Ergodicity of some dynamics of DNA sequences

MaRDI QIDQ5133293zbMATH OpenFDO

Authors Mikael Falconnet, Nina Gantert, Ellen Saada

Publication date 12 November 2020

Full work available at URL https://arxiv.org/abs/1903.06455, http://math-mprf.org/journal/articles/id1589/

zbMATH Keywords

ergodicitycouplingdualityinteracting particle systemsJukes-Cantor modeldynamics of DNA sequencessubstitution processes

Mathematics Subject Classification ID

Protein sequences, DNA sequences (92D20) Interacting random processes; statistical mechanics type models; percolation theory (60K35) Continuous-time Markov processes on general state spaces (60J25) Interacting particle systems in time-dependent statistical mechanics (82C22)

Abstract: We define interacting particle systems on configurations of the integer lattice (with values in some finite alphabet) by the superimposition of two dynamics: a substitution process with finite range rates, and a circular permutation mechanism(called "cut-and-paste") with possibly unbounded range. The model is motivated by the dynamics of DNA sequences: we consider an ergodic model for substitutions, the RN+YpR model ([BGP08]), with three particular cases, the models JC+cpg,T92+cpg, and RNc+YpR. We investigate whether they remain ergodic with the additional cut-and-paste mechanism, which models insertions and deletions of nucleotides. Using either duality or attractiveness techniques, we provide various sets of sufficient conditions, concerning only the substitution rates, for ergodicity of the superimposed process. They imply ergodicity of the models JC+cpg, T92+cpg as well as the attractive RNc+YpR, all with an additional cut-and-paste mechanism.

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