probiotic activity used in the treatment of ulcerative colitis, and a carcinogenic activity under host inflammatory conditions. To date, functional small molecules from this pathway have not been reported. Here we implemented a comparative metabolomics and targeted structural network analyses approach to identify a catalog of small molecules dependent on the colibactin pathway from the meningitis isolate E. coli IHE3034 and the probiotic E. coli Nissle 1917. The structures of 10 pathway-dependent small molecules are proposed based on structural characterizations and network relationships. The network will provide a roadmap for the structural and functional elucidation of a variety of other small molecules encoded by the pathway. From the characterized small molecule set, in vitro bacterial growth inhibitory and mammalian CNS receptor antagonist activities are presented.

  7. OXPHOS-Dependent Cells Identify Environmental Disruptors of Mitochondrial Function

    Science.gov (United States)

    Mitochondrial dysfunction is associated with numerous chronic diseases including metabolic syndrome. Environmental chemicals can impair mitochondrial function through numerous mechanisms such as membrane disruption, complex inhibition and electron transport chain uncoupling. Curr...

  8. Spin-Dependent Structure Function $g_1$ at Small x

    CERN Document Server

    Ermolaev, B I; Troyan, S I

    2004-01-01

    Accounting for double-logarithms of x and running QCD coupling leads to expressions for both the non-singlet and singlet components of $g_1$. These expressions manifest the Regge asymptotics when x ->0 and differ considerably from the DGLAP expressions at small values of x.

  9. Shape-dependent global deformation modes of large protein structures

    Science.gov (United States)

    Miloshevsky, Gennady V.; Hassanein, Ahmed; Jordan, Peter C.

    2010-05-01

    Conformational changes are central to the functioning of pore-forming proteins that open and close their molecular gates in response to external stimuli such as pH, ionic strength, membrane voltage or ligand binding. Normal mode analysis (NMA) is used to identify and characterize the slowest motions in the gA, KcsA, ClC-ec1, LacY and LeuT Aa proteins at the onset of gating. Global deformation modes of the essentially cylindrical gA, KcsA, LacY and LeuT Aa biomolecules are reminiscent of global twisting, transverse and longitudinal motions in a homogeneous elastic rod. The ClC-ec1 protein executes a splaying motion in the plane perpendicular to the lipid bilayer. These global collective deformations are determined by protein shape. New methods, all-atom Monte Carlo Normal Mode Following and its simplification using a rotation-translation of protein blocks (RTB), are described and applied to gain insight into the nature of gating transitions in gA and KcsA. These studies demonstrate the severe limitations of standard NMA in characterizing the structural rearrangements associated with gating transitions. Comparison of all-atom and RTB transition pathways in gA clearly illustrates the impact of the rigid protein block approximation and the need to include all degrees of freedom and their relaxation in computational studies of protein gating. The effects of atomic level structure, pH, hydrogen bonding and charged residues on the large-scale conformational changes associated with gating transitions are discussed.

  10. Transverse-momentum-dependent fragmentation functions in e+e- annihilation

    Science.gov (United States)

    Garzia, Isabella; Giordano, Francesca

    2016-06-01

    Fragmentation functions are non-perturbative functions used to describe the formation of colorless, observable hadrons starting from a colored, partonic initial state. The knowledge of these functions are based on the experimental data, and a good parameterization of the fragmentation processes can shed light on the confining aspect of QCD, and are also a key ingredient in accessing nucleon parton distribution functions in semi-inclusive deep inelastic scattering and proton-proton collisions. In the last decade, a strong interest has risen about the transverse-momentum-dependent (TMD) fragmentation functions, which can be used as tools to probe the 3D-structure of nucleons, and to investigate the Q2 evolution of TMD objects. In this review we will summarize the existing light-quarks fragmentation related measurements from the BaBar, Belle, and BESIII e + e - experiments; in particular, we will focus on the polarized TMD Collins fragmentation functions, emerging from correlations between the transverse polarization of the fragmenting parton and the direction of the resulting hadrons.

  11. Structure-based inference of molecular functions of proteins of unknown function from Berkeley Structural Genomics Center

    Energy Technology Data Exchange (ETDEWEB)

    Kim, Sung-Hou; Shin, Dong Hae; Hou, Jingtong; Chandonia, John-Marc; Das, Debanu; Choi, In-Geol; Kim, Rosalind; Kim, Sung-Hou

    2007-09-02

    Advances in sequence genomics have resulted in an accumulation of a huge number of protein sequences derived from genome sequences. However, the functions of a large portion of them cannot be inferred based on the current methods of sequence homology detection to proteins of known functions. Three-dimensional structure can have an important impact in providing inference of molecular function (physical and chemical function) of a protein of unknown function. Structural genomics centers worldwide have been determining many 3-D structures of the proteins of unknown functions, and possible molecular functions of them have been inferred based on their structures. Combined with bioinformatics and enzymatic assay tools, the successful acceleration of the process of protein structure determination through high throughput pipelines enables the rapid functional annotation of a large fraction of hypothetical proteins. We present a brief summary of the process we used at the Berkeley Structural Genomics Center to infer molecular functions of proteins of unknown function.

  12. Structure-based inference of molecular functions of proteins of unknown function from Berkeley Structural Genomics Center.

    Science.gov (United States)

    Shin, Dong Hae; Hou, Jingtong; Chandonia, John-Marc; Das, Debanu; Choi, In-Geol; Kim, Rosalind; Kim, Sung-Hou

    2007-09-01

    Advances in sequence genomics have resulted in an accumulation of a huge number of protein sequences derived from genome sequences. However, the functions of a large portion of them cannot be inferred based on the current methods of sequence homology detection to proteins of known functions. Three-dimensional structure can have an important impact in providing inference of molecular function (physical and chemical function) of a protein of unknown function. Structural genomics centers worldwide have been determining many 3-D structures of the proteins of unknown functions, and possible molecular functions of them have been inferred based on their structures. Combined with bioinformatics and enzymatic assay tools, the successful acceleration of the process of protein structure determination through high throughput pipelines enables the rapid functional annotation of a large fraction of hypothetical proteins. We present a brief summary of the process we used at the Berkeley Structural Genomics Center to infer molecular functions of proteins of unknown function.

  13. Classical Solutions of Path-Dependent PDEs and Functional Forward-Backward Stochastic Systems

    Directory of Open Access Journals (Sweden)

    Shaolin Ji

    2013-01-01

    Full Text Available In this paper we study the relationship between functional forward-backward stochastic systems and path-dependent PDEs. In the framework of functional Itô calculus, we introduce a path-dependent PDE and prove that its solution is uniquely determined by a functional forward-backward stochastic system.

  14. Neisserial surface lipoproteins: structure, function and biogenesis.

    Science.gov (United States)

    Hooda, Yogesh; Shin, Hyejin E; Bateman, Thomas J; Moraes, Trevor F

    2017-03-01

    The surface of many Gram-negative bacteria contains lipidated protein molecules referred to as surface lipoproteins or SLPs. SLPs play critical roles in host immune evasion, nutrient acquisition and regulation of the bacterial stress response. The focus of this review is on the SLPs present in Neisseria, a genus of bacteria that colonise the mucosal surfaces of animals. Neisseria contains two pathogens of medical interest, namely Neisseria meningitidis and N. gonorrhoeae. Several SLPs have been identified in Neisseria and their study has elucidated key strategies used by these pathogens to survive inside the human body. Herein, we focus on the identification, structure and function of SLPs that have been identified in Neisseria. We also survey the translocation pathways used by these SLPs to reach the cell surface. Specifically, we elaborate on the strategies used by neisserial SLPs to translocate across the outer membrane with an emphasis on Slam, a novel outer membrane protein that has been implicated in SLP biogenesis. Taken together, the study of SLPs in Neisseria illustrates the widespread roles played by this family of proteins in Gram-negative bacteria. © FEMS 2017. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

  15. Effects of Detrital Subsidies on Soft-Sediment Ecosystem Function Are Transient and Source-Dependent.

    Directory of Open Access Journals (Sweden)

    Rebecca V Gladstone-Gallagher

    Full Text Available Detrital subsidies from marine macrophytes are prevalent in temperate estuaries, and their role in structuring benthic macrofaunal communities is well documented, but the resulting impact on ecosystem function is not understood. We conducted a field experiment to test the effects of detrital decay on soft-sediment primary production, community metabolism and nutrient regeneration (measures of ecosystem function. Twenty four (2 m2 plots were established on an intertidal sandflat, to which we added 0 or 220 g DW m-2 of detritus from either mangroves (Avicennia marina, seagrass (Zostera muelleri, or kelp (Ecklonia radiata (n = 6 plots per treatment. Then, after 4, 17 and 46 d we measured ecosystem function, macrofaunal community structure and sediment properties. We hypothesized that (1 detrital decay would stimulate benthic primary production either by supplying nutrients to the benthic macrophytes, or by altering the macrofaunal community; and (2 ecosystem responses would depend on the stage and rate of macrophyte decay (a function of source. Avicennia detritus decayed the slowest with a half-life (t50 of 46 d, while Zostera and Ecklonia had t50 values of 28 and 2.6 d, respectively. However, ecosystem responses were not related to these differences. Instead, we found transient effects (up to 17 d of Avicennia and Ecklonia detritus on benthic primary production, where initially (4 d these detrital sources suppressed primary production, but after 17 d, primary production was stimulated in Avicennia plots relative to controls. Other ecosystem function response variables and the macrofaunal community composition were not altered by the addition of detritus, but did vary with time. By sampling ecosystem function temporally, we were able to capture the in situ transient effects of detrital subsidies on important benthic ecosystem functions.

