Ref HAL: hal-01806569_v1
DOI: 10.1063/1.5023707
WoS: 000432853800077
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18 Citations
Résumé:

We propose a new scheme to parameterize effective potentials that can be used to simulate atomic systems such as oxide glasses. As input data for the optimization, we use the radial distribution functions of the liquid and the vibrational density of state of the glass, both obtained from ab initio simulations, as well as experimental data on the pressure dependence of the density of the glass. For the case of silica, we find that this new scheme facilitates finding pair potentials that are significantly more accurate than the previous ones even if the functional form is the same, thus demonstrating that even simple two-body potentials can be superior to more complex three-body potentials. We have tested the new potential by calculating the pressure dependence of the elastic moduli and found a good agreement with the corresponding experimental data.

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Ref Arxiv: 1801.09638
DOI: 10.1088/1361-648X/aab0c9
WoS: WOS:000427389700004
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14 Citations
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Computer simulations give precious insight into the microscopic behavior of supercooled liquids and glasses, but their typical time scales are orders of magnitude shorter than the experimentally relevant ones. We recently closed this gap for a class of models of size polydisperse fluids, which we successfully equilibrate beyond laboratory time scales by means of the swap Monte Carlo algorithm. In this contribution, we study the interplay between compositional and geometric local orders in a model of polydisperse hard spheres equilibrated with this algorithm. Local compositional order has a weak state dependence, while local geometric order associated to icosahedral arrangements grows more markedly but only at very high density. We quantify the correlation lengths and the degree of sphericity associated to icosahedral structures and compare these results to those for the Wahnström Lennard-Jones mixture. Finally, we analyze the structure of very dense samples that partially crystallized following a pattern incompatible with conventional fractionation scenarios. The crystal structure has the symmetry of aluminum diboride and involves a subset of small and large particles with size ratio approximately equal to 0.5.

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Ref Arxiv: 1803.00887
DOI: 10.1103/PhysRevE.97.052139
WoS: 000433291900005
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7 Citations
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We develop a power series method for the nonequilibrium steady state of the inhomogeneous one-dimensional totally asymmetric simple exclusion process (TASEP) in contact with two particle reservoirs and with site-dependent hopping rates in the bulk. The power series is performed in the entrance or exit rates governing particle exchange with the reservoirs, and the corresponding particle current is computed analytically up to the cubic term in the entry or exit rate, respectively. We also show how to compute higher-order terms using combinatorial objects known as Young tableaux. Our results address the long outstanding problem of finding the exact nonequilibrium steady state of the inhomogeneous TASEP. The findings are particularly relevant to the modelling of mRNA translation in which the rate of translation initiation, corresponding to the entrance rate in the TASEP, is typically small.

Ref HAL: hal-01735760_v1
DOI: 10.1103/PhysRevE.97.012403
WoS: WOS:000423129000005
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2 Citations
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Cilia are elastic hairlike protuberances of the cell membrane found in various unicellular organisms and in several tissues of most living organisms. In some tissues such as the airway tissues of the lung, the coordinated beating of cilia induce a fluid flow of crucial importance as it allows the continuous cleaning of our bronchia, known as mucociliary clearance. While most of the models addressing the question of collective dynamics and metachronal wave consider homogeneous carpets of cilia, experimental observations rather show that cilia clusters are heterogeneously distributed over the tissue surface. The purpose of this paper is to investigate the role of spatial heterogeneity on the coherent beating of cilia using a very simple one dimensional model for cilia known as the rower model. We systematically study systems consisting of a few rowers to hundreds of rowers and we investigate the conditions for the emergence of collective beating. When considering a small number of rowers, a phase drift occurs, hence a bifurcation in beating frequency is observed as the distance between rowers clusters is changed. In the case of many rowers, a distribution of frequencies is observed. We found in particular the pattern of the patchy structure that shows the best robustness in collective beating behavior, as the density of cilia is varied over a wide range.

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Ref Arxiv: 1708.07678
DOI: 10.1103/PhysRevLett.120.128101
WoS: 000427804000009
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14 Citations
Résumé:

One of the greatest challenges in biophysical models of translation is to identify coding sequences features that affect the rate of translation and therefore the overall protein production in the cell. We propose an analytic method to solve a translation model based on the inhomogeneous totally asymmetric simple exclusion process, which allow us to unveil simple design principles of nucleotide sequences determining protein production rates. Our solution shows an excellent agreement when compared to numerical genome-wide simulations of S. cerevisiae transcript sequences and predicts that the first 10 codons, together with the value of the initiation rate, are the main determinants of protein production rate. Finally, we interpret the obtained analytic results based on the evolutionary role of codons' choice for regulating translation rates and ribosome densities.

Commentaires: 5 pages, 3 figures, Supplemental Material (3 pages)

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Ref Arxiv: 1705.00855
DOI: 10.1063/1.5006924
WoS: 000431291900023
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5 Citations
Résumé:

In a dense colloidal suspension at a volume fraction slightly lower than that of its glass transition, we follow the trajectories of an assembly of tracers over a large time window. We define a local activity, which quantifies the local tendency of the system to rearrange. We determine the statistics of the time and space integrated activity, and we argue that it develops a low activity tail that comes on a par with the onset of glassy behavior and heterogeneous dynamics. These rare events may be interpreted as the reflection of an underlying dynamic phase transition.

Commentaires: 10 pages, 15 figures