Ab initio bubble-driven denaturation of double-stranded DNA: Self-mechanical theory

- The model equation of the open-sites dynamics along the ds-DNA is derived within a self-mechanical viewpoint.
- The dynamics around the ground state condensate are the basis for the ab initio DNA denaturation.
- The open-sites dynamics are represented by traveling waves with elastic properties.
- The different scenarios of head-on collisions are properly discussed.

Among the different theoretical models of the open-site-driven DNA-denaturation found in the literature, very few interests are actually paid to the fundamental unzipping process of the double-stranded DNA within the vicinity of its ground state condensate. In this paper, we address an alternative to better understand the process of denaturation of such a macromolecule by investigating the onset of its dynamics around its equilibrium state. We show that from the initiation of the transcription bubble by the promoter to the termination state, the open-states of the strands evolve dynamically while generating some localized waveguide channels with elastic scattering properties. We properly discuss the nonlinear dynamics of these structures within the viewpoint of the self-mechanical theory while inferring to the physical structure of the findings and their potential issues.