  16. Calcium-dependent mitochondrial function and dysfunction in neurons.

    Science.gov (United States)

    Pivovarova, Natalia B; Andrews, S Brian

    2010-09-01

    Calcium is an extraordinarily versatile signaling ion, encoding cellular responses to a wide variety of external stimuli. In neurons, mitochondria can accumulate enormous amounts of calcium, with the consequence that mitochondrial calcium uptake, sequestration and release play pivotal roles in orchestrating calcium-dependent responses as diverse as gene transcription and cell death. In this review, we consider the basic chemistry of calcium as a 'sticky' cation, which leads to extremely high bound/free ratios, and discuss areas of current interest or controversy. Topics addressed include methodologies for measuring local intracellular calcium, mitochondrial calcium buffering and loading capacity, mitochondrially directed spatial calcium gradients, and the role of calcium overload-dependent mitochondrial dysfunction in glutamate-evoked excitotoxic injury and neurodegeneration. Finally, we consider the relationship between delayed calcium de-regulation, the mitochondrial permeability transition and the generation of reactive oxygen species, and propose a unified view of the 'source specificity' and 'calcium overload' models of N-methyl-d-aspartate (NMDA) receptor-dependent excitotoxicity. Non-NMDA receptor mechanisms of excitotoxicity are discussed briefly. Journal compilation © 2010 FEBS. No claim to original US government works.

  17. Nepheline structural and chemical dependence on melt composition

    Energy Technology Data Exchange (ETDEWEB)

    Marcial, José; Crum, Jarrod; Neill, Owen; McCloy, John

    2016-02-01

    Nepheline crystallizes upon slow-cooling in some melts concentrated in Na2O and Al2O3, which can result in a residual glass phase of low chemical durability. Nepheline can incorporate many components often found in high-level waste radioactive borosilicate glass, including glass network ions (e.g., Si, Al, Fe), alkali metals (e.g., Cs, K, Na, and possibly Li), alkaline-earth metals (e.g., Ba, Sr, Ca, Mg), and transition metals (e.g., Mn, and possibly Cr, Zn, Ni). When crystallized from melts of different compositions, nepheline chemistry varies as a function of starting glass composition. Five simulated high level nuclear waste borosilicate glasses shown to crystallize large fractions of nepheline on slow cooling, were selected for study. These melts constituted a range of Al2O3, B2O3, CaO, Na2O, K2O, Fe2O3, and SiO2 compositions. Compositional analyses of nepheline crystals in glass by electron probe micro-analysis (EPMA) indicate that boron is unlikely to be present in any significant concentration, if at all, in nepheline. Also, several models are presented for calculating the fraction of vacancies in the nepheline structure.

  18. The functional central limit theorem for strong near-epoch dependent random variables

    Institute of Scientific and Technical Information of China (English)

    QIU Jin; LIN Zhengyan

    2004-01-01

    The functional central limit theorem for strong near-epoch dependent sequences of random variables is proved.The conditions given improve on previous results in the literature concerning dependence and heterogeneity.

  19. Sound power radiation from a vibrating structure in terms of structure-dependent radiation modes

    Science.gov (United States)

    Ji, Lin; Bolton, J. Stuart

    2015-01-01

    As a good supplement of conventional acoustic radiation modes (a-modes), a set of so-called "structure-dependent radiation modes" (s-modes) is introduced to describe the sound power radiation from a vibrating structure. Differing from a-modes, s-modes are determined by not only the acoustic resistance matrix of the structure but also the frequency-independent normal modes of the structure. Such a new definition has the following main advantages over the conventional one: (1) it can reflect directly the influences of dynamic properties (e.g., boundary conditions) of the structures on its sound power radiation; (2) the number of s-modes generated is generally less than that of a-modes since the former depends on the number of structural modes involved in the vibration while the latter depends on the number of segmented elemental radiators of the structure, and consequently, the demand for large data storage can be greatly alleviated, especially for large structures and/or higher frequency vibrations; (3) the set of s-modes possesses a better convergence than that of a-modes because the higher ordered s-modes can decay more rapidly than the same ordered a-modes. Two baffled, finite, models, i.e., a simple beam and a thin plate, are employed to investigate numerically the acoustic properties of s-modes, and then compared with those of a-modes. It has been shown that the two sets of radiation modes share a very similar frequency-dependent behavior in that the radiation efficiency falls off very rapidly with increasing mode order at low frequency range (typically with kl<1). Meanwhile, the number of s-modes required to describe the total sound power radiation is found to be the same as that of a-modes. Consequently, an appropriate truncation of a-modes can be achieved by using the number of vibrational modes involved. Nevertheless, the odd-ordered (even-ordered) s-modes are found only associated with the odd-numbered (even-ordered) structural modes. In case of only few

  20. The Morphological Type Dependence of K-band Luminosity Functions

    CERN Document Server

    Devereux, Nick; Willner, S P; Ashby, M L N; Willmer, C N A

    2009-01-01

    Differential 2.2um (K-band) luminosity functions are presented for a complete sample of 1570 nearby Vgsr < 3000 km/s, where Vgsr is the velocity measured with respect to the Galactic standard of rest), bright (K < 10 mag), galaxies segregated by visible morphology. The K-band luminosity function for late-type spirals follows a power law that rises towards low luminosities whereas the K-band luminosity functions for ellipticals, lenticulars and bulge-dominated spirals are peaked with a fall off at both high and low luminosities. However, each morphological type (E, S0, S0/a-Sab, Sb-Sbc, Sc-Scd) contributes approximately equally to the overall K-band luminosity density in the local universe, and by inference, the stellar mass density as well.

  1. Radiation Feedback, Fragmentation, and the Environmental Dependence of the Initial Mass Function

    CERN Document Server

    Krumholz, Mark R; Klein, Richard I; McKee, Christopher F

    2010-01-01

    The fragmentation of star-forming interstellar clouds, and the resulting stellar initial mass function (IMF), is determined largely by the temperature structure of the collapsing gas. Since radiation feedback from embedded stars can modify this as collapse proceeds, feedback plays an important role in determining the IMF. However, the effects and importance of radiative heating are likely to depend strongly on the surface density of the collapsing clouds, which determines both their effectiveness at trapping radiation and the accretion luminosities of the stars forming within them. In this paper we report a suite of adaptive mesh refinement radiation-hydrodynamic simulations using the ORION code in which we isolate the effect of column density on fragmentation by following the collapse of clouds of varying column density while holding the mass, initial density and velocity structure, and initial virial ratio fixed. We find that radiation does not significantly modify the overall star formation rate or efficie...

  2. Ligand binding-dependent functions of the lipocalin NLaz: an in vivo study in Drosophila.

    Science.gov (United States)

    Ruiz, Mario; Ganfornina, Maria D; Correnti, Colin; Strong, Roland K; Sanchez, Diego

    2014-04-01

    Lipocalins are small extracellular proteins mostly described as lipid carriers. The Drosophila lipocalin NLaz (neural Lazarillo) modulates the IIS pathway and regulates longevity, stress resistance, and behavior. Here, we test whether a native hydrophobic pocket structure is required for NLaz to perform its functions. We use a point mutation altering the binding pocket (NLaz(L130R)) and control mutations outside NLaz binding pocket. Tryptophan fluorescence titration reveals that NLaz(L130R) loses its ability to bind ergosterol and the pheromone 7(z)-tricosene but retains retinoic acid binding. Using site-directed transgenesis in Drosophila, we test the functionality of the ligand binding-altered lipocalin at the organism level. NLaz-dependent life span reduction, oxidative stress and starvation sensitivity, aging markers accumulation, and deficient courtship are rescued by overexpression of NLaz(WT), but not of NLaz(L130R). Transcriptional responses to aging and oxidative stress show a large set of age-responsive genes dependent on the integrity of NLaz binding pocket. Inhibition of IIS activity and modulation of oxidative stress and infection-responsive genes are binding pocket-dependent processes. Control of energy metabolites on starvation appears to be, however, insensitive to the modification of the NLaz binding pocket.

  3. Optoelectronic Properties of Carbon Nanorings: Excitonic Effects from Time-Dependent Density Functional Theory

    CERN Document Server

    Wong, Bryan M

    2009-01-01

    The electronic structure and size-scaling of optoelectronic properties in cycloparaphenylene carbon nanorings are investigated using time-dependent density functional theory (TDDFT). The TDDFT calculations on these molecular nanostructures indicate that the lowest excitation energy surprisingly becomes larger as the carbon nanoring size is increased, in contradiction with typical quantum confinement effects. In order to understand their unusual electronic properties, I performed an extensive investigation of excitonic effects by analyzing electron-hole transition density matrices and exciton binding energies as a function of size in these nanoring systems. The transition density matrices allow a global view of electronic coherence during an electronic excitation, and the exciton binding energies give a quantitative measure of electron-hole interaction energies in the nanorings. Based on overall trends in exciton binding energies and their spatial delocalization, I find that excitonic effects play a vital role...

