Investigation of DNA denaturation in Peyrard-Bishop-Dauxois model by molecular dynamics method

Abstract

The phase transition of (PolyA/PolyT)100 duplex into the denaturated state is studied in the Peyrard-Bishop-Dauxois model by the method of direct molecular-dynamical modeling. The temperature dependencies of the total energy and heat capacity of the duplex are calculated. The convergence of the dependence of heat capacity on the number of realizations is shown. The approach applied can be used to calculate the statistical properties of the duplexes of any length and nucleotide composition.

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References

  1. 1.

    R.M. Wartell, A.S. Benight, Phys. Rep. 126, 67 (1985)

    ADS  Article  Google Scholar 

  2. 2.

    M. Peyrard, A.R. Bishop, Phys. Rev. Lett. 62, 2755 (1989)

    ADS  Article  Google Scholar 

  3. 3.

    T. Dauxois, M.J. Peyrard, Phys. Rev. E 47, 44 (1993)

    ADS  Article  Google Scholar 

  4. 4.

    T. Dauxois, M. Peyrard, A.R. Bishop, Phys. Rev. E. 47, 684 (1993)

    ADS  Article  Google Scholar 

  5. 5.

    B.S. Alexandrov, L.T. Wille, K.Ø. Rasmussen, A.R. Bishop, K.B. Blagoev, Phys. Rev. E 74, 050901 (2006)

    ADS  Article  Google Scholar 

  6. 6.

    F. De los Santos, O. Al Hammal, M.A. Muñoz, Phys. Rev. E 77, 1 (2008)

    Article  Google Scholar 

  7. 7.

    W.G. Swope, H.C. Andersen, P.H. Berens, K.R. Wilson, J. Chem. Phys. 76, 637 (1982)

    ADS  Article  Google Scholar 

  8. 8.

    W.G. Hoover, A.J.C. Ladd, B. Moran, Phys. Rev. Lett. 48, 1818 (1982)

    ADS  Article  Google Scholar 

  9. 9.

    N.K. Balabaev, A.S. Lemak, J. Phys. Chem. 69, 28 (1995)

    Google Scholar 

  10. 10.

    A.S. Lemak, N.K. Balabaev, Mol. Simul. 15, 223 (1995)

    Article  Google Scholar 

  11. 11.

    A.S. Lemak, N.K. Balabaev, J. Comput. Chem. 17, 1685 (1996)

    Article  Google Scholar 

  12. 12.

    T. Dauxois, M.J. Payrard, Phys. Rev. E 51, 4027 (1995)

    ADS  Article  Google Scholar 

  13. 13.

    M.J. Zoli, Phys. Rev. E 79, 041927 (2009)

    ADS  Article  Google Scholar 

  14. 14.

    P. Vaitiekunas, C.-R. Colyn, P.L. Privalov, Nucleic Acids Res. 43, 8577 (2015)

    Article  Google Scholar 

  15. 15.

    S. Srivastava, N. Singh, J. Chem. Phys. 134, 21 (2011)

    Google Scholar 

  16. 16.

    J. Marmur, P. Doty, J. Mol. Biol. 5, 109 (1962)

    Article  Google Scholar 

  17. 17.

    M. Joyeux, S. Buyukdagli, Phys. Rev. E 72, 051902 (2005)

    ADS  Article  Google Scholar 

  18. 18.

    H.J.C. Berendsen, J.P.M. Postma, W.F. van Gunsteren, A. Di Nola, J.R. Haak, J. Chem. Phys. 81, 3684 (1984)

    ADS  Article  Google Scholar 

  19. 19.

    W.G. Hoover, Phys. Rev. A 31, 1695 (1985)

    ADS  Article  Google Scholar 

  20. 20.

    P.L. Privalov, N.N. Khechinashvili, J. Mol. Biol. 86, 665 (1974)

    Article  Google Scholar 

  21. 21.

    W. Ebeling, V. Podlipchuk, A. Valuev, Physica A 217, 22 (1995)

    ADS  Article  Google Scholar 

  22. 22.

    A. Campa, A. Giansanti, Phys. Rev. E 58, 3585 (1998)

    ADS  Article  Google Scholar 

  23. 23.

    V. Sadovnichy, A. Tikhonravov, V.l. Voevodin, V. Opanasenko,Computational Science (CRC Press, Boca Raton, USA, 2013)

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Correspondence to Ilya Viatcheslavovitch Likhachev.

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Likhachev, I.V., Lakhno, V.D. Investigation of DNA denaturation in Peyrard-Bishop-Dauxois model by molecular dynamics method. Eur. Phys. J. B 92, 253 (2019). https://doi.org/10.1140/epjb/e2019-90741-6

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Keywords

  • Statistical and Nonlinear Physics