The boson peak in silicate glasses: insight from molecular dynamics.

In the low-frequency regime, ≈1 THz, glasses show an anomalous excess in their vibrational density of states called the boson peak (BP). The origin of BP has been a subject of debate since its first discovery a few decades ago. Although BP has been the focus of numerous studies, no conclusive answers have been found about its origins, which remained elusive to date. Here, we present results based on molecular dynamics of several binary and ternary silicate glasses with different network intermediates and modifier oxides. The vibrational density of states and the BP are reported for all the studied glasses. Their correlation with the elastic constant C44, structural, and dynamical properties are extensively discussed in terms of Voronoi atomic volume and the vibrational mean square displacement of Q4 species specifically. We also question the classical classification of alkali oxides as modifiers, and we suggest that Li2O plays the role of pseudo-intermediate oxide in lithium silicate glasses. This claim is supported by the effect of Li on various vibrational modes, and this effect differs from the other alkali metals. Furthermore, we demonstrate a correlation between the BP intensities and both the Voronoi volume of the Q4 and Q3 units and vibrational mean square displacements.

Nucleic Acids under Stress: Understanding and Simulating Nucleobase Fragmentation Pathways.

The effects of radiations on nucleic acids and their constituents is widely studied across several research fields using different experimental and theoretical protocols. While a large number of studies were performed in this context, many fundamental physical and chemical effects are still being investigated, particularly involving the effect of the biological environment. As an example, the interpretation of experimental nucleic acid bases mass spectra, and hence inferring their reactivity in complex environment still poses great challenge. This Minireview summarizes recent theoretical advancements aiming to predict and interpret the reactivity of nucleic acid bases. We focus not only on the understanding of the inherent fragmentation pathways of isolated nucleobases but also on the modeling of a realistic nano-environments highlighting the importance of molecular dynamics simulations and the non-innocent role of the environment and also the possibility to open novel fragmentation pathways.

Atomistic insights into the structure and elasticity of densified 45S5 bioactive glasses.

Glasses have applications in regenerative medicine due to their bioactivity, enabling interactions with hard and soft tissues. Soda-lime phosphosilicate glasses, such as 45S5, represent a model system of bioactive glasses. Regardless of their importance as bioactive materials, the relationship between the structure, density, and cooling process has not been studied in detail. This hinders further development of glasses as biomaterials. We used molecular dynamics simulations to study the elastic and structural properties of densified 45S5 bioactive glass and liquids over a wide range of densities. We performed a systematic analysis of the glass structure to density relationship to correlate the change in the properties with the structural change to enhance the mechanical properties of bioactive glasses while preserving their bioactive nature. The results show that the glass structure tends to be repolymerized, as indicated by increased network connectivity and a tetrahedral to octahedral polyhedral transition. We were able to tailor the elastic properties while keeping the bioactivity of the glass. The results presented here will provide some guidance to develop bioactive glasses with enhanced mechanical properties.

Structure-Elasticity Relationship of Potassium Silicate Glasses from Brillouin Light Scattering Spectroscopy and Molecular Dynamics Simulations.

Brillouin light scattering (BLS) spectroscopy and molecular dynamic (MD) simulations allowed the identification of a relationship between the elastic properties and the structure of K-containing glasses of formula (K2O)x-(SiO2)1-x, having different K2O concentrations. Excellent agreement was observed between experimental data and simulations. The peculiar elastic properties observed for these potassium silicate glasses have been extensively discussed in terms of structural and energetic features of the materials. Elastic properties were shown to be strongly dependent on the asymmetry of potential energy in the K-BO interactions and the K-NBO interactions. A low K2O content (below 10-15% K2O) appeared to be in favor of K+-BO interactions and high asymmetry of potential energy, whereas a high K2O content (from 10 to 15% K2O) was in favor of K+-NBO interactions with lower asymmetry. Our results suggest a possible explanation to the observed anomalous dependence of elastic properties of potassium silicate glasses with K2O amount.

Ionic self-diffusion and the glass transition anomaly in aluminosilicates.

The glass transition temperature (Tg) is the temperature after which a supercooled liquid undergoes a dynamical arrest. Usually, glass network modifiers (e.g., Na2O) affect the behavior of Tg. However, in aluminosilicate glasses, the effect of different modifiers on Tg is still unclear and shows an anomalous behavior. Here, based on molecular dynamics simulations, we show that Tg decreases with increasing charge balancing cation field strength (FS) in the aluminosilicate glasses, which is an anomalous behavior as compared to other oxide glasses. The results show that the origins of this anomaly come from the dynamics of the supercooled liquid above Tg, which in turn is correlated to pair excess entropy. Our results deepen our understanding of the effect of different modifiers on the properties of the aluminosilicate glasses.

DNA Nucleobase under Ionizing Radiation: Unexpected Proton Transfer by Thymine Cation in Water Nanodroplets.

