Abstract
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.
Highlights
The deoxyribonucleic acid DNA is a thread-like chain of nucleotides carrying the genetic information of all organisms
We show that mobile breather can lead to the observed breathing, but the amplitude of the breather is determinant for the transient conformational fluctuations of DNA
The stability of dark breathers using of the symmetric Morse potential have been obtained with the Floquet’s theory
Summary
The deoxyribonucleic acid DNA is a thread-like chain of nucleotides carrying the genetic information of all organisms. The coding sequences for genes and regulatory information are located in DNA and is marginally stable and undergoes a “melting phase transition”. There are many experimental ways to study the fluctuations or breathing of DNA: hydrogen exchange, formaldehyde probing, protein-nucleic acid interactions, DNA replication, DNA base analogue spectroscopy, single molecule DNA-protein interactions, two-dimensional fluorescence spectroscopy[1]. The interaction between the viscous potential and external forces prevent DNA to unzip perfectly but allows DNA to split at a certain distance from its original position[2]. S. Flach gives the theory of the “discrete breathers” and applications[3]
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