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Mathematical Problems in Engineering
Volume 2009, Article ID 215815, 14 pages
Review Article

Simulation Algorithm That Conserves Energy and Momentum for Molecular Dynamics of Systems Driven by Switching Potentials

Department of Chemistry, University of Malaya, 50603 Kuala Lumpur, Malaysia

Received 26 November 2008; Revised 10 March 2009; Accepted 28 May 2009

Academic Editor: Jerzy Warminski

Copyright © 2009 Christopher G. Jesudason. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

Linked References

  6. J. Xu, S. Kjelstrup, and D. Bedeaux, “Molecular dynamics simulations of a chemical reaction; conditions for local equilibrium in a temperature gradient,” Physical Chemistry Chemical Physics, vol. 8, pp. 2017–2027, 2006. View at Google Scholar
  7. S. Nosé, “A unified formulation of the constant temperature molecular dynamics methods,” The Journal of Chemical Physics, vol. 81, no. 1, pp. 511–519, 1984. View at Google Scholar
  8. S. Nosé, “A molecular dynamics method for simulation in the canonical ensemble,” Molecular Physics, vol. 52, pp. 255–268, 1984. View at Google Scholar
  9. W. G. Hoover, “Canonical dynamics: equilibrium phase-space distributions,” Physical Review A, vol. 31, no. 3, pp. 1695–1697, 1985. View at Publisher · View at Google Scholar
  10. W. G. Hoover, “Constant-pressure equations of motion,” Physical Review A, vol. 34, no. 3, pp. 2499–2500, 1986. View at Publisher · View at Google Scholar
  11. D. Frenkel and B. Smit, Understanding Molecular Simulations: From Algorithms to Applications, vol. 1 of Computational Science Series, Academic Press, San Diego, Calif, USA, 2nd edition, 2002.
  12. D. Persano Adorno, N. Pizzolato, and B. Spagnolo, “The influence of noise on electron dynamics in semiconductors driven by a periodic electric field,” Journal of Statistical Mechanics: Theory and Experiment, vol. 2009, no. 1, Article ID P01039, 10 pages, 2009. View at Publisher · View at Google Scholar
  13. D. Persano Adorno, M. Zarcone, and G. Ferrante, “Far-infrared harmonic generation in semiconductors: a Monte Carlo simulation,” Laser Physics, vol. 10, no. 1, pp. 310–315, 2000. View at Google Scholar
  14. G. J. Martyna, D. J. Tobias, and M. L. Klein, “Constant pressure molecular dynamics algorithms,” The Journal of Chemical Physics, vol. 101, no. 5, pp. 4177–4189, 1994. View at Google Scholar
  15. H. J. C. Berendsen, J. P. M. Postma, W. F. Van Gunsteren, A. DiNola, and J. R. Haak, “Molecular dynamics with coupling to an external bath,” The Journal of Chemical Physics, vol. 81, no. 8, pp. 3684–3690, 1984. View at Google Scholar
  16. M. E. Tuckerman and G. J. Martyna, “Understanding modern molecular dynamics: techniques and applications,” Journal of Physical Chemistry B, vol. 104, no. 2, pp. 159–178, 2000. View at Google Scholar
  17. J. M. Haile, Molecular Dynamics Simulation, John Wiley & Sons, New York, NY, USA, 1992.
  18. C. G. Jesudason, “Model hysteresis dimer molecule. I. Equilibrium properties,” Journal of Mathematical Chemistry, vol. 42, no. 4, pp. 859–891, 2007. View at Publisher · View at Google Scholar
  19. T. Baer and W. L. Hase, Unimolecular Reaction Dynamics, Oxford University Press, Oxford, UK, 1996.
  20. Z. G. Fthenakis, “Applicability of the Hunjan-Ramaswamy global optimization method,” Physical Review E, vol. 70, no. 6, Article ID 066704, 8 pages, 2004. View at Publisher · View at Google Scholar
  21. G. S. Fanourgakis and S. C. Farantos, “Potential functions and static and dynamic properties of Mgm+Arn (m=1,2; n=118) clusters,” Journal of Physical Chemistry, vol. 100, pp. 3900–3909, 1996. View at Google Scholar
  22. D. R. Bevan, L. Li, L. G. Pedersen, and T. A. Darden, “Molecular dynamics simulations of the d(CCAACGTTGG)2 decamer: influence of the crystal environment,” Biophysical Journal, vol. 78, no. 2, pp. 668–682, 2000. View at Google Scholar
  23. E. Duffour and P. Malfreyt, “MD simulations of the collision between a copper ion and a polyethylene surface: an application to the plasma-insulating material interaction,” Polymer, vol. 45, no. 13, pp. 4565–4575, 2004. View at Publisher · View at Google Scholar
  24. I. Bena, C. Van den Broeck, R. Kawai, and K. Lindenberg, “Nonlinear response with dichotomous noise,” Physical Review E, vol. 66, no. 4, Article ID 045603, 4 pages, 2002. View at Publisher · View at Google Scholar
  25. M. P. Allen and D. J. Tildesley, Computer Simulation of Liquids, Oxford University Press, Oxford, UK, 1992.