Publications

2012

• Sodium selenide toxicity is mediated by O2-dependent DNA breaks.
  
  • Peyroche Gerald
  • Saveanu Cosmin
  • Dauplais Marc
  • Lazard Myriam
  • Beuneu Francois
  • Decourty Laurence
  • Malabat Christophe
  • Jacquier Alain
  • Blanquet Sylvain
  • Plateau Pierre
  PLoS ONE, Public Library of Science, 2012, 7 (5), pp.e36343. Hydrogen selenide is a recurrent metabolite of selenium compounds. However, few experiments studied the direct link between this toxic agent and cell death. To address this question, we first screened a systematic collection of Saccharomyces cerevisiae haploid knockout strains for sensitivity to sodium selenide, a donor for hydrogen selenide (H(2)Se/HSe(-/)Se(2-)). Among the genes whose deletion caused hypersensitivity, homologous recombination and DNA damage checkpoint genes were over-represented, suggesting that DNA double-strand breaks are a dominant cause of hydrogen selenide toxicity. Consistent with this hypothesis, treatment of S. cerevisiae cells with sodium selenide triggered G2/M checkpoint activation and induced in vivo chromosome fragmentation. In vitro, sodium selenide directly induced DNA phosphodiester-bond breaks via an O(2)-dependent reaction. The reaction was inhibited by mannitol, a hydroxyl radical quencher, but not by superoxide dismutase or catalase, strongly suggesting the involvement of hydroxyl radicals and ruling out participations of superoxide anions or hydrogen peroxide. The (*)OH signature could indeed be detected by electron spin resonance upon exposure of a solution of sodium selenide to O(2). Finally we showed that, in vivo, toxicity strictly depended on the presence of O(2). Therefore, by combining genome-wide and biochemical approaches, we demonstrated that, in yeast cells, hydrogen selenide induces toxic DNA breaks through an O(2)-dependent radical-based mechanism. (10.1371/journal.pone.0036343)
  DOI : 10.1371/journal.pone.0036343
• Kinetic Monte-Carlo simulation of the homoepitaxial growth of MgO\001\ thin films by molecular deposition
  
  • Antoshchenkova Ekaterina
  • Hayoun Marc
  • Finocchi Fabio
  • Geneste Grégory
  Surface Science : A Journal Devoted to the Physics and Chemistry of Interfaces, Elsevier, 2012, 606 (5-6), pp.605-614. A lattice-based kinetic Monte-Carlo (KMC) code has been developed to investigate the MgO\001\ crystal growth from deposition of MgO molecules, as a prototypical case of the growth of oxide thin films. The KMC approach has been designed on the basis of an extensive database including all possible diffusion mechanisms. The corresponding activation energies have been computed through first-principles calculations at zero temperature or from Arrhenius plots of the frequencies obtained by molecular dynamics simulations with empirical potentials. Crystal growth occurs layer by layer, as experimentally observed, and the diffusion of admolecules leads to a high capacity of nucleation, which is enhanced by vacancy diffusion. We have characterized the growth through surface roughness, size distribution and density of the islands, and filling ratios of the growing layers. Moreover, we have analysed the influence of each elementary mechanism on the growth. The best quality of the deposited layers is reached for temperatures larger than 700 K and for pressures smaller than 0.1 Torr. For these conditions, the simulated surface roughness is fully consistent with available experimental results. (C) 2011 Elsevier B.V. All rights reserved. (10.1016/j.susc.2011.11.026)
  DOI : 10.1016/j.susc.2011.11.026
• p Doping in Expanded Phases of ZnO: An Ab Initio Study
  
  • Hapiuk D.
  • Marques Miguel A. L.
  • Melinon P.
  • Flores-Livas Jose A.
  • Botti Silvana
  • Masenelli Bruno
  Physical Review Letters, American Physical Society, 2012, 108 (11), pp.NA. The issue of p doping in nanostructured cagelike ZnO is investigated by state-of-the-art calculations. Our study is focused on one prototypical structure, namely, sodalite, for which we show that p-type doping is possible for elements of the V, VI, and VII columns of the periodic table. However, some dopants tend to form dimers, thus impairing the stability of this kind of doping. This difference of behavior is discussed, and two criteria are proposed to ensure stable p doping. (10.1103/PhysRevLett.108.115903)
  DOI : 10.1103/PhysRevLett.108.115903
• Point defect stability in gamma irradiated aluminoborosilicate glasses: Influence of Yb3+ doping ions
  
  • Ollier N.
  • Pukhkaya V.
  Nuclear Instruments and Methods in Physics Research Section B: Beam Interactions with Materials and Atoms, Elsevier, 2012, 277, pp.121. Yb-doped aluminoborosilicate were irradiated with gamma rays at 10(4), 10(5), 10(6) and 10(7) Gy. The thermal stability as well as the recovery at room temperature of paramagnetic point defects such as Boron Oxygen Hole Center (BOHC), peroxy radicals and E' center were studied. At first, doping with Yb induced a saturation of the E' defect production and more importantly, the E' center recovering temperature was decreased by 50 degrees C. E' and BOHC defects both showed a limited stability at room temperature. By doping with Yb the glasses, the fading time of defects and in particular the BOHC defect recovery was modified. The BOHC defect showed moreover a larger sensitivity to photobleaching compared to the E' centers. Crown Copyright (C) 2012 Published by Elsevier B.V. All rights reserved. (10.1016/j.nimb.2011.12.053)
  DOI : 10.1016/j.nimb.2011.12.053
• Ion-matter interaction: the three-dimensional version of the thermal spike model. Application to nanoparticle irradiation with swift heavy ions NA
  
