Proton structure functions at small x

DOE PAGES

Hentschinski, Martin

2015-11-03

Proton structure functions are measured in electron-proton collision through inelastic scattering of virtual photons with virtuality Q on protons; x denotes the momentum fraction carried by the struck parton. Proton structure functions are currently described with excellent accuracy in terms of scale dependent parton distribution functions, defined in terms of collinear factorization and DGLAP evolution in Q. With decreasing x however, parton densities increase and are ultimately expected to saturate. In this regime DGLAP evolution will finally break down and non-linear evolution equations w.r.t x are expected to take over. In the first part of the talk we present recentmore » result on an implementation of physical DGLAP evolution. Unlike the conventional description in terms of parton distribution functions, the former describes directly the Q dependence of the measured structure functions. It is therefore physical insensitive to factorization scheme and scale ambiguities. It therefore provides a more stringent test of DGLAP evolution and eases the manifestation of (non-linear) small x effects. It however requires a precise measurement of both structure functions F 2 and F L, which will be only possible at future facilities, such as an Electron Ion Collider. In the second part we present a recent analysis of the small x region of the combined HERA data on the structure function F 2. We demonstrate that (linear) next-to-leading order BFKL evolution describes the effective Pomeron intercept, determined from the combined HERA data, once a resummation of collinear enhanced terms is included and the renormalization scale is fixed using the BLM optimal scale setting procedure. We also provide a detailed description of the Q and x dependence of the full structure functions F 2 in the small x region, as measured at HERA. As a result, predictions for the structure function F L are found to be in agreement with the existing HERA data.« less

Measurements of the nucleon structure function in the range 0.002 < x < 0.17 and 00.2 < Q2 < 8 GeV2 in deuterium, carbon and calcium

NASA Astrophysics Data System (ADS)

European Muon Collaboration; Arneodo, M.; Arvidson, A.; Aubert, J. J.; Badelek, B.; Beaufays, J.; Bee, C. P.; Benchouk, C.; Berghoff, G.; Bird, I. G.; Blum, D.; Böhm, E.; de Bouard, X.; Brasse, F. W.; Braun, H.; Broll, C.; Brown, S. C.; Brück, H.; Calén, H.; Chima, J. S.; Ciborowski, J.; Clifft, R.; Coignet, G.; Combley, F.; Coughlan, J.; d'Agostini, G.; Dahlgren, S.; Derado, I.; Dreyer, T.; Drees, J.; Düren, M.; Eckardt, V.; Edwards, A.; Edwards, M.; Ernst, T.; Eszes, G.; Favier, J.; Ferrero, M. I.; Figiel, J.; Flauger, W.; Foster, J.; Gabathuler, E.; Gajewski, J.; Gamet, R.; Geddes, N.; Grafström, P.; Gustafsson, L.; Haas, J.; Hagberg, E.; Hasert, F. J.; Hayman, P.; Heusse, P.; Jaffre, M.; Jacholkowska, A.; Janata, F.; Jancso, G.; Johnson, A. S.; Kabuss, E. M.; Kellner, G.; Krüger, A.; Krüger, J.; Kullander, S.; Landgraf, U.; Lanske, D.; Loken, J.; Long, K.; Maire, M.; Malecki, P.; Manz, A.; Maselli, S.; Mohr, W.; Montanet, F.; Montgomery, H. E.; Nagy, E.; Nassalski, J.; Norton, P. R.; Oakham, F. G.; Osborne, A. M.; Pascaud, C.; Pawlik, B.; Payre, P.; Peroni, C.; Peschel, H.; Pessard, H.; Pettingale, J.; Pietrzyk, B.; Poensgen, B.; Pötsch, M.; Renton, P.; Ribarics, P.; Rith, K.; Rondio, E.; Sandacz, A.; Scheer, M.; Schlagböhmer, A.; Schiemann, H.; Schmitz, N.; Schneegans, M.; Scholz, M.; Schouten, M.; Schröder, T.; Schultze, K.; Sloan, T.; Stier, H. E.; Studt, M.; Taylor, G. N.; Thenard, J. M.; Thompson, J. C.; de la Torre, A.; Toth, J.; Urban, L.; Urban, L.; Wallucks, W.; Whalley, M.; Wheeler, S.; Williams, W. S. C.; Wimpenny, S. J.; Windmolders, R.; Wolf, G.

1990-03-01

Small angle scattering of 280 GeV positive muons by deuterium, carbon and calcium has been measured at scattering angles down to 2 mrad. The nucleon structure function F2 extracted from deuterium does not show a significant x dependence in the measured range of Q2 and its Q2 dependence is linear in logQ2. For calcium, a depletion of F2 is observed at low x by 30% as compared with the values at x = 0.1 where F2(Ca) and F2 (D) are not significantly different. This depletion is attributed to shadowing. The carbon structure function exhibits a similar, but less pronounced, x dependence. Such behaviour is observed to be independent of Q2. The data are consistent with those obtained from other charged lepton experiments both at similar and higher values of x and Q2 and considerably extend the range of the measurements down to the low values of x to be measured in forthcoming experiments at HERA.

High-pressure structural study of MnF 2

DOE PAGES

Stavrou, Elissaios; Yao, Yansun; Goncharov, Alexander F.; ...

2015-02-01

In this study, manganese fluoride (MnF 2) with the tetragonal rutile-type structure has been studied using a synchrotron angle-dispersive powder x-ray diffraction and Raman spectroscopy in a diamond anvil cell up to 60 GPa at room temperature combined with first-principles density functional calculations. The experimental data reveal two pressure-induced structural phase transitions with the following sequence: rutile → SrI 2 type (3 GPa)→ α–PbCl 2 type (13 GPa). Complete structural information, including interatomic distances, has been determined in the case of MnF 2 including the exact structure of the debated first high-pressure phase. First-principles density functional calculations confirm this phasemore » transition sequence, and the two calculated transition pressures are in excellent agreement with the experiment. Lattice dynamics calculations also reproduce the experimental Raman spectra measured for the ambient and high-pressure phases. The results are discussed in line with the possible practical use of rutile-type fluorides in general and specifically MnF 2 as a model compound to reveal the HP structural behavior of rutile-type SiO 2 (Stishovite).« less

Beauty, charm, and F{sub L} at HERA: New data vs. Early predictions

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

Nikolaev, N. N.; Zoller, V. R., E-mail: zoller@itep.r

One of the well-known effects of the asymptotic freedom is splitting of the leading-log BFKL pomeron into a series of isolated poles in complex angular momentum plane. Following our earlier works we explore the phenomenological consequences of the emerging BFKL-Regge factorized expansion for the small-x charm (F{sub 2}{sup c}) and beauty (F{sub 2}{sup b}) structure functions of the proton. As we found earlier, the colordipole approach to the BFKL dynamics predicts uniquely decoupling of subleading hard BFKL exchanges from F{sub 2}{sup c} at moderately large Q{sup 2}. We predicted precocious BFKL asymptotics of F{sub 2}{sup c} (x,Q{sup 2}) with interceptmore » of the rightmost BFKL pole {alpha}{sub P}(0) - 1 = {Delta}{sub P} {approx} 0.4. High-energy open beauty photo- and electroproduction probes the vacuum exchange at much smaller distances and detects significant corrections to the BFKL asymptotics coming from the subleading vacuum poles. In view of the accumulation of the experimental data on small -xF{sub 2}{sup c} and F{sub 2}{sup b} we extended our early predictions to the kinematical domain covered by new HERA measurements. Our structure functions obtained in 1999 agree well with the determination of both F{sub 2}{sup c} and F{sub 2}{sup b} by the H1 published in 2006 but contradict very recent (2008, preliminary)H1 results on F{sub 2}{sup b}. We present also comparison of our early predictions for the longitudinal structure function F{sub L} with recent H1 data (2008) taken at very low Bjorken x. We comment on the electromagnetic corrections to the Okun-Pomeranchuk theorem.« less

Measurement of the proton structure function F 2 from the 1993 HERA data

NASA Astrophysics Data System (ADS)

Derrick, M.; Krakauer, D.; Magill, S.; Musgrave, B.; Repond, J.; Schlereth, J.; Stanek, R.; Talaga, R. L.; Thron, J.; Arzarello, F.; Ayad, R.; Bari, G.; Basile, M.; Bellagamba, L.; Boscherini, D.; Bruni, A.; Bruni, G.; Bruni, P.; Cara Romeo, G.; Castellini, G.; Chiarini, M.; Cifarelli, L.; Cindolo, F.; Ciralli, F.; Contin, A.; D'Auria, S.; Frasconi, F.; Giusti, P.; Iacobucci, G.; Laurenti, G.; Levi, G.; Margotti, A.; Massam, T.; Nania, R.; Nemoz, C.; Palmonari, F.; Polini, A.; Sartorelli, G.; Timellini, R.; Zamora Garcia, Y.; Zichichi, A.; Bargende, A.; Crittenden, J.; Desch, K.; Diekmann, B.; Doeker, T.; Feld, L.; Frey, A.; Geerts, M.; Geitz, G.; Grothe, M.; Hartmann, H.; Haun, D.; Heinloth, K.; Hilger, E.; Jakob, H.-P.; Katz, U. F.; Mari, S. M.; Mass, A.; Mengel, S.; Mollen, J.; Paul, E.; Rembser, Ch.; Schattevoy, R.; Schneider, J.-L.; Schramm, D.; Stamm, J.; Wedemeyer, R.; Campbell-Robson, S.; Cassidy, A.; Dyce, N.; Foster, B.; George, S.; Gilmore, R.; Heath, G. P.; Heath, H. F.; Llewellyn, T. J.; Morgado, C. J. S.; Norman, D. J. P.; O'Mara, J. A.; Tapper, R. J.; Wilson, S. S.; Yoshida, R.; Rau, R. R.; Arneodo, M.; Iannotti, L.; Schioppa, M.; Susinno, G.; Bernstein, A.; Caldwell, A.; Gialas, I.; Parsons, J. A.; Ritz, S.; Sciulli, F.; Straub, P. B.; Wai, L.; Yang, S.; Borzemski, P.; Chwastowski, J.; Eskreys, A.; Piotrzkowski, K.; Zachara, M.; Zawiejski, L.; Adamczyk, L.; Bednarek, B.; Eskreys, K.; Jeleń, K.; Kisielewska, D.; Kowalski, T.; Rulikowska-Zarębska, E.; Suszycki, L.; Zając, J.; Kędzierski, T.; Kotański, A.; Przybycień, M.; Bauerdick, L. A. T.; Behrens, U.; Bienlein, J. K.; Böttcher, S.; Coldewey, C.; Drews, G.; Flasiński, M.; Gilkinson, D. J.; Göttlicher, P.; Gutjahr, B.; Haas, T.; Hagge, L.; Hain, W.; Hasell, D.; Heßling, H.; Hultschig, H.; Iga, Y.; Joos, P.; Kasemann, M.; Klanner, R.; Koch, W.; Köpke, L.; Kötz, U.; Kowalski, H.; Kröger, W.; Krüger, J.; Labs, J.; Ladage, A.; Löhr, B.; Löwe, M.; Lüke, D.; Mainusch, J.; Mańczak, O.; Ng, J. S. T.; Nickel, S.; Notz, D.; Ohrenberg, K.; Roco, M.; Rohde, M.; Roldán, J.; Schneekloth, U.; Schulz, W.; Selonke, F.; Stiliaris, E.; Voß, T.; Westphal, D.; Wolf, G.; Youngman, C.; Grabosch, H. J.; Leich, A.; Meyer, A.; Rethfeldt, C.; Schlenstedt, S.; Barbagli, G.; Pelfer, P.; Anzivino, G.; Maccarrone, G.; de Pasquale, S.; Qian, S.; Votano, L.; Bamberger, A.; Freidhof, A.; Poser, T.; Söldner-Rembold, S.; Schroeder, J.; Theisen, G.; Trefzger, T.; Brook, N. H.; Bussey, P. J.; Doyle, A. T.; Fleck, I.; Jamieson, V. A.; Saxon, D. H.; Utley, M. L.; Wilson, A. S.; Dannemann, A.; Holm, U.; Horstmann, D.; Kammerlocher, H.; Krebs, B.; Neumann, T.; Sinkus, R.; Wick, K.; Badura, E.; Burow, B. D.; Fürtjes, A.; Lohrmann, E.; Milewski, J.; Nakahata, M.; Pavel, N.; Poelz, G.; Schott, W.; Terron, J.; Zetsche, F.; Bacon, T. C.; Beuselinck, R.; Butterworth, I.; Gallo, E.; Harris, V. L.; Hung, B. H.; Long, K. R.; Miller, D. B.; Morawitz, P. P. O.; Prinias, A.; Sedgbeer, J. K.; Whitfield, A. F.; Mallik, U.; McCliment, E.; Wang, M. Z.; Zhang, Y.; Cloth, P.; Filges, D.; An, S. H.; Hong, S. M.; Nam, S. W.; Park, S. K.; Suh, M. H.; Yon, S. H.; Imlay, R.; Kartik, S.; Kim, H.-J.; McNeil, R. R.; Metcalf, W.; Nadendla, V. K.; Barreiro, F.; Cases, G.; Graciani, R.; Hernández, J. M.; Hervás, L.; Labarga, L.; Del Peso, J.; Puga, J.; de Trocóniz, J. F.; Ikraiam, F.; Mayer, J. K.; Smith, G. R.; Corriveau, F.; Hanna, D. S.; Hartmann, J.; Hung, L. W.; Lim, J. N.; Matthews, C. G.; Mitchell, J. W.; Patel, P. M.; Sinclair, L. E.; Stairs, D. G.; St. Laurent, M.; Ullmann, R.; Bashkirov, V.; Dolgoshein, B. A.; Stifutkin, A.; Bashindzhagyan, G. L.; Ermolov, P. F.; Gladilin, L. K.; Golubkov, Y. A.; Kobrin, V. D.; Kuzmin, V. A.; Proskuryakov, A. S.; Savin, A. A.; Shcheglova, L. M.; Solomin, A. N.; Zotov, N. P.; Bentvelsen, S.; Botje, M.; Chlebana, F.; Dake, A.; Engelen, J.; de Jong, P.; de Kamps, M.; Kooijman, P.; Kruse, A.; O'Dell, V.; Tenner, A.; Tiecke, H.; Verkerke, W.; Vreeswijk, M.; Wiggers, L.; de Wolf, E.; van Woudenberg, R.; Acosta, D.; Bylsma, B.; Durkin, L. S.; Honscheid, K.; Li, C.; Ling, T. Y.; McLean, K. W.; Murray, W. N.; Park, I. H.; Romanowski, T. A.; Seidlein, R.; Bailey, D. S.; Blair, G. A.; Byrne, A.; Cashmore, R. J.; Cooper-Sarkar, A. M.; Daniels, D.; Devenish, R. C. E.; Harnew, N.; Lancaster, M.; Luffman, P. E.; Lindemann, L.; McFall, J.; Nath, C.; Quadt, A.; Uijterwaal, H.; Walczak, R.; Wilson, F. F.; Yip, T.; Abbiendi, G.; Bertolin, A.; Brugnera, R.; Carlin, R.; Dal Corso, F.; de Giorgi, M.; Dosselli, U.; Gasparini, F.; Limentani, S.; Morandin, M.; Posocco, M.; Stanco, L.; Stroili, R.; Voci, C.; Bulmahn, J.; Butterworth, J. M.; Feild, R. G.; Oh, B. Y.; Whitmore, J. J.; D'Agostini, G.; Iori, M.; Marini, G.; Mattioli, M.; Nigro, A.; Tassi, E.; Hart, J. C.; McCubbin, N. A.; Prytz, K.; Shah, T. P.; Short, T. L.; Barberis, E.; Cartiglia, N.; Dubbs, T.; Heusch, C.; van Hook, M.; Hubbard, B.; Lockman, W.; Rahn, J. T.; Sadrozinski, H. F.-W.; Seiden, A.; Biltzinger, J.; Seifert, R. J.; Walenta, A. H.; Zech, G.; Abramowicz, H.; Briskin, G.; Dagan, S.; Levy, A.; Hasegawa, T.; Hazumi, M.; Ishii, T.; Kuze, M.; Mine, S.; Nagasawa, Y.; Nagira, T.; Nakao, M.; Suzuki, I.; Tokushuku, K.; Yamada, S.; Yamazaki, Y.; Chiba, M.; Hamatsu, R.; Hirose, T.; Homma, K.; Kitamura, S.; Nagayama, S.; Nakamitsu, Y.; Cirio, R.; Costa, M.; Ferrero, M. I.; Lamberti, L.; Maselli, S.; Peroni, C.; Sacchi, R.; Solano, A.; Staiano, A.; Dardo, M.; Bandyopadhyay, D.; Benard, F.; Brkic, M.; Crombie, M. B.; Gingrich, D. M.; Hartner, G. F.; Joo, K. K.; Levman, G. M.; Martin, J. F.; Orr, R. S.; Sampson, C. R.; Teuscher, R. J.; Catterall, C. D.; Jones, T. W.; Kaziewicz, P. B.; Lane, J. B.; Saunders, R. L.; Shulman, J.; Blankenship, K.; Kochocki, J.; Lu, B.; Mo, L. W.; Bogusz, W.; Charchula, K.; Ciborowski, J.; Gajewski, J.; Grzelak, G.; Kasprzak, M.; Krzyżanowski, M.; Muchorowski, K.; Nowak, R. J.; Pawlak, J. M.; Tymieniecka, T.; Wróblewski, A. K.; Zakrzewski, J. A.; Żarnecki, A. F.; Adamus, M.; Eisenberg, Y.; Glasman, C.; Karshon, U.; Revel, D.; Shapira, A.; Ali, I.; Behrens, B.; Dasu, S.; Fordham, C.; Foudas, C.; Goussiou, A.; Loveless, R. J.; Reeder, D. D.; Silverstein, S.; Smith, W. H.; Tsurugai, T.; Bhadra, S.; Frisken, W. R.; Furutani, K. M.

1995-09-01

The ZEUS detector has been used to measure the proton structure function F 2. During 1993 HERA collided 26.7 GeV electrons on 820 GeV protons. The data sample corresponds to an integrated luminosity of 0.54 pb-1, representing a twenty fold increase in statistics compared to that of 1992. Results are presented for 7< Q 2<104 GeV2 and x values as low as 3×10-4. The rapid rise in F 2 as x decreases observed previously is now studied in greater detail and persists for Q 2 values up to 500 GeV2.

Direct Observation of Quark-Hadron Duality in the Free Neutron {ital F}{sub 2} Structure Function

DOE PAGES

Niculescu, I.; Niculescu, G.; Melnitchouk, W.; ...

2015-05-21

Using the recently published data from the BONuS(Barely Off-shell Nucleon Structure) experiment at Jefferson Lab, which utilized a spectator tagging technique to extract the inclusive electron-free neutron scattering cross section, we obtain the first direct observation of quark-hadron duality in the neutron F-2 structure function. The data are used to reconstruct the lowest few (N = 2, 4, and 6) moments of F-2 in the three prominent nucleon resonance regions, as well as the moments integrated over the entire resonance region. Comparison with moments computed from global parametrizations of parton distribution functions suggest that quark-hadron duality holds locally for themore » neutron in the second and third resonance regions down to Q(2) approximate to 1 GeV2, with violations possibly up to 20% observed in the first resonance region.« less

A measurement of the proton structure function F2( x, Q2)

NASA Astrophysics Data System (ADS)

Ahmed, T.; Aid, S.; Akhundov, A.; Andreev, V.; Andrieu, B.; Appuhn, R.-D.; Arpagaus, M.; Babaev, A.; Baehr, J.; Bán, J.; Baranov, P.; Barrelet, E.; Bartel, W.; Barth, M.; Bassler, U.; Beck, H. P.; Behrend, H.-J.; Belousov, A.; Berger, Ch.; Bergstein, H.; Bernardi, G.; Bernet, R.; Bertrand-Coremans, G.; Besançon, M.; Beyer, R.; Biddulph, P.; Bizot, J. C.; Blobel, V.; Borras, K.; Botterweck, F.; Boudry, V.; Braemer, A.; Brasse, F.; Braunschweig, W.; Brisson, V.; Bruncko, D.; Brune, C.; Buchholz, R.; Büngener, L.; Bürger, J.; Büsser, F. W.; Buniatian, A.; Burke, S.; Buschhorn, G.; Campbell, A. J.; Carli, T.; Charles, F.; Clarke, D.; Clegg, A. B.; Clerbaux, B.; Colombo, M.; Contreras, J. G.; Cormack, C.; Coughlan, J. A.; Courau, A.; Coutures, Ch.; Cozzika, G.; Criegge, L.; Cussans, D. G.; Cvach, J.; Dagoret, S.; Dainton, J. B.; Danilov, M.; Dau, W. D.; Daum, K.; David, M.; Deffur, E.; Delcourt, B.; Del Buono, L.; De Roeck, A.; De Wolf, E. A.; Di Nezza, P.; Dollfus, C.; Dowell, J. D.; Dreis, H. B.; Droutskoi, V.; Duboc, J.; Düllmann, D.; Dünger, O.; Duhm, H.; Ebert, J.; Ebert, T. R.; Eckerlin, G.; Efremenko, V.; Egli, S.; Ehrlichmann, H.; Eichenberger, S.; Eichler, R.; Eisele, F.; Eisenhandler, E.; Ellison, R. J.; Elsen, E.; Erdmann, M.; Erdmann, W.; Evrard, E.; Favart, L.; Fedotov, A.; Feeken, D.; Felst, R.; Feltesse, J.; Ferencei, J.; Ferrarotto, F.; Flamm, K.; Fleischer, M.; Flieser, M.; Flügge, G.; Fomenko, A.; Fominykh, B.; Forbush, M.; Formánek, J.; Foster, J. M.; Franke, G.; Fretwurst, E.; Gabathuler, E.; Gabathuler, K.; Gamerdinger, K.; Garvey, J.; Gayler, J.; Gebauer, M.; Gellrich, A.; Genzel, H.; Gerhards, R.; Goerlach, U.; Goerlich, L.; Gogitidze, N.; Goldberg, M.; Goldner, D.; Gonzalez-Pineiro, B.; Gorelov, I.; Goritchev, P.; Grab, C.; Grässler, H.; Grässler, R.; Greenshaw, T.; Grindhammer, G.; Gruber, A.; Gruber, C.; Haack, J.; Haidt, D.; Hajduk, L.; Hamon, O.; Hampel, M.; Hanlon, E. M.; Hapke, M.; Haynes, W. J.; Heatherington, J.; Heinzelmann, G.; Henderson, R. C. W.; Henschel, H.; Herma, R.; Herynek, I.; Hess, M. F.; Hildesheim, W.; Hill, P.; Hiller, K. H.; Hilton, C. D.; Hladký, J.; Hoeger, K. C.; Höppner, M.; Horisberger, R.; Hudgson, V. L.; Huet, Ph.; Hütte, M.; Hufnagel, H.; Ibbotson, M.; Itterbeck, H.; Jabiol, M.-A.; Jacholkowska, A.; Jacobsson, C.; Jaffre, M.; Janoth, J.; Jansen, T.; Jönsson, L.; Johannsen, K.; Johnson, D. P.; Johnson, L.; Jung, H.; Kalmus, P. I. P.; Kant, D.; Kaschowitz, R.; Kasselmann, P.; Kathage, U.; Katzy, J.; Kaufmann, H. H.; Kazarian, S.; Kenyon, I. R.; Kermiche, S.; Keuker, C.; Kiesling, C.; Klein, M.; Kleinwort, C.; Knies, G.; Ko, W.; Köhler, T.; Köhne, J.; Kolanoski, H.; Kole, F.; Kolya, S. D.; Korbel, V.; Korn, M.; Kostka, P.; Kotelnikov, S. K.; Krämerkämper, T.; Krasny, M. W.; Krehbiel, H.; Krücker, D.; Krüger, U.; Krüner-Marquis, U.; Kubenka, J. P.; Küster, H.; Kuhlen, M.; Kurča, T.; Kurzhöfer, J.; Kuznik, B.; Lacour, D.; Lamarche, F.; Lander, R.; Landon, M. P. J.; Lange, W.; Lanius, P.; Laporte, J.-F.; Lebedev, A.; Leverenz, C.; Levonian, S.; Ley, Ch.; Lindner, A.; Lindström, G.; Linsel, F.; Lipinski, J.; List, B.; Loch, P.; Lohmander, H.; Lopez, G. C.; Lubimov, V.; Lüke, D.; Magnussen, N.; Malinovski, E.; Mani, S.; Maraček, R.; Marage, P.; Marks, J.; Marshall, R.; Martens, J.; Martin, R.; Martyn, H.-U.; Martyniak, J.; Masson, S.; Mavroidis, T.; Maxfield, S. J.; McMahon, S. J.; Mehta, A.; Meier, K.; Mercer, D.; Merz, T.; Meyer, C. A.; Meyer, H.; Meyer, J.; Mikocki, S.; Milstead, D.; Moreau, F.; Morris, J. V.; Mroczko, E.; Müller, G.; Müller, K.; Murín, P.; Nagovizin, V.; Nahnhauer, R.; Naroska, B.; Naumann, Th.; Newman, P. R.; Newton, D.; Neyret, D.; Nguyen, H. K.; Nicholls, T. C.; Niebergall, F.; Niebuhr, C.; Nisius, R.; Nowak, G.; Noyes, G. W.; Nyberg-Werther, M.; Oakden, M.; Oberlack, H.; Obrock, U.; Olsson, J. E.; Panaro, E.; Panitch, A.; Pascaud, C.; Patel, G. D.; Peppel, E.; Perez, E.; Phillips, J. P.; Pichler, Ch.; Pitzl, D.; Pope, G.; Prell, S.; Prosi, R.; Rädel, G.; Raupach, F.; Reimer, P.; Reinshagen, S.; Ribarics, P.; Rick, H.; Riech, V.; Riedlberger, J.; Riess, S.; Rietz, M.; Rizvi, E.; Robertson, S. M.; Robmann, P.; Roloff, H. E.; Roosen, R.; Rosenbauer, K.; Rostovtsev, A.; Rouse, F.; Royon, C.; Rüter, K.; Rusakov, S.; Rybicki, K.; Rylko, R.; Sahlmann, N.; Sanchez, E.; Sankey, D. P. C.; Savitsky, M.; Schacht, P.; Schiek, S.; Schleper, P.; von Schlippe, W.; Schmidt, C.; Schmidt, D.; Schmidt, G.; Schöning, A.; Schröder, V.; Schuhmann, E.; Schwab, B.; Schwind, A.; Seehausen, U.; Sefkow, F.; Seidel, M.; Sell, R.; Semenov, A.; Shekelyan, V.; Sheviakov, I.; Shooshtari, H.; Shtarkov, L. N.; Siegmon, G.; Siewert, U.; Sirois, Y.; Skillicorn, I. O.; Smirnov, P.; Smith, J. R.; Soloviev, Y.; Spiekermann, J.; Spitzer, H.; Starosta, R.; Steenbock, M.; Steffen, P.; Steinberg, R.; Stella, B.; Stephens, K.; Stier, J.; Stiewe, J.; Stösslein, U.; Strachota, J.; Straumann, U.; Struczinski, W.; Sutton, J. P.; Tapprogge, S.; Taylor, R. E.; Tchernyshov, V.; Thiebaux, C.; Thompson, G.; Truöl, P.; Turnau, J.; Tutas, J.; Uelkes, P.; Usik, A.; Valkár, S.; Valkárová, A.; Vallée, C.; Van Esch, P.; Van Mechelen, P.; Vartapetian, A.; Vazdik, Y.; Vecko, M.; Verrecchia, P.; Villet, G.; Wacker, K.; Wagener, A.; Wagener, M.; Walker, I. W.; Walther, A.; Weber, G.; Weber, M.; Wegener, D.; Wegner, A.; Wellisch, H. P.; West, L. R.; Willard, S.; Winde, M.; Winter, G.-G.; Wright, A. E.; Wünsch, E.; Wulff, N.; Yiou, T. P.; Žáček, J.; Zarbock, D.; Zhang, Z.; Zhokin, A.; Zimmer, M.; Zimmermann, W.; Zomer, F.; Zuber, K.; H1 Collaboration

1995-02-01

A measurement of the proton structure function F2( x, Q2) is reported for momentum transfers squared Q2 between 4.5 GeV 2 and 1600 GeV 2 and for Bjorken x between 1.8 × 10 -14 and 0.13 using data collected by the HERA experiment H1 in 1993. It is observed that F2 increases significantly with decreasing x, confirming our previous measurement made with one tenth of the data available in this analysis. The Q2 dependence is approximately logarithmic over the full kinematic range covered. The subsample of deep inelastic events with a large pseudo-rapidity gap in the hadronic energy flow close to the proton remnant is used to measure the "diffractive" contribution to F2.

Measurement of the structure function of the nearly free neutron using spectator tagging in inelastic 2H(e ,e'ps )X scattering with CLAS

NASA Astrophysics Data System (ADS)

Tkachenko, S.; Baillie, N.; Kuhn, S. E.; Zhang, J.; Arrington, J.; Bosted, P.; Bültmann, S.; Christy, M. E.; Fenker, H.; Griffioen, K. A.; Kalantarians, N.; Keppel, C. E.; Melnitchouk, W.; Tvaskis, V.; Adhikari, K. P.; Aghasyan, M.; Amaryan, M. J.; Anefalos Pereira, S.; Avakian, H.; Ball, J.; Baltzell, N. A.; Battaglieri, M.; Bedlinskiy, I.; Biselli, A. S.; Briscoe, W. J.; Brooks, W. K.; Burkert, V. D.; Carman, D. S.; Celentano, A.; Chandavar, S.; Charles, G.; Cole, P. L.; Contalbrigo, M.; Cortes, O.; Crede, V.; D'Angelo, A.; Dashyan, N.; De Vita, R.; De Sanctis, E.; Deur, A.; Djalali, C.; Dodge, G. E.; Doughty, D.; Dupre, R.; Egiyan, H.; El Alaoui, A.; El Fassi, L.; Elouadrhiri, L.; Eugenio, P.; Fedotov, G.; Fleming, J. A.; Garillon, B.; Gevorgyan, N.; Ghandilyan, Y.; Gilfoyle, G. P.; Giovanetti, K. L.; Girod, F. X.; Goetz, J. T.; Golovatch, E.; Gothe, R. W.; Guidal, M.; Guo, L.; Hafidi, K.; Hakobyan, H.; Hanretty, C.; Harrison, N.; Hattawy, M.; Hicks, K.; Ho, D.; Holtrop, M.; Hyde, C. E.; Ilieva, Y.; Ireland, D. G.; Ishkhanov, B. S.; Jo, H. S.; Keller, D.; Khandaker, M.; Kim, A.; Kim, W.; King, P. M.; Klein, A.; Klein, F. J.; Koirala, S.; Kubarovsky, V.; Kuleshov, S. V.; Lenisa, P.; Lewis, S.; Livingston, K.; Lu, H.; MacCormick, M.; MacGregor, I. J. D.; Markov, N.; Mayer, M.; McKinnon, B.; Mineeva, T.; Mirazita, M.; Mokeev, V.; Montgomery, R. A.; Moutarde, H.; Munoz Camacho, C.; Nadel-Turonski, P.; Niccolai, S.; Niculescu, G.; Niculescu, I.; Osipenko, M.; Pappalardo, L. L.; Paremuzyan, R.; Park, K.; Pasyuk, E.; Phillips, J. J.; Pisano, S.; Pogorelko, O.; Pozdniakov, S.; Price, J. W.; Procureur, S.; Protopopescu, D.; Puckett, A. J. R.; Rimal, D.; Ripani, M.; Rizzo, A.; Rosner, G.; Rossi, P.; Roy, P.; Sabatié, F.; Schott, D.; Schumacher, R. A.; Seder, E.; Senderovich, I.; Sharabian, Y. G.; Simonyan, A.; Smith, G. D.; Sober, D. I.; Sokhan, D.; Stepanyan, S.; Stepanyan, S. S.; Strauch, S.; Tang, W.; Ungaro, M.; Vlassov, A. V.; Voskanyan, H.; Voutier, E.; Walford, N. K.; Watts, D.; Wei, X.; Weinstein, L. B.; Wood, M. H.; Zana, L.; Zonta, I.; CLAS Collaboration

2014-04-01

Background: Much less is known about neutron structure than that of the proton due to the absence of free neutron targets. Neutron information is usually extracted from data on nuclear targets such as deuterium, requiring corrections for nuclear binding and nucleon off-shell effects. These corrections are model dependent and have significant uncertainties, especially for large values of the Bjorken scaling variable x . As a consequence, the same data can lead to different conclusions, for example, about the behavior of the d quark distribution in the proton at large x . Purpose: The Barely Off-shell Nucleon Structure experiment at Jefferson Lab measured the inelastic electron-deuteron scattering cross section, tagging spectator protons in coincidence with the scattered electrons. This method reduces nuclear binding uncertainties significantly and has allowed for the first time a (nearly) model-independent extraction of the neutron structure function F2(x ,Q2) in the resonance and deep-inelastic regions. Method: A novel compact radial time projection chamber was built to detect protons with momentum between 70 and 150 MeV/c and over a nearly 4 π angular range. For the extraction of the free-neutron structure function F2n, spectator protons at backward angles (>100∘ relative to the momentum transfer) and with momenta below 100 MeV/c were selected, ensuring that the scattering took place on a nearly free neutron. The scattered electrons were detected with Jefferson Lab's CLAS spectrometer, with data taken at beam energies near 2, 4, and 5 GeV. Results: The extracted neutron structure function F2n and its ratio to the inclusive deuteron structure function F2d are presented in both the resonance and the deep-inelastic regions for momentum transfer squared Q2 between 0.7 and 5 GeV2/c2 , invariant mass W between 1 and 2.7 GeV/c2 , and Bjorken x between 0.25 and 0.6 (in the deep-inelastic scattering region). The dependence of the semi-inclusive cross section on the spectator proton momentum and angle is investigated, and tests of the spectator mechanism for different kinematics are performed. Conclusions: Our data set on the structure function ratio F2n/F2d can be used to study neutron resonance excitations, test quark-hadron duality in the neutron, develop more precise parametrizations of structure functions, and investigate binding effects (including possible mechanisms for the nuclear EMC effect) and provide a first glimpse of the asymptotic behavior of d /u at x →1 .

Q{sub 2} evolution of parton distributions at small values of x: Effective scale for combined H1 and ZEUS data on the structure function F{sub 2}

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

Kotikov, A. V., E-mail: kotikov@theor.jinr.ru; Shaikhatdenov, B. G.

2015-06-15

An expression for the structure function F{sub 2} in the form of Bessel functions at small values of the Bjorken variable x is used. This expression was derived for a flat initial condition in the Dokshitzer-Gribov-Lipatov-Altarelli-Parisi (DGLAP) evolution equations. The argument of the strong coupling constant was chosen in such a way as to annihilate the singular part of the anomalous dimensions in the next-to-leading-order of perturbation theory. This choice, together with the frozen and analytic versions of the strong coupling constant, is used to analyze combined data of the H1 and ZEUS Collaborations obtained recently for the structure functionmore » F{sub 2}.« less

Constraints on the large-x d/u ratio from electron--nucleus scattering at x>1

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

O. Hen, A. Accardi, W. Melnitchouk and E. Piasetzky

2011-12-01

Recently the ratio of neutron to proton structure functions F{sub 2}{sup n}/F{sub 2}{sup p} was extracted from a phenomenological correlation between the strength of the nuclear EMC effect and inclusive electron-nucleus cross section ratios at x > 1. Within conventional models of nuclear smearing, this 'in-medium correction' (IMC) extraction constrains the size of nuclear effects in the deuteron structure functions, from which the neutron structure function F{sub 2}{sup n} is usually extracted. The IMC data determine the resulting proton d/u quark distribution ratio, extrapolated to x = 1, to be 0.23 {+-} 0.09 with a 90% confidence level. This ismore » well below the SU(6) symmetry limit of 1/2 and significantly above the scalar diquark dominance limit of 0.« less

Measurement of the structure functions F 2 and xF 3 and comparison with QCD predictions including kinematical and dynamical higher twist effects

NASA Astrophysics Data System (ADS)

Varvell, K.; Cooper-Sarkar, A. M.; Parker, M. A.; Sansum, R. A.; Aderholz, M.; Armenise, N.; Baton, J. P.; Bullock, F. W.; Berggren, M.; Bertrand, D.; Brisson, V.; Burkot, W.; Calcchio, M.; Claytoh, E. F.; Coghen, T.; Erriquez, O.; Fitch, P. J.; Gerbier, G.; Guy, J.; Hulth, P. O.; Iaselli, G.; Jones, G. T.; Kasper, P.; Klein, H.; Kochowski, C.; Marage, P.; Mermikides, M.; Middleton, R. P.; Morrison, D. R. O.; Mobayyen, M. M.; Natali, S.; Neveu, M.; Nuzzo, S.; O'Neale, S. W.; Petiau, P.; Petrides, A.; Ruggieri, F.; Sacton, J.; Simopoulou, E.; Vallee, C.; Vayaki, A.; Venus, W. A.; Wachsmuth, H.; Wells, J.; Wittek, W.

1987-03-01

The isoscalar nucleon structure functions F 2( x, Q 2) and xF 3( x, Q 2) are measured in the range 0< Q 2<64 GeV2, 1.7< W 2<250 GeV2, x<0.7 using ν andbar v interactions on neon in BEBC. The data are used to evaluate possible higher twist contributions and to determine their impact on the evaluation of the QCD parameter Λ. In contrast to previous analyses reaching to such low W 2 values, it is found that a lowΛ _{overline {MS} } value in the neighbourhood of 100 MeV describes the data adequately and that the contribution of dynamical higher twist effects is small and negative.

F2Dock: Fast Fourier Protein-Protein Docking

PubMed Central

Bajaj, Chandrajit; Chowdhury, Rezaul; Siddavanahalli, Vinay

2009-01-01

The functions of proteins is often realized through their mutual interactions. Determining a relative transformation for a pair of proteins and their conformations which form a stable complex, reproducible in nature, is known as docking. It is an important step in drug design, structure determination and understanding function and structure relationships. In this paper we extend our non-uniform fast Fourier transform docking algorithm to include an adaptive search phase (both translational and rotational) and thereby speed up its execution. We have also implemented a multithreaded version of the adaptive docking algorithm for even faster execution on multicore machines. We call this protein-protein docking code F2Dock (F2 = Fast Fourier). We have calibrated F2Dock based on an extensive experimental study on a list of benchmark complexes and conclude that F2Dock works very well in practice. Though all docking results reported in this paper use shape complementarity and Coulombic potential based scores only, F2Dock is structured to incorporate Lennard-Jones potential and re-ranking docking solutions based on desolvation energy. PMID:21071796

Role of electrochemically in-house synthesized and functionalized graphene nanofillers in the structural performance of epoxy matrix composites.

PubMed

Sahoo, Sumanta Kumar; Ray, Bankim Chandra; Mallik, Archana

2017-06-21

The present study focuses on the intriguing enhancement in the mechanical properties of an epoxy-based composite structure resulting from the incorporation of in-house synthesized functionalized graphene nanosheets (f-GNSs) as nanofillers. The f-GNSs were obtained by anionic electrochemical intercalation and exfoliation with 2 M H 2 SO 4 , HClO 4 , and HNO 3 protic electrolytes. The structural properties of the as-synthesized GNSs were analyzed by XRD and Raman spectroscopy. The (002) and (001) lattice planes of graphene and graphene oxide are observed at around 24.5° and 11° (2θ), respectively, in the XRD spectra. The characteristic peaks at around 1345, 1590, and 2700 cm -1 correspond to the D, G, and 2D bands of the GNSs in the Raman spectra. Quantification of the functional groups and sp 2 contents in the GNSs were further analyzed by XPS. Morphological characterization of the f-GNSs reveals that the exfoliated carbon sheets consist of 2-8 layers. The composites are then fabricated by addition of these f-GNSs nanofillers, and the effect of the wt% of the nanofillers on the mechanical properties of the composites is analyzed with the three-point bend test and fractography analysis through interfacial morphological analysis. The addition of 0.1 wt% of nitric-acid-exfoliated f-GNSs nanofiller results in maximum increases of 42.6% and 28.2% in the flexural strengths of neat epoxy resin and glass fiber/epoxy polymer composite structures, respectively. Similarly, the moduli increase by 33.5% and 57.7% in the neat epoxy resin and glass fiber/epoxy polymer composite structures, respectively. The effect of epoxy/f-GNSs interfacial bonding in the composite structure was studied by DSC analysis.

The Osmium(VIII) Oxofluoro Cations OsO(2)F(3)(+) and F(cis-OsO(2)F(3))(2)(+): Syntheses, Characterization by (19)F NMR Spectroscopy and Raman Spectroscopy, X-ray Crystal Structure of F(cis-OsO(2)F(3))(2)(+)Sb(2)F(11)(-), and Density Functional Theory Calculations of OsO(2)F(3)(+), ReO(2)F(3), and F(cis-OsO(2)F(3))(2)(+).

PubMed

Casteel, William J.; Dixon, David A.; Mercier, Hélène P. A.; Schrobilgen, Gary J.

1996-07-17

Osmium dioxide tetrafluoride, cis-OsO(2)F(4), reacts with the strong fluoride ion acceptors AsF(5) and SbF(5) in anhydrous HF and SbF(5) solutions to form orange salts. Raman spectra are consistent with the formation of the fluorine-bridged diosmium cation F(cis-OsO(2)F(3))(2)(+), as the AsF(6)(-) and Sb(2)F(11)(-) salts, respectively. The (19)F NMR spectra of the salts in HF solution are exchange-averaged singlets occurring at higher frequency than those of the fluorine environments of cis-OsO(2)F(4). The F(cis-OsO(2)F(3))(2)(+)Sb(2)F(11)(-) salt crystallizes in the orthorhombic space group Imma. At -107 degrees C, a = 12.838(3) Å, b = 10.667(2) Å, c = 11.323(2) Å, V = 1550.7(8) Å(3), and Z = 4. Refinement converged with R = 0.0469 [R(w) = 0.0500]. The crystal structure consists of discrete fluorine-bridged F(cis-OsO(2)F(3))(2)(+) and Sb(2)F(11)(-) ions in which the fluorine bridge of the F(cis-OsO(2)F(3))(2)(+) cation is trans to an oxygen atom (Os-O 1.676 Å) of each OsO(2)F(3) group. The angle at the bridge is 155.2(8) degrees with a bridging Os---F(b) distance of 2.086(3) Å. Two terminal fluorine atoms (Os-F 1.821 Å) are cis to the two oxygen atoms (Os-O 1.750 Å), and two terminal fluorine atoms of the OsO(2)F(3) group are trans to one another (1.813 Å). The OsO(2)F(3)(+) cation was characterized by (19)F NMR and by Raman spectroscopy in neat SbF(5) solution but was not isolable in the solid state. The NMR and Raman spectroscopic findings are consistent with a trigonal bipyramidal cation in which the oxygen atoms and a fluorine atom occupy the equatorial plane and two fluorine atoms are in axial positions. Density functional theory calculations show that the crystallographic structure of F(cis-OsO(2)F(3))(2)(+) is the energy-minimized structure and the energy-minimized structures of the OsO(2)F(3)(+) cation and ReO(2)F(3) are trigonal bipyramidal having C(2)(v)() point symmetry. Attempts to prepare the OsOF(5)(+) cation by oxidative fluorination of cis-OsO(2)F(4) with KrF(+)AsF(6)(-) in anhydrous HF proved unsuccessful.

Asymptotic 3-loop heavy flavor corrections to the charged current structure functions FLW+-W-(x ,Q2) and F2W+-W-(x ,Q2)

NASA Astrophysics Data System (ADS)

Behring, A.; Blümlein, J.; Falcioni, G.; De Freitas, A.; von Manteuffel, A.; Schneider, C.

2016-12-01

We derive the massive Wilson coefficients for the heavy flavor contributions to the nonsinglet charged current deep-inelastic scattering structure functions FLW+(x ,Q2)-FLW-(x ,Q2) and F2W+(x ,Q2)-F2W-(x ,Q2) in the asymptotic region Q2≫m2 to 3-loop order in quantum chromodynamics at general values of the Mellin variable N and the momentum fraction x . Besides the heavy quark pair production, also the single heavy flavor excitation s →c contributes. Numerical results are presented for the charm quark contributions, and consequences on the unpolarized Bjorken sum rule and Adler sum rule are discussed.

Nuclear medium effects in structure functions of nucleon at moderate Q2

NASA Astrophysics Data System (ADS)

Haider, H.; Zaidi, F.; Sajjad Athar, M.; Singh, S. K.; Ruiz Simo, I.

2015-11-01

Recent experiments performed on inclusive electron scattering from nuclear targets have measured the nucleon electromagnetic structure functions F1 (x ,Q2), F2 (x ,Q2) and FL (x ,Q2) in 12C, 27Al, 56Fe and 64Cu nuclei. The measurements have been done in the energy region of 1 GeV2

Generalized zeta function representation of groups and 2-dimensional topological Yang-Mills theory: The example of GL(2, #Mathematical Double-Struck Capital F#{sub q}) and PGL(2, #Mathematical Double-Struck Capital F#{sub q})

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

Roche, Ph., E-mail: philippe.roche@univ-montp2.fr

We recall the relation between zeta function representation of groups and two-dimensional topological Yang-Mills theory through Mednikh formula. We prove various generalisations of Mednikh formulas and define generalization of zeta function representations of groups. We compute some of these functions in the case of the finite group GL(2, #Mathematical Double-Struck Capital F#{sub q}) and PGL(2, #Mathematical Double-Struck Capital F#{sub q}). We recall the table characters of these groups for any q, compute the Frobenius-Schur indicator of their irreducible representations, and give the explicit structure of their fusion rings.

Measurement of the F 2 structure function in deep inelastic e + p scattering using 1994 data from the ZEUS detector at HERA

NASA Astrophysics Data System (ADS)

Derrick, M.; Krakauer, D.; Magill, S.; Mikunas, D.; Musgrave, B.; Okrasinski, J. R.; Repond, J.; Stanek, R.; Talaga, R. L.; Zhang, H.; Mattingly, M. C. K.; Anselmo, F.; Antonioli, P.; Bari, G.; Basile, M.; Bellagamba, L.; Boscherini, D.; Bruni, A.; Bruni, G.; Bruni, P.; Romeo, G. Cara; Castellini, G.; Cifarelli, L.; Cindolo, F.; Contin, A.; Corradi, M.; Gialas, I.; Giusti, P.; Iacobucci, G.; Laurenti, G.; Levi, G.; Margotti, A.; Massam, T.; Nania, R.; Palmonari, F.; Pesci, A.; Polini, A.; Sartorelli, G.; Garcia, Y. Zamora; Zichichi, A.; Amelung, C.; Bornheim, A.; Crittenden, J.; Deffner, R.; Doeker, T.; Eckert, M.; Feld, L.; Frey, A.; Geerts, M.; Grothe, M.; Hartmann, H.; Heinloth, K.; Heinz, L.; Hilger, E.; Jakob, H.-P.; Katz, U. F.; Mengel, S.; Paul, E.; Pfeiffer, M.; Rembser, Ch.; Schramm, D.; Stamm, J.; Wedemeyer, R.; Campbell-Robson, S.; Cassidy, A.; Cottingham, W. N.; Dyce, N.; Foster, B.; George, S.; Hayes, M. E.; Heath, G. P.; Heath, H. F.; Piccioni, D.; Roff, D. G.; Tapper, R. J.; Yoshida, R.; Arneodo, M.; Ayad, R.; Capua, M.; Garfagnini, A.; Iannotti, L.; Schioppa, M.; Susinno, G.; Caldwell, A.; Cartiglia, N.; Jing, Z.; Liu, W.; Parsons, J. A.; Ritz, S.; Sciulli, F.; Straub, P. B.; Wai, L.; Yang, S.; Zhu, Q.; Borzemski, P.; Chwastowski, J.; Eskreys, A.; Jakubowski, Z.; Przybycień, M. B.; Zachara, M.; Zawiejski, L.; Adamczyk, L.; Bednarek, B.; Jeleń, K.; Kisielewska, D.; Kowalski, T.; Przybycien, M.; Rulikowska-Zarębska, E.; Suszycki, L.; Zając, J.; Duliński, Z.; Kotański, A.; Abbiendi, G.; Bauerdick, L. A. T.; Behrens, U.; Beier, H.; Bienlein, J. K.; Cases, G.; Deppe, O.; Desler, K.; Drews, G.; Flasiński, M.; Gilkinson, D. J.; Glasman, C.; Göttlicher, P.; Große-Knetter, J.; Haas, T.; Hain, W.; Hasell, D.; Heßling, H.; Iga, Y.; Johnson, K. F.; Joos, P.; Kasemann, M.; Klanner, R.; Koch, W.; Kötz, U.; Kowalski, H.; Labs, J.; Ladage, A.; Löhr, B.; Löwe, M.; Lüke, D.; Mainusch, J.; Mańczak, O.; Milewski, J.; Monteiro, T.; Ng, J. S. T.; Notz, D.; Ohrenberg, K.; Piotrzkowski, K.; Roco, M.; Rohde, M.; Roldán, J.; Schneekloth, U.; Schulz, W.; Selonke, F.; Surrow, B.; Tassi, E.; Voß, T.; Westphal, D.; Wolf, G.; Wollmer, U.; Youngman, C.; Zeuner, W.; Grabosch, H. J.; Kharchilava, A.; Mari, S. M.; Meyer, A.; Schlenstedt, S.; Wulff, N.; Barbagli, G.; Gallo, E.; Pelfer, P.; Maccarrone, G.; de Pasquale, S.; Votano, L.; Bamberger, A.; Eisenhardt, S.; Trefzger, T.; Wölfle, S.; Bromley, J. T.; Brook, N. H.; Bussey, P. J.; Doyle, A. T.; Saxon, D. H.; Sinclair, L. E.; Utley, M. L.; Wilson, A. S.; Dannemann, A.; Holm, U.; Horstmann, D.; Sinkus, R.; Wick, K.; Burow, B. D.; Hagge, L.; Lohrmann, E.; Poelz, G.; Schott, W.; Zetsche, F.; Bacon, T. C.; Brümmer, N.; Butterworth, I.; Harris, V. L.; Howell, G.; Hung, B. H. Y.; Lamberti, L.; Long, K. R.; Miller, D. B.; Pavel, N.; Prinias, A.; Sedgbeer, J. K.; Sideris, D.; Whitfield, A. F.; Mallik, U.; Wang, M. Z.; Wang, S. M.; Wu, J. T.; Cloth, P.; Filges, D.; An, S. H.; Cho, G. H.; Ko, B. J.; Lee, S. B.; Nam, S. W.; Park, H. S.; Park, S. K.; Kartik, S.; Kim, H.-J.; McNeil, R. R.; Metcalf, W.; Nadendla, V. K.; Barreiro, F.; Fernandez, J. P.; Graciani, R.; Hernández, J. M.; Hervás, L.; Labarga, L.; Martinez, M.; Del Peso, J.; Puga, J.; Terron, J.; de Trocóniz, J. F.; Corriveau, F.; Hanna, D. S.; Hartmann, J.; Hung, L. W.; Lim, J. N.; Matthews, C. G.; Patel, P. M.; Riveline, M.; Stairs, D. G.; St-Laurent, M.; Ullmann, R.; Zacek, G.; Tsurugai, T.; Bashkirov, V.; Dolgoshein, B. A.; Stifutkin, A.; Bashindzhagyan, G. L.; Ermolov, P. F.; Gladilin, L. K.; Golubkov, Yu. A.; Kobrin, V. D.; Korzhavina, I. A.; Kuzmin, V. A.; Lukina, O. Yu.; Proskuryakov, A. S.; Savin, A. A.; Shcheglova, L. M.; Solomin, A. N.; Zotov, N. P.; Botje, M.; Chlebana, F.; Engelen, J.; de Kamps, M.; Kooijman, P.; Kruse, A.; van Sighem, A.; Tiecke, H.; Verkerke, W.; Vossebeld, J.; Vreeswijk, M.; Wiggers, L.; de Wolf, E.; van Woudenberg, R.; Acosta, D.; Bylsma, B.; Durkin, L. S.; Gilmore, J.; Li, C.; Ling, T. Y.; Nylander, P.; Park, I. H.; Romanowski, T. A.; Bailey, D. S.; Cashmore, R. J.; Cooper-Sarkar, A. M.; Devenish, R. C. E.; Harnew, N.; Lancaster, M.; Lindemann, L.; McFall, J. D.; Nath, C.; Noyes, V. A.; Quadt, A.; Tickner, J. R.; Uijterwaal, H.; Walczak, R.; Waters, D. S.; Wilson, F. F.; Yip, T.; Bertolin, A.; Brugnera, R.; Carlin, R.; Dal Corso, F.; de Giorgi, M.; Dosselli, U.; Limentani, S.; Morandin, M.; Posocco, M.; Stanco, L.; Stroili, R.; Voci, C.; Zuin, F.; Bulmahn, J.; Feild, R. G.; Oh, B. Y.; Whitmore, J. J.; D'Agostini, G.; Marini, G.; Nigro, A.; Hart, J. C.; McCubbin, N. A.; Shah, T. P.; Barberis, E.; Dubbs, T.; Heusch, C.; van Hook, M.; Lockman, W.; Rahn, J. T.; Sadrozinski, H. F.-W.; Seiden, A.; Williams, D. C.; Biltzinger, J.; Seifert, R. J.; Schwarzer, O.; Walenta, A. H.; Zech, G.; Abramowicz, H.; Briskin, G.; Dagan, S.; Levy, A.; Fleck, J. I.; Inuzuka, M.; Ishii, T.; Kuze, M.; Mine, S.; Nakao, M.; Suzuki, I.; Tokushuku, K.; Umemori, K.; Yamada, S.; Yamazaki, Y.; Chiba, M.; Hamatsu, R.; Hirose, T.; Homma, K.; Kitamura, S.; Matsushita, T.; Yamauchi, K.; Cirio, R.; Costa, M.; Ferrero, M. I.; Maselli, S.; Peroni, C.; Sacchi, R.; Solano, A.; Staiano, A.; Dardo, M.; Bailey, D. C.; Benard, F.; Brkic, M.; Fagerstroem, C.-P.; Hartner, G. F.; Joo, K. K.; Levman, G. M.; Martin, J. F.; Orr, R. S.; Polenz, S.; Sampson, C. R.; Simmons, D.; Teuscher, R. J.; Butterworth, J. M.; Catterall, C. D.; Jones, T. W.; Kaziewicz, P. B.; Lane, J. B.; Saunders, R. L.; Shulman, J.; Sutton, M. R.; Lu, B.; Mo, L. W.; Bogusz, W.; Ciborowski, J.; Gajewski, J.; Grzelak, G.; Kasprzak, M.; Krzyżanowski, M.; Muchorowski, K.; Nowak, R. J.; Pawlak, J. M.; Tymieniecka, T.; Wróblewski, A. K.; Zakrzewski, J. A.; Żarnecki, A. F.; Adamus, M.; Coldewey, C.; Eisenberg, Y.; Hochman, D.; Karshon, U.; Revel, D.; Zer-Zion, D.; Badgett, W. F.; Breitweg, J.; Chapin, D.; Cross, R.; Dasu, S.; Foudas, C.; Loveless, R. J.; Mattingly, S.; Reeder, D. D.; Silverstein, S.; Smith, W. H.; Vaiciulis, A.; Wodarczyk, M.; Bhadra, S.; Cardy, M. L.; Frisken, W. R.; Khakzad, M.; Murray, W. N.; Schmidke, W. B.

1996-09-01

We present measurements of the structure function F 2 in e + p scattering at HERA in the range 3.5 GeV2< Q 2<5000 GeV2. A new reconstruction method has allowed a significant improvement in the resolution of the kinematic variables and an extension of the kinematic region covered by the experiment. At Q 2<35 GeV2 the range in x now spans 6.3·10-5< x<0.08 providing overlap with measurements from fixed target experiments. At values of Q 2 above 1000 GeV2 the x range extends to 0.5. Systematic errors below 5% have been achieved for most of the kinematic region. The structure function rises as x decreases; the rise becomes more pronounced as Q 2 increases. The behaviour of the structure function data is well described by next-to-leading order perturbative QCD as implemented in the DGLAP evolution equations.

Determination of the longitudinal proton structure function FL(x,Q2) at low x

NASA Astrophysics Data System (ADS)

Adloff, C.; Aid, S.; Anderson, M.; Andreev, V.; Andrieu, B.; Arndt, C.; Babaev, A.; Bähr, J.; Bán, J.; Ban, Y.; Baranov, P.; Barrelet, E.; Barschke, R.; Bartel, W.; Barth, M.; Bassler, U.; Beck, H. P.; Beck, M.; Behrend, H.-J.; Belousov, A.; Berger, Ch.; Bernardi, G.; Bertrand-Coremans, G.; Besançon, M.; Beyer, R.; Biddulph, P.; Bispham, P.; Bizot, J. C.; Blobel, V.; Blümlein, J.; Borras, K.; Botterweck, F.; Boudry, V.; Braemer, A.; Braunschweig, W.; Brisson, V.; Brückner, W.; Bruel, P.; Bruncko, D.; Brune, C.; Buchholz, R.; Büngener, L.; Bürger, J.; Büsser, F. W.; Buniatian, A.; Burke, S.; Burton, M. J.; Calvet, D.; Campbell, A. J.; Carli, T.; Charlet, M.; Clarke, D.; Clegg, A. B.; Clerbaux, B.; Cocks, S.; Contreras, J. G.; Cormack, C.; Coughlan, J. A.; Courau, A.; Cousinou, M.-C.; Cozzika, G.; Criegee, L.; Cussans, D. G.; Cvach, J.; Dagoret, S.; Dainton, J. B.; Dau, W. D.; Daum, K.; David, M.; Davis, C. L.; Delcourt, B.; de Roeck, A.; de Wolf, E. A.; Dirkmann, M.; Dixon, P.; di Nezza, P.; Dlugosz, W.; Dollfus, C.; Donovan, K. T.; Dowell, J. D.; Dreis, H. B.; Droutskoi, A.; Dünger, O.; Duhm, H.; Ebert, J.; Ebert, T. R.; Eckerlin, G.; Efremenko, V.; Egli, S.; Eichler, R.; Eisele, F.; Eisenhandler, E.; Elsen, E.; Erdmann, M.; Erdmann, W.; Fahr, A. B.; Favart, L.; Fedotov, A.; Felst, R.; Feltesse, J.; Ferencei, J.; Ferrarotto, F.; Flamm, K.; Fleischer, M.; Flieser, M.; Flügge, G.; Fomenko, A.; Formánek, J.; Foster, J. M.; Franke, G.; Fretwurst, E.; Gabathuler, E.; Gabathuler, K.; Gaede, F.; Garvey, J.; Gayler, J.; Gebauer, M.; Genzel, H.; Gerhards, R.; Glazov, A.; Goerlich, L.; Gogitidze, N.; Goldberg, M.; Goldner, D.; Golec-Biernat, K.; Gonzalez-Pineiro, B.; Gorelov, I.; Grab, C.; Grässler, H.; Greenshaw, T.; Griffiths, R. K.; Grindhammer, G.; Gruber, A.; Gruber, C.; Hadig, T.; Haidt, D.; Hajduk, L.; Haller, T.; Hampel, M.; Haynes, W. J.; Heinemann, B.; Heinzelmann, G.; Henderson, R. C. W.; Henschel, H.; Herynek, I.; Hess, M. F.; Hewitt, K.; Hildesheim, W.; Hiller, K. H.; Hilton, C. D.; Hladký, J.; Höppner, M.; Hoffmann, D.; Holtom, T.; Horisberger, R.; Hudgson, V. L.; Hütte, M.; Ibbotson, M.; İşsever, Ç.; Itterbeck, H.; Jacholkowska, A.; Jacobsson, C.; Jaffre, M.; Janoth, J.; Jansen, D. M.; Jansen, T.; Jönsson, L.; Johnson, D. P.; Jung, H.; Kalmus, P. I. P.; Kander, M.; Kant, D.; Kaschowitz, R.; Kathage, U.; Katzy, J.; Kaufmann, H. H.; Kaufmann, O.; Kausch, M.; Kazarian, S.; Kenyon, I. R.; Köhler, T.; Köhne, J. H.; Kolanoski, H.; Kolya, S. D.; Korbel, V.; Kostka, P.; Kotelnikov, S. K.; Krämerkämper, T.; Krehbiel, H.; Krücker, D.; Küster, H.; Kuhlen, M.; Kurča, T.; Kurzhöfer, J.; Lacour, D.; Laforge, B.; Landon, M. P. J.; Lange, W.; Langenegger, U.; Lebedev, A.; Lehner, F.; Levonian, S.; Lindström, G.; Lindstroem, M.; Linsel, F.; Lipinski, J.; List, B.; Lobo, G.; Loch, P.; Lomas, J. W.; Lopez, G. C.; Lubimov, V.; Lüke, D.; Lytkin, L.; Magnussen, N.; Malinovski, E.; Maraček, R.; Marage, P.; Marks, J.; Marshall, R.; Martens, J.; Martin, G.; Martin, R.; Martyn, H.-U.; Martyniak, J.; Mavroidis, T.; Maxfield, S. J.; McMahon, S. J.; Mehta, A.; Meier, K.; Metlica, F.; Meyer, A.; Meyer, A.; Meyer, H.; Meyer, J.; Meyer, P.-O.; Migliori, A.; Mikocki, S.; Milstead, D.; Moeck, J.; Moreau, F.; Morris, J. V.; Mroczko, E.; Müller, D.; Müller, G.; Müller, K.; Murín, P.; Nagovizin, V.; Nahnhauer, R.; Naroska, B.; Naumann, Th.; Négri, I.; Newman, P. R.; Newton, D.; Nguyen, H. K.; Nicholls, T. C.; Niebergall, F.; Niebuhr, C.; Niedzballa, Ch.; Niggli, H.; Nowak, G.; Noyes, G. W.; Nunnemann, T.; Nyberg-Werther, M.; Oakden, M.; Oberlack, H.; Olsson, J. E.; Ozerov, D.; Palmen, P.; Panaro, E.; Panitch, A.; Pascaud, C.; Patel, G. D.; Pawletta, H.; Peppel, E.; Perez, E.; Phillips, J. P.; Pieuchot, A.; Pitzl, D.; Pope, G.; Povh, B.; Prell, S.; Rabbertz, K.; Rädel, G.; Reimer, P.; Reinshagen, S.; Riemersma, S.; Rick, H.; Riepenhausen, F.; Riess, S.; Rizvi, E.; Robmann, P.; Roloff, H. E.; Roosen, R.; Rosenbauer, K.; Rostovtsev, A.; Rouse, F.; Royon, C.; Rüter, K.; Rusakov, S.; Rybicki, K.; Sankey, D. P. C.; Schacht, P.; Schiek, S.; Schleif, S.; Schleper, P.; von Schlippe, W.; Schmidt, D.; Schmidt, G.; Schoeffel, L.; Schöning, A.; Schröder, V.; Schuhmann, E.; Schwab, B.; Sefkow, F.; Sell, R.; Semenov, A.; Shekelyan, V.; Sheviakov, I.; Shtarkov, L. N.; Siegmon, G.; Siewert, U.; Sirois, Y.; Skillicorn, I. O.; Smirnov, P.; Solochenko, V.; Soloviev, Y.; Specka, A.; Spiekermann, J.; Spielman, S.; Spitzer, H.; Squinabol, F.; Steffen, P.; Steinberg, R.; Steiner, H.; Steinhart, J.; Stella, B.; Stellberger, A.; Stier, J.; Stiewe, J.; Stößlein, U.; Stolze, K.; Straumann, U.; Struczinski, W.; Sutton, J. P.; Tapprogge, S.; Taševský, M.; Tchernyshov, V.; Tchetchelnitski, S.; Theissen, J.; Thiebaux, C.; Thompson, G.; Tobien, N.; Todenhagen, R.; Truöl, P.; Tsipolitis, G.; Turnau, J.; Tutas, J.; Tzamariudaki, E.; Uelkes, P.; Usik, A.; Valkár, S.; Valkárová, A.; Vallée, C.; Vandenplas, D.; van Esch, P.; van Mechelen, P.; Vazdik, Y.; Verrecchia, P.; Villet, G.; Wacker, K.; Wagener, A.; Wagener, M.; Waugh, B.; Weber, G.; Weber, M.; Wegener, D.; Wegner, A.; Wengler, T.; Werner, M.; West, L. R.; Wilksen, T.; Willard, S.; Winde, M.; Winter, G.-G.; Wittek, C.; Wobisch, M.; Wünsch, E.; ŽáČek, J.; Zarbock, D.; Zhang, Z.; Zhokin, A.; Zini, P.; Zomer, F.; Zsembery, J.; Zuber, K.; Zurnedden, M.

1997-02-01

A measurement of the inclusive cross section for the deep-inelastic scattering of positrons off protons at HERA is presented at momentum transfers 8.5 <= Q2 <= 35 GeV2 and large inelasticity = 0.7, i.e. for the Bjorken-x range 0.00013 <= x <= 0.00055. Using a next-to-leading order QCD fit to the structure function F2 at lower y values, the contribution of F2 to the measured cross section at high y is calculated and, by subtraction, the longitudinal structure function FL is determined for the first time with an average value of FL = 0.52+/-0.03 (stat)+0.25-0.22 (syst) at Q2 = 15.4 GeV2 and x = 0.000243.

Theoretical characterization of the F(2)O(3) molecule by coupled-cluster methods.

PubMed

Huang, Ming-Ju; Watts, John D

2010-09-23

Coupled-cluster calculations with extended basis sets that include noniterative connected triple excitations (CCSD(T)) have been used to study the FOOOF isomer of F(2)O(3). Second-order Moller-Plessett perturbation theory (MP2) and density-functional theory (B3LYP functional) calculations have also been performed for comparison. Two local minima of similar energy, namely, conformers of C(2) and C(s) symmetry have been located. Structures, harmonic vibrational frequencies, and standard enthalpies and free energies of formation have been calculated. The calculated bond lengths of F(2)O(3) are more characteristic of those in F(2)O and a "normal" peroxide than the unusual bond lengths in F(2)O(2). Both conformers have equal F-O and O-O bond lengths, contrary to a recent suggestion of an unsymmetrical structure. The harmonic vibrational frequencies can aid possible identification of gaseous F(2)O(3). The calculated Δ(f)H° and Δ(f)G° are 110 and 173 kJ mol(-1), respectively. These values are based on extrapolation of CCSD(T) results with augmented triple- and quadruple-ζ basis sets and are expected to be within chemical accuracy (i.e., 1 kcal mol(-1) or 4 kJ mol(-1)). F(2)O(3) is calculated to be stable to decomposition to either FO + FOO or F(2) + O(3), but unstable to decomposition to its elements, to F(2)O(2) + (1)/(2)O(2), and to F(2)O + O(2).

Electronic structure and magnetic anisotropies of antiferromagnetic transition-metal difluorides

NASA Astrophysics Data System (ADS)

Corrêa, Cinthia Antunes; Výborný, Karel

2018-06-01

We compare calculations based on density functional theory (DFT) with available experimental data and analyze the origin of magnetic anisotropies in MnF2, FeF2, CoF2, and NiF2. We confirm that the magnetic anisotropy of MnF2 stems almost completely from the dipolar interaction, while magnetocrystalline anisotropy energy (originating in spin-orbit interaction) plays a dominant role in the other three compounds, and discuss how it depends on the details of band structure. The latter is critically compared to available optical measurements. The case of CoF2, where magnetocrystalline anisotropy energy strongly depends on U (the Hubbard parameter in DFT +U ), is put into contrast with FeF2 where theoretical predictions of magnetic anisotropies are nearly quantitative.

Structural characterisation of some vanillic Mannich bases: Experimental and theoretical study

NASA Astrophysics Data System (ADS)

Petrović, Vladimir P.; Simijonović, Dušica; Novaković, Sladjana B.; Bogdanović, Goran A.; Marković, Svetlana; Petrović, Zorica D.

2015-10-01

In this paper, synthesis and structural determination of 2-[1-(N-4-fluorophenylamino)-1-(4-hydroxy-3-methoxyphenyl)]methylcyclohexanone (MB-F) is presented. To determine the structure of this new compound, IR and NMR spectral characterisation was performed experimentally and theoretically. Simulation of spectral data was carried out using three functionals: B3LYP, B3LYP-D2, and M06-2X. The results obtained for MB-F were compared to those attained for similar, known compound 2-[1-(N-phenylamino)-1-(4-hydroxy-3-methoxyphenyl)]methylcyclohexanone (MB-H), whose crystal structure is presented here. Taking into account all experimental and theoretical findings, the structure of MB-F was proposed.

Correlation of Factor IXa Subsite Modulations with Effects on Substrate Discrimination

PubMed Central

Neuenschwander, Pierre F.; Deadmond, Kimberly J.; Zepeda, Karla; Rutland, Joshua

2012-01-01

Summary Background A key feature of factor IXa (fIXa) is its allosteric transformation from an enzymatically latent form into a potent procoagulant. Whilst several small molecules have been found capable of partially effecting fIXa function (i.e. ethylene glycol, calcium ion and LMWH), the resulting modest changes in peptidolytic activity have made the study of their mechanisms of action challenging. Since these effects yield hints into potential regulatory forces that may be operational in full expression of fIXa coagulant activity, their description remains of high interest. Studies of crystal structures have yielded insight into structural changes induced by these effectors, but there remains a paucity of information to correlate any given structural change with specific consequences on fIXa function. Objectives To correlate structural changes induced by these modulators with defined consequences in fIXa substrate discrimination and function. Methods A peptidomics-based MS approach was used to examine patterns of hydrolysis of four combinatorial chemistry-derived pentapeptide libraries by fIXa under various conditions in a soluble, active enzyme system. Results Ethylene glycol specifically alters the S3 subsite of fIXa to render it more tolerant to side chains at the P3 substrate position, while calcium enhances tolerance at the S2 subsite. In contrast, LMWH alters both S2 and S1' subsites. Conclusions These results demonstrate the role of plasticity in regulating fIXa function with respect to discrimination of extended substrate sequences, as well as provide crucial insight into active site modulations that may be capitalized upon by various physiological cofactors of fIXa and in future drug design. PMID:22212890

Synthesis and structural characterization of the hexagonal anti-perovskite Na{sub 2}CaVO{sub 4}F

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

Green, Robert L., E-mail: rgreen@flpoly.org; Avdeev, Maxim; School of Chemistry, The University of Sydney, Sydney, NSW 2006

The structural details of the ordered hexagonal oxyfluoride Na{sub 2}CaVO{sub 4}F prepared by solid-state synthesis using stoichiometric amounts of V{sub 2}O{sub 5}, CaCO{sub 3}, Na{sub 2}CO{sub 3} and NaF were characterized using high-resolution neutron powder diffraction. The structural changes between 25 °C and 750 °C revealed that the two structural subunits in this material behave different when heated: there is an expansion of the face-shared FNa{sub 4}Ca{sub 2} octahedra while the VO{sub 4} tetrahedra due to increased thermal disorder reveal marginal bond contractions. Bond valences and the global instability index point to significant structural disorder at 750 °C. - Graphicalmore » abstract: The structure of the novel oxyfluoride Na{sub 2}CaVO{sub 4}F is studied at room temperature and high-temperatures. The structure can be viewed as layers of compression and elongation of polyhedral subunits, which change as a function of temperature. - Highlights: • The novel oxyfluoride, Na{sub 2}CaVO{sub 4}F, is synthesized via solid-state method. • High-resolution neutron diffraction data is used to analyze the structure of Na{sub 2}CaVO{sub 4}F. • Structural subunits exhibit expansion and contraction with increasing temperature. • Higher temperatures increase instability within the structure of Na{sub 2}CaVO{sub 4}F.« less

Electrical conductivity and electromagnetic interference shielding of epoxy nanocomposite foams containing functionalized multi-wall carbon nanotubes

NASA Astrophysics Data System (ADS)

Li, Jiantong; Zhang, Guangcheng; Zhang, Hongming; Fan, Xun; Zhou, Lisheng; Shang, Zhengyang; Shi, Xuetao

2018-01-01

Epoxy/functionalized multi-wall carbon nanotube (EP/F-MWCNT) microcellular foams were fabricated through a supercritical CO2 (scCO2) foaming method. MWCNTs with carboxylation treatment were disentangled by using alpha-zirconium phosphate (ZrP) assisting dispersion method and functionalized with sulfanilamide. The F-MWCNTs were redispersed in acetone for mixing with epoxy resins to prepare nanocomposites. It was found that the dispersion of MWCNTs could be improved, thus heterogeneous nucleation effect of F-MWCNTs took place effectively during the foaming process, resulting in the formation of microcellular structure with larger cell density and smaller cell size. The volume conductivity and electromagnetic interference shielding performance of foamed EP/F-MWCNT nanocomposites were studied. When the F-MWCNT addition was 5 wt%, the conductivity of the foamed EP/F-MWCNT nanocomposites was 3.02 × 10-4 S/cm and the EMI shielding effectiveness (SE) reached 20.5 dB, significantly higher than the corresponding results of nanocomposite counterparts, indicating that introducing microcellular structure in EP/F-MWCNT nanocomposites would beneficial to improve their electrical conductivity and electromagnetic interference shielding performance.

The complete O (αs2) non-singlet heavy flavor corrections to the structure functions g1,2ep (x ,Q2), F1,2,Lep (x ,Q2), F1,2,3ν (ν bar) (x ,Q2) and the associated sum rules

NASA Astrophysics Data System (ADS)

Blümlein, Johannes; Falcioni, Giulio; De Freitas, Abilio

2016-09-01

We calculate analytically the flavor non-singlet O (αs2) massive Wilson coefficients for the inclusive neutral current non-singlet structure functions F1,2,Lep (x ,Q2) and g1,2ep (x ,Q2) and charged current non-singlet structure functions F1,2,3ν (ν bar) p (x ,Q2), at general virtualities Q2 in the deep-inelastic region. Numerical results are presented. We illustrate the transition from low to large virtualities for these observables, which may be contrasted to basic assumptions made in the so-called variable flavor number scheme. We also derive the corresponding results for the Adler sum rule, the unpolarized and polarized Bjorken sum rules and the Gross-Llewellyn Smith sum rule. There are no logarithmic corrections at large scales Q2 and the effects of the power corrections due to the heavy quark mass are of the size of the known O (αs4) corrections in the case of the sum rules. The complete charm and bottom corrections are compared to the approach using asymptotic representations in the region Q2 ≫mc,b2. We also study the target mass corrections to the above sum rules.

A next-to-leading-order QCD analysis of neutrino-iron structure functions at the Tevatron

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

Seligman, William Glenn

1997-01-01

Nucleon structure functions measured in neutrino-iron and antineutrino-iron charged-current interactions are presented. The data were taken in two high-energy high-statistics runs by the LAB-E detector at the Fermilab Tevatron. Structure functions are extracted from a sample of 950,000 neutrino and 170,000 antineutrino events with neutrino energies from 30 to 360 GeV. The structure functions F 2 and xF 3 are compared with the predictions of perturbative Quantum Chromodynamics (PQCD). The combined non-singlet and singlet evolution in the context of PQCD gives value of ΛNLO,(4)/MS = 337 ± 28 (exp.) MeV, which corresponds to α S(M Z 2) = 0.119 ±more » 0.002 (exp.) ± 0.004 (theory), and with a gluon distribution given by xG(x,Q 0 2 = 5GeV 2) = (2.22 ± 0.34) x (1 - x) 4.65±0.68.« less

A measurement of the proton structure function F2( x, Q2) at low x and low Q2 at HERA

NASA Astrophysics Data System (ADS)

Adloff, C.; Aid, S.; Anderson, M.; Andreev, V.; Andrieu, B.; Arkadov, V.; Arndt, C.; Ayyaz, I.; Babaev, A.; Bähr, J.; Bán, J.; Ban, Y.; Baranov, P.; Barrelet, E.; Barschke, R.; Bartel, W.; Bassler, U.; Beck, H. P.; Beck, M.; Behrend, H.-J.; Belousov, A.; Berger, Ch.; Bernardi, G.; Bertrand-Coremans, G.; Beyer, R.; Biddulph, P.; Bispham, P.; Bizot, J. C.; Borras, K.; Botterweck, F.; Boudry, V.; Bourov, S.; Braemer, A.; Braunschweig, W.; Brisson, V.; Brückner, W.; Bruel, P.; Bruncko, D.; Brune, C.; Buchholz, R.; Büngener, L.; Bürger, J.; Büsser, F. W.; Buniatian, A.; Burke, S.; Burton, M. J.; Buschhorn, G.; Calvet, D.; Campbell, A. J.; Carli, T.; Charlet, M.; Clarke, D.; Clerbaux, B.; Cocks, S.; Contreras, J. G.; Cormack, C.; Coughlan, J. A.; Courau, A.; Cousinou, M.-C.; Cox, B. E.; Cozzika, G.; Cussans, D. G.; Cvach, J.; Dagoret, S.; Dainton, J. B.; Dau, W. D.; Daum, K.; David, M.; Davis, C. L.; De Roeck, A.; De Wolf, E. A.; Delcourt, B.; Dirkmann, M.; Dixon, P.; Dlugosz, W.; Dollfus, C.; Donovan, K. T.; Dowell, J. D.; Dreis, H. B.; Droutskoi, A.; Ebert, J.; Ebert, T. R.; Eckerlin, G.; Efremenko, V.; Egli, S.; Eichler, R.; Eisele, F.; Eisenhandler, E.; Elsen, E.; Erdmann, M.; Fahr, A. B.; Favart, L.; Fedotov, A.; Felst, R.; Feltesse, J.; Ferencei, J.; Ferrarotto, F.; Flamm, K.; Fleischer, M.; Flieser, M.; Flügge, G.; Fomenko, A.; Formánek, J.; Foster, J. M.; Franke, G.; Gabathuler, E.; Gabathuler, K.; Gaede, F.; Garvey, J.; Gayler, J.; Gebauer, M.; Genzel, H.; Gerhards, R.; Glazov, A.; Goerlich, L.; Gogitidze, N.; Goldberg, M.; Goldner, D.; Golec-Biernat, K.; Gonzalez-Pineiro, B.; Gorelov, I.; Grab, C.; Grässler, H.; Greenshaw, T.; Griffiths, R. K.; Grindhammer, G.; Gruber, A.; Gruber, C.; Hadig, T.; Haidt, D.; Hajduk, L.; Haller, T.; Hampel, M.; Haynes, W. J.; Heinemann, B.; Heinzelmann, G.; Henderson, R. C. W.; Henschel, H.; Herynek, I.; Hess, M. F.; Hewitt, K.; Hiller, K. H.; Hilton, C. D.; Hladký, J.; Höppner, M.; Hoffmann, D.; Holtom, T.; Horisberger, R.; Hudgson, V. L.; Hütte, M.; Ibbotson, M.; İşsever, Ç.; Itterbeck, H.; Jacholkowska, A.; Jacobsson, C.; Jacquet, M.; Jaffre, M.; Janoth, J.; Jansen, D. M.; Jönsson, L.; Johnson, D. P.; Jung, H.; Kalmus, P. I. P.; Kander, M.; Kant, D.; Kathage, U.; Katzy, J.; Kaufmann, H. H.; Kaufmann, O.; Kausch, M.; Kazarian, S.; Kenyon, I. R.; Kermiche, S.; Keuker, C.; Kiesling, C.; Klein, M.; Kleinwort, C.; Knies, G.; Köhler, T.; Köhne, J. H.; Kolanoski, H.; Kolya, S. D.; Korbel, V.; Kostka, P.; Kotelnikov, S. K.; Krämerkämper, T.; Krasny, M. W.; Krehbiel, H.; Krücker, D.; Küpper, A.; Küster, H.; Kuhlen, M.; Kurča, T.; Kurzhöfer, J.; Laforge, B.; Landon, M. P. J.; Lange, W.; Langenegger, U.; Lebedev, A.; Lehner, F.; Lemaitre, V.; Levonian, S.; Lindstroem, M.; Linsel, F.; Lipinski, J.; List, B.; Lobo, G.; Lomas, J. W.; Lopez, G. C.; Lubimov, V.; Lüke, D.; Lytkin, L.; Magnussen, N.; Mahlke-Krüger, H.; Malinovski, E.; Maraček, R.; Marage, P.; Marks, J.; Marshall, R.; Martens, J.; Martin, G.; Martin, R.; Martyn, H.-U.; Martyniak, J.; Mavroidis, T.; Maxfield, S. J.; McMahon, S. J.; Mehta, A.; Meier, K.; Merkel, P.; Metlica, F.; Meyer, A.; Meyer, A.; Meyer, H.; Meyer, J.; Meyer, P.-O.; Migliori, A.; Mikocki, S.; Milstead, D.; Moeck, J.; Moreau, F.; Morris, J. V.; Mroczko, E.; Müller, D.; Walter, T.; Müller, K.; Murín, P.; Nagovizin, V.; Nahnhauer, R.; Naroska, B.; Naumann, Th.; Négri, I.; Newman, P. R.; Newton, D.; Nguyen, H. K.; Nicholls, T. C.; Niebergall, F.; Niebuhr, C.; Niedzballa, Ch.; Niggli, H.; Nowak, G.; Nunnemann, T.; Nyberg-Werther, M.; Oberlack, H.; Olsson, J. E.; Ozerov, D.; Palmen, P.; Panaro, E.; Panitch, A.; Pascaud, C.; Passaggio, S.; Patel, G. D.; Pawletta, H.; Peppel, E.; Perez, E.; Phillips, J. P.; Pieuchot, A.; Pitzl, D.; Pöschl, R.; Pope, G.; Povh, B.; Prell, S.; Rabbertz, K.; Rädel, G.; Reimer, P.; Rick, H.; Riess, S.; Rizvi, E.; Robmann, P.; Roosen, R.; Rosenbauer, K.; Rostovtsev, A.; Rouse, F.; Royon, C.; Rüter, K.; Rusakov, S.; Rybicki, K.; Sankey, D. P. C.; Schacht, P.; Schiek, S.; Schleif, S.; Schleper, P.; von Schlippe, W.; Schmidt, D.; Schmidt, G.; Schoeffel, L.; Schöning, A.; Schröder, V.; Schuhmann, E.; Schwab, B.; Sefkow, F.; Semenov, A.; Shekelyan, V.; Sheviakov, I.; Shtarkov, L. N.; Siegmon, G.; Siewert, U.; Sirois, Y.; Skillicorn, I. O.; Sloan, T.; Smirnov, P.; Smith, M.; Solochenko, V.; Soloviev, Y.; Specka, A.; Spiekermann, J.; Spielman, S.; Spitzer, H.; Squinabol, F.; Steffen, P.; Steinberg, R.; Steinhart, J.; Stella, B.; Stellberger, A.; Stier, J.; Stiewe, J.; Stöβlein, U.; Stolze, K.; Straumann, U.; Struczinski, W.; Sutton, J. P.; Tapprogge, S.; Taševský, M.; Tchernyshov, V.; Tchetchelnitski, S.; Theissen, J.; Thompson, G.; Thompson, P. D.; Tobien, N.; Todenhagen, R.; Truöl, P.; Tsipolitis, G.; Turnau, J.; Tzamariudaki, E.; Uelkes, P.; Usik, A.; Valkár, S.; Valkárová, A.; Valĺee, C.; Van Esch, P.; Van Mechelen, P.; Vandenplas, D.; Vazdik, Y.; Verrecchia, P.; Villet, G.; Wacker, K.; Wagener, A.; Wagener, M.; Wallny, R.; Waugh, B.; Weber, G.; Weber, M.; Wegener, D.; Wegner, A.; Wengler, T.; Werner, M.; West, L. R.; Wiesand, S.; Wilksen, T.; Willard, S.; Winde, M.; Winter, G.-G.; Wittek, C.; Wobisch, M.; Wollatz, H.; Wünsch, E.; Žáček, J.; Zarbock, D.; Zhang, Z.; Zhokin, A.; Zini, P.; Zomer, F.; Zsembery, J.; zurNedden, M.; H1 Collaboration

1997-02-01

The results of a measurement of the proton structure function F2( x, Q2) and the virtual photon-proton cross section are reported for momentum transfers squared Q2 between 0.35 GeV 2 and 3.5 GeV 2 and for Bjorken- x values down to 6 × 10 -6 using data collected by the HERA experiment H1 in 1995. The data represent an increase in kinematic reach to lower x and Q2 values of about a factor of 5 compared to previous H1 measurements. Including measurements from fixed target experiments the rise of F2 with decreasing x is found to be less steep for the lowest Q2 values measured. Phenomenological models at low Q2 are compared with the data.

