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9. Molecular Dynamics Simulations in Biology, Chemistry and Physics

  • P. Entel
  • W.A. Adeagbo
  • M. Sugihara
  • G. Rollmann
  • A.T. Zayak
  • M. Kreth
  • K. Kadau
Part II Simulation from Nanoscopic Systems to Macroscopic Materials
Part of the Lecture Notes in Physics book series (LNP, volume 642)

Abstract

We review recent progress in understanding fundamental processes in biology, chemistry and physics on the basis of ab initio and molecular dynamics simulations. The first step of the visual process involving the excitation of bovine rhodopsin after absorption of light is taken as an example from biochemistry to demonstrate what is nowadays possible to simulate numerically. The act of freezing of water has recently been simulated, for the first time successfully, by scientists from chemistry. Martensitic transformation in bulk and nanophase materials, a typical and hitherto not completely solved problem from solid state physics, is used to illustrate the achievements of multimillion atoms simulations.

Keywords

Molecular Dynamic Simulation Martensitic Transformation Guest Molecule Radial Distribution Function Water Cluster 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

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References

  1. 1. W.G. Hoover, A. Ladd, B. Moran: Phys. Rev. Lett. 48, 1818 (1982)CrossRefGoogle Scholar
  2. 2. S. Nosé: J. Chem. Phys. 81, 511 (1984); S. Nosé: Mol. Phys. 52, 255 (1984)CrossRefGoogle Scholar
  3. 3. W.G. Hoover: Phys. Rev. A 31, 1695 (1985).CrossRefGoogle Scholar
  4. 4. M. Parrinello: A. Rahman, Phys. Rev. Lett. 45, 1196 (1980)Google Scholar
  5. 5. D. Frenkel, B. Smit: Understanding Molecular Simulation – From Algorithms to Applications, Computational Science Series 1, 2nd edn. (Academic Press, San Diego 2002)Google Scholar
  6. 6. K.A. Fichthorn, M.L. Merrick, M. Scheffler: Appl. Phys. A 75, 79 (2002)CrossRefGoogle Scholar
  7. 7. A. Voter: J. Chem. Phys. 106, 4665 (1997)CrossRefGoogle Scholar
  8. 8. J. VandeVondele, U. Rothlisberger: J. Chem. Phys. 113, 4863 (2000); A. Passerone, M. Parrinello: Phys. Rev. Lett. 87, 83002 (2001)CrossRefGoogle Scholar
  9. 9. Bridging Time Scales: Molecular Simulations for the Next Decade, Lecture Notes in Physics, LNP 605, ed. by P. Nielaba, M. Mareschal, G. Ciccotti (Springer, Berlin 2002)Google Scholar
  10. 10. S.R. Shenoy, T. Lookman, A. Saxena, A.R. Bishop: Phys. Rev. B 60, R12537 (1999)Google Scholar
  11. 11. P. Cartoni, U. Rothlisberger, M. Parrinello: Acc. Chem. Res. 35, 455 (2002)CrossRefPubMedGoogle Scholar
  12. 12. M. E. Colombo, L. Guidoni, A. Laio, A. Magiskato, P. Maurer, S. Piana, U. Roehrig, K. Spiegel, J. VandeVondele, U. Roethlisberger: Chimica 56, 11 (2002)Google Scholar
