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Chechetkin V.R.,Troitsk Institute of Innovation and Thermonuclear Investigations TRINITI | Lobzin V.V.,University of Sydney
Journal of Theoretical Biology | Year: 2011

The standard genetic code is known to be much more efficient in minimizing adverse effects of misreading errors and one-point mutations in comparison with a random code having the same structure, i.e. the same number of codons coding for each particular amino acid. We study the inverse problem, how the code structure affects the optimal physico-chemical parameters of amino acids ensuring the highest stability of the genetic code. It is shown that the choice of two or more amino acids with given properties determines unambiguously all the others. In this sense the code structure determines strictly the optimal parameters of amino acids or the corresponding scales may be derived directly from the genetic code. In the code with the structure of the standard genetic code the resulting values for hydrophobicity obtained in the scheme "leave one out" and in the scheme with fixed maximum and minimum parameters correlate significantly with the natural scale. The comparison of the optimal and natural parameters allows assessing relative impact of physico-chemical and error-minimization factors during evolution of the genetic code. As the resulting optimal scale depends on the choice of amino acids with given parameters, the technique can also be applied to testing various scenarios of the code evolution with increasing number of codified amino acids. Our results indicate the co-evolution of the genetic code and physico-chemical properties of recruited amino acids. © 2010 Elsevier Ltd.

Chechetkin V.R.,Troitsk Institute of Innovation and Thermonuclear Investigations TRINITI
Physics Letters, Section A: General, Atomic and Solid State Physics | Year: 2011

Periodic patterns play the important regulatory and structural roles in genomic DNA sequences. Commonly, the underlying periodicities should be understood in a broad statistical sense, since the corresponding periodic patterns have been strongly distorted by the random point mutations and insertions/deletions during molecular evolution. The latent periodicities in DNA sequences can be efficiently displayed by Fourier transform. The criteria of significance for observed periodicities are obtained via the comparison versus the counterpart characteristics of the reference random sequences. We show that the restrictions imposed on the significance criteria by the rigorous spectral sum rules can be rationally described with De Finetti distribution. This distribution provides the convenient intermediate asymptotic form between Rayleigh distribution and exact combinatoric theory. © 2011 Elsevier B.V.

Chechetkin V.R.,Troitsk Institute of Innovation and Thermonuclear Investigations TRINITI
Physics Letters, Section A: General, Atomic and Solid State Physics | Year: 2013

The main statistical distributions applicable to the analysis of genome architecture and genome tracks are briefly discussed and critically assessed. Although the observed features in distributions of element lengths can be equally well fitted by the different statistical approximations, the interpretation of observed regularities may strongly depend on the chosen scheme. We discuss the possible evolution scenarios and describe the main characteristics obtained with different distributions. The expression for the assessment of levels in hierarchical chromatin folding is derived and the quantitative measure of genome architecture inhomogeneity is suggested. This theory provides the ground for the regular statistical study of genome architecture and genome tracks. © 2013 Elsevier B.V. All rights reserved.

Balakirev E.S.,University of California at Irvine | Balakirev E.S.,RAS A.V. Zhirmunsky Institute of Marine Biology | Chechetkin V.R.,Troitsk Institute of Innovation and Thermonuclear Investigations TRINITI | Lobzin V.V.,University of Sydney | Ayala F.J.,University of California at Irvine
Methods in Molecular Biology | Year: 2014

Spectral entropy and GC content analyses reveal comprehensive structural features of DNA sequences. To illustrate the signifcance of these features, we analyze the β-esterase gene cluster, including the Est-6 gene and the ψEst-6 putative pseudogene, in seven species of the Drosophila melanogaster subgroup. The spectral entropies show distinctly lower structural ordering for ψEst-6 than for Est-6 in all species studied. However, entropy accumulation is not a completely random process for either gene and it shows to be nucleotide dependent. Furthermore, GC content in synonymous positions is uniformly higher in Est-6 than in ψEst-6, in agreement with the reduced GC content generally observed in pseudogenes and nonfunctional sequences. The observed differences in entropy and GC content refect an evolutionary shift associated with the process of pseudogenization and subsequent functional divergence of ψEst-6 and Est-6 after the duplication event. The data obtained show the relevance and signifcance of entropy and GC content analyses for pseudogene identifcation and for the comparative study of gene–pseudogene evolution. © Springer Science+Business Media New York 2014.

Klimenko E.Yu.,RAS Research Center Kurchatov Institute | Chechetkin V.R.,Troitsk Institute of Innovation and Thermonuclear Investigations TRINITI | Khayrutdinov R.R.,Troitsk Institute of Innovation and Thermonuclear Investigations TRINITI | Solodovnikov S.G.,Troitsk Institute of Innovation and Thermonuclear Investigations TRINITI
Cryogenics | Year: 2010

A general scheme for electrodynamics of composite multifilament superconductors is presented. Our approach is based on an anisotropic continuum model for a multifilament wire taking into account smooth dependence of superconductor conductivity on temperature, magnetic field and current density. The electrodynamics equations are self-consistently treated together with heat transfer. On the base of this scheme, 2D codes were developed for simulation of non-stationary processes in composite superconductors. A comparison of current density dynamics in twisted and non-twisted multifilament wires is presented as an example. The dynamics of current density in a twisted wire proved to be determined by two characteristic times and differs from the predictions based on the critical state model. © 2010 Elsevier Ltd. All rights reserved.

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