Éditeur(s) : HAL CCSD Elsevier
Résumé : International audience
Talc is a hydrous magnesium rich layered silicate that is widely disseminated in the Earth from the seafloor to over 100 km depth, in ultra-high pressure metamorphism of oceanic crust. In this paper we determine the single crystal elastic constants at pressures from 0 to 12 GPa of talc triclinic (C 1¯) and monoclinic (C2/c) polytypes using ab initio methods. We find that talc has an extraordinarily high elastic anisotropy at zero pressure that reduces with increasing pressure. The exceptional anisotropy is complemented by a negative Poisson's ratio for many directions in crystal space. Calculations show that talc is not only one of very few common minerals to exhibit auxetic behaviour, but the magnitude of this effect may be the largest reported so far for a mineral. The compression (Vp) and shear (Vs) wave velocity anisotropy is 80% and 85% for the triclinic polytype. At pressures where talc is known be stable in the Earth (up to 5 GPa) the Vp and Vs anisotropy is reduced to about 40% for both velocities, which is still a very high value. Vp is slow parallel to the c-axis and fast perpendicular to it. This remains unchanged with increasing pressure and is observed in both polytypes. The shear wave splitting (difference between fast and slow S-wave velocities) at low pressure has high values in the plane normal to the c-axis, with a maximum near the alow asterisk-axis in the triclinic and the b-axis in the monoclinic polytype. The c-axis is the direction of minimum splitting. The pattern of shear wave splitting does not change significantly with pressure. The volume fraction of talc varies between 11 and 41% for hydrated mantle rocks, but the lack of data on the crystallographic preferred orientation (CPO) precludes a detailed analysis of the impact of talc on seismic anisotropy in subduction zones. However, it is highly likely that CPO can easily develop in zones of deformation due to the platy habit of talc crystals. For random aggregates of talc, the isotropic Vp, Vs and Vp/Vs ratio have significantly lower values than those of antigorite and may explain low-velocity regions in the mantle wedge. Vp/Vs ratios are more complex in anisotropic media because there are fast and slow S-waves, resulting in Vp/Vs1 and Vp/Vs2 ratios for every propagation direction, making interpretation difficult in deformed polycrystalline talc with a CPO. Talc on the subduction plate boundary can strongly influence guided wave velocity as CPO would develop in this region of intense shearing. The very low coefficient of friction (< 0.1) of talc above 100 °C could also explain silent earthquakes at shallow depths (ca 30 km) along the subduction plate boundaries, frequently responsible for tsunami.
ISSN: 0012-821X

hal-00411481
https://hal.archives-ouvertes.fr/hal-00411481
DOI : 10.1016/j.epsl.2008.07.047

Éditeur(s) : HAL CCSD Elsevier
Résumé : International audience
Predicting the impact of underground engineering on the environment requires the knowledge of natural media at different scales. In particular, understanding basic phenomena controlling the properties of rocks in the presence of complex fluids necessitates a detailed atomic description of the solid/fluid/solid contacts, the subject of Part I of the present study. First, building the solid interspace between two different crystals in a non-periodic situation is achieved using the ab initio and molecular mechanics code GenMol (TM). A description of the fluid confined within the interspace is then derived from the original genetic iterative multi-species (GIMS) algorithm implemented in the same code. This approach consists of equilibrating chemical potentials, cycle after cycle and species after species, between the confined fluid and the free natural fluid. An elementary iteration for a species k consists of different steps incrementing the number N-k of particles k, with other numbers N-k remaining constant. At each step, an optimum fluid composition is obtained by a genetic process distributing the fluid particles on a grid by stochastic shots, followed in fine by a refining process. The effectiveness of the GIMS approach is demonstrated in the case study of a fluid confined between two (0 0 1) kaolinite faces, with apertures h varying between 4 and 10 A. connected to a 9-species external solution [H2O, Cl-, Na+ CO2(aq), NaCl(aq), Ca2+, Mg2+, HCO3-, H3O+] where concentrations are ranging from 55 to 10(-4) mol/L. The results show a drastic variation in the solute/solvent and cations/ions ratios in the confined fluid when aperture h is lowered to less than 1 nm. These results obtained with a very rapid convergence of the iterative algorithm combined with a very competitive genetic optimizer are validated with high precision on a free solution. This description of contacts between crystals is original and unattainable by standard crystal interface approaches. It opens the way to understanding and/or predicting phenomena between crystals in a complex natural environment, such as adhesion or repulsion investigated in the Part II of this study.
ISSN: 0022-0248

hal-00544569
https://hal.archives-ouvertes.fr/hal-00544569
DOI : 10.1016/j.jcrysgro.2010.08.009

