Thermal and mechanical properties of a DNA model with solvation barrier

TL;DR

This paper investigates the thermal and mechanical behavior of DNA denaturation using a mesoscopic model that includes solvent interaction, analyzing bubble formation and stability, and applying PCA to understand dynamical behavior.

Contribution

It introduces a modified Peyrard-Bishop-Dauxois model with solvent effects and demonstrates the effectiveness of PCA in analyzing DNA dynamics.

Findings

Model parameters fitted to homogeneous A-T sequences

PCA accurately captures DNA dynamical behavior

Results align with biological observations

Abstract

We study the thermal and mechanical behavior of DNA denaturation in the frame of the mesoscopic Peyrard- Bishop-Dauxois model with the inclusion of solvent interaction. By analyzing the melting transition of a homogeneous A-T sequence, we are able to set suitable values of the parameters of the model and study the formation and stability of bubbles in the system. Then, we focus on the case of the P5 promoter sequence and use the Principal Component Analysis of the trajectories to extract the main information on the dynamical behavior of the system. We find that this analysis method gives an excellent agreement with previous biological results.