QUANTAS: a Python software for the analysis of thermodynamics and elastic behavior of solids from ab initio quantum mechanical simulations and experimental data

Mineralogy, petrology and materials science are fundamental disciplines not only for the basic knowledge and classification of solid phases but also for their technological applications, which are becoming increasingly demanding and challenging. Characterization and design of materials are of utmost importance and usually need knowledge of the thermodynamics and mechanical stability of solids. Alongside well known experimental approaches, in recent years the advances in both quantum mechanical methods and computational power have placed theoretical investigations as a complementary useful and powerful tool in this kind of study. In order to aid both theoreticians and experimentalists, an open-source Python-based software, QUANTAS, has been developed. QUANTAS provides a fast, flexible, easy-to-use and extensible platform for calculating the thermodynamics and elastic behavior of crystalline solid phases, starting from both experimental and ab initio data

Structural and elastic behaviour of aragonite at high-pressure: A contribution from first-principle simulations

Aragonite (CaCO3, space group Pmcn) is an important mineral for both geological and biological reasons, being one of the phases that recycles carbon in deep Earth conditions and the product of biomineralization of several terrestrial and marine organisms, respectively. Because of its ubiquity, aragonite has been the subject of several investigations to understand its elastic behaviour and stability at different P-T conditions, but the results reported in literature are still very scattered. Aiming at providing further details on this topic, in the present work we determined the structural and elastic properties of aragonite at absolute zero (0 K) within the Density Functional Theory framework, using a posteriori correction to include the weak long-range interactions. The equation of state parameters for this mineral phase, calculated between 0 GPa – 25 GPa, were K0 = 80.2(7) GPa, K’ = 4.37(10) and V0 = 223.00(6) Å3, in good agreement with the bulk modulus calculated from the elastic moduli (KR = 78.49 GPa). The results were compared to previous experimental and theoretical data, finding them in line with some specific studies, and show that some structural features (e.g., the carbonate ion aplanarity) could be related to the mechanism of phase transition to the post-aragonite phase at high pressure. The present work highlights the importance of including van der Waals interactions in the physical treatment of the structural and elastic properties of aragonite, and further extends the knowledge of the behaviour of this mineral as a function of pressure

Structural and Elastic Behaviour of Sodalite Na8(Al6Si6O24)Cl2 at High-Pressure by First-Principle Simulations

Sodalite Na8(Al6Si6O24)Cl2 (space group P-43n) is an important mineral belonging to the zeolite group, with several and manyfold fundamental and technological applications. Despite the interest in this mineral from different disciplines, very little is known regarding the high-pressure elastic properties. The present study aims at filling this knowledge gap, reporting the equation of state and the elastic moduli of sodalite calculated in a wide pressure range, from –6 GPa to 22 GPa. The results were obtained from Density Functional Theory simulations carried out with Gaussian-type basis sets and the well-known hybrid functional B3LYP. The DFT-D3 a posteriori correction to include the van der Waals interactions in the physical treatment of the mineral was also applied. The calculated equation of state parameters at 0 GPa and absolute zero (0 K), i.e., K0 = 70.15(7) GPa, K’ = 4.46(2) and V0 = 676.85(3) Å3 are in line with the properties derived from the stiffness tensor, and in agreement with the few experimental data reported in literature. Sodalite was found mechanically instable when compressed above 15.6 GPa

Effect of shape and thickness of asbestos bundles and fibres on EDS microanalysis: A Monte Carlo simulation

Quantitative microanalysis of tiny asbestos mineral fibres by scanning electron microscopy equipped with energy-dispersive X-ray spectroscopy (SEM-EDS) still represents a complex analytical issue. This complexity arises from the variable fibre shape and small thickness (< 5 μm) compared with the penetration of the incident electron beam. Here, we present the results of Monte Carlo simulations of chrysotile, crocidolite and amosite fibres (and bundles of fibres) of circular and square section and thicknesses from 0.1 μm to 10 μm, to investigate the effect of shape and thickness on SEM-EDS microanalysis. The influence of shape and thickness on the simulated spectrum was investigated for electron beam energies of 5, 15 and 25 keV, respectively. A strong influence of the asbestos bundles and fibres shape and thickness on the detected EDS X-ray intensity was observed. The X-ray intensity trends as a function of fibre thickness showed a non-linear dependence for all the elements and minerals. In general, the X-ray intensities showed a considerable reduction for thicknesses below about 5 μm at 5 keV, 2 μm at 15 keV, and 5 μm at 25 keV. Correction parameters, k-ratios, for the asbestos fibre thickness effect, are reported

Layer charge and heavy metals structures in hydrated 2 : 1 silicates:state of the art and new advances on cadmium