The effect of ionizing radiation on DNA constituents is a widely studied fundamental process using experimental and computational techniques. In particular, radiation effects on nucleobases are usually tackled by mass spectrometry in which the nucleobase is embedded in a water nanodroplet. Here, we present a multiscale theoretical study revealing the effects and the dynamics of water droplets towards neutral and ionized thymine. In particular, by using both hybrid quantum mechanics/molecular mechanics and full ab initio molecular dynamics, we reveal an unexpected proton transfer from thymine cation to a nearby water molecule. This leads to the formation of a neutral radical thymine and a Zundel structure, while the hydrated proton localizes at the interface between the deprotonated thymine and the water droplet. This observation opens entirely novel perspectives concerning the reactivity and further fragmentation of ionized nucleobases.

Ab Initio Study of the Stepwise versus Concerted Fragmentation Pathways in Microhydrated Thymine Radical Cations.

Thymine radiation-induced fragmentation is characterised by ring opening and the loss of HNCO/NCO. These pathways have been investigated using DFT calculations in the presence of zero, one and two water molecules. In addition to the already characterised stepwise fragmentation mechanism, we propose a novel concerted pathway reported here for the first time. We show that both the stepwise and concerted mechanisms are competitive with activation energies of 2.05 eV and 2.00 eV, respectively, in the gas phase. The effect of microhydration on these mechanisms are examined based on the most stable conformations found by an exploration of the potential energy surface performed by using DFT-based ab initio molecular dynamics. Microhydration is also accompanied by an increase in the activation energies, with respect to gas phase, amounting to 0.47 eV-an increase that is associated to a stabilising effect of water in agreement with recent experimental studies. However, we also point out that this effect is greatly dependent on the specific water arrangement around thymine and could be limited to only 0.13 eV for some configurations.

Ionization and fragmentation of uracil upon microhydration.

We study at the DFT level the ionization and the fragmentation of uracil in the presence of zero, one and two water molecules, to unravel the effect of microhydration on the reactivity of this nucleobase. We show that the microhydration lowers the adiabatic and vertical ionization potentials by 0.41 eV and 0.22 eV, respectively. Furthermore, microhydration increases the activation energies of the different dissociation channels up to 0.5 eV and restricts the formation of some fragments, in particular those corresponding to the C5-C6 fragmentation pathway. For the first time, our theoretical study shows new transition states and minima not found for the gas phase, hence indicating a change in the fragmentation mechanisms, as well as a stabilizing effect of microhydration, confirming previous experimental studies.

Effect of Sodium Oxide Modifier on Structural and Elastic Properties of Silicate Glass.

Molecular dynamics (MD) simulations and Brillouin light scattering (BLS) spectroscopy experiments have been carried to study the structure of sodium silicate glasses (SiO2)(100-X)(Na2O)X, where X ranges from 0 to 45 at room temperature. The MD-obtained glass structures have been subjected to energy minimization at zero temperature to extract the elastic constants also obtained by BLS spectroscopy. The structures obtained are in good agreement with the structural experimental data realized by different techniques. The simulations show that the values of the elastic constants as a function of X (i.e., Na2O mol %) agree well with those measured by BLS spectroscopy. The variations of elastic constants C11 and C44 as a function of Na2O mol % are discussed and correlated to structural results and potential energies of oxygen atoms.

Highly sensitive pseudo-differential ac-nanocalorimeter for the study of the glass transition.

We present a nanocalorimeter designed for the measurement of the dynamic heat capacity of thin films. The microfabricated sensor, the thermal conditioning of the sensor, as well as the highly stable and low noise electronic chain allow measurements of the real and imaginary parts of the complex specific heat with a resolution Δ C/C of about 10(-5). The performances of this quasi-differential nanocalorimeter were tested on a model of polymeric glass-former, the polyvinyl acetate (PVAc). The high stability and low noise of the device are essential for accurate studies on non-equilibrium slow relaxing systems such as glasses.

The calculation of proton and secondary electron stopping powers in liquid water.

The stopping power of energetic protons in liquid water has been calculated using a new model based on different theoretical and semi-empirical approaches. In this model, we consider the relativistic corrections along with the electronic and nuclear stopping power. The present work accounts for the different interactions made with electrons and nuclei inside the target. Interactions of the incident particle with the target's electrons dominate in the high energy regime; in the low energy regime, the interactions of the projectile with the target nuclei contribute importantly and are included in the calculation. We also compute the stopping cross sections and the stopping power of secondary electrons ejected from proton and hydrogen ionization impact, and generated by hydrogen electron loss processes. The consideration of secondary electrons' stopping power can contribute to the study of nano-dosimetry. Our results are in good agreement with existing experimental data. This calculation model can be useful for different applications in medical physics and space radiation health, such as hadron therapy for cancer treatment or radiation protection for astronauts.