Ergodicity of some dynamics of DNA sequences

zbMATH Open1456.60186arXiv1903.06455MaRDI QIDQ5133293FDOQ5133293

Authors: Mikael Falconnet, Nina Gantert, Ellen Saada 

Publication date: 12 November 2020

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.

Full work available at URL: https://arxiv.org/abs/1903.06455

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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)

Cited In (5)

• On the spectral criteria of disorder in nonperiodic sequences: application to inflation models, symbolic dynamics and DNA sequences
• Solvable models of neighbor-dependent substitution processes
• Dynamics of the life history of a DNA-repeat sequence
• Title not available (Why is that?)
• Quantifying local randomness in human DNA and RNA sequences using Erdös motifs

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