  4. Problem Decomposition Method to Compute an Optimal Cover for a Set of Functional Dependencies

    Directory of Open Access Journals (Sweden)

    Vitalie COTELEA

    2011-12-01

    Full Text Available The paper proposes a problem decomposition method for building optimal cover for a set of functional dependencies to decrease the solving time. At the beginning, the paper includes an overview of the covers of functional dependencies. There are considered definitions and properties of non redundant covers for sets of functional dependencies, reduced and canonical covers as well as equivalence classes of functional dependencies, minimum and optimal covers. Then, a theoretical tool for inference of functional dependencies is proposed, which possesses the uniqueness property. And finally, the set of attributes of the relational schema is divided into equivalence classes of attributes that will serve as the basis for building optimal cover for a set of functional dependencies.

  5. Tuning of the excited state properties of phenylenevinylene oligomers : A time-dependent density functional theory study

    NARCIS (Netherlands)

    Grozema, FC; Telesca, R; Snijders, JG; Siebbeles, LDA

    2003-01-01

    This paper discusses a time-dependent density functional theory study of the effect of molecular structure on the excited state polarizability of conjugated molecules. A short phenylenevinylene oligomer containing three phenyl rings (PV2, distyryl benzene) is taken as a model system. Introduction of

  6. Time-dependent current-density-functional theory for metals

    NARCIS (Netherlands)

    Romaniello, Pina

    2006-01-01

    Materials have been used throughout history for their structural properties, e.g. ductility, elasticity, hardness etc., and later also for their physical properties, i.e., for their characteristic response to external perturbances. These last properties have been investigated in this thesis by using

  7. Left temporal lobe structural and functional abnormality underlying auditory hallucinations

    Directory of Open Access Journals (Sweden)

    Kenneth Hugdahl

    2009-05-01

    Full Text Available In this article, we review recent findings from our laboratory that auditory hallucinations in schizophrenia are internally generated speech mis-representations lateralized to the left superior temporal gyrus and sulcus. Such experiences are, moreover, not cognitively suppressed due to enhanced attention to the voices and failure of fronto-parietal executive control functions. An overview of diagnostic questionnaires for scoring of symptoms is presented, together with a review of behavioural, structural and functional MRI data. Functional imaging data have either shown increased or decreased activation depending on whether patients have been presented an external stimulus or not during scanning. Structural imaging data have shown reduction of grey matter density and volume in the same areas in the temporal lobe. The behavioral and neuroimaging findings are moreover hypothesized to be related to glutamate hypofunction in schizophrenia. We propose a model for the understanding of auditory hallucinations that trace the origin of auditory hallucinations to uncontrolled neuronal firing in the speech areas in the left temporal lobe, which is not suppressed by volitional cognitive control processes, due to dysfunctional fronto-parietal executive cortical networks.

  8. Overexpression of neurofilament H disrupts normal cell structure and function

    Science.gov (United States)

    Szebenyi, Gyorgyi; Smith, George M.; Li, Ping; Brady, Scott T.

    2002-01-01

    Studying exogenously expressed tagged proteins in live cells has become a standard technique for evaluating protein distribution and function. Typically, expression levels of experimentally introduced proteins are not regulated, and high levels are often preferred to facilitate detection. However, overexpression of many proteins leads to mislocalization and pathologies. Therefore, for normative studies, moderate levels of expression may be more suitable. To understand better the dynamics of intermediate filament formation, transport, and stability in a healthy, living cell, we inserted neurofilament heavy chain (NFH)-green fluorescent protein (GFP) fusion constructs in adenoviral vectors with tetracycline (tet)-regulated promoters. This system allows for turning on or off the synthesis of NFH-GFP at a selected time, for a defined period, in a dose-dependent manner. We used this inducible system for live cell imaging of changes in filament structure and cell shape, motility, and transport associated with increasing NFH-GFP expression. Cells with low to intermediate levels of NFH-GFP were structurally and functionally similar to neighboring, nonexpressing cells. In contrast, overexpression led to pathological alterations in both filament organization and cell function. Copyright 2002 Wiley-Liss, Inc.

  9. A Phase-Dependent Hypothesis for Locomotor Functions of Human Foot Complex

    Institute of Scientific and Technical Information of China (English)

    Lei Ren; David Howard; Lu-quan Ren; Chris Nester; Li-mei Tian

    2008-01-01

    The human foot is a very complex structure comprising numerous bones, muscles, ligaments and synovial joints. As the only component in contact with the ground, the foot complex delivers a variety of biomechanical functions during human locomotion, e.g. body support and propulsion, stability maintenance and impact absorption. These need the human foot to be rigid and damped to transmit ground reaction forces to the upper body and maintain body stability, and also to be compliant and resilient to moderate risky impacts and save energy. How does the human foot achieve these apparent conflicting functions? In this study, we propose a phase-dependent hypothesis for the overall locomotor functions of the human foot complex based on in-vivo measurements of human natural gait and simulation results of a mathematical foot model. We propse that foot functions are highly dependent on gait phase, which is a major characteristics of human locomotion. In early stance just after heel strike,the foot mainly works as a shock absorber by moderating high impacts using the viscouselastic heel pad in both. vertical and horizontal directions. In mid-stance phase(~80% of stance phase), the foot complex can be considered as a springy rocker,reserving external mechanical work using the foot arch whilst moving ground contact point forward along a curved path to maintain body stability. In late stance after heel off, the foot complex mainly serves as a force modulator like a gear box,modulating effective mechanical advantages of ankle plantiflexor muscles using metatarsal-phalangeal joints. A sound understanding of how diverse functions are implemented in a simple foot segment during human locomotion might be useful to gain insight into the overall foot locomotor functions and hence to facilitate clinical diagnosis, rehabilitation product design and humanoid robot development.

  10. Bounds on Transverse Momentum Dependent Distribution and Fragmentation Functions

    Science.gov (United States)

    Bacchetta, A.; Boglione, M.; Henneman, A.; Mulders, P. J.

    2000-07-01

    We give bounds on the distribution and fragmentation functions that appear at leading order in deep inelastic one-particle inclusive leptoproduction or in Drell-Yan processes. These bounds simply follow from positivity of the defining matrix elements and are an important guidance in estimating the magnitude of the azimuthal and spin asymmetries in these processes.

  11. Bounds on transverse momentum dependent distribution and fragmentation functions

    CERN Document Server

    Bacchetta, A; Henneman, A A; Mulders, P J

    2000-01-01

    We give bounds on the distribution and fragmentation functions that appear at leading order in deep inelastic 1-particle inclusive leptoproduction or in Drell-Yan processes. These bounds simply follow from positivity of the defining matrix elements and are an important guidance in estimating the magnitude of the azimuthal and spin asymmetries in these processes.

  12. Lipid dependence of ABC transporter localization and function

    NARCIS (Netherlands)

    Klappe, Karin; Hummel, Ina; Hoekstra, Dick; Kok, Jan Willem

    2009-01-01

    Lipid rafts have been implicated in many cellular functions, including protein and lipid transport and signal transduction. ATP-binding cassette (ABC) transporters have also been localized in these membrane domains. In this review the evidence for this specific localization will be evaluated and dis

  13. Lipid dependence of ABC transporter localization and function

    NARCIS (Netherlands)

    Klappe, Karin; Hummel, Ina; Hoekstra, Dick; Kok, Jan Willem

    2009-01-01

    Lipid rafts have been implicated in many cellular functions, including protein and lipid transport and signal transduction. ATP-binding cassette (ABC) transporters have also been localized in these membrane domains. In this review the evidence for this specific localization will be evaluated and dis

  14. Lipid dependence of ABC transporter localization and function

    NARCIS (Netherlands)

    Klappe, Karin; Hummel, Ina; Hoekstra, Dick; Kok, Jan Willem

    2009-01-01

    Lipid rafts have been implicated in many cellular functions, including protein and lipid transport and signal transduction. ATP-binding cassette (ABC) transporters have also been localized in these membrane domains. In this review the evidence for this specific localization will be evaluated and

  15. Density-dependence of functional spiking networks in vitro

    Energy Technology Data Exchange (ETDEWEB)

    Ham, Michael I [Los Alamos National Laboratory; Gintautuas, Vadas [Los Alamos National Laboratory; Rodriguez, Marko A [Los Alamos National Laboratory; Bettencourt, Luis M A [Los Alamos National Laboratory; Bennett, Ryan [UNIV OF NORTH TEXAS; Santa Maria, Cara L [UNIV OF NORTH TEXAS

    2008-01-01

    During development, the mammalian brain differentiates into specialized regions with unique functional abilities. While many factors contribute to this functional specialization, we explore the effect neuronal density can have on neuronal interactions. Two types of networks, dense (50,000 neurons and glia support cells) and sparse (12,000 neurons and glia support cells), are studied. A competitive first response model is applied to construct activation graphs that represent pairwise neuronal interactions. By observing the evolution of these graphs during development in vitro we observe that dense networks form activation connections earlier than sparse networks, and that link-!llltropy analysis of the resulting dense activation graphs reveals that balanced directional connections dominate. Information theoretic measures reveal in addition that early functional information interactions (of order 3) are synergetic in both dense and sparse networks. However, during development in vitro, such interactions become redundant in dense, but not sparse networks. Large values of activation graph link-entropy correlate strongly with redundant ensembles observed in the dense networks. Results demonstrate differences between dense and sparse networks in terms of informational groups, pairwise relationships, and activation graphs. These differences suggest that variations in cell density may result in different functional specialization of nervous system tissue also in vivo.

