Dark breather using symmetric Morse, solvent and external potentials for DNA breathing

• Main Authors: Hernan Oscar Cortez Gutierrez, Milton Milciades Cortez Gutierrez, Girady Iara Cortez Fuentes Rivera, Liv Jois Cortez Fuentes Rivera, Deolinda Fuentes Rivera Vallejo
• Format: Article
• Language: English
• Published: Universidade Estadual Paulista 2019-01-01
• Series: Eclética Química
• Online Access: https://revista.iq.unesp.br/ojs/index.php/ecletica/article/view/422

We analyze the dynamics and the quantum thermodynamics of DNA in Symmetric-Peyrard-Bishop-Dauxois model (S-PBD) with solvent and external potentials and describe the transient conformational fluctuations using dark breather and the ground state wave function of the associate Schrodinger differential equation.  We used the S-PBD, the Floquet theory, quantum thermodynamic and finite difference methods. We show that for lower coupling dark breather is present.  We estimate the fluctuations or breathing of DNA. For the S-PBD model we have the stability of dark breather for k<0.004 and mobile breathers with coupling k=0.004. The fluctuations of the dark breather in the S-PBD model is approximately zero with the quantum thermodynamics. The viscous and external potential effect is direct proportional to hydrogen bond stretching.