Structural properties of a calcium aluminosilicate glass from molecular-dynamics simulations: A finite size effects study

We study a calcium aluminosilicate glass of composition (SiO$_2$)$_{0.67}$-(Al$_2$O$_3$)$_{0.12}$-(CaO)$_{0.21}$ by means of molecular-dynamics (MD) simulations, using a potential made of two-body and three-body interactions. In order to prepare small samples that can subsequently be studied by first-principles, the finite size effects on the liquid dynamics and on the glass structural properties are investigated. We find that finite size effects affect the Si-O-Si and Si-O-Al angular distributions, the first peaks of the Si-O, Al-O and Ca-O pair correlation functions, the Ca coordination and the oxygen atoms environment in the smallest system (100 atoms). We give evidence that these finite size effects can be directly attributed to the use of three-body interactions.Comment: 36 pages, 14 figures. Journal of Chem. Phys., in pres

Detection of the tagged or untagged photons in acousto-optic imaging of thick highly scattering media by photorefractive adaptive holography

We propose an original adaptive wavefront holographic setup based on the photorefractive effect (PR), to make real-time measurements of acousto-optic signals in thick scattering media, with a high flux collection at high rates for breast tumor detection. We describe here our present state of art and understanding on the problem of breast imaging with PR detection of the acousto-optic signal

Back-translation for discovering distant protein homologies

Frameshift mutations in protein-coding DNA sequences produce a drastic change in the resulting protein sequence, which prevents classic protein alignment methods from revealing the proteins' common origin. Moreover, when a large number of substitutions are additionally involved in the divergence, the homology detection becomes difficult even at the DNA level. To cope with this situation, we propose a novel method to infer distant homology relations of two proteins, that accounts for frameshift and point mutations that may have affected the coding sequences. We design a dynamic programming alignment algorithm over memory-efficient graph representations of the complete set of putative DNA sequences of each protein, with the goal of determining the two putative DNA sequences which have the best scoring alignment under a powerful scoring system designed to reflect the most probable evolutionary process. This allows us to uncover evolutionary information that is not captured by traditional alignment methods, which is confirmed by biologically significant examples.Comment: The 9th International Workshop in Algorithms in Bioinformatics (WABI), Philadelphia : \'Etats-Unis d'Am\'erique (2009

Molecular dynamics simulation of radiation damage in glasses

Molecular dynamics simulations of the ballistic effects arising from displacement cascades in glasses have been investigated in silica and in a SiO 2 -B 2 O 3 -Na 2 O glass. In both glasses the T-O-T′ angle (where T and T′ are network formers) diminishes, despite radiation causes opposite effects: while the ternary glass swells and silica becomes denser. We show that radiation-induced modifications of macroscopic glass properties result from structural change at medium/range, reflecting an increasing disorder and internal energy of the system. A local thermal quenching model is proposed to account for the effects of ballistic collisions. The core of a displacement cascade is heated by the passage of the projectile, then rapidly quenched, leading to a process that mimics a local thermal quenching. The observed changes in both the mechanical and structural properties of glasses eventually reach saturation at 2 10 18 α/g as the accumulated energy increases. The passage of a single projectile is sufficient to reach the maximum degree of damage, confirming the hypothesis postulated in the swelling model proposed by J.A.C. Marples

The importance of major mergers in the build up of stellar mass in brightest cluster galaxies at z=1

Recent independent results from numerical simulations and observations have shown that brightest cluster galaxies (BCGs) have increased their stellar mass by a factor of almost two between z~0.9 and z~0.2. The numerical simulations further suggest that more than half this mass is accreted through major mergers. Using a sample of 18 distant galaxy clusters with over 600 spectroscopically confirmed cluster members between them, we search for observational evidence that major mergers do play a significant role. We find a major merger rate of 0.38 +/- 0.14 mergers per Gyr at z~1. While the uncertainties, which stem from the small size of our sample, are relatively large, our rate is consistent with the results that are derived from numerical simulations. If we assume that this rate continues to the present day and that half of the mass of the companion is accreted onto the BCG during these mergers, then we find that this rate can explain the growth in the stellar mass of the BCGs that is observed and predicted by simulations. Major mergers therefore appear to be playing an important role, perhaps even the dominant one, in the build up of stellar mass in these extraordinary galaxies.Comment: 15 pages, 6 figures, accepted for publication in MNRAS. Reduced data will be made available through the ESO archiv