Density Functional Study of Structures and Electron Affinities of BrO4F/BrO4F−

PubMed Central

Gong, Liangfa; Xiong, Jieming; Wu, Xinmin; Qi, Chuansong; Li, Wei; Guo, Wenli

2009-01-01

The structures, electron affinities and bond dissociation energies of BrO4F/BrO4F− species have been investigated with five density functional theory (DFT) methods with DZP++ basis sets. The planar F-Br…O2…O2 complexes possess 3A′ electronic state for neutral molecule and 4A′ state for the corresponding anion. Three types of the neutral-anion energy separations are the adiabatic electron affinity (EAad), the vertical electron affinity (EAvert), and the vertical detachment energy (VDE). The EAad value predicted by B3LYP method is 4.52 eV. The bond dissociation energies De (BrO4F → BrO4-mF + Om) (m = 1–4) and De− (BrO4F− → BrO4-mF− + Om and BrO4F− → BrO4-mF + Om−) are predicted. The adiabatic electron affinities (EAad) were predicted to be 4.52 eV for F-Br…O2…O2 (3A′←4A′) (B3LYP method). PMID:19742128

Variola virus F1L is a Bcl-2-like protein that unlike its vaccinia virus counterpart inhibits apoptosis independent of Bim

PubMed Central

Marshall, B; Puthalakath, H; Caria, S; Chugh, S; Doerflinger, M; Colman, P M; Kvansakul, M

2015-01-01

Subversion of host cell apoptosis is an important survival strategy for viruses to ensure their own proliferation and survival. Certain viruses express proteins homologous in sequence, structure and function to mammalian pro-survival B-cell lymphoma 2 (Bcl-2) proteins, which prevent rapid clearance of infected host cells. In vaccinia virus (VV), the virulence factor F1L was shown to be a potent inhibitor of apoptosis that functions primarily be engaging pro-apoptotic Bim. Variola virus (VAR), the causative agent of smallpox, harbors a homolog of F1L of unknown function. We show that VAR F1L is a potent inhibitor of apoptosis, and unlike all other characterized anti-apoptotic Bcl-2 family members lacks affinity for the Bim Bcl-2 homology 3 (BH3) domain. Instead, VAR F1L engages Bid BH3 as well as Bak and Bax BH3 domains. Unlike its VV homolog, variola F1L only protects against Bax-mediated apoptosis in cellular assays. Crystal structures of variola F1L bound to Bid and Bak BH3 domains reveal that variola F1L forms a domain-swapped Bcl-2 fold, which accommodates Bid and Bak BH3 in the canonical Bcl-2-binding groove, in a manner similar to VV F1L. Despite the observed conservation of structure and sequence, variola F1L inhibits apoptosis using a startlingly different mechanism compared with its VV counterpart. Our results suggest that unlike during VV infection, Bim neutralization may not be required during VAR infection. As molecular determinants for the human-specific tropism of VAR remain essentially unknown, identification of a different mechanism of action and utilization of host factors used by a VAR virulence factor compared with its VV homolog suggest that studying VAR directly may be essential to understand its unique tropism. PMID:25766319

Variola virus F1L is a Bcl-2-like protein that unlike its vaccinia virus counterpart inhibits apoptosis independent of Bim.

PubMed

Marshall, B; Puthalakath, H; Caria, S; Chugh, S; Doerflinger, M; Colman, P M; Kvansakul, M

2015-03-12

Subversion of host cell apoptosis is an important survival strategy for viruses to ensure their own proliferation and survival. Certain viruses express proteins homologous in sequence, structure and function to mammalian pro-survival B-cell lymphoma 2 (Bcl-2) proteins, which prevent rapid clearance of infected host cells. In vaccinia virus (VV), the virulence factor F1L was shown to be a potent inhibitor of apoptosis that functions primarily be engaging pro-apoptotic Bim. Variola virus (VAR), the causative agent of smallpox, harbors a homolog of F1L of unknown function. We show that VAR F1L is a potent inhibitor of apoptosis, and unlike all other characterized anti-apoptotic Bcl-2 family members lacks affinity for the Bim Bcl-2 homology 3 (BH3) domain. Instead, VAR F1L engages Bid BH3 as well as Bak and Bax BH3 domains. Unlike its VV homolog, variola F1L only protects against Bax-mediated apoptosis in cellular assays. Crystal structures of variola F1L bound to Bid and Bak BH3 domains reveal that variola F1L forms a domain-swapped Bcl-2 fold, which accommodates Bid and Bak BH3 in the canonical Bcl-2-binding groove, in a manner similar to VV F1L. Despite the observed conservation of structure and sequence, variola F1L inhibits apoptosis using a startlingly different mechanism compared with its VV counterpart. Our results suggest that unlike during VV infection, Bim neutralization may not be required during VAR infection. As molecular determinants for the human-specific tropism of VAR remain essentially unknown, identification of a different mechanism of action and utilization of host factors used by a VAR virulence factor compared with its VV homolog suggest that studying VAR directly may be essential to understand its unique tropism.

The Modeling and Control of Acoustic/Structure Interaction Problems via Piezoceramic Actuators: 2-D Numerical Examples

DTIC Science & Technology

1992-04-01

the voltage applied to the it" patch, K ’ is a parameter which depends on the geometry and piezoceramic...in the state space II L 2(fQ) x L2 (F0 ). Here L2(Q) is the quotient space of L2 over the constant functions. The use of the quotient space results...form of the problem, we also define the Hilbert space V = fti(Q) x H(F 0 ) where h!(Q) is the quotient space of Il’ over the constant functions

A measurement and QCD analysis of the proton structure function F2 ( x, Q2) at HERA

NASA Astrophysics Data System (ADS)

Aid, S.; Andreev, V.; Andrieu, B.; Appuhn, R.-D.; Arpagaus, M.; Babaev, A.; Bähr, J.; Bán, J.; Ban, Y.; Baranov, P.; Barrelet, E.; Barschke, R.; Bartel, W.; Barth, M.; Bassler, U.; Beck, H. P.; Behrend, H.-J.; Belousov, A.; Berger, Ch.; Bernardi, G.; Bernet, R.; Bertrand-Coremans, G.; Besançoni, M.; Beyer, R.; Biddulph, P.; Bispham, P.; Bizot, J. C.; Blobel, V.; Borras, K.; Botterweck, F.; Boudry, V.; Braemer, A.; Braunschweig, W.; Brisson, V.; Bruncko, D.; Brune, C.; Buchholz, R.; Büngener, L.; BurgerF. W. Büsser, J.; Buniatian, A.; Burke, S.; Burton, M. J.; Buschhorn, G.; Campbell, A. J.; Carli, T.; Charles, F.; Charlet, M.; Clarke, D.; Clegg, A. B.; Clerbaux, B.; Cocks, S.; Contreras, J. G.; Cormack, C.; Coughlan, J. A.; Courau, A.; Cousinou, M.-C.; Cozzika, G.; Criegee, L.; Cussans, D. G.; Cvach, J.; Dagoret, S.; Dainton, J. B.; Dau, W. D.; Daum, K.; David, M.; Davis, C. L.; Delcourt, B.; De Roeck, A.; De Wolf, E. A.; Dirkmann, M.; Dixon, P.; Di Nezza, P.; Dlugosz, W.; Dollfus, C.; Dowell, J. D.; Dreis, H. B.; Droutskoi, A.; Düllmann, D.; Dünger, O.; Duhm, H.; Ebert, J.; Ebert, T. R.; Eckerlin, G.; Efremenko, V.; Egli, S.; Eichler, R.; Eisele, F.; Eisenhandler, E.; Ellison, R. J.; Elsen, E.; Erdmann, M.; Erdmann, W.; Evrard, E.; Fahr, A. B.; Favart, L.; Fedotov, A.; Feeken, D.; Felst, R.; Feltesse, J.; Ferencei, J.; Ferrarotto, F.; Flamm, K.; Fleischer, M.; Flieser, M.; Flügge, G.; Fomenko, A.; Fominykh, B.; Formánek, J.; Foster, J. M.; Franke, G.; Fretwurst, E.; Gabathuler, E.; Gabathuler, K.; Gaede, F.; Garvey, J.; Gayler, J.; Gebauer, M.; Gellrich, A.; Genzel, H.; Gerhards, R.; Glazov, A.; Goerlach, U.; Goerlich, L.; Gogitidze, N.; Goldberg, M.; Goldner, D.; Golec-Biernat, K.; Gonzalez-Pineiro, B.; Gorelov, I.; Grab, C.; Grässler, H.; Grässler, R.; Greenshaw, T.; Griffiths, R.; Grindhammer, G.; Gruber, A.; Gruber, C.; Haack, J.; Haidt, D.; Hajduk, L.; Hampel, M.; Haynes, W. J.; Heinzelmann, G.; Henderson, R. C. W.; Henschel, H.; Herynek, I.; Hess, M. F.; Hildesheim, W.; Hiller, K. H.; Hilton, C. D.; Hladký, J.; Hoeger, K. C.; Höppner, M.; Hoffmann, D.; Holtom, T.; Horisberger, R.; Hudgson, V. L.; Hütte, M.; Hufnagel, H.; Ibbotson, M.; Itterbeck, H.; Jacholkowska, A.; Jacobsson, C.; Jaffre, M.; Janoth, J.; Jansen, T.; Jönsson, L.; Johannsen, K.; Johnson, D. P.; Johnson, L.; Jung, H.; Kalmus, P. I. P.; Kander, M.; Kant, D.; Kaschowitz, R.; Kathage, U.; Katzy, J.; Kaufmann, H. H.; Kazarian, S.; Kenyon, I. R.; Kermiche, S.; Keuker, C.; Kiesling, C.; Klein, M.; Kleinwort, C.; Knies, G.; Köhler, T.; Köhne, J. H.; Kolanoski, H.; Kole, F.; Kolya, S. D.; Korbel, V.; Korn, M.; Kostka, P.; Kotelnikov, S. K.; Krämerkämper, T.; Krasny, M. W.; Krehbie, H.; Krücker, D.; Krüger, U.; Krüner-Marquis, U.; Küster, H.; Kuhlen, M.; Kurča, T.; Kurzhöfer, J.; Lacour, D.; Laforge, B.; Lander, R.; Landon, M. P. J.; Lange, W.; Langenegger, U.; Laporte, J.-F.; Lebedev, A.; Lehner, F.; Leverenz, C.; Levonian, S.; Ley, Ch.; Lindström, G.; Lindstroem, M.; Link, J.; Linsel, F.; Lipinski, J.; List, B.; Lobo, G.; Lohmander, H.; Lomas, J. W.; Lopez, G. C.; Lubimov, V.; Lüke, D.; Magnussen, N.; Malinovski, E.; Mani, S.; Maraček, R.; Marage, P.; Marks, J.; Marshall, R.; Martens, J.; Martin, G.; Martin, R.; Martyn, H.-U.; Martyniak, J.; Mavroidis, T.; Maxfield, S. J.; McMahon, S. J.; Mehta, A.; Meier, K.; Merz, T.; Meyer, A.; MeyerH. Meyer, A.; Meyer, J.; Meyer, P.-O.; Migliori, A.; Mikocki, S.; Milstead, D.; Moeck, J.; Moreau, F.; Morris, J. V.; Mroczko, E.; Müller, D.; Müller, G.; Müller, K.; Murín, P.; Nagovizin, V.; Nahnhauer, R.; Naroska, B.; Naumann, Th.; Newman, P. R.; Newton, D.; Neyret, D.; Nguyen, H. K.; Nicholls, T. C.; Niebergall, F.; Niebuhr, C.; Niedzballa, Ch.; Niggli, H.; Nisius, R.; Nowak, G.; Noyes, G. W.; Nyberg-Werther, M.; Oakden, M.; Oberlack, H.; Obrock, U.; Olsson, J. E.; Ozerov, D.; Palmen, P.; Panaro, E.; Panitch, A.; Pascaud, C.; Patel, G. D.; Pawletta, H.; Peppel, E.; Perez, E.; Phillips, J. P.; Pieuchot, A.; Pitzl, D.; Pope, G.; Prell, S.; Prosi, R.; Rabbertz, K.; Rädel, G.; Raupach, F.; Reimer, P.; Reinshagen, S.; Rick, H.; Riech, V.; Riedlberger, J.; Riepenhausen, F.; Riess, S.; Rizvi, E.; Robertson, S. M.; Robmann, P.; Roloff, H. E.; Roosen, R.; Rosenbauer, K.; Rostovtsev, A.; Rouse, F.; Royon, C.; Rüter, K.; Rusakov, S.; Rybicki, K.; Sahlmann, N.; Sankey, D. P. C.; Schacht, P.; Schiek, S.; Schleif, S.; Schleper, P.; von Schlippe, W.; Schmidt, D.; Schmidt, G.; Schöning, A.; Schröder, V.; Schuhmann, E.; Schwab, B.; Sefkow, F.; Seidel, M.; Sell, R.; Semenov, A.; Shekelyan, V.; Sheviakov, I.; Shtarkov, L. N.; Siegmon, G.; Siewert, U.; Sirois, Y.; Skillicorn, I. O.; Smirnov, P.; Smith, J. R.; Solochenko, V.; Soloviev, H.; Specka, A.; Spiekermann, J.; Spielman, S.; Spitzer, H.; Squinabl, F.; Starosta, R.; Steenbock, M.; Steffen, P.; Steinberg, R.; Steiner, H.; Stella, B.; Stellberger, A.; Stier, J.; Stiewe, J.; Stößlein, U.; Stolze, K.; Straumann, U.; Struczinski, W.; Sutton, J. P.; Tapprogge, S.; Taševský, M.; Tchernyshov, V.; Tchetchelnitski, S.; Theissen, J.; Thiebaux, C.; Thompson, G.; Truöl, P.; Turnau, J.; Tutas, J.; Uelkes, P.; Usik, A.; Valkár, S.; Valkárová, A.; Vallée, C.; Vandenplas, D.; Van Esch, P.; Van Mechelen, P.; Vazdik, Y.; Verrecchi, P.; Villet, G.; Wacker, K.; Wagener, A.; Wagener, M.; Walther, A.; Waugh, B.; Weber, G.; Weber, M.; Wegener, D.; Wegner, A.; Wengler, T.; Werner, M.; West, L. R.; Wilksen, T.; Willard, S.; Winde, M.; Winter, G.-G.; Wittek, C.; Wünsch, E.; Žáček, J.; Zarbock, D.; Zhang, Z.; Zhokin, A.; Zimmer, M.; Zomer, F.; Zsembery, J.; Zuber, K.; zurNedden, M.; Kaufmannxa, O.; H1 Collaboration

1996-02-01

A new measurement of the proton structure function F2 ( x, Q2) is reported for momentum transfers squared Q2 between ].5 GeV 2 and 5000 GeV 2 and for Bjorken x between 3 · 10 -5 and 0.32 using data collected by the HERA experiment H1 in 1994. The data represent an increase in statistics by a factor of ten with respect to the analysis of the 1993 data. Substantial extension of the kinematic range towards low Q2 and x has been achieved using dedicated data samples and events with initial state photon radiation. The structure function is found to increase significantly with decreasing x, even in the lowest accessible Q2 region. The data are well described by a Next to Leading Order QCD fit and the gluon density is extracted.

Structures of the Ca2+-regulated photoprotein obelin Y138F mutant before and after bioluminescence support the catalytic function of a water molecule in the reaction.

PubMed

Natashin, Pavel V; Ding, Wei; Eremeeva, Elena V; Markova, Svetlana V; Lee, John; Vysotski, Eugene S; Liu, Zhi-Jie

2014-03-01

Ca(2+)-regulated photoproteins, which are responsible for light emission in a variety of marine coelenterates, are a highly valuable tool for measuring Ca(2+) inside living cells. All of the photoproteins are a single-chain polypeptide to which a 2-hydroperoxycoelenterazine molecule is tightly but noncovalently bound. Bioluminescence results from the oxidative decarboxylation of 2-hydroperoxycoelenterazine, generating protein-bound coelenteramide in an excited state. Here, the crystal structures of the Y138F obelin mutant before and after bioluminescence are reported at 1.72 and 1.30 Å resolution, respectively. The comparison of the spatial structures of the conformational states of Y138F obelin with those of wild-type obelin gives clear evidence that the substitution of Tyr by Phe does not affect the overall structure of both Y138F obelin and its product following Ca(2+) discharge compared with the corresponding conformational states of wild-type obelin. Despite the similarity of the overall structures and internal cavities of Y138F and wild-type obelins, there is a substantial difference: in the cavity of Y138F obelin a water molecule corresponding to W2 in wild-type obelin is not found. However, in Ca(2+)-discharged Y138F obelin this water molecule now appears in the same location. This finding, together with the observed much slower kinetics of Y138F obelin, clearly supports the hypothesis that the function of a water molecule in this location is to catalyze the 2-hydroperoxycoelenterazine decarboxylation reaction by protonation of a dioxetanone anion before its decomposition into the excited-state product. Although obelin differs from other hydromedusan Ca(2+)-regulated photoproteins in some of its properties, they are believed to share a common mechanism.

Lattice dynamics of Cs2NaYbF6 and Cs2NaYF6 elpasolites: Ab initio calculation

NASA Astrophysics Data System (ADS)

Chernyshev, V. A.; Petrov, V. P.; Nikiforov, A. E.; Zakir'yanov, D. O.

2015-06-01

The ab initio calculations of the crystal structure and the phonon spectrum of Cs2NaYbF6 and Cs2NaYF6 crystals with the elpasolite structure have been performed. The frequencies and types of fundamental vibrations have been determined. The calculations have been performed in the framework of the density functional theory using the molecular orbital method with hybrid functionals in the CRYSTAL09 program developed for the simulation of periodic structures. The outer 5 s and 5 p shells of the rare-earth ion have been described in Gaussian-type basis sets. The influence of inner shells, including 4 f electron shells, on the outer shells has been described using the pseudopotential. It has been shown that this approach allows the description of the phonon spectrum with the inclusion of the splitting of the longitudinal and transverse optical modes.

A density functional study of silicon fullerene endohedral X@Si20F20 and exohedral X-Si20F20 (X=O2-, S2-, Se2-) complexes

NASA Astrophysics Data System (ADS)

Behzadi, Hadi; Esrafili, Mehdi D.; Manzetti, Sergio; Roonasi, Payman

2014-02-01

This study reports the structure and electronic properties of three stable endohedral X@Si20F20 and exohedral X-Si20F20 (X=O2-, S2-, Se2-) complexes. The study revealed that the endohedral complexes with S2- and Se2- result as energy minimum structures, with the guest anion located in the cage center. In the case of endohedral O2--complexes, the pattern is quite different whereas the O2- complexes dramatically deviated from the architecture of S2- and Se2-, by having O2- located toward one of silicon atoms in the cage. With respect to the exohedral form, the energy minimized structure is obtained by positioning the anion between two silicon atoms and forming two Si-X bonds. For both cases, the strength of the interactions is calculated to increase accordingly to the pattern: Se2-@Si20F20 (Se2--Si20F20)

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

Anderson, Brian B.; Kirkegaard, Marie C.; Miskowiec, Andrew J.

Uranyl fluoride (UO 2F 2) is a hygroscopic powder with two main structural phases: an anhydrous crystal and a partially hydrated crystal of the same R¯3m symmetry. The formally closed-shell electron structure of anhydrous UO 2F 2 is amenable to density functional theory calculations. We use density functional perturbation theory (DFPT) to calculate the vibrational frequencies of the anhydrous crystal structure and employ complementary inelastic neutron scattering and temperature-dependent Raman scattering to validate those frequencies. As a model closed-shell actinide, we investigated the effect of LDA, GGA, and non-local vdW functionals as well as the spherically-averaged Hubbard +U correction onmore » vibrational frequencies, electronic structure, and geometry of anhydrous UO 2F 2. A particular choice of U eff = 5.5 eV yields the correct U Oyl bond distance and vibrational frequencies for the characteristic Eg and A1g modes that are within the resolution of experiment. Inelastic neutron scattering and Raman scattering suggest a degree of water coupling to the lattice vibrations in the more experimentally accessible partially hydrated UO 2F 2 system, with the symmetric O-U-O stretching vibration shifted approximately 47 cm -1 lower in energy compared to the anhydrous structure. Evidence of water interaction with the uranyl ion is present from a two-peak decomposition of the uranyl stretching vibration in the Raman spectra and anion hydrogen stretching vibrations in the inelastic neutron scattering spectra. A first-order dehydration phase transition temperature is definitively identified to be 125 °C using temperature-dependent Raman scattering.« less

Vibrational Properties of Anhydrous and Partially Hydrated Uranyl Fluoride

DOE PAGES

Anderson, Brian B.; Kirkegaard, Marie C.; Miskowiec, Andrew J.; ...

2017-01-01

Uranyl fluoride (UO 2F 2) is a hygroscopic powder with two main structural phases: an anhydrous crystal and a partially hydrated crystal of the same R¯3m symmetry. The formally closed-shell electron structure of anhydrous UO 2F 2 is amenable to density functional theory calculations. We use density functional perturbation theory (DFPT) to calculate the vibrational frequencies of the anhydrous crystal structure and employ complementary inelastic neutron scattering and temperature-dependent Raman scattering to validate those frequencies. As a model closed-shell actinide, we investigated the effect of LDA, GGA, and non-local vdW functionals as well as the spherically-averaged Hubbard +U correction onmore » vibrational frequencies, electronic structure, and geometry of anhydrous UO 2F 2. A particular choice of U eff = 5.5 eV yields the correct U Oyl bond distance and vibrational frequencies for the characteristic Eg and A1g modes that are within the resolution of experiment. Inelastic neutron scattering and Raman scattering suggest a degree of water coupling to the lattice vibrations in the more experimentally accessible partially hydrated UO 2F 2 system, with the symmetric O-U-O stretching vibration shifted approximately 47 cm -1 lower in energy compared to the anhydrous structure. Evidence of water interaction with the uranyl ion is present from a two-peak decomposition of the uranyl stretching vibration in the Raman spectra and anion hydrogen stretching vibrations in the inelastic neutron scattering spectra. A first-order dehydration phase transition temperature is definitively identified to be 125 °C using temperature-dependent Raman scattering.« less

Theoretical calculations of high-pressure phases of NiF2: An ab initio constant-pressure study

NASA Astrophysics Data System (ADS)

Kürkçü, Cihan; Merdan, Ziya; Öztürk, Hülya

2016-12-01

We have studied the structural properties of the antiferromagnetic NiF2 tetragonal structure with P42/ mnm symmetry using density functional theory (DFT) under rapid hydrostatic pressure up to 400 GPa. For the exchange correlation energy we used the local density approximation (LDA) of Ceperley and Alder (CA). Two phase transformations are successfully observed through the simulations. The structures of XF2-type compounds crystallize in rutile-type structure. NiF2 undergoes phase transformations from the tetragonal rutile-type structure with space group P42/ mnm to orthorhombic CaCl2-type structure with space group Pnnm and from this orthorhombic phase to monoclinic structure with space group C2/ m at 152 GPa and 360 GPa, respectively. These phase changes are also studied by total energy and enthalpy calculations. According to these calculations, we perdict these phase transformations at about 1.85 and 30 GPa.

Assigning the Cerium Oxidation State for CH2CeF2 and OCeF2 Based on Multireference Wave Function Analysis.

PubMed

Mooßen, Oliver; Dolg, Michael

2016-06-09

The geometric and electronic structure of the recently experimentally studied molecules ZCeF2 (Z = CH2, O) was investigated by density functional theory (DFT) and wave function-based ab initio methods. Special attention was paid to the Ce-Z metal-ligand bonding, especially to the nature of the interaction between the Ce 4f and the Z 2p orbitals and the possible multiconfigurational character arising from it, as well as to the assignment of an oxidation state of Ce reflecting the electronic structure. Complete active space self-consistent field (CASSCF) calculations were performed, followed by orbital rotations in the active orbital space. The methylene compound CH2CeF2 has an open-shell singlet ground state, which is characterized by a two-configurational wave function in the basis of the strongly mixed natural CASSCF orbitals. The system can also be described in a very compact way by the dominant Ce 4f(1) C 2p(1) configuration, if nearly pure Ce 4f and C 2p orbitals are used. In the basis of these localized orbitals, the molecule is almost monoconfigurational and should be best described as a Ce(III) system. The singlet ground state of the oxygen OCeF2 complex is of closed-shell character when a monoconfigurational wave function with very strongly mixed Ce 4f and O 2p CASSCF natural orbitals is used for the description. The transformation to orbitals localized on the cerium and oxygen atoms leads to a multiconfigurational wave function and reveals characteristics of a mixed valent Ce(IV)/Ce(III) compound. Additionally, the interactions of the localized active orbitals were analyzed by evaluating the expectation values of the charge fluctuation operator and the local spin operator. The Ce 4f and C 2p orbital interaction of the CH2CeF2 compound is weakly covalent and resembles the interaction of the H 1s orbitals in a stretched hydrogen dimer. In contrast, the interaction of the localized active orbitals for OCeF2 shows ionic character. Calculated vibrational Ce-C and Ce-O stretching frequencies at the DFT, CASSCF, second-order Rayleigh-Schrödinger perturbation theory (RS2C), multireference configuration interaction (MRCI), as well as single, doubles, and perturbative triples coupled cluster (CCSD(T)) level are reported and compared to experimental infrared absorption data in a Ne and Ar matrix.

ns2np4 (n = 4, 5) lone pair triplets whirling in M*F2E3 (M* = Kr, Xe): Stereochemistry and ab initio analyses

NASA Astrophysics Data System (ADS)

Galy, Jean; Matar, Samir F.

2017-02-01

The stereochemistry of ns2np4 (n = 4, 5) lone pair LP characterizing noble gas Kr and Xe (labeled M*) in M*F2 difluorides is examined within coherent crystal chemistry and ab initio visualizations. M*2+ in such oxidation state brings three lone pairs (E) and difluorides are formulated M*F2E3. The analyses use electron localization function (ELF) obtained within density functional theory calculations showing the development of the LP triplets whirling {E3} quantified in the relevant chemical systems. Detailed ELF data analyses allowed showing that in α KrF2E3 and isostructural XeF2E3 difluorides the three E electronic clouds merge or hybridize into a torus and adopt a perfect gyration circle with an elliptical section, while in β KrF2 the network architecture deforms the whole torus into an ellipsoid shape. Original precise metrics are provided for the torus in the different compounds under study. In KrF2 the geometric changes upon β → α phase transition is schematized and mechanisms for the transformation with temperature or pressure are proposed. The results are further highlighted by electronic band structure calculations which show similar features of equal band gaps of 3 eV in both α and β KrF2 and a reorganization of frontier orbitals due to the different orientations of the F-Kr-F linear molecule in the two tetragonal structures.

Pressure-induced photoluminescence in Mn2+-doped BaF2 and SrF2 fluorites

NASA Astrophysics Data System (ADS)

Hernández, Ignacio; Rodríguez, Fernando

2003-01-01

This work reports an effective way for inducing room temperature photoluminescence (PL) in Mn2+-doped BaF2 and SrF2 using high-pressure techniques. The aim is to understand the surprising PL behavior exhibited by Mn2+ at the cubal site of the fluorite structure. While Mn2+-doped CaF2 shows a green PL with quantum yield close to 1 at room temperature, Mn2+-doped MF2 (M=Ba,Sr) is not PL either at room temperature (SrF2) or at any temperature (BaF2) at ambient pressure. We associate the loss of Mn2+ PL on passing from CaF2 to SrF2 or BaF2 with nonradiative multiphonon relaxation whose thermal activation energy decreases along the series CaF2→SrF2→BaF2. A salient feature of this work deals with the increase of activation energy induced by pressure. It leads to a quantum yield enhancement, which favors PL recovery. Furthermore, the activation energy mainly depends on the crystal volume per molecule irrespective of the crystal structure or the local symmetry around the impurity. In this way, the relevance of the fluorite-to-cotunnite phase transition is analyzed in connection with the PL properties of the investigated compounds. The PL spectrum and the corresponding lifetime are reported for both structural phases as a function of pressure.

A Next-to-Leading Order QCD Analysis of Neutrino - Iron Structure Functions at the Tevatron

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

Seligman, William Glenn

1997-01-01

Nucleon structure functions measured in neutrino-iron and antineutrinoiron charged-current interactions are presented. The data were taken in two high-energy high-statistics runs by the LAB-E detector at the Fermilab Tevatron. Structure functions are extracted from a sample of 950,000 neutrino and 170,000 antineutrino events with neutrino energies from 30 to 360 Ge V. The structure functionsmore » $$F_2$$ and $$xF_3$$ are compared with the the predictions of perturbative Quantum Chromodynamics (PQCD). The combined non-singlet and singlet evolution in the context of PQCD gives NL0(4) . 2 value of $$\\Lambda^{NLO,(4)}_{\\overline MS}$$ = 337 ± 28 (exp.) MeV, which corresponds to $$\\alpha_s$$ ($$M^2_z$$) = 0.119 ± 0.002 (exp.) ± 0.004 (theory), and with a gluon distribution given by $$xG(x,Q^2_0 = 5 GeV^2$$ ) = (2.22±0.34) x ($$1-x)^{4.65 \\pm 0.68}$$« less

BID-F1 and BID-F2 Domains of Bartonella henselae Effector Protein BepF Trigger Together with BepC the Formation of Invasome Structures

PubMed Central

Truttmann, Matthias C.; Guye, Patrick; Dehio, Christoph

2011-01-01

The gram-negative, zoonotic pathogen Bartonella henselae (Bhe) translocates seven distinct Bartonella effector proteins (Beps) via the VirB/VirD4 type IV secretion system (T4SS) into human cells, thereby interfering with host cell signaling [1], [2]. In particular, the effector protein BepG alone or the combination of effector proteins BepC and BepF trigger massive F-actin rearrangements that lead to the establishment of invasome structures eventually resulting in the internalization of entire Bhe aggregates [2], [3]. In this report, we investigate the molecular function of the effector protein BepF in the eukaryotic host cell. We show that the N-terminal [E/T]PLYAT tyrosine phosphorylation motifs of BepF get phosphorylated upon translocation but do not contribute to invasome-mediated Bhe uptake. In contrast, we found that two of the three BID domains of BepF are capable to trigger invasome formation together with BepC, while a mutation of the WxxxE motif of the BID-F1 domain inhibited its ability to contribute to the formation of invasome structures. Next, we show that BepF function during invasome formation can be replaced by the over-expression of constitutive-active Rho GTPases Rac1 or Cdc42. Finally we demonstrate that BID-F1 and BID-F2 domains promote the formation of filopodia-like extensions in NIH 3T3 and HeLa cells as well as membrane protrusions in HeLa cells, suggesting a role for BepF in Rac1 and Cdc42 activation during the process of invasome formation. PMID:22043280

BID-F1 and BID-F2 domains of Bartonella henselae effector protein BepF trigger together with BepC the formation of invasome structures.

PubMed

Truttmann, Matthias C; Guye, Patrick; Dehio, Christoph

2011-01-01

The gram-negative, zoonotic pathogen Bartonella henselae (Bhe) translocates seven distinct Bartonella effector proteins (Beps) via the VirB/VirD4 type IV secretion system (T4SS) into human cells, thereby interfering with host cell signaling [1], [2]. In particular, the effector protein BepG alone or the combination of effector proteins BepC and BepF trigger massive F-actin rearrangements that lead to the establishment of invasome structures eventually resulting in the internalization of entire Bhe aggregates [2], [3]. In this report, we investigate the molecular function of the effector protein BepF in the eukaryotic host cell. We show that the N-terminal [E/T]PLYAT tyrosine phosphorylation motifs of BepF get phosphorylated upon translocation but do not contribute to invasome-mediated Bhe uptake. In contrast, we found that two of the three BID domains of BepF are capable to trigger invasome formation together with BepC, while a mutation of the WxxxE motif of the BID-F1 domain inhibited its ability to contribute to the formation of invasome structures. Next, we show that BepF function during invasome formation can be replaced by the over-expression of constitutive-active Rho GTPases Rac1 or Cdc42. Finally we demonstrate that BID-F1 and BID-F2 domains promote the formation of filopodia-like extensions in NIH 3T3 and HeLa cells as well as membrane protrusions in HeLa cells, suggesting a role for BepF in Rac1 and Cdc42 activation during the process of invasome formation.

E2F transcription factor-1 deficiency reduces pathophysiology in the mouse model of Duchenne muscular dystrophy through increased muscle oxidative metabolism.

PubMed

Blanchet, Emilie; Annicotte, Jean-Sébastien; Pradelli, Ludivine A; Hugon, Gérald; Matecki, Stéfan; Mornet, Dominique; Rivier, François; Fajas, Lluis

2012-09-01

E2F1 deletion leads to increased mitochondrial number and function, increased body temperature in response to cold and increased resistance to fatigue with exercise. Since E2f1-/- mice show increased muscle performance, we examined the effect of E2f1 genetic inactivation in the mdx background, a mouse model of Duchenne muscular dystrophy (DMD). E2f1-/-;mdx mice demonstrated a strong reduction of physiopathological signs of DMD, including preservation of muscle structure, decreased inflammatory profile, increased utrophin expression, resulting in better endurance and muscle contractile parameters, comparable to normal mdx mice. E2f1 deficiency in the mdx genetic background increased the oxidative metabolic gene program, mitochondrial activity and improved muscle functions. Interestingly, we observed increased E2F1 protein levels in DMD patients, suggesting that E2F1 might represent a promising target for the treatment of DMD.

Influence of genome-scale RNA structure disruption on the replication of murine norovirus—similar replication kinetics in cell culture but attenuation of viral fitness in vivo

PubMed Central

McFadden, Nora; Arias, Armando; Dry, Inga; Bailey, Dalan; Witteveldt, Jeroen; Evans, David J.; Goodfellow, Ian; Simmonds, Peter

2013-01-01

Mechanisms by which certain RNA viruses, such as hepatitis C virus, establish persistent infections and cause chronic disease are of fundamental importance in viral pathogenesis. Mammalian positive-stranded RNA viruses establishing persistence typically possess genome-scale ordered RNA secondary structure (GORS) in their genomes. Murine norovirus (MNV) persists in immunocompetent mice and provides an experimental model to functionally characterize GORS. Substitution mutants were constructed with coding sequences in NS3/4- and NS6/7-coding regions replaced with sequences with identical coding and (di-)nucleotide composition but disrupted RNA secondary structure (F1, F2, F1/F2 mutants). Mutants replicated with similar kinetics to wild-type (WT) MNV3 in RAW264.7 cells and primary macrophages, exhibited similar (highly restricted) induction and susceptibility to interferon-coupled cellular responses and equal replication fitness by serial passaging of co-cultures. In vivo, both WT and F1/F2 mutant viruses persistently infected mice, although F1, F2 and F1/F2 mutant viruses were rapidly eliminated 1–7 days post-inoculation in competition experiments with WT. F1/F2 mutants recovered from tissues at 9 months showed higher synonymous substitution rates than WT and nucleotide substitutions that potentially restored of RNA secondary structure. GORS plays no role in basic replication of MNV but potentially contributes to viral fitness and persistence in vivo. PMID:23630317

Measurement of the proton structure function F2 and σγ*ptot at low Q2 and very low x at HERA

NASA Astrophysics Data System (ADS)

Breitweg, J.; Derrick, M.; Krakauer, D.; Magill, S.; Mikunas, D.; Musgrave, B.; Repond, J.; Stanek, R.; Talaga, R. L.; Yoshida, R.; Zhang, H.; Mattingly, M. C. K.; Anselmo, F.; Antonioli, P.; Bari, G.; Basile, M.; Bellagamba, L.; Boscherini, D.; Bruni, A.; Bruni, G.; Romeo, G. Cara; Castellini, G.; Cifarelli, L.; Cindolo, F.; Contin, A.; Corradi, M.; de Pasquale, S.; Gialas, I.; Giusti, P.; Iacobucci, G.; Laurenti, G.; Levi, G.; Margotti, A.; Massam, T.; Nania, R.; Palmonari, F.; Pesci, A.; Polini, A.; Ricci, F.; Sartorelli, G.; Garcia, Y. Zamora; Zichichi, A.; Amelung, C.; Bornheim, A.; Brock, I.; Coböken, K.; Crittenden, J.; Deffner, R.; Eckert, M.; Grothe, M.; Hartmann, H.; Heinloth, K.; Heinz, L.; Hilger, E.; Jakob, H.-P.; Katz, U. F.; Kerger, R.; Paul, E.; Pfeiffer, M.; Rembser, Ch.; Stamm, J.; Wedemeyer, R.; Wieber, H.; Bailey, D. S.; Campbell-Robson, S.; Cottingham, W. N.; Foster, B.; Hall-Wilton, R.; Hayes, M. E.; Heath, G. P.; Heath, H. F.; Piccioni, D.; Roff, D. G.; Tapper, R. J.; Arneodo, M.; Ayad, R.; Capua, M.; Garfagnini, A.; Iannotti, L.; Schioppa, M.; Susinno, G.; Kim, J. Y.; Lee, J. H.; Lim, I. T.; Pac, M. Y.; Caldwell, A.; Cartiglia, N.; Jing, Z.; Liu, W.; Mellado, B.; Parsons, J. A.; Ritz, S.; Sampson, S.; Sciulli, F.; Straub, P. B.; Zhu, Q.; Borzemski, P.; Chwastowski, J.; Eskreys, A.; Jakubowski, Z.; Przybycień, M. B.; Zachara, M.; Zawiejski, L.; Adamczyk, L.; Bednarek, B.; Jeleń, J.; Kisielewska, D.; Kowalski, T.; Przybycień, M.; Rulikowska-Zarȩbska, E.; Suszycki, L.; Zajac, J.; Duliński, Z.; Kotański, A.; Abbiendi, G.; Bauerdick, L. A. T.; Behrens, U.; Beier, H.; Bienlein, J. K.; Cases, G.; Deppe, O.; Desler, K.; Drews, G.; Fricke, U.; Gilkinson, D. J.; Glasman, C.; Göttlicher, P.; Große-Knetter, J.; Haas, T.; Hain, W.; Hasell, D.; Johnson, K. F.; Kasemann, M.; Koch, W.; Kötz, U.; Kowalski, H.; Labs, J.; Lindemann, L.; Löhr, B.; Löwe, M.; Mańczak, O.; Milewski, J.; Monteiro, T.; Ng, J. S. T.; Notz, D.; Ohrenberg, K.; Park, I. H.; Pellegrino, A.; Pelucchi, F.; Piotrzkowski, K.; Roco, M.; Rohde, M.; Roldán, J.; Ryan, J. J.; Savin, A. A.; Schneekloth, U.; Selonke, F.; Surrow, B.; Tassi, E.; Voß, T.; Westphal, D.; Wolf, G.; Wollmer, U.; Youngman, C.; Żarnecki, A. F.; Zeuner, W.; Burow, B. D.; Grabosch, H. J.; Meyer, A.; Schlenstedt, S.; Barbagli, G.; Gallo, E.; Pelfer, P.; Maccarrone, G.; Votano, L.; Bamberger, A.; Eisenhardt, S.; Markun, P.; Trefzger, T.; Wölfle, S.; Bromley, J. T.; Brook, N. H.; Bussey, P. J.; Doyle, A. T.; Saxon, D. H.; Sinclair, L. E.; Strickland, E.; Utley, M. L.; Waugh, R.; Wilson, A. S.; Bohnet, I.; Gendner, N.; Holm, U.; Meyer-Larsen, A.; Salehi, H.; Wick, K.; Gladilin, L. K.; Horstmann, D.; Kçira, D.; Klanner, R.; Lohrmann, E.; Poelz, G.; Schott, W.; Zetsche, F.; Bacon, T. C.; Butterworth, I.; Cole, J. E.; Harris, V. L.; Howell, G.; Hung, B. H. Y.; Lamberti, L.; Long, K. R.; Miller, D. B.; Pavel, N.; Prinias, A.; Sedgbeer, J. K.; Sideris, D.; Whitfield, A. F.; Mallik, U.; Wang, S. M.; Wu, J. T.; Cloth, P.; Filges, D.; Fleck, J. I.; Ishii, T.; Kuze, M.; Nakao, M.; Tokushuku, K.; Yamada, S.; Yamazaki, Y.; An, S. H.; Lee, S. B.; Nam, S. W.; Park, H. S.; Park, S. K.; Barreiro, F.; Fernández, J. P.; García, G.; Graciani, R.; Hernández, J. M.; Hervás, L.; Labarga, L.; Martínez, M.; del Peso, J.; Puga, J.; Terrón, J.; de Trocóniz, J. F.; Corriveau, F.; Hanna, D. S.; Hartmann, J.; Hung, L. W.; Lim, J. N.; Murray, W. N.; Ochs, A.; Riveline, M.; Stairs, D. G.; St-Laurent, M.; Ullmann, R.; Tsurugai, T.; Bashkirov, V.; Dolgoshein, B. A.; Stifutkin, A.; Bashindzhagyan, G. L.; Ermolov, P. F.; Golubkov, Yu. A.; Khein, L. A.; Korotkova, N. A.; Korzhavina, I. A.; Kuzmin, V. A.; Lukina, O. Yu.; Proskuryakov, A. S.; Shcheglova, L. M.; Solomin, A. N.; Zotkin, S. A.; Bokel, C.; Botje, M.; Brümmer, N.; Chlebana, F.; Engelen, J.; Kooijman, P.; van Sighem, A.; Tiecke, H.; Tuning, N.; Verkerke, W.; Vossebeld, J.; Vreeswijk, M.; Wiggers, L.; de Wolf, E.; Acosta, D.; Bylsma, B.; Durkin, L. S.; Gilmore, J.; Ginsburg, C. M.; Kim, C. L.; Ling, T. Y.; Nylander, P.; Romanowski, T. A.; Blaikley, H. E.; Cashmore, R. J.; Cooper-Sarkar, A. M.; Devenish, R. C. E.; Edmonds, J. K.; Harnew, N.; Lancaster, M.; McFall, J. D.; Nath, C.; Noyes, V. A.; Quadt, A.; Ruske, O.; Tickner, J. R.; Uijterwaal, H.; Walczak, R.; Waters, D. S.; Bertolin, A.; Brugnera, R.; Carlin, R.; dal Corso, F.; Dosselli, U.; Limentani, S.; Morandin, M.; Posocco, M.; Stanco, L.; Stroili, R.; Voci, C.; Bulmahn, J.; Feild, R. G.; Oh, B. Y.; Okrasiński, J. R.; Whitmore, J. J.; Iga, Y.; D'Agostini, G.; Marini, G.; Nigro, A.; Raso, M.; Hart, J. C.; McCubbin, N. A.; Shah, T. P.; Epperson, D.; Heusch, C.; Rahn, J. T.; Sadrozinski, H. F.-W.; Seiden, A.; Williams, D. C.; Schwarzer, O.; Walenta, A. H.; Abramowicz, H.; Briskin, G.; Dagan, S.; Doeker, T.; Kananov, S.; Levy, A.; Abe, T.; Fusayasu, T.; Inuzuka, M.; Nagano, K.; Suzuki, I.; Umemori, K.; Yamashita, T.; Hamatsu, R.; Hirose, T.; Homma, K.; Kitamura, S.; Matsushita, T.; Yamauchi, K.; Cirio, R.; Costa, M.; Ferrero, M. I.; Maselli, S.; Monaco, V.; Peroni, C.; Petrucci, M. C.; Sacchi, R.; Solano, A.; Staiano, A.; Dardo, M.; Bailey, D. C.; Brkic, M.; Fagerstroem, C.-P.; Hartner, G. F.; Joo, K. K.; Levman, G. M.; Martin, J. F.; Orr, R. S.; Polenz, S.; Sampson, C. R.; Simmons, D.; Teuscher, R. J.; Butterworth, J. M.; Catterall, C. D.; Jones, T. W.; Kaziewicz, P. B.; Lane, J. B.; Saunders, R. L.; Shulman, J.; Sutton, M. R.; Lu, B.; Mo, L. W.; Ciborowski, J.; Grzelak, G.; Kasprzak, M.; Muchorowski, K.; Nowak, R. J.; Pawlak, J. M.; Pawlak, R.; Tymieniecka, T.; Wróblewski, A. K.; Zakrzewski, J. A.; Adamus, M.; Coldewey, C.; Eisenberg, Y.; Hochman, D.; Karshon, U.; Revel, D.; Badgett, W. F.; Chapin, D.; Cross, R.; Dasu, S.; Foudas, C.; Loveless, R. J.; Mattingly, S.; Reeder, D. D.; Smith, W. H.; Vaiciulis, A.; Wodarczyk, M.; Bhadra, S.; Frisken, W. R.; Khakzad, M.; Schmidke, W. B.

1997-02-01

A small electromagnetic sampling calorimeter, installed in the ZEUS experiment in 1995, significantly enhanced the acceptance for very low x and low Q2 inelastic neutral current scattering, e+p -> e+X, at HERA. A measurement of the proton structure function F2 and the total virtual photon-proton (γ*p) cross-section is presented for 0.11 <= Q2 <= 0.65 GeV2 and 2 × 10-6 <= x <= 6 × 10-5, corresponding to a range in the γ*p c.m. energy of 100 <= W <= 230 GeV. Comparisons with various models are also presented.

Plant functional traits and canopy structure control the relationship between photosynthetic CO2 uptake and far-red sun-induced fluorescence in a Mediterranean grassland under different nutrient availability.

PubMed

Migliavacca, Mirco; Perez-Priego, Oscar; Rossini, Micol; El-Madany, Tarek S; Moreno, Gerardo; van der Tol, Christiaan; Rascher, Uwe; Berninger, Anna; Bessenbacher, Verena; Burkart, Andreas; Carrara, Arnaud; Fava, Francesco; Guan, Jin-Hong; Hammer, Tiana W; Henkel, Kathrin; Juarez-Alcalde, Enrique; Julitta, Tommaso; Kolle, Olaf; Martín, M Pilar; Musavi, Talie; Pacheco-Labrador, Javier; Pérez-Burgueño, Andrea; Wutzler, Thomas; Zaehle, Sönke; Reichstein, Markus

2017-05-01

Sun-induced fluorescence (SIF) in the far-red region provides a new noninvasive measurement approach that has the potential to quantify dynamic changes in light-use efficiency and gross primary production (GPP). However, the mechanistic link between GPP and SIF is not completely understood. We analyzed the structural and functional factors controlling the emission of SIF at 760 nm (F 760 ) in a Mediterranean grassland manipulated with nutrient addition of nitrogen (N), phosphorous (P) or nitrogen-phosphorous (NP). Using the soil-canopy observation of photosynthesis and energy (SCOPE) model, we investigated how nutrient-induced changes in canopy structure (i.e. changes in plant forms abundance that influence leaf inclination distribution function, LIDF) and functional traits (e.g. N content in dry mass of leaves, N%, Chlorophyll a+b concentration (Cab) and maximum carboxylation capacity (V cmax )) affected the observed linear relationship between F 760 and GPP. We conclude that the addition of nutrients imposed a change in the abundance of different plant forms and biochemistry of the canopy that controls F 760 . Changes in canopy structure mainly control the GPP-F 760 relationship, with a secondary effect of Cab and V cmax . In order to exploit F 760 data to model GPP at the global/regional scale, canopy structural variability, biodiversity and functional traits are important factors that have to be considered. © 2017 The Authors. New Phytologist © 2017 New Phytologist Trust.

Ultrasound assisted simultaneous reduction and direct functionalization of graphene oxide with thermal and cytotoxicity profile.

PubMed

Maktedar, Shrikant S; Avashthi, Gopal; Singh, Man

2017-01-01

The new sonochemical approach for simultaneous reduction and direct functionalization of graphene oxide (GrO) has been developed. The GrO was functionalized with 2-Aminobenzoxazole (2-ABOZ) in twenty min with complete deletion of hazardous steps. The significance of ultrasound was exemplified with the comparative conventional methods. The newly prepared f-(2-ABOZ)GrO was extensively characterized with near edge X-ray absorption fine structure (NEXAFS) spectroscopy, 13 C solid state NMR, XPS, XRD, HRTEM, SAED, AFM, Raman, UV-vis, FTIR and TGA. The thermal stability of f-(2-ABOZ)GrO was confirmed with total percentage weight loss in TGA. The biological activity of f-(2-ABOZ)GrO was explored with MCF-7 and Vero cell lines. The inherent cytotoxicity was evaluated with SRB assay at 10, 20, 40 and 80μgmL -1 . The estimated cell viabilities were >78% with f-(2-ABOZ) GrO. A high cytocompatibility of f-(2-ABOZ)GrO was ensured with in vitro evaluation on living cell lines, and low toxicity of f-(2-ABOZ)GrO was confirmed its excellent biocompatibility. The morphological effect on Vero cell line evidently supports the formation of biocompatible f-(2-ABOZ)GrO. Therefore, f-(2-ABOZ)GrO was emerged as an advanced functional material for thermally stable biocompatible coatings. Copyright © 2016 Elsevier B.V. All rights reserved.

Structure-Function Correlation of G6, a Novel Small Molecule Inhibitor of Jak2

PubMed Central

Majumder, Anurima; Govindasamy, Lakshmanan; Magis, Andrew; Kiss, Róbert; Polgár, Tímea; Baskin, Rebekah; Allan, Robert W.; Agbandje-McKenna, Mavis; Reuther, Gary W.; Keserű, György M.; Bisht, Kirpal S.; Sayeski, Peter P.

2010-01-01

Somatic mutations in the Jak2 protein, such as V617F, cause aberrant Jak/STAT signaling and can lead to the development of myeloproliferative neoplasms. This discovery has led to the search for small molecule inhibitors that target Jak2. Using structure-based virtual screening, our group recently identified a novel small molecule inhibitor of Jak2 named G6. Here, we identified a structure-function correlation of this compound. Specifically, five derivative compounds of G6 having structural similarity to the original lead compound were obtained and analyzed for their ability to (i) inhibit Jak2-V617F-mediated cell growth, (ii) inhibit the levels of phospho-Jak2, phospho-STAT3, and phospho-STAT5; (iii) induce apoptosis in human erythroleukemia cells; and (iv) suppress pathologic cell growth of Jak2-V617F-expressing human bone marrow cells ex vivo. Additionally, we computationally examined the interactions of these compounds with the ATP-binding pocket of the Jak2 kinase domain. We found that the stilbenoid core-containing derivatives of G6 significantly inhibited Jak2-V617F-mediated cell proliferation in a time- and dose-dependent manner. They also inhibited phosphorylation of Jak2, STAT3, and STAT5 proteins within cells, resulting in higher levels of apoptosis via the intrinsic apoptotic pathway. Finally, the stilbenoid derivatives inhibited the pathologic growth of Jak2-V617F-expressing human bone marrow cells ex vivo. Collectively, our data demonstrate that G6 has a stilbenoid core that is indispensable for maintaining its Jak2 inhibitory potential. PMID:20667821

Charge structure of the hadronic final state in deep-inelastic muon-nucleon scattering

NASA Astrophysics Data System (ADS)

Arneodo, M.; Arvidson, A.; Aubert, J. J.; Bedełek, J.; Beaufays, J.; Bee, C. P.; Benchouk, C.; Berghoff, G.; Bird, I.; Blum, D.; Böhm, E.; de Bouard, X.; Brasse, F. W.; Braun, H.; Broll, C.; Brown, S.; Brück, H.; Calen, H.; Chima, J. S.; Ciborowski, J.; Clifft, R.; Coignet, G.; Combley, F.; Coughlan, J.; D'Agostini, G.; Dahlgren, S.; Dengler, F.; Derado, I.; Dreyer, T.; Drees, J.; Düren, M.; Eckardt, V.; Edwards, A.; Edwards, M.; Ernst, T.; Eszes, G.; Favier, J.; Ferrero, M. I.; Figiel, J.; Flauger, W.; Foster, J.; Ftáčnik, J.; Gabathuler, E.; Gajewski, J.; Gamet, R.; Gayler, J.; Geddes, N.; Grafström, P.; Grard, F.; Haas, J.; Hagberg, E.; Hasert, F. J.; Hayman, P.; Heusse, P.; Jaffré, M.; Jachołkowska, A.; Janata, F.; Jancsó, G.; Johnson, A. S.; Kabuss, E. M.; Kellner, G.; Korbel, V.; Krüger, J.; Kullander, S.; Landgraf, U.; Lanske, D.; Loken, J.; Long, K.; Maire, M.; Malecki, P.; Manz, A.; Maselli, S.; Mohr, W.; Montanet, F.; Montgomery, H. E.; Nagy, E.; Nassalski, J.; Norton, P. R.; Oakham, F. G.; Osborne, A. M.; Pascaud, C.; Pawlik, B.; Payre, P.; Peroni, C.; Peschel, H.; Pessard, H.; Pettinghale, J.; Pietrzyk, B.; Pietrzyk, U.; Pönsgen, B.; Pötsch, M.; Renton, P.; Ribarics, P.; Rith, K.; Rondio, E.; Sandacz, A.; Scheer, M.; Schlagböhmer, A.; Schiemann, H.; Schmitz, N.; Schneegans, M.; Schneider, A.; Scholz, M.; Schröder, T.; Schultze, K.; Sloan, T.; Stier, H. E.; Studt, M.; Taylor, G. N.; Thénard, J. M.; Thompson, J. C.; de La Torre, A.; Toth, J.; Urban, L.; Wallucks, W.; Whalley, M.; Wheeler, S.; Williams, W. S. C.; Wimpenny, S. J.; Windmolders, R.; Wolf, G.

1988-09-01

The general charge properties of the hadronic final state produced in μ + p and μ + d interactions at 280 GeV are investigated. Quark charge retention and local charge compensation is observed. The ratio F {2/ n }/ F {2/ p } of the neutron to proton structure function is derived from the measurement of the average hadronic charge in μ d interactions.

The phase diagrams of KCaF3 and NaMgF3 by ab initio simulations

NASA Astrophysics Data System (ADS)

Jakymiw, Clément; Vočadlo, Lidunka; Dobson, David P.; Bailey, Edward; Thomson, Andrew R.; Brodholt, John P.; Wood, Ian G.; Lindsay-Scott, Alex

2018-04-01

ABF3 compounds have been found to make valuable low-pressure analogues for high-pressure silicate phases that are present in the Earth's deep interior and that may also occur in the interiors of exoplanets. The phase diagrams of two of these materials, KCaF3 and NaMgF3, have been investigated in detail by static ab initio computer simulations based on density functional theory. Six ABF3 polymorphs were considered, as follows: the orthorhombic perovskite structure (GdFeO3-type; space group Pbnm); the orthorhombic CaIrO3 structure ( Cmcm; commonly referred to as the "post-perovskite" structure); the orthorhombic Sb2S3 and La2S3 structures (both Pmcn); the hexagonal structure previously suggested in computer simulations of NaMgF3 ( P63/ mmc); the monoclinic structure found to be intermediate between the perovskite and CaIrO3 structures in CaRhO3 ( P21/ m). Volumetric and axial equations of state of all phases considered are presented. For KCaF3, as expected, the perovskite phase is shown to be the most thermodynamically stable at atmospheric pressure. With increasing pressure, the relative stability of the KCaF3 phases then follows the sequence: perovskite → La2S3 structure → Sb2S3 structure → P63/ mmc structure; the CaIrO3 structure is never the most stable form. Above about 2.6 GPa, however, none of the KCaF3 polymorphs are stable with respect to dissociation into KF and CaF2. The possibility that high-pressure KCaF3 polymorphs might exist metastably at 300 K, or might be stabilised by chemical substitution so as to occur within the standard operating range of a multi-anvil press, is briefly discussed. For NaMgF3, the transitions to the high-pressure phases occur at pressures outside the normal range of a multi-anvil press. Two different sequences of transitions had previously been suggested from computer simulations. With increasing pressure, we find that the relative stability of the NaMgF3 phases follows the sequence: perovskite → CaIrO3 structure → Sb2S3 structure → P63/ mmc structure. However, only the perovskite and CaIrO3 structures are stable with respect to dissociation into NaF and MgF2.

Synthesis, fungicidal activity, structure-activity relationships (SARs) and density functional theory (DFT) studies of novel strobilurin analogues containing arylpyrazole rings.

PubMed

Liu, Yuanyuan; Lv, Kunzhi; Li, Yi; Nan, Qiuli; Xu, Jinyuan

2018-05-18

A series of novel strobilurin analogues (1a-1f, 2a-2e, 3a-3e) containing arylpyrazole rings were synthesized and characterized by NMR spectroscopy. The structures of 1f, 2b and 3b were also determined by single crystal X-ray diffraction analysis. These analogues were collected together with other twenty-eight similar compounds 4a-4f, 5a-5h, 6a-6h and 7a-7f from our previous studies, for in vitro bioassays and thorough structure-activity relationships (SARs) studies. Most compounds exhibited excellent-to-good fungicidal activity against Rhizoctonia solani, especially 5c, 7a, 6c, and 3b with 98.94%, 83.40%, 71.40% and 65.87% inhibition rates at 0.1 μg mL -1 , respectively, better than commercial pyraclostrobin. Comparative molecular field analysis (CoMFA) was employed to study three-dimensional quantitative structure-activity relationships (3D-QSARs). Density functional theory (DFT) calculation was also carried out to provide more information regarding SARs. The present work provided some hints for developing novel strobilurin fungicides.

Evolution of the orbitals Dy-4f in the DyB2 compound using the LDA, PBE approximations, and the PBE0 hybrid functional

NASA Astrophysics Data System (ADS)

Rasero Causil, Diego; Ortega López, César; Espitia Rico, Miguel

2018-04-01

Computational calculations of total energy based on density functional theory were used to investigate the structural, electronic, and magnetic properties of the DyB2 compounds in the hexagonal structure. The calculations were carried out by means of the full-potential linearized augmented plane wave (FP-LAPW) method, employing the computational Wien2k package. The local density approximation (LDA) and the generalized gradient approximation (GGA) were used for the electron-electron interactions. Additionally, we used the functional hybrid PBE0 for a better description the electronic and magnetic properties, because the DyB2 compound is a strongly-correlated system. We found that the calculated lattice constant agrees well with the values reported theoretically and experimentally. The density of states (DOS) calculation shows that the compound exhibits a metallic behavior and has magnetic properties, with a total magnetic moment of 5.47 μ0/cell determined mainly by the 4f states of the rare earth elements. The functional PBE0 shows a strong localization of the Dy-4f orbitals.

Complementary aspects of diffusion imaging and fMRI; I: structure and function.

PubMed

Mulkern, Robert V; Davis, Peter E; Haker, Steven J; Estepar, Raul San Jose; Panych, Lawrence P; Maier, Stephan E; Rivkin, Michael J

2006-05-01

Studying the intersection of brain structure and function is an important aspect of modern neuroscience. The development of magnetic resonance imaging (MRI) over the last 25 years has provided new and powerful tools for the study of brain structure and function. Two tools in particular, diffusion imaging and functional MRI (fMRI), are playing increasingly important roles in elucidating the complementary aspects of brain structure and function. In this work, we review basic technical features of diffusion imaging and fMRI for studying the integrity of white matter structural components and for determining the location and extent of cortical activation in gray matter, respectively. We then review a growing body of literature in which the complementary aspects of diffusion imaging and fMRI, applied as separate examinations but analyzed in tandem, have been exploited to enhance our knowledge of brain structure and function.

Role of 4 f electrons in crystallographic and magnetic complexity

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

Pathak, Arjun K.; Paudyal, Durga; Mudryk, Yaroslav

2017-08-09

Here, the functionality of many magnetic materials critically depends on first manipulating and then taking advantage of highly nonlinear changes of properties that occur during phase transformations. Unique to lanthanides, property-defining 4f electrons are highly localized and, as commonly accepted, play little to no role in chemical bonding. Yet here we demonstrate that the competition between 4f-electron energy landscapes of Dy (4f 9) and Er (4f 11) is the key element of the puzzle required to explain complex interplay of magnetic and structural features observed in Er 1–xDy xCo 2, and likely many other mixed lanthanide systems. Unlike the parentmore » binaries—DyCo 2 and ErCo 2—Er 1–xDy xCo 2 exhibits two successive magnetostructural transitions: a first order at TC, followed by a second order in the ferrimagnetically ordered state. Supported by first-principles calculations, our results offer new opportunities for targeted design of magnetic materials with multiple functionalities, and also provide a critical insight into the role of 4f electrons in controlling the magnetism and structure of lanthanide intermetallics.« less

F-BAR family proteins, emerging regulators for cell membrane dynamic changes-from structure to human diseases.

PubMed

Liu, Suxuan; Xiong, Xinyu; Zhao, Xianxian; Yang, Xiaofeng; Wang, Hong

2015-05-09

Eukaryotic cell membrane dynamics change in curvature during physiological and pathological processes. In the past ten years, a novel protein family, Fes/CIP4 homology-Bin/Amphiphysin/Rvs (F-BAR) domain proteins, has been identified to be the most important coordinators in membrane curvature regulation. The F-BAR domain family is a member of the Bin/Amphiphysin/Rvs (BAR) domain superfamily that is associated with dynamic changes in cell membrane. However, the molecular basis in membrane structure regulation and the biological functions of F-BAR protein are unclear. The pathophysiological role of F-BAR protein is unknown. This review summarizes the current understanding of structure and function in the BAR domain superfamily, classifies F-BAR family proteins into nine subfamilies based on domain structure, and characterizes F-BAR protein structure, domain interaction, and functional relevance. In general, F-BAR protein binds to cell membrane via F-BAR domain association with membrane phospholipids and initiates membrane curvature and scission via Src homology-3 (SH3) domain interaction with its partner proteins. This process causes membrane dynamic changes and leads to seven important cellular biological functions, which include endocytosis, phagocytosis, filopodium, lamellipodium, cytokinesis, adhesion, and podosome formation, via distinct signaling pathways determined by specific domain-binding partners. These cellular functions play important roles in many physiological and pathophysiological processes. We further summarize F-BAR protein expression and mutation changes observed in various diseases and developmental disorders. Considering the structure feature and functional implication of F-BAR proteins, we anticipate that F-BAR proteins modulate physiological and pathophysiological processes via transferring extracellular materials, regulating cell trafficking and mobility, presenting antigens, mediating extracellular matrix degradation, and transmitting signaling for cell proliferation.

Domain organization and crystal structure of the catalytic domain of E.coli RluF, a pseudouridine synthase that acts on 23S rRNA

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

Sunita,S.; Zhenxing, H.; Swaathi, J.

2006-01-01

Pseudouridine synthases catalyze the isomerization of uridine to pseudouridine ({psi}) in rRNA and tRNA. The pseudouridine synthase RluF from Escherichia coli (E.C. 4.2.1.70) modifies U2604 in 23S rRNA, and belongs to a large family of pseudouridine synthases present in all kingdoms of life. Here we report the domain architecture and crystal structure of the catalytic domain of E. coli RluF at 2.6 Angstroms resolution. Limited proteolysis, mass spectrometry and N-terminal sequencing indicate that RluF has a distinct domain architecture, with the catalytic domain flanked at the N and C termini by additional domains connected to it by flexible linkers. Themore » structure of the catalytic domain of RluF is similar to those of RsuA and TruB. RluF is a member of the RsuA sequence family of {psi}-synthases, along with RluB and RluE. Structural comparison of RluF with its closest structural homologues, RsuA and TruB, suggests possible functional roles for the N-terminal and C-terminal domains of RluF.« less

Regulatory and structural properties differentiating the chromosomal and the bacteriophage-associated Escherichia coli O157:H7 Cu, Zn superoxide dismutases.

PubMed

D'Orazio, Melania; Scotti, Raffaella; Nicolini, Laura; Cervoni, Laura; Rotilio, Giuseppe; Battistoni, Andrea; Gabbianelli, Roberta

2008-10-01

Highly virulent enterohemorrhagic Escherichia coli O157:H7 strains possess three sodC genes encoding for periplasmic Cu, Zn superoxide dismutases: sodC, which is identical to the gene present in non-pathogenic E. coli strains, and sodC-F1 and sodC-F2, two nearly identical genes located within lambdoid prophage sequences. The significance of this apparent sodC redundancy in E. coli O157:H7 has not yet been investigated. We report that strains deleted of one or more sodC genes are less resistant than the wild type strain to a challenge with hydrogen peroxide, thus confirming their involvement in the bacterial antioxidant apparatus. To understand if the different sodC genes have truly overlapping functions, we have carried out a comparison of the functional, structural and regulatory properties of the various E. coli O157:H7 SodC enzymes. We have found that the chromosomal and prophagic sodC genes are differentially regulated in vitro. sodC is exclusively expressed in aerobic cultures grown to the stationary phase. In contrast, sodC-F1 and sodC-F2 are expressed also in the logarithmic phase and in anaerobic cultures. Moreover, the abundance of SodC-F1/SodC-F2 increases with respect to that of SodC in bacteria recovered from infected Caco-2 cells, suggesting higher expression/stability of SodC-F1/SodC-F2 in intracellular environments. This observation correlates with the properties of the proteins. In fact, monomeric SodC and dimeric SodC-F1/SodC-F2 are characterized by sharp differences in catalytic activity, metal affinity, protease resistance and stability. Our data show that the chromosomal and bacteriophage-associated E. coli O157:H7 sodC genes have different regulatory properties and encode for proteins with distinct structural/functional features, suggesting that they likely play distinctive roles in bacterial protection from reactive oxygen species. In particular, dimeric SodC-F1 and SodC-F2 possess physico-chemical properties which make these enzymes more suitable than SodC to resist the harsh environmental conditions which are encountered by bacteria within the infected host.

Analysis of the local structure around Cr3+ centers in perovskite KMgF3 using both ab initio (DFT) and semi-empirical (SPM) calculations

NASA Astrophysics Data System (ADS)

Emül, Y.; Erbahar, D.; Açıkgöz, M.

2014-11-01

The local structure around Cr3+ centers in perovskite KMgF3 crystal have been investigated through the applications of both an ab-initio, density functional theory (DFT), and a semi empirical, superposition model (SPM), analyses. A supercell approach is used for DFT calculations. All the tetragonal (Cr3+-VMg and Cr3+-Li+), trigonal (Cr3+-VK), and CrF5O cluster centers have been considered with various structural models based on the previously suggested experimental inferences. The significant structural changes around the Cr3+ centers induced by Mg2+ or K+ vacancies and the Li substitution at those vacancy sites have been determined and discussed by means of charge distribution. This study provides insight on both the roles of Mg2+ and K+ vacancies and Li+ ion in the local structural properties around Cr3+ centers in KMgF3.

Simple systematization of vibrational excitation cross-section calculations for resonant electron-molecule scattering in the boomerang and impulse models.

PubMed

Sarma, Manabendra; Adhikari, S; Mishra, Manoj K

2007-01-28

Vibrational excitation (nu(f)<--nu(i)) cross-sections sigma(nu(f)<--nu(i) )(E) in resonant e-N(2) and e-H(2) scattering are calculated from transition matrix elements T(nu(f),nu(i) )(E) obtained using Fourier transform of the cross correlation function , where psi(nu(i))(R,t) approximately =e(-iH(A(2))-(R)t/h phi(nu(i))(R) with time evolution under the influence of the resonance anionic Hamiltonian H(A(2) (-))(A(2) (-)=N(2)(-)/H(2) (-)) implemented using Lanczos and fast Fourier transforms. The target (A(2)) vibrational eigenfunctions phi(nu(i))(R) and phi(nu(f))(R) are calculated using Fourier grid Hamiltonian method applied to potential energy (PE) curves of the neutral target. Application of this simple systematization to calculate vibrational structure in e-N(2) and e-H(2) scattering cross-sections provides mechanistic insights into features underlying presence/absence of structure in e-N(2) and e-H(2) scattering cross-sections. The results obtained with approximate PE curves are in reasonable agreement with experimental/calculated cross-section profiles, and cross correlation functions provide a simple demarcation between the boomerang and impulse models.

Functional brain networks reconstruction using group sparsity-regularized learning.

PubMed

Zhao, Qinghua; Li, Will X Y; Jiang, Xi; Lv, Jinglei; Lu, Jianfeng; Liu, Tianming

2018-06-01

Investigating functional brain networks and patterns using sparse representation of fMRI data has received significant interests in the neuroimaging community. It has been reported that sparse representation is effective in reconstructing concurrent and interactive functional brain networks. To date, most of data-driven network reconstruction approaches rarely take consideration of anatomical structures, which are the substrate of brain function. Furthermore, it has been rarely explored whether structured sparse representation with anatomical guidance could facilitate functional networks reconstruction. To address this problem, in this paper, we propose to reconstruct brain networks utilizing the structure guided group sparse regression (S2GSR) in which 116 anatomical regions from the AAL template, as prior knowledge, are employed to guide the network reconstruction when performing sparse representation of whole-brain fMRI data. Specifically, we extract fMRI signals from standard space aligned with the AAL template. Then by learning a global over-complete dictionary, with the learned dictionary as a set of features (regressors), the group structured regression employs anatomical structures as group information to regress whole brain signals. Finally, the decomposition coefficients matrix is mapped back to the brain volume to represent functional brain networks and patterns. We use the publicly available Human Connectome Project (HCP) Q1 dataset as the test bed, and the experimental results indicate that the proposed anatomically guided structure sparse representation is effective in reconstructing concurrent functional brain networks.

The effect of diffuse basis functions on valence bond structural weights

NASA Astrophysics Data System (ADS)

Galbraith, John Morrison; James, Andrew M.; Nemes, Coleen T.

2014-03-01

Structural weights and bond dissociation energies have been determined for H-F, H-X, and F-X molecules (-X = -OH, -NH2, and -CH3) at the valence bond self-consistent field (VBSCF) and breathing orbital valence bond (BOVB) levels of theory with the aug-cc-pVDZ and 6-31++G(d,p) basis sets. At the BOVB level, the aug-cc-pVDZ basis set yields a counterintuitive ordering of ionic structural weights when the initial heavy atom s-type basis functions are included. For H-F, H-OH, and F-X, the ordering follows chemical intuition when these basis functions are not included. These counterintuitive weights are shown to be a result of the diffuse polarisation function on one VB fragment being spatially located, in part, on the other VB fragment. Except in the case of F-CH3, this problem is corrected with the 6-31++G(d,p) basis set. The initial heavy atom s-type functions are shown to make an important contribution to the VB orbitals and bond dissociation energies and, therefore, should not be excluded. It is recommended to not use diffuse basis sets in valence bond calculations unless absolutely necessary. If diffuse basis sets are needed, the 6-31++G(d,p) basis set should be used with caution and the structural weights checked against VBSCF values which have been shown to follow the expected ordering in all cases.

Role of 5f electrons in the structural stability of light actinide (Th-U) mononitrides under pressure.

PubMed

Modak, P; Verma, Ashok K

2016-03-28

Pressure induced structural sequences and their mechanism for light actinide (Th-U) mononitrides were studied as a function of 5f-electron number using first-principles total energy and electronic structure calculations. Zero pressure lattice constants, bulk module and C11 elastic module vary systematically with 5f-electron number implying its direct role on crystal binding. There is a critical 5f-electron number below which the system makes B1-B2 and above it B1-R3̄m-B2 structural sequence under pressure. Also, the B1-B2 transition pressure increases with increasing 5f-electron number whereas an opposite trend is obtained for the B1-R3̄m transition pressure. The ascending of N p anti-bonding states through the Fermi level at high pressure is responsible for the structural instability of the system. Above the critical 5f-electron number in the system a narrow 5f-band occurs very close to the Fermi level which allows the system to lower its symmetry via band Jahn-Teller type lattice distortion and the system undergoes a B1-R3̄m phase transition. However, below the critical 5f-electron number this mechanism is not favorable due to a lack of sufficient 5f-state occupancy and thus the system undergoes a B1-B2 phase transition like other ionic solids.

Investigation of structural and luminescent properties of Ce{sup 3+}/Mn{sup 2+} ions-doped Ca{sub 5}(PO{sub 4}){sub 3}F

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

Zhang, Lei; Fu, Zuoling, E-mail: zlfu@jlu.edu.cn; Wu, Zhijian

Graphical abstract: The structural and luminescent properties FAP: Ce{sup 3+} and FAP: Ce{sup 3+}, Mn{sup 2+} were investigated in detail by the spectral measurement and theoretical calculation. The emission of Ce{sup 3+} is fitted by two Gaussian functions dashed lines in wavenumber to further confirm the Ce{sup 3+} ion simultaneously occupy the 4f and 6h sites Ca{sub 5}(PO{sub 4})F host. - Highlights: • A simple hydrothermal method has been used to prepare Ca{sub 5}(PO{sub 4}){sub 3}F: Ce{sup 3+}, Mn{sup 2+} powders with structural and luminescent analysis. • The emission of Ce{sup 3+} is fitted by two Gaussian functions to confirmmore » the Ce{sup 3+} ion simultaneously to occupy the 4f and 6h sites in Ca{sub 5}(PO{sub 4}){sub 3}F host. • Due to an efficient energy transfer, the existence of Ce{sup 3+} (sensitizer) can dramatically enhance the green emission of Mn{sup 2+} (activator) in co-doped samples. - Abstract: Ce{sup 3+}/Mn{sup 2+} ions-doped oxyapatite calcium fluorapatite [Ca{sub 5}(PO{sub 4}){sub 3}F, FAP] has been successfully synthesized by a facile one-step hydrothermal method. The luminescent properties of Ce{sup 3+}- and Ce{sup 3+}/Mn{sup 2+}- activated FAP phosphors were investigated using the photoluminescence (PL) and photoluminescence excitation (PLE) spectra. The emission of Ce{sup 3+} was fitted by two Gaussian functions with dashed lines in wavenumber to confirm the Ce{sup 3+} ion simultaneously to occupy the 4f and 6h sites in Ca{sub 5}(PO{sub 4}){sub 3}F host, which was consistent with the calculated results of crystal field based on chemical bond theory. In addition, the existence of Ce{sup 3+} (sensitizer) can dramatically enhance the green emission of Mn{sup 2+} (activator) in Ce{sup 3+}/Mn{sup 2+} ions co-doped samples due to an efficient energy transfer from Ce{sup 3+} to Mn{sup 2+}. All of these results could help us understand the site assignments and optical properties of the rare earth ions doped in hexagonal Ca{sub 5}(PO{sub 4}){sub 3}F.« less

4f fine-structure levels as the dominant error in the electronic structures of binary lanthanide oxides.

PubMed

Huang, Bolong

2016-04-05

The ground-state 4f fine-structure levels in the intrinsic optical transition gaps between the 2p and 5d orbitals of lanthanide sesquioxides (Ln2 O3 , Ln = La…Lu) were calculated by a two-way crossover search for the U parameters for DFT + U calculations. The original 4f-shell potential perturbation in the linear response method were reformulated within the constraint volume of the given solids. The band structures were also calculated. This method yields nearly constant optical transition gaps between Ln-5d and O-2p orbitals, with magnitudes of 5.3 to 5.5 eV. This result verifies that the error in the band structure calculations for Ln2 O3 is dominated by the inaccuracies in the predicted 4f levels in the 2p-5d transition gaps, which strongly and non-linearly depend on the on-site Hubbard U. The relationship between the 4f occupancies and Hubbard U is non-monotonic and is entirely different from that for materials with 3d or 4d orbitals, such as transition metal oxides. This new linear response DFT + U method can provide a simpler understanding of the electronic structure of Ln2 O3 and enables a quick examination of the electronic structures of lanthanide solids before hybrid functional or GW calculations. © 2015 Wiley Periodicals, Inc.

High-Resolution Structure and Mechanism of an F/V-Hybrid Rotor Ring in a Na+-coupled ATP Synthase

PubMed Central

Matthies, Doreen; Zhou, Wenchang; Klyszejko, Adriana L.; Anselmi, Claudio; Yildiz, Özkan; Brandt, Karsten; Müller, Volker; Faraldo-Gómez, José D.; Meier, Thomas

2014-01-01

All rotary ATPases catalyze the interconversion of ATP and ADP-Pi through a mechanism that is coupled to the transmembrane flow of H+ or Na+. Physiologically, however, F/A-type enzymes specialize in ATP synthesis driven by downhill ion diffusion, while eukaryotic V-type ATPases function as ion pumps. To begin to rationalize the molecular basis for this functional differentiation, we solved the crystal structure of the Na+-driven membrane rotor of the Acetobacterium woodii ATP synthase, at 2.1 Å resolution. Unlike known structures, this rotor ring is a 9:1 heteromer of F- and V-type c-subunits, and therefore features a hybrid configuration of ion-binding sites along its circumference. Molecular and kinetic simulations are used to dissect the mechanisms of Na+ recognition and rotation of this c-ring, and to explain the functional implications of the V-type c-subunit. These structural and mechanistic insights indicate an evolutionary path between synthases and pumps involving adaptations in the rotor ring. PMID:25381992

Self-limited growth of the CaF nanowire on the Si(5 5 12)-2 × 1 template

NASA Astrophysics Data System (ADS)

Kim, Hidong; Duvjir, Ganbat; Dugerjav, Otgonbayar; Li, Huiting; Motlak, Moaaed; Arvisbaatar, Amarmunkh; Seo, Jae M.

2012-10-01

The atomic structure and interfacial bonding of the ordered-and-isolated CaF nanowires on Si(5 5 12)-2 × 1 have been disclosed by scanning tunneling microscopy and synchrotron photoemission spectroscopy. Initially, CaF molecules dissociated from thermally deposited CaF2 molecules are adsorbed preferentially on the chain structures of Si(5 5 12)-2 × 1 held at 500 °C. With increasing CaF2 deposition amount, one-dimensional (1D) CaF nanowires composed of (113) and (111) facets are formed. The line density of these CaF nanowires increases as a function of deposition amount. Finally, at a submonolayer coverage, the surface is saturated with these 1D nanowires except for the (225) subunit, while the original period of Si(5 5 12)-2 × 1, 5.35 nm, is preserved. It has been deduced by the present studies that, owing to these preferential adsorption of CaF and facet-dependent growth of a CaF layer within a unit periodic length of Si(5 5 12)-2 × 1, such a self-limited growth of the CaF nanowire with a high aspect ratio becomes possible.

The effect of hippocampal function, volume and connectivity on posterior cingulate cortex functioning during episodic memory fMRI in mild cognitive impairment.

PubMed

Papma, Janne M; Smits, Marion; de Groot, Marius; Mattace Raso, Francesco U; van der Lugt, Aad; Vrooman, Henri A; Niessen, Wiro J; Koudstaal, Peter J; van Swieten, John C; van der Veen, Frederik M; Prins, Niels D

2017-09-01

Diminished function of the posterior cingulate cortex (PCC) is a typical finding in early Alzheimer's disease (AD). It is hypothesized that in early stage AD, PCC functioning relates to or reflects hippocampal dysfunction or atrophy. The aim of this study was to examine the relationship between hippocampus function, volume and structural connectivity, and PCC activation during an episodic memory task-related fMRI study in mild cognitive impairment (MCI). MCI patients (n = 27) underwent episodic memory task-related fMRI, 3D-T1w MRI, 2D T2-FLAIR MRI and diffusion tensor imaging. Stepwise linear regression analysis was performed to examine the relationship between PCC activation and hippocampal activation, hippocampal volume and diffusion measures within the cingulum along the hippocampus. We found a significant relationship between PCC and hippocampus activation during successful episodic memory encoding and correct recognition in MCI patients. We found no relationship between the PCC and structural hippocampal predictors. Our results indicate a relationship between PCC and hippocampus activation during episodic memory engagement in MCI. This may suggest that during episodic memory, functional network deterioration is the most important predictor of PCC functioning in MCI. • PCC functioning during episodic memory relates to hippocampal functioning in MCI. • PCC functioning during episodic memory does not relate to hippocampal structure in MCI. • Functional network changes are an important predictor of PCC functioning in MCI.

Structure-Function of the Cytochrome b 6f Complex of Oxygenic Photosynthesis

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

Cramer, W. A.; Yamashita, E.; Baniulis, D.

2014-03-20

Structure–function of the major integral membrane cytochrome b 6f complex that functions in cyanobacteria, algae, and green plants to transfer electrons between the two reaction center complexes in the electron transport chain of oxygenic photosynthesis is discussed in the context of recently obtained crystal structures of the complex and soluble domains of cytochrome f and the Rieske iron–sulfur protein. The energy-transducing function of the complex, generation of the proton trans-membrane electrochemical potential gradient, centers on the oxidation/reduction pathways of the plastoquinol/plastoquinone (QH 2/Q), the proton donor/acceptor within the complex. These redox reactions are carried out by five redox prosthetic groupsmore » embedded in each monomer, the high potential two iron–two sulfur cluster and the heme of cytochrome f on the electropositive side (p) of the complex, two noncovalently bound b-type hemes that cross the complex and the membrane, and a covalently bound c-type heme (c n) on the electronegative side (n). These five redox-active groups are organized in high- (cyt f/[2Fe–2S] and low-potential (hemes b p, b n, c n) electron transport pathways that oxidize and reduce the quinol and quinone on the p- and n-sides in a Q-cycle-type mechanism, while translocating as many as 2 H + to the p-side aqueous side for every electron transferred through the high potential chain to the photosystem I reaction center. The presence of heme c n and the connection of the n-side of the membrane and b 6f complex to the cyclic electron transport chain indicate that the Q cycle in the oxygenic photosynthetic electron transport chain differs from those connected to the bc 1 complex in the mitochondrial respiratory chain and the chain in photosynthetic bacteria. Inferences from the structure and C2 symmetry of the complex for the pathway of QH 2/Q transfer within the complex, problems posed by the presence of lipid in the inter-monomer cavity, and the narrow portal for QH2 passage through the p-side oxidation site proximal to the [2Fe–2S] cluster are discussed.« less

The Cytochrome b 6 f Complex: Biophysical Aspects of Its Functioning in Chloroplasts.

PubMed

Tikhonov, Alexander N

2018-01-01

This chapter presents an overview of structural properties of the cytochrome (Cyt) b 6 f complex and its functioning in chloroplasts. The Cyt b 6 f complex stands at the crossroad of photosynthetic electron transport pathways, providing connectivity between Photosystem (PSI) and Photosysten II (PSII) and pumping protons across the membrane into the thylakoid lumen. After a brief review of the chloroplast electron transport chain, the consideration is focused on the structural organization of the Cyt b 6 f complex and its interaction with plastoquinol (PQH 2 , reduced form of plastoquinone), a mediator of electron transfer from PSII to the Cyt b 6 f complex. The processes of PQH 2 oxidation by the Cyt b 6 f complex have been considered within the framework of the Mitchell's Q-cycle. The overall rate of the intersystem electron transport is determined by PQH 2 turnover at the quinone-binding site Q o of the Cyt b 6 f complex. The rate of PQH 2 oxidation is controlled by the intrathylakoid pH in , which value determines the protonation/deprotonation events in the Q o -center. Two other regulatory mechanisms associated with the Cyt b 6 f complex are briefly overviewed: (i) redistribution of electron fluxes between alternative (linear and cyclic) pathways, and (ii) "state transitions" related to redistribution of solar energy between PSI and PSII.

Informatics-Aided Density Functional Theory Study on the Li Ion Transport of Tavorite-Type LiMTO4F (M(3+)-T(5+), M(2+)-T(6+)).

PubMed

Jalem, Randy; Kimura, Mayumi; Nakayama, Masanobu; Kasuga, Toshihiro

2015-06-22

The ongoing search for fast Li-ion conducting solid electrolytes has driven the deployment surge on density functional theory (DFT) computation and materials informatics for exploring novel chemistries before actual experimental testing. Existing structure prototypes can now be readily evaluated beforehand not only to map out trends on target properties or for candidate composition selection but also for gaining insights on structure-property relationships. Recently, the tavorite structure has been determined to be capable of a fast Li ion insertion rate for battery cathode applications. Taking this inspiration, we surveyed the LiMTO4F tavorite system (M(3+)-T(5+) and M(2+)-T(6+) pairs; M is nontransition metals) for solid electrolyte use, identifying promising compositions with enormously low Li migration energy (ME) and understanding how structure parameters affect or modulate ME. We employed a combination of DFT computation, variable interaction analysis, graph theory, and a neural network for building a crystal structure-based ME prediction model. Candidate compositions that were predicted include LiGaPO4F (0.25 eV), LiGdPO4F (0.30 eV), LiDyPO4F (0.30 eV), LiMgSO4F (0.21 eV), and LiMgSeO4F (0.11 eV). With chemical substitutions at M and T sites, competing effects among Li pathway bottleneck size, polyanion covalency, and local lattice distortion were determined to be crucial for controlling ME. A way to predict ME for multiple structure types within the neural network framework was also explored.

Structures and electron affinities of the di-arsenic fluorides As2Fn/As2Fn- (n=1-8).

PubMed

Kasalová, Veronika; Schaefer, Henry F

2005-04-15

Developments in the preparation of new materials for microelectronics are focusing new attention on molecular systems incorporating several arsenic atoms. A systematic investigation of the As2Fn/As2Fn- systems was carried out using Density Functional Theory methods and a DZP++ quality basis set. Global and low-lying local geometric minima and relative energies are discussed and compared. The three types of neutral-anion separations reported in this work are: the adiabatic electron affinity (EAad), the vertical electron affinity (EAvert), and the vertical detachment energy (VDE). Harmonic vibrational frequencies pertaining to the global minimum for each compound are reported. From the first four studied species (As2Fn, n=1-4), all neutral molecules and their anions are shown to be stable with respect to As-As bond breaking. The neutral As2F molecule and its anion are predicted to have Cs symmetry. We find the trans F-As-As-F isomer of C2h symmetry and a pyramidalized vinylidene-like As-As-F2- isomer of Cs symmetry to be the global minima for the As2F2 and As2F2- species, respectively. The lowest lying minima of As2F3 and As2F3- are vinyl radical-like structures F-As-As-F2 of Cs symmetry. The neutral As2F4 global minimum is a trans-bent (like Si2H4) F2-As-As-F2 isomer of C2 symmetry, while its anion is predicted to have an unusual fluorine-bridged (C(1)) structure. The global minima of the neutral As2Fn species, n=5-8, are weakly bound complexes, held together by dipole-dipole interactions. All such structures have the AsFm-AsFn form, where (m,n) is (2,3) for As2F5, (3,3) for As2F6, (4,3) for As2F7), and (5,3) for As2F8. For As2F8 the beautiful pentavalent F4As-AsF4 structure (analogous to the stable AsF5 molecule) lies about 30 kcal/mol above the AsF3 . . . AsF5 complex. The stability of AsF(5) depends crucially on the strong As-F bonds, and replacing one of these with an As-As bond (in F4As-AsF4) has a very negative impact on the molecule's stability. The anions As2Fn-, n=5-8, are shown to be stable with respect to the As-As bond breaking, and we predict that all of them have fluorine-bridged or fluorine-linked structures. The zero-point vibrational energy corrected adiabatic electron affinities are predicted to be 2.28 eV (As2F), 1.95 eV (As2F2), 2.39 eV (As2F3), 1.71 eV (As2F4), 2.72 eV (As2F5), 1.79 eV (As2F6), 5.26 eV (As2F7), and 3.40 eV (As2F8) from the BHLYP method. Vertical detachment energies are rather large, especially for species with fluorine-bridged global minima, having values up to 6.45 eV (As2F7, BHLYP).

