Ref HAL: hal-01531104_v1
PMID 28558053
DOI: 10.1371/journal.pcbi.1005555
WoS: 000402889500040
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10 Citations
Résumé:

The well established phenomenon of ribosome drop-off plays crucial roles in translational accuracy and nutrient starvation responses during protein translation. When cells are under stress conditions, such as amino acid starvation or aminoacyl-tRNA depletion due to a high level of recombinant protein expression, ribosome drop-off can substantially affect the efficiency of protein expression. Here we introduce a mathematical model that describes the effects of ribosome drop-off on the ribosome density along the mRNA and on the concomitant protein synthesis rate. Our results show that ribosome premature termination may lead to non-intuitive ribosome density profiles, such as a ribosome density which increases from the 5' to the 3' end. Importantly, the model predicts that the effects of ribosome drop-off on the translation rate are mRNA-specific, and we quantify their resilience to drop-off, showing that the mRNAs which present ribosome queues are much less affected by ribosome drop-off than those which do not. Moreover, among those mRNAs that do not present ribosome queues, resilience to drop-off correlates positively with the elongation rate, so that sequences using fast codons are expected to be less affected by ribosome drop-off. This result is consistent with a genome-wide analysis of S. cerevisiae, which reveals that under favourable growth conditions mRNAs coding for proteins involved in the translation machinery, known to be highly codon biased and using preferentially fast codons, are highly resilient to ribosome drop-off. Moreover, in physiological conditions, the translation rate of mRNAs coding for regulatory, stress-related proteins, is less resilient to ribosome drop-off. This model therefore allows analysis of variations in the translational efficiency of individual mRNAs by accounting for the full range of known ribosome behaviours, as well as explaining mRNA-specific variations in ribosome density emerging from ribosome profiling studies.

Ref HAL: hal-02178694_v1
Ref Arxiv: 1606.03108
Ref INSPIRE: 1508910
DOI: 10.1103/PhysRevE.95.012112
WoS: 000391864200001
Ref. & Cit.: NASA ADS
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2 Citations
Résumé:

Ising spin-glass models with bimodal, Gaussian, uniform, and Laplacian interaction distributions in dimension five are studied through detailed numerical simulations. The data are analyzed in both the finite-size scaling regime and the thermodynamic limit regime. It is shown that the values of critical exponents and of dimensionless observables at criticality are model dependent. Models in a single universality class have identical values for each of these critical parameters, so Ising spin-glass models in dimension five with different interaction distributions each lie in different universality classes. This result confirms conclusions drawn from measurements in dimension four and dimension two.

Ref HAL: hal-01461389_v1
DOI: 10.1088/1742-5468/aa4e92
WoS: 000395732100001
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16 Citations

Ref HAL: hal-01437143_v1
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Résumé:

Computer simulations give precious insight into the microscopic behavior of amorphous materials, but their typical timescales are orders of magnitude shorter than the experimentally relevant ones. We close this enormous gap for a class of polydisperse models, which we successfully equilibrate beyond experimental timescales by means of the swap Monte Carlo algorithm. This numerical advance allows us to address some crucial outstanding questions, such as the relationship between jamming and glass transitions and the relevance of an entropy crisis for glass formation.

Ref HAL: hal-01435941_v1
Ref Arxiv: 1609.07979
DOI: 10.1063/1.4972525
WoS: 000393431000021
Ref. & Cit.: NASA ADS
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16 Citations
Résumé:

Classical particle systems characterized by continuous size polydispersity, such as colloidal materials, are not straightforwardly described using statistical mechanics, since fundamental issues may arise from particle distinguishability. Because the mixing entropy in such systems is divergent in the thermodynamic limit we show that the configurational entropy estimated from standard computational approaches to characterize glassy states also diverges. This reasoning would suggest that polydisperse materials cannot undergo a glass transition, in contradiction to experiments. We explain that this argument stems from the confusion between configurations in phase space and states defined by free energy minima, and propose a simple method to compute a finite and physically meaningful configurational entropy in continuously polydisperse systems. Physically, the proposed approach relies on an effective description of the system as an $M^*$-component system with a finite $M^*$, for which finite mixing and configurational entropies are obtained. We show how to directly determine $M^*$ from computer simulations in a range of glass-forming models with different size polydispersities, characterized by hard and soft interparticle interactions, and by additive and non-additive interactions. Our approach provides consistent results in all cases and demonstrates that the configurational entropy of polydisperse system exists, is finite, and can be quantitatively estimated.

Commentaires: 13 pages, 4 figures. v2: Published version. Réf Journal: J. Chem. Phys. 146, 014502 (2017)