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

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. 1/f noise. PACS 05.10.Gg-Stochastic models in statistical physics and nonlinear dynamics PACS 89.75.Fb-Self-organization in complex systems, PACS 05.65.+b-Self-organised criticality PACS 87.14.gk-DNA MSC 60G18 Probability theory and stochastic processes: self-similar processes MSC 37K40 Dynamical systems: Soliton theory, asymptotic behavior of solutions MSC 92C45 Biology and other natural sciences: Kinetics in biochemical problems