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Methodology

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Nanoscale Fluid Transport

Part of the book series: Springer Theses ((Springer Theses))

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Abstract

Molecular modeling techniques have been extensively used in studying fluid flow in nanochannels. In this Chapter I discuss the basic background of equilibrium and non-equilibrium molecular dynamics simulations. 

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References

  1. Van der Spoel, D., et al. (2005). GROMACS: Fast, flexible, and free. Journal of Computational Chemistry, 26(16), 1701–1718.

    Article  Google Scholar 

  2. Berendsen, H. J. C., Postma, J. P. M., Van Gunsteren, W. F., & Hermans, J. (1981). Intermolecular forces. Dordrecht: Reidel.

    Google Scholar 

  3. Berendsen, H. J. C., Grigera, J. R., & Straatsma, T. P. (1987). The missing term in effective pair potentials. Journal of Physical Chemistry, 91(24), 6269–6271.

    Article  CAS  Google Scholar 

  4. Abascal, J. L. F., & Vega, C. (2005). A general purpose model for the condensed phases of water: TIP4P/2005. The Journal of Chemical Physics, 123(23), 234505.

    Article  CAS  Google Scholar 

  5. Jorgensen, W. L., Chandrasekhar, J., Madura, J. D., Impey, R. W., & Klein, M. L. (1983). Comparison of simple potential functions for simulating liquid water. The Journal of Chemical Physics, 79(2), 926–935.

    Article  CAS  Google Scholar 

  6. Mahoney, M. W., & Jorgensen, W. L. (2000). A five-site model for liquid water and the reproduction of the density anomaly by rigid, nonpolarizable potential functions. The Journal of Chemical Physics, 112(20), 8910–8922.

    Article  CAS  Google Scholar 

  7. Gonzalez, M. A., & Abascal, J. L. F. (2011). A flexible model for water based on TIP4P/2005. The Journal of Chemical Physics, 135(22), 224516–224523.

    Article  Google Scholar 

  8. Lamoureux, G., Harder, E., Vorobyov, I. V., Roux, B., & MacKerell, A. D. (2006). A polarizable model of water for molecular dynamics simulations of biomolecules. Chemical Physics Letters, 418(1–3), 245–249.

    Article  CAS  Google Scholar 

  9. Ryckaert, J.-P., Ciccotti, G., & Berendsen, H. (1977). Numerical integration of the cartesian equations of motion of a system with constraints: Molecular dynamics of n-alkanes. Journal of Computational Physics, 23(3), 327–341.

    Article  CAS  Google Scholar 

  10. Mark, P., & Nilsson, L. (2001). Structure and dynamics of the TIP3P, SPC, and SPC/E water models at 298 K. Journal of Physical Chemistry A, 105(43), 9954–9960.

    Article  CAS  Google Scholar 

  11. Pusztai, L., Pizio, O., & Sokolowski, S. (2008). Comparison of interaction potentials of liquid water with respect to their consistency with neutron diffraction data of pure heavy water. The Journal of Chemical Physics, 129(18), 184103.

    Article  Google Scholar 

  12. Krynicki, K., Green, C. D., & Sawyer, D. W. (1978). Pressure and temperature-dependence of self-diffusion in water. Faraday Discussions, 66, 199–208.

    Article  Google Scholar 

  13. Mahoney, M. W., & Jorgensen, W. L. (2001). Diffusion constant of the TIP5P model of liquid water. The Journal of Chemical Physics, 114(1), 363–366.

    Article  CAS  Google Scholar 

  14. Vega, C., & Abascal, J. L. F. (2011). Simulating water with rigid non-polarizable models: A general perspective. Physical Chemistry Chemical Physics: PCCP, 13(44), 19663–19688.

    Article  CAS  Google Scholar 

  15. Ho, T. A., et al. (2011). Interfacial water on crystalline silica: A comparative molecular dynamics simulation study. Molecular Simulation, 37(3), 172–195.

    Article  CAS  Google Scholar 

  16. Basconi, J. E., & Shirts, M. R. (2013). Effects of temperature control algorithms on transport properties and kinetics in molecular dynamics simulations. Journal of Chemical Theory and Computation, 9(7), 2887–2899.

    Article  CAS  Google Scholar 

  17. Thompson, P. A., & Troian, S. M. (1997). A general boundary condition for liquid flow at solid surfaces. Nature, 389(6649), 360.

    Article  CAS  Google Scholar 

  18. Lauga, E., Brenner, M., & Stone, H. (2007). Handbook of experimental fluid dynamics. New York: Springer.

    Google Scholar 

  19. Ho, T. A., Papavassiliou, D. V., Lee, L. L., & Striolo, A. (2011). Liquid water can slip on a hydrophilic surface. Proceedings of the National Academy of Sciences, 108(39), 16170–16175.

    Article  CAS  Google Scholar 

  20. Cohen-Tanugi, D., & Grossman, J. C. (2012). Water Desalination across nanoporous graphene. Nano Letters, 12(7), 3602–3608.

    Article  CAS  Google Scholar 

  21. Holt, J. K., et al. (2006). Fast mass transport through sub-2-nanometer carbon nanotubes. Science, 312(5776), 1034–1037.

    Article  CAS  Google Scholar 

  22. Whitby, M., & Quirke, N. (2007). Fluid flow in carbon nanotubes and nanopipes. Nature Nanotechnology, 2(2), 87–94.

    Article  CAS  Google Scholar 

  23. Toton, D., Lorenz, C. D., Rompotis, N., Martsinovich, N., & Kantorovich, L. (2010). Temperature control in molecular dynamic simulations of non-equilibrium processes. Journal of Physics: Condensed Matter, 22(7), 074205.

    Google Scholar 

  24. Zhu, W., Singer, S. J., Zheng, Z., & Conlisk, A. T. (2005). Electro-osmotic flow of a model electrolyte. Physical Review E, 71(4), 041501.

    Article  Google Scholar 

  25. Freund, J. B. (2002). Electro-osmosis in a nanometer-scale channel studied by atomistic simulation. The Journal of Chemical Physics, 116(5), 2194–2200.

    Article  CAS  Google Scholar 

  26. Qiao, R., & Aluru, N. R. (2003). Ion concentrations and velocity profiles in nanochannel electroosmotic flows. The Journal of Chemical Physics, 118(10), 4692–4701.

    Article  CAS  Google Scholar 

  27. Khare, R., de Pablo, J., & Yethiraj, A. (1997). Molecular simulation and continuum mechanics study of simple fluids in non-isothermal planar couette flows. The Journal of Chemical Physics, 107(7), 2589–2596.

    Article  CAS  Google Scholar 

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Correspondence to Tuan Anh Ho .

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Ho, T.A. (2017). Methodology. In: Nanoscale Fluid Transport. Springer Theses. Springer, Cham. https://doi.org/10.1007/978-3-319-47003-0_2

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