  16. The Dependency Structure of Coordinate Phrases: A Corpus Approach

    Science.gov (United States)

    Temperley, David

    2005-01-01

    Hudson (1990) proposes that each conjunct in a coordinate phrase forms dependency relations with heads or dependents outside the coordinate phrase (the "multi-head" view). This proposal is tested through corpus analysis of Wall Street Journal text. For right-branching constituents (such as direct-object NPs), a short-long preference for conjunct…

  17. Axon extension in the fast and slow lanes: substratum-dependent engagement of myosin II functions.

    Science.gov (United States)

    Ketschek, Andrea R; Jones, Steven L; Gallo, Gianluca

    2007-09-01

    Axon extension involves the coordinated regulation of the neuronal cytoskeleton. Actin filaments drive protrusion of filopodia and lamellipodia while microtubules invade the growth cone, thereby providing structural support for the nascent axon. Furthermore, in order for axons to extend the growth cone must attach to the substratum. Previous work indicates that myosin II activity inhibits the advance of microtubules into the periphery of growth cones, and myosin II has also been implicated in mediating integrin-dependent cell attachment. However, it is not clear how the functions of myosin II in regulating substratum attachment and microtubule advance are integrated during axon extension. We report that inhibition of myosin II function decreases the rate of axon extension on laminin, but surprisingly promotes extension rate on polylysine. The differential effects of myosin II inhibition on axon extension rate are attributable to myosin II having the primary function of mediating substratum attachment on laminin, but not on polylysine. Conversely, on polylysine the primary function of myosin II is to inhibit microtubule advance into growth cones. Thus, the substratum determines the role of myosin II in axon extension by controlling the functions of myosin II that contribute to extension.

  18. Renormalization Scheme Dependence and the Renormalization Group Beta Function

    OpenAIRE

    Chishtie, F. A.; McKeon, D. G. C.

    2016-01-01

    The renormalization that relates a coupling "a" associated with a distinct renormalization group beta function in a given theory is considered. Dimensional regularization and mass independent renormalization schemes are used in this discussion. It is shown how the renormalization $a^*=a+x_2a^2$ is related to a change in the mass scale $\\mu$ that is induced by renormalization. It is argued that the infrared fixed point is to be a determined in a renormalization scheme in which the series expan...

  19. Size dependence of complex refractive index function of growing nanoparticles

    Science.gov (United States)

    Eremin, A.; Gurentsov, E.; Popova, E.; Priemchenko, K.

    2011-08-01

    The evidence of the change of the complex refractive index function E( m) of carbon and iron nanoparticles as a function of their size was found from two-color time-resolved laser-induced incandescence (TiRe-LII) measurements. Growing carbon particles were observed from acetylene pyrolysis behind a shock wave and iron particles were synthesized by pulse Kr-F excimer laser photo-dissociation of Fe(CO)5. The magnitudes of refractive index function were found through the fitting of two independently measured values of particle heat up temperature, determined by two-color pyrometry and from the known energy of the laser pulse and the E( m) variation. Small carbon particles of about 1-14 nm in diameter had a low value of E( m)˜0.05-0.07, which tends to increase up to a value of 0.2-0.25 during particle growth up to 20 nm. Similar behavior for iron particles resulted in E( m) rise from ˜0.1 for particles 1-3 nm in diameter up to ˜0.2 for particles >12 nm in diameter.

  20. Structured Connectivity Shapes Microcircuit Function in the Prefrontal Cortex.

    Directory of Open Access Journals (Sweden)

    Stefanos Stefanou - Stamatiadis

    2014-03-01

    Full Text Available The application of new experimental techniques in vivo has shed light on the wiring diagram of cortical networks, revealing the highly non-random connectivity of pyramidal neurons. This structured connectivity is characterized by distance-dependent formation of neuronal clusters and over-represented structural ‘motifs’ (Perin 2011, Ko 2013. In the prefrontal cortex (PFC in particular, pyramidal neurons were shown to form hyper-clusters, compared to other sensory regions. Yet, very little is known about the functional properties of these microcircuits and their role in Persistent Activity (PA, a well known function of the PFC. PA is the spiking activity that persists beyond the stimulus presentation and is considered to be the cellular correlate of working memory. Although, PA was traditionally assumed to emerge in large scale networks, recent in vivo data in the PFC suggest that small microcircuits mediate its functional output (Durstwitz, 2010. Motivated by the above findings this work probes the role of realistic connectivity constraints in shaping the functional output of PFC, through simulations of biophysically and morphologically detailed PFC circuits. Towards this goal, we used a compartmental modeling approach, whereby layer 5 PFC pyramidal neurons are modeled with detailed morphological and biophysical properties. Three different types of interneurons were also implemented; the Fast-spiking (FS, Regular-spiking (RS, and Irregular-spiking (IS. These were biophysically detailed, yet morphologically simplified. Microcircuits consisted of 75 pyramidal neurons, 13 FS, 6 RS and 6 IS. Properties (location /number /amplitude /kinetics of both excitatory and inhibitory synapses were extensively validated against experimental data. The network model was used to investigate the effect of connectivity on the emergence of persistent activity. Two different connectivity profiles of pyramidal cells were implemented: one highly non

  1. Unveiling Dimensionality Dependence of Glassy Dynamics: 2D Infinite Fluctuation Eclipses Inherent Structural Relaxation

    Science.gov (United States)

    Shiba, Hayato; Yamada, Yasunori; Kawasaki, Takeshi; Kim, Kang

    2016-12-01

    By using large-scale molecular dynamics simulations, the dynamics of two-dimensional (2D) supercooled liquids turns out to be dependent on the system size, while the size dependence is not pronounced in three-dimensional (3D) systems. It is demonstrated that the strong system-size effect in 2D amorphous systems originates from the enhanced fluctuations at long wavelengths which are similar to those of 2D crystal phonons. This observation is further supported by the frequency dependence of the vibrational density of states, consisting of the Debye approximation in the low-wave-number limit. However, the system-size effect in the intermediate scattering function becomes negligible when the length scale is larger than the vibrational amplitude. This suggests that the finite-size effect in a 2D system is transient and also that the structural relaxation itself is not fundamentally different from that in a 3D system. In fact, the dynamic correlation lengths estimated from the bond-breakage function, which do not suffer from those enhanced fluctuations, are not size dependent in either 2D or 3D systems.

  2. Functional neuroanatomy in depressed patients with sexual dysfunction: blood oxygenation level dependent functional MR imaging

    Energy Technology Data Exchange (ETDEWEB)

    Yang, Jong Chul [Chonnam National Univ. Hospital, Kwangju (Korea, Republic of)

    2004-06-15

    To demonstrate the functional neuroanatomy associated with sexual arousal visually evoked in depressed males who have underlying sexual dysfunction using Blood Oxygenation Level Dependent-based fMRI. Ten healthy volunteers (age range 21-55: mean 32.5 years), and 10 depressed subjects (age range 23-51: mean 34.4 years, mean Beck Depression Inventory score of 39.6 {+-} 5.9, mean Hamilton Rating Scale Depression (HAMD)-17 score of 33.5 {+-} 6.0) with sexual arousal dysfunction viewed erotic and neutral video films during functional magnetic resonance imaging (fMRI) with 1.5 T MR scanner (GE Signa Horizon). The fMRI data were obtained from 7 oblique planes using gradient-echo EPI (flip angle/TR/TE=90 .deg. /6000 ms/50 ms). The visual stimulation paradigm began with 60 sec of black screen, 150 sec of neutral stimulation with a documentary video film, 30 sec of black screen, 150 sec of sexual stimulation with an erotic video film followed by 30 sec of black screen. The brain activation maps and their quantification were analyzed by SPM99 program. There was a significant difference of brain activation between two groups during visual sexual stimulation. In depressed subjects, the level of activation during the visually evoked sexual arousal was significantly less than that of healthy volunteers, especially in the cerebrocortical areas of the hypothalamus, thalamus, caudate nucleus, and inferior and superior temporal gyri. On the other hand, the cerebral activation patterns during the neutral condition in both groups showed no significant differences ({rho} < 0.01). This study is the first demonstration of the functional neuroanatomy of the brain associated with sexual dysfunction in depressed patients using fMRI. In order to validate our physiological neuroscience results, further studies that would include patients with other disorders and sexual dysfunction, and depressed patients without sexual dysfunction and their treatment response are needed.

