Ref HAL: hal-01382770_v1
Ref Arxiv: 1602.07589
DOI: 10.1088/1742-5468/2016/07/074012
WoS: WOS:000381379800041
Ref. & Cit.: NASA ADS
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10 Citations
Résumé:

We study the structure of inactive states in a prototypical model glass, the Kob-Andersen binary Lennard-Jones mixture. These inactive states are obtained by transition path sampling and are at dynamical phase coexistence with an active equilibrium state. Configurations in the inactive states are kinetically stable and are located in deeper basins of the energy landscape than their active counterparts. By analyzing trajectory-to-trajectory fluctuations within the inactive state, we assess correlations between kinetic stability, energy and other structural properties. We show that measures of local order associated to stable local packings and bond-orientational order are weakly correlated with energy and kinetic stability. We discuss what kinds of structural measurement might capture the relevant dynamical features of the inactive state.

Ref HAL: hal-01382401_v1
Ref Arxiv: 1606.00641
DOI: 10.1039/C6SM01322H
WoS: 000382113400007
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32 Citations
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We study the glassy dynamics taking place in dense assemblies of athermal active particles that are driven solely by a nonequilibrium self-propulsion mechanism. Active forces are modeled as an Ornstein-Uhlenbeck stochastic process, characterized by a persistence time and an effective temperature, and particles interact via a Lennard-Jones potential that yields well-studied glassy behavior in the Brownian limit, obtained as the persistence time vanishes. By increasing the persistence time, the system departs more strongly from thermal equilibrium and we provide a comprehensive numerical analysis of the structure and dynamics of the resulting active fluid. Finite persistence times profoundly affect the static structure of the fluid and give rise to nonequilibrium velocity correlations that are absent in thermal systems. Despite these nonequilibrium features, for any value of the persistence time we observe a nonequilibrium glass transition as the effective temperature is decreased. Surprisingly, increasing departure from thermal equilibrium is found to promote (rather than suppress) the glassy dynamics. Overall, our results suggest that with increasing persistence time, microscopic properties of the active fluid change quantitatively, but the broad features of the nonequilibrium glassy dynamics observed with decreasing the effective temperature remain qualitatively similar to those of thermal glass-formers.

Commentaires: Soft Matter 12, 7136 (2016)

Ref HAL: hal-01379497_v1
DOI: 10.1117/12.2237337
WoS: 000389019400015
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A scaling analysis of the extraordinary transmission by subwavelength holes is provided. The structure under study is a lamellar grating. The grating can be described by homogeneous permittivity and permeability tensors. The permeability is dispersive and the peaks of transmission result from a Bragg condition

Ref HAL: hal-01374628_v1
PMID 27714069
DOI: 10.1039/c6nr04930c
WoS: 000385383100021
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13 Citations
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We propose the principles of structural organization in spherical nanoassemblies with icosahedral symmetry constituted by asymmetric protein molecules. The approach modifies the paradigmatic geometrical Caspar and Klug (CK) model of icosahedral viral capsids and demonstrates the common origin of both the "anomalous" and conventional capsid structures. In contrast to all previous models of "anomalous" viral capsids the proposed modified model conserves the basic structural principles of the CK approach and reveals the common hidden symmetry underlying all small viral shells. We demonstrate the common genesis of the "anomalous" and conventional capsids and explain their structures in the same frame. The organization principles are derived from the group theory analysis of the positional order on the spherical surface. The relationship between the modified CK geometrical model and the theory of two-dimensional spherical crystallization is discussed. We also apply the proposed approach to complex double-shelled capsids and capsids with protruding knob-like proteins. The introduced notion of commensurability for the concentric nanoshells explains the peculiarities of their organization and helps to predict analogous, but yet undiscovered, double-shelled viral capsid nanostructures.

Ref HAL: hal-01371450_v1
Ref Arxiv: 1511.03573
DOI: 10.1103/PhysRevE.94.032605
WoS: 000383878500004
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16 Citations
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The growing sluggishness of glass-forming liquids is thought to be accompanied by growing structural order. The nature of such order, however, remains hotly debated. A decade ago, point-to-set (PTS) correlation lengths were proposed as measures of amorphous order in glass formers, but recent results raise doubts as to their generality. Here, we extend the definition of PTS correlations to agnostically capture any type of growing order in liquids, be it local or amorphous. This advance enables the formulation of a clear distinction between slowing down due to conventional critical ordering and that due to glassiness, and provides a unified framework to assess the relative importance of specific local order and generic amorphous order in glass formation.

Commentaires: 12 pages, 8 figures; v2: Fig.4 added, presentation improved. Data relevant to this work can be accessed at http://doi.org/10.7924/G8BG2KWP. Réf Journal: Phys. Rev. E 94, 032605 (2016)

Ref HAL: hal-02060317_v1
PMID 27407108
DOI: 10.1093/nar/gkw630
WoS: 000388016900022
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10 Citations
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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-01367394_v1
DOI: 10.1063/1.4959118
WoS: WOS:000381679800040
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10 Citations
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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.