The thermal denaturation of the Peyrard-Bishop model with an external potential

DOI10.1088/0031-8949/86/01/015802MaRDI QIDQ2844908zbMATH OpenOpenAlexFDO

Authors Amira Sulaiman, F. P. Zen, H. Alatas, L. T. Handoko

Publication date 20 August 2013

Published in Physica Scripta (Search for Journal in Brave)

Full work available at URL https://arxiv.org/abs/1109.5118

Mathematics Subject Classification ID

Biochemistry, molecular biology (92C40) Protein sequences, DNA sequences (92D20) Taxonomy, cladistics, statistics in mathematical biology (92B10)

Abstract: The impact of various types of external potentials to the Peyrard-Bishop DNA denaturation is investigated through statistical mechanics approach. The partition function is obtained using transfer integral method, and further the stretching of hydrogen bond is calculated using time independent perturbation method. It is shown that all types of external potentials accelerate the denaturation processes at lower temperature. In particular, it is argued that the Gaussian potential with infinitesimal width reproduces a constant force at one end of DNA sequence as already done in some previous works.

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Cited in

(9)

• Statistical mechanics of DNA mutation using SUSY quantum mechanics
• Dynamics of DNA breathing in the Peyrard-Bishop model with damping and external force
• DNA base pairs openings perturbed by the surrounding medium
• Nonlinear dynamics of microtubules
• Twisting short dsDNA with applied tension
• Thermal properties of a DNA denaturation with solvent interaction
• On the pseudo-Schrödinger equation approximation of the transfer-integral operator for 1-dimensional DNA models
• EFFECTS OF MODEL PARAMETERS IN THERMODYNAMICS OF THE PNJL MODEL
• An elastic model of DNA under thermal induced stress

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