The gluon density of the proton at low x from a QCD analysis of F2

NASA Astrophysics Data System (ADS)

Aid, S.; Andreev, V.; Andrieu, B.; Appuhn, R.-D.; Arpagaus, M.; Babaev, A.; Baehr, J.; Bán, J.; Ban, Y.; Baranov, P.; Barrelet, E.; Barschke, R.; Bartel, W.; Barth, M.; Bassler, U.; Beck, H. P.; Behrend, H.-J.; Belousov, A.; Berger, Ch.; Bernardi, G.; Bernet, R.; Bertrand-Coremans, G.; Besançon, M.; Beyer, R.; Biddulph, P.; Bispham, P.; Bizot, J. C.; Blobel, V.; Borras, K.; Botterweck, F.; Boudry, V.; Braemer, A.; Brasse, F.; Braunschweig, W.; Brisson, V.; Bruncko, D.; Brune, C.; Buchholz, R.; Büngener, L.; Bürger, J.; Büsser, F. W.; Buniatian, A.; Burke, S.; Burton, M.; Buschhorn, G.; Campbell, A. J.; Carli, T.; Charles, F.; Charlet, M.; Clarke, D.; Clegg, A. B.; Clerbaux, B.; Colombo, M.; Contreras, J. G.; Cormack, C.; Coughlan, J. A.; Courau, A.; Coutures, Ch.; Cozzika, G.; Criegee, L.; Cussans, D. G.; Cvach, J.; Dagoret, S.; Dainton, J. B.; Dau, W. D.; Daum, K.; David, M.; Delcourt, B.; Del Buono, L.; De Roeck, A.; De Wolf, E. A.; Di Nezza, P.; Dollfus, C.; Dowell, J. D.; Dreis, H. B.; Droutskoi, A.; Duboc, J.; Düllmann, D.; Dünger, O.; Duhm, H.; Ebert, J.; Ebert, T. R.; Eckerlin, G.; Efremenko, V.; Egli, S.; Ehrlichmann, H.; Eichenberger, S.; Eichler, R.; Eisele, F.; Eisenhandler, E.; Ellison, R. J.; Elsen, E.; Erdmann, M.; Erdmann, W.; Evrard, E.; Favart, L.; Fedotov, A.; Feeken, D.; Felst, R.; Feltesse, J.; Ferencei, J.; Ferrarotto, F.; Flamm, K.; Fleischer, M.; Flieser, M.; Flügge, G.; Fomenko, A.; Fominykh, B.; Forbush, M.; Formánek, J.; Foster, J. M.; Franke, G.; Fretwurst, E.; Gabathuler, E.; Gabathuler, K.; Gamerdinger, K.; Garvey, J.; Gayler, J.; Gebauer, M.; Gellrich, A.; Genzel, H.; Gerhards, R.; Goerlach, U.; Goerlich, L.; Gogitidze, N.; Goldberg, M.; Goldner, D.; Gonzalez-Pineiro, B.; Gorelov, I.; Goritchev, P.; Grab, C.; Grässler, H.; Grässler, R.; Greenshaw, T.; Grindhammer, G.; Gruber, A.; Gruber, C.; Haack, J.; Haidt, D.; Hajduk, L.; Hamon, O.; Hampel, M.; Hanlon, E. M.; Hapke, M.; Haynes, W. J.; Heatherington, J.; Heinzelmann, G.; Henderson, R. C. W.; Henschel, H.; Herynek, I.; Hess, M. F.; Hildesheim, W.; Hill, P.; Hiller, K. H.; Hilton, C. D.; Hladký, J.; Hoeger, K. C.; Höppner, M.; Horisberger, R.; Hudgson, V. L.; Huet, Ph.; Hütte, M.; Hufnagel, H.; Ibbotson, M.; Itterbeck, H.; Jabiol, M.-A.; Jacholkowska, A.; Jacobsson, C.; Jaffre, M.; Janoth, J.; Jansen, T.; Jönsson, L.; Johnson, D. P.; Johnson, L.; Jung, H.; Kalmus, P. I. P.; Kant, D.; Kaschowitz, R.; Kasselmann, P.; Kathage, U.; Katzy, J.; Kaufmann, H. H.; Kazarian, S.; Kenyon, I. R.; Kermiche, S.; Keuker, C.; Kiesling, C.; Klein, M.; Kleinwort, C.; Knies, G.; Ko, W.; Köhler, T.; Köhne, J. H.; Kolanoski, H.; Kole, F.; Kolya, S. D.; Korbel, V.; Korn, M.; Kostka, P.; Kotelnikov, S. K.; Krämerkämper, T.; Krasny, M. W.; Krehbiel, H.; Krücker, D.; Krüger, U.; Krüner-Marquis, U.; Kubenka, J. P.; Küster, H.; Kuhlen, M.; Kurča, T.; Kurzhöfer, J.; Kuznik, B.; Lacour, D.; Lamarche, F.; Lander, R.; Landon, M. P. J.; Lange, W.; Lanius, P.; Laporte, J.-F.; Lebedev, A.; Leverenz, C.; Levonian, S.; Ley, Ch.; Lindner, A.; Lindström, G.; Link, J.; Linsel, F.; Lipinski, J.; List, B.; Lobo, G.; Loch, P.; Lohmander, H.; Lomas, J.; Lopez, G. C.; Lubimov, V.; Lüke, D.; Magnussen, N.; Malinovski, E.; Mani, S.; Maraček, R.; Marage, P.; Marks, J.; Marshall, R.; Martens, J.; Martin, R.; Martyn, H.-U.; Martyniak, J.; Masson, S.; Mavroidis, T.; Maxfield, S. J.; McMahon, S. J.; Mehta, A.; Meier, K.; Mercer, D.; Merz, T.; Meyer, C. A.; Meyer, H.; Meyer, J.; Migliori, A.; Mikocki, S.; Milstead, D.; Moreau, F.; Morris, J. V.; Mroczko, E.; Müller, G.; Müller, K.; Murín, P.; Nagovizin, V.; Nahnhauer, R.; Naroska, B.; Naumann, Th.; Newman, P. R.; Newton, D.; Neyret, D.; Nguyen, H. K.; Nicholls, T. C.; Niebergall, F.; Niebuhr, C.; Niedzballa, Ch.; Nisius, R.; Nowak, G.; Noyes, G. W.; Nyberg-Werther, M.; Oakden, M.; Oberlack, H.; Obrock, U.; Olsson, J. E.; Ozerov, D.; Panaro, E.; Panitch, A.; Pascaud, C.; Patel, G. D.; Peppel, E.; Perez, E.; Phillips, J. P.; Pichler, Ch.; Pieuchot, A.; Pitzl, D.; Pope, G.; Prell, S.; Prosi, R.; Rabbertz, K.; Rädel, G.; Raupach, F.; Reimer, P.; Reinshagen, S.; Ribarics, P.; Rick, H.; Riech, V.; Riedlberger, J.; Riess, S.; Rietz, M.; Rizvi, E.; Robertson, S. M.; Robmann, P.; Roloff, H. E.; Roosen, R.; Rosenbauer, K.; Rostovtsev, A.; Rouse, F.; Royon, C.; Rüter, K.; Rusakov, S.; Rybicki, K.; Rylko, R.; Sahlmann, N.; Sanchez, E.; Sankey, D. P. C.; Schacht, P.; Schiek, S.; Schleper, P.; von Schlippe, W.; Schmidt, C.; Schmidt, D.; Schmidt, G.; Schöning, A.; Schröder, V.; Schuhmann, E.; Schwab, B.; Schwind, A.; Sefkow, F.; Seidel, M.; Sell, R.; Semenov, A.; Shekelyan, V.; Sheviakov, I.; Shooshtari, H.; Shtarkov, L. N.; Siegmon, G.; Siewert, U.; Sirois, Y.; Skillicorn, I. O.; Smirnov, P.; Smith, J. R.; Solochenko, V.; Soloviev, Y.; Spiekermann, J.; Spielman, S.; Spitzer, H.; Starosta, R.; Steenbock, M.; Steffen, P.; Steinberg, R.; Stella, B.; Stephens, K.; Stier, J.; Stiewe, J.; Stösslein, U.; Stolze, K.; Strachota, J.; Straumann, U.; Struczinski, W.; Sutton, J. P.; Tapprogge, S.; Tchernyshov, V.; Thiebaux, C.; Thompson, G.; Truöl, P.; Turnau, J.; Tutas, J.; Uelkes, P.; Usik, A.; Valkár, S.; Valkárová, A.; Vallée, C.; Van Esch, P.; Van Mechelen, P.; Vartapetian, A.; Vazdik, Y.; Verrecchia, P.; Villet, G.; Wacker, K.; Wagener, A.; Wagener, M.; Walker, I. W.; Walther, A.; Weber, G.; Weber, M.; Wegener, D.; Wegner, A.; Wellisch, H. P.; West, L. R.; Willard, S.; Willard, S.; Winde, M.; Winter, G.-G.; Wittek, C.; Wright, A. E.; Wünsch, E.; Wulff, N.; Yiou, T. P.; Žáček, J.; Zarbock, D.; Zhang, Z.; Zhokin, A.; Zimmer, M.; Zimmermann, W.; Zomer, F.; Zuber, K.; H1 Collaboration

1995-02-01

We present a QCD analysis of the proton structure function F2 measured by the H1 experiment at HERA, combined with data from previous fixed target experiments. The gluon density is extracted from the scaling violations of F2 in the range 2 · 10 -4 < x < 3 · 10 -2 and compared with an approximate solution of the QCD evolution equations. The gluon density is found to rise steeply with decreasing x.

An in situ polymerization approach for the synthesis of superhydrophobic and superoleophilic nanofibrous membranes for oil-water separation

NASA Astrophysics Data System (ADS)

Shang, Yanwei; Si, Yang; Raza, Aikifa; Yang, Liping; Mao, Xue; Ding, Bin; Yu, Jianyong

2012-11-01

Superhydrophobic and superoleophilic nanofibrous membranes exhibiting robust oil-water separation performance were prepared by a facile combination of electrospun cellulose acetate (CA) nanofibers and a novel in situ polymerized fluorinated polybenzoxazine (F-PBZ) functional layer that incorporated silica nanoparticles (SiO2 NPs). By employing the F-PBZ/SiO2 NPs modification, the pristine hydrophilic CA nanofibrous membranes were endowed with a superhydrophobicity with the water contact angle of 161° and a superoleophilicity with the oil contact angle of 3°. Surface morphological studies have indicated that the wettability of resultant membranes could be manipulated by tuning the surface composition as well as the hierarchical structures. The quantitative hierarchical roughness analysis using the N2 adsorption method has confirmed the major contribution of SiO2 NPs on enhancing the porous structure, and a detailed correlation between roughness and solid-liquid interface pinning is proposed. Furthermore, the as-prepared membranes exhibited fast and efficient separation for oil-water mixtures and excellent stability over a wide range of pH conditions, which would make them a good candidate in industrial oil-polluted water treatments and oil spill cleanup, and also provided a new insight into the design and development of functional nanofibrous membranes through F-PBZ modification.Superhydrophobic and superoleophilic nanofibrous membranes exhibiting robust oil-water separation performance were prepared by a facile combination of electrospun cellulose acetate (CA) nanofibers and a novel in situ polymerized fluorinated polybenzoxazine (F-PBZ) functional layer that incorporated silica nanoparticles (SiO2 NPs). By employing the F-PBZ/SiO2 NPs modification, the pristine hydrophilic CA nanofibrous membranes were endowed with a superhydrophobicity with the water contact angle of 161° and a superoleophilicity with the oil contact angle of 3°. Surface morphological studies have indicated that the wettability of resultant membranes could be manipulated by tuning the surface composition as well as the hierarchical structures. The quantitative hierarchical roughness analysis using the N2 adsorption method has confirmed the major contribution of SiO2 NPs on enhancing the porous structure, and a detailed correlation between roughness and solid-liquid interface pinning is proposed. Furthermore, the as-prepared membranes exhibited fast and efficient separation for oil-water mixtures and excellent stability over a wide range of pH conditions, which would make them a good candidate in industrial oil-polluted water treatments and oil spill cleanup, and also provided a new insight into the design and development of functional nanofibrous membranes through F-PBZ modification. Electronic supplementary information (ESI) available: Detailed synthesis and structural confirmation of BAF-tfa, FT-IR results, OCA results and Movie S1. See DOI: 10.1039/c2nr33063f

Structural, electronic and magnetic properties of Au-based monolayer derivatives in honeycomb structure

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

Kapoor, Pooja, E-mail: pupooja16@gmail.com; Sharma, Munish; Ahluwalia, P. K.

2016-05-23

We present electronic properties of atomic layer of Au, Au{sub 2}-N, Au{sub 2}-O and Au{sub 2}-F in graphene-like structure within the framework of density functional theory (DFT). The lattice constant of derived monolayers are found to be higher than the pristine Au monolayer. Au monolayer is metallic in nature with quantum ballistic conductance calculated as 4G{sub 0}. Similarly, Au{sub 2}-N and Au{sub 2}-F monolayers show 4G{sub 0} and 2G{sub 0} quantum conductance respectively while semiconducting nature with calculated band gap of 0.28 eV has been observed for Au{sub 2}-O monolayer. Most interestingly, half metalicity has been predicted for Au{sub 2}-Nmore » and Au{sub 2}-F monolayers. Our findings may have importance for the application of these monolayers in nanoelectronic and spintronics.« less

Origin of generalized entropies and generalized statistical mechanics for superstatistical multifractal systems

NASA Astrophysics Data System (ADS)

Gadjiev, Bahruz; Progulova, Tatiana

2015-01-01

We consider a multifractal structure as a mixture of fractal substructures and introduce a distribution function f (α), where α is a fractal dimension. Then we can introduce g(p)˜ ∫- ln p μe-yf(y)dy and show that the distribution functions f (α) in the form of f(α) = δ(α-1), f(α) = δ(α-θ) , f(α) = 1/α-1 , f(y)= y α-1 lead to the Boltzmann - Gibbs, Shafee, Tsallis and Anteneodo - Plastino entropies conformably. Here δ(x) is the Dirac delta function. Therefore the Shafee entropy corresponds to a fractal structure, the Tsallis entropy describes a multifractal structure with a homogeneous distribution of fractal substructures and the Anteneodo - Plastino entropy appears in case of a power law distribution f (y). We consider the Fokker - Planck equation for a fractal substructure and determine its stationary solution. To determine the distribution function of a multifractal structure we solve the two-dimensional Fokker - Planck equation and obtain its stationary solution. Then applying the Bayes theorem we obtain a distribution function for the entire system in the form of q-exponential function. We compare the results of the distribution functions obtained due to the superstatistical approach with the ones obtained according to the maximum entropy principle.

26 CFR 301.7430-1 - Exhaustion of administrative remedies.

Code of Federal Regulations, 2010 CFR

2010-04-01

... March 3, in the name of F. On April 2, F pays the entire liability thereby satisfying the lien. On May 2... revenue ruling which holds that ear piercing does not affect a function or structure of the body within... piercing and, following an examination, receives a notice of proposed deficiency (30-day letter...

26 CFR 301.7430-1 - Exhaustion of administrative remedies.

Code of Federal Regulations, 2014 CFR

2014-04-01

... March 3, in the name of F. On April 2, F pays the entire liability thereby satisfying the lien. On May 2... revenue ruling which holds that ear piercing does not affect a function or structure of the body within... piercing and, following an examination, receives a notice of proposed deficiency (30-day letter...

26 CFR 301.7430-1 - Exhaustion of administrative remedies.

Code of Federal Regulations, 2013 CFR

2013-04-01

... March 3, in the name of F. On April 2, F pays the entire liability thereby satisfying the lien. On May 2... revenue ruling which holds that ear piercing does not affect a function or structure of the body within... piercing and, following an examination, receives a notice of proposed deficiency (30-day letter...

26 CFR 301.7430-1 - Exhaustion of administrative remedies.

Code of Federal Regulations, 2012 CFR

2012-04-01

... March 3, in the name of F. On April 2, F pays the entire liability thereby satisfying the lien. On May 2... revenue ruling which holds that ear piercing does not affect a function or structure of the body within... piercing and, following an examination, receives a notice of proposed deficiency (30-day letter...

26 CFR 301.7430-1 - Exhaustion of administrative remedies.

Code of Federal Regulations, 2011 CFR

2011-04-01

... March 3, in the name of F. On April 2, F pays the entire liability thereby satisfying the lien. On May 2... revenue ruling which holds that ear piercing does not affect a function or structure of the body within... piercing and, following an examination, receives a notice of proposed deficiency (30-day letter...

Density functional theory study on aqueous aluminum-fluoride complexes: exploration of the intrinsic relationship between water-exchange rate constants and structural parameters for monomer aluminum complexes.

PubMed

Jin, Xiaoyan; Qian, Zhaosheng; Lu, Bangmei; Yang, Wenjing; Bi, Shuping

2011-01-01

Density functional theory (DFT) calculation is carried out to investigate the structures, (19)F and (27)Al NMR chemical shifts of aqueous Al-F complexes and their water-exchange reactions. The following investigations are performed in this paper: (1) the microscopic properties of typical aqueous Al-F complexes are obtained at the level of B3LYP/6-311+G**. Al-OH(2) bond lengths increase with F(-) replacing inner-sphere H(2)O progressively, indicating labilizing effect of F(-) ligand. The Al-OH(2) distance trans to fluoride is longer than other Al-OH(2) distance, accounting for trans effect of F(-) ligand. (19)F and (27)Al NMR chemical shifts are calculated using GIAO method at the HF/6-311+G** level relative to F(H(2)O)(6)(-) and Al(H(2)O)(6)(3+) references, respectively. The results are consistent with available experimental values; (2) the dissociative (D) activated mechanism is observed by modeling water-exchange reaction for [Al(H(2)O)(6-i)F(i)]((3-i)+) (i = 1-4). The activation energy barriers are found to decrease with increasing F(-) substitution, which is in line with experimental rate constants (k(ex)). The log k(ex) of AlF(3)(H(2)O)(3)(0) and AlF(4)(H(2)O)(2)(-) are predicted by three ways. The results indicate that the correlation between log k(ex) and Al-O bond length as well as the given transmission coefficient allows experimental rate constants to be predicted, whereas the correlation between log k(ex) and activation free energy is poor; (3) the environmental significance of this work is elucidated by the extension toward three fields, that is, polyaluminum system, monomer Al-organic system and other metal ions system with high charge-to-radius ratio.

Altered Actin Dynamics and Functions of Osteoblast-Like Cells in Parabolic Flight may Involve ERK1/2

NASA Astrophysics Data System (ADS)

Dai, Zhongquan; Tan, Yingjun; Yang, Fen; Qu, Lina; Zhang, Hongyu; Wan, Yumin; Li, Yinghui

2011-01-01

Osteoblasts are sensitive to mechanical stressors such as gravity and alter their cytoskeletons and functions to adapt; however, the contribution of gravity to this phenomenon is not well understood. In this study, we investigated the effects of acute gravitational changes on the structure and function of osteoblast ROS17/2.8 as generated by parabolic flight. The changes in microfilament cytoskeleton was observed by immunofluorescence stain of Texas red conjugated Phalloidin and Alexa Fluor 488 conjugated DNase I for F-actin and G-actin, respectively. To examine osteoblast function, ALP (alkaline phosphatase) activity, osteocalcin secretions and the expression of ALP, COL1A1 (collagen type I alpha 1 chain) and osteocalcin were detected by modified Gomori methods, radioimmunity and RT-PCR, respectively. Double fluorescence staining of phosphorylated p44/42 and F-actin were performed to observe their colocalization relationship. The established semi-quantitative analysis method of fluorescence intensity of EGFP was used to detect the activity changes of COL1A1 promoter in EGFP-ROS cells with MAPK inhibitor PD98059 or F-actin inhibitor cytochalasin B. Results indicate that the altered gravity induced the reorganization of microfilament cytoskeletons of osteoblasts. After 3 h parabolic flight, F-actin of osteoblast cytoskeleton became thicker and directivity, whereas G-actin shrunk and became more concentrated at the edge of nucleus. The excretion of osteocalcin, the activity of ALP and the expression of mRNA decreased. Colocalization analysis indicated that phosphorylated p44/42 MAPK was coupled with F-actin. Inhibitor PD98059 and cytochalasin B decreased the fluorescence intensity of EGFP-ROS cells. Above results suggest that short time gravity variations induce the adjustment of osteoblast structure and functional and ERK1/2 signaling maybe involve these responses. We believe that it is an adaptive method of the osteoblasts to gravity alteration that structure alteration inhibits the function performing.

Sum rules across the unpolarized Compton processes involving generalized polarizabilities and moments of nucleon structure functions

NASA Astrophysics Data System (ADS)

Lensky, Vadim; Hagelstein, Franziska; Pascalutsa, Vladimir; Vanderhaeghen, Marc

2018-04-01

We derive two new sum rules for the unpolarized doubly virtual Compton scattering process on a nucleon, which establish novel low-Q2 relations involving the nucleon's generalized polarizabilities and moments of the nucleon's unpolarized structure functions F1(x ,Q2) and F2(x ,Q2). These relations facilitate the determination of some structure constants which can only be accessed in off-forward doubly virtual Compton scattering, not experimentally accessible at present. We perform an empirical determination for the proton and compare our results with a next-to-leading-order chiral perturbation theory prediction. We also show how these relations may be useful for a model-independent determination of the low-Q2 subtraction function in the Compton amplitude, which enters the two-photon-exchange contribution to the Lamb shift of (muonic) hydrogen. An explicit calculation of the Δ (1232 )-resonance contribution to the muonic-hydrogen 2 P -2 S Lamb shift yields -1 ±1 μ eV , confirming the previously conjectured smallness of this effect.

Connectivity of glass structure. Oxygen number

NASA Astrophysics Data System (ADS)

Medvedev, E. F.; Min'ko, N. I.

2018-03-01

With reference to mathematics, crystal chemistry and chemical technology of synthesis of glass structures in the solution (sol-gel technology), the paper is devoted to the study of the degree of connectivity of a silicon-oxygen backbone (fSi) and the oxygen number (R) [1]. It reveals logical contradictions and uncertainty of mathematical expressions of parameters, since fSi is not similar to the oxygen number. The connectivity of any structure is a result of various types of bonds: ion-covalent, donor-acceptor, hydrogen bonds, etc. Besides, alongside with SiO2, many glass compositions contain other glass-forming elements due to tetrahedral sites thus formed. The connectivity function of a glassy network with any set of glass-forming elements is roughly ensured by connectivity factor Y [2], which has monovalent elements loosening a glassy network. The paper considers the existence of various structural motives in hydrogen-impermeable glasses containing B2O3, Al2O3, PbO, Na2O, K2O and rare-earth elements. Hence, it also describes gradual nucleation, change of crystal forms, and structure consolidation in the process of substance intake from a matrix solution according to sol-gel technology. The crystal form varied from two-dimensional plates to three-dimensional and dendritical ones [3]. Alternative parameters, such as the oxygen number (O) and the structure connectivity factor (Y), were suggested. Functional dependence of Y=f(O) to forecast the generated structures was obtained for two- and multicomponent glass compositions.

Functions and requirements document for interim store solidified high-level and transuranic waste

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

Smith-Fewell, M.A., Westinghouse Hanford

1996-05-17

The functions, requirements, interfaces, and architectures contained within the Functions and Requirements (F{ampersand}R) Document are based on the information currently contained within the TWRS Functions and Requirements database. The database also documents the set of technically defensible functions and requirements associated with the solidified waste interim storage mission.The F{ampersand}R Document provides a snapshot in time of the technical baseline for the project. The F{ampersand}R document is the product of functional analysis, requirements allocation and architectural structure definition. The technical baseline described in this document is traceable to the TWRS function 4.2.4.1, Interim Store Solidified Waste, and its related requirements, architecture,more » and interfaces.« less

Surface-Based fMRI-Driven Diffusion Tractography in the Presence of Significant Brain Pathology: A Study Linking Structure and Function in Cerebral Palsy

PubMed Central

Cunnington, Ross; Boyd, Roslyn N.; Rose, Stephen E.

2016-01-01

Diffusion MRI (dMRI) tractography analyses are difficult to perform in the presence of brain pathology. Automated methods that rely on cortical parcellation for structural connectivity studies often fail, while manually defining regions is extremely time consuming and can introduce human error. Both methods also make assumptions about structure-function relationships that may not hold after cortical reorganisation. Seeding tractography with functional-MRI (fMRI) activation is an emerging method that reduces these confounds, but inherent smoothing of fMRI signal may result in the inclusion of irrelevant pathways. This paper describes a novel fMRI-seeded dMRI-analysis pipeline based on surface-meshes that reduces these issues and utilises machine-learning to generate task specific white matter pathways, minimising the requirement for manually-drawn ROIs. We directly compared this new strategy to a standard voxelwise fMRI-dMRI approach, by investigating correlations between clinical scores and dMRI metrics of thalamocortical and corticomotor tracts in 31 children with unilateral cerebral palsy. The surface-based approach successfully processed more participants (87%) than the voxel-based approach (65%), and provided significantly more-coherent tractography. Significant correlations between dMRI metrics and five clinical scores of function were found for the more superior regions of these tracts. These significant correlations were stronger and more frequently found with the surface-based method (15/20 investigated were significant; R2 = 0.43–0.73) than the voxelwise analysis (2 sig. correlations; 0.38 & 0.49). More restricted fMRI signal, better-constrained tractography, and the novel track-classification method all appeared to contribute toward these differences. PMID:27487011

Structure-function analysis and genetic interactions of the SmG, SmE, and SmF subunits of the yeast Sm protein ring.

PubMed

Schwer, Beate; Kruchten, Joshua; Shuman, Stewart

2016-09-01

A seven-subunit Sm protein ring forms a core scaffold of the U1, U2, U4, and U5 snRNPs that direct pre-mRNA splicing. Using human snRNP structures to guide mutagenesis in Saccharomyces cerevisiae, we gained new insights into structure-function relationships of the SmG, SmE, and SmF subunits. An alanine scan of 19 conserved amino acids of these three proteins, comprising the Sm RNA binding sites or inter-subunit interfaces, revealed that, with the exception of Arg74 in SmF, none are essential for yeast growth. Yet, for SmG, SmE, and SmF, as for many components of the yeast spliceosome, the effects of perturbing protein-RNA and protein-protein interactions are masked by built-in functional redundancies of the splicing machine. For example, tests for genetic interactions with non-Sm splicing factors showed that many benign mutations of SmG, SmE, and SmF (and of SmB and SmD3) were synthetically lethal with null alleles of U2 snRNP subunits Lea1 and Msl1. Tests of pairwise combinations of SmG, SmE, SmF, SmB, and SmD3 alleles highlighted the inherent redundancies within the Sm ring, whereby simultaneous mutations of the RNA binding sites of any two of the Sm subunits are lethal. Our results suggest that six intact RNA binding sites in the Sm ring suffice for function but five sites may not. © 2016 Schwer et al.; Published by Cold Spring Harbor Laboratory Press for the RNA Society.

Substituent effects on furan-phenylene copolymer for photovoltaic improvement: A density functional study

NASA Astrophysics Data System (ADS)

Janprapa, Nuttaporn; Vchirawongkwin, Viwat; Kritayakornupong, Chinapong

2018-06-01

The structural, electronic and photovoltaic properties of furan-phenylene copolymer ((Fu-co-Ph)4) and its derivatives were evaluated using density functional theory (DFT) and time-dependent density functional theory (TD-DFT). The calculated band gaps of pristine furan and phenylene are in good agreement with the available experimental data. The lower band gap value of 2.72 eV was obtained from -NO2 and -NHCH3 substituents, leading to broader solar absorption range. With respected to the reorganization energy, -OCH3, -NHCH3, -OH, -SCH3, -CH3, -CF3, -NO2, and -F substituted (Fu-co-Ph)4 structures were classified as better electron donor materials. For combination with PC61BM, -NO2, -CN, -CF3 and -F functionalized copolymers demonstrated significantly higher open circuit voltage (Voc) values ranging from 1.07 to 2.10 eV. Our results revealed that electron withdrawing group substitution on furan-phenylene copolymers was an effective way for improving electronic and optical properties of donor materials used in photovoltaic applications.

Evaluation of Road Performance Based on International Roughness Index and Falling Weight Deflectometer

NASA Astrophysics Data System (ADS)

Hasanuddin; Setyawan, A.; Yulianto, B.

2018-03-01

Assessment to the performance of road pavement is deemed necessary to improve the management quality of road maintenance and rehabilitation. This research to evaluate the road base on functional and structural and recommendations handling done. Assessing the pavement performance is conducted with functional and structural evaluation. Functional evaluation of pavement is based on the value of IRI (International Roughness Index) which among others is derived from reading NAASRA for analysis and recommended road handling. Meanwhile, structural evaluation of pavement is done by analyzing deflection value based on FWD (Falling Weight Deflectometer) data resulting in SN (Structural Number) value. The analysis will result in SN eff (Structural Number Effective) and SN f (Structural Number Future) value obtained from comparing SN eff to SN f value that leads to SCI (Structural Condition Index) value. SCI value implies the possible recommendation for handling pavement. The study done to Simpang Tuan-Batas Kota Jambi road segment was based on functional analysis. The study indicated that the road segment split into 12 segments in which segment 1, 3, 5, 7, 9, and 11 were of regular maintenance, segment 2, 4, 8, 10, 12 belonged to periodic maintenance, and segment 6 was of rehabilitation. The structural analysis resulted in 8 segments consisting of segment 1 and 2 recommended for regular maintenance, segment 3, 4, 5, and 7 for functional overlay, and 6 and 8 were of structural overlay.

Structural and Biochemical Investigation of PglF from Campylobacter jejuni Reveals a New Mechanism for a Member of the Short Chain Dehydrogenase/Reductase Superfamily

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

Riegert, Alexander S.; Thoden, James B.; Schoenhofen, Ian C.

Within recent years it has become apparent that protein glycosylation is not limited to eukaryotes. Indeed, in Campylobacter jejuni, a Gram-negative bacterium, more than 60 of its proteins are known to be glycosylated. One of the sugars found in such glycosylated proteins is 2,4-diacetamido-2,4,6-trideoxy-α-d-glucopyranose, hereafter referred to as QuiNAc4NAc. The pathway for its biosynthesis, initiating with UDP-GlcNAc, requires three enzymes referred to as PglF, PglE, and PlgD. The focus of this investigation is on PglF, an NAD+-dependent sugar 4,6-dehydratase known to belong to the short chain dehydrogenase/reductase (SDR) superfamily. Specifically, PglF catalyzes the first step in the pathway, namely, themore » dehydration of UDP-GlcNAc to UDP-2-acetamido-2,6-dideoxy-α-d-xylo-hexos-4-ulose. Most members of the SDR superfamily contain a characteristic signature sequence of YXXXK where the conserved tyrosine functions as a catalytic acid or a base. Strikingly, in PglF, this residue is a methionine. Here we describe a detailed structural and functional investigation of PglF from C. jejuni. For this investigation five X-ray structures were determined to resolutions of 2.0 Å or better. In addition, kinetic analyses of the wild-type and site-directed variants were performed. On the basis of the data reported herein, a new catalytic mechanism for a SDR superfamily member is proposed that does not require the typically conserved tyrosine residue.« less

Theoretical Study of Decomposition Pathways for HArF and HKrF

NASA Technical Reports Server (NTRS)

Chaban, Galina M.; Lundell, Jan; Gerber, R. Benny; Kwak, Donchan (Technical Monitor)

2002-01-01

To provide theoretical insights into the stability and dynamics of the new rare gas compounds HArF and HKrF, reaction paths for decomposition processes HRgF to Rg + HF and HRgF to H + Rg + F (Rg = Ar, Kr) are calculated using ab initio electronic structure methods. The bending channels, HRgF to Rg + HF, are described by single-configurational MP2 and CCSD(T) electronic structure methods, while the linear decomposition paths, HRgF to H + Rg + F, require the use of multi-configurational wave functions that include dynamic correlation and are size extensive. HArF and HKrF molecules are found to be energetically stable with respect to atomic dissociation products (H + Rg + F) and separated by substantial energy barriers from Rg + HF products, which ensure their kinetic stability. The results are compatible with experimental data on these systems.

Neutral-current weak interactions at an EIC

DOE PAGES

Zhao, Y. X.; Deshpande, A.; Huang, J.; ...

2017-03-21

Here, a simulation study of measurements of neutral current structure functions of the nucleon at the future high-energy and high-luminosity polarized electron-ion collider (EIC) is presented. A new series of γ-Z interference structure functions, F γZ 1, F γZ 3, g γZ 1, g γZ 5 become accessible via parity-violating asymmetries in polarized electron-nucleon deep inelastic scattering (DIS). Within the context of the quark-parton model, they provide a unique and, in some cases, yet-unmeasured combination of unpolarized and polarized parton distribution functions. The uncertainty projections for these structure functions using electron-proton collisions are considered for various EIC beam energy configurations.more » Also presented are uncertainty projections for measurements of the weak mixing angle sin 2θ W using electron-deuteron collisions which cover a much higher Q 2 than that accessible in fixed target measurements. QED and QCD radiative corrections and effects of detector smearing are included with the calculations.« less

Ferroelectricity in d0 double perovskite fluoroscandates

NASA Astrophysics Data System (ADS)

Charles, Nenian; Rondinelli, James M.

2015-08-01

Ferroelectricity in strain-free and strained double perovskite fluorides, Na3ScF6 and K2NaScF6 , is investigated using first-principles density functional theory. Although the experimental room temperature crystal structures of these fluoroscandates are centrosymmetric, i.e., Na3ScF6 (P 21/n ) and K2NaScF6 (F m 3 ¯m ), lattice dynamical calculations reveal that soft polar instabilities exist in each prototypical cubic phase and that the modes harden as the tolerance factor approaches unity. Thus the double fluoroperovskites bear some similarities to A B O3 perovskite oxides; however, in contrast, these fluorides exhibit large acentric displacements of alkali metal cations (Na, K) rather than polar displacements of the transition metal cations. Biaxial strain investigations of the centrosymmetric and polar Na3ScF6 and K2NaScF6 phases reveal that the paraelectric structures are favored under compressive strain, whereas polar structures with in-plane electric polarizations (˜5 -18 μ C cm-2 ) are realized at sufficiently large tensile strains. The electric polarization and stability of the polar structures for both chemistries are found to be further enhanced and stabilized by a coexisting single octahedral tilt system. Our results suggest that polar double perovskite fluorides may be realized by suppression of octahedral rotations about more than one Cartesian axis; structures exhibiting in- or out-of-phase octahedral rotations about the c axis are more susceptible to polar symmetries.

The oxidation state of sulfur in apatite: A new oxybarometer?

NASA Astrophysics Data System (ADS)

Fiege, A.; Konecke, B.; Kim, Y.; Simon, A. C.; Becker, U.; Parat, F.

2016-12-01

Oxygen fugacity (fO2) of magmatic and hydrothermal systems influences, for instance, crystallization and degassing processes as well as metal solubilities in melts and fluids. Apatite is a ubiquitous mineral in magmatic and hydrothermal environments that can record and preserve volatile zonation. It can contain several thousand μg/g of the redox sensitive element sulfur (S), making S-in-apatite a potential fO2 sensor. Despite the polyvalent properties of S (e.g., S2-, S4+, S6+), the oxidation state and incorporation mechanisms of S in the apatite structure are poorly understood. In this study, the oxidation state of S-in-apatite as a function of fO2 is investigated using X-ray absorption near-edge structures (XANES) spectroscopy at the S K-edge. Apatites crystallized from lamproitic melts at 1000°C, 300 MPa and over a broad range of fO2 and sulfur fugacities (fS2) were measured. Peaks corresponding to S6+ ( 2482 eV), S4+ ( 2478 eV) and S2- ( 2470 eV) were identified in apatite. The integrated S6+/STotal (STotal = S6+ + S4+ + S2-) peak area ratios show a distinct positive correlation with fO2, increasing from 0.17 at FMQ+0 to 0.96 at FMQ+3. Ab-initio calculations were performed to further understand the energetics and geometry of incorporation of S6+, S4+ and S2- into the apatite (F-, Cl-, OH-) end-members. The results confirm that apatite can contain three different oxidations states of S (S6+, S4+, S2-) as a function of fO2. This makes apatite probably the first geologically relevant mineral to incorporate reduced (S2-), intermediate (S4+), and oxidized (S6+) S in variable proportions. We emphasize that the strong dependence of the S oxidation state in apatite as a function of fO2 is also coupled with changing S content of apatite and co-existing melt (i.e., with changing fS2), resulting in a complex correlation between [1] apatite-melt (or fluid) partitioning, [2] redox conditions and [3] the melt and/or fluid composition, making the application of previously determined S apatite-melt partitioning coefficient debatable. Upon calibration over a range of geologically relevant T-P-X-fO2-fS2, S-in-apatite can serve as a powerful oxybarometer to quantify fO2.

The molecular structures and conformation of o-selenobenzyl fluoride derivatives, ArSeX (Ar=C 6H 4CH 2F; X=CN, Cl, Me): ab initio and DFT calculations

NASA Astrophysics Data System (ADS)

Jeong, Myongho; Kwon, Younghi

2000-10-01

Ab initio and density functional theory methods are applied to investigate the molecular structures, intramolecular orbital interactions, and 19F and 77Se NMR chemical shifts of o-selenobenzyl fluoride derivatives, ArSeX ( Ar= C6H4CH2F; X= CN, Cl, Me) , at both RHF and B3LYP levels with the basis sets 6-311G ∗∗ and 6-311+G ∗∗. There are two stable rotational conformers for ArSeX. The energy differences between both conformers for each compound are small (within 2 kcal/mol) at various levels.

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

NASA Astrophysics Data System (ADS)

Wu, Xueyuan

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

Inferring multi-scale neural mechanisms with brain network modelling

PubMed Central

Schirner, Michael; McIntosh, Anthony Randal; Jirsa, Viktor; Deco, Gustavo

2018-01-01

The neurophysiological processes underlying non-invasive brain activity measurements are incompletely understood. Here, we developed a connectome-based brain network model that integrates individual structural and functional data with neural population dynamics to support multi-scale neurophysiological inference. Simulated populations were linked by structural connectivity and, as a novelty, driven by electroencephalography (EEG) source activity. Simulations not only predicted subjects' individual resting-state functional magnetic resonance imaging (fMRI) time series and spatial network topologies over 20 minutes of activity, but more importantly, they also revealed precise neurophysiological mechanisms that underlie and link six empirical observations from different scales and modalities: (1) resting-state fMRI oscillations, (2) functional connectivity networks, (3) excitation-inhibition balance, (4, 5) inverse relationships between α-rhythms, spike-firing and fMRI on short and long time scales, and (6) fMRI power-law scaling. These findings underscore the potential of this new modelling framework for general inference and integration of neurophysiological knowledge to complement empirical studies. PMID:29308767

Measurements of the separated longitudinal structure function F L from hydrogen and deuterium targets at low Q 2

DOE PAGES

Tvaskis, V.; Tvaskis, A.; Niculescu, I.; ...

2018-04-26

Structure functions, as measured in lepton-nucleon scattering, have proven to be very useful in studying the partonic dynamics within the nucleon. Furthermore, it is experimentally difficult to separately determine the longitudinal and transverse structure functions, and consequently there are substantially less data available in particular for the longitudinal structure function. Here, we present separated structure functions for hydrogen and deuterium at low four-momentum transfer squared, Q 2 < 1 GeV 2, and compare them with parton distribution parametrization and k T factorization approaches. While differences are found, the parametrizations generally agree with the data, even at the very low-Q 2more » scale of the data. The deuterium data show a smaller longitudinal structure function and a smaller ratio of longitudinal to transverse cross section, R, than the proton. This suggests either an unexpected difference in R for the proton and the neutron or a suppression of the gluonic distribution in nuclei.« less

Measurements of the separated longitudinal structure function F L from hydrogen and deuterium targets at low Q 2

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

Tvaskis, V.; Tvaskis, A.; Niculescu, I.

Structure functions, as measured in lepton-nucleon scattering, have proven to be very useful in studying the partonic dynamics within the nucleon. Furthermore, it is experimentally difficult to separately determine the longitudinal and transverse structure functions, and consequently there are substantially less data available in particular for the longitudinal structure function. Here, we present separated structure functions for hydrogen and deuterium at low four-momentum transfer squared, Q 2 < 1 GeV 2, and compare them with parton distribution parametrization and k T factorization approaches. While differences are found, the parametrizations generally agree with the data, even at the very low-Q 2more » scale of the data. The deuterium data show a smaller longitudinal structure function and a smaller ratio of longitudinal to transverse cross section, R, than the proton. This suggests either an unexpected difference in R for the proton and the neutron or a suppression of the gluonic distribution in nuclei.« less

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

Njema, H.; Debbichi, M., E-mail: mourad_fsm@yahoo.fr; Boughzala, K.

Highlights: • The structural and electronic properties of apatites with the general formula Ca{sub 10−x}La{sub x}(PO{sub 4}){sub 6−x}(SiO{sub 4}){sub x}F{sub 2} (0 ≤ x ≤ 6) have been investigated by means of the density functional theory. • The calculated enthalpy of formation of the compounds increased with the substitution degree. • The decrease in stability is probably due to the disorder induced in the Ca/LaO{sub 6}F polyhedron, following the substitution. - Abstract: The apatite-type compounds Ca{sub 10−x}La{sub x}(PO{sub 4}){sub 6−x}(SiO{sub 4}){sub x}F{sub 2} with 0 ≤ x ≤ 6 were prepared using a high temperature solid state reaction and weremore » characterized by X-ray diffraction. The crystal structure, chemical bonding, electronic structure and formation energy of all relaxed structures were analyzed by density functional theory (DFT). The calculated results show that the predicted geometry can well reproduce the structural parameters. The incorporation of La{sup 3+} into the fluorapatite (FA) structure induced especially at the level of the S(2) sites a certain disorder which is responsible for the weakening in the stability with x. Excellent agreement were obtained between the calculated and experimental results. Moreover, the band structure indicates that despite the reduction of the band gap with x content all materials remain insulating.« less

Conservation and divergence of C-terminal domain structure in the retinoblastoma protein family

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

Liban, Tyler J.; Medina, Edgar M.; Tripathi, Sarvind

The retinoblastoma protein (Rb) and the homologous pocket proteins p107 and p130 negatively regulate cell proliferation by binding and inhibiting members of the E2F transcription factor family. The structural features that distinguish Rb from other pocket proteins have been unclear but are critical for understanding their functional diversity and determining why Rb has unique tumor suppressor activities. We describe here important differences in how the Rb and p107 C-terminal domains (CTDs) associate with the coiled-coil and marked-box domains (CMs) of E2Fs. We find that although CTD–CM binding is conserved across protein families, Rb and p107 CTDs show clear preferences formore » different E2Fs. A crystal structure of the p107 CTD bound to E2F5 and its dimer partner DP1 reveals the molecular basis for pocket protein–E2F binding specificity and how cyclin-dependent kinases differentially regulate pocket proteins through CTD phosphorylation. Our structural and biochemical data together with phylogenetic analyses of Rb and E2F proteins support the conclusion that Rb evolved specific structural motifs that confer its unique capacity to bind with high affinity those E2Fs that are the most potent activators of the cell cycle.« less

Mechanism-based corrector combination restores ΔF508-CFTR folding and function

PubMed Central

Okiyoneda, Tsukasa; Veit, Guido; Dekkers, Johanna F.; Bagdany, Miklos; Soya, Naoto; Xu, Haijin; Roldan, Ariel; Verkman, Alan S.; Kurth, Mark; Simon, Agnes; Hegedus, Tamas; Beekman, Jeffrey M.; Lukacs, Gergely L.

2013-01-01

The most common cystic fibrosis (CF) mutation, ΔF508 in the nucleotide binding domain-1 (NBD1), impairs CFTR coupled-domain folding, plasma membrane (PM) expression, function and stability. VX-809, a promising investigational corrector of ΔF508-CFTR misprocessing, has limited clinical benefit and incompletely understood mechanism, hampering drug development. Based on the effect of second site suppressor mutations, robust ΔF508-CFTR correction likely requires stabilization of NBD1 and the membrane spanning domains (MSDs)-NBD1 interface, both established primary conformational defects. Here, we elucidated the molecular targets of available correctors; class-I stabilizes the NBD1-MSD1/2 interface, class-II targets NBD2, and only chemical chaperones, surrogates of class-III correctors, stabilize the human ΔF508-NBD1. While VX-809 can correct missense mutations primarily destabilizing the NBD1-MSD1/2 interface, functional PM expression of ΔF508-CFTR also requires compounds that counteract the NBD1 and NBD2 stability defects in CF bronchial epithelial cells and intestinal organoids. Thus, structure-guided corrector combination represents an effective approach for CF therapy. PMID:23666117

A Theoretical Study of Structural, Electronic and Vibrational Properties of Small Fluoride Clusters

NASA Astrophysics Data System (ADS)

Waters, Kevin; Pandey, Ratnesh; Nigam, Sandeep; He, Haiying; Pingle, Subhash; Pandey, Avinash; Pandey, Ravindra

2014-03-01

Alkaline earth metal fluorides are an interesting family of ionic crystals having a wide range of applications in solid state lasers, luminescence, scintillators, to name just a few. In this work, small stoichiometric clusters of (MF2)n (M = Mg, Ca Sr, Ba, n =1-6) were studied for structural, vibrational and electronic properties using first-principles methods based on density functional theory. A clear trend of structural and electronic structure evolution was found for all the alkaline earth metal fluorides when the cluster size n increases from 1 to 6. Our study reveals that these fluoride clusters mimic the bulk-like behavior at the very small size. Among the four series of metal fluorides, however, (MgF2)n clusters stands out to be different in its preference of equilibrium structures owing to the much smaller ionic radius of Mg and the higher degree of covalency in the Mg-F bonding. The calculated binding energy, highest stretching frequency, ionization potential, and HOMO-LUMO gap decrease from MgF2 to BaF2 for the same cluster size. These variations are explained in terms of the change in the ionic radius and the basicity of the metal ions.

The interplay between tissue plasminogen activator domains and fibrin structures in the regulation of fibrinolysis: kinetic and microscopic studies

PubMed Central

Thelwell, Craig; Williams, Stella C.; Silva, Marta M. C. G.; Szabó, László; Kolev, Krasimir

2011-01-01

Regulation of tissue-type plasminogen activator (tPA) depends on fibrin binding and fibrin structure. tPA structure/function relationships were investigated in fibrin formed by high or low thrombin concentrations to produce a fine mesh and small pores, or thick fibers and coarse structure, respectively. Kinetics studies were performed to investigate plasminogen activation and fibrinolysis in the 2 types of fibrin, using wild-type tPA (F-G-K1-K2-P, F and K2 binding), K1K1-tPA (F-G-K1-K1-P, F binding), and delF-tPA (G-K1-K2-P, K2 binding). There was a trend of enzyme potency of tPA > K1K1-tPA > delF-tPA, highlighting the importance of the finger domain in regulating activity, but the differences were less apparent in fine fibrin. Fine fibrin was a better surface for plasminogen activation but more resistant to lysis. Scanning electron and confocal microscopy using orange fluorescent fibrin with green fluorescent protein-labeled tPA variants showed that tPA was strongly associated with agglomerates in coarse but not in fine fibrin. In later lytic stages, delF-tPA-green fluorescent protein diffused more rapidly through fibrin in contrast to full-length tPA, highlighting the importance of finger domain-agglomerate interactions. Thus, the regulation of fibrinolysis depends on the starting nature of fibrin fibers and complex dynamic interaction between tPA and fibrin structures that vary over time. PMID:20966169

On Monotone Embedding in Information Geometry (Open Access)

DTIC Science & Technology

2015-06-25

the non-parametric ( infinite - dimensional ) setting, as well [4,6], with the α-connection structure cast in a more general way. Theorem 1 of [4] gives... the weighting function for taking the expectation of random variables in calculating the Riemannian metric (G = 1 reduces to F - geometry , with the ...is a trivial rewriting of the convex function f used by [2]. This paper will start in Section 1

Functionalized C@TiO2 hollow spherical architecture for multifunctional applications.

PubMed

Chattopadhyay, Shreyasi; Mishra, Manish Kr; De, Goutam

2016-03-28

Hierarchical anatase titania (TiO2) with a hollow spherical architecture decorated with functionalized carbon dots (C(F)@THS) was synthesized by a solvothermal decomposition of titanium(IV) isopropoxide (TTIP) in the presence of a solution mixture containing thiourea and citric acid. Interestingly, the concomitant presence of thiourea and citric acid has been found to be essential to obtain such hierarchical hollow architecture because individual constituents produced non-hollow spheres when hydrothermally treated with TTIP. The co-existence of these two constituents also accelerates the growth of hollow spheres. BET surface area study of C(F)@THS revealed the existence of a slit like mesoporosity with a surface area value of 81 m(2) g(-1). Time dependent FESEM and TEM studies confirmed the formation of nanoflake like structures in the intermediate stages followed by the growth of a hollow spherical architecture. We proposed that these nanoflakes get accumulated on the bubble surface to form such hollow spherical morphology. The PL spectral study and Raman shift of the as prepared C(F)@THS confirmed the presence of functionalized graphitic C dots on the surface. A thorough XPS analysis was conducted to explore the nature and relative atomic concentration of the functional groups (-COOH, -CONH2, -NH2). This C(F)@THS sample showed very fast and selective dye (methylene blue and methyl violet) adsorption ability (even from a mixture of two different dye solutions) due to these δ-site containing functional groups on the surface. As C(F)@THS showed only two times reusability for adsorption, the dye adsorbed C(F)@THS was calcined at 450 °C in air to yield organic free anatase TiO2 hollow spheres (THS) with a retention of the original structure. THS was recycled as an efficient and a reusable photocatalyst (k = 9.36 × 10(-2) min(-1)) as well as a photoanode in dye sensitized solar cells (DSSCs) having Jsc value of 19.58 mA cm(-2) with overall efficiency of 6.48%.

Measurements of d 2 n and A 1 n : Probing the neutron spin structure

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

Flay, D.; Posik, M.; Parno, D. S.

We report on the results of the E06-014 experiment performed at Jefferson Lab in Hall A, where a precision measurement of the twist-3 matrix element d(2) of the neutron (d(2)(n)) was conducted. The quantity d(2)(n) represents the average color Lorentz force a struck quark experiences in a deep inelastic electron scattering event off a neutron due to its interaction with the hadronizing remnants. This color force was determined from a linear combination of the third moments of the He-3 spin structure functions, g(1) and g(2), after nuclear corrections had been applied to these moments. The structure functions were obtained frommore » a measurement of the unpolarized cross section and of double-spin asymmetries in the scattering of a longitudinally polarized electron beam from a transversely and a longitudinally polarized He-3 target. The measurement kinematics included two average Q(2) bins of 3.2 GeV2 and 4.3 GeV2, and Bjorken-x 0.25 <= x <= 0.90 covering the deep inelastic and resonance regions. We have found that d(2)(n) is small and negative for < Q(2)> = 3.2 GeV2, and even smaller for < Q(2)> = 4.3 GeV2, consistent with the results of a lattice QCD calculation. The twist-4 matrix element f(2)(n) was extracted by combining our measured d(2)(n) with the world data on the first moment in x of g(1)(n), Gamma(n)(1). We found f(2)(n) to be roughly an order of magnitude larger than d(2)(n). Utilizing the extracted d(2)(n) and f(2)(n) data, we separated the Lorentz color force into its electric and magnetic components, F-E(y,n) and F-B(y,n), and found them to be equal and opposite in magnitude, in agreement with the predictions from an instanton model but not with those from QCD sum rules. Furthermore, using the measured double-spin asymmetries, we have extracted the virtual photon-nucleon asymmetry on the neutron A(1)(n), the structure function ratio g(1)(n)/F-1(n), and the quark ratios (Delta u + Delta(u) over bar)/(u + (u) over bar) and (Delta d + Delta(d) over bar)/(d + (d) over bar). These results were found to be consistent with deep-inelastic scattering world data and with the prediction of the constituent quark model but at odds with the perturbative quantum chromodynamics predictions at large x.« less

Antihuman factor VIII C2 domain antibodies in hemophilia A mice recognize a functionally complex continuous spectrum of epitopes dominated by inhibitors of factor VIII activation

PubMed Central

Meeks, Shannon L.; Healey, John F.; Parker, Ernest T.; Barrow, Rachel T.

2007-01-01

The diversity of factor VIII (fVIII) C2 domain antibody epitopes was investigated by competition enzyme-linked immunosorbent assay (ELISA) using a panel of 56 antibodies. The overlap patterns produced 5 groups of monoclonal antibodies (MAbs), designated A, AB, B, BC, and C, and yielded a set of 18 distinct epitopes. Group-specific loss of antigenicity was associated with mutations at the Met2199/Phe2200 phospholipid binding β-hairpin (group AB MAbs) and at Lys2227 (group BC MAbs), which allowed orientation of the epitope structure as a continuum that covers one face of the C2 β-sandwich. MAbs from groups A, AB, and B inhibit the binding of fVIIIa to phospholipid membranes. Group BC was the most common group and displayed the highest specific fVIII inhibitor activities. MAbs in this group are type II inhibitors that inhibit the activation of fVIII by either thrombin or factor Xa and poorly inhibit the binding of fVIII to phospholipid membranes or von Willebrand factor (VWF). Group BC MAbs are epitopically and mechanistically distinct from the extensively studied group C MAb, ESH8. These results reveal the structural and functional complexity of the anti-C2 domain antibody response and indicate that interference with fVIII activation is a major attribute of the inhibitor landscape. PMID:17848617

The roles of 4f- and 5f-orbitals in bonding: A magnetochemical, crystal field, density functional theory, and multi-reference wavefunction study

DOE PAGES

Lukens, Wayne W.; Speldrich, Manfred; Yang, Ping; ...

2016-05-31

The electronic structures of 4f 3/5f 3 Cp" 3M and Cp" 3M·alkylisocyanide complexes, where Cp" is 1,3-bis-(trimethylsilyl)cyclopentadienyl, are explored with a focus on the splitting of the f-orbitals, which provides information about the strengths of the metal–ligand interactions. While the f-orbital splitting in many lanthanide complexes has been reported in detail, experimental determination of the f-orbital splitting in actinide complexes remains rare in systems other than halide and oxide compounds, since the experimental approach, crystal field analysis, is generally significantly more difficult for actinide complexes than for lanthanide complexes. In this study, a set of analogous neodymium(III) and uranium(III) tris-cyclopentadienylmore » complexes and their isocyanide adducts was characterized by electron paramagnetic resonance (EPR) spectroscopy and magnetic susceptibility. The crystal field model was parameterized by combined fitting of EPR and susceptibility data, yielding an accurate description of f-orbital splitting. The isocyanide derivatives were also studied using density functional theory, resulting in f-orbital splitting that is consistent with crystal field fitting, and by multi-reference wavefunction calculations that support the electronic structure analysis derived from the crystal-field calculations. The results highlight that the 5f-orbitals, but not the 4f-orbitals, are significantly involved in bonding to the isocyanide ligands. The main interaction between isocyanide ligand and the metal center is a σ-bond, with additional 5f to π* donation for the uranium complexes. As a result, while interaction with the isocyanide π*-orbitals lowers the energies of the 5f xz2 and 5f yz2-orbitals, spin–orbit coupling greatly reduces the population of 5f xz2 and 5f yz2 in the ground state.« less

Function-specific and Enhanced Brain Structural Connectivity Mapping via Joint Modeling of Diffusion and Functional MRI.

PubMed

Chu, Shu-Hsien; Parhi, Keshab K; Lenglet, Christophe

2018-03-16

A joint structural-functional brain network model is presented, which enables the discovery of function-specific brain circuits, and recovers structural connections that are under-estimated by diffusion MRI (dMRI). Incorporating information from functional MRI (fMRI) into diffusion MRI to estimate brain circuits is a challenging task. Usually, seed regions for tractography are selected from fMRI activation maps to extract the white matter pathways of interest. The proposed method jointly analyzes whole brain dMRI and fMRI data, allowing the estimation of complete function-specific structural networks instead of interactively investigating the connectivity of individual cortical/sub-cortical areas. Additionally, tractography techniques are prone to limitations, which can result in erroneous pathways. The proposed framework explicitly models the interactions between structural and functional connectivity measures thereby improving anatomical circuit estimation. Results on Human Connectome Project (HCP) data demonstrate the benefits of the approach by successfully identifying function-specific anatomical circuits, such as the language and resting-state networks. In contrast to correlation-based or independent component analysis (ICA) functional connectivity mapping, detailed anatomical connectivity patterns are revealed for each functional module. Results on a phantom (Fibercup) also indicate improvements in structural connectivity mapping by rejecting false-positive connections with insufficient support from fMRI, and enhancing under-estimated connectivity with strong functional correlation.

Brain functional BOLD perturbation modelling for forward fMRI and inverse mapping

PubMed Central

Robinson, Jennifer; Calhoun, Vince

2018-01-01

Purpose To computationally separate dynamic brain functional BOLD responses from static background in a brain functional activity for forward fMRI signal analysis and inverse mapping. Methods A brain functional activity is represented in terms of magnetic source by a perturbation model: χ = χ0 +δχ, with δχ for BOLD magnetic perturbations and χ0 for background. A brain fMRI experiment produces a timeseries of complex-valued images (T2* images), whereby we extract the BOLD phase signals (denoted by δP) by a complex division. By solving an inverse problem, we reconstruct the BOLD δχ dataset from the δP dataset, and the brain χ distribution from a (unwrapped) T2* phase image. Given a 4D dataset of task BOLD fMRI, we implement brain functional mapping by temporal correlation analysis. Results Through a high-field (7T) and high-resolution (0.5mm in plane) task fMRI experiment, we demonstrated in detail the BOLD perturbation model for fMRI phase signal separation (P + δP) and reconstructing intrinsic brain magnetic source (χ and δχ). We also provided to a low-field (3T) and low-resolution (2mm) task fMRI experiment in support of single-subject fMRI study. Our experiments show that the δχ-depicted functional map reveals bidirectional BOLD χ perturbations during the task performance. Conclusions The BOLD perturbation model allows us to separate fMRI phase signal (by complex division) and to perform inverse mapping for pure BOLD δχ reconstruction for intrinsic functional χ mapping. The full brain χ reconstruction (from unwrapped fMRI phase) provides a new brain tissue image that allows to scrutinize the brain tissue idiosyncrasy for the pure BOLD δχ response through an automatic function/structure co-localization. PMID:29351339

Heteromeric amino acid transporters. In search of the molecular bases of transport cycle mechanisms.

PubMed

Palacín, Manuel; Errasti-Murugarren, Ekaitz; Rosell, Albert

2016-06-15

Heteromeric amino acid transporters (HATs) are relevant targets for structural studies. On the one hand, HATs are involved in inherited and acquired human pathologies. On the other hand, these molecules are the only known examples of solute transporters composed of two subunits (heavy and light) linked by a disulfide bridge. Unfortunately, structural knowledge of HATs is scarce and limited to the atomic structure of the ectodomain of a heavy subunit (human 4F2hc-ED) and distant prokaryotic homologues of the light subunits that share a LeuT-fold. Recent data on human 4F2hc/LAT2 at nanometer resolution revealed 4F2hc-ED positioned on top of the external loops of the light subunit LAT2. Improved resolution of the structure of HATs, combined with conformational studies, is essential to establish the structural bases for light subunit recognition and to evaluate the functional relevance of heavy and light subunit interactions for the amino acid transport cycle. © 2016 Authors; published by Portland Press Limited.

An Overview of the Common Fluid Models Used in Fluid-Structure Interactions

DTIC Science & Technology

1991-08-05

inverse transform of (63) and us- ing the relation f (t - a) = exp (iwa)f(0) (64) for arbitrary (reasonably behaved) f, with f = C and a = r/c since...lri( r - ) - F -la* exp(ikr)dS’ using (53). The inverse transform of this equation gives 3 rV (Xi, t) = 2Vi c + T r3’fV+(- C (an ))dS’ (72) upon...T, when it exists, has the property rl-Tf= T=rf = f for a generic function f, the Laplace transform and inverse transform being examples of such a T

Enhanced electronic and magnetic properties by functionalization of monolayer GaS via substitutional doping and adsorption.

PubMed

Ur Rahman, Altaf; Rahman, Gul; Kratzer, Peter

2018-05-16

The structural, electronic, and magnetic properties of two-dimensional (2D) GaS are investigated using density functional theory (DFT). After confirming that the pristine 2D GaS is a non-magnetic, indirect band gap semiconductor, we consider N and F as substitutional dopants or adsorbed atoms. Except for N substituting for Ga (N Ga ), all considered cases are found to possess a magnetic moment. Fluorine, both in its atomic and molecular form, undergoes a highly exothermic reaction with GaS. Its site preference (F S or F Ga ) as substitutional dopant depends on Ga-rich or S-rich conditions. Both for F Ga and F adsorption at the Ga site, a strong F-Ga bond is formed, resulting in broken bonds within the GaS monolayer. As a result, F Ga induces p-type conductivity in GaS, whereas F S induces a dispersive, partly occupied impurity band about 0.5 e below the conduction band edge of GaS. Substitutional doping with N at both the S and the Ga site is exothermic when using N atoms, whereas only the more favourable site under the prevailing conditions can be accessed by the less reactive N 2 molecules. While N Ga induces a deep level occupied by one electron at 0.5 eV above the valence band, non-magnetic N S impurities in sufficiently high concentrations modify the band structure such that a direct transition between N-induced states becomes possible. This effect can be exploited to render monolayer GaS a direct-band gap semiconductor for optoelectronic applications. Moreover, functionalization by N or F adsorption on GaS leads to in-gap states with characteristic transition energies that can be used to tune light absorption and emission. These results suggest that GaS is a good candidate for design and construction of 2D optoelectronic and spintronics devices.

Evidence Coupling Increased Hexosamine Biosynthesis Pathway Activity to Membrane Cholesterol Toxicity and Cortical Filamentous Actin Derangement Contributing to Cellular Insulin Resistance†

PubMed Central

Bhonagiri, Padma; Pattar, Guruprasad R.; Habegger, Kirk M.; McCarthy, Alicia M.; Tackett, Lixuan

2011-01-01

Hyperinsulinemia is known to promote the progression/worsening of insulin resistance. Evidence reveals a hidden cost of hyperinsulinemia on plasma membrane (PM) phosphatidylinositol 4,5-bisphosphate (PIP2)-regulated filamentous actin (F-actin) structure, components critical to the normal operation of the insulin-regulated glucose transport system. Here we delineated whether increased glucose flux through the hexosamine biosynthesis pathway (HBP) causes PIP2/F-actin dysregulation and subsequent insulin resistance. Increased glycosylation events were detected in 3T3-L1 adipocytes cultured under conditions closely resembling physiological hyperinsulinemia (5 nm insulin; 12 h) and in cells in which HBP activity was amplified by 2 mm glucosamine (GlcN). Both the physiological hyperinsulinemia and experimental GlcN challenge induced comparable losses of PIP2 and F-actin. In addition to protecting against the insulin-induced membrane/cytoskeletal abnormality and insulin-resistant state, exogenous PIP2 corrected the GlcN-induced insult on these parameters. Moreover, in accordance with HBP flux directly weakening PIP2/F-actin structure, pharmacological inhibition of the rate-limiting HBP enzyme [glutamine-fructose-6-phosphate amidotransferase (GFAT)] restored PIP2-regulated F-actin structure and insulin responsiveness. Conversely, overexpression of GFAT was associated with a loss of detectable PM PIP2 and insulin sensitivity. Even less invasive challenges with glucose, in the absence of insulin, also led to PIP2/F-actin dysregulation. Mechanistically we found that increased HBP activity increased PM cholesterol, the removal of which normalized PIP2/F-actin levels. Accordingly, these data suggest that glucose transporter-4 functionality, dependent on PIP2 and/or F-actin status, can be critically compromised by inappropriate HBP activity. Furthermore, these data are consistent with the PM cholesterol accrual/toxicity as a mechanistic basis of the HBP-induced defects in PIP2/F-actin structure and impaired glucose transporter-4 regulation. PMID:21712361

Electronic structures and geometries of the XF{sub 3} (X = Cl, Br, I, At) fluorides

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

Sergentu, Dumitru-Claudiu; CEISAM, UMR CNRS 6230, Université de Nantes, 2 Rue de la Houssinière, BP 92208, 44322 Nantes Cedex 3; Amaouch, Mohamed

The potential energy surfaces of the group 17 XF{sub 3} (X = Cl, Br, I, At) fluorides have been investigated for the first time with multiconfigurational wave function theory approaches. In agreement with experiment, bent T-shaped C{sub 2v} structures are computed for ClF{sub 3}, BrF{sub 3}, and IF{sub 3}, while we predict that an average D{sub 3h} structure would be experimentally observed for AtF{sub 3}. Electron correlation and scalar relativistic effects strongly reduce the energy difference between the D{sub 3h} geometry and the C{sub 2v} one, along the XF{sub 3} series, and in the X = At case, spin-orbit couplingmore » also slightly reduces this energy difference. AtF{sub 3} is a borderline system where the D{sub 3h} structure becomes a minimum, i.e., the pseudo-Jahn-Teller effect is inhibited since electron correlation and scalar-relativistic effects create small energy barriers leading to the global C{sub 2v} minima, although both types of effects interfere.« less

Wave Propagation and Dynamics of Lattice Structures.

DTIC Science & Technology

1984-05-01

Progress in Solid Mechanics, North Holand Publishing Company, Amsterdam, 1960. [7) Y. K. Linn, and T. J. McDaniel, ’n)amics of Beam Type Periodic...deformation. -99- APPENDIX F FREQUENCY RESPONSE AND IMPULSE RESPONSE FUNCTIONS FOR LONGITUDINAL VIBRATION IN AN ELASTIC ROD Figure F1 shows the elastic rod to b...6 (F38) Rearranging eqn. (F38), .HE(w) = e’ 4e~3 ~e e 2 e1" +e " 6 e r (F39) Mlultiplying eqn. ( F1 =39) by 6Ŕ 6- and aragn te - . e 6 -e _ aix

Genetic and Diagnostic Biomarker Development in ASD Toddlers Using Resting State Functional MRI

DTIC Science & Technology

2017-11-01

and activation-based fMRI from the Courchesne lab report the presence of structural and functional abnormality in these structures by ages 1 to 2...young ages. With this invaluable resource, we will identify early developmental patterns of intrinsic functional network abnormalities in ASD infants...all infants and toddlers, analyses also investigate whether there may be subtypes of abnormal intrinsic connectivity patterns based on early clinical

Chemical Makeup and Hydrophilic Behavior of Graphene Oxide Nanoribbons after Low-Temperature Fluorination.

PubMed

Romero Aburto, Rebeca; Alemany, Lawrence B; Weldeghiorghis, Thomas K; Ozden, Sehmus; Peng, Zhiwei; Lherbier, Aurélien; Botello Méndez, Andrés Rafael; Tiwary, Chandra Sekhar; Taha-Tijerina, Jaime; Yan, Zheng; Tabata, Mika; Charlier, Jean-Christophe; Tour, James M; Ajayan, Pulickel M

2015-07-28

Here we investigated the fluorination of graphene oxide nanoribbons (GONRs) using H2 and F2 gases at low temperature, below 200 °C, with the purpose of elucidating their structure and predicting a fluorination mechanism. The importance of this study is the understanding of how fluorine functional groups are incorporated in complex structures, such as GONRs, as a function of temperature. The insight provided herein can potentially help engineer application-oriented materials for several research and industrial sectors. Direct (13)C pulse magic angle spinning (MAS) nuclear magnetic resonance (NMR) confirmed the presence of epoxy, hydroxyl, ester and ketone carbonyl, tertiary alkyl fluorides, as well as graphitic sp(2)-hybridized carbon. Moreover, (19)F-(13)C cross-polarization MAS NMR with (1)H and (19)F decoupling confirmed the presence of secondary alkyl fluoride (CF2) groups in the fluorinated graphene oxide nanoribbon (FGONR) structures fluorinated above 50 °C. First-principles density functional theory calculations gained insight into the atomic arrangement of the most dominant chemical groups. The fluorinated GONRs present atomic fluorine percentages in the range of 6-35. Interestingly, the FGONRs synthesized up to 100 °C, with 6-19% of atomic fluorine, exhibit colloidal similar stability in aqueous environments when compared to GONRs. This colloidal stability is important because it is not common for materials with up to 19% fluorine to have a high degree of hydrophilicity.

Conformational heterogeneity in the C-terminal zinc fingers of human MTF-1: an NMR and zinc-binding study.

PubMed

Giedroc, D P; Chen, X; Pennella, M A; LiWang, A C

2001-11-09

The human metalloregulatory transcription factor, metal-response element (MRE)-binding transcription factor-1 (MTF-1), contains six TFIIIA-type Cys(2)-His(2) motifs, each of which was projected to form well-structured betabetaalpha domains upon Zn(II) binding. In this report, the structure and backbone dynamics of a fragment containing the unusual C-terminal fingers F4-F6 has been investigated. (15)N heteronuclear single quantum coherence (HSQC) spectra of uniformly (15)N-labeled hMTF-zf46 show that Zn(II) induces the folding of hMTF-zf46. Analysis of the secondary structure of Zn(3) hMTF-zf46 determined by (13)Calpha chemical shift indexing and the magnitude of (3)J(Halpha-HN) clearly reveal that zinc fingers F4 and F6 adopt typical betabetaalpha structures. An analysis of the heteronuclear backbone (15)N relaxation dynamics behavior is consistent with this picture and further reveals independent tumbling of the finger domains in solution. Titration of apo-MTF-zf46 with Zn(II) reveals that the F4 domain binds Zn(II) significantly more tightly than do the other two finger domains. In contrast to fingers F4 and F6, the betabetaalpha fold of finger F5 is unstable and only partially populated at substoichiometric Zn(II); a slight molar excess of zinc results in severe conformational exchange broadening of all F5 NH cross-peaks. Finally, although Cd(II) binds to apo-hMTF-zf46 as revealed by intense S(-)-->Cd(II) absorption, a non-native structure results; addition of stoichiometric Zn(II) to the Cd(II) complex results in quantitative refolding of the betabetaalpha structure in F4 and F6. The functional implications of these results are discussed.

Synthesis and Crystal and Electronic Structures of the Dinuclear Platinum Compounds [PEtPh(3)](2)[Pt(2)(&mgr;-PPh(2))(2)(C(6)F(5))(4)] and [Pt(2)(&mgr;-PPh(2))(2)(C(6)F(5))(4)]: A Computational Study by Density Functional Theory.

PubMed

Alonso, Ester; Casas, José M.; Cotton, F. Albert; Feng, Xuejung; Forniés, Juan; Fortuño, Consuelo; Tomas, Milagros

1999-11-01

The electrolytic behavior of the dinuclear complexes [NBu(4)](2)[MM'(&mgr;-PPh(2))(2)(C(6)F(5))(4)] (M = M' = Pt (1), Pd (1a); M = Pt, M' = Pd (1b)) has been studied, showing electrochemically irreversible oxidation and related reduction processes. The chemical oxidation of the binuclear compound for M = M' = Pt, results in the formation of the binuclear Pt(III) compound [Pt(2)(&mgr;-PPh(2))(2)(C(6)F(5))(4)]. The crystal structure analysis of both complexes has been carried out, showing very similar structures with similar Pt-C and Pt-P distances and analogous skeletons. However the Pt-Pt distances are very different, 3.621(1) Å for the Pt(II) compound and 2.7245(7) Å for the Pt(III) derivative (as are the parameters geometrically related to this Pt-Pt distance), suggesting that, in the Pt(III) compound, there is a strong Pt-Pt bond. Results of DFT calculations on [Pt(2)(&mgr;-PH(2))(2)(C(6)F(5))(4)](n)()(-) (n = 2, 0) agree very well with the crystallographic data and indicate that, in the Pt(III) compound, there is approximately a single sigma bond between the metal atoms.

The effect of hydrochloric acid addition to increase carbon nanotubes dispersibility as drug delivery system by covalent functionalization

NASA Astrophysics Data System (ADS)

Wulan, P. P. D. K.; Ulwani, S. H.; Wulandari, H.; Purwanto, W. W.; Mulia, K.

2018-03-01

This study is to obtain the effect of adding hydrochloric acid (HCl) to the mixture of sulfuric acid (H2SO4) and HNO3 in CNT covalent functionalization. HCl expected to increase the dispersibility of functionalized CNT by improving the dispersion time period done with H2SO4 or HNO3. Functionalization used mixture of H2SO4 and HNO3 with volume ratio of 3:1. Covalent functionalization used 0.5 grams of MWCNT ultra sonicated in 50mL HNO3 with and mixture of H2SO4 and HNO3. Additions of 200 mL HCl used variation of molarity from 1M, 2M, 3M, 4M, 5M to 6M. CNT were oxidized to form carboxylic and hydroxyl bonds on the surface that increase dispersibility of CNT. FTIR spectrums showed the existences of carboxyl and hydroxyl group on spectra of 2600-3700 cm-1 and 900-1400 cm-1. Dispersion tests, which showed functionalized CNT (f-CNT) dispersion capabilities, were done by dissolving f-CNT in water. The study resulted that 6M f-CNT (NSC6) gave the best dispersion with zeta potential value of -37.1mV. NSC6 gave the longest dispersion time which was 20 days until f-CNT settle again. SEM-EDS micrographs showed the surface structure of 6M f-CNT without significant damage and no longer contain impurities of Fe, Ni, and Cl.

Identification and characterisation of midbrain nuclei using optimised functional magnetic resonance imaging

PubMed Central

Limbrick-Oldfield, Eve H.; Brooks, Jonathan C.W.; Wise, Richard J.S.; Padormo, Francesco; Hajnal, Jo V.; Beckmann, Christian F.; Ungless, Mark A.

2012-01-01

Localising activity in the human midbrain with conventional functional MRI (fMRI) is challenging because the midbrain nuclei are small and located in an area that is prone to physiological artefacts. Here we present a replicable and automated method to improve the detection and localisation of midbrain fMRI signals. We designed a visual fMRI task that was predicted would activate the superior colliculi (SC) bilaterally. A limited number of coronal slices were scanned, orientated along the long axis of the brainstem, whilst simultaneously recording cardiac and respiratory traces. A novel anatomical registration pathway was used to optimise the localisation of the small midbrain nuclei in stereotactic space. Two additional structural scans were used to improve registration between functional and structural T1-weighted images: an echo-planar image (EPI) that matched the functional data but had whole-brain coverage, and a whole-brain T2-weighted image. This pathway was compared to conventional registration pathways, and was shown to significantly improve midbrain registration. To reduce the physiological artefacts in the functional data, we estimated and removed structured noise using a modified version of a previously described physiological noise model (PNM). Whereas a conventional analysis revealed only unilateral SC activity, the PNM analysis revealed the predicted bilateral activity. We demonstrate that these methods improve the measurement of a biologically plausible fMRI signal. Moreover they could be used to investigate the function of other midbrain nuclei. PMID:21867762

Measurement of the EMC effect in the deuteron

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

Griffioen, Keith A.; Arrington, John R.; Christy, M. Eric

2015-07-21

We have determined the structure function ratiomore » $$R^d_{\\rm EMC}=F_2^d/(F_2^n+F_2^p)$$ from recently published $$F_2^n/F_2^d$$ data taken by the BONuS experiment using CLAS at Jefferson Lab. This ratio deviates from unity, with a slope $$dR_{\\rm EMC}^{d}/dx= -0.10\\pm 0.05$$ in the range of Bjorken $x$ from 0.35 to 0.7, for invariant mass $W>1.4$ GeV and $Q^2>1$ GeV$^2$. The observed EMC effect for these kinematics is consistent with conventional nuclear physics models that include off-shell corrections, as well as with empirical analyses that find the EMC effect proportional to the probability of short-range nucleon-nucleon correlations.« less

Comparison of the F2 Structure Function in Iron as Measured by Charged Lepton and Neutrino Probes

NASA Astrophysics Data System (ADS)

Kalantarians, Narbe; Christy, Eric; Keppel, Cynthia

2017-09-01

World data for the F2 structure function for Iron, as measured by multiple charged lepton and neutrino deep inelastic scattering experiments, are compared. Data obtained from charged lepton and neutrino scattering at larger values of x are in remarkably good agreement with a simple invocation of the 18/5 rule, while a discrepancy in the behavior of the data obtained from the different probes well beyond the data uncertainties is observed in the shadowing/anti-shadowing transition region where the Bjorken scaling variable x is less than 0.15. The data are compared to theoretical calculations. Details and results of the data comparison will be presented, along with future plans.

HOTCFGM-2D: A Coupled Higher-Order Theory for Cylindrical Structural Components with Bi-Directionally Components with Bi-Directionally Graded Microstructures

NASA Technical Reports Server (NTRS)

Pindera, Marek-Jerzy; Aboudi, Jacob

2000-01-01

The objective of this two-year project was to develop and deliver to the NASA-Glenn Research Center a two-dimensional higher-order theory, and related computer codes, for the analysis and design of cylindrical functionally graded materials/structural components for use in advanced aircraft engines (e.g., combustor linings, rotor disks, heat shields, brisk blades). To satisfy this objective, two-dimensional version of the higher-order theory, HOTCFGM-2D, and four computer codes based on this theory, for the analysis and design of structural components functionally graded in the radial and circumferential directions were developed in the cylindrical coordinate system r-Theta-z. This version of the higher-order theory is a significant generalization of the one-dimensional theory, HOTCFGM-1D, developed during the FY97 for the analysis and design of cylindrical structural components with radially graded microstructures. The generalized theory is applicable to thin multi-phased composite shells/cylinders subjected to steady-state thermomechanical, transient thermal and inertial loading applied uniformly along the axial direction such that the overall deformation is characterized by a constant average axial strain. The reinforcement phases are uniformly distributed in the axial direction, and arbitrarily distributed in the radial and circumferential direction, thereby allowing functional grading of the internal reinforcement in the r-Theta plane. The four computer codes fgmc3dq.cylindrical.f, fgmp3dq.cylindrical.f, fgmgvips3dq.cylindrical.f, and fgmc3dq.cylindrical.transient.f are research-oriented codes for investigating the effect of functionally graded architectures, as well as the properties of the multi-phase reinforcement, in thin shells subjected to thermomechanical and inertial loading, on the internal temperature, stress and (inelastic) strain fields. The reinforcement distribution in the radial and circumferential directions is specified by the user. The thermal and inelastic properties of the individual phases can vary with temperature. The inelastic phases are presently modeled by the power-law creep model generalized to multi-directional loading (within fgmc3dq.cylindrical.f and fgmc3dq.cylindrical.transient.f for steady-state and transient thermal loading, respectively), and incremental plasticity and GVIPS unified viscoplasticity theories (within the steady-state loading versions fgmp3dq.cylindrical.f and fgmgvips3dq.cylindrical.f).

Crystal structure of cbbF from Zymomonas mobilis and its functional implication

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

Hwang, Hyo-Jeong; Park, Suk-Youl; Kim, Jeong-Sun, E-mail: jsunkim@chonnam.ac.kr

2014-02-28

Highlights: • The crystal structure of one cbbF from Zymomonas mobilis was revealed. • Scores of residues form two secondary structures with a non-polar protruded residue. • It exists as a dimeric form in solution. - Abstract: A phosphate group at the C1-atom of inositol-monophosphate (IMP) and fructose-1,6-bisphosphate (FBP) is hydrolyzed by a phosphatase IMPase and FBPase in a metal-dependent way, respectively. The two enzymes are almost indiscernible from each other because of their highly similar sequences and structures. Metal ions are bound to residues on the β1- and β2-strands and one mobile loop. However, FBP has another phosphate andmore » FBPases exist as a higher oligomeric state, which may discriminate FBPases from IMPases. There are three genes annotated as FBPases in Zymomonas mobilis, termed also cbbF (ZmcbbF). The revealed crystal structure of one ZmcbbF shows a globular structure formed by five stacked layers. Twenty-five residues in the middle of the sequence form an α-helix and a β-strand, which occupy one side of the catalytic site. A non-polar Leu residue among them is protruded to the active site, pointing out unfavorable access of a bulky charged group to this side. In vitro assays have shown its dimeric form in solution. Interestingly, two β-strands of β1 and β2 are disordered in the ZmcbbF structure. These data indicate that ZmcbbF might structurally belong to IMPase, and imply that its active site would be reorganized in a yet unreported way.« less

Electronic structure and metallization of cubic GdH{sub 3} under pressure: Ab initio many-body GW calculations

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

Kong, Bo, E-mail: kong79@yeah.net, E-mail: yachao.zhang@pku.edu.cn; Guizhou Provincial Key Laboratory of Computational Nano-Material Science, Guizhou Education University, Guiyang 550018; Zhang, Yachao, E-mail: kong79@yeah.net, E-mail: yachao.zhang@pku.edu.cn

The electronic structures of the cubic GdH{sub 3} are extensively investigated using the ab initio many-body GW calculations treating the Gd 4f electrons either in the core (4f-core) or in the valence states (4f-val). Different degrees of quasiparticle (QP) self-consistent calculations with the different starting points are used to correct the failures of the GGA/GGA + U/HSE03 calculations. In the 4f-core case, GGA + G{sub 0}W{sub 0} calculations give a fundamental band gap of 1.72 eV, while GGA+ GW{sub 0} or GGA + GW calculations present a larger band gap. In the 4f-val case, the nonlocal exchange-correlation (xc) functional HSE03 can account much better for the strong localizationmore » of the 4f states than the semilocal or Hubbard U corrected xc functional in the Kohn–Sham equation. We show that the fundamental gap of the antiferromagnetic (AFM) or ferromagnetic (FM) GdH{sub 3} can be opened up by solving the QP equation with improved starting point of eigenvalues and wave functions given by HSE03. The HSE03 + G{sub 0}W{sub 0} calculations present a fundamental band gap of 2.73 eV in the AFM configuration, and the results of the corresponding GW{sub 0} and GW calculations are 2.89 and 3.03 eV, respectively. In general, for the cubic structure, the fundamental gap from G{sub 0}W{sub 0} calculations in the 4f-core case is the closest to the real result. By G{sub 0}W{sub 0} calculations in the 4f-core case, we find that H or Gd defects can strongly affect the band structure, especially the H defects. We explain the mechanism in terms of the possible electron correlation on the hydrogen site. Under compression, the insulator-to-metal transition in the cubic GdH{sub 3} occurs around 40 GPa, which might be a satisfied prediction.« less

Theoretical study of mixed LiLnX4 (Ln = La, Dy; X = F, Cl, Br, I) rare earth/alkali halide complexes.

PubMed

Groen, C P; Oskam, A; Kovács, A

2000-12-25

The structure, bonding and vibrational properties of the mixed LiLnX4 (Ln = La, Dy; X = F, Cl, Br, I) rare earth/alkali halide complexes were studied using various quantum chemical methods (HF, MP2 and the Becke3-Lee-Yang-Parr exchange-correlation density functional) in conjunction with polarized triple-zeta valence basis sets and quasi-relativistic effective core potentials for the heavy atoms. Our comparative study indicated the superiority of MP2 theory while the HF and B3-LYP methods as well as less sophisticated basis sets failed for the correct energetic relations. In particular, f polarization functions on Li and X proved to be important for the Li...X interaction in the complexes. From the three characteristic structures of such complexes, possessing 1-(C3v), 2-(C2v), or 3-fold coordination (C3v) between the alkali metal and the bridging halide atoms, the bi- and tridentate forms are located considerably lower on the potential energy surface then the monodentate isomer. Therefore only the bi- and tridentate isomers have chemical relevance. The monodentate isomer is only a high-lying local minimum in the case of X = F. For X = Cl, Br, and I this structure is found to be a second-order saddle point. The bidentate structure was found to be the global minimum for the systems with X = F, Cl, and Br. However, the relative stability with respect to the tridentate structure is very small (1-5 kJ/mol) for the heavier halide derivatives and the relative order is reversed in the case of the iodides. The energy difference between the three structures and the dissociation energy decrease in the row F to I. The ionic bonding in the complexes was characterized by natural charges and a topological analysis of the electron density distribution according to Bader's theorem. Variation of the geometrical and bonding characteristics between the lanthanum and dysprosium complexes reflects the effect of "lanthanide contraction". The calculated vibrational data indicate that infrared spectroscopy may be an effective tool for experimental investigation and characterization of LiLnX4 molecules.

Structure prediction and analysis of MxaF from obligate, facultative and restricted facultative methylobacterium.

PubMed

Singh, Raghvendra Pratap; Singh, Ram Nageena; Srivastava, Manish K; Srivastava, Alok Kumar; Kumar, Sudheer; Dubey, Ramesh Chandra; Sharma, Arun Kumar

2012-01-01

Methylobacteria are ubiquitous in the biosphere which are capable of growing on C1 compounds such as formate, formaldehyde, methanol and methylamine as well as on a wide range of multi-carbon growth substrates such as C2, C3 and C4 compounds due to the methylotrophic enzymes methanol dehydrogenase (MDH). MDH is performing these functions with the help of a key protein mxaF. Unfortunately, detailed structural analysis and homology modeling of mxaF is remains undefined. Hence, the objective of this research is the characterization and three dimensional modeling of mxaF protein from three different methylotrophs by using I-TASSER server. The predicted model were further optimize and validate by Profile 3D, Errat, Verifiy3-D and PROCHECK server. Predicted and best evaluated models have been successfully deposited to PMDB database with PMDB ID PM0077505, PM0077506 and PM0077507. Active site identification revealed 11, 13 and 14 putative functional site residues in respected models. It may play a major role during protein-protein, and protein-cofactor interactions. This study can provide us an ab-initio and detail information to understand the structure, mechanism of action and regulation of mxaF protein.

Structure prediction and analysis of MxaF from obligate, facultative and restricted facultative methylobacterium

PubMed Central

Singh, Raghvendra Pratap; Singh, Ram Nageena; Srivastava, Manish K; Srivastava, Alok Kumar; Kumar, Sudheer; Dubey, Ramesh Chandra; Sharma, Arun Kumar

2012-01-01

Methylobacteria are ubiquitous in the biosphere which are capable of growing on C1 compounds such as formate, formaldehyde, methanol and methylamine as well as on a wide range of multi-carbon growth substrates such as C2, C3 and C4 compounds due to the methylotrophic enzymes methanol dehydrogenase (MDH). MDH is performing these functions with the help of a key protein mxaF. Unfortunately, detailed structural analysis and homology modeling of mxaF is remains undefined. Hence, the objective of this research is the characterization and three dimensional modeling of mxaF protein from three different methylotrophs by using I-TASSER server. The predicted model were further optimize and validate by Profile 3D, Errat, Verifiy3-D and PROCHECK server. Predicted and best evaluated models have been successfully deposited to PMDB database with PMDB ID PM0077505, PM0077506 and PM0077507. Active site identification revealed 11, 13 and 14 putative functional site residues in respected models. It may play a major role during protein-protein, and protein-cofactor interactions. This study can provide us an ab-initio and detail information to understand the structure, mechanism of action and regulation of mxaF protein. PMID:23275704

Structural abnormalities and altered regional brain activity in multiple sclerosis with simple spinal cord involvement.

