Strand separation in negatively supercoiled dna
Christian Mazza (University of Lyon)
TL;DR
This paper presents a statistical mechanics model for DNA strand separation influenced by negative supercoiling, focusing on how supercoiling affects denaturation localization considering DNA base composition.
Contribution
It introduces a combined mean field and random field Ising model to analyze DNA denaturation under supercoiling, incorporating base composition effects.
Findings
Supercoiling influences denaturation localization.
Base composition (AT vs GC) affects denaturation patterns.
Small perimeter hypothesis simplifies the model analysis.
Abstract
We consider a model for strand separation in negatively supercoiled dna, and study the effect of supercoiling on the localization of denaturation, using notions from statistical mechanics. The model is based on on mean field Ising system, coupled with a random field one dimensional ISing model. The effect of the word in AT and Gc associated with the DNA on localization of denaturation is studied under the hypothesis of small perimeter.
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Taxonomy
TopicsProtein Structure and Dynamics · Theoretical and Computational Physics · Algorithms and Data Compression