@article {142, title = {Optimized molecular reconstruction procedure combining hybrid reverse Monte Carlo and molecular dynamics}, journal = {The Journal of Chemical Physics}, volume = {142}, year = {2015}, month = {Mar-21-2015}, pages = {Article Number: 114112}, abstract = {

We report an efficient atom-scale reconstruction method that consists of combining the Hybrid Reverse Monte Carlo algorithm (HRMC) with Molecular Dynamics (MD) in the framework of a simulated annealing technique. In the spirit of the experimentally constrained molecular relaxation technique [Biswas et al., Phys. Rev. B 69, 195207 (2004)], this modified procedure offers a refined strategy in the field of reconstruction techniques, with special interest for heterogeneous and disordered solids such as amorphous porous materials. While the HRMC method generates physical structures, thanks to the use of energy penalties, the combination with MD makes the method at least one order of magnitude faster than HRMC simulations to obtain structures of similar quality. Furthermore, in order to ensure the transferability of this technique, we provide rational arguments to select the various input parameters such as the relative weight of the energy penalty with respect to the structure optimization. By applying the method to disordered porous carbons, we show that adsorption properties provide data to test the global texture of the reconstructed sample but are only weakly sensitive to the presence of defects. In contrast, the vibrational properties such as the phonon density of states are found to be very sensitive to the local structure of the sample.

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}, issn = {0021-9606}, doi = {10.1063/1.4914921}, author = {Bousige, Colin and Botan, Alexandru and Franz-Josef Ulm and Roland Jean-Marc Pellenq and Benoit A. Coasne} } @article {141, title = {Organic{\textendash}Clay Interfacial Chemical Bonds Probed by ab Initio Calculations}, journal = {The Journal of Physical Chemistry C}, volume = {119}, year = {2015}, month = {Mar-26-2015}, pages = {6511 - 6517}, abstract = {
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Evaluating the nature of binding of the organic phase (called kerogen) with clays and other minerals in gas and oil shale is of critical importance for developing optimal processes for hydrocarbon extraction and recovery. Here we report the results of an ab initio reactive study of a gaseous oil/clay interface, which consists of grafting fragments of sp3 methane and sp2 benzene onto the basal surface of illite. Methane and benzene fragments were selected as they correspond to the simplest monomers of the immature (aliphatic sp3 carbon atoms) and mature (aromatic sp2 carbon atoms) stages of the kerogen macromolecule while illite is encountered in many shale formations. We find that the methyl or phenyl radicals always bond upright to one of the outmost Si atoms of the clay phase, while the H atom attaches to the inner Al\–OH group forming a water molecule. The covalent attachment of the radicals to the oxygen atoms of the clay surface is always less favorable than to the silicon atoms. The energetics of these grafted adducts are discussed along with the maturation state of the shale. An unanticipated signature of the covalent Si\–C binding is the formation of hypervalent Si complexes, characterized by elongated bonds at the oil/clay interface. We complement our atomistic modeling by simulating IR spectra of the two covalently grafted interfaces (methyl\–illite and phenyl\–illite) which fingerprint elongated Si\–C bonds in the frequency range 1100\–1250 cm\–1. This novel finding should have a large impact on the understanding of fracking conditions in shales through this tight- and loose-bonded organic/inorganic interface.

}, issn = {1932-7447}, doi = {10.1021/jp510885f}, author = {Bocquet, Marie-Laure and Benoit A. Coasne and Roland Jean-Marc Pellenq and Franz-Josef Ulm} } @article {262, title = {Order and disorder in calcium{\textendash}silicate{\textendash}hydrate}, journal = {The Journal of Chemical Physics}, volume = {140}, year = {2014}, month = {Jun-07-2014}, pages = {Article Number: 214503}, abstract = {

