Thermal and mechanical properties of a DNA model with solvation barrier

Details Thermal and mechanical properties of a DNA model with solvation barrier Thermal and mechanical properties of a DNA model with solvation barrier

2010-09-08

arxiv.org/abs/1009.1501v1

Phys. Rev. E 82, 031916 (2010) [8 pages]

Physics

Biological Physics

Physical Review E (in press)

Scientific paper

10.1103/PhysRevE.82.031916

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.

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