Shear instabilities of freely standing thermotropic smectic-A films

In this Letter we discuss theoretically the instabilities of thermotropic freely standing smectic-A films under shear flow\cite{re:wu}. We show that, in Couette geometry, the centrifugal force pushes the liquid crystal toward the outer boundary and induces smectic layer dilation close to the outer boundary. Under strong shear, this effect induces a layer buckling instability. The critical shear rate is proportional to $1/\sqrt{d}$, where $d$ is the thickness of the film.Comment: 12 pages, 2 figure

Self-healing capacity of nuclear glass observed by NMR spectroscopy

Safe management of high level nuclear waste is a worldwide significant issue for which vitrification has been selected by many countries. There exists a crucial need for improving our understanding of the ageing of the glass under irradiation. While external irradiation by ions provides a rapid simulation of damage induced by alpha decays, short lived actinide doping is more representative of the reality. Here, we report radiological NMR experiments to compare the damage in International Simplified Glass (ISG) when irradiated by these two methods. In the 0.1 mole percent 244Cm doped glass, accumulation of high alpha decay only shows small modifications of the local structure, in sharp contrast to heavy ion irradiation. These results reveal the ability of the alpha particle to partially repair the damage generated by the heavy recoil nuclei highlighting the radiation resistance of nuclear glass and the difficulty to accurately simulate its behaviour by single ion beam irradiations

Shear induced instabilities in layered liquids

Motivated by the experimentally observed shear-induced destabilization and reorientation of smectic A like systems, we consider an extended formulation of smectic A hydrodynamics. We include both, the smectic layering (via the layer displacement u and the layer normal p) and the director n of the underlying nematic order in our macroscopic hydrodynamic description and allow both directions to differ in non equilibrium situations. In an homeotropically aligned sample the nematic director does couple to an applied simple shear, whereas the smectic layering stays unchanged. This difference leads to a finite (but usually small) angle between n and p, which we find to be equivalent to an effective dilatation of the layers. This effective dilatation leads, above a certain threshold, to an undulation instability of the layers. We generalize our earlier approach [Rheol. Acta, vol.39(3), 15] and include the cross couplings with the velocity field and the order parameters for orientational and positional order and show how the order parameters interact with the undulation instability. We explore the influence of various material parameters on the instability. Comparing our results to recent experiments and molecular dynamic simulations, we find a good qualitative agreement.Comment: 15 pages, 12 figures, accepted for publication in PR

The Thermal Structural Transition of α-Crystallin Inhibits the Heat Induced Self-Aggregation

-crystallin, the major constituent of human lens, is a member of the heat-shock proteins family and it is known to have a quaternary structural transition at . The presence of calcium ions and/or temperature changes induce supramolecular self-aggregation, a process of relevance in the cataractogenesis. Here we investigate the potential effect of the bovine -crystallin's structural transition on the self-aggregation process. Along all the temperatures investigated, aggregation proceeds by forming intermediate molecular assemblies that successively aggregate in clusters. The final morphology of the aggregates, above and below , is similar, but the aggregation kinetics are completely different. The size of the intermediate molecular assemblies, and their repulsive energy barrier show a marked increase while crossing . Our results highlight the key role of heat modified form of -crystallin in protecting from aggregation and preserving the transparency of the lens under hyperthermic conditions

The Importance of Major Mergers in the Build Up of Stellar Mass in Brightest Cluster Galaxies at \u3cem\u3ez\u3c/em\u3e = 1

Recent independent results from numerical simulations and observations have shown that brightest cluster galaxies (BCGs) have increased their stellar mass by a factor of almost 2 between z ∼ 0.9 and z ∼ 0.2. The numerical simulations further suggest that more than half this mass is accreted through major mergers. Using a sample of 18 distant galaxy clusters with over 600 spectroscopically confirmed cluster members between them, we search for observational evidence that major mergers do play a significant role. We find a major merger rate of 0.38 ± 0.14 mergers per Gyr at z ∼ 1. While the uncertainties, which stem from the small size of our sample, are relatively large, our rate is consistent with the results that are derived from numerical simulations. If we assume that this rate continues to the present day and that half of the mass of the companion is accreted on to the BCG during these mergers, then we find that this rate can explain the growth in the stellar mass of the BCGs that is observed and predicted by simulations. Major mergers therefore appear to be playing an important role, perhaps even the dominant one, in the build up of stellar mass in these extraordinary galaxies