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Elasticity and Stability of Clathrate Hydrate: Role of Guest Molecule Motions

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      Abstract

      Molecular dynamic simulations were performed to determine the elastic constants of carbon dioxide (CO2) and methane (CH4) hydrates at one hundred pressure–temperature data points, respectively. The conditions represent marine sediments and permafrost zones where gas hydrates occur. The shear modulus and Young’s modulus of the CO2 hydrate increase anomalously with increasing temperature, whereas those of the CH4 hydrate decrease regularly with increase in temperature. We ascribe this anomaly to the kinetic behavior of the linear CO2 molecule, especially those in the small cages. The cavity space of the cage limits free rotational motion of the CO2 molecule at low temperature. With increase in temperature, the CO2 molecule can rotate easily, and enhance the stability and rigidity of the CO2 hydrate. Our work provides a key database for the elastic properties of gas hydrates, and molecular insights into stability changes of CO2 hydrate from high temperature of ~5 °C to low decomposition temperature of ~−150 °C.

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      Canonical dynamics: Equilibrium phase-space distributions

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        GROMACS 4:  Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation.

        Molecular simulation is an extremely useful, but computationally very expensive tool for studies of chemical and biomolecular systems. Here, we present a new implementation of our molecular simulation toolkit GROMACS which now both achieves extremely high performance on single processors from algorithmic optimizations and hand-coded routines and simultaneously scales very well on parallel machines. The code encompasses a minimal-communication domain decomposition algorithm, full dynamic load balancing, a state-of-the-art parallel constraint solver, and efficient virtual site algorithms that allow removal of hydrogen atom degrees of freedom to enable integration time steps up to 5 fs for atomistic simulations also in parallel. To improve the scaling properties of the common particle mesh Ewald electrostatics algorithms, we have in addition used a Multiple-Program, Multiple-Data approach, with separate node domains responsible for direct and reciprocal space interactions. Not only does this combination of algorithms enable extremely long simulations of large systems but also it provides that simulation performance on quite modest numbers of standard cluster nodes.
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          A smooth particle mesh Ewald method

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            Author and article information

            Affiliations
            [1 ]ISNI 0000 0004 0372 2033, GRID grid.258799.8, Environment and Resource System Engineering, , Kyoto University, ; Kyoto, 615-8540 Japan
            [2 ]ISNI 0000 0001 2242 4849, GRID grid.177174.3, International Institute for Carbon-Neutral Energy Research (I2CNER), , Kyushu University, ; Fukuoka, 819-0395 Japan
            [3 ]ISNI 0000 0001 2151 536X, GRID grid.26999.3d, Center for Engineering, Research into Artifacts (RACE), , the University of Tokyo, ; Chiba, 277-8568 Japan
            [4 ]ISNI 0000 0001 2242 4849, GRID grid.177174.3, Department of Earth Resources Engineering, , Kyushu University, ; Fukuoka, 819-0395 Japan
            [5 ]GRID grid.468640.8, , Fukada Geological Institute, ; Tokyo, 113-0021 Japan
            Contributors
            ORCID: http://orcid.org/0000-0002-8832-1778, liang@race.u-tokyo.ac.jp
            murata.sumihiko.6v@kyoto-u.ac.jp
            Journal
            Sci Rep
            Sci Rep
            Scientific Reports
            Nature Publishing Group UK (London )
            2045-2322
            2 May 2017
            2 May 2017
            2017
            : 7
            28465527
            5431056
            1369
            10.1038/s41598-017-01369-0
            © The Author(s) 2017

            Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.

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