Raman spectroscopy is one of the key experimental methods for the structuralanalysis of glasses, thanks to its simple application and its sensitivity to variations ofcomposition or atomic-scale order. However, the inherent disorder of the glassystructure results to broad and overlapping peaks in the spectra, rendering theirquantitative analysis a challenging task and resulting in a mostly phenomenologicalinterpretation. This drawback can be addressed by the use of modern and accuratetheoretical tools, such as ab-initio vibrational spectroscopies. In this work we havestudied three simple sodosilicate glasses, prepared using a combined classical/ab-initio approach. For these structures, we have used density functional theory (DFT) tocalculate their vibrational density of states, as well as their Raman and IR spectra.The main advantage of the DFT calculations is that the resulting spectra can bedirectly correlated with the structural models and, most importantly, the vibrationalspectrum can be decomposed into exact contributions arising from individualstructural units. In the case of the sodosilicate glasses, we have identifiedcorrelations between spectral characteristics and stoichiometry, the effect of thepresence of bridging and non-bridging oxygens, the contributions of smaller or largerSi-O-Si angles, as well as the ones arising from the presence of the so-called Q-species. These results open the way for the study of even more complex glasses andaid in the interpretation of experimental spectra.

Silicate glasses possess a central role in glass technology due to their multiple applications ranging from optical devices to the immobilization of nuclear waste. Raman spectroscopy is a key method for the investigation of their structure and the study of their properties. However, the inherent structural disorder found in glasses results in very broad and overlapping peaks in their spectra. In this context, an accurate theoretical modeling of the spectra can be proven to be invaluable in order to optimize their performance and tailor their fabrication method to match requirements for future applications. In this work, we present results on binary sodo-silicate glasses [xNa2O- (1-x)SiO2], which have been prepared by combining classical and ab-initio Molecular Dynamics. The Raman spectra (polarized and unpolarized), as well as the IR spectra, have been obtained using the Quantum Espresso package [1] in the GGA framework by employing norm-conserving pseudopotentials. Calibration runs have been carried out on the crystalline α-quartz and Na2SiO3 systems in order to optimize the choice of pseudopotentials. Concerning the glasses under study, we focused on the effect of local structural units, such as Q-species and their interconnection, alongside the role of sodium atom content in order to assign the corresponding bands. The initial results show very good agreement with previous theoretical and experimental spectra [2-5], while the ongoing decomposition relative to the exact contributions from each of the structural units of the glasses is expected to provide insight to the interpretation of the experimental spectra.References[1] P. Gianozzi et al., J. Phys.: Condens. Matter 21, 395502 (2009).[2] S. Ispas, N. Zotov, S. de Wispelaere, W. Kob, J. Non-Cryst. Solids 351, 1144 (2005).[3] N. Zotov, H. Keppler, Phys. Chem. Minerals 25, 259 (1998).[4] B. Hehlen, D.R. Neuville, J. Phys. Chem. B 119, 4093 (2015).[5] B.O. Mysen, J.D. Frantz, Contrib. Mineral. Petrol. 117, 1 (1994).

Gene expression and cellular physiology are deeply connected. In this talk I present a few ideas on how I imagine to relate those processes with a mathematical model.

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 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?). Here I will explain how the transcript efficiency can be dictated by ribosome abundances, codon usage and transcript length. We propose an approach based on the standard exclusion process, a 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 and gene expression data, which are well reproduced qualitatively and quantitatively. The proposed mathematical framework also 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.

It has been widely reported that the jamming transition point phi_J is not uniquely determined but shows protocol dependence.Whereas phi_J is obtained around 65% in three dimensions by compressing a dilute hard sphere fluid,higher value of phi_J is attained when a dense thermally equilibrated fluid is compressed.Recently, we develop a very efficient thermalization setting of a hard sphere system which is composed of continuous polydispersity of the particle diameters and a non-local swap Monte-Carlo algorithm.This method enabled us to thermalize the hard sphere fluid up to nearly 66%, which is beyond phi_J of the system obtained by the compression of dilute states.By compressing these high density equilibrium fluids, we obtain an unprecedentedly wide range of phi_J, so-called J-line, from around 65% to almost 70%.These denser phi_J states also have on average 6 contact number per particle (isostaticity).Also, the power law singularity near contact in the radial distribution function is observed over the entire J-line with a fixed exponent whose value is consistent with the prediction of the mean-field theory. Furthermore, we examine local and global structural properties of high density jammed states.Even though the isostaticity and critical behavior are preserved over the entire J-line, the high density jammed states show qualitatively distinct structural properties compared to the lowest jamming transition point, phi_J = 65%, which has been widely studied in the past.Especially, we demonstrate the following local and global structural properties.Growing local order:Even though our jammed configurations are all isostatic, they do differ at the local structure level.We reveal this by a combination of bond-orientational order analysis and Voronoi tessellation.This analysis detects growing icosahedral order with increasing phi_J and shows no signs of crystallization in our configurations.Disturbing the hyperuniformity: Hyperuniformity, which corresponds to vanishing of the density (or volume fraction) fluctuations at long wavelengths is believed to be one of the characteristic properties of the jamming transition point.We analyze the two body correlation function of the volume fraction to examine the hyperuniformity in our system.We observe excitations at small wavenumbers which disturb the hyperunifromity at the high density jammed states.Also, these excitations increase with increasing phi_J.Suppression of the finite size effect: It has been argued that the jamming transition is a phase transition which occurs at the thermodynamic limit.Also, several length scales diverging at phi_J are well characterized as a consequences of the isostaticity of the system.However, the length scale which causes finite size effects at the jamming transition is not yet understood. We study finite size effects for two protocols, compression of dilute and of dense fluids.Interestingly, we find that finite size effects are significantly suppressed by the protocol using compression of the dense fluid.This observation implies that the length scale causing finite size effects is not related to the isostaticity of the system.Instead we discuss the mechanism of the finite size effect of the jamming transition using an analogy with the potential energy landscape thermal systems.

We implement and optimize a particle-swap Monte Carlo algorithm that allows us to thermalize a polydisperse system of hard spheres up to unprecedentedly large volume fractions, where previous algorithms and experiments fail to equilibrate. We show that no glass singularity intervenes before the jamming density, which we independently determine through two distinct nonequilibrium protocols. We demonstrate that equilibrium fluid and nonequilibrium jammed states can have the same density, showing that the jamming transition cannot be the end point of the fluid branch.