  3. Prefrontal response and frontostriatal functional connectivity to monetary reward in abstinent alcohol-dependent young adults

    National Research Council Canada - National Science Library

    Forbes, Erika E; Rodriguez, Eric E; Musselman, Samuel; Narendran, Rajesh

    2014-01-01

    ... function that are central to addiction. In addition, few studies have examined function in these regions during young adulthood, when exposure is less chronic than in typical samples of alcohol-dependent adults...

  4. Transverse momentum dependent gluon fragmentation functions from J/ψπ production at e{sup +}e{sup -} colliders

    Energy Technology Data Exchange (ETDEWEB)

    Zhang, Guang-Peng [Peking University, Center for High Energy Physics, Beijing (China)

    2015-10-15

    The back-to-back J/ψ and π associated production at e{sup +}e{sup -} colliders is proposed to detect the gluon transverse momentum dependent (TMD) fragmentation functions. TMD factorization is assumed for this process. With a spinless pion, unpolarized and linearly polarized gluon TMD fragmentation functions can be defined. It is found that at parton level the hadronic tensor can be described by three independent structure functions. As a result, there are three independent angular distributions, of which the cos 2φ azimuthal asymmetry is sensitive to the linearly polarized gluon fragmentation function. (orig.)

  5. Competition between magnetic field dependent band structure and coherent backscattering in multiwall carbon nanotubes

    Science.gov (United States)

    Stojetz, B.; Roche, S.; Miko, C.; Triozon, F.; Forró, L.; Strunk, C.

    2007-03-01

    Magnetotransport measurements in large diameter multiwall carbon nanotubes (20 40 nm) demonstrate the competition of a magnetic-field dependent bandstructure and Altshuler Aronov Spivak oscillations. By means of an efficient capacitive coupling to a backgate electrode, the magnetoconductance oscillations are explored as a function of Fermi level shift. Changing the magnetic field orientation with respect to the tube axis and by ensemble averaging, allows the contributions of different Aharonov Bohm phases to be identified. The results are in qualitative agreement with numerical calculations of the band structure and the conductance.

  6. Orbital-Dependent Density Functionals for Chemical Catalysis

    Science.gov (United States)

    2011-02-16

    Biradical ...transferred  state  is  a   biradical .  The   lowest-­‐energy  adiabatic  singlet  state  shows  at  least  two  minima  along... biradical )  at  intermediate  approach  (Ca⋯C  distance  ≈2.5–2.7   Å)  with  molecular  orbital  structure  ϕ1ϕ2,

  7. Electromagnetism and multiple-valued loop-dependent wave functionals

    CERN Document Server

    Leal, Lorenzo

    2009-01-01

    We quantize the Maxwell theory in the presence of a electric charge in a "dual" Loop Representation, i.e. a geometric representation of magnetic Faraday's lines. It is found that the theory can be seen as a theory without sources, except by the fact that the wave functional becomes multivalued. This can be seen as the dual counterpart of what occurs in Maxwell theory with a magnetic pole, when it is quantized in the ordinary Loop Representation. The multivaluedness can be seen as a result of the multiply-connectedness of the configuration space of the quantum theory.

  8. Nucleon structure functions in noncommutative space-time

    CERN Document Server

    Rafiei, Ali; Mirjalili, Abolfazl

    2016-01-01

    In the context of noncommutative space-time, we investigate the nucleon structure functions which plays an important role to identify the internal structure of nucleons. We use the corrected vertices and employ new vertices that appear in two approaches of noncommutativity and calculate the proton structure functions in terms of noncommutative tensor \\theta_{\\mu\

  9. Density dependence in an age-structured population of great tits: identifying the critical age classes.

    Science.gov (United States)

    Gamelon, Marlène; Grøtan, Vidar; Engen, Steinar; Bjørkvoll, Eirin; Visser, Marcel E; Saether, Bernt-Erik

    2016-09-01

    Classical approaches for the analyses of density dependence assume that all the individuals in a population equally respond and equally contribute to density dependence. However, in age-structured populations, individuals of different ages may differ in their responses to changes in population size and how they contribute to density dependence affecting the growth rate of the whole population. Here we apply the concept of critical age classes, i.e., a specific scalar function that describes how one or a combination of several age classes affect the demographic rates negatively, in order to examine how total density dependence acting on the population growth rate depends on the age-specific population sizes. In a 38-yr dataset of an age-structured great tit (Parus major) population, we find that the age classes, including the youngest breeding females, were the critical age classes for density regulation. These age classes correspond to new breeders that attempt to take a territory and that have the strongest competitive effect on other breeding females. They strongly affected population growth rate and reduced recruitment and survival rates of all breeding females. We also show that depending on their age class, females may differently respond to varying density. In particular, the negative effect of the number of breeding females was stronger on recruitment rate of the youngest breeding females. These findings question the classical assumptions that all the individuals of a population can be treated as having an equal contribution to density regulation and that the effect of the number of individuals is age independent. Our results improve our understanding of density regulation in natural populations.

  10. Inorganic pyrophosphatases: structural diversity serving the function

    Science.gov (United States)

    Samygina, V. R.

    2016-05-01

    The review is devoted to ubiquitous enzymes, inorganic pyrophosphatases, which are essential in all living organisms. Despite the long history of investigations, these enzymes continue to attract interest. The review focuses on the three-dimensional structures of various representatives of this class of proteins. The structural diversity, the relationship between the structure and some properties of pyrophosphatases and various mechanisms of enzyme action related to the structural diversity of these enzymes are discussed. Interactions of pyrophosphatase with other proteins and possible practical applications are considered. The bibliography includes 56 references.

  11. Dependence of optical structure of coke from black coal on petrologic peculiarities of the coal

    Energy Technology Data Exchange (ETDEWEB)

    Proskuryakov, A.E.; Stankevich, A.S.; Podchishchaeva, N.I.; Shkoller, M.B.

    1988-01-01

    Analyzes factors that influence optical structure of coke from Kuzbass black coal. An optical microscope (magnification 800-2,000 times) was used. On the basis of investigations 8 types of optical structures in coke were determined: an isotropic structure, fine grain structure, medium grain structure, large grain structure, fibre-like structure, inertinite structure and a relict structure. The following criteria for determining optical structures are used: optical character of coke matter, grain size, grain geometry, microlites and primary structure. Using regression analysis, dependence of the optical structures on the following indices were derived: vitrinite reflectivity, vitrinite content and reduction degree. 12 refs.

  12. A Determination of the Neutron Spin Structure Function

    Energy Technology Data Exchange (ETDEWEB)

    Hughes, Emlyn W

    2003-08-18

    The authors report the results of the experiment E142 which measured the spin dependent structure function of the neutron, g{sub 1}{sup n}(x, Q{sup 2}). The experiment was carried out at the Stanford Linear Accelerator Center by measuring an asymmetry in the deep inelastic scattering of polarized electrons from a polarized {sup 3}He target, at electron energies from 19 to 26 GeV. The structure function was determined over the kinematic range 0.03 < BJorken x < 0.6 and 1.0 < Q{sup 2} < 5.5 (GeV/c){sup 2}. An evaluation of the integral {integral}{sub 0}{sup 1} g{sub 1}{sup n}(x,Q{sup 2})dx at fixed Q{sup 2} = 2 (GeV/c){sup 2} yields the final result {Lambda}{sub 1}{sup n} = -0.032 {+-} 0.006 (stat.) {+-} 0.009 (syst.). This result, when combined with the integral of the proton spin structure function measured in other experiments, confirms the fundamental Bjorken sum rule with O({alpha}{sub s}{sup 3}) corrections to within one standard deviation. This is a major success for perturbative Quantum Chromodynamics. Some ancillary results include the findings that the Ellis-Jaffe sum rule for the neutron is violated at the 2 {sigma} level, and that the total contribution of the quarks to the helicity of the nucleon is 0.36 {+-} 0.10. The strange sea polarization is estimated to be small and negative, {Delta}s = -0.07 {+-} 0.04.

  13. Properties and structure of peat humic acids depending on humification and precursor biota in bogs

    Science.gov (United States)

    Klavins, Maris; Purmalis, Oskars

    2013-04-01

    Humic substances form most of the organic component of soil, peat and natural waters, but their structure and properties very much differs depending on their source. The aim of this study is to characterize humic acids from raised bog peat profiles to evaluate the homogeneity of humic acids isolated from the bog bodies and study peat humification impact on properties of humic acids. A major impact on the structure of peat humic acids have raised bog biota (dominantly represented by bryophytes of different origin) void of lignin. For characterization of peat humic acids their elemental (CHNOS), functional (-COOH, phenolic OH) analysis, spectroscopic characterization (UV, fluorescence, FTIR, 1H NMR, CP/MAS 13C NMR, ESR) and degradation studies (Py-GC/MS) were done. Peat humic acids (HA) have an intermediate position between the living organic matter and coal organic matter and their structure is formed in a process in which more labile structures (carbohydrates, amino acids, etc.) are destroyed, but thermodynamically more stable aromatic and polyaromatic structures emerge. Comparatively, the studied peat HAs are at the start of the transformation process of living organic matter. Concentrations of carboxyl and phenolic hydroxyl groups changes depending on the depth of peat from which HAs have been isolated: and carboxylic acidity is increasing with depth of peat location and the humification degree. The ability to influence the surface tension of peat humic acids isolated from a well-characterized bog profile demonstrates dependence on age and humification degree. With increase of the humification degree and age of humic acids, their molecular complexity and ability to influence surface tension decreases; even so, the impact of the biological precursor (peat-forming bryophytes and plants) can be identified.

