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Exciton and phonon dynamics in the presence of an impurity in a two-dimensional alpha-helix chain: Formation, stability and interactions of breathers

Author

Listed:
  • Ondoua, R.Y.
  • Mimshe Fewu, J.C.
  • Abouem A. Ribama, R.
  • Youssoufa, M.
  • Tabi, C.B.
  • Ekobena Fouda, H.P.
  • Nguenang, J.P.

Abstract

This paper examines the impact of mass impurity on exciton–phonon dynamics in a two-dimensional alpha-helix protein chain. Using the semi-discrete approximation and the multiple time scale method, we derive discrete and continuous two-dimensional nonlinear Schrödinger equations, respectively. Besides the mass impurity defect, two other parameters of the system under study attracted our attention, namely, the dipole–dipole interaction coefficient and the off-diagonal coupling parameter. Through intensive numerical simulations, firstly, the effect of these parameters was verified on the energy localization in the alpha-helix by means of the two-dimensional breather propagation. A transition between stability and instability is clearly manifested in the spatial evolution of the mode. Then, an analysis of the time evolution and stability of the impure mode in this model is made. Finally, we examine the complex dynamics that emerge when local modes, called breathers, interact with an impurity in our model. Some physical phenomena appear in this work, the total barrier phenomenon, the excitation phenomenon, the dissipation phenomenon and the partial barrier phenomenon, to name a few. One biological implication of this work is that laser pulses could be used to generate controlled breathers, activating therapeutic proteins such as light-sensitive ion channels.

Suggested Citation

  • Ondoua, R.Y. & Mimshe Fewu, J.C. & Abouem A. Ribama, R. & Youssoufa, M. & Tabi, C.B. & Ekobena Fouda, H.P. & Nguenang, J.P., 2025. "Exciton and phonon dynamics in the presence of an impurity in a two-dimensional alpha-helix chain: Formation, stability and interactions of breathers," Chaos, Solitons & Fractals, Elsevier, vol. 201(P1).
    • Handle: RePEc:eee:chsofr:v:201:y:2025:i:p1:s0960077925012457
    DOI: 10.1016/j.chaos.2025.117232
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    References listed on IDEAS

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    1. Djoufack, Z.I. & Kenmogne, Fabien & Nguenang, J.P. & Kenfack-Jiotsa, A., 2021. "Dynamics of solitons with periodic loops intrinsic localized modes and modulational instability in a quantum 2D nonlinear square Klein-Gordon chain," Chaos, Solitons & Fractals, Elsevier, vol. 142(C).
    2. R. Abouem A. Ribama & Z. I. Djoufack & J. P. Nguenang, 2022. "Breather-impurity interactions and modulational instability in a quantum 2D Klein–Gordon chain," The European Physical Journal B: Condensed Matter and Complex Systems, Springer;EDP Sciences, vol. 95(5), pages 1-19, May.
    3. Daniel, M. & Latha, M.M., 2001. "A generalized Davydov soliton model for energy transfer in alpha helical proteins," Physica A: Statistical Mechanics and its Applications, Elsevier, vol. 298(3), pages 351-370.
    4. Daniel, M. & Latha, M.M., 1997. "Soliton in discrete and continuum alpha helical proteins with higher-order excitations," Physica A: Statistical Mechanics and its Applications, Elsevier, vol. 240(3), pages 526-546.
    5. R. Ondoua & C. Tabi & H. Ekobena Fouda & A. Mohamadou & T. Kofané, 2012. "Discrete energy transport in the perturbed Ablowitz-Ladik equation for Davydov model of α-helix proteins," The European Physical Journal B: Condensed Matter and Complex Systems, Springer;EDP Sciences, vol. 85(9), pages 1-6, September.
    6. Djoufack, Z.I. & Ribama, R. Abouem A. & Nguenang, J.P., 2023. "Impurity–impurity and impurity–breather interactions combined with energy localization in a quantum 1D Klein–Gordon chain," Chaos, Solitons & Fractals, Elsevier, vol. 168(C).
    7. 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.
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