Modelling of a standard gas mixtures generator with computational fluid dynamics

Monitoring VOC for climate change and for indoor and outdoor air quality at trace level concentrations need reference standard materials at high metrological performance. To improve this performance, the description of phenomena involved in mixtures generation by rigorous models is mandatory. A model to describe diffusion cells of a primary generator was developed and validated with experimental data. A good agreement was found between the uncertainties of measurements and calculations

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

Solubility-consistent force field simulations for aqueous metal carbonate systems using graphical processing units

Crystallization of alkaline earth metal carbonates from water is important for biomineralization and environmental geochemistry. Here, large-scale computer simulations are a useful approach to complement experimental studies by providing atomistic insights and even by quantitatively determining the thermodynamics of individual steps. However, this is dependent on the existence of force field models that are sufficiently accurate while being computationally efficient enough to sample complex systems. Here, we introduce a revised force field for aqueous alkaline earth metal carbonates that reproduces both the solubilities of the crystalline anhydrous minerals, as well as the hydration free energies of the ions. The model is also designed to run efficiently on graphical processing units thereby reducing the cost of such simulations. The performance of the revised force field is compared against previous results for important properties relevant to crystallization, including ion-pairing and mineral-water interfacial structure and dynamics. This article is part of a discussion meeting issue 'Supercomputing simulations of advanced materials'

Impact of constitutional copy number variants on biological pathway evolution

Background: Inherited Copy Number Variants (CNVs) can modulate the expression levels of individual genes. However, little is known about how CNVs alter biological pathways and how this varies across different populations. To trace potential evolutionary changes of well-described biological pathways, we jointly queried the genomes and the transcriptomes of a collection of individuals with Caucasian, Asian or Yoruban descent combining high-resolution array and sequencing data. Results: We implemented an enrichment analysis of pathways accounting for CNVs and genes sizes and detected significant enrichment not only in signal transduction and extracellular biological processes, but also in metabolism pathways. Upon the estimation of CNV population differentiation (CNVs with different polymorphism frequencies across populations), we evaluated that 22% of the pathways contain at least one gene that is proximal to a CNV (CNV-gene pair) that shows significant population differentiation. The majority of these CNV-gene pairs belong to signal transduction pathways and 6% of the CNV-gene pairs show statistical association between the copy number states and the transcript levels. Conclusions: The analysis suggested possible examples of positive selection within individual populations including NF-kB, MAPK signaling pathways, and Alu/L1 retrotransposition factors. Altogether, our results suggest that constitutional CNVs may modulate subtle pathway changes through specific pathway enzymes, which may become fixed in some populations

A hierarchical Naïve Bayes Model for handling sample heterogeneity in classification problems: an application to tissue microarrays

BACKGROUND: Uncertainty often affects molecular biology experiments and data for different reasons. Heterogeneity of gene or protein expression within the same tumor tissue is an example of biological uncertainty which should be taken into account when molecular markers are used in decision making. Tissue Microarray (TMA) experiments allow for large scale profiling of tissue biopsies, investigating protein patterns characterizing specific disease states. TMA studies deal with multiple sampling of the same patient, and therefore with multiple measurements of same protein target, to account for possible biological heterogeneity. The aim of this paper is to provide and validate a classification model taking into consideration the uncertainty associated with measuring replicate samples. RESULTS: We propose an extension of the well-known Naïve Bayes classifier, which accounts for biological heterogeneity in a probabilistic framework, relying on Bayesian hierarchical models. The model, which can be efficiently learned from the training dataset, exploits a closed-form of classification equation, thus providing no additional computational cost with respect to the standard Naïve Bayes classifier. We validated the approach on several simulated datasets comparing its performances with the Naïve Bayes classifier. Moreover, we demonstrated that explicitly dealing with heterogeneity can improve classification accuracy on a TMA prostate cancer dataset. CONCLUSION: The proposed Hierarchical Naïve Bayes classifier can be conveniently applied in problems where within sample heterogeneity must be taken into account, such as TMA experiments and biological contexts where several measurements (replicates) are available for the same biological sample. The performance of the new approach is better than the standard Naïve Bayes model, in particular when the within sample heterogeneity is different in the different classes

Suya Taco and Sol de Mayo mafic complexes from eastern Sierras Pampeanas, Argentina: Evidence for the emplacement of primitive OIB-like magmas into deep crustal levels at a late stage of the Pampean orogeny

The age and petrogenetic features of the Suya Taco and Sol de Mayo mafic complexes reported here provide important new insights into the tectonic setting and evolution of the Pampean orogen. Specifically, the results of this study support models that are capable of explaining the introduction of non-arc mantle-derived mafic magmas into the developing orogen at or very near the time of its metamorphic peak. Although a continental collision model for the Pampean orogen cannot be categorically ruled out, an additional slab break-off or lower crustal delamination event immediately following collision would be required in order to account for the observations presented here. Alternatively, the recently proposed hypothesis of subduction of a mid-ocean ridge beneath an accretionary prism as the cause for Pampean orogeny can account for rise of non-arc, OIB-like mafic magmas through an already thickened supracrustalassemblage, as well as the close spatial and temporal association of this magmatism with the development of high-grade granulitic metamorphic and migmatitic assemblages in the Pampean supracrustal rocks.Fil: Tibaldi, Alina María. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Córdoba; Argentina. Universidad Nacional de Río Cuarto. Facultad de Ciencias Exactas, Fisicoquímicas y Naturales. Departamento de Geología; ArgentinaFil: Otamendi, Juan Enrique. Universidad Nacional de Río Cuarto. Facultad de Ciencias Exactas, Fisicoquímicas y Naturales. Departamento de Geología; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Córdoba; ArgentinaFil: Gromet, L. P.. University Brown; Estados UnidosFil: Demichelis, A. H.. Universidad Nacional de Río Cuarto. Facultad de Ciencias Exactas, Fisicoquímicas y Naturales. Departamento de Geología; Argentin

Toward the realization of reproducible AFM measurements of elastic modulus in biological samples

partially_open6The validation of the AFM method for elastic modulus E measurement in soft materials (E <5 MPa) is still missing. The interest of measurements in materials with E <5 MPa is mainly biological, including soft tissues and single cells. For the diagnosis of malignant human tumors, a change in cell elasticity, within tissues, has recently been recognized as a marker of metastatic potential. To measure a cell elasticity difference, reproducible E measurements in biological samples are needed. In this work a robust method for a metrological validation of E measurements in the range 500–5000 kPa was developed, based on the realization of thick E standard samples and on the study of the interactions between the measurement process and the sample at micro- and nano-scale. E measurement reproducibility limit of 4% has been reached. This allows designing a very sensitive and reproducible measurement of E in biological samples representing thus a powerful diagnostic tool for cancer detection.partially_openA. Demichelis; C. Divieto; L. Mortati; S. Pavarelli; G. Sassi; M. SassiDemichelis, A.; Divieto, C.; Mortati, L.; Pavarelli, S.; Sassi, G.; Sassi, M

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

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