  14. The structural basis of nuclear function.

    Science.gov (United States)

    Jackson, D A; Cook, P R

    1995-01-01

    Most models for transcription and replication involve polymerases that track along the template. We review here experiments that suggest an alternative in which polymerization occurs as the template slides past a polymerase fixed to a large structure in the eukaryotic nucleus--a "factory" attached to a nucleoskeleton. This means that higher-order structure dictates how and when DNA is replicated or transcribed.

  15. Structural and functional properties of hemp seed protein products.

    Science.gov (United States)

    Malomo, Sunday A; He, Rong; Aluko, Rotimi E

    2014-08-01

    The effects of pH and protein concentration on some structural and functional properties of hemp seed protein isolate (HPI, 84.15% protein content) and defatted hemp seed protein meal (HPM, 44.32% protein content) were determined. The HPI had minimum protein solubility (PS) at pH 4.0, which increased as pH was decreased or increased. In contrast, the HPM had minimum PS at pH 3.0, which increased at higher pH values. Gel electrophoresis showed that some of the high molecular weight proteins (>45 kDa) present in HPM were not well extracted by the alkali and were absent or present in low ratio in the HPI polypeptide profile. The amino acid composition showed that the isolation process increased the Arg/Lys ratio of HPI (5.52%) when compared to HPM (3.35%). Intrinsic fluorescence and circular dichroism data indicate that the HPI proteins had a well-defined structure at pH 3.0, which was lost as pH value increased. The differences in structural conformation of HPI at different pH values were reflected as better foaming capacity at pH 3.0 when compared to pH 5.0, 7.0, and 9.0. At 10 and 25 mg/mL protein concentrations, emulsions formed by the HPM had smaller oil droplet sizes (higher quality), when compared to the HPI-formed emulsions. In contrast at 50 mg/mL protein concentration, the HPI-formed emulsions had smaller oil droplet sizes (except at pH 3.0). We conclude that the functional properties of hemp seed protein products are dependent on structural conformations as well as protein concentration and pH.

  16. Structure and Function Evolution of Thiolate Monolayers on Gold

    Energy Technology Data Exchange (ETDEWEB)

    Edwards, Grant Alvin [Iowa State Univ., Ames, IA (United States)

    2006-01-01

    The use of n-alkanethiolate self-assembled monolayers on gold has blossomed in the past few years. These systems have functioned as models for common interfaces. Thiolate monolayers are ideal because they are easily modified before or after deposition. The works contained within this dissertation include interfacial characterization (inbred reflection absorption spectroscopy, ellipsometry, contact angle, scanning probe microscopy, and heterogeneous electron-transfer kinetics) and various modeling scenarios. The results of these characterizations present ground-breaking insights into the structure, function, and reproducible preparation of these monolayers. Surprisingly, three interfacial properties (electron-transfer, contact angle, and ellipsometry) were discovered to depend directly on the odd-even character of the monolayer components. Molecular modeling was utilized to investigate adlayer orientation, and suggests that these effects are adlayer structure specific. Finally, the electric force microscopy and theoretical modeling investigations of monolayer samples are presented, which show that the film dielectric constant, thickness, and dipole moment directly affect image contrast. In addition, the prospects for utilization of this emerging technique are outlined.

  17. Structure and function evolution of thiolate monolayers on gold

    Energy Technology Data Exchange (ETDEWEB)

    Edwards, Grant Alvin [Iowa State Univ., Ames, IA (United States)

    2006-01-01

    The use of n-alkanethiolate self-assembled monolayers on gold has blossomed in the past few years. These systems have functioned as models for common interfaces. Thiolate monolayers are ideal because they are easily modified before or after deposition. The works contained within this dissertation include interfacial characterization (infrared reflection absorption spectroscopy, ellipsometry, contact angle, scanning probe microscopy, and heterogeneous electron-transfer kinetics) and various modeling scenarios. The results of these characterizations present ground-breaking insights into the structure, function, and reproducible preparation of these monolayers. Surprisingly, three interfacial properties (electron-transfer, contact angle, and ellipsometry) were discovered to depend directly on the odd-even character of the monolayer components. Molecular modeling was utilized to investigate adlayer orientation, and suggests that these effects are adlayer structure specific. Finally, the electric force microscopy and theoretical modeling investigations of monolayer samples are presented, which show that the film dielectric constant, thickness, and dipole moment directly affect image contrast. In addition, the prospects for utilization of this emerging technique are outlined.

  18. Extracellular matrix structure and nano-mechanics determine megakaryocyte function.

    Science.gov (United States)

    Malara, Alessandro; Gruppi, Cristian; Pallotta, Isabella; Spedden, Elise; Tenni, Ruggero; Raspanti, Mario; Kaplan, David; Tira, Maria Enrica; Staii, Cristian; Balduini, Alessandra

    2011-10-20

    Cell interactions with matrices via specific receptors control many functions, with chemistry, physics, and membrane elasticity as fundamental elements of the processes involved. Little is known about how biochemical and biophysical processes integrate to generate force and, ultimately, to regulate hemopoiesis into the bone marrow-matrix environment. To address this hypothesis, in this work we focus on the regulation of MK development by type I collagen. By atomic force microscopy analysis, we demonstrate that the tensile strength of fibrils in type I collagen structure is a fundamental requirement to regulate cytoskeleton contractility of human MKs through the activation of integrin-α2β1-dependent Rho-ROCK pathway and MLC-2 phosphorylation. Most importantly, this mechanism seemed to mediate MK migration, fibronectin assembly, and platelet formation. On the contrary, a decrease in mechanical tension caused by N-acetylation of lysine side chains in type I collagen completely reverted these processes by preventing fibrillogenesis.

  19. Alphavirus RNA synthesis and non-structural protein functions.

    Science.gov (United States)

    Rupp, Jonathan C; Sokoloski, Kevin J; Gebhart, Natasha N; Hardy, Richard W

    2015-09-01

    The members of the genus Alphavirus are positive-sense RNA viruses, which are predominantly transmitted to vertebrates by a mosquito vector. Alphavirus disease in humans can be severely debilitating, and depending on the particular viral species, infection may result in encephalitis and possibly death. In recent years, alphaviruses have received significant attention from public health authorities as a consequence of the dramatic emergence of chikungunya virus in the Indian Ocean islands and the Caribbean. Currently, no safe, approved or effective vaccine or antiviral intervention exists for human alphavirus infection. The molecular biology of alphavirus RNA synthesis has been well studied in a few species of the genus and represents a general target for antiviral drug development. This review describes what is currently understood about the regulation of alphavirus RNA synthesis, the roles of the viral non-structural proteins in this process and the functions of cis-acting RNA elements in replication, and points to open questions within the field.

  20. Structural Diversity and Function of Xyloglucan Sidechain Substituents

    Directory of Open Access Journals (Sweden)

    Alex Schultink

    2014-11-01

    Full Text Available Xyloglucan (XyG is a hemicellulose found in the cell walls of all land plants including early-divergent groups such as liverworts, hornworts and mosses. The basic structure of XyG, a xylosylated glucan, is similar in all of these plants but additional substituents can vary depending on plant family, tissue, and developmental stage. A comprehensive list of known XyG sidechain substituents is assembled including their occurrence within plant families, thereby providing insight into the evolutionary origin of the various sidechains. Recent advances in DNA sequencing have enabled comparative genomics approaches for the identification of XyG biosynthetic enzymes in Arabidopsis thaliana as well as in non-model plant species. Characterization of these biosynthetic genes not only allows the determination of their substrate specificity but also provides insights into the function of the various substituents in plant growth and development.

  1. Socio-demographic factors related to functional limitations and care dependency among older Egyptians

    NARCIS (Netherlands)

    Boggatz, Thomas; Farid, Tamer; Mohammedin, Ahmed; Dijkstra, Ate; Lohrmann, Christa; Dassen, Theo

    P>Title. Socio-demographic factors related to functional limitations and care dependency among older Egyptians. Aim. This paper is a report of a study determining the relationship of socio-demographic factors to functional limitations and care dependency among older care recipients and non-care

  2. Fast Algorithms of Mining Probability Functional Dependency Rules in Relational Database

    Institute of Scientific and Technical Information of China (English)

    TAO Xiaopeng; ZHOU Aoying; HU Yunfa

    2000-01-01

    This paper defines a new kind of rule, probability functional dependency rule. The functional dependency degree can be depicted by this kind of rule. Five algorithms, from the simple to the complex, are presented to mine this kind of rule in different condition. The related theorems are proved to ensure the high efficiency and the correctness of the above algorithms.