PubMed

Yin, Ping; Liu, Yi; Xiong, Hua; Han, Yongliang; Sah, Shambhu Kumar; Zeng, Chun; Wang, Jingjie; Li, Yongmei

2018-02-01

To assess the changes of the structural and functional abnormalities in multiple sclerosis with simple spinal cord involvement (MS-SSCI) by using resting-state functional MRI (RS-fMRI), voxel based morphology (VBM) and diffusion tensor tractography. The amplitude of low-frequency fluctuation (ALFF) of 22 patients with MS-SSCI and 22 healthy controls (HCs) matched for age, gender and education were compared by using RS-fMRI. We also compared the volume, fractional anisotropy (FA) and apparent diffusion coefficient of the brain regions in baseline brain activity by using VBM and diffusion tensor imaging. The relationships between the expanded disability states scale (EDSS) scores, changed parameters of structure and function were further explored. (1) Compared with HCs, the ALFF of the bilateral hippocampus and right middle temporal gyrus in MS-SSCI decreased significantly. However, patients exhibited increased ALFF in the left middle frontal gyrus, left posterior cingulate gyrus and right middle occipital gyrus ( two-sample t-test, after AlphaSim correction, p < 0.01, voxel size > 40). The volume of right middle frontal gyrus reduced significantly (p < 0.01). The FA and ADC of right hippocampus, the FA of left hippocampus and right middle temporal gyrus were significantly different. (2) A significant correlation between EDSS scores and ALFF was noted only in the left posterior cingulate gyrus. Our results detected structural and functional abnormalities in MS-SSCI and functional parameters were associated with clinical abnormalities. Multimodal imaging plays an important role in detecting structural and functional abnormalities in MS-SSCI. Advances in knowledge: This is the first time to apply RS-fMRI, VBM and diffusion tensor tractography to study the structural and functional abnormalities in MS-SSCI, and to explore its correlation with EDSS score.

Second harmonic generation from metallo-dielectric multilayered structures in the plasmonic regime.

PubMed

Mattiucci, Nadia; D'Aguanno, Giuseppe; Bloemer, Mark J

2010-11-08

We present a theoretical study on second harmonic generation from metallo-dielectric multilayered structures in the plasmonic regime. In particular we analyze the behavior of structures made of Ag (silver) and MgF2 (magnesium-fluoride) due to the straightforward procedure to grow these materials with standard sputtering or thermal evaporation techniques. A systematic study is performed which analyzes four different kinds of elementary cells--namely (Ag/MgF2)N, (MgF2/Ag)N, (Ag/MgF2/Ag)N and (MgF2/Ag/MgF2)N--as function of the number of periods (N) and the thickness of the layers. We predict the conversion efficiency to be up to three orders of magnitude greater than the conversion efficiency found in the non-plasmonic regime and we point out the best geometries to achieve these conversion efficiencies. We also underline the role played by the short-range/long-range plasmons and leaky waves in the generation process. We perform a statistical study to demonstrate the robustness of the SH process in the plasmonic regime against the inevitable variations in the thickness of the layers. Finally, we show that a proper choice of the output medium can further improve the conversion efficiency reaching an enhancement of almost five orders of magnitude with respect to the non plasmonic regime.

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

PubMed

Rahaman, Badiur; Saha-Dasgupta, T

2007-07-25

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

Structural basis for olivetolic acid formation by a polyketide cyclase from Cannabis sativa.

PubMed

Yang, Xinmei; Matsui, Takashi; Kodama, Takeshi; Mori, Takahiro; Zhou, Xiaoxi; Taura, Futoshi; Noguchi, Hiroshi; Abe, Ikuro; Morita, Hiroyuki

2016-03-01

In polyketide biosynthesis, ring formation is one of the key diversification steps. Olivetolic acid cyclase (OAC) from Cannabis sativa, involved in cannabinoid biosynthesis, is the only known plant polyketide cyclase. In addition, it is the only functionally characterized plant α+β barrel (DABB) protein that catalyzes the C2-C7 aldol cyclization of the linear pentyl tetra-β-ketide CoA as the substrate, to generate olivetolic acid (OA). Herein, we solved the OAC apo and OAC-OA complex binary crystal structures at 1.32 and 1.70 Å resolutions, respectively. The crystal structures revealed that the enzyme indeed belongs to the DABB superfamily, as previously proposed, and possesses a unique active-site cavity containing the pentyl-binding hydrophobic pocket and the polyketide binding site, which have never been observed among the functionally and structurally characterized bacterial polyketide cyclases. Furthermore, site-directed mutagenesis studies indicated that Tyr72 and His78 function as acid/base catalysts at the catalytic center. Structural and/or functional studies of OAC suggested that the enzyme lacks thioesterase and aromatase activities. These observations demonstrated that OAC employs unique catalytic machinery utilizing acid/base catalytic chemistry for the formation of the precursor of OA. The structural and functional insights obtained in this work thus provide the foundation for analyses of the plant polyketide cyclases that will be discovered in the future. Structural data reported in this paper are available in the Protein Data Bank under the accession numbers 5B08 for the OAC apo, 5B09 for the OAC-OA binary complex and 5B0A, 5B0B, 5B0C, 5B0D, 5B0E, 5B0F and 5B0G for the OAC His5Q, Ile7F, Tyr27F, Tyr27W, Val59M, Tyr72F and His78S mutant enzymes, respectively. © 2016 Federation of European Biochemical Societies.

Dual roles of f electrons in mixing Al 3 p character into d -orbital conduction bands for lanthanide and actinide dialuminides

DOE PAGES

Altman, Alison B.; Pemmaraju, C. D.; Alayoglu, Selim; ...

2018-01-15

Correlated electron phenomena in lanthanide and actinide materials are driven by a complex interplay between the f and d orbitals. Here in this study, aluminum K-edge x-ray absorption spectroscopy and density functional theory calculations are used to evaluate the electronic structure of the dialuminides, MAl 2 (M = Ce, Sm, Eu, Yb, Lu, U, and Pu). The results show how the energy and occupancy of the 4f or 5f orbitals impacts mixing of Al 3p character into the 5d or 6d conduction bands, which has implications for understanding the magnetic and structural properties of correlated electron systems.

Three-phase heterostructures f-NiFe2O4/PANI/PI EMI shielding fabric with high Microwave Absorption Performance

NASA Astrophysics Data System (ADS)

Wang, Yu; Wang, Wei; Yu, Dan

2017-12-01

In this work, a three-phase heterostructures f-NiFe2O4/PANI/PI EMI shielding fabric with a layer by layer structure was designed and prepared to obtain excellent microwave attenuation performance. Firstly, PANI/PI fabric was prepared via in-situ deposition method. Then, the NiFe2O4 nanoparticles functionalized by oleic acid were uniformly dispersed in epoxy resin and coated on the top and bottom of PANI/PI fabric with 0.041 mm total thickness. The investigation of chemical structure and surface morphologies indicated the composite structure of f-NiFe2O4/PANI/PI fabric. Various parameters like magnetic property, reflection loss and attenuation constant were used to evaluate its microwave attenuation performance. The results demonstrated that the 30f-NiFe2O4/PANI/PI fabric had a highest attenuation effectiveness with the minimum reflection loss value of -42.5 dB (>90% attenuation) at 12.5 GHz and the effective absorption bandwidth was 3.4 GHz. The study of attenuation mechanism indicated that the dielectric loss from PANI, the magnetic loss caused by f-NiFe2O4 and the layer by layer structure effectively improved microwave attenuation performance of composite fabric. Furthermore, the favorable flexibility and dimensional stability of this resultant fabric would allow the composite fabric for a long time service under pressure or foldable conditions. In sum, the study clearly indicated that three-phase heterostructures f-NiFe2O4/PANI/PI fabric was a good candidate as electromagnetic shielding materials in many fields.

13C and 19F solid-state NMR and X-ray crystallographic study of halogen-bonded frameworks featuring nitrogen-containing heterocycles.

PubMed

Szell, Patrick M J; Gabriel, Shaina A; Gill, Russell D D; Wan, Shirley Y H; Gabidullin, Bulat; Bryce, David L

2017-03-01

Halogen bonding is a noncovalent interaction between the electrophilic region of a halogen (σ-hole) and an electron donor. We report a crystallographic and structural analysis of halogen-bonded compounds by applying a combined X-ray diffraction (XRD) and solid-state nuclear magnetic resonance (SSNMR) approach. Single-crystal XRD was first used to characterize the halogen-bonded cocrystals formed between two fluorinated halogen-bond donors (1,4-diiodotetrafluorobenzene and 1,3,5-trifluoro-2,4,6-triiodobenzene) and several nitrogen-containing heterocycles (acridine, 1,10-phenanthroline, 2,3,5,6-tetramethylpyrazine, and hexamethylenetetramine). New structures are reported for the following three cocrystals, all in the P2 1 /c space group: acridine-1,3,5-trifluoro-2,4,6-triiodobenzene (1/1), C 6 F 3 I 3 ·C 13 H 9 N, 1,10-phenanthroline-1,3,5-trifluoro-2,4,6-triiodobenzene (1/1), C 6 F 3 I 3 ·C 12 H 8 N 2 , and 2,3,5,6-tetramethylpyrazine-1,3,5-trifluoro-2,4,6-triiodobenzene (1/1), C 6 F 3 I 3 ·C 8 H 12 N 2 . 13 C and 19 F solid-state magic-angle spinning (MAS) NMR is shown to be a convenient method to characterize the structural features of the halogen-bond donor and acceptor, with chemical shifts attributable to cocrystal formation observed in the spectra of both nuclides. Cross polarization (CP) from 19 F to 13 C results in improved spectral sensitivity in characterizing the perfluorinated halogen-bond donor when compared to conventional 1 H CP. Gauge-including projector-augmented wave density functional theory (GIPAW DFT) calculations of magnetic shielding constants, along with optimization of the XRD structures, provide a final set of structures in best agreement with the experimental 13 C and 19 F chemical shifts. Data for carbons bonded to iodine remain outliers due to well-known relativistic effects.

Comparison of the structure function F 2 as measured by charged lepton and neutrino scattering from iron targets

DOE PAGES

Kalantarians, N.; Keppel, C.; Christy, M. E.

2017-09-12

A comparison study of world data for the structure function F 2 for Iron, as measured by both charged lepton and neutrino scattering experiments, is presented. Consistency of results for both charged lepton and neutrino scattering is observed for the full global data set in the valence regime. Consistency is also observed at low x for the various neutrino data sets, as well as for the charged lepton data sets, independently. However, data from the two probes exhibit differences on the order of 15% in the shadowing/anti-shadowing transition region where the Bjorken scaling variable x is < 0.15. This observationmore » is indicative that neutrino probes of nucleon structure might be sensitive to different nuclear effects than charged lepton probes. Details and results of the data comparison are here presented.« less

Comparison of the structure function F 2 as measured by charged lepton and neutrino scattering from iron targets

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

Kalantarians, N.; Keppel, C.; Christy, M. E.

A comparison study of world data for the structure function F 2 for Iron, as measured by both charged lepton and neutrino scattering experiments, is presented. Consistency of results for both charged lepton and neutrino scattering is observed for the full global data set in the valence regime. Consistency is also observed at low x for the various neutrino data sets, as well as for the charged lepton data sets, independently. However, data from the two probes exhibit differences on the order of 15% in the shadowing/anti-shadowing transition region where the Bjorken scaling variable x is < 0.15. This observationmore » is indicative that neutrino probes of nucleon structure might be sensitive to different nuclear effects than charged lepton probes. Details and results of the data comparison are here presented.« less

Combined Approach for the Structural Characterization of Alkali Fluoroscandates: Solid-State NMR, Powder X-ray Diffraction, and Density Functional Theory Calculations.

PubMed

Rakhmatullin, Aydar; Polovov, Ilya B; Maltsev, Dmitry; Allix, Mathieu; Volkovich, Vladimir; Chukin, Andrey V; Boča, Miroslav; Bessada, Catherine

2018-02-05

The structures of several fluoroscandate compounds are presented here using a characterization approach combining powder X-ray diffraction and solid-state NMR. The structure of K 5 Sc 3 F 14 was fully determined from Rietveld refinement performed on powder X-ray diffraction data. Moreover, the local structures of NaScF 4 , Li 3 ScF 6 , KSc 2 F 7 , and Na 3 ScF 6 compounds were studied in detail from solid-state 19 F and 45 Sc NMR experiments. The 45 Sc chemical shift ranges for six- and seven-coordinated scandium environments were defined. The 19 F chemical shift ranges for bridging and terminal fluorine atoms were also determined. First-principles calculations of the 19 F and 45 Sc NMR parameters were carried out using plane-wave basis sets and periodic boundary conditions (CASTEP), and the results were compared with the experimental data. A good agreement between the calculated shielding constants and experimental chemical shifts was obtained. This demonstrates the good potential of computational methods in spectroscopic assignments of solid-state 45 Sc NMR spectroscopy.

Optimization of single crystals of solid electrolytes with tysonite-type structure (LaF3) for conductivity at 293 K: 2. Nonstoichiometric phases R 1- y M y F3- y ( R = La-Lu, Y; M = Sr, Ba)

NASA Astrophysics Data System (ADS)

Sorokin, N. I.; Sobolev, B. P.; Krivandina, E. A.; Zhmurova, Z. I.

2015-01-01

Single crystals of fluorine-conducting solid electrolytes R 1 - y Sr y F3 - y and R 1 - y Ba y F3 - y ( R = La-Lu, Y) with a tysonite-type structure (LaF3) have been optimized for room-temperature conductivity σ293 K. The optimization is based on high-temperature measurements of σ( T) in two-component nonstoichiometric phases R 1 - y M y F3 - y ( M = Sr, Ba) as a function of the MF2 content. Optimization for thermal stability is based on studying the phase diagrams of MF2- RF3 systems ( M = Sr, Ba) and the behavior of nonstoichiometric crystals upon heating when measuring temperature dependences σ( T). Single crystals of many studied R 1 - y Sr y F3 - y and R 1 - y Ba y F3 - y phases have σ293 K values large enough to use these materials in solid-state electrochemical devices (chemical sensors, fluorine-ion batteries, accumulators, etc.) operating at room temperature.

Photocatalytic activity of CdS and Ag2S quantum dots deposited on poly(amidoamine) functionalized carbon nanotubes

PubMed Central

Neelgund, Gururaj M.; Oki, Aderemi

2011-01-01

Two novel ternary nanocatalysts, f-MWCNTs-CdS and f-MWCNTs-Ag2S were successfully constructed by covalent grafting of fourth generation (G4) hyperbranched, crosslinked poly(amidoamine) (PAMAM) to carboxylated multi-walled carbon nanotubes (MWCNTs-COOH) and subsequent deposition of CdS or Ag2S quantum dots (QDs). The structural transformation, surface potential, and morphology of functionalized MWCNTs (f-MWCNTs) and nanocatalysts were characterized by UV-vis spectrophotometer, Fourier transform infrared spectroscopy, powder X-ray diffraction, Raman spectroscopy, thermogravimetric analysis, scanning electron microscopy and energy dispersive spectroscopy. Transmission electron microscopy reveals the effective anchoring of QDs on f-MWCNTs. The catalytic activity of nanocatalysts was evaluated by photodegradation of methyl orange under illumination of UV light. The coupling of MWCNTs, PAMAM and CdS or Ag2S QDs significantly enhanced the catalytic efficiency of nanocatalysts. The rate constants for degradation of methyl orange in presence of nanocatalysts were calculated using the Langmuir-Hinshelwood model. Overall, the excellence in photodegradation was accomplished by hybridizing f-MWCNTs with CdS or Ag2S PMID:22267895

Methyltransferase That Modifies Guanine 966 of the 16 S rRNA: FUNCTIONAL IDENTIFICATION AND TERTIARY STRUCTURE*

PubMed Central

Lesnyak, Dmitry V.; Osipiuk, Jerzy; Skarina, Tatiana; Sergiev, Petr V.; Bogdanov, Alexey A.; Edwards, Aled; Savchenko, Alexei; Joachimiak, Andrzej; Dontsova, Olga A.

2010-01-01

N2-Methylguanine 966 is located in the loop of Escherichia coli 16 S rRNA helix 31, forming a part of the P-site tRNA-binding pocket. We found yhhF to be a gene encoding for m2G966 specific 16 S rRNA methyltransferase. Disruption of the yhhF gene by kanamycin resistance marker leads to a loss of modification at G966. The modification could be rescued by expression of recombinant protein from the plasmid carrying the yhhF gene. Moreover, purified m2G966 methyltransferase, in the presence of S-adenosylomethionine (AdoMet), is able to methylate 30 S ribosomal subunits that were purified from yhhF knock-out strain in vitro. The methylation is specific for G966 base of the 16 S rRNA. The m2G966 methyltransferase was crystallized, and its structure has been determined and refined to 2.05 Å. The structure closely resembles RsmC rRNA methyltransferase, specific for m2G1207 of the 16 S rRNA. Structural comparisons and analysis of the enzyme active site suggest modes for binding AdoMet and rRNA to m2G966 methyltransferase. Based on the experimental data and current nomenclature the protein expressed from the yhhF gene was renamed to RsmD. A model for interaction of RsmD with ribosome has been proposed. PMID:17189261

Methyltransferase that modifies guanine 966 of the 16 S rRNA: functional identification and tertiary structure.

PubMed

Lesnyak, Dmitry V; Osipiuk, Jerzy; Skarina, Tatiana; Sergiev, Petr V; Bogdanov, Alexey A; Edwards, Aled; Savchenko, Alexei; Joachimiak, Andrzej; Dontsova, Olga A

2007-02-23

N(2)-Methylguanine 966 is located in the loop of Escherichia coli 16 S rRNA helix 31, forming a part of the P-site tRNA-binding pocket. We found yhhF to be a gene encoding for m(2)G966 specific 16 S rRNA methyltransferase. Disruption of the yhhF gene by kanamycin resistance marker leads to a loss of modification at G966. The modification could be rescued by expression of recombinant protein from the plasmid carrying the yhhF gene. Moreover, purified m(2)G966 methyltransferase, in the presence of S-adenosylomethionine (AdoMet), is able to methylate 30 S ribosomal subunits that were purified from yhhF knock-out strain in vitro. The methylation is specific for G966 base of the 16 S rRNA. The m(2)G966 methyltransferase was crystallized, and its structure has been determined and refined to 2.05A(.) The structure closely resembles RsmC rRNA methyltransferase, specific for m(2)G1207 of the 16 S rRNA. Structural comparisons and analysis of the enzyme active site suggest modes for binding AdoMet and rRNA to m(2)G966 methyltransferase. Based on the experimental data and current nomenclature the protein expressed from the yhhF gene was renamed to RsmD. A model for interaction of RsmD with ribosome has been proposed.

Measurements of d 2 n and A 1 n : Probing the neutron spin structure

DOE PAGES

Flay, D.; Posik, M.; Parno, D. S.; ...

2016-09-06

We report on the results of the E06-014 experiment performed at Jefferson Lab in Hall A, where a precision measurement of the twist-3 matrix elementmore » $$d_2$$ of the neutron ($$d_{2}^{n}$$) was conducted. This quantity represents the average color Lorentz force a struck quark experiences in a deep inelastic electron scattering event off a neutron due to its interaction with the hadronizing remnants. This color force was determined from a linear combination of the third moments of the spin structure functions $$g_1$$ and $$g_2$$ on $$^{3}$$He after nuclear corrections had been applied to these moments. The kinematics included two average $$Q^{2}$$ bins of $3.2$ GeV$$^{2}$$ and $4.3$ GeV$$^{2}$$, and Bjorken-$x$ $$0.25 \\leq x \\leq 0.90$$ covering the DIS and resonance regions. We found $$d_2^n$$ to be small and negative for $ = 3.2$ GeV$$^{2}$$, and smaller for $ = 4.3$ GeV$$^{2}$$, consistent with a lattice QCD calculation. The twist-4 matrix element $$f_{2}^{n}$$ was extracted by combining our $$d_{2}^{n}$$ with the world data on $$\\Gamma_{1}^{n} = \\int_{0}^{1} g_{1}^{n} dx$$. We found $$f_{2}^{n}$$ to be roughly an order of magnitude larger than $$d_{2}^{n}$$. Utilizing the extracted $$d_{2}^{n}$$ and $$f_{2}^{n}$$ data, we separated the color force into its electric and magnetic components, $$F_{E}^{y,n}$$ and $$F_{B}^{y,n}$$, and found them to be equal and opposite in magnitude, in agreement with instanton model predictions but not with those from QCD sum rules. Additionally, we have extracted the neutron virtual photon-nucleon asymmetry $$A_{1}^{n}$$, the structure function ratio $$g_{1}^{n}/F_{1}^{n}$$, and the quark ratios $$(\\Delta u + \\Delta \\bar{u})/(u + \\bar{u})$$ and $$(\\Delta d + \\Delta \\bar{d})/(d + \\bar{d})$$. Lastly, these results were found to be consistent with DIS world data and with the prediction of the constituent quark model but at odds with those of perturbative QCD at large $x$.« less

Materials Data on Sb4Au(Xe2F11)2 (SG:2) by Materials Project

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

Kristin Persson

Computed materials data using density functional theory calculations. These calculations determine the electronic structure of bulk materials by solving approximations to the Schrodinger equation. For more information, see https://materialsproject.org/docs/calculations

Materials Data on W5(O2F11)2 (SG:2) by Materials Project

DOE Data Explorer

Kristin Persson

2014-07-09

Computed materials data using density functional theory calculations. These calculations determine the electronic structure of bulk materials by solving approximations to the Schrodinger equation. For more information, see https://materialsproject.org/docs/calculations

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

Clark, Richard A.; McNamara, Bruce K.; Barinaga, Charles J.

The first electron ionization mass spectrum of tellurium hexafluoride (TeF6) is reported. The starting material was produced by direct fluorination of Te metal or TeO2 with nitrogen trifluoride. Formation of TeF6 was confirmed through cryogenic capture of the tellurium fluorination product and analysis through Raman spectroscopy. The eight natural abundance isotopes were observed for each of the set of fragment ions: TeF5+, TeF4+ TeF3+, TeF2+, TeF1+, and Te+, Te2+. A trend in increasing abundance was observed for the even fluoride bearing ions: TeF1+ < TeF3+ < TeF5+, and a decreasing abundance was observed for the even fragment series: Te(0)+ >more » TeF2+ > TeF4+ > TeF6+, with the molecular ion TeF6+ not observed at all. Density functional theory based electronic structure calculations were used to calculate optimized ground state geometries of these gas phase species and their relative stabilities explain the trends in the data and the lack of observed signal for TeF6+.« less

Structure and Mutagenesis of the Parainfluenza Virus 5 Hemagglutinin-Neuraminidase Stalk Domain Reveals a Four-Helix Bundle and the Role of the Stalk in Fusion Promotion

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

Bose, Sayantan; Welch, Brett D.; Kors, Christopher A.

2014-10-02

Paramyxovirus entry into cells requires the fusion protein (F) and a receptor binding protein (hemagglutinin-neuraminidase [HN], H, or G). The multifunctional HN protein of some paramyxoviruses, besides functioning as the receptor (sialic acid) binding protein (hemagglutinin activity) and the receptor-destroying protein (neuraminidase activity), enhances F activity, presumably by lowering the activation energy required for F to mediate fusion of viral and cellular membranes. Before or upon receptor binding by the HN globular head, F is believed to interact with the HN stalk. Unfortunately, until recently none of the receptor binding protein crystal structures have shown electron density for the stalkmore » domain. Parainfluenza virus 5 (PIV5) HN exists as a noncovalent dimer-of-dimers on the surface of cells, linked by a single disulfide bond in the stalk. Here we present the crystal structure of the PIV5-HN stalk domain at a resolution of 2.65 {angstrom}, revealing a four-helix bundle (4HB) with an upper (N-terminal) straight region and a lower (C-terminal) supercoiled part. The hydrophobic core residues are a mix of an 11-mer repeat and a 3- to 4-heptad repeat. To functionally characterize the role of the HN stalk in F interactions and fusion, we designed mutants along the PIV5-HN stalk that are N-glycosylated to physically disrupt F-HN interactions. By extensive study of receptor binding, neuraminidase activity, oligomerization, and fusion-promoting functions of the mutant proteins, we found a correlation between the position of the N-glycosylation mutants on the stalk structure and their neuraminidase activities as well as their abilities to promote fusion.« less

Structure and Mutagenesis of the Parainfluenza Virus 5 Hemagglutinin-Neuraminidase Stalk Domain Reveals a Four-Helix Bundle and the Role of the Stalk in Fusion Promotion▿

PubMed Central

Bose, Sayantan; Welch, Brett D.; Kors, Christopher A.; Yuan, Ping; Jardetzky, Theodore S.; Lamb, Robert A.

2011-01-01

Paramyxovirus entry into cells requires the fusion protein (F) and a receptor binding protein (hemagglutinin-neuraminidase [HN], H, or G). The multifunctional HN protein of some paramyxoviruses, besides functioning as the receptor (sialic acid) binding protein (hemagglutinin activity) and the receptor-destroying protein (neuraminidase activity), enhances F activity, presumably by lowering the activation energy required for F to mediate fusion of viral and cellular membranes. Before or upon receptor binding by the HN globular head, F is believed to interact with the HN stalk. Unfortunately, until recently none of the receptor binding protein crystal structures have shown electron density for the stalk domain. Parainfluenza virus 5 (PIV5) HN exists as a noncovalent dimer-of-dimers on the surface of cells, linked by a single disulfide bond in the stalk. Here we present the crystal structure of the PIV5-HN stalk domain at a resolution of 2.65 Å, revealing a four-helix bundle (4HB) with an upper (N-terminal) straight region and a lower (C-terminal) supercoiled part. The hydrophobic core residues are a mix of an 11-mer repeat and a 3- to 4-heptad repeat. To functionally characterize the role of the HN stalk in F interactions and fusion, we designed mutants along the PIV5-HN stalk that are N-glycosylated to physically disrupt F-HN interactions. By extensive study of receptor binding, neuraminidase activity, oligomerization, and fusion-promoting functions of the mutant proteins, we found a correlation between the position of the N-glycosylation mutants on the stalk structure and their neuraminidase activities as well as their abilities to promote fusion. PMID:21994464

R6/2 Huntington's disease mice develop early and progressive abnormal brain metabolism and seizures.

PubMed

Cepeda-Prado, Efrain; Popp, Susanna; Khan, Usman; Stefanov, Dimitre; Rodríguez, Jorge; Menalled, Liliana B; Dow-Edwards, Diana; Small, Scott A; Moreno, Herman

2012-05-09

A hallmark feature of Huntington's disease pathology is the atrophy of brain regions including, but not limited to, the striatum. Though MRI studies have identified structural CNS changes in several Huntington's disease (HD) mouse models, the functional consequences of HD pathology during the progression of the disease have yet to be investigated using in vivo functional MRI (fMRI). To address this issue, we first established the structural and functional MRI phenotype of juvenile HD mouse model R6/2 at early and advanced stages of disease. Significantly higher fMRI signals [relative cerebral blood volumes (rCBVs)] and atrophy were observed in both age groups in specific brain regions. Next, fMRI results were correlated with electrophysiological analysis, which showed abnormal increases in neuronal activity in affected brain regions, thus identifying a mechanism accounting for the abnormal fMRI findings. [(14)C] 2-deoxyglucose maps to investigate patterns of glucose utilization were also generated. An interesting mismatch between increases in rCBV and decreases in glucose uptake was observed. Finally, we evaluated the sensitivity of this mouse line to audiogenic seizures early in the disease course. We found that R6/2 mice had an increased susceptibility to develop seizures. Together, these findings identified seizure activity in R6/2 mice and show that neuroimaging measures sensitive to oxygen metabolism can be used as in vivo biomarkers, preceding the onset of an overt behavioral phenotype. Since fMRI-rCBV can also be obtained in patients, we propose that it may serve as a translational tool to evaluate therapeutic responses in humans and HD mouse models.

On F-Algebras M p  (1 < p < ∞) of Holomorphic Functions

PubMed Central

Meštrović, Romeo

2014-01-01

We consider the classes M p (1 < p < ∞) of holomorphic functions on the open unit disk 𝔻 in the complex plane. These classes are in fact generalizations of the class M introduced by Kim (1986). The space M p equipped with the topology given by the metric ρ p defined by ρ p(f, g) = ||f − g||p = (∫ 0 2πlogp(1 + M(f − g)(θ))(dθ/2π))1/p, with f, g∈M p and Mf(θ) = sup0⩽r<1 ⁡|f(re iθ)|, becomes an F-space. By a result of Stoll (1977), the Privalov space N p (1 < p < ∞) with the topology given by the Stoll metric d p is an F-algebra. By using these two facts, we prove that the spaces M p and N p coincide and have the same topological structure. Consequently, we describe a general form of continuous linear functionals on M p (with respect to the metric ρ p). Furthermore, we give a characterization of bounded subsets of the spaces M p. Moreover, we give the examples of bounded subsets of M p that are not relatively compact. PMID:24672388

Molecular and ultrastructural analysis of forisome subunits reveals the principles of forisome assembly

PubMed Central

Müller, Boje; Groscurth, Sira; Menzel, Matthias; Rüping, Boris A.; Twyman, Richard M.; Prüfer, Dirk; Noll, Gundula A.

2014-01-01

Background and Aims Forisomes are specialized structural phloem proteins that mediate sieve element occlusion after wounding exclusively in papilionoid legumes, but most studies of forisome structure and function have focused on the Old World clade rather than the early lineages. A comprehensive phylogenetic, molecular, structural and functional analysis of forisomes from species covering a broad spectrum of the papilionoid legumes was therefore carried out, including the first analysis of Dipteryx panamensis forisomes, representing the earliest branch of the Papilionoideae lineage. The aim was to study the molecular, structural and functional conservation among forisomes from different tribes and to establish the roles of individual forisome subunits. Methods Sequence analysis and bioinformatics were combined with structural and functional analysis of native forisomes and artificial forisome-like protein bodies, the latter produced by expressing forisome genes from different legumes in a heterologous background. The structure of these bodies was analysed using a combination of confocal laser scanning microscopy (CLSM), scanning electron microscopy (SEM) and transmission electron microscopy (TEM), and the function of individual subunits was examined by combinatorial expression, micromanipulation and light microscopy. Key Results Dipteryx panamensis native forisomes and homomeric protein bodies assembled from the single sieve element occlusion by forisome (SEO-F) subunit identified in this species were structurally and functionally similar to forisomes from the Old World clade. In contrast, homomeric protein bodies assembled from individual SEO-F subunits from Old World species yielded artificial forisomes differing in proportion to their native counterparts, suggesting that multiple SEO-F proteins are required for forisome assembly in these plants. Structural differences between Medicago truncatula native forisomes, homomeric protein bodies and heteromeric bodies containing all possible subunit combinations suggested that combinations of SEO-F proteins may fine-tune the geometric proportions and reactivity of forisomes. Conclusions It is concluded that forisome structure and function have been strongly conserved during evolution and that species-dependent subsets of SEO-F proteins may have evolved to fine-tune the structure of native forisomes. PMID:24694827

Crystal structure of YHI9, the yeast member of the phenazine biosynthesis PhzF enzyme superfamily.

PubMed

Liger, Dominique; Quevillon-Cheruel, Sophie; Sorel, Isabelle; Bremang, Michael; Blondeau, Karine; Aboulfath, Ilham; Janin, Joël; van Tilbeurgh, Herman; Leulliot, Nicolas

2005-09-01

In the Pseudomonas bacterial genomes, the PhzF proteins are involved in the production of phenazine derivative antibiotic and antifungal compounds. The PhzF superfamily however also encompasses proteins in all genomes from bacteria to eukaryotes, for which no function has been assigned. We have determined the three dimensional crystal structure at 2.05 A resolution of YHI9, the yeast member of the PhzF family. YHI9 has a fold similar to bacterial diaminopimelate epimerase, revealing a bimodular structure with an internal symmetry. Residue conservation identifies a putative active site at the interface between the two domains. Evolution of this protein by gene duplication, gene fusion and domain swapping from an ancestral gene containing the "hot dog" fold, identifies the protein as a "kinked double hot dog" fold. Copyright 2005 Wiley-Liss, Inc.

Membrane-Induced Structural Rearrangement and Identification of a Novel Membrane Anchor in Talin F2F3

PubMed Central

Arcario, Mark J.; Tajkhorshid, Emad

2014-01-01

Experimental challenges associated with characterization of the membrane-bound form of talin have prevented us from understanding the molecular mechanism of its membrane-dependent integrin activation. Here, utilizing what we believe to be a novel membrane mimetic model, we present a reproducible model of membrane-bound talin observed across multiple independent simulations. We characterize both local and global membrane-induced structural transitions that successfully reconcile discrepancies between biochemical and structural studies and provide insight into how talin might modulate integrin function. Membrane binding of talin, captured in unbiased simulations, proceeds through three distinct steps: initial electrostatic recruitment of the F2 subdomain to anionic lipids via several basic residues; insertion of an initially buried, conserved hydrophobic anchor into the membrane; and association of the F3 subdomain with the membrane surface through a large, interdomain conformational change. These latter two steps, to our knowledge, have not been observed or described previously. Electrostatic analysis shows talin F2F3 to be highly polarized, with a highly positive underside, which we attribute to the initial electrostatic recruitment, and a negative top face, which can help orient the protein optimally with respect to the membrane, thereby reducing the number of unproductive membrane collision events. PMID:25418091

Workshop on Functional and Structural Relationships and Factor Analysis (1983). Summary of Research Interests of Participants.

DTIC Science & Technology

1983-01-01

J. Amer. Statist. Assoc. 75, 687-692. Dahm, P. F., Helton, B. and Fuller, W. A. (1983), Generalized least squares estimation of the genotypic ...with applications to -"insect development times". Austral. J. Statist. 23, 204-213. [2] Angus , J.F., R. Morton and C. Schafer. (1981). "Phasic

Research into Traveling Wave Control in Flexible Structures

DTIC Science & Technology

1990-06-15

Displacement is the measured variable in all of the rod examples. Y = F I s i n(k + k 0) _______________ ikEA 21- k [ (24)- -- .r k k 0 F - Choosing m = 4 in...the value of Eq. (25) function of position is given by becomes U2 for that mode. U(X)= F 4 ( 2 e + e (21) Figure 3 shows the magnitudes of the ikEA ...for providing a reasonable length sensor. ___ sin(k_ The dash-dot curve in Fig. 4 shows the ikEA 1- _ 2 1- e-as (28) magnitude and phase of a

Structure of the d-alanylgriseoluteic acid biosynthetic protein EhpF, an atypical member of the ANL superfamily of adenylating enzymes

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

Bera, Asim K.; Atanasova, Vesna; Gamage, Swarna

2010-06-01

The structure of EhpF from P. agglomerans has been solved alone and in complex with phenazine-1,6-dicarboxylate. Apo EhpF was solved and refined in two different space groups at 1.95 and 2.3 Å resolution and the EhpF–phenazine-1,6-dicarboxylate complex structure was determined at 2.8 Å resolution. The structure of EhpF, a 41 kDa protein that functions in the biosynthetic pathway leading to the broad-spectrum antimicrobial compound d-alanylgriseoluteic acid (AGA), is reported. A cluster of approximately 16 genes, including ehpF, located on a 200 kbp plasmid native to certain strains of Pantoea agglomerans encodes the proteins that are required for the conversion ofmore » chorismic acid to AGA. Phenazine-1,6-dicarboxylate has been identified as an intermediate in AGA biosynthesis and deletion of ehpF results in accumulation of this compound in vivo. The crystallographic data presented here reveal that EhpF is an atypical member of the acyl-CoA synthase or ANL superfamily of adenylating enzymes. These enzymes typically catalyze two-step reactions involving adenylation of a carboxylate substrate followed by transfer of the substrate from AMP to coenzyme A or another phosphopantetheine. EhpF is distinguished by the absence of the C-terminal domain that is characteristic of enzymes from this family and is involved in phosphopantetheine binding and in the second half of the canonical two-step reaction that is typically observed. Based on the structure of EhpF and a bioinformatic analysis, it is proposed that EhpF and EhpG convert phenazine-1,6-dicarboxylate to 6-formylphenazine-1-carboxylate via an adenylyl intermediate.« less

Structure of the Newcastle disease virus F protein in the post-fusion conformation

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

Swanson, Kurt; Wen, Xiaolin; Leser, George P.

2010-11-17

The paramyxovirus F protein is a class I viral membrane fusion protein which undergoes a significant refolding transition during virus entry. Previous studies of the Newcastle disease virus, human parainfluenza virus 3 and parainfluenza virus 5 F proteins revealed differences in the pre- and post-fusion structures. The NDV Queensland (Q) F structure lacked structural elements observed in the other two structures, which are key to the refolding and fusogenic activity of F. Here we present the NDV Australia-Victoria (AV) F protein post-fusion structure and provide EM evidence for its folding to a pre-fusion form. The NDV AV F structure containsmore » heptad repeat elements missing in the previous NDV Q F structure, forming a post-fusion six-helix bundle (6HB) similar to the post-fusion hPIV3 F structure. Electrostatic and temperature factor analysis of the F structures points to regions of these proteins that may be functionally important in their membrane fusion activity.« less

[DPOAE in tinnitus patients with cochlear hearing loss considering hyperacusis and misophonia].

PubMed

Sztuka, Aleksandra; Pośpiech, Lucyna; Gawron, Wojciech; Dudek, Krzysztof

2006-01-01

The most probable place generating tinnitus in auditory pathway are outer hair cells (OHC) inside cochlea. To asses their activity otoacoustic emission is used. The goal of the investigation was estimation the features of otoemission DPOAE in groups with tinnitus patients with cochlear hearing loss, estimation of diagnostic value of DPOAE parameters for analysis of function of the cochlea in investigated patients emphasizing DPOAE parameters most useful in localizing tinnitus generators and estimation of hypothetic influence of hyperacusis and misophony on parameters of DPOAE in tinnitus patients with cochlear hearing loss. The material of the study were 42 tinnitus patients with cochlear hearing loss. In the control group there were 21 patients without tinnitus with the same type of hearing loss. Then tinnitus patients were divided into three subgroups--with hyperacusis, misophony and without both of them, based on audiologic findings. after taking view on tinnitus and physical examination in all the patients pure tone and impedance audiometry, supratreshold tests, ABR and audiometric average and discomfort level were evaluated. Then otoemission DPOAE was measured in three procedures. First the amplitudes of two points per octave were assessed, in second--"fine structure" method-- 16-20 points per octave (f2/f1 = 1.2, L1 = L2 = 70 dB). Third procedure included recording of growth rate function in three series for input tones of value f2 = 2002, 4004, 6006 Hz (f2/f1= 1.22) and levels L1=L2, growing by degrees of 5dB in each series. DPOAE amplitudes in recording of 2 points per octave and fine structure method are very valuable parameters for estimation of cochlear function in tinnitus patients with cochlear hearing loss. Decreasing of DPOAE amplitudes in patients with cochlear hearing loss and tinnitus suggests significant role of OHC pathology, unbalanced by IHC injury in generation of tinnitus in patients with hearing loss of cochlear localization. DPOAE fine structure provides us the additional information about DPOAE amplitude recorded in two points per octave, spreading the amount of frequencies f2, where differences are noticed in comparison of two groups--tinnitus patients and control. Function growth rate cannot be the only parameter in estimation of DPOAE in tinnitus patients with cochlear hearing loss, also including subjects with hyperacusis and misophony. Hyperacusis has important influence on DPOAE amplitude, increases essentially amplitude of DPOAE in the examined group of tinnitus patients.

Materials Data on KCu2P2H3(O4F)2 (SG:12) by Materials Project

DOE Data Explorer

Kristin Persson

2016-04-23

Computed materials data using density functional theory calculations. These calculations determine the electronic structure of bulk materials by solving approximations to the Schrodinger equation. For more information, see https://materialsproject.org/docs/calculations

3D topology of orientation columns in visual cortex revealed by functional optical coherence tomography.

PubMed

Nakamichi, Yu; Kalatsky, Valery A; Watanabe, Hideyuki; Sato, Takayuki; Rajagopalan, Uma Maheswari; Tanifuji, Manabu

2018-04-01

Orientation tuning is a canonical neuronal response property of six-layer visual cortex that is encoded in pinwheel structures with center orientation singularities. Optical imaging of intrinsic signals enables us to map these surface two-dimensional (2D) structures, whereas lack of appropriate techniques has not allowed us to visualize depth structures of orientation coding. In the present study, we performed functional optical coherence tomography (fOCT), a technique capable of acquiring a 3D map of the intrinsic signals, to study the topology of orientation coding inside the cat visual cortex. With this technique, for the first time, we visualized columnar assemblies in orientation coding that had been predicted from electrophysiological recordings. In addition, we found that the columnar structures were largely distorted around pinwheel centers: center singularities were not rigid straight lines running perpendicularly to the cortical surface but formed twisted string-like structures inside the cortex that turned and extended horizontally through the cortex. Looping singularities were observed with their respective termini accessing the same cortical surface via clockwise and counterclockwise orientation pinwheels. These results suggest that a 3D topology of orientation coding cannot be fully anticipated from 2D surface measurements. Moreover, the findings demonstrate the utility of fOCT as an in vivo mesoscale imaging method for mapping functional response properties of cortex in the depth axis. NEW & NOTEWORTHY We used functional optical coherence tomography (fOCT) to visualize three-dimensional structure of the orientation columns with millimeter range and micrometer spatial resolution. We validated vertically elongated columnar structure in iso-orientation domains. The columnar structure was distorted around pinwheel centers. An orientation singularity formed a string with tortuous trajectories inside the cortex and connected clockwise and counterclockwise pinwheel centers in the surface orientation map. The results were confirmed by comparisons with conventional optical imaging and electrophysiological recordings.

Markov models for fMRI correlation structure: Is brain functional connectivity small world, or decomposable into networks?

PubMed

Varoquaux, G; Gramfort, A; Poline, J B; Thirion, B

2012-01-01

Correlations in the signal observed via functional Magnetic Resonance Imaging (fMRI), are expected to reveal the interactions in the underlying neural populations through hemodynamic response. In particular, they highlight distributed set of mutually correlated regions that correspond to brain networks related to different cognitive functions. Yet graph-theoretical studies of neural connections give a different picture: that of a highly integrated system with small-world properties: local clustering but with short pathways across the complete structure. We examine the conditional independence properties of the fMRI signal, i.e. its Markov structure, to find realistic assumptions on the connectivity structure that are required to explain the observed functional connectivity. In particular we seek a decomposition of the Markov structure into segregated functional networks using decomposable graphs: a set of strongly-connected and partially overlapping cliques. We introduce a new method to efficiently extract such cliques on a large, strongly-connected graph. We compare methods learning different graph structures from functional connectivity by testing the goodness of fit of the model they learn on new data. We find that summarizing the structure as strongly-connected networks can give a good description only for very large and overlapping networks. These results highlight that Markov models are good tools to identify the structure of brain connectivity from fMRI signals, but for this purpose they must reflect the small-world properties of the underlying neural systems. Copyright © 2012 Elsevier Ltd. All rights reserved.

Materials Data on Fe3(O2F)2 (SG:1) by Materials Project

DOE Data Explorer

Kristin Persson

2015-01-21

Computed materials data using density functional theory calculations. These calculations determine the electronic structure of bulk materials by solving approximations to the Schrodinger equation. For more information, see https://materialsproject.org/docs/calculations

Materials Data on Sr2BN2F (SG:62) by Materials Project

DOE Data Explorer

Kristin Persson

2014-11-02

Computed materials data using density functional theory calculations. These calculations determine the electronic structure of bulk materials by solving approximations to the Schrodinger equation. For more information, see https://materialsproject.org/docs/calculations

Materials Data on Ca2BN2F (SG:62) by Materials Project

DOE Data Explorer

Kristin Persson

2014-11-02

Computed materials data using density functional theory calculations. These calculations determine the electronic structure of bulk materials by solving approximations to the Schrodinger equation. For more information, see https://materialsproject.org/docs/calculations

Materials Data on CaSn2F6 (SG:2) by Materials Project

DOE Data Explorer

Kristin Persson

2014-07-09

Computed materials data using density functional theory calculations. These calculations determine the electronic structure of bulk materials by solving approximations to the Schrodinger equation. For more information, see https://materialsproject.org/docs/calculations

Study on the “3F-in-1” Sustainable Reconstruction of Rural Architecture from Placeality Perspective--A Case Study of Caiyuan Village in Jingmen City, Hubei Province

NASA Astrophysics Data System (ADS)

Fangyu, Fu; Yu, Cao

2017-05-01

This paper takes Caiyuan Village in Jingmen City of Hubei Province as the research object, analyzes the production, life and ecological functions of rural buildings and the “3F-in-1” inherent mechanism from the local perspective. Based on the concept analysis of placeality and “3F-in-1”, this paper clarifies the relationship among the value of life function, production function, ecological function so as to analyze the “3F-in-1” mode of rural architecture with placeality. On this basis, this thesis puts forward the strategy of sustainable spatial transformation (1) preserve the traditional overall spatial structure of villages, (2) improve the adaptability and function of rural architecture, (3) extend the rural social culture, (4) pay attention to local perception, with a view to explore an organic system design method for the exhibition of placeality and sustainable development of beautiful countryside.

Relationship between left ventricular mechanics and low free triiodothyronine levels after myocardial infarction: a prospective study.

PubMed

Jankauskienė, Edita; Orda, Paulius; Barauskienė, Greta; Mickuvienė, Narseta; Brožaitienė, Julija; Vaškelytė, Jolanta Justina; Bunevičius, Robertas

2016-04-01

Low free triiodothyronine (fT3) levels following acute myocardial infarction (AMI) are associated with greater impairment in cardiac mechanics compared with patients with AMI who have normal values of thyroid hormones. The objectives are to investigate left ventricular (LV) function and mechanics during a 6-month follow-up after myocardial infarction and to evaluate their prognostic implication using two-dimensional (2D) echocardiography and 2D speckle-tracking echocardiography in patients with low fT3 levels. The study design is prospective cohort study. One hundred forty patients with first-onset AMI were grouped according to serum fT3 levels: low fT3 group (fT3 <3.2 pmol/L; n = 44) and control group (fT3 >3.2 pmol/L; n = 96). Low levels of fT3 were associated with greater LV diameters and LV end-diastolic volume, and decreased systolic LV function. Systolic apical and basal rotation, peak systolic global longitudinal strain and strain rate, and LV twist and torsion were significantly decreased in the low fT3 group. The prognostic implication for predicting low fT3 levels was evaluated using ROC analysis. LV end-diastolic diameter index is the most sensitive (94.12 %), but has low specificity (37.93 %; area = 0.659, p = 0.01). By contrast, LV end-systolic volume is the most specific (94.03 %), but has low sensitivity (26.32 %; area = 0.594, p = 0.04). Low fT3 levels are significantly associated with worse LV mechanics. Low fT3 levels are important for prediction of LV structure, function, rotation, and deformation parameters during the late post-myocardial infarction period.

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

Pantelis, Evaggelos, E-mail: vpantelis@phys.uoa.g; Medical Physics Laboratory, Medical School, University of Athens, Athens; Papadakis, Nikolaos

Purpose: To study the efficacy of the integration of functional magnetic resonance imaging (fMRI) and diffusion tensor imaging tractography data into stereotactic radiosurgery clinical practice. Methods and Materials: fMRI and tractography data sets were acquired and fused with corresponding anatomical MR and computed tomography images of patients with arteriovenous malformation (AVM), astrocytoma, brain metastasis, or hemangioma and referred for stereotactic radiosurgery. The acquired data sets were imported into a CyberKnife stereotactic radiosurgery system and used to delineate the target, organs at risk, and nearby functional structures and fiber tracts. Treatment plans with and without the incorporation of the functional structuresmore » and the fiber tracts into the optimization process were developed and compared. Results: The nearby functional structures and fiber tracts could receive doses of >50% of the maximum dose if they were excluded from the planning process. In the AVM case, the doses received by the Broadmann-17 structure and the optic tract were reduced to 700 cGy from 1,400 cGy and to 1,200 cGy from 2,000 cGy, respectively, upon inclusion into the optimization process. In the metastasis case, the motor cortex received 850 cGy instead of 1,400 cGy; and in the hemangioma case, the pyramidal tracts received 780 cGy instead of 990 cGy. In the astrocytoma case, the dose to the motor cortex bordering the lesion was reduced to 1,900 cGy from 2,100 cGy, and therefore, the biologically equivalent dose in three fractions was delivered instead. Conclusions: Functional structures and fiber tracts could receive high doses if they were not considered during treatment planning. With the aid of fMRI and tractography images, they can be delineated and spared.« less

Compounds that correct F508del-CFTR trafficking can also correct other protein trafficking diseases: an in vitro study using cell lines

PubMed Central

2013-01-01

Background Many genetic diseases are due to defects in protein trafficking where the mutant protein is recognized by the quality control systems, retained in the endoplasmic reticulum (ER), and degraded by the proteasome. In many cases, the mutant protein retains function if it can be trafficked to its proper cellular location. We have identified structurally diverse correctors that restore the trafficking and function of the most common mutation causing cystic fibrosis, F508del-CFTR. Most of these correctors do not act directly as ligands of CFTR, but indirectly on other pathways to promote folding and correction. We hypothesize that these proteostasis regulators may also correct other protein trafficking diseases. Methods To test our hypothesis, we used stable cell lines or transient transfection to express 2 well-studied trafficking disease mutations in each of 3 different proteins: the arginine-vasopressin receptor 2 (AVPR2, also known as V2R), the human ether-a-go-go-related gene (KCNH2, also known as hERG), and finally the sulfonylurea receptor 1 (ABCC8, also known as SUR1). We treated cells expressing these mutant proteins with 9 structurally diverse F508del-CFTR correctors that function through different cellular mechanisms and assessed whether correction occurred via immunoblotting and functional assays. Results were deemed significantly different from controls by a one-way ANOVA (p < 0.05). Results Here we show that F508del-CFTR correctors RDR1, KM60 and KM57 also correct some mutant alleles of other protein trafficking diseases. We also show that one corrector, the cardiac glycoside ouabain, was found to alter the glycosylation of all mutant alleles tested. Conclusions Correctors of F508del-CFTR trafficking might have broader applications to other protein trafficking diseases. PMID:23316740

X2Y2 isomers: tuning structure and relative stability through electronegativity differences (X = H, Li, Na, F, Cl, Br, I; Y = O, S, Se, Te).

PubMed

El-Hamdi, Majid; Poater, Jordi; Bickelhaupt, F Matthias; Solà, Miquel

2013-03-04

We have studied the XYYX and X2YY isomers of the X2Y2 species (X = H, Li, Na, F, Cl, Br, I; Y = O, S, Se, Te) using density functional theory at the ZORA-BP86/QZ4P level. Our computations show that, over the entire range of our model systems, the XYYX isomers are more stable than the X2YY forms except for X = F and Y = S and Te, for which the F2SS and F2TeTe isomers are slightly more stable. Our results also point out that the Y-Y bond length can be tuned quite generally through the X-Y electronegativity difference. The mechanism behind this electronic tuning is the population or depopulation of the π* in the YY fragment.

Glycosylated SV2 and Gangliosides as Dual Receptors for Botulinum Neurotoxin Serotype F

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

Fu, Zhuji; Chen, Chen; Barbieri, Joseph T.

2010-02-22

Botulinum neurotoxin causes rapid flaccid paralysis through the inhibition of acetylcholine release at the neuromuscular junction. The seven BoNT serotypes (A-G) have been proposed to bind motor neurons via ganglioside-protein dual receptors. To date, the structure-function properties of BoNT/F host receptor interactions have not been resolved. Here, we report the crystal structures of the receptor binding domains (HCR) of BoNT/A and BoNT/F and the characterization of the dual receptors for BoNT/F. The overall polypeptide fold of HCR/A is essentially identical to the receptor binding domain of the BoNT/A holotoxin, and the structure of HCR/F is very similar to that ofmore » HCR/A, except for two regions implicated in neuronal binding. Solid phase array analysis identified two HCR/F binding glycans: ganglioside GD1a and oligosaccharides containing an N-acetyllactosamine core. Using affinity chromatography, HCR/F bound native synaptic vesicle glycoproteins as part of a protein complex. Deglycosylation of glycoproteins using {alpha}(1-3,4)-fucosidase, endo-{beta}-galactosidase, and PNGase F disrupted the interaction with HCR/F, while the binding of HCR/B to its cognate receptor, synaptotagmin I, was unaffected. These data indicate that the HCR/F binds synaptic vesicle glycoproteins through the keratan sulfate moiety of SV2. The interaction of HCR/F with gangliosides was also investigated. HCR/F bound specifically to gangliosides that contain {alpha}2,3-linked sialic acid on the terminal galactose of a neutral saccharide core (binding order GT1b = GD1a GM3; no binding to GD1b and GM1a). Mutations within the putative ganglioside binding pocket of HCR/F decreased binding to gangliosides, synaptic vesicle protein complexes, and primary rat hippocampal neurons. Thus, BoNT/F neuronal discrimination involves the recognition of ganglioside and protein (glycosylated SV2) carbohydrate moieties, providing a structural basis for the high affinity and specificity of BoNT/F for neurons.« less

Measurement of the nucleon structure function F 2 in the nuclear medium and evaluation of its moments

DOE PAGES

Osipenko, M.

2010-06-01

We report on the measurement of inclusive electron scattering off a carbon target performed with CLAS at Jefferson Laboratory. A combination of three different beam energies 1.161, 2.261 and 4.461 GeV allowed us to reach an invariant mass of the final-state hadronic system W ≈ 2.4 GeV with four-momentum transfers Q 2 ranging from 0.2 to 5 GeV 2. These data, together with previous measurements of the inclusive electron scattering off proton and deuteron, which cover a similar continuous two-dimensional region of Q 2 and Bjorken variable x, permit the study of nuclear modifications of the nucleon structure. By usingmore » these, as well as other world data, we evaluated the F 2 structure function and its moments. Using an OPE-based twist expansion, we studied the Q 2-evolution of the moments, obtaining a separation of the leading-twist and the total higher-twist terms. The carbon-to-deuteron ratio of the leading-twist contributions to the F 2 moments exhibits the well known EMC effect, compatible with that discovered previously in x-space. The total higher-twist term in the carbon nucleus appears, although with large systematic uncertainites, to be smaller with respect to the deuteron case for n < 7, suggesting partial parton deconfinement in nuclear matter. Lastly, we speculate that the spatial extension of the nucleon is changed when it is immersed in the nuclear medium.« less

Preservation of cardiac function by prolonged action potentials in mice deficient of KChIP2.

PubMed

Grubb, Søren; Aistrup, Gary L; Koivumäki, Jussi T; Speerschneider, Tobias; Gottlieb, Lisa A; Mutsaers, Nancy A M; Olesen, Søren-Peter; Calloe, Kirstine; Thomsen, Morten B

2015-08-01

Inherited ion channelopathies and electrical remodeling in heart disease alter the cardiac action potential with important consequences for excitation-contraction coupling. Potassium channel-interacting protein 2 (KChIP2) is reduced in heart failure and interacts under physiological conditions with both Kv4 to conduct the fast-recovering transient outward K(+) current (Ito,f) and with CaV1.2 to mediate the inward L-type Ca(2+) current (ICa,L). Anesthetized KChIP2(-/-) mice have normal cardiac contraction despite the lower ICa,L, and we hypothesized that the delayed repolarization could contribute to the preservation of contractile function. Detailed analysis of current kinetics shows that only ICa,L density is reduced, and immunoblots demonstrate unaltered CaV1.2 and CaVβ₂ protein levels. Computer modeling suggests that delayed repolarization would prolong the period of Ca(2+) entry into the cell, thereby augmenting Ca(2+)-induced Ca(2+) release. Ca(2+) transients in disaggregated KChIP2(-/-) cardiomyocytes are indeed comparable to wild-type transients, corroborating the preserved contractile function and suggesting that the compensatory mechanism lies in the Ca(2+)-induced Ca(2+) release event. We next functionally probed dyad structure, ryanodine receptor Ca(2+) sensitivity, and sarcoplasmic reticulum Ca(2+) load and found that increased temporal synchronicity of the Ca(2+) release in KChIP2(-/-) cardiomyocytes may reflect improved dyad structure aiding the compensatory mechanisms in preserving cardiac contractile force. Thus the bimodal effect of KChIP2 on Ito,f and ICa,L constitutes an important regulatory effect of KChIP2 on cardiac contractility, and we conclude that delayed repolarization and improved dyad structure function together to preserve cardiac contraction in KChIP2(-/-) mice. Copyright © 2015 the American Physiological Society.

Strong Dependence of Hydration State of F-Actin on the Bound Mg(2+)/Ca(2+) Ions.

PubMed

Suzuki, Makoto; Imao, Asato; Mogami, George; Chishima, Ryotaro; Watanabe, Takahiro; Yamaguchi, Takaya; Morimoto, Nobuyuki; Wazawa, Tetsuichi

2016-07-21

Understanding of the hydration state is an important issue in the chemomechanical energetics of versatile biological functions of polymerized actin (F-actin). In this study, hydration-state differences of F-actin by the bound divalent cations are revealed through precision microwave dielectric relaxation (DR) spectroscopy. G- and F-actin in Ca- and Mg-containing buffer solutions exhibit dual hydration components comprising restrained water with DR frequency f2 (fw). The hydration state of F-actin is strongly dependent on the ionic composition. In every buffer tested, the HMW signal Dhyme (≡ (f1 - fw)δ1/(fwδw)) of F-actin is stronger than that of G-actin, where δw is DR-amplitude of bulk solvent and δ1 is that of HMW in a fixed-volume ellipsoid containing an F-actin and surrounding water in solution. Dhyme value of F-actin in Ca2.0-buffer (containing 2 mM Ca(2+)) is markedly higher than in Mg2.0-buffer (containing 2 mM Mg(2+)). Moreover, in the presence of 2 mM Mg(2+), the hydration state of F-actin is changed by adding a small fraction of Ca(2+) (∼0.1 mM) and becomes closer to that of the Ca-bound form in Ca2.0-buffer. This is consistent with the results of the partial specific volume and the Cotton effect around 290 nm in the CD spectra, indicating a change in the tertiary structure and less apparent change in the secondary structure of actin. The number of restrained water molecules per actin (N2) is estimated to be 1600-2100 for Ca2.0- and F-buffer and ∼2500 for Mg2.0-buffer at 10-15 °C. These numbers are comparable to those estimated from the available F-actin atomic structures as in the first water layer. The number of HMW molecules is roughly explained by the volume between the equipotential surface of -kT/2e and the first water layer of the actin surface by solving the Poisson-Boltzmann equation using UCSF Chimera.

Structure and function of conjugative pili: monoclonal antibodies as probes for structural variants of F pili.

PubMed Central

Grossman, T H; Frost, L S; Silverman, P M

1990-01-01

The lac-tra operon fusion plasmid pTG801 contains the known F plasmid DNA transfer (tra) genes required by Escherichia coli to elaborate functional F pili (T. Grossman and P. M. Silverman, J. Bacteriol. 171:650-656, 1989). Here, we show that these pili are actually structural variants of normal F pili and that the F plasmid must contain additional genes that affect pilus structure and function. We confirmed a previous report that two monoclonal antibodies that recognize epitopes at and near the amino terminus of F pilin do not decorate the sides of normal F pili, as determined by immunogold electron microscopy. However, both antibodies laterally decorated pTG801 pili. The epitope for one of the antibodies has been shown to include the amino-terminal acetyl group of F pilin, which must therefore also be present on pTG801 pilin. Normal antibody staining was restored to pTG801 pili when cells contained, in addition to pTG801, the compatible plasmid pRS31, which must therefore include at least one gene affecting F-pilus structure. One candidate, traD, was excluded as the sole such gene, since traD+ derivatives of a pTG801 strain still elaborated pili that could be laterally decorated with antibody. Moreover, although traD alone restored RNA bacteriophage R17 infectivity to pTG801 cells, as expected, it did not mimic pRS31 in restoring to pTG801 pili other characteristics of normal F pili. We conclude that pRS31 contains as yet uncharacterized genes required for elaboration of structurally normal F pili. Finally, we identified vesicular material, especially abundant in cultures of pTG801 transformants, that stained heavily with the anti-F-pilin monoclonal antibodies. This material may reflect the inner membrane pool of F pilin. Images FIG. 3 FIG. 4 FIG. 5 PMID:1689713

Structural similarities of human and mammalian lipocalins, and their function in innate immunity and allergy.

PubMed

Jensen-Jarolim, E; Pacios, L F; Bianchini, R; Hofstetter, G; Roth-Walter, F

2016-03-01

Owners and their domestic animals via skin shedding and secretions, mutually exchange microbiomes, potential pathogens and innate immune molecules. Among the latter especially lipocalins are multifaceted: they may have an immunomodulatory function and, furthermore, they represent one of the most important animal allergen families. The amino acid identities, as well as their structures by superposition modeling were compared among human lipocalins, hLCN1 and hLCN2, and most important animal lipocalin allergens, such as Can f 1, Can f 2 and Can f 4 from dog, Fel d 4 from cats, Bos d 5 from cow's milk, Equ c 1 from horses, and Mus m 1 from mice, all of them representing major allergens. The β-barrel fold with a central molecular pocket is similar among human and animal lipocalins. Thereby, lipocalins are able to transport a variety of biological ligands in their highly conserved calyx-like cavity, among them siderophores with the strongest known capability to complex iron (Fe(3+) ). Levels of human lipocalins are elevated in nonallergic inflammation and cancer, associated with innate immunoregulatory functions that critically depend on ligand load. Accordingly, deficient loading of lipocalin allergens establishes their capacity to induce Th2 hypersensitivity. Our similarity analysis of human and mammalian lipocalins highlights their function in innate immunity and allergy. © 2015 The Authors. Allergy Published by John Wiley & Sons Ltd.

Homogeneous and heterogeneous noncovalent dimers of formaldehyde and thioformaldehyde: structures, energetics, and vibrational frequencies.

PubMed

Van Dornshuld, Eric; Holy, Christina M; Tschumper, Gregory S

2014-05-08

This work provides the first characterization of five stationary points of the homogeneous thioformaldehyde dimer, (CH2S)2, and seven stationary points of the heterogeneous formaldehyde/thioformaldehyde dimer, CH2O/CH2S, with correlated ab initio electronic structure methods. Full geometry optimizations and corresponding harmonic vibrational frequencies were computed with second-order Møller-Plesset perturbation theory (MP2) and 13 different density functionals in conjunction with triple-ζ basis sets augmented with diffuse and multiple sets of polarization functions. The MP2 results indicate that the three stationary points of (CH2S)2 and four of CH2O/CH2S are minima, in contrast to two stationary points of the formaldehyde dimer, (CH2O)2. Single-point energies were also computed using the explicitly correlated MP2-F12 and CCSD(T)-F12 methods and basis sets as large as heavy-aug-cc-pVTZ. The (CH2O)2 and CH2O/CH2S MP2 and MP2-F12 binding energies deviated from the CCSD(T)-F12 binding energies by no more than 0.2 and 0.4 kcal mol(-1), respectively. The (CH2O)2 and CH2O/CH2S global minimum is the same at every level of theory. However, the MP2 methods overbind (CH2S)2 by as much as 1.1 kcal mol(-1), effectively altering the energetic ordering of the thioformaldehyde dimer minima relative to the CCSD(T)-F12 energies. The CCSD(T)-F12 binding energies of the (CH2O)2 and CH2O/CH2S stationary points are quite similar, with the former ranging from around -2.4 to -4.6 kcal mol(-1) and the latter from about -1.1 to -4.4 kcal mol(-1). Corresponding (CH2S)2 stationary points have appreciably smaller CCSD(T)-F12 binding energies ranging from ca. -1.1 to -3.4 kcal mol(-1). The vibrational frequency shifts upon dimerization are also reported for each minimum on the MP2 potential energy surfaces.

Tunneling current in HfO2 and Hf0.5Zr0.5O2-based ferroelectric tunnel junction

NASA Astrophysics Data System (ADS)

Dong, Zhipeng; Cao, Xi; Wu, Tong; Guo, Jing

2018-03-01

Ferroelectric tunnel junctions (FTJs) have been intensively explored for future low power data storage and information processing applications. Among various ferroelectric (FE) materials studied, HfO2 and H0.5Zr0.5O2 (HZO) have the advantage of CMOS process compatibility. The validity of the simple effective mass approximation, for describing the tunneling process in these materials, is examined by computing the complex band structure from ab initio simulations. The results show that the simple effective mass approximation is insufficient to describe the tunneling current in HfO2 and HZO materials, and quantitative accurate descriptions of the complex band structures are indispensable for calculation of the tunneling current. A compact k . p Hamiltonian is parameterized to and validated by ab initio complex band structures, which provides a method for efficiently and accurately computing the tunneling current in HfO2 and HZO. The device characteristics of a metal/FE/metal structure and a metal/FE/semiconductor (M-F-S) structure are investigated by using the non-equilibrium Green's function formalism with the parameterized effective Hamiltonian. The result shows that the M-F-S structure offers a larger resistance window due to an extra barrier in the semiconductor region at off-state. A FTJ utilizing M-F-S structure is beneficial for memory design.

Materials Data on Te5(O2F11)2 (SG:88) by Materials Project

DOE Data Explorer

Kristin Persson

2016-02-04

Computed materials data using density functional theory calculations. These calculations determine the electronic structure of bulk materials by solving approximations to the Schrodinger equation. For more information, see https://materialsproject.org/docs/calculations

Materials Data on Sr2SnSe3F2 (SG:62) by Materials Project

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

Kristin Persson

2014-11-02

Computed materials data using density functional theory calculations. These calculations determine the electronic structure of bulk materials by solving approximations to the Schrodinger equation. For more information, see https://materialsproject.org/docs/calculations

Materials Data on Ba2SnSe3F2 (SG:62) by Materials Project

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

Kristin Persson

2014-11-02

Computed materials data using density functional theory calculations. These calculations determine the electronic structure of bulk materials by solving approximations to the Schrodinger equation. For more information, see https://materialsproject.org/docs/calculations

Materials Data on Ba2SnS3F2 (SG:62) by Materials Project

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

Kristin Persson

2014-11-02

Computed materials data using density functional theory calculations. These calculations determine the electronic structure of bulk materials by solving approximations to the Schrodinger equation. For more information, see https://materialsproject.org/docs/calculations

Materials Data on Sr2SnS3F2 (SG:62) by Materials Project

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

Kristin Persson

2014-11-02

Computed materials data using density functional theory calculations. These calculations determine the electronic structure of bulk materials by solving approximations to the Schrodinger equation. For more information, see https://materialsproject.org/docs/calculations

Materials Data on Rb2Be3Cd2F12 (SG:198) by Materials Project

DOE Data Explorer

Kristin Persson

2014-11-02

Computed materials data using density functional theory calculations. These calculations determine the electronic structure of bulk materials by solving approximations to the Schrodinger equation. For more information, see https://materialsproject.org/docs/calculations

Materials Data on Na2LiBe2F7 (SG:113) by Materials Project

DOE Data Explorer

Kristin Persson

2014-11-02

Computed materials data using density functional theory calculations. These calculations determine the electronic structure of bulk materials by solving approximations to the Schrodinger equation. For more information, see https://materialsproject.org/docs/calculations

Materials Data on K2SrBe2F8 (SG:166) by Materials Project

DOE Data Explorer

Kristin Persson

2014-11-02

Computed materials data using density functional theory calculations. These calculations determine the electronic structure of bulk materials by solving approximations to the Schrodinger equation. For more information, see https://materialsproject.org/docs/calculations

Materials Data on K2Mg2Be3F12 (SG:198) by Materials Project

DOE Data Explorer

Kristin Persson

2014-11-02

Computed materials data using density functional theory calculations. These calculations determine the electronic structure of bulk materials by solving approximations to the Schrodinger equation. For more information, see https://materialsproject.org/docs/calculations

Materials Data on Br3N(O2F5)2 (SG:18) by Materials Project

DOE Data Explorer

Kristin Persson

2014-07-09

Computed materials data using density functional theory calculations. These calculations determine the electronic structure of bulk materials by solving approximations to the Schrodinger equation. For more information, see https://materialsproject.org/docs/calculations

In situ sonochemical reduction and direct functionalization of graphene oxide: A robust approach with thermal and biomedical applications.

PubMed

Maktedar, Shrikant S; Mehetre, Shantilal S; Avashthi, Gopal; Singh, Man

2017-01-01

The rapid, robust, scalable and non-hazardous sonochemical approach for in situ reduction and direct functionalization of graphene oxide has been developed for non-toxic biomedical applications. The graphene oxide (GrO) was directly functionalized with tryptamine (TA) without using any hazardous acylating and coupling reagents. The reaction was completed within 20min. An impact of ultrasound was inferred for a direct functionalization with other conventional methods. The evolved electronic states were confirmed with near edge X-ray absorption fine structure (NEXAFS). The direct covalent functionalization and formation of f-(TA) GrO was proven with FTIR, 13 C solid state NMR, XPS, XRD, Raman' HRTEM, AFM and TGA. The total percentage weight loss in TGA confirms an enhanced thermal stability of f-(TA) GrO. The f-(TA) GrO was further explored for an investigation of in vitro antimicrobial activity to ensure the health and environmental safety. An outstanding antibacterial activity of f-(TA) GrO was found against gram positive Staphylococcus aureus at MIC 128mgmL -1 . It confirms a suitability of f-(TA) GrO for thermally stable antibacterial coating. The f-(TA) GrO showed 39.14-48.9% antioxidant activities, evaluated with 2,2-diphenyl-1-picrylhydrazyl (DPPH) free radical assay. The inherent cytotoxicity of f-(TA) GrO was evaluated with SRB assay to living cells, MCF-7 and Vero. The estimated cell viabilities were >80% upon addition of f-(TA) GrO over a wide concentration range of 10-80μgmL -1 . The high cytocompatibility of f-(TA) GrO confirms the low toxicity and an excellent biocompatibility. The morphological effect on Vero cell line, evidently confirmed the biocompatibility of f-(TA) GrO. Therefore, f-(TA) GrO was emerged as an advanced functional biomaterial for thermal and biomedical applications. Copyright © 2016 Elsevier B.V. All rights reserved.

Structure and Function of the Splice Variants of TMPRSS2-ERG, a Prevalent Genomic Alteration in Prostate Cancer

DTIC Science & Technology

2012-09-01

apoptosis through VE-cadherin. Blood 2008; 111: 3498–3506. 20 Ellett F, Kile BT, Lieschke GJ. The role of the ETS factor erg in zebrafish...angiogenesis and endothelial apoptosis through VE-cadherin. Blood 111, 3498–3506 (2008). 46. Ellett, F., Kile , B. T. & Lieschke, G. J. The role of

The 3D Structure of the Binding Pocket of the Human Oxytocin Receptor for Benzoxazine Antagonists, Determined by Molecular Docking, Scoring Functions and 3D-QSAR Methods

NASA Astrophysics Data System (ADS)

Jójárt, Balázs; Martinek, Tamás A.; Márki, Árpád

2005-05-01

Molecular docking and 3D-QSAR studies were performed to determine the binding mode for a series of benzoxazine oxytocin antagonists taken from the literature. Structural hypotheses were generated by docking the most active molecule to the rigid receptor by means of AutoDock 3.05. The cluster analysis yielded seven possible binding conformations. These structures were refined by using constrained simulated annealing, and the further ligands were aligned in the refined receptor by molecular docking. A good correlation was found between the estimated Δ G bind and the p K i values for complex F. The Connolly-surface analysis, CoMFA and CoMSIA models q CoMFA 2 = 0.653, q CoMSA 2 = 0.630 and r pred,CoMFA 2 = 0.852 , r pred,CoMSIA 2 = 0.815) confirmed the scoring function results. The structural features of the receptor-ligand complex and the CoMFA and CoMSIA fields are in closely connected. These results suggest that receptor-ligand complex F is the most likely binding hypothesis for the studied benzoxazine analogs.

Crystal structure of the Vibrio cholerae colonization factor TcpF and identification of a functional immunogenic site.

PubMed

Megli, Christina J; Yuen, Alex S W; Kolappan, Subramaniapillai; Richardson, Malcolm R; Dharmasena, Madushini N; Krebs, Shelly J; Taylor, Ronald K; Craig, Lisa

2011-06-03

Vibrio cholerae relies on two main virulence factors--toxin-coregulated pilus (TCP) and cholera toxin--to cause the gastrointestinal disease cholera. TCP is a type IV pilus that mediates bacterial autoagglutination and colonization of the intestine. TCP is encoded by the tcp operon, which also encodes TcpF, a protein of unknown function that is secreted by V. cholerae in a TCP-dependent manner. Although TcpF is not required for TCP biogenesis, a tcpF mutant has a colonization defect in the infant mouse cholera model that is as severe as a pilus mutant. Furthermore, TcpF antisera protect against V. cholerae infection. TcpF has no apparent sequence homology to any known protein. Here, we report the de novo X-ray crystal structure of TcpF and the identification of an epitope that is critical for its function as a colonization factor. A monoclonal antibody recognizing this epitope is protective against V. cholerae challenge and adds to the protection provided by an anti-TcpA antibody. These data suggest that TcpF has a novel function in V. cholerae colonization and define a region crucial for this function. Copyright © 2011 Elsevier Ltd. All rights reserved.

Diabetes and exocrine pancreatic insufficiency in E2F1/E2F2 double-mutant mice.

PubMed

Iglesias, Ainhoa; Murga, Matilde; Laresgoiti, Usua; Skoudy, Anouchka; Bernales, Irantzu; Fullaondo, Asier; Moreno, Bernardino; Lloreta, José; Field, Seth J; Real, Francisco X; Zubiaga, Ana M

2004-05-01

E2F transcription factors are thought to be key regulators of cell growth control. Here we use mutant mouse strains to investigate the function of E2F1 and E2F2 in vivo. E2F1/E2F2 compound-mutant mice develop nonautoimmune insulin-deficient diabetes and exocrine pancreatic dysfunction characterized by endocrine and exocrine cell dysplasia, a reduction in the number and size of acini and islets, and their replacement by ductal structures and adipose tissue. Mutant pancreatic cells exhibit increased rates of DNA replication but also of apoptosis, resulting in severe pancreatic atrophy. The expression of genes involved in DNA replication and cell cycle control was upregulated in the E2F1/E2F2 compound-mutant pancreas, suggesting that their expression is repressed by E2F1/E2F2 activities and that the inappropriate cell cycle found in the mutant pancreas is likely the result of the deregulated expression of these genes. Interestingly, the expression of ductal cell and adipocyte differentiation marker genes was also upregulated, whereas expression of pancreatic cell marker genes were downregulated. These results suggest that E2F1/E2F2 activity negatively controls growth of mature pancreatic cells and is necessary for the maintenance of differentiated pancreatic phenotypes in the adult.

Comparison of S. cerevisiae F-BAR domain structures reveals a conserved inositol phosphate binding site

PubMed Central

Moravcevic, Katarina; Alvarado, Diego; Schmitz, Karl R.; Kenniston, Jon A.; Mendrola, Jeannine M.; Ferguson, Kathryn M.; Lemmon, Mark A.

2015-01-01

SUMMARY F-BAR domains control membrane interactions in endocytosis, cytokinesis, and cell signaling. Although generally thought to bind curved membranes containing negatively charged phospholipids, numerous functional studies argue that differences in lipid-binding selectivities of F-BAR domains are functionally important. Here, we compare membrane-binding properties of the S. cerevisiae F-BAR domains in vitro and in vivo. Whereas some F-BAR domains (such as Bzz1p and Hof1p F-BARs) bind equally well to all phospholipids, the F-BAR domain from the RhoGAP Rgd1p preferentially binds phosphoinositides. We determined X-ray crystal structures of F-BAR domains from Hof1p and Rgd1p, the latter bound to an inositol phosphate. The structures explain phospholipid-binding selectivity differences, and reveal an F-BAR phosphoinositide binding site that is fully conserved in a mammalian RhoGAP called Gmip, and is partly retained in certain other F-BAR domains. Our findings reveal previously unappreciated determinants of F-BAR domain lipid-binding specificity, and provide a basis for its prediction from sequence. PMID:25620000

High-level ab initio predictions for the ionization energy, electron affinity, and heats of formation of cyclopentadienyl radical, cation, and anion, C5H5/C5H5+/C5H5-.

PubMed

Lo, Po-Kam; Lau, Kai-Chung

2014-04-03

The ionization energy (IE), electron affinity (EA), and heats of formation (ΔH°f0/ΔH°f298) for cyclopentadienyl radical, cation, and anion, C5H5/C5H5(+)/C5H5(-), have been calculated by wave function-based ab initio CCSDT/CBS approach, which involves approximation to complete basis set (CBS) limit at coupled-cluster level with up to full triple excitations (CCSDT). The zero-point vibrational energy correction, core-valence electronic correction, scalar relativistic effect, and higher-order corrections beyond the CCSD(T) wave function are included in these calculations. The allylic [C5H5((2)A2)] and dienylic [C5H5((2)B1)] forms of cyclopentadienyl radical are considered: the ground state structure exists in the dienyl form and it is about 30 meV more stable than the allylic structure. Both structures are lying closely and are interconvertible along the normal mode of b2 in-plane vibration. The CCSDT/CBS predictions (in eV) for IE[C5H5(+)((3)A1')←C5H5((2)B1)] = 8.443, IE[C5H5(+)((1)A1)←C5H5((2)B1)] = 8.634 and EA[C5H5(-)((1)A1')←C5H5((2)B1)] = 1.785 are consistent with the respective experimental values of 8.4268 ± 0.0005, 8.6170 ± 0.0005, and 1.808 ± 0.006, obtained from photoelectron spectroscopic measurements. The ΔH°f0/ΔH°f298's (in kJ/mol) for C5H5/C5H5(+)/C5H5(-) have also been predicted by the CCSDT/CBS method: ΔH°f0/ΔH°f298[C5H5((2)B1)] = 283.6/272.0, ΔH°f0/ΔH°f298[C5H5(+)((3)A1')] = 1098.2/1086.9, ΔH°f0/ΔH°f298[C5H5(+)((1)A1)] = 1116.6/1106.0, and ΔH°f0/ΔH°f298[C5H5(-)((1)A1')] = 111.4/100.0. The comparisons between the CCSDT/CBS predictions and the experimental values suggest that the CCSDT/CBS procedure is capable of predicting reliable IE(C5H5)'s and EA(C5H5) with uncertainties of ± 17 and ± 23 meV, respectively.

Mild hydrothermal crystal growth of new uranium(IV) fluorides, Na3.13Mg1.43U6F30 and Na2.50Mn1.75U6F30: Structures, optical and magnetic properties

NASA Astrophysics Data System (ADS)

Yeon, Jeongho; Smith, Mark D.; Tapp, Joshua; Möller, Angela; zur Loye, Hans-Conrad

2016-04-01

Two new uranium(IV) fluorides, Na3.13Mg1.43U6F30 (1) and Na2.50Mn1.75U6F30 (2), were synthesized through an in situ mild hydrothermal route, and were structurally characterized by single crystal X-ray diffraction. The compounds exhibit complex crystal structures composed of corner- or edge-shared UF9 and MF6 (M=Mg, Mn) polyhedra, forming hexagonal channels in the three-dimensional framework, in which ordered or disordered divalent metal and sodium atoms reside. The large hexagonal voids contain the nearly regular M(II)F6 octahedra and sodium ions, whereas the small hexagonal cavities include M(II) and sodium ions on a mixed-occupied site. Magnetic susceptibility measurements yielded effective magnetic moments of 8.36 and 11.6 μB for 1 and 2, respectively, confirming the presence and oxidation states of U(IV) and Mn(II). The large negative Weiss constants indicate the spin gap between a triplet and a singlet state in the U(IV). Magnetization data as a function of applied fields revealed that 2 exhibits paramagnetic behavior due to the nonmagnetic singlet ground state of U(IV) at low temperature. UV-vis diffuse reflectance and X-ray photoelectron spectroscopy data were also analyzed.

Controlled surface functionality of magnetic nanoparticles by layer-by-layer assembled nano-films

NASA Astrophysics Data System (ADS)

Choi, Daheui; Son, Boram; Park, Tai Hyun; Hong, Jinkee

2015-04-01

Over the past several years, the preparation of functionalized nanoparticles has been aggressively pursued in order to develop desired structures, compositions, and structural order. Among the various nanoparticles, iron oxide magnetic nanoparticles (MNPs) have shown great promise because the material generated using these MNPs can be used in a variety of biomedical applications and possible bioactive functionalities. In this study, we report the development of various functionalized MNPs (F-MNPs) generated using the layer-by-layer (LbL) self-assembly method. To provide broad functional opportunities, we fabricated F-MNP bio-toolbox by using three different materials: synthetic polymers, natural polymers, and carbon materials. Each of these F-MNPs displays distinct properties, such as enhanced thickness or unique morphologies. In an effort to explore their biomedical applications, we generated basic fibroblast growth factor (bFGF)-loaded F-MNPs. The bFGF-loaded F-MNPs exhibited different release mechanisms and loading amounts, depending on the film material and composition order. Moreover, bFGF-loaded F-MNPs displayed higher biocompatibility and possessed superior proliferation properties than the bare MNPs and pure bFGF, respectively. We conclude that by simply optimizing the building materials and the nanoparticle's film composition, MNPs exhibiting various bioactive properties can be generated.Over the past several years, the preparation of functionalized nanoparticles has been aggressively pursued in order to develop desired structures, compositions, and structural order. Among the various nanoparticles, iron oxide magnetic nanoparticles (MNPs) have shown great promise because the material generated using these MNPs can be used in a variety of biomedical applications and possible bioactive functionalities. In this study, we report the development of various functionalized MNPs (F-MNPs) generated using the layer-by-layer (LbL) self-assembly method. To provide broad functional opportunities, we fabricated F-MNP bio-toolbox by using three different materials: synthetic polymers, natural polymers, and carbon materials. Each of these F-MNPs displays distinct properties, such as enhanced thickness or unique morphologies. In an effort to explore their biomedical applications, we generated basic fibroblast growth factor (bFGF)-loaded F-MNPs. The bFGF-loaded F-MNPs exhibited different release mechanisms and loading amounts, depending on the film material and composition order. Moreover, bFGF-loaded F-MNPs displayed higher biocompatibility and possessed superior proliferation properties than the bare MNPs and pure bFGF, respectively. We conclude that by simply optimizing the building materials and the nanoparticle's film composition, MNPs exhibiting various bioactive properties can be generated. Electronic supplementary information (ESI) available. See DOI: 10.1039/c4nr07373h

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

Bae, Brian; Cobb, Ryan E.; DeSieno, Matthew A.

The enzyme FrbF from Streptomyces rubellomurinus has attracted significant attention due to its role in the biosynthesis of the antimalarial phosphonate FR-900098. The enzyme catalyzes acetyl transfer onto the hydroxamate of the FR-900098 precursors cytidine 5'-monophosphate-3-aminopropylphosphonate and cytidine 5'-monophosphate-N-hydroxy-3-aminopropylphosphonate. Despite the established function as a bona fide N-acetyltransferase, FrbF shows no sequence similarity to any member of the GCN5-like N-acetyltransferase (GNAT) superfamily. Here, we present the 2.0 {angstrom} resolution crystal structure of FrbF in complex with acetyl-CoA, which demonstrates a unique architecture that is distinct from those of canonical GNAT-like acetyltransferases. We also utilized the co-crystal structure to guide structure-functionmore » studies that identified the roles of putative active site residues in the acetyltransferase mechanism. The combined biochemical and structural analyses of FrbF provide insights into this previously uncharacterized family of N-acetyltransferases and also provide a molecular framework toward the production of novel N-acyl derivatives of FR-900098.« less

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

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

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

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

Fusing DTI and FMRI Data: A Survey of Methods and Applications

PubMed Central

Zhu, Dajiang; Zhang, Tuo; Jiang, Xi; Hu, Xintao; Chen, Hanbo; Yang, Ning; Lv, Jinglei; Han, Junwei; Guo, Lei; Liu, Tianming

2014-01-01

The relationship between brain structure and function has been one of the centers of research in neuroimaging for decades. In recent years, diffusion tensor imaging (DTI) and functional magnetic resonance imaging (fMRI) techniques have been widely available and popular in cognitive and clinical neurosciences for examining the brain’s white matter (WM) micro-structures and gray matter (GM) functions, respectively. Given the intrinsic integration of WM/GM and the complementary information embedded in DTI/fMRI data, it is natural and well-justified to combine these two neuroimaging modalities together to investigate brain structure and function and their relationships simultaneously. In the past decade, there have been remarkable achievements of DTI/fMRI fusion methods and applications in neuroimaging and human brain mapping community. This survey paper aims to review recent advancements on methodologies and applications in incorporating multimodal DTI and fMRI data, and offer our perspectives on future research directions. We envision that effective fusion of DTI/fMRI techniques will play increasingly important roles in neuroimaging and brain sciences in the years to come. PMID:24103849

Molecular Investigations of the Structure and Function of the Protein Phosphatase 1:Spinophilin:Inhibitor-2 Heterotrimeric Complex

PubMed Central

Dancheck, Barbara; Ragusa, Michael J.; Allaire, Marc; Nairn, Angus C.; Page, Rebecca; Peti, Wolfgang

2011-01-01

Regulation of the major ser/thr phosphatase Protein Phosphatase 1 (PP1) is controlled by a diverse array of targeting and inhibitor proteins. Though many PP1 regulatory proteins share at least one PP1 binding motif, usually the RVxF motif, it was recently discovered that certain pairs of targeting and inhibitor proteins bind PP1 simultaneously to form PP1 heterotrimeric complexes. To date, structural information for these heterotrimeric complexes, and, in turn, how they direct PP1 activity is entirely lacking. Using a combination of NMR spectroscopy, biochemistry and small angle X-ray scattering (SAXS), we show that major structural rearrangements in both spinophilin (targeting) and Inhibitor-2 (I-2, inhibitor) are essential for the formation of the heterotrimeric PP1:spinophilin:I-2 (PSI) complex. The RVxF motif of I-2 is released from PP1 during the formation of PSI, making the less prevalent SILK motif of I-2 essential for complex stability. The release of the I-2 RVxF motif allows for enhanced flexibility of both I-2 and spinophilin in the heterotrimeric complex. In addition, we used inductively coupled plasma atomic emission spectroscopy to show that PP1 contains two metals in both heterodimeric complexes (PP1:spinophilin and PP1:I2) and PSI, demonstrating that PSI retains the biochemical characteristics of the PP1:I2 holoenzyme. Finally, we combined the NMR and biochemical data with SAXS and molecular dynamics simulations to generate a structural model of the full heterotrimeric PSI complex. Collectively, these data reveal the molecular events that enable PP1 heterotrimeric complexes to exploit both the targeting and inhibitory features of the PP1-regulatory proteins to form multi-functional PP1 holoenzymes. PMID:21218781

Theoretical understanding of ruthenium(II) based fluoride sensor derived from 4,5-bis(benzimidazol-2-yl)imidazole (H3ImBzim) and bipyridine: electronic structure and binding nature.

