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Self-organised criticality in base-pair breathing in DNA with a defect

By Ciprian-Ionut Duduiala, Jonathan A. D. Wattis and Charles A Laughton

Abstract

We analyse base-pair breathing in a DNA sequence of 12 base-pairs with a defective base at its centre. We use both all-atom molecular dynamics (MD) simulations and a system of stochastic differential equations (SDE). In both cases, Fourier analysis of the trajectories reveals self-organised critical behaviour in the breathing of base-pairs. The Fourier Transforms (FT) of the interbase distances show power-law behaviour with gradients close to -1. The scale-invariant behaviour we have found provides evidence for the view that base-pair breathing corresponds to the nucleation stage of large-scale DNA opening (or 'melting') and that this process is a (second-order) phase transition. Although the random forces in our SDE system were introduced as white noise, FTs of the displacements exhibit pink noise, as do the displacements in the AMBER/MD simulations.Comment: 18 pages, 8 figure

Topics: Physics - Biological Physics, Condensed Matter - Soft Condensed Matter, Mathematics - Dynamical Systems, Nonlinear Sciences - Adaptation and Self-Organizing Systems, Quantitative Biology - Biomolecules
Year: 2011
DOI identifier: 10.1016/j.physd.2011.04.018
OAI identifier: oai:arXiv.org:1104.4201
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