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Four-state quantum chain as a model of sequence evolution

Joachim Hermisson·Holger Wagner·Michael Baake
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Abstract

A variety of selection-mutation models for DNA (or RNA) sequences, well known in molecular evolution, can be translated into a model of coupled Ising quantum chains. This correspondence is used to investigate the genetic variability and error threshold behaviour in dependence of possible fitness landscapes. In contrast to the two-state models treated hitherto, the model explicitly takes the four-state nature of the nucleotide alphabet into account and allowes for the distinction of mutation rates for the different base substitutions, as given by standard mutation schemes of molecular phylogeny. As a consequence of this refined treatment, new phase diagrams for the error threshold behaviour are obtained, with appearance of a novel phase in which the nucleotide ordering of the wildtype sequence is only partially conserved. Explicit analytic and numeric results are presented for evolution dynamics and equilibrium behaviour in a number of accessible situations, such as quadratic fitness landscapes and the Kimura 2 parameter mutation scheme.

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Joachim Hermisson, Holger Wagner, Michael Baake. 2000-08-08. Four-state quantum chain as a model of sequence evolution. https://arxiv.org/abs/cond-mat/0008123

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