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(408) Production(s) de l'année 2015
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Deformation of sodium borosilicate glasses under load using Molecular Dynamics simulations 
Auteur(s): Kilymis D., Delaye Jean-Marc, Ispas S.
Conference: CECAM workshop, Chemical and Structural Transformations in Materials Under Mechanical Load (Laussane, CH, 2015-09-01)
Ref HAL: hal-01939439_v1
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Résumé: In this study we present the results of nanoindentation and isostatic compression simulations of sodium borosilicate glasses using Molecular Dynamics, alongside experimental results obtained by Raman spectroscopy. For nanoindentation, three glasses with varying sodium content were simulated both in their pristine form, as well as a “disordered” one, which is analogous to the real irradiated glass and exhibits a swollen and more depolymerized network. The results indicate a very low increase of coordination of the silicon atoms, in contrast to boron and sodium. Densification occurs by the decrease of free volume and takes place in regions rich in glass formers. On the contrary, we observed evidence of high shear flow around sodium atoms. In the compression simulations, the pristine forms of the glasses were brought to a pressure of 20 GPa and then decompressed again. We found that the amount of free volume has a major influence on the amount of densification, alongside the percentage of three-coordinated boron. At the same time, sodium creates soft regions in the glass that can be more easily compressed. The results are then compared to Raman spectra collected on the imprint marks of experimentally indented borosilicate glasses.
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Finite size effects and recycling in the protein production line
Auteur(s): Ciandrini L.
(Séminaires)
Institute for Complex Systems and Mathematical Biology (ICSMB) (Aberdeen, GB), 2015-05-25 |
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Ribosome recycling as a main determinant of experimental ribosome densities
Auteur(s): Ciandrini L.
Conference: EMBO fellows’ meeting (Heidelberg, DE, 2015-06-18)
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Transcript length as a main determinant of mRNA translation efficiency
Auteur(s): Ciandrini L.
Conference: Quantitative Methods in Gene Regulation III (Cambridge, GB, 2015-12-07)
Ref HAL: hal-01939067_v1
Exporter : BibTex | endNote
Résumé: Proteins are the basis of cellular functions, yet key parameters regulating protein synthesis remain elusive. Understanding the fine mechanisms of this regulation is a major goal of molecular and systems biology, and this knowledge will support many “synthetic biological” applications. We have the ambitious goal of providing a comprehensive modeling framework of one of the last steps of protein synthesis, namely mRNA translation. In this presentation I will focus from a modeler’s point of view, on the role of translation initiation and how this step is mainly dictated by ribosome abundances, finite size effects and recycling. We propose an approach based on the standard exclusion process, prototypic lattice gas model. This mathematical framework considers long-range dynamical effects often neglected in standard translation models. The model is compared to experimental ribosome density data, which are well reproduced qualitatively and quantitatively. The proposed mathematical framework thus describes the origins of the well-known and yet not understood relation between transcript efficiency and its length. We also speculate on the role of transcript length in the competition for ribosomes among different mRNAs.
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Raman studies of graphene
Auteur(s): Anglaret E.
(Séminaires)
IEF (Orsay, FR), 2015-07-01 |
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Raman studies of graphene
Auteur(s): Anglaret E.
(Séminaires)
IEF (Orsay, FR), 2015-07-01 |
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Nanomaterials for SERS
Auteur(s): Anglaret E.
(Séminaires)
CRPP (Bordeaux, FR), 2015-06-19 |
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