Éditeur(s) : HAL CCSD Elsevier
Résumé : International audience
We use first first-principle methods and the Peierls-Nabarro model to evaluate the resistance to glide, characterized by the Peierls stress, of glide systems for end-member MgSiO3 Perovskite at mantle pressures. [010](100) is the easiest glide system in Mg-Perovskite at all pressures. Peierls stresses increase systematically with pressure for all systems except [001](010), indicating the importance of lattice friction at lower mantle pressures. The ratio of the maximum Peierls stress for each system relative to the [010](100) value defines their critical resolved shear stress (CRSS). These CRSS are used in a visco-plastic self-consistent homogenization model to predict the evolution of crystal preferred orientations (CPO) during deformation of polycrystalline Mg-Perovskite. In axial compression, [100] tends to align with the compression direction, in agreement with in situ observations in axial compression experiments. In simple shear, [010] concentrates near the shear direction and (100), although more dispersed, tends to align near the shear plane, consistent with the dominant activity of the easier [010](100) system. The calculated seismic anisotropy for a 100% Mg-Perovskite aggregate using the CPO in simple shear and the elastic constants Of MgSiO3 perovskite at lower mantle pressures and temperatures is weak (>3% for P-waves with and >2% for S-waves) and decreases with increasing temperature and pressure. P-waves show the fastest propagation parallel to the lineation and S-waves fast polarization is in the foliation at 38 GPa and normal to the lineation at 88 GPa. This weak anisotropy is consistent with global seismological observations of a nearly isotropic lower mantle. There are however two regions where strain-induced Mg-Perovskite CPO could contribute to anisotropy; a) low temperature regions in the uppermost lower mantle, where the predicted S-wave polarization anisotropy may attain 1.6% with a fast polarization parallel to the foliation, b) in high high-temperature domains in the D '' layer, where Mg-Perovskite may be the major stable phase, leading to polarization of fast S-waves normal to the lineation for propagation directions at high angle to the lineation and an apparent isotropy for all other propagation directions.
ISSN: 0012-821X

hal-00411460
https://hal.archives-ouvertes.fr/hal-00411460
DOI : 10.1016/j.epsl.2008.03.058

Éditeur(s) : HAL CCSD Wiley
Résumé : International audience
A relevant and accurate description of three-dimensional (3D) protein structures can be achieved by characterizing recurrent local structures. In a previous study, we developed a library of 120 3D structural prototypes encompassing all known 11-residues long local protein structures and ensuring a good quality of structural approximation. A local structure prediction method was also proposed. Here, overlapping properties of local protein structures in global ones are taken into account to characterize frequent local networks. At the same time, we propose a new long local structure prediction strategy which involves the use of evolutionary information coupled with Support Vector Machines (SVMs). Our prediction is evaluated by a stringent geometrical assessment. Every local structure prediction with a Calpha RMSD less than 2.5 A from the true local structure is considered as correct. A global prediction rate of 63.1% is then reached, corresponding to an improvement of 7.7 points compared with the previous strategy. In the same way, the prediction of 88.33% of the 120 structural classes is improved with 8.65% mean gain. 85.33% of proteins have better prediction results with a 9.43% average gain. An analysis of prediction rate per local network also supports the global improvement and gives insights into the potential of our method for predicting super local structures. Moreover, a confidence index for the direct estimation of prediction quality is proposed. Finally, our method is proved to be very competitive with cutting-edge strategies encompassing three categories of local structure predictions. Proteins 2009. (c) 2009 Wiley-Liss, Inc.
ISSN: 0887-3585

inserm-00348740
http://www.hal.inserm.fr/inserm-00348740
http://www.hal.inserm.fr/inserm-00348740/document
http://www.hal.inserm.fr/inserm-00348740/file/Bornot_Proteins_2009_preprint_version.pdf
http://www.hal.inserm.fr/inserm-00348740/file/inserm-00348740_edited.pdf