PubMed

Wang, Jian; Bai, Fu-Quan; Xia, Bao-Hui; Sun, Lei; Zhang, Hong-Xing

2011-03-17

Using density functional theory (DFT) approach, we assessed the newly developed fluoride sensor: [(bpy)(2)Ru(H(3)ImBzim)](2+) (denoted as 1, where H(3)ImBzim = 4,5-bis(benzimidazol-2-yl)imidazole and byp = 2,2'-bipyridine). On the basis of our benchmark test, a PBE0 functional with a LanL2DZ basis set was chosen to explore the electronic structure of 1 in both ground and singlet excited states in acetonitrile solution. Both absorption bands at 426 and 352 nm are assigned as metal-to-ligand charge-transfer transition characters. By analyzing the difference of absorption spectrum between the binding adducts and the experimental measurement, the fluoride detection process was found to be driven by the proton transfer model, which makes 1 not only capable of detecting fluoride, but also for other Bønster base anions. And the result is in general accordance with the experimental observations. We hope the current exploration can give some knowledge about the detection mechanism of the F(-) anion sensor and provide some inspiration for the design of functional molecular detectors for F(-) anion.

The stability of quadratic-reciprocal functional equation

NASA Astrophysics Data System (ADS)

Song, Aimin; Song, Minwei

2018-04-01

A new quadratic-reciprocal functional equation f ((k +1 )x +k y )+f ((k +1 )x -k y )=2/f (x )f (y )[(k+1 ) 2f (y )+k2f (x )] [(k+1)2f (y )-k2f (x )] 2 is introduced. The Hyers-Ulam stability for the quadratic-reciprocal functional equations is proved in Banach spaces using the direct method and the fixed point method, respectively.

Snapshots of the maltose transporter during ATP hydrolysis

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

Oldham, Michael L.; Chen, Jue

2011-12-05

ATP-binding cassette transporters are powered by ATP, but the mechanism by which these transporters hydrolyze ATP is unclear. In this study, four crystal structures of the full-length wild-type maltose transporter, stabilized by adenosine 5{prime}-({beta},{gamma}-imido)triphosphate or ADP in conjunction with phosphate analogs BeF{sub 3}{sup -}, VO{sub 4}{sup 3-}, or AlF{sub 4}{sup -}, were determined to 2.2- to 2.4-{angstrom} resolution. These structures led to the assignment of two enzymatic states during ATP hydrolysis and demonstrate specific functional roles of highly conserved residues in the nucleotide-binding domain, suggesting that ATP-binding cassette transporters catalyze ATP hydrolysis via a general base mechanism.

Materials Data on Sb4PdC4(O2F11)2 (SG:14) by Materials Project

DOE Data Explorer

Kristin Persson

2014-07-09

Computed materials data using density functional theory calculations. These calculations determine the electronic structure of bulk materials by solving approximations to the Schrodinger equation. For more information, see https://materialsproject.org/docs/calculations

Materials Data on Sb4PtC4(O2F11)2 (SG:14) by Materials Project

DOE Data Explorer

Kristin Persson

2016-02-04

Computed materials data using density functional theory calculations. These calculations determine the electronic structure of bulk materials by solving approximations to the Schrodinger equation. For more information, see https://materialsproject.org/docs/calculations

Materials Data on Ba4Fe3(S3F2)2 (SG:62) by Materials Project

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

Kristin Persson

2016-04-23

Computed materials data using density functional theory calculations. These calculations determine the electronic structure of bulk materials by solving approximations to the Schrodinger equation. For more information, see https://materialsproject.org/docs/calculations

Materials Data on K3Sb2N2O6F7 (SG:12) by Materials Project

DOE Data Explorer

Kristin Persson

2014-07-09

Computed materials data using density functional theory calculations. These calculations determine the electronic structure of bulk materials by solving approximations to the Schrodinger equation. For more information, see https://materialsproject.org/docs/calculations

Materials Data on KNaMg2Si4(O5F)2 (SG:12) by Materials Project

DOE Data Explorer

Kristin Persson

2014-07-09

Computed materials data using density functional theory calculations. These calculations determine the electronic structure of bulk materials by solving approximations to the Schrodinger equation. For more information, see https://materialsproject.org/docs/calculations

Materials Data on FeCu2H21(O5F4)2 (SG:1) by Materials Project

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

Kristin Persson

2014-07-09

Computed materials data using density functional theory calculations. These calculations determine the electronic structure of bulk materials by solving approximations to the Schrodinger equation. For more information, see https://materialsproject.org/docs/calculations

TMEM16 proteins: unknown structure and confusing functions.

PubMed

Picollo, Alessandra; Malvezzi, Mattia; Accardi, Alessio

2015-01-16

The TMEM16 family of membrane proteins, also known as anoctamins, plays key roles in a variety of physiological functions that range from ion transport to phospholipid scrambling and to regulating other ion channels. The first two family members to be functionally characterized, TMEM16A (ANO1) and TMEM16B (ANO2), form Ca(2+)-activated Cl(-) channels and are important for transepithelial ion transport, olfaction, phototransduction, smooth muscle contraction, nociception, cell proliferation and control of neuronal excitability. The roles of other family members, such as TMEM16C (ANO3), TMEM16D (ANO4), TMEM16F (ANO6), TMEM16G (ANO7) and TMEM16J (ANO9), remain poorly understood and controversial. These homologues were reported to be phospholipid scramblases, ion channels, to have both functions or to be regulatory subunits of other channels. Mutations in TMEM16F cause Scott syndrome, a bleeding disorder caused by impaired Ca(2+)-dependent externalization of phosphatidylserine in activated platelets, suggesting that this homologue might be a scramblase. However, overexpression of TMEM16F has also been associated with a remarkable number of different ion channel types, raising the possibility that this protein might be involved in both ion and lipid transports. The recent identification of an ancestral TMEM16 homologue with intrinsic channel and scramblase activities supports this hypothesis. Thus, the TMEM16 family might have diverged in two or three different subclasses, channels, scramblases and dual-function channel/scramblases. The structural bases and functional implication of such a functional diversity within a single protein family remain to be elucidated and the links between TMEM16 functions and human physiology and pathologies need to be investigated. Copyright © 2014 Elsevier Ltd. All rights reserved.

Structural and functional insights into the lipopolysaccharide ABC transporter LptB2FG.

PubMed

Dong, Haohao; Zhang, Zhengyu; Tang, Xiaodi; Paterson, Neil G; Dong, Changjiang

2017-08-09

The cell surface of most Gram-negative bacteria contains lipopolysaccharide that is essential for their viability and drug resistance. A 134-kDa protein complex LptB 2 FG is unique among ATP-binding cassette transporters because it extracts lipopolysaccharide from the external leaflet of the inner membrane and propels it along a filament that extends across the periplasm to directly deliver lipopolysaccharide into the external leaflet of the outer membrane. Here we report the crystal structure of the lipopolysaccharide transporter LptB 2 FG from Klebsiella pneumoniae, in which both LptF and LptG are composed of a β-jellyroll-like periplasmic domain and six α-helical segments in the transmembrane domain. LptF and LptG form a central cavity containing highly conserved hydrophobic residues. Structural and functional studies suggest that LptB 2 FG uses an alternating lateral access mechanism to extract lipopolysaccharide and traffic it along the hydrophobic cavity toward the transporter's periplasmic domains.Lipopolysaccharides (LPS) are synthesized at the periplasmic side of the inner membrane of Gram-negative bacteria and are then extracted by the LptB 2 FG complex during the first step of LPS transport to the outer membrane. Here the authors present the LptB 2 FG structure, which supports an alternating lateral access mechanism for LPS extraction.

Generalized uncertainty principles and quantum field theory

NASA Astrophysics Data System (ADS)

Husain, Viqar; Kothawala, Dawood; Seahra, Sanjeev S.

2013-01-01

Quantum mechanics with a generalized uncertainty principle arises through a representation of the commutator [x^,p^]=if(p^). We apply this deformed quantization to free scalar field theory for f±=1±βp2. The resulting quantum field theories have a rich fine scale structure. For small wavelength modes, the Green’s function for f+ exhibits a remarkable transition from Lorentz to Galilean invariance, whereas for f- such modes effectively do not propagate. For both cases Lorentz invariance is recovered at long wavelengths.

Chaotic Expansions of Elements of the Universal Enveloping Superalgebra Associated with a Z2-graded Quantum Stochastic Calculus

NASA Astrophysics Data System (ADS)

Eyre, T. M. W.

Given a polynomial function f of classical stochastic integrator processes whose differentials satisfy a closed Ito multiplication table, we can express the stochastic derivative of f as We establish an analogue of this formula in the form of a chaotic decomposition for Z2-graded theories of quantum stochastic calculus based on the natural coalgebra structure of the universal enveloping superalgebra.

Functional determinants of ras interference 1 mutants required for their inhbitory activity on endocytosis

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

Galvis, Adriana; Giambini, Hugo; Villasana, Zoilmar

In this study, we initiated experiments to address the structure-function relationship of Rin1. A total of ten substitute mutations were created, and their effects on Rin1 function were examined. Of the ten mutants, four of them (P541A, E574A, Y577F, T580A) were defective in Rab5 binding, while two other Rin1 mutants (D537A, Y561F) partially interacted with Rab5. Mutations in several other residues (Y506F, Y523F, T572A, Y578F) resulted in partial loss of Rab5 function. Biochemical studies showed that six of them (D537A, P541A, Y561F, E574A, Y577F, T580A) were unable to activate Rab5 in an in vitro assay. In addition, Rin1: D537A andmore » Rin1: Y561F mutants showed dominant inhibition of Rab5 function. Consistent with the biochemical studies, we observed that these two Rin1 mutants have lost their ability to stimulate the endocytosis of EGF, form enlarged Rab5-positive endosomes, or support in vitro endosome fusion. Based on these data, our results showed that mutations in the Vps9 domain of Rin1 lead to a loss-of-function phenotype, indicating a specific structure-function relationship between Rab5 and Rin1.« less

Density functional studies on the exchange interaction of a dinuclear Gd(iii)-Cu(ii) complex: method assessment, magnetic coupling mechanism and magneto-structural correlations.

PubMed

Rajaraman, Gopalan; Totti, Federico; Bencini, Alessandro; Caneschi, Andrea; Sessoli, Roberta; Gatteschi, Dante

2009-05-07

Density functional calculations have been performed on a [Gd(iii)Cu(ii)] complex [L(1)CuGd(O(2)CCF(3))(3)(C(2)H(5)OH)(2)] () (where L(1) is N,N'-bis(3-ethoxy-salicylidene)-1,2-diamino-2-methylpropanato) with an aim of assessing a suitable functional within the DFT formalism to understand the mechanism of magnetic coupling and also to develop magneto-structural correlations. Encouraging results have been obtained in our studies where the application of B3LYP on the crystal structure of yields a ferromagnetic J value of -5.8 cm(-1) which is in excellent agreement with the experimental value of -4.42 cm(-1) (H = JS(Gd).S(Cu)). After testing varieties of functional for the method assessment we recommend the use of B3LYP with a combination of an effective core potential basis set. For all electron basis sets the relativistic effects should be incorporated either via the Douglas-Kroll-Hess (DKH) or zeroth-order regular approximation (ZORA) methods. A breakdown approach has been adopted where the calculations on several model complexes of have been performed. Their wave functions have been analysed thereafter (MO and NBO analysis) in order to gain some insight into the coupling mechanism. The results suggest, unambiguously, that the empty Gd(iii) 5d orbitals have a prominent role on the magnetic coupling. These 5d orbitals gain partial occupancy via Cu(ii) charge transfer as well as from the Gd(iii) 4f orbitals. A competing 4f-3d interaction associated with the symmetry of the complex has also been observed. The general mechanism hence incorporates both contributions and sets forth rather a prevailing mechanism for the 3d-4f coupling. The magneto-structural correlations reveal that there is no unique parameter which the J values are strongly correlated with, but an exponential relation to the J value found for the O-Cu-O-Gd dihedral angle parameter is the most credible correlation.

Analyzing and Assessing Brain Structure with Graph Connectivity Measures

DTIC Science & Technology

2014-05-09

structural brain networks, i.e. determining which regions of the brain are physically connected. Meanwhile, functional MRI ( fMRI ) yields an image of...produced by fMRI is a map of which parts are of the brain are active and which are not at a given time. In creating functional networks, regions of...the brain which often activitate together, i.e., often show up on fMRI as deoxygenated regions together, are considered connected. DTI allows the

Effect of lead fluoride incorporation on the structure and luminescence properties of tungsten sodium phosphate glasses

NASA Astrophysics Data System (ADS)

Nardi, Rachel Prado Russo Delorenzo; Braz, Celso Eduardo; de Camargo, Andrea S. S.; Ribeiro, Sidney J. L.; Rocha, Lucas A.; Cassanjes, Fábia Castro; Poirier, Gael

2015-11-01

Tungsten phosphate glasses are known to be promising materials for several applications in optics such as non linear optical properties, lower phonon energy or photochromic effects related with tungsten oxide incorporation inside the phosphate network. In this study, lead fluoride has been incorporated in a 60NaPO3-40WO3 glass composition according to the ternary molar compositions (100 - x)[0.6NaPO3-0.4WO3]-xPbF2 with x varying from 0 to 60 mol%. The structural changes as a function of composition were investigated by thermal analysis, UV-visible absorption, Raman spectroscopy, X-ray diffraction of the crystallized samples, and Eu3+ emission in the visible. While DSC analyzes points out a strong decrease in the glass network connectivity and higher crystallization tendency with increasing PbF2 contents, Raman spectra clearly identify a progressive incorporation of PbF2 in the phosphate network with the formation of terminal Psbnd F and Wsbnd F bonds. These results are also in agreement with the crystallization of β-PbF2 observed for the most lead fluoride concentrated samples. Investigation of Eu3+ emission data in the visible showed longer 5D0 excited state lifetime values and higher quantum efficiencies. These results are discussed in terms of the assumption of higher local symmetry around Eu3+ with increasing PbF2 contents.

AgPO2F2 and Ag9(PO2F2)14: the first Ag(i) and Ag(i)/Ag(ii) difluorophosphates with complex crystal structures.

PubMed

Malinowski, Przemysław J; Kurzydłowski, Dominik; Grochala, Wojciech

2015-12-07

The reaction of AgF2 with P2O3F4 yields a mixed valence Ag(I)/Ag(II) difluorophosphate salt with AgAg(PO2F2)14 stoichiometry - the first Ag(ii)-PO2F2 system known. This highly moisture sensitive brown solid is thermally stable up to 120 °C, which points at further feasible extension of the chemistry of Ag(ii)-PO2F2 systems. The crystal structure shows a very complex bonding pattern, comprising of polymeric Ag(PO2F2)14(4-) anions and two types of Ag(I) cations. One particular Ag(II) site present in the crystal structure of Ag9(PO2F2)14 is the first known example of square pyramidal penta-coordinated Ag(ii) in an oxo-ligand environment. Ag(i)PO2F2 - the product of the thermal decomposition of Ag9(PO2F2)14 - has also been characterized by thermal analysis, IR spectroscopy and X-ray powder diffraction. It has a complicated crystal structure as well, which consists of infinite 1D [Ag(I)O4/2] chains which are linked to more complex 3D structures via OPO bridges. The PO2F2(-) anions bind to cations in both compounds as bidentate oxo-ligands. The terminal F atoms tend to point inside the van der Waals cavities in the crystal structure of both compounds. All important structural details of both title compounds were corroborated by DFT calculations.

Spectroscopic and theoretical investigation of the electronic states of layered perovskite oxyfluoride S r2Ru O3F2 thin films

NASA Astrophysics Data System (ADS)

Chikamatsu, Akira; Kurauchi, Yuji; Kawahara, Keisuke; Onozuka, Tomoya; Minohara, Makoto; Kumigashira, Hiroshi; Ikenaga, Eiji; Hasegawa, Tetsuya

2018-06-01

We investigated the electronic structure of a layered perovskite oxyfluoride S r2Ru O3F2 thin film by hard x-ray photoemission spectroscopy (HAXPES) and soft x-ray absorption spectroscopy (XAS) as well as density functional theory (DFT)-based calculations. The core-level HAXPES spectra suggested that S r2Ru O3F2 is a Mott insulator. The DFT calculations described the total and site-projected density of states and the band dispersion for the optimized crystal structure of S r2Ru O3F2 , predicting that R u4 + takes a high-spin configuration of (xy ) ↑(yz ,z x ) ↑↑(3z2-r2 ) ↑ and that S r2Ru O3F2 has an indirect band gap of 0.7 eV with minima at the M ,A and X ,R points. HAXPES spectra near the Fermi level and the angular-dependent O 1 s XAS spectra of the S r2Ru O3F2 thin film, corresponding to the valence band and conduction band density of states, respectively, were drastically different compared to those of the S r2Ru O4 film, suggesting that the changes in the electronic states were mainly driven by the substitution of an oxygen atom coordinated to Ru by fluorine and subsequent modification of the crystal field.

An improved analysis of proton structure function F2(x,t) at small x

NASA Astrophysics Data System (ADS)

Machahari, Luxmi; Choudhury, D. K.

2018-04-01

We report an improved analysis of Taylor approximated coupled DGLAP equations for singlet F2S(x,t) and gluon G( x, t) distributions at small x pursued in recent years. To that end, we assume a plausible t-dependent relation between the singlet and gluon distribution valid at small x and omit the boundary condition F2S (1, t) = 0, for any t which needs large x extrapolation of small x solution. We observe that in general two inequivalent t-evolutions of F2S (x, t) and G( x, t) are possible. Theoretical advantages of one over the other are discussed and compared with the recently compiled data in order to choose the best one. Phenomenological range of validity of solutions is also reported.

The OsO(3)F(+) and mu-F(OsO(3)F)(2)(+) cations: their syntheses and study by Raman and (19)F NMR spectroscopy and electron structure calculations and X-ray crystal structures of [OsO(3)F][PnF(6)] (Pn = As, Sb), [OsO(3)F][HF](2)[AsF(6)], [OsO(3)F][HF][SbF(6)], and [OsO(3)F][Sb(3)F(16)].

PubMed

Gerken, Michael; Dixon, David A; Schrobilgen, Gary J

2002-01-28

The fluoride ion donor properties of OsO(3)F(2) have been investigated. The salts [OsO(3)F][AsF(6)], [OsO(3)F][HF](2)[AsF(6)], mu-F(OsO(3)F)(2)[AsF(6)], [OsO(3)F][HF](2)[SbF(6)], and [OsO(3)F][HF][SbF(6)] have been prepared by reaction of OsO(3)F(2) with AsF(5) and SbF(5) in HF solvent and have been characterized in the solid state by Raman spectroscopy. The single-crystal X-ray diffraction studies of [OsO(3)F][AsF(6)] (P2(1)/n, a = 7.0001(11) A, c = 8.8629(13) A, beta = 92.270(7) degrees, Z = 4, and R(1) = 0.0401 at -126 degrees C), [OsO(3)F][SbF(6)] (P2(1)/c, a = 5.4772(14) A, b = 10.115(3) A, c = 12.234(3) A, beta = 99.321(5) degrees, Z = 4, and R(1) = 0.0325 at -173 degrees C), [OsO(3)F][HF](2)[AsF(6)] (P2(1)/n, a = 5.1491(9) A, b = 8.129(2) A, c = 19.636(7) A, beta = 95.099(7) degrees, Z = 4, and R(1) = 0.0348 at -117 degrees C), and [OsO(3)F][HF][SbF(6)] (Pc, a = 5.244(4) A, b = 9.646(6) A, c = 15.269(10) A, beta = 97.154(13) degrees, Z = 4, and R(1) = 0.0558 at -133 degrees C) have shown that the OsO(3)F(+) cations exhibit strong contacts to the anions and HF solvent molecules giving rise to cyclic, dimeric structures in which the osmium atoms have coordination numbers of 6. The reaction of OsO(3)F(2) with neat SbF(5) yielded [OsO(3)F][Sb(3)F(16)], which has been characterized by (19)F NMR spectroscopy in SbF(5) and SO(2)ClF solvents and by Raman spectroscopy and single-crystal X-ray diffraction in the solid state (P4(1)m, a = 10.076(6) A, c = 7.585(8) A, Z = 2, and R(1) = 0.0858 at -113 degrees C). The weak fluoride ion basicity of the Sb(3)F(16)(-) anion resulted in an OsO(3)F(+) cation (C(3)(v) point symmetry) that is well isolated from the anion and in which the osmium is four-coordinate. The geometrical parameters and vibrational frequencies of OsO(3)F(+), ReO(3)F, mu-F(OsO(3)F)(2)(+), (FO(3)Os--FPnF(5))(2), and (FO(3)Os--(HF)(2)--FPnF(5))(2) (Pn = As, Sb) have been calculated using density functional theory methods.

A multi writable thiophene-based selective and reversible chromogenic fluoride probe with dual -NH functionality

NASA Astrophysics Data System (ADS)

Vishwakarma, Siddharth; Kumar, Ajit; Pandey, Abha; Upadhyay, K. K.

2017-01-01

A chromogenic fluoride probe bearing bis imine groups having dual -NH functionality (BSB) has been designed, synthesised and structurally characterized by its single crystal X-ray diffraction studies. The BSB could visually and spectroscopically recognise F- with high selectivity over other anions by exhibiting intense chromogenic response (from colourless to red) for F- in acetonitrile solution. The UV-visible titration and 1H NMR titration experiments indicated that the observed changes occur via a combined process including hydrogen bonding and deprotonation between the BSB and F-. Moreover theoretical calculations at the Density Functional Theory (DFT) level shed further light upon probe design strategy and the nature of interactions between BSB and F-. The limit of detection and binding constant of BSB towards F- were found to be 6.9 × 10- 7 M and 1.42 ± 0.069 × 108 M- 2 respectively. Finally, by using F- and H+ as chemical inputs and the absorbance as output, a INHIBIT logic gate was constructed, which exhibits "Multi-write" ability without obvious degradation in its optical output.

2D massless Dirac Fermi gas model of superconductivity in the surface state of a topological insulator at high magnetic fields

NASA Astrophysics Data System (ADS)

Zhuravlev, Vladimir; Duan, Wenye; Maniv, Tsofar

2017-10-01

The Nambu-Gorkov Green's function approach is applied to strongly type-II superconductivity in a 2D spin-momentum-locked (Weyl) Fermi gas model at high perpendicular magnetic fields. The resulting phase diagram can be mapped onto that derived for the standard, parabolic band-structure model, having the same Fermi surface parameters, E F and v, but with cyclotron effective mass m\\ast=EF/2v2 . Significant deviations from the predicted mapping are found only for very small E F , when the Landau-Level filling factors are smaller than unity, and E F shrinks below the cutoff energy.

[Characterization and microbial community shifts of rice strawdegrading microbial consortia].

PubMed

Wang, Chunfang; Ma, Shichun; Huang, Yan; Liu, Laiyan; Fan, Hui; Deng, Yu

2016-12-04

To study the relationship between microbial community and degradation rate of rice straw, we compared and analyzed cellulose-decomposing ability, microbial community structures and shifts of microbial consortia F1 and F2. We determined exoglucanase activity by 3, 5-dinitrosalicylic acid colorimetry. We determined content of cellulose, hemicellulose and lignin in rice straw by Van Soest method, and calculated degradation rates of rice straw by the weight changes before and after a 10-day incubation. We analyzed and compared the microbial communities and functional microbiology shifts by clone libraries, Miseq analysis and real time-PCR based on the 16S rRNA gene and cel48 genes. Total degradation rate, cellulose, and hemicellulose degradation rate of microbial consortia F1 were significantly higher than that of F2. The variation trend of exoglucanase activity in both microbial consortia F1 and F2 was consistent with that of cel48 gene copies. Microbial diversity of F1 was complex with aerobic bacteria as dominant species, whereas that of F2 was simple with a high proportion of anaerobic cellulose decomposing bacteria in the later stage of incubation. In the first 4 days, unclassified Bacillales and Bacillus were dominant in both F1 and F2. The dominant species and abundance became different after 4-day incubation, Bacteroidetes and Firmicutes were dominant phyla of F1 and F2, respectively. Although Petrimonas and Pusillimonas were common dominant species in F1 and F2, abundance of Petrimonas in F2 (38.30%) was significantly higher than that in F1 (9.47%), and the abundance of Clostridiales OPB54 in F2 increased to 14.85% after 8-day incubation. The abundance of cel48 gene related with cellulose degradation rate and exoglucanase activity, and cel48 gene has the potential as a molecular marker to monitor the process of cellulose degradation. Microbial community structure has a remarkable impact on the degradation efficiency of straw cellulose, and Petrimonas, Paenibacillus, Bacillales, Clostridiales were vital species for microbial consortia F1 and F2 decomposing rice straw.

Ferromagnetism in half-metallic quaternary FeVTiAl Heusler compound

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

Bhat, Tahir Mohiuddin; Bhat, Idris Hamid; Yousuf, Saleem

The electronic structure and magnetic properties of FeVTiAl quaternary Heusler alloy have been investigated within the density functional theory framework. The material was found completely spin-polarized half-metallic Ferromagnet in the ground state with F-43m structure. The structural stability was further confirmed by calculating different elastic constants in the cubic phase. Present study predicts an energy band gap of 0.72 eV calculated in localized minority spin channel at an equilibrium lattice parameter of 6.0Å. The calculated total spin magnetic moment of 2 µ{sub B}/f.u. is in agreement with the Slater-Pauling rule for full Heusler alloys.

Soluble expression, purification and characterization of the full length IS2 Transposase.

PubMed

Lewis, Leslie A; Astatke, Mekbib; Umekubo, Peter T; Alvi, Shaheen; Saby, Robert; Afrose, Jehan

2011-10-27

The two-step transposition pathway of insertion sequences of the IS3 family, and several other families, involves first the formation of a branched figure-of-eight (F-8) structure by an asymmetric single strand cleavage at one optional donor end and joining to the flanking host DNA near the target end. Its conversion to a double stranded minicircle precedes the second insertional step, where both ends function as donors. In IS2, the left end which lacks donor function in Step I acquires it in Step II. The assembly of two intrinsically different protein-DNA complexes in these F-8 generating elements has been intuitively proposed, but a barrier to testing this hypothesis has been the difficulty of isolating a full length, soluble and active transposase that creates fully formed synaptic complexes in vitro with protein bound to both binding and catalytic domains of the ends. We address here a solution to expressing, purifying and structurally analyzing such a protein. A soluble and active IS2 transposase derivative with GFP fused to its C-terminus functions as efficiently as the native protein in in vivo transposition assays. In vitro electrophoretic mobility shift assay data show that the partially purified protein prepared under native conditions binds very efficiently to cognate DNA, utilizing both N- and C-terminal residues. As a precursor to biophysical analyses of these complexes, a fluorescence-based random mutagenesis protocol was developed that enabled a structure-function analysis of the protein with good resolution at the secondary structure level. The results extend previous structure-function work on IS3 family transposases, identifying the binding domain as a three helix H + HTH bundle and explaining the function of an atypical leucine zipper-like motif in IS2. In addition gain- and loss-of-function mutations in the catalytic active site define its role in regional and global binding and identify functional signatures that are common to the three dimensional catalytic core motif of the retroviral integrase superfamily. Intractably insoluble transposases, such as the IS2 transposase, prepared by solubilization protocols are often refractory to whole protein structure-function studies. The results described here have validated the use of GFP-tagging and fluorescence-based random mutagenesis in overcoming this limitation at the secondary structure level.

Soluble expression, purification and characterization of the full length IS2 Transposase

PubMed Central

2011-01-01

Background The two-step transposition pathway of insertion sequences of the IS3 family, and several other families, involves first the formation of a branched figure-of-eight (F-8) structure by an asymmetric single strand cleavage at one optional donor end and joining to the flanking host DNA near the target end. Its conversion to a double stranded minicircle precedes the second insertional step, where both ends function as donors. In IS2, the left end which lacks donor function in Step I acquires it in Step II. The assembly of two intrinsically different protein-DNA complexes in these F-8 generating elements has been intuitively proposed, but a barrier to testing this hypothesis has been the difficulty of isolating a full length, soluble and active transposase that creates fully formed synaptic complexes in vitro with protein bound to both binding and catalytic domains of the ends. We address here a solution to expressing, purifying and structurally analyzing such a protein. Results A soluble and active IS2 transposase derivative with GFP fused to its C-terminus functions as efficiently as the native protein in in vivo transposition assays. In vitro electrophoretic mobility shift assay data show that the partially purified protein prepared under native conditions binds very efficiently to cognate DNA, utilizing both N- and C-terminal residues. As a precursor to biophysical analyses of these complexes, a fluorescence-based random mutagenesis protocol was developed that enabled a structure-function analysis of the protein with good resolution at the secondary structure level. The results extend previous structure-function work on IS3 family transposases, identifying the binding domain as a three helix H + HTH bundle and explaining the function of an atypical leucine zipper-like motif in IS2. In addition gain- and loss-of-function mutations in the catalytic active site define its role in regional and global binding and identify functional signatures that are common to the three dimensional catalytic core motif of the retroviral integrase superfamily. Conclusions Intractably insoluble transposases, such as the IS2 transposase, prepared by solubilization protocols are often refractory to whole protein structure-function studies. The results described here have validated the use of GFP-tagging and fluorescence-based random mutagenesis in overcoming this limitation at the secondary structure level. PMID:22032517

Materials Data on K8Ti5P2(O4F11)2 (SG:14) by Materials Project

DOE Data Explorer

Kristin Persson

2016-07-14

Computed materials data using density functional theory calculations. These calculations determine the electronic structure of bulk materials by solving approximations to the Schrodinger equation. For more information, see https://materialsproject.org/docs/calculations

Why phase errors affect the electron function more than amplitude errors.

PubMed

Lattman, Eaton; DeRosier, David

2008-03-01

If Fexp(ialpha) are the set of structure factors for a structure f, the amplitudes can be converted to those of an uncorrelated structure g (amplitude swapping) by multiplying each F by the positive number G/F. Correspondingly, the image f is convoluted with k, the Fourier transform of G/F; k has a large peak at the origin, so that f * k approximately f. For swapped phases, the image f is convoluted with l, the Fourier transform of exp(iDeltaalpha), where Deltaalpha, the phase difference between F and G, is a random variable; l does not have a large peak at the origin, so that f * l does not resemble f. The paper provides quantitative descriptions of these arguments.

Hydrothermal synthesis of novel Mn3O4 nano-octahedrons with enhanced supercapacitors performances

NASA Astrophysics Data System (ADS)

Jiang, Hao; Zhao, Ting; Yan, Chaoyi; Ma, Jan; Li, Chunzhong

2010-10-01

Uniform and single-crystalline Mn3O4 nano-octahedrons have been successfully synthesized by a simple ethylenediaminetetraacetic acid disodium salt (EDTA-2Na) assisted hydrothermal route. The octahedron structures exhibit a high geometric symmetry with smooth surfaces and the mean side length of square base of octahedrons is ~160 nm. The structure is reckoned to provide superior functional properties and the nano-size achieved in the present work is noted to further facilitate the material property enhancement. The formation process was proposed to begin with a ``dissolution-recrystallization'' which is followed by an ``Ostwald ripening'' mechanism. The Mn3O4 nano-octahedrons exhibited an enhanced specific capacitance of 322 F g-1 compared with the truncated octahedrons with specific capacitances of 244 F g-1, making them a promising electrode material for supercapacitors.Uniform and single-crystalline Mn3O4 nano-octahedrons have been successfully synthesized by a simple ethylenediaminetetraacetic acid disodium salt (EDTA-2Na) assisted hydrothermal route. The octahedron structures exhibit a high geometric symmetry with smooth surfaces and the mean side length of square base of octahedrons is ~160 nm. The structure is reckoned to provide superior functional properties and the nano-size achieved in the present work is noted to further facilitate the material property enhancement. The formation process was proposed to begin with a ``dissolution-recrystallization'' which is followed by an ``Ostwald ripening'' mechanism. The Mn3O4 nano-octahedrons exhibited an enhanced specific capacitance of 322 F g-1 compared with the truncated octahedrons with specific capacitances of 244 F g-1, making them a promising electrode material for supercapacitors. Electronic supplementary information (ESI) available: TEM images; EDTA-2Na reaction details. See DOI: 10.1039/c0nr00257g

Factors influencing inapplicability of cosolvency-induced model on organic acid sorption onto humic substance from methanol mixture.

PubMed

Kim, Minhee; Kim, Juhee; Kim, Jeong-Gyu; Hyun, Seunghun

2015-10-01

Applicability of cosolvency model for describing the sorption of organic acids to humic substance was investigated by analyzing dataset of sorption (K m) and solubility (S m) of selected solutes (benzoic acid, 1-naphthoic acid, 2,4-dichlorophenoxyacetic acid, and 2,4,6-trichlorophenol (2,4,6-TCP)) as a function of pH(appCME) (apparent pH of liquid phase) and f c (methanol volume fractions). For all solutes, the K m decreased with f c with the K m reduction being less than the S m-based prediction. The slope of log K m-f c plot in the three organic carboxylic acids was well correlated with their cosolvency power, whereas the data of organic phenolic acid (2,4,6-TCP) was placed above the trend, indicating the different actions of functional groups. The occurrence of Ca(2+) bridge between carboxylate and negatively charged humic surface may explain this phenomenon. Normalizing the K m to the corresponding S m (α' = K m/S m) was not in unity over the pH(app)-f c range but decreased with f c, indicating a possible structural modification of sorption domain favoring extra sorption. For a given solute, the α' of neutral species was always greater than that of anionic species, showing that extra interaction will be likely at pH(app)

Electronic structure properties of UO2 as a Mott insulator

NASA Astrophysics Data System (ADS)

Sheykhi, Samira; Payami, Mahmoud

2018-06-01

In this work using the density functional theory (DFT), we have studied the structural, electronic and magnetic properties of uranium dioxide with antiferromagnetic 1k-, 2k-, and 3k-order structures. Ordinary approximations in DFT, such as the local density approximation (LDA) or generalized gradient approximation (GGA), usually predict incorrect metallic behaviors for this strongly correlated electron system. Using Hubbard term correction for f-electrons, LDA+U method, as well as using the screened Heyd-Scuseria-Ernzerhof (HSE) hybrid functional for the exchange-correlation (XC), we have obtained the correct ground-state behavior as an insulator, with band gaps in good agreement with experiment.

High-functionality star-branched macromolecules: polymer size and virial coefficients.

PubMed

Randisi, Ferdinando; Pelissetto, Andrea

2013-10-21

We perform high-statistics Monte Carlo simulations of a lattice model to compute the radius of gyration Rg, the center-to-end distance, the monomer distribution, and the second and third virial coefficients of star polymers for a wide range of functionalities f, 6 ≤ f ≤ 120. We consider systems with a large number L of monomers per arm (100 is approximately < L is approximately < 1000 for f ≤ 40 and 100 is approximately < L is approximately < 400 for f = 80, 120), which allows us to determine accurately all quantities in the scaling regime. Results are extrapolated to determine the behavior of the different quantities in the limit f → ∞. Structural results are finally compared with the predictions of the Daoud-Cotton model. It turns out that the blob picture of a star polymer is essentially correct up to the corona radius Rc, which depends on f and which varies from 0.7Rg for f = 6 to 1.0Rg for f = 40. The outer region (r > Rc), in which the monomer distribution decays exponentially, shrinks as f increases, but it does not disappear in the scaling regime even in the limit f → ∞. We also consider the Daoud-Cotton scaling relation Rg (2)~f(1-ν)L(2ν), which is found to hold only for f > 100.

Analytic derivation of the next-to-leading order proton structure function F2p(x ,Q2) based on the Laplace transformation

NASA Astrophysics Data System (ADS)

Khanpour, Hamzeh; Mirjalili, Abolfazl; Tehrani, S. Atashbar

2017-03-01

An analytical solution based on the Laplace transformation technique for the Dokshitzer-Gribov-Lipatov-Altarelli-Parisi (DGLAP) evolution equations is presented at next-to-leading order accuracy in perturbative QCD. This technique is also applied to extract the analytical solution for the proton structure function, F2p(x ,Q2) , in the Laplace s space. We present the results for the separate parton distributions of all parton species, including valence quark densities, the antiquark and strange sea parton distribution functions (PDFs), and the gluon distribution. We successfully compare the obtained parton distribution functions and the proton structure function with the results from GJR08 [Gluck, Jimenez-Delgado, and Reya, Eur. Phys. J. C 53, 355 (2008)], 10.1140/epjc/s10052-007-0462-9 and KKT12 [Khanpour, Khorramian, and Tehrani, J. Phys. G 40, 045002 (2013)], 10.1088/0954-3899/40/4/045002 parametrization models as well as the x -space results using QCDnum code. Our calculations show a very good agreement with the available theoretical models as well as the deep inelastic scattering (DIS) experimental data throughout the small and large values of x . The use of our analytical solution to extract the parton densities and the proton structure function is discussed in detail to justify the analysis method, considering the accuracy and speed of calculations. Overall, the accuracy we obtain from the analytical solution using the inverse Laplace transform technique is found to be better than 1 part in 104 to 105. We also present a detailed QCD analysis of nonsinglet structure functions using all available DIS data to perform global QCD fits. In this regard we employ the Jacobi polynomial approach to convert the results from Laplace s space to Bjorken x space. The extracted valence quark densities are also presented and compared to the JR14, MMHT14, NNPDF, and CJ15 PDFs sets. We evaluate the numerical effects of target mass corrections (TMCs) and higher twist (HT) terms on various structure functions, and compare fits to data with and without these corrections.

Bold-Independent Computational Entropy Assesses Functional Donut-Like Structures in Brain fMRI Images

PubMed Central

Peters, James F.; Ramanna, Sheela; Tozzi, Arturo; İnan, Ebubekir

2017-01-01

We introduce a novel method for the measurement of information level in fMRI (functional Magnetic Resonance Imaging) neural data sets, based on image subdivision in small polygons equipped with different entropic content. We show how this method, called maximal nucleus clustering (MNC), is a novel, fast and inexpensive image-analysis technique, independent from the standard blood-oxygen-level dependent signals. MNC facilitates the objective detection of hidden temporal patterns of entropy/information in zones of fMRI images generally not taken into account by the subjective standpoint of the observer. This approach befits the geometric character of fMRIs. The main purpose of this study is to provide a computable framework for fMRI that not only facilitates analyses, but also provides an easily decipherable visualization of structures. This framework commands attention because it is easily implemented using conventional software systems. In order to evaluate the potential applications of MNC, we looked for the presence of a fourth dimension's distinctive hallmarks in a temporal sequence of 2D images taken during spontaneous brain activity. Indeed, recent findings suggest that several brain activities, such as mind-wandering and memory retrieval, might take place in the functional space of a four dimensional hypersphere, which is a double donut-like structure undetectable in the usual three dimensions. We found that the Rényi entropy is higher in MNC areas than in the surrounding ones, and that these temporal patterns closely resemble the trajectories predicted by the possible presence of a hypersphere in the brain. PMID:28203153

Bold-Independent Computational Entropy Assesses Functional Donut-Like Structures in Brain fMRI Images.

PubMed

Peters, James F; Ramanna, Sheela; Tozzi, Arturo; İnan, Ebubekir

2017-01-01

We introduce a novel method for the measurement of information level in fMRI (functional Magnetic Resonance Imaging) neural data sets, based on image subdivision in small polygons equipped with different entropic content. We show how this method, called maximal nucleus clustering (MNC), is a novel, fast and inexpensive image-analysis technique, independent from the standard blood-oxygen-level dependent signals. MNC facilitates the objective detection of hidden temporal patterns of entropy/information in zones of fMRI images generally not taken into account by the subjective standpoint of the observer. This approach befits the geometric character of fMRIs. The main purpose of this study is to provide a computable framework for fMRI that not only facilitates analyses, but also provides an easily decipherable visualization of structures. This framework commands attention because it is easily implemented using conventional software systems. In order to evaluate the potential applications of MNC, we looked for the presence of a fourth dimension's distinctive hallmarks in a temporal sequence of 2D images taken during spontaneous brain activity. Indeed, recent findings suggest that several brain activities, such as mind-wandering and memory retrieval, might take place in the functional space of a four dimensional hypersphere, which is a double donut-like structure undetectable in the usual three dimensions. We found that the Rényi entropy is higher in MNC areas than in the surrounding ones, and that these temporal patterns closely resemble the trajectories predicted by the possible presence of a hypersphere in the brain.

Wavelet decomposition analysis in the two-flash multifocal ERG in early glaucoma: a comparison to ganglion cell analysis and visual field.

PubMed

Brandao, Livia M; Monhart, Matthias; Schötzau, Andreas; Ledolter, Anna A; Palmowski-Wolfe, Anja M

2017-08-01

To further improve analysis of the two-flash multifocal electroretinogram (2F-mfERG) in glaucoma in regard to structure-function analysis, using discrete wavelet transform (DWT) analysis. Sixty subjects [35 controls and 25 primary open-angle glaucoma (POAG)] underwent 2F-mfERG. Responses were analyzed with the DWT. The DWT level that could best separate POAG from controls was compared to the root-mean-square (RMS) calculations previously used in the analysis of the 2F-mfERG. In a subgroup analysis, structure-function correlation was assessed between DWT, optical coherence tomography and automated perimetry (mf103 customized pattern) for the central 15°. Frequency level 4 of the wavelet variance analysis (144 Hz, WVA-144) was most sensitive (p < 0.003). It correlated positively with RMS but had a better AUC. Positive relations were found between visual field, WVA-144 and GCIPL thickness. The highest predictive factor for glaucoma diagnostic was seen in the GCIPL, but this improved further by adding the mean sensitivity and WVA-144. mfERG using WVA analysis improves glaucoma diagnosis, especially when combined with GCIPL and MS.

Analytic Morse/long-range potential energy surfaces and "adiabatic-hindered-rotor" treatment for a symmetric top-linear molecule dimer: A case study of CH3F-H2

NASA Astrophysics Data System (ADS)

Zhang, Xiao-Long; Ma, Yong-Tao; Zhai, Yu; Li, Hui

2018-03-01

A first effective six-dimensional ab initio potential energy surface (PES) for CH3F-H2 which explicitly includes the intramolecular Q3 stretching normal mode of the CH3F monomer is presented. The electronic structure computations have been carried out at the explicitly correlated coupled cluster level of theory [CCSD(T)-F12a] with an augmented correlation-consistent triple zeta basis set. Five-dimensional analytical intermolecular PESs for ν3(CH3F) = 0 and 1 are then obtained by fitting the vibrationally averaged potentials to the Morse/Long-Range (MLR) potential function form. The MLR function form is applied to the nonlinear molecule-linear molecule case for the first time. These fits to 25 015 points have root-mean-square deviations of 0.74 cm-1 and 0.082 cm-1 for interaction energies less than 0.0 cm-1. Using the adiabatic hindered-rotor approximation, three-dimensional PESs for CH3F-paraH2 are generated from the 5D PESs over all possible orientations of the hydrogen monomer. The infrared and microwave spectra for CH3F-paraH2 dimer are predicted for the first time. These analytic PESs can be used for modeling the dynamical behavior in CH3F-(H2)N clusters, including the possible appearance of microscopic superfluidity.

Noble-Gas Difluoride Complexes of Mercury(II): The Syntheses and Structures of Hg(OTeF 5) 2·1.5NgF 2 (Ng = Xe, Kr) and Hg(OTeF 5) 2

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

DeBackere, John R.; Mercier, Helene P. A; Schrobilgen, Gary J.

2014-02-03

The synthesis of high-purity Hg(OTeF 5) 2 has resulted in its structural characterization in the solid state by Raman spectroscopy and single-crystal X-ray diffraction (XRD) and in solution by 19F NMR spectroscopy. The crystal structure of Hg(OTeF 5) 2 (-173 °C) consists of discrete Hg(OTeF 5) 2 units having gauche-conformations that interact through long Hg---O and Hg---F intramolecular contacts to give a chain structure. Furthermore, the Lewis acidity of Hg(OTeF 5) 2 toward NgF 2 (Ng = Xe, Kr) was investigated in SO 2ClF solvent and shown to form stable coordination complexes with NgF 2 at -78 °C. Both complexesmore » were characterized by low-temperature Raman spectroscopy (-155 °C) and single-crystal XRD. The complexes are isostructural and are formulated as Hg(OTeF 5) 2·1.5NgF 2. The Hg(OTeF 5) 2 units of Hg(OTeF 5) 2·1.5NgF 2 also have gauche-conformations and are linked through bridging NgF 2 molecules, also resulting in chain structures. The complexes represent the only examples of coordination compounds where NgF 2 coordinates to mercury in a neutral covalent compound and the only example of mercury coordinated to KrF 2. Moreover, the Hg(OTeF 5) 2·1.5KrF 2 complex is the only KrF 2 complex known to contain a bridging KrF 2 ligand. Energy-minimized gas-phase geometries and vibrational frequencies for the model compounds, [Hg(OTeF5) 2] 3 and [Hg(OTeF 5) 2] 3·2NgF 2, were obtained and provide good approximations of the local environments of Hg(OTeF 5) 2 and NgF 2 in the crystal structures of Hg(OTeF5)2 and Hg(OTeF 5) 2·1.5NgF 2. Assignments of the Raman spectra of Hg(OTeF 5) 2 and Hg(OTeF 5) 2·1.5NgF 2 are based on the calculated vibrational frequencies of the model compounds. Natural bond orbital analyses provided the associated bond orders, valencies, and natural population analysis charges.« less

Materials Data on KHo2F7 (SG:12) by Materials Project

DOE Data Explorer

Kristin Persson

2016-05-18

Computed materials data using density functional theory calculations. These calculations determine the electronic structure of bulk materials by solving approximations to the Schrodinger equation. For more information, see https://materialsproject.org/docs/calculations

Materials Data on CuF2 (SG:14) by Materials Project

DOE Data Explorer

Kristin Persson

2015-01-27

Computed materials data using density functional theory calculations. These calculations determine the electronic structure of bulk materials by solving approximations to the Schrodinger equation. For more information, see https://materialsproject.org/docs/calculations

Materials Data on BaF2 (SG:225) by Materials Project

DOE Data Explorer

Kristin Persson

2014-11-02

Computed materials data using density functional theory calculations. These calculations determine the electronic structure of bulk materials by solving approximations to the Schrodinger equation. For more information, see https://materialsproject.org/docs/calculations

Materials Data on PdF2 (SG:136) by Materials Project

DOE Data Explorer

Kristin Persson

2015-02-09

Computed materials data using density functional theory calculations. These calculations determine the electronic structure of bulk materials by solving approximations to the Schrodinger equation. For more information, see https://materialsproject.org/docs/calculations

Materials Data on AgSnF6 (SG:2) by Materials Project

DOE Data Explorer

Kristin Persson

2014-11-02

Computed materials data using density functional theory calculations. These calculations determine the electronic structure of bulk materials by solving approximations to the Schrodinger equation. For more information, see https://materialsproject.org/docs/calculations

Materials Data on TiAgF6 (SG:2) by Materials Project

DOE Data Explorer

Kristin Persson

2014-11-02

Computed materials data using density functional theory calculations. These calculations determine the electronic structure of bulk materials by solving approximations to the Schrodinger equation. For more information, see https://materialsproject.org/docs/calculations

Materials Data on CaF2 (SG:62) by Materials Project

DOE Data Explorer

Kristin Persson

2014-11-02

Computed materials data using density functional theory calculations. These calculations determine the electronic structure of bulk materials by solving approximations to the Schrodinger equation. For more information, see https://materialsproject.org/docs/calculations

Materials Data on C(ClF)2 (SG:43) by Materials Project

DOE Data Explorer

Kristin Persson

2014-11-02

Computed materials data using density functional theory calculations. These calculations determine the electronic structure of bulk materials by solving approximations to the Schrodinger equation. For more information, see https://materialsproject.org/docs/calculations

Materials Data on MgF2 (SG:12) by Materials Project

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

Kristin Persson

2014-07-09

Computed materials data using density functional theory calculations. These calculations determine the electronic structure of bulk materials by solving approximations to the Schrodinger equation. For more information, see https://materialsproject.org/docs/calculations

Materials Data on MgF2 (SG:205) by Materials Project

DOE Data Explorer

Kristin Persson

2014-11-02

Computed materials data using density functional theory calculations. These calculations determine the electronic structure of bulk materials by solving approximations to the Schrodinger equation. For more information, see https://materialsproject.org/docs/calculations

Materials Data on MgF2 (SG:136) by Materials Project

DOE Data Explorer

Kristin Persson

2014-11-02

Computed materials data using density functional theory calculations. These calculations determine the electronic structure of bulk materials by solving approximations to the Schrodinger equation. For more information, see https://materialsproject.org/docs/calculations

Comparison of Saccharomyces cerevisiae F-BAR domain structures reveals a conserved inositol phosphate binding site.

PubMed

Moravcevic, Katarina; Alvarado, Diego; Schmitz, Karl R; Kenniston, Jon A; Mendrola, Jeannine M; Ferguson, Kathryn M; Lemmon, Mark A

2015-02-03

F-BAR domains control membrane interactions in endocytosis, cytokinesis, and cell signaling. Although they are generally thought to bind curved membranes containing negatively charged phospholipids, numerous functional studies argue that differences in lipid-binding selectivities of F-BAR domains are functionally important. Here, we compare membrane-binding properties of the Saccharomyces cerevisiae F-BAR domains in vitro and in vivo. Whereas some F-BAR domains (such as Bzz1p and Hof1p F-BARs) bind equally well to all phospholipids, the F-BAR domain from the RhoGAP Rgd1p preferentially binds phosphoinositides. We determined X-ray crystal structures of F-BAR domains from Hof1p and Rgd1p, the latter bound to an inositol phosphate. The structures explain phospholipid-binding selectivity differences and reveal an F-BAR phosphoinositide binding site that is fully conserved in a mammalian RhoGAP called Gmip and is partly retained in certain other F-BAR domains. Our findings reveal previously unappreciated determinants of F-BAR domain lipid-binding specificity and provide a basis for its prediction from sequence. Copyright © 2015 Elsevier Ltd. All rights reserved.

Comparison of Saccharomyces cerevisiae F-BAR Domain Structures Reveals a Conserved Inositol Phosphate Binding Site

DOE PAGES

Moravcevic, Katarina; Alvarado, Diego; Schmitz, Karl R.; ...

2015-01-22

F-BAR domains control membrane interactions in endocytosis, cytokinesis, and cell signaling. Although they are generally thought to bind curved membranes containing negatively charged phospholipids, numerous functional studies argue that differences in lipid-binding selectivities of F-BAR domains are functionally important. Here in this paper, we compare membrane-binding properties of the Saccharomyces cerevisiae F-BAR domains in vitro and in vivo. Whereas some F-BAR domains (such as Bzz1p and Hof1p F-BARs) bind equally well to all phospholipids, the F-BAR domain from the RhoGAP Rgd1p preferentially binds phosphoinositides. We determined X-ray crystal structures of F-BAR domains from Hof1p and Rgd1p, the latter bound tomore » an inositol phosphate. The structures explain phospholipid-binding selectivity differences and reveal an F-BAR phosphoinositide binding site that is fully conserved in a mammalian RhoGAP called Gmip and is partly retained in certain other F-BAR domains. In conclusion, our findings reveal previously unappreciated determinants of F-BAR domain lipid-binding specificity and provide a basis for its prediction from sequence.« less

Structural Basis for Suppression of a Host Antiviral Response by Influenza A Virus

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

Das,K.; Ma, L.; Xiao, R.

2008-01-01

Influenza A viruses are responsible for seasonal epidemics and high mortality pandemics. A major function of the viral NS1A protein, a virulence factor, is the inhibition of the production of IFN-{beta}{beta} mRNA and other antiviral mRNAs. The NS1A protein of the human influenza A/Udorn/72 (Ud) virus inhibits the production of these antiviral mRNAs by binding the cellular 30-kDa subunit of the cleavage and polyadenylation specificity factor (CPSF30), which is required for the 3' end processing of all cellular pre-mRNAs. Here we report the 1.95- Angstroms resolution X-ray crystal structure of the complex formed between the second and third zinc fingermore » domain (F2F3) of CPSF30 and the C-terminal domain of the Ud NS1A protein. The complex is a tetramer, in which each of two F2F3 molecules wraps around two NS1A effector domains that interact with each other head-to-head. This structure identifies a CPSF30 binding pocket on NS1A comprised of amino acid residues that are highly conserved among human influenza A viruses. Single amino acid changes within this binding pocket eliminate CPSF30 binding, and a recombinant Ud virus expressing an NS1A protein with such a substitution is attenuated and does not inhibit IFN-{beta} pre-mRNA processing. This binding pocket is a potential target for antiviral drug development. The crystal structure also reveals that two amino acids outside of this pocket, F103 and M106, which are highly conserved (>99%) among influenza A viruses isolated from humans, participate in key hydrophobic interactions with F2F3 that stabilize the complex.« less

Exploring the charge localization and band gap opening of borophene: a first-principles study.

PubMed

Kistanov, Andrey A; Cai, Yongqing; Zhou, Kun; Srikanth, Narasimalu; Dmitriev, Sergey V; Zhang, Yong-Wei

2018-01-18

Recently synthesized two-dimensional (2D) boron, borophene, exhibits a novel metallic behavior rooted in the s-p orbital hybridization, distinctively different from other 2D materials such as sulfides/selenides and semi-metallic graphene. This unique feature of borophene implies new routes for charge delocalization and band gap opening. Herein, using first-principles calculations, we explore the routes to localize the carriers and open the band gap of borophene via chemical functionalization, ribbon construction, and defect engineering. The metallicity of borophene is found to be remarkably robust against H- and F-functionalization and the presence of vacancies. Interestingly, a strong odd-even oscillation of the electronic structure with width is revealed for H-functionalized borophene nanoribbons, while an ultra-high work function (∼7.83 eV) is found for the F-functionalized borophene due to its strong charge transfer to the atomic adsorbates.

Motor Flow Instabilities - Part 1

DTIC Science & Technology

2004-01-01

by the flow, the structure motions (as possibly affecting the mean and unsteady flows). Finally, the model should be able: a) to propagate the...combustion responses function determinations, Dedicated models for combustion mechanisms and fluid- structure couplings, Dedicated and documented test...associated with these large motors (recall that f1L ≈ a/2L) rendered such oscillations undesirable since they were able to couple to the structural modes

A Conserved Region in the F2 Subunit of Paramyxovirus Fusion Proteins Is Involved In Fusion Regulation▿

PubMed Central

Gardner, Amanda E.; Dutch, Rebecca E.

2007-01-01

Paramyxoviruses utilize both an attachment protein and a fusion (F) protein to drive virus-cell and cell-cell fusion. F exists functionally as a trimer of two disulfide-linked subunits: F1 and F2. Alignment and analysis of a set of paramyxovirus F protein sequences identified three conserved blocks (CB): one in the fusion peptide/heptad repeat A domain, known to play important roles in fusion promotion, one in the region between the heptad repeats of F1 (CBF1) (A. E. Gardner, K. L. Martin, and R. E. Dutch, Biochemistry 46:5094-5105, 2007), and one in the F2 subunit (CBF2). To analyze the functions of CBF2, alanine substitutions at conserved positions were created in both the simian virus 5 (SV5) and Hendra virus F proteins. A number of the CBF2 mutations resulted in folding and expression defects. However, the CBF2 mutants that were properly expressed and trafficked had altered fusion promotion activity. The Hendra virus CBF2 Y79A and P89A mutants showed significantly decreased levels of fusion, whereas the SV5 CBF2 I49A mutant exhibited greatly increased cell-cell fusion relative to that for wild-type F. Additional substitutions at SV5 F I49 suggest that both side chain volume and hydrophobicity at this position are important in the folding of the metastable, prefusion state and the subsequent triggering of membrane fusion. The recently published prefusogenic structure of parainfluenza virus 5/SV5 F (H. S. Yin et al., Nature 439:38-44, 2006) places CBF2 in direct contact with heptad repeat A. Our data therefore indicate that this conserved region plays a critical role in stabilizing the prefusion state, likely through interactions with heptad repeat A, and in triggering membrane fusion. PMID:17507474

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

Wu, Pei-Hsin; Chung, Hsiao-Wen; Tsai, Ping-Huei

Purpose: One of the technical advantages of functional magnetic resonance imaging (fMRI) is its precise localization of changes from neuronal activities. While current practice of fMRI acquisition at voxel size around 3 × 3 × 3 mm{sup 3} achieves satisfactory results in studies of basic brain functions, higher spatial resolution is required in order to resolve finer cortical structures. This study investigated spatial resolution effects on brain fMRI experiments using balanced steady-state free precession (bSSFP) imaging with 0.37 mm{sup 3} voxel volume at 3.0 T. Methods: In fMRI experiments, full and unilateral visual field 5 Hz flashing checkerboard stimulations weremore » given to healthy subjects. The bSSFP imaging experiments were performed at three different frequency offsets to widen the coverage, with functional activations in the primary visual cortex analyzed using the general linear model. Variations of the spatial resolution were achieved by removing outerk-space data components. Results: Results show that a reduction in voxel volume from 3.44 × 3.44 × 2 mm{sup 3} to 0.43 × 0.43 × 2 mm{sup 3} has resulted in an increase of the functional activation signals from (7.7 ± 1.7)% to (20.9 ± 2.0)% at 3.0 T, despite of the threefold SNR decreases in the original images, leading to nearly invariant functional contrast-to-noise ratios (fCNR) even at high spatial resolution. Activation signals aligning nicely with gray matter sulci at high spatial resolution would, on the other hand, have possibly been mistaken as noise at low spatial resolution. Conclusions: It is concluded that the bSSFP sequence is a plausible technique for fMRI investigations at submillimeter voxel widths without compromising fCNR. The reduction of partial volume averaging with nonactivated brain tissues to retain fCNR is uniquely suitable for high spatial resolution applications such as the resolving of columnar organization in the brain.« less

Structural and Functional Divergence of the Aldolase Fold in Toxoplasma gondii

DOE PAGES

Tonkin, Michelle L.; Halavaty, Andrei S.; Ramaswamy, Raghavendran; ...

2014-10-02

Parasites of the phylum Apicomplexa are highly successful pathogens of humans and animals worldwide. As obligate intracellular parasites, they have significant energy requirements for invasion and gliding motility that are supplied by various metabolic pathways. Aldolases have emerged as key enzymes involved in these pathways, and all apicomplexans express one or both of fructose 1,6-bisphosphate (F16BP) aldolase and 2-deoxyribose 5-phosphate (dR5P) aldolase (DERA). Intriguingly, Toxoplasma gondii, a highly successful apicomplexan parasite, expresses F16BP aldolase (TgALD1), d5RP aldolase (TgDERA), and a divergent dR5P aldolase-like protein (TgDPA) exclusively in the latent bradyzoite stage. While the importance of TgALD1 in glycolysis is wellmore » established and TgDERA is also likely to be involved in parasite metabolism, the detailed function of TgDPA remains elusive. Here, to gain mechanistic insight into the function of different T. gondii aldolases, we first determined the crystal structures of TgALD1 and TgDPA. Structural analysis revealed that both aldolases adopt a TIM barrel fold accessorized with divergent secondary structure elements. Structural comparison of TgALD1 and TgDPA with members of their respective enzyme families revealed that, while the active-site residues are conserved in TgALD1, key catalytic residues are absent in TgDPA. Consistent with this observation, biochemical assays showed that, while TgALD1 was active on F16BP, TgDPA was inactive on dR5P. In conclusion, intriguingly, both aldolases are competent to bind polymerized actin in vitro. Altogether, structural and biochemical analyses of T. gondii aldolase and aldolase-like proteins reveal diverse functionalization of the classic TIM barrel aldolase fold.« less

Structural and functional divergence of the aldolase fold in Toxoplasma gondii.

PubMed

Tonkin, Michelle L; Halavaty, Andrei S; Ramaswamy, Raghavendran; Ruan, Jiapeng; Igarashi, Makoto; Ngô, Huân M; Boulanger, Martin J

2015-02-27

Parasites of the phylum Apicomplexa are highly successful pathogens of humans and animals worldwide. As obligate intracellular parasites, they have significant energy requirements for invasion and gliding motility that are supplied by various metabolic pathways. Aldolases have emerged as key enzymes involved in these pathways, and all apicomplexans express one or both of fructose 1,6-bisphosphate (F16BP) aldolase and 2-deoxyribose 5-phosphate (dR5P) aldolase (DERA). Intriguingly, Toxoplasma gondii, a highly successful apicomplexan parasite, expresses F16BP aldolase (TgALD1), d5RP aldolase (TgDERA), and a divergent dR5P aldolase-like protein (TgDPA) exclusively in the latent bradyzoite stage. While the importance of TgALD1 in glycolysis is well established and TgDERA is also likely to be involved in parasite metabolism, the detailed function of TgDPA remains elusive. To gain mechanistic insight into the function of different T. gondii aldolases, we first determined the crystal structures of TgALD1 and TgDPA. Structural analysis revealed that both aldolases adopt a TIM barrel fold accessorized with divergent secondary structure elements. Structural comparison of TgALD1 and TgDPA with members of their respective enzyme families revealed that, while the active-site residues are conserved in TgALD1, key catalytic residues are absent in TgDPA. Consistent with this observation, biochemical assays showed that, while TgALD1 was active on F16BP, TgDPA was inactive on dR5P. Intriguingly, both aldolases are competent to bind polymerized actin in vitro. Altogether, structural and biochemical analyses of T. gondii aldolase and aldolase-like proteins reveal diverse functionalization of the classic TIM barrel aldolase fold. Copyright © 2014 Elsevier Ltd. All rights reserved.

Assessment of brain activity during voluntary anal sphincter contraction: Comparative study in women with and without fecal incontinence.

PubMed

Parés, D; Martínez-Vilalta, M; Ortiz, H; Soriano-Mas, C; Maestre-Gonzalez, Y; Pujol, J; Grande, L

2018-04-14

Voluntary anal sphincter function is driven by an extended network of brain structures, most of which are still unknown. Disturbances in this function may cause fecal incontinence. The aim of this study was to characterize the cerebral areas involved in voluntary contraction of the anorectal sphincter in healthy women and in a group of patients with fecal incontinence by using a standardized functional magnetic resonance imaging (fMRI) protocol. This comparative study included 12 healthy women (mean age 53.17 ± 4.93 years) and 12 women with fecal incontinence (56.25 ± 6.94 years). An MRI-compatible anal manometer was used to register voluntary external anal sphincter contraction. During brain fMRI imaging, participants were cued to perform 10-s series of self-paced anal sphincter contractions at an approximate rate of 1 Hz. Brain structures linked to anal sphincter contractions were mapped and the findings were compared between the 2 study groups. There were no differences in the evoked brain activity between the 2 groups. In healthy women, group fMRI analysis revealed significant activations in medial primary motor cortices, supplementary motor area, bilateral putamen, and cerebellum, as well as in the supramarginal gyrus and visual areas. In patients with fecal incontinence, the activation pattern involved similar regions without significant differences with healthy women. This brain fMRI-anorectal protocol was able to map the brain regions linked to voluntary anal sphincter function in healthy and women with fecal incontinence. © 2018 John Wiley & Sons Ltd.

Reproductive toxicity evaluation of dietary butyl benzyl phthalate (BBP) in rats.

PubMed

Tyl, Rochelle W; Myers, Christina B; Marr, Melissa C; Fail, Patricia A; Seely, John C; Brine, Dolores R; Barter, Robert A; Butala, John H

2004-01-01

Butyl benzyl phthalate (BBP) was administered in the diet at 0, 750, 3750, and 11,250 ppm ad libitum to 30 rats per sex per dose for two offspring generations, one litter/breeding pair/generation, through weaning of F2 litters. Adult F0 systemic toxicity and adult F1 systemic and reproductive toxicity were present at 11,250 ppm (750 mg/kg per day). At 11,250 ppm, there were reduced F1 and F2 male anogenital distance (AGD) and body weights/litter during lactation, delayed acquisition of puberty in F1 males and females, retention of nipples and areolae in F1 and F2 males, and male reproductive system malformations. At 3750 ppm (250 mg/kg per day), only reduced F1 and F2 offspring male AGD was present. There were no effects on parents or offspring at 750 ppm (50 mg/kg per day). The F1 parental systemic and reproductive toxicity no observable adverse effect level (NOAEL) was 3750 ppm. The offspring toxicity NOAEL was 3750 ppm. The offspring toxicity no observable effect level (NOEL) was 750 ppm, based on the presence of reduced AGD in F1 and F2 males at birth at 3750 ppm, but no effects on reproductive development, structures, or functions.

Quark-hadron duality and parity violating asymmetry of electroweak reactions in the {delta} region

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

Matsui, K.; Sato, T.; Lee, T.-S.H.

2005-08-01

A dynamical model [T. Sato and T.-S. H. Lee, Phys. Rev. C 54, 2660 (1996); 63, 055201 (2001); T. Sato, D. Uno, and T.-S. H. Lee, ibid. 67, 065201 (2003)] of electroweak pion production reactions in the {delta}(1232) region has been extended to include the neutral current contributions for examining the local quark-hadron duality in neutrino-induced reactions and for investigating how the axial N-{delta} form factor can be determined by the parity violating asymmetry of N(e{sup {yields}},e{sup '}) reactions. We first show that the recent data of (e,e{sup '}) structure functions F{sub 1} and F{sub 2}, which exhibit the quark-hadronmore » duality, are in good agreement with our predictions. For possible future experimental tests, we then predict that the structure functions F{sub 1},F{sub 2}, and F{sub 3} for ({nu},e) and ({nu},{nu}{sup '}) processes also show the similar quark-hadron duality. The spin-dependent structure functions g{sub 1} and g{sub 2} of (e,e{sup '}) have also been calculated from our model. It is found that the local quark-hadron duality is not seen in the calculated g{sub 1} and g{sub 2}, while our results for g{sub 1} and some polarization observables associated with the exclusive p(e{sup {yields}},e{sup '}{pi}) and p{sup {yields}}(e{sup {yields}},e{sup '}{pi}) reactions are in reasonably good agreement with the recent data. In the study of parity violating asymmetry A of N(e{sup {yields}},e{sup '}) reactions, the relative importance between the nonresonant mechanisms and the {delta} excitation is investigated by taking into account the unitarity condition. Predictions are made for using the data of A to test the axial N-{delta} form factors determined previously in the studies of N({nu}{sub {mu}},{mu}{sup -}{pi}) reactions. The predicted asymmetry A are also compared with the parton model predictions for future experimental investigations of quark-hadron duality.« less

Decoupling the NLO-coupled QED⊗QCD, DGLAP evolution equations, using Laplace transform method

NASA Astrophysics Data System (ADS)

Mottaghizadeh, Marzieh; Eslami, Parvin; Taghavi-Shahri, Fatemeh

2017-05-01

We analytically solved the QED⊗QCD-coupled DGLAP evolution equations at leading order (LO) quantum electrodynamics (QED) and next-to-leading order (NLO) quantum chromodynamics (QCD) approximations, using the Laplace transform method and then computed the proton structure function in terms of the unpolarized parton distribution functions. Our analytical solutions for parton densities are in good agreement with those from CT14QED (1.2952 < Q2 < 1010) (Ref. 6) global parametrizations and APFEL (A PDF Evolution Library) (2 < Q2 < 108) (Ref. 4). We also compared the proton structure function, F2p(x,Q2), with the experimental data released by the ZEUS and H1 collaborations at HERA. There is a nice agreement between them in the range of low and high x and Q2.

E2F function in muscle growth is necessary and sufficient for viability in Drosophila

PubMed Central

Zappia, Maria Paula; Frolov, Maxim V.

2016-01-01

The E2F transcription factor is a key cell cycle regulator. However, the inactivation of the entire E2F family in Drosophila is permissive throughout most of animal development until pupation when lethality occurs. Here we show that E2F function in the adult skeletal muscle is essential for animal viability since providing E2F function in muscles rescues the lethality of the whole-body E2F-deficient animals. Muscle-specific loss of E2F results in a significant reduction in muscle mass and thinner myofibrils. We demonstrate that E2F is dispensable for proliferation of muscle progenitor cells, but is required during late myogenesis to directly control the expression of a set of muscle-specific genes. Interestingly, E2f1 provides a major contribution to the regulation of myogenic function, while E2f2 appears to be less important. These findings identify a key function of E2F in skeletal muscle required for animal viability, and illustrate how the cell cycle regulator is repurposed in post-mitotic cells. PMID:26823289

A multi-functional guanine derivative for studying the DNA G-quadruplex structure.

PubMed

Ishizuka, Takumi; Zhao, Pei-Yan; Bao, Hong-Liang; Xu, Yan

2017-10-23

In the present study, we developed a multi-functional guanine derivative, 8F G, as a G-quadruplex stabilizer, a fluorescent probe for the detection of G-quadruplex formation, and a 19 F sensor for the observation of the G-quadruplex. We demonstrate that the functional nucleoside bearing a 3,5-bis(trifluoromethyl)benzene group at the 8-position of guanine stabilizes the DNA G-quadruplex structure and fluoresces following the G-quadruplex formation. Furthermore, we show that the functional sensor can be used to directly observe DNA G-quadruplexes by 19 F-NMR in living cells. To our knowledge, this is the first study showing that the nucleoside derivative simultaneously allows for three kinds of functions at a single G-quadruplex DNA. Our results suggest that the multi-functional nucleoside derivative can be broadly used for studying the G-quadruplex structure and serves as a powerful tool for examining the molecular basis of G-quadruplex formation in vitro and in living cells.

Reactive Oxygen Species-Inducible ECF σ Factors of Bradyrhizobium japonicum

PubMed Central

Masloboeva, Nadezda; Reutimann, Luzia; Stiefel, Philipp; Follador, Rainer; Leimer, Nadja; Hennecke, Hauke; Mesa, Socorro; Fischer, Hans-Martin

2012-01-01

Extracytoplasmic function (ECF) σ factors control the transcription of genes involved in different cellular functions, such as stress responses, metal homeostasis, virulence-related traits, and cell envelope structure. The genome of Bradyrhizobium japonicum, the nitrogen-fixing soybean endosymbiont, encodes 17 putative ECF σ factors belonging to nine different ECF σ factor families. The genes for two of them, ecfQ (bll1028) and ecfF (blr3038), are highly induced in response to the reactive oxygen species hydrogen peroxide (H2O2) and singlet oxygen (1O2). The ecfF gene is followed by the predicted anti-σ factor gene osrA (blr3039). Mutants lacking EcfQ, EcfF plus OsrA, OsrA alone, or both σ factors plus OsrA were phenotypically characterized. While the symbiotic properties of all mutants were indistinguishable from the wild type, they showed increased sensitivity to singlet oxygen under free-living conditions. Possible target genes of EcfQ and EcfF were determined by microarray analyses, and candidate genes were compared with the H2O2-responsive regulon. These experiments disclosed that the two σ factors control rather small and, for the most part, distinct sets of genes, with about half of the genes representing 13% of the members of H2O2-responsive regulon. To get more insight into transcriptional regulation of both σ factors, the 5′ ends of ecfQ and ecfF mRNA were determined. The presence of conserved sequence motifs in the promoter region of ecfQ and genes encoding EcfQ-like σ factors in related α-proteobacteria suggests regulation via a yet unknown transcription factor. By contrast, we have evidence that ecfF is autoregulated by transcription from an EcfF-dependent consensus promoter, and its product is negatively regulated via protein-protein interaction with OsrA. Conserved cysteine residues 129 and 179 of OsrA are required for normal function of OsrA. Cysteine 179 is essential for release of EcfF from an EcfF-OsrA complex upon H2O2 stress while cysteine 129 is possibly needed for EcfF-OsrA interaction. PMID:22916258

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

Huang, Li; Wang, Yilin; Werner, Philipp

Understanding the electronic properties of actinide oxides under pressure poses a great challenge for experimental and theoretical studies. Here, we investigate the electronic structure of cubic phase uranium dioxide at different volumes using a combination of density functional theory and dynamical mean-field theory. The ab initio calculations predict an orbital-selective insulator-metal transition at a moderate pressure of ~45 GPa. At this pressure the uranium's 5f 5/2 state becomes metallic, while the 5f 7/2 state remains insulating up to about 60 GPa. In the metallic state, we observe a rapid decrease of the 5f occupation and total angular momentum with pressure.more » Simultaneously, the so-called "Zhang-Rice state", which is of predominantly 5f 5/2 character, quickly disappears after the transition into the metallic phase.« less

Peroxide Activation for Electrophilic Reactivity by the Binuclear Non-heme Iron Enzyme AurF

DOE PAGES

Park, Kiyoung; Li, Ning; Kwak, Yeonju; ...

2017-05-01

Binuclear non-heme iron enzymes activate O 2 for diverse chemistries that include oxygenation of organic substrates and hydrogen atom abstraction. This process often involves the formation of peroxo-bridged biferric intermediates, only some of which can perform electrophilic reactions. To elucidate the geometric and electronic structural requirements to activate peroxo reactivity, the active peroxo intermediate in 4-aminobenzoate N-oxygenase (AurF) has been characterized spectroscopically and computationally. A magnetic circular dichroism study of reduced AurF shows that its electronic and geometric structures are poised to react rapidly with O 2. Nuclear resonance vibrational spectroscopic definition of the peroxo intermediate formed in this reactionmore » shows that the active intermediate has a protonated peroxo bridge. Density functional theory computations on the structure established here show that the protonation activates peroxide for electrophilic/single-electron-transfer reactivity. As a result, this activation of peroxide by protonation is likely also relevant to the reactive peroxo intermediates in other binuclear non-heme iron enzymes.« less

Peroxide Activation for Electrophilic Reactivity by the Binuclear Non-heme Iron Enzyme AurF

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

Park, Kiyoung; Li, Ning; Kwak, Yeonju

Binuclear non-heme iron enzymes activate O 2 for diverse chemistries that include oxygenation of organic substrates and hydrogen atom abstraction. This process often involves the formation of peroxo-bridged biferric intermediates, only some of which can perform electrophilic reactions. To elucidate the geometric and electronic structural requirements to activate peroxo reactivity, the active peroxo intermediate in 4-aminobenzoate N-oxygenase (AurF) has been characterized spectroscopically and computationally. A magnetic circular dichroism study of reduced AurF shows that its electronic and geometric structures are poised to react rapidly with O 2. Nuclear resonance vibrational spectroscopic definition of the peroxo intermediate formed in this reactionmore » shows that the active intermediate has a protonated peroxo bridge. Density functional theory computations on the structure established here show that the protonation activates peroxide for electrophilic/single-electron-transfer reactivity. As a result, this activation of peroxide by protonation is likely also relevant to the reactive peroxo intermediates in other binuclear non-heme iron enzymes.« less

Exploring the thermal expansion of fluorides and oxyfluorides with rhenium trioxide-type structures: From negative to positive thermal expansion

NASA Astrophysics Data System (ADS)

Greve, Benjamin K.

This thesis explores the thermal expansion and high pressure behavior of some materials with the ReO3 structure type. This structure is simple and has, in principle, all of the features necessary for negative thermal expansion (NTE) arising from the transverse thermal motion of the bridging anions and the coupled rotation of rigid units; however, ReO 3 itself only exhibits mild NTE across a narrow temperature range at low temperatures. ReO3 is metallic because of a delocalized d-electron, and this may contribute to the lack of NTE in this material. The materials examined in this thesis are all based on d 0 metal ions so that the observed thermal expansion behavior should arise from vibrational, rather than electronic, effects. In Chapter 2, the thermal expansion of scandium fluoride, ScF3 , is examined using a combination of in situ synchrotron X-ray and neutron variable temperature diffraction. ScF3 retains the cubic ReO3 structure across the entire temperature range examined (10 - 1600 K) and exhibits pronounced negative thermal expansion at low temperatures. The magnitude of NTE in this material is comparable to that of cubic ZrW2O8, which is perhaps the most widely studied NTE material, at room temperature and below. This is the first report of NTE in an ReO3 type structure across a wide temperature range. Chapter 3 presents a comparison between titanium oxyfluoride, TiOF 2, and a vacancy-containing titanium hydroxyoxyfluoride, Ti x(O/OH/F)3. TiOF2 was originally reported to adopt the cubic ReO3 structure type under ambient conditions, therefore the initial goal for this study was to examine the thermal expansion of this material and determine if it displayed interesting behavior such as NTE. During the course of the study, it was discovered that the original synthetic method resulted in Tix(O/OH/F)3, which does adopt the cubic ReO3 structure type. The chemical composition of the hydroxyoxyfluoride is highly dependent upon synthesis conditions and subsequent heat treatments. This material readily pyrohydrolyizes at low temperatures (≈350 K). It was also observed that TiOF does not adopt the cubic ReO 3 structure; at room temperature it adopts a rhombohedrally distorted variant of the ReO3 structure. Positive thermal expansion was observed for TiOF2 from 120 K through decomposition into TiO2. At ≈400 K, TiOF2 undergoes a structural phase transition from rhombohedral to cubic symmetry. High pressure diffraction studies revealed a cubic to rhombohedral phase transition for Tix(O/OH/F) 3 between 0.5-1 GPa. No phase transitions were observed for TiOF 2 on compression. In Chapter 4, an in situ variable pressure-temperature diffraction experiment examining the effects of pressure on the coefficients of thermal expansion (CTE) for ScF3 and TaO2F is presented. In the manufacture and use of composites, which is a possible application for low and NTE materials, stresses may be experienced. Pressure was observed to have a negligible effect on cubic ScF3's CTE; however, for TaO 2F the application of modest pressures, such as those that might be experienced in the manufacture or use of composites, has a major effect on its CTE. This effect is associated with a pressure-induced phase transition from cubic to rhombohedral symmetry upon compression. TaO2F was prepared from the direct reaction of Ta2O5 with TaF 5 and from the digestion of Ta2O5 in hot hydrofluoric acid. The effects of pressure on the two samples of TaO2F were qualitatively similar. The slightly different properties for the samples are likely due to differences in their thermal history leading to differing arrangements of oxide and fluoride in these disordered materials. In Chapter 5, the local structures of TiOF2 and TaO2 F are examined using pair distribution functions (PDFs) obtained from X-ray total scattering experiments. In these materials, the anions (O/F) are disordered over the available anion positions. While traditional X-ray diffraction provides detailed information about the average structures of these materials, it is not sufficient to fully understand their thermal expansion. Fits of simple structural models to the low r portions of PDFs for these materials indicate the presence of geometrically distinct M -X-M (M = Ti, Ta; X = O, F) linkages, and a simple analysis of the TaO2F variable temperature PDFs indicates that these distinct links respond differently to temperature.

Jahn-Teller transition in TiF3 investigated using density-functional theory

NASA Astrophysics Data System (ADS)

Perebeinos, Vasili; Vogt, Tom

2004-03-01

We use first-principles density-functional theory to calculate the electronic and magnetic properties of TiF3 using the full-potential-linearized augmented-plane-wave method. The local density approximation (LDA) predicts a fully saturated ferromagnetic metal and finds degenerate energy minima for high- and low-symmetry structures. The experimentally observed Jahn-Teller phase transition at Tc=370 K cannot be driven by the electron-phonon interaction alone, which is usually described accurately by the LDA. Electron correlations beyond the LDA are essential to lift the degeneracy of the singly occupied Ti t2g orbital. Although the on-site Coulomb correlations are important, the direction of the t2g-level splitting is determined by dipole-dipole interactions. The LDA+U functional predicts an aniferromagnetic insulator with an orbitally ordered ground state. The input parameters U=8.1 eV and J=0.9 eV for the Ti 3d orbital were found by varying the total charge on the TiF2-6 ion using the molecular NRLMOL code. We estimate the Heisenberg exchange constant for spin 1/2 on a cubic lattice to be approximately 24 K. The symmetry lowering energy in LDA+U is about 900 K per TiF3 formula unit.

Quantum-chemical study of the effect of ligands on the structure and properties of gold clusters

NASA Astrophysics Data System (ADS)

Golosnaya, M. N.; Pichugina, D. A.; Oleinichenko, A. V.; Kuz'menko, N. E.

2017-02-01

The structures of [Au4(dpmp)2X2]2+clusters, where X =-C≡CH,-CH3,-SCH3,-F,-Cl,-Br,-I, dpmp is bis((diphenylphosphino)methyl)(phenyl)phosphine, are calculated at the level of density functional theory with the PBE functional and a modified Dirac-Coulomb-Breit Hamiltonian in an all-electron basis set (Λ). Using the example of [Au4(dpmp)2(C≡CC6H5)2]2+, the interatomic distances and bond angles calculated by means of PBE0/LANL2DZ, TPSS/LANL2DZ, TPSSh/LANL2DZ, and PBE/Λ are compared to X-ray crystallography data. It is shown that PBE/Λ yields the most accurate calculation of the geometrical parameters of this cluster. The ligand effect on the electronic stability of a cluster and the stability in reactions of decomposition into different fragments is studied, along with the capability of ligand exchange. Stability is predicted for [Au4(dpmp)2F2]2+ and [Au4(dpmp)2(SCH3)2]2+, while [Au4(dpmp)2I2]2+ cluster is unstable and its decomposes into two identical fragments is supposed.

Structure and function of Neisseria gonorrhoeae MtrF illuminates a class of antimetabolite efflux pumps

DOE PAGES

Su, Chih -Chia; Bolla, Jani  Reddy; Kumar, Nitin; ...

2015-04-01

Neisseria gonorrhoeae is an obligate human pathogen and the causative agent of the sexually transmitted disease gonorrhea. The control of this disease has been compromised by the increasing proportion of infections due to antibiotic-resistant strains, which are growing at an alarming rate. N. gonorrhoeae MtrF is an integral membrane protein that belongs to the AbgT family of transporters for which no structural information is available. Here, we describe the crystal structure of MtrF, revealing a dimeric molecule with architecture distinct from all other families of transporters. MtrF is a bowl-shaped dimer with a solvent-filled basin extending from the cytoplasm tomore » halfway across the membrane bilayer. Each subunit of the transporter contains nine transmembrane helices and two hairpins, posing a plausible pathway for substrate transport. A combination of the crystal structure and biochemical functional assays suggests that MtrF is an antibiotic efflux pump mediating bacterial resistance to sulfonamide antimetabolite drugs.« less

Structure and function of Neisseria gonorrhoeae MtrF illuminates a class of antimetabolite efflux pumps

PubMed Central

Su, Chih-Chia; Bolla, Jani Reddy; Kumar, Nitin; Radhakrishnan, Abhijith; Long, Feng; Delmar, Jared A.; Chou, Tsung-Han; Rajashankar, Kanagalaghatta R.; Shafer, William M.; Yu, Edward W.

2015-01-01

SUMMARY Neisseria gonorrhoeae is an obligate human pathogen and the causative agent of the sexually-transmitted disease gonorrhea. The control of this disease has been compromised by the increasing proportion of infections due to antibiotic-resistant strains, which are growing at an alarming rate. N. gonorrhoeae MtrF is an integral membrane protein, which belongs to the AbgT family of transporters for which no structural information is available. Here we describe the crystal structure of MtrF, revealing a dimeric molecule with architecture distinct from all other families of transporters. MtrF is a bowl-shaped dimer with a solvent-filled basin extending from the cytoplasm to halfway across the membrane bilayer. Each subunit of the transporter contains nine transmembrane helices and two hairpins, posing a plausible pathway for substrate transport. A combination of the crystal structure and biochemical functional assays suggests that MtrF is an antibiotic efflux pump, mediating bacterial resistance to sulfonamide antimetabolite drugs. PMID:25818299

Genomic structure, expression pattern, and functional characterization of transcription factor E2F-2 from black tiger shrimp (Penaeus monodon)

PubMed Central

Zhao, Chao; Qiu, Lihua

2017-01-01

Transcription factor E2F-2 is a regulator of cell cycle. Researchers identified E2F-2 genes from yeasts to humans, but few reports investigated E2F-2 gene from black tiger shrimp. In the present study, we cloned E2F-2 gene from black tiger shrimp (Penaeus monodon). Full-length PmE2F-2 complementary DNA sequence measures 3,189 bp with an open reading frame of 1,371 bp. Complete PmE2F-2 genomic sequence (17,305 bp) of P. monodon contains nine exons, which are separated by eight introns. Quantitative real-time polymerase chain reaction (qRT-PCR) analysis indicated that PmE2F-2 is highly expressed in hepatopancreas and ovaries of P. monodon. Highest PmE2F-2 expression levels were observed in stage III ovarian development of P. monodon. PmE2F-2 expression levels were significantly augmented in ovaries of P. monodon after 5-hydroxytryptamine injection and eyestalk ablation. RNA interference experiments were conducted to examine PmE2F-2, PmCDK2, and PmCyclin E expression profiles. PmE2F-2 was successfully knocked down in ovaries and hepatopancreas via double-stranded RNA (dsRNA)–E2F-2 injection. In the same organs, PmE2F-2 expression localization and level were investigated through in situ hybridization, which revealed consistent results with those of qRT-PCR. After dsRNA—E2F-2 injection, gonadosomatic index of shrimp was significantly lower than those following dsRNA—GFP and phosphate-buffered solution injections. Therefore, PmE2F-2 may be involved in ovarian maturation in P. monodon. PMID:28558060

Joint representation of consistent structural and functional profiles for identification of common cortical landmarks.

