A new structural model for disorder in vaterite from first-principles calculations

Both of the previously proposed Pbnm and P6522 ordered structures for vaterite are found to be unstable transition states using first principles methods. Five stable structures are located, the lowest energy one being of P3221 symmetry. Since interconversion between these structures requires only thermal energy, this provides an additional source of disorder within the vaterite structure

Assessing Thermochemical Properties of Materials through Ab initio Quantum-mechanical Methods: The Case of α-Al2O3

The thermochemical behavior of α-Al2O3 corundum in the whole temperature range 0–2317 K (melting point) and under pressures up to 12 GPa is predicted by applying ab initio methods based on the density functional theory (DFT), the use of a local basis set and periodic-boundary conditions. Thermodynamic properties are treated both within and beyond the harmonic approximation to the lattice potential. In particular, a recent implementation of the quasi-harmonic approximation, in the Crystal program, is here shown to provide a reliable description of the thermal expansion coefficient, entropy, constant-volume and constant-pressure specific heats, and temperature dependence of the bulk modulus, nearly up to the corundum melting temperature. This is a remarkable outcome suggesting α-Al2O3 to be an almost perfect quasi-harmonic crystal. The effect of using different computational parameters and DFT functionals belonging to different levels of approximations on the accuracy of the thermal properties is tested, providing a reference for further studies involving alumina polymorphs and, more generally, quasi-ionic minerals

Tetrahedrally bonded ternary amorphous semiconductor alloys

The properties of tetrahedrally bonded ternary amorphous semiconductors a-CSiSn:H and a-CSiGe:H are reviewed with particular emphasis on the temperature dependence of dark conductivity and the coordination in random networks. It is shown here that the dark conductivity as a function of the temperature strongly depends on the carbon content and, more precisely, on the proportion of sp3 and sp2 sites in the carbon. Ternary alloys with different carbon contents are compared to binary alloys using the average coordination number. The ternary alloys have an average coordination number close to the optimal value predicted for amorphous covalent networks

Improving plastic management by means of people awareness

In past decades the usage of plastic has seen a tremendous increment. This raise is mainly caused by industrial development and by the spread of this material in every aspect of people life, from food package to aerospace application. For sure plastic has a key role in society and it is not possible to erase, nevertheless its overuse has a serious impact on the environment as well know. In particular, just a few percentage of the total amount of plastic is recycled, the rest has to be landfilled or burnt causing serious pollution side effect. This poor circularity in plastic value chain is mainly caused by difficulties in sorting processes and expensiveness of recycling. By the way a great part of plastic applications could be avoided without implying a reduction in life quality for the people. In addition, a better education in plastic objects shopping and plastic waste management could decrease the difficulties in sorting and recycling. One of the crucial reason why these applications and incorrect behaviour are still present is that the information on alternatives are not present or very hard to be found. In the present paper a novel platform to enhance a more plastic-free life is presented. First a detailed description of the problem is stated, then the process to achieve the proposed solution is described. Finally the platform prototype is analysed in details among its functionalities

Optimizing copy number variation analysis using genome-wide short sequence oligonucleotide arrays

The detection of copy number variants (CNV) by array-based platforms provides valuable insight into understanding human diversity. However, suboptimal study design and data processing negatively affect CNV assessment. We quantitatively evaluate their impact when short-sequence oligonucleotide arrays are applied (Affymetrix Genome-Wide Human SNP Array 6.0) by evaluating 42 HapMap samples for CNV detection. Several processing and segmentation strategies are implemented, and results are compared to CNV assessment obtained using an oligonucleotide array CGH platform designed to query CNVs at high resolution (Agilent). We quantitatively demonstrate that different reference models (e.g. single versus pooled sample reference) used to detect CNVs are a major source of inter-platform discrepancy (up to 30%) and that CNVs residing within segmental duplication regions (higher reference copy number) are significantly harder to detect (P < 0.0001). After adjusting Affymetrix data to mimic the Agilent experimental design (reference sample effect), we applied several common segmentation approaches and evaluated differential sensitivity and specificity for CNV detection, ranging 39–77% and 86–100% for non-segmental duplication regions, respectively, and 18–55% and 39–77% for segmental duplications. Our results are relevant to any array-based CNV study and provide guidelines to optimize performance based on study-specific objectives