  3. Socio-demographic factors related to functional limitations and care dependency among older Egyptians

    NARCIS (Netherlands)

    Boggatz, Thomas; Farid, Tamer; Mohammedin, Ahmed; Dijkstra, Ate; Lohrmann, Christa; Dassen, Theo

    2010-01-01

    P>Title. Socio-demographic factors related to functional limitations and care dependency among older Egyptians. Aim. This paper is a report of a study determining the relationship of socio-demographic factors to functional limitations and care dependency among older care recipients and non-care reci

  4. Structural Brain Connectivity Constrains within-a-Day Variability of Direct Functional Connectivity

    Directory of Open Access Journals (Sweden)

    Bumhee Park

    2017-08-01

    Full Text Available The idea that structural white matter connectivity constrains functional connectivity (interactions among brain regions has widely been explored in studies of brain networks; studies have mostly focused on the “average” strength of functional connectivity. The question of how structural connectivity constrains the “variability” of functional connectivity remains unresolved. In this study, we investigated the variability of resting state functional connectivity that was acquired every 3 h within a single day from 12 participants (eight time sessions within a 24-h period, 165 scans per session. Three different types of functional connectivity (functional connectivity based on Pearson correlation, direct functional connectivity based on partial correlation, and the pseudo functional connectivity produced by their difference were estimated from resting state functional magnetic resonance imaging data along with structural connectivity defined using fiber tractography of diffusion tensor imaging. Those types of functional connectivity were evaluated with regard to properties of structural connectivity (fiber streamline counts and lengths and types of structural connectivity such as intra-/inter-hemispheric edges and topological edge types in the rich club organization. We observed that the structural connectivity constrained the variability of direct functional connectivity more than pseudo-functional connectivity and that the constraints depended strongly on structural connectivity types. The structural constraints were greater for intra-hemispheric and heterologous inter-hemispheric edges than homologous inter-hemispheric edges, and feeder and local edges than rich club edges in the rich club architecture. While each edge was highly variable, the multivariate patterns of edge involvement, especially the direct functional connectivity patterns among the rich club brain regions, showed low variability over time. This study suggests that

  5. On the dynamics of the age structure, dependency, and consumption

    Science.gov (United States)

    Hock, Heinrich

    2013-01-01

    We examine the effects of population aging due to declining fertility and rising elderly life expectancy on consumption possibilities in the presence of intergenerational transfers. Our analysis is based on a highly tractable continuous-time overlapping generations model in which the population is divided into three groups (youth dependents, workers, and elderly dependents) and lifecourse transitions take place in a probabilistic fashion. We show that the consumption-maximizing response to greater longevity in highly developed countries is an increase in fertility. However, with larger transfer payments, the actual fertility response will likely be the opposite, leading to further population aging. PMID:24353374

  6. Phase dependent structural and electronic properties of lanthanum orthophosphate (LaPO4)

    Science.gov (United States)

    Neupane, M. R.; Garrett, G. A.; Rudin, S.; Andzelm, J. W.

    2016-05-01

    We study the phase-dependent structural and electronic properties of bulk LaPO4, using density functional theory (DFT). The applicability of conventional semi-local and hybrid functionals in predicting structural and electronic properties of monoclinic and hexagonal LaPO4 is evaluated by comparing results to available experimental data. The monoclinic LaPO4 was found to be more stable than the hexagonal phase in ambient conditions with a small energy difference, suggesting a possibility of a phase transition. Both the phases in the bulk form are found to be diamagnetic with indirect energy gaps. These results are consistent with available experimental results. In the monoclinic phase, the hybrid functionals predict indirect band gap at about 8 eV. Furthermore, the calculated indirect-direct transition energy offset (ΔE) in the hexagonal phase was three times lower than the monoclinic phase. Our calculations based on hybrid functionals also reveal that the states near the conduction band edge in the hexagonal LaPO4 are strongly hybridized between La and PO4 states. By analyzing the band dispersion around the band edges, we show that the hexagonal phase has lighter electron effective mass, as compared to the monoclinic phase. With a larger energy gap, smaller ΔE, and smaller electron effective mass, the hexagonal LaPO4 might be a promising candidate material as an n-type transparent oxide.

  7. Stability of soil microbial structure and activity depends on microbial diversity.

    Science.gov (United States)

    Tardy, Vincent; Mathieu, Olivier; Lévêque, Jean; Terrat, Sébastien; Chabbi, Abad; Lemanceau, Philippe; Ranjard, Lionel; Maron, Pierre-Alain

    2014-04-01

    Despite the central role of microbes in soil processes, empirical evidence concerning the effect of their diversity on soil stability remains controversial. Here, we addressed the ecological insurance hypothesis by examining the stability of microbial communities along a gradient of soil microbial diversity in response to mercury pollution and heat stress. Diversity was manipulated by dilution extinction approach. Structural and functional stabilities of microbial communities were assessed from patterns of genetic structure and soil respiration after the stress. Dilution led to the establishment of a consistent diversity gradient, as revealed by 454 sequencing of ribosomal genes. Diversity stability was enhanced in species-rich communities whatever the stress whereas functional stability was improved with increasing diversity after heat stress, but not after mercury pollution. This discrepancy implies that the relevance of ecological insurance for soil microbial communities might depend on the type of stress. Our results also suggest that the significance of microbial diversity for soil functional stability might increase with available soil resources. This could have strong repercussions in the current 'global changes' context because it suggests that the combined increased frequencies of extreme climatic events, nutrient loading and biotic exploitation may amplify the functional consequences of diversity decrease.

  8. Context-Dependent Functional Divergence of the Notch Ligands DLL1 and DLL4 In Vivo.

    Directory of Open Access Journals (Sweden)

    Kristina Preuße

    2015-06-01

    Full Text Available Notch signalling is a fundamental pathway that shapes the developing embryo and sustains adult tissues by direct communication between ligand and receptor molecules on adjacent cells. Among the ligands are two Delta paralogues, DLL1 and DLL4, that are conserved in mammals and share a similar structure and sequence. They activate the Notch receptor partly in overlapping expression domains where they fulfil redundant functions in some processes (e.g. maintenance of the crypt cell progenitor pool. In other processes, however, they appear to act differently (e.g. maintenance of foetal arterial identity raising the questions of how similar DLL1 and DLL4 really are and which mechanism causes the apparent context-dependent divergence. By analysing mice that conditionally overexpress DLL1 or DLL4 from the same genomic locus (Hprt and mice that express DLL4 instead of DLL1 from the endogenous Dll1 locus (Dll1Dll4ki, we found functional differences that are tissue-specific: while DLL1 and DLL4 act redundantly during the maintenance of retinal progenitors, their function varies in the presomitic mesoderm (PSM where somites form in a Notch-dependent process. In the anterior PSM, every cell expresses both Notch receptors and ligands, and DLL1 is the only activator of Notch while DLL4 is not endogenously expressed. Transgenic DLL4 cannot replace DLL1 during somitogenesis and in heterozygous Dll1Dll4ki/+ mice, the Dll1Dll4ki allele causes a dominant segmentation phenotype. Testing several aspects of the complex Notch signalling system in vitro, we found that both ligands have a similar trans-activation potential but that only DLL4 is an efficient cis-inhibitor of Notch signalling, causing a reduced net activation of Notch. These differential cis-inhibitory properties are likely to contribute to the functional divergence of DLL1 and DLL4.

  9. Structure and function of yeast alcohol dehydrogenase

    Directory of Open Access Journals (Sweden)

    VLADIMIR LESKOVAC

    2000-04-01

    Full Text Available 1. Introduction 2. Isoenzymes of YADH 3. Substrate specificity 4. Kinetic mechanism 5. Primary structure 6. The active site 7. Mutations in the yeast enzyme 8. Chemical mechanism 9. Binding of coenzymes 10. Hydride transfer

  10. Measurement of the Electron Structure Function at LEP energies

    CERN Document Server

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

    2010-01-01

    The hadronic part of the Electron Structure Function (ESF) has been measured for the first time, using e+e- data collected by the DELPHI experiment at LEP, at centre-of-mass energies sqrt(s) = 91.2-209.5 GeV. The data analysis is simpler than that of the measurement of the photon structure function. The ESF data are compared to predictions of phenomenological models based on the photon structure function. It is shown that the quasi-real photon virtuality contribution is significant. The presented data can serve as a cross-check of the photon structure function analyses and help in refining existing parametrizations.

  11. Continuous compliance compensation of position-dependent flexible structures

    NARCIS (Netherlands)

    Kontaras, Nikolaos; Heertjes, Marcel; Zwart, Hans

    2016-01-01

    The implementation of lightweight high-performance motion systems in lithography and other applications imposes lower requirements on actuators, amplifiers, and cooling. However, the decreased stiffness of lightweight designs increases the effect of structural flexibilities especially when the point

  12. Polymer-Dependent Layer Structures in Montmorillonite Nanocomposites

    Directory of Open Access Journals (Sweden)

    Justyna Strankowska

    2011-12-01

    Full Text Available We have studied structural differences among tetrahedral and octahedral sodium Montmorillonite layer arrangements in naturally occurring and synthetic montmorillonite clay minerals, as well as their poly(ethylene oxide and poly(ε-coprolatone polymer nanocomposites.

