rotein synthesis rates are determined, at the translational level, by properties of the transcript’s sequence. The e ciency of an mRNA can be tuned by varying the ribosome binding sites controlling the recruitment of the ribosomes, or the codon usage establishing the speed of protein elongation. In this work we propose transcript length as a further key determinant of translation e ciency. Based on a physical model that considers the kinetics of ribosomes advancing on the mRNA and di using in its surrounding, as well as mRNA circularisation and ribosome drop-o , we explain how the transcript length may play a central role in establishing ribosome recruitment and the overall translation rate of an mRNA. According to our results, the proximity of the 3′ end to the ribosomal recruitment site of the mRNA could induce a feedback in the translation process that would favour the recycling of ribosomes. We also demonstrate how this process may be involved in shaping the experimental ribosome density-gene length dependence. Finally, we argue that cells could exploit this mechanism to adjust and balance the usage of its ribosomal resources.

Protein synthesis rates are determined, at the translational level, by properties of the transcript’s sequence. The efficiency of an mRNA can be tuned by varying the ribosome binding sites controlling the recruitment of the ribosomes, or the codon usage establishing the speed of protein elongation. In this work we promote transcript length as a further key determinant of translation efficiency. Based on a physical model that considers the kinetics ofribosomes advancing on the mRNA and diffusing in its surrounding, we explain how the transcript length might play a central role in establishing ribosome recruitment and the overall translation rate of an mRNA. We also demonstrate how this process might be involved in shaping the experimental ribosome density-gene length dependence. Finally, we argue that cells could exploit this mechanism to adjust and balance the usage of its ribosomal resources.

La compréhension du mécanisme de la formation du verre est l'un des importants problèmes ouverts en recherche sur la matière condensée. De nombreuses questions restent sans réponse, en raison d'une énorme augmentation des temps de relaxation pendant le processus de refroidissement qui ne permet pas l'exploration des propriétés d'équilibre des liquides surfondus à très basses températures. Les simulations numériques des liquides surfondus sont actuellement en mesure d'atteindre l'équilibre à des températures comparables à la température du crossover de la théorie de couplages de modes, qui est bien supérieure à la température de transition vitreuse expérimentale. En conséquence, les simulations plus lentes que les expériences pour équilibrer un liquide surfondu par un facteur d'environ huit ordres de grandeur. Les progrès réalisés pour combler cet écart ont été lents et résultent essentiellement d'améliorations de l'architecture des ordinateurs. Dans cette thèse, nous résolvons en partie le problème de la thermalisation à basse température de liquides surfondus dans des simulations numériques. Nous combinons l'utilisation d'un algorithme Monte Carlo, connu sous le nom d'algorithme de swap, avec la conception de nouveaux modèles de formateurs de verre. Nous examinons systématiquement des nombreux systèmes, à la fois des mélanges discrets de particules, ainsi que des systèmes a polydispersité continue. Nous discutons le rôle que la polydispersité et la forme du potentiel entre particules jouent pour éviter la cristallisation et parvenir efficacement à des régimes de température inexplorés. De plus, nous étudions les processus dynamiques à l’œuvre pendant une simulation de swap Monte Carlo. Nous démontrons que, dans certains cas, notre technique permet de produire des configurations équilibrées à des températures inaccessibles même dans des expériences. Dans ce régime de température complètement nouveau, nous examinons plusieurs questions ouvertes concernant la physique de la transition vitreuse. Nous montrons qu'un fluide de sphères dures peut être équilibré jusqu'à la densité critique du jamming, et même au-delà. Nous mesurons l'entropie configurationelle dans un liquide refroidi à très basse température. Nous mettons en évidence une forte dépendance dimensionnelle, qui suggère l'existence d'une transition vitreuse idéale à une température finie en trois dimensions et à son absence en deux dimensions. Nous détectons l'augmentation de l'ordre amorphe quantifié par une longueur statique point-to-set pendant la formation du verre. Nous mesurons les exposants critiques introduits dans la théorie de champ moyen des verres beaucoup plus proche de la température critique prédite dans la théorie. Enfin, nous révélons l'absence de transition géométrique caractérisant le paysage d’énergie potentiel au travers de la température du crossover de la théorie de couplages de modes.Les modèles et les algorithmes développés dans cette thèse déplacent les études des liquides surfoundus vers un territoire entièrement nouveau, en réduisant l'écart entre la théorie et les expériences, ce qui nous amène plus proche de la solution du problème de la transition vitreuse.