PubMed

Zhang, Shu; Zhao, Yu; Jiang, Xi; Shen, Dinggang; Liu, Tianming

2018-06-01

In the brain mapping field, there have been significant interests in representation of structural/functional profiles to establish structural/functional landmark correspondences across individuals and populations. For example, from the structural perspective, our previous studies have identified hundreds of consistent DICCCOL (dense individualized and common connectivity-based cortical landmarks) landmarks across individuals and populations, each of which possess consistent DTI-derived fiber connection patterns. From the functional perspective, a large collection of well-characterized HAFNI (holistic atlases of functional networks and interactions) networks based on sparse representation of whole-brain fMRI signals have been identified in our prior studies. However, due to the remarkable variability of structural and functional architectures in the human brain, it is challenging for earlier studies to jointly represent the connectome-scale structural and functional profiles for establishing a common cortical architecture which can comprehensively encode both structural and functional characteristics across individuals. To address this challenge, we propose an effective computational framework to jointly represent the structural and functional profiles for identification of consistent and common cortical landmarks with both structural and functional correspondences across different brains based on DTI and fMRI data. Experimental results demonstrate that 55 structurally and functionally common cortical landmarks can be successfully identified.

Pressure-driven insulator-metal transition in cubic phase UO 2

DOE PAGES

Huang, Li; Wang, Yilin; Werner, Philipp

2017-09-21

Understanding the electronic properties of actinide oxides under pressure poses a great challenge for experimental and theoretical studies. Here, we investigate the electronic structure of cubic phase uranium dioxide at different volumes using a combination of density functional theory and dynamical mean-field theory. The ab initio calculations predict an orbital-selective insulator-metal transition at a moderate pressure of ~45 GPa. At this pressure the uranium's 5f 5/2 state becomes metallic, while the 5f 7/2 state remains insulating up to about 60 GPa. In the metallic state, we observe a rapid decrease of the 5f occupation and total angular momentum with pressure.more » Simultaneously, the so-called "Zhang-Rice state", which is of predominantly 5f 5/2 character, quickly disappears after the transition into the metallic phase.« less

Pressure-driven insulator-metal transition in cubic phase UO2

NASA Astrophysics Data System (ADS)

Huang, Li; Wang, Yilin; Werner, Philipp

2017-09-01

Understanding the electronic properties of actinide oxides under pressure poses a great challenge for experimental and theoretical studies. Here, we investigate the electronic structure of cubic phase uranium dioxide at different volumes using a combination of density functional theory and dynamical mean-field theory. The ab initio calculations predict an orbital-selective insulator-metal transition at a moderate pressure of ∼45 GPa. At this pressure the uranium's 5f 5/2 state becomes metallic, while the 5f 7/2 state remains insulating up to about 60 GPa. In the metallic state, we observe a rapid decrease of the 5f occupation and total angular momentum with pressure. Simultaneously, the so-called “Zhang-Rice state”, which is of predominantly 5f 5/2 character, quickly disappears after the transition into the metallic phase.

Materials Data on Ca(AuF6)2 (SG:115) by Materials Project

DOE Data Explorer

Kristin Persson

2016-02-04

Computed materials data using density functional theory calculations. These calculations determine the electronic structure of bulk materials by solving approximations to the Schrodinger equation. For more information, see https://materialsproject.org/docs/calculations

Materials Data on AgP(XeF5)2 (SG:140) by Materials Project

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

Kristin Persson

2014-07-09

Computed materials data using density functional theory calculations. These calculations determine the electronic structure of bulk materials by solving approximations to the Schrodinger equation. For more information, see https://materialsproject.org/docs/calculations

Materials Data on Mg(AuF4)2 (SG:14) by Materials Project

DOE Data Explorer

Kristin Persson

2016-02-04

Computed materials data using density functional theory calculations. These calculations determine the electronic structure of bulk materials by solving approximations to the Schrodinger equation. For more information, see https://materialsproject.org/docs/calculations

Materials Data on K2PdF4 (SG:12) by Materials Project

DOE Data Explorer

Kristin Persson

2014-11-02

Computed materials data using density functional theory calculations. These calculations determine the electronic structure of bulk materials by solving approximations to the Schrodinger equation. For more information, see https://materialsproject.org/docs/calculations

Materials Data on AsS(ClF2)3 (SG:19) by Materials Project

DOE Data Explorer

Kristin Persson

2014-07-09

Computed materials data using density functional theory calculations. These calculations determine the electronic structure of bulk materials by solving approximations to the Schrodinger equation. For more information, see https://materialsproject.org/docs/calculations

Materials Data on AsS(BrF2)3 (SG:14) by Materials Project

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

Kristin Persson

2016-07-14

Computed materials data using density functional theory calculations. These calculations determine the electronic structure of bulk materials by solving approximations to the Schrodinger equation. For more information, see https://materialsproject.org/docs/calculations

Materials Data on LiCu2F5 (SG:133) by Materials Project

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

Kristin Persson

2016-02-05

Computed materials data using density functional theory calculations. These calculations determine the electronic structure of bulk materials by solving approximations to the Schrodinger equation. For more information, see https://materialsproject.org/docs/calculations

Materials Data on BeTl2F4 (SG:62) by Materials Project

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

Kristin Persson

2014-07-09

Computed materials data using density functional theory calculations. These calculations determine the electronic structure of bulk materials by solving approximations to the Schrodinger equation. For more information, see https://materialsproject.org/docs/calculations

Materials Data on Cs2KAgF6 (SG:225) by Materials Project

DOE Data Explorer

Kristin Persson

2014-11-02

Computed materials data using density functional theory calculations. These calculations determine the electronic structure of bulk materials by solving approximations to the Schrodinger equation. For more information, see https://materialsproject.org/docs/calculations

Materials Data on BaEr2F8 (SG:12) by Materials Project

DOE Data Explorer

Kristin Persson

2014-11-02

Computed materials data using density functional theory calculations. These calculations determine the electronic structure of bulk materials by solving approximations to the Schrodinger equation. For more information, see https://materialsproject.org/docs/calculations

Materials Data on Cs2AgF4 (SG:139) by Materials Project

DOE Data Explorer

Kristin Persson

2014-11-02

Computed materials data using density functional theory calculations. These calculations determine the electronic structure of bulk materials by solving approximations to the Schrodinger equation. For more information, see https://materialsproject.org/docs/calculations

Materials Data on Rb2SiF6 (SG:225) by Materials Project

DOE Data Explorer

Kristin Persson

2014-11-02

Computed materials data using density functional theory calculations. These calculations determine the electronic structure of bulk materials by solving approximations to the Schrodinger equation. For more information, see https://materialsproject.org/docs/calculations

Materials Data on CaB2F8 (SG:61) by Materials Project

DOE Data Explorer

Kristin Persson

2014-11-02

Computed materials data using density functional theory calculations. These calculations determine the electronic structure of bulk materials by solving approximations to the Schrodinger equation. For more information, see https://materialsproject.org/docs/calculations

Materials Data on Na2MgInF7 (SG:62) by Materials Project

DOE Data Explorer

Kristin Persson

2014-11-02

Computed materials data using density functional theory calculations. These calculations determine the electronic structure of bulk materials by solving approximations to the Schrodinger equation. For more information, see https://materialsproject.org/docs/calculations

Materials Data on BaGaBO3F2 (SG:176) by Materials Project

DOE Data Explorer

Kristin Persson

2014-11-02

Computed materials data using density functional theory calculations. These calculations determine the electronic structure of bulk materials by solving approximations to the Schrodinger equation. For more information, see https://materialsproject.org/docs/calculations

Materials Data on K2SiF6 (SG:186) by Materials Project

DOE Data Explorer

Kristin Persson

2014-11-02

Computed materials data using density functional theory calculations. These calculations determine the electronic structure of bulk materials by solving approximations to the Schrodinger equation. For more information, see https://materialsproject.org/docs/calculations

Materials Data on BaAlBO3F2 (SG:176) by Materials Project

DOE Data Explorer

Kristin Persson

2014-11-02

Computed materials data using density functional theory calculations. These calculations determine the electronic structure of bulk materials by solving approximations to the Schrodinger equation. For more information, see https://materialsproject.org/docs/calculations

Materials Data on BaZnCO3F2 (SG:176) by Materials Project

DOE Data Explorer

Kristin Persson

2014-11-02

Computed materials data using density functional theory calculations. These calculations determine the electronic structure of bulk materials by solving approximations to the Schrodinger equation. For more information, see https://materialsproject.org/docs/calculations

Materials Data on K2ZrF6 (SG:63) by Materials Project

DOE Data Explorer

Kristin Persson

2014-11-02

Computed materials data using density functional theory calculations. These calculations determine the electronic structure of bulk materials by solving approximations to the Schrodinger equation. For more information, see https://materialsproject.org/docs/calculations

Materials Data on Na2MgPO4F (SG:60) by Materials Project

DOE Data Explorer

Kristin Persson

2014-11-02

Computed materials data using density functional theory calculations. These calculations determine the electronic structure of bulk materials by solving approximations to the Schrodinger equation. For more information, see https://materialsproject.org/docs/calculations

Materials Data on TiTl2F6 (SG:164) by Materials Project

DOE Data Explorer

Kristin Persson

2014-11-02

Computed materials data using density functional theory calculations. These calculations determine the electronic structure of bulk materials by solving approximations to the Schrodinger equation. For more information, see https://materialsproject.org/docs/calculations

Materials Data on KRb2GaF6 (SG:225) by Materials Project

DOE Data Explorer

Kristin Persson

2014-11-02

Computed materials data using density functional theory calculations. These calculations determine the electronic structure of bulk materials by solving approximations to the Schrodinger equation. For more information, see https://materialsproject.org/docs/calculations

Materials Data on K2IrF6 (SG:164) by Materials Project

DOE Data Explorer

Kristin Persson

2014-11-02

Computed materials data using density functional theory calculations. These calculations determine the electronic structure of bulk materials by solving approximations to the Schrodinger equation. For more information, see https://materialsproject.org/docs/calculations

Materials Data on Na2PO3F (SG:19) by Materials Project

DOE Data Explorer

Kristin Persson

2014-11-02

Computed materials data using density functional theory calculations. These calculations determine the electronic structure of bulk materials by solving approximations to the Schrodinger equation. For more information, see https://materialsproject.org/docs/calculations

Materials Data on Tl2SnF6 (SG:164) by Materials Project

DOE Data Explorer

Kristin Persson

2014-11-02

Computed materials data using density functional theory calculations. These calculations determine the electronic structure of bulk materials by solving approximations to the Schrodinger equation. For more information, see https://materialsproject.org/docs/calculations

Materials Data on LiV2O5F (SG:18) by Materials Project

DOE Data Explorer

Kristin Persson

2014-07-09

Computed materials data using density functional theory calculations. These calculations determine the electronic structure of bulk materials by solving approximations to the Schrodinger equation. For more information, see https://materialsproject.org/docs/calculations

Materials Data on NaSn2F5 (SG:133) by Materials Project

DOE Data Explorer

Kristin Persson

2014-11-02

Computed materials data using density functional theory calculations. These calculations determine the electronic structure of bulk materials by solving approximations to the Schrodinger equation. For more information, see https://materialsproject.org/docs/calculations

Materials Data on Sn2ClF3 (SG:198) by Materials Project

DOE Data Explorer

Kristin Persson

2014-11-02

Computed materials data using density functional theory calculations. These calculations determine the electronic structure of bulk materials by solving approximations to the Schrodinger equation. For more information, see https://materialsproject.org/docs/calculations

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

Zhu, Jia, E-mail: jia-zhu@jxnu.edu.cn, E-mail: zhangyf@fzu.edu.cn; Zhang, Hui; Tong, Yawen

The structures and electronic properties of bimetallic oxide CrW{sub 2}O{sub 9} clusters supported on the perfect and defective MgO(001) surfaces with three different color centers, F{sub S}{sup 0}, F{sub S}{sup +}, and F{sub S}{sup 2+} centers, respectively, have been investigated by density functional theory calculations. Our results show that the configurations, adsorption energies, charge transfers, and bonding modes of dispersed CrW{sub 2}O{sub 9} clusters are sensitive to the charge states of the F{sub S} centers. Compared with the gas-phase configuration, the CrW{sub 2}O{sub 9} clusters supported on the defective surfaces are distorted dramatically, which exhibit different chain structures. On themore » perfect MgO surface, the depositions of clusters do not involve obvious charge transfer, while the situation is quite different on the defective MgO(001) surfaces in which significant electron transfer occurs from the surface to the cluster. Interestingly, this effect becomes more remarkable for electron-rich oxygen vacancies (F{sub S}{sup 0} center) than that for electron-poor oxygen vacancies (F{sub S}{sup +} and F{sub S}{sup 2+} centers). Furthermore, our work reveals a progressive Brønsted acid sites where spin density preferentially localized around the Cr atoms not the W atoms for all kinds of F{sub S}-centers, indicating the better catalytic activities can be expected for CrW{sub 2}O{sub 9} cluster on defective MgO(001) surfaces with respect to the W{sub 3}O{sub 9} cluster.« less

Structure of the F–actin–tropomyosin complex

PubMed Central

von der Ecken, Julian; Müller, Mirco; Lehman, William; Manstein, Dietmar J.; Penczek, Pawel A.; Raunser, Stefan

2015-01-01

Filamentous actin (F-actin) is the major protein of muscle thin filaments, and actin microfilaments are the main component of the eukaryotic cytoskeleton. Mutations in different actin isoforms lead to early-onset autosomal dominant non-syndromic hearing loss1, familial thoracic aortic aneurysms and dissections2, and multiple variations of myopathies3. In striated muscle fibres, the binding of myosin motors to actin filaments is mainly regulated by tropomyosin and troponin4,5. Tropomyosin also binds to F-actin in smooth muscle and in non-muscle cells and stabilizes and regulates the filaments there in the absence of troponin6. Although crystal structures for monomeric actin (G-actin) are available7, a high-resolution structure of F-actin is still missing, hampering our understanding of how disease-causing mutations affect the function of thin muscle filaments and microfilaments. Here we report the three-dimensional structure of F-actin at a resolution of 3.7 ångstroms in complex with tropomyosin at a resolution of 6.5ångstroms, determined by electron cryomicroscopy. The structure reveals that the D-loop is ordered and acts as a central region for hydrophobic and electrostatic interactions that stabilize the F-actin filament. We clearly identify the density corresponding to ADP and Mg2+ and explain the possible effect of prominent disease-causing mutants. A comparison of F-actin with G-actin reveals the conformational changes during filament formation and identifies the D-loop as their key mediator. We also confirm that negatively charged tropomyosin interacts with a positively charged groove on F-actin. Comparison of the position of tropomyosin in F-actin–tropomyosin with its position in our previously determined actin–tropomyosin–myosin structure8 reveals a myosin-induced transition of tropomyosin. Our results allow us to understand the role of individual mutations in the genesis of actin- and tropomyosin-related diseases and will serve as a strong foundation for the targeted development of drugs. PMID:25470062

Oxygen dose responsiveness of human fetal airway smooth muscle cells.

PubMed

Hartman, William R; Smelter, Dan F; Sathish, Venkatachalem; Karass, Michael; Kim, Sunchin; Aravamudan, Bharathi; Thompson, Michael A; Amrani, Yassine; Pandya, Hitesh C; Martin, Richard J; Prakash, Y S; Pabelick, Christina M

2012-10-15

Maintenance of blood oxygen saturation dictates supplemental oxygen administration to premature infants, but hyperoxia predisposes survivors to respiratory diseases such as asthma. Although much research has focused on oxygen effects on alveoli in the setting of bronchopulmonary dysplasia, the mechanisms by which oxygen affects airway structure or function relevant to asthma are still under investigation. We used isolated human fetal airway smooth muscle (fASM) cells from 18-20 postconceptual age lungs (canalicular stage) to examine oxygen effects on intracellular Ca(2+) ([Ca(2+)](i)) and cellular proliferation. fASM cells expressed substantial smooth muscle actin and myosin and several Ca(2+) regulatory proteins but not fibroblast or epithelial markers, profiles qualitatively comparable to adult human ASM. Fluorescence Ca(2+) imaging showed robust [Ca(2+)](i) responses to 1 μM acetylcholine (ACh) and 10 μM histamine (albeit smaller and slower than adult ASM), partly sensitive to zero extracellular Ca(2+). Compared with adult, fASM showed greater baseline proliferation. Based on this validation, we assessed fASM responses to 10% hypoxia through 90% hyperoxia and found enhanced proliferation at <60% oxygen but increased apoptosis at >60%, effects accompanied by appropriate changes in proliferative vs. apoptotic markers and enhanced mitochondrial fission at >60% oxygen. [Ca(2+)](i) responses to ACh were enhanced for <60% but blunted at >60% oxygen. These results suggest that hyperoxia has dose-dependent effects on structure and function of developing ASM, which could have consequences for airway diseases of childhood. Thus detrimental effects on ASM should be an additional consideration in assessing risks of supplemental oxygen in prematurity.

Oxygen dose responsiveness of human fetal airway smooth muscle cells

PubMed Central

Hartman, William R.; Smelter, Dan F.; Sathish, Venkatachalem; Karass, Michael; Kim, Sunchin; Aravamudan, Bharathi; Thompson, Michael A.; Amrani, Yassine; Pandya, Hitesh C.; Martin, Richard J.; Prakash, Y. S.

2012-01-01

Maintenance of blood oxygen saturation dictates supplemental oxygen administration to premature infants, but hyperoxia predisposes survivors to respiratory diseases such as asthma. Although much research has focused on oxygen effects on alveoli in the setting of bronchopulmonary dysplasia, the mechanisms by which oxygen affects airway structure or function relevant to asthma are still under investigation. We used isolated human fetal airway smooth muscle (fASM) cells from 18–20 postconceptual age lungs (canalicular stage) to examine oxygen effects on intracellular Ca2+ ([Ca2+]i) and cellular proliferation. fASM cells expressed substantial smooth muscle actin and myosin and several Ca2+ regulatory proteins but not fibroblast or epithelial markers, profiles qualitatively comparable to adult human ASM. Fluorescence Ca2+ imaging showed robust [Ca2+]i responses to 1 μM acetylcholine (ACh) and 10 μM histamine (albeit smaller and slower than adult ASM), partly sensitive to zero extracellular Ca2+. Compared with adult, fASM showed greater baseline proliferation. Based on this validation, we assessed fASM responses to 10% hypoxia through 90% hyperoxia and found enhanced proliferation at <60% oxygen but increased apoptosis at >60%, effects accompanied by appropriate changes in proliferative vs. apoptotic markers and enhanced mitochondrial fission at >60% oxygen. [Ca2+]i responses to ACh were enhanced for <60% but blunted at >60% oxygen. These results suggest that hyperoxia has dose-dependent effects on structure and function of developing ASM, which could have consequences for airway diseases of childhood. Thus detrimental effects on ASM should be an additional consideration in assessing risks of supplemental oxygen in prematurity. PMID:22923637

Pushing spatial and temporal resolution for functional and diffusion MRI in the Human Connectome Project

PubMed Central

Uğurbil, Kamil; Xu, Junqian; Auerbach, Edward J.; Moeller, Steen; Vu, An; Duarte-Carvajalino, Julio M.; Lenglet, Christophe; Wu, Xiaoping; Schmitter, Sebastian; Van de Moortele, Pierre Francois; Strupp, John; Sapiro, Guillermo; De Martino, Federico; Wang, Dingxin; Harel, Noam; Garwood, Michael; Chen, Liyong; Feinberg, David A.; Smith, Stephen M.; Miller, Karla L.; Sotiropoulos, Stamatios N; Jbabdi, Saad; Andersson, Jesper L; Behrens, Timothy EJ; Glasser, Matthew F.; Van Essen, David; Yacoub, Essa

2013-01-01

The human connectome project (HCP) relies primarily on three complementary magnetic resonance (MR) methods. These are: 1) resting state functional MR imaging (rfMRI) which uses correlations in the temporal fluctuations in an fMRI time series to deduce ‘functional connectivity’; 2) diffusion imaging (dMRI), which provides the input for tractography algorithms used for the reconstruction of the complex axonal fiber architecture; and 3) task based fMRI (tfMRI), which is employed to identify functional parcellation in the human brain in order to assist analyses of data obtained with the first two methods. We describe technical improvements and optimization of these methods as well as instrumental choices that impact speed of acquisition of fMRI and dMRI images at 3 Tesla, leading to whole brain coverage with 2 mm isotropic resolution in 0.7 second for fMRI, and 1.25 mm isotropic resolution dMRI data for tractography analysis with three-fold reduction in total data acquisition time. Ongoing technical developments and optimization for acquisition of similar data at 7 Tesla magnetic field are also presented, targeting higher resolution, specificity of functional imaging signals, mitigation of the inhomogeneous radio frequency (RF) fields and power deposition. Results demonstrate that overall, these approaches represent a significant advance in MR imaging of the human brain to investigate brain function and structure. PMID:23702417

Origin of the SN2 benzylic effect.

PubMed

Galabov, Boris; Nikolova, Valia; Wilke, Jeremiah J; Schaefer, Henry F; Allen, Wesley D

2008-07-30

The S N2 identity exchange reactions of the fluoride ion with benzyl fluoride and 10 para-substituted derivatives (RC6H 4CH 2F, R = CH3, OH, OCH 3, NH2, F, Cl, CCH, CN, COF, and NO2) have been investigated by both rigorous ab initio methods and carefully calibrated density functional theory. Groundbreaking focal-point computations were executed for the C6H5CH 2F + F (-) and C 6H 5CH2Cl + Cl (-) SN2 reactions at the highest possible levels of electronic structure theory, employing complete basis set (CBS) extrapolations of aug-cc-pV XZ (X = 2-5) Hartree-Fock and MP2 energies, and including higher-order electron correlation via CCSD/aug-cc-pVQZ and CCSD(T)/aug-cc-pVTZ coupled cluster wave functions. Strong linear dependences are found between the computed electrostatic potential at the reaction-center carbon atom and the effective SN2 activation energies within the series of para-substituted benzyl fluorides. An activation strain energy decomposition indicates that the SN2 reactivity of these benzylic compounds is governed by the intrinsic electrostatic interaction between the reacting fragments. The delocalization of nucleophilic charge into the aromatic ring in the SN2 transition states is quite limited and should not be considered the origin of benzylic acceleration of SN2 reactions. Our rigorous focal-point computations validate the benzylic effect by establishing SN2 barriers for (F (-), Cl (-)) identity exchange in (C6H5CH2F, C6H 5CH2Cl) that are lower than those of (CH3F, CH3Cl) by (3.8, 1.6) kcal mol (-1), in order.

Improved hole-injection and power efficiency of organic light-emitting diodes using an ultrathin cerium fluoride buffer layer

NASA Astrophysics Data System (ADS)

Lu, Hsin-Wei; Kao, Po-Ching; Chu, Sheng-Yuan

2016-09-01

In this study, the efficiency of organic light-emitting diodes (OLEDs) was enhanced by depositing a CeF3 film as an ultra-thin buffer layer between the ITO and NPB hole transport layer, with the structure configuration ITO/CeF3 (1 nm)/NPB (40 nm)/Alq3 (60 nm)/LiF (1 nm)/Al (150 nm). The enhancement mechanism was systematically investigated via several approaches. The work function increased from 4.8 eV (standard ITO electrode) to 5.2 eV (1-nm-thick UV-ozone treated CeF3 film deposited on the ITO electrode). The turn-on voltage decreased from 4.2 V to 4.0 V at 1 mA/cm2, the luminance increased from 7588 cd/m2 to 10820 cd/m2, and the current efficiency increased from 3.2 cd/A to 3.5 cd/A when the 1-nm-thick UV-ozone treated CeF3 film was inserted into the OLEDs.

Behavior of Halogen Bonds of the Y-X⋅⋅⋅π Type (X, Y=F, Cl, Br, I) in the Benzene π System, Elucidated by Using a Quantum Theory of Atoms in Molecules Dual-Functional Analysis.

PubMed

Sugibayashi, Yuji; Hayashi, Satoko; Nakanishi, Waro

2016-08-18

The nature of halogen bonds of the Y-X-✶-π(C6 H6 ) type (X, Y=F, Cl, Br, and I) have been elucidated by using the quantum theory of atoms in molecules (QTAIM) dual-functional analysis (QTAIM-DFA), which we proposed recently. Asterisks (✶) emphasize the presence of bond-critical points (BCPs) in the interactions in question. Total electron energy densities, Hb (rc ), are plotted versus Hb (rc )-Vb (rc )/2 [=(ħ(2) /8m)∇(2) ρb (rc )] for the interactions in QTAIM-DFA, in which Vb (rc ) are potential energy densities at the BCPs. Data for perturbed structures around fully optimized structures were used for the plots, in addition to those of the fully optimized ones. The plots were analyzed by using the polar (R, θ) coordinate for the data of fully optimized structures with (θp , κp ) for those that contained the perturbed structures; θp corresponds to the tangent line of the plot and κp is the curvature. Whereas (R, θ) corresponds to the static nature, (θp , κp ) represents the dynamic nature of the interactions. All interactions in Y-X-✶-π(C6 H6 ) are classified by pure closed-shell interactions and characterized to have vdW nature, except for Y-I-✶-π(C6 H6 ) (Y=F, Cl, Br) and F-Br-✶-π(C6 H6 ), which have typical hydrogen-bond nature without covalency. I-I-✶-π(C6 H6 ) has a borderline nature between the two. Y-F-✶-π(C6 H6 ) (Y=Br, I) were optimized as bent forms, in which Y-✶-π interactions were detected. The Y-✶-π interactions in the bent forms are predicted to be substantially weaker than those in the linear F-Y-✶-π(C6 H6 ) forms. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Synthesis, crystal structure, Hirshfeld surface analysis, spectroscopic characterization, reactivity study by DFT and MD approaches and molecular docking study of a novel chalcone derivative

NASA Astrophysics Data System (ADS)

Arshad, Suhana; Pillai, Renjith Raveendran; Zainuri, Dian Alwani; Khalib, Nuridayanti Che; Razak, Ibrahim Abdul; Armaković, Stevan; Armaković, Sanja J.; Panicker, C. Yohannan; Van Alsenoy, C.

2017-05-01

In the present study, the title compound named as (E)-1-(4-bromophenyl)-3-(4-(trifluoromethyl)phenyl)prop-2-en-1-one was synthesized and structurally characterized by single-crystal X-ray diffraction. The compound crystallizes in monoclinic crystal system in P21/c space group, unit cell parameters a = 16.7629 (12) Å, b = 13.9681 (10) Å, c = 5.8740 (4) Å, β = 96.3860 (12)° and Z = 4. Hirshfeld surface analysis revealed that the molecular structure is dominated by H⋯H, C⋯H/H⋯C, Br⋯F/F⋯Br and F⋯F contacts. The FT-IR spectrum was recorded and interpreted in details with the aid of Density Functional Theory (DFT) calculations and Potential Energy Distribution (PED) analysis. Average local ionization energies (ALIE) and Fukui functions have been used as quantum-molecular descriptors to locate the molecule sites that could be of importance from the aspect of reactivity. Degradation properties have been assessed by calculations of bond dissociation energies (BDE) for hydrogen abstraction and the rest of the single acyclic bonds, while molecular dynamics (MD) simulations were used in order to calculate radial distribution functions and determine the atoms with significant interactions with water. In order to understand how the title molecule inhibits and hence increases the catalytic efficiency of MOA-B enzyme, molecular docking study was performed.

An in situ polymerization approach for the synthesis of superhydrophobic and superoleophilic nanofibrous membranes for oil-water separation.

PubMed

Shang, Yanwei; Si, Yang; Raza, Aikifa; Yang, Liping; Mao, Xue; Ding, Bin; Yu, Jianyong

2012-12-21

Superhydrophobic and superoleophilic nanofibrous membranes exhibiting robust oil-water separation performance were prepared by a facile combination of electrospun cellulose acetate (CA) nanofibers and a novel in situ polymerized fluorinated polybenzoxazine (F-PBZ) functional layer that incorporated silica nanoparticles (SiO(2) NPs). By employing the F-PBZ/SiO(2) NPs modification, the pristine hydrophilic CA nanofibrous membranes were endowed with a superhydrophobicity with the water contact angle of 161° and a superoleophilicity with the oil contact angle of 3°. Surface morphological studies have indicated that the wettability of resultant membranes could be manipulated by tuning the surface composition as well as the hierarchical structures. The quantitative hierarchical roughness analysis using the N(2) adsorption method has confirmed the major contribution of SiO(2) NPs on enhancing the porous structure, and a detailed correlation between roughness and solid-liquid interface pinning is proposed. Furthermore, the as-prepared membranes exhibited fast and efficient separation for oil-water mixtures and excellent stability over a wide range of pH conditions, which would make them a good candidate in industrial oil-polluted water treatments and oil spill cleanup, and also provided a new insight into the design and development of functional nanofibrous membranes through F-PBZ modification.

Removal of distal protein–water hydrogen bonds in a plant epoxide hydrolase increases catalytic turnover but decreases thermostability

PubMed Central

Thomaeus, Ann; Naworyta, Agata; Mowbray, Sherry L.; Widersten, Mikael

2008-01-01

A putative proton wire in potato soluble epoxide hydrolase 1, StEH1, was identified and investigated by means of site-directed mutagenesis, steady-state kinetic measurements, temperature inactivation studies, and X-ray crystallography. The chain of hydrogen bonds includes five water molecules coordinated through backbone carbonyl oxygens of Pro186, Leu266, His269, and the His153 imidazole. The hydroxyl of Tyr149 is also an integrated component of the chain, which leads to the hydroxyl of Tyr154. Available data suggest that Tyr154 functions as a final proton donor to the anionic alkylenzyme intermediate formed during catalysis. To investigate the role of the putative proton wire, mutants Y149F, H153F, and Y149F/H153F were constructed and purified. The structure of the Y149F mutant was solved by molecular replacement and refined to 2.0 Å resolution. Comparison with the structure of wild-type StEH1 revealed only subtle structural differences. The hydroxyl group lost as a result of the mutation was replaced by a water molecule, thus maintaining a functioning hydrogen bond network in the proton wire. All mutants showed decreased catalytic efficiencies with the R,R-enantiomer of trans-stilbene oxide, whereas with the S,S-enantiomer, k cat/K M was similar or slightly increased compared with the wild-type reactions. k cat for the Y149F mutant with either TSO enantiomer was increased; thus the lowered enzyme efficiencies were due to increases in K M. Thermal inactivation studies revealed that the mutated enzymes were more sensitive to elevated temperatures than the wild-type enzyme. Hence, structural alterations affecting the hydrogen bond chain caused increases in k cat but lowered thermostability. PMID:18515642

Removal of distal protein-water hydrogen bonds in a plant epoxide hydrolase increases catalytic turnover but decreases thermostability.

PubMed

Thomaeus, Ann; Naworyta, Agata; Mowbray, Sherry L; Widersten, Mikael

2008-07-01

A putative proton wire in potato soluble epoxide hydrolase 1, StEH1, was identified and investigated by means of site-directed mutagenesis, steady-state kinetic measurements, temperature inactivation studies, and X-ray crystallography. The chain of hydrogen bonds includes five water molecules coordinated through backbone carbonyl oxygens of Pro(186), Leu(266), His(269), and the His(153) imidazole. The hydroxyl of Tyr(149) is also an integrated component of the chain, which leads to the hydroxyl of Tyr(154). Available data suggest that Tyr(154) functions as a final proton donor to the anionic alkylenzyme intermediate formed during catalysis. To investigate the role of the putative proton wire, mutants Y149F, H153F, and Y149F/H153F were constructed and purified. The structure of the Y149F mutant was solved by molecular replacement and refined to 2.0 A resolution. Comparison with the structure of wild-type StEH1 revealed only subtle structural differences. The hydroxyl group lost as a result of the mutation was replaced by a water molecule, thus maintaining a functioning hydrogen bond network in the proton wire. All mutants showed decreased catalytic efficiencies with the R,R-enantiomer of trans-stilbene oxide, whereas with the S,S-enantiomer, k (cat)/K (M) was similar or slightly increased compared with the wild-type reactions. k (cat) for the Y149F mutant with either TSO enantiomer was increased; thus the lowered enzyme efficiencies were due to increases in K (M). Thermal inactivation studies revealed that the mutated enzymes were more sensitive to elevated temperatures than the wild-type enzyme. Hence, structural alterations affecting the hydrogen bond chain caused increases in k (cat) but lowered thermostability.

Calculated high-pressure structural properties, lattice dynamics and quasi particle band structures of perovskite fluorides KZnF3, CsCaF3 and BaLiF3

NASA Astrophysics Data System (ADS)

Vaitheeswaran, G.; Kanchana, V.; Zhang, Xinxin; Ma, Yanming; Svane, A.; Christensen, N. E.

2016-08-01

A detailed study of the high-pressure structural properties, lattice dynamics and band structures of perovskite structured fluorides KZnF3, CsCaF3 and BaLiF3 has been carried out by means of density functional theory. The calculated structural properties including elastic constants and equation of state agree well with available experimental information. The phonon dispersion curves are in good agreement with available experimental inelastic neutron scattering data. The electronic structures of these fluorides have been calculated using the quasi particle self-consistent GW approximation. The GW calculations reveal that all the fluorides studied are wide band gap insulators, and the band gaps are significantly larger than those obtained by the standard local density approximation, thus emphasizing the importance of quasi particle corrections in perovskite fluorides.

Calculated high-pressure structural properties, lattice dynamics and quasi particle band structures of perovskite fluorides KZnF3, CsCaF3 and BaLiF3.

PubMed

Vaitheeswaran, G; Kanchana, V; Zhang, Xinxin; Ma, Yanming; Svane, A; Christensen, N E

2016-08-10

A detailed study of the high-pressure structural properties, lattice dynamics and band structures of perovskite structured fluorides KZnF3, CsCaF3 and BaLiF3 has been carried out by means of density functional theory. The calculated structural properties including elastic constants and equation of state agree well with available experimental information. The phonon dispersion curves are in good agreement with available experimental inelastic neutron scattering data. The electronic structures of these fluorides have been calculated using the quasi particle self-consistent [Formula: see text] approximation. The [Formula: see text] calculations reveal that all the fluorides studied are wide band gap insulators, and the band gaps are significantly larger than those obtained by the standard local density approximation, thus emphasizing the importance of quasi particle corrections in perovskite fluorides.

Mild hydrothermal crystal growth of new uranium(IV) fluorides, Na{sub 3.13}Mg{sub 1.43}U{sub 6}F{sub 30} and Na{sub 2.50}Mn{sub 1.75}U{sub 6}F{sub 30}: Structures, optical and magnetic properties

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

Yeon, Jeongho; Smith, Mark D.; Tapp, Joshua

Two new uranium(IV) fluorides, Na{sub 3.13}Mg{sub 1.43}U{sub 6}F{sub 30} (1) and Na{sub 2.50}Mn{sub 1.75}U{sub 6}F{sub 30} (2), were synthesized through an in situ mild hydrothermal route, and were structurally characterized by single crystal X-ray diffraction. The compounds exhibit complex crystal structures composed of corner- or edge-shared UF{sub 9} and MF{sub 6} (M=Mg, Mn) polyhedra, forming hexagonal channels in the three-dimensional framework, in which ordered or disordered divalent metal and sodium atoms reside. The large hexagonal voids contain the nearly regular M(II)F{sub 6} octahedra and sodium ions, whereas the small hexagonal cavities include M(II) and sodium ions on a mixed-occupied site.more » Magnetic susceptibility measurements yielded effective magnetic moments of 8.36 and 11.6 µ{sub B} for 1 and 2, respectively, confirming the presence and oxidation states of U(IV) and Mn(II). The large negative Weiss constants indicate the spin gap between a triplet and a singlet state in the U(IV). Magnetization data as a function of applied fields revealed that 2 exhibits paramagnetic behavior due to the nonmagnetic singlet ground state of U(IV) at low temperature. UV–vis diffuse reflectance and X-ray photoelectron spectroscopy data were also analyzed. - Graphical abstract: Two new quaternary U(IV) fluorides, Na{sub 3.13}Mg{sub 1.43}U{sub 6}F{sub 30} and Na{sub 2.50}Mn{sub 1.75}U{sub 6}F{sub 30}, were crystallized via an in situ reduction step of U(VI) to U(IV) under mild hydrothermal conditions. The compounds show complex crystal structures based on the 3-D building block of U{sub 6}F{sub 30}. Magnetic property measurements revealed that the U(IV) exhibits a nonmagnetic singlet ground state at low temperature with a spin gap. - Highlights: • Na{sub 3.13}Mg{sub 1.43}U{sub 6}F{sub 30} and Na{sub 2.50}Mn{sub 1.75}U{sub 6}F{sub 30} have been synthesized and characterized. • The U(IV) fluorides exhibit complex three-dimensional crystal structures. • The optical properties were investigated. • Magnetic susceptibility data were collected.« less

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

Gantayat, S., E-mail: subhra-gantayat@rediffmail.com; Rout, D.; Swain, S. K.

The effect of the functionalization of multiwalled carbon nanotube on the structure and electrical properties of composites was investigated. Samples based on epoxy resin with different weight percentage of MWCNTs were prepared and characterized. The interaction between MWCNT & epoxy resin was noticed by Fourier transform infrared spectroscopy (FTIR). The structure of functionalized multiwalled carbon nanotube (f-MWCNT) reinforced epoxy composite was studied by field emission scanning electron microscope (FESEM). The dispersion of f-MWCNT in epoxy resin was evidenced by high resolution transmission electron microscope (HRTEM). Electrical properties of epoxy/f-MWCNT nanocomposites were measured & the result indicated that the conductivity increasedmore » with increasing concentration of f-MWCNTs.« less

Energetic Diagrams and Structural Properties of Monohaloacetylenes HC≡CX (X = F, Cl, Br).

PubMed

Khiri, D; Hochlaf, M; Chambaud, G

2016-08-04

Highly correlated electronic wave functions within the Multi Reference Configuration Interaction (MRCI) approach are used to study the stability and the formation processes of the monohaloacetylenes HCCX and monohalovinylidenes C2HX (X = F, Cl, Br) in their electronic ground state. These tetra-atomics can be formed through the reaction of triatomic fragments C2F, C2Cl, and C2Br with a hydrogen atom or of C2H with halogen atoms via barrierless reactions, whereas the reactions between the diatomics [C2 + HX] need to overcome barriers of 1.70, 0.89, and 0.58 eV for X = F, Cl, and Br. It is found that the linear HCCX isomers, in singlet symmetry, are more stable than the singlet C2HX iso-forms by 1.995, 2.083, and 1.958 eV for X = F, Cl, and Br. The very small isomerization barriers from iso to linear forms are calculated 0.067, 0.044, and 0.100 eV for F, Cl, and Br systems. The dissociation energies of the HCCX systems (without ZPE corrections), resulting from the breaking of the CX bond, are calculated to be 5.647, 4.691, and 4.129 eV for X = F, Cl, Br, respectively. At the equilibrium geometry of the X(1)Σ(+) state of HCCX, the vertical excitation energies in singlet and triplet symmetries are all larger than the respective dissociation energies. Stable excited states are found only as (3)A', (3)A″, and (1)A″ monohalovinylidene structures.

Modes of Paramyxovirus Fusion: a Henipavirus perspective

PubMed Central

Lee, Benhur; Akyol-Ataman, Zeynep

2011-01-01

Henipavirus is a new genus of paramyxovirus that uses protein-based receptors (EphrinB2 and EphrinB3) for virus entry. Paramyxovirus entry requires the coordinated action of the fusion (F) and attachment viral envelope glycoproteins. Receptor binding to the attachment protein triggers F to undergo a conformational cascade that results in membrane fusion. The accumulation of structural and functional studies on many paramyxoviral fusion and attachment proteins, including recent structures of Nipah and Hendra virus G bound and unbound to cognate ephrinB receptors, indicate that henipavirus entry and fusion differs mechanistically from paramyxoviruses that use glycan-based receptors. PMID:21511478

Aggregation, adsorption, and surface properties of multiply end-functionalized polystyrenes.

PubMed

Ansari, Imtiyaz A; Clarke, Nigel; Hutchings, Lian R; Pillay-Narrainen, Amilcar; Terry, Ann E; Thompson, Richard L; Webster, John R P

2007-04-10

The properties of polystyrene blends containing deuteriopolystyrene, multiply end-functionalized with C8F17 fluorocarbon groups, are strikingly analogous to those of surfactants in solution. These materials, denoted FxdPSy, where x is the number of fluorocarbon groups and y is the molecular weight of the dPS chain in kg/mol, were blended with unfunctionalized polystyrene, hPS. Nuclear reaction analysis experiments show that FxdPSy polymers adsorb spontaneously to solution and blend surfaces, resulting in a reduction in surface energy inferred from contact angle analysis. Aggregation of functionalized polymers in the bulk was found to be sensitive to FxdPSy structure and closely related to surface properties. At low concentrations, the functionalized polymers are freely dispersed in the hPS matrix, and in this range, the surface excess concentration grows sharply with increasing bulk concentration. At higher concentrations, surface excess concentrations and contact angles reach a plateau, small-angle neutron scattering data indicate small micellar aggregates of six to seven F2dPS10 polymer chains and much larger aggregates of F4dPS10. Whereas F2dPS10 aggregates are miscible with the hPS matrix, F4dPS10 forms a separate phase of multilamellar vesicles. Using neutron reflectometry (NR), we found that the extent of the adsorbed layer was approximately half the lamellar spacing of the multilamellar vesicles. NR data were fitted using an error function profile to describe the concentration profile of the adsorbed layer, and reasonable agreement was found with concentration profiles predicted by the SCFT model. The thermodynamic sticking energy of the fluorocarbon-functionalized polymer chains to the blend surface increases from 5.3kBT for x = 2 to 6.6kBT for x = 4 but appears to be somewhat dependent upon the blend concentration.

Ferroelectric ferrimagnetic LiFe2F6 : Charge-ordering-mediated magnetoelectricity

NASA Astrophysics Data System (ADS)

Lin, Ling-Fang; Xu, Qiao-Ru; Zhang, Yang; Zhang, Jun-Jie; Liang, Yan-Ping; Dong, Shuai

2017-12-01

Trirutile-type LiFe2F6 is a charge-ordered material with an Fe2 +/Fe3 + configuration. Here, its physical properties, including magnetism, electronic structure, phase transition, and charge ordering, are studied theoretically. On one hand, the charge ordering leads to improper ferroelectricity with a large polarization. On the other hand, its magnetic ground state can be tuned from the antiferromagnetic to ferrimagnetic by moderate compressive strain. Thus, LiFe2F6 can be a rare multiferroic with both large magnetization and polarization. Most importantly, since the charge ordering is the common ingredient for both ferroelectricity and magnetization, the net magnetization may be fully switched by flipping the polarization, rendering intrinsically strong magnetoelectric effects and desirable functions.

Neuroimaging in epilepsy.

PubMed

Sidhu, Meneka Kaur; Duncan, John S; Sander, Josemir W

2018-05-17

Epilepsy neuroimaging is important for detecting the seizure onset zone, predicting and preventing deficits from surgery and illuminating mechanisms of epileptogenesis. An aspiration is to integrate imaging and genetic biomarkers to enable personalized epilepsy treatments. The ability to detect lesions, particularly focal cortical dysplasia and hippocampal sclerosis, is increased using ultra high-field imaging and postprocessing techniques such as automated volumetry, T2 relaxometry, voxel-based morphometry and surface-based techniques. Statistical analysis of PET and single photon emission computer tomography (STATISCOM) are superior to qualitative analysis alone in identifying focal abnormalities in MRI-negative patients. These methods have also been used to study mechanisms of epileptogenesis and pharmacoresistance.Recent language fMRI studies aim to localize, and also lateralize language functions. Memory fMRI has been recommended to lateralize mnemonic function and predict outcome after surgery in temporal lobe epilepsy. Combinations of structural, functional and post-processing methods have been used in multimodal and machine learning models to improve the identification of the seizure onset zone and increase understanding of mechanisms underlying structural and functional aberrations in epilepsy.

Synthesis of extended polycyclic aromatic hydrocarbons by oxidative tandem spirocyclization and 1,2-aryl migration

NASA Astrophysics Data System (ADS)

Zhang, Xuan; Xu, Zhanqiang; Si, Weili; Oniwa, Kazuaki; Bao, Ming; Yamamoto, Yoshinori; Jin, Tienan

2017-04-01

The extended polycyclic aromatic hydrocarbons (PAHs) have received significant interdisciplinary attention due to their semiconducting applications in diverse organic electronics as well as intriguing structural interests of well-defined graphene segments. Herein, a highly efficient oxidative spirocyclization and 1,2-aryl migration tandem synthetic method for the construction of extended polyaromatic hydrocarbons (PAHs) has been developed. The CuCl-catalyst/PhCO3 tBu or DDQ oxidation system in the presence of trifluoroacetic acid enables the selective single-electron oxidation to take place preferentially at the more electron-rich alkene moiety of o-biphenylyl-substituted methylenefluorenes, giving rise to the subsequent tandem process. A variety of structurally diverse extended PAHs including functionalized dibenzo[g,p]chrysenes, benzo[f]naphtho[1,2-s]picene, hexabenzo[a,c,fg,j,l,op]tetracene, tetrabenzo[a,c,f,m]phenanthro[9,10-k]tetraphene, tetrabenzo[a,c,f,k]phenanthro[9,10-m]tetraphene, tetrabenzo[a,c,f,o]phenanthro[9,10-m]picene and S-type helicene have been readily synthesized.

Theoretical study on the electronic structures and phosphorescent properties of four Ir(III) complexes with different substituents on the ancillary ligand

NASA Astrophysics Data System (ADS)

Han, Deming; Shang, Xiaohong; Zhang, Gang; Zhao, Lihui

2013-12-01

The geometry structures, electronic structures, absorption and phosphorescent properties of four Ir(III) complexes {[(F2-ppy)2Ir(pta-X)], where F2-ppy = (2,4-difluoro)phenylpyridine; pta = pyridine-1,2,4-triazole; X = -CF3; -H; -CH3; -N(CH3)2}, are investigated using the density functional method. The results reveal that the electron-accepting group -CF3 has no obvious effect on absorption and emission properties, while the substitutive group -N(CH3)2 with strong electron-donating ability has obvious effect on the emission properties. The mobility of hole and electron were studied computationally based on the Marcus-Hush theory. Calculations of ionisation potential and electron affinity were used to evaluate the injection abilities of holes and electrons into these complexes. We hope that this theoretical work can provide a suitable guide to the future design and synthesis of novel phosphorescent materials for use in the organic light-emitting diodes.

Rough-pipe flows and the existence of fully developed turbulence

NASA Astrophysics Data System (ADS)

Gioia, G.; Chakraborty, Pinaki; Bombardelli, Fabián A.

2006-03-01

It is widely believed that at high Reynolds number (Re) all turbulent flows approach a limiting state of "fully developed turbulence" in which the statistics of the velocity fluctuations are independent of Re. Nevertheless, direct measurements of the velocity fluctuations have failed to yield firm empirical evidence that even the second-order structure function becomes independent of Re at high Re, let alone structure functions of higher order. Here we relate the friction coefficient (f) of rough-pipe flows to the second-order structure function. Then we show that in light of experimental measurements of f our results yield unequivocal evidence that the second-order structure function becomes independent of Re at high Re, compatible with the existence of fully developed turbulence.

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

Flay, D.; Posik, M.; Parno, D. S.

We report on the results of the E06-014 experiment performed at Jefferson Lab in Hall A, where a precision measurement of the twist-3 matrix elementmore » $$d_2$$ of the neutron ($$d_{2}^{n}$$) was conducted. This quantity represents the average color Lorentz force a struck quark experiences in a deep inelastic electron scattering event off a neutron due to its interaction with the hadronizing remnants. This color force was determined from a linear combination of the third moments of the spin structure functions $$g_1$$ and $$g_2$$ on $$^{3}$$He after nuclear corrections had been applied to these moments. The kinematics included two average $$Q^{2}$$ bins of $3.2$ GeV$$^{2}$$ and $4.3$ GeV$$^{2}$$, and Bjorken-$x$ $$0.25 \\leq x \\leq 0.90$$ covering the DIS and resonance regions. We found $$d_2^n$$ to be small and negative for $ = 3.2$ GeV$$^{2}$$, and smaller for $ = 4.3$ GeV$$^{2}$$, consistent with a lattice QCD calculation. The twist-4 matrix element $$f_{2}^{n}$$ was extracted by combining our $$d_{2}^{n}$$ with the world data on $$\\Gamma_{1}^{n} = \\int_{0}^{1} g_{1}^{n} dx$$. We found $$f_{2}^{n}$$ to be roughly an order of magnitude larger than $$d_{2}^{n}$$. Utilizing the extracted $$d_{2}^{n}$$ and $$f_{2}^{n}$$ data, we separated the color force into its electric and magnetic components, $$F_{E}^{y,n}$$ and $$F_{B}^{y,n}$$, and found them to be equal and opposite in magnitude, in agreement with instanton model predictions but not with those from QCD sum rules. Additionally, we have extracted the neutron virtual photon-nucleon asymmetry $$A_{1}^{n}$$, the structure function ratio $$g_{1}^{n}/F_{1}^{n}$$, and the quark ratios $$(\\Delta u + \\Delta \\bar{u})/(u + \\bar{u})$$ and $$(\\Delta d + \\Delta \\bar{d})/(d + \\bar{d})$$. Lastly, these results were found to be consistent with DIS world data and with the prediction of the constituent quark model but at odds with those of perturbative QCD at large $x$.« less

Synthesis of polybenzoxazine based nitrogen-rich porous carbons for carbon dioxide capture

NASA Astrophysics Data System (ADS)

Wan, Liu; Wang, Jianlong; Feng, Chong; Sun, Yahui; Li, Kaixi

2015-04-01

Nitrogen-rich porous carbons (NPCs) were synthesized from 1,5-dihydroxynaphthalene, urea, and formaldehyde based on benzoxazine chemistry by a soft-templating method with KOH chemical activation. They possess high surface areas of 856.8-1257.8 m2 g-1, a large pore volume of 0.15-0.65 cm3 g-1, tunable pore structure, high nitrogen content (5.21-5.32 wt%), and high char yields. The amount of the soft-templating agent F127 has multiple influences on the textural and chemical properties of the carbons, affecting the surface area and pore structure, impacting the compositions of nitrogen species and resulting in an improvement of the CO2 capture performance. At 1 bar, high CO2 uptake of 4.02 and 6.35 mmol g-1 at 25 and 0 °C was achieved for the sample NPC-2 with a molar ratio of F127 : urea = 0.010 : 1. This can be attributed to its well-developed micropore structure and abundant pyridinic nitrogen, pyrrolic nitrogen and pyridonic nitrogen functionalities. The sample NPC-2 also exhibits a remarkable selectivity for CO2/N2 separation and a fast adsorption/desorption rate and can be easily regenerated. This suggests that the polybenzoxazine-based NPCs are desirable for CO2 capture because of possessing a high micropore surface area, a large micropore volume, appropriate pore size distribution, and a large number of basic nitrogen functionalities.Nitrogen-rich porous carbons (NPCs) were synthesized from 1,5-dihydroxynaphthalene, urea, and formaldehyde based on benzoxazine chemistry by a soft-templating method with KOH chemical activation. They possess high surface areas of 856.8-1257.8 m2 g-1, a large pore volume of 0.15-0.65 cm3 g-1, tunable pore structure, high nitrogen content (5.21-5.32 wt%), and high char yields. The amount of the soft-templating agent F127 has multiple influences on the textural and chemical properties of the carbons, affecting the surface area and pore structure, impacting the compositions of nitrogen species and resulting in an improvement of the CO2 capture performance. At 1 bar, high CO2 uptake of 4.02 and 6.35 mmol g-1 at 25 and 0 °C was achieved for the sample NPC-2 with a molar ratio of F127 : urea = 0.010 : 1. This can be attributed to its well-developed micropore structure and abundant pyridinic nitrogen, pyrrolic nitrogen and pyridonic nitrogen functionalities. The sample NPC-2 also exhibits a remarkable selectivity for CO2/N2 separation and a fast adsorption/desorption rate and can be easily regenerated. This suggests that the polybenzoxazine-based NPCs are desirable for CO2 capture because of possessing a high micropore surface area, a large micropore volume, appropriate pore size distribution, and a large number of basic nitrogen functionalities. Electronic supplementary information (ESI) available: Elemental and XPS analyses and XPS peak positions and relative content of N species in the NPCs. See DOI: 10.1039/c4nr07409b

Removal design report for the 108-F Biological Laboratory

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

NONE

1997-09-01

Most of the 100-F facilities were deactivated with the reactor and have since been demolished. Of the dozen or so reactor-related structures, only the 105-F Reactor Building and the 108-F Biology Laboratory remain standing today. The 108-F Biology Laboratory was intended to be used as a facility for the mixing and addition of chemicals used in the treatment of the reactor cooling water. Shortly after F Reactor began operation, it was determined that the facility was not needed for this purpose. In 1949, the building was converted for use as a biological laboratory. In 1962, the lab was expanded bymore » adding a three-story annex to the original four-story structure. The resulting lab had a floor area of approximately 2,883 m{sup 2} (main building and annex) that operated until 1973. The building contained 47 laboratories, a number of small offices, a conference room, administrative section, lunch and locker rooms, and a heavily shielded, high-energy exposure cell. The purpose of this removal design report is to establish the methods of decontamination and decommissioning and the supporting functions associated with facility removal and disposal.« less

Shock Compression Response of Calcium Fluoride (CaF2)

NASA Astrophysics Data System (ADS)

Root, Seth

2017-06-01

The fluorite crystal structure is a textbook lattice that is observed for many systems, such as CaF2, Mg2 Si, and CeO2. Specifically, CaF2 is a useful material for studying the fluorite system because it is readily available as a single crystal. Under static compression, CaF2 is known to have at least three solid phases: fluorite, cotunnite, and a Ni2 In phase. Along the Hugoniot CaF2 undergoes a fluorite to cotunnite phase transition, however, at higher shock pressures it is unknown whether CaF2 undergoes another solid phase transition or melts directly from the cotunnite phase. In this work, we conducted planar shock compression experiments on CaF2 using Sandia's Z-machine and a two-stage light gun up to 900 GPa. In addition, we use density functional theory (DFT) based quantum molecular dynamics (QMD) simulations to provide insight into the CaF2 state along the Hugoniot. In collaboration with: Michael Desjarlais, Ray Lemke, Patricia Kalita, Scott Alexander, Sandia National Laboratories. Sandia National Laboratories is a multi-mission laboratory managed and operated by Sandia Corporation, a wholly owned subsidiary of Lockheed Martin Corporation, for the U.S. Department of Energy's National Nuclear Security Administration under contract DE-AC04-94AL850.

Small molecule correctors of F508del-CFTR discovered by structure-based virtual screening

NASA Astrophysics Data System (ADS)

Kalid, Ori; Mense, Martin; Fischman, Sharon; Shitrit, Alina; Bihler, Hermann; Ben-Zeev, Efrat; Schutz, Nili; Pedemonte, Nicoletta; Thomas, Philip J.; Bridges, Robert J.; Wetmore, Diana R.; Marantz, Yael; Senderowitz, Hanoch

2010-12-01

Folding correctors of F508del-CFTR were discovered by in silico structure-based screening utilizing homology models of CFTR. The intracellular segment of CFTR was modeled and three cavities were identified at inter-domain interfaces: (1) Interface between the two Nucleotide Binding Domains (NBDs); (2) Interface between NBD1 and Intracellular Loop (ICL) 4, in the region of the F508 deletion; (3) multi-domain interface between NBD1:2:ICL1:2:4. We hypothesized that compounds binding at these interfaces may improve the stability of the protein, potentially affecting the folding yield or surface stability. In silico structure-based screening was performed at the putative binding-sites and a total of 496 candidate compounds from all three sites were tested in functional assays. A total of 15 compounds, representing diverse chemotypes, were identified as F508del folding correctors. This corresponds to a 3% hit rate, tenfold higher than hit rates obtained in corresponding high-throughput screening campaigns. The same binding sites also yielded potentiators and, most notably, compounds with a dual corrector-potentiator activity (dual-acting). Compounds harboring both activity types may prove to be better leads for the development of CF therapeutics than either pure correctors or pure potentiators. To the best of our knowledge this is the first report of structure-based discovery of CFTR modulators.

Uncovering the Origin of Divergence in the CsM(CrO 4) 2 (M = La, Pr, Nd, Sm, Eu; Am) Family through Examination of the Chemical Bonding in a Molecular Cluster and by Band Structure Analysis

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

Galley, Shane S.; Arico, Alexandra A.; Lee, Tsung-Han

A series of f-block chromates, CsM(CrO 4) 2 (M = La, Pr, Nd, Sm, Eu; Am), were prepared revealing notable differences between the Am III derivatives and their lanthanide analogs. While all compounds form similar layered structures, the americium compound exhibits polymorphism and adopts both a structure isomorphous with the early lanthanides as well as one that possesses lower symmetry. Both polymorphs are dark red and possess band gaps that are smaller than the Ln III compounds. In order to probe the origin of these differences, the electronic structure of α-CsSm(CrO 4) 2, α-CsEu(CrO 4) 2, and α-CsAm(CrO 4) 2more » were studied using both a molecular cluster approach featuring hybrid density functional theory and QTAIM analysis and by the periodic LDA+GA and LDA+DMFT methods. Notably, the covalent contributions to bonding by the f orbitals were found to be more than twice as large in the Am III chromate than in the Sm III and Eu III compounds, and even larger in magnitude than the Am-5f spin–orbit splitting in this system. Our analysis indicates also that the Am–O covalency in α-CsAm(CrO 4) 2 is driven by the degeneracy of the 5f and 2p orbitals, and not by orbital overlap.« less

Uncovering the Origin of Divergence in the CsM(CrO 4) 2 (M = La, Pr, Nd, Sm, Eu; Am) Family through Examination of the Chemical Bonding in a Molecular Cluster and by Band Structure Analysis

DOE PAGES

Galley, Shane S.; Arico, Alexandra A.; Lee, Tsung-Han; ...

2018-01-10

A series of f-block chromates, CsM(CrO 4) 2 (M = La, Pr, Nd, Sm, Eu; Am), were prepared revealing notable differences between the Am III derivatives and their lanthanide analogs. While all compounds form similar layered structures, the americium compound exhibits polymorphism and adopts both a structure isomorphous with the early lanthanides as well as one that possesses lower symmetry. Both polymorphs are dark red and possess band gaps that are smaller than the Ln III compounds. In order to probe the origin of these differences, the electronic structure of α-CsSm(CrO 4) 2, α-CsEu(CrO 4) 2, and α-CsAm(CrO 4) 2more » were studied using both a molecular cluster approach featuring hybrid density functional theory and QTAIM analysis and by the periodic LDA+GA and LDA+DMFT methods. Notably, the covalent contributions to bonding by the f orbitals were found to be more than twice as large in the Am III chromate than in the Sm III and Eu III compounds, and even larger in magnitude than the Am-5f spin–orbit splitting in this system. Our analysis indicates also that the Am–O covalency in α-CsAm(CrO 4) 2 is driven by the degeneracy of the 5f and 2p orbitals, and not by orbital overlap.« less

Germylenes: structures, electron affinities, and singlet-triplet gaps of the conventional XGeCY(3) (X = H, F, Cl, Br, and I; Y = F and Cl) species and the unexpected cyclic XGeCY(3) (Y = Br and I) systems.

PubMed

Bundhun, Ashwini; Abdallah, Hassan H; Ramasami, Ponnadurai; Schaefer, Henry F

2010-12-23

A systematic investigation of the X-Ge-CY(3) (X = H, F, Cl, Br, and I; Y = F, Cl, Br, and I) species is carried out using density functional theory. The basis sets used for all atoms (except iodine) in this work are of double-ζ plus polarization quality with additional s- and p-type diffuse functions, and denoted DZP++. Vibrational frequency analyses are performed to evaluate zero-point energy corrections and to determine the nature of the stationary points located. Predicted are four different forms of neutral-anion separations: adiabatic electron affinity (EA(ad)), zero-point vibrational energy corrected EA(ad(ZPVE)), vertical electron affinity (EA(vert)), and vertical detachment energy (VDE). The electronegativity (χ) reactivity descriptor for the halogens (X = F, Cl, Br, and I) is used as a tool to assess the interrelated properties of these germylenes. The topological position of the halogen atom bound to the divalent germanium center is well correlated with the trend in the electron affinities and singlet-triplet gaps. For the expected XGeCY(3) structures (X = H, F, Cl, Br, and I; Y = F and Cl), the predicted trend in the electron affinities is well correlated with simpler germylene derivatives (J. Phys. Chem. A 2009, 113, 8080). The predicted EA(ad(ZPVE)) values with the BHLYP functional range from 1.66 eV (FGeCCl(3)) to 2.20 eV (IGeCF(3)), while the singlet-triplet splittings range from 1.28 eV (HGeCF(3)) to 2.22 eV (FGeCCl(3)). The XGeCY(3) (Y = Br and I) species are most often characterized by three-membered cyclic systems involving the divalent germanium atom, the carbon atom, and a halogen atom.

Functionalized guanidinium chloride based colourimetric sensors for fluoride and acetate: single crystal X-ray structural evidence of -NH deprotonation and complexation.

PubMed

Bose, Purnandhu; Ahamed, B Nisar; Ghosh, Pradyut

2011-03-21

A series of new symmetrically functionalized guanidinium chlorides (S1-S10) are synthesized in good yields and their sensing ability toward anions is studied in MeCN-DMF (24 : 1) (v/v). The absorption bands of these molecules in the presence of anions are tuned by varying the functional groups attached to the guanidinium moiety (which resembles urea) with respect to (i) aromaticity (S1-S4), (ii) electron induction effect (S1, S5-S9), (iii) positional isomeric effect (S7-S9), (iv) indole functionality (S10) of the conjugated aryl units. Anions that are above Cl(-) in the Hofmeister series (F(-), AcO(-), H(2)PO(4)(-)) are eligible as an analyte in this series of molecules whereas less basic anions than Cl(-) do not cause any interference. Thus, this series of molecules are suitable for the detection of anions in the narrow window of the Hofmeister series. Out of all the anions, only fluoride causes vivid colour changes from yellow to red to reddish orange and finally to blue, irrespective of the increasing aromaticity, induction and positional isomeric effect of the substituent that is attached to the guanidinium moiety. Interestingly, S9 has shown the ability to sense distinctly both F(-) and AcO(-) colourimetrically. Further S10, a sensor attached with indole functionality shows selective sensing of F(-) colourimetrically with a NIR signature at ∼930 nm though both these outputs are very unstable in nature. Stability constants for complex formation of S1-S10 (except S5) with F(-), AcO(-) are calculated by UV-vis titration experiments. Finally single crystal X-ray structural studies on the species 1 formed upon treating S6 with sodium fluoride confirms -NH deprotonation, whereas the reaction of S6 and S2 with sodium benzoate shows 1:1 host:guest binding that results in complexes 2 and 3 respectively.

Coordinated autoinhibition of F-BAR domain membrane binding and WASp activation by Nervous Wreck.

PubMed

Stanishneva-Konovalova, Tatiana B; Kelley, Charlotte F; Eskin, Tania L; Messelaar, Emily M; Wasserman, Steven A; Sokolova, Olga S; Rodal, Avital A

2016-09-20

Membrane remodeling by Fes/Cip4 homology-Bin/Amphiphysin/Rvs167 (F-BAR) proteins is regulated by autoinhibitory interactions between their SRC homology 3 (SH3) and F-BAR domains. The structural basis of autoregulation, and whether it affects interactions of SH3 domains with other cellular ligands, remain unclear. Here we used single-particle electron microscopy to determine the structure of the F-BAR protein Nervous Wreck (Nwk) in both soluble and membrane-bound states. On membrane binding, Nwk SH3 domains do not completely dissociate from the F-BAR dimer, but instead shift from its concave surface to positions on either side of the dimer. Unexpectedly, along with controlling membrane binding, these autoregulatory interactions inhibit the ability of Nwk-SH3a to activate Wiskott-Aldrich syndrome protein (WASp)/actin related protein (Arp) 2/3-dependent actin filament assembly. In Drosophila neurons, Nwk autoregulation restricts SH3a domain-dependent synaptopod formation, synaptic growth, and actin organization. Our results define structural rearrangements in Nwk that control F-BAR-membrane interactions as well as SH3 domain activities, and suggest that these two functions are tightly coordinated in vitro and in vivo.

Highly Efficient Multiple-Anchored Fluorescent Probe for the Detection of Aniline Vapor Based on Synergistic Effect: Chemical Reaction and PET.

PubMed

Jiao, Zinuo; Zhang, Yu; Xu, Wei; Zhang, Xiangtao; Jiang, Haibo; Wu, Pengcheng; Fu, Yanyan; He, Qingguo; Cao, Huimin; Cheng, Jiangong

2017-05-26

A multiple-anchored fluorescent probe ((((hexane-1,6-diylbis(2,7-bis(4-formyl)-phenyl)-9H-fluorine-9,9-diyl))-bis(hexane-6,1-diyl))-bis(9H-carbazole-9,3,6-triyl))-tetrakis(benzene-4,1-diyl))-tetraformyl-(8FP-2F) with eight aldehyde groups was designed and synthesized. The molecule has four branches and highly twisted structure. Furthermore, it tends to self-assemble into nanospheres, which is beneficial for gaseous analyte penetration and high fluorescence quantum efficiency. Among gaseous analytes, detection of aniline vapor is extraordinarily important in the control of environmental issues and human diseases. Herein, 8FP-2F was introduced to detect aniline vapor with distinguished sensitivity and selectivity via simple Schiff base reaction at room temperature. After exposure to saturate aniline vapor, the 89% fluorescence of 8FP-2F was quenched in 50 s and the detection limit was as low as 3 ppb. Further study showed the suitable HOMO/LUMO energy levels and matched orbital symmetry between probe and aniline molecules ensured chemical reaction and PET process work together. The synergistic effect resulted in a significant sensing performance and fluorescence quenching toward aniline vapor. Moreover, the multiple active sites structure of 8FP-2F means it could be applied for constructing many interesting structures and highly efficient organic optoelectronic functional materials.

Some notes on the Roman domination number and Italian domination number in graphs

NASA Astrophysics Data System (ADS)

Hajibaba, Maryam; Jafari Rad, Nader

2017-09-01

An Italian dominating function (or simply, IDF) on a graph G = (V, E) is a function f : V → {0, 1, 2} that satisfies the property that for every vertex v ∈ V, with f(v) = 0, Σ u∈N(v) f(u) ≥ 2. The weight of an Italian dominating function f is defined as w(f) = f(V ) = Σ u∈V f(u). The minimum weight among all of the Italian dominating functions on a graph G is called the Italian domination number of G, and is denoted by γI (G). A double Roman dominating function (or simply, DRDF) is a function f : V → {0, 1, 2, 3} having the property that if f(v) = 0 for a vertex v, then v has at least two adjacent vertices assigned 2 under f or one adjacent vertex assigned 3 under f, and if f(v) = 1, then v has at least one neighbor with f(w) ≥ 2. The weight of a DRDF f is defined as the sum f(V) = Σ v∈V f(v), and the minimum weight of a DRDF on G is the double Roman domination number of G, denoted by γdR (G). In this paper we show that γdR (G)/2 ≤ γI (G) ≤ 2γdR (G)/3, and characterize all trees T with γI (T) = 2γdR (T)/3.

Partial covariance based functional connectivity computation using Ledoit-Wolf covariance regularization.

PubMed

Brier, Matthew R; Mitra, Anish; McCarthy, John E; Ances, Beau M; Snyder, Abraham Z

2015-11-01

Functional connectivity refers to shared signals among brain regions and is typically assessed in a task free state. Functional connectivity commonly is quantified between signal pairs using Pearson correlation. However, resting-state fMRI is a multivariate process exhibiting a complicated covariance structure. Partial covariance assesses the unique variance shared between two brain regions excluding any widely shared variance, hence is appropriate for the analysis of multivariate fMRI datasets. However, calculation of partial covariance requires inversion of the covariance matrix, which, in most functional connectivity studies, is not invertible owing to rank deficiency. Here we apply Ledoit-Wolf shrinkage (L2 regularization) to invert the high dimensional BOLD covariance matrix. We investigate the network organization and brain-state dependence of partial covariance-based functional connectivity. Although RSNs are conventionally defined in terms of shared variance, removal of widely shared variance, surprisingly, improved the separation of RSNs in a spring embedded graphical model. This result suggests that pair-wise unique shared variance plays a heretofore unrecognized role in RSN covariance organization. In addition, application of partial correlation to fMRI data acquired in the eyes open vs. eyes closed states revealed focal changes in uniquely shared variance between the thalamus and visual cortices. This result suggests that partial correlation of resting state BOLD time series reflect functional processes in addition to structural connectivity. Copyright © 2015 Elsevier Inc. All rights reserved.

Partial covariance based functional connectivity computation using Ledoit-Wolf covariance regularization

PubMed Central

Brier, Matthew R.; Mitra, Anish; McCarthy, John E.; Ances, Beau M.; Snyder, Abraham Z.

2015-01-01

Functional connectivity refers to shared signals among brain regions and is typically assessed in a task free state. Functional connectivity commonly is quantified between signal pairs using Pearson correlation. However, resting-state fMRI is a multivariate process exhibiting a complicated covariance structure. Partial covariance assesses the unique variance shared between two brain regions excluding any widely shared variance, hence is appropriate for the analysis of multivariate fMRI datasets. However, calculation of partial covariance requires inversion of the covariance matrix, which, in most functional connectivity studies, is not invertible owing to rank deficiency. Here we apply Ledoit-Wolf shrinkage (L2 regularization) to invert the high dimensional BOLD covariance matrix. We investigate the network organization and brain-state dependence of partial covariance-based functional connectivity. Although RSNs are conventionally defined in terms of shared variance, removal of widely shared variance, surprisingly, improved the separation of RSNs in a spring embedded graphical model. This result suggests that pair-wise unique shared variance plays a heretofore unrecognized role in RSN covariance organization. In addition, application of partial correlation to fMRI data acquired in the eyes open vs. eyes closed states revealed focal changes in uniquely shared variance between the thalamus and visual cortices. This result suggests that partial correlation of resting state BOLD time series reflect functional processes in addition to structural connectivity. PMID:26208872

Materials Data on CaP2Xe5F22 (SG:33) by Materials Project

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

Kristin Persson

Computed materials data using density functional theory calculations. These calculations determine the electronic structure of bulk materials by solving approximations to the Schrodinger equation. For more information, see https://materialsproject.org/docs/calculations

Materials Data on CdP2Xe5F22 (SG:33) by Materials Project

DOE Data Explorer

Kristin Persson

2014-07-09

Computed materials data using density functional theory calculations. These calculations determine the electronic structure of bulk materials by solving approximations to the Schrodinger equation. For more information, see https://materialsproject.org/docs/calculations

Materials Data on BaSb2Xe5F22 (SG:69) by Materials Project

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

Kristin Persson

Computed materials data using density functional theory calculations. These calculations determine the electronic structure of bulk materials by solving approximations to the Schrodinger equation. For more information, see https://materialsproject.org/docs/calculations

Materials Data on SnH4C2NO4F (SG:14) by Materials Project

DOE Data Explorer

Kristin Persson

2014-11-02

Computed materials data using density functional theory calculations. These calculations determine the electronic structure of bulk materials by solving approximations to the Schrodinger equation. For more information, see https://materialsproject.org/docs/calculations

Materials Data on Cs2NaAl3F12 (SG:166) by Materials Project

DOE Data Explorer

Kristin Persson

2014-11-02

Computed materials data using density functional theory calculations. These calculations determine the electronic structure of bulk materials by solving approximations to the Schrodinger equation. For more information, see https://materialsproject.org/docs/calculations

Materials Data on Rb3NaBe2F8 (SG:164) by Materials Project

DOE Data Explorer

Kristin Persson

2014-11-02

Computed materials data using density functional theory calculations. These calculations determine the electronic structure of bulk materials by solving approximations to the Schrodinger equation. For more information, see https://materialsproject.org/docs/calculations

Materials Data on Cs2LiAl3F12 (SG:166) by Materials Project

DOE Data Explorer

Kristin Persson

2014-11-02

Computed materials data using density functional theory calculations. These calculations determine the electronic structure of bulk materials by solving approximations to the Schrodinger equation. For more information, see https://materialsproject.org/docs/calculations

Materials Data on CaAs2(XeF5)4 (SG:4) by Materials Project

DOE Data Explorer

Kristin Persson

2016-02-04

Computed materials data using density functional theory calculations. These calculations determine the electronic structure of bulk materials by solving approximations to the Schrodinger equation. For more information, see https://materialsproject.org/docs/calculations

Structural investigation of α-LaZr2F11 by coupling X-ray powder diffraction, 19F solid state NMR and DFT calculations

NASA Astrophysics Data System (ADS)

Martineau, Charlotte; Legein, Christophe; Body, Monique; Péron, Olivier; Boulard, Brigitte; Fayon, Franck

2013-03-01

α-LaZr2F11 has been synthesized by solid state reaction. Its crystal structure has been refined from X-ray powder diffraction data (space group no. 72 Ibam, a=7.785(1) Å, b=10.086(1) Å and c=11.102(1) Å). α-LaZr2F11 contains one La, one Zr and four F inequivalent crystallographic sites. F3 and F4 are shared between one ZrF73- polyhedron and one LaF85- polyhedron, while F1 and F2 bridge two ZrF73- polyhedra. 19F 1D MAS NMR spectra of α-LaZr2F11 are in agreement with the proposed structural model. Assignment of the 19F resonances to the corresponding crystallographic sites has been performed on the basis of both their relative intensities and their correlation patterns in a 19F 2D dipolar-based double-quantum recoupling MAS NMR spectrum. DFT calculations of the 19F chemical shielding tensors have been performed using the GIPAW method implemented in the NMR-CASTEP code, for the experimental structure and two PBE-DFT geometry optimized structures of α-LaZr2F11 (atomic position optimization and full geometry optimization with rescaling of the unit cell volume to the experimental value). Computations were done with and without using a modified La pseudopotential allowing the treatment of the 4f localized empty orbitals of La3+. A relatively nice agreement between the experimental 19F isotropic and anisotropic chemical shifts and the values calculated for the proposed structural model is obtained.

Interacting cytoplasmic loops of subunits a and c of Escherichia coli F1F0 ATP synthase gate H+ transport to the cytoplasm.

PubMed

Steed, P Ryan; Kraft, Kaitlin A; Fillingame, Robert H

2014-11-25

H(+)-transporting F1F0 ATP synthase catalyzes the synthesis of ATP via coupled rotary motors within F0 and F1. H(+) transport at the subunit a-c interface in transmembranous F0 drives rotation of a cylindrical c10 oligomer within the membrane, which is coupled to rotation of subunit γ within the α3β3 sector of F1 to mechanically drive ATP synthesis. F1F0 functions in a reversible manner, with ATP hydrolysis driving H(+) transport. ATP-driven H(+) transport in a select group of cysteine mutants in subunits a and c is inhibited after chelation of Ag(+) and/or Cd(+2) with the substituted sulfhydryl groups. The H(+) transport pathway mapped via these Ag(+)(Cd(+2))-sensitive Cys extends from the transmembrane helices (TMHs) of subunits a and c into cytoplasmic loops connecting the TMHs, suggesting these loop regions could be involved in gating H(+) release to the cytoplasm. Here, using select loop-region Cys from the single cytoplasmic loop of subunit c and multiple cytoplasmic loops of subunit a, we show that Cd(+2) directly inhibits passive H(+) transport mediated by F0 reconstituted in liposomes. Further, in extensions of previous studies, we show that the regions mediating passive H(+) transport can be cross-linked to each other. We conclude that the loop-regions in subunits a and c that are implicated in H(+) transport likely interact in a single structural domain, which then functions in gating H(+) release to the cytoplasm.

Adaptation of brain functional and structural networks in aging.

PubMed

Lee, Annie; Ratnarajah, Nagulan; Tuan, Ta Anh; Chen, Shen-Hsing Annabel; Qiu, Anqi

2015-01-01

The human brain, especially the prefrontal cortex (PFC), is functionally and anatomically reorganized in order to adapt to neuronal challenges in aging. This study employed structural MRI, resting-state fMRI (rs-fMRI), and high angular resolution diffusion imaging (HARDI), and examined the functional and structural reorganization of the PFC in aging using a Chinese sample of 173 subjects aged from 21 years and above. We found age-related increases in the structural connectivity between the PFC and posterior brain regions. Such findings were partially mediated by age-related increases in the structural connectivity of the occipital lobe within the posterior brain. Based on our findings, it is thought that the PFC reorganization in aging could be partly due to the adaptation to age-related changes in the structural reorganization of the posterior brain. This thus supports the idea derived from task-based fMRI that the PFC reorganization in aging may be adapted to the need of compensation for resolving less distinctive stimulus information from the posterior brain regions. In addition, we found that the structural connectivity of the PFC with the temporal lobe was fully mediated by the temporal cortical thickness, suggesting that the brain morphology plays an important role in the functional and structural reorganization with aging.

Reconstitution and functional comparison of purified GlpF and AqpZ, the glycerol and water channels from Escherichia coli.

PubMed

Borgnia, M J; Agre, P

2001-02-27

A large family of membrane channel proteins selective for transport of water (aquaporins) or water plus glycerol (aquaglyceroporins) has been found in diverse life forms. Escherichia coli has two members of this family-a water channel, AqpZ, and a glycerol facilitator, GlpF. Despite having similar primary amino acid sequences and predicted structures, the oligomeric state and solute selectivity of AqpZ and GlpF are disputed. Here we report biochemical and functional characterizations of affinity-purified GlpF and compare it to AqpZ. Histidine-tagged (His-GlpF) and hemagglutinin-tagged (HA-GlpF) polypeptides encoded by a bicistronic construct were expressed in bacteria. HA-GlpF and His-GlpF appear to form oligomers during Ni-nitrilotriacetate affinity purification. Sucrose gradient sedimentation analyses showed that the oligomeric state of octyl glucoside-solubilized GlpF varies: low ionic strength favors subunit dissociation, whereas Mg(2+) stabilizes tetrameric assembly. Reconstitution of affinity-purified GlpF into proteoliposomes increases glycerol permeability more than 100-fold and water permeability up to 10-fold compared with control liposomes. Glycerol and water permeability of GlpF both occur with low Arrhenius activation energies and are reversibly inhibited by HgCl(2). Our studies demonstrate that, unlike AqpZ, a water-selective stable tetramer, purified GlpF exists in multiple oligomeric forms under nondenaturing conditions and is highly permeable to glycerol but less well permeated by water.

DPOAE in estimation of the function of the cochlea in tinnitus patients with normal hearing.

PubMed

Sztuka, Aleksandra; Pospiech, Lucyna; Gawron, Wojciech; Dudek, Krzysztof

2010-02-01

The most probable place generating tinnitus in the auditory pathway is the outer hair cells (OHCs) inside the cochlea. Otoacoustic emissions are used to assess their activity. The objective of the investigation was to measure the features of distortion product otoacoustic emissions (DPOAE) in a group of tinnitus patients without hearing loss, estimate the diagnostic value of the parameters for the analysis of cochlear function in the patients, emphasizing those most useful in localizing tinnitus generators, and determine the hypothetical influence of hyperacusis and misophony on DPOAE parameters in tinnitus patients. The material consisted of 44 patients with tinnitus and without hearing loss. In the control group were 33 patients without tinnitus with the same state of hearing. The tinnitus patients were divided into three subgroups: those with hyperacusis, those with misophonia, and those with neither. After collecting medical history and performing clinical examination of all the patients, tonal and impedance audiometry, ABR, and discomfort level were evaluated. Then DPOAE were measured using three procedures. First the amplitudes of two points per octave were assessed, second the "fine structure" method with 16-20 points per octave (f2/f1=1.22, L1=L2=70 dB), and the third procedure included recording the growth function in three series for input tones of f2=2002, 4004, and 6006Hz (f2/f1=1.22) and L1=L2 levels increasing by increments of 5 dB in each series. Hyperacusis was found in 63% and misophonia in 10% of the tinnitus patients with no hearing loss. DPOAE amplitudes in recordings with two points per octave and the fine structure method are very valuable parameters for estimating cochlear function in tinnitus patients with normal hearing. Function growth rate cannot be the only parameter in measuring DPOAE in tinnitus patients, including subjects with hyperacusis and misophonia. The markedly higher DPOAE amplitudes in the group of tinnitus patients without hearing loss suggest that tinnitus may be caused by increased motility of the OHCs induced by decreasing efferent fiber activity, and not by OHC failure. Hyperacusis significantly increases the amplitude of DPOAE in tinnitus patients with no hearing loss. Copyright (c) 2009 Elsevier Ireland Ltd. All rights reserved.

A multi writable thiophene-based selective and reversible chromogenic fluoride probe with dual -NH functionality.

PubMed

Vishwakarma, Siddharth; Kumar, Ajit; Pandey, Abha; Upadhyay, K K

2017-01-05

A chromogenic fluoride probe bearing bis imine groups having dual -NH functionality (BSB) has been designed, synthesised and structurally characterized by its single crystal X-ray diffraction studies. The BSB could visually and spectroscopically recognise F(-) with high selectivity over other anions by exhibiting intense chromogenic response (from colourless to red) for F(-) in acetonitrile solution. The UV-visible titration and (1)H NMR titration experiments indicated that the observed changes occur via a combined process including hydrogen bonding and deprotonation between the BSB and F(-). Moreover theoretical calculations at the Density Functional Theory (DFT) level shed further light upon probe design strategy and the nature of interactions between BSB and F(-). The limit of detection and binding constant of BSB towards F(-) were found to be 6.9×10(-7)M and 1.42±0.069×10(8)M(-2) respectively. Finally, by using F(-)and H(+) as chemical inputs and the absorbance as output, a INHIBIT logic gate was constructed, which exhibits "Multi-write" ability without obvious degradation in its optical output. Copyright © 2016 Elsevier B.V. All rights reserved.

Syntheses, Raman spectroscopy and crystal structures of alkali hexa­fluorido­rhenates(IV) revisited

PubMed Central

Louis-Jean, James; Salamat, Ashkan; Pham, Chien Thang; Poineau, Frederic

2018-01-01

The A 2[ReF6] (A = K, Rb and Cs) salts are isotypic and crystallize in the trigonal space group type P m1, adopting the K2[GeF6] structure type. Common to all A 2[ReF6] structures are slightly distorted octa­hedral [ReF6]2− anions with an average Re—F bond length of 1.951 (8) Å. In those salts, symmetry lowering on the local [ReF6]2− anions from Oh (free anion) to D 3d (solid-state structure) occur. The distortions of the [ReF6]2− anions, as observed in their Raman spectra, are correlated to the size of the counter-cations.

Syntheses, Raman spectroscopy and crystal structures of alkali hexafluoridorhenates(IV) revisited

DOE PAGES

Louis-Jean, James; Mariappan Balasekaran, Samundeeswari; Smith, Dean; ...

2018-04-06

The A 2[ReF 6] (A = K, Rb and Cs) salts are isotypic and crystallize in the trigonal space group type Pmore » $$\\bar{3}$$m1, adopting the K 2[GeF 6] structure type. Common to all A 2[ReF 6] structures are slightly distorted octa­hedral [ReF 6] 2- anions with an average Re—F bond length of 1.951 (8) Å. In these salts, symmetry lowering on the local [ReF 6] 2- anions from O h (free anion) to D 3d (solid-state structure) occur. The distortions of the [ReF 6] 2- anions, as observed in their Raman spectra, are correlated to the size of the counter-cations.« less

Disrupted topology of the resting state structural connectome in middle-aged APOE ε4 carriers.

PubMed

Korthauer, L E; Zhan, L; Ajilore, O; Leow, A; Driscoll, I

2018-05-24

The apolipoprotein E (APOE) ε4 allele is the best characterized genetic risk factor for Alzheimer's disease to date. Older APOE ε4 carriers (aged 60 + years) are known to have disrupted structural and functional connectivity, but less is known about APOE-associated network integrity in middle age. The goal of this study was to characterize APOE-related differences in network topology in middle age, as disentangling the early effects of healthy versus pathological aging may aid early detection of Alzheimer's disease and inform treatments. We performed resting state functional magnetic resonance imaging (rs-fMRI) and diffusion tensor imaging (DTI) in healthy, cognitively normal, middle-aged adults (age 40-60; N = 76, 38 APOE ε4 carriers). Graph theoretical analysis was used to calculate local and global efficiency of 1) a whole brain rs-fMRI network; 2) a whole brain DTI network; and 3) the resting state structural connectome (rsSC), an integrated functional-structural network derived using functional-by-structural hierarchical (FSH) mapping. Our results indicated no APOE ε4-associated differences in network topology of the rs-fMRI or DTI networks alone. However, ε4 carriers had significantly lower global and local efficiency of the integrated rsSC compared to non-carriers. Furthermore, ε4 carriers were less resilient to targeted node failure of the rsSC, which mimics the neuropathological process of Alzheimer's disease. Collectively, these findings suggest that integrating multiple neuroimaging modalities and employing graph theoretical analysis may reveal network-level vulnerabilities that may serve as biomarkers of age-related cognitive decline in middle age, decades before the onset of overt cognitive impairment. Copyright © 2018. Published by Elsevier Inc.

Thermodynamic controls on element partitioning between titanomagnetite and andesitic-dacitic silicate melts

NASA Astrophysics Data System (ADS)

Sievwright, R. H.; Wilkinson, J. J.; O'Neill, H. St. C.; Berry, A. J.

