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)

Understanding the motion of nanoparticles in polymer solutionsand melts is a problem of broad importance, with applications tomany different fields, such as material science, biophysics, andmedicine. If the nanoparticles are larger than the polymer's radiusof gyration, their structure and dynamics can be well described interms of effective pair potentials. However, much remains to beunderstood in the so-called “protein limit”, where the size of thenanoparticles becomes comparable to or smaller than that ofthe polymers. Moreover, most of the previous study consideringthis size range have only focused on the dilute nanoparticleregime, which is easier to handle since inter-nanoparticleinteraction can be neglected and the properties of the polymersolution/melt are expected to be unchanged.Using molecular dynamics simulations, we study the dynamic andstructural properties of a semidilute polymer solution containingwell dispersed spherical nanoparticles of size smaller than thepolymer's radius of gyration. We consider various nanoparticlediameters and a broad range of nanoparticle volume fractions,up to values for which the inter-nanoparticle interactionbecomes important.We find that the polymers slow down when the nanoparticleconcentration is increased, in qualitative agreement with theconfinement parameter theory (Choi et al.,ACS Macro Lett.2013,2,485−490), according to which polymers slow downbecause they have to squeeze through “bottlenecks” created bythe presence of the nanoparticles. Also the nanoparticles slowdown when their concentration is increased, with the magnitudeof the slowing down depending in a non-trivial way on their size.Surprisingly, if the concentration of the nanoparticles is increasedpast the range in which the nanoparticle dispersion is good, thediffusivities of polymers and nanoparticles reach a minimum andthen start to increase.

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.

Dense active materials

Lectures on entropy