This study will discuss how layer charge can affect chemical speciation and topology of heavy metals adsorbed to 2:1 layer silicates, by providing: i) an overview of literature data; ii) experimental data on Cd complexes adsorbed by 2:1 layer silicates with different layer charge (montmorillonite and vermiculite); iii) a comparison between our results and literature data. This study will also be supported by several different experimental techniques such as chemical and thermal analyses, X-ray powder diffraction and X-ray absorption spectroscopy.Based on our data Cd atoms were found to complex water molecules in both clay minerals and to show four-fold coordination in montmorillonite (CdO distances of 2.24 Å) and six-fold coordination in vermiculite (CdO distances of 2.16 and 2.28 Å). Furthermore our models clearly suggest that Cd mainly bonds to interlayer water, without neglecting the more limited, but still significant, Cd multinuclear surface complexes at the octahedral broken edges. Both clay minerals show H2O/Cd ratio, as evidenced by thermal analyses, drastically higher than expected from X-ray adsorption spectroscopy data, thus implying that most of the water molecules are only loosely coordinated to interlayer cations

Probing the statistical decay and alpha-clustering effects in 12c+12c and 14n+10b reactions

An experimental campaign has been undertaken at INFN Laboratori Nazionali di Legnaro, Italy, in order to progress in our understanding of the statistical properties of light nuclei at excitation energies above particle emission threshold, by measuring exclusive data from fusion-evaporation reactions. A first reaction 12C+12C at 7.9 AMeV beam energy has been measured, using the GARFIELD+Ring Counter experimental setup. Fusion-evaporation events have been exclusively selected. The comparison to a dedicated Hauser-Feshbach calculation allows us to give constraints on the nuclear level density at high excitation energy for light systems ranging from C up to Mg. Out-of-equilibrium emission has been evidenced and attributed both to entrance channel effects favoured by the cluster nature of reaction partners and, in more dissipative events, to the persistence of cluster correlations well above the 24Mg threshold for 6 alphas decay. The 24Mg compound nucleus has been studied with a new measurement 14N + 10B at 5.7 AMeV. The comparison between the two datasets would allow us to further constrain the level density of light nuclei. Deviations from a statistical behaviour can be analyzed to get information on nuclear clustering.Comment: 4 pages, 2 figures, Contribution to conference proceedings of the 25th International Nuclear Physics Conference (INPC 2013

Phosphorylated cofilin-2 is more prone to oxidative modifications on Cys39 and favors amyloid fibril formation

Cofilins are small protein of the actin depolymerizing family. Actin polymerization/depolymerization is central to a number of critical cellular physiological tasks making cofilin a key protein for several physiological functions of the cell. Cofilin activity is mainly regulated by phosphorylation on serine residue 3 making this post-translational modification key to the regulation of myofilament integrity. In fact, in this form, the protein segregates in myocardial aggregates in human idiopathic dilated cardiomyopathy. Since myofilament network is an early target of oxidative stress we investigated the molecular changes induced by oxidation on cofilin isoforms and their interplay with the protein phosphorylation state to get insight on whether/how those changes may predispose to early protein aggregation. Using different and complementary approaches we characterized the aggregation properties of cofilin-2 and its phosphomimetic variant (S3D) in response to oxidative stress in silico, in vitro and on isolated cardiomyocytes. We found that the phosphorylated (inactive) form of cofilin-2 is mechanistically linked to the formation of an extended network of fibrillar structures induced by oxidative stress via the formation of a disulfide bond between Cys39 and Cys80. Such phosphorylation-dependent effect is likely controlled by changes in the hydrogen bonding network involving Cys39. We found that the sulfide ion inhibits the formation of such structures. This might represent the mechanism for the protective effect of the therapeutic agent Na2S on ischemic injury

Energy measurement and fragment identification using digital signals from partially depleted Si detectors

A study of identification properties of a Si-Si DE-E telescope exploiting an underdepleted residual-energy detector has been performed. Five different bias voltages have been used, one corresponding to full depletion, the others associated with a depleted layer ranging from 90% to 60% of the detector thickness. Fragment identification has been performed using either the DE-E technique or Pulse Shape Analysis (PSA). Both detectors are reverse mounted: particles enter from the low field side, to enhance the PSA performance. The achieved charge and mass resolution has been quantitatively expressed using a Figure of Merit (FoM). Charge collection efficiency has been evaluated and the possibility of energy calibration corrections has been considered. We find that the DE-E performance is not affected by incomplete depletion even when only 60% of the wafer is depleted. Isotopic separation capability improves at lower bias voltages with respect to full depletion, though charge identification thresholds are higher than at full depletion. Good isotopic identification via PSA has been obtained from a partially depleted detector whose doping uniformity is not good enough for isotopic identification at full depletion.Comment: 13 pages, 10 figures 5 tables; submitted to European Physical Journal