We have carried out combined classical and ab initio molecular dynamics (MD)simulations in order to investigate the structural and vibrational properties of severalborosilicate glasses. We have considered rather simple ternary compositions withvarying SiO 2 , B 2 O 3 or Na 2 O concentrations, or more complex compositionscontaining equally CaO, Al 2 O 3 or MgO. The ab initio calculations have been carriedout within the density functional theory framework as implemented in the VASPcode. The classical MD simulations were carried out using different effective pairpotentials.We have studied the local structure of the various structural units, and inparticular we have focused on the structures around the boron atoms and how theseare embedded into the network. We have investigated how the Na atoms aredistributed around the [3] B triangles and [4] B tetrahedra. Furthermore, we have foundthat the Na distribution associated to a BO 4 tetrahedron is different from thatcorresponding to a SiO 4 tetrahedron in that the former gives rise to a distribution thatis significantly more structured.The vibrational properties have been equally studied within the ab initio approach,and we have identified the contributions of the various species as well as those ofthe local structural units. We have also calculated the dielectric function ε(ω) as wellas the absorption spectra. The latter are in good quantitative agreement withexperimental data. The results obtained in this work confirm that the atomisticsimulations, in particular the ab initio ones, give access to a better understanding ofcomplex borosilicate glasses since their structural and vibrational properties can beextracted with a good accuracy and compare very well to experimental data.

We have parameterized empirical potentials for molecular dynamics (MD) simulations ofmulti-component silicate glasses. The main motivation has been to improve predictions ofstatic properties like elastic moduli and dynamic properties like vibrational density of states(VDOS) that MD simulations have generally not been able to estimate correctly, while stillusing a simple functional form for computational efficiency.Our approach has been to fit the potentials to data extracted from accurate first principlescalculations to predict both the static and dynamic properties correctly, by explicitly incor-porating the radial distribution function (RDF) and the VDOS into the cost function of thefitting scheme. The current optimization scheme is an extension of a recent work using asinput only the structural data from the ab initio simulations, and which has been applied inthe past to obtain a reliable potential for amorphous silica [1,2].The newly developed potentials will be used to study the elastic response of multi-componentoxide glasses to external stimuli such as high temperatures, high pressures and high strains,and their deformation modes under different loading conditions.A. Carré, J. Horbach, S. Ispas, W. Kob, Europhys. Lett. 82 (2008) 17001.A. Carré, S. Ispas, J. Horbach, W. Kob, Comput. Mater. Sci. 124 (2016) 323

Density functional theory is used to calculate the vibrational properties of pure silica and sodo-silicateglasses with 20, 25, and 33 mol% of Na2O. The infrared and Raman spectra are calculated and the full responses aredecomposed into principal structural components (PSC). Those are for example the SiO4n--tetrahedra with n nonbrigdingoxygens defining the Qn-species at the origin of the structured feature at high frequency, and the Si-O-Sibridges leading the broad Raman R-band at intermediate frequencies. Our results confirm that Si-O-Si bending inbridges with large angle vibrate preferentially at lower frequencies than those with low angle. In addition, the spectralresponse of the Q2-species is bimodal and overlaps with that of the Q3, while the Q4 response covers almost all ofthe spectral range of the Qn-band. The ab-initio individual spectral responses of the PSC are used to reconstruct theexperimental Raman responses. Contrary to the commonly used multi-Gaussian decomposition, this approachprovides unambiguous band-assignments and hence a more accurate way to probe the structural and chemicalproperties of glasses from their spectroscopic signature.