Cluster-scaling, chaotic order and coherence in DNA (1011.4840v4)

Abstract: Different numerical mappings of the DNA sequences have been studied using a new cluster-scaling method and the well known spectral methods. It is shown, in particular, that the nucleotide sequences in DNA molecules have robust cluster-scaling properties. These properties are relevant to both types of nucleotide pair-bases interactions: hydrogen bonds and stacking interactions. It is shown that taking into account the cluster-scaling properties can help to improve heterogeneous models of the DNA dynamics. It is also shown that a chaotic (deterministic) order, rather than a stochastic randomness, controls the energy minima positions of the stacking interactions in the DNA sequences on large scales. The chaotic order results in a large-scale chaotic coherence between the two complimentary DNA-duplex's sequences. A competition between this broad-band chaotic coherence and the resonance coherence produced by genetic code has been briefly discussed. The Arabidopsis plant genome (which is a model plant for genome analysis) and two human genes: BRCA2 and NRXN1, have been considered as examples.