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Statistical thermodynamics of DNA with open states

Author

Listed:
  • Nikitiuk, Aleksandr S.
  • Bayandin, Yuriy V.
  • Naimark, Oleg B.

Abstract

The study in the open states plays an important role in understanding the laws of DNA biological activity. The techniques of statistical thermodynamics are potentially able of providing a general framework for understanding the influence of the open states on DNA functionality. In this paper, we develop statistically based DNA thermodynamics with the open states. There were ascertained the internal variables related to the DNA open states which were introduced for determining nucleotides interaction. Besides, there was found the free energy form corresponding to the structural-scaling parameter playing the role of the ≪effective temperature≫ of the open state’s induced thermodynamics. Following the open state statistical thermodynamic model, the DNA dynamics was studied as compared with the Peyrard–Bishop–Dauxois model. The ≪critical≫ dynamics was ascertained in characteristic ranges of the structural-scaling parameter as a form of the open states collective modes, providing the functionality of the DNA dynamics.

Suggested Citation

  • Nikitiuk, Aleksandr S. & Bayandin, Yuriy V. & Naimark, Oleg B., 2022. "Statistical thermodynamics of DNA with open states," Physica A: Statistical Mechanics and its Applications, Elsevier, vol. 607(C).
    • Handle: RePEc:eee:phsmap:v:607:y:2022:i:c:s0378437122007142
    DOI: 10.1016/j.physa.2022.128156
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    References listed on IDEAS

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    1. Honchar, Yulian & von Ferber, Christian & Holovatch, Yurij, 2021. "Variety of scaling laws for DNA thermal denaturation," Physica A: Statistical Mechanics and its Applications, Elsevier, vol. 573(C).
    2. Shekaari, Ashkan & Jafari, Mahmoud, 2019. "Statistical mechanical modeling of a DNA nanobiostructure at the base-pair level," Physica A: Statistical Mechanics and its Applications, Elsevier, vol. 518(C), pages 80-88.
    3. Resendis-Antonio, O. & Garcia-Colin, L.S. & Larralde, H., 2003. "A statistical model of DNA denaturation," Physica A: Statistical Mechanics and its Applications, Elsevier, vol. 318(3), pages 435-446.
    4. Tabi, C.B. & Dang Koko, A. & Oumarou Doko, R. & Ekobena Fouda, H.P. & Kofané, T.C., 2016. "Modulated charge patterns and noise effect in a twisted DNA model with solvent interaction," Physica A: Statistical Mechanics and its Applications, Elsevier, vol. 442(C), pages 498-509.
    5. Agarwal, J. & Hennig, D., 2003. "Breather solutions of a nonlinear DNA model including a longitudinal degree of freedom," Physica A: Statistical Mechanics and its Applications, Elsevier, vol. 323(C), pages 519-533.
    6. Causo, Maria Serena & Coluzzi, Barbara & Grassberger, Peter, 2002. "A simple model for DNA denaturation transition," Physica A: Statistical Mechanics and its Applications, Elsevier, vol. 314(1), pages 607-612.
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