Probing the Multiple Structures of Vaterite through Combined Computational and Experimental Raman Spectroscopy

First-principles Raman spectra have been computed for several new vaterite structural models that have been recently proposed, and compared with spectra recorded on a set of biogenic, geological and synthetic samples. This set includes new measurements collected on Herdamania momus spicules (Great Barrier Reef, Queensland, Australia), which are known to have purity and crystallinity that are higher than for other biogenic samples. Overall, due to the close structural connection between the various models, the computed Raman spectra are found to be broadly similar. However, the spectra obtained for the two most stable models (monoclinic C2 and trigonal P3221, corresponding to two different polytypes of vaterite) exhibit features that are in excellent agreement with the experimental spectra, whereas the other theoretical structures show minor peaks that are not observed experimentally. When comparing the spectra for the two lowest energy structural models (C2 and P3221), the differences are too small to discriminate between these candidates. The Raman spectrum of Herdamania momus is of higher quality with respect to spectra obtained in previous studies on other biogenic samples. However, there is no significant and systematic difference with respect to samples of geological and synthetic origin

A model for the generic alpha relaxation of viscous liquids

Dielectric measurements on molecular liquids just above the glass transition indicate that alpha relaxation is characterized by a generic high-frequency loss varying as $\omega^{-1/2}$, whereas deviations from this come from one or more low-lying beta processes [Olsen et al, Phys. Rev. Lett. {\bf 86} (2001) 1271]. Assuming that long-wavelength fluctuations dominate the dynamics, a model for the dielectric alpha relaxation based on the simplest coupling between the density and dipole density fields is proposed here. The model, which is solved in second order perturbation theory in the Gaussian approximation, reproduces the generic features of alpha relaxation

Simulation of Calcium Phosphate Pre-Nucleation Clusters in Aqueous Solution: Association Beyond Ion Pairing

© 2019 American Chemical Society. Classical molecular dynamics simulations and free energy methods have been used to obtain a better understanding of the molecular processes occurring prior to the first nucleation event for calcium phosphate biominerals. The association constants for the formation of negatively charged complexes containing calcium and phosphate ions in aqueous solution have been computed, and these results suggest that the previously proposed calcium phosphate building unit, [Ca(HPO4)3]4-, should only be present in small amounts under normal experimental conditions. However, the presence of an activation barrier for the removal of an HPO42- ion from this complex indicates that this species could be kinetically trapped. Aggregation pathways involving CaHPO4, [Ca(HPO4)2]2-, and [Ca(HPO4)3]4- complexes have been explored with the finding that dimerization is favorable up to a Ca/HPO4 ratio of 1:2

SNP panel identification assay (SPIA): a genetic-based assay for the identification of cell lines

Translational research hinges on the ability to make observations in model systems and to implement those findings into clinical applications, such as the development of diagnostic tools or targeted therapeutics. Tumor cell lines are commonly used to model carcinogenesis. The same tumor cell line can be simultaneously studied in multiple research laboratories throughout the world, theoretically generating results that are directly comparable. One important assumption in this paradigm is that researchers are working with the same cells. However, recent work using high throughput genomic analyses questions the accuracy of this assumption. Observations by our group and others suggest that experiments reported in the scientific literature may contain pre-analytic errors due to inaccurate identities of the cell lines employed. To address this problem, we developed a simple approach that enables an accurate determination of cell line identity by genotyping 34 single nucleotide polymorphisms (SNPs). Here, we describe the empirical development of a SNP panel identification assay (SPIA) compatible with routine use in the laboratory setting to ensure the identity of tumor cell lines and human tumor samples throughout the course of long term research use

Thermodynamically Consistent Force Field for Molecular Dynamics Simulations of Alkaline-Earth Carbonates and Their Aqueous Speciation

In recent years atomistic simulations have become increasingly important in providing molecular insight to complement experiments. Even for the seemingly simple case of ion-pair formation a detailed atomistic picture of the structure and relative stability of the contact, solvent-shared and solvent-separated ion pairs can only be readily achieved by computer simulation. Here a new force field parametrization for the alkaline-earth carbonate interactions in water has been developed by fitting against experimental thermodynamic and structural data. We demonstrate that the present force field can accurately reproduce the dynamics and thermodynamics of the ions in solution, which is the key to producing quantitatively accurate data that can be compared against experiment