  • Dufour Ch
  • Khomenkov V.
  • Rizza G.
  • Toulemonde M.
  Journal of Physics D: Applied Physics, IOP Publishing, 2012, 45 (6), pp.NA. In the framework of swift heavy ion-matter interaction, the thermal spike has proved its worth for nearly two decades. This paper deals with the necessary refinement of the computation due to the kind of materials of interest, i.e. nanomaterials such as multilayered systems or composite films constituted of nanocylinders or nanospheres embedded in an insulating matrix. The three-dimensional computation of the thermal spike model is applied for the first time in the case of ions striking layers containing spherical nanoparticles embedded in a silica matrix. The temperature profiles calculated at each point (x, y, z) of the target for a total duration up to 10(-10) s and different values of ion impact parameter allow a possible explanation of the particle shape change under irradiation with swift heavy ions having an energy of several MeVamu(-1) (10.1088/0022-3727/45/6/065302)
  DOI : 10.1088/0022-3727/45/6/065302
• Raman activity of sp(3) carbon allotropes under pressure: A density functional theory study
  
  • Flores-Livas Jose A.
  • Lehtovaara Lauri
  • Amsler Maximilian
  • Goedecker Stefan
  • Pailhes Stephane
  • Botti Silvana
  • San Miguel Alfonso
  • Marques Miguel A. L.
  Physical Review B: Condensed Matter and Materials Physics (1998-2015), American Physical Society, 2012, 85 (15), pp.NA. Raman spectroscopy is a powerful tool to study the intrinsic vibrational characteristics of crystals, and, therefore, it is an adequate technique to explore phase transitions of carbon under pressure. However, the diamond-anvil cell, which is used in experiments to apply pressure, appears as a broad intense feature in the spectra. This feature lies, unfortunately, in the same range as the principal modes of recently proposed sp(3) carbon structures. As these modes are hard to distinguish from the diamond cell background, we analyze all Raman-active modes present in the sp(3) carbon structures in order to find detectable fingerprint features for an experimental identification. (10.1103/PhysRevB.85.155428)
  DOI : 10.1103/PhysRevB.85.155428
• Positron annihilation in latex templated macroporous silica films: pore size and ortho-positronium escape
  
  • Liszkay L.
  • Guillemot F.
  • Corbel C.
  • Boilot J.P.
  • Gacoin T.
  • Barthel E.
  • Pérez A.
  • Barthe M.F.
  • Desgardin P.
  • Crivelli P.
  • Gendotti U.
  • Rubbia A.
  New Journal of Physics, Institute of Physics: Open Access Journals, 2012, 14, pp.065009. Depth profling of positron annihilation characteristics has been used to investigate the pore size distribution in macroporous PMMA latex templated SiO2 films deposited on glass or Si and prepared with 11-70% porosity. The correlation between the annihilation characteristics shows that o-Ps escape (re-emission) into vacuum occurs in all films with a porosity threshold that is pore size dependent. For 60 ± 2% porosity, the o-Ps reemission yield decreases from ~ 0:25 to ~ 0:11 as the pore size increases from 32 to 75 nm. The o-Ps reemission yield is shown to vary linearly with the specific surface area per mass unit and the slope is independent of pore size, 9:1±0:4 g cm-1. For 32 nm pores, the o-Ps annihilation lifetimes in the films, 17(2)ns and 106(5) ns, show that o-Ps annihilates from micropores with small effective size (1:4 ± 4 nm) and from macropores with large effective size (~ 32 nm). Above the porosity threshold, the o-Ps-escape model predicts the annihilation lifetime in the films to be 19±2 ns. Our results imply that o-Ps effciently detects the microporosity present in the silica walls. At low porosity, its capture into the micropores competes with its capture into the macropores. At higher porosity (when the distance between micropores and macropores become small), this capture into the micropores assists the capture into the macropores. (10.1088/1367-2630/14/6/065009)
  DOI : 10.1088/1367-2630/14/6/065009
• Clusters dissolution of Yb³⁺ in codoped SiO₂-Al₂O₃-P₂O₅ glass fiber and its relevance to photodarkening
  
  • Deschamps T.
  • Ollier N.
  • Vezin H.
  • Gonnet C.
  The Journal of Chemical Physics, American Institute of Physics, 2012, 136, pp.014503-1 - 014503-4. Using a combination of pulse electron paramagnetic resonance and photoluminescence spectroscopy, we demonstrate the major role of phosphorous rather than aluminium in the rare-earth dissolution process, an essential advance in telecommunication and solid laser fields. Our results also provide new insight into the micro-structural origin of the photodarkening process occurring in Yb doped fiber. (10.1063/1.3673792)
  DOI : 10.1063/1.3673792
• Nucleation of single wall carbon nanotubes of various chiralities
  
  • Beuneu F.
  Solid State Communications, Elsevier, 2012, 152 (13), pp.1155. A simple model for the nucleation and growth of single wall carbon nanotubes from a graphene sheet at the surface of a metallic catalyst saturated in carbon is developed. It enables to predict the geometry and energy of tube embryos of all possible chiralities, as well as the way that they can grow. It is shown that armchair-like chiralities are energy preferred for geometrical reasons. This result is discussed and compared to experimental literature. © 2012 Elsevier Ltd. All rights reserved. (10.1016/j.ssc.2012.03.041)
  DOI : 10.1016/j.ssc.2012.03.041