2017-08-01

Titanomagnetite-melt partitioning of Mg, Mn, Al, Ti, Sc, V, Co, Ni, Cu, Zn, Ga, Zr, Nb, Mo, Hf and Ta was investigated experimentally as a function of oxygen fugacity ( fO2) and temperature ( T) in an andesitic-dacitic bulk-chemical compositional range. In these bulk systems, at constant T, there are strong increases in the titanomagnetite-melt partitioning of the divalent cations (Mg2+, Mn2+, Co2+, Ni2+, Zn2+) and Cu2+/Cu+ with increasing fO2 between 0.2 and 3.7 log units above the fayalite-magnetite-quartz buffer. This is attributed to a coupling between magnetite crystallisation and melt composition. Although melt structure has been invoked to explain the patterns of mineral-melt partitioning of divalent cations, a more rigorous justification of magnetite-melt partitioning can be derived from thermodynamic principles, which accounts for much of the supposed influence ascribed to melt structure. The presence of magnetite-rich spinel in equilibrium with melt over a range of fO2 implies a reciprocal relationship between a(Fe2+O) and a(Fe3+O1.5) in the melt. We show that this relationship accounts for the observed dependence of titanomagnetite-melt partitioning of divalent cations with fO2 in magnetite-rich spinel. As a result of this, titanomagnetite-melt partitioning of divalent cations is indirectly sensitive to changes in fO2 in silicic, but less so in mafic bulk systems.

First measurement of the deep-inelastic structure of proton diffraction

NASA Astrophysics Data System (ADS)

Ahmed, T.; Aid, S.; Andreev, V.; Andrieu, B.; Appuhn, R.-D.; Arpagaus, M.; Babaev, A.; Baehr, J.; Bán, J.; Ban, Y.; Baranov, P.; Barrelet, E.; Bartel, W.; Barth, M.; Bassler, U.; Beck, H. P.; Behrend, H.-J.; Belousov, A.; Berger, Ch.; Bernardi, G.; Bernet, R.; Bertrand-Coremans, G.; Besançon, M.; Beyer, R.; Biddulph, P.; Bispham, P.; Bizot, J. C.; Blobel, V.; Borras, K.; Botterweck, F.; Boudry, V.; Braemer, A.; Brasse, F.; Braunschweig, W.; Brisson, V.; Bruncko, D.; Brune, C.; Buchholz, R.; Büngener, L.; Bürger, J.; Büsser, F. W.; Buniatian, A.; Burke, S.; Burton, M.; Buschhorn, G.; Campbell, A. J.; Carli, T.; Charles, F.; Clarke, D.; Clegg, A. B.; Clerbaux, B.; Colombo, M.; Contreras, J. G.; Cormack, C.; Coughlan, J. A.; Courau, A.; Coutures, Ch.; Cozzika, G.; Criegee, L.; Cussans, D. G.; Cvach, J.; Dagoret, S.; Dainton, J. B.; Dau, W. D.; Daum, K.; David, M.; Deffur, E.; Delcourt, B.; Del Buono, L.; De Roeck, A.; De Wolf, E. A.; Di Nezza, P.; Dollfus, C.; Dowell, J. D.; Dreis, H. B.; Droutskoi, A.; Duboc, J.; Düllmann, D.; Dünger, O.; Duhm, H.; Ebert, J.; Ebert, T. R.; Eckerlin, G.; Efremenko, V.; Egli, S.; Ehrlichmann, H.; Eichenberger, S.; Eichler, R.; Eckerlin, G.; Efremenko, V.; Egli, S.; Ehrlichmann, H.; Eichenberger, S.; Eichler, R.; Eisele, F.; Eisenhandler, E.; Ellison, R. J.; Elsen, E.; Erdmann, M.; Erdmann, W.; Evrard, E.; Favart, L.; Fedotov, A.; Feeken, D.; Felst, R.; Feltesse, J.; Ferencei, J.; Ferrarotto, F.; Flamm, K.; Fleischer, M.; Flieser, M.; Flügge, G.; Fomenko, A.; Forbush, M.; Formánek, J.; Foster, J. M.; Franke, G.; Fretwurst, E.; Gabathuler, E.; Gabathuler, K.; Gamerdinger, K.; Garvey, J.; Gayler, J.; Gebauer, M.; Gellrich, A.; Genzel, H.; Gerhards, R.; Goerlach, U.; Goerlich, L.; Gogitidze, N.; Goldberg, M.; Goldner, D.; Gonzalez-Pineiro, B.; Gorelov, I.; Goritchev, P.; Grab, C.; Grässler, H.; Grässler, R.; Greenshaw, T.; Grindhammer, G.; Gruber, A.; Gruber, C.; Haack, J.; Haidt, D.; Hajduk, L.; Hamon, O.; Hampel, M.; Hanlon, E. M.; Hapke, M.; Haynes, W. J.; Heatherington, J.; Heinzelmann, G.; Henderson, R. C. W.; Henschel, H.; Herynek, I.; Hess, M. F.; Hildesheim, W.; Hill, P.; Hiller, K. H.; Hilton, C. D.; Hladký, J.; Hoeger, K. C.; Höppner, M.; Horisberger, R.; Hudgson, V. L.; Huet, Ph.; Hütte, M.; Hufnagel, H.; Ibbotson, M.; Itterbeck, H.; Jabiol, M.-A.; Jacholkowska, A.; Jacobsson, C.; Jaffre, M.; Janoth, J.; Jansen, T.; Jönsson, L.; Johnson, D. P.; Johnson, L.; Jung, H.; Kalmus, P. I. P.; Kant, D.; Kaschowitz, R.; Kasselmann, P.; Kathage, U.; Katzy, J.; Kaufmann, H. H.; Kazarian, S.; Kenyon, I. R.; Kermiche, S.; Keuker, C.; Kiesling, C.; Klein, M.; Kleinwort, C.; Knies, G.; Ko, W.; Köhler, T.; Köhne, J. H.; Kolanoski, H.; Kole, F.; Kolva, S. D.; Korbel, V.; Korn, M.; Kostka, P.; Kotelnikov, S. K.; Krämerkämper, T.; Krasny, M. W.; Krehbiel, H.; Krücker, D.; Krüger, U.; Krüner-Marquis, U.; Kubenka, J. P.; Küster, H.; Kuhlen, M.; Kurča, T.; Kurzhöfer, J.; Kuznik, B.; Lacour, D.; Lamarche, F.; Lander, R.; Landon, M. P. J.; Lange, W.; Lanius, P.; Laporte, J.-F.; Lebedev, A.; Leverenz, C.; Levonian, S.; Ley, Ch.; Lindner, A.; Lindström, G.; Link, J.; Linsel, F.; Lipinski, J.; List, B.; Lobo, G.; Loch, P.; Lohmander, H.; Lomas, J.; Lopez, G. C.; Lubimov, V.; Lüke, D.; Magnussen, N.; Malinovski, E.; Mani, S.; Maraček, R.; Marage, P.; Marks, J.; Marshall, R.; Martens, J.; Martin, R.; Martyn, H.-U.; Martyniak, J.; Masson, S.; Mavroidis, T.; Maxfield, S. J.; McMahon, S. J.; Mehta, A.; Meier, K.; Mercer, D.; Merz, T.; Meyer, C. A.; Meyer, H.; Meyer, J.; Mikocki, S.; Milstead, D.; Moreau, F.; Morris, J. V.; Mroczko, E.; Müller, G.; Müller, K.; Murín, P.; Nagovizin, V.; Nahnhauer, R.; Naroska, B.; Naumann, Th.; Newman, P. R.; Newton, D.; Neyret, D.; Nguyen, H. K.; Nicholls, T. C.; Niebergall, F.; Niebuhr, C.; Niedzballa, Ch.; Nisius, R.; Nowak, G.; Noyes, G. W.; Nyberg-Werther, M.; Oakden, M.; Oberlack, H.; Obrock, U.; Olsson, J. E.; Ozerov, D.; Panaro, E.; Panitch, A.; Pascaud, C.; Patel, G. D.; Peppel, E.; Perez, E.; Phillips, J. P.; Pichler, Ch.; Pitzl, D.; Pope, G.; Prell, S.; Prosi, R.; Rabbertz, K.; Rädel, G.; Raupach, F.; Reimer, P.; Reinshagen, S.; Ribarics, P.; Rick, H.; Riech, V.; Riedlberger, J.; Riess, S.; Rietz, M.; Rizvi, E.; Robertson, S. M.; Robmann, P.; Roloff, H. E.; Roosen, R.; Rosenbauer, K.; Rostovtsev, A.; Rouse, F.; Royon, C.; Rüter, K.; Rusakov, S.; Rybicki, K.; Rylko, R.; Sahlmann, N.; Sanchez, E.; Sankey, D. P. C.; Schacht, P.; Schiek, S.; Schleper, P.; von Schlippe, W.; Schmidt, C.; Schmidt, D.; Schmidt, G.; Schöning, A.; Schröder, V.; Schuhmann, E.; Schwab, B.; Schwind, A.; Sefkow, F.; Seidel, M.; Sell, R.; Semenov, A.; Shekelyan, V.; Sheviakov, I.; Shooshtari, H.; Shtarkov, L. N.; Siegmon, G.; Siewert, U.; Sirois, Y.; Skillicorn, I. O.; Smirnov, P.; Smith, J. R.; Solochenko, V.; Soloviev, Y.; Spiekermann, J.; Spitzer, H.; Starosta, R.; Steenbock, M.; Steffen, P.; Steinberg, R.; Stella, B.; Stephens, K.; Stier, J.; Stiewe, J.; Stösslein, U.; Stolze, K.; Strachota, J.; Straumann, U.; Struczinski, W.; Sutton, J. P.; Tapprogge, S.; Taylor, R. E.; Tchernyshov, V.; Thiebaux, C.; Thompson, G.; Truöl, P.; Turnau, J.; Tutas, J.; Uelkes, P.; Usik, A.; Valkár, S.; Valkárová, A.; Vallée, C.; Van Esch, P.; Van Mechelen, P.; Vartapetian, A.; Vazdik, Y.; Verrecchia, P.; Villet, G.; Wacker, K.; Wagener, A.; Wagener, M.; Walker, I. W.; Walther, A.; Weber, G.; Weber, M.; Wegener, D.; Wegner, A.; Wellisch, H. P.; West, L. R.; Willard, S.; Winde, M.; Winter, G.-G.; Wittek, C.; Wright, A. E.; Wünsch, E.; Wulff, N.; Yiou, T. P.; Žáček, J.; Zarbock, D.; Zhang, Z.; Zhokin, A.; Zimmer, M.; Zimmermann, W.; Zomer, F.; Zuber, K.; H1 Collaboration

1995-02-01

A measurement is presented, using data taken with the H1 detector at HERA, of the contribution of diffractive interactions to deep-inelastic electron-proton ( ep) scattering in the kinematic range 8.5 < Q2 < 50GeV 2, 2.4 × 10 -4 < Bjorken- x < 0.0133, and 3.7 × 10 -4 < χp < 0.043. The diffractive contribution to the proton structure function F2( x, Q2) is evaluated as a function of the appropriate deep-inelastic scattering variables χp, Q2, β (= {χ}/{χ p}) using a class of deep-inelastic ep scattering events with no hadronic energy flow in an interval of pseudo-rapidity adjacent to the proton beam direction. the dependence of this contribution on χp is measured to be χp- n with n = 1.19 ± 0.06 (stat.) ± 0.07 (syst.) independent of β and Q2, which is consistent with both a diffractive interpretation and a factorisable ep diffractive cross section. A first measurement of the deep-inelastic structure of the pomeron in the form of the Q2 and β dependences of a factorised structure function is presented. For all measured β, this structure function is observed to be consistent with scale invariance.

Structural Studies of Perfluoroaryldiselenadiazolyl Radicals: Insights into Dithiadiazolyl Chemistry.

PubMed

Melen, Rebecca L; Less, Robert J; Pask, Christopher M; Rawson, Jeremy M

2016-11-21

The synthesis and structural characterization of a series of perfluoroaryldiselenadiazolyls [DSeDA; p-XC 6 F 4 CNSeSeN (X = F, Cl, Br, CF 3 , NO 2 , and CN for 2a-2f, respectively)] are described. Concentration-dependent solution UV/vis measurements on 2a follow the Beer-Lambert law and the transitions assigned through time-dependent density functional theory (TD-DFT) studies, indicating little propensity for dimerization in solution (10 -3 -10 -4 M). Solution electron paramagnetic resonance (EPR) spectra reveal that these radicals exhibit a broad featureless singlet around g = 2.04 but form well-resolved anisotropic EPR spectra in frozen solution, from which spin densities were determined and found to reflect an increase in the spin density at the chalcogen in relation to the corresponding dithiadiazolyl (DTDA) radicals, p-XC 6 F 4 CNSSN. The solid-state structures of 2a and 2d-2f all adopt spin-paired cis-cofacial dimers in which the dimers are held together via multicenter π*-π* "pancake bonding" interactions. Conversely, 2b and 2c exhibit an orthogonal mode of association, which is unique to DSeDA chemistry but which also affords a singlet ground state evidenced by SQUID magnetometry. The more sterically demanding diselenadiazolyl radical 2f was also prepared and exhibits a trans-antarafacial dimerization mode. DFT studies [UPBE0-D3 ccPVTZ-PP(-F)++] on the model radical HCNSeSeN confirm that each dimer is a stable energy minimum on the potential energy surface, reproducing well the experimental geometric parameters with relative stability in the order cis-cofacial > orthogonal > trans-antarafacial. Computational studies reflect stronger dimerization for DSeDA radicals in relation to their sulfur analogues, consistent with the experimental observation: While 2a and 2d are isomorphous with their corresponding DTDA radicals, 2b, 2c, and 2e-2g are all dimeric, in contrast to their DTDA analogues, which are monomeric in the solid-state. A study on 2f reveals that significant geometric strain accumulates in order to support the propensity for both cis dimerization and intermolecular CN···Se interactions. Conversely, p-NCC 6 F 4 CNSSN likely forfeits dimerization in the analogous packing motif in order to release strain but retains the favorable intermolecular CN···S interactions.

Mechanism of Hydrogen Production in [Fe-Fe]-Hydrogenase: A Density Functional Theory Study (Preprint)

DTIC Science & Technology

2007-03-01

of NiFe hydrogenases. Dalton Transactions 2003,4030-4038. (9) Armstrong, F. A., Hydrogenases: active site puzzles and progress. Current Opinion in...DFT Investigation of Structural, Electronic, and Catalytic Properties of Diiron Complexes Related to the [2Fe]H Subcluster of Fe-Only Hydrogenases...Hydrogenases: Effects of Redox State and Ligand Characteristics on Structural, Electronic, and Reactivity Properties of Complexes Related to the [2Fe]H

Structure and magnetic properties of oxychalcogenides A2F2Fe2OQ2 (A = Sr, Ba; Q = S, Se) with Fe2O square planar layers representing an antiferromagnetic checkerboard spin lattice.

PubMed

Kabbour, Houria; Janod, Etienne; Corraze, Benoît; Danot, Michel; Lee, Changhoon; Whangbo, Myung-Hwan; Cario, Laurent

2008-07-02

The oxychalcogenides A2F2Fe2OQ2 (A = Sr, Ba; Q = S, Se), which contain Fe2O square planar layers of the anti-CuO2 type, were predicted using a modular assembly of layered secondary building units and subsequently synthesized. The physical properties of these compounds were characterized using magnetic susceptibility, electrical resistivity, specific heat, (57)Fe Mossbauer, and powder neutron diffraction measurements and also by estimating their exchange interactions on the basis of first-principles density functional theory electronic structure calculations. These compounds are magnetic semiconductors that undergo a long-range antiferromagnetic ordering below 83.6-106.2 K, and their magnetic properties are well-described by a two-dimensional Ising model. The dominant antiferromagnetic spin exchange interaction between S = 2 Fe(2+) ions occurs through corner-sharing Fe-O-Fe bridges. Moreover, the calculated spin exchange interactions show that the A2F2Fe2OQ2 (A = Sr, Ba; Q = S, Se) compounds represent a rare example of a frustrated antiferromagnetic checkerboard lattice.

Structures, internal rotor potentials, and thermochemical properties for a series of nitrocarbonyls, nitroolefins, corresponding nitrites, and their carbon centered radicals.

PubMed

Snitsiriwat, Suarwee; Asatryan, Rubik; Bozzelli, Joseph W

2011-12-01

Structures, enthalpy (Δ(f)H°(298)), entropy (S°(T)), and heat capacity (C(p)(T)) are determined for a series of nitrocarbonyls, nitroolefins, corresponding nitrites, and their carbon centered radicals using the density functional B3LYP and composite CBS-QB3 calculations. Enthalpies of formation (Δ(f)H°(298)) are determined at the B3LYP/6-31G(d,p), B3LYP/6-31+G(2d,2p), and composite CBS-QB3 levels using several work reactions for each species. Entropy (S) and heat capacity (C(p)(T)) values from vibration, translational, and external rotational contributions are calculated using the rigid-rotor-harmonic-oscillator approximation based on the vibration frequencies and structures obtained from the density functional studies. Contribution to Δ(f)H(T), S, and C(p)(T) from the analysis on the internal rotors is included. Recommended values for enthalpies of formation of the most stable conformers of nitroacetone cc(═o)cno2, acetonitrite cc(═o)ono, nitroacetate cc(═o)no2, and acetyl nitrite cc(═o)ono are -51.6 kcal mol(-1), -51.3 kcal mol(-1), -45.4 kcal mol(-1), and -58.2 kcal mol(-1), respectively. The calculated Δ(f)H°(298) for nitroethylene c═cno2 is 7.6 kcal mol(-1) and for vinyl nitrite c═cono is 7.2 kcal mol(-1). We also found an unusual phenomena: an intramolecular transfer reaction (isomerization) with a low barrier (3.6 kcal mol(-1)) in the acetyl nitrite. The NO of the nitrite (R-ONO) in CH(3)C(═O')ONO moves to the C═O' oxygen in a motion of a stretching frequency and then a shift to the carbonyl oxygen (marked as O' for illustration purposes). © 2011 American Chemical Society

First principle study of electronic structures and optical properties of Ce-doped SiO2

NASA Astrophysics Data System (ADS)

Cong, Wei-Yan; Lu, Ying-Bo; Zhang, Peng; Guan, Cheng-Bo

2018-05-01

Electronic structures and optical properties of Silicon dioxide (SiO2) systems with and without cerium(Ce) dopant were calculated using the density functional theory. We find that after the Ce incorporation, a new localized impurity band appears between the valance band maximum (VBM) and the conduction band minimum (CBM) of SiO2 system, which is induced mainly by the Ce-4f orbitals. The localized impurity band constructs a bridge between the valence band and the conduction band, making the electronic transition much easier. The calculated optical properties show that in contrast from the pure SiO2 sample, absorption in the visible-light region is found in Ce-doped SiO2 system, which originates from the transition between the valence band and Ce-4f dominated impurity band, as well as the electronic transition from Ce-4f states to Ce-5d states. All calculated results indicate that Ce doping is an effective strategy to improve the optical performance of SiO2 sample, which is in agreement with the experimental results.

Molecular basis of the fructose-2,6-bisphosphatase reaction of PFKFB3: Transition state and the C-terminal function

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

Cavalier, Michael C.; Kim, Song-Gun; Neau, David

2012-03-22

The molecular basis of fructose-2,6-bisphosphatase (F-2,6-P{sub 2}ase) of 6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase (PFKFB) was investigated using the crystal structures of the human inducible form (PFKFB3) in a phospho-enzyme intermediate state (PFKFB3-P {center_dot} F-6-P), in a transition state-analogous complex (PFKFB3 {center_dot} AlF{sub 4}), and in a complex with pyrophosphate (PFKFB3 {center_dot} PP{sub i}) at resolutions of 2.45, 2.2, and 2.3 {angstrom}, respectively. Trapping the PFKFB3-P {center_dot} F-6-P intermediate was achieved by flash cooling the crystal during the reaction, and the PFKFB3 {center_dot} AlF{sub 4} and PFKFB3 {center_dot} PP{sub i} complexes were obtained by soaking. The PFKFB3 {center_dot} AlF{sub 4} and PFKFB3 {center_dot} PP{sub i}more » complexes resulted in removing F-6-P from the catalytic pocket. With these structures, the structures of the Michaelis complex and the transition state were extrapolated. For both the PFKFB3-P formation and break down, the phosphoryl donor and the acceptor are located within {approx}5.1 {angstrom}, and the pivotal point 2-P is on the same line, suggesting an 'in-line' transfer with a direct inversion of phosphate configuration. The geometry suggests that NE2 of His253 undergoes a nucleophilic attack to form a covalent N-P bond, breaking the 2O-P bond in the substrate. The resulting high reactivity of the leaving group, 2O of F-6-P, is neutralized by a proton donated by Glu322. Negative charges on the equatorial oxygen of the transient bipyramidal phosphorane formed during the transfer are stabilized by Arg252, His387, and Asn259. The C-terminal domain (residues 440-446) was rearranged in PFKFB3 {center_dot} PP{sub i}, implying that this domain plays a critical role in binding of substrate to and release of product from the F-2,6-P{sub 2}ase catalytic pocket. These findings provide a new insight into the understanding of the phosphoryl transfer reaction.« less

Exploration of structural stability in deleterious nsSNPs of the XPA gene: A molecular dynamics approach.

PubMed

Nagasundaram, N; Priya Doss, C George

2011-01-01

Distinguishing the deleterious from the massive number of non-functional nsSNPs that occur within a single genome is a considerable challenge in mutation research. In this approach, we have used the existing in silico methods to explore the mutation-structure-function relationship in the XPAgene. We used the Sorting Intolerant From Tolerant (SIFT), Polymorphism Phenotyping (PolyPhen), I-Mutant 2.0, and the Protein Analysis THrough Evolutionary Relationships methods to predict the effects of deleterious nsSNPs on protein function and evaluated the impact of mutation on protein stability by Molecular Dynamics simulations. By comparing the scores of all the four in silico methods, nsSNP with an ID rs104894131 at position C108F was predicted to be highly deleterious. We extended our Molecular dynamics approach to gain insight into the impact of this non-synonymous polymorphism on structural changes that may affect the activity of the XPAgene. Based on the in silico methods score, potential energy, root-mean-square deviation, and root-mean-square fluctuation, we predict that deleterious nsSNP at position C108F would play a significant role in causing disease by the XPA gene. Our approach would present the application of in silicotools in understanding the functional variation from the perspective of structure, evolution, and phenotype.

Fabrication of superhydrophobic coating for preventing microleakage in a dental composite restoration.

PubMed

Cao, Danfeng; Zhang, Yingchao; Li, Yao; Shi, Xiaoyu; Gong, Haihuan; Feng, Dan; Guo, Xiaowei; Shi, Zuosen; Zhu, Song; Cui, Zhanchen

2017-09-01

Superhydrophobic coatings were successfully fabricated by photo-crosslinked polyurethane (PU) and organic fluoro group-functionalized SiO 2 nanoparticles (F-SiO 2 NPs), and were introduced for preventing microleakage in a dental composite restoration. The F-SiO 2 NPs possessed low surface energy and the PU can not only improve the mechanical stability but also promote F-SiO 2 NPs to form multiscale structure, which could facilitate the properties of the as-prepared superhydrophobic coating by synergetic effect. The morphology and properties of the resulted superhydrophobic coatings with different PU/F-SiO 2 ratios were studied using 1 H NMR spectrum, fourier transform infrared spectra, scanning electron microscopy, atomic force microscopy and UV-vis spectrophotometry. The results showed that the superhydrophobic coatings with low PU/F-SiO 2 ratio (1:3) possessed excellent hierarchical papillae structure with trapped air pockets, high contact angle (160.1°), low sliding angle (<1°) and good transparency. Additionally, MTT experiments results certified the prominent cell viability and biocompatibility for clinical application. Based on its fantastically superhydrophobic property, the as-prepared superhydrophobic coatings effectively prevented water permeation in resin composite restoration evaluation. This research may provide an effective method to solve the problem of microleakage and will efficiently increase the success rate of dental composite restorations. Copyright © 2017 Elsevier B.V. All rights reserved.

Oral Administration of a Select Mixture of Bacillus Probiotics Affects the Gut Microbiota and Goblet Cell Function following Escherichia coli Challenge in Newly Weaned Pigs of Genotype MUC4 That Are Supposed To Be Enterotoxigenic E. coli F4ab/ac Receptor Negative.

PubMed

Zhang, Wei; Zhu, Yao-Hong; Zhou, Dong; Wu, Qiong; Song, Dan; Dicksved, Johan; Wang, Jiu-Feng

2017-02-01

Structural disruption of the gut microbiota and impaired goblet cell function are collateral etiologic factors in enteric diseases. Low, moderate, or high doses of a Bacillus licheniformis-B. subtilis mixture (BLS mix) were orally administered to piglets of genotype MUC4 that are supposed to be F4-expressing enterotoxigenic Escherichia coli strain (F4 + ETEC) F4ab/ac receptor negative (i.e., MUC4-resistant piglets) for 1 week before F4 + ETEC challenge. The luminal contents were collected from the mucosa of the colon on day 8 after F4 + ETEC challenge. The BLS mix attenuated E. coli-induced expansion of Bacteroides uniformis, Eubacterium eligens, Acetanaerobacterium, and Sporobacter populations. Clostridium and Turicibacter populations increased following F4 + ETEC challenge in pigs pretreated with low-dose BLS mix. Lactobacillus gasseri and Lactobacillus salivarius populations increased after administration of BLS mix during E. coli infection. The beneficial effects of BLS mix were due in part to the expansion of certain Clostridium, Lactobacillus, and Turicibacter populations, with a corresponding increase in the number of goblet cells in the ileum via upregulated Atoh1 expression, in turn increasing MUC2 production and thus preserving the mucus barrier and enhancing host defenses against enteropathogenic bacteria. However, excessive BLS mix consumption may increase the risk for enteritis, partly through disruption of colonic microbial ecology, characterized by expansion of Proteobacteria and impaired goblet cell function in the ileum. Our findings suggest that oral administration of BLS mix reprograms the gut microbiota and enhances goblet cell function to ameliorate enteritis. The present study is important for improving our understanding of the protective role of probiotics against Escherichia coli infection in piglets. Structural disruption of the gut microbiota and impaired goblet cell function are collateral etiologic factors in enteric diseases. In this study, low, moderate, or high doses of a Bacillus licheniformis-B. subtilis mixture (BLS mix) were orally administered to MUC4-resistant piglets for 1 week before the F4-expressing ETEC strain (F4 + ETEC) challenge. Our findings suggest that oral administration of BLS mix reprograms the gut microbiota and enhances goblet cell function to ameliorate enteritis. Copyright © 2017 American Society for Microbiology.

Oral Administration of a Select Mixture of Bacillus Probiotics Affects the Gut Microbiota and Goblet Cell Function following Escherichia coli Challenge in Newly Weaned Pigs of Genotype MUC4 That Are Supposed To Be Enterotoxigenic E. coli F4ab/ac Receptor Negative

PubMed Central

Zhang, Wei; Zhou, Dong; Wu, Qiong; Song, Dan; Dicksved, Johan; Wang, Jiu-Feng

2016-01-01

ABSTRACT Structural disruption of the gut microbiota and impaired goblet cell function are collateral etiologic factors in enteric diseases. Low, moderate, or high doses of a Bacillus licheniformis-B. subtilis mixture (BLS mix) were orally administered to piglets of genotype MUC4 that are supposed to be F4-expressing enterotoxigenic Escherichia coli strain (F4+ ETEC) F4ab/ac receptor negative (i.e., MUC4-resistant piglets) for 1 week before F4+ ETEC challenge. The luminal contents were collected from the mucosa of the colon on day 8 after F4+ ETEC challenge. The BLS mix attenuated E. coli-induced expansion of Bacteroides uniformis, Eubacterium eligens, Acetanaerobacterium, and Sporobacter populations. Clostridium and Turicibacter populations increased following F4+ ETEC challenge in pigs pretreated with low-dose BLS mix. Lactobacillus gasseri and Lactobacillus salivarius populations increased after administration of BLS mix during E. coli infection. The beneficial effects of BLS mix were due in part to the expansion of certain Clostridium, Lactobacillus, and Turicibacter populations, with a corresponding increase in the number of goblet cells in the ileum via upregulated Atoh1 expression, in turn increasing MUC2 production and thus preserving the mucus barrier and enhancing host defenses against enteropathogenic bacteria. However, excessive BLS mix consumption may increase the risk for enteritis, partly through disruption of colonic microbial ecology, characterized by expansion of Proteobacteria and impaired goblet cell function in the ileum. Our findings suggest that oral administration of BLS mix reprograms the gut microbiota and enhances goblet cell function to ameliorate enteritis. IMPORTANCE The present study is important for improving our understanding of the protective role of probiotics against Escherichia coli infection in piglets. Structural disruption of the gut microbiota and impaired goblet cell function are collateral etiologic factors in enteric diseases. In this study, low, moderate, or high doses of a Bacillus licheniformis-B. subtilis mixture (BLS mix) were orally administered to MUC4-resistant piglets for 1 week before the F4-expressing ETEC strain (F4+ ETEC) challenge. Our findings suggest that oral administration of BLS mix reprograms the gut microbiota and enhances goblet cell function to ameliorate enteritis. PMID:27881419

Insight into the C-F bond mechanism of molecular analogs for antibacterial drug design.

PubMed

Liu, Junna; Lv, Biyu; Liu, Huaqing; Li, Xin; Yin, Weiping

2018-06-01

The activities of biological molecules usually rely on both of intra-molecular and intermolecular interactions between their function groups. These interactions include interonic attraction theory, Van der Waal's forces and the function of geometry on the individual molecules, whether they are naturally or synthetic. The purpose of this study was to evaluate the antibacterial activity of C-F bond compound using combination of experiments verification and theoretical calculation. We target on the insect natural products from the maggots of Chrysomyis megacephala Fabricius. Based on density functional theory(DFT) and B3LYP method, a theoretical study of the C-F bond on fluoride was designed to explore compounds 2 and 4 antibacterial structure-activity relationship. With the progress in DFT, first-principle calculation based on DFT has gradually become a routine method for drug design, quantum chemistry and other science fields.

Increased brain connectivity and activation after cognitive rehabilitation in Parkinson's disease: a randomized controlled trial.

PubMed

Díez-Cirarda, María; Ojeda, Natalia; Peña, Javier; Cabrera-Zubizarreta, Alberto; Lucas-Jiménez, Olaia; Gómez-Esteban, Juan Carlos; Gómez-Beldarrain, Maria Ángeles; Ibarretxe-Bilbao, Naroa

2017-12-01

Cognitive rehabilitation programs have demonstrated efficacy in improving cognitive functions in Parkinson's disease (PD), but little is known about cerebral changes associated with an integrative cognitive rehabilitation in PD. To assess structural and functional cerebral changes in PD patients, after attending a three-month integrative cognitive rehabilitation program (REHACOP). Forty-four PD patients were randomly divided into REHACOP group (cognitive rehabilitation) and a control group (occupational therapy). T1-weighted, diffusion weighted and functional magnetic resonance images (fMRI) during resting-state and during a memory paradigm (with learning and recognition tasks) were acquired at pre-treatment and post-treatment. Cerebral changes were assessed with repeated measures ANOVA 2 × 2 for group x time interaction. During resting-state fMRI, the REHACOP group showed significantly increased brain connectivity between the left inferior temporal lobe and the bilateral dorsolateral prefrontal cortex compared to the control group. Moreover, during the recognition fMRI task, the REHACOP group showed significantly increased brain activation in the left middle temporal area compared to the control group. During the learning fMRI task, the REHACOP group showed increased brain activation in the left inferior frontal lobe at post-treatment compared to pre-treatment. No significant structural changes were found between pre- and post-treatment. Finally, the REHACOP group showed significant and positive correlations between the brain connectivity and activation and the cognitive performance at post-treatment. This randomized controlled trial suggests that an integrative cognitive rehabilitation program can produce significant functional cerebral changes in PD patients and adds evidence to the efficacy of cognitive rehabilitation programs in the therapeutic approach for PD.

Quantification of 18F-fluorocholine kinetics in patients with prostate cancer.

PubMed

Verwer, Eline E; Oprea-Lager, Daniela E; van den Eertwegh, Alfons J M; van Moorselaar, Reindert J A; Windhorst, Albert D; Schwarte, Lothar A; Hendrikse, N Harry; Schuit, Robert C; Hoekstra, Otto S; Lammertsma, Adriaan A; Boellaard, Ronald

2015-03-01

Choline kinase is upregulated in prostate cancer, resulting in increased (18)F-fluoromethylcholine uptake. This study used pharmacokinetic modeling to validate the use of simplified methods for quantification of (18)F-fluoromethylcholine uptake in a routine clinical setting. Forty-minute dynamic PET/CT scans were acquired after injection of 204 ± 9 MBq of (18)F-fluoromethylcholine, from 8 patients with histologically proven metastasized prostate cancer. Plasma input functions were obtained using continuous arterial blood-sampling as well as using image-derived methods. Manual arterial blood samples were used for calibration and correction for plasma-to-blood ratio and metabolites. Time-activity curves were derived from volumes of interest in all visually detectable lymph node metastases. (18)F-fluoromethylcholine kinetics were studied by nonlinear regression fitting of several single- and 2-tissue plasma input models to the time-activity curves. Model selection was based on the Akaike information criterion and measures of robustness. In addition, the performance of several simplified methods, such as standardized uptake value (SUV), was assessed. Best fits were obtained using an irreversible compartment model with blood volume parameter. Parent fractions were 0.12 ± 0.4 after 20 min, necessitating individual metabolite corrections. Correspondence between venous and arterial parent fractions was low as determined by the intraclass correlation coefficient (0.61). Results for image-derived input functions that were obtained from volumes of interest in blood-pool structures distant from tissues of high (18)F-fluoromethylcholine uptake yielded good correlation to those for the blood-sampling input functions (R(2) = 0.83). SUV showed poor correlation to parameters derived from full quantitative kinetic analysis (R(2) < 0.34). In contrast, lesion activity concentration normalized to the integral of the blood activity concentration over time (SUVAUC) showed good correlation (R(2) = 0.92 for metabolite-corrected plasma; 0.65 for whole-blood activity concentrations). SUV cannot be used to quantify (18)F-fluoromethylcholine uptake. A clinical compromise could be SUVAUC derived from 2 consecutive static PET scans, one centered on a large blood-pool structure during 0-30 min after injection to obtain the blood activity concentrations and the other a whole-body scan at 30 min after injection to obtain lymph node activity concentrations. © 2015 by the Society of Nuclear Medicine and Molecular Imaging, Inc.

Materials Data on Sb4OsC6(O3F11)2 (SG:14) by Materials Project

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

Kristin Persson

Computed materials data using density functional theory calculations. These calculations determine the electronic structure of bulk materials by solving approximations to the Schrodinger equation. For more information, see https://materialsproject.org/docs/calculations

Materials Data on Sb4RuC6(O3F11)2 (SG:14) by Materials Project

DOE Data Explorer

Kristin Persson

2016-02-04

Computed materials data using density functional theory calculations. These calculations determine the electronic structure of bulk materials by solving approximations to the Schrodinger equation. For more information, see https://materialsproject.org/docs/calculations

Materials Data on FeSb4C6(O3F11)2 (SG:14) by Materials Project

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

Kristin Persson

Computed materials data using density functional theory calculations. These calculations determine the electronic structure of bulk materials by solving approximations to the Schrodinger equation. For more information, see https://materialsproject.org/docs/calculations

Materials Data on BaNaCe2C4O12F (SG:194) by Materials Project

DOE Data Explorer

Kristin Persson

2016-02-10

Computed materials data using density functional theory calculations. These calculations determine the electronic structure of bulk materials by solving approximations to the Schrodinger equation. For more information, see https://materialsproject.org/docs/calculations

Abnormal functional connectivity and cortical integrity influence dominant hand motor disability in multiple sclerosis: a multimodal analysis.

PubMed

Zhong, Jidan; Nantes, Julia C; Holmes, Scott A; Gallant, Serge; Narayanan, Sridar; Koski, Lisa

2016-12-01

Functional reorganization and structural damage occur in the brains of people with multiple sclerosis (MS) throughout the disease course. However, the relationship between resting-state functional connectivity (FC) reorganization in the sensorimotor network and motor disability in MS is not well understood. This study used resting-state fMRI, T1-weighted and T2-weighted, and magnetization transfer (MT) imaging to investigate the relationship between abnormal FC in the sensorimotor network and upper limb motor disability in people with MS, as well as the impact of disease-related structural abnormalities within this network. Specifically, the differences in FC of the left hemisphere hand motor region between MS participants with preserved (n = 17) and impaired (n = 26) right hand function, compared with healthy controls (n = 20) was investigated. Differences in brain atrophy and MT ratio measured at the global and regional levels were also investigated between the three groups. Motor preserved MS participants had stronger FC in structurally intact visual information processing regions relative to motor impaired MS participants. Motor impaired MS participants showed weaker FC in the sensorimotor and somatosensory association cortices and more severe structural damage throughout the brain compared with the other groups. Logistic regression analysis showed that regional MTR predicted motor disability beyond the impact of global atrophy whereas regional grey matter volume did not. More importantly, as the first multimodal analysis combining resting-state fMRI, T1-weighted, T2-weighted and MTR images in MS, we demonstrate how a combination of structural and functional changes may contribute to motor impairment or preservation in MS. Hum Brain Mapp 37:4262-4275, 2016. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

Structural and phylogenetic analysis of Rhodobacter capsulatus NifF: uncovering general features of nitrogen-fixation (nif)-flavodoxins.

PubMed

Pérez-Dorado, Inmaculada; Bortolotti, Ana; Cortez, Néstor; Hermoso, Juan A

2013-01-09

Analysis of the crystal structure of NifF from Rhodobacter capsulatus and its homologues reported so far reflects the existence of unique structural features in nif flavodoxins: a leucine at the re face of the isoalloxazine, an eight-residue insertion at the C-terminus of the 50's loop and a remarkable difference in the electrostatic potential surface with respect to non-nif flavodoxins. A phylogenetic study on 64 sequences from 52 bacterial species revealed four clusters, including different functional prototypes, correlating the previously defined as "short-chain" with the firmicutes flavodoxins and the "long-chain" with gram-negative species. The comparison of Rhodobacter NifF structure with other bacterial flavodoxin prototypes discloses the concurrence of specific features of these functional electron donors to nitrogenase.

Functional and structural abnormalities associated with empathy in patients with schizophrenia: An fMRI and VBM study

PubMed Central

Singh, Sadhana; Modi, Shilpi; Goyal, Satnam; Kaur, Prabhjot; Singh, Namita; Bhatia, Triptish; Deshpande, Smita N; Khushu, Subash

2016-01-01

Empathy deficit is a core feature of schizophrenia which may lead to social dysfunction. The present study was carried out to investigate functional and structural abnormalities associated with empathy in patients with schizophrenia using functional magnetic resonance imaging (fMRI) and voxel-based morphometry (VBM). A sample of 14 schizophrenia patients and 14 healthy control subjects matched for age, sex and education were examined with structural high-resolution T1-weighted MRI; fMRI images were obtained during empathy task in the same session. The analysis was carried out using SPM8 software. On behavioural assessment, schizophrenic patients (83.00±29.04) showed less scores for sadness compared to healthy controls (128.70±22.26) (p<0.001). fMRI results also showed reduced clusters of activation in the bilateral fusiform gyrus, left lingual gyrus, left middle and inferior occipital gyrus in schizophrenic subjects as compared to controls during empathy task. In the same brain areas, VBM results also showed reduced grey and white matter volumes. The present study provides an evidence for an association between structural alterations and disturbed functional brain activation during empathy task in persons affected with schizophrenia. These findings suggest a biological basis for social cognition deficits in schizophrenics. PMID:25963262

Functional and structural abnormalities associated with empathy in patients with schizophrenia: An fMRI and VBM study.

PubMed

Singh, Sadhana; Modi, Shilpi; Goyal, Satnam; Kaur, Prabhjot; Singh, Namita; Bhatia, Triptish; Deshpande, Smita N; Khushu, Subash

2015-06-01

Empathy deficit is a core feature of schizophrenia which may lead to social dysfunction. The present study was carried out to investigate functional and structural abnormalities associated with empathy in patients with schizophrenia using functional magnetic resonance imaging (fMRI) and voxel-based morphometry (VBM). A sample of 14 schizophrenia patients and 14 healthy control subjects matched for age, sex and education were examined with structural highresolution T1-weighted MRI; fMRI images were obtained during empathy task in the same session. The analysis was carried out using SPM8 software. On behavioural assessment, schizophrenic patients (83.00+-29.04) showed less scores for sadness compared to healthy controls (128.70+-22.26) (p less than 0.001). fMRI results also showed reduced clusters of activation in the bilateral fusiform gyrus, left lingual gyrus, left middle and inferior occipital gyrus in schizophrenic subjects as compared to controls during empathy task. In the same brain areas, VBM results also showed reduced grey and white matter volumes. The present study provides an evidence for an association between structural alterations and disturbed functional brain activation during empathy task in persons affected with schizophrenia. These findings suggest a biological basis for social cognition deficits in schizophrenics.

Scorpion-Toxin Mimics of CD4 in Complex with Human Immunodeficiency Virus gp120: Crystal Structures, Molecular Mimicry, and Neutralization Breadth

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

Huang, Chih-chin; Stricher, Francois; Martin, Loic

The binding surface on CD4 for the HIV-1 gp120 envelope glycoprotein has been transplanted previously onto a scorpion-toxin scaffold. Here, we use X-ray crystallography to characterize atomic-level details of gp120 with this transplant, CD4M33. Despite known envelope flexibility, the conformation of gp120 induced by CD4M33 was so similar to that induced by CD4 that localized measures were required to distinguish ligand-induced differences from lattice variation. To investigate relationships between structure, function, and mimicry, an F23 analog of CD4M33 was devised. Structural and thermodynamic analyses showed F23 to be a better molecular mimic of CD4 than CD4M33. F23 also showed increasedmore » neutralization breadth, against diverse isolates of HIV-1, HIV-2, and SIVcpz. Our results lend insight into the stability of the CD4 bound conformation of gp120, define measures that quantify molecular mimicry as a function of evolutionary distance, and suggest how such evaluations might be useful in developing mimetic antagonists with increased neutralization breadth.« less

Covalent character and electric field dependence of H2-AgX (X = F - I).

PubMed

Li, Xinying

2018-06-16

Mechanisms of Ag-X and Ag…H 2 interactions and stabilities of T-shaped H 2 -AgX (X = F - I) series were investigated at the CCSD(T) level. The "no-density" bond with smaller positive Laplacian and ELF values in interaction regions, as well as considerable delocalization index values, suggest weak covalent "charge-shift" character for the Ag…H 2 interaction. Structure and stability dependence on the electric field were investigated at the MP2 level. Relative total energy curves show obvious parabolic character, and the plots can be fitted by quadratic polynomials as functions of electric field strength.

Structure and possible mechanism of the CcbJ methyltransferase from Streptomyces caelestis.

PubMed

Bauer, Jacob; Ondrovičová, Gabriela; Najmanová, Lucie; Pevala, Vladimír; Kameník, Zdeněk; Koštan, Július; Janata, Jiří; Kutejová, Eva

2014-04-01

The S-adenosyl-L-methionine (SAM)-dependent methyltransferase CcbJ from Streptomyces caelestis catalyzes one of the final steps in the biosynthesis of the antibiotic celesticetin, methylation of the N atom of its proline moiety, which greatly enhances the activity of the antibiotic. Since several celesticetin variants exist, this enzyme may be able to act on a variety of substrates. The structures of CcbJ determined by MAD phasing at 3.0 Å resolution, its native form at 2.7 Å resolution and its complex with S-adenosyl-L-homocysteine (SAH) at 2.9 Å resolution are reported here. Based on these structures, three point mutants, Y9F, Y17F and F117G, were prepared in order to study its behaviour as well as docking simulations of both CcbJ-SAM-substrate and CcbJ-SAH-product complexes. The structures show that CcbJ is a class I SAM-dependent methyltransferase with a wide active site, thereby suggesting that it may accommodate a number of different substrates. The mutation results show that the Y9F and F117G mutants are almost non-functional, while the Y17F mutant has almost half of the wild-type activity. In combination with the docking studies, these results suggest that Tyr9 and Phe117 are likely to help to position the substrate for the methyl-transfer reaction and that Tyr9 may also facilitate the reaction by removing an H(+) ion. Tyr17, on the other hand, seems to operate by helping to stabilize the SAM cofactor.

Crystal Structure of the Pre-fusion Nipah Virus Fusion Glycoprotein Reveals a Novel Hexamer-of-Trimers Assembly.

PubMed

Xu, Kai; Chan, Yee-Peng; Bradel-Tretheway, Birgit; Akyol-Ataman, Zeynep; Zhu, Yongqun; Dutta, Somnath; Yan, Lianying; Feng, YanRu; Wang, Lin-Fa; Skiniotis, Georgios; Lee, Benhur; Zhou, Z Hong; Broder, Christopher C; Aguilar, Hector C; Nikolov, Dimitar B

2015-12-01

Nipah virus (NiV) is a paramyxovirus that infects host cells through the coordinated efforts of two envelope glycoproteins. The G glycoprotein attaches to cell receptors, triggering the fusion (F) glycoprotein to execute membrane fusion. Here we report the first crystal structure of the pre-fusion form of the NiV-F glycoprotein ectodomain. Interestingly this structure also revealed a hexamer-of-trimers encircling a central axis. Electron tomography of Nipah virus-like particles supported the hexameric pre-fusion model, and biochemical analyses supported the hexamer-of-trimers F assembly in solution. Importantly, structure-assisted site-directed mutagenesis of the interfaces between F trimers highlighted the functional relevance of the hexameric assembly. Shown here, in both cell-cell fusion and virus-cell fusion systems, our results suggested that this hexamer-of-trimers assembly was important during fusion pore formation. We propose that this assembly would stabilize the pre-fusion F conformation prior to cell attachment and facilitate the coordinated transition to a post-fusion conformation of all six F trimers upon triggering of a single trimer. Together, our data reveal a novel and functional pre-fusion architecture of a paramyxoviral fusion glycoprotein.

Genetic and Functional Diversity of Human Immunodeficiency Virus Type 1 Subtype B Nef Primary Isolates

PubMed Central

Foster, John L.; Molina, Rene P.; Luo, Tianci; Arora, Vivek K.; Huang, Yaoxing; Ho, David D.; Garcia, J. Victor

2001-01-01

We have characterized the functional integrity of seven primary Nef isolates: five from a long-term nonprogressing human immunodeficiency virus (HIV)-infected individual and one each from two patients with AIDS. One of the seven Nefs was defective for CD4 downregulation, two others were defective for PAK-2 activation, and one Nef was defective for PAK-2 activation and major histocompatibility complex (MHC) class I downregulation. Five of the Nefs were tested and found to be functional for the enhancement of virus particle infectivity. The structural basis for each of the functional defects has been analyzed by constructing a consensus nef, followed by mutational analysis of the variant amino acid residues. Mutations A29V and F193I were deleterious to CD4 downregulation and PAK-2 activation, respectively, while S189R rendered Nef defective for both MHC class I downregulation and PAK-2 activation. A search of the literature identified HIVs from five patients with Nefs predominantly mutated at F193 and from one patient with Nefs predominantly mutated at A29. A29 is highly conserved in all HIV subtypes except for subtype E. F193 is conserved in subtype B (and possibly in the closely related subtype D), but none of the other HIV group M subtypes. Our results suggest that functional distinctions may exist between HIV subtypes. PMID:11160665

Galactose-depleted xyloglucan is dysfunctional and leads to dwarfism in Arabidopsis.

PubMed

Kong, Yingzhen; Peña, Maria J; Renna, Luciana; Avci, Utku; Pattathil, Sivakumar; Tuomivaara, Sami T; Li, Xuemei; Reiter, Wolf-Dieter; Brandizzi, Federica; Hahn, Michael G; Darvill, Alan G; York, William S; O'Neill, Malcolm A

2015-04-01

Xyloglucan is a polysaccharide that has important roles in the formation and function of the walls that surround growing land plant cells. Many of these plants synthesize xyloglucan that contains galactose in two different side chains (L and F), which exist in distinct molecular environments. However, little is known about the contribution of these side chains to xyloglucan function. Here, we show that Arabidopsis (Arabidopsis thaliana) mutants devoid of the F side chain galactosyltransferase MURUS3 (MUR3) form xyloglucan that lacks F side chains and contains much less galactosylated xylose than its wild-type counterpart. The galactose-depleted xyloglucan is dysfunctional, as it leads to mutants that are dwarfed with curled rosette leaves, short petioles, and short inflorescence stems. Moreover, cell wall matrix polysaccharides, including xyloglucan and pectin, are not properly secreted and instead accumulate within intracellular aggregates. Near-normal growth is restored by generating mur3 mutants that produce no detectable amounts of xyloglucan. Thus, cellular processes are affected more by the presence of the dysfunctional xyloglucan than by eliminating xyloglucan altogether. To identify structural features responsible for xyloglucan dysfunction, xyloglucan structure was modified in situ by generating mur3 mutants that lack specific xyloglucan xylosyltransferases (XXTs) or that overexpress the XYLOGLUCAN L-SIDE CHAIN GALACTOSYLTRANSFERASE2 (XLT2) gene. Normal growth was restored in the mur3-3 mutant overexpressing XLT2 and in mur3-3 xxt double mutants when the dysfunctional xyloglucan was modified by doubling the amounts of galactosylated side chains. Our study assigns a role for galactosylation in normal xyloglucan function and demonstrates that altering xyloglucan side chain structure disturbs diverse cellular and physiological processes. © 2015 American Society of Plant Biologists. All Rights Reserved.

A Neutral Silicon/Phosphorus Frustrated Lewis Pair.

PubMed

Waerder, Benedikt; Pieper, Martin; Körte, Leif A; Kinder, Timo A; Mix, Andreas; Neumann, Beate; Stammler, Hans-Georg; Mitzel, Norbert W

2015-11-02

Frustrated Lewis pairs (FLPs) have a great potential for activation of small molecules. Most known FLP systems are based on boron or aluminum atoms as acid functions, few on zinc, and only two on boron-isoelectronic silicenium cation systems. The first FLP system based on a neutral silane, (C2F5)3SiCH2P(tBu)2 (1), was prepared from (C2F5)3SiCl with C2F5 groups of very high electronegativity and LiCH2P(tBu)2. 1 is capable of cleaving hydrogen, and adds CO2 and SO2. Hydrogen splitting was confirmed by H/D scrambling reactions. The structures of 1, its CO2 and SO2 adducts, and a decomposition product with CO2 were elucidated by X-ray diffraction. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Functional Connectivity Mapping in the Animal Model: Principles and Applications of Resting-State fMRI

PubMed Central

Gorges, Martin; Roselli, Francesco; Müller, Hans-Peter; Ludolph, Albert C.; Rasche, Volker; Kassubek, Jan

2017-01-01

“Resting-state” fMRI has substantially contributed to the understanding of human and non-human functional brain organization by the analysis of correlated patterns in spontaneous activity within dedicated brain systems. Spontaneous neural activity is indirectly measured from the blood oxygenation level-dependent signal as acquired by echo planar imaging, when subjects quietly “resting” in the scanner. Animal models including disease or knockout models allow a broad spectrum of experimental manipulations not applicable in humans. The non-invasive fMRI approach provides a promising tool for cross-species comparative investigations. This review focuses on the principles of “resting-state” functional connectivity analysis and its applications to living animals. The translational aspect from in vivo animal models toward clinical applications in humans is emphasized. We introduce the fMRI-based investigation of the non-human brain’s hemodynamics, the methodological issues in the data postprocessing, and the functional data interpretation from different abstraction levels. The longer term goal of integrating fMRI connectivity data with structural connectomes obtained with tracing and optical imaging approaches is presented and will allow the interrogation of fMRI data in terms of directional flow of information and may identify the structural underpinnings of observed functional connectivity patterns. PMID:28539914

Evolution of Quasiparticle Excitations in a Doped Hubbard Model

NASA Astrophysics Data System (ADS)

Hess, D. W.; Deisz, J. J.; Serene, J. W.

1997-03-01

Self-consistent calculations in the fluctuation exchange approximation for the 2D Hubbard model at half-filling show the evolution of anomalous structure in the self-energy at low energy with decreasing temperature. This structure is inconsistent with a Fermi liquid interpretation of evolving quasiparticle excitations.(J.J. Deisz, D.W. Hess, J.W. Serene, Phys. Rev. Lett. 76), 1312 (1996). Here we present calculations for a doped 2D Hubbard model with U=4t, n = 0.87 and for temperatures down to ~ 0.01t. Unlike the self-energy of the half-filled case, the slope of Re Σ(k_F, \\varepsilon) remains negative and | Im Σ(k_F, \\varepsilon)| shows no anomalous structure and is roughly parabolic at low energy with a very small magnitude at \\varepsilon = 0. In contrast to the `shadows' of antiferromagnetic order observed for half-filling, structure observed in the single-particle spectral function for momenta not on the Fermi surface are consistent with the characteristic depression at \\varepsilon =0 expected for an evolving Fermi liquid.(See e.g.) P.G. Mc Queen, D.W. Hess, J.W. Serene, Phys. Rev. Lett. 71, 129 (1993). No anomalous structure associated with incipient antiferromagnetic order is evident in the momentum distribution function.

Alkylphenol Xenoestrogens with Varying Carbon Chain Lengths Differentially and Potently Activate Signaling and Functional Responses in GH3/B6/F10 Somatomammotropes

PubMed Central

Kochukov, Mikhail Y.; Jeng, Yow-Jiun; Watson, Cheryl S.

2009-01-01

Background Alkylphenols varying in their side-chain lengths [ethyl-, propyl-, octyl-, and nonylphenol (EP, PP, OP, and NP, respectively)] and bisphenol A (BPA) represent a large group of structurally related xenoestrogens that have endocrine-disruptive effects. Their rapid nongenomic effects that depend on structure for cell signaling and resulting functions are unknown. Objectives We compared nongenomic estrogenic activities of alkylphenols with BPA and 17β-estradiol (E2) in membrane estrogen receptor-α–enriched GH3/B6/F10 pituitary tumor cells. These actions included calcium (Ca) signaling, prolactin (PRL) release, extracellular-regulated kinase (ERK) phosphorylation, and cell proliferation. Methods We imaged Ca using fura-2, measured PRL release via radioimmunoassay, detected ERK phosphorylation by fixed cell immunoassay, and estimated cell number using the crystal violet assay. Results All compounds caused increases in Ca oscillation frequency and intracellular Ca volume at 100 fM to 1 nM concentrations, although long-chain alkylphenols were most effective. All estrogens caused rapid PRL release at concentrations as low as 1 fM to 10 pM; the potency of EP, PP, and NP exceeded that of E2. All compounds at 1 nM produced similar increases in ERK phosphorylation, causing rapid peaks at 2.5–5 min, followed by inactivation and additional 60-min peaks (except for BPA). Dose–response patterns of ERK activation at 5 min were similar for E2, BPA, and PP, whereas EP caused larger effects. Only E2 and NP increased cell number. Some rapid estrogenic responses showed correlations with the hydrophobicity of estrogenic molecules; the more hydrophobic OP and NP were superior at Ca and cell proliferation responses, whereas the less hydrophobic EP and PP were better at ERK activations. Conclusions Alkylphenols are potent estrogens in evoking these nongenomic responses contributing to complex functions; their hydrophobicity can largely predict these behaviors. PMID:19479013

Autoxidation and Oxygen Binding Properties of Recombinant Hemoglobins with Substitutions at the αVal-62 or βVal-67 Position of the Distal Heme Pocket*

PubMed Central

Tam, Ming F.; Rice, Natalie W.; Maillett, David H.; Simplaceanu, Virgil; Ho, Nancy T.; Tam, Tsuey Chyi S.; Shen, Tong-Jian; Ho, Chien

2013-01-01

The E11 valine in the distal heme pocket of either the α- or β-subunit of human adult hemoglobin (Hb A) was replaced by leucine, isoleucine, or phenylalanine. Recombinant proteins were expressed in Escherichia coli and purified for structural and functional studies. 1H NMR spectra were obtained for the CO and deoxy forms of Hb A and the mutants. The mutations did not disturb the α1β2 interface in either form, whereas the H-bond between αHis-103 and βGln-131 in the α1β1 interfaces of the deoxy α-subunit mutants was weakened. Localized structural changes in the mutated heme pocket were detected for the CO form of recombinant Hb (rHb) (αV62F), rHb (βV67I), and rHb (βV67F) compared with Hb A. In the deoxy form the proximal histidyl residue in the β-subunit of rHb (βV67F) has been altered. Furthermore, the interactions between the porphyrin ring and heme pocket residues have been perturbed in rHb (αV62I), rHb (αV62F), and rHb (βV67F). Functionally, the oxygen binding affinity (P50), cooperativity (n50), and the alkaline Bohr Effect of the three α-subunit mutants and rHb (βV67L) are similar to those of Hb A. rHb (βV67I) and rHb (βV67F) exhibit low and high oxygen affinity, respectively. rHb (βV67F) has P50 values lower that those reported for rHb (αL29F), a B10 mutant studied previously in our laboratory (Wiltrout, M. E., Giovannelli, J. L., Simplaceanu, V., Lukin, J. A., Ho, N. T., and Ho, C. (2005) Biochemistry 44, 7207–7217). These E11 mutations do not slow down the autoxidation and azide-induced oxidation rates of the recombinant proteins. Results from this study provide new insights into the roles of E11 mutants in the structure-function relationship in hemoglobin. PMID:23867463

Structure-function relationships during segregated and integrated network states of human brain functional connectivity.

PubMed

Fukushima, Makoto; Betzel, Richard F; He, Ye; van den Heuvel, Martijn P; Zuo, Xi-Nian; Sporns, Olaf

2018-04-01

Structural white matter connections are thought to facilitate integration of neural information across functionally segregated systems. Recent studies have demonstrated that changes in the balance between segregation and integration in brain networks can be tracked by time-resolved functional connectivity derived from resting-state functional magnetic resonance imaging (rs-fMRI) data and that fluctuations between segregated and integrated network states are related to human behavior. However, how these network states relate to structural connectivity is largely unknown. To obtain a better understanding of structural substrates for these network states, we investigated how the relationship between structural connectivity, derived from diffusion tractography, and functional connectivity, as measured by rs-fMRI, changes with fluctuations between segregated and integrated states in the human brain. We found that the similarity of edge weights between structural and functional connectivity was greater in the integrated state, especially at edges connecting the default mode and the dorsal attention networks. We also demonstrated that the similarity of network partitions, evaluated between structural and functional connectivity, increased and the density of direct structural connections within modules in functional networks was elevated during the integrated state. These results suggest that, when functional connectivity exhibited an integrated network topology, structural connectivity and functional connectivity were more closely linked to each other and direct structural connections mediated a larger proportion of neural communication within functional modules. Our findings point out the possibility of significant contributions of structural connections to integrative neural processes underlying human behavior.

Density functional theory calculations for armchair stanene nanoribbons with fluorine and sulfur functionalization

NASA Astrophysics Data System (ADS)

Zhang, J.; Lang, X. Y.; Jiang, Q.

2018-07-01

A systematic density functional theory calculation has been carried out to study the effect of edge terminating of F and S elements with different edge natures on the structure and electronic properties of armchair stanene nanoribbons (ASnNRs). Moreover, the corresponding size (ribbon width Na) dependence on these properties is also considered. The energy gap was found to be oscillated as a function of Na and could be classified into three distinct groups of 3m, 3m + 1 and 3m + 2. In addition, the energy gaps of ASnNRs saturated by S atoms differ from that did by F and H atoms in vibration trends as well VBM and CBM changes, where the energy gap is a direct energy gap with a moderate size.

Structure–function analysis and genetic interactions of the SmG, SmE, and SmF subunits of the yeast Sm protein ring

PubMed Central

Schwer, Beate; Kruchten, Joshua; Shuman, Stewart

2016-01-01

A seven-subunit Sm protein ring forms a core scaffold of the U1, U2, U4, and U5 snRNPs that direct pre-mRNA splicing. Using human snRNP structures to guide mutagenesis in Saccharomyces cerevisiae, we gained new insights into structure–function relationships of the SmG, SmE, and SmF subunits. An alanine scan of 19 conserved amino acids of these three proteins, comprising the Sm RNA binding sites or inter-subunit interfaces, revealed that, with the exception of Arg74 in SmF, none are essential for yeast growth. Yet, for SmG, SmE, and SmF, as for many components of the yeast spliceosome, the effects of perturbing protein–RNA and protein–protein interactions are masked by built-in functional redundancies of the splicing machine. For example, tests for genetic interactions with non-Sm splicing factors showed that many benign mutations of SmG, SmE, and SmF (and of SmB and SmD3) were synthetically lethal with null alleles of U2 snRNP subunits Lea1 and Msl1. Tests of pairwise combinations of SmG, SmE, SmF, SmB, and SmD3 alleles highlighted the inherent redundancies within the Sm ring, whereby simultaneous mutations of the RNA binding sites of any two of the Sm subunits are lethal. Our results suggest that six intact RNA binding sites in the Sm ring suffice for function but five sites may not. PMID:27417296

Covalency in the f element-chalcogen bond. computational studies of M[N(EPR2)2]3 (M = La, Ce, Pr, Pm, Eu, U, Np, Pu, Am, Cm; E = O, S, Se, Te; R = H, (i)Pr, Ph).

PubMed

Ingram, Kieran I M; Tassell, Matthew J; Gaunt, Andrew J; Kaltsoyannis, Nikolas

2008-09-01

The geometric and electronic structures of the title complexes have been studied using scalar relativistic, gradient-corrected density functional theory. Extension of our previous work on six-coordinate M[N(EPH 2) 2] 3 (M = La, Ce, U, Pu; E = O, S, Se, Te), models for the experimentally characterized M[N(EP (i)Pr 2) 2] 3, yields converged geometries for all of the other 4f and 5f metals studied and for all four group 16 elements. By contrast, converged geometries for nine-coordinate M[N(EPPh 2) 2] 3 are obtained only for E = S and Se. Comparison of the electronic structures of six- and nine-coordinate M[N(EPH 2) 2] 3 suggests that coordination of the N atoms produces only minor changes in the metal-chalcogen interactions. Six-coordinate Eu[N(EPH 2) 2] 3 and Am[N(EPH 2) 2] 3 with the heavier group 16 donors display geometric and electronic properties rather different from those of the other members of the 4f and 5f series, in particular, longer than expected Eu-E and Am-E bond lengths, smaller reductions in charge difference between M and E down group 16, and larger f populations. The latter are interpreted not as evidence of f-based metal-ligand covalency but rather as being indicative of ionic metal centers closer to M (II) than M (III). The Cm complexes are found to be very ionic, with very metal-localized f orbitals and Cm (III) centers. The implications of the results for the separation of the minor actinides from nuclear wastes are discussed, as is the validity of using La (III)/U (III) comparisons as models for minor actinide/Eu systems.

Anionic ordering and thermal properties of FeF3·3H2O.

PubMed

Burbano, Mario; Duttine, Mathieu; Borkiewicz, Olaf; Wattiaux, Alain; Demourgues, Alain; Salanne, Mathieu; Groult, Henri; Dambournet, Damien

2015-10-05

Iron fluoride trihydrate can be used to prepare iron hydroxyfluoride with the hexagonal-tungsten-bronze (HTB) type structure, a potential cathode material for batteries. To understand this phase transformation, a structural description of β-FeF3·3H2O is first performed by means of DFT calculations and Mössbauer spectroscopy. The structure of this compound consists of infinite chains of [FeF6]n and [FeF2(H2O)4]n. The decomposition of FeF3·3H2O induces a collapse and condensation of these chains, which lead to the stabilization, under specific conditions, of a hydroxyfluoride network FeF3-x(OH)x with the HTB structure. The release of H2O and HF was monitored by thermal analysis and physical characterizations during the decomposition of FeF3·3H2O. An average distribution of FeF4(OH)2 distorted octahedra in HTB-FeF3-x(OH)x was obtained subsequent to the thermal hydrolysis/olation of equatorial anionic positions involving F(-) and H2O. This study provides a clear understanding of the structure and thermal properties of FeF3·3H2O, a material that can potentially bridge the recycling of pickling sludge from the steel industry by preparing battery electrodes.

Anionic ordering and thermal properties of FeF 3·3H 2O

DOE PAGES

Burbano, Mario; Duttine, Mathieu; Borkiewicz, Olaf; ...

2015-09-17

In this study, iron fluoride tri-hydrate can be used to prepare iron hydroxyfluoride with the Hexagonal-Tungsten-Bronze (HTB) type structure, a potential cathode material for batteries. To understand this phase transformation, a structural description of β-FeF 3·3H 2O is first performed by means of DFT calculations and Mössbauer spectroscopy. The structure of this compound consists of infinite chains of [FeF 6]n and [FeF 2(H2O) 4] n. The decomposition of FeF 3·3H 2O induces a collapse and condensation of these chains, which lead to the stabilization, under specific conditions, of a hydroxyfluoride network FeF 3-x(OH) x with the HTB structure. The releasemore » of H 2O and HF was monitored by thermal analysis and physical characterizations during the decomposition of FeF 3·3H 2O. An average distribution of FeF 4(OH) 2 distorted octahedra in HTB-FeF 3-x(OH) x was obtained subsequent to the thermal hydrolysis/olation of equatorial anionic positions involving F- and H 2O. This study provides a clear understanding of the structure and thermal properties of FeF 3·3H 2O, a material that can potentially bridge the recycling of pickling sludge from the steel industry by preparing battery electrodes.« less

Structure of the Newcastle disease virus hemagglutinin-neuraminidase (HN) ectodomain reveals a four-helix bundle stalk

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

Yuan, Ping; Swanson, Kurt A.; Leser, George P.

2014-10-02

The paramyxovirus hemagglutinin-neuraminidase (HN) protein plays multiple roles in viral entry and egress, including binding to sialic acid receptors, activating the fusion (F) protein to activate membrane fusion and viral entry, and cleaving sialic acid from carbohydrate chains. HN is an oligomeric integral membrane protein consisting of an N-terminal transmembrane domain, a stalk region, and an enzymatically active neuraminidase (NA) domain. Structures of the HN NA domains have been solved previously; however, the structure of the stalk region has remained elusive. The stalk region contains specificity determinants for F interactions and activation, underlying the requirement for homotypic F and HNmore » interactions in viral entry. Mutations of the Newcastle disease virus HN stalk region have been shown to affect both F activation and NA activities, but a structural basis for understanding these dual affects on HN functions has been lacking. Here, we report the structure of the Newcastle disease virus HN ectodomain, revealing dimers of NA domain dimers flanking the N-terminal stalk domain. The stalk forms a parallel tetrameric coiled-coil bundle (4HB) that allows classification of extensive mutational data, providing insight into the functional roles of the stalk region. Mutations that affect both F activation and NA activities map predominantly to the 4HB hydrophobic core, whereas mutations that affect only F-protein activation map primarily to the 4HB surface. Two of four NA domains interact with the 4HB stalk, and residues at this interface in both the stalk and NA domain have been implicated in HN function.« less

Tau PET in Alzheimer disease and mild cognitive impairment.

PubMed

Cho, Hanna; Choi, Jae Yong; Hwang, Mi Song; Lee, Jae Hoon; Kim, You Jin; Lee, Hye Mi; Lyoo, Chul Hyoung; Ryu, Young Hoon; Lee, Myung Sik

2016-07-26

To investigate the topographical distribution of tau pathology and its effect on functional and structural changes in patients with Alzheimer disease (AD) and mild cognitive impairment (MCI) by using (18)F-AV-1451 PET. We included 20 patients with AD, 15 patients with MCI, and 20 healthy controls, and performed neuropsychological function tests, MRI, as well as (18)F-florbetaben (for amyloid) and (18)F-AV-1451 (for tau) PET scans. By using the regional volume-of-interest masks extracted from MRIs, regional binding values of standardized uptake value ratios and volumes were measured. We compared regional binding values among 3 diagnostic groups and identified correlations among the regional binding values, performance in each cognitive function test, and regional atrophy. (18)F-AV-1451 binding was increased only in the entorhinal cortex in patients with MCI, while patients with AD exhibited greater binding in most cortical regions. In the 35 patients with MCI and AD, (18)F-AV-1451 binding in most of the neocortex increased with a worsening of global cognitive function. The visual and verbal memory functions were associated with the extent of (18)F-AV-1451 binding, especially in the medial temporal regions. The (18)F-AV-1451 binding also correlated with the severity of regional atrophy of the cerebral cortex. Tau PET imaging with (18)F-AV-1451 could serve as an in vivo biomarker for the evaluation of AD-related tau pathology and monitoring disease progression. The accumulation of pathologic tau is more closely related to functional and structural deterioration in the AD spectrum than β-amyloid. © 2016 American Academy of Neurology.

Functional-structural reorganisation of the neuronal network for auditory perception in subjects with unilateral hearing loss: Review of neuroimaging studies.

PubMed

Heggdal, Peder O Laugen; Brännström, Jonas; Aarstad, Hans Jørgen; Vassbotn, Flemming S; Specht, Karsten

2016-02-01

This paper aims to provide a review of studies using neuroimaging to measure functional-structural reorganisation of the neuronal network for auditory perception after unilateral hearing loss. A literature search was performed in PubMed. Search criterions were peer reviewed original research papers in English completed by the 11th of March 2015. Twelve studies were found to use neuroimaging in subjects with unilateral hearing loss. An additional five papers not identified by the literature search were provided by a reviewer. Thus, a total of 17 studies were included in the review. Four different neuroimaging methods were used in these studies: Functional magnetic resonance imaging (fMRI) (n = 11), diffusion tensor imaging (DTI) (n = 4), T1/T2 volumetric images (n = 2), magnetic resonance spectroscopy (MRS) (n = 1). One study utilized two imaging methods (fMRI and T1 volumetric images). Neuroimaging techniques could provide valuable information regarding the effects of unilateral hearing loss on both auditory and non-auditory performance. fMRI-studies showing a bilateral BOLD-response in patients with unilateral hearing loss have not yet been followed by DTI studies confirming their microstructural correlates. In addition, the review shows that an auditory modality-specific deficit could affect multi-modal brain regions and their connections. Copyright © 2015 Elsevier B.V. All rights reserved.

Immunology Research in Israel.

DTIC Science & Technology

1985-11-14

sonCLSIIDFG6S 1 .01 56 *3 2 . 1.8. 11111.2 1111 . MICROCOPY RESOLU TION TEST CHART W NAIN L 8UE OSTNA1936 - Ilile I.. - t"t 4-. r; I...pursued by Israel.i scientists include investigation of irmuno- globulin genes, structure-f unction analysis of antibodies and regulation of antibody...investigation of immuno- that had been first formulated by M. globulin genes, structure-function anal- Sela and R. Arnon. D. Givol pioneered in ysis of

Materials Data on ZrH16C5N2O3F4 (SG:41) by Materials Project

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

Kristin Persson

2016-02-11

Computed materials data using density functional theory calculations. These calculations determine the electronic structure of bulk materials by solving approximations to the Schrodinger equation. For more information, see https://materialsproject.org/docs/calculations

Exploring the Reduction of Fuel Consumption for Ship-to-Shore Connectors of the Marine Expeditionary Brigade

DTIC Science & Technology

2013-12-01

include the Command Element (CE), the Aviation Combat Element (ACE), the Ground Combat Element ( GCE ), and the Combat Service Support Element (CSSE) (from...35 Figure 9. The upper level functional architecture for EW12 shows the three primary functions of F1-Assemble the Seabase, F2...Function F2-Perform Assault is decomposed to obtain the lower level specific functions. From this decomposition, the sub-function of F2.2- Gain Entry

All-thiol-stabilized Ag44 and Au12Ag32 nanoparticles with single-crystal structures.

PubMed

Yang, Huayan; Wang, Yu; Huang, Huaqi; Gell, Lars; Lehtovaara, Lauri; Malola, Sami; Häkkinen, Hannu; Zheng, Nanfeng

2013-01-01

Noble metal nanoparticles stabilized by organic ligands are important for applications in assembly, site-specific bioconjugate labelling and sensing, drug delivery and medical therapy, molecular recognition and molecular electronics, and catalysis. Here we report crystal structures and theoretical analysis of three Ag44(SR)30 and three Au12Ag32(SR)30 intermetallic nanoclusters stabilized with fluorinated arylthiols (SR=SPhF, SPhF2 or SPhCF3). The nanocluster forms a Keplerate solid of concentric icosahedral and dodecahedral atom shells, protected by six Ag2(SR)5 units. Positive counterions in the crystal indicate a high negative charge of 4(-) per nanoparticle, and density functional theory calculations explain the stability as an 18-electron superatom shell closure in the metal core. Highly featured optical absorption spectra in the ultraviolet-visible region are analysed using time-dependent density functional perturbation theory. This work forms a basis for further understanding, engineering and controlling of stability as well as electronic and optical properties of these novel nanomaterials.

K(3)TaF(8) from laboratory X-ray powder data.

PubMed

Smrcok, Lubomír; Cerný, Radovan; Boca, Miroslav; Macková, Iveta; Kubíková, Blanka

2010-02-01

The crystal structure of tripotassium octafluoridotantalate, K(3)TaF(8), determined from laboratory powder diffraction data by the simulated annealing method and refined by total energy minimization in the solid state, is built from discrete potassium cations, fluoride anions and monocapped trigonal-prismatic [TaF(7)](2-) ions. All six atoms in the asymmetric unit are in special positions of the P6(3)mc space group: the Ta and one F atom in the 2b (3m) sites, the K and two F atoms in the 6c (m) sites, and one F atom in the 2a (3m) site. The structure consists of face-sharing K(6) octahedra with a fluoride anion at the center of each octahedron, forming chains of composition [FK(3)](2+) running along [001] with isolated [TaF(7)](2-) trigonal prisms in between. The structure of the title compound is different from the reported structure of Na(3)TaF(8) and represents a new structure type.

Experimental observation of charge-shift bond in fluorite CaF2.

PubMed

Stachowicz, Marcin; Malinska, Maura; Parafiniuk, Jan; Woźniak, Krzysztof

2017-08-01

On the basis of a multipole refinement of single-crystal X-ray diffraction data collected using an Ag source at 90 K to a resolution of 1.63 Å -1 , a quantitative experimental charge density distribution has been obtained for fluorite (CaF 2 ). The atoms-in-molecules integrated experimental charges for Ca 2+ and F - ions are +1.40 e and -0.70 e, respectively. The derived electron-density distribution, maximum electron-density paths, interaction lines and bond critical points along Ca 2+ ...F - and F - ...F - contacts revealed the character of these interactions. The Ca 2+ ...F - interaction is clearly a closed shell and ionic in character. However, the F - ...F - interaction has properties associated with the recently recognized type of interaction referred to as `charge-shift' bonding. This conclusion is supported by the topology of the electron localization function and analysis of the quantum theory of atoms in molecules and crystals topological parameters. The Ca 2+ ...F - bonded radii - measured as distances from the centre of the ion to the critical point - are 1.21 Å for the Ca 2+ cation and 1.15 Å for the F - anion. These values are in a good agreement with the corresponding Shannon ionic radii. The F - ...F - bond path and bond critical point is also found in the CaF 2 crystal structure. According to the quantum theory of atoms in molecules and crystals, this interaction is attractive in character. This is additionally supported by the topology of non-covalent interactions based on the reduced density gradient.

First Observation of Photoinduced Magnetization for the Cyano-Bridged 3d 4f Heterobimetallic Assembly Nd(DMF)4(H2O)3(μ-CN)Fe(CN)5ṡH2O (DMF=N,N-Dimethylformamide)

NASA Astrophysics Data System (ADS)

Li, Guangming; Akitsu, Takashiro; Sato, Osamu; Einaga, Yasuaki

2004-12-01

Photoinduced magnetization of the cyano-bridged 3d 4f hetero-bimetallic assembly Nd (DMF)4(H2O)3(μ-CN)Fe(CN)5ṡH2O (1) (DMF=N,N-dimethylformamide) is described in this paper. The χM T values are enhanced by about 45% after UV light illumination in the temperature range of 5 50 K. We propose that UV light illumination induces a structural distortion in 1. This small structural change is propagated by molecular interactions in the inorganic network. Furthermore, the cooperativity resulting from the molecular interaction functions to increase the activation energy of the relaxation processes, which makes observation of the photoexcited state possible. The flexible network structure through the hydrogen bonds in 1 plays an essential role for the photoinduced phenomenon. This finding may open up a new domain for developing molecule-based magnetic materials.

Thermally induced anchoring of fullerene in copolymers with Si-bridging atom: Spectroscopic evidences

NASA Astrophysics Data System (ADS)

Marchiori, Cleber F. N.; Garcia-Basabe, Yunier; de A. Ribeiro, Fabio; Koehler, Marlus; Roman, Lucimara S.; Rocco, Maria Luiza M.

2017-01-01

We use X-ray photoelectron spectroscopy (XPS), Near-edge X-ray absorption fine structure (NEXAFS), resonant Auger spectroscopy (RAS), Attenuation Total Reflection Infrared (ATR-IR) and Atomic Force Microscopy (AFM) to study the blend between the copolymer poly[2,7-(9,9-bis(2-ethylhexyl)-dibenzosilole)-alt-4,7-bis(thiophen-2-yl)benzo-2,1,3-thiadiazole] (PSiF-DBT) and the fullerene derivative PC71BM submitted to different annealing temperatures. Those measurements indicate that there is an incidental anchoring of a fullerene derivative to the Si-bridging atoms of a copolymer induced by thermal annealing of the film. Insights about the physical properties of one possible PSiF-DBT/PC71BM anchored structure are obtained using Density Functional Theory calculations. Since the performance of organic photovoltaic based on polymer-fullerene blends depends on the chemical structure of the blend components, the anchoring effect might affect the photovoltaic properties of those devices.

Structural and functional network connectivity breakdown in Alzheimer’s disease studied with magnetic resonance imaging techniques.

PubMed

Filippi, Massimo; Agosta, Federica

2011-01-01

Patients with Alzheimer’s disease (AD) experience a brain network breakdown, reflecting disconnection at both the structural and functional system level. Resting-state (RS) functional MRI (fMRI) studies demonstrated that the regional coherence of the fMRI signal is significantly altered in patients with AD and amnestic mild cognitive impairment. Diffusion tensor (DT) MRI has made it possible to track fiber bundle projections across the brain, revealing a substantially abnormal interplay of “critical” white matter tracts in these conditions. The observed agreement between the results of RS fMRI and DT MRI tractography studies in healthy individuals is encouraging and offers interesting hypotheses to be tested in patients with AD, a MCI, and other dementias in order to improve our understanding of their pathobiology in vivo. In this review,we describe the major findings obtained in AD using RS fMRI and DT MRI tractography, and discuss how the relationship between structure and function of the brain networks in AD may be better understood through the application of MR-based technology. This research endeavor holds a great promise in clarifying the mechanisms of cognitive decline in complex chronic neurodegenerative disorders.

Anatomical guidance for functional near-infrared spectroscopy: AtlasViewer tutorial

PubMed Central

Aasted, Christopher M.; Yücel, Meryem A.; Cooper, Robert J.; Dubb, Jay; Tsuzuki, Daisuke; Becerra, Lino; Petkov, Mike P.; Borsook, David; Dan, Ippeita; Boas, David A.

2015-01-01

Abstract. Functional near-infrared spectroscopy (fNIRS) is an optical imaging method that is used to noninvasively measure cerebral hemoglobin concentration changes induced by brain activation. Using structural guidance in fNIRS research enhances interpretation of results and facilitates making comparisons between studies. AtlasViewer is an open-source software package we have developed that incorporates multiple spatial registration tools to enable structural guidance in the interpretation of fNIRS studies. We introduce the reader to the layout of the AtlasViewer graphical user interface, the folder structure, and user files required in the creation of fNIRS probes containing sources and detectors registered to desired locations on the head, evaluating probe fabrication error and intersubject probe placement variability, and different procedures for estimating measurement sensitivity to different brain regions as well as image reconstruction performance. Further, we detail how AtlasViewer provides a generic head atlas for guiding interpretation of fNIRS results, but also permits users to provide subject-specific head anatomies to interpret their results. We anticipate that AtlasViewer will be a valuable tool in improving the anatomical interpretation of fNIRS studies. PMID:26157991

First-principle calculations of crystal structures, electronic structures, and optical properties of RETaO4 (RE = Y, La, Sm, Eu, Dy, Er)

NASA Astrophysics Data System (ADS)

Ma, Zhuang; Zheng, Jiayi; Wang, Song; Gao, Lihong

2018-01-01

It is an effective method to protect components from high power laser damage using high reflective materials. The rare earth tantalates RETaO4 with high dielectric constant suggests that they may have very high reflectivity, according to the relationship between dielectric constant and reflectivity. The crystal structures, electronic structures, and optical properties of RETaO4 (RE=Y, La, Sm, Eu, Dy, Er) have been studied by first-principle calculations. With the increasing atomic number of RE (i.e., the number of 4f electrons), a 4f electron shell moves from the bottom of conduction band to the forbidden gap and then to the valence band. The relationship between the electronic structures and optical properties is explored. The electron transitions among O 2p states, RE 4f states, and Ta 5d states have a key effect on optical properties such as dielectric function, absorption coefficient, and reflectivity. For the series of RETaO4, the appearance of the 4f electronic states will obviously promote the improvement of reflectivity. When the 4f states appear at the middle of the forbidden gap, the reflectivity reaches the maximum. The reflectivity of EuTaO4 at 1064 nm is up to 93.47%, indicating that it has potential applications in the antilaser radiation area.

Chemical Changes in Layered Ferroelectric Semiconductors Induced by Helium Ion Beam

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

Belianinov, Alex; Burch, Matthew J.; Hysmith, Holland E.

Transitioning to multi-material systems as either interfaced 2D materials or 3D heterostructures can lead to the next generation multi-functional device architectures. Combined direct physical and chemical nanoscale control of these systems offers a new way to tailor material and device functionality as functional structures reach their physical limit. Transition metal thiophosphate (TPS), Cu 1-xIn 1+x/3P 2S 6, that have ferroelectric polarization behavior as layered crystals at room temperature and above make them attractive candidates for direct material sculpting of both chemical and functional properties. The bulk material exhibits stable ferroelectric polarization corroborated by domain structures, rewritable polarization, and hysteresis loops.more » Our previous studies have demonstrated that ferroic order persists on the surface and that spinoidal decomposition of ferroelectric and paraelectric phases occurs in non-stoichiometric Cu/In ratio formulations. Here, we elucidate the chemical changes induced through helium ion irradiation in the TPS family library with varying Cu/In ratio formulations using correlated AFM and ToF-SIMS imaging. We correlate nano- and micro- structures that scale, in area and volume, to the total dose of the helium ion beam, as well as the overall copper concentration in the sample. Furthermore, our ToF-SIMS results show that ion irradiation leads to oxygen penetration as a function of Cu concentration, and proceeds along the Cu domains to the stopping distance of the helium ions in the TPS material. These results opens up new opportunities to understand and implement ferroicly coupled van der Waal devices into an existing framework of 2D heterostructures by locally tuning material chemistry and functionality.« less

Chemical Changes in Layered Ferroelectric Semiconductors Induced by Helium Ion Beam

DOE PAGES

Belianinov, Alex; Burch, Matthew J.; Hysmith, Holland E.; ...

2017-11-30

Transitioning to multi-material systems as either interfaced 2D materials or 3D heterostructures can lead to the next generation multi-functional device architectures. Combined direct physical and chemical nanoscale control of these systems offers a new way to tailor material and device functionality as functional structures reach their physical limit. Transition metal thiophosphate (TPS), Cu 1-xIn 1+x/3P 2S 6, that have ferroelectric polarization behavior as layered crystals at room temperature and above make them attractive candidates for direct material sculpting of both chemical and functional properties. The bulk material exhibits stable ferroelectric polarization corroborated by domain structures, rewritable polarization, and hysteresis loops.more » Our previous studies have demonstrated that ferroic order persists on the surface and that spinoidal decomposition of ferroelectric and paraelectric phases occurs in non-stoichiometric Cu/In ratio formulations. Here, we elucidate the chemical changes induced through helium ion irradiation in the TPS family library with varying Cu/In ratio formulations using correlated AFM and ToF-SIMS imaging. We correlate nano- and micro- structures that scale, in area and volume, to the total dose of the helium ion beam, as well as the overall copper concentration in the sample. Furthermore, our ToF-SIMS results show that ion irradiation leads to oxygen penetration as a function of Cu concentration, and proceeds along the Cu domains to the stopping distance of the helium ions in the TPS material. These results opens up new opportunities to understand and implement ferroicly coupled van der Waal devices into an existing framework of 2D heterostructures by locally tuning material chemistry and functionality.« less

A covariant model for the gamma N -> N(1535) transition at high momentum transfer

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

G. Ramalho, M.T. Pena

2011-08-01

A relativistic constituent quark model is applied to the gamma N -> N(1535) transition. The N(1535) wave function is determined by extending the covariant spectator quark model, previously developed for the nucleon, to the S11 resonance. The model allows us to calculate the valence quark contributions to the gamma N -> N(1535) transition form factors. Because of the nucleon and N(1535) structure the model is valid only for Q^2> 2.3 GeV^2. The results are compared with the experimental data for the electromagnetic form factors F1* and F2* and the helicity amplitudes A_1/2 and S_1/2, at high Q^2.

