We propose a new scheme to parametrize effective pair potentials that can be used to simulate oxideglasses. As input data for the optimization we use the radial distribution functions of the liquid andthe vibrational density of state of the glass, both obtained from ab initio simulations, as well asexperimental data on the pressure and/or composition dependence of the density and the elasticmoduli of the glass [1].For the case of silica we find that this new scheme allows to find potentials that are significantlyaccurate than previous ones even if the functional form is the same, thus demonstrating that evensimple two-body potentials can be superior to more complex three-body potentials. We have testedthe new potential by calculating the pressure dependence of the elastic moduli and find a goodagreement with the corresponding experimental data.For binary alkali (lithium, sodium, potassium) silicate glasses, the new potentials allow to reproducethe composition dependence of both density and elastic moduli. Further, we examine thecapabilities of these potentials for studying ternary compositions containing two alkali oxides, andwe find that they are reliable even if they have been developed for binary compositions.Simplicity of the functional form also makes these potentials computationally more efficient thanpotentials with more complex functional forms, and hence more suitable for simulations involvinglarge length and/or time scales scales.[1] S. Sundararaman, L. Huang, S. Ispas, and W. Kob, ”New optimization scheme to obtaininteraction potentials for oxide glasses”, J. Chem. Phys. 148 194504 (2018)

In this talk I will present our understanding on the relation between codon and ribosome usage, and its link to bacterial growth rate.

How the Neveu-Schwarz string was discovered is the result of a most unlikely sequence of four coincidences.

Proteins are the basis of cellular functions, yet key parameters regulating protein synthesis remain elusive. Understanding the fine mechanisms of regulation is a major goal of molecular and systems biology, and this knowledge will support many synthetic biology applications.We have the ambitious goal of providing a biophysical modelling framework of one of the last steps in protein synthesis, namely mRNA translation. Our work focuses on translation initiation and elongation, which relative role is highly debated in the literature: is the ribosome recruitment or the codon bias determining the expression of a gene? We explain how the transcript efficiency can be dictated by ribosome abundances, codon usage and transcript length.We propose analytical and simulation methods to investigate translation models based on an inhomogeneous exclusion process, the prototypical non-equilibrium traffic model in one dimension. We show that the first codons, together with the value of the initiation rate, are the main determinants of protein production. Finally, we interpret the obtained analytical results based on the evolutionary role of codons’ choice for regulating translation rates and ribosome usage.

The vibrational properties of three sodosilicate glasses have been investigated in the framework of Density Functional Theory. The Raman spectra are calculated and the results compare well with the experimental observations. The vibrational analysis confirms the presence of Si-O-Si bending as well as breathing modes of small rings at intermediate frequencies. The Qn Raman-feature at high frequency is decomposed into Q2, Q3, and Q4 vibrational species. Interestingly, the results suggests a large overlap between the three contributions as well as spectral shapes that are not necessarily unimodal nor Gaussian, as frequently assumed in the treatment of the experimental data. Raman scattering of ternary alumino-silicate glasses with alkali and alkaline-earth cations (Mg, Ca, Sr, Ba, Na,...) has also been performed. In these glasses, vibrational signatures of cations are clearly evidenced at low frequency in the depolarized (VH) spectra. Raman scattering by cations at low-frequency is confirmed by the computational data in the sodo-silicates. In the alumino-silicate glasses the responses associate to different types of motions. The analysis allows separating the contribution arising from network modifier cations to that originating from charge compensator ones.

We use computer simulations to probe the thermodynamic and dynamic properties of a glass-former that undergoes an ideal glass-transition because ofthe presence of randomly pinned particles.We find that even deep in the equilibrium glass state the system relaxes to some extent because ofthe presence of localized excitations that allow the systemto access different inherent structures,giving thus rise to a non-trivial contribution to the entropy. By calculating with high accuracy thevibrational part of the entropy, we show that also in the equilibrium glass state thermodynamicsand dynamics give a coherent picture and that glasses shouldnot be seen as a disordered solid inwhich the particles undergo just vibrational motion but instead as a system with a highly nonlinearinternal dynamics.

We propose a new scheme to parametrize effective pair potentials that can be used tosimulate oxide glasses. As input data for the optimization we use the radial distributionfunctions of the liquid and the vibrational density of state of the glass, both obtained fromab initio simulations, as well as experimental data on the pressure and/or composition de-pendence of the density and the elastic moduli of the glass [1].For the case of silica we find that this new scheme allows to find potentials that are signifi-cantly accurate than previous ones even if the functional form is the same, thus demonstratingthat even simple two-body potentials can be superior to more complex three-body poten-tials. We have tested the new potential by calculating the pressure dependence of the elasticmoduli and find a good agreement with the corresponding experimental data.For binary alkali (lithium, sodium, potassium) silicate glasses, the new potentials allowto reproduce the composition dependence of both density and elastic moduli. Further, weexamine the capabilities of these potentials for studying ternary compositions containing twoalkali oxides, and we find that they are reliable even if they have been developed for binarycompositions.Simplicity of the functional form also makes these potentials computationally more efficientthan potentials with more complex functional forms, and hence more suitable for simulationsinvolving large length and/or time scales scales.S. Sundararaman, L. Huang, S. Ispas, and W. Kob, ”New optimization scheme to obtaininteraction potentials for oxide glasses”, submitted (2018)