  13. 13. M. Elstner, D. Porezag, G. Jungnickel, J. Elsner, M. Haugk, T. Frauenheim, S. Suhai, G. Seifert: Phys. Rev. B 58, 7260 (1998)CrossRefGoogle Scholar
  14. 14. Q. Cui, M. Elstner, T. Frauenheim, E. Kaxiras, M. Karpuls: J. Phys. Chem. B 105, 569 (2001).CrossRefGoogle Scholar
  15. 15. U. Saalmann, R. Schmidt: Z. Phys. D 38, 153 (1996)CrossRefGoogle Scholar
  16. 16. G.W. Robinson, S.-B. Zhu, S. Singh, M.W. Evans: Water in Biology, Chemistry and Physics – Experimental Overviews and Computational Methodologies, World Scientific Series in Contemporary Chemical Physics – Vol. 9 (World Scientific, Singapore 1996)Google Scholar
  17. 17. Proceedings of the First International Symposium on Physical, Chemical and Biological Properties of Stable Water ( I E TM ) Clusters, ed. by S.Y.Lo, B. Bonavida (World Scientific, Singapore 1998)Google Scholar
  18. 18. M. Chaplin: http://www.sbu.ac.uk/water/Google Scholar
  19. 19. A. Bizzarri, S. Cannistraro: J. Phys. Chem B 106, 6617 (2002)CrossRefGoogle Scholar
  20. 20. M.E. Tuckerman: J. Phys.: Condens. Matter 14, R 1297 (2002)Google Scholar
  21. 21. D. Marx, M.E. Tuckerman, J. Hutter, M. Parrinello: Nature 397, 601 (1999)CrossRefGoogle Scholar
  22. 22. U.W. Schmitt, G.A. Voth: J. Chem. Phys. 111, 9361 (1999)CrossRefGoogle Scholar
  23. 23. L.M. Ramaniah, M. Parrinello, M. Bernasconi: J. Chem. Phys. 111, 1595 (1999)CrossRefGoogle Scholar
  24. 24. M. Benoit, D. Marx, M. Parrinello: Nature 392, 258 (1998)CrossRefGoogle Scholar
  25. 25. J.M. Sorenson, G. Hura, R.M. Glaeser, T. Head-Gordon: J. Chem. Phys. 113, 9149 (2000)CrossRefGoogle Scholar
  26. 26. A.K. Soper: Chem. Phys. 258, 121 (2000)CrossRefGoogle Scholar
  27. 27. S. Izvekov, G.A. Voth: J. Chem. Phys. 116, 10372 (2002)CrossRefGoogle Scholar
  28. 28. R. Car, M. Parrinello: Phys. Rev. Lett. 55, 2471 (1985)CrossRefGoogle Scholar
  29. 29. A.D. Becke: Phys. Rev. A 38, 3098 (1988); C. Lee, W. Yang, R.C. Parr: Phys. Rev. B 37, 785 (1988)CrossRefGoogle Scholar
  30. 30. N. Troullier, J.L. Martins: Phys. Rev. B 43, 1993 (1991)Google Scholar
  31. 31. G. Kresse, J. Furthmüller: Phys. Rev. B 54, 11169 (1996)CrossRefGoogle Scholar
  32. 32. A. Wallqvist, R.D. Mountain: ‘Molecular Models of Water: Derivation and Description’. In: Reviews in Computational Chemistry, Vol. 13, ed. by K.B. Lipkowitz, D.B. Boyd (Wiley-VCH, New York 1999), pp. 183–247Google Scholar
  33. 33. G.A. Jeffrey: An Introduction to Hydrogen Bonding, (Oxford University Press, Oxford 1997)Google Scholar
  34. 34. M. Matsumoto, S. Saito, I. Ohmine: Nature 416, 409 (2002) (http://www.nature. com/nature). Figure 2 used by courtesy of Iwao Ohmine, Chemistry Department, Nagoya University, JapanCrossRefPubMedGoogle Scholar
  35. 35. W.L. Jorgensen, J. Chandrasekhar, J.D. Madura: J. Chem. Phys. 79, 926 (1983)CrossRefGoogle Scholar
  36. 36. P.J. Steinhardt, D.R. Nelson, M. Ronchetti: Phys. Rev. B 28, 784 (1983)CrossRefGoogle Scholar