Éditeur(s) : HAL CCSD Elsevier
Résumé : The Duffy antigen/receptor for chemokine (DARC) is an erythrocyte receptor for malaria parasites (Plasmodium vivax and Plasmodium knowlesi) and for chemokines. In contrast to other chemokine receptors, DARC is a promiscuous receptor that binds chemokines of both CC and CXC classes. The four extracellular domains (ECDs) of DARC are essential for its interaction with chemokines, whilst the first (ECD1) is sufficient for the interaction with malaria erythrocyte-binding protein. In this study, we elaborate and analyze structural models of the DARC. The construction of the 3D models is based on a comparative modeling process and on the use of many procedures to predict transmembrane segments and to detect far homologous proteins with known structures. Threading, ab initio, secondary structure and Protein Blocks approaches are used to build a very large number of models. The conformational exploration of the ECDs is performed with simulated annealing. The second and fourth ECDs are strongly constrained. On the contrary, the ECD1 is highly flexible, but seems composed of three consecutive regions: a small beta-sheet, a linker region and a structured loop. The chosen structural models encompass most of the biochemical features and reflect the known experimental data. They may be used to analyze functional interaction properties.
ISSN: 0006-3002

inserm-00143373
http://www.hal.inserm.fr/inserm-00143373
http://www.hal.inserm.fr/inserm-00143373/document
http://www.hal.inserm.fr/inserm-00143373/file/de_Brevern_BBA_2005.pdf
DOI : 10.1016/j.bbagen.2005.05.016

Éditeur(s) : HAL CCSD Springer Verlag
Résumé : International audience
Intrinsic tribological properties of lamellar compounds are usually attributed to the presence of van der Waals gaps in their structure through which interlayer interactions are weak. The controlled variation of the distances and interactions between graphene layers by intercalation of electrophilic species in graphite is used in order to explore more deeply the friction reduction properties of low-dimensional compounds. Three graphite intercalation compounds with antimony pentachloride, iron trichloride and aluminium trichloride are studied. Their tribological properties are correlated to their structural parameters, and the interlayer interactions are deduced from ab initio bands structure calculations.
ISSN: 1023-8883

hal-00767639
https://hal.archives-ouvertes.fr/hal-00767639
https://hal.archives-ouvertes.fr/hal-00767639/document
https://hal.archives-ouvertes.fr/hal-00767639/file/Delbe_6330.pdf
DOI : 10.1007/s11249-012-9981-0

Éditeur(s) : HAL CCSD Elsevier
Résumé : International audience
This work deals with the problem of finding for a given industrial target the molecule conformation leading to the most efficient crystal polymorph and/or designing unknown crystal packing of new molecules. The originality of the method relies first on constraining the domain of the most probable crystals, before converging towards the predicted packing by a double genetic-refining optimization algorithm. Validation of this approach is discussed on the case study of 46 energetic crystal compounds, using the semi Ab Initio and Molecular Mechanics code GenMol™. This validation shows that all observed structures are retrieved in any circumstances with a relatively high number of good rankings.
ISSN: 0022-0248

hal-00857875
https://hal.archives-ouvertes.fr/hal-00857875
DOI : 10.1016/j.jcrysgro.2009.04.002

Éditeur(s) : HAL CCSD World Scientific Publishing
Résumé : International audience
We present a new, alternative interpretation of the vector-tensor multiplet as a two-form in central charge superspace. This approach provides a geometric description of the (nontrivial) central charge transformations ab initio and is naturally generalized to include couplings of Chern-Simons forms to the antisymmetric tensor gauge field, giving rise to a N=2 supersymmetric version of the Green-Schwarz anomaly cancellation mechanism.
ISSN: 0217-751X

hal-00769900
https://hal.univ-antilles.fr/hal-00769900
DOI : 10.1142/S0217751X98000792