Despite advances in the characterization and modeling of cement hydrates, the atomic order in Calcium\–Silicate\–Hydrate (C\–S\–H), the binding phase of cement, remains an open question. Indeed, in contrast to the former crystalline model, recent molecular models suggest that the nanoscale structure of C\–S\–H is amorphous. To elucidate this issue, we analyzed the structure of a realistic simulated model of C\–S\–H, and compared the latter to crystalline tobermorite, a natural analogue of C\–S\–H, and to an artificial ideal glass. The results clearly indicate that C\–S\–H appears as amorphous, when averaged on all atoms. However, an analysis of the order around each atomic species reveals that its structure shows an intermediate degree of order, retaining some characteristics of the crystal while acquiring an overall glass-like disorder. Thanks to a detailed quantification of order and disorder, we show that, while C\–S\–H retains some signatures of a tobermorite-like layered structure, hydrated species are completely amorphous.

}, issn = {0021-9606}, doi = {10.1063/1.4878656}, author = {Mathieu Bauchy and Mohammad Javad Abdolhosseini Qomi and Franz-Josef Ulm and Roland Jean-Marc Pellenq} } @article {66, title = {Optimizing water permeability through the hourglass shape of aquaporins}, journal = {Proceedings of the National Academy of Sciences}, volume = {110}, year = {2013}, month = {Oct-08-2013}, pages = {16367{\textendash}16372}, abstract = {

The ubiquitous aquaporin channels are able to conduct water across cell membranes, combining the seemingly antagonist functions of a very high selectivity with a remarkable permeability. Whereas molecular details are obvious keys to perform these tasks, the overall efficiency of transport in such nanopores is also strongly limited by viscous dissipation arising at the connection between the nanoconstriction and the nearby bulk reservoirs. In this contribution, we focus on these so-called entrance effects and specifically examine whether the characteristic hourglass shape of aquaporins may arise from a geometrical optimum for such hydrodynamic dissipation. Using a combination of finite-element calculations and analytical modeling, we show that conical entrances with suitable opening angle can indeed provide a large increase of the overall channel permeability. Moreover, the optimal opening angles that maximize the permeability are found to compare well with the angles measured in a large variety of aquaporins. This suggests that the hourglass shape of aquaporins could be the result of a natural selection process toward optimal hydrodynamic transport. Finally, in a biomimetic perspective, these results provide guidelines to design artificial nanopores with optimal performances.

}, doi = {10.1073/pnas.1306447110}, author = {Simon Gravelle and Joly, Laurent and Detcheverry, Fran{\c c}ois and Christophe Ybert and Cottin-Bizonne, C{\'e}cile and Lyd{\'e}ric Bocquet} } @proceedings {353, title = {Onset of Immersed Granular Avalanches by DEM-LBM Approach}, journal = {9th International Workshop on Buifurcation and Degradation in Geomaterials (IWBDG 2011)}, volume = {Springer Series in Geomechanics and Geoengineering - ADVANCES IN BIFURCATION AND DEGRADATION IN GEOMATERIALS}, year = {2011}, month = {May-28-2011}, pages = {109 - 115}, publisher = {Springer Netherlands}, address = {MAY 23-26 2011 Porquerolles, FRANCE}, abstract = {

We present 3D grain-fluid simulations based on the discrete element method interfaced with the lattice Boltzmann method and applied to investigate the initiation of underwater granular flows. We prepare granular beds of 800 spherical grains with different values of the initial solid fraction in a biperiodic rectangular box. In order to trigger an avalanche, the bed is instantaneously tilted to a finite slope angle above the maximum angle of stability. We simulate the dynamics of the transient flow for different solid fractions. In agreement with the experimental work of Iverson (Water Resour Res 36(7):1897\–1910, 2000) and Pailha et\ al. (Phys Fluids 20(11):111701, 2008), we find that the flow onset is controlled by the initial solid fraction.

}, isbn = {978-94-007-1420-5}, issn = {1866-8755}, doi = {10.1007/978-94-007-1421-210.1007/978-94-007-1421-2_14}, author = {Jean-Yves Delenne and Mansouri, M. and Farhang Radja{\"\i} and Moulay Sa{\"\i}d El Youssoufi and Seridi, A.}, editor = {St{\'e}phane Bonelli and Dascalu, Cristian and Fran{\c c}ois Nicot} }