  37. 37. W.A. Adeagbo, P. Entel: Phase Transitions, submittedGoogle Scholar
  38. 38. A. Vegiri, S.C. Farantos: J. Chem. Phys. 98, 4059 (1993)CrossRefGoogle Scholar
  39. 39. H. Kabrede, R. Hentschke: J. Phys. Chem. 107, 3914 (2003)CrossRefGoogle Scholar
  40. 40. D.J. Wales, I. Ohmine: J. Chem. Phys. 98, 7245 (1993)CrossRefGoogle Scholar
  41. 41. S. Lee, J. Kim, S.J. Lee, K.S. Kim: Phys. Rev. Lett. 79, 2038 (1997)CrossRefGoogle Scholar
  42. 42. W.B. Wayne, M.M. Rhodes: J. Chem. Phys. 98, 4413 (1993)CrossRefGoogle Scholar
  43. 43. J.L. Atwood, J.E.D. Davies, D.D. MacNicol, F. Vöegtle, J.M. Lehn: Comprehensive Supramolecular Chemistry, (Elsevier, Oxford 1996)Google Scholar
  44. 44. B.K. Lipkowitz: Chem. Rev. 98, 1829 (1998)CrossRefPubMedGoogle Scholar
  45. 45. W. Saegner, J. Jacob, K. Steiner, D. Hoffman, H. Sanbe, K. Koizumi, S.M. Smith, T. Takaha: Chem. Rev. 98, 1787 (1998)CrossRefPubMedGoogle Scholar
  46. 46. J. Szejtli: J. Mater. Chem. 7, 575 (1997)CrossRefGoogle Scholar
  47. 47. W.A. Adeagbo, V. Buss, P. Entel: Phase Transitions, submittedGoogle Scholar
  48. 48. J. Ding, T. Steiner, W. Saenger: Acta Cryst. B 47, 731 (1991)CrossRefGoogle Scholar
  49. 49. B. Manunza, S. Deiana, M. Pintore, C. Gessa: J. Molec. Struct. (Theochem) 419, 133 (1997)CrossRefPubMedGoogle Scholar
  50. 50. G. Wald: Science 162, 230 (1968)PubMedGoogle Scholar
  51. 51. R.W. Schoenlein, L.A. Peteanu, R.A. Mathies, C.V. Shank: Science 254, 412 (1991)PubMedGoogle Scholar
  52. 52. S.J. Hug, J.W. Lewis, C.M. Einterz, T.E. Thorgeirsson, D.S. Kliger: Biochemistry 29, 1475 (1990)PubMedGoogle Scholar
  53. 53. B. Borhan, M.L. Souto, H. Imai, Y. Shichda, K. Nakanishi: Science 288, 2209 (2000)CrossRefPubMedGoogle Scholar
  54. 54. J.E. Kim, D.W. McCamant, L. Zhu, R.A. Mathies: J. Phys. Chem. B 105, 1240 (2001)CrossRefGoogle Scholar
  55. 55. A.G. Doukas, R.H. Callender, T.G. Ebrey: Biochemistry 17, 2430 (1978)PubMedGoogle Scholar
  56. 56. T. Okada, K. Palczewski, K.P. Hofmann: Trends Biochem. Sci. 26, 318 (2001)CrossRefPubMedGoogle Scholar
  57. 57. Y. Shichida, H. Imai, T. Okada: Cell. Mol. Life Sci. 54, 1299 (1998). Figure 8 used by courtesy of Tetsuji Okada, AIST Tokyo, JapanCrossRefPubMedGoogle Scholar
  58. 58. L. Tang, T.G. Ebrey, S. Subramaniam: Israel Jour. Chem. 35, 193 (1995)Google Scholar
  59. 59. T. Okada, I. Le Trong, B.A. Fox, C.A. Behnke, R.E. Stenkamp, K. Palczewski: J. Struct. Biol. 130, 73 (2000)CrossRefPubMedGoogle Scholar
  60. 60. T. Okada, K. Palczewski: Current Opinion Struct. Biol. 11, 420 (2001)CrossRefGoogle Scholar
  61. 61. K. Palczewski, T. Kumasaka, T. Hori, C.A. Behnke, H. Motoshima, B.A. Fox, I. LeTrong, D.C. Teller, T. Okada, R.E. Stenkamp, M. Yamamoto, M. Miyano: Science 289, 739 (2000) (http://www.sciencemag.org). Figure 6 used by courtesy of Krzysztof Placzewski, Department of Ophthalmology, University of Washington, USAPubMedGoogle Scholar
