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Universality of long-range correlations in expansion–randomization systems

P W Messer1, M Lässig2 and P F Arndt1

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We study the stochastic dynamics of sequences evolving by single-site mutations, segmental duplications, deletions, and random insertions. These processes are relevant for the evolution of genomic DNA. They define a universality class of non-equilibrium 1D expansion–randomization systems with generic stationary long-range correlations in a regime of growing sequence length. We obtain explicitly the two-point correlation function of the sequence composition and the distribution function of the composition bias in sequences of finite length. The characteristic exponent χ of these quantities is determined by the ratio of two effective rates, which are explicitly calculated for several specific sequence evolution dynamics of the universality class. Depending on the value of χ, we find two different scaling regimes, which are distinguished by the detectability of the initial composition bias. All analytic results are accurately verified by numerical simulations. We also discuss the non-stationary build-up and decay of correlations, as well as more complex evolutionary scenarios, where the rates of the processes vary in time. Our findings provide a possible example for the emergence of universality in molecular biology.


Keywords

models for evolution (theory)

mutational and evolutionary processes (theory)

dynamics (theory)

PACS

87.15.Cc Folding: thermodynamics, statistical mechanics, models, and pathways

87.14.G- Nucleic acids

02.50.Ey Stochastic processes

87.15.A- Theory, modeling, and computer simulation

87.15.H- Dynamics of biomolecules

MSC

92C40 Biochemistry, molecular biology

92B15 General biostatistics (See also 62P10)

92D20 Protein sequences, DNA sequences

62L10 Sequential analysis

Subjects

Computational physics

Biological physics

Dates

Issue 10 (October 2005)

Received 11 August 2005, accepted for publication 19 September 2005

Published 6 October 2005



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