Thermal and mechanical properties of a DNA model with solvation barrier
arXiv:1009.1501 · doi:10.1103/PhysRevE.82.031916
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.
arXiv commentPhysical Review E (in press)
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Cited by in corpus (10)
- Effect of salt concentration on the stability of heterogeneous DNA
- Heterogeneity and chaos in the Peyrard-Bishop-Dauxois DNA model
- Thermal and mechanical denaturation properties of a DNA model with three sites per nucleotide
- Distributions of Bubble Lifetimes and Bubble Lengths in DNA
- Mesoscopic Model for Free Energy Landscape Analysis of DNA sequences
- Bubble lifetimes in DNA gene promoters and their mutations affecting transcription
- Modeling the interaction of DNA with alternating fields
- Unzipping of DNA under the influence of external fields
- Towards spectrally selective catastrophic response
- Distribution of Base Pair Alternations in a Periodic DNA Chain: Application of Polya Counting to a Physical System