Complexity measures for the evolutionary categorization of organisms

Provata, A.; Nicolis, C.; Nicolis, Grégoire

doi:10.1016/j.compbiolchem.2014.08.004

Cited by 13 publications

(9 citation statements)

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“…Besides, the evolution of DNA sequences under repeated replications can be simulated using kinetic models of DNA polymerases. As seen in figure 5, the base pairs A:T become more frequent than C:G from replication to replication in agreement with the higher probability to find A or T in different genomes [39,40]. The reason is that the average physiological concentration [dATP] + [dTTP] is larger than [dCTP] + [dGTP] [31].…”

Section: (D) Molecular Evolutionsupporting

confidence: 66%

Kinetics and thermodynamics of living copolymerization processes

Gaspard

2016

Phil. Trans. R. Soc. A.

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Theoretical advances are reported on the kinetics and thermodynamics of free and template-directed living copolymerizations. Until recently, the kinetic theory of these processes had only been established in the fully irreversible regime, in which the attachment rates are only considered. However, the entropy production is infinite in this regime and the approach to thermodynamic equilibrium cannot be investigated. For this purpose, the detachment rates should also be included. Inspite of this complication, the kinetics can be exactly solved in the regimes of steady growth and depolymerization. In this way, analytical expressions are obtained for the mean growth velocity, the statistical properties of the copolymer sequences, as well as the thermodynamic entropy production. The results apply to DNA replication, transcription and translation, allowing us to understand important aspects of molecular evolution.This article is part of the themed issue 'Multiscale modelling at the physics-chemistry-biology interface'.

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Section: (D) Molecular Evolutionsupporting

confidence: 66%

Kinetics and thermodynamics of living copolymerization processes

Gaspard

2016

Phil. Trans. R. Soc. A.

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“…In general, the sequence may have any kind of statistical correlations among the successive monomeric units. On the one hand, systematic studies have shown that DNA sequences of biological species manifest statistical correlations that cannot be described by low order Markov chains [56][57][58]. On the other hand, arbitrary DNA sequences can be synthesized with modern technologies [59,60].…”

Section: B Kinetic Schemementioning

confidence: 99%

“…This quantity, which is often called information Shannon entropy, is studied to characterize the complexity of DNA symbolic sequences in various biological organisms [56][57][58]. The overall disorder per nucleotide is observed to vary from the value D(α) ≃ 1.339 assuming the sequence α is a first-order Markov chain, down to D(α) ≃ 1.273 if α is a 8 th -order Markov chain, which suggests the existence of long-range correlations besides the fact that the four nucleotides occur with unequal probabilities in typical DNA sequences [57,58]. In the present paper, the template is supposed to be a Bernoulli chain with equal probabilities ν 1 (n) = It should be pointed out that the sequence carries information to the extent that it is replicated, transcripted, or translated into proteins in living organisms.…”

Section: Thermodynamics and Sequence Disordermentioning

confidence: 99%

Kinetics and thermodynamics of exonuclease-deficient DNA polymerases

Gaspard

2016

Phys. Rev. E

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A kinetic theory is developed for exonuclease-deficient DNA polymerases, based on the experimental observation that the rates depend not only on the newly incorporated nucleotide, but also on the previous one, leading to the growth of Markovian DNA sequences from a Bernoullian template. The dependences on nucleotide concentrations and template sequence are explicitly taken into account. In this framework, the kinetic and thermodynamic properties of DNA replication, in particular, the mean growth velocity, the error probability, and the entropy production in terms of the rate constants and the concentrations are calculated analytically. Theory is compared with numerical simulations for the DNA polymerases of T7 viruses and human mitochondria.

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“…( 3) Note that in general, on the same strand P˛→ˇis not equal to Pˇ→ ( Provata et al, 2014). The largest transition probability for a given nucleotide (maximum value per row) is marked in bold.…”

Section: First-order Markov Model Based On Dimer Frequenciesmentioning

confidence: 99%