Ref HAL: hal-02060317_v1
PMID 27407108
DOI: 10.1093/nar/gkw630
WoS: 000388016900022
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10 Citations
Résumé:

tRNA gene copy number is a primary determinant of tRNA abundance and therefore the rate at which each tRNA delivers amino acids to the ribosome during translation. Low-abundance tRNAs decode rare codons slowly, but it is unclear which genes might be subject to tRNA-mediated regulation of expression. Here, those mRNA targets were identified via global simulation of translation. In-silico mRNA translation rates were compared for each mRNA in both wild-type and a [Formula: see text] sup70-65 mutant, which exhibits a pseudohyphal growth phenotype and a 75% slower CAG codon translation rate. Of 4900 CAG-containing mRNAs, 300 showed significantly reduced in silico translation rates in a simulated tRNA mutant. Quantitative immunoassay confirmed that the reduced translation rates of sensitive mRNAs were [Formula: see text] concentration-dependent. Translation simulations showed that reduced [Formula: see text] concentrations triggered ribosome queues, which dissipated at reduced translation initiation rates. To validate this prediction experimentally, constitutive gcn2 kinase mutants were used to reduce in vivo translation initiation rates. This repaired the relative translational rate defect of target mRNAs in the sup70-65 background, and ameliorated sup70-65 pseudohyphal growth phenotypes. We thus validate global simulation of translation as a new tool to identify mRNA targets of tRNA-specific gene regulation.

Ref HAL: hal-01393714_v1
DOI: 10.1103/PhysRevB.94.081201
WoS: WOS:000381889700002
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10 Citations
Résumé:

We show that the spin-lattice relaxation in n-type insulating GaAs is dramatically accelerated at low magnetic fields. The origin of this effect, which cannot be explained in terms of well-known diffusion-limited hyperfine relaxation, is found in the quadrupole relaxation, induced by fluctuating donor charges. Therefore, quadrupole relaxation, which governs low field nuclear spin relaxation in semiconductor quantum dots, but was so far supposed to be harmless to bulk nuclei spins in the absence of optical pumping, can be studied and harnessed in the much simpler model environment of n-GaAs bulk crystal.

Ref HAL: hal-01367394_v1
DOI: 10.1063/1.4959118
WoS: WOS:000381679800040
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10 Citations
Résumé:

We have carried out classical molecular dynamics simulations in order to get insight into the atomistic mechanisms of the deformation during nanoindentation of the pristine and irradiated forms of a sodium borosilicate glass. In terms of the glass hardness, we have found that the primary factor affecting the decrease of hardness after irradiation is depolymerization rather than free volume, and we argue that this is a general trend applicable to other borosilicate glasses with similar compositions. We have analyzed the changes of the short- and medium-range structures under deformation and found that the creation of oxygen triclusters is an important mechanism in order to describe the deformation of highly polymerized borosilicate glasses and is essential in the understanding of the folding of large rings under stress. We have equally found that the less polymerized glasses present a higher amount of relative densification, while the analysis of bond-breaking during the nanoindentation has showed that shear flow is more likely to appear around sodium atoms. The results provided in this study can be proven to be useful in the interpretation of experimental results.

Ref HAL: hal-01367384_v1
Ref Arxiv: 1507.04120
DOI: 10.1103/PhysRevE.94.022615
WoS: 000382177400007
Ref. & Cit.: NASA ADS
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44 Citations
Résumé:

We use computer simulations to analyse the yielding transition during large-amplitude oscillatory shear of a simple model for soft jammed solids. Simultaneous analysis of global mechanical response and particle-scale motion demonstrates that macroscopic yielding, revealed by a smooth crossover in mechanical properties, is accompanied by a sudden change in the particle dynamics, which evolves from non-diffusive motion to irreversible diffusion as the amplitude of the shear is increased. We provide numerical evidence that this sharp change corresponds to a non-equilibrium first-order dynamic phase transition, thus establishing the existence of a well-defined microscopic dynamic signature of the yielding transition in amorphous materials in oscillatory shear.

Commentaires: 7 pages, 4 figures, Phys. Rev. E (in press). Réf Journal: Phys. Rev. E 94, 022615 (2016)

Ref HAL: hal-01366597_v1
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Opto-electronic properties of single-walled carbon nanotubes can be significantly modified by chromophore confinement into their hollow core. For instance, charge transfers are evidenced from Raman data analysis. First, by exciting nanotubes far from the optical absorption of the molecule, the Raman G-band signal exhibits a weak but significant up or downshift depending on the nanotube diameters. This behavior is consistent with a permanent electron transfer to the nanotube in the framework of the renormalization process 1. In addition, close to the molecule resonance, the magnitude of the G-band shift is enhanced for small diameter tubes, evidencing a photo-induced electron transfer. Finally, the Breit-Wigner-Fano lineshape (characteristic of electron-phonon coupling) of the Raman G-band can be strongly reduced for defective metallic nanotubes. After molecule functionalization, this peculiar profile is recovered, suggesting a back donation of electrons to the nanotube. Photoluminescence properties of semiconducting nanotubes are also significantly modified by chromophore confinement. The nanotube emission intensity is amplified after encapsulation. This exaltation depends on the nanotube diameter, and can be related to diameters exactly fitting the molecule size. The origin of the photoluminescence enhancement will be discussed.

Ref HAL: hal-01366306_v1
Ref Arxiv: 1607.02271
DOI: 10.1021/acsmacrolett.6b00516
WoS: 000385913800002
Ref. & Cit.: NASA ADS
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6 Citations
Résumé:

We investigate the nucleation and propagation of cracks in self-assembled viscoelastic fluids, which are made of surfactant micellesreversibly linked by telechelic polymers. The morphology of the micelles can be continuously tuned, from spherical to rodlike towormlike, thus producing transient double networks when the micelles are sufficiently long and entangled and transient singlenetworks otherwise. For a single network, we show that cracks nucleate when the sample deformation rate involved is comparable tothe relaxation time scale of the network. For a double network, by contrast, significant rearrangements of the micelles occuras a crack nucleates and propagates. We show that birefringence develops at the crack tip over a finite length, ξ, whichcorresponds to the length scale over which micelle alignment occurs. We find that ξ is larger for slower cracks, suggesting anincrease of ductility.

Ref HAL: hal-01365923_v1
DOI: 10.1103/PhysRevB.94.075430
WoS: 000381889000007
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9 Citations
Résumé:

We examine the excitonic nature of the E33 optical transition of the individual free-standing index-identified(23,7) single-walled carbon nanotube by means of the measurements of its radial-breathing-mode and G-modeRaman excitation profiles. We confirm that it is impossible to determine unambiguously the nature of its E33optical transition (excitonic vs band to band) based only on the excitation profiles. Nevertheless, by combiningRaman scattering, Rayleigh scattering, and optical absorption measurements on strictly the same individual(23,7) single-walled carbon nanotube, we show that the absorption, Rayleigh spectra, and Raman excitationprofiles of the longitudinal and transverse G modes are best fitted by considering the nature of the E33 transitionas excitonic. The fit of the three sets of data gives close values of the transition energy E33 and damping parameter. This comparison shows that the fit of the Raman excitation profiles provides with good accuracy the energy and damping parameter of the excitonic optical transitions in single-walled carbon nanotubes.