title: DNA viewed as an out-of-equilibrium structure.
abstract: The complexity of the primary structure of human DNA is explored using methods from nonequilibrium statistical mechanics, dynamical systems theory, and information theory. A collection of statistical analyses is performed on the DNA data and the results are compared with sequences derived from different stochastic processes. The use of χ^{2} tests shows that DNA can not be described as a low order Markov chain of order up to r=6. Although detailed balance seems to hold at the level of a binary alphabet, it fails when all four base pairs are considered, suggesting spatial asymmetry and irreversibility. Furthermore, the block entropy does not increase linearly with the block size, reflecting the long-range nature of the correlations in the human genomic sequences. To probe locally the spatial structure of the chain, we study the exit distances from a specific symbol, the distribution of recurrence distances, and the Hurst exponent, all of which show power law tails and long-range characteristics. These results suggest that human DNA can be viewed as a nonequilibrium structure maintained in its state through interactions with a constantly changing environment. Based solely on the exit distance distribution accounting for the nonequilibrium statistics and using the Monte Carlo rejection sampling method, we construct a model DNA sequence. This method allows us to keep both long- and short-range statistical characteristics of the native DNA data. The model sequence presents the same characteristic exponents as the natural DNA but fails to capture spatial correlations and point-to-point details.
authors.affiliation: Institute of Nanoscience and Nanotechnology, National Center for Scientific Research "Demokritos", 15310 Athens, Greece and Interdisciplinary Center for Nonlinear Phenomena and Complex Systems, Université Libre de Bruxelles, Campus Plaine, CP. 231, 1050 Bruxelles, Belgium.
authors.forename: A
authors.initials: A
authors.lastname: Provata
authors.affiliation: Institut Royal Météorologique de Belgique, 3 Avenue Circulaire, 1180 Bruxelles, Belgium.
authors.forename: C
authors.initials: C
authors.lastname: Nicolis
authors.affiliation: Interdisciplinary Center for Nonlinear Phenomena and Complex Systems, Université Libre de Bruxelles, Campus Plaine, CP. 231, 1050 Bruxelles, Belgium.
authors.forename: G
authors.initials: G
authors.lastname: Nicolis
mesh_terms: D001483:Base Sequence; D003198:Computer Simulation; D004247:DNA / Q000737:chemistry* / Q000235:genetics*; D019277:Entropy; D006801:Humans; D016247:Information Storage and Retrieval / Q000379:methods; D008390:Markov Chains; D008956:Models, Chemical; D008957:Models, Genetic; D015233:Models, Statistical; D008969:Molecular Sequence Data; D017422:Sequence Analysis, DNA / Q000379:methods*
chemical_list: D004247:DNA