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

Study of the variation of the optical properties of calcite with applied stress, useful for specific rock and material mechanics

Calcite (CaCO3, trigonal crystal system, space group R3 ¯ c) is a ubiquitous carbonate phase commonly found on the Earth’s crust that finds many useful applications in both scientific (mineralogy, petrology, geology) and technological fields (optics, sensors, materials technology) because of its peculiar anisotropic physical properties. Among them, photoelasticity, i.e., the variation of the optical properties of the mineral (including birefringence) with the applied stress, could find usefulness in determining the stress state of a rock sample containing calcite by employing simple optical measurements. However, the photoelastic tensor is not easily available from experiments, and affected by high uncertainties. Here we present a theoretical Density Functional Theory approach to obtain both elastic and photoelastic properties of calcite, considering realistic experimental conditions (298 K, 1 atm). The results were compared with those available in literature, further extending the knowledge of the photoelasticity of calcite, and clarifying an experimental discrepancy in the sign of the p41 photoelastic tensor component measured in past investigations. The methods here described and applied to a well-known crystalline material can be used to obtain the photoelastic properties of other minerals and/or materials at desired pressure and temperature conditions

Fibre-reinforced geopolymer composites micro-nanochemistry by SEM-EDS simulations

The focus of the present study is on fibre-reinforced geopolymer composites, whose optimization and application necessarily need a detailed chemical characterization at the micro-nanoscale. In this regard, many geopolymer composites presenting micro and nanometric architectures pose a challenge for scanning electron microscopy with energy dispersive X-ray microanalysis (SEM-EDS) quantification, because of several potential sources of errors. For this reason, the present work reports a SEM-EDS Monte Carlo approach to carefully investigate the complex physical phenomena related to the cited quantification errors. The model used for this theoretical analysis is a simplified fibre-reinforced geopolymer with basalt-derived glass fibres immersed in a potassium-poly(sialatesiloxo) matrix. The simulated SEM-EDS spectra showed a strong influence on the measured X-ray intensity of (i) the sample nano-to-micro architecture, (ii) the electron beam probing energy and (iii) the electron probe-sample-EDS detector relative position. The results showed that, compared to a bulk material, the X-ray intensity for a nano-micrometric sized specimen may give rise to potential underestimation and/or overestimation of the elemental composition of the sample. The proposed Monte Carlo approach indicated the optimal instrumental setup depending on the sample and on the specific SEM-EDS equipment here considered

Duration of stages of the Middle Phalanx Maturation method in a contemporary population: A 6-year longitudinal analysis

Objective: To determine the duration and age at the beginning of each stage corresponding to the circumpubertal period in the Middle Phalanx Maturation method (MPM) and to assess the differences between males and females. Materials and Methods: Sets of X-rays of the middle phalanx of the third finger taken at 6-month intervals were analysed for 246 skeletal Class I subjects (102 females and 144 males) between 9 and 15 years of age. After staging, the duration of each stage was derived from chronological ages, and the difference between males and females for both duration and age at the beginning of each stage was investigated. Results: The median duration for MPS2 and MPS3 was 1 year for both sexes, while MPS4 showed a median duration of 1 year in females and 9 months in males, with no significant differences between the sexes. Mean age at the beginning of MPS2 was 10y11m for females and 11y11m for males; for MPS3, it was 11y8m for females and 13y1m for males; for MPS4, it was 12y9m for females and 13y11m for males; for MPS5, it was 13y4m for females and 14y3m for males. The differences between the sexes were statistically significant for all the stages (P <.001). Conclusions: This study confirms, with relevant sample size, the median duration of 1 year for each MPM stage from MPS2 to MPS4. Despite the distinctive interindividual variability, the interquartile range is 6 months or less for all but one interval, confirming the soundness of the results

Unraveling vitamin B12-responsive gene regulation in Algae

Photosynthetic microalgae play a vital role in primary productivity and biogeochemical cycling in both marine and freshwater systems across the globe. However, the growth of these cosmopolitan organisms depends on the bioavailability of nutrients such as vitamins. Approximately one-half of all microalgal species requires vitamin B12 as a growth supplement. The major determinant of algal B12 requirements is defined by the isoform of methionine synthase possessed by an alga, such that the presence of the B12- independent methionine synthase (METE) enables growth without this vitamin. Moreover, the widespread but phylogenetically unrelated distribution of B12 auxotrophy across the algal lineages suggests that the METE gene has been lost multiple times in evolution. Given that METE expression is repressed by the presence of B12, prolonged repression by a reliable source of the vitamin could lead to the accumulation of mutations and eventually gene loss. Here, we probe METE gene regulation by B12 and methionine/folate cycle metabolites in both marine and freshwater microalgal species. In addition, we identify a B12-responsive element of Chlamydomonas reinhardtii METE using a reporter gene approach. We show that complete repression of the reporter occurs via a region spanning 2574 to 290 bp upstream of the METE start codon. A proteomics study reveals that two other genes (S-Adenosylhomocysteine hydrolase and Serine hydroxymethyltransferase2) involved in the methionine-folate cycle are also repressed by B12 in C. reinhardtii. The strong repressible nature and high sensitivity of the B12-responsive element has promising biotechnological applications as a cost-effective regulatory gene expression tool.BBSRC (BB/I013164/1)SNSF (PBEZA-115703; PA00P3-124169)CNP

Kek-6: A truncated-Trk-like receptor for Drosophila neurotrophin 2 regulates structural synaptic plasticity.

Neurotrophism, structural plasticity, learning and long-term memory in mammals critically depend on neurotrophins binding Trk receptors to activate tyrosine kinase (TyrK) signaling, but Drosophila lacks full-length Trks, raising the question of how these processes occur in the fly. Paradoxically, truncated Trk isoforms lacking the TyrK predominate in the adult human brain, but whether they have neuronal functions independently of full-length Trks is unknown. Drosophila has TyrK-less Trk-family receptors, encoded by the kekkon (kek) genes, suggesting that evolutionarily conserved functions for this receptor class may exist. Here, we asked whether Keks function together with Drosophila neurotrophins (DNTs) at the larval glutamatergic neuromuscular junction (NMJ). We tested the eleven LRR and Ig-containing (LIG) proteins encoded in the Drosophila genome for expression in the central nervous system (CNS) and potential interaction with DNTs. Kek-6 is expressed in the CNS, interacts genetically with DNTs and can bind DNT2 in signaling assays and co-immunoprecipitations. Ligand binding is promiscuous, as Kek-6 can also bind DNT1, and Kek-2 and Kek-5 can also bind DNT2. In vivo, Kek-6 is found presynaptically in motoneurons, and DNT2 is produced by the muscle to function as a retrograde factor at the NMJ. Kek-6 and DNT2 regulate NMJ growth and synaptic structure. Evidence indicates that Kek-6 does not antagonise the alternative DNT2 receptor Toll-6. Instead, Kek-6 and Toll-6 interact physically, and together regulate structural synaptic plasticity and homeostasis. Using pull-down assays, we identified and validated CaMKII and VAP33A as intracellular partners of Kek-6, and show that they regulate NMJ growth and active zone formation downstream of DNT2 and Kek-6. The synaptic functions of Kek-6 could be evolutionarily conserved. This raises the intriguing possibility that a novel mechanism of structural synaptic plasticity involving truncated Trk-family receptors independently of TyrK signaling may also operate in the human brain