  62. 62. D.C. Teller, T. Okada, C.A. Behnke, K. Palczewki, R.E. Stenkamp: Biochemistry 40, 7761 (2001)CrossRefPubMedGoogle Scholar
  63. 63. T. Okada, Y. Fujiyohi, M. Silow, J. Navarro, E.M. Landau, Y. Schichida: Proc. Natl. Acad. Sci. U.S.A. 99, 5982 (2002)CrossRefPubMedGoogle Scholar
  64. 64. V. Buss, M. Sugihara, P. Entel, J. Hafner: Z. Angew. Chemie, acceptedGoogle Scholar
  65. 65. M. Sugihara, V. Buss, P. Entel, M. Elstner, T. Frauenheim: Biochemistry 41, 15239 (2002)CrossRefGoogle Scholar
  66. 66. M. Han, B.S. DeDecker, S.O. Smith: Biophys. J. 65, 6111 (1993)Google Scholar
  67. 67. M. Han, S.O. Smith: Biochemistry 34, 1425 (1995)PubMedGoogle Scholar
  68. 68. P. Garriga, J. Manyosa: Biochemistry 528, 17 (2002)CrossRefGoogle Scholar
  69. 69. U.F.Röhrig, L. Guidoni, U. Rhothilinsberger: Biochemistry 41, 10799 (2002)CrossRefPubMedGoogle Scholar
  70. 70. E.C.Y. Yan, M.A. Kazmi, S. De, B.S.W. Chang, C. Seibert, E.P. Marin, R.A. Mathies, T.P. Sakmar: Biochemistry 41, 3620 (2002)CrossRefPubMedGoogle Scholar
  71. 71. J.-P. Perdew, Y. Wang: Phys. Rev. 45, 13244 (1992)CrossRefGoogle Scholar
  72. 72. E.F. Wassermann: ‘Invar: Moment-volume instabilities in transition metals and alloys’. In: Ferromagnetic Materials, ed. by K.H.J. Buschow, E.P. Wohlfarth (Elsevier, Amsterdam 1990) pp. 237–322Google Scholar
  73. 73. A.D. Bozhko, A.N. Vasil’ev, V.V. Khovailo, I.E. Dikshtein, V.V. Koledov, S.M. Seletskii, A.A. Tulaikova, A.A. Cherechukin, V.G. Shavrov, V.D. Buchelnikov: JETP 88, 957 (1999)CrossRefGoogle Scholar
  74. 74. M. Schröter, H. Ebert, H. Akai, P. Entel, E. Hoffmann, G.G. Reddy: Phys. Rev. B 52, 188 (1995)CrossRefGoogle Scholar
  75. 75. V. Crisan, P. Entel, H. Ebert, H. Akai, D.D. Johnson, J.B. Staunton, Phys. Rev. B 66, 014416 (2002)Google Scholar
  76. 76. P. Entel, R. Meyer, K. Kadau, H.C. Herper, E. Hoffmann: Eur. Phys. J. B 5, 379 (1998)CrossRefGoogle Scholar
  77. 77. K. Kadau: Molekulardynamik-Simulationen von strukturellen Phasenumwandlungen in Festkörpern, Nanopartikeln und ultradünnen Filmen. PhD Thesis, Gerhard-Mercator-Universität Duisburg, Duisburg (2001)Google Scholar
  78. 78. M.S. Daw, M.I. Baskes: Phys. Rev. B 26, 6443 (1983)Google Scholar
  79. 79. V.V. Khovailo, T. Takagi, A.D. Bozhko, M. Matsumoto, J. Tani, V.G. Shavrov: J. Phys.: Condens. Matter 13, 9655 (2001)CrossRefGoogle Scholar
  80. 80. A.N. Vasil’ev, A.D. Bozhko, V.V. Khovailo, I.E. Dikshtein, V.G. Shavrov, V.D. Buchelnikov, M. Matsumoto, S. Suzuki, T. Takagi, J. Tani: Phys. Rev. B 59, 1113 (1999)CrossRefGoogle Scholar
  81. 81. V.D. Buchelnikov, A.T. Zayak, A.N. Vasil’ev, T. Takagi: Int. J. Appl. Electromagn. Mechan. 1, 2, 19 (2000)Google Scholar
  82. 82. V.D. Buchelnikov, A.T. Zayak, A.N. Vasil’ev, D.L. Dalidovich, V.G. Shavrov, T. Takagi, V.V. Khovailo: JETP 92, 1010 (2001)CrossRefGoogle Scholar