  13. Relativistic density functional for nuclear structure

    CERN Document Server

    2016-01-01

    This book aims to provide a detailed introduction to the state-of-the-art covariant density functional theory, which follows the Lorentz invariance from the very beginning and is able to describe nuclear many-body quantum systems microscopically and self-consistently. Covariant density functional theory was introduced in nuclear physics in the 1970s and has since been developed and used to describe the diversity of nuclear properties and phenomena with great success. In order to provide an advanced and updated textbook of covariant density functional theory for graduate students and nuclear physics researchers, this book summarizes the enormous amount of material that has accumulated in the field of covariant density functional theory over the last few decades as well as the latest developments in this area. Moreover, the book contains enough details for readers to follow the formalism and theoretical results, and provides exhaustive references to explore the research literature.

  14. Experimental febrile seizures induce age-dependent structural plasticity and improve memory in mice.

    Science.gov (United States)

    Tao, K; Ichikawa, J; Matsuki, N; Ikegaya, Y; Koyama, R

    2016-03-24

    Population-based studies have demonstrated that children with a history of febrile seizure (FS) perform better than age-matched controls at hippocampus-dependent memory tasks. Here, we report that FSs induce two distinct structural reorganizations in the hippocampus and bidirectionally modify future learning abilities in an age-dependent manner. Compared with age-matched controls, adult mice that had experienced experimental FSs induced by hyperthermia (HT) on postnatal day 14 (P14-HT) performed better in a cognitive task that requires dentate granule cells (DGCs). The enhanced memory performance correlated with an FS-induced persistent increase in the density of large mossy fiber terminals (LMTs) of the DGCs. The memory enhancement was not observed in mice that had experienced HT-induced seizures at P11 which exhibited abnormally located DGCs in addition to the increased LMT density. The ectopic DGCs of the P11-HT mice were abolished by the diuretic bumetanide, and this pharmacological treatment unveiled the masked memory enhancement. Thus, this work provides a novel basis for age-dependent structural plasticity in which FSs influence future brain function. Copyright © 2016 IBRO. Published by Elsevier Ltd. All rights reserved.

  15. Cobamide structure depends on both lower ligand availability and CobT substrate specificity.

    Science.gov (United States)

    Crofts, Terence S; Seth, Erica C; Hazra, Amrita B; Taga, Michiko E

    2013-10-24

    Cobamides are members of the vitamin B12 family of cofactors that function in a variety of metabolic processes and are synthesized only by prokaryotes. Cobamides produced by different organisms vary in the structure of the lower axial ligand. Here we explore the molecular factors that control specificity in the incorporation of lower ligand bases into cobamides. We find that the cobT gene product, which activates lower ligand bases for attachment, limits the range of lower ligand bases that can be incorporated by bacteria. Furthermore, we demonstrate that the substrate specificity of CobT can be predictably altered by changing two active site residues. These results demonstrate that sequence variations in cobT homologs contribute to cobamide structural diversity. This analysis could open new routes to engineering specific cobamide production and understanding cobamide-dependent processes. Copyright © 2013 Elsevier Ltd. All rights reserved.

  16. Structural phase-dependent hole localization and transport in bismuth vanadate

    Science.gov (United States)

    Kweon, Kyoung E.; Hwang, Gyeong S.

    2013-05-01

    We present theoretical evidence for the phase dependence of hole localization and transport in bismuth vanadate (BiVO4). Our hybrid density-functional theory calculations predict that, in the tetragonal phase [tetragonal scheelite BiVO4 (ts-BiVO4)], an excess hole tends to localize around a BiO8 polyhedron with strong lattice distortion, whereas, in the monoclinic phase [monoclinic scheelite BiVO4 (ms-BiVO4)], it spreads over many lattice sites. The phase-dependent behavior is likely related to the higher structural stability of ms-BiVO4 than ts-BiVO4, which may suppress hole-induced lattice distortions. Our study also demonstrates that the relatively weakly localized hole in ms-BiVO4 undergoes faster diffusion compared to the case of ts-BiVO4, irrespective of the fact that the degrees of localization and mobility vary depending on the choice of exchange-correlation functional. The mobility difference may provide an explanation for the enhanced photocatalytic activity of ms-BiVO4 over ts-BiVO4 for water oxidation, considering that the increased mobility would lead to an increase in the hole current to the catalyst surface.

  17. Time-dependent density functional studies of nuclear quantum dynamics in large amplitudes

    CERN Document Server

    Wen, Kai; Fang, Ni; Nakatsukasa, Takashi

    2015-01-01

    The time-dependent density functional theory (TDDFT) provides a unified description of the structure and reaction. The linear approximation leads to the random-phase approximation (RPA) which is capable of describing a variety of collective motion in a harmonic regime. Beyond the linear regime, we present applications of the TDDFT to nuclear fusion and fission reaction. In particular, the extraction of the internuclear potential and the inertial mass parameter is performed using two different methods. A fusion hindrance mechanism for heavy systems is investigated from the microscopic point of view. The canonical collective variables are determined by the adiabatic self-consistent collective coordinate method. Preliminary results of the spontaneous fission path, the potential, and the collective mass parameter are shown for 8Be --> alpha+alpha.

  18. Functional annotation by identification of local surface similarities: a novel tool for structural genomics

    Directory of Open Access Journals (Sweden)

    Zanzoni Andreas

    2005-08-01

    Full Text Available Abstract Background Protein function is often dependent on subsets of solvent-exposed residues that may exist in a similar three-dimensional configuration in non homologous proteins thus having different order and/or spacing in the sequence. Hence, functional annotation by means of sequence or fold similarity is not adequate for such cases. Results We describe a method for the function-related annotation of protein structures by means of the detection of local structural similarity with a library of annotated functional sites. An automatic procedure was used to annotate the function of local surface regions. Next, we employed a sequence-independent algorithm to compare exhaustively these functional patches with a larger collection of protein surface cavities. After tuning and validating the algorithm on a dataset of well annotated structures, we applied it to a list of protein structures that are classified as being of unknown function in the Protein Data Bank. By this strategy, we were able to provide functional clues to proteins that do not show any significant sequence or global structural similarity with proteins in the current databases. Conclusion This method is able to spot structural similarities associated to function-related similarities, independently on sequence or fold resemblance, therefore is a valuable tool for the functional analysis of uncharacterized proteins. Results are available at http://cbm.bio.uniroma2.it/surface/structuralGenomics.html

  19. What function tells about structure in heterogeneous aquifers

    Science.gov (United States)

    Lischeid, Gunnar; Steidl, Jörg; Merz, Christoph; Dannowski, Ralf

    2016-04-01

    Hydogeologists and water resources managers are interested in the functional aspects of groundwater systems, that is, the temporal behaviour of groundwater head, patterns of groundwater flow pathways or residence time distribution. These functional aspects highly depend on the structure of the respective aquifer, e.g., on the extent and inclination of confining layers or on the geometry of fissures in hardrock aquifers. Thus a sound knowledge of the prevailing features of the aquifer's structure is a necessary prerequisite for groundwater resources management and application of groundwater models. There is urgent need for efficient ways to extract relevant information from easily available data. When certain structures in the subsurface have a major effect on the functioning of a groundwater system sophisticated analysis of the latter might be used to infer the former in an inverse approach. Then in a next step this information could be used, e.g., for constraining groundwater models. Unless, e.g., for a naïve implementation of geophysical data in groundwater models, the approach outlined here ensures that only structures relevant for hydrogeological functioning are considered, thus minimizing the model structure uncertainty. This approach has been applied in the Quillow catchment in Northeast Germany, a region with a very complex setting of pleistocenic unconsolidated sediments of 200 m thickness, where numerous layers of varying permeability intersect to unknown numbers and extent. Here the key problem is the identification of confining layers that effectively separate different aquifers. Different approaches were combined. Firstly, a principal component analysis was applied to time series of groundwater head from 10 groundwater wells in the study region, allowing to differentiate between different effects on groundwater dynamics. Corresponding to other studies published recently, groundwater head dynamics in the first place depended on the degree of

  20. Molecular and structural advances in tissue factor-dependent coagulation.

    Science.gov (United States)

    Kirchhofer, D; Banner, D W

    1997-11-01

    The tissue factor:factor VIIa (TF-F.VIIa) complex is considered the physiological initiator of blood coagulation. Besides its role in normal hemostasis, this enzyme complex has been found to play an important role in various thrombotic disorders and thus has become an attractive target for the development of new anticoagulants. Recently, significant progress has been made in regard to structural and molecular aspects of TF-VIIa-initiated coagulation. A rather complete picture on how tissue factor binds to factor VIIa has emerged and is discussed in detail in this review. Also, the combined data of the TF-F.VIIa crystal structure, of naturally occurring F.VII variants, and of mutagenesis studies provide a framework to discuss molecular aspects of the tissue factor-mediated enhancement of F.VIIa catalytic efficiency and the recognition of macromolecular substrates. F.VIIa as a member of the serine protease family has an active site homologous to other coagulation factors. The release of the coordinates of the crystal structures of F.X and F.IX, together with the earlier determined thrombin structure, now allows a detailed comparison of these active centers with respect to the development of specific and potent active site inhibitors. This structural and molecular information about the TF-F.VIIa complex and other coagulation enzymes adds to our understanding of blood coagulation and should further the development of new classes of anticoagulants. (Trends Cardiovasc Med 1997;7:316-324). © 1997, Elsevier Science Inc.