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

DOI10.1016/J.PHYSD.2011.04.018zbMATH Open1223.92011arXiv1104.4201OpenAlexW2010123939MaRDI QIDQ720690FDOQ720690

Authors: Ciprian-Ionuţ Duduială, Jonathan A. D. Wattis, Charles A. Laughton 

Publication date: 11 October 2011

Published in: Physica D (Search for Journal in Brave)

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.

Full work available at URL: https://arxiv.org/abs/1104.4201

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zbMATH Keywords

stochastic differential equations\(1/f\) noise

Mathematics Subject Classification ID

Biochemistry, molecular biology (92C40) Dynamical systems in biology (37N25) Numerical methods for wavelets (65T60) Stochastic ordinary differential equations (aspects of stochastic analysis) (60H10)

Cites Work

• Self-organized criticality
• Cellular Automata Modeling of Physical Systems
• Modelling DNA at the mesoscale: a challenge for nonlinear science?
• Small random perturbations of dynamical systems and the definition of attractors
• Nonlinear breathing modes due to a defect in a DNA chain

Cited In (1)

• Nonlinear breathing modes due to a defect in a DNA chain

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