  83. 83. A.T. Zayak, V.D. Buchelnikov, P. Entel: Phase Transitions 75, 243 (2002)CrossRefGoogle Scholar
  84. 84. A.T. Zayak, P. Entel, J. Enkovaara, A. Ayuela, R.M. Nieminen: cond-mat/0304315 (2003)Google Scholar
  85. 85. C.B. Bungaro, K.M. Rabe, A. Dal Corso: cond-mat/0304349 (2003)Google Scholar
  86. 86. A. Zheludev, S.M. Shapiro, P. Wochner, A. Schwartz, M. Wall, L.E. Tanner: Phase Transitions 51, 11310 (1995)CrossRefGoogle Scholar
  87. 87. J. Schiøtz, F.D.D. Tolla, K.W. Jacobsen: Nature 391, 561 (1998)CrossRefGoogle Scholar
  88. 88. R.W. Siegel, G.E. Fougere: ‘Mechanical properties of nanophase materials’. In: Nanophase Materials, Synthesis – Properties – Applications, NATO ASI Series E, vol. 260, ed. by G.C. Hadjipanayis, R.W. Siegel (Kluwer, Dordrecht 1990), pp. 233Google Scholar
  89. 89. K. Asaka, Y. Hirotsu, T. Tadaki: ‘Martensitic transformation in nanometer-sized particles of Fe-Ni alloys’. In: ICOMAT 98: International Conference on Martensitic Transformations at San Carlos de Bariloche, Argentina, December 7–11, 1998, ed. by M. Ahlers, G. Kostorz, M.Sade, Mater. Sci. Engin. A 273–275, 257 (1999)Google Scholar
  90. 90. K. Kadau, P. Entel, T.C. Germann, P.S. Lomdahl, B.L. Holian: ‘Large-scale molecular-dynamics study of the nucleation process of martensite in Fe–Ni alloys’. In: ESOMAT 2000: Fifth European Symposium on Martensitic Transformations and Shape Memory Alloys at Como, Italy, September 4–8, 2000, ed. by G. Airoldi, S. Besseghini, J. Physique IV (France) 11, Pr8–17 (2001)Google Scholar
  91. 91. P.S. Lomdahl, P. Tamayo, N.G. Jensen, D.M. Beazley: ‘50 GFlops molecular dynamics on the CM-5’. In: Proceedings of Supercomputing 93, ed. by G.S. Ansell (IEEE Computer Society Press, Los Alamitos, CA, 1993) pp. 520–527Google Scholar
  92. 92. D.M. Beazley, P.S. Lomdahl: Computers in Physics 11, 230 (1997)Google Scholar
  93. 93. http://bifrost.lanl.gov/MD/MD.htmlGoogle Scholar
  94. 94. J.W.W. Frenken, P.M. Maree, J.F. van der Veen: Phys. Rev. B 34, 7506 (1986)CrossRefGoogle Scholar
  95. 95. H. Reichert, O. Klein, H. Dosch, M. Denk, V. Honkimäki, T. Lippmann, G. Reiter: Nature 408, 839 (2000)CrossRefPubMedGoogle Scholar
  96. 96. P. Buffat, J.-P. Borel: Phys. Rev. A 13, 2287 (1976)CrossRefGoogle Scholar
  97. 97. M. Schmidt, J. Dongers, Th. Hippler, H. Haberland: Phys. Rev. Lett. 90, 103401 (2003)CrossRefGoogle Scholar

Authors and Affiliations

  • P. Entel
    • 1
  • W.A. Adeagbo
    • 1
  • M. Sugihara
    • 1
  • G. Rollmann
    • 1
  • A.T. Zayak
    • 1
  • M. Kreth
    • 1
  • K. Kadau
    • 2
  1. 1.Institute of Physics, University of Duisburg–Essen, 47048 DuisburgGermany
  2. 2.Los Alamos National Laboratory, T–11, MS B262, Los Alamos, NM 87545USA

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