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| Volume 20 Issue 2 Year 2025 | ||
Comment to “Melting of genomic DNA: Predictive modeling by nonlinear lattice dynamics”. The problem of entropy and end effects in the Peyard – Bishop – Dauxois model
Shigaev A.S. Institute of Mathematical Problems of Biology RAS, Keldysh Institute of Applied Mathematics of Russian Academy of Sciences, Pushchino, Russia
Abstract. The problem of finding the optimal combination of parameters of the Peyard – Bishop-Dauxois model is considered using one of the new reparametrizations proposed by N. Theodorakopoulos. The relationship between the parameters of the inter-site potential of the model and the entropy gain in large open regions of DNA is analyzed. The direct transfer of the properties of long DNAs to short chains is shown to be unacceptable due to different contributions of the loop entropy during melting. The erroneousness of taking into account the finite nature of stacking interactions “directly” through a radical change in the parameters of the inter-site potential of the Peyard – Bishop – Dauxois model is demonstrated.
Key words: Peyrard – Bishop – Dauxois model, parametrization, loop entropy, DNA open states
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Table of Contents
Original Article
Shigaev A.S. Comment to “Melting of genomic DNA: Predictive modeling by nonlinear lattice dynamics”. The problem of entropy and end effects in the Peyard – Bishop – Dauxois model. Ìàthematical biology and bioinformatics. 2025;20(2):363-368. doi: 10.17537/2025.20.363 (published in Russian) Abstract (rus.) Abstract (eng.) Full text (rus., pdf) References
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