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Physique Théorique
(51) Production(s) de l'année 2022
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Physical modeling of ribosomes along mRNA: estimating kinetic rates from ribosome profiling experiments
Auteur(s): Walter J.-C.
Conférence invité: RNA Club (Montpellier, FR, 2022-10-12)
Texte intégral en Openaccess :
Ref HAL: hal-03815334_v1
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Résumé: Gene expression consists in the synthesis of proteins from the information encoded on DNA. One of the two main steps of gene expression is the translation of messenger RNA (mRNA) into polypeptide sequences of amino acids. Here, by taking into account mRNA degradation, we model the motion of ribosomes along mRNA with a ballistic model where particles advance along a filament without excluded volume interactions. Unidirectional models of transport have previously been used to fit the average density of ribosomes obtained by the experimental ribo-sequencing (Ribo-seq) technique. In this case an inverse fit gives access to the kinetic rates: the position-dependent speeds and the entry rate of ribosomes onto mRNA. The degradation rate is not, however, accounted for and experimental data from different experiments are needed to have enough parameters for the fit. Here, we propose an entirely novel experimental setup and theoretical framework consisting in splitting the mRNAs into categories depending on the number of ribosomes from one to four. We solve analytically the ballistic model for a fixed number of ribosomes per mRNA, study the different regimes of degradation, and propose a criteria for the quality of the inverse fit. The proposed method provides a high sensitivity to the mRNA degradation rate. The additional equations coming from using the monosome (single ribosome) and polysome (arbitrary number) ribo-seq profiles enable us to determine all the kinetic rates in terms of the experimentally accessible mRNA degradation rate.
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Collective dynamics in a glass-former with Mari-Kurchan interactions
Auteur(s): Nishikawa Y., Ikeda A., Berthier L.
(Article) Publié:
The Journal Of Chemical Physics, vol. p.244503 (2022)
Texte intégral en Openaccess :
Ref HAL: hal-03807702_v1
Ref Arxiv: 2204.05130
DOI: 10.1063/5.0096356
Ref. & Cit.: NASA ADS
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Résumé: We numerically study the equilibrium relaxation dynamics of a two-dimensional Mari-Kurchan glass model. The tree-like structure of particle interactions forbids both non-trivial structural motifs and the emergence of a complex free-energy landscape leading to a thermodynamic glass transition, while the finite-dimensional nature of the model prevents the existence of a mode-coupling singularity. Nevertheless, the equilibrium relaxation dynamics is shown to be in excellent agreement with simulations performed in conventional glass-formers. Averaged time-correlation functions display a phenomenology typical of supercooled liquids, including the emergence of an excess signal in relaxation spectra at intermediate frequencies. We show that this evolution is accompanied by strong signatures of collective and heterogeneous dynamics which cannot be interpreted in terms of single particle hopping and emerge from dynamic facilitation. Our study demonstrates that an off-lattice interacting particle model with extremely simple structural correlations displays quantitatively realistic glassy dynamics.
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Supersymmetric black holes and modularity
Auteur(s): Alexandrov S.
Conférence invité: Théorie, Univers et Gravitation (Montpellier, FR, 2022-10-04)
Ref HAL: hal-03811118_v1
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Résumé: I'll give a review of the role that modular symmetry plays in description of BPS black holes and counting of their microstates.
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Topological aspects of periodic and aperiodic photonic crystals
Auteur(s): Rousseau E., Kling Emmanuel, Felbacq D.
Conference: SPIE Nanoscience + Engineering (San Diego, FR, 2022-08-21)
Texte intégral en Openaccess :
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D-instantons in Calabi-Yau compactifications
Auteur(s): Alexandrov S.
Conférence invité: String Field Theory 2022 (Prague, CZ, 2023-09-12)
Ref HAL: hal-03811120_v1
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Résumé: Euclidean D-branes wrapped on non-trivial cycles of a Calabi-Yau threefold are known to affect the metric on the hypermultiplet moduli space determining the effective action of type II strings on such manifolds. After reviewing the existing results on the instanton corrected metric following from a combination of constraints imposed by supersymmetry and dualities, I'll show how the D-instanton effects can be computed by a direct worldsheet approach. This required solving several conceptual and technical problems, which also paved the way for extension of this approach to compactifications with lower supersymmetry. The talk is based on joint work with A. Sen and B. Stefanski.
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