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Nonequilibrium Effects in DNA Microarrays: A Multiplatform Study 
Auteur(s): Walter J.-C., Kroll Myriam, Hooyberghs Jeff, Carlon Enrico
(Article) Publié:
The Journal Of Physical Chemistry B, vol. 115 p.6732 (2011)
Texte intégral en Openaccess : 
Ref HAL: hal-00872421_v1
PMID 21542593
DOI: 10.1021/jp2014034
WoS: 000290652100038
Exporter : BibTex | endNote
4 Citations
Résumé: It has recently been shown that in some DNA microarrays the time needed to reach thermal equilibrium may largely exceed the typical experimental time, which is about 15 h in standard protocols (Hooyberghs et al. Phys. Rev. E 2010, 81, 012901). In this paper we discuss how this breakdown of thermo-dynamic equilibrium could be detected in microarray experiments without resorting to real time hybridization data, which are difficult to implement in standard experimental conditions. The method is based on the analysis of the distribution of fluorescence intensities I from different spots for probes carrying base mismatches. In thermal equilibrium and at sufficiently low concentrations, log I is expected to be linearly related to the hybridization free energy ΔG with a slope equal to 1/RTexp, where Texp is the experimental temperature and R is the gas constant. The breakdown of equilibrium results in the deviation from this law. A model for hybridization kinetics explaining the observed experimental behavior is discussed, the so-called 3-state model. It predicts that deviations from equilibrium yield a proportionality of log I to ΔG/RTeff. Here, Teff is an "effective" temperature, higher than the experimental one. This behavior is indeed observed in some experiments on Agilent arrays [Hooyberghs et al. Phys. Rev. E 2010, 81, 012901 and Hooyberghs et al. Nucleic Acids Res. 2009, 37, e53]. We analyze experimental data from two other microarray platforms and discuss, on the basis of the results, the attainment of equilibrium in these cases. Interestingly, the same 3-state model predicts a (dynamical) saturation of the signal at values below the expected one at equilibrium.
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Equilibrium winding angle of a polymer around a bar
Auteur(s): Walter J.-C., Barkema Gerard, Carlon Enrico
(Article) Publié:
Journal Of Statistical Mechanics: Theory And Experiment, vol. p.P10020 (2011)
Texte intégral en Openaccess :
Ref Arxiv: 1110.4782
DOI: 10.1088/1742-5468/2011/10/P10020
WoS: 000296709800021
Ref. & Cit.: NASA ADS
13 Citations
Résumé: The winding angle probability distribution of a planar self-avoiding walk has been known exactly since a long time: it has a gaussian shape with a variance growing as $<\theta^2>\sim \ln L$. For the three-dimensional case of a walk winding around a bar, the same scaling is suggested, based on a first-order epsilon-expansion. We tested this three-dimensional case by means of Monte Carlo simulations up to length $L\approx25\,000$ and using exact enumeration data for sizes $L\le20$. We find that the variance of the winding angle scales as $<\theta^2>\sim (\ln L)^{2\alpha}$, with $\alpha=0.75(1)$. The ratio $\gamma = <\theta^4>/<\theta^2>^2=3.74(5)$ is incompatible with the gaussian value $\gamma =3$, but consistent with the observation that the tail of the probability distribution function $p(\theta)$ is found to decrease slower than a gaussian function. These findings are at odds with the existing first-order $\epsilon$-expansion results.
Commentaires: 18 pages, 12 figures, 1 table
Journal: J. Stat. Mech. (2011) P10020
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