Intracellular degradation of chemically functionalized carbon nanotubes using a long-term primary microglial culture model

NASA Astrophysics Data System (ADS)

Bussy, Cyrill; Hadad, Caroline; Prato, Maurizio; Bianco, Alberto; Kostarelos, Kostas

2015-12-01

Chemically functionalized carbon nanotubes (f-CNTs) have been used in proof-of-concept studies to alleviate debilitating neurological conditions. Previous in vivo observations in brain tissue have suggested that microglia - acting as resident macrophages of the brain - play a critical role in the internalization of f-CNTs and their partial in situ biodegradation following a stereotactic administration in the cortex. At the same time, several reports have indicated that immune cells such as neutrophils, eosinophils and even macrophages could participate in the processing of carbon nanomaterials via oxidation processes leading to degradation, with surface properties acting as modulators of CNT biodegradability. In this study we questioned whether degradability of f-CNTs within microglia could be modulated depending on the type of surface functionalization used. We investigated the kinetics of degradation of multi-walled carbon nanotubes (MWNTs) functionalized via different chemical strategies that were internalized within isolated primary microglia over three months. A cellular model of rat primary microglia that can be maintained in cell culture for a long period of time was first developed. The Raman structural signature of the internalized f-CNTs was then studied directly in cells over a period of up to three months, following a single exposure to a non-cytotoxic concentration of three different f-CNTs (carboxylated, aminated and both carboxylated and aminated). Structural modifications suggesting partial but continuous degradation were observed for all nanotubes irrespective of their surface functionalization. Carboxylation was shown to promote more pronounced structural changes inside microglia over the first two weeks of the study.Chemically functionalized carbon nanotubes (f-CNTs) have been used in proof-of-concept studies to alleviate debilitating neurological conditions. Previous in vivo observations in brain tissue have suggested that microglia - acting as resident macrophages of the brain - play a critical role in the internalization of f-CNTs and their partial in situ biodegradation following a stereotactic administration in the cortex. At the same time, several reports have indicated that immune cells such as neutrophils, eosinophils and even macrophages could participate in the processing of carbon nanomaterials via oxidation processes leading to degradation, with surface properties acting as modulators of CNT biodegradability. In this study we questioned whether degradability of f-CNTs within microglia could be modulated depending on the type of surface functionalization used. We investigated the kinetics of degradation of multi-walled carbon nanotubes (MWNTs) functionalized via different chemical strategies that were internalized within isolated primary microglia over three months. A cellular model of rat primary microglia that can be maintained in cell culture for a long period of time was first developed. The Raman structural signature of the internalized f-CNTs was then studied directly in cells over a period of up to three months, following a single exposure to a non-cytotoxic concentration of three different f-CNTs (carboxylated, aminated and both carboxylated and aminated). Structural modifications suggesting partial but continuous degradation were observed for all nanotubes irrespective of their surface functionalization. Carboxylation was shown to promote more pronounced structural changes inside microglia over the first two weeks of the study. Electronic supplementary information (ESI) available. See DOI: 10.1039/c5nr06625e

Defects in oxide surfaces studied by atomic force and scanning tunneling microscopy

PubMed Central

König, Thomas; Simon, Georg H; Heinke, Lars; Lichtenstein, Leonid

2011-01-01

Summary Surfaces of thin oxide films were investigated by means of a dual mode NC-AFM/STM. Apart from imaging the surface termination by NC-AFM with atomic resolution, point defects in magnesium oxide on Ag(001) and line defects in aluminum oxide on NiAl(110), respectively, were thoroughly studied. The contact potential was determined by Kelvin probe force microscopy (KPFM) and the electronic structure by scanning tunneling spectroscopy (STS). On magnesium oxide, different color centers, i.e., F0, F+, F2+ and divacancies, have different effects on the contact potential. These differences enabled classification and unambiguous differentiation by KPFM. True atomic resolution shows the topography at line defects in aluminum oxide. At these domain boundaries, STS and KPFM verify F2+-like centers, which have been predicted by density functional theory calculations. Thus, by determining the contact potential and the electronic structure with a spatial resolution in the nanometer range, NC-AFM and STM can be successfully applied on thin oxide films beyond imaging the topography of the surface atoms. PMID:21977410

Effect of different surfactants on structural and optical properties of Ce3+ and Tb3+ co-doped BiPO4 nanostructures

NASA Astrophysics Data System (ADS)

Lakshminarayana, G.; Dao, T. D.; Chen, K.; Sharma, Manoj; Takeda, T.; Brik, M. G.; Kityk, I. V.; Singh, Sarabjot; Nagao, T.

2015-01-01

In this paper we report on the Ce3+ and Tb3+ ions co-doped bismuth phosphate (BiPO4) nanostructures that were synthesized by a simple precipitation method using different surfactants such as glycerol/H2O, glycerol/ethylene glycol, oleic acid, and ethylene glycol. The structural (X-ray diffraction, scanning electron microscopy, tunneling electron microscopy), functional groups analysis (Fourier transform infrared and Raman spectroscopy), thermal (thermogravimetry and differential thermal analysis), and optical (photoluminescence, photoluminescence-excitation) properties were investigated. The structural and morphological analysis confirms the pure hexagonal crystal structure of the synthesized nanostructures. From the measured Fourier transform infrared (FTIR) and Raman spectra various functional groups such as υ3 stretching vibration of the PO4 group, and δ(O-P-O) and υ4 (PO4) vibrations including the υ2 and υ1 bending modes of the PO4 units are identified. Based on the thermal analysis, for all the studied samples an exothermic peak between 680 °C and 700 °C was observed due to phase transition from hexagonal to high temperature monoclinic. The Ce3+and Tb3+ codoped samples show spectrally broad 5d → 4f luminescence in the blue (centered at 459 nm) wavelength region under the direct optical excitation of Ce3+ at 417 nm. Similarly, Tb3+ has revealed four main emission bands (5D4 → 7F6, 5, 4 and 3) at 490 nm, 545 nm, 585 nm and 621 nm with 378 nm (7F6 → 5G6) as the excitation wavelength, including three more weak emission bands at 647 nm, 669 nm, and 681 nm which could be assigned to 5D4 → 7F2, 1, 0 emission transitions. Among them, 545 nm (5D4 → 7F5) has shown bright green emission. The Ce3+ and Tb3+ codoped sample synthesized with pure oleic acid have shown relatively high green emission intensity for Tb3+, and relatively weak blue emission intensity for Ce3+ under their respective optical excitation wavelengths.

Effect of structural evolution of ZnO/HfO2 nanocrystals on Eu2+/Eu3+ emission in glass-ceramic waveguides for photonic applications

NASA Astrophysics Data System (ADS)

Ghosh, Subhabrata; N, Shivakiran Bhaktha B.

2018-06-01

Eu-doped 70SiO2–23HfO2–7ZnO (mol%) glass-ceramic waveguides have been fabricated by sol-gel method as a function of heat-treatment temperatures for on-chip blue-light emitting source applications. Structural evolution of spherical ZnO and spherical as well as rod-like HfO2 nanocrystalline structures have been observed with heat-treatments at different temperatures. Initially, in the as-prepared samples at 900 ◦C, both, Eu2+ as well as Eu3+ ions are found to be present in the ternary matrix. With controlled heat-treatments of up to 1000 ◦C for 2 h, local environment of Eu-ions become more crystalline in nature and the reduction of Eu3+ to Eu2+ takes place in such ZnO/HfO2 crystalline environments. In these ternary glass-ceramic waveguides, heat-treated at higher temperatures, the blue-light emission characteristic, which is the signature of 4f 65d \\to 4f 7 energy level transition of Eu2+ ions is found to be greatly enhanced. The as-prepared glass-ceramic waveguides exhibit a propagation loss of 0.4 ± 0.2 dB cm‑1 at 632.8 nm. Though the propagation losses increase with the growth of nanocrystals, the added functionalities achieved in the optimally heat-treated Eu-doped 70SiO2–23HfO2–7ZnO (mol%) waveguides, make them a viable functional optical material for the fabrication of on-chip blue-light emitting sources for integrated optic applications.

Effect of structural evolution of ZnO/HfO2 nanocrystals on Eu2+/Eu3+ emission in glass-ceramic waveguides for photonic applications.

PubMed

Ghosh, Subhabrata; Bhaktha B N, Shivakiran

2018-06-01

Eu-doped 70SiO 2 -23HfO 2 -7ZnO (mol%) glass-ceramic waveguides have been fabricated by sol-gel method as a function of heat-treatment temperatures for on-chip blue-light emitting source applications. Structural evolution of spherical ZnO and spherical as well as rod-like HfO 2 nanocrystalline structures have been observed with heat-treatments at different temperatures. Initially, in the as-prepared samples at 900 ◦ C, both, Eu 2+ as well as Eu 3+ ions are found to be present in the ternary matrix. With controlled heat-treatments of up to 1000 ◦ C for 2 h, local environment of Eu-ions become more crystalline in nature and the reduction of Eu 3+ to Eu 2+ takes place in such ZnO/HfO 2 crystalline environments. In these ternary glass-ceramic waveguides, heat-treated at higher temperatures, the blue-light emission characteristic, which is the signature of 4f 6 5d [Formula: see text] 4f 7 energy level transition of Eu 2+ ions is found to be greatly enhanced. The as-prepared glass-ceramic waveguides exhibit a propagation loss of 0.4 ± 0.2 dB cm -1 at 632.8 nm. Though the propagation losses increase with the growth of nanocrystals, the added functionalities achieved in the optimally heat-treated Eu-doped 70SiO 2 -23HfO 2 -7ZnO (mol%) waveguides, make them a viable functional optical material for the fabrication of on-chip blue-light emitting sources for integrated optic applications.

Electron induced ionization of plasma processing gases: C4F x (x  =  1–8) and the isomers of C4F6 and C4F8

NASA Astrophysics Data System (ADS)

Gupta, Dhanoj; Choi, Heechol; Kwon, Deuk-Chul; Yoon, Jung-Sik; Song, Mi-Young

2018-04-01

The total ionization cross section (Q ion) for C4F x (x  =  1–8) fluorocarbons and the isomers of C4F6 and C4F8 molecules are calculated from ionization threshold to 5 keV using the binary-encounter bethe method. The targets are fully optimized using the Hartree–Fock (HF) method and density function theory (DFT) for their minimum energy structure and orbital parameters. The present Q ion with HF parameters showed good agreement with the experimental data for 1,3-C4F6, 2-C4F6, 2-C4F8 and 1-C4F8. On the other hand, the Q ion with DFT parameters are in good accordance with the recent theoretical results for 1,3-C4F6 and 2-C4F6. The Q ion for c-C4F8 showed much variation among the various results. The isomer effect in Q ion is negligible for the isomers of C4F6 and C4F8 molecules. The calculation of Q ion for C4F, C4F2, C4F3, C4F4, C4F5, c-C4F6, C4F7 and iso-C4F8 is a maiden attempt. The present cross section data are important quantities for low temperature plasma modeling especially related to the fluorocarbon plasmas.

Inducing rye 1R chromosome structural changes in common wheat cv. Chinese spring by the gametocidal chromosome 2C of Aegilops cylindrica.

PubMed

Shi, Fang; Liu, Kun-Fan; Endo, Takashi R; Wang, Dao-Wen

2005-05-01

To generate 1 R deletion and translocation lines, we introduced a 2C chromosome,which was derived from Aegilops cylindrica and was known to have a gametocidal function when added monosomically into common wheat cv. Chinese Spring (CS) and its derivative, into a wheat-rye 1R chromosome disomic addition line (CS-1R"). When the individuals with chromosome constitution 21" + 1R" + 2C' (2n = 45) were selfed, the 1R chromosome structural changes were found to be induced with high frequency (24.1%) among the progenies. By using C-banding and GISH analysis, we analyzed 1R structural changes in 46 F3 individuals, which came from 23 F2 plants. The rearranged 1R chromosomes could be characterized in about 85% of the F3 individuals. This included telosome 1RL (39.1%), iso-chromosome 1 RL (2.2%), whole arm translocation involving 1RL (32.6%), telosome 1RS (4.3%), iso-chromosome 1RS (4.3%), and 1R deletion mutant with break point in the long arm (2.2%). The mutant 1R lines obtained in this study will potentially be useful in mapping the chromosome locations of agronomically important genes located in 1R. This study also demonstrated that molecular markers might be used to identify wheat chromosome arm involved in translocation with 1R.

Revealing topological organization of human brain functional networks with resting-state functional near infrared spectroscopy.

PubMed

Niu, Haijing; Wang, Jinhui; Zhao, Tengda; Shu, Ni; He, Yong

2012-01-01

The human brain is a highly complex system that can be represented as a structurally interconnected and functionally synchronized network, which assures both the segregation and integration of information processing. Recent studies have demonstrated that a variety of neuroimaging and neurophysiological techniques such as functional magnetic resonance imaging (MRI), diffusion MRI and electroencephalography/magnetoencephalography can be employed to explore the topological organization of human brain networks. However, little is known about whether functional near infrared spectroscopy (fNIRS), a relatively new optical imaging technology, can be used to map functional connectome of the human brain and reveal meaningful and reproducible topological characteristics. We utilized resting-state fNIRS (R-fNIRS) to investigate the topological organization of human brain functional networks in 15 healthy adults. Brain networks were constructed by thresholding the temporal correlation matrices of 46 channels and analyzed using graph-theory approaches. We found that the functional brain network derived from R-fNIRS data had efficient small-world properties, significant hierarchical modular structure and highly connected hubs. These results were highly reproducible both across participants and over time and were consistent with previous findings based on other functional imaging techniques. Our results confirmed the feasibility and validity of using graph-theory approaches in conjunction with optical imaging techniques to explore the topological organization of human brain networks. These results may expand a methodological framework for utilizing fNIRS to study functional network changes that occur in association with development, aging and neurological and psychiatric disorders.

A detailed study of the proton structure functions in deep inelastic muon-proton scattering

NASA Astrophysics Data System (ADS)

Aubert, J. J.; Bassompierre, G.; Becks, K. H.; Best, C.; Böhm, E.; de Bouard, X.; Brasse, F. W.; Broll, C.; Brown, S.; Carr, J.; Clifft, R. W.; Cobb, J. H.; Coignet, G.; Combley, F.; D'Agostini, G.; Dau, W. D.; Davies, J. K.; Déclais, Y.; Dobinson, R. W.; Dosselli, U.; Drees, J.; Edwards, A. W.; Edwards, M.; Favier, J.; Ferrero, M. I.; Flauger, W.; Gabathuler, E.; Gamet, R.; Gayler, J.; Gerhardt, V.; Gössling, C.; Haas, J.; Hamacher, K.; Hayman, P.; Henckes, M.; Korbel, V.; Landgraf, U.; Leenen, M.; Maire, M.; Mohr, W.; Montgomery, H. E.; Moser, K.; Mount, R. P.; Nassalski, J.; Norton, P. R.; McNicholas, J.; Osborne, A. M.; Payre, P.; Peroni, C.; Pessard, H.; Pietrzyk, U.; Rith, K.; Schneegans, M.; Sloan, T.; Stier, H. E.; Stockhausen, W.; Thénard, J. M.; Thompson, J. C.; Urban, L.; Wahlen, H.; Whalley, M.; Williams, W. S. C.; Williamson, J.; Wimpenny, S. J.; European Muon Collaboration

1985-09-01

The x and Q2 dependence of the single photon exchange cross section d 2σ/d Q2d x and the proton structure functions F2( x, Q2) and R( x, Q2) have been measured in deep inelastic muon proton scattering in the region 0.02 < x < 0.8 and 3 < Q2 < 190 GeV 2. By comparing data at different incident muon energies R was found to have little kinematic dependence and an average value of -0.010 ± 0.037 (stat.) ± 0.102 (stat.). The observed deviations from scaling gave the value of Λ overlineMS, the QCD mass scale parameter, to be 105 -45+55 (stat.) -45+85 (syst.) MeV. The fraction of the momentum of the nucleon carried by gluons was found to be ˜56% at Q2˜22.5 GeV 2. It is shown that to obtain a description of the data for F2( x, Q2) together with that measured in deep inelastic electron-proton scattering at lower Q2 it is necessary to include additional higher twist contributions. The value of Λ overlineMS remains unchanged with the inclusion of these contributions which were found to have an x-dependence of the form x3/(1 - x).

Preclinical Positron Emission Tomographic Imaging of Acute Hyperoxia Therapy of Chronic Hypoxia during Pregnancy.

PubMed

Zheleznyak, Alexander; Garbow, Joel R; Neeman, Michal; Lapi, Suzanne E

2015-01-01

The goal of this work was to study the efficacy of the positron emission tomography (PET) tracers 2-deoxy-2-[18F]fluoro-D-glucose ([18F]FDG) and 64Cu-diacetyl-bis(N4-methylthiosemicarbazone) ([64Cu]ATSM) and in monitoring placental and fetal functional response to acute hyperoxia in late-term pregnant mice subjected to experimentally induced chronic hypoxia. E15 mice were maintained at 12% inspired oxygen for 72 hours and then imaged during oxygen inhalation with either [18F]FDG to monitor nutrient transport or 64Cu-ATSM to establish the presence of hypoxia. Computed tomography (CT) with contrast allowed clear visualization of both placentas and fetuses. The average ratio of fetal to placental [18F]FDG uptake was 0.45 ± 0.1 for the hypoxic animals and 0.55 ± 0.1 for the normoxic animals, demonstrating a significant decrease (p = .0002) in placental function in dams exposed to chronic hypoxic conditions. Hypoxic placentas and fetuses retained more 64Cu-ATSM compared to normoxic placentas and fetuses. Herein we report first-in-mouse PET imaging of fetuses employing both tracers [18F]FDG (metabolism) and 64Cu-ATSM (hypoxia). [18F]FDG PET/CT imaging allowed clear visualization of placental-fetal structures and supported quantification of tracer uptake, making this a sensitive tool for monitoring placental function in preclinical rodent models. These measurements illustrate the potentially irreversible damage generated by chronic exposure to hypoxia, which cannot be corrected by acute exposure to hyperoxia.

Distortion product otoacoustic emissions provide clues to hearing mechanisms in the frog ear

NASA Astrophysics Data System (ADS)

Vassilakis, Pantelis N.; Meenderink, Sebastiaan W. F.; Narins, Peter M.

2004-12-01

2 f1-f2 and 2 f2-f1 distortion product otoacoustic emissions (DPOAEs) were recorded from both ears of male and female Rana pipiens pipiens and Rana catesbeiana. The input-output (I/O) curves obtained from the amphibian papilla (AP) of both frog species are analogous to I/O curves recorded from mammals suggesting that, similarly to the mammalian cochlea, there may be an amplification process present in the frog AP. DPOAE level dependence on L1-L2 is different from that in mammals and consistent with intermodulation distortion expectations. Therefore, if a mechanical structure in the frog inner ear is functioning analogously to the mammalian basilar membrane, it must be more broadly tuned. DPOAE audiograms were obtained for primary frequencies spanning the animals' hearing range and selected stimulus levels. The results confirm that DPOAEs are produced in both papillae, with R. catesbeiana producing stronger emissions than R. p. pipiens. Consistent with previously reported sexual dimorphism in the mammalian and anuran auditory systems, females of both species produce stronger emissions than males. Moreover, it appears that 2 f1-f2 in the frog is generated primarily at the DPOAE frequency place, while 2 f2-f1 is generated primarily at a frequency place around the primaries. Regardless of generation place, both emissions within the AP may be subject to the same filtering mechanism, possibly the tectorial membrane..

Structural Basis of Response Regulator Dephosphorylation by Rap Phosphatases

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

V Parashar; N Mirouze; D Dubnau

2011-12-31

Bacterial Rap family proteins have been most extensively studied in Bacillus subtilis, where they regulate activities including sporulation, genetic competence, antibiotic expression, and the movement of the ICEBs1 transposon. One subset of Rap proteins consists of phosphatases that control B. subtilis and B. anthracis sporulation by dephosphorylating the response regulator Spo0F. The mechanistic basis of Rap phosphatase activity was unknown. Here we present the RapH-Spo0F X-ray crystal structure, which shows that Rap proteins consist of a 3-helix bundle and a tetratricopeptide repeat domain. Extensive biochemical and genetic functional studies reveal the importance of the observed RapH-Spo0F interactions, including the catalyticmore » role of a glutamine in the RapH 3-helix bundle that inserts into the Spo0F active site. We show that in addition to dephosphorylating Spo0F, RapH can antagonize sporulation by sterically blocking phosphoryl transfer to and from Spo0F. Our structure-function analysis of the RapH-Spo0F interaction identified Rap protein residues critical for Spo0F phosphatase activity. This information enabled us to assign Spo0F phosphatase activity to a Rap protein based on sequence alone, which was not previously possible. Finally, as the ultimate test of our newfound understanding of the structural requirements for Rap phosphatase function, a non-phosphatase Rap protein that inhibits the binding of the response regulator ComA to DNA was rationally engineered to dephosphorylate Spo0F. In addition to revealing the mechanistic basis of response regulator dephosphorylation by Rap proteins, our studies support the previously proposed T-loop-Y allostery model of receiver domain regulation that restricts the aromatic 'switch' residue to an internal position when the {beta}4-{alpha}4 loop adopts an active-site proximal conformation.« less

Electronic structure and bonding properties of potassium (K) on graphite under external electric field.

NASA Astrophysics Data System (ADS)

Tapia, Alejandro; Canto, Gabriel

2005-03-01

The effect of an external electric field on the potassium (K) adsorption on the graphite surface, are studied by means of first-principles total-energy calculations. The results were obtained with the pseudopotentials LCAO method (SIESTA code) and the Generalized Gradient Approximation (GGA) for the exchange-correlation potential. The structural parameters, bonding properties, and electronic structure of the K-graphite system are studied in the triangular (2x2) overlayer phase as a function of the external electric field magnitude. We find an important change in the K-graphite bonding as a consequence of the charge transfer from the adatom towards the substrate induced by the electric field. The results are discussed in the light of the experimental observed difussion of K into graphite induced by external electric fields. This work was supported by Consejo Nacional de Ciencia y Tecnolog'ia (CONACYT, M'exico) under Grants No. 43830-F and No. 44831-F.

Changes of Visual Pathway and Brain Connectivity in Glaucoma: A Systematic Review

PubMed Central

Nuzzi, Raffaele; Dallorto, Laura; Rolle, Teresa

2018-01-01

Background: Glaucoma is a leading cause of irreversible blindness worldwide. The increasing interest in the involvement of the cortical visual pathway in glaucomatous patients is due to the implications in recent therapies, such as neuroprotection and neuroregeneration. Objective: In this review, we outline the current understanding of brain structural, functional, and metabolic changes detected with the modern techniques of neuroimaging in glaucomatous subjects. Methods: We screened MEDLINE, EMBASE, CINAHL, CENTRAL, LILACS, Trip Database, and NICE for original contributions published until 31 October 2017. Studies with at least six patients affected by any type of glaucoma were considered. We included studies using the following neuroimaging techniques: functional Magnetic Resonance Imaging (fMRI), resting-state fMRI (rs-fMRI), magnetic resonance spectroscopy (MRS), voxel- based Morphometry (VBM), surface-based Morphometry (SBM), diffusion tensor MRI (DTI). Results: Over a total of 1,901 studies, 56 case series with a total of 2,381 patients were included. Evidence of neurodegenerative process in glaucomatous patients was found both within and beyond the visual system. Structural alterations in visual cortex (mainly reduced cortex thickness and volume) have been demonstrated with SBM and VBM; these changes were not limited to primary visual cortex but also involved association visual areas. Other brain regions, associated with visual function, demonstrated a certain grade of increased or decreased gray matter volume. Functional and metabolic abnormalities resulted within primary visual cortex in all studies with fMRI and MRS. Studies with rs-fMRI found disrupted connectivity between the primary and higher visual cortex and between visual cortex and associative visual areas in the task-free state of glaucomatous patients. Conclusions: This review contributes to the better understanding of brain abnormalities in glaucoma. It may stimulate further speculation about brain plasticity at a later age and therapeutic strategies, such as the prevention of cortical degeneration in patients with glaucoma. Structural, functional, and metabolic neuroimaging methods provided evidence of changes throughout the visual pathway in glaucomatous patients. Other brain areas, not directly involved in the processing of visual information, also showed alterations. PMID:29896087

Phospho-selective mechanisms of arrestin conformations and functions revealed by unnatural amino acid incorporation and 19F-NMR

PubMed Central

Yang, Fan; Yu, Xiao; Liu, Chuan; Qu, Chang-Xiu; Gong, Zheng; Liu, Hong-Da; Li, Fa-Hui; Wang, Hong-Mei; He, Dong-Fang; Yi, Fan; Song, Chen; Tian, Chang-Lin; Xiao, Kun-Hong; Wang, Jiang-Yun; Sun, Jin-Peng

2015-01-01

Specific arrestin conformations are coupled to distinct downstream effectors, which underlie the functions of many G-protein-coupled receptors (GPCRs). Here, using unnatural amino acid incorporation and fluorine-19 nuclear magnetic resonance (19F-NMR) spectroscopy, we demonstrate that distinct receptor phospho-barcodes are translated to specific β-arrestin-1 conformations and direct selective signalling. With its phosphate-binding concave surface, β-arrestin-1 ‘reads' the message in the receptor phospho-C-tails and distinct phospho-interaction patterns are revealed by 19F-NMR. Whereas all functional phosphopeptides interact with a common phosphate binding site and induce the movements of finger and middle loops, different phospho-interaction patterns induce distinct structural states of β-arrestin-1 that are coupled to distinct arrestin functions. Only clathrin recognizes and stabilizes GRK2-specific β-arrestin-1 conformations. The identified receptor-phospho-selective mechanism for arrestin conformation and the spacing of the multiple phosphate-binding sites in the arrestin enable arrestin to recognize plethora phosphorylation states of numerous GPCRs, contributing to the functional diversity of receptors. PMID:26347956

Synthesis and characterization of new fluoride-containing manganese vanadates A{sub 2}Mn{sub 2}V{sub 2}O{sub 7}F{sub 2} (A=Rb, Cs) and Mn{sub 2}VO{sub 4}F

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

Sanjeewa, Liurukara D.; McGuire, Michael A.; Smith Pellizzeri, Tiffany M.

2016-09-15

Large single crystals of A{sub 2}Mn{sub 2}V{sub 2}O{sub 7}F{sub 2} (A=Rb, Cs) and Mn{sub 2}VO{sub 4}F were grown using a high-temperature (~600 °C) hydrothermal technique. Single crystal X-ray diffraction and powder X-ray diffraction were utilized to characterize the structures, which both possess MnO{sub 4}F{sub 2} building blocks. The A{sub 2}Mn{sub 2}V{sub 2}O{sub 7}F{sub 2} series crystallizes as a new structure type in space group Pbcn (No. 60), Z=4 (Rb{sub 2}Mn{sub 2}V{sub 2}O{sub 7}F{sub 2}: a=7.4389(17) Å, b=11.574(3) Å, c=10.914(2) Å; Cs{sub 2}Mn{sub 2}V{sub 2}O{sub 7}F{sub 2}: a=7.5615(15) Å, b=11.745(2) Å, c=11.127(2) Å). The structure is composed of zigzag chains ofmore » edge-sharing MnO{sub 4}F{sub 2} units running along the a-axis, and interconnected through V{sub 2}O{sub 7} pyrovanadate groups. Temperature dependent magnetic susceptibility measurements on this interesting one-dimensional structural feature based on Mn{sup 2+} indicated that Cs{sub 2}Mn{sub 2}V{sub 2}O{sub 7}F{sub 2} is antiferromagnetic with a Neél temperature, T{sub N}=~3 K and a Weiss constant, θ, of −11.7(1) K. Raman and infrared spectra were also analyzed to identify the fundamental V–O vibrational modes in Cs{sub 2}Mn{sub 2}V{sub 2}O{sub 7}F{sub 2}. Mn{sub 2}(VO{sub 4})F crystalizes in the monoclinic space group of C2/c (no. 15), Z=8 with unit cell parameters of a=13.559(2) Å, b=6.8036(7) Å, c=10.1408(13) Å and β=116.16(3)°. The structure is associated with those of triplite and wagnerite. Dynamic fluorine disorder gives rise to complex alternating chains of five-and six-coordinate Mn{sup 2+}. These interpenetrating chains are additionally connected through isolated VO{sub 4} tetrahedra to form the condensed structure. - Graphical abstract: New vanadate fluorides A{sub 2}Mn{sub 2}V{sub 2}O{sub 7}F{sub 2} (A=Rb, Cs) and Mn{sub 2}(VO{sub 4})F have been synthesized hydrothermally. Upon cooling, the one-dimensional Mn(II) substructure results in antiferromagnetic ordering. Display Omitted - Highlights: • Single crystals of A{sub 2}Mn{sub 2}V{sub 2}O{sub 7}F{sub 2}, (A=Rb, Cs) and Mn{sub 2}VO{sub 4}F were grown hydrothermally. • The use of fluoride mineralizers in the synthesis led to the formation of new compounds without OH{sup −} groups. • The structure of A{sub 2}Mn{sub 2}V{sub 2}O{sub 7}F{sub 2} features zigzag chains of MnO{sub 4}F{sub 2} units. • Cs{sub 2}Mn{sub 2}V{sub 2}O{sub 7}F{sub 2} exhibits antiferromagnetic ordering with a Neel temperature of ~3 K. • Mn{sub 2}VO{sub 4}F possesses a condensed framework structure with disordered fluorine atoms.« less

Trapping of Li(+) Ions by [ThFn](4-n) Clusters Leading to Oscillating Maxwell-Stefan Diffusivity in the Molten Salt LiF-ThF4.

PubMed

Chakraborty, Brahmananda; Kidwai, Sharif; Ramaniah, Lavanya M

2016-08-18

A molten salt mixture of lithium fluoride and thorium fluoride (LiF-ThF4) serves as a fuel as well as a coolant in the most sophisticated molten salt reactor (MSR). Here, we report for the first time dynamic correlations, Onsager coefficients, Maxwell-Stefan (MS) diffusivities, and the concentration dependence of density and enthalpy of the molten salt mixture LiF-ThF4 at 1200 K in the composition range of 2-45% ThF4 and also at eutectic composition in the temperature range of 1123-1600 K using Green-Kubo formalism and equilibrium molecular dynamics simulations. We have observed an interesting oscillating pattern for the MS diffusivity for the cation-cation pair, in which ĐLi-Th oscillates between positive and negative values with the amplitude of the oscillation reducing as the system becomes rich in ThF4. Through the velocity autocorrelation function, vibrational density of states, radial distribution function analysis, and structural snapshots, we establish an interplay between the local structure and multicomponent dynamics and predict that formation of negatively charged [ThFn](4-n) clusters at a higher ThF4 mole % makes positively charged Li(+) ions oscillate between different clusters, with their range of motion reducing as the number of [ThFn](4-n) clusters increases, and finally Li(+) ions almost get trapped at a higher ThF4% when the electrostatic force on Li(+) exerted by various surrounding clusters gets balanced. Although reports on variations of density and enthalpy with temperature exist in the literature, for the first time we report variations of the density and enthalpy of LiF-ThF4 with the concentration of ThF4 (mole %) and fit them with the square root function of ThF4 concentration, which will be very useful for experimentalists to obtain data over a range of concentrations from fitting the formula for design purposes. The formation of [ThFn](4-n) clusters and the reduction in the diffusivity of the ions at a higher ThF4% may limit the percentage of ThF4 that can be used in the MSR to optimize the neutron economy.

Structural and functional insight into the carbohydrate receptor binding of F4 fimbriae-producing enterotoxigenic Escherichia coli.

PubMed

Moonens, Kristof; Van den Broeck, Imke; De Kerpel, Maia; Deboeck, Francine; Raymaekers, Hanne; Remaut, Han; De Greve, Henri

2015-03-27

Enterotoxigenic Escherichia coli (ETEC) strains are important causes of intestinal disease in humans and lead to severe production losses in animal farming. A range of fimbrial adhesins in ETEC strains determines host and tissue tropism. ETEC strains expressing F4 fimbriae are associated with neonatal and post-weaning diarrhea in piglets. Three naturally occurring variants of F4 fimbriae (F4ab, F4ac, and F4ad) exist that differ in the primary sequence of their major adhesive subunit FaeG, and each features a related yet distinct receptor binding profile. Here the x-ray structure of FaeGad bound to lactose provides the first structural insight into the receptor specificity and mode of binding by the poly-adhesive F4 fimbriae. A small D'-D″-α1-α2 subdomain grafted on the immunoglobulin-like core of FaeG hosts the carbohydrate binding site. Two short amino acid stretches Phe(150)-Glu(152) and Val(166)-Glu(170) of FaeGad bind the terminal galactose in the lactosyl unit and provide affinity and specificity to the interaction. A hemagglutination-based assay with E. coli expressing mutant F4ad fimbriae confirmed the elucidated co-complex structure. Interestingly, the crucial D'-α1 loop that borders the FaeGad binding site adopts a different conformation in the two other FaeG variants and hints at a heterogeneous binding pocket among the FaeG serotypes. © 2015 by The American Society for Biochemistry and Molecular Biology, Inc.

Calculation of exchange integrals and Curie temperature for La-substituted barium hexaferrites.

PubMed

Wu, Chuanjian; Yu, Zhong; Sun, Ke; Nie, Jinlan; Guo, Rongdi; Liu, Hai; Jiang, Xiaona; Lan, Zhongwen

2016-10-31

As the macro behavior of the strength of exchange interaction, state of the art of Curie temperature T c , which is directly proportional to the exchange integrals, makes sense to the high-frequency and high-reliability microwave devices. Challenge remains as finding a quantitative way to reveal the relationship between the Curie temperature and the exchange integrals for doped barium hexaferrites. Here in this report, for La-substituted barium hexaferrites, the electronic structure has been determined by the density functional theory (DFT) and generalized gradient approximation (GGA). By means of the comparison between the ground and relative state, thirteen exchange integrals have been calculated as a function of the effective value U eff . Furthermore, based on the Heisenberg model, the molecular field approximation (MFA) and random phase approximation (RPA), which provide an upper and lower bound of the Curie temperature T c , have been adopted to deduce the Curie temperature T c . In addition, the Curie temperature T c derived from the MFA are coincided well with the experimental data. Finally, the strength of superexchange interaction mainly depends on 2b-4f 1 , 4f 2 -12k, 2a-4f 1 , and 4f 1 -12k interactions.

Measurement of protein unfolding/refolding kinetics and structural characterization of hidden intermediates by NMR relaxation dispersion

PubMed Central

Meinhold, Derrick W.; Wright, Peter E.

2011-01-01

Detailed understanding of protein function and malfunction hinges on the ability to characterize transiently populated states and the transitions between them. Here, we use 15N, , and 13CO NMR R2 relaxation dispersion to investigate spontaneous unfolding and refolding events of native apomyoglobin. Above pH 5.0, dispersion is dominated by processes involving fluctuations of the F-helix region, which is invisible in NMR spectra. Measurements of R2 dispersion for residues contacted by the F-helix region in the native (N) structure reveal a transient state formed by local unfolding of helix F and undocking from the protein core. A similar state was detected at pH 4.75–4.95 and determined to be an on-pathway intermediate (I1) in a linear three-state unfolding scheme (N⇆I1⇆MG) leading to a transiently populated molten globule (MG) state. The slowest steps in unfolding and refolding are N → I1 (36 s-1) and MG → I1 (26 s-1), respectively. Differences in chemical shift between N and I1 are very small, except in regions adjacent to helix F, showing that their core structures are similar. Chemical shift changes between the N and MG states, obtained from R2 dispersion, reveal that the transient MG state is structurally similar to the equilibrium MG observed previously at high temperature and low pH. Analysis of MG state chemical shifts shows the location of residual helical structure in the transient intermediate and identifies regions that unfold or rearrange into nonnative structure during the N → MG transition. The experiments also identify regions of energetic frustration that “crack” during unfolding and impede the refolding process. PMID:21562212

Ion release and in vitro enamel fluoride uptake associated with pit and fissure sealants containing microencapsulated remineralizing agents.

PubMed

Burbank, Brant D; Cooper, Ryan L; Kava, Alyssa; Hartjes, Jennifer M; McHale, William A; Latta, Mark A; Gross, Stephen M

2017-04-01

To determine if pit-and-fissure sealants with microencapsulated remineralizing agents with sustained release of fluoride, calcium and phosphate ions could promote enamel fluoride uptake by demineralized tooth structure. Sealants that contained 5 w/w% microcapsules with aqueous solutions of 5M Ca(NO3)2 or 0.8M NaF or 6.0M K2HPO4 or a mixture of all three were prepared. Ion release profiles were measured as a function of time. Enamel fluoride uptake by demineralized tooth structure was determined. Sustained release of fluoride, calcium and phosphate ions from a sealant was demonstrated. Fluoride uptake by demineralized enamel was significantly increased compared to a control sealant manufactured without microcapsules (P< 0.01). Bovine enamel that contained 2.2±2.1 µg F/g of enamel prior to exposure to a sealant without microcapsules had 2.3±0.5 after 90 days. Enamel exposed to sealant with 5w/% NaF microcapsules went from 3.5±3.5 µg F/g of enamel prior to exposure to 148±76 after 90 days. Enamel exposed to sealant with 2 w/w% NaF, 2 w/w% Ca(NO3)2 and 1 w/w% K2HPO4 microcapsules went from 1.7±0.7 µg F/g of enamel prior to exposure to 190±137 after 90 days. Sealants with encapsulated remineralizing agents were capable of releasing biologically available fluoride, calcium, and phosphate ions. Incorporation of these microcapsules in pit and fissure sealants is a promising method for remineralization determined by enamel fluoride uptake measurements.

ATM-dependent E2F1 accumulation in the nucleolus is an indicator of ribosomal stress in early response to DNA damage

PubMed Central

Jin, Ya-Qiong; An, Guo-Shun; Ni, Ju-Hua; Li, Shu-Yan; Jia, Hong-Ti

2014-01-01

The nucleolus plays a major role in ribosome biogenesis. Most genotoxic agents disrupt nucleolar structure and function, which results in the stabilization/activation of p53, inducing cell cycle arrest or apoptosis. Likewise, transcription factor E2F1 as a DNA damage responsive protein also plays roles in cell cycle arrest, DNA repair, or apoptosis in response to DNA damage through transcriptional response and protein–protein interaction. Furthermore, E2F1 is known to be involved in regulating rRNA transcription. However, how E2F1 displays in coordinating DNA damage and nucleolar stress is unclear. In this study, we demonstrate that ATM-dependent E2F1 accumulation in the nucleolus is a characteristic feature of nucleolar stress in early response to DNA damage. We found that at the early stage of DNA damage, E2F1 accumulation in the nucleolus was an ATM-dependent and a common event in p53-suficient and -deficient cells. Increased nucleolar E2F1 was sequestered by the nucleolar protein p14ARF, which repressed E2F1-dependent rRNA transcription initiation, and was coupled with S phase. Our data indicate that early accumulation of E2F1 in the nucleolus is an indicator for nucleolar stress and a component of ATM pathway, which presumably buffers elevation of E2F1 in the nucleoplasm and coordinates the diversifying mechanisms of E2F1 acts in cell cycle progression and apoptosis in early response to DNA damage. PMID:24675884

ATM-dependent E2F1 accumulation in the nucleolus is an indicator of ribosomal stress in early response to DNA damage.

PubMed

Jin, Ya-Qiong; An, Guo-Shun; Ni, Ju-Hua; Li, Shu-Yan; Jia, Hong-Ti

2014-01-01

The nucleolus plays a major role in ribosome biogenesis. Most genotoxic agents disrupt nucleolar structure and function, which results in the stabilization/activation of p53, inducing cell cycle arrest or apoptosis. Likewise, transcription factor E2F1 as a DNA damage responsive protein also plays roles in cell cycle arrest, DNA repair, or apoptosis in response to DNA damage through transcriptional response and protein-protein interaction. Furthermore, E2F1 is known to be involved in regulating rRNA transcription. However, how E2F1 displays in coordinating DNA damage and nucleolar stress is unclear. In this study, we demonstrate that ATM-dependent E2F1 accumulation in the nucleolus is a characteristic feature of nucleolar stress in early response to DNA damage. We found that at the early stage of DNA damage, E2F1 accumulation in the nucleolus was an ATM-dependent and a common event in p53-suficient and -deficient cells. Increased nucleolar E2F1 was sequestered by the nucleolar protein p14ARF, which repressed E2F1-dependent rRNA transcription initiation, and was coupled with S phase. Our data indicate that early accumulation of E2F1 in the nucleolus is an indicator for nucleolar stress and a component of ATM pathway, which presumably buffers elevation of E2F1 in the nucleoplasm and coordinates the diversifying mechanisms of E2F1 acts in cell cycle progression and apoptosis in early response to DNA damage.

An approach to functionally relevant clustering of the protein universe: Active site profile-based clustering of protein structures and sequences.

PubMed

Knutson, Stacy T; Westwood, Brian M; Leuthaeuser, Janelle B; Turner, Brandon E; Nguyendac, Don; Shea, Gabrielle; Kumar, Kiran; Hayden, Julia D; Harper, Angela F; Brown, Shoshana D; Morris, John H; Ferrin, Thomas E; Babbitt, Patricia C; Fetrow, Jacquelyn S

2017-04-01

Protein function identification remains a significant problem. Solving this problem at the molecular functional level would allow mechanistic determinant identification-amino acids that distinguish details between functional families within a superfamily. Active site profiling was developed to identify mechanistic determinants. DASP and DASP2 were developed as tools to search sequence databases using active site profiling. Here, TuLIP (Two-Level Iterative clustering Process) is introduced as an iterative, divisive clustering process that utilizes active site profiling to separate structurally characterized superfamily members into functionally relevant clusters. Underlying TuLIP is the observation that functionally relevant families (curated by Structure-Function Linkage Database, SFLD) self-identify in DASP2 searches; clusters containing multiple functional families do not. Each TuLIP iteration produces candidate clusters, each evaluated to determine if it self-identifies using DASP2. If so, it is deemed a functionally relevant group. Divisive clustering continues until each structure is either a functionally relevant group member or a singlet. TuLIP is validated on enolase and glutathione transferase structures, superfamilies well-curated by SFLD. Correlation is strong; small numbers of structures prevent statistically significant analysis. TuLIP-identified enolase clusters are used in DASP2 GenBank searches to identify sequences sharing functional site features. Analysis shows a true positive rate of 96%, false negative rate of 4%, and maximum false positive rate of 4%. F-measure and performance analysis on the enolase search results and comparison to GEMMA and SCI-PHY demonstrate that TuLIP avoids the over-division problem of these methods. Mechanistic determinants for enolase families are evaluated and shown to correlate well with literature results. © 2017 The Authors Protein Science published by Wiley Periodicals, Inc. on behalf of The Protein Society.

Synthesis and characterization of new fluoride-containing manganese vanadates A2Mn2V2O7F2 (A=Rb, Cs) and Mn2VO4F

NASA Astrophysics Data System (ADS)

Sanjeewa, Liurukara D.; McGuire, Michael A.; Smith Pellizzeri, Tiffany M.; McMillen, Colin D.; Ovidiu Garlea, V.; Willett, Daniel; Chumanov, George; Kolis, Joseph W.

2016-09-01

Large single crystals of A2Mn2V2O7F2 (A=Rb, Cs) and Mn2VO4F were grown using a high-temperature (~600 °C) hydrothermal technique. Single crystal X-ray diffraction and powder X-ray diffraction were utilized to characterize the structures, which both possess MnO4F2 building blocks. The A2Mn2V2O7F2 series crystallizes as a new structure type in space group Pbcn (No. 60), Z=4 (Rb2Mn2V2O7F2: a=7.4389(17) Å, b=11.574(3) Å, c=10.914(2) Å; Cs2Mn2V2O7F2: a=7.5615(15) Å, b=11.745(2) Å, c=11.127(2) Å). The structure is composed of zigzag chains of edge-sharing MnO4F2 units running along the a-axis, and interconnected through V2O7 pyrovanadate groups. Temperature dependent magnetic susceptibility measurements on this interesting one-dimensional structural feature based on Mn2+ indicated that Cs2Mn2V2O7F2 is antiferromagnetic with a Neél temperature, TN=~3 K and a Weiss constant, θ, of -11.7(1) K. Raman and infrared spectra were also analyzed to identify the fundamental V-O vibrational modes in Cs2Mn2V2O7F2. Mn2(VO4)F crystalizes in the monoclinic space group of C2/c (no. 15), Z=8 with unit cell parameters of a=13.559(2) Å, b=6.8036(7) Å, c=10.1408(13) Å and β=116.16(3)°. The structure is associated with those of triplite and wagnerite. Dynamic fluorine disorder gives rise to complex alternating chains of five-and six-coordinate Mn2+. These interpenetrating chains are additionally connected through isolated VO4 tetrahedra to form the condensed structure.

Synthesis and characterization of new fluoride-containing manganese vanadates A 2Mn 2V 2O 7F 2 (A=Rb, Cs) and Mn 2VO 4F

DOE PAGES

Sanjeewa, Liurukara D.; McGuire, Michael A.; Smith Pellizzeri, Tiffany M.; ...

2016-05-10

In large single crystals of A 2Mn 2V 2O 7F 2 (A=Rb, Cs) and Mn 2VO 4F were grown using a high-temperature (~600 °C) hydrothermal technique. We utilized single crystal X-ray diffraction and powder X-ray diffraction in order to characterize the structures, which both possess MnO 4F 2 building blocks. The A 2Mn 2V 2O 7F 2 series crystallizes as a new structure type in space group Pbcn (No. 60), Z=4 (Rb 2Mn 2V 2O 7F 2: a=7.4389(17) Å, b=11.574(3) Å, c=10.914(2) Å; Cs 2Mn 2V 2O 7F 2: a=7.5615(15) Å, b=11.745(2) Å, c=11.127(2) Å). The structure is composed ofmore » zigzag chains of edge-sharing MnO 4F 2 units running along the a-axis, and interconnected through V 2O 7 pyrovanadate groups. Temperature dependent magnetic susceptibility measurements on this interesting one-dimensional structural feature based on Mn 2+ indicated that Cs 2Mn 2V 2O 7F 2 is antiferromagnetic with a Neél temperature, TN=~3 K and a Weiss constant, θ, of -11.7(1) K. Raman and infrared spectra were also analyzed to identify the fundamental V–O vibrational modes in Cs 2Mn 2V 2O 7F 2. Mn 2(VO 4)F crystalizes in the monoclinic space group of C2/c (no. 15), Z=8 with unit cell parameters of a=13.559(2) Å, b=6.8036(7) Å, c=10.1408(13) Å and β=116.16(3)°. The structure is associated with those of triplite and wagnerite. Dynamic fluorine disorder gives rise to complex alternating chains of five-and six-coordinate Mn 2+. Our interpenetrating chains are additionally connected through isolated VO 4 tetrahedra to form the condensed structure.« less

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

Chang Jenghwa; Kowalski, Alex; Hou, Bob

The purpose of this work was to study the feasibility of incorporating functional magnetic resonance imaging (fMRI) information for intensity modulated radiotherapy (IMRT) treatment planning of brain tumors. Three glioma patients were retrospectively replanned for radiotherapy (RT) with additional fMRI information. The fMRI of each patient was acquired using a bilateral finger-tapping paradigm with a gradient echo EPI (Echo Planer Imaging) sequence. The fMRI data were processed using the Analysis of Functional Neuroimaging (AFNI) software package for determining activation volumes, and the volumes were fused with the simulation computed tomography (CT) scan. The actived pixels in left and right primarymore » motor cortexes (PMCs) were contoured as critical structures for IMRT planning. The goal of replanning was to minimize the RT dose to the activation volumes in the PMC regions, while maintaining a similar coverage to the planning target volume (PTV) and keeping critical structures within accepted dose tolerance. Dose-volume histograms of the treatment plans with and without considering the fMRI information were compared. Beam angles adjustment or additional beams were needed for 2 cases to meet the planning criteria. Mean dose to the contralateral and ipsilateral PMC was significantly reduced by 66% and 55%, respectively, for 1 patient. For the other 2 patients, mean dose to contralateral PMC region was lowered by 73% and 69%. In general, IMRT optimization can reduce the RT dose to the PMC regions without compromising the PTV coverage or sparing of other critical organs. In conclusion, it is feasible to incorporate the fMRI information into the RT treatment planning. IMRT planning allows a significant reduction in RT dose to the PMC regions, especially if the region does not lie within the PTV.« less

Phase equilibria in the NaF-CdO-NaPO{sub 3} system at 873 K and crystal structure and physico-chemical characterizations of the new Na{sub 2}CdPO{sub 4}F fluorophosphate

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

Aboussatar, Mohamed; Laboratoire de Physico-Chimie de l’État Solide, Faculté des Sciences de Sfax, Université de Sfax, BP 1171, 3000 Sfax; Mbarek, Aïcha

Isothermal sections of the diagram representing phase relationships in the NaF-CdO-NaPO{sub 3} system have been investigated by solid state reactions and powder X-ray diffraction. This phase diagram investigation confirms the polymorphism of the NaCdPO{sub 4} side component and the structure of the ß high temperature polymorph (orthorhombic, space group Pnma and unit cell parameters a=9.3118(2), b=7.0459(1), c=5.1849(1) Å has been refined. A new fluorophosphate, Na{sub 2}CdPO{sub 4}F, has been discovered and its crystal structure determined and refined from powder X-ray diffraction data. It exhibits a new 3D structure with orthorhombic symmetry, space group Pnma and unit cell parameters a=5.3731(1), b=6.8530(1),more » c=12.2691(2) Å. The structure is closely related to those of the high temperature polymorph of the nacaphite Na{sub 2}CaPO{sub 4}F and the fluorosilicate Ca{sub 2}NaSiO{sub 4}F but differs essentially in the cationic repartition since the structure is fully ordered with one Na site (8d) and one Cd site (4c). Relationships with other Na{sub 2}M{sup II}PO{sub 4}F (M{sup II}=Mg, Ca, Mn, Fe, Co, Ni) have been examined and the crystal-chemical and topographical analysis of these fluorophosphates is briefly reviewed. IR, Raman, optical and {sup 19}F, {sup 23}Na, {sup 31}P MAS NMR characterizations of Na{sub 2}CdPO{sub 4}F have been investigated. - Graphical abstract: The structure of the compound Na{sub 2}CdPO{sub 4}F, discovered during the study of the phase relationships in the NaF-CdO-NaPO{sub 3} system, has been determined and compared with other Na{sub 2}M{sup II}PO{sub 4}F fluorophosphates. - Highlights: • XRD analysis of the isothermal section of the NaF-CdO-NaPO{sub 3} system at 923 K. • Rietveld refinement of the high temperature polymorph β-NaCdPO{sub 4}. • Crystal structure of the new Na{sub 2}CdPO{sub 4}F fluorophosphate determined from powder XRD. • Crystal structure - composition relationships of Na{sub 2}M{sup II}PO{sub 4}F compounds are reviewed. • IR, Raman, optical and {sup 19}F, {sup 23}Na, {sup 31}P MAS NMR characterizations of Na{sub 2}CdPO{sub 4}F.« less

Explicit Performance in Girls and Implicit Processing in Boys: A Simultaneous fNIRS–ERP Study on Second Language Syntactic Learning in Young Adolescents

PubMed Central

Sugiura, Lisa; Hata, Masahiro; Matsuba-Kurita, Hiroko; Uga, Minako; Tsuzuki, Daisuke; Dan, Ippeita; Hagiwara, Hiroko; Homae, Fumitaka

2018-01-01

Learning a second language (L2) proceeds with individual approaches to proficiency in the language. Individual differences including sex, as well as working memory (WM) function appear to have strong effects on behavioral performance and cortical responses in L2 processing. Thus, by considering sex and WM capacity, we examined neural responses during L2 sentence processing as a function of L2 proficiency in young adolescents. In behavioral tests, girls significantly outperformed boys in L2 tests assessing proficiency and grammatical knowledge, and in a reading span test (RST) assessing WM capacity. Girls, but not boys, showed significant correlations between L2 tests and RST scores. Using functional near-infrared spectroscopy (fNIRS) and event-related potential (ERP) simultaneously, we measured cortical responses while participants listened to syntactically correct and incorrect sentences. ERP data revealed a grammaticality effect only in boys in the early time window (100–300 ms), implicated in phrase structure processing. In fNIRS data, while boys had significantly increased activation in the left prefrontal region implicated in syntactic processing, girls had increased activation in the posterior language-related region involved in phonology, semantics, and sentence processing with proficiency. Presumably, boys implicitly focused on rule-based syntactic processing, whereas girls made full use of linguistic knowledge and WM function. The present results provide important fundamental data for learning and teaching in L2 education. PMID:29568265

Common Evolutionary Origin for the Rotor Domain of Rotary Atpases and Flagellar Protein Export Apparatus

PubMed Central

Kishikawa, Jun-ichi; Ibuki, Tatsuya; Nakamura, Shuichi; Nakanishi, Astuko; Minamino, Tohru; Miyata, Tomoko; Namba, Keiichi; Konno, Hiroki; Ueno, Hiroshi; Imada, Katsumi; Yokoyama, Ken

2013-01-01

The V1- and F1- rotary ATPases contain a rotor that rotates against a catalytic A3B3 or α3β3 stator. The rotor F1-γ or V1-DF is composed of both anti-parallel coiled coil and globular-loop parts. The bacterial flagellar type III export apparatus contains a V1/F1-like ATPase ring structure composed of FliI6 homo-hexamer and FliJ which adopts an anti-parallel coiled coil structure without the globular-loop part. Here we report that FliJ of Salmonella enterica serovar Typhimurium shows a rotor like function in Thermus thermophilus A3B3 based on both biochemical and structural analysis. Single molecular analysis indicates that an anti-parallel coiled-coil structure protein (FliJ structure protein) functions as a rotor in A3B3. A rotary ATPase possessing an F1-γ-like protein generated by fusion of the D and F subunits of V1 rotates, suggesting F1-γ could be the result of a fusion of the genes encoding two separate rotor subunits. Together with sequence comparison among the globular part proteins, the data strongly suggest that the rotor domains of the rotary ATPases and the flagellar export apparatus share a common evolutionary origin. PMID:23724081

Structural and functional deficits in human amblyopia.

PubMed

Lv, Bin; He, Huiguang; Li, Xingfeng; Zhang, Zhiqiang; Huang, Wei; Li, Meng; Lu, Guangming

2008-05-23

Many neuroimaging tools have been used to assess the site of the cortical deficits in human amblyopia. In this paper, we aimed at detecting the structural and functional deficits in humans with amblyopia, with the aid of anatomic magnetic resonance imaging (aMRI) and functional MRI (fMRI). We designed the visual stimulus to investigate the functional deficits, and delineated the V1/V2 areas by retinotopic mapping. Then we performed the brain parcellation to calculate the volume of the subcortical structure on each individual, and reconstructed the cortical surfaces to measure the cortical thickness. At last, the statistical comparison was carried out to find the structural abnormities and their relationship to the functional deficits. Compared with the normal controls, it is found that the hemisphere difference existed on the unilateral amblyopia subjects, and the functional deficit might come along with the changes in the cortical volume, especially in the occipital lobe. The examined results may provide insight to the study of the neural substrates of amblyopia.

Crystallization and Preliminary X-ray Analysis of Der f 2, a Potent Allergen Derived from the House Dust Mite

NASA Technical Reports Server (NTRS)

Roeber, Dana; Achari, Aniruddha; Takai, Toshiro; Okumura, Yasushi; Scott, David L.; Curreri, Peter (Technical Monitor)

2002-01-01

Although a number of allergens have been identified and isolated, the underlying molecular basis for the potent immune response is poorly understood. House dust mites (Dermatophugoides sp.) are particularly ubiquitous contributors to atopy in developed countries. The rhinitis, dermatitis, and asthma associated with allergic reactions to these arthropods are often caused by relatively small (125-129 amino acids) mite proteins of unclear biological function. Der f 2, a major allergen from the mite Dermatophagoides farinae, has been recombinantly expressed and characterized. The Der f 2 protein has been crystallized in our laboratory and a native data set collected at a synchrotron source. The crystals belong to the orthorhombic space group I422 with unit cell parameters of a = 95.2 Angstroms, b = 95.2 Angstroms, and c = 103.3 Angstroms. An essentially complete (97.2%) data set has been collected to 2.4 Angstroms. Attempts to solve the crystal structure of Der f 2 by molecular replacement using the available NMR coordinates for either Der f 2 or Der p 2 (the homologous protein from D. pterovssinus) failed to reveal a creditable solution.

Combining electronic structure and many-body theory with large databases: A method for predicting the nature of 4 f states in Ce compounds

NASA Astrophysics Data System (ADS)

Herper, H. C.; Ahmed, T.; Wills, J. M.; Di Marco, I.; Björkman, T.; Iuşan, D.; Balatsky, A. V.; Eriksson, O.

2017-08-01

Recent progress in materials informatics has opened up the possibility of a new approach to accessing properties of materials in which one assays the aggregate properties of a large set of materials within the same class in addition to a detailed investigation of each compound in that class. Here we present a large scale investigation of electronic properties and correlated magnetism in Ce-based compounds accompanied by a systematic study of the electronic structure and 4 f -hybridization function of a large body of Ce compounds. We systematically study the electronic structure and 4 f -hybridization function of a large body of Ce compounds with the goal of elucidating the nature of the 4 f states and their interrelation with the measured Kondo energy in these compounds. The hybridization function has been analyzed for more than 350 data sets (being part of the IMS database) of cubic Ce compounds using electronic structure theory that relies on a full-potential approach. We demonstrate that the strength of the hybridization function, evaluated in this way, allows us to draw precise conclusions about the degree of localization of the 4 f states in these compounds. The theoretical results are entirely consistent with all experimental information, relevant to the degree of 4 f localization for all investigated materials. Furthermore, a more detailed analysis of the electronic structure and the hybridization function allows us to make precise statements about Kondo correlations in these systems. The calculated hybridization functions, together with the corresponding density of states, reproduce the expected exponential behavior of the observed Kondo temperatures and prove a consistent trend in real materials. This trend allows us to predict which systems may be correctly identified as Kondo systems. A strong anticorrelation between the size of the hybridization function and the volume of the systems has been observed. The information entropy for this set of systems is about 0.42. Our approach demonstrates the predictive power of materials informatics when a large number of materials is used to establish significant trends. This predictive power can be used to design new materials with desired properties. The applicability of this approach for other correlated electron systems is discussed.

Dissociation of functional and anatomical brain abnormalities in unaffected siblings of schizophrenia patients.

PubMed

Guo, Wenbin; Song, Yan; Liu, Feng; Zhang, Zhikun; Zhang, Jian; Yu, Miaoyu; Liu, Jianrong; Xiao, Changqing; Liu, Guiying; Zhao, Jingping

2015-05-01

Schizophrenia patients and their unaffected siblings share similar brain functional and structural abnormalities. However, no study is engaged to investigate whether and how functional abnormalities are related to structural abnormalities in unaffected siblings. This study was undertaken to examine the association between functional and anatomical abnormalities in unaffected siblings. Forty-six unaffected siblings of schizophrenia patients and 46 age-, sex-, and education-matched healthy controls underwent structural and resting-state functional magnetic resonance imaging scanning. Voxel-based morphometry (VBM), amplitude of low-frequency fluctuation (ALFF) and fractional ALFF (fALFF) were utilized to analyze imaging data. The VBM analysis showed gray matter volume decreases in the fronto-temporal regions (the left middle temporal gyrus and right inferior frontal gyrus, orbital part) and increases in basal ganglia system (the left putamen). Functional abnormalities measured by ALFF and fALFF mainly involved in the fronto-limbic-sensorimotor circuit (decreased ALFF in bilateral middle frontal gyrus and the right middle cingulate gyrus, and decreased fALFF in the right inferior frontal gyrus, orbital part; and increased ALFF in the left fusiform gyrus and left lingual gyrus, and increased fALFF in bilateral calcarine cortex). No significant correlation was found between functional and anatomical abnormalities in the sibling group. A dissociation pattern of brain regions with functional and anatomical abnormalities is observed in unaffected siblings. Our findings suggest that brain functional and anatomical abnormalities might be present independently in unaffected siblings of schizophrenia patients. Copyright © 2014 International Federation of Clinical Neurophysiology. Published by Elsevier Ireland Ltd. All rights reserved.

Learning from eponyms: George F. Odland and Odland bodies

PubMed Central

Joshi, Rajiv

2014-01-01

Odland bodies (lamellar) bodies are small sub-cellular structures of size 200-300 nm that are present in the upper spinous and granular cell layers of the epidermis. These act as processing and repository areas for lipids that contribute to the epidermal permeability barrier. They also contain proteases, cathepsin D, kallikrein and other proteins including corneo-desmosins. Recent information also credits them with a role in the local innate immune response as they contain beta 2 defensins, which are anti-microbial peptides with potent activity against Gram-negative bacteria and candida. Odland bodies are important for maintaining homeostasis of the epidermis and are involved in epidermal permeability barrier function, desquamation of keratinocytes, formation of the cornified envelope and in local anti-microbial immunity. This article reviews the structure and functions of these bodies with a brief biography of George F. Odland who first described these bodies in 1960 and whose name is eponymically associated with them. PMID:25165659

Oxygen-rich hierarchical porous carbon derived from artemia cyst shells with superior electrochemical performance.

PubMed

Zhao, Yufeng; Ran, Wei; He, Jing; Song, Yanfang; Zhang, Chunming; Xiong, Ding-Bang; Gao, Faming; Wu, Jinsong; Xia, Yongyao

2015-01-21

In this study, three-dimensional (3D) hierarchical porous carbon with abundant functional groups is produced through a very simple low-cost carbonization of Artemia cyst shells. The unique hierarchical porous structure of this material, combining large numbers of micropores and macropores, as well as reasonable amount of mesopores, is proven favorable to capacitive behavior. The abundant oxygen functional groups from the natural carbon precursor contribute stable pseudocapacitance. As-prepared sample exhibits high specific capacitance (369 F g(-1) in 1 M H2SO4 and 349 F g(-1) in 6 M KOH), excellent cycling stability with capacitance retention of 100% over 10 000 cycles, and promising rate performance. This work not only describes a simple way to produce high-performance carbon electrode materials for practical application, but also inspires an idea for future structure design of porous carbon.

Changes in Gray Matter Density, Regional Homogeneity, and Functional Connectivity in Methamphetamine-Associated Psychosis: A Resting-State Functional Magnetic Resonance Imaging (fMRI) Study.

PubMed

Zhang, Shengyu; Hu, Qiang; Tang, Tao; Liu, Chao; Li, Chengchong; Zang, Yin-Yin; Cai, Wei-Xiong

2018-06-13

BACKGROUND Using regional homogeneity (ReHo) blood oxygen level-dependent functional MR (BOLD-fMRI), we investigated the structural and functional alterations of brain regions among patients with methamphetamine-associated psychosis (MAP). MATERIAL AND METHODS This retrospective study included 17 MAP patients, 16 schizophrenia (SCZ) patients, and 18 healthy controls. Informed consent was obtained from all patients before the clinical assessment, the severity of clinical symptoms was evaluated prior to the fMRI scanning, and then images were acquired and preprocessed after each participant received 6-min fRMI scanning. The participants all underwent BOLD-fMRI scanning. Voxel-based morphometry was used to measure gray matter density (GMD). Resting-state fMRI (rs-fMRI) was conducted to analyze functional MR, ReHo, and functional connectivity (FC). RESULTS GMD analysis results suggest that MAP patients, SCZ patients, and healthy volunteers show different GMDs within different brain regions. Similarly, the ReHo analysis results suggest that MAP patients, SCZ patients, and healthy volunteers have different GMDs within different brain regions. Negative correlations were found between ReHo- and the PANSS-positive scores within the left orbital interior frontal gyrus (L-orb-IFG) of MAP patients. ReHo- and PANSS-negative scores of R-SFG were negatively correlated among SCZ patients. The abnormal FC of R-MFG showed a negative correlation with the PANSS score among MAP patients. CONCLUSIONS The abnormalities in brain structure and FC were associated with the development of MAP.

Concerted Motions Networking Pores and Distant Ferroxidase Centers Enable Bacterioferritin Function and Iron Traffic£ξ

PubMed Central

Yao, Huili; Rui, Huan; Kumar, Ritesh; Eshelman, Kate; Lovell, Scott; Battaile, Kevin P.; Im, Wonpil; Rivera, Mario

2015-01-01

X-ray crystallography, molecular dynamics (MD) simulations and biochemistry were utilized to investigate the effect of introducing hydrophobic interactions in the 4-fold (N148L and Q151L) and B-pores (D34F) of Pseudomonas aeruginosa bacterioferritin B (BfrB) on BfrB function. The structures show only local structural perturbations and confirm the anticipated hydrophobic interactions. Surprisingly, structures obtained after soaking crystals in Fe2+-containing crystallization solution revealed that although iron loads into the ferroxidase centers of the mutants, the side chains of ferroxidase ligands E51 and H130 do not reorganize to bind the iron ions, as is seen in the wt BfrB structures. Similar experiments with a double mutant (C89S/K96C) prepared to introduce changes outside the pores show competent ferroxidase centers that function akin to those in wt BfrB. MD simulations comparing wt BfrB with the D34F and N148L mutants show that the mutants exhibit significantly reduced flexibility, and reveal a network of concerted motions linking ferroxidase centers and 4-fold and B-pores, which are important for imparting ferroxidase centers in BfrB with the required flexibility to function efficiently. In agreement, the efficiency of Fe2+ oxidation and uptake of the 4-fold and B-pore mutants in solution is significantly compromised relative to wt or C89S/K96C BfrB. Finally, our structures show a large number of previously unknown iron binding sites in the interior cavity and B-pores of BfrB, which reveal in unprecedented detail conduits followed by iron and phosphate ions across the BfrB shell, as well as paths in the interior cavity that may facilitate nucleation of the iron phosphate mineral. PMID:25640193

Exploration of structural stability in deleterious nsSNPs of the XPA gene: A molecular dynamics approach

PubMed Central

NagaSundaram, N; Priya Doss, C George

2011-01-01

Background: Distinguishing the deleterious from the massive number of non-functional nsSNPs that occur within a single genome is a considerable challenge in mutation research. In this approach, we have used the existing in silico methods to explore the mutation-structure-function relationship in the XPAgene. Materials and Methods: We used the Sorting Intolerant From Tolerant (SIFT), Polymorphism Phenotyping (PolyPhen), I-Mutant 2.0, and the Protein Analysis THrough Evolutionary Relationships methods to predict the effects of deleterious nsSNPs on protein function and evaluated the impact of mutation on protein stability by Molecular Dynamics simulations. Results: By comparing the scores of all the four in silico methods, nsSNP with an ID rs104894131 at position C108F was predicted to be highly deleterious. We extended our Molecular dynamics approach to gain insight into the impact of this non-synonymous polymorphism on structural changes that may affect the activity of the XPAgene. Conclusion: Based on the in silico methods score, potential energy, root-mean-square deviation, and root-mean-square fluctuation, we predict that deleterious nsSNP at position C108F would play a significant role in causing disease by the XPA gene. Our approach would present the application of in silicotools in understanding the functional variation from the perspective of structure, evolution, and phenotype. PMID:22190868

Comparison of noncovalent interactions of zigzag and armchair carbon nanotubes with heterocyclic and aromatic compounds: Imidazole and benzene, imidazophenazines, and tetracene

NASA Astrophysics Data System (ADS)

Zarudnev, Eugene S.; Stepanian, Stepan G.; Adamowicz, Ludwik; Leontiev, Victor S.; Karachevtsev, Victor A.

2017-02-01

We study non-covalent functionalization of SWCNT by linear heterocyclic compounds such as imidazophenazine (F1) and its derivatives (F2-F4). MP2 and DFT/M05-2X quantum-chemical methods are used to determine the structures and the interaction energies of complexes formed by F1-F4 with the zigzag(10,10) and armchair(6,6) nanotubes. The calculations show that for small diameter nanotubes the binding energies with zigzag nanotubes are stronger than with armchair nanotubes. But above the diameter of 1.4 nm the interaction energies for the armchair nanotubes become larger than for the zigzag nanotubes. Experimental measurements demonstrates that the ratio of the integral intensity of the resonance Raman bands assigned to the RBM modes of semiconducting nanotubes to the integral intensity of the metallic nanotubes increases for supernatant of SWCNT:F4 (1,2,3-triazole-[4,5-d]-phenazine) hybrids solved in 1-Methyl-2-pyrrolidone as compared to this ratio in sediment samples. It demonstrates that the linear heterocyclic compounds can be used for separating SWCNTs with different electron-conduction types.

Decoupling of the Leading Order DGLAP Evolution Equation with Spin Dependent Structure Functions

NASA Astrophysics Data System (ADS)

Azadbakht, F. Teimoury; Boroun, G. R.

2018-02-01

We propose an analytical solution for DGLAP evolution equations with polarized splitting functions at the Leading Order (LO) approximation based on the Laplace transform method. It is shown that the DGLAP evolution equations can be decoupled completely into two second order differential equations which then are solved analytically by using the initial conditions δ FS(x,Q2)=F[partial δ FS0(x), δ FS0(x)] and {δ G}(x,Q2)=G[partial δ G0(x), δ G0(x)]. We used this method to obtain the polarized structure function of the proton as well as the polarized gluon distribution function inside the proton and compared the numerical results with experimental data of COMPASS, HERMES, and AAC'08 Collaborations. It was found that there is a good agreement between our predictions and the experiments.

Mutations in the novel protocadherin PCDH15 cause Usher syndrome type 1F.

PubMed

Alagramam, K N; Yuan, H; Kuehn, M H; Murcia, C L; Wayne, S; Srisailpathy, C R; Lowry, R B; Knaus, R; Van Laer, L; Bernier, F P; Schwartz, S; Lee, C; Morton, C C; Mullins, R F; Ramesh, A; Van Camp, G; Hageman, G S; Woychik, R P; Smith, R J; Hagemen, G S

2001-08-01

We have determined the molecular basis for Usher syndrome type 1F (USH1F) in two families segregating for this type of syndromic deafness. By fluorescence in situ hybridization, we placed the human homolog of the mouse protocadherin Pcdh15 in the linkage interval defined by the USH1F locus. We determined the genomic structure of this novel protocadherin, and found a single-base deletion in exon 10 in one USH1F family and a nonsense mutation in exon 2 in the second. Consistent with the phenotypes observed in these families, we demonstrated expression of PCDH15 in the retina and cochlea by RT-PCR and immunohistochemistry. This report shows that protocadherins are essential for maintenance of normal retinal and cochlear function.

The Structure of Optimum Interpolation Functions.

DTIC Science & Technology

1983-02-01

Daniel F. Merriam, ed., Plenum Press, 1970. 2. Hiroshi Akima, "Comments on ’Optimal Contour Mapping Using Universal Kriging’ by Ricardo 0. Olea ," (with...Kriging," Mathematical Geology 14 (1982), 249-257. 21 27. Ricardo 0. Olea , "Optimal Contour Mapping Using Universal Kriging," J. of Geophysical Res. 79

On the topological stability of continuous functions in certain spaces related to Fourier series

NASA Astrophysics Data System (ADS)

Lebedev, Vladimir V.

2010-04-01

We show that the following properties of a continuous function f on the circle \\mathbb T are equivalent: the sequence \\widehat{f\\circ h} of the Fourier coefficients of the superposition f\\circ h belongs to the weak l^1 for every homeomorphism h of the circle onto itself; f is a function of bounded quadratic variation. We obtain similar results for spaces of functions whose sequence of Fourier coefficients belongs to the weak l^p, 1, for spaces A_p of functions f with \\widehat{f}\\in l^p, for the Sobolev spaces W_2^\\lambda, and for other spaces of functions on \\mathbb T. Under rather general assumptions on a space \\mathbb X of functions on the circle, we give a necessary condition for a given continuous function f to stay in \\mathbb X for every change of variable. We also consider the multidimensional case, which is essentially different from the one-dimensional case. In particular, we show that if p<2 and f is a continuous function on the torus \\mathbb T^d, d\\ge2, such that f\\circ h\\in A_p(\\mathbb T^d) for every homeomorphism h\\colon \\mathbb T^d\\to\\mathbb T^d, then f is constant.

THE PRENATAL PARENTAL REFLECTIVE FUNCTIONING QUESTIONNAIRE: EXPLORING FACTOR STRUCTURE AND CONSTRUCT VALIDITY OF A NEW MEASURE IN THE FINN BRAIN BIRTH COHORT PILOT STUDY.

PubMed

Pajulo, Marjukka; Tolvanen, Mimmi; Karlsson, Linnea; Halme-Chowdhury, Elina; Öst, Camilla; Luyten, Patrick; Mayes, Linda; Karlsson, Hasse

2015-01-01

Parental reflective functioning (PRF) is the capacity to focus on experience and feelings in oneself and in the child. Individual differences in PRF reportedly affect child attachment and socioemotional development. In this study, we report work on developing a questionnaire to assess PRF during pregnancy (Prenatal Parental Reflective Functioning Questionnaire; P-PRFQ). The factor structure of the 33-item version of the P-PRFQ was explored using pilot study data from the Finn Brain Birth Cohort Study (n = 124 mothers, n = 82 fathers). Construct validity was assessed against the Pregnancy Interview (PI; A. Slade, L. Grunebaum, L. Huganir, & M. Reeves, 1987, 2002, 2011) in a subsample of 29 mothers from the same pilot sample. Exploratory and confirmatory factor analysis resulted in a 14-item P-PRFQ, with three factors which seem to capture relevant aspects of prenatal parental mentalization-F1: "Opacity of mental states," F2: "Reflecting on the fetus-child," and F3: "The dynamic nature of the mental states." Functioning of the factor structure was further tested in the large cohort with 600 mothers and 600 fathers. Correlations with the PI result were high, both regarding total and factor scores of the P-PRFQ. Cost-effective tools to assess key areas of early parenting are needed for both research and clinical purposes. The 14-item P-PRFQ seems to be an applicable and promising new tool for assessing very early parental mentalizing capacity. © 2015 Michigan Association for Infant Mental Health.

Pseudocapacitive organic catechol derivative-functionalized three-dimensional graphene aerogel hybrid electrodes for high-performance supercapacitors

NASA Astrophysics Data System (ADS)

Choi, Jaewon; Yang, MinHo; Kim, Sung-Kon

2017-11-01

Bio-inspired and environmentally friendly chemical functionalization is a successful way to a new class of hybrid electrode materials for applications in energy storage. Quinone (Q)-hydroquinone (QH2) couples, a prototypical example of organic redox systems, provide fast and reversible proton-coupled electron-transfer reactions which lead to increased capacity. To achieve high capacitance and rate performance, constructing three-dimensional (3D) continuous porous structure is highly desirable. Here we report the hybrid electrodes (GA-C) consisting of 3D graphene aerogel (GA) functionalized with organic redox-active material, catechol derivative, for application to high-performance supercapacitors. The catechol derivative is adsorbed on the surface of GA through non-covalent interactions and promotes fast and reversible Q/QH2 faradaic reactions, providing large specific capacitance of 188 F g-1 at a current of 1 A g-1 and a specific energy of ∼25 Wh kg-1 at a specific power of ∼18,000 W kg-1. 3D continuous porous structure of GA electrode facilitates ion and electron transports, resulting in high rate performance (∼140 F g-1 at a current of 10 A g-1).

A2TiF 5· nH 2O ( A=K, Rb, or Cs; n=0 or 1): Synthesis, structure, characterization, and calculations of three new uni-dimensional titanium fluorides

NASA Astrophysics Data System (ADS)

Jo, Vinna; Woo Lee, Dong; Koo, Hyun-Joo; Ok, Kang Min

2011-04-01

Three new uni-dimensional alkali metal titanium fluoride materials, A2TiF 5· nH 2O ( A=K, Rb, or Cs; n=0 or 1) have been synthesized by hydrothermal reactions. The structures of A2TiF 5· nH 2O have been determined by single-crystal X-ray diffraction. The Ti 4+ cations have been reduced to Ti 3+ during the synthesis reactions. All three A2TiF 5· nH 2O materials contain novel 1-D chain structures that are composed of the slightly distorted Ti 3+F 6 corner-sharing octahedra attributable to the Jahn-Teller distortion. The coordination environment of the alkali metal cations plays an important role to determine the degree of turning in the chain structures. Complete structural analyses, Infrared and UV-vis diffuse reflectance spectra, and thermal analyses are presented, as are electronic structure calculations.

A phenome-wide examination of neural and cognitive function.

PubMed

Poldrack, R A; Congdon, E; Triplett, W; Gorgolewski, K J; Karlsgodt, K H; Mumford, J A; Sabb, F W; Freimer, N B; London, E D; Cannon, T D; Bilder, R M

2016-12-06

This data descriptor outlines a shared neuroimaging dataset from the UCLA Consortium for Neuropsychiatric Phenomics, which focused on understanding the dimensional structure of memory and cognitive control (response inhibition) functions in both healthy individuals (130 subjects) and individuals with neuropsychiatric disorders including schizophrenia (50 subjects), bipolar disorder (49 subjects), and attention deficit/hyperactivity disorder (43 subjects). The dataset includes an extensive set of task-based fMRI assessments, resting fMRI, structural MRI, and high angular resolution diffusion MRI. The dataset is shared through the OpenfMRI project, and is formatted according to the Brain Imaging Data Structure (BIDS) standard.

Structural Basis of Substrate Specificity and Regiochemistry in the MycF/TylF Family of Sugar O -Methyltransferases.

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

Bernard, Steffen M.; Akey, David L.; Tripathi, Ashootosh

Sugar moieties in natural products are frequently modified by O-methylation. In the biosynthesis of the macrolide antibiotic mycinamicin, methylation of a 6'-deoxyallose substituent occurs in a stepwise manner first at the 2'- and then the 3'-hydroxyl groups to produce the mycinose moiety in the final product. The timing and placement of the O-methylations impact final stage C-H functionalization reactions mediated by the P450 monooxygenase MycG. The structural basis of pathway ordering and substrate specificity is unknown. A series of crystal structures of MycF, the 3'-O-methyltransferase, including the free enzyme and complexes with S-adenosyl homocysteine (SAH), substrate, product, and unnatural substrates,more » show that SAM binding induces substantial ordering that creates the binding site for the natural substrate, and a bound metal ion positions the substrate for catalysis. A single amino acid substitution relaxed the 2'-methoxy specificity but retained regiospecificity. The engineered variant produced a new mycinamicin analog, demonstrating the utility of structural information to facilitate bioengineering approaches for the chemoenzymatic synthesis of complex small molecules containing modified sugars. Using the MycF substrate complex and the modeled substrate complex of a 4'-specific homolog, active site residues were identified that correlate with the 3'- or 4'- specificity of MycF family members and define the protein and substrate features that direct the regiochemistry of methyltransfer. Lastly, this classification scheme will be useful in the annotation of new secondary metabolite pathways that utilize this family of enzymes.« less

Structural Basis of Substrate Specificity and Regiochemistry in the MycF/TylF Family of Sugar O -Methyltransferases.

DOE PAGES

Bernard, Steffen M.; Akey, David L.; Tripathi, Ashootosh; ...

2015-02-18

Sugar moieties in natural products are frequently modified by O-methylation. In the biosynthesis of the macrolide antibiotic mycinamicin, methylation of a 6'-deoxyallose substituent occurs in a stepwise manner first at the 2'- and then the 3'-hydroxyl groups to produce the mycinose moiety in the final product. The timing and placement of the O-methylations impact final stage C-H functionalization reactions mediated by the P450 monooxygenase MycG. The structural basis of pathway ordering and substrate specificity is unknown. A series of crystal structures of MycF, the 3'-O-methyltransferase, including the free enzyme and complexes with S-adenosyl homocysteine (SAH), substrate, product, and unnatural substrates,more » show that SAM binding induces substantial ordering that creates the binding site for the natural substrate, and a bound metal ion positions the substrate for catalysis. A single amino acid substitution relaxed the 2'-methoxy specificity but retained regiospecificity. The engineered variant produced a new mycinamicin analog, demonstrating the utility of structural information to facilitate bioengineering approaches for the chemoenzymatic synthesis of complex small molecules containing modified sugars. Using the MycF substrate complex and the modeled substrate complex of a 4'-specific homolog, active site residues were identified that correlate with the 3'- or 4'- specificity of MycF family members and define the protein and substrate features that direct the regiochemistry of methyltransfer. Lastly, this classification scheme will be useful in the annotation of new secondary metabolite pathways that utilize this family of enzymes.« less

Crystallization and preliminary X-ray analysis of Der f 2, a potent allergen derived from the house dust mite (Dermatophagoides farinae)

NASA Technical Reports Server (NTRS)

Roeber, Dana; Achari, Aniruddha; Takai, Toshiro; Okumura, Yasushi; Scott, David L.

2003-01-01

Although a number of allergens have been identified and isolated, the underlying molecular basis for the potent immune response is poorly understood. House dust mites (Dermatophagoides sp.) are ubiquitous contributors to atopy in developed countries. The rhinitis, dermatitis and asthma associated with allergic reactions to these arthropods are frequently caused by relatively small (125-129 amino acids) mite proteins of unknown biological function. Der f 2, a major allergen from the mite D. farinae, has been recombinantly expressed, characterized and crystallized. The crystals belong to the tetragonal space group I4(1)22, with unit-cell parameters a = b = 95.2, c = 103.3 A. An essentially complete (97.2%) data set has been collected to 2.4 A at a synchrotron source. Attempts to solve the crystal structure of Der f 2 by molecular replacement using the NMR coordinates for either Der f 2 or Der p 2 (the homologous protein from D. pteronyssinus) failed, but preliminary searches using the crystalline Der p 2 atomic coordinates appear to be promising.

Salt forms of the pharmaceutical amide dihydrocarbamazepine.

PubMed

Buist, Amanda R; Kennedy, Alan R

2016-02-01

Carbamazepine (CBZ) is well known as a model active pharmaceutical ingredient used in the study of polymorphism and the generation and comparison of cocrystal forms. The pharmaceutical amide dihydrocarbamazepine (DCBZ) is a less well known material and is largely of interest here as a structural congener of CBZ. Reaction of DCBZ with strong acids results in protonation of the amide functionality at the O atom and gives the salt forms dihydrocarbamazepine hydrochloride {systematic name: [(10,11-dihydro-5H-dibenzo[b,f]azepin-5-yl)(hydroxy)methylidene]azanium chloride, C15H15N2O(+)·Cl(-)}, dihydrocarbamazepine hydrochloride monohydrate {systematic name: [(10,11-dihydro-5H-dibenzo[b,f]azepin-5-yl)(hydroxy)methylidene]azanium chloride monohydrate, C15H15N2O(+)·Cl(-)·H2O} and dihydrocarbamazepine hydrobromide monohydrate {systematic name: [(10,11-dihydro-5H-dibenzo[b,f]azepin-5-yl)(hydroxy)methylidene]azanium bromide monohydrate, C15H15N2O(+)·Br(-)·H2O}. The anhydrous hydrochloride has a structure with two crystallographically independent ion pairs (Z' = 2), wherein both cations adopt syn conformations, whilst the two hydrated species are mutually isostructural and have cations with anti conformations. Compared to neutral dihydrocarbamazepine structures, protonation of the amide group is shown to cause changes to both the molecular (C=O bond lengthening and C-N bond shortening) and the supramolecular structures. The amide-to-amide and dimeric hydrogen-bonding motifs seen for neutral polymorphs and cocrystalline species are replaced here by one-dimensional polymeric constructs with no direct amide-to-amide bonds. The structures are also compared with, and shown to be closely related to, those of the salt forms of the structurally similar pharmaceutical carbamazepine.

Analysis of crystal structure of Arabidopsis MPK6 and generation of its mutants with higher activity

PubMed Central

Wang, Bo; Qin, Xinghua; Wu, Juan; Deng, Hongying; Li, Yuan; Yang, Hailian; Chen, Zhongzhou; Liu, Guoqin; Ren, Dongtao

2016-01-01

Mitogen-activated protein kinase (MAPK) cascades, which are the highly conserved signalling modules in eukaryotic organisms, have been shown to play important roles in regulating growth, development, and stress responses. The structures of various MAPKs from yeast and animal have been solved, and structure-based mutants were generated for their function analyses, however, the structures of plant MAPKs remain unsolved. Here, we report the crystal structure of Arabidopsis MPK6 at a 3.0 Å resolution. Although MPK6 is topologically similar to ERK2 and p38, the structures of the glycine-rich loop, MAPK insert, substrate binding sites, and L16 loop in MPK6 show notable differences from those of ERK2 and p38. Based on the structural comparison, we constructed MPK6 mutants and analyzed their kinase activity both in vitro and in planta. MPK6F364L and MPK6F368L mutants, in which Phe364 and Phe368 in the L16 loop were changed to Leu, respectively, acquired higher intrinsic kinase activity and retained the normal MAPKK activation property. The expression of MPK6 mutants with basal activity is sufficient to induce camalexin biosynthesis; however, to induce ethylene and leaf senescence, the expression of MPK6 mutants with higher activity is required. The results suggest that these mutants can be used to analyze the specific biological functions of MPK6. PMID:27160427

The Crystal Structure of the Escherichia coli Autoinducer-2 Processing Protein LsrF

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

Diaz, Z.; Xavier, K; Miller, S

2009-01-01

Many bacteria produce and respond to the quorum sensing signal autoinducer-2 (AI-2). Escherichia coli and Salmonella typhimurium are among the species with the lsr operon, an operon containing AI-2 transport and processing genes that are up regulated in response to AI-2. One of the Lsr proteins, LsrF, has been implicated in processing the phosphorylated form of AI-2. Here, we present the structure of LsrF, unliganded and in complex with two phospho-AI-2 analogues, ribose-5-phosphate and ribulose-5-phosphate. The crystal structure shows that LsrF is a decamer of (??)8-barrels that exhibit a previously unseen N-terminal domain swap and have high structural homology withmore » aldolases that process phosphorylated sugars. Ligand binding sites and key catalytic residues are structurally conserved, strongly implicating LsrF as a class I aldolase.« less

Small Maf proteins (MafF, MafG, MafK): History, structure and function.

PubMed

Katsuoka, Fumiki; Yamamoto, Masayuki

2016-07-25

The small Maf proteins (sMafs) are basic region leucine zipper (bZIP)-type transcription factors. The basic region of the Maf family is unique among the bZIP factors, and it contributes to the distinct DNA-binding mode of this class of proteins. MafF, MafG and MafK are the three vertebrate sMafs, and no functional differences have been observed among them in terms of their bZIP structures. sMafs form homodimers by themselves, and they form heterodimers with cap 'n' collar (CNC) proteins (p45 NF-E2, Nrf1, Nrf2, and Nrf3) and also with Bach proteins (Bach1 and Bach2). Because CNC and Bach proteins cannot bind to DNA as monomers, sMafs are indispensable partners that are required by CNC and Bach proteins to exert their functions. sMafs lack the transcriptional activation domain; hence, their homodimers act as transcriptional repressors. In contrast, sMafs participate in transcriptional activation or repression depending on their heterodimeric partner molecules and context. Mouse genetic analyses have revealed that various biological pathways are under the regulation of CNC-sMaf heterodimers. In this review, we summarize the history and current progress of sMaf studies in relation to their partners. Copyright © 2016 Elsevier B.V. All rights reserved.