Base pairs opening and bubble transport in damped DNA dynamics with transport memory effects

Joseph Brizar Okaly, Fabien Ii Ndzana, Rosalie Laure Woulaché, Conrad Bertrand Tabi, Timoleón Crépin Kofané

Research output: Contribution to journalArticle

Abstract

Transport memory effects on nonlinear wave propagation are addressed in a damped Peyrard-Bishop-Dauxois model of DNA dynamics. Under the continuum and overdamped limits, the multiple-scale expansion method is employed to show that an open-state configuration of the DNA molecule is described by a complex nonlinear Schrödinger equation. For the latter, solutions are proposed as bright solitons, which suitably represent the open-state configuration that takes place along the DNA molecule in the form of bubbles. A good agreement between numerical experiments and analytical predictions on the impact of memory effects on the angular frequency, velocity, width, and amplitude of the moving bubble is obtained. It also appears that memory effects can modify qualitatively and quantitatively the nonlinear dynamics of DNA, including the energy brought by enzymes for the initiation of the processes of replication and transcription.

Original languageEnglish
Article number093103
JournalChaos
Volume29
Issue number9
DOIs
Publication statusPublished - Sep 1 2019

Fingerprint

Memory Effect
Damped
Bubble
DNA
bubbles
deoxyribonucleic acid
Data storage equipment
Nonlinear Wave Propagation
Molecules
Configuration
Multiple Scales
Transcription
Nonlinear Dynamics
Replication
Solitons
Nonlinear Equations
Enzymes
Continuum
configurations
Numerical Experiment

All Science Journal Classification (ASJC) codes

  • Statistical and Nonlinear Physics
  • Mathematical Physics
  • Physics and Astronomy(all)
  • Applied Mathematics

Cite this

Okaly, Joseph Brizar ; Ndzana, Fabien Ii ; Woulaché, Rosalie Laure ; Tabi, Conrad Bertrand ; Kofané, Timoleón Crépin. / Base pairs opening and bubble transport in damped DNA dynamics with transport memory effects. In: Chaos. 2019 ; Vol. 29, No. 9.
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Base pairs opening and bubble transport in damped DNA dynamics with transport memory effects. / Okaly, Joseph Brizar; Ndzana, Fabien Ii; Woulaché, Rosalie Laure; Tabi, Conrad Bertrand; Kofané, Timoleón Crépin.

In: Chaos, Vol. 29, No. 9, 093103, 01.09.2019.

Research output: Contribution to journalArticle

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T1 - Base pairs opening and bubble transport in damped DNA dynamics with transport memory effects

AU - Okaly, Joseph Brizar

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AU - Woulaché, Rosalie Laure

AU - Tabi, Conrad Bertrand

AU - Kofané, Timoleón Crépin

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AB - Transport memory effects on nonlinear wave propagation are addressed in a damped Peyrard-Bishop-Dauxois model of DNA dynamics. Under the continuum and overdamped limits, the multiple-scale expansion method is employed to show that an open-state configuration of the DNA molecule is described by a complex nonlinear Schrödinger equation. For the latter, solutions are proposed as bright solitons, which suitably represent the open-state configuration that takes place along the DNA molecule in the form of bubbles. A good agreement between numerical experiments and analytical predictions on the impact of memory effects on the angular frequency, velocity, width, and amplitude of the moving bubble is obtained. It also appears that memory effects can modify qualitatively and quantitatively the nonlinear dynamics of DNA, including the energy brought by enzymes for the initiation of the processes of replication and transcription.

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