DNA viewed as an out-of-equilibrium structure.
Phys Rev E Stat Nonlin Soft Matter Phys
; 89(5): 052105, 2014 May.
Article
em En
| MEDLINE
| ID: mdl-25353737
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.
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Coleções:
01-internacional
Base de dados:
MEDLINE
Assunto principal:
DNA
/
Modelos Estatísticos
/
Análise de Sequência de DNA
/
Modelos Químicos
/
Modelos Genéticos
Tipo de estudo:
Health_economic_evaluation
/
Prognostic_studies
/
Risk_factors_studies
Limite:
Humans
Idioma:
En
Revista:
Phys Rev E Stat Nonlin Soft Matter Phys
Assunto da revista:
BIOFISICA
/
FISIOLOGIA
Ano de publicação:
2014
Tipo de documento:
Article
País de afiliação:
Bélgica