<p>The Peyrard-Bishop-Dauxois (PBD) model is a notable representation of DNA, offering valuable insights due to its helicoidal structure. This configuration brings distant nucleotides into close proximity through hydrogen bonds facilitated by water filaments. This paper focuses on the fifth-order approximation of breather modes and solvent interactions within the helicoidal PBD model. We initiate our study by deriving the discrete nonlinear differential equation governing polynucleotide motion via Hamiltonian formalism. Subsequently, we obtain the linear dispersion law for small-amplitude waves. Utilizing the reductive perturbation method, we then derive the Quintic nonlinear Schrödinger equation (QNLSE), incorporating solvent interaction parameters. A comprehensive modulational instability analysis is conducted, followed by an analytical examination of an exact solution using direct integration. Our findings indicate that solvent interactions significantly influence the amplitude of bright solitons and the breather mode’s pulse.</p>

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Fifth Order Approximation and Solvent Interaction in Helicoidal Peyrard-Bishop-Dauxois Model of DNA

  • Arnaud Djine,
  • Serge Bruno Yamgoué,
  • Nkeh Oma Nfor

摘要

The Peyrard-Bishop-Dauxois (PBD) model is a notable representation of DNA, offering valuable insights due to its helicoidal structure. This configuration brings distant nucleotides into close proximity through hydrogen bonds facilitated by water filaments. This paper focuses on the fifth-order approximation of breather modes and solvent interactions within the helicoidal PBD model. We initiate our study by deriving the discrete nonlinear differential equation governing polynucleotide motion via Hamiltonian formalism. Subsequently, we obtain the linear dispersion law for small-amplitude waves. Utilizing the reductive perturbation method, we then derive the Quintic nonlinear Schrödinger equation (QNLSE), incorporating solvent interaction parameters. A comprehensive modulational instability analysis is conducted, followed by an analytical examination of an exact solution using direct integration. Our findings indicate that solvent interactions significantly influence the amplitude of bright solitons and the breather mode’s pulse.