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

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...

Dynamic model of base pair breathing in a DNA chain with a defect.

We model and analyze a short section of a DNA chain with a defect, with the aim of understanding how the frequency, amplitude, and localization of breathing events depend on the strength of the bonds between base pairs, both along the chain and between the chains. Our results show that the presence of a defect in the chain permits the existence of a localized breather mode. The models we analyz...

Studies in self-organised criticality

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Applying Self-Organised Criticality to Evolutionary Algorithms

On the role of self-organised criticality in accretion systems

Self-organised criticality (SOC) has been suggested as a potentially powerful unifying paradigm for interpreting the structure of, and signals from, accretion systems. After reviewing the most promising sites where SOC might be observable, we consider the theoretical arguments for supposing that SOC can occur in accretion discs. Perhaps